Genetic resistance prediction against antimicrobial drugs in microorganism using structural changes in the genome

The present invention relates to a method of determining an infection of a patient with at least one microorganism, particularly a bacterial microorganism, potentially resistant to antimicrobial drug treatment, a method of selecting a treatment of a patient suffering from an infection with at least one microorganism, particularly bacterial microorganism, and a method of determining structural changes of the genome of the microorganism, particularly bacterial microorganism, comprising at least one gene, as well as computer program products used in these methods.

Antibiotic resistance is a form of drug resistance whereby a sub-population of a microorganism, e.g. a strain of a bacterial species, can survive and multiply despite exposure to an antibiotic drug. It is a serious health concern for the individual patient as well as a major public health issue. Timely treatment of a bacterial infection requires the analysis of clinical isolates obtained from patients with regard to antibiotic resistance, in order to select an efficacious therapy. Generally, for this purpose an association of the identified resistance with a certain microorganism (i.e. ID) is necessary.

Antibacterial drug resistance (ADR) represents a major health burden. According to the World Health Organization's antimicrobial resistance global report on surveillance, ADR leads to 25,000 deaths per year in Europe and 23,000 deaths per year in the US. In Europe, 2.5 million extra hospital days lead to societal cost of 1.5 billion euro. In the US, the direct cost of 2 million illnesses leads to 20 billion dollar direct cost. The overall cost is estimated to be substantially higher, reducing the gross domestic product (GDP) by up to 1.6%.

In general the mechanisms for resistance of bacteria against antimicrobial treatments rely to a very substantial part on the organism's genetics. The respective genes or molecular mechanisms are either encoded in the genome of the bacteria or on plasmids that can be interchanged between different bacteria. The most common resistance mechanisms include:

1) Efflux pumps are high-affinity reverse transport systems located in the membrane that transports the antibiotic out of the cell, e.g. resistance to tetracycline.

2) Specific enzymes modify the antibiotic in a way that it loses its activity. In the case of streptomycin, the antibiotic is chemically modified so that it will no longer bind to the ribosome to block protein synthesis.

3) An enzyme is produced that degrades the antibiotic, thereby inactivating it. For example, the penicillinases are a group of beta-lactamase enzymes that cleave the beta lactam ring of the penicillin molecule.

In addition, some pathogens show natural resistance against drugs. For example, an organism can lack a transport system for an antibiotic or the target of the antibiotic molecule is not present in the organism.

Pathogens that are in principle susceptible to drugs can become resistant by modification of existing genetic material (e.g. spontaneous mutations for antibiotic resistance, happening in a frequency of one in about 100 mio bacteria in an infection) or the acquisition of new genetic material from another source. One example is horizontal gene transfer, a process where genetic material contained in small packets of DNA can be transferred between individual bacteria of the same species or even between different species. Horizontal gene transfer may happen by transduction, transformation or conjugation.

Generally, testing for susceptibility/resistance to antimicrobial agents is performed by culturing organisms in different concentrations of these agents.

In brief, agar plates are inoculated with patient sample (e.g. urine, sputum, blood, stool) overnight. On the next day individual colonies are used for identification of organisms, either by culturing or using mass spectroscopy. Based on the identity of organisms new plates containing increasing concentration of drugs used for the treatment of these organisms are inoculated and grown for additional 12-24 hours. The lowest drug concentration which inhibits growth (minimal inhibitory concentration—MIC) is used to determine susceptibility/resistance for tested drugs. The process takes at least 2 to 3 working days during which the patient is treated empirically. Automated systems exist from several companies, e.g. Biomeriux (Vitek), Beckman Coulter (Microscan). A significant reduction of time-to-result is needed especially in patients with life-threatening disease and to overcome the widespread misuse of antibiotics.

Recent developments include PCR based test kits for fast bacterial identification (e.g. Biomerieux Biofire Tests, Curetis Unyvero Tests). With these test the detection of selected resistance loci is possible for a very limited number of drugs, but no correlation to culture based AST is given. Mass spectroscopy is increasingly used for identification of pathogens in clinical samples (e.g. Bruker Biotyper), and research is ongoing to establish methods for the detection of susceptibility/resistance against antibiotics.

The use of molecular techniques for direct detection of MRSA has become more commonplace especially for screening purposes. Resistance to methicillin is mediated via the mec operon which is part of the staphylococcal cassette chromosome mec (SCCmec). Recently PCR tests were introduced that are based on the detection of the right extremity sequence of the SCCmec in combination with S. aureus specific marker. Initial reports exist that describe culture based susceptibility reports despite detection of the presence of a resistance conferring gene.

For some drugs such it is known that at least two targets are addressed, e.g. in case of Ciprofloxacin (drug bank ID 00537; http://www.drugbank.ca/drugs/DB00537) targets include DNA Topoisomerase IV, DNA Topoisomerase II and DNA Gyrase. It can be expected that this is also the case for other drugs although the respective secondary targets have not been identified yet. In case of a common regulation, both relevant genetic sites would naturally show a co-correlation or redundancy.

It is known that drug resistance can be associated with genetic polymorphisms. This holds for viruses, where resistance testing is established clinical practice (e.g. HIV genotyping). More recently, it has been shown that resistance has also genetic causes in bacteria and even higher organisms, such as humans where tumors resistance against certain cytostatic agents can be linked to genomic mutations.

Wozniak et al. (BMC Genomics 2012, 13(Suppl 7):S23) disclose genetic determinants of drug resistance in Staphylococcus aureus based on genotype and phenotype data. Stoesser et al. disclose prediction of antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data (J Antimicrob Chemother 2013; 68: 2234-2244).

Chewapreecha et al (Chewapreecha et al (2014) Comprehensive Identification of single nucleotid polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes. PLoS Genet 10(8): e1004547) used a comparable approach to identify mutations in gram-positive Streptococcus Pneumonia.

In recent studies, genetic tests are taken into account that consider variations in the genome of a microorganism, e.g. a bacterial microorganism. In previous works it could be shown that a faster decision for a treatment could be made using changes in single bases. However, this does not necessarily apply to all antimicrobial drugs, e.g. antibiotics, tested.

The fast and accurate detection of infections with microorganisms, particularly microbial species, e.g. Staphylococcus aureus, and the prediction of response to anti-microbial therapy represent a high unmet clinical need.

This need is addressed by the present invention.

SUMMARY OF THE INVENTION

The inventors found out that structural variations in the genome that relate to more than one base, particularly at least one gene or more genes in an open reading frame can be related to resistance/susceptibility of microorganisms, particularly bacterial microorganisms, to antimicrobial, e.g. antibiotic, drugs. For example, an efflux pump can be present on a plasmid additionally in a genome. Such efflux pump then can transport a medicine/drug like an antibiotic out of the organism, so that it cannot be effective. Thus, a bacterium having such efflux pump on a plasmid is resistant.

According to a first aspect, the present invention relates to a method of determining structural variations in a genome of a microorganism, particularly a bacterial microorganism, comprising at least a change in the genome comprising more than one base, comprising:

obtaining or providing a first data set of gene sequences of a plurality of clinical isolates of the microorganism, wherein optionally at least a part of the gene sequences of the first data set are assembled; and/or obtaining or providing a first data set of gene sequences of a plurality of clinical isolates of the microorganism and aligning the gene sequences of the first data set to at least one, preferably one, reference sequence;

analyzing the gene sequences of the first data set for structural variations of the genome comprising at least a change in the genome comprising more than one base to obtain a third data set of structural variants;

providing a second data set of antimicrobial drug, e.g. antibiotic, resistance and/or susceptibility of the plurality of clinical isolates of the microorganism;

correlating the third data set with the second data set and statistically analyzing the correlation; and

determining the structural variations in the genome of the microorganism associated with antimicrobial drug, e.g. antibiotic, resistance.

A second aspect of the present invention relates to a diagnostic method of determining an infection of a patient with a microorganism, particularly a bacterial microorganism potentially resistant to antimicrobial drug treatment, comprising the steps of:

a) obtaining or providing a sample containing or suspected of containing a microorganism, particularly a bacterial microorganism, from the patient;

b) determining the presence of at least one structural variation in at least one genetic sequence of the microorganism, particularly bacterial microorganism, as determined by the method of the first aspect, wherein the presence of said at least one structural variation is indicative of an infection with an antimicrobial drug resistant microorganism in said patient.

A third asped of the present invention relates to a method of selecting a treatment of a patient suffering from an infection with a potentially resistant microorganism, particularly bacterial microorganism, comprising the steps of:

a) obtaining or providing a sample containing or suspected of containing a microorganism, particularly a bacterial microorganism, from the patient;

b) determining the presence of at least one structural variation in at least one genetic sequence of the microorganism, particularly bacterial microorganism, as determined by the method of any one of claims 1 to 3, wherein the presence of said at least one structural variation is indicative of a resistance to one or more antimicrobial drugs;

c) identifying said at least one or more antimicrobial drugs; and

d) selecting one or more antimicrobial drugs different from the ones identified in step c) and being suitable for the treatment of the infection with the microorga

A fourth aspect of the present invention relates to a method of determining structural variations of a genome of a microorganism for a clinical isolate of the microorganism, particularly a bacterial microorganism, comprising: obtaining or providing at least one gene sequence of the clinical isolate of the microorganism, particularly the bacterial microorganism; and determining the presence of structural variations in the at least one gene sequence of the clinical isolate of the microorganism, particularly bacterial microorganism, as determined by the method of the first aspect.

In a fifth aspect the present invention relates to one or more computer program products comprising computer executable instructions which, when executed, perform a method according to any one of the first to the fourth aspect of the present invention.

Further aspects and embodiments of the invention are disclosed in the dependent claims and can be taken from the following description, figures and examples, without being limited thereto.

FIGURES

The enclosed drawings should illustrate embodiments of the present invention and convey a further understanding thereof. In connection with the description they serve as explanation of concepts and principles of the invention. Other embodiments and many of the stated advantages can be derived in relation to the drawings. The elements of the drawings are not necessarily to scale towards each other. Identical, functionally equivalent and acting equal features and components are denoted in the figures of the drawings with the same reference numbers, unless noted otherwise.

FIG. 1 shows schematically a read-out concept for a diagnostic test according to a method of the present invention.

DETAILED DESCRIPTION OF THE PRESENT INVENTION

Definitions

Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.

An “antimicrobial drug” in the present invention refers to a group of drugs that includes antibiotics, antifungals, antiprotozoals, and antivirals. According to certain embodiments, the antimicrobial drug is an antibiotic.

The term “nucleic acid molecule” refers to a polynucleotide molecule having a defined sequence. It comprises DNA molecules, RNA molecules, nucleotide analog molecules and combinations and derivatives thereof, such as DNA molecules or RNA molecules with incorporated nucleotide analogs or cDNA.

The term “nucleic acid sequence information” relates to an information which can be derived from the sequence of a nucleic acid molecule, such as the sequence itself or a variation in the sequence as compared to a reference sequence.

The term “mutation” relates to a variation in the sequence as compared to a reference sequence. Such a reference sequence can be a sequence determined in a predominant wild type organism or a reference organism, e.g. a defined and known bacterial strain or substrain. A mutation is for example a deletion of one or multiple nucleotides, an insertion of one or multiple nucleotides, or substitution of one or multiple nucleotides, duplication of one or a sequence of multiple nucleotides, translocation of one or a sequence of multiple nucleotides, e.g. also a single nucleotide polymorphism (SNP).

In the context of the present invention a “sample” is a sample which comprises at least one nucleic acid molecule from a bacterial microorganism. Examples for samples are: cells, tissue, body fluids, biopsy specimens, blood, urine, saliva, sputum, plasma, serum, cell culture supernatant, swab sample and others. According to certain embodiments, the sample is a patient sample (clinical isolate).

New and highly efficient methods of sequencing nucleic acids referred to as next generation sequencing have opened the possibility of large scale genomic analysis. The term “next generation sequencing” or “high throughput sequencing” refers to high-throughput sequencing technologies that parallelize the sequencing process, producing thousands or millions of sequences at once. Examples include Massively Parallel Signature Sequencing (MPSS), Polony sequencing, 454 pyrosequencing, Illumina (Solexa) sequencing, SOLiD sequencing, Ion semiconductor sequencing, DNA nanoball sequencing, Helioscope(™) single molecule sequencing, Single Molecule SMRT(™) sequencing, Single Molecule real time (RNAP) sequencing, Nanopore DNA sequencing, Sequencing By Hybridization, Amplicon Sequencing, GnuBio.

Within the present description the term “microorganism” comprises the term microbe. The type of microorganism is not particularly restricted, unless noted otherwise or obvious, and, for example, comprises bacteria, viruses, fungi, microscopic algae and protozoa, as well as combinations thereof. According to certain aspects, it refers to one or more bacterial species, being either Gram-negative or Gram-positive, particularly one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species.

A reference to a microorganism or microorganisms in the present description comprises a reference to one microorganism as well a plurality of microorganisms, e.g. two, three, four, five, six or more microorganisms.

A vertebrate within the present invention refers to animals having a vertebrae, which includes mammals—including humans, birds, reptiles, amphibians and fishes. The present invention thus is not only suitable for human medicine, but also for veterinary medicine.

According to certain embodiments, the patient in the present methods is a vertebrate, more preferably a mammal and most preferred a human patient.

Before the invention is described in exemplary detail, it is to be understood that this invention is not limited to the particular component parts of the process steps of the methods described herein as such methods may vary. It is also to be understood that the terminology used herein is for purposes of describing particular embodiments only, and is not intended to be limiting. It must be noted that, as used in the specification and the appended claims, the singular forms “a,” “an” and “the” include singular and/or plural referents unless the context clearly dictates otherwise. For example, the term “a” as used herein can be understood as one single entity or in the meaning of “one or more” entities. It is also to be understood that plural forms include singular and/or plural referents unless the context clearly dictates otherwise. It is moreover to be understood that, in case parameter ranges are given which are delimited by numeric values, the ranges are deemed to include these limitation values.

Regarding the dosage of the antimicrobial, e.g. antibiotic, drugs, it is referred to the established principles of pharmacology in human and veterinary medicine. For example, Forth, Henschler, Rummel “Allgemeine and spezielle Pharmakologie and Toxikologie”, 9th edition, 2005 might be used as a guideline. Regarding the formulation of a ready-to-use medicament, reference is made to “Remington, The Science and Practice of Pharmacy”, 22^ndedition, 2013.

Assembling of a gene sequence can be carried out by any known method and is not particularly limited.

According to certain embodiments, mutations that were found using alignments can also be compared or matched with alignment-free methods, e.g. for detecting single base exchanges, for example based on contigs that were found by assemblies. For example, reads obtained from sequencing can be assembled to contigs and the contigs can be compared to each other.

A structural variation comprising a change in the genome comprising more than one base refers to a structural variation wherein at least two bases in a gene sequence of a genome of a microorganism that are adjacent are changed, and can refer to e.g. a deletion of multiple (2 or more) nucleotides, an insertion of multiple (2 or more) nucleotides, a substitution of multiple (2 or more) nucleotides, a duplication of a sequence of multiple (2 or more) nucleotides, or a translocation of a sequence of multiple (2 or more) nucleotide. According to certain embodiments, a structural variation can comprise bigger parts sections of the genome, e.g. at least one whole gene in the genome of the microorganism, or even more genes in an open reading frame.

In the present invention, not specific changes of single nucleotides are determined, but a determination is based on bigger parts of the genome, as above.

In the present invention, a reference sequence is not particularly limited, as long as it is useful as a reference for one or more unknown gene sequences in one or more samples, It can for example be one or more reference genomes, a pan genome or one or more centroids. According to certain embodiments, the reference sequences comprise one or more centroids, wherein a centroid is a representative of a gene group/family/cluster of a genome, e.g. of a microorganism. Centroids can be for example extracted from the database MetaRef (http://metaref.org/), which was used in the present examples, with the extraction from the data base being carried out particularly on Nov. 24, 2014. After the extraction the data from the MetaRef database can be updated continually for further experiments. A list of centroids can be extracted for each organism separately or as a whole. In the present examples a list of centroids was extracted for each organism. The centroid information, e.g. for annotation, can be extracted from databases like IMG (http://img.jgi.doe.gov/), as in the present case, or NCBI.

providing a second data set of antimicrobial drug, e.g. antibiotic, resistance and/or susceptibility of the plurality of clinical isolates of the microorganism;

correlating the third data set with the second data set and statistically analyzing the correlation; and

determining the structural variations in the genome of the microorganism associated with antimicrobial drug, e.g. antibiotic, resistance.

In this method, as well as the other methods of the invention, the first data set of gene sequences of a plurality of clinical isolates can be provided or obtained in any way, preferably non-invasive, and can be e.g. provided from in vitro samples.

According to certain embodiments, the obtaining or providing of gene sequences of a plurality of clinical isolates in this method—as well as the other methods of the invention—can comprise the following:

A sample of a vertebrate, e.g. a human, e.g. is provided or obtained and nucleic acid sequences, e.g. DNA or RNA sequences, are recorded by a known method for recording nucleic acid, which is not particularly limited. For example, nucleic acid can be recorded by a sequencing method, wherein any sequencing method is appropriate, particularly sequencing methods wherein a multitude of sample components, as e.g. in a blood sample, can be analyzed for nucleic acids and/or nucleic acid fragments and/or parts thereof contained therein in a short period of time, including the nucleic acids and/or nucleic acid fragments and/or parts thereof of at least one microorganism of interest, particularly a bacterial microorganism. For example, sequencing can be carried out using polymerase chain reaction (PCR), particularly multiplex PCR, or high throughput sequencing or next generation sequencing, preferably using high-throughput sequencing. For sequencing, preferably an in vitro sample is used.

The data obtained by the sequencing can be in any format, and can then be used to identify the nucleic acids of the microorganism to be identified, by known methods, e.g. fingerprinting methods, comparing genomes and/or aligning to at least one, or more, reference sequences of one or more species of the microorganism of interest, e.g. a reference genome and/or centroids, etc., forming a third data set of, optionally aligned, genes for a microorganism-discarding additional data from other sources, e.g. the vertebrate. For the present method, also the raw data can be used and/or assemblies, at least in part, can be used for forming the third data set. Thus, according to certain embodiments, at least a part of the gene sequences of the first data set can be assembled, wherein assembly can be carried out by any known method and is not particularly limited. In addition, also data from reference sequences, e.g. centroids and/or genomes of known species, e.g. from bacterial species that are already known, e.g. from databases like MetaRef and/or at the NCBI, can be used in the first data set and/or for evaluation of the first data set.

For some organisms, it might be useful in genome-wide association studies to reference the points of interest, e.g. structural variations, to one constant reference for enhanced standardization. In case of the human with a high consistency of the genome and 99% identical sequences among individuals this is easy and represents the standard, as corresponding reference genomes are available in databases.

In case of organisms that trigger infectious diseases (e.g. bacteria and viruses) this is much more difficult, though, and particularly also genetic variations that are not on genes, particularly known genes, can be missed when aligning sequence data to a reference genome. One possibility to overcome this is to fall back on a virtual pan-genome which contains all sequences of a certain genus or to perform reference free variation calling. A further possibility is the analysis of a huge amount of reference sequences, e.g. from MetaRef, and even all available references, which is much more complex. Therein all n references from a database (e.g. RefSeq) are extracted and compared with the newly sequenced bacterial genomes k. After this, matrices (% of mapped reads, % of covered genome) can be applied and the data can be compared to several reference sequences. In such a case, n×k complete alignments are carried out. Having a big number of references, stable results can be obtained.

In the present method, gene sequence of the first data set can also be assembled, at least in part, according to certain embodiments with known methods, e.g. by de-novo assembly or mapping assembly. The sequence assembly is not particularly limited, and any known genome assembler can be used, e.g. based on Sanger, 454, Solexa, Illumina, SOLid technologies, etc., as well as hybrids/mixtures thereof.

According to certain embodiments, the data of nucleic acids of different origin than the microorganism of interest, e.g. a bacterial microorganism, can be removed after the nucleic acids of interest are identified, e.g. by filtering the data out. Such data can e.g. include nucleic acids of a patient, e.g. the vertebrate, e.g. human, and/or other microorganisms, etc. This can be done by e.g. computational subtraction, as developed by Meyerson et al. 2002. For this, also aligning to the genome of the vertebrate, etc., is possible. For aligning, several alignment-tools are available. This way the original data amount from the sample can be drastically reduced.

After such removal of “excess” data, obtaining the third data set can be carried out for the microorganism, e.g. a bacterial microorganism, as described above.

Using these techniques, structural variations in the genome, e.g. in the gene sequences, of the microorganism of interest, e.g. a bacterial microorganism, can be obtained for various species.

When testing these same species for antimicrobial drug, e.g. antibiotic, susceptibility of a number of antimicrobial drugs, e.g. antibiotics, e.g. using standard culturing methods on dishes with antimicrobial drug, e.g. antibiotic, intake, as e.g. described below, the results of these antimicrobial drug, e.g. antibiotic, susceptibility tests can then be cross-referenced/correlated with the structural variations in the genome of the respective microorganism. Using several, e.g. 50 or more than 50, 100 or more than 100, 200 or more than 200, 400 or more than 400, 800 or more than 800, or 900 or more than 900 different isolates of the same or different species of a microorganism, statistical analysis can be carried out on the obtained cross-referenced data between genetic variations and antimicrobial drug, e.g. antibiotic, susceptibility for these microorganisms, using known methods.

Regarding culturing methods, samples of microorganisms can be e.g. cultured overnight. On the next day individual colonies can be used for identification of organisms, either by culturing or using mass spectroscopy. Based on the identity of organisms new plates containing increasing concentration of antibiotics used for the treatment of these organisms are inoculated and grown for additional 12-24 hours. The lowest drug concentration which inhibits growth (minimal inhibitory concentration—MIC) can be used to determine susceptibility/resistance for tested antibiotics.

Also, resistance testing can be carried out by determining e.g. known resistance genes in the different isolates, like in case of methicillin resistant Staphylococcus aureus (MRSA) and methicillin susceptible Staphylococcus aureus (MSSA). For determining resistances, respectively susceptibility, the data from culturing methods and/or from determining known resistance genes, as well as data obtained in different ways, e.g. based on mass spectrometry (possibly also in connection with culturing) can be used.

Correlation of the genetic variations with antimicrobial drug, e.g. antibiotic, resistance can be carried out in a usual way and is not particularly limited. For example, resistances can be correlated to structural variances in the whole genome of the respective microorganism or only parts thereof, for example only coding parts of the genome. In some cases even only genetic variations in genes, e.g. certain genes, or certain mutations in genes can be determined. After correlation, statistical analysis can be carried out.

According to certain embodiments, the data of the first data set can be filtered prior to a possible annotation to a pan-genome and/or reference genome(s) and the correlation with the resistance/susceptibility data.

For example, to reduce the number of similar annotations they can be filtered and aggregated by one or more of the following:

- Only annotations for which the considered structural variation lies on a protein can be kept and the further data discarded
- Only annotations which do not contain “hypothetical proteins” can be kept
- Annotations can be sorted by identification number (ID) and gene product
- For a unique pair of IDs and gene products only the first annotation can be kept, e.g in case of multiple genes in a genome

Also, according to certain embodiments, the following structural variations can be excluded:

1. Constant features and phenotypes (same value or only NA) can be removed (e.g. centroids present in all samples or phenotypes with the result “resistant” for all samples)

2. Almost constant features and phenotypes can also removed, e.g. features whose most frequent value was in >=95% of all samples, ignoring NA values, can be removed (e.g. a centroid is present in >=95% of all samples)

Also phenotypes whose most frequent value was in >=90% of all samples, ignoring NA values, can be removed (e.g. >=90% of all samples are resistant)

3. In addition, as is the case in the present examples for the Gram-positive bacteria S. aureus (Gram neg. bacteria in the Examples did not have partially missing data for phenotypes), only drugs with non-missing data for at least 10% of the samples can be kept.

For statistical analysis, as in the examples, e.g. Fisher's exact two-sided test can be applied with subsequent p-value adjustment over all phenotypes together using FDR and p-value threshold of 0.01 (1e-2). Additionally, 10 permutation tests can be performed by permuting each phenotype separately and applying Fisher's exact test to the centroid presence matrix and permuted phenotypes. The results then can be further filtered by centroid annotation, i.e.

1. Centroids without a gene product name can be removed

2. Centroids whose gene product name contains “putative”, “predicted” or “hypothetical” can be removed

3. If there are centroids with same gene product name and gene symbol than only the first one can be kept

4. Centroids without GeneBank accession can be removed

According to certain embodiments, the structural variations can be annotated to a pan-genome of the microorganism and/or annotated to one or more reference sequences, e.g. centroids, of the microorganism. The construction of a pan-genome is not particularly limited and can be done using known methods.

However, other suitable reference genomes (e.g. used in the Examples, but also for other microorganisms) can be found at publicly available data bases like at the NCBI or from MetaRef.

Statistical analysis of the correlation of the gene mutations with antimicrobial drug, e.g. antibiotic, resistance is not particularly limited and can be carried out, depending on e.g. the amount of data, in different ways, for example using analysis of variance (ANOVA), Student's t-test or Fisher's exact test, for example with a sample size n of 50, 100, 200, 300, 400, 500 or 600, and a level of significance (a-error-level) of e.g. 0.05 or smaller, e.g. 0.05, preferably 0.01 or smaller. A statistical value can be obtained for each structural variation and/or each genetic sequence in the genome as well as for all antibiotics tested, a group of antibiotics or a single antibiotic. The obtained p-values can also be adapted for statistical errors, if needed.

For statistically sound results a multitude of individuals should be sampled, with n=50, 100, 200, 300, 400, 500 or 600, and a level of significance (a-error-level) of e.g. 0.05 or smaller, e.g. 0.05, preferably 0.01 or smaller. According to certain embodiments, particularly significant results can be obtained for n=200, 300, 400, 500 or 600.

For statistically sound results a multitude of individuals should be sampled, with n=50 or more, 100 or more, 200 or more, 300 or more, 400 or more, 500 or more or 600 or more, and a level of significance (a-error-level) of e.g. 0.05 or smaller, e.g. 0.05, preferably 0.01 or smaller. According to certain embodiments, particularly significant results can be obtained for n=200 or more, 300 or more, 400 or more, 500 or more or 600 or more.

After the above procedure has been carried out for the individual strains of bacterial species in the Examples, the data disclosed in Tables 1 to 24 were obtained for the statistically best correlations between structural variations and antimicrobial drug, e.g. antibiotic, resistances. In the tables, tables with an odd number, e.g. 1, 3, 5, represent the top 50 results for the statistical analysis as described above, i.e. the structural variations with the best p-value (denoted best_pv in the tables) for at least one antibiotic, whereas the tables with an even number show the top 50 results regarding p-value with at least one drug class ratio of 1.0, so that the structural variation applies to a multitude of drugs and at least a specific drug class, wherein the following applies:

Drug class ratio=number of significant drugs of that class/number of tested drugs of that class For example, if two fluoroquinolones were tested but only one has significant p-value, then the drug class ratio for fluoroquinolones is 0.5.

Genetic variations in the gene sequences given in Tables 1 to 24, with regard to the several reference sequences as above, were proven as valid markers for antimicrobial drug, e.g. antibiotic, resistance. According to certain embodiments, structural variations in at least the gene sequences and/or relating to at least the whole sequences between the start coordinate (denoted “Start.Coord” in the tables) and the end coordinate (denoted “End.Coord” in the tables) of the genes, particularly relating to the whole sequence between the start coordinate and the end coordinate, given for consecutive numbers (“No.”) 1 to 50 with the highest p-values, as above, in Tables 1-24 are obtained by the present method.

When referring to the second data set, wherein the second data set e.g. comprises, respectively is, a set of antimicrobial drug, e.g. antibiotic, resistances of a plurality of clinical isolates, this can, within the scope of the invention, also refer to a self-learning data base that, whenever a new sample is analyzed, can take this sample into the second data set and thus expand its data base. The second data set thus does not have to be static and can be expanded, either by external input or by incorporating new data due to self-learning. This is, however, not restricted to the first aspect of the invention, but applies to other aspects of the invention that refer to a second data set, which does not necessarily have to refer to antimicrobial drug resistance. The same applies, where applicable, to the first data set, e.g. in the first aspect.

According to certain embodiments of the first aspect, the structural variations are detected alignment-free. According to certain embodiments, the structural variations are annotated to a pan-genome of the microorganism and/or annotated to one or more reference sequences.

According to certain embodiments, statistical analysis in the present methods is carried can be carried using Fisher's test with p<10⁻³, preferably p<10⁻⁶, further preferably p<10⁻⁹.

The method of the first aspect of the present invention, as well as related methods, e.g. according to the 2^nd, 3^rdand 4^thaspect, can, according to certain embodiments, comprise correlating different genetic sites to each other. This way even higher statistical significance can be achieved.

According to certain embodiments of the method of the first aspect and related methods-as above, the second data set can be provided by culturing the clinical isolates of the microorganism on agar plates provided with antimicrobial drugs, e.g. antibiotics, at different concentrations, and the second data can be obtained by taking the minimal concentration of the plates that inhibits growth of the respective microorganism.

According to certain embodiments of the method of the first aspect and related methods, the microorganism is a Gram positive bacterial microorganism, particularly a Staphylococcus species, particularly Staphylococcus aureus, and the antimicrobial drug, e.g. antibiotic drug, is selected from the group consisting of β-lactams, β-lactam inhibitors, quinolines and derivatives thereof, e.g. fluoroquinolones, aminoglycosides, glycopeptides, lincosamides, macrolides, nitrofuranes, oxazolidinones polyketides, respectively tetracyclines, and folate synthesis inhibitors, e.g. benzene derived/sulfonamide antibiotics, preferably from the group consisting of Amoxicillin/Clavulanate, Ampicillin, Ampicillin/Sulbactam, Azithromycin, Cefalothin, Cefazolin, Cefepime, Cefotaxime, Cefoxitin, Ceftriaxone, Cefuroxime, Chloramphenicol, Ciprofloxacin, Clindamycin, Daptomycin, Ertapenem, Erythromycin, Fosfomycin, Fusidic acid, Gentamicin, Imipenem, Levofloxacin, Linezolid, Meropenem, Methicillin, Moxifloxacin, Mupirocin, Nitrofurantoin, Norfloxacin, Ofloxacin, Oxacillin, Penicillin G, Piperacillin/Tazobactam, Quinupristin/Dalfopristin, Rifampicin, Teicoplanin, Tetracycline, Tigecycline, Tobramycin, Trimethoprim/Sulfamethoxazole, and Vancomycin, further preferably from the group consisting of Amoxicillin/Clavulanate, Ampicillin, Ampicillin/Sulbactam, Azithromycin, Cefalothin, Cefazolin, Cefepime, Cefotaxime, Cefoxitin, Ceftriaxone, Cefuroxime, Chloramphenicol, Ciprofloxacin, Clindamycin, Daptomycin, Ertapenem, Erythromycin, Fosfomycin, Fusidic acid, Gentamicin, Imipenem, Levofloxacin, Linezolid, Meropenem, Moxifloxacin, Mupirocin, Nitrofurantoin, Norfloxacin, Ofloxacin, Oxacillin, Penicillin G, Piperacillin/Tazobactam, Quinupristin/Dalfopristin, Rifampicin, Teicoplanin, Tetracycline, Tigecycline, Tobramycin, Trimethoprim/Sulfamethoxazole, and Vancomycin.

According to certain embodiments of the method of the first aspect and related methods, the microorganism is a Gram negative bacterial microorganism, particularly one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, and/or Shigella species, particularly as denoted in the Examples, and the antimicrobial drug, e.g. antibiotic, is at least one selected from the group of β-lactams, β-lactam inhibitors, quinolines and derivatives thereof, aminoglycosides, polyketides, respectively tetracyclines, and folate synthesis inhibitors, preferably from the group consisting of Amoxicillin/K Clavulanate (AUG), Ampicillin (AM), Aztreonam (AZT), Cefazolin (CFZ), Cefepime (CPM), Cefotaxime (CFT), Ceftazidime (CAZ), Ceftriaxone (CAX), Cefuroxime (CRM), Cephalotin (CF), Ciprofloxacin (CP), Ertapenem (ETP), Gentamicin (GM), Imipenem (IMP), Levofloxacin (LVX), Meropenem (MER), Piperacillin/Tazobactam (P/T), Ampicillin/Sulbactam (A/S), Tetracycline (TE), Tobramycin (TO), and Trimethoprim/Sulfamethoxazole (T/S).

According to certain embodiments, structural variations in at least the gene sequences and/or relating to at least the whole sequences between the start coordinate (denoted “Start.Coord” in the tables) and the end coordinate (denoted “End.Coord” in the tables) of the genes, particularly relating to the whole sequence between the start coordinate and the end coordinate, given for consecutive numbers (“No.”) 1 to 50 with the highest p-values, as above, in Tables 1-24 are obtained by the present method, and the antibiotic is at least one chosen from the class of antibiotics in the column designated “sign_phenos_class”, particularly the one in the column designated “best_pheno_class”, preferably wherein the antibiotic is at least one chosen from the ones in the column designated “sign_phenos”, particularly the one in the column designated “best_pheno”.

a) obtaining or providing a sample containing or suspected of containing a microorganism, particularly a bacterial microorganism, from the patient;

With this method, any mutations in the genome of a microorganism, e.g. the bacterial species given above and below in the Examples, e.g. a clinical isolate with an unknown strain of the microorganism, particularly bacterial microorganism, correlated with antimicrobial drug, e.g. antibiotic, resistance can be determined and a thorough antimicrobial drug, e.g. antibiotic, resistance profile can be established which can add information to a profile which considers only changes in single bases, e.g. single nucleotide polymorphisms (SNPs).

Again, the different steps can herein be carried out as described with regard to the first aspect of the present invention.

According to this aspect, an infection with a microorganism, particularly a bacterial microorganism, in a patient can be determined using sequencing methods, as well as a resistance to antimicrobial drugs, e.g. antibiotics, of the microorganism can be determined in a short amount of time compared to conventional methods.

a) obtaining or providing a sample containing or suspected of containing a microorganism, particularly a bacterial microorganism, from the patient;

b) determining the presence of at least one structural variation in at least one genetic sequence of the microorganism, particularly bacterial microorganism, as determined by the method of any one of claims 1 to 3, wherein the presence of said at least one structural variation is indicative of a resistance to one or more antimicrobial drugs;

c) identifying said at least one or more antimicrobial drugs; and

d) selecting one or more antimicrobial drugs different from the ones identified in step c) and being suitable for the treatment of the infection with the microorganism, particularly the bacterial microorganism.

This method can be carried out similarly to the second aspect of the invention and enables a fast was to select a suitable treatment with antibiotics for any infection with an unknown microorganism, particularly bacterial microorganism, e.g. Staphylococcus aureus.

In this method, as well as similar ones, no aligning is necessary, as the unknown sample can be directly correlated, after the genome or genome sequences are produced, with the second data set, and thus genetic variations and antimicrobial drug, e.g. antibiotic, resistances can be determined. The first data set can be assembled, for example, using known techniques.

According to certain embodiments, statistical analysis in the present method is carried out using Fisher's test with p<10⁻³, preferably p<10⁻⁶, preferably p<10⁻⁹. Also, according to certain embodiments, the method further comprises correlating different genetic sites to each other.

With this method, antimicrobial drug, e.g. antibiotic, resistances in an unknown isolate of a microorganism, e.g. Staphylococcus aureus, can be determined.

A simple read out concept for a diagnostic test as described in this aspect is shown schematically in FIG. 1.

According to FIG. 1, a sample 1, e.g. blood from a patient, is used for molecular testing 2, e.g. using next generation sequencing (NGS), and then a molecular fingerprint 3 is taken, e.g. in case of NGS a sequence of selected genomic/plasmid regions or the whole genome is assembled. This is then compared to a reference library 4 containing several reference sequences and/or a pan-genome, i.e. selected sequences or the whole sequence are/is compared to one or more reference sequences and/or a pan-genome, and structural variations (,sequence/gene additions/deletions, etc.) are correlated with susceptibility/resistance profiles of reference sequences the reference library. The reference library 4 herein contains many genomes and/or a pan-genome and is different from a reference genome. Then the result 5 is reported which can comprise ID (pathogen identification), i.e. a list of all (pathogenic) species identified in the sample, and AST (antimicrobial susceptibility testing), i.e. a list including a susceptibility/resistance profile for all species listed, based on structural variations.

Again, in the third and fourth aspect, the different steps can herein be carried out as described with regard to the first aspect of the present invention.

In certain embodiments the computer program product is one on which program commands or program codes of a computer program for executing said method are stored. According to certain embodiments the computer program product is a storage medium. As noted above, the computer program products of the present invention can be self-learning, e.g. with respect to the first and second data sets.

In order to obtain the best possible information from the highly complex genetic data and develop an optimum model for diagnostic and therapeutical uses as well as the methods of the present invention—which can be applied stably in clinical routine—a thorough in silico analysis can be necessary. The proposed principle is based on a combination of different approaches, e.g. assembly of the gene sequences and/or genome of the microorganisms, at least in part and optionally annotating the sequences to one or more reference sequences and/or a pan-genome, and/or alignment of the sequence data of the clinical isolate to be determined with one or more reference sequences and/or a pan-genome, and correlation of structural variations found in every sample, e.g. from each patient, respectively an unknown clinical isolate, with all references and drugs, e.g. antibiotics, or only one or some of them, and search for structural variations which occur in one or several drug and one or several strains.

Using the above steps a list of structural variations s with regard to one or more reference sequences and/or a pan-genome is generated. These can be stored in databases and statistical models can be derived from the databases. The statistical models can be based on at least one or more structural variations in at least one or more sequences. Statistical models that can be trained can be combined from structural variations and sequences. Examples of algorithms that can produce such models are association Rules, Support Vector Machines, Decision Trees, Decision Forests, Discriminant-Analysis, Cluster-Methods, and many more.

The goal of the training is to allow a reproducible, standardized application during routine procedures.

For this, for example, gene sequences or parts thereof can be sequenced from a patient to be diagnosed. Afterwards, core characteristics can be derived from the sequence data which can be used to predict resistance. These are the points in the database used for the final model, i.e. at least one structural variation, but also combinations of structural variations, etc.

The corresponding characteristics can be used as input for the statistical model and thus enable a prognosis for new patients. Not only the information regarding all resistances of all microorganisms, against all or only some or one drugs, e.g. antibiotics, can be integrated in a computer decision support tool, but also corresponding directives (e.g. EUCAST) so that only treatment proposals are made that are in line with the directives.

An eighth aspect of the present invention relates to the use of the computer program product according to the fifth aspect, e.g. for determining structural variations of a genome of a microorganism for a clinical isolate of the microorganism in the fourth aspect of the invention and/or for use in the diagnostic method of the second method of the invention and/or for selecting a treatment in the third aspect of the present invention and/or in the method of the first aspect of the present invention.

A sixth aspect of the present invention discloses a diagnostic method of determining an infection of a patient with a microorganism, preferably a bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species), potentially resistant to antimicrobial drug, e.g. antibiotic, treatment, comprising the steps of:

a) obtaining or providing a sample containing or suspected of containing at least one microorganism, preferably a bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species), from the patient;

b) determining the presence of at least one structural variation in at least two sequences from the group of sequences annotated with Nos. 1-50 with regard to the reference sequences, particularly centroids (denoted “Scaffold.External.Accession”), with the sequences names, particularly centroid names (denoted “Scaffold.Name”), given in Tables 1 to 24, particularly with the reference genomes and genome names given in Tables 1 a to 24 a, wherein the presence of said at least two structural variations is indicative of an infection with an antimicrobial drug, e.g. antibiotic, resistant microorganism, preferably bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species), in said patient.

As noted above, genetic variations in the gene sequences given in Tables 1 to 24, with regard to the several reference sequences as above, were proven as valid markers for antimicrobial drug, e.g. antibiotic, resistance. According to certain embodiments, structural variations in at least the gene sequences and/or relating to at least the whole sequences between the start coordinate (denoted “Start.Coord” in the tables) and the end coordinate (denoted “End.Coord” in the tables) of the genes, particularly relating to the whole sequence between the start coordinate and the end coordinate, given for consecutive numbers (“No.”) 1 to 50 with the highest p-values, as above, in Tables 1-24 are obtained by the present method.

An infection of a patient with a microorganism, preferably a bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species), potentially resistant to antimicrobial drug treatment herein means an infection of a patient with a microorganism, preferably a bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species), wherein it is unclear if the microorganism, preferably bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species), is susceptible to treatment with a specific antimicrobial drug or if it is resistant to the antimicrobial drug.

In step b) above, as well as corresponding steps, at least one structural variation in at least two positions is determined, so that in total at least two structural variations are determined, wherein the two structural variations are in different positions, respectively are different sequences.

In this method, as well as the other methods of the invention, the sample can be provided or obtained in any way, preferably non-invasive, and can be e.g. provided as an in vitro sample or prepared as in vitro sample.

According to certain aspects, structural variations in at least two, three, four, five, six, seven, eight, nine or ten positions, respectively sequences, are determined in any of the methods of the present invention, e.g. in at least two positions, respectively sequences, or in at least three positions, respectively sequences. Instead of testing only single positions, respectively sequences, a combination of several variant positions, respectively sequences, can improve the prediction accuracy and further reduce false positive findings that are influenced by other factors. Therefore, it is in particular preferred to determine the presence of structural variations in 2, 3, 4, 5, 6, 7, 8 or 9 (or more) sequences selected from the respective Table 1-24.

According to certain embodiments, the obtaining or providing a sample containing or suspected of containing at least one microorganism, preferably a bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species), from the patient in this method—as well as the other methods of the invention—can comprise the following:

A sample of a vertebrate, e.g. a human, e.g. is provided or obtained and nucleic acid sequences, e.g. DNA or RNA sequences, are recorded by a known method for recording nucleic acid, which is not particularly limited. For example, nucleic acid can be recorded by a sequencing method, wherein any sequencing method is appropriate, particularly sequencing methods wherein a multitude of sample components, as e.g. in a blood sample, can be analyzed for nucleic acids and/or nucleic acid fragments and/or parts thereof contained therein in a short period of time, including the nucleic acids and/or nucleic acid fragments and/or parts thereof of the microorganism. For example, sequencing can be carried out using polymerase chain reaction (PCR), particularly multiplex PCR, or high throughput sequencing or next generation sequencing, preferably using high-throughput sequencing. For sequencing, preferably an in vitro sample is used.

The data obtained by the sequencing can be in any format, and can then be analyzed as described with regard to the first to fourth aspect of the present invention.

In a seventh aspect, the present invention relates to a method of selecting a treatment of a patient suffering from an infection with a potentially resistant microorganism, preferably a bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species), comprising the steps of:

c) identifying said at least one or more antimicrobial, e.g. antibiotic, drugs; and

d) selecting one or more antimicrobial, e.g. antibiotic, drugs different from the ones identified in step c) and being suitable for the treatment of the infection with the microorganism, preferably bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species).

In this method, the steps a) of obtaining or providing a sample and b) of determining the presence of at least one structural variation are as in the method of the sixth aspect.

The identification of the at least one or more antimicrobial, e.g. antibiotic, drug in step c) is then based on the results obtained in step b) and corresponds to the antimicrobial, e.g. antibiotic, drug(s) that correlate(s) with the structural variations. Once these antimicrobial drugs, e.g. antibiotics, are ruled out, the remaining antimicrobial drugs, e.g. antibiotic drugs/antibiotics, can be selected in step d) as being suitable for treatment.

In the description, references to the sixth and seventh aspect also apply to the 9^th, 10^th, 11^thand 12^thaspect, referring to the same positions, respectively sequences, unless clear from the context that they don't apply.

According to certain embodiments, the microorganism is a Gram positive bacterial microorganism, particularly a Staphylococcus species, particularly Staphylococcus aureus, and the antimicrobial drug, e.g. antibiotic drug, is selected from the group consisting of β-lactams, β-lactam inhibitors, quinolines and derivatives thereof, e.g. fluoroquinolones, aminoglycosides, glycopeptides, lincosamides, macrolides, nitrofuranes, oxazolidinones polyketides, respectively tetracyclines, and folate synthesis inhibitors, e.g. benzene derived/sulfonamide antibiotics, preferably from the group consisting of Amoxicillin/Clavulanate, Ampicillin, Ampicillin/Sulbactam, Azithromycin, Cefalothin, Cefazolin, Cefepime, Cefotaxime, Cefoxitin, Ceftriaxone, Cefuroxime, Chloramphenicol, Ciprofloxacin, Clindamycin, Daptomycin, Ertapenem, Erythromycin, Fosfomycin, Fusidic acid, Gentamicin, Imipenem, Levofloxacin, Linezolid, Meropenem, Methicillin, Moxifloxacin, Mupirocin, Nitrofurantoin, Norfloxacin, Ofloxacin, Oxacillin, Penicillin G, Piperacillin/Tazobactam, Quinupristin/Dalfopristin, Rifampicin, Teicoplanin, Tetracycline, Tigecycline, Tobramycin, Trimethoprim/Sulfamethoxazole, and Vancomycin, further preferably from the group consisting of Amoxicillin/Clavulanate, Ampicillin, Ampicillin/Sulbactam, Azithromycin, Cefalothin, Cefazolin, Cefepime, Cefotaxime, Cefoxitin, Ceftriaxone, Cefuroxime, Chloramphenicol, Ciprofloxacin, Clindamycin, Daptomycin, Ertapenem, Erythromycin, Fosfomycin, Fusidic acid, Gentamicin, Imipenem, Levofloxacin, Linezolid, Meropenem, Moxifloxacin, Mupirocin, Nitrofurantoin, Norfloxacin, Ofloxacin, Oxacillin, Penicillin G, Piperacillin/Tazobactam, Quinupristin/Dalfopristin, Rifampicin, Teicoplanin, Tetracycline, Tigecycline, Tobramycin, Trimethoprim/Sulfamethoxazole, and Vancomycin.

According to certain embodiments, the microorganism is a Gram negative bacterial microorganism, particularly one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, and/or Shigella species, particularly as denoted in the Examples, and the antimicrobial drug, e.g. antibiotic, is at least one selected from the group of β-lactams, β-lactam inhibitors, quinolines and derivatives thereof, aminoglycosides, polyketides, respectively tetracyclines, and folate synthesis inhibitors, preferably from the group consisting of Amoxicillin/K Clavulanate (AUG), Ampicillin (AM), Aztreonam (AZT), Cefazolin (CFZ), Cefepime (CPM), Cefotaxime (CFT), Ceftazidime (CAZ), Ceftriaxone (CAX), Cefuroxime (CRM), Cephalotin (CF), Ciprofloxacin (CP), Ertapenem (ETP), Gentamicin (GM), Imipenem (IMP), Levofloxacin (LVX), Meropenem (MER), Piperacillin/Tazobactam (P/T), Ampicillin/Sulbactam (A/S), Tetracycline (TE), Tobramycin (TO), and Trimethoprim/Sulfamethoxazole (T/S).

In the methods of the invention the resistance of the microorganism, preferably bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species), to one or more antimicrobial, e.g. antibiotic, drugs can be determined according to certain embodiments.

According to certain embodiments of the sixth and/or seventh aspect of the invention, the resistance of the microorganism, preferably bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species), against 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 16, 17, 18, 19, 20 or more antibiotic drugs is determined.

According to certain embodiments of the sixth and/or seventh aspect of the invention, determining the nucleic acid sequence information with the sequences having a structural variation or the presence of a structural variation comprises using a next generation sequencing or high throughput sequencing method. According to preferred embodiments of the sixth and/or seventh aspect of the invention, a partial or entire genome sequence of a microorganism, preferably a bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species), is determined by using a next generation sequencing or high throughput sequencing method.

A ninth aspect of the present invention is directed to a method of treating a patient suffering from an antimicrobial drug, e.g. antibiotic, resistant infection with a microorganism, preferably a bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species), comprising the steps of:

c) identifying said at least one or more antimicrobial, e.g. antibiotic, drugs;

d) selecting one or more antimicrobial, e.g. antibiotic, drugs different from the ones identified in step c) and being suitable for the treatment of the infection with the microorganism, preferably a bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species); and

e) treating the patient with said one or more antimicrobial, e.g. antibiotic, drugs.

Herein, steps a) to d) can be carried out as described with respect to the seventh aspect. Step e) can be sufficiently carried out without being restricted and can be done e.g. non-invasively.

A tenth aspect of the present invention discloses a diagnostic method of determining an infection of a patient with a microorganism, preferably a bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species), potentially resistant to antimicrobial drug, e.g. antibiotic, treatment, comprising the steps of:

b) determining the presence of at least one structural variation in at least one sequence from the group of sequences annotated with Nos. 1-50 with regard to the reference sequences, particularly centroids (denoted “Scaffold.External.Accession”), with the sequences names, particularly centroid names (denoted “Scaffold.Name”), given in Tables 1 to 24, particularly with the reference genomes and genome names given in Tables 1 to24 a, wherein the presence of said at least one structural variation is indicative of an infection with an antimicrobial drug, e.g. antibiotic, resistant microorganism, preferably a bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species), in said patient.

In an eleventh aspect, the present invention relates to a method of selecting a treatment of a patient suffering from an infection with a potentially resistant microorganism, preferably a bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species), comprising the steps of:

c) identifying said at least one or more antimicrobial, e.g. antibiotic, drugs; and

d) selecting one or more antimicrobial, e.g. antibiotic, drugs different from the ones identified in step c) and being suitable for the treatment of the infection with the microorganism, preferably a bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species).

Again, in the tenth and the eleventh aspect the steps correspond to those in the sixth or seventh aspect, although only a mutation in at least one gene is determined.

A twelfth aspect of the present invention is directed to a method of treating a patient suffering from an antimicrobial drug, e.g. antibiotic, resistant infection with a microorganism, preferably a bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species), comprising the steps of:

c) identifying said at least one or more antimicrobial, e.g. antibiotic, drugs;

d) selecting one or more antimicrobial, e.g. antibiotic, drugs different from the ones identified in step c) and being suitable for the treatment of the infection with the microorganism, preferably a bacterial microorganism, particularly one as noted above (i.e. one or more of Acinetobacter, Escherichia, e.g. E.coli, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species); and e) treating the patient with said one or more antimicrobial, e.g. antibiotic, drugs.

Also in the twelfth aspect of the invention, steps a) to d) are analogous to the steps in the method of the ninth aspect of the present invention. Step e) can again be sufficiently carried out without being restricted and can be done e.g. non-invasively.

EXAMPLES

The present invention will now be described in detail with reference to several examples thereof. However, these examples are illustrative and do not limit the scope of the invention.

Example 1

Acinetobacter, Particularly Acinetobacter Baumanii

Whole genome sequencing was carried out in addition to classical antimicrobial susceptibility testing of the same isolates for a cohort of 448 specimens. This allowed performing genome wide correlation studies to find genetic variants (e.g. point mutations, small insertions and deletion, larger structural variants, plasmid copy number gains, gene dosage effects) in the genome and plasmids that are significantly correlated to the resistance against one or several drugs. The approach also allows for comparing the relevant sites in the genome to each other.

In the approach the different sources of genetic resistance regarding structural variances as well as the different ways of how bacteria can become resistant were covered. By measuring clinical isolates collected in a broad geographical area and across a broad time span of three decades a complete picture going far beyond the rather artificial step of laboratory generated resistance mechanisms was tried to be generated.

To this end, a set of 21 clinically relevant antimicrobial agents with 5 different modes of action was put together, and the minimally inhibitory concentration (MIC) of the 21 drugs for the Acinetobacter isolates was measured.

The detailed procedure is given in the following:

Bacterial Strains

The inventors selected 448 Acinetobacter strains from the microbiology strain collection at Siemens Healthcare Diagnostics (West Sacramento, Calif.) for susceptibility testing and whole genome sequencing.

Antimicrobial Susceptibility Testing (AST) Panels Frozen reference AST panels were prepared following Clinical Laboratory Standards Institute (CLSI) recommendations. The following antimicrobial agents (with μg/ml concentrations shown in parentheses) were included in the panels:

Amoxicillin/K Clavulanate (0.5/0.25-64/32), Ampicillin (0.25-128), Ampicillin/Sulbactam (0.5/0.25-64/32), Aztreonam (0.25-64), Cefazolin (0.5-32), Cefepime (0.25-64), Cefotaxime (0.25-128), Ceftazidime (0.25-64), Ceftriaxone (0.25-128), Cefuroxime (1-64), Cephalothin (1-64), Ciprofloxacin (0.015-8), Ertepenem (0.12-32), Gentamicin (0.12-32), Imipenem (0.25-32), Levofloxacin (0.25-16), Meropenem (0.12-32), Piperacillin/Tazobactam (0.25/4-256/4), Tetracycline (0.5-64), Tobramycin (0.12-32), and Trimethoprim/Sulfamethoxazole (0.25/4.7-32/608). Prior to use with clinical isolates, AST panels were tested with QC strains. AST panels were considered acceptable for testing with clinical isolates when the QC results met QC ranges described by CLSI16.

Inoculum Preparation

Isolates were cultured on trypticase soy agar with 5% sheep blood (BBL, Cockeysville, Md.) and incubated in ambient air at 35±1° C. for 18-24 h. Isolated colonies (4-5 large colonies or 5-10 small colonies) were transferred to a 3 ml Sterile Inoculum Water (Siemens) and emulsified to a final turbidity of a 0.5 McFarland standard. 2 ml of this suspension was added to 25 ml Inoculum Water with Pluronic-F (Siemens). Using the Inoculator (Siemens) specific for frozen AST panels, 5 μl of the cell suspension was transferred to each well of the AST panel. The inoculated AST panels were incubated in ambient air at 35±1° C. for 16-20 h. Panel results were read visually, and minimal inhibitory concentrations (MIC) were determined.

DNA Extraction

Four streaks of each Gram-negative bacterial isolate cultured on trypticase soy agar containing 5% sheep blood and cell suspensions were made in sterile 1.5 ml collection tubes containing 50 μl Nuclease-Free Water (AM9930, Life Technologies). Bacterial isolate samples were stored at −20° C. until nucleic acid extraction. The Tissue Preparation System (TPS) (096D0382-02_01_B, Siemens) and the VERSANT® Tissue Preparation Reagents (TPR) kit (10632404B, Siemens) were used to extract DNA from these bacterial isolates. Prior to extraction, the bacterial isolates were thawed at room temperature and were pelleted at 2000 G for 5 seconds. The DNA extraction protocol DNAext was used for complete total nucleic acid extraction of 48 isolate samples and eluates, 50 μl each, in 4 hours. The total nucleic acid eluates were then transferred into 96-Well qPCR Detection Plates (401341, Agilent Technologies) for RNase A digestion, DNA quantitation, and plate DNA concentration standardization processes. RNase A (AM2271, Life Technologies) which was diluted in nuclease-free water following manufacturer's instructions was added to 50 μl of the total nucleic acid eluate for a final working concentration of 20 μg/ml. Digestion enzyme and eluate mixture were incubated at 37° C. for 30 minutes using Siemens VERSANT® Amplification and Detection instrument. DNA from the RNase digested eluate was quantitated using the Quant-iT™ PicoGreen dsDNA Assay (P11496, Life Technologies) following the assay kit instruction, and fluorescence was determined on the Siemens VERSANT® Amplification and Detection instrument. Data analysis was performed using Microsoft® Excel 2007. 25 μl of the quantitated DNA eluates were transferred into a new 96-Well PCR plate for plate DNA concentration standardization prior to library preparation. Elution buffer from the TPR kit was used to adjust DNA concentration. The standardized DNA eluate plate was then stored at −80° C. until library preparation.

Next Generation Sequencing

Prior to library preparation, quality control of isolated bacterial DNA was conducted using a Qubit 2.0 Fluorometer (Qubit dsDNA BR Assay Kit, Life Technologies) and an Agilent 2200 TapeStation (Genomic DNA ScreenTape, Agilent Technologies). NGS libraries were prepared in 96 well format using NexteraXT DNA Sample Preparation Kit and NexteraXT Index Kit for 96 Indexes (Illumina) according to the manufacturer's protocol. The resulting sequencing libraries were quantified in a qPCR-based approach using the KAPA SYBR FAST qPCR MasterMix Kit (Peqlab) on a ViiA 7 real time PCR system (Life Technologies). 96 samples were pooled per lane for paired-end sequencing (2×100bp) on Illumina Hiseq2000 or Hiseq2500 sequencers using TruSeq PE Cluster v3 and TruSeq SBS v3 sequncing chemistry (Illumina). Basic sequencing quality parameters were determined using the FastQC quality control tool for high throughput sequence data (Babraham Bioinformatics Institute).

Data Analysis

For each organism in the examples, a list of centroids was extracted from MetaRef (http://metaref.org/). Herein, centroids were representatives of genes, etc. in a group/family/cluster. Data for information/annotation regarding the centroids was extracted from the database IMG (http://img.jgi.doe.gov/).

For Acinetobacter, 1380 centroids of A. baumannii were used as reference sequences, extracted from MetaRef.

The centroid presence in samples was evaluated as follows: Sequences of centroids were aligned against the de novo assemblies using BLASTn (http://blast.ncbi.nlm.nih.gov/Blast.cgi).

The following parameters were used:

- BLAST db type: “fasta” and “nucl”
- word size: 11 (default)
- gapopen: 3 (default 5)
- gapextend: 2 (default)
- penalty: −2 (default −3)
- reward: 1 (default)

A centroids was considered as present if the alignment result contained at least one hit with

- min. 80% identity of assembly sequence and centroid sequence
- min. 80% of centroid sequence was aligned, computed as

$centroidcoverage = \frac{centoidalignmentend - centroidalignmentstart + 1}{centroidlength}$

In the results, a centroid was coded as 0/1 (absent/present)

Association testing and result filtering:

The input data was further filtered as follows to reduce the amount of data:

- 1. Constant features and phenotypes (same value or only NA) were removed (e.g. centroids present in all samples or phenotypes with “resistant” for all samples)
- 2. Almost constant features and phenotypes were removed:
  - Features whose most frequent value was in >=95% of all samples, ignoring NA values (e.g. a centroid is present in >=95% of all samples), were removed
  - Penotypes whose most frequent value was in >=90% of all samples, ignoring NA values (e.g. >=95% of all samples are resistant), were removed 3. Particularly for S. aureus in Example 12, only drugs with non-missing data for at least 10% of the samples were kept

For statistical analysis, Fisher's exact two-sided test was applied with subsequent p-value adjustment over all phenotypes together using FDR and p-value threshold of 0.01 (1e-2). Additionally, 10 permutation tests were performed by permuting each phenotype separately and applying Fisher's exact test to the centroid presence matrix and permuted phenotypes. The results were further filtered by centroid annotation, i.e.

- 1. Centroids without a gene product name were removed
- 2. Centroids whose gene product name contains “putative”, “predicted” or “hypothetical” were removed
- 3. If there are centroids with same gene product name and gene symbol than only the first one was kept
- 4. Centroids without GeneBank accession were removed

After the above procedure has been carried out, the data disclosed in Tables 1 and 2 were obtained for the statistically best correlations between structural variations and antimicrobial drug, e.g. antibiotic, resistances. Table 1 (as well as the odd Tables 3, 5, 7, 9, 11, 13, 15, 17, 19, 21 and 23 in Examples 2 to 12) represents the top 50 results for structural variations with the best p-value (denoted best_pv in the tables) for at least one antibiotic, whereas Table 2 (as well as the even Tables 4, 6, 8, 10, 12, 14, 16, 18, 20, 22 and 24 in Examples 2 to 12) shows the top 50 results regarding p-value with at least one drug class ratio of 1.0, so that the structural variation applies to a multitude of drugs and at least a specific drug class, wherein the following applies:

Drug class ratio=number of significant drugs of that class/number of tested drugs of that class

For example, if two fluoroquinolones were tested but only one has significant p-value, then the drug class ratio for fluoroquinolones is 0.5.

In Tables 1 and 2, as well as also the following Tables 3 to 24 in Examples 2 to 12, the columns are designated as follows:

- No.: Consecutive number from 1-50, corresponding to the best p-values
- best_pheno: Phenotype (drug) with smallest adj. p-value
- best_pheno_class: drug class of best drug
- best_pv: adj. p-value of best phenotype calculated using Fisher's exact test and adjusted by FDR (Benjamini Hochberg) method (Benjamini Hochberg, 1995)
- sign_phenos: names of all phenotypes with significant adj. p-value separated by “i”
- sign_phenos_class: drug classes of all significant drugs
- num_<drug class>: number of significant drugs of that drug class
- <phenotype>_pv_adj: adjusted p-value of the phenotype calculated using Fisher's exact test and adjusted by FDR (Benjamini Hochberg) method (Benjamini Hochberg, 1995)
- Centroid (gene) annotation:
  - Locus.Tag: Locus of the gene in the genome
  - Gene.Symbol: Gene symbol
  - GeneBank.Accession: GeneBank ID for the gene
  - Chromosom: If gene lies on a plasmids, this column contains plasmid name
  - Start.Coord/End.Coord: Start and end coordinates of the gene
  - Strand: “+” for forward and “−” for reverse strand
  - Scaffold.ID: (IMG) ID of the scaffold containing the gene
  - Scaffold.External.Accession: Non-IMG ID, e.g. as annotated at the NCBI, RefSeq ID
  - Scaffold.Name: Genome name and scaffold external accession ID

TABLE 1a

Data for Acinetobacter, particularly Acinetobacter baumanii

Scaffold.External

No.
Accession
Scaffold.Name
best_pv

1
CP001921

Acinetobacter baumannii 1656-2: CP001921
7.16783907123597e−62

2
NZ_ACYR01000063

Acinetobacter sp. 6013113 NZ_ACYR01000063: NZ_ACYR01000063
1.39202289199418e−61

3
NC_009085

Acinetobacter baumannii ATCC 17978: NC_009085
1.43720401820086e−56

4
NC_011595

Acinetobacter baumannii AB307-0294: NC_011595
5.41948460225177e−51

5
NC_011595

Acinetobacter baumannii AB307-0294: NC_011595
7.00413054521082e−47

6
NC_011586

Acinetobacter baumannii AB0057: NC_011586
2.06435524702153e−46

7
NC_011586

Acinetobacter baumannii AB0057: NC_011586
8.98962816077673e−46

8
NC_011595

Acinetobacter baumannii AB307-0294: NC_011595
2.76883973579195e−44

9
NC_011586

Acinetobacter baumannii AB0057: NC_011586
6.86281420221907e−43

10
NZ_ABXK01000013

Acinetobacter baumannii AB900: NZ_ABXK01000013
5.20862955909241e−42

11
NZ_GG704495

Acinetobacter sp. RUH2624 genomic scaffold supercont1.1: NZ_GG704495
9.06181183555984e−42

12
NZ_GG704515

Acinetobacter sp. RUH2624 genomic scaffold supercont1.21: NZ_GG704515
9.06181183555984e−42

13
NZ_GG704515

Acinetobacter sp. RUH2624 genomic scaffold supercont1.21: NZ_GG704515
9.06181183555984e−42

14
NC_014259

Acinetobacter sp. DR1 chromosome: NC_014259
9.06181183555984e−42

15
NZ_GG704949

Acinetobacter calcoaceticus RUH2202 genomic scaffold supercont1.1:
9.06181183555984e−42

NZ_GG704949

16
NZ_GG704515

Acinetobacter sp. RUH2624 genomic scaffold supercont1.21: NZ_GG704515
9.06181183555984e−42

17
CP002177

Acinetobacter calcoaceticus PHEA-2: CP002177
9.06181183555984e−42

18
NZ_GG704515

Acinetobacter sp. RUH2624 genomic scaffold supercont1.21: NZ_GG704515
3.84309843417235e−41

19
NZ_GG704495

Acinetobacter sp. RUH2624 genomic scaffold supercont1.1: NZ_GG704495
3.89818602393582e−41

20
NC_005966

Acinetobacter sp. ADP1: NC_005966
1.28694655921313e−40

21
NZ_GG704515

Acinetobacter sp. RUH2624 genomic scaffold supercont1.21: NZ_GG704515
1.49093940399756e−40

22
NC_011595

Acinetobacter baumannii A3307-0294: NC_011595
7.70079013246134e−40

23
CP002522

Acinetobacter baumannii TCDC-AB0715: CP002522
9.96749396638303e−40

24
NC_011595

Acinetobacter baumannii AB307-0294: NC_011595
1.66049576626689e−39

25
NC_011586

Acinetobacter baumannii AB0057: NC_011586
2.08472354496451e−39

26
NC_014259

Acinetobacter sp. DR1 chromosome: NC_014259
6.40954171412503e−39

27
NZ_GG705093

Acinetobacter lwoffii SH145 genomic scaffold supercont1.39: NZ_GG705093
1.2155660857651e−38

28
NZ_ACYQ01000024

Acinetobacter sp. 6013150 NZ_ACYQ01000024: NZ_ACYQ01000024
2.19910980623625e−38

29
NZ_GG704532

Acinetobacter sp. RUH2624 genomic scaffold supercont1.38: NZ_GG704532
5.31361687748575e−38

30
NZ_ACYS01000159

Acinetobacter sp. 6014059 NZ_ACYS01000159: NZ_ACYS01000159
6.25755791192393e−38

31
NC_010611

Acinetobacter baumannii ACICU: NC_010611
1.6998208344511e−37

32
NZ_GG753601

Acinetobacter sp. SH024 genomic scaffold supercont1.2: NZ_GG753601
2.25174704599278e−37

33
CP002522

Acinetobacter baumannii TCDC-AB0715: CP002522
2.43979456355917e−37

34
NZ_GG704979

Acinetobacter johnsonii SH046 genomic scaffold supercont1.16: NZ_GG704979
3.21441196797496e−37

35
NC_011586

Acinetobacter baumannii AB0057: NC_011586
4.65662453496211e−37

36
NC_011586

Acinetobacter baumannii AB0057: NC_011586
4.97462543315347e−37

37
NC_010611

Acinetobacter baumannii ACICU: NC_010611
5.86970772802613e−37

38
CP002522

Acinetobacter baumannii TCDC-AB0715: CP002522
5.86970772802613e−37

39
NZ_ABXK01000021

Acinetobacter baumannii AB900: NZ_ABXK01000021
7.97065298524188e−37

40
CP001921

Acinetobacter baumannii 1656-2: CP001921
8.02210311363916e−37

41
NZ_ACYQ01000067

Acinetobacter sp. 6013150 NZ_ACYQ01000067: NZ_ACYQ01000067
1.04988843673196e−36

42
NZ_GG704579

Acinetobacter baumannii ATCC 19606 genomic scaffold supercont1.8:
2.27416603584469e−36

NZ_GG704579

43
NC_010611

Acinetobacter baumannii ACICU: NC_010611
2.41369225680075e−36

44
NZ_ADMT01000124

Acinetobacter haemolyticus ATCC 19194 contig00185: NZ_ADMT01000124
8.1885528903387e−36

45
NC_011586

Acinetobacter baumannii AB0057: NC_011586
8.6668830227109e−36

46
CP002177

Acinetobacter calcoaceticus PHEA-2: CP002177
1.06688951972352e−35

47
NZ_GG704579

Acinetobacter baumannii ATCC 19606 genomic scaffold supercont1.8:
1.73119071134862e−35

NZ_GG704579

48
NC_011595

Acinetobacter baumannii AB307-0294: NC_011595
2.17923094612776e−35

49
NZ_GG704499

Acinetobacter sp. RUH2624 genomic scaffold supercont1.5: NZ_GG704499
2.56827101997287e−35

50
CP002522

Acinetobacter baumannii TCDC-AB0715: CP002522
2.89444275071491e−35

TABLE 1b

Data for Acinetobacter, particularly Acinetobacter baumanii (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

2
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

3
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

4
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

5
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

6
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

7
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

8
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

9
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

10
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

11
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

12
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

13
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

14
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

15
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

16
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

17
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

18
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

19
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

20
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

21
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

22
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

23
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

24
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

25
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

26
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

27
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

28
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

29
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

30
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

31
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

32
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

33
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

34
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

35
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

36
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

37
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

38
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

39
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

40
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

41
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

42
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

43
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

44
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

45
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

46
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

47
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

48
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

49
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

50
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

TABLE 1c

Data for Acinetobacter, particularly Acinetobacter baumanii (continued)

No.
num_aminoglycoside
num_fluoroquinolone
num_lactam
num_other

1
2
2
2
1

2
2
2
2
1

3
2
2
2
1

4
2
2
2
1

5
2
2
2
1

6
2
2
2
1

7
2
2
2
1

8
2
2
2
1

9
2
2
2
1

10
2
2
2
1

11
2
2
2
1

12
2
2
2
1

13
2
2
2
1

14
2
2
2
1

15
2
2
2
1

16
2
2
2
1

17
2
2
2
1

18
2
2
2
1

19
2
2
2
1

20
2
2
2
1

21
2
2
2
1

22
2
2
2
1

23
2
2
2
1

24
2
2
2
1

25
2
2
2
1

26
2
2
2
1

27
2
2
2
1

28
2
2
2
1

29
2
2
2
1

30
2
2
2
1

31
2
2
2
1

32
2
2
2
1

33
2
2
2
1

34
2
2
2
1

35
2
2
2
1

36
2
2
2
1

37
2
2
2
1

38
2
2
2
1

39
2
2
2
1

40
2
2
2
1

41
2
2
2
1

42
2
2
2
1

43
2
2
2
1

44
2
2
2
1

45
2
2
2
1

46
2
2
2
1

47
2
2
2
1

48
2
2
2
1

49
2
2
2
1

50
2
2
2
1

TABLE 1d

Data for Acinetobacter, particularly Acinetobacter baumanii (continued)

No.
CP_pv_adj
GM_pv_adj
IMP_pv_adj
LVX_pv_adj
MER_pv_adj
TO_pv_adj
T/S_pv_adj

1
7.17E−34
7.62E−37
2.99E−16
2.51E−58
1.71E−29
3.85E−19
7.12E−37

2
1.39E−61
2.93E−36
2.52E−16
1.14E−57
1.26E−28
1.01E−18
2.48E−36

3
1.44E−56
1.41E−30
7.92E−24
2.33E−56
4.63E−35
1.23E−15
1.16E−31

4
5.42E−51
1.20E−26
3.83E−16
1.97E−49
3.77E−19
6.39E−14
5.70E−30

5
7.00E−47
7.36E−25
7.07E−15
3.32E−45
1.76E−24
2.16E−14
1.06E−32

6
2.06E−46
1.72E−23
1.92E−08
3.46E−46
2.40E−18
1.64E−13
3.34E−31

7
8.99E−46
1.85E−24
2.19E−15
2.93E−44
1.16E−24
3.33E−14
3.29E−31

8
2.77E−44
1.51E−23
2.19E−15
5.38E−43
1.16E−24
3.33E−14
3.45E−30

9
6.86E−43
1.15E−22
4.78E−15
1.09E−41
3.50E−24
5.85E−13
2.90E−29

10
5.21E−42
7.13E−19
3.88E−19
3.01E−41
3.46E−19
1.35E−06
1.20E−22

11
9.06E−42
1.74E−21
5.28E−11
6.20E−39
2.05E−18
9.48E−14
2.09E−27

12
9.06E−42
1.40E−20
1.57E−11
1.29E−40
2.50E−19
2.12E−13
1.47E−25

13
9.06E−42
1.40E−20
1.57E−11
1.29E−40
2.50E−19
2.12E−13
1.47E−25

14
9.06E−42
1.26E−22
4.71E−10
1.24E−38
1.59E−17
1.36E−14
1.16E−28

15
9.06E−42
1.40E−20
1.57E−11
1.29E−40
2.50E−19
2.12E−13
1.47E−25

16
9.06E−42
1.40E−20
1.57E−11
1.29E−40
2.50E−19
2.12E−13
1.47E−25

17
9.06E−42
1.40E−20
1.57E−11
1.29E−40
2.50E−19
2.12E−13
1.47E−25

18
3.84E−41
4.26E−21
5.48E−11
2.25E−38
2.28E−18
1.85E−13
1.34E−28

19
3.90E−41
3.00E−22
8.17E−10
4.60E−38
3.07E−17
2.60E−14
3.05E−28

20
1.29E−40
2.54E−23
8.32E−09
2.28E−37
2.98E−16
7.17E−15
4.45E−29

21
1.49E−40
1.06E−20
9.78E−11
8.02E−38
4.26E−18
3.58E−13
1.41E−26

22
7.70E−40
2.19E−21
2.55E−13
8.73E−40
2.71E−22
1.30E−12
9.73E−29

23
9.97E−40
1.94E−20
5.69E−10
6.32E−37
5.09E−15
3.42E−13
4.53E−25

24
1.66E−39
2.25E−21
1.11E−11
4.74E−37
9.11E−19
4.30E−12
6.58E−28

25
6.97E−38
2.51E−23
4.39E−17
2.08E−39
2.11E−31
2.81E−20
2.62E−29

26
6.41E−39
8.82E−20
8.32E−09
2.28E−37
8.45E−15
5.48E−12
1.80E−23

27
1.21E−36
6.79E−22
2.00E−18
1.22E−38
1.37E−30
1.91E−20
1.86E−29

28
2.20E−38
6.34E−16
1.51E−04
3.00E−37
3.02E−15
2.23E−05
5.58E−26

29
2.16E−37
5.62E−21
1.99E−11
5.31E−38
4.07E−20
1.62E−14
1.79E−33

30
6.26E−38
1.31E−11
3.04E−05
7.55E−37
2.46E−19
5.99E−05
3.36E−19

31
1.70E−37
9.89E−20
4.00E−15
6.17E−33
1.59E−19
1.06E−07
5.60E−19

32
2.25E−37
3.62E−20
5.26E−16
3.31E−34
9.82E−23
4.38E−09
5.82E−22

33
2.44E−37
6.97E−16
4.33E−14
7.77E−37
9.30E−19
4.18E−07
1.39E−20

34
3.21E−37
1.12E−20
1.05E−11
3.70E−36
1.02E−20
3.75E−13
1.16E−24

35
4.66E−37
5.92E−20
3.00E−11
4.04E−32
8.17E−17
5.55E−10
2.22E−21

36
4.97E−37
9.12E−20
3.90E−11
7.27E−35
8.20E−18
2.95E−11
2.78E−26

37
5.87E−37
1.44E−15
3.36E−14
2.00E−36
3.55E−19
3.60E−07
3.09E−20

38
5.87E−37
1.44E−15
2.29E−13
2.00E−36
2.38E−18
1.01E−06
4.30E−21

39
7.97E−37
1.41E−20
4.11E−10
1.69E−34
6.22E−17
1.57E−12
9.61E−26

40
8.02E−36
1.02E−16
8.36E−13
8.02E−37
6.77E−18
2.61E−10
1.91E−19

41
1.05E−36
5.82E−22
6.09E−07
1.09E−33
3.93E−12
9.82E−13
1.13E−26

42
2.17E−18
1.05E−13
2.19E−05
7.67E−17
1.44E−05
1.58E−19
2.27E−36

43
2.04E−35
2.18E−16
4.05E−13
2.41E−36
4.89E−18
7.30E−10
2.59E−18

44
2.30E−34
4.36E−15
1.44E−11
8.19E−36
1.06E−16
9.26E−09
1.67E−18

45
8.67E−36
6.11E−17
3.23E−06
1.48E−32
1.25E−11
1.06E−09
8.79E−25

46
1.07E−35
6.07E−21
9.46E−09
3.15E−33
4.04E−15
6.09E−14
1.52E−24

47
2.15E−17
3.02E−13
2.37E−05
3.26E−16
2.56E−05
2.12E−19
1.73E−35

48
2.18E−35
2.69E−18
1.65E−04
2.17E−32
2.13E−10
9.38E−10
2.81E−21

49
2.57E−35
5.01E−23
1.62E−06
3.27E−32
1.19E−11
4.78E−13
2.98E−26

50
2.89E−35
4.58E−19
5.87E−06
4.77E−32
5.92E−13
2.05E−11
8.30E−23

TABLE 1e

Data for Acinetobacter, particularly Acinetobacter baumanii (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
ABK1_1135

ADX02769

2
A60131_010100011170

ZP_06783174

3
A1S_0690

YP_001083736

4
ABBFA_001710

YP_002325613

5
ABBFA_001640

YP_002325543

6
AB57_1876

YP_002319238

7
AB57_2151

YP_002319507

8
ABBFA_001638

YP_002325541

9
AB57_2147

YP_002319503

10
AbauAB_010100009672

ZP_04661877

11
HMPREF0014_00181

ZP_05823167

12
HMPREF0014_02450

ZP_05825436

13
HMPREF0014_02452

ZP_05825438

14
AOLE_17735

YP_003733805

15
HMPREF0012_01352

ZP_06057184

16
HMPREF0014_02453

ZP_05825439

17
BDGL_001498
ocd2
ADY82084

18
HMPREF0014_02489

ZP_05825475

19
HMPREF0014_00004

ZP_05822990

20
ACIAD0370
rbfA
YP_045140

21
HMPREF0014_02492

ZP_05825478

22
ABBFA_001637

YP_002325540

23
ABTW07_1894

ADX92323

24
ABBFA_000343

YP_002324276

25
AB57_2771

YP_002320110

26
AOLE_17690

YP_003733796

27
HMPREF0017_03097

ZP_06071176

28
A6013_010100003618

ZP_06795427

29
HMPREF0014_03338

ZP_05826324

30
A6014_010100015962

ZP_06788050

31
ACICU_00639
filE
YP_001845298

32
HMPREF0013_02137

ZP_06692288

33
ABTW07_2865

ADX93289

34
HMPREF0016_03291

ZP_06064821

35
AB57_2131

YP_002319487

36
AB57_3624
pilV
YP_002320921

37
ACICU_02614

YP_001847273

38
ABTW07_2863

ADX93287

39
AbauAB_010100013685

ZP_04662667

40
ABK1_2278

ADX03912

41
A6013_010100009420

ZP_06796568

42
HMPREF0010_03320

ZP_05829937

43
ACICU_01819

YP_001846478

44
HMP0015_1294

ZP_06727085

45
AB57_1430

YP_002318806

46
BDGL_000595

ADY81181

47
HMPREF0010_03319

ZP_05829936

48
ABBFA_001847

YP_002325750

49
HMPREF0014_00860

ZP_05823846

50
ABTW07_1891

ADX92320

TABLE 1f

Data for Acinetobacter, particularly

Acinetobacter baumanii (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
1235814
1236425
+
650377914

2
64
768
+
647008664

3
821275
822057
+
640069344

4
1834753
1835667
−
643348583

5
1759838
1761280
+
643348583

6
1966831
1969149
+
643348581

7
2232790
2233716
−
643348581

8
1757930
1758571
−
643348583

9
2226774
2228099
+
643348581

10
63870
65015
−
645061599

11
195165
195419
+
647535325

12
27528
28301
−
647535345

13
31818
33023
−
647535345

14
3783514
3783789
+
648028017

15
1494626
1495630
+
646207323

16
33027
34796
−
647535345

17
1603798
1604811
+
650377930

18
74534
74893
+
647535345

19
1819
2325
−
647535325

20
363575
363976
+
637000277

21
76454
76681
+
647535345

22
1757594
1757890
−
643348583

23
2004366
2004983
+
650378014

24
370977
371978
+
643348583

25
2838051
2838620
−
643348581

26
3773081
3773467
+
648028017

27
716
1162
+
646207467

28
6958
7416
−
647008417

29
12541
13101
−
647535362

30
7588
7713
+
647009002

31
705957
707216
+
642555129

32
856694
857281
−
647536755

33
3040319
3041707
−
650378014

34
4553
4768
−
646207353

35
2213458
2214801
−
643348581

36
3730668
3731222
−
643348581

37
2775538
2776941
+
642555129

38
3038397
3039893
−
650378014

39
70983
71513
−
645061607

40
2403829
2405136
+
650377914

41
2603
3454
+
647008460

42
159696
159998
+
647535409

43
1941428
1942675
+
642555129

44
1088
2629
−
647018944

45
1505450
1506382
+
643348581

46
622112
622732
+
650377930

47
158794
159609
+
647535409

48
1980078
1981988
−
643348583

49
126664
127845
+
647535329

50
1999835
2001676
+
650378014

TABLE 2a

Data for Acinetobacter, particularly Acinetobacter baumanii

No.
Scaffold.External.Accession
Scaffold.Name
best_pv

1
CP001921

Acinetobacter baumannii 1656-2: CP001921
7.16783907123597e−62

2
NZ_ACYR01000063

Acinetobacter sp. 6013113 NZ_ACYR01000063:
1.39202289199418e−61

NZ_ACYR01000063

3
NC_009085

Acinetobacter baumannii ATCC 17978: NC_009085
1.43720401820086e−56

4
NC_011595

Acinetobacter baumannii AB307-0294: NC_011595
5.41948460225177e−51

5
NC_011595

Acinetobacter baumannii AB307-0294: NC_011595
7.00413054521082e−47

6
NC_011586

Acinetobacter baumannii AB0057: NC_011586
2.06435524702153e−46

7
NC_011586

Acinetobacter baumannii AB0057: NC_011586
8.98962816077673e−46

8
NC_011595

Acinetobacter baumannii AB307-0294: NC_011595
2.76883973579195e−44

9
NC_011586

Acinetobacter baumannii AB0057: NC_011586
6.86281420221907e−43

10
NZ_ABXK01000013

Acinetobacter baumannii AB900: NZ_ABXK01000013
5.20862955909241e−42

11
NZ_GG704495

Acinetobacter sp. RUH2624 genomic scaffold
9.06181183555984e−42

supercont1.1: NZ_GG704495

12
NZ_GG704515

Acinetobacter sp. RUH2624 genomic scaffold
9.06181183555984e−42

supercont1.21: NZ_GG704515

13
NZ_GG704515

Acinetobacter sp. RUH2624 genomic scaffold
9.06181183555984e−42

supercont1.21: NZ_GG704515

14
NC_014259

Acinetobacter sp. DR1 chromosome: NC_014259
9.06181183555984e−42

15
NZ_GG704949

Acinetobacter calcoaceticus RUH2202 genomic
9.06181183555984e−42

scaffold supercont1.1: NZ_GG704949

16
NZ_GG704515

Acinetobacter sp. RUH2624 genomic scaffold
9.06181183555984e−42

supercont1.21: NZ_GG704515

17
CP002177

Acinetobacter calcoaceticus PHEA-2: CP002177
9.06181183555984e−42

18
NZ_GG704515

Acinetobacter sp. RUH2624 genomic scaffold
3.84309843417235e−41

supercont1.21: NZ_GG704515

19
NZ_GG704495

Acinetobacter sp. RUH2624 genomic scaffold
3.89818602393582e−41

supercont1.1: NZ_GG704495

20
NC_005966

Acinetobacter sp. ADP1: NC_005966
1.28694655921313e−40

21
NZ_GG704515

Acinetobacter sp. RUH2624 genomic scaffold
1.49093940399756e−40

supercont1.21: NZ_GG704515

22
NC_011595

Acinetobacter baumannii AB307-0294: NC_011595
7.70079013246134e−40

23
CP002522

Acinetobacter baumannii TCDC-AB0715: CP002522
9.96749396638303e−40

24
NC_011595

Acinetobacter baumannii AB307-0294: NC_011595
1.66049576626689e−39

25
NC_011586

Acinetobacter baumannii AB0057: NC_011586
2.08472354496451e−39

26
NC_014259

Acinetobacter sp. DR1 chromosome: NC_014259
6.40954171412503e−39

27
NZ_GG705093

Acinetobacter lwoffii SH145 genomic scaffold
1.2155660857651e−38

supercont1.39: NZ_GG705093

28
NZ_ACYQ01000024

Acinetobacter sp. 6013150 NZ_ACYQ01000024:
2.19910980623625e−38

NZ_ACYQ01000024

29
NZ_GG704532

Acinetobacter sp. RUH2624 genomic scaffold
5.31361687748575e−38

supercont1.38: NZ_GG704532

30
NZ_ACYS01000159

Acinetobacter sp. 6014059 NZ_ACYS01000159:
6.25755791192393e−38

NZ_ACYS01000159

31
NC_010611

Acinetobacter baumannii ACICU: NC_010611
1.6998208344511e−37

32
NZ_GG753601

Acinetobacter sp. SH024 genomic scaffold
2.25174704599278e−37

supercont1.2: NZ_GG753601

33
CP002522

Acinetobacter baumannii TCDC-AB0715: CP002522
2.43979456355917e−37

34
NZ_GG704979

Acinetobacter johnsonii SH046 genomic scaffold
3.21441196797496e−37

supercont1.16: NZ_GG704979

35
NC_011586

Acinetobacter baumannii AB0057: NC_011586
4.65662453496211e−37

36
NC_011586

Acinetobacter baumannii AB0057: NC_011586
4.97462543315347e−37

37
NC_010611

Acinetobacter baumannii ACICU: NC_010611
5.86970772802613e−37

38
CP002522

Acinetobacter baumannii TCDC-AB0715: CP002522
5.86970772802613e−37

39
NZ_ABXK01000021

Acinetobacter baumannii AB900: NZ_ABXK01000021
7.97065298524188e−37

40
CP001921

Acinetobacter baumannii 1656-2: CP001921
8.02210311363916e−37

41
NZ_ACYQ01000067

Acinetobacter sp. 6013150 NZ_ACYQ01000067:
1.04988843673196e−36

NZ_ACYQ01000067

42
NZ_GG704579

Acinetobacter baumannii ATCC 19606 genomic
2.27416603584469e−36

scaffold supercont1.8: NZ_GG704579

43
NC_010611

Acinetobacter baumannii ACICU: NC_010611
2.41369225680075e−36

44
NZ_ADMT01000124

Acinetobacter haemolyticus ATCC 19194
8.1885528903387e−36

contig00185: NZ_ADMT01000124

45
NC_011586

Acinetobacter baumannii AB0057: NC_011586
8.6668830227109e−36

46
CP002177

Acinetobacter calcoaceticus PHEA-2: CP002177
1.06688951972352e−35

47
NZ_GG704579

Acinetobacter baumannii ATCC 19606 genomic
1.73119071134862e−35

scaffold supercont1.8: NZ_GG704579

48
NC_011595

Acinetobacter baumannii AB307-0294: NC_011595
2.17923094612776e−35

49
NZ_GG704499

Acinetobacter sp. RUH2624 genomic scaffold
2.56827101997287e−35

supercont1.5: NZ_GG704499

50
CP002522

Acinetobacter baumannii TCDC-AB0715: CP002522
2.89444275071491e−35

TABLE 2b

Data for Acinetobacter, particularly Acinetobacter baumanii (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

2
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

3
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

4
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

5
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

6
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

7
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

8
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

9
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

10
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

11
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

12
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

13
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

14
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

15
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

16
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

17
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

18
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

19
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

20
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

21
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

22
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

23
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

24
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

25
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

26
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

27
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

28
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

29
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

30
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

31
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

32
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

33
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

34
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

35
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

36
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

37
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

38
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

39
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

40
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

41
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

42
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

43
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

44
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

45
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

46
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

47
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

48
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

49
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

50
CP; GM; IMP; LVX; MER; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

TABLE 2c

Data for Acinetobacter, particularly Acinetobacter baumanii (continued)

No.
num_aminoglycoside
num_fluoroquinolone
num_lactam
num_other

1
2
2
2
1

2
2
2
2
1

3
2
2
2
1

4
2
2
2
1

5
2
2
2
1

6
2
2
2
1

7
2
2
2
1

8
2
2
2
1

9
2
2
2
1

10
2
2
2
1

11
2
2
2
1

12
2
2
2
1

13
2
2
2
1

14
2
2
2
1

15
2
2
2
1

16
2
2
2
1

17
2
2
2
1

18
2
2
2
1

19
2
2
2
1

20
2
2
2
1

21
2
2
2
1

22
2
2
2
1

23
2
2
2
1

24
2
2
2
1

25
2
2
2
1

26
2
2
2
1

27
2
2
2
1

28
2
2
2
1

29
2
2
2
1

30
2
2
2
1

31
2
2
2
1

32
2
2
2
1

33
2
2
2
1

34
2
2
2
1

35
2
2
2
1

36
2
2
2
1

37
2
2
2
1

38
2
2
2
1

39
2
2
2
1

40
2
2
2
1

41
2
2
2
1

42
2
2
2
1

43
2
2
2
1

44
2
2
2
1

45
2
2
2
1

46
2
2
2
1

47
2
2
2
1

48
2
2
2
1

49
2
2
2
1

50
2
2
2
1

TABLE 2d

Data for Acinetobacter, particularly Acinetobacter baumanii (continued)

No.
CP_pv_adj
GM_pv_adj
IMP_pv_adj
LVX_pv_adj
MER_pv_adj
TO_pv_adj
T/S_pv_adj

1
7.17E−62
7.62E−37
2.99E−16
2.51E−58
1.71E−29
3.85E−19
7.12E−37

2
1.39E−61
2.93E−36
2.52E−16
1.14E−57
1.26E−28
1.01E−18
2.48E−36

3
1.44E−56
1.41E−30
7.92E−24
2.33E−56
4.63E−35
1.23E−15
1.16E−31

4
5.42E−51
1.20E−26
3.83E−16
1.97E−49
3.77E−19
6.39E−14
5.70E−30

5
7.00E−47
7.36E−25
7.07E−15
3.32E−45
1.76E−24
2.16E−14
1.06E−32

6
2.06E−46
1.72E−23
1.92E−08
3.46E−46
2.40E−18
1.64E−13
3.34E−31

7
8.99E−46
1.85E−24
2.19E−15
2.93E−44
1.16E−24
3.33E−14
3.29E−31

8
2.77E−44
1.51E−23
2.19E−15
5.38E−43
1.16E−24
3.33E−14
3.45E−30

9
6.86E−43
1.15E−22
4.78E−15
1.09E−41
3.50E−24
5.85E−13
2.90E−29

10
5.21E−42
7.13E−19
3.88E−19
3.01E−41
3.46E−19
1.35E−06
1.20E−22

11
9.06E−42
1.74E−21
5.28E−11
6.20E−39
2.05E−18
9.48E−14
2.09E−27

12
9.06E−42
1.40E−20
1.57E−11
1.29E−40
2.50E−19
2.12E−13
1.47E−25

13
9.06E−42
1.40E−20
1.57E−11
1.29E−40
2.50E−19
2.12E−13
1.47E−25

14
9.06E−42
1.26E−22
4.71E−10
1.24E−38
1.59E−17
1.36E−14
1.16E−28

15
9.06E−42
1.40E−20
1.57E−11
1.29E−40
2.50E−19
2.12E−13
1.47E−25

16
9.06E−42
1.40E−20
1.57E−11
1.29E−40
2.50E−19
2.12E−13
1.47E−25

17
9.06E−42
1.40E−20
1.57E−11
1.29E−40
2.50E−19
2.12E−13
1.47E−25

18
3.84E−41
4.26E−21
5.48E−11
2.25E−38
2.28E−18
1.85E−13
1.34E−28

19
3.90E−41
3.00E−22
8.17E−10
4.60E−38
3.07E−17
2.60E−14
3.05E−28

20
1.29E−40
2.54E−23
8.32E−09
2.28E−37
2.98E−16
7.17E−15
4.45E−29

21
1.49E−40
1.06E−20
9.78E−11
8.02E−38
4.26E−18
3.58E−13
1.41E−26

22
7.70E−40
2.19E−21
2.55E−13
8.73E−40
2.71E−22
1.30E−12
9.73E−29

23
9.97E−40
1.94E−20
5.69E−10
6.32E−37
5.09E−15
3.42E−13
4.53E−25

24
1.66E−39
2.25E−21
1.11E−11
4.74E−37
9.11E−19
4.30E−12
6.58E−28

25
6.97E−38
2.51E−23
4.39E−17
2.08E−39
2.11E−31
2.81E−20
2.62E−29

26
6.41E−39
8.82E−20
8.32E−09
2.28E−37
8.45E−15
5.48E−12
1.80E−23

27
1.21E−36
6.79E−22
2.00E−18
1.22E−38
1.37E−30
1.91E−20
1.86E−29

28
2.20E−38
6.34E−16
0.00015078
3.00E−37
3.02E−15
2.23E−05
5.58E−26

29
2.16E−37
5.62E−21
1.99E−11
5.31E−38
4.07E−20
1.62E−14
1.79E−33

30
6.26E−38
1.31E−11
3.04E−05
7.55E−37
2.46E−19
5.99E−05
3.36E−19

31
1.70E−37
9.89E−20
4.00E−15
6.17E−33
1.59E−19
1.06E−07
5.60E−19

32
2.25E−37
3.62E−20
5.26E−16
3.31E−34
9.82E−23
4.38E−09
5.82E−22

33
2.44E−37
6.97E−16
4.33E−14
7.77E−37
9.30E−19
4.18E−07
1.39E−20

34
3.21E−37
1.12E−20
1.05E−11
3.70E−36
1.02E−20
3.75E−13
1.16E−24

35
4.66E−37
5.92E−20
3.00E−11
4.04E−32
8.17E−17
5.55E−10
2.22E−21

36
4.97E−37
9.12E−20
3.90E−11
7.27E−35
8.20E−18
2.95E−11
2.78E−26

37
5.87E−37
1.44E−15
3.36E−14
2.00E−36
3.55E−19
3.60E−07
3.09E−20

38
5.87E−37
1.44E−15
2.29E−13
2.00E−36
2.38E−18
1.01E−06
4.30E−21

39
7.97E−37
1.41E−20
4.11E−10
1.69E−34
6.22E−17
1.57E−12
9.61E−26

40
8.02E−36
1.02E−16
8.36E−13
8.02E−37
6.77E−18
2.61E−10
1.91E−19

41
1.05E−36
5.82E−22
6.09E−07
1.09E−33
3.93E−12
9.82E−13
1.13E−26

42
2.17E−18
1.05E−13
2.19E−05
7.67E−17
1.44E−05
1.58E−19
2.27E−36

43
2.04E−35
2.18E−16
4.05E−13
2.41E−36
4.89E−18
7.30E−10
2.59E−18

44
2.30E−34
4.36E−15
1.44E−11
8.19E−36
1.06E−16
9.26E−09
1.67E−18

45
8.67E−36
6.11E−17
3.23E−06
1.48E−32
1.25E−11
1.06E−09
8.79E−25

46
1.07E−35
6.07E−21
9.46E−09
3.15E−33
4.04E−15
6.09E−14
1.52E−24

47
2.15E−17
3.02E−13
2.37E−05
3.26E−16
2.56E−05
2.12E−19
1.73E−35

48
2.18E−35
2.69E−18
0.00016455
2.17E−32
2.13E−10
9.38E−10
2.81E−21

49
2.57E−35
5.01E−23
1.62E−06
3.27E−32
1.19E−11
4.78E−13
2.98E−26

50
2.89E−35
4.58E−19
5.87E−06
4.77E−32
5.92E−13
2.05E−11
8.30E−23

TABLE 2e

Data for Acinetobacter, particularly Acinetobacter baumanii (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
ABK1_1135

ADX02769

2
A60131_010100011170

ZP_06783174

3
A1S_0690

YP_001083736

4
ABBFA_001710

YP_002325613

5
ABBFA_001640

YP_002325543

6
AB57_1876

YP_002319238

7
AB57_2151

YP_002319507

8
ABBFA_001638

YP_002325541

9
AB57_2147

YP_002319503

10
AbauAB_010100009672

ZP_04661877

11
HMPREF0014_00181

ZP_05823167

12
HMPREF0014_02450

ZP_05825436

13
HMPREF0014_02452

ZP_05825438

14
AOLE_17735

YP_003733805

15
HMPREF0012_01352

ZP_06057184

16
HMPREF0014_02453

ZP_05825439

17
BDGL_001498
ocd2
ADY82084

18
HMPREF0014_02489

ZP_05825475

19
HMPREF0014_00004

ZP_05822990

20
ACIAD0370
rbfA
YP_045140

21
HMPREF0014_02492

ZP_05825478

22
ABBFA_001637

YP_002325540

23
ABTW07_1894

ADX92323

24
ABBFA_000343

YP_002324276

25
AB57_2771

YP_002320110

26
AOLE_17690

YP_003733796

27
HMPREF0017_03097

ZP_06071176

28
A6013_010100003618

ZP_06795427

29
HMPREF0014_03338

ZP_05826324

30
A6014_010100015962

ZP_06788050

31
ACICU_00639
filE
YP_001845298

32
HMPREF0013_02137

ZP_06692288

33
ABTW07_2865

ADX93289

34
HMPREF0016_03291

ZP_06064821

35
AB57_2131

YP_002319487

36
AB57_3624
pilV
YP_002320921

37
ACICU_02614

YP_001847273

38
ABTW07_2863

ADX93287

39
AbauAB_010100013685

ZP_04662667

40
ABK1_2278

ADX03912

41
A6013_010100009420

ZP_06796568

42
HMPREF0010_03320

ZP_05829937

43
ACICU_01819

YP_001846478

44
HMP0015_1294

ZP_06727085

45
AB57_1430

YP_002318806

46
BDGL_000595

ADY81181

47
HMPREF0010_03319

ZP_05829936

48
ABBFA_001847

YP_002325750

49
HMPREF0014_00860

ZP_05823846

50
ABTW07_1891

ADX92320

TABLE 2f

Data for Acinetobacter, particularly Acinetobacter baumanii (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
1235814
1236425
+
650377914

2
64
768
+
647008664

3
821275
822057
+
640069344

4
1834753
1835667
−
643348583

5
1759838
1761280
+
643348583

6
1966831
1969149
+
643348581

7
2232790
2233716
−
643348581

8
1757930
1758571
−
643348583

9
2226774
2228099
+
643348581

10
63870
65015
−
645061599

11
195165
195419
+
647535325

12
27528
28301
−
647535345

13
31818
33023
−
647535345

14
3783514
3783789
+
648028017

15
1494626
1495630
+
646207323

16
33027
34796
−
647535345

17
1603798
1604811
+
650377930

18
74534
74893
+
647535345

19
1819
2325
−
647535325

20
363575
363976
+
637000277

21
76454
76681
+
647535345

22
1757594
1757890
−
643348583

23
2004366
2004983
+
650378014

24
370977
371978
+
643348583

25
2838051
2838620
−
643348581

26
3773081
3773467
+
648028017

27
716
1162
+
646207467

28
6958
7416
−
647008417

29
12541
13101
−
647535362

30
7588
7713
+
647009002

31
705957
707216
+
642555129

32
856694
857281
−
647536755

33
3040319
3041707
−
650378014

34
4553
4768
−
646207353

35
2213458
2214801
−
643348581

36
3730668
3731222
−
643348581

37
2775538
2776941
+
642555129

38
3038397
3039893
−
650378014

39
70983
71513
−
645061607

40
2403829
2405136
+
650377914

41
2603
3454
+
647008460

42
159696
159998
+
647535409

43
1941428
1942675
+
642555129

44
1088
2629
−
647018944

45
1505450
1506382
+
643348581

46
622112
622732
+
650377930

47
158794
159609
+
647535409

48
1980078
1981988
−
643348583

49
126664
127845
+
647535329

50
1999835
2001676
+
650378014

Examples 2 and 3: Enterobacter, particularly Enterobacter aerogenes and Enterobacter cloacae

The procedure was carried out as in Example 1, except that the following microorganisms were used:+

Bacterial Strains

The inventors selected 695 Enterobacter strains, particularly 298 for Enterobacter aerogenes and 397 for Enterobacter cloacae, from the microbiology strain collection at Siemens Healthcare Diagnostics (West Sacramento, Calif.) for susceptibility testing and whole genome sequencing.

From MetaRef, 5220 centroids of E. aerogenes were used as reference sequences for E. aerogenes, and 4734 centroids of E. cloacae were used as reference sequences for E. cloacae.

The results for Enterobacter aerogenes are shown in Tables 3 (corresponding to Table 1) and 4 (corresponding to Table 2), and the results for Enterobacter cloacae are shown in Tables 5 (corresponding to Table 1) and 6 (corresponding to Table 2).

TABLE 3a

Data for Enterobacter, particularly Enterobacter aerogenes

Scaffold.External.

No.
Accession
Scaffold.Name
best_pv

1
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
1.01047730430126e−10

2
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
1.01047730430126e−10

3
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
2.21893843673589e−10

4
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
7.36056945497466e−08

5
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
9.81164607784395e−08

6
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
9.81164607784395e−08

7
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
3.92206261774063e−06

8
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
9.95623777570528e−06

9
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.000635187711382771

10
NC_009778

Enterobacter sakazakii ATCC BAA-894: NC_009778
0.000701852165838025

11
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.000717841336438945

12
NZ_GG745509

Klebsiella sp. 1_1_55 genomic scaffold supercont1.2:
0.000881981942215321

NZ_GG745509

13
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
0.000881981942215321

14
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.000960532001115215

15
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00108645793188005

16
NZ_ADTJ01000031

Escherichia coli MS 198-1 E_coli198-1-1.0_Cont45.1:
0.00108724371491948

NZ_ADTJ01000031

17
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.0016524197402272

18
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00184130315909336

19
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00187260357604506

20
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00191687062572367

21
NZ_ACZD01000042

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC
0.00208337132265191

13884 contig00042: NZ_ACZD01000042

22
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00208337132265191

23
NZ_ADTJ01000031

Escherichia coli MS 198-1 E_coli198-1-1.0_Cont45.1:
0.00241352185546859

NZ_ADTJ01000031

24
NZ_ADTJ01000031

Escherichia coli MS 198-1 E_coli198-1-1.0_Cont45.1:
0.00245969973695216

NZ_ADTJ01000031

25
AM946981

Escherichia coli BL21(DE3): AM946981
0.00327316953478549

26
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00327864620009511

27
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00334082507673483

28
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00342044194519721

29
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00349516820070151

30
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00391582859992096

31
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.0039468230846432

32
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.0042274756954506

33
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00458480687490629

34
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00458480687490629

35
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00458480687490629

36
NC_012731

Klebsiella pneumoniae NTUH-K2044: NC_012731
0.00458480687490629

37
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00482300882771186

38
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00495283743056749

39
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00495283743056749

40
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00503080982688659

41
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00529748534762393

42
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00585931541937669

43
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00585931541937669

44
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00585931541937669

45
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00585931541937669

46
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00648651344338336

47
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00648651344338336

48
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00648651344338336

49
NZ_GG745510

Klebsiella sp. 1_1_55 genomic scaffold supercont1.3:
0.00659680763861341

NZ_GG745510

50
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00667294667231188

TABLE 3b

Data for Enterobacter, particularly Enterobacter aerogenes (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
AZT; CAX; CAZ; CFT; CP; CRM; LVX;
aminoglycoside; fluoroquinolone; lactam;
CP
fluoroquinolone

P/T; TO; T/S
other

2
AZT; CAX; CAZ; CFT; CP; CRM;
aminoglycoside; fluoroquinolone; lactam;
CP
fluoroquinolone

LVX; P/T; TO; T/S
other

3
AZT; CAX; CAZ; CFT; CP; CRM;
aminoglycoside; fluoroquinolone; lactam;
CP
fluoroquinolone

LVX; P/T; TO; T/S
other

4
CP; LVX; TO; T/S
aminoglycoside; fluoroquinolone; other
CP
fluoroquinolone

5
AZT; CAX; CAZ; CFT; CP; CRM; LVX; P/T; T/S
fluoroquinolone; lactam; other
CP
fluoroquinolone

6
AZT; CP; LVX; P/T; T/S
fluoroquinolone; lactam; other
CP
fluoroquinolone

7
CP; LVX; T/S
fluoroquinolone; other
CP
fluoroquinolone

8
CP; LVX; T/S
fluoroquinolone; other
CP
fluoroquinolone

9
AZT; CAX; CAZ; CFT; P/T
lactam
CFT
lactam

10
AZT; CAX; CAZ; CFT; CRM; P/T
lactam
AZT
lactam

11
CAX; CFT; CRM
lactam
CRM
lactam

12
AZT; CAX; CAZ; CFT; P/T
lactam
CAX
lactam

13
AZT; CAX; CAZ; CFT; P/T
lactam
CAX
lactam

14
TO
aminoglycoside
TO
aminoglycoside

15
AZT; CAX; CAZ; CFT; CRM; P/T
lactam
CAX
lactam

16
CP; LVX
fluoroquinolone
CP
fluoroquinolone

17
AZT; CAX; CAZ; CFT; CP; P/T
fluoroquinolone; lactam
P/T
lactam

18
AZT; CAX; CAZ; CFT; CP; P/T
fluoroquinolone; lactam
CAX
lactam

19
AZT; CAX; CAZ; CFT; CRM
lactam
CAX
lactam

20
CAX; CAZ; CFT
lactam
CAX
lactam

21
CAX; CAZ; CFT; CRM; P/T
lactam
CAX
lactam

22
CAX; CAZ; CFT; CRM; P/T
lactam
CAX
lactam

23
TO
aminoglycoside
TO
aminoglycoside

24
TO
aminoglycoside
TO
aminoglycoside

25
AZT; CAX; CAZ; CFT
lactam
CAX
lactam

26
CP
fluoroquinolone
CP
fluoroquinolone

27
AZT; CAX; CAZ; CFT; CRM; P/T
lactam
CAX
lactam

28
CAX; CAZ; CFT; CRM; P/T
lactam
CAX
lactam

29
AZT; CAX; CAZ; CFT
lactam
CAX
lactam

30
AZT; CAX; CAZ; CFT; P/T
lactam
AZT
lactam

31
AZT; CAX; CFT
lactam
CAX
lactam

32
AZT; CAX
lactam
CAX
lactam

33
CAX; CFT
lactam
CAX
lactam

34
CAX; CFT
lactam
CAX
lactam

35
CAX; CP
fluoroquinolone; lactam
CP
fluoroquinolone

36
CAX; CFT
lactam
CAX
lactam

37
CAX; CFT; CRM; P/T
lactam
CRM
lactam

38
AZT; CAX; CFT
lactam
CFT
lactam

39
AZT; CAX; CFT
lactam
CFT
lactam

40
CAX
lactam
CAX
lactam

41
CAX
lactam
CAX
lactam

42
AZT; CAX
lactam
AZT
lactam

43
CAX
lactam
CAX
lactam

44
AZT; CAX
lactam
AZT
lactam

45
AZT; CAX; CFT
lactam
CAX
lactam

46
AZT; CAX
lactam
CAX
lactam

47
AZT; CAX
lactam
CAX
lactam

48
AZT; CAX
lactam
CAX
lactam

49
CAX
lactam
CAX
lactam

50
CAX
lactam
CAX
lactam

TABLE 3c

Data for Enterobacter, particularly Enterobacter aerogenes (continued)

No.
num_aminoglycoside
num_fluoroquinolone
num_lactam
num_other

1
1
2
6
1

2
1
2
6
1

3
1
2
6
1

4
1
2
0
1

5
0
2
6
1

6
0
2
2
1

7
0
2
0
1

8
0
2
0
1

9
0
0
5
0

10
0
0
6
0

11
0
0
3
0

12
0
0
5
0

13
0
0
5
0

14
1
0
0
0

15
0
0
6
0

16
0
2
0
0

17
0
1
5
0

18
0
1
5
0

19
0
0
5
0

20
0
0
3
0

21
0
0
5
0

22
0
0
5
0

23
1
0
0
0

24
1
0
0
0

25
0
0
4
0

26
0
1
0
0

27
0
0
6
0

28
0
0
5
0

29
0
0
4
0

30
0
0
5
0

31
0
0
3
0

32
0
0
2
0

33
0
0
2
0

34
0
0
2
0

35
0
1
1
0

36
0
0
2
0

37
0
0
4
0

38
0
0
3
0

39
0
0
3
0

40
0
0
1
0

41
0
0
1
0

42
0
0
2
0

43
0
0
1
0

44
0
0
2
0

45
0
0
3
0

46
0
0
2
0

47
0
0
2
0

48
0
0
2
0

49
0
0
1
0

50
0
0
1
0

TABLE 3d

Data for Enterobacter, particularly Enterobacter aerogenes (continued)

No.
AZT_pv_adj
CAX_pv_adj
CAZ_pv_adj
CFT_pv_adj
CP_pv_adj

1
8.22E−04
2.45E−04
3.83E−04
4.31E−04
1.01E−10

2
1.32E−03
4.48E−04
7.06E−04
7.76E−04
1.01E−10

3
3.27E−03
1.99E−03
4.43E−03
3.01E−03
2.22E−10

4
2.06E−02
1.86E−02
2.29E−02
2.41E−02
7.36E−08

5
4.29E−03
2.32E−04
6.91E−04
7.06E−04
9.81E−08

6
8.86E−03
1.82E−02
1.77E−02
1.84E−02
9.81E−08

7
5.47E−01
1.61E−02
4.75E−02
4.90E−02
3.92E−06

8
6.96E−01
3.29E−02
9.63E−02
9.80E−02
9.96E−06

9
4.82E−03
9.01E−04
1.84E−03
6.35E−04
3.94E−02

10
7.02E−04
3.95E−03
6.47E−03
6.18E−03
2.19E−02

11
1.74E−02
4.82E−03
1.41E−02
4.93E−03
4.78E−01

12
5.48E−03
8.82E−04
6.43E−03
2.81E−03
2.06E−01

13
5.48E−03
8.82E−04
6.43E−03
2.81E−03
2.06E−01

14
6.13E−01
3.30E−01
3.24E−01
4.36E−01
1.68E−02

15
3.27E−03
1.09E−03
2.08E−03
3.16E−03
1.86E−02

16
1.54E−01
7.15E−02
8.90E−02
1.12E−01
1.09E−03

17
3.27E−03
5.44E−03
6.66E−03
5.44E−03
6.21E−03

18
5.86E−03
1.84E−03
2.44E−03
3.43E−03
5.30E−03

19
2.04E−03
1.87E−03
6.34E−03
2.86E−03
4.83E−01

20
2.06E−02
1.92E−03
6.18E−03
3.56E−03
1.74E−01

21
2.06E−02
2.08E−03
6.49E−03
5.34E−03
4.77E−01

22
2.06E−02
2.08E−03
6.49E−03
5.34E−03
4.77E−01

23
3.45E−01
2.11E−01
2.09E−01
2.56E−01
4.61E−02

24
2.34E−01
1.31E−01
1.03E−01
1.64E−01
1.86E−02

25
3.92E−03
3.27E−03
9.44E−03
4.58E−03
6.15E−01

26
1.66E−02
3.39E−02
3.18E−02
4.22E−02
3.28E−03

27
3.46E−03
3.34E−03
5.74E−03
5.48E−03
2.58E−01

28
1.26E−02
3.42E−03
6.74E−03
5.59E−03
6.42E−02

29
5.74E−03
3.50E−03
9.56E−03
4.82E−03
4.25E−01

30
3.92E−03
5.86E−03
9.75E−03
7.85E−03
4.70E−01

31
5.99E−03
3.95E−03
1.08E−02
5.34E−03
5.16E−01

32
8.78E−03
4.23E−03
2.75E−02
1.06E−02
3.44E−01

33
2.32E−02
4.58E−03
2.06E−02
9.82E−03
6.54E−01

34
2.32E−02
4.58E−03
2.06E−02
9.82E−03
6.54E−01

35
2.01E−02
5.71E−03
1.85E−02
1.46E−02
4.58E−03

36
2.32E−02
4.58E−03
2.06E−02
9.82E−03
6.54E−01

37
3.09E−02
6.66E−03
2.19E−02
9.73E−03
4.29E−01

38
9.88E−03
8.78E−03
1.16E−02
4.95E−03
1.65E−01

39
9.88E−03
8.78E−03
1.16E−02
4.95E−03
1.65E−01

40
3.62E−02
5.03E−03
2.31E−02
1.38E−02
2.47E−01

41
1.54E−02
5.30E−03
1.43E−02
1.12E−02
6.43E−02

42
5.86E−03
9.44E−03
1.23E−02
2.06E−02
7.63E−02

43
1.15E−02
5.86E−03
1.39E−02
1.38E−02
2.62E−01

44
5.86E−03
9.44E−03
1.23E−02
2.06E−02
7.63E−02

45
9.73E−03
5.86E−03
1.64E−02
6.17E−03
4.25E−01

46
7.89E−03
6.49E−03
3.09E−02
1.64E−02
2.98E−01

47
7.89E−03
6.49E−03
3.09E−02
1.64E−02
2.98E−01

48
7.89E−03
6.49E−03
3.09E−02
1.64E−02
2.98E−01

49
1.20E−02
6.60E−03
1.12E−02
1.82E−02
2.16E−01

50
1.38E−02
6.67E−03
2.06E−02
1.64E−02
3.23E−01

TABLE 3e

Data for Enterobacter, particularly Enterobacter aerogenes (continued)

No.
CRM_pv_adj
LVX_pv_adj
P/T_pv_adj
TO_pv_adj
T/S_pv_adj

1
4.55E−04
5.22E−07
2.23E−04
2.03E−04
1.88E−06

2
8.93E−04
7.25E−07
2.87E−04
2.45E−04
2.53E−06

3
1.47E−03
8.82E−07
4.54E−03
2.55E−04
3.69E−06

4
1.86E−02
5.08E−05
2.73E−02
3.92E−03
3.62E−05

5
9.61E−04
7.96E−07
9.64E−04
1.26E−02
1.69E−03

6
1.46E−02
1.31E−04
8.95E−03
2.06E−02
8.55E−03

7
4.85E−02
6.35E−04
2.98E−01
9.28E−02
9.01E−04

8
1.03E−01
9.82E−04
4.28E−01
1.13E−01
1.44E−03

9
1.08E−02
2.67E−01
3.56E−03
5.09E−01
2.87E−01

10
1.66E−03
1.39E−01
5.16E−03
8.93E−02
1.08E−01

11
7.18E−04
5.91E−01
1.76E−02
7.39E−01
9.14E−01

12
7.03E−02
6.77E−01
6.85E−03
7.65E−01
9.68E−01

13
7.03E−02
6.77E−01
6.85E−03
7.65E−01
9.68E−01

14
8.23E−01
8.17E−02
2.13E−01
9.61E−04
2.24E−02

15
4.37E−03
2.22E−01
9.03E−03
2.02E−01
2.91E−01

16
4.57E−02
7.49E−03
2.26E−01
4.29E−01
4.38E−02

17
3.26E−02
1.15E−01
1.65E−03
1.93E−02
4.43E−02

18
1.64E−02
1.66E−01
9.73E−03
4.25E−01
6.31E−01

19
3.50E−03
6.96E−01
3.47E−02
1
1

20
1.20E−02
4.90E−01
1.60E−02
1
7.91E−01

21
2.40E−03
9.70E−01
9.40E−03
4.93E−01
6.15E−01

22
2.40E−03
9.70E−01
9.40E−03
4.93E−01
6.15E−01

23
5.50E−01
2.07E−01
1.23E−01
2.41E−03
4.88E−02

24
5.46E−01
9.58E−02
1.16E−01
2.46E−03
7.04E−02

25
1.40E−02
8.28E−01
4.99E−02
9.45E−01
8.28E−01

26
4.65E−02
5.56E−02
1.64E−02
4.80E−02
1.26E−02

27
9.73E−03
5.14E−01
9.59E−03
7.93E−01
8.06E−01

28
5.86E−03
3.56E−01
4.54E−03
3.41E−01
5.47E−01

29
2.85E−02
7.23E−01
6.42E−02
8.28E−01
6.13E−01

30
1.82E−02
6.97E−01
5.99E−03
6.87E−01
9.71E−01

31
1.59E−02
8.28E−01
7.52E−02
8.28E−01
7.23E−01

32
1.61E−02
6.13E−01
9.20E−02
9.51E−01
8.47E−01

33
8.16E−02
9.71E−01
3.93E−02
3.34E−01
7.11E−01

34
8.16E−02
9.71E−01
3.93E−02
3.34E−01
7.11E−01

35
5.70E−02
3.62E−02
1.61E−02
1.47E−01
4.48E−02

36
8.16E−02
9.71E−01
3.93E−02
3.34E−01
7.11E−01

37
4.82E−03
3.59E−01
5.54E−03
7.80E−01
2.77E−01

38
1.33E−02
4.16E−01
4.96E−02
7.39E−01
5.42E−01

39
1.33E−02
4.16E−01
4.96E−02
7.39E−01
5.42E−01

40
1.95E−02
5.02E−01
5.98E−02
2.35E−01
2.07E−01

41
4.20E−02
2.18E−01
1.19E−02
2.02E−01
4.53E−01

42
7.24E−02
4.76E−01
1.76E−02
9.62E−01
7.80E−01

43
6.56E−02
5.59E−01
9.19E−02
8.66E−01
1

44
7.24E−02
4.76E−01
1.76E−02
9.62E−01
7.80E−01

45
1.76E−02
7.23E−01
1.10E−01
8.28E−01
7.24E−01

46
1.84E−02
6.37E−01
9.12E−02
7.39E−01
1

47
1.84E−02
6.37E−01
9.12E−02
7.39E−01
1

48
1.84E−02
6.37E−01
9.12E−02
7.39E−01
1

49
7.35E−02
7.11E−01
1.15E−02
5.12E−01
3.68E−01

50
1.28E−01
6.61E−01
1.11E−01
9.60E−01
1

TABLE 3f

Data for Enterobacter, particularly Enterobacter aerogenes (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
EAE_18905

YP_004593967

2
EAE_18910

YP_004593968

3
EAE_20750

YP_004594334

4
EAE_20680

YP_004594322

5
EAE_10325

YP_004592260

6
EAE_15945

YP_004593379

7
EAE_24270

YP_004595026

8
EAE_19175

YP_004594021

9
EAE_17360

YP_004593662

10
ESA_03685

YP_001439725

11
EAE_20530
tynA
YP_004594292

12
HMPREF0485_02019

ZP_06549619

13
Kvar_3843

YP_003440755

14
EAE_19000

YP_004593986

15
EAE_21240

YP_004594432

16
HMPREF9552_00257

ZP_07114469

17
EAE_11550

YP_004592503

18
EAE_21235

YP_004594431

19
EAE_24605
flk
YP_004595093

20
EAE_17355

YP_004593661

21
HMPREF0484_0684

ZP_06013668

22
EAE_06855

YP_004591574

23
HMPREF9552_00255

ZP_07114467

24
HMPREF9552_00247

ZP_07114459

25
B21_02377
ybl112
CAQ32894

26
EAE_00560

YP_004590329

27
EAE_02625
aphA
YP_004590739

28
EAE_10300

YP_004592255

29
EAE_23410

YP_004594860

30
EAE_02640

YP_004590742

31
EAE_23150

YP_004594808

32
EAE_23330

YP_004594844

33
EAE_06345

YP_004591472

34
EAE_06340

YP_004591471

35
EAE_23435

YP_004594865

36
KP1_5319
wabN
YP_002921814

37
EAE_22395

YP_004594657

38
EAE_06770

YP_004591557

39
EAE_06775

YP_004591558

40
EAE_06430
ligB
YP_004591489

41
EAE_15075

YP_004593207

42
EAE_03420

YP_004590898

43
EAE_23445

YP_004594867

44
EAE_03430

YP_004590900

45
EAE_23415

YP_004594861

46
EAE_06330

YP_004591469

47
EAE_06320

YP_004591467

48
EAE_06325

YP_004591468

49
HMPREF0485_03181

ZP_06550780

50
EAE_23450

YP_004594868

TABLE 3g

Data for Enterobacter, particularly Enterobacter aerogenes (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
4057377
4057994
−
650716122

2
4057994
4059313
−
650716122

3
4444576
4447206
−
650716122

4
4432502
4433842
−
650716122

5
2202535
2203893
−
650716122

6
3439556
3442066
+
650716122

7
5174177
5175436
+
650716122

8
4113374
4114306
−
650716122

9
3748049
3748279
+
650716122

10
3623778
3624146
+
640753067

11
4396852
4399119
+
650716122

12
347124
347486
+
647536390

13
4046094
4046396
−
646312028

14
4078519
4079427
+
650716122

15
4545796
4546983
−
650716122

16
14233
15036
+
648286894

17
2477524
2479728
+
650716122

18
4544187
4545296
+
650716122

19
5241493
5242410
+
650716122

20
3747138
3747791
+
650716122

21
5606
5998
+
647009789

22
1421376
1421699
+
650716122

23
12357
13376
+
648286894

24
7786
8685
−
648286894

25
2517630
2518469
+
646862300

26
114571
115482
+
650716122

27
557964
558680
−
650716122

28
2197515
2198873
+
650716122

29
4974131
4974946
−
650716122

30
560166
561344
−
650716122

31
4919559
4920611
+
650716122

32
4955309
4956457
+
650716122

33
1317545
1318672
+
650716122

34
1316472
1317548
+
650716122

35
4979540
4980544
+
650716122

36
5064271
5065293
−
646564530

37
4777378
4777638
−
650716122

38
1404935
1406026
−
650716122

39
1406073
1406483
+
650716122

40
1331758
1333431
−
650716122

41
3235642
3239709
+
650716122

42
718097
718942
−
650716122

43
4982582
4983136
−
650716122

44
720009
720686
+
650716122

45
4975309
4976445
−
650716122

46
1314302
1315078
−
650716122

47
1312221
1313129
+
650716122

48
1313194
1314276
+
650716122

49
538177
539649
+
647536391

50
4983148
4984038
−
650716122

TABLE 4a

Data for Enterobacter, particularly Enterobacter aerogenes

Scaffold.External.

No.
Accession
Scaffold.Name
best_pv

1
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
1.01047730430126e−10

2
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
1.01047730430126e−10

3
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
2.21893843673589e−10

4
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
7.36056945497466e−08

5
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
9.81164607784395e−08

6
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
9.81164607784395e−08

7
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
3.92206261774063e−06

8
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
9.95623777570528e−06

9
NC_009778

Enterobacter sakazakii ATCC BAA-894: NC_009778
0.000701852165838025

10
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.000960532001115215

11
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00108645793188005

12
NZ_ADTJ01000031

Escherichia coli MS 198-1 E_coli198-1-1.0_Cont45.1:
0.00108724371491948

NZ_ADTJ01000031

13
NZ_ADTJ01000031

Escherichia coli MS 198-1 E_coli198-1-1.0_Cont45.1:
0.00241352185546859

NZ_ADTJ01000031

14
NZ_ADTJ01000031

Escherichia coli MS 198-1 E_coli198-1-1.0_Cont45.1:
0.00245969973695216

NZ_ADTJ01000031

15
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00334082507673483

16
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
0.00795925223735345

TABLE 4b

Data for Enterobacter, particularly Enterobacter aerogenes (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
AZT; CAX; CAZ; CFT; CP; CRM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CP
fluoroquinolone

other

2
AZT; CAX; CAZ; CFT; CP; CRM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CP
fluoroquinolone

other

3
AZT; CAX; CAZ; CFT; CP; CRM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CP
fluoroquinolone

other

4
CP; LVX; TO; T/S
aminoglycoside; fluoroquinolone; other
CP
fluoroquinolone

5
AZT; CAX; CAZ; CFT; CP; CRM; LVX; P/T; T/S
fluoroquinolone; lactam; other
CP
fluoroquinolone

6
AZT; CP; LVX; P/T; T/S
fluoroquinolone; lactam; other
CP
fluoroquinolone

7
CP; LVX; T/S
fluoroquinolone; other
CP
fluoroquinolone

8
CP; LVX; T/S
fluoroquinolone; other
CP
fluoroquinolone

9
AZT; CAX; CAZ; CFT; CRM; P/T
lactam
AZT
lactam

10
TO
aminoglycoside
TO
aminoglycoside

11
AZT; CAX; CAZ; CFT; CRM; P/T
lactam
CAX
lactam

12
CP; LVX
fluoroquinolone
CP
fluoroquinolone

13
TO
aminoglycoside
TO
aminoglycoside

14
TO
aminoglycoside
TO
aminoglycoside

15
AZT; CAX; CAZ; CFT; CRM; P/T
lactam
CAX
lactam

16
TO
aminoglycoside
TO
aminoglycoside

TABLE 4c

Data for Enterobacter, particularly Enterobacter aerogenes (continued)

No.
num_aminoglycoside
num_fluoroquinolone
num_lactam
num_other

1
1
2
6
1

2
1
2
6
1

3
1
2
6
1

4
1
2
0
1

5
0
2
6
1

6
0
2
2
1

7
0
2
0
1

8
0
2
0
1

9
0
0
6
0

10
1
0
0
0

11
0
0
6
0

12
0
2
0
0

13
1
0
0
0

14
1
0
0
0

15
0
0
6
0

16
1
0
0
0

TABLE 4d

Data for Enterobacter, particularly Enterobacter aerogenes (continued)

No.
AZT_pv_adj
CAX_pv_adj
CAZ_pv_adj
CFT_pv_adj
CP_pv_adj

1
8.22E−04
2.45E−04
3.83E−04
4.31E−04
1.01E−10

2
1.32E−03
4.48E−04
7.06E−04
7.76E−04
1.01E−10

3
3.27E−03
1.99E−03
4.43E−03
3.01E−03
2.22E−10

4
2.06E−02
1.86E−02
2.29E−02
2.41E−02
7.36E−08

5
4.29E−03
2.32E−04
6.91E−04
7.06E−04
9.81E−08

6
8.86E−03
1.82E−02
1.77E−02
1.84E−02
9.81E−08

7
5.47E−01
1.61E−02
4.75E−02
4.90E−02
3.92E−06

8
6.96E−01
3.29E−02
9.63E−02
9.80E−02
9.96E−06

9
7.02E−04
3.95E−03
6.47E−03
6.18E−03
2.19E−02

10
6.13E−01
3.30E−01
3.24E−01
4.36E−01
1.68E−02

11
3.27E−03
1.09E−03
2.08E−03
3.16E−03
1.86E−02

12
1.54E−01
7.15E−02
8.90E−02
1.12E−01
1.09E−03

13
3.45E−01
2.11E−01
2.09E−01
2.56E−01
4.61E−02

14
2.34E−01
1.31E−01
1.03E−01
1.64E−01
1.86E−02

15
3.46E−03
3.34E−03
5.74E−03
5.48E−03
2.58E−01

16
3.30E−01
2.07E−01
1.34E−01
1.68E−01
8.94E−01

TABLE 4e

Data for Enterobacter, particularly Enterobacter aerogenes (continued)

No.
CRM_pv_adj
LVX_pv_adj
P/T_pv_adj
TO_pv_adj
T/S_pv_adj

1
4.55E−04
5.22E−07
2.23E−04
2.03E−04
1.88E−06

2
8.93E−04
7.25E−07
2.87E−04
2.45E−04
2.53E−06

3
1.47E−03
8.82E−07
4.54E−03
2.55E−04
3.69E−06

4
1.86E−02
5.08E−05
2.73E−02
3.92E−03
3.62E−05

5
9.61E−04
7.96E−07
9.64E−04
1.26E−02
1.69E−03

6
1.46E−02
1.31E−04
8.95E−03
2.06E−02
8.55E−03

7
4.85E−02
6.35E−04
2.98E−01
9.28E−02
9.01E−04

8
1.03E−01
9.82E−04
4.28E−01
1.13E−01
1.44E−03

9
1.66E−03
1.39E−01
5.16E−03
8.93E−02
1.08E−01

10
8.23E−01
8.17E−02
2.13E−01
9.61E−04
2.24E−02

11
4.37E−03
2.22E−01
9.03E−03
2.02E−01
2.91E−01

12
4.57E−02
7.49E−03
2.26E−01
4.29E−01
4.38E−02

13
5.50E−01
2.07E−01
1.23E−01
2.41E−03
4.88E−02

14
5.46E−01
9.58E−02
1.16E−01
2.46E−03
7.04E−02

15
9.73E−03
5.14E−01
9.59E−03
7.93E−01
8.06E−01

16
8.88E−01
8.87E−01
4.35E−02
7.96E−03
8.87E−01

TABLE 4f

Data for Enterobacter, particularly Enterobacter aerogenes (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
EAE_18905

YP_004593967

2
EAE_18910

YP_004593968

3
EAE_20750

YP_004594334

4
EAE_20680

YP_004594322

5
EAE_10325

YP_004592260

6
EAE_15945

YP_004593379

7
EAE_24270

YP_004595026

8
EAE_19175

YP_004594021

9
ESA_03685

YP_001439725

10
EAE_19000

YP_004593986

11
EAE_21240

YP_004594432

12
HMPREF9552_00257

ZP_07114469

13
HMPREF9552_00255

ZP_07114467

14
HMPREF9552_00247

ZP_07114459

15
EAE_02625
aphA
YP_004590739

16
EAE_18950

YP_004593976

TABLE 4g

Data for Enterobacter, particularly

Enterobacter aerogenes (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
4057377
4057994
−
650716122

2
4057994
4059313
−
650716122

3
4444576
4447206
−
650716122

4
4432502
4433842
−
650716122

5
2202535
2203893
−
650716122

6
3439556
3442066
+
650716122

7
5174177
5175436
+
650716122

8
4113374
4114306
−
650716122

9
3623778
3624146
+
640753067

10
4078519
4079427
+
650716122

11
4545796
4546983
−
650716122

12
14233
15036
+
648286894

13
12357
13376
+
648286894

14
7786
8685
−
648286894

15
557964
558680
−
650716122

16
4069127
4070251
−
650716122

TABLE 5a

Data for Enterobacter, particularly Enterobacter cloacae

Scaffold.External.

No.
Accession
Scaffold.Name
best_pv

1
NC_013509

Edwardsiella tarda EIB202 plasmid pEIB202: NC_013509
5.49490970435242e−27

2
NC_014107

Enterobacter cloacae subsp. cloacae ATCC 13047 plasmid
5.83313344212793e−25

pECL_A: NC_014107

3
NC_009838

Escherichia coli APEC O1 plasmid pAPEC-O1-R: NC_009838
5.83313344212793e−25

4
NC_009838

Escherichia coli APEC O1 plasmid pAPEC-O1-R: NC_009838
5.83313344212793e−25

5
NC_014107

Enterobacter cloacae subsp. cloacae ATCC 13047 plasmid
1.25162242820201e−24

pECL_A: NC_014107

6
NC_014107

Enterobacter cloacae subsp. cloacae ATCC 13047 plasmid
2.31689992231266e−24

pECL_A: NC_014107

7
NC_014107

Enterobacter cloacae subsp. cloacae ATCC 13047 plasmid
2.46438038993034e−24

pECL_A: NC_014107

8
NC_014107

Enterobacter cloacae subsp. cloacae ATCC 13047 plasmid
2.46438038993034e−24

pECL_A: NC_014107

9
NZ_GG657370

Citrobacter sp. 30_2 genomic scaffold supercont1.5:
2.46438038993034e−24

NZ_GG657370

10
NZ_GG657370

Citrobacter sp. 30_2 genomic scaffold supercont1.5:
1.59357817134779e−23

NZ_GG657370

11
NC_009838

Escherichia coli APEC O1 plasmid pAPEC-O1-R: NC_009838
1.59357817134779e−23

12
NC_009778

Enterobacter sakazakii ATCC BAA-894: NC_009778
2.83245228849161e−23

13
NC_014107

Enterobacter cloacae subsp. cloacae ATCC 13047 plasmid
2.83245228849161e−23

pECL_A: NC_014107

14
NZ_ADUD01000537

Escherichia coli MS 196-1 E_coli196-1-1.0_Cont1482.1:
9.1281268279348e−23

NZ_ADUD01000537

15
NC_014121

Enterobacter cloacae subsp. cloacae ATCC 13047
2.16502306009163e−22

chromosome: NC_014121

16
NZ_ABFH01000001

Salmonella enterica subsp. enterica serovar Virchow str.
4.49434330590708e−22

SL491, unfinished sequence: NZ_ABFH01000001

17
NC_004741

Shigella flexneri 2a str. 2457T: NC_004741
1.02679325501045e−21

18
NC_014121

Enterobacter cloacae subsp. cloacae ATCC 13047
1.4942758061424e−21

chromosome: NC_014121

19
NZ_AFBO01000168

Klebsiella sp. MS 92-3 K_spMS92-3-1.0_Cont398.10:
2.33876952186319e−21

NZ_AFBO01000168

20
NC_014121

Enterobacter cloacae subsp. cloacae ATCC 13047
7.16913512003583e−16

chromosome: NC_014121

21
CP001383

Shigella flexneri 2002017: CP001383
1.0532279235518e−15

22
CP001637

Escherichia coli DH1: CP001637
4.34714801916322e−15

23
NZ_ADWT01000006

Escherichia coli MS 124-1 E_coliMS124-1-1.0.1_Cont5.1:
2.30933700130366e−14

NZ_ADWT01000006

24
NZ_ADTR01000359

Escherichia coli MS 21-1 E_coli21-1-1.0_Cont669.1:
3.84987338572512e−13

NZ_ADTR01000359

25
NC_014121

Enterobacter cloacae subsp. cloacae ATCC 13047
5.47488441522503e−11

chromosome: NC_014121

26
NZ_AAJV01000019

Escherichia coli E22, unfinished sequence:
9.06569667406974e−10

NZ_AAJV01000019

27
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
1.83557061686134e−09

genome.: FP929040

28
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
3.37768924887661e−09

genome.: FP929040

29
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
5.84222468117604e−09

genome.: FP929040

30
NZ_AFHR01000043

Enterobacter hormaechei ATCC 49162 contig00043:
8.80996353751187e−09

NZ_AFHR01000043

31
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
1.29388450812614e−08

genome.: FP929040

32
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
1.29388450812614e−08

genome.: FP929040

33
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
1.29388450812614e−08

genome.: FP929040

34
NZ_AFHR01000073

Enterobacter hormaechei ATCC 49162 contig00073:
1.29388450812614e−08

NZ_AFHR01000073

35
NZ_AFHR01000073

Enterobacter hormaechei ATCC 49162 contig00073:
1.29388450812614e−08

NZ_AFHR01000073

36
NZ_AFHR01000034

Enterobacter hormaechei ATCC 49162 contig00034:
1.29388450812614e−08

NZ_AFHR01000034

37
NZ_AFHR01000073

Enterobacter hormaechei ATCC 49162 contig00073:
2.23051874499664e−08

NZ_AFHR01000073

38
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
2.39066831640169e−08

genome.: FP929040

39
NZ_AFHR01000062

Enterobacter hormaechei ATCC 49162 contig00062:
2.39066831640169e−08

NZ_AFHR01000062

40
NC_014618

Enterobacter cloacae SCF1 chromosome: NC_014618
2.76892470483105e−08

41
NC_014618

Enterobacter cloacae SCF1 chromosome: NC_014618
3.01843352491008e−08

42
NZ_ABWM01000064

Enterobacter cancerogenus ATCC 35316, unfinished
4.40355882800235e−08

sequence: NZ_ABWM01000064

43
NC_014121

Enterobacter cloacae subsp. cloacae ATCC 13047
4.44394973624704e−08

chromosome: NC_014121

44
NZ_GG657370

Citrobacter sp. 30_2 genomic scaffold supercont1.5:
5.11952538533182e−08

NZ_GG657370

45
NC_014618

Enterobacter cloacae SCF1 chromosome: NC_014618
5.14762193286233e−08

46
NZ_AFHR01000015

Enterobacter hormaechei ATCC 49162 contig00015:
5.14762193286233e−08

NZ_AFHR01000015

47
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
5.31046635969439e−08

genome.: FP929040

48
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
5.31046635969439e−08

genome.: FP929040

49
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
5.31046635969439e−08

genome.: FP929040

50
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
5.31046635969439e−08

genome.: FP929040

TABLE 5b

Data for Enterobacter, particularly Enterobacter cloacae (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
AZT; CAX; CAZ; CFT; CP; CPE; CRM; ETP; GM; LVX;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

P/T; TO; T/S
other

2
AZT; CAX; CAZ; CFT; CP; CPE; CRM; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

TO; T/S
other

3
AZT; CAX; CAZ; CFT; CP; CPE; CRM; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

TO; T/S
other

4
AZT; CAX; CAZ; CFT; CP; CPE; CRM; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

TO; T/S
other

5
AZT; CAX; CAZ; CFT; CP; CPE; CRM; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

TO; T/S
other

6
AZT; CAX; CAZ; CFT; CP; CPE; ETP; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

TO; T/S
other

7
AZT; CAX; CAZ; CFT; CP; CPE; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
T/S
other

other

8
AZT; CAX; CAZ; CFT; CP; CPE; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
T/S
other

other

9
AZT; CAX; CAZ; CFT; CP; CPE; CRM; GM; LVX; TO;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

T/S
other

10
AZT; CAX; CAZ; CFT; CP; CPE; CRM; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

TO; T/S
other

11
AZT; CAX; CAZ; CFT; CP; CPE; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
T/S
other

other

12
AZT; CAX; CAZ; CFT; CP; CPE; CRM; GM; LVX; TO;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

T/S
other

13
AZT; CAX; CAZ; CFT; CP; CPE; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
T/S
other

other

14
AZT; CAX; CAZ; CFT; CP; CPE; CRM; ETP; GM; LVX;
aminoglycoside; fluoroquinolone; lactam;
GM
aminoglycoside

P/T; TO; T/S
other

15
AZT; CAX; CAZ; CFT; CP; CPE; CRM; ETP; GM; LVX;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

P/T; TO; T/S
other

16
AZT; CAX; CAZ; CFT; CP; CPE; CRM; ETP; GM; LVX;
aminoglycoside; fluoroquinolone; lactam;
GM
aminoglycoside

P/T; TO; T/S
other

17
AZT; CAX; CAZ; CFT; CP; CPE; CRM; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
GM
aminoglycoside

TO; T/S
other

18
AZT; CAX; CAZ; CFT; CP; CPE; CRM; ETP; GM; LVX;
aminoglycoside; fluoroquinolone; lactam;
TO
aminoglycoside

P/T; TO; T/S
other

19
AZT; CAX; CAZ; CFT; CP; CPE; CRM; ETP; GM; LVX;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

P/T; TO; T/S
other

20
AZT; CAX; CAZ; CFT; CP; CPE; CRM; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
TO
aminoglycoside

TO; T/S
other

21
AZT; CAX; CAZ; CFT; CP; CPE; GM; LVX; P/T; TO;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

T/S
other

22
AZT; CAX; CAZ; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
T/S
other

other

23
AZT; CAX; CAZ; CFT; CP; CPE; GM; LVX; P/T; TO;
aminoglycoside; fluoroquinolone; lactam;
GM
aminoglycoside

T/S
other

24
AZT; CAX; CAZ; CFT; CP; CPE; GM; LVX; P/T; TO;
aminoglycoside; fluoroquinolone; lactam;
GM
aminoglycoside

T/S
other

25
AZT; CAX; CAZ; CFT; CP; CPE; ETP; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
TO
aminoglycoside

TO; T/S
other

26
AZT; CAX; CAZ; CFT; CP; CPE; ETP; GM; LVX; TO;
aminoglycoside; fluoroquinolone; lactam;
TO
aminoglycoside

T/S
other

27
AZT; CAX; CAZ; CFT; CP; CPE; GM; LVX; P/T; TO;
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

T/S
other

28
AZT; CAX; CAZ; CFT; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
CPE
lactam

29
AZT; CAX; CAZ; CFT; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

30
AZT; CAZ; CFT; CP; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

31
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

32
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

33
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

34
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

35
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

36
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

37
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

38
CP; CPE; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

39
CP; CPE; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

40
AZT; CAX; CAZ; CFT; CRM; GM; P/T; TO; T/S
aminoglycoside; lactam; other
T/S
other

41
AZT; CAX; CAZ; CFT; CP; CPE; ETP; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

TO; T/S
other

42
CP; CPE; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

43
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

44
AZT; CAX; CAZ; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
T/S
other

other

45
CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

46
CP; CPE; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

47
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

48
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

49
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

50
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

TABLE 5c

Data for Enterobacter, particularly Enterobacter cloacae (continued)

No.
num_aminoglycoside
num_fluoroquinolone
num_lactam
num_other

1
2
2
8
1

2
2
2
7
1

3
2
2
7
1

4
2
2
7
1

5
2
2
7
1

6
2
2
7
1

7
2
2
5
1

8
2
2
5
1

9
2
2
6
1

10
2
2
7
1

11
2
2
5
1

12
2
2
6
1

13
2
2
5
1

14
2
2
8
1

15
2
2
8
1

16
2
2
8
1

17
2
2
7
1

18
2
2
8
1

19
2
2
8
1

20
2
2
7
1

21
2
2
6
1

22
2
2
5
1

23
2
2
6
1

24
2
2
6
1

25
2
2
7
1

26
2
2
6
1

27
2
2
6
1

28
2
1
6
0

29
2
1
6
1

30
2
2
5
1

31
2
1
5
1

32
2
1
5
1

33
2
1
5
1

34
2
1
5
1

35
2
1
5
1

36
2
1
5
1

37
2
1
5
1

38
2
2
1
1

39
2
2
1
1

40
2
0
6
1

41
2
2
7
1

42
2
2
1
1

43
2
1
5
1

44
2
2
5
1

45
2
1
4
1

46
2
2
1
1

47
2
1
5
1

48
2
1
5
1

49
2
1
5
1

50
2
1
5
1

TABLE 5d

Data for Enterobacter, particularly Enterobacter cloacae (continued)

No.
AZT_pv_adj
CAX_pv_adj
CAZ_pv_adj
CFT_pv_adj
CP_pv_adj

1
3.58E−10
7.39E−09
2.80E−11
3.62E−09
5.27E−08

2
4.06E−06
7.65E−06
8.35E−07
8.00E−07
3.72E−07

3
4.06E−06
7.65E−06
8.35E−07
8.00E−07
3.72E−07

4
4.06E−06
7.65E−06
8.35E−07
8.00E−07
3.72E−07

5
8.70E−07
8.75E−06
5.21E−07
5.80E−07
1.18E−06

6
1.92E−12
2.08E−13
5.48E−12
1.92E−12
4.74E−09

7
2.20E−05
4.05E−05
4.94E−06
4.85E−06
7.75E−07

8
2.20E−05
4.05E−05
4.94E−06
4.85E−06
7.75E−07

9
6.62E−06
1.21E−05
1.34E−06
1.27E−06
3.72E−07

10
3.70E−06
6.73E−06
7.48E−07
7.08E−07
2.65E−06

11
3.46E−05
6.07E−05
7.99E−06
7.84E−06
7.16E−07

12
6.62E−06
1.21E−05
1.34E−06
1.27E−06
3.14E−06

13
2.20E−05
4.05E−05
4.94E−06
4.85E−06
7.75E−07

14
2.41E−09
3.66E−10
2.89E−10
1.33E−09
1.31E−11

15
6.79E−08
4.49E−08
1.13E−08
3.99E−08
4.19E−12

16
3.51E−09
1.67E−09
8.09E−10
8.35E−10
5.65E−12

17
3.11E−11
6.47E−11
7.01E−12
5.47E−11
1.53E−06

18
4.36E−12
6.39E−12
5.85E−13
5.48E−12
5.70E−07

19
6.79E−08
4.49E−08
1.13E−08
3.99E−08
3.61E−11

20
5.39E−09
1.23E−08
5.84E−09
6.70E−09
5.19E−07

21
3.36E−07
5.25E−07
5.19E−07
3.74E−06
3.91E−05

22
4.53E−07
8.07E−07
7.17E−07
6.01E−06
7.16E−05

23
1.62E−07
3.02E−07
2.83E−08
5.65E−08
9.46E−05

24
8.58E−09
1.75E−08
5.92E−08
2.01E−07
7.82E−07

25
5.28E−06
5.19E−07
1.32E−06
7.50E−07
1.27E−05

26
3.71E−05
2.06E−06
1.56E−05
9.73E−06
1.34E−04

27
2.41E−04
8.91E−05
8.91E−05
4.87E−04
5.72E−04

28
2.12E−03
7.75E−04
1.61E−03
5.63E−03
2.33E−02

29
3.60E−03
1.44E−03
1.46E−03
6.84E−03
1.58E−02

30
1.63E−03
1.30E−02
1.26E−03
9.88E−03
1.03E−03

31
8.73E−03
1.90E−03
3.60E−03
1.54E−02
2.18E−02

32
8.73E−03
1.90E−03
3.60E−03
1.54E−02
2.18E−02

33
8.73E−03
1.90E−03
3.60E−03
1.54E−02
2.18E−02

34
8.73E−03
1.90E−03
3.60E−03
1.54E−02
2.18E−02

35
8.73E−03
1.90E−03
3.60E−03
1.54E−02
2.18E−02

36
8.73E−03
1.90E−03
3.60E−03
1.54E−02
2.18E−02

37
9.06E−03
2.62E−03
4.92E−03
1.99E−02
2.22E−02

38
3.58E−02
1.04E−02
1.75E−02
5.31E−02
2.20E−05

39
5.33E−02
1.78E−02
2.85E−02
7.63E−02
6.85E−05

40
8.52E−05
3.90E−05
6.01E−06
2.49E−05
1.29E−02

41
4.11E−06
7.41E−04
4.26E−05
1.08E−03
6.16E−05

42
4.35E−02
1.36E−02
2.23E−02
6.48E−02
2.37E−05

43
8.79E−03
2.56E−03
4.80E−03
1.96E−02
2.95E−02

44
5.44E−03
1.03E−03
6.23E−04
1.01E−03
1.45E−04

45
1.49E−02
4.69E−03
8.56E−03
3.09E−02
3.86E−02

46
2.22E−01
6.69E−02
1.35E−01
3.01E−01
6.26E−04

47
8.87E−03
1.93E−03
3.69E−03
1.56E−02
3.05E−02

48
8.87E−03
1.93E−03
3.69E−03
1.56E−02
3.05E−02

49
8.87E−03
1.93E−03
3.69E−03
1.56E−02
3.05E−02

50
8.87E−03
1.93E−03
3.69E−03
1.56E−02
3.05E−02

TABLE 5e

Data for Enterobacter, particularly

Enterobacter cloacae (continued)

No.
CPE_pv_adj
CRM_pv_adj
ETP_pv_adj
GM_pv_adj

1
2.76E−09
1.20E−03
1.29E−04
3.48E−19

2
2.95E−05
2.74E−03
5.44E−02
5.95E−17

3
2.95E−05
2.74E−03
5.44E−02
5.95E−17

4
2.95E−05
2.74E−03
5.44E−02
5.95E−17

5
5.40E−05
2.87E−03
9.20E−02
6.93E−16

6
3.27E−08
3.20E−02
6.76E−03
1.07E−19

7
6.14E−05
1.06E−02
5.77E−02
2.51E−16

8
6.14E−05
1.06E−02
5.77E−02
2.51E−16

9
5.81E−05
2.77E−03
7.62E−02
4.00E−16

10
5.02E−05
3.99E−03
3.88E−02
2.55E−15

11
5.72E−05
1.10E−02
5.64E−02
1.59E−16

12
5.81E−05
6.94E−03
4.04E−02
4.15E−15

13
1.93E−05
1.06E−02
5.77E−02
2.51E−16

14
5.33E−09
5.60E−04
8.61E−04
9.13E−23

15
1.62E−07
1.89E−03
7.13E−04
4.13E−22

16
1.55E−08
1.01E−03
1.04E−03
4.49E−22

17
5.31E−08
9.22E−03
1.04E−02
1.03E−21

18
1.37E−08
1.77E−03
7.24E−03
1.52E−21

19
3.31E−08
1.89E−03
6.74E−03
5.26E−21

20
5.79E−05
2.43E−03
5.85E−02
1.07E−14

21
8.87E−03
1.21E−02
2.44E−01
2.97E−08

22
1.76E−02
1.63E−02
2.41E−01
7.76E−08

23
2.82E−06
7.01E−02
5.22E−02
2.31E−14

24
3.31E−04
2.06E−02
1.04E−02
3.85E−13

25
1.65E−04
1.14E−01
1.77E−03
5.27E−08

26
1.92E−04
5.27E−02
1.45E−03
1.24E−08

27
1.84E−09
3.12E−02
9.47E−02
3.86E−04

28
3.38E−09
2.11E−01
1.66E−01
6.74E−04

29
5.84E−09
6.96E−02
2.65E−01
9.71E−04

30
8.81E−09
1.75E−01
1.27E−01
2.57E−04

31
1.29E−08
8.58E−02
3.28E−01
1.48E−03

32
1.29E−08
8.58E−02
3.28E−01
1.48E−03

33
1.29E−08
8.58E−02
3.28E−01
1.48E−03

34
1.29E−08
8.58E−02
3.28E−01
1.48E−03

35
1.29E−08
8.58E−02
3.28E−01
1.48E−03

36
1.29E−08
8.58E−02
3.28E−01
1.48E−03

37
2.23E−08
8.52E−02
3.28E−01
1.51E−03

38
2.39E−08
4.38E−01
5.64E−02
4.16E−03

39
2.39E−08
4.38E−01
5.64E−02
4.16E−03

40
1.69E−01
6.82E−04
7.60E−01
2.98E−04

41
3.02E−08
3.74E−02
3.81E−04
1.38E−04

42
4.40E−08
3.77E−01
5.72E−02
4.38E−03

43
4.44E−08
6.75E−02
3.31E−01
2.17E−03

44
2.31E−02
4.84E−02
6.10E−02
1.15E−06

45
5.15E−08
8.55E−02
2.60E−01
3.19E−03

46
5.15E−08
7.80E−02
4.73E−01
1.13E−03

47
5.31E−08
1.08E−01
2.67E−01
2.37E−03

48
5.31E−08
1.08E−01
2.67E−01
2.37E−03

49
5.31E−08
1.08E−01
2.67E−01
2.37E−03

50
5.31E−08
1.08E−01
2.67E−01
2.37E−03

TABLE 5f

Data for Enterobacter, particularly

Enterobacter cloacae (continued)

No.
LVX_pv_adj
P/T_pv_adj
TO_pv_adj
T/S_pv_adj

1
8.81E−09
1.52E−04
2.06E−19
5.49E−27

2
2.74E−08
6.34E−03
2.69E−20
5.83E−25

3
2.74E−08
6.34E−03
2.69E−20
5.83E−25

4
2.74E−08
6.34E−03
2.69E−20
5.83E−25

5
5.07E−07
6.25E−03
9.93E−19
1.25E−24

6
1.21E−11
4.05E−05
5.70E−21
2.32E−24

7
5.15E−08
1.58E−02
1.59E−19
2.46E−24

8
5.15E−08
1.58E−02
1.59E−19
2.46E−24

9
7.06E−08
1.10E−02
1.73E−19
2.46E−24

10
3.37E−07
8.08E−03
1.06E−18
1.59E−23

11
4.09E−08
2.07E−02
9.23E−20
1.59E−23

12
3.72E−07
1.10E−02
1.95E−18
2.83E−23

13
5.15E−08
1.58E−02
1.59E−19
2.83E−23

14
1.31E−11
2.13E−07
5.43E−22
1.85E−22

15
4.19E−12
8.40E−07
8.04E−22
2.17E−22

16
5.65E−12
5.70E−07
2.63E−21
1.03E−21

17
1.00E−08
4.60E−04
1.44E−21
4.11E−18

18
2.49E−09
1.68E−04
1.49E−21
4.99E−18

19
4.19E−12
8.40E−07
7.92E−21
2.34E−21

20
6.44E−09
2.28E−04
7.17E−16
1.02E−15

21
8.28E−05
6.44E−04
3.80E−10
1.05E−15

22
1.82E−04
9.24E−04
1.96E−09
4.35E−15

23
1.55E−05
1.40E−04
3.69E−14
6.50E−11

24
7.82E−07
1.61E−04
8.30E−12
1.21E−11

25
3.34E−06
3.34E−03
5.47E−11
4.91E−08

26
6.31E−06
1.70E−02
9.07E−10
5.12E−08

27
2.79E−05
2.12E−03
1.68E−04
4.44E−04

28
2.35E−03
8.21E−03
2.41E−03
3.78E−02

29
1.41E−03
2.25E−03
9.05E−04
1.74E−03

30
1.97E−05
1.77E−03
8.04E−05
5.50E−04

31
2.08E−03
5.50E−03
1.36E−03
3.40E−03

32
2.08E−03
5.50E−03
1.36E−03
3.40E−03

33
2.08E−03
5.50E−03
1.36E−03
3.40E−03

34
2.08E−03
5.50E−03
1.36E−03
3.40E−03

35
2.08E−03
5.50E−03
1.36E−03
3.40E−03

36
2.08E−03
5.50E−03
1.36E−03
3.40E−03

37
2.10E−03
7.39E−03
1.42E−03
3.42E−03

38
1.40E−06
4.00E−02
2.39E−03
8.45E−04

39
5.74E−06
7.03E−02
2.39E−03
8.45E−04

40
1.29E−02
8.60E−03
1.87E−05
2.77E−08

41
6.73E−06
8.68E−06
4.49E−05
2.53E−04

42
1.52E−06
4.87E−02
2.44E−03
8.72E−04

43
3.07E−03
5.47E−03
1.99E−03
2.25E−03

44
1.45E−04
6.88E−03
4.69E−06
5.12E−08

45
3.22E−03
9.52E−03
2.86E−03
3.22E−03

46
6.11E−05
1.82E−01
2.53E−04
3.05E−04

47
3.31E−03
5.73E−03
2.11E−03
5.16E−03

48
3.31E−03
5.73E−03
2.11E−03
5.16E−03

49
3.31E−03
5.73E−03
2.11E−03
5.16E−03

50
3.31E−03
5.73E−03
2.11E−03
5.16E−03

TABLE 5g

Data for Enterobacter, particularly Enterobacter cloacae (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
ETAE_p041
folP
YP_003297635
plasmid pEIB202

2
ECL_A197

YP_003602692
plasmid pECL_A

3
APECO1_O1R60
terY1
YP_001481413
plasmid pAPEC-O1-R

4
APECO1_O1R58
terY2
YP_001481411
plasmid pAPEC-O1-R

5
ECL_A215

YP_003602710
plasmid pECL_A

6
ECL_A245

YP_003602738
plasmid pECL_A

7
ECL_A211

YP_003602706
plasmid pECL_A

8
ECL_A213

YP_003602708
plasmid pECL_A

9
CSAG_04328

ZP_04559059

10
CSAG_04340

ZP_04559071

11
APECO1_O1R72
terD
YP_001481425
plasmid pAPEC-O1-R

12
ESA_01791

YP_001437881

13
ECL_A210

YP_003602705
plasmid pECL_A

14
HMPREF9551_04611

ZP_07191964

15
ECL_03822
merP
YP_003614305

16
Salmoentericaenterica_010100000105

ZP_02702049

17
S2707
parA
NP_838057

18
ECL_03815

YP_003614298

19
HMPREF9538_01300

ZP_08303641

20
ECL_00479

YP_003610994

21
SFxv_1737

ADA73942

22
EcDH1_2078

ACX39734

23
HMPREF9347_01086

ZP_07208640

24
HMPREF9530_03894

ZP_07153755

25
ECL_00391

YP_003610906

26
EcolE2_01002790

ZP_00728858

27
ENC_13410

CBK85143

28
ENC_03420

CBK84384

29
ENC_31170

CBK86512

30
HMPREF9086_2435

ZP_08498173

31
ENC_11900

CBK85029

32
ENC_02650

CBK84321

33
ENC_02700

CBK84325

34
HMPREF9086_4455
amsH2
ZP_08500191

35
HMPREF9086_4454
yccY2
ZP_08500190

36
HMPREF9086_2100
yjdF
ZP_08497838

37
HMPREF9086_4460
ligA2
ZP_08500196

38
ENC_28850

CBK86326

39
HMPREF9086_3524
gatAX
ZP_08499260

40
Entcl_2219

YP_003941757

41
Entcl_2207

YP_003941745

42
ENTCAN_03923

ZP_03284103

43
ECL_01132

YP_003611642

44
CSAG_04209

ZP_04558940

45
Entcl_0777

YP_003940336

46
HMPREF9086_0855

ZP_08496597

47
ENC_21030

CBK85719

48
ENC_20990

CBK85716

49
ENC_21000

CBK85717

50
ENC_21040

CBK85720

TABLE 5h

Data for Enterobacter, particularly

Enterobacter cloacae (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
32101
32916
−
646311959

2
142295
142936
−
646564617

3
68792
69511
−
640753093

4
67490
68131
−
640753093

5
156077
157318
+
646564617

6
176747
177670
−
646564617

7
153338
154378
+
646564617

8
155073
155648
+
646564617

9
377133
378173
−
646206736

10
388284
389441
+
646206736

11
80263
80841
+
640753093

12
1731242
1732198
−
640753067

13
152860
153315
+
646564617

14
97
531
−
648293053

15
3908948
3909223
+
646564624

16
16271
16636
−
641778223

17
2602155
2602892
−
637000219

18
3903410
3903712
+
646564624

19
6404
6640
+
651333085

20
482851
484329
−
646564624

21
1636971
1637258
−
646862363

22
2232606
2232845
+
646862383

23
2726
5692
−
648294279

24
1918
3231
−
648290583

25
409807
410283
+
646564624

26
14395
15375
+
638358747

27
1397946
1398188
−
650378029

28
360699
361856
+
650378029

29
3151035
3151685
−
650378029

30
192614
193519
+
651335147

31
1250898
1252163
+
650378029

32
274155
276332
−
650378029

33
280790
281458
−
650378029

34
111547
112680
−
651335177

35
111116
111559
−
651335177

36
33364
34074
+
651335138

37
117314
119053
−
651335177

38
2904606
2905577
−
650378029

39
8440
9756
−
651335166

40
2349542
2349967
+
649633020

41
2334593
2335594
−
649633020

42
28272
29567
−
643006662

43
1168855
1169388
+
646564624

44
254005
255187
−
646206736

45
812618
813094
+
649633020

46
13947
15560
−
651335119

47
2148896
2151391
+
650378029

48
2145171
2145458
+
650378029

49
2145486
2146736
+
650378029

50
2151395
2152267
−
650378029

TABLE 6a

Data for Enterobacter, particularly Enterobacter cloacae

Scaffold.external.

No.
Accession
Scaffold.Name
best_pv

1
NC_013509

Edwardsiella tarda EIB202 plasmid pEIB202: NC_013509
5.49490970435242e−27

2
NC_014107

Enterobacter cloacae subsp. cloacae ATCC 13047 plasmid
5.83313344212793e−25

pECL_A: NC_014107

3
NC_009838

Escherichia coli APEC O1 plasmid pAPEC-O1-R: NC_009838
5.83313344212793e−25

4
NC_009838

Escherichia coli APEC O1 plasmid pAPEC-O1-R: NC_009838
5.83313344212793e−25

5
NC_014107

Enterobacter cloacae subsp. cloacae ATCC 13047 plasmid
1.25162242820201e−24

pECL_A: NC_014107

6
NC_014107

Enterobacter cloacae subsp. cloacae ATCC 13047 plasmid
2.31689992231266e−24

pECL_A: NC_014107

7
NC_014107

Enterobacter cloacae subsp. cloacae ATCC 13047 plasmid
2.46438038993034e−24

pECL_A: NC_014107

8
NC_014107
Enterobacter cloacae subsp. cloacae ATCC 13047 plasmid
2.46438038993034e−24

pECL_A: NC_014107

9
NZ_GG657370

Citrobacter sp. 30_2 genomic scaffold supercont1.5:
2.46438038993034e−24

NZ_GG657370

10
NZ_GG657370

Citrobacter sp. 30_2 genomic scaffold supercont1.5:
1.59357817134779e−23

NZ_GG657370

11
NC_009838

Escherichia coli APEC O1 plasmid pAPEC-O1-R: NC_009838
1.59357817134779e−23

12
NC_009778

Enterobacter sakazakii ATCC BAA-894: NC_009778
2.83245228849161e−23

13
NC_014107

Enterobacter cloacae subsp. cloacae ATCC 13047 plasmid
2.83245228849161e−23

pECL_A: NC_014107

14
NZ_ADUD01000537

Escherichia coli MS 196-1 E_coli196-1-1.0_Cont1482.1:
9.1281268279348e−23

NZ_ADUD01000537

15
NC_014121

Enterobacter cloacae subsp. cloacae ATCC 13047
2.16502306009163e−22

chromosome: NC_014121

16
NZ_ABFH01000001

Salmonella enterica subsp. enterica serovar Virchow
4.49434330590708e−22

str. SL491, unfinished sequence: NZ_ABFH01000001

17
NC_004741

Shigella flexneri 2a str. 2457T: NC_004741
1.02679325501045e−21

18
NC_014121

Enterobacter cloacae subsp. cloacae ATCC 13047
1.4942758061424e−21

chromosome: NC_014121

19
NZ_AFBO01000168

Klebsiella sp. MS 92-3 K_spMS92-3-1.0_Cont398.10:
2.33876952186319e−21

NZ_AFBO01000168

20
NC_014121

Enterobacter cloacae subsp. cloacae ATCC 13047
7.16913512003583e−16

chromosome: NC_014121

21
CP001383

Shigella flexneri 2002017: CP001383
1.0532279235518e−15

22
CP001637

Escherichia coli DH1: CP001637
4.34714801916322e−15

23
NZ_ADWT01000006

Escherichia coli MS 124-1 E_coliMS124-1.1.0.1_Cont5.1:
2.30933700130366e−14

NZ_ADWT01000006

24
NZ_ADTR01000359

Escherichia coli MS 21-1 E_coli21-1-1.0_Cont669.1:
3.84987338572512e−13

NZ_ADTR01000359

25
NC_014121

Enterobacter cloacae subsp. cloacae ATCC 13047
5.47488441522503e−11

chromosome: NC_014121

26
NZ_AAJV01000019

Escherichia coli E22, unfinished sequence:
9.06569667406974e−10

NZ_AAJV01000019

27
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
1.83557061686134e−09

genome.: FP929040

28
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
3.37768924887661e−09

genome.: FP929040

29
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
5.84222468117604e−09

genome.: FP929040

30
NZ_AFHR01000043

Enterobacter hormaechei ATCC 49162 contig00043:
8.80996353751187e−09

NZ_AFHR01000043

31
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
1.29388450812614e−08

genome.: FP929040

32
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
1.29388450812614e−08

genome.: FP929040

33
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
1.29388450812614e−08

genome.: FP929040

34
NZ_AFHR01000073

Enterobacter hormaechei ATCC 49162 contig00073:
1.29388450812614e−08

NZ_AFHR01000073

35
NZ_AFHR01000073

Enterobacter hormaechei ATCC 49162 contig00073:
1.29388450812614e−08

NZ_AFHR01000073

36
NZ_AFHR01000034

Enterobacter hormaechei ATCC 49162 contig00034:
1.29388450812614e−08

NZ_AFHR01000034

37
NZ_AFHR01000073

Enterobacter hormaechei ATCC 49162 contig00073:
2.23051874499664e−08

NZ_AFHR01000073

38
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
2.39066831640169e−08

genome.: FP929040

39
NZ_AFHR01000062

Enterobacter hormaechei ATCC 49162 contig00062:
2.39066831640169e−08

NZ_AFHR01000062

40
NC_014618

Enterobacter cloacae SCF1 chromosome: NC_014618
2.76892470483105e−08

41
NC_014618

Enterobacter cloacae SCF1 chromosome: NC_014618
3.01843352491008e−08

42
NZ_ABWM01000064

Enterobacter cancerogenus ATCC 35316, unfinished
4.40355882800235e−08

sequence: NZ_ABWM01000064

43
NC_014121

Enterobacter cloacae subsp. cloacae ATCC 13047
4.44394973624704e−08

chromosome: NC_014121

44
NZ_GG657370

Citrobacter sp. 30_2 genomic scaffold supercont1.5:
5.11952538533182e−08

NZ_GG657370

45
NC_014618

Enterobacter cloacae SCF1 chromosome: NC_014618
5.14762193286233e−08

46
NZ_AFHR01000015

Enterobacter hormaechei ATCC 49162 contig00015:
5.14762193286233e−08

NZ_AFHR01000015

47
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
5.31046635969439e−08

genome.: FP929040

48
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
5.31046635969439e−08

genome.: FP929040

49
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
5.31046635969439e−08

genome.: FP929040

50
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft
5.31046635969439e−08

genome.: FP929040

TABLE 6b

Data for Enterobacter, particularly Enterobacter cloacae (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
AZT; CAX; CAZ; CFT; CP; CPE; CRM; ETP; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

TO; T/S
other

2
AZT; CAX; CAZ; CFT; CP; CPE; CRM; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

TO; T/S
other

3
AZT; CAX; CAZ; CFT; CP; CPE; CRM; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

TO; T/S
other

4
AZT; CAX; CAZ; CFT; CP; CPE; CRM; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

TO; T/S
other

5
AZT; CAX; CAZ; CFT; CP; CPE; CRM; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

TO; T/S
other

6
AZT; CAX; CAZ; CFT; CP; CPE; ETP; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

TO; T/S
other

7
AZT; CAX; CAZ; CFT; CP; CPE; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
T/S
other

other

8
AZT; CAX; CAZ; CFT; CP; CPE; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
T/S
other

other

9
AZT; CAX; CAZ; CFT; CP; CPE; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
T/S
other

other

10
AZT; CAX; CAZ; CFT; CP; CPE; CRM; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

TO; T/S
other

11
AZT; CAX; CAZ; CFT; CP; CPE; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
T/S
other

other

12
AZT; CAX; CAZ; CFT; CP; CPE; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
T/S
other

other

13
AZT; CAX; CAZ; CFT; CP; CPE; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
T/S
other

other

14
AZT; CAX; CAZ; CFT; CP; CPE; CRM; ETP; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
GM
aminoglycoside

TO; T/S
other

15
AZT; CAX; CAZ; CFT; CP; CPE; CRM; ETP; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

TO; T/S
other

16
AZT; CAX; CAZ; CFT; CP; CPE; CRM; ETP; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
GM
aminoglycoside

TO; T/S
other

17
AZT; CAX; CAZ; CFT; CP; CPE; CRM; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
GM
aminogiycoside

TO; T/S
other

18
AZT; CAX; CAZ; CFT; CP; CPE; CRM; ETP; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
TO
aminogiycoside

TO; T/S
other

19
AZT; CAX; CAZ; CFT; CP; CPE; CRM; ETP; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
T/S
other

TO; T/S
other

20
AZT; CAX; CAZ; CFT; CP; CPE; CRM; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
TO
aminogiycoside

TO; T/S
other

21
AZT; CAX; CAZ; CFT; CP; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
T/S
other

other

22
AZT; CAX; CAZ; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
T/S
other

other

23
AZT; CAX; CAZ; CFT; CP; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
GM
aminogiycoside

other

24
AZT; CAX; CAZ; CFT; CP; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
GM
aminogiycoside

other

25
AZT; CAX; CAZ; CFT; CP; CPE; ETP; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
TO
aminogiycoside

TO; T/S
other

26
AZT; CAX; CAZ; CFT; CP; CPE; ETP; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
TO
aminogiycoside

other

27
AZT; CAX; CAZ; CFT; CP; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

28
AZT; CAX; CAZ; CFT; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
CPE
lactam

29
AZT; CAX; CAZ; CFT; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

30
AZT; CAZ; CFT; CP; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

31
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

32
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

33
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

34
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

35
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

36
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

37
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

38
CP; CPE; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

39
CP; CPE; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

40
AZT; CAX; CAZ; CFT; CRM; GM; P/T; TO; T/S
aminoglycoside; lactam; other
T/S
other

41
AZT; CAX; CAZ; CFT; CP; CPE; ETP; GM; LVX; P/T;
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

TO; T/S
other

42
CP; CPE; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

43
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

44
AZT; CAX; CAZ; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
T/S
other

other

45
CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

46
CP; CPE; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

47
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

48
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

49
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

50
AZT; CAX; CAZ; CPE; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam;
CPE
lactam

other

TABLE 6c

Data for Enterobacter, particularly Enterobacter cloacae (continued)

No.
num_aminoglycoside
num_fluoroquinolone
num_lactam
num_other

1
2
2
8
1

2
2
2
7
1

3
2
2
7
1

4
2
2
7
1

5
2
2
7
1

6
2
2
7
1

7
2
2
5
1

8
2
2
5
1

9
2
2
6
1

10
2
2
7
1

11
2
2
5
1

12
2
2
6
1

13
2
2
5
1

14
2
2
8
1

15
2
2
8
1

16
2
2
8
1

17
2
2
7
1

18
2
2
8
1

19
2
2
8
1

20
2
2
7
1

21
2
2
6
1

22
2
2
5
1

23
2
2
6
1

24
2
2
6
1

25
2
2
7
1

26
2
2
6
1

27
2
2
6
1

28
2
1
6
0

29
2
1
6
1

30
2
2
5
1

31
2
1
5
1

32
2
1
5
1

33
2
1
5
1

34
2
1
5
1

35
2
1
5
1

36
2
1
5
1

37
2
1
5
1

38
2
2
1
1

39
2
2
1
1

40
2
0
6
1

41
2
2
7
1

42
2
2
1
1

43
2
1
5
1

44
2
2
5
1

45
2
1
4
1

46
2
2
1
1

47
2
1
5
1

48
2
1
5
1

49
2
1
5
1

50
2
1
5
1

TABLE 6d

Data for Enterobacter, particularly Enterobacter cloacae (continued)

No.
AZT_pv_adj
CAX_pv_adj
CAZ_pv_adj
CFT_pv_adj
CP_pv_adj

1
3.58E−10
7.39E−09
2.80E−11
3.62E−09
5.27E−08

2
4.06E−06
7.65E−06
8.35E−07
8.00E−07
3.72E−07

3
4.06E−06
7.65E−06
8.35E−07
8.00E−07
3.72E−07

4
4.06E−06
7.65E−06
8.35E−07
8.00E−07
3.72E−07

5
8.70E−07
8.75E−06
5.21E−07
5.80E−07
1.18E−06

6
1.92E−12
2.08E−13
5.48E−12
1.92E−12
4.74E−09

7
2.20E−05
4.05E−05
4.94E−06
4.85E−06
7.75E−07

8
2.20E−05
4.05E−05
4.94E−06
4.85E−06
7.75E−07

9
6.62E−06
1.21E−05
1.34E−06
1.27E−06
3.72E−07

10
3.70E−06
6.73E−06
7.48E−07
7.08E−07
2.65E−06

11
3.46E−05
6.07E−05
7.99E−06
7.84E−06
7.16E−07

12
6.62E−06
1.21E−05
1.34E−06
1.27E−06
3.14E−06

13
2.20E−05
4.05E−05
4.94E−06
4.85E−06
7.75E−07

14
2.41E−09
3.66E−10
2.89E−10
1.33E−09
1.31E−11

15
6.79E−08
4.49E−08
1.13E−08
3.99E−08
4.19E−12

16
3.51E−09
1.67E−09
8.09E−10
8.35E−10
5.65E−12

17
3.11E−11
6.47E−11
7.01E−12
5.47E−11
1.53E−06

18
4.36E−12
6.39E−12
5.85E−13
5.48E−12
5.70E−07

19
6.79E−08
4.49E−08
1.13E−08
3.99E−08
3.61E−11

20
5.39E−09
1.23E−08
5.84E−09
6.70E−09
5.19E−07

21
3.36E−07
5.25E−07
5.19E−07
3.74E−06
3.91E−05

22
4.53E−07
8.07E−07
7.17E−07
6.01E−06
7.16E−05

23
1.62E−07
3.02E−07
2.83E−08
5.65E−08
9.46E−05

24
8.58E−09
1.75E−08
5.92E−08
2.01E−07
7.82E−07

25
5.28E−06
5.19E−07
1.32E−06
7.50E−07
1.27E−05

26
3.71E−05
2.06E−06
1.56E−05
9.73E−06
1.34E−04

27
2.41E−04
8.91E−05
8.91E−05
4.87E−04
5.72E−04

28
2.12E−03
7.75E−04
1.61E−03
5.63E−03
2.33E−02

29
3.60E−03
1.44E−03
1.46E−03
6.84E−03
1.58E−02

30
1.63E−03
1.30E−02
1.26E−03
9.88E−03
1.03E−03

31
8.73E−03
1.90E−03
3.60E−03
1.54E−02
2.18E−02

32
8.73E−03
1.90E−03
3.60E−03
1.54E−02
2.18E−02

33
8.73E−03
1.90E−03
3.60E−03
1.54E−02
2.18E−02

34
8.73E−03
1.90E−03
3.60E−03
1.54E−02
2.18E−02

35
8.73E−03
1.90E−03
3.60E−03
1.54E−02
2.18E−02

36
8.73E−03
1.90E−03
3.60E−03
1.54E−02
2.18E−02

37
9.06E−03
2.62E−03
4.92E−03
1.99E−02
2.22E−02

38
3.58E−02
1.04E−02
1.75E−02
5.31E−02
2.20E−05

39
5.33E−02
1.78E−02
2.85E−02
7.63E−02
6.85E−05

40
8.52E−05
3.90E−05
6.01E−06
2.49E−05
1.29E−02

41
4.11E−06
7.41E−04
4.26E−05
1.08E−03
6.16E−05

42
4.35E−02
1.36E−02
2.23E−02
6.48E−02
2.37E−05

43
8.79E−03
2.56E−03
4.80E−03
1.96E−02
2.95E−02

44
5.44E−03
1.03E−03
6.23E−04
1.01E−03
1.45E−04

45
1.49E−02
4.69E−03
8.56E−03
3.09E−02
3.86E−02

46
2.22E−01
6.69E−02
1.35E−01
3.01E−01
6.26E−04

47
8.87E−03
1.93E−03
3.69E−03
1.56E−02
3.05E−02

48
8.87E−03
1.93E−03
3.69E−03
1.56E−02
3.05E−02

49
8.87E−03
1.93E−03
3.69E−03
1.56E−02
3.05E−02

50
8.87E−03
1.93E−03
3.69E−03
1.56E−02
3.05E−02

TABLE 6e

Data for Enterobacter, particularly

Enterobacter cloacae (continued)

No.
CPE_pv_adj
CRM_pv_adj
ETP_pv_adj
GM_pv_adj

1
2.76E−09
1.20E−03
1.29E−04
3.48E−19

2
2.95E−05
2.74E−03
5.44E−02
5.95E−17

3
2.95E−05
2.74E−03
5.44E−02
5.95E−17

4
2.95E−05
2.74E−03
5.44E−02
5.95E−17

5
5.40E−05
2.87E−03
9.20E−02
6.93E−16

6
3.27E−08
3.20E−02
6.76E−03
1.07E−19

7
6.14E−05
1.06E−02
5.77E−02
2.51E−16

8
6.14E−05
1.06E−02
5.77E−02
2.51E−16

9
5.81E−05
2.77E−03
7.62E−02
4.00E−16

10
5.02E−05
3.99E−03
3.88E−02
2.55E−15

11
5.72E−05
1.10E−02
5.64E−02
1.59E−16

12
5.81E−05
6.94E−03
4.04E−02
4.15E−15

13
1.93E−05
1.06E−02
5.77E−02
2.51E−16

14
5.33E−09
5.60E−04
8.61E−04
9.13E−23

15
1.62E−07
1.89E−03
7.13E−04
4.13E−22

16
1.55E−08
1.01E−03
1.04E−03
4.49E−22

17
5.31E−08
9.22E−03
1.04E−02
1.03E−21

18
1.37E−08
1.77E−03
7.24E−03
1.52E−21

19
3.31E−08
1.89E−03
6.74E−03
5.26E−21

20
5.79E−05
2.43E−03
5.85E−02
1.07E−14

21
8.87E−03
1.21E−02
2.44E−01
2.97E−08

22
1.76E−02
1.63E−02
2.41E−01
7.76E−08

23
2.82E−06
7.01E−02
5.22E−02
2.31E−14

24
3.31E−04
2.06E−02
1.04E−02
3.85E−13

25
1.65E−04
1.14E−01
1.77E−03
5.27E−08

26
1.92E−04
5.27E−02
1.45E−03
1.24E−08

27
1.84E−09
3.12E−02
9.47E−02
3.86E−04

28
3.38E−09
2.11E−01
1.66E−01
6.74E−04

29
5.84E−09
6.96E−02
2.65E−01
9.71E−04

30
8.81E−09
1.75E−01
1.27E−01
2.57E−04

31
1.29E−08
8.58E−02
3.28E−01
1.48E−03

32
1.29E−08
8.58E−02
3.28E−01
1.48E−03

33
1.29E−08
8.58E−02
3.28E−01
1.48E−03

34
1.29E−08
8.58E−02
3.28E−01
1.48E−03

35
1.29E−08
8.58E−02
3.28E−01
1.48E−03

36
1.29E−08
8.58E−02
3.28E−01
1.48E−03

37
2.23E−08
8.52E−02
3.28E−01
1.51E−03

38
2.39E−08
4.38E−01
5.64E−02
4.16E−03

39
2.39E−08
4.38E−01
5.64E−02
4.16E−03

40
1.69E−01
6.82E−04
7.60E−01
2.98E−04

41
3.02E−08
3.74E−02
3.81E−04
1.38E−04

42
4.40E−08
3.77E−01
5.72E−02
4.38E−03

43
4.44E−08
6.75E−02
3.31E−01
2.17E−03

44
2.31E−02
4.84E−02
6.10E−02
1.15E−06

45
5.15E−08
8.55E−02
2.60E−01
3.19E−03

46
5.15E−08
7.80E−02
4.73E−01
1.13E−03

47
5.31E−08
1.08E−01
2.67E−01
2.37E−03

48
5.31E−08
1.08E−01
2.67E−01
2.37E−03

49
5.31E−08
1.08E−01
2.67E−01
2.37E−03

50
5.31E−08
1.08E−01
2.67E−01
2.37E−03

TABLE 6f

Data for Enterobacter, particularly

Enterobacter cloacae (continued)

No.
LVX_pv_adj
P/T_pv_adj
TO_pv_adj
T/S_pv_adj

1
8.81E−09
1.52E−04
2.06E−19
5.49E−27

2
2.74E−08
6.34E−03
2.69E−20
5.83E−25

3
2.74E−08
6.34E−03
2.69E−20
5.83E−25

4
2.74E−08
6.34E−03
2.69E−20
5.83E−25

5
5.07E−07
6.25E−03
9.93E−19
1.25E−24

6
1.21E−11
4.05E−05
5.70E−21
2.32E−24

7
5.15E−08
1.58E−02
1.59E−19
2.46E−24

8
5.15E−08
1.58E−02
1.59E−19
2.46E−24

9
7.06E−08
1.10E−02
1.73E−19
2.46E−24

10
3.37E−07
8.08E−03
1.06E−18
1.59E−23

11
4.09E−08
2.07E−02
9.23E−20
1.59E−23

12
3.72E−07
1.10E−02
1.95E−18
2.83E−23

13
5.15E−08
1.58E−02
1.59E−19
2.83E−23

14
1.31E−11
2.13E−07
5.43E−22
1.85E−22

15
4.19E−12
8.40E−07
8.04E−22
2.17E−22

16
5.65E−12
5.70E−07
2.63E−21
1.03E−21

17
1.00E−08
4.60E−04
1.44E−21
4.11E−18

18
2.49E−09
1.68E−04
1.49E−21
4.99E−18

19
4.19E−12
8.40E−07
7.92E−21
2.34E−21

20
6.44E−09
2.28E−04
7.17E−16
1.02E−15

21
8.28E−05
6.44E−04
3.80E−10
1.05E−15

22
1.82E−04
9.24E−04
1.96E−09
4.35E−15

23
1.55E−05
1.40E−04
3.69E−14
6.50E−11

24
7.82E−07
1.61E−04
8.30E−12
1.21E−11

25
3.34E−06
3.34E−03
5.47E−11
4.91E−08

26
6.31E−06
1.70E−02
9.07E−10
5.12E−08

27
2.79E−05
2.12E−03
1.68E−04
4.44E−04

28
2.35E−03
8.21E−03
2.41E−03
3.78E−02

29
1.41E−03
2.25E−03
9.05E−04
1.74E−03

30
1.97E−05
1.77E−03
8.04E−05
5.50E−04

31
2.08E−03
5.50E−03
1.36E−03
3.40E−03

32
2.08E−03
5.50E−03
1.36E−03
3.40E−03

33
2.08E−03
5.50E−03
1.36E−03
3.40E−03

34
2.08E−03
5.50E−03
1.36E−03
3.40E−03

35
2.08E−03
5.50E−03
1.36E−03
3.40E−03

36
2.08E−03
5.50E−03
1.36E−03
3.40E−03

37
2.10E−03
7.39E−03
1.42E−03
3.42E−03

38
1.40E−06
4.00E−02
2.39E−03
8.45E−04

39
5.74E−06
7.03E−02
2.39E−03
8.45E−04

40
1.29E−02
8.60E−03
1.87E−05
2.77E−08

41
6.73E−06
8.68E−06
4.49E−05
2.53E−04

42
1.52E−06
4.87E−02
2.44E−03
8.72E−04

43
3.07E−03
5.47E−03
1.99E−03
2.25E−03

44
1.45E−04
6.88E−03
4.69E−06
5.12E−08

45
3.22E−03
9.52E−03
2.86E−03
3.22E−03

46
6.11E−05
1.82E−01
2.53E−04
3.05E−04

47
3.31E−03
5.73E−03
2.11E−03
5.16E−03

48
3.31E−03
5.73E−03
2.11E−03
5.16E−03

49
3.31E−03
5.73E−03
2.11E−03
5.16E−03

50
3.31E−03
5.73E−03
2.11E−03
5.16E−03

TABLE 6g

Data for Enterobacter, particularly Enterobacter cloacae (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
ETAE_p041
folP
YP_003297635
plasmid pEIB202

2
ECL_A197

YP_003602692
plasmid pECL_A

3
APECO1_O1R60
terY1
YP_001481413
plasmid pAPEC-O1-R

4
APECO1_O1R58
terY2
YP_001481411
plasmid pAPEC-O1-R

5
ECL_A215

YP_003602710
plasmid pECL_A

6
ECL_A245

YP_003602738
plasmid pECL_A

7
ECL_A211

YP_003602706
plasmid pECL_A

8
ECL_A213

YP_003602708
plasmid pECL_A

9
CSAG_04328

ZP_04559059

10
CSAG_04340

ZP_04559071

11
APECO1_O1R72
terD
YP_001481425
plasmid pAPEC-O1-R

12
ESA_01791

YP_001437881

13
ECL_A210

YP_003602705
plasmid pECL_A

14
HMPREF9551_04611

ZP_07191964

15
ECL_03822
merP
YP_003614305

16
Salmoentericaenterica_010100000105

ZP_02702049

17
S2707
parA
NP_838057

18
ECL_03815

YP_003614298

19
HMPREF9538_01300

ZP_08303641

20
ECL_00479

YP_003610994

21
SFxv_17317

ADA73942

22
EcDH1_2078

ACX39734

23
HMPREF9347_01086

ZP_07208640

24
HMPREF9530_03894

ZP_07153755

25
ECL_00391

YP_003610906

26
EcolE2_01002790

ZP_00728858

27
ENC_13410

CBK85143

28
ENC_03420

CBK84384

29
ENC_31170

CBK86512

30
HMPREF9086_2435

ZP_08498173

31
ENC_11900

CBK85029

32
ENC_02650

CBK84321

33
ENC_02700

CBK84325

34
HMPREF9086_4455
amsH2
ZP_08500191

35
HMPREF9086_4454
yccY2
ZP_08500190

36
HMPREF9086_2100
yjdF
ZP_08497838

37
HMPREF9086_4460
ligA2
ZP_08500196

38
ENC_28850

CBK86326

39
HMPREF9086_3524
gatAX
ZP_08499260

40
Entcl_2219

YP_003941757

41
Entcl_2207

YP_003941745

42
ENTCAN_03923

ZP_03284103

43
ECL_01132

YP_003611642

44
CSAG_04209

ZP_04558940

45
Entcl_0777

YP_003940336

46
HMPREF9086_0855

ZP_08496597

47
ENC_21030

CBK85719

48
ENC_20990

CBK85716

49
ENC_21000

CBK85717

50
ENC_21040

CBK85720

TABLE 6h

Data for Enterobacter, particularly

Enterobacter cloacae (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
32101
32916
−
646311959

2
142295
142936
−
646564617

3
68792
69511
−
640753093

4
67490
68131
−
640753093

5
156077
157318
+
646564617

6
176747
177670
−
646564617

7
153338
154378
+
646564617

8
155073
155648
+
646564617

9
377133
378173
−
646206736

10
388284
389441
+
646206736

11
80263
80841
+
640753093

12
1731242
1732198
−
640753067

13
152860
153315
+
646564617

14
97
531
−
648293053

15
3908948
3909223
+
646564624

16
16271
16636
−
641778223

17
2602155
2602892
−
637000219

18
3903410
3903712
+
646564624

19
6404
6640
+
651333085

20
482851
484329
−
646564624

21
1636971
1637258
−
646862363

22
2232606
2232845
+
646862383

23
2726
5692
−
648294279

24
1918
3231
−
648290583

25
409807
410283
+
646564624

26
14395
15375
+
638358747

27
1397946
1398188
−
650378029

28
360699
361856
+
650378029

29
3151035
3151685
−
650378029

30
192614
193519
+
651335147

31
1250898
1252163
+
650378029

32
274155
276332
−
650378029

33
280790
281458
−
650378029

34
111547
112680
−
651335177

35
111116
111559
−
651335177

36
33364
34074
+
651335138

37
117314
119053
−
651335177

38
2904606
2905577
−
650378029

39
8440
9756
−
651335166

40
2349542
2349967
+
649633020

41
2334593
2335594
−
649633020

42
28272
29567
−
643006662

43
1168855
1169388
+
646564624

44
254005
255187
−
646206736

45
812618
813094
+
649633020

46
13947
15560
−
651335119

47
2148896
2151391
+
650378029

48
2145171
2145458
+
650378029

49
2145486
2146736
+
650378029

50
2151395
2152267
−
650378029

Example 4:

Escherichia, particularly E. coli

The procedure was carried out as in Example 1, except that the following microorganisms were used:

Bacterial Strains

The inventors selected 1144 E.coli strains from the microbiology strain collection at Siemens Healthcare Diagnostics (West Sacramento, Calif.) for susceptibility testing and whole genome sequencing.

From MetaRef, 318 centroids of E.coli were used as reference sequences.

The results for E.coli are shown in Tables 7 (corresponding to Table 1) and 8 (corresponding to Table 2).

TABLE 7a

Data for Escherichia, particularly E. coli

Scaffold.External.

No.
Accession
Scaffold.Name
best_pv

1
NC_011083

Salmonella enterica subsp. enterica serovar Heidelberg str.
3.5041948925527e−207

SL476: NC_011083

2
NZ_AAJT01000012

Escherichia coli B7A, unfinished sequence: NZ_AAJT01000012
1.62252621621877e−119

3
NZ_ADWV01000045

Escherichia coli MS 107-1 E_coliMS107-1-1.0.1_Cont44.1:
6.24750842070913e−97

NZ_ADWV01000045

4
NC_009651

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid
8.77735582031733e−96

pKPN5: NC_009651

5
NZ_ADUB01000261

Escherichia coli MS 175-1 E_coli175-1-1.0_Cont542.3:
1.23709746311649e−80

NZ_ADUB01000261

6
NC_011092

Salmonella enterica subsp. enterica serovar Schwarzengrund
2.41688550175243e−75

str. CVM19633 plasmid pCVM19633_110: NC_011092

7
NZ_ADWV01000056

Escherichia coli MS 107-1 E_coliMS107-1-1.0.1_Cont55.1:
7.68091736117399e−72

NZ_ADWV01000056

8
NZ_AAJX01000089

Escherichia coli B171, unfinished sequence: NZ_AAJX01000089
1.57772112100981e−71

9
NC_011743

Escherichia fergusonii ATCC 35469 plasmid pEFER: NC_011743
1.0118246517332e−69

10
NC_013509

Edwardsiella tarda EIB202 plasmid pEIB202: NC_013509
1.23255842888535e−68

11
NZ_GG749218

Escherichia coli FVEC1412 genomic scaffold supercont1.13:
6.77313303746994e−68

NZ_GG749218

12
NC_013509

Edwardsiella tarda EIB202 plasmid pEIB202: NC_013509
1.94619564613577e−64

13
NZ_GG749218

Escherichia coli FVEC1412 genomic scaffold supercont1.13:
1.86737834552034e−63

NZ_GG749218

14
NC_013717

Citrobacter rodentium ICC168 plasmid pCROD1: NC_013717
7.42780365363135e−62

15
NC_013717

Citrobacter rodentium ICC168 plasmid pCROD1: NC_013717
3.07751376659308e−61

16
NZ_ADWS01000089

Escherichia coli MS 145-7 E_coliMS145-7-1.0.1_Cont88.1:
1.7351795845908e−60

NZ_ADWS01000089

17
NC_011751

Escherichia coli UMN026: NC_011751
2.44317906034667e−60

18
NC_011751

Escherichia coli UMN026: NC_011751
6.73588199342071e−60

19
NZ_ADWV01000056

Escherichia coli MS 107-1 E_coliMS107-1-1.0.1_Cont55.1:
2.62943019143703e−59

NZ_ADWV01000056

20
NC_010488

Escherichia coli SECEC SMS-3-5 plasmid pSMS35_130: NC_010488
3.46702381924878e−47

21
NZ_ADTM01000311

Escherichia coli MS 182-1 E_coli182-1-1.0_Cont460.3:
4.65308035729244e−46

NZ_ADTM01000311

22
NZ_ADWS01000095

Escherichia coli MS 145-7 E_coliMS145-7-1.0.1_Cont94.1:
7.71451120848483e−46

NZ_ADWS01000095

23
NZ_ADTM01000311

Escherichia coli MS 182-1 E_coli182-1-1.0_Cont460.3:
1.08551755499227e−44

NZ_ADTM01000311

24
NC_009650

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid
4.89761264283562e−44

pKPN4: NC_009650

25
NZ_ADWV01000017

Escherichia coli MS 107-1 E_coliMS107-1-1.0.1_Cont16.1:
6.97693050178087e−44

NZ_ADWV01000017

26
NC_009650

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid
9.68294892967391e−44

pKPN4: NC_009650

27
NZ_GG665811

Escherichia sp. 1_1_43 genomic scaffold supercont1.1:
3.5843867496487e−43

NZ_GG665811

28
NZ_ADTL01000051

Escherichia coli MS 115-1 E_coli115-1-1.0_Cont158.2:
3.5843867496487e−43

NZ_ADTL01000051

29
AP011957

Salmonella enterica subsp. enterica serovar Typhimurium str.
5.53805522527039e−43

T000240 DNA: AP011957

30
NC_011282

Klebsiella pneumoniae 342 plasmid pKP187: NC_011282
2.71226651272988e−42

31
NZ_ABHR01000011

Escherichia coli O157:H7 str. EC4401, unfinished sequence:
8.45082785112866e−42

NZ_ABHR01000011

32
NC_010488

Escherichia coli SECEC SMS-3-5 plasmid pSMS35_130: NC_010488
1.02749291231853e−41

33
NZ_AFBO01000013

Klebsiella sp. MS 92-3 K_spMS92-3-l.0_Cont24.1:
1.46909169086738e−41

NZ_AFBO01000013

34
CP002797

Escherichia coli NA114: CP002797
2.43588122712712e−41

35
NZ_ABHK01000002

Escherichia coli O157:H7 str. EC4206, unfinished sequence:
2.60702932643171e−41

NZ_ABHK01000002

36
NZ_GG657366

Citrobacter sp. 30_2 genomic scaffold supercont1.1:
2.60702932643171e−41

NZ_GG657366

37
NC_011353

Escherichia coli O157:H7 str. EC4115: NC_011353
2.60702932643171e−41

38
NZ_ABWL01000012

Citrobacter youngae ATCC 29220 C_sp-1.0_Cont2.3:
3.21133372679738e−41

NZ_ABWL01000012

39
AP009378

Escherichia coli SE15 DNA: AP009378
3.68640118720819e−41

40
NZ_ACXN01000074

Escherichia coli O157:H7 str. FRIK966: NZ_ACXN01000074
5.75695041652081e−41

41
NC_007384

Shigella sonnei Ss046: NC_007384
6.75951367822551e−41

42
NZ_ABWL01000012

Citrobacter youngae ATCC 29220 C_sp-1.0_Cont2.3:
8.12681193093067e−41

NZ_ABWL01000012

43
NZ_ADTL01000083

Escherichia coli MS 115-1 E_coli115-1-1.0_Cont264.1:
8.12681193093067e−41

NZ_ADTL01000083

44
AC_000091

Escherichia coli W3110 DNA: AC_000091
8.12681193093067e−41

45
NZ_ADUD01000537

Escherichia coli MS 196-1 E_colil96-1-1.0_Cont1482.1:
1.06521634399457e−40

NZ_ADUD01000537

46
NC_011083

Salmonella enterica subsp. enterica serovar Heidelberg str.
1.84998224240006e−40

SL476: NC_011083

47
CP001383

Shigella flexneri 2002017: CP001383
1.89942261631873e−40

48
NZ_ADTR01000134

Escherichia coli MS 21-1 E_coli21-1-1.0_Cont296.1:
3.35939290103889e−40

NZ_ADTR01000134

49
NC_009650

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid
3.76989142366575e−40

pKPN4: NC_009650

50
NC_004851

Shigella flexneri 2a str. 301 plasmid pCP301: NC_004851
8.68449218790606e−39

TABLE 7b

Data for Escherichia, particularly E. coli (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
AM; A/S; AUG; CAX; CP; CRM; GM;
aminoglycoside; fluoroquinolone; lactam; other
AM
lactam

LVX; TO; T/S

2
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; LVX; TO; T/S

3
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; LVX; TO; T/S

4
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; LVX; TO; T/S

5
AM; A/S; AUG; CRM
lactam
AM
lactam

6
AM; A/S; AUG
lactam
AM
lactam

7
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; LVX; TO; T/S

8
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; LVX; TO; T/S

9
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; LVX; TO; T/S

10
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; LVX; TO; T/S

11
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; LVX; TO; T/S

12
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; LVX; TO; T/S

13
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; LVX; TO; T/S

14
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

15
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

16
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; LVX; TO; T/S

17
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; LVX; TO; T/S

18
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; LVX; TO; T/S

19
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; LVX; TO; T/S

20
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; LVX; TO; T/S

21
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
CAX
lactam

CRM; GM; LVX; TO; T/S

22
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; LVX; TO; T/S

23
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
AM
lactam

CRM; GM; LVX; TO; T/S

24
AM; A/S; AUG; CAX; CFT; CP; CRM;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

GM; LVX; TO; T/S

25
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; LVX; T/S

26
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; TO; T/S

27
AM; AUG; AZT; CAX; CFT; CP; CRM;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

GM; LVX; TO; T/S

28
AM; AUG; AZT; CAX; CFT; CP; CRM;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

GM; LVX; TO; T/S

29
AM; A/S; AUG; CAX; CFT; CP; CRM;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

GM; LVX; T/S

30
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

31
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

CRM; GM; LVX; TO; T/S

32
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

33
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

34
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

35
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

36
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

37
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

38
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

39
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

40
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

CRM; GM; LVX; TO; T/S

41
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

42
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

43
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

44
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

45
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; T/S

46
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

47
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

48
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

49
AM; A/S; AUG; T/S
lactam; other
T/S
other

50
AM; A/S; AUG; AZT; CAX; CFT; CP;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

CRM; GM; LVX; TO; T/S

TABLE 7c

Data for Escherichia, particularly E. coli (continued)

No.
num_aminoglycoside
num_fluoroquinolone
num_lactam
num_other

1
2
2
5
1

2
2
2
7
1

3
2
2
7
1

4
2
2
7
1

5
0
0
4
0

6
0
0
3
0

7
2
2
7
1

8
2
2
7
1

9
2
2
7
1

10
2
2
7
1

11
2
2
7
1

12
2
2
7
1

13
2
2
7
1

14
2
2
7
1

15
2
2
7
1

16
2
2
7
1

17
2
2
7
1

18
2
2
7
1

19
2
2
7
1

20
2
2
7
1

21
2
2
7
1

22
2
2
7
1

23
2
2
7
1

24
2
2
6
1

25
1
2
7
1

26
2
1
7
1

27
2
2
6
1

28
2
2
6
1

29
1
2
6
1

30
2
2
7
1

31
2
2
7
1

32
2
2
7
1

33
2
2
7
1

34
2
2
7
1

35
2
2
7
1

36
2
2
7
1

37
2
2
7
1

38
2
2
7
1

39
2
2
7
1

40
2
2
7
1

41
2
2
7
1

42
2
2
7
1

43
2
2
7
1

44
2
2
7
1

45
1
1
7
1

46
2
2
7
1

47
2
2
7
1

48
2
2
7
1

49
0
0
3
1

50
2
2
7
1

TABLE 7d

Data for Escherichia, particularly E. coli (continued)

No.
AM_pv_adj
A/S_pv_adj
AUG_pv_adj
AZT_pv_adj

1
3.50E−207
1.39E−175
2.23E−54
1.94E−02

2
3.12E−58
4.85E−48
1.56E−20
2.24E−14

3
2.85E−46
1.23E−39
2.49E−17
7.44E−15

4
2.62E−45
3.93E−39
1.12E−17
7.82E−14

5
1.24E−80
9.93E−72
2.04E−21
1.77E−02

6
2.42E−75
1.11E−66
8.58E−21
6.08E−02

7
1.01E−26
2.48E−22
5.21E−09
2.11E−04

8
4.88E−38
1.20E−35
3.67E−16
6.67E−10

9
2.35E−59
7.04E−49
2.73E−24
1.89E−06

10
2.35E−59
7.04E−49
1.31E−23
5.63E−06

11
1.84E−24
1.82E−23
1.33E−10
1.05E−06

12
2.51E−64
6.77E−56
3.88E−22
9.19E−04

13
2.79E−25
9.09E−23
1.32E−08
1.48E−03

14
2.94E−45
2.43E−34
1.15E−22
2.63E−14

15
1.58E−45
1.72E−34
1.75E−22
1.91E−14

16
3.26E−28
1.85E−21
2.00E−08
1.16E−05

17
1.44E−20
2.94E−18
5.11E−07
1.25E−04

18
6.63E−29
5.38E−22
1.16E−08
1.11E−05

19
6.41E−30
1.52E−22
9.58E−09
6.45E−06

20
4.62E−35
3.20E−30
5.19E−17
2.18E−07

21
1.82E−09
8.62E−11
2.50E−17
1.74E−39

22
3.88E−27
4.06E−27
4.62E−12
9.38E−06

23
1.09E−44
2.09E−39
1.05E−16
2.10E−06

24
2.75E−28
8.80E−22
3.79E−08
1.79E−02

25
6.10E−28
3.56E−20
2.25E−09
8.28E−04

26
5.97E−23
1.19E−15
1.39E−06
1.28E−03

27
4.17E−03
3.66E−02
4.90E−07
1.65E−14

28
4.17E−03
3.66E−02
4.90E−07
1.65E−14

29
1.37E−28
1.45E−21
8.41E−09
2.36E−02

30
5.88E−10
1.33E−07
1.85E−09
7.58E−11

31
1.14E−08
2.28E−05
5.66E−08
3.43E−16

32
1.96E−09
3.67E−07
4.28E−09
1.44E−10

33
2.88E−09
5.08E−07
4.50E−09
1.51E−10

34
1.07E−10
2.85E−08
1.31E−06
4.19E−06

35
4.32E−08
6.04E−05
1.49E−07
4.44E−16

36
8.33E−08
9.79E−05
2.97E−07
4.44E−16

37
8.33E−08
9.79E−05
2.97E−07
4.44E−16

38
3.07E−08
4.70E−05
1.02E−07
7.64E−16

39
4.14E−12
7.23E−10
1.20E−05
1.17E−03

40
1.57E−07
1.55E−04
4.17E−07
7.80E−16

41
2.15E−07
1.95E−04
5.61E−07
8.13E−16

42
1.55E−07
1.54E−04
3.95E−07
8.67E−16

43
1.55E−07
1.54E−04
3.95E−07
8.67E−16

44
1.55E−07
1.54E−04
3.95E−07
8.67E−16

45
3.13E−28
1.97E−20
2.60E−09
3.55E−04

46
1.16E−10
3.41E−08
3.47E−07
2.45E−06

47
2.72E−09
3.18E−07
2.44E−07
1.12E−10

48
2.66E−09
8.84E−08
1.21E−05
1.64E−08

49
4.47E−24
6.61E−18
2.77E−06
2.45E−01

50
2.16E−06
8.47E−04
1.36E−06
7.02E−16

TABLE 7e

Data for Escherichia, particularly E. coli (continued)

No.
CAX_pv_adj
CFT_pv_adj
CP_pv_adj
CRM_pv_adj

1
9.08E−03
5.54E−02
2.29E−17
2.63E−05

2
4.55E−21
9.31E−20
3.14E−43
1.15E−19

3
4.33E−19
1.87E−17
1.53E−32
5.07E−17

4
6.85E−18
2.28E−16
6.99E−31
7.62E−16

5
1.28E−02
7.14E−02
5.78E−01
3.21E−04

6
1.41E−01
3.53E−01
2.23E−01
3.75E−02

7
2.25E−06
3.51E−06
1.44E−38
1.55E−08

8
3.18E−15
1.35E−14
4.48E−11
1.70E−12

9
2.34E−05
5.15E−06
1.74E−15
7.72E−10

10
5.80E−05
9.14E−06
6.46E−15
2.18E−09

11
6.82E−10
3.64E−09
1.69E−49
1.37E−10

12
5.59E−03
1.88E−03
1.12E−09
2.39E−05

13
9.17E−05
2.37E−04
1.28E−36
6.73E−06

14
8.04E−16
5.19E−14
7.03E−61
9.05E−21

15
5.55E−16
2.31E−14
2.47E−60
6.03E−21

16
5.30E−07
2.10E−06
1.38E−39
8.69E−08

17
1.67E−06
3.95E−06
1.23E−38
5.25E−08

18
4.67E−07
1.87E−06
6.39E−39
5.20E−08

19
4.17E−07
1.68E−06
2.84E−39
4.28E−08

20
5.95E−11
4.86E−10
4.79E−07
1.46E−09

21
4.65E−46
9.26E−45
3.20E−19
1.06E−36

22
5.55E−08
2.77E−08
8.59E−09
1.64E−09

23
4.89E−09
9.33E−07
3.24E−25
8.32E−08

24
8.50E−03
9.80E−03
5.28E−05
4.13E−03

25
4.82E−05
7.11E−05
5.83E−03
5.89E−04

26
1.31E−04
1.77E−04
7.59E−03
2.84E−03

27
2.32E−15
2.75E−17
6.79E−43
2.56E−16

28
2.32E−15
2.75E−17
6.79E−43
2.56E−16

29
3.66E−03
4.47E−03
4.75E−03
2.48E−03

30
6.25E−11
6.54E−10
4.02E−42
2.80E−12

31
6.60E−17
2.67E−17
8.45E−42
2.23E−17

32
7.29E−11
7.76E−10
1.57E−41
5.31E−12

33
7.91E−11
8.46E−10
2.18E−41
1.70E−11

34
4.29E−06
1.52E−06
1.28E−40
1.80E−07

35
1.31E−16
5.36E−17
3.96E−41
4.26E−17

36
1.31E−16
5.36E−17
3.96E−41
4.26E−17

37
1.31E−16
5.36E−17
3.96E−41
4.26E−17

38
1.43E−16
5.77E−17
4.56E−41
1.17E−17

39
6.46E−05
1.74E−04
2.25E−40
1.80E−06

40
2.55E−16
1.06E−16
5.76E−41
7.39E−17

41
2.58E−16
1.06E−16
1.05E−40
7.84E−17

42
2.68E−16
1.10E−16
1.19E−40
2.23E−17

43
2.68E−16
1.10E−16
1.19E−40
2.23E−17

44
2.68E−16
1.10E−16
1.19E−40
2.23E−17

45
1.90E−05
2.89E−05
6.00E−03
1.99E−04

46
1.84E−06
5.25E−07
1.05E−39
6.76E−08

47
8.60E−10
4.43E−09
9.49E−40
8.85E−14

48
2.36E−11
1.27E−10
4.92E−38
2.22E−11

49
1.07E−01
1.14E−01
1.50E−02
6.49E−02

50
4.02E−16
1.67E−16
1.34E−38
7.42E−18

TABLE 7f

Data for Escherichia, particularly E. coli (continued)

No.
GM_pv_adj
LVX_pv_adj
TO_pv_adj
T/S_pv_adj

1
2.40E−14
2.96E−16
6.56E−10
5.59E−55

2
9.02E−31
5.84E−43
3.02E−26
1.62E−119

3
3.09E−28
1.25E−33
1.52E−27
6.25E−97

4
1.19E−27
5.56E−32
5.30E−27
8.78E−96

5
5.50E−01
4.74E−01
9.96E−02
3.77E−02

6
8.08E−01
2.88E−01
8.73E−01
1.21E−01

7
2.33E−13
1.57E−38
6.37E−15
7.68E−72

8
4.17E−11
5.22E−11
1.79E−08
1.58E−71

9
7.23E−11
6.17E−14
8.00E−05
1.01E−69

10
2.80E−10
1.39E−13
8.00E−05
1.23E−68

11
1.18E−18
2.49E−49
2.67E−22
6.77E−68

12
7.65E−07
1.10E−08
7.07E−03
1.95E−64

13
1.21E−16
1.92E−37
4.13E−18
1.87E−63

14
4.86E−26
7.43E−62
5.25E−32
2.58E−39

15
2.72E−26
3.08E−61
2.92E−32
4.30E−39

16
1.39E−16
1.68E−39
1.59E−17
1.74E−60

17
5.78E−18
2.01E−39
1.91E−19
2.44E−60

18
1.02E−16
7.87E−39
1.17E−17
6.74E−60

19
7.38E−17
3.56E−39
8.56E−18
2.63E−59

20
6.73E−07
9.82E−07
5.94E−07
3.47E−47

21
5.34E−12
1.45E−19
7.00E−09
2.74E−06

22
3.89E−07
1.14E−08
2.09E−05
7.71E−46

23
6.04E−13
2.10E−24
3.47E−12
1.02E−37

24
8.52E−06
1.56E−04
7.54E−03
4.90E−44

25
9.39E−05
9.80E−03
1.28E−02
6.98E−44

26
2.16E−04
1.65E−02
9.49E−03
9.68E−44

27
1.81E−12
3.58E−43
2.05E−13
2.13E−06

28
1.81E−12
3.58E−43
2.05E−13
2.13E−06

29
1.08E−04
8.15E−03
5.44E−02
5.54E−43

30
1.81E−12
2.71E−42
4.67E−11
6.64E−17

31
3.65E−19
9.37E−42
2.80E−17
3.20E−18

32
3.61E−12
1.03E−41
9.37E−11
2.18E−16

33
3.86E−12
1.47E−41
9.73E−11
2.45E−16

34
1.03E−13
2.44E−41
2.22E−16
4.82E−04

35
4.79E−19
2.61E−41
5.83E−17
9.95E−18

36
4.79E−19
2.61E−41
5.83E−17
3.03E−17

37
4.79E−19
2.61E−41
5.83E−17
3.03E−17

38
8.47E−19
3.21E−41
6.04E−17
3.36E−18

39
3.56E−12
3.69E−41
8.59E−15
1.04E−04

40
8.74E−19
6.20E−41
6.42E−17
5.21E−17

41
9.35E−19
6.76E−41
6.96E−17
8.31E−17

42
1.03E−18
8.13E−41
1.27E−16
2.95E−17

43
1.03E−18
8.13E−41
1.27E−16
2.95E−17

44
1.03E−18
8.13E−41
1.27E−16
2.95E−17

45
9.79E−05
1.29E−02
1.33E−02
1.07E−40

46
1.98E−13
1.85E−40
4.73E−16
4.17E−04

47
2.68E−16
1.90E−40
1.10E−17
2.80E−08

48
1.27E−13
3.36E−40
7.14E−14
3.41E−07

49
1.15E−02
2.48E−02
4.44E−01
3.77E−40

50
1.50E−18
8.68E−39
9.76E−17
2.56E−15

TABLE 7g

Data for Escherichia, particularly E. coli (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
SeHA_C1580
blaT
YP_002045448

2
EcolB7_01001258

ZP_00717086

3
HMPREF9345_05066

ZP_07100147

4
KPN_pKPN5p08201

YP_001338811
plasmid pKPN5

5
HMPREF9547_03104

ZP_07169558

6
SeSA_B0079

YP_002112958
plasmid

pCVM19633_110

7
HMPREF9345_05232

ZP_07100311

8
EcolB_01004576

ZP_00708527

9
pEFER_0049

YP_002394596
plasmid pEFER

10
ETAE_p040

YP_003297634
plasmid pEIB202

11
ECGG_04429

ZP_06648541

12
ETAE_p041
folP
YP_003297635
plasmid pEIB202

13
ECGG_04434

ZP_06648545

14
ROD_p1051
pemI
YP_003368450
plasmid pCROD1

15
ROD_p1061
pemK
YP_003368451
plasmid pCROD1

16
HMPREF9348_05540

ZP_07692671

17
ECUMN_4816
aadA
YP_002415408

18
ECUMN_4827
mphA
YP_002415417

19
HMPREF9345_05223

ZP_07100302

20
EcSMS35_A0150

YP_001740030
plasmid pSMS35_130

21
HMPREF9548_03778

ZP_07141582

22
HMPREF9348_05561

ZP_07692692

23
HMPREF9548_03784

ZP_07141588

24
KPN_pKPN4p07064

YP_001338673
plasmid pKPN4

25
HMPREF9345_03525

ZP_07098656

26
KPN_pKPN4p07068
merC
YP_001338677
plasmid pKPN4

27
ESCG_01010

ZP_04871321

28
HMPREF9540_00466

ZP_07133313

29
STMDT12_C39340

BAJ38877

30
KPK_A0022
sopB
YP_002235674
plasmid pKP187

31
EcoliO157_010100014809

ZP_02780941

32
EcSMS35_A0072
sopB
YP_001739960
plasmid pSMS35_130

33
HMPREF9538_00090

ZP_08302456

34
ECNA114_2444

AEG37278

35
EschericcoliO157_010100006568

ZP_02749755

36
CSAG_00128

ZP_04560798

37
ECH74115_0422
mhpA
YP_002268988

38
CIT292_01335

ZP_03835561

39
ECSF_1165

BAI54705

40
EscherichiacoliO157EcO_010100009454

ZP_05948572

41
SSON_0329
mhpD
YP_309341

42
CIT292_01336

ZP_03835562

43
HMPREF9540_00984

ZP_07133822

44
Missing
mhpE
AP_001004

locus_tag:AC_000091.cds340.373092..374105

45
HMPREF9551_04611

ZP_07191964

46
SeHA_C2638

YP_002046450

47
SFxv_0758

ADA73054

48
HMPREF9530_01431

ZP_07151340

49
KPN_pKPN4p07069
merA
YP_001338678
plasmid pKPN4

50
CP0077

NP_858210
plasmid pCP301

TABLE 7h

Data for Escherichia, particularly E. coli (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
1525960
1526820
+
642555218

2
77515
77910
+
638358454

3
4715
5554
−
648294624

4
34908
35255
−
640753021

5
3248
3841
+
648291919

6
68933
70240
+
642555219

7
5252
5572
−
648294635

8
3555
4568
+
638359041

9
48658
49503
+
643692014

10
31237
32040
−
646311959

11
19278
19826
+
647536609

12
32101
32916
−
646311959

13
22618
23823
+
647536609

14
3339
3596
+
646311988

15
3529
3930
+
646311988

16
461
1045
−
649994953

17
4994882
4995670
+
644736335

18
5003053
5003958
−
644736335

19
1167
2405
+
648294635

20
118542
119474
+
641522668

21
4493
5755
+
648288593

22
209
661
+
649994959

23
8819
9535
+
648288593

24
23310
24614
−
640753020

25
1071
1307
−
648294596

26
25970
27664
−
640753020

27
241682
242032
+
646206991

28
192
443
+
648287910

29
4084530
4085237
−
651053007

30
12106
13071
−
643348532

31
123136
123969
−
641781714

32
53664
54635
−
641522668

33
5657
6832
+
651332930

34
2476906
2477910
−
651053098

35
369676
370620
+
641780393

36
146099
147763
+
646206732

37
430810
432474
+
643348548

38
25505
26449
+
643891503

39
1248345
1249289
+
646862305

40
20015
20965
+
645964942

41
356486
357301
+
640427102

42
26463
27344
+
643891503

43
7204
8217
+
648287942

44
373092
374105
+
637000000

45
97
531
−
648293053

46
2550781
2552010
+
642555218

47
734541
734921
+
646862363

48
8
643
−
648290358

49
27716
28177
−
640753020

50
61397
61579
+
637000224

TABLE 8a

Data for Escherichia, particularly E. coli

Scaffold.External.

No.
Accession
Scaffold.Name
best_pv

1
NC_011083

Salmonella enterica subsp. enterica serovar Heidelberg
3.5041948925527e−207

str. SL476: NC_011083

2
NZ_AAJT01000012

Escherichia coli B7A, unfinished sequence: NZ_AAJT01000012
1.62252621621877e−119

3
NZ_ADWV01000045

Escherichia coli MS 107-1 E_coliMS107-1-1.0.1_Cont44.1:
6.24750842070913e−97

NZ_ADWV01000045

4
NC_009651

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid
8.77735582031733e−96

pKPN5: NC_009651

5
NZ_ADWV01000056

Escherichia coli MS 107-1 E_coliMS107-1-1.0.1_Cont55.1:
7.68091736117399e−72

NZ_ADWV01000056

6
NZ_AAJX01000089

Escherichia coli B171, unfinished sequence:
1.57772112100981e−71

NZ_AAJX01000089

7
NC_011743

Escherichia fergusonii ATCC 35469 plasmid pEFER: NC_011743
1.0118246517332e−69

8
NC_013509

Edwardsiella tarda EIB202 plasmid pEIB202: NC_013509
1.23255842888535e−68

9
NZ_GG749218

Escherichia coli FVEC1412 genomic scaffold supercont1.13:
6.77313303746994e−68

NZ_GG749218

10
NC_013509

Edwardsiella tarda EIB202 plasmid pEIB202: NC_013509
1.94619564613577e−64

11
NZ_GG749218

Escherichia coli FVEC1412 genomic scaffold supercont1.13:
1.86737834552034e−63

NZ_GG749218

12
NC_013717

Citrobacter rodentium ICC168 plasmid pCROD1: NC_013717
7.42780365363135e−62

13
NC_013717

Citrobacter rodentium ICC168 plasmid pCROD1: NC_013717
3.07751376659308e−61

14
NZ_ADWS01000089

Escherichia coli MS 145-7 E_coliMS145-7-1.0.1_Cont88.1:
1.7351795845908e−60

NZ_ADWS01000089

15
NC_011751

Escherichia coli UMN026: NC_011751
2.44317906034667e−60

16
NC_011751

Escherichia coli UMN026: NC_011751
6.73588199342071e−60

17
NZ_ADWV01000056

Escherichia coli MS 107-1 E_coliMS107-1-1.0.1_Cont55.1:
2.62943019143703e−59

NZ_ADWV01000056

18
NC_010488

Escherichia coli SECEC SMS-3-5 plasmid pSMS35_130:
3.46702381924878e−47

NC_010488

19
NZ_ADTM01000311

Escherichia coli MS 182-1 E_coli182-1-1.0_Cont460.3:
4.65308035729244e−46

NZ_ADTM01000311

20
NZ_ADWS01000095

Escherichia coli MS 145-7 E_coliMS145-7-1.0.1_Cont94.1:
7.71451120848483e−46

NZ_ADWS01000095

21
NZ_ADTM01000311

Escherichia coli MS 182-1 E_coli182-1-1.0_Cont460.3:
1.08551755499227e−44

NZ_ADTM01000311

22
NC_009650

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid
4.89761264283562e−44

pKPN4: NC_009650

23
NZ_ADWV01000017

Escherichia coli MS 107-1 E_coliMS107-1-1.0.1_Cont16.1:
6.97693050178087e−44

NZ_ADWV01000017

24
NC_009650

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid
9.68294892967391e−44

pKPN4: NC_009650

25
NZ_GG665811

Escherichia sp. 1_1_43 genomic scaffold supercont1.1:
3.5843867496487e−43

NZ_GG665811

26
NZ_ADTL01000051

Escherichia coli MS 115-1 E_coli115-1-1.0_Cont158.2:
3.5843867496487e−43

NZ_ADTL01000051

27
AP011957

Salmonella enterica subsp. enterica serovar Typhimurium
5.53805522527039e−43

str. T000240 DNA: AP011957

28
NC_011282

Klebsiella pneumoniae 342 plasmid pKP187: NC_011282
2.71226651272988e−42

29
NZ_ABHR01000011

Escherichia coli O157:H7 str. EC4401, unfinished sequence:
8.45082785112866e−42

NZ_ABHR01000011

30
NC_010488

Escherichia coli SECEC SMS-3-5 plasmid pSMS35_130:
1.02749291231853e−41

NC_010488

31
NZ_AFBO01000013

Klebsiella sp. MS 92-3 K_spMS92-3-l.0_Cont24.1:
1.46909169086738e−41

NZ_AFBO01000013

32
CP002797

Escherichia coli NA114: CP002797
2.43588122712712e−41

33
NZ_ABHK01000002

Escherichia coli O157:H7 str. EC4206, unfinished sequence:
2.60702932643171e−41

NZ_ABHK01000002

34
NZ_GG657366

Citrobacter sp. 30_2 genomic scaffold supercont1.1:
2.60702932643171e−41

NZ_GG657366

35
NC_011353

Escherichia coli O157:H7 str. EC4115: NC_011353
2.60702932643171e−41

36
NZ_ABWL01000012

Citrobacter youngae ATCC 29220 C_sp-1.0_Cont2.3:
3.21133372679738e−41

NZ_ABWL01000012

37
AP009378

Escherichia coli SE15 DNA: AP009378
3.68640118720819e−41

38
NZ_ACXN01000074

Escherichia coli O157:H7 str. FRIK966: NZ_ACXN01000074
5.75695041652081e−41

39
NC_007384

Shigella sonnei Ss046: NC_007384
6.75951367822551e−41

40
NZ_ABWL01000012

Citrobacter youngae ATCC 29220 C_sp-1.0_Cont2.3:
8.12681193093067e−41

NZ_ABWL01000012

41
NZ_ADTL01000083

Escherichia coli MS 115-1 E_coli115-1-1.0_Cont264.1:
8.12681193093067e−41

NZ_ADTL01000083

42
AC_000091

Escherichia coli W3110 DNA: AC_000091
8.12681193093067e−41

43
NZ_ADUD01000537

Escherichia coli MS 196-1 E_coli196-1-1.0_Cont1482.1:
1.06521634399457e−40

NZ_ADUD01000537

44
NC_011083

Salmonella enterica subsp. enterica serovar Heidelberg
1.84998224240006e−40

str. SL476: NC_011083

45
CP001383

Shigella flexneri 2002017: CP001383
1.89942261631873e−40

46
NZ_ADTR01000134

Escherichia coli MS 21-1 E_coli21-1-1.0_Cont296.1:
3.35939290103889e−40

NZ_ADTR01000134

47
NC_009650

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid
3.76989142366575e−40

pKPN4: NC_009650

48
NC_004851

Shigella flexneri 2a str. 301 plasmid pCP301: NC_004851
8.68449218790606e−39

49
NC_007607

Shigella dysenteriae Sd197 plasmid pSD1_197: NC_007607
2.27746826869945e−38

50
NZ_ADTL01000280

Escherichia coli MS 115-1 E_coli115-1-1.0_Cont677.5:
4.92053652141975e−38

NZ_ADTL01000280

TABLE 8b

Data for Escherichia, particularly E. coli (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
AM; A/S; AUG; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
AM
lactam

2
AM; A/S; AUG; AZ T; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

TO; T/S

3
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

TO; T/S

4
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

TO; T/S

5
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

TO; T/S

6
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

TO; T/S

7
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

TO; T/S

8
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

TO; T/S

9
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

TO; T/S

10
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

TO; T/S

11
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

TO; T/S

12
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

13
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

14
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

TO; T/S

15
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

TO; T/S

16
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

TO; T/S

17
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

TO; T/S

18
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

TO; T/S

19
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
CAX
lactam

TO; T/S

20
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

TO; T/S

21
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
AM
lactam

TO; T/S

22
AM; A/S; AUG; CAX; CFT; CP; CRM; GM; LVX; TO;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

T/S

23
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

T/S

24
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; TO;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

T/S

25
AM; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX; TO;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

T/S

26
AM; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX; TO;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

T/S

27
AM; A/S; AUG; CAX; CFT; CP; CRM; GM; LVX; T/S
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

28
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

29
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

TO; T/S

30
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

31
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

32
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

33
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

34
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

35
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

36
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

37
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

38
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

TO; T/S

39
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

40
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

41
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

42
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

43
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; T/S
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

44
AM; A/S; AUG; AZT; CAX; CFT; CP; C RM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

45
AM; A/S; AUG; AZT; CAX; CFT; CP; C RM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

46
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

47
AM; A/S; AUG; T/S
lactam; other
T/S
other

48
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

49
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

50
AM; A/S; AUG; AZT; CAX; CFT; CP; CRM; GM; LVX;
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TO; T/S

TABLE 8c

Data for Escherichia, particularly E. coli (continued)

No.
num_aminoglycoside
num_fluoroquinolone
num_lactam
num_other

1
2
2
5
1

2
2
2
7
1

3
2
2
7
1

4
2
2
7
1

5
2
2
7
1

6
2
2
7
1

7
2
2
7
1

8
2
2
7
1

9
2
2
7
1

10
2
2
7
1

11
2
2
7
1

12
2
2
7
1

13
2
2
7
1

14
2
2
7
1

15
2
2
7
1

16
2
2
7
1

17
2
2
7
1

18
2
2
7
1

19
2
2
7
1

20
2
2
7
1

21
2
2
7
1

22
2
2
6
1

23
1
2
7
1

24
2
1
7
1

25
2
2
6
1

26
2
2
6
1

27
1
2
6
1

28
2
2
7
1

29
2
2
7
1

30
2
2
7
1

31
2
2
7
1

32
2
2
7
1

33
2
2
7
1

34
2
2
7
1

35
2
2
7
1

36
2
2
7
1

37
2
2
7
1

38
2
2
7
1

39
2
2
7
1

40
2
2
7
1

41
2
2
7
1

42
2
2
7
1

43
1
1
7
1

44
2
2
7
1

45
2
2
7
1

46
2
2
7
1

47
0
0
3
1

48
2
2
7
1

49
2
2
7
1

50
2
2
7
1

TABLE 8d

Data for Escherichia, particularly E. coli (continued)

No.
AM_pv_adj
A/S_pv_adj
AUG_pv_adj
AZT_pv_adj

1
3.50E−207
1.39E−175
2.23E−54
1.94E−02

2
3.12E−58
4.85E−48
1.56E−20
2.24E−14

3
2.85E−46
1.23E−39
2.49E−17
7.44E−15

4
2.62E−45
3.93E−39
1.12E−17
7.82E−14

5
1.01E−26
2.48E−22
5.21E−09
2.11E−04

6
4.88E−38
1.20E−35
3.67E−16
6.67E−10

7
2.35E−59
7.04E−49
2.73E−24
1.89E−06

8
2.35E−59
7.04E−49
1.31E−23
5.63E−06

9
1.84E−24
1.82E−23
1.33E−10
1.05E−06

10
2.51E−64
6.77E−56
3.88E−22
9.19E−04

11
2.79E−25
9.09E−23
1.32E−08
1.48E−03

12
2.94E−45
2.43E−34
1.15E−22
2.63E−14

13
1.58E−45
1.72E−34
1.75E−22
1.91E−14

14
3.26E−28
1.85E−21
2.00E−08
1.16E−05

15
1.44E−20
2.94E−18
5.11E−07
1.25E−04

16
6.63E−29
5.38E−22
1.16E−08
1.11E−05

17
6.41E−30
1.52E−22
9.58E−09
6.45E−06

18
4.62E−35
3.20E−30
5.19E−17
2.18E−07

19
1.82E−09
8.62E−11
2.50E−17
1.74E−39

20
3.88E−27
4.06E−27
4.62E−12
9.38E−06

21
1.09E−44
2.09E−39
1.05E−16
2.10E−06

22
2.75E−28
8.80E−22
3.79E−08
1.79E−02

23
6.10E−28
3.56E−20
2.25E−09
8.28E−04

24
5.97E−23
1.19E−15
1.39E−06
1.28E−03

25
4.17E−03
3.66E−02
4.90E−07
1.65E−14

26
4.17E−03
3.66E−02
4.90E−07
1.65E−14

27
1.37E−28
1.45E−21
8.41E−09
2.36E−02

28
5.88E−10
1.33E−07
1.85E−09
7.58E−11

29
1.14E−08
2.28E−05
5.66E−08
3.43E−16

30
1.96E−09
3.67E−07
4.28E−09
1.44E−10

31
2.88E−09
5.08E−07
4.50E−09
1.51E−10

32
1.07E−10
2.85E−08
1.31E−06
4.19E−06

33
4.32E−08
6.04E−05
1.49E−07
4.44E−16

34
8.33E−08
9.79E−05
2.97E−07
4.44E−16

35
8.33E−08
9.79E−05
2.97E−07
4.44E−16

36
3.07E−08
4.70E−05
1.02E−07
7.64E−16

37
4.14E−12
7.23E−10
1.20E−05
1.17E−03

38
1.57E−07
1.55E−04
4.17E−07
7.80E−16

39
2.15E−07
1.95E−04
5.61E−07
8.13E−16

40
1.55E−07
1.54E−04
3.95E−07
8.67E−16

41
1.55E−07
1.54E−04
3.95E−07
8.67E−16

42
1.55E−07
1.54E−04
3.95E−07
8.67E−16

43
3.13E−28
1.97E−20
2.60E−09
3.55E−04

44
1.16E−10
3.41E−08
3.47E−07
2.45E−06

45
2.72E−09
3.18E−07
2.44E−07
1.12E−10

46
2.66E−09
8.84E−08
1.21E−05
1.64E−08

47
4.47E−24
6.61E−18
2.77E−06
2.45E−01

48
2.16E−06
8.47E−04
1.36E−06
7.02E−16

49
4.99E−06
1.53E−03
2.46E−06
1.26E−15

50
1.11E−05
1.86E−03
1.74E−06
1.63E−14

TABLE 8e

Data for Escherichia, particularly E. coli (continued)

No.
CAX_pv_adj
CFT_pv_adj
CP_pv_adj
CRM_pv_adj

1
9.08E−03
5.54E−02
2.29E−17
2.63E−05

2
4.55E−21
9.31E−20
3.14E−43
1.15E−19

3
4.33E−19
1.87E−17
1.53E−32
5.07E−17

4
6.85E−18
2.28E−16
6.99E−31
7.62E−16

5
2.25E−06
3.51E−06
1.44E−38
1.55E−08

6
3.18E−15
1.35E−14
4.48E−11
1.70E−12

7
2.34E−05
5.15E−06
1.74E−15
7.72E−10

8
5.80E−05
9.14E−06
6.46E−15
2.18E−09

9
6.82E−10
3.64E−09
1.69E−49
1.37E−10

10
5.59E−03
1.88E−03
1.12E−09
2.39E−05

11
9.17E−05
2.37E−04
1.28E−36
6.73E−06

12
8.04E−16
5.19E−14
7.03E−61
9.05E−21

13
5.55E−16
2.31E−14
2.47E−60
6.03E−21

14
5.30E−07
2.10E−06
1.38E−39
8.69E−08

15
1.67E−06
3.95E−06
1.23E−38
5.25E−08

16
4.67E−07
1.87E−06
6.39E−39
5.20E−08

17
4.17E−07
1.68E−06
2.84E−39
4.28E−08

18
5.95E−11
4.86E−10
4.79E−07
1.46E−09

19
4.65E−46
9.26E−45
3.20E−19
1.06E−36

20
5.55E−08
2.77E−08
8.59E−09
1.64E−09

21
4.89E−09
9.33E−07
3.24E−25
8.32E−08

22
8.50E−03
9.80E−03
5.28E−05
4.13E−03

23
4.82E−05
7.11E−05
5.83E−03
5.89E−04

24
1.31E−04
1.77E−04
7.59E−03
2.84E−03

25
2.32E−15
2.75E−17
6.79E−43
2.56E−16

26
2.32E−15
2.75E−17
6.79E−43
2.56E−16

27
3.66E−03
4.47E−03
4.75E−03
2.48E−03

28
6.25E−11
6.54E−10
4.02E−42
2.80E−12

29
6.60E−17
2.67E−17
8.45E−42
2.23E−17

30
7.29E−11
7.76E−10
1.57E−41
5.31E−12

31
7.91E−11
8.46E−10
2.18E−41
1.70E−11

32
4.29E−06
1.52E−06
1.28E−40
1.80E−07

33
1.31E−16
5.36E−17
3.96E−41
4.26E−17

34
1.31E−16
5.36E−17
3.96E−41
4.26E−17

35
1.31E−16
5.36E−17
3.96E−41
4.26E−17

36
1.43E−16
5.77E−17
4.56E−41
1.17E−17

37
6.46E−05
1.74E−04
2.25E−40
1.80E−06

38
2.55E−16
1.06E−16
5.76E−41
7.39E−17

39
2.58E−16
1.06E−16
1.05E−40
7.84E−17

40
2.68E−16
1.10E−16
1.19E−40
2.23E−17

41
2.68E−16
1.10E−16
1.19E−40
2.23E−17

42
2.68E−16
1.10E−16
1.19E−40
2.23E−17

43
1.90E−05
2.89E−05
6.00E−03
1.99E−04

44
1.84E−06
5.25E−07
1.05E−39
6.76E−08

45
8.60E−10
4.43E−09
9.49E−40
8.85E−14

46
2.36E−11
1.27E−10
4.92E−38
2.22E−11

47
1.07E−01
1.14E−01
1.50E−02
6.49E−02

48
4.02E−16
1.67E−16
1.34E−38
7.42E−18

49
4.46E−16
1.95E−16
3.53E−38
1.42E−17

50
4.97E−15
2.04E−15
7.83E−38
2.27E−17

TABLE 8f

Data for Escherichia, particularly E. coli (continued)

No.
GM_pv_adj
LVX_pv_adj
TO_pv_adj
T/S_pv_adj

1
2.40E−14
2.96E−16
6.56E−10
5.59E−55

2
9.02E−31
5.84E−43
3.02E−26
1.62E−119

3
3.09E−28
1.25E−33
1.52E−27
6.25E−97

4
1.19E−27
5.56E−32
5.30E−27
8.78E−96

5
2.33E−13
1.57E−38
6.37E−15
7.68E−72

6
4.17E−11
5.22E−11
1.79E−08
1.58E−71

7
7.23E−11
6.17E−14
8.00E−05
1.01E−69

8
2.80E−10
1.39E−13
8.00E−05
1.23E−68

9
1.18E−18
2.49E−49
2.67E−22
6.77E−68

10
7.65E−07
1.10E−08
7.07E−03
1.95E−64

11
1.21E−16
1.92E−37
4.13E−18
1.87E−63

12
4.86E−26
7.43E−62
5.25E−32
2.58E−39

13
2.72E−26
3.08E−61
2.92E−32
4.30E−39

14
1.39E−16
1.68E−39
1.59E−17
1.74E−60

15
5.78E−18
2.01E−39
1.91E−19
2.44E−60

16
1.02E−16
7.87E−39
1.17E−17
6.74E−60

17
7.38E−17
3.56E−39
8.56E−18
2.63E−59

18
6.73E−07
9.82E−07
5.94E−07
3.47E−47

19
5.34E−12
1.45E−19
7.00E−09
2.74E−06

20
3.89E−07
1.14E−08
2.09E−05
7.71E−46

21
6.04E−13
2.10E−24
3.47E−12
1.02E−37

22
8.52E−06
1.56E−04
7.54E−03
4.90E−44

23
9.39E−05
9.80E−03
1.28E−02
6.98E−44

24
2.16E−04
1.65E−02
9.49E−03
9.68E−44

25
1.81E−12
3.58E−43
2.05E−13
2.13E−06

26
1.81E−12
3.58E−43
2.05E−13
2.13E−06

27
1.08E−04
8.15E−03
5.44E−02
5.54E−43

28
1.81E−12
2.71E−42
4.67E−11
6.64E−17

29
3.65E−19
9.37E−42
2.80E−17
3.20E−18

30
3.61E−12
1.03E−41
9.37E−11
2.18E−16

31
3.86E−12
1.47E−41
9.73E−11
2.45E−16

32
1.03E−13
2.44E−41
2.22E−16
4.82E−04

33
4.79E−19
2.61E−41
5.83E−17
9.95E−18

34
4.79E−19
2.61E−41
5.83E−17
3.03E−17

35
4.79E−19
2.61E−41
5.83E−17
3.03E−17

36
8.47E−19
3.21E−41
6.04E−17
3.36E−18

37
3.56E−12
3.69E−41
8.59E−15
1.04E−04

38
8.74E−19
6.20E−41
6.42E−17
5.21E−17

39
9.35E−19
6.76E−41
6.96E−17
8.31E−17

40
1.03E−18
8.13E−41
1.27E−16
2.95E−17

41
1.03E−18
8.13E−41
1.27E−16
2.95E−17

42
1.03E−18
8.13E−41
1.27E−16
2.95E−17

43
9.79E−05
1.29E−02
1.33E−02
1.07E−40

44
1.98E−13
1.85E−40
4.73E−16
4.17E−04

45
2.68E−16
1.90E−40
1.10E−17
2.80E−08

46
1.27E−13
3.36E−40
7.14E−14
3.41E−07

47
1.15E−02
2.48E−02
4.44E−01
3.77E−40

48
1.50E−18
8.68E−39
9.76E−17
2.56E−15

49
3.08E−18
2.28E−38
1.98E−16
1.91E−14

50
2.46E−16
4.92E−38
8.76E−15
4.31E−13

TABLE 8g

Data for Escherichia, particularly E. coli (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
SeHA_C1580
blaT
YP_002045448

2
EcolB7_01001258

ZP_00717086

3
HMPREF9345_05066

ZP_07100147

4
KPN_pKPN5p08201

YP_001338811
plasmid pKPN5

5
HMPREF9345_05232

ZP_07100311

6
EcolB_01004576

ZP_00708527

7
pEFER_0049

YP_002394596
plasmid pEFER

8
ETAE_p040

YP_003297634
plasmid pEIB202

9
ECGG_04429

ZP_06648541

10
ETAE_p041
folP
YP_003297635
plasmid pEIB202

11
ECGG_04434

ZP_06648545

12
ROD_p1051
pemI
YP_003368450
plasmid pCROD1

13
ROD_p1061
pemK
YP_003368451
plasmid pCROD1

14
HMPREF9348_05540

ZP_07692671

15
ECUMN_4816
aadA
YP_002415408

16
ECUMN_4827
mphA
YP_002415417

17
HMPREF9345_05223

ZP_07100302

18
EcSMS35_A0150

YP_001740030
plasmid pSMS35_130

19
HMPREF9548_03778

ZP_07141582

20
HMPREF9348_05561

ZP_07692692

21
HMPREF9548_03784

ZP_07141588

22
KPN_pKPN4p07064

YP_001338673
plasmid pKPN4

23
HMPREF9345_03525

ZP_07098656

24
KPN_pKPN4p07068
merC
YP_001338677
plasmid pKPN4

25
ESCG_01010

ZP_04871321

26
HMPREF9540_00466

ZP_07133313

27
STMDT12_C39340

BAJ38877

28
KPK_A0022
sopB
YP_002235674
plasmid pKP187

29
EcoliO157_010100014809

ZP_02780941

30
EcSMS35_A0072
sopB
YP_001739960
plasmid pSMS35_130

31
HMPREF9538_00090

ZP_08302456

32
ECNA114_2444

AEG37278

33
EschericcoliO157_010100006568

ZP_02749755

34
CSAG_00128

ZP_04560798

35
ECH74115_0422
mhpA
YP_002268988

36
CIT292_01335

ZP_03835561

37
ECSF_1165

BAI54705

38
EscherichiacoliO157EcO_010100009454

ZP_05948572

39
SSON_0329
mhpD
YP_309341

40
CIT292_01336

ZP_03835562

41
HMPREF9540_00984

ZP_07133822

42
Missing
mhpE
AP_001004

locus_tag:AC_000091.cds340.373092..374105

43
HMPREF9551_04611

ZP_07191964

44
SeHA_C2638

YP_002046450

45
SFxv_0758

ADA73054

46
HMPREF9530_01431

ZP_07151340

47
KPN_pKPN4p07069
merA
YP_001338678
plasmid pKPN4

48
CP0077

NP_858210
plasmid pCP301

49
SDY_P083

YP_406084
plasmid pSD1_197

50
HMPREF9540_03398

ZP_07136184

TABLE 8h

Data for Escherichia, particularly E. coli (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
1525960
1526820
+
642555218

2
77515
77910
+
638358454

3
4715
5554
−
648294624

4
34908
35255
−
640753021

5
5252
5572
−
648294635

6
3555
4568
+
638359041

7
48658
49503
+
643692014

8
31237
32040
−
646311959

9
19278
19826
+
647536609

10
32101
32916
−
646311959

11
22618
23823
+
647536609

12
3339
3596
+
646311988

13
3529
3930
+
646311988

14
461
1045
−
649994953

15
4994882
4995670
+
644736335

16
5003053
5003958
−
644736335

17
1167
2405
+
648294635

18
118542
119474
+
641522668

19
4493
5755
+
648288593

20
209
661
+
649994959

21
8819
9535
+
648288593

22
23310
24614
−
640753020

23
1071
1307
−
648294596

24
25970
27664
−
640753020

25
241682
242032
+
646206991

26
192
443
+
648287910

27
4084530
4085237
−
651053007

28
12106
13071
−
643348532

29
123136
123969
−
641781714

30
53664
54635
−
641522668

31
5657
6832
+
651332930

32
2476906
2477910
−
651053098

33
369676
370620
+
641780393

34
146099
147763
+
646206732

35
430810
432474
+
643348548

36
25505
26449
+
643891503

37
1248345
1249289
+
646862305

38
20015
20965
+
645964942

39
356486
357301
+
640427102

40
26463
27344
+
643891503

41
7204
8217
+
648287942

42
373092
374105
+
637000000

43
97
531
−
648293053

44
2550781
2552010
+
642555218

45
734541
734921
+
646862363

46
8
643
−
648290358

47
27716
28177
−
640753020

48
61397
61579
+
637000224

49
69343
69615
−
640427105

50
3415
4356
−
648288139

Examples 5 and 6
Klebsiella, particularly K. oxytoca and K. pneumoniae

The procedure was carried out as in Example 1, except that the following microorganisms were used:

Bacterial Strains

The inventors selected 1568 Klebsiella strains, particularly 1179 for Klebsiella pneumonia and 389 for Klebsiella oxytoca, from the microbiology strain collection at Siemens Healthcare Diagnostics (West Sacramento, Calif.) for susceptibility testing and whole genome sequencing.

From MetaRef, 1640 centroids of Klebsiella species were used as reference sequences for K. oxytoca, and 1641 centroids of K. pneumoniae were uses as reference sequences of K. pneumoniae.

The results for K. oxytoca are shown in Tables 9 (corresponding to Table 1) and 10 (corresponding to Table 2), and the results for K. pneumonia are shown in Tables 11 (corresponding to Table 1) and 12 (corresponding to Table 2).

TABLE 9a

Data for Klebsiella, particularly K. oxytoca

No.
Scaffold.External.Accession
Scaffold.Name
best_pv

1
NC_011283

Klebsiella pneumoniae 342: NC_011283
7.24545119859105e−19

2
NZ_GG745508

Klebsiella sp. 1_1_55 genomic scaffold supercont1.1:
7.24545119859105e−19

NZ_GG745508

3
NC_011283

Klebsiella pneumoniae 342: NC_011283
1.17347446332913e−17

4
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
9.82145388713083e−17

5
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
4.06768464186916e−16

6
NZ_ACZD01000230

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
4.06768464186916e−16

contig00265: NZ_ACZD01000230

7
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

8
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
6.05465029985694e−16

9
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
6.05465029985694e−16

10
NZ_GG745509

Klebsiella sp. 1_1_55 genomic scaffold supercont1.2:
6.05465029985694e−16

NZ_GG745509

11
NZ_GG745508

Klebsiella sp. 1_1_55 genomic scaffold supercont1.1:
6.05465029985694e−16

NZ_GG745508

12
NC_011283

Klebsiella pneumoniae 342: NC_011283
6.05465029985694e−16

13
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

14
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

15
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

16
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

17
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

18
NZ_GG745512

Klebsiella sp. 1_1_55 genomic scaffold supercont1.5:
6.05465029985694e−16

NZ_GG745512

19
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

20
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

21
NZ_GG745508

Klebsiella sp. 1_1_55 genomic scaffold supercont1.1:
6.05465029985694e−16

NZ_GG745508

22
NC_009648

Klebsiella pneumoniae subsp. pneumoniae MGH 78578:
6.05465029985694e−16

NC_009648

23
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

24
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

25
NC_012731

Klebsiella pneumoniae NTUH-K2044: NC_012731
6.05465029985694e−16

26
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

27
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

28
NZ_GG745508

Klebsiella sp. 1_1_55 genomic scaffold supercont1.1:
6.05465029985694e−16

NZ_GG745508

29
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

30
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

31
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

32
NZ_GG745508

Klebsiella sp. 1_1_55 genomic scaffold supercont1.1:
6.05465029985694e−16

NZ_GG745508

33
NZ_GG745508

Klebsiella sp. 1_1_55 genomic scaffold supercont1.1:
6.05465029985694e−16

NZ_GG745508

34
NC_012731

Klebsiella pneumoniae NTUH-K2044: NC_012731
6.05465029985694e−16

35
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
6.05465029985694e−16

36
NC_011283

Klebsiella pneumoniae 342: NC_011283
6.05465029985694e−16

37
NZ_AFBO01000503

Klebsiella sp. MS 92-3 K_spMS92-3-1.0_Cont988.13:
6.05465029985694e−16

NZ_AFBO01000503

38
NZ_GG745509

Klebsiella sp. 1_1_55 genomic scaffold supercont1.2:
6.05465029985694e−16

NZ_GG745509

39
NZ_GG745509

Klebsiella sp. 1_1_55 genomic scaffold supercont1.2:
6.05465029985694e−16

NZ_GG745509

40
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

41
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

42
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

43
NC_009648

Klebsiella pneumoniae subsp. pneumoniae MGH 78578:
6.05465029985694e−16

NC_009648

44
NZ_GG745509

Klebsiella sp. 1_1_55 genomic scaffold supercont1.2:
6.05465029985694e−16

NZ_GG745509

45
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

46
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

47
NZ_AFBO01000685

Klebsiella sp. MS 92-3 K_spMS92-3-1.0_Cont1649.3:
6.05465029985694e−16

NZ_AFBO01000685

48
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
6.05465029985694e−16

49
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

50
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

TABLE 9b

Data for Klebsiella, particularly K. oxytoca (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
A/S; AUG; CP; CRM; LVX; P/T
fluoroquinolone; lactam
A/S
lactam

2
A/S; AUG; CP; CRM; LVX; P/T
fluoroquinolone; lactam
A/S
lactam

3
A/S; AUG; CRM; LVX; P/T
fluoroquinolone; lactam
A/S
lactam

4
A/S; AUG; CP; CRM; LVX; P/T
fluoroquinolone; lactam
A/S
lactam

5
A/S; CP; LVX
fluoroquinolone; lactam
A/S
lactam

6
A/S; AUG; CP; CRM; LVX; P/T
fluoroquinolone; lactam
A/S
lactam

7
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

8
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

9
A/S; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

10
A/S; AUG; CP; LVX
fluoroquinolone; lactam
A/S
lactam

11
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

12
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

13
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

14
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

15
A/S; CP; LVX
fluoroquinolone; lactam
A/S
lactam

16
A/S; AUG; CP; CRM; LVX; P/T
fluoroquinolone; lactam
A/S
lactam

17
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

18
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

19
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

20
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

21
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

22
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

23
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

24
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

25
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

26
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

27
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

28
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

29
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

30
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

31
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

32
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

33
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

34
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

35
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

36
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

37
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

38
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

39
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

40
A/S; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

41
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

42
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

43
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

44
A/S; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

45
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

46
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

47
A/S; CP; LVX
fluoroquinolone; lactam
A/S
lactam

48
A/S; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

49
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

50
A/S; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

TABLE 9c

Data for Klebsiella, particularly K. oxytoca (continued)

No.
num_fluoroquinolone
num_lactam

1
2
4

2
2
4

3
1
4

4
2
4

5
2
1

6
2
4

7
2
3

8
2
3

9
1
2

10
2
2

11
2
3

12
2
3

13
2
3

14
2
3

15
2
1

16
2
4

17
2
3

18
2
3

19
2
3

20
2
3

21
2
3

22
2
3

23
2
3

24
2
3

25
2
3

26
2
3

27
2
3

28
2
3

29
2
3

30
2
3

31
2
3

32
2
3

33
2
3

34
2
3

35
2
3

36
2
3

37
2
3

38
2
3

39
2
3

40
1
2

41
2
3

42
2
3

43
2
3

44
1
2

45
2
3

46
2
3

47
2
1

48
1
2

49
2
3

50
1
2

TABLE 9d

Data for Klebsiella, particularly K. oxytoca (continued)

No.
A/S_pv_adj
AUG_pv_adj
AZT_pv_adj
CAX_pv_adj
CFT_pv_adj

1
7.25E−19
1.72E−03
1.02E−01
7.63E−02
1.14E−01

2
7.25E−19
1.72E−03
1.02E−01
7.63E−02
1.14E−01

3
1.17E−17
2.11E−03
1.25E−02
1.67E−02
3.76E−02

4
9.82E−17
1.48E−03
1.97E−02
1.37E−02
6.22E−02

5
4.07E−16
1.01E−02
2.64E−02
3.46E−02
3.40E−02

6
4.07E−16
2.92E−04
3.51E−02
2.48E−02
4.69E−02

7
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

8
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

9
6.05E−16
1.93E−02
7.20E−02
7.25E−02
5.85E−02

10
6.05E−16
9.84E−03
4.51E−02
3.38E−02
2.50E−02

11
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

12
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

13
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

14
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

15
6.05E−16
1.01E−02
4.61E−02
3.45E−02
3.46E−02

16
6.05E−16
5.13E−03
2.58E−02
1.89E−02
1.75E−02

17
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

18
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

19
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

20
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

21
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

22
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

23
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

24
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

25
6.05E−16
5.42E−03
3.46E−02
1.98E−02
2.46E−02

26
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

27
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

28
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

29
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

30
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

31
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

32
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

33
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

34
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

35
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

36
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

37
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

38
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

39
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

40
6.05E−16
1.96E−02
7.24E−02
9.30E−02
5.85E−02

41
6.05E−16
7.42E−03
3.51E−02
2.53E−02
2.48E−02

42
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

43
6.05E−16
7.42E−03
3.51E−02
2.53E−02
2.48E−02

44
6.05E−16
1.96E−02
7.24E−02
9.30E−02
5.85E−02

45
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

46
6.05E−16
7.42E−03
3.51E−02
2.53E−02
2.48E−02

47
6.05E−16
1.84E−02
7.73E−02
5.74E−02
4.41E−02

48
6.05E−16
1.96E−02
7.24E−02
9.30E−02
5.85E−02

49
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

50
6.05E−16
1.96E−02
7.24E−02
9.30E−02
5.85E−02

TABLE 9e

Data for Klebsiella, particularly K. oxytoca (continued)

No.
CP_pv_adj
CRM_pv_adj
LVX_pv_adj
P/T_pv_adj

1
4.47E−03
3.22E−03
3.33E−05
4.21E−03

2
4.47E−03
3.22E−03
3.33E−05
4.21E−03

3
4.19E−02
3.50E−03
2.38E−03
7.73E−03

4
2.12E−04
4.16E−03
5.03E−07
3.38E−03

5
2.11E−03
1.38E−02
6.28E−05
1.93E−02

6
6.71E−04
1.62E−03
8.24E−07
2.85E−03

7
1.30E−03
7.85E−03
5.53E−05
1.37E−02

8
1.30E−03
7.85E−03
5.53E−05
1.37E−02

9
6.62E−02
2.94E−03
1.50E−03
3.78E−02

10
1.98E−03
1.03E−02
5.68E−05
1.89E−02

11
1.30E−03
7.85E−03
5.53E−05
1.37E−02

12
1.30E−03
7.85E−03
5.53E−05
1.37E−02

13
1.30E−03
7.85E−03
5.53E−05
1.37E−02

14
1.30E−03
7.85E−03
5.53E−05
1.37E−02

15
1.26E−03
1.04E−02
3.08E−05
1.93E−02

16
7.58E−04
6.15E−03
5.93E−05
9.93E−03

17
1.30E−03
7.85E−03
5.53E−05
1.37E−02

18
1.30E−03
7.85E−03
5.53E−05
1.37E−02

19
1.30E−03
7.85E−03
5.53E−05
1.37E−02

20
1.30E−03
7.85E−03
5.53E−05
1.37E−02

21
1.30E−03
7.85E−03
5.53E−05
1.37E−02

22
1.30E−03
7.85E−03
5.53E−05
1.37E−02

23
1.30E−03
7.85E−03
5.53E−05
1.37E−02

24
1.30E−03
7.85E−03
5.53E−05
1.37E−02

25
3.39E−03
6.15E−03
1.55E−04
1.03E−02

26
1.30E−03
7.85E−03
5.53E−05
1.37E−02

27
1.30E−03
7.85E−03
5.53E−05
1.37E−02

28
1.30E−03
7.85E−03
5.53E−05
1.37E−02

29
1.30E−03
7.85E−03
5.53E−05
1.37E−02

30
1.30E−03
7.85E−03
5.53E−05
1.37E−02

31
1.30E−03
7.85E−03
5.53E−05
1.37E−02

32
1.30E−03
7.85E−03
5.53E−05
1.37E−02

33
1.30E−03
7.85E−03
5.53E−05
1.37E−02

34
1.30E−03
7.85E−03
5.53E−05
1.37E−02

35
1.30E−03
7.85E−03
5.53E−05
1.37E−02

36
1.30E−03
7.85E−03
5.53E−05
1.37E−02

37
1.30E−03
7.85E−03
5.53E−05
1.37E−02

38
1.30E−03
7.85E−03
5.53E−05
1.37E−02

39
1.30E−03
7.85E−03
5.53E−05
1.37E−02

40
9.00E−02
4.08E−03
1.50E−03
4.97E−02

41
1.97E−03
7.93E−03
5.53E−05
1.39E−02

42
1.30E−03
7.85E−03
5.53E−05
1.37E−02

43
1.97E−03
7.93E−03
5.53E−05
1.39E−02

44
9.00E−02
4.08E−03
1.50E−03
4.97E−02

45
1.30E−03
7.85E−03
5.53E−05
1.37E−02

46
1.97E−03
7.93E−03
5.53E−05
1.39E−02

47
7.43E−03
1.01E−02
2.47E−04
3.31E−02

48
9.00E−02
4.08E−03
1.50E−03
4.97E−02

49
1.30E−03
7.85E−03
5.53E−05
1.37E−02

50
9.00E−02
4.08E−03
1.50E−03
4.97E−02

TABLE 9f

Data for Klebsiella, particularly K. oxytoca (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
KPK_2590

YP_002238421

2
HMPREF0485_01216

ZP_06548816

3
KPK_0292

YP_002236174

4
EAE_11985

YP_004592590

5
Kvar_2784

YP_003439702

6
HMPREF0484_4675
add
ZP_06017656

7
Kvar_2381

YP_003439305

8
KPN2242_04295

AEJ96779

9
KPN2242_08680

AEJ97652

10
HMPREF0485_01916

ZP_06549516

11
HMPREF0485_01247

ZP_06548847

12
KPK_2622

YP_002238453

13
Kvar_2568

YP_003439490

14
Kvar_0816

YP_003437758

15
Kvar_4643

YP_003441547

16
Kvar_3771

YP_003440683

17
Kvar_1596

YP_003438533

18
HMPREF0485_03998

ZP_06551594

19
Kvar_2140

YP_003439069

20
Kvar_3380

YP_003440292

21
HMPREF0485_00446

ZP_06548046

22
KPN_00275

YP_001333958

23
Kvar_1589

YP_003438526

24
Kvar_1856

YP_003438789

25
KP1_3016

YP_002919724

26
Kvar_5099

YP_003442002

27
Kvar_0479

YP_003437421

28
HMPREF0485_00450

ZP_06548050

29
Kvar_1586

YP_003438523

30
Kvar_1598

YP_003438535

31
Kvar_1597

YP_003438534

32
HMPREF0485_00443

ZP_06548043

33
HMPREF0485_00453

ZP_06548053

34
KP1_2851

YP_002919569

35
KPN2242_01120

AEJ96149

36
KPK_2936

YP_002238762

37
HMPREF9538_03901

ZP_08306208

38
HMPREF0485_02477

ZP_06550077

39
HMPREF0485_01831

ZP_06549431

40
Kvar_3258

YP_003440171

41
Kvar_3395

YP_003440307

42
Kvar_3210

YP_003440127

43
KPN_00277

YP_001333960

44
HMPREF0485_02605

ZP_06550204

45
Kvar_1604

YP_003438541

46
Kvar_4545

YP_003441451

47
HMPREF9538_05113

ZP_08307402

48
KPN2242_08695

AEJ97655

49
Kvar_4742

YP_003441646

50
Kvar_3261

YP_003440174

TABLE 9g

Data for Klebsiella, particularly K. oxytoca (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
2648871
2649476
+
643348533

2
1355295
1356167
−
647536389

3
321413
321955
−
643348533

4
2576463
2577677
−
650716122

5
2889784
2890686
−
646312028

6
12390
13076
+
647009977

7
2489613
2491040
+
646312028

8
925860
926771
−
651053122

9
1837699
1838718
+
651053122

10
237063
237326
+
647536390

11
1387256
1388314
+
647536389

12
2680912
2681727
+
643348533

13
2679911
2680687
+
646312028

14
851698
852411
+
646312028

15
4934923
4936932
+
646312028

16
3964905
3966425
+
646312028

17
1721712
1722182
−
646312028

18
140912
141796
+
647536393

19
2255010
2255996
+
646312028

20
3519306
3520322
−
646312028

21
523538
524377
−
647536389

22
311624
312142
+
640753018

23
1716249
1716779
+
646312028

24
1971206
1973212
−
646312028

25
2878963
2879583
+
646564530

26
5455245
5456423
−
646312028

27
509672
510736
+
646312028

28
528513
529175
−
647536389

29
1711303
1712709
−
646312028

30
1723564
1724937
−
646312028

31
1722169
1723554
−
646312028

32
520902
521159
−
647536389

33
531062
532510
−
647536389

34
2717504
2718439
+
646564530

35
230663
231895
−
651053122

36
2983904
2984626
+
643348533

37
15395
16450
+
651333420

38
872347
873972
+
647536390

39
149922
150884
−
647536390

40
3387706
3389424
−
646312028

41
3535340
3535786
+
646312028

42
3340882
3341376
−
646312028

43
312969
315452
+
640753018

44
1009891
1010898
+
647536390

45
1730820
1734335
+
646312028

46
4822901
4823620
+
646312028

47
52
390
−
651333602

48
1839612
1840562
+
651053122

49
5039066
5040004
+
646312028

50
3391540
3392502
+
646312028

TABLE 10a

Data for Klebsiella, particularly K. oxytoca

Scaffold.External.

No.
Accession
Scaffold.Name
best_pv

1
NC_011283

Klebsiella pneumoniae 342: NC_011283
7.24545119859105e−19

2
NZ_GG745508

Klebsiella sp. 1_1_55 genomic scaffold supercont1.1: NZ_GG745508
7.24545119859105e−19

3
NC_015663

Enterobacter aerogenes KCTC 2190 chromosome: NC_015663
9.82145388713083e−17

4
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
4.06768464186916e−16

5
NZ_ACZD01000230

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
4.06768464186916e−16

contig00265: NZ_ACZD01000230

6
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

7
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
6.05465029985694e−16

8
NZ_GG745509

Klebsiella sp. 1_1_55 genomic scaffold supercont1.2: NZ_GG745509
6.05465029985694e−16

9
NZ_GG745508

Klebsiella sp. 1_1_55 genomic scaffold supercont1.1: NZ_GG745508
6.05465029985694e−16

10
NC_011283

Klebsiella pneumoniae 342: NC_011283
6.05465029985694e−16

11
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

12
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

13
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

14
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

15
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

16
NZ_GG745512

Klebsiella sp. 1_1_55 genomic scaffold supercont1.5: NZ_GG745512
6.05465029985694e−16

17
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

18
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

19
NZ_GG745508

Klebsiella sp. 1_1_55 genomic scaffold supercont1.1: NZ_GG745508
6.05465029985694e−16

20
NC_009648

Klebsiella pneumoniae subsp. pneumoniae MGH 78578: NC_009648
6.05465029985694e−16

21
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

22
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

23
NC_012731

Klebsiella pneumoniae NTUH-K2044: NC_012731
6.05465029985694e−16

24
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

25
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

26
NZ_GG745508

Klebsiella sp. 1_1_55 genomic scaffold supercont1.1: NZ_GG745508
6.05465029985694e−16

27
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

28
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

29
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

30
NZ_GG745508

Klebsiella sp. 1_1_55 genomic scaffold supercont1.1: NZ_GG745508
6.05465029985694e−16

31
NZ_GG745508

Klebsiella sp. 1_1_55 genomic scaffold supercont1.1: NZ_GG745508
6.05465029985694e−16

32
NC_012731

Klebsiella pneumoniae NTUH-K2044: NC_012731
6.05465029985694e−16

33
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
6.05465029985694e−16

34
NC_011283

Klebsiella pneumoniae 342: NC_011283
6.05465029985694e−16

35
NZ_AFBO01000503

Klebsiella sp. MS 92-3 K_spMS92-3-1.0_Cont988.13:
6.05465029985694e−16

NZ_AFBO01000503

36
NZ_GG745509

Klebsiella sp. 1_1_55 genomic scaffold supercont1.2: NZ_GG745509
6.05465029985694e−16

37
NZ_GG745509

Klebsiella sp. 1_1_55 genomic scaffold supercont1.2: NZ_GG745509
6.05465029985694e−16

38
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

39
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

40
NC_009648

Klebsiella pneumoniae subsp. pneumoniae MGH 78578: NC_009648
6.05465029985694e−16

41
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

42
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

43
NZ_AFBO01000685

Klebsiella sp. MS 92-3 K_spMS92-3-1.0_Cont1649.3:
6.05465029985694e−16

NZ_AFBO01000685

44
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

45
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

46
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.05465029985694e−16

47
NC_009648

Klebsiella pneumoniae subsp. pneumoniae MGH 78578: NC_009648
6.05465029985694e−16

48
NC_011283

Klebsiella pneumoniae 342: NC_011283
6.05465029985694e−16

49
NC_014500

Dickeya dadantii 3937 chromosome: NC_014500
6.05465029985694e−16

50
NC_011283

Klebsiella pneumoniae 342: NC_011283
6.05465029985694e−16

TABLE 10b

Data for Klebsiella, particularly K. oxytoca (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
A/S; AUG; CP; CRM; LVX; P/T
fluoroquinolone; lactam
A/S
lactam

2
A/S; AUG; CP; CRM; LVX; P/T
fluoroquinolone; lactam
A/S
lactam

3
A/S; AUG; CP; CRM; LVX; P/T
fluoroquinolone; lactam
A/S
lactam

4
A/S; CP; LVX
fluoroquinolone; lactam
A/S
lactam

5
A/S; AUG; CP; CRM; LVX; P/T
fluoroquinolone; lactam
A/S
lactam

6
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

7
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

8
A/S; AUG; CP; LVX
fluoroquinolone; lactam
A/S
lactam

9
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

10
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

11
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

12
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

13
A/S; CP; LVX
fluoroquinolone; lactam
A/S
lactam

14
A/S; AUG; CP; CRM; LVX; P/T
fluoroquinolone; lactam
A/S
lactam

15
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

16
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

17
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

18
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

19
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

20
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

21
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

22
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

23
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

24
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

25
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

26
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

27
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

28
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

29
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

30
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

31
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

32
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

33
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

34
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

35
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

36
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

37
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

38
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

39
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

40
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

41
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

42
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

43
A/S; CP; LVX
fluoroquinolone; lactam
A/S
lactam

44
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

45
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

46
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

47
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

48
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

49
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

50
A/S; AUG; CP; CRM; LVX
fluoroquinolone; lactam
A/S
lactam

TABLE 10c

Data for Klebsiella, particularly K. oxytoca (continued)

No.
num_fluoroquinolone
num_lactam

1
2
4

2
2
4

3
2
4

4
2
1

5
2
4

6
2
3

7
2
3

8
2
2

9
2
3

10
2
3

11
2
3

12
2
3

13
2
1

14
2
4

15
2
3

16
2
3

17
2
3

18
2
3

19
2
3

20
2
3

21
2
3

22
2
3

23
2
3

24
2
3

25
2
3

26
2
3

27
2
3

28
2
3

29
2
3

30
2
3

31
2
3

32
2
3

33
2
3

34
2
3

35
2
3

36
2
3

37
2
3

38
2
3

39
2
3

40
2
3

41
2
3

42
2
3

43
2
1

44
2
3

45
2
3

46
2
3

47
2
3

48
2
3

49
2
3

50
2
3

TABLE 10d

Data for Klebsiella, particularly K. oxytoca (continued)

No.
A/S_pv_adj
AUG_pv_adj
AZT_pv_adj
CAX_pv_adj
CFT_pv_adj

1
7.25E−19
1.72E−03
1.02E−01
7.63E−02
1.14E−01

2
7.25E−19
1.72E−03
1.02E−01
7.63E−02
1.14E−01

3
9.82E−17
1.48E−03
1.97E−02
1.37E−02
6.22E−02

4
4.07E−16
1.01E−02
2.64E−02
3.46E−02
3.40E−02

5
4.07E−16
2.92E−04
3.51E−02
2.48E−02
4.69E−02

6
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

7
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

8
6.05E−16
9.84E−03
4.51E−02
3.38E−02
2.50E−02

9
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

10
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

11
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

12
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

13
6.05E−16
1.01E−02
4.61E−02
3.45E−02
3.46E−02

14
6.05E−16
5.13E−03
2.58E−02
1.89E−02
1.75E−02

15
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

16
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

17
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

18
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

19
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

20
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

21
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

22
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

23
6.05E−16
5.42E−03
3.46E−02
1.98E−02
2.46E−02

24
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

25
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

26
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

27
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

28
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

29
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

30
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

31
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

32
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

33
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

34
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

35
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

36
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

37
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

38
6.05E−16
7.42E−03
3.51E−02
2.53E−02
2.48E−02

39
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

40
6.05E−16
7.42E−03
3.51E−02
2.53E−02
2.48E−02

41
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

42
6.05E−16
7.42E−03
3.51E−02
2.53E−02
2.48E−02

43
6.05E−16
1.84E−02
7.73E−02
5.74E−02
4.41E−02

44
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

45
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

46
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

47
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

48
6.05E−16
7.42E−03
3.51E−02
2.53E−02
2.48E−02

49
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

50
6.05E−16
7.34E−03
3.46E−02
2.50E−02
2.46E−02

TABLE 10e

Data for Klebsiella, particularly K. oxytoca (continued)

No.
CP_pv_adj
CRM_pv_adj
LVX_pv_adj
P/T_pv_adj

1
4.47E−03
3.22E−03
3.33E−05
4.21E−03

2
4.47E−03
3.22E−03
3.33E−05
4.21E−03

3
2.12E−04
4.16E−03
5.03E−07
3.38E−03

4
2.11E−03
1.38E−02
6.28E−05
1.93E−02

5
6.71E−04
1.62E−03
8.24E−07
2.85E−03

6
1.30E−03
7.85E−03
5.53E−05
1.37E−02

7
1.30E−03
7.85E−03
5.53E−05
1.37E−02

8
1.98E−03
1.03E−02
5.68E−05
1.89E−02

9
1.30E−03
7.85E−03
5.53E−05
1.37E−02

10
1.30E−03
7.85E−03
5.53E−05
1.37E−02

11
1.30E−03
7.85E−03
5.53E−05
1.37E−02

12
1.30E−03
7.85E−03
5.53E−05
1.37E−02

13
1.26E−03
1.04E−02
3.08E−05
1.93E−02

14
7.58E−04
6.15E−03
5.93E−05
9.93E−03

15
1.30E−03
7.85E−03
5.53E−05
1.37E−02

16
1.30E−03
7.85E−03
5.53E−05
1.37E−02

17
1.30E−03
7.85E−03
5.53E−05
1.37E−02

18
1.30E−03
7.85E−03
5.53E−05
1.37E−02

19
1.30E−03
7.85E−03
5.53E−05
1.37E−02

20
1.30E−03
7.85E−03
5.53E−05
1.37E−02

21
1.30E−03
7.85E−03
5.53E−05
1.37E−02

22
1.30E−03
7.85E−03
5.53E−05
1.37E−02

23
3.39E−03
6.15E−03
1.55E−04
1.03E−02

24
1.30E−03
7.85E−03
5.53E−05
1.37E−02

25
1.30E−03
7.85E−03
5.53E−05
1.37E−02

26
1.30E−03
7.85E−03
5.53E−05
1.37E−02

27
1.30E−03
7.85E−03
5.53E−05
1.37E−02

28
1.30E−03
7.85E−03
5.53E−05
1.37E−02

29
1.30E−03
7.85E−03
5.53E−05
1.37E−02

30
1.30E−03
7.85E−03
5.53E−05
1.37E−02

31
1.30E−03
7.85E−03
5.53E−05
1.37E−02

32
1.30E−03
7.85E−03
5.53E−05
1.37E−02

33
1.30E−03
7.85E−03
5.53E−05
1.37E−02

34
1.30E−03
7.85E−03
5.53E−05
1.37E−02

35
1.30E−03
7.85E−03
5.53E−05
1.37E−02

36
1.30E−03
7.85E−03
5.53E−05
1.37E−02

37
1.30E−03
7.85E−03
5.53E−05
1.37E−02

38
1.97E−03
7.93E−03
5.53E−05
1.39E−02

39
1.30E−03
7.85E−03
5.53E−05
1.37E−02

40
1.97E−03
7.93E−03
5.53E−05
1.39E−02

41
1.30E−03
7.85E−03
5.53E−05
1.37E−02

42
1.97E−03
7.93E−03
5.53E−05
1.39E−02

43
7.43E−03
1.01E−02
2.47E−04
3.31E−02

44
1.30E−03
7.85E−03
5.53E−05
1.37E−02

45
1.30E−03
7.85E−03
5.53E−05
1.37E−02

46
1.30E−03
7.85E−03
5.53E−05
1.37E−02

47
1.30E−03
7.85E−03
5.53E−05
1.37E−02

48
1.97E−03
4.47E−03
5.53E−05
1.39E−02

49
1.30E−03
7.85E−03
5.53E−05
1.37E−02

50
1.30E−03
7.85E−03
5.53E−05
1.37E−02

TABLE 10f

Data for Klebsiella, particularly K. oxytoca (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
KPK_2590

YP_002238421

2
HMPREF0485_01216

ZP_06548816

3
EAE_11985

YP_004592590

4
Kvar_2784

YP_003439702

5
HMPREF0484_4675
add
ZP_06017656

6
Kvar_2381

YP_003439305

7
KPN2242_04295

AEJ96779

8
HMPREF0485_01916

ZP_06549516

9
HMPREF0485_01247

ZP_06548847

10
KPK_2622

YP_002238453

11
Kvar_2568

YP_003439490

12
Kvar_0816

YP_003437758

13
Kvar_4643

YP_003441547

14
Kvar_3771

YP_003440683

15
Kvar_1596

YP_003438533

16
HMPREF0485_03998

ZP_06551594

17
Kvar_2140

YP_003439069

18
Kvar_3380

YP_003440292

19
HMPREF0485_00446

ZP_06548046

20
KPN_00275

YP_001333958

21
Kvar_1589

YP_003438526

22
Kvar_1856

YP_003438789

23
KP1_3016

YP_002919724

24
Kvar_5099

YP_003442002

25
Kvar_0479

YP_003437421

26
HMPREF0485_00450

ZP_06548050

27
Kvar_1586

YP_003438523

28
Kvar_1598

YP_003438535

29
Kvar_1597

YP_003438534

30
HMPREF0485_00443

ZP_06548043

31
HMPREF0485_00453

ZP_06548053

32
KP1_2851

YP_002919569

33
KPN2242_01120

AEJ96149

34
KPK_2936

YP_002238762

35
HMPREF9538_03901

ZP_08306208

36
HMPREF0485_02477

ZP_06550077

37
HMPREF0485_01831

ZP_06549431

38
Kvar_3395

YP_003440307

39
Kvar_3210

YP_003440127

40
KPN_00277

YP_001333960

41
Kvar_1604

YP_003438541

42
Kvar_4545

YP_003441451

43
HMPREF9538_05113

ZP_08307402

44
Kvar_4742

YP_003441646

45
Kvar_2570

YP_003439492

46
Kvar_2569

YP_003439491

47
KPN_04505
melA
YP_001338127

48
KPK_1698
nifA
YP_002237549

49
Dda3937_02155
nifH
YP_003884784

50
KPK_1712
nifK
YP_002237563

TABLE 10g

Data for Klebsiella, particularly K. oxytoca (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
2648871
2649476
+
643348533

2
1355295
1356167
−
647536389

3
2576463
2577677
−
650716122

4
2889784
2890686
−
646312028

5
12390
13076
+
647009977

6
2489613
2491040
+
646312028

7
925860
926771
−
651053122

8
237063
237326
+
647536390

9
1387256
1388314
+
647536389

10
2680912
2681727
+
643348533

11
2679911
2680687
+
646312028

12
851698
852411
+
646312028

13
4934923
4936932
+
646312028

14
3964905
3966425
+
646312028

15
1721712
1722182
−
646312028

16
140912
141796
+
647536393

17
2255010
2255996
+
646312028

18
3519306
3520322
−
646312028

19
523538
524377
−
647536389

20
311624
312142
+
640753018

21
1716249
1716779
+
646312028

22
1971206
1973212
−
646312028

23
2878963
2879583
+
646564530

24
5455245
5456423
−
646312028

25
509672
510736
+
646312028

26
528513
529175
−
647536389

27
1711303
1712709
−
646312028

28
1723564
1724937
−
646312028

29
1722169
1723554
−
646312028

30
520902
521159
−
647536389

31
531062
532510
−
647536389

32
2717504
2718439
+
646564530

33
230663
231895
−
651053122

34
2983904
2984626
+
643348533

35
15395
16450
+
651333420

36
872347
873972
+
647536390

37
149922
150884
−
647536390

38
3535340
3535786
+
646312028

39
3340882
3341376
−
646312028

40
312969
315452
+
640753018

41
1730820
1734335
+
646312028

42
4822901
4823620
+
646312028

43
52
390
−
651333602

44
5039066
5040004
+
646312028

45
2681431
2682066
+
646312028

46
2680692
2681420
+
646312028

47
4930190
4931542
+
640753018

48
1752865
1754439
−
643348533

49
4321869
4322750
−
648028072

50
1766440
1768002
−
643348533

TABLE 11a

Data for Klebsiella, particularly K. pneumoniae

Scaffold.External.

No.
Accession
Scaffold.Name
best_pv

1
NC_007384

Shigella sonnei Ss046: NC_007384
1.21395823682916e−119

2
NC_011083

Salmonella enterica subsp. enterica serovar Heidelberg str. SL476:
1.70517984237646e−115

NC_011083

3
NZ_ADWV01000045

Escherichia coli MS 107-1 E_coliMS107-1-1.0.1_Cont44.1:
3.12333368944279e−110

NZ_ADWV01000045

4
NC_009651

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid pKPN5:
1.8490215255217e−103

NC_009651

5
NZ_ABFH01000001

Salmonella enterica subsp. enterica serovar Virchow str. SL491,
4.16211077482132e−97

unfinished sequence: NZ_ABFH01000001

6
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
1.34397014479151e−80

7
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
1.21342816034335e−71

8
NZ_ACZD01000070

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
4.42089689687353e−61

contig00070: NZ_ACZD01000070

9
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
8.41004168548543e−61

10
NC_011282

Klebsiella pneumoniae 342 plasmid pKP187: NC_011282
8.41004168548543e−61

11
NZ_ACZD01000070

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
8.41004168548543e−61

contig00070: NZ_ACZD01000070

12
NZ_ADTP01000323

Escherichia coli MS 69-1 E_coli69-1-1.0_Cont630.1: NZ_ADTP01000323
4.94539115664213e−60

13
NC_009793
Citrobacter koseri ATCC BAA-895 plasmid pCK03: NC_009793
5.71878021049123e−59

14
NZ_ACZD01000005

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
1.22977045856913e−58

contig00005: NZ_ACZD01000005

15
NZ_ACZD01000127

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
1.49068550300511e−58

contig00129: NZ_ACZD01000127

16
NZ_GG745515

Klebsiella sp. 1_1_55 genomic scaffold supercont1.8: NZ_GG745515
7.09566707309011e−58

17
NZ_AAJX01000089

Escherichia coli B171, unfinished sequence: NZ_AAJX01000089
1.65409147045657e−56

18
NZ_ACZD01000005

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
7.54090407593199e−55

contig00005: NZ_ACZD01000005

19
NZ_AFBO01000042

Klebsiella sp. MS 92-3 K_spMS92-3-1.0_Cont91.1: NZ_AFBO01000042
2.8348333685311e−54

20
NC_009649

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid pKPN3:
2.8348333685311e−54

NC_009649

21
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
2.83530891190408e−54

22
NC_009649

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid pKPN3:
4.89541334527925e−54

NC_009649

23
NZ_AFBO01000042

Klebsiella sp. MS 92-3 K_spMS92-3-1.0_Cont91.1: NZ_AFBO01000042
2.18592863711471e−53

24
NC_009649

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid pKPN3:
2.18592863711471e−53

NC_009649

25
NZ_ACZD01000127

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
1.08576020331202e−52

contig00129: NZ_ACZD01000127

26
NZ_ACZD01000127

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
1.37521017661703e−52

contig00129: NZ_ACZD01000127

27
NZ_ACZD01000127

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
2.1362800317976e−52

contig00129: NZ_ACZD01000127

28
NC_014121

Enterobacter cloacae subsp. cloacae ATCC 13047 chromosome: NC_014121
2.21381524453565e−51

29
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
6.53846908249994e−51

30
NZ_GG745512

Klebsiella sp. 1_1_55 genomic scaffold supercont1.5: NZ_GG745512
2.78992804201171e−50

31
NZ_CAAZ01000154

Salmonella enterica subsp. enterica serovar Typhi str. E98-3139,
4.10919139010377e−50

unfinished sequence: NZ_CAAZ01000154

32
NZ_ACZD01000127

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
6.10670380866266e−50

contig00129: NZ_ACZD01000127

33
NZ_ACZD01000127

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
1.00996840886331e−49

contig00129: NZ_ACZD01000127

34
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
1.33344542353295e−48

35
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
3.00269800428115e−48

36
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
3.13126971411145e−48

37
NZ_ACZD01000127

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
3.13126971411145e−48

contig00129: NZ_ACZD01000127

38
NC_014121

Enterobacter cloacae subsp. cloacae ATCC 13047 chromosome: NC_014121
3.79149056816214e−48

39
NZ_AFBO01000625

Klebsiella sp. MS 92-3 K_spMS92-3-1.0_Cont1175.2: NZ_AFBO01000625
2.5975548233422e−47

40
NZ_ACZD01000127

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
1.05391699509183e−46

contig00129: NZ_ACZD01000127

41
NC_011092

Salmonella enterica subsp. enterica serovar Schwarzengrund str.
4.42178242563847e−46

CVM19633 plasmid pCVM19633_110: NC_011092

42
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.65483065085068e−46

43
NC_012912

Dickeya zeae Ech1591: NC_012912
1.05262166415392e−45

44
NC_013509

Edwardsiella tarda EIB202 plasmid pEIB202: NC_013509
1.24074600175825e−45

45
AP011957

Salmonella enterica subsp. enterica serovar Typhimurium str. T000240
2.46270503642371e−45

DNA: AP011957

46
NC_006856

Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
9.02631418377704e−45

plasmid pSC138: NC_006856

47
AP011957

Salmonella enterica subsp. enterica serovar Typhimurium str. T000240
3.37821430101762e−44

DNA: AP011957

48
NZ_AFBO01000232

Klebsiella sp. MS 92-3 K_spMS92-3-1.0_Cont505.1: NZ_AFBO01000232
4.87973844618098e−43

49
NC_004631

Salmonella enterica subsp. enterica serovar Typhi Ty2: NC_004631
1.54269244019591e−42

50
NC_006625

Klebsiella pneumoniae NTUH-K2044 plasmid pK2044: NC_006625
1.89874529968327e−42

TABLE 11b

Data for Klebsiella, particularly K. pneumoniae (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
TO
aminoglycoside

ETP; GM; LVX; P/T; TO; T/S

2
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
AUG
lactam

ETP; GM; LVX; P/T; TO; T/S

3
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

ETP; GM; LVX; P/T; TO; T/S

4
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

ETP; GM; LVX; P/T; TO; T/S

5
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

ETP; GM; LVX; P/T; TO; T/S

6
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

ETP; GM; LVX; P/T; TO; T/S

7
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

ETP; GM; LVX; P/T; TO; T/S

8
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

ETP; CM; LVX; P/T; TO; T/S

9
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

ETP; GM; LVX; P/T; TO; T/S

10
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

ETP; GM; LVX; P/T; TO; T/S

11
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

ETP; GM; LVX; P/T; TO; T/S

12
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
CAZ
lactam

ETP; GM; LVX; P/T; TO; T/S

13
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
AUG
lactam

ETP; GM; LVX; P/T; TO; T/S

14
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

ETP; GM; LVX; P/T; TO; T/S

15
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
TO
aminoglycoside

ETP; GM; LVX; P/T; TO; T/S

16
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

ETP; GM; LVX; P/T; TO; T/S

17
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

ETP; GM; LVX; P/T; TO; T/S

18
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

ETP; GM; LVX; P/T; TO; T/S

19
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
P/T
lactam

ETP; GM; LVX; P/T; TO; T/S

20
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
P/T
lactam

ETP; GM; LVX; P/T; TO; T/S

21
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
TO
aminoglycoside

ETP; GM; LVX; P/T; TO; T/S

22
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
P/T
lactam

ETP; GM; LVX; P/T; TO; T/S

23
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
P/T
lactam

ETP; GM; LVX; P/T; TO; T/S

24
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
P/T
lactam

ETP; GM; LVX; P/T; TO; T/S

25
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
TO
aminoglycoside

ETP; GM; LVX; P/T; TO; T/S

26
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
TO
aminoglycoside

ETP; GM; LVX; P/T; TO; T/S

27
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
TO
aminoglycoside

ETP; GM; LVX; P/T; TO; T/S

28
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

ETP; GM; LVX; P/T; TO; T/S

29
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

ETP; GM; LVX; P/T; TO; T/S

30
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

ETP; GM; LVX; P/T; TO; T/S

31
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

ETP; GM; LVX; P/T; TO; T/S

32
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

ETP; GM; LVX; P/T; TO; T/S

33
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

ETP; GM; LVX; P/T; TO; T/S

34
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

ETP; GM; LVX; P/T; TO; T/S

35
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

ETP; GM; LVX; P/T; TO; T/S

36
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

ETP; GM; LVX; P/T; TO; T/S

37
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

ETP; GM; LVX; P/T; TO; T/S

38
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

ETP; GM; LVX; P/T; TO; T/S

39
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CM; LVX; P/T; TO; T/S

40
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

ETP; GM; LVX; P/T; TO; T/S

41
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
AUG
lactam

ETP; GM; LVX; P/T; TO; T/S

42
AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM; ETP ;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

LVX; P/T; TO; T/S

43
AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM; ETP ;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

LVX; P/T; TO; T/S

44
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

ETP; GM; LVX; P/T; TO; T/S

45
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
TO
aminoglycoside

ETP; GM; LVX; P/T; TO; T/S

46
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
TO
aminoglycoside

ETP; GM; LVX; P/T; TO; T/S

47
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
AUG
lactam

ETP; GM; LVX; P/T; TO; T/S

48
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

ETP; GM; LVX; P/T; TO; T/S

49
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

ETP; GM; LVX; P/T; TO; T/S

50
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

ETP; GM; LVX; P/T; TO; T/S

TABLE 11c

Data for Klebsiella, particularly K. pneumoniae (continued)

No.
num_aminoglycoside
num_fluoroquinolone
num_lactam
num_other

1
2
2
10
1

2
2
2
10
1

3
2
2
10
1

4
2
2
10
1

5
2
2
10
1

6
2
2
10
1

7
2
2
10
1

8
2
2
10
1

9
2
2
10
1

10
2
2
10
1

11
2
2
10
1

12
2
2
10
1

13
2
2
10
1

14
2
2
10
1

15
2
2
10
1

16
2
2
10
1

17
2
2
10
1

18
2
2
10
1

19
2
2
10
1

20
2
2
10
1

21
2
2
10
1

22
2
2
10
1

23
2
2
10
1

24
2
2
10
1

25
2
2
10
1

26
2
2
10
1

27
2
2
10
1

28
2
2
10
1

29
2
2
10
1

30
2
2
10
1

31
2
2
10
1

32
2
2
10
1

33
2
2
10
1

34
2
2
10
1

35
2
2
10
1

36
2
2
10
1

37
2
2
10
1

38
2
2
10
1

39
2
2
9
1

40
2
2
10
1

41
2
2
10
1

42
1
2
9
1

43
1
2
9
1

44
2
2
10
1

45
2
2
10
1

46
2
2
10
1

47
2
2
10
1

48
2
2
10
1

49
2
2
10
1

50
2
2
10
1

TABLE 11d

Data for Klebsiella, particularly K. pneumoniae (continued)

No.
A/S_pv_adj
AUG_pv_adj
AZT_pv_adj
CAX_pv_adj
CAZ_pv_adj

1
1.28E−76
1.24E−105
4.06E−95
3.39E−95
5.99E−93

2
1.18E−98
1.71E−115
9.09E−91
6.55E−88
1.66E−96

3
1.08E−81
5.85E−86
2.76E−94
4.16E−97
6.84E−100

4
5.55E−76
3.05E−84
1.38E−91
2.64E−96
5.33E−94

5
1.22E−70
3.41E−71
1.41E−80
1.50E−83
6.22E−90

6
7.70E−21
1.03E−41
8.20E−48
2.50E−44
2.69E−46

7
8.54E−16
4.34E−29
4.54E−38
5.50E−34
1.34E−34

8
2.62E−12
1.74E−24
1.49E−26
2.74E−25
2.84E−24

9
5.20E−12
2.50E−24
3.69E−26
7.31E−25
7.66E−24

10
5.20E−12
2.50E−24
3.69E−26
7.31E−25
7.66E−24

11
5.20E−12
2.50E−24
3.69E−26
7.31E−25
7.66E−24

12
3.32E−43
1.75E−59
1.48E−54
9.28E−55
4.95E−60

13
2.41E−43
5.72E−59
4.20E−53
2.96E−53
2.14E−58

14
2.47E−16
8.57E−27
1.49E−34
1.96E−31
8.83E−33

15
1.72E−35
6.40E−55
1.25E−44
4.12E−43
1.61E−46

16
3.04E−18
5.19E−32
4.83E−36
2.23E−35
1.91E−32

17
1.02E−47
9.19E−45
1.85E−48
9.17E−53
6.18E−56

18
3.51E−17
3.04E−23
8.29E−30
1.21E−27
9.29E−29

19
1.03E−40
7.90E−52
1.41E−37
4.81E−39
9.97E−38

20
1.03E−40
7.90E−52
1.41E−37
4.81E−39
9.97E−38

21
8.56E−34
4.84E−53
8.75E−43
2.41E−41
9.43E−45

22
5.13E−42
1.10E−52
3.02E−38
9.55E−40
3.15E−38

23
1.11E−41
3.84E−52
1.00E−37
3.11E−39
8.03E−38

24
1.11E−41
3.84E−52
1.00E−37
3.11E−39
8.03E−38

25
8.85E−33
1.54E−51
2.83E−42
1.24E−40
2.88E−44

26
1.96E−32
2.54E−52
2.98E−42
1.41E−40
3.55E−44

27
5.12E−32
6.70E−50
1.84E−40
2.34E−38
1.33E−42

28
1.65E−30
3.00E−47
1.96E−38
1.37E−36
4.94E−39

29
4.43E−31
1.45E−47
2.29E−39
1.06E−37
3.63E−40

30
6.99E−12
2.37E−26
2.77E−24
5.28E−24
2.55E−26

31
2.78E−31
7.62E−46
1.11E−38
5.40E−37
1.95E−39

32
9.62E−32
1.45E−47
2.29E−39
1.06E−37
3.63E−40

33
2.27E−31
2.28E−47
3.20E−39
1.66E−37
5.77E−40

34
9.74E−28
9.40E−43
1.44E−35
7.30E−34
3.24E−36

35
1.57E−28
2.77E−42
6.21E−36
1.59E−34
2.14E−36

36
3.41E−27
2.34E−43
7.21E−36
4.53E−33
9.07E−37

37
3.41E−27
2.34E−43
7.21E−36
4.53E−33
9.07E−37

38
2.00E−30
7.61E−47
1.00E−38
1.06E−37
3.63E−40

39
8.29E−47
2.48E−33
3.67E−37
5.57E−42
2.74E−43

40
1.53E−27
6.97E−43
2.91E−36
2.70E−35
5.96E−38

41
1.75E−44
4.42E−46
2.16E−37
1.21E−36
1.12E−42

42
4.51E−02
4.66E−12
9.77E−17
3.13E−16
9.90E−15

43
5.37E−02
5.73E−12
1.27E−16
6.11E−16
1.15E−14

44
6.65E−31
4.17E−32
1.40E−25
3.69E−27
1.78E−29

45
6.15E−34
5.78E−41
2.29E−36
9.94E−38
1.48E−38

46
3.01E−32
3.12E−38
7.22E−37
3.96E−36
6.00E−37

47
4.35E−41
3.38E−44
1.49E−30
1.42E−33
1.82E−29

48
6.41E−31
1.63E−41
3.24E−33
2.26E−36
1.97E−31

49
2.54E−11
2.61E−18
8.71E−21
1.23E−18
1.87E−19

50
2.38E−23
3.76E−29
2.21E−27
4.97E−29
1.37E−29

TABLE 11e

Data for Klebsiella, particularly K. pneumoniae (continued)

No.
CFT_pv_adj
CP_pv_adj
CPE_pv_adj
CRM_pv_adj
ETP_pv_adj

1
2.17E−99
2.40E−85
2.31E−68
1.21E−82
1.87E−58

2
2.52E−83
1.28E−61
4.61E−66
7.83E−57
8.20E−51

3
3.93E−93
2.17E−58
2.89E−43
3.32E−73
3.54E−24

4
1.52E−90
4.25E−60
1.75E−43
2.59E−71
1.63E−23

5
3.61E−77
1.76E−47
1.47E−36
5.14E−62
6.31E−21

6
2.84E−46
1.53E−54
2.89E−63
1.06E−36
1.34E−80

7
8.43E−36
1.96E−43
3.06E−55
3.95E−29
1.21E−71

8
5.55E−27
2.63E−33
6.90E−40
1.01E−20
4.42E−61

9
1.58E−26
5.49E−33
1.32E−39
2.40E−20
8.41E−61

10
1.58E−26
5.49E−33
1.32E−39
2.40E−20
8.41E−61

11
1.58E−26
5.49E−33
1.32E−39
4.98E−21
8.41E−61

12
4.39E−54
4.96E−60
1.80E−51
7.75E−50
7.02E−53

13
1.26E−52
1.35E−58
1.72E−50
4.57E−49
3.71E−52

14
1.28E−31
2.00E−30
6.27E−42
1.20E−29
1.23E−58

15
2.05E−41
2.56E−52
7.76E−46
3.74E−32
5.20E−48

16
1.52E−36
2.10E−37
5.58E−48
5.62E−28
7.10E−58

17
9.26E−49
4.16E−22
1.22E−19
9.42E−36
5.55E−05

18
6.27E−28
1.02E−25
4.83E−36
7.62E−29
7.54E−55

19
9.92E−40
2.65E−39
2.28E−41
4.71E−28
1.10E−32

20
9.92E−40
2.65E−39
2.28E−41
4.71E−28
1.10E−32

21
1.47E−40
1.18E−49
1.74E−45
2.18E−32
1.46E−46

22
2.00E−40
6.22E−40
7.04E−42
1.08E−28
5.10E−33

23
6.77E−40
2.32E−39
3.78E−41
2.22E−28
3.70E−32

24
6.77E−40
2.32E−39
3.78E−41
2.22E−28
3.70E−32

25
4.69E−40
3.62E−49
1.06E−44
1.70E−33
2.11E−45

26
4.89E−40
1.97E−49
1.88E−45
2.34E−32
8.59E−46

27
5.94E−39
1.13E−47
2.46E−43
3.44E−33
1.93E−49

28
3.32E−36
2.21E−51
1.87E−44
1.56E−31
1.83E−41

29
2.69E−37
6.54E−51
4.48E−44
2.19E−30
3.44E−41

30
1.39E−24
6.75E−31
1.12E−35
5.11E−15
2.79E−50

31
1.34E−36
4.11E−50
1.67E−43
1.45E−31
8.85E−41

32
2.69E−37
6.11E−50
4.48E−44
2.19E−30
3.44E−41

33
6.74E−37
1.01E−49
6.91E−44
1.07E−30
4.69E−41

34
3.28E−34
1.33E−48
1.41E−40
1.52E−30
7.40E−43

35
3.72E−36
3.00E−48
1.67E−40
8.05E−31
2.56E−43

36
1.04E−34
3.13E−48
5.88E−41
1.06E−29
3.84E−43

37
1.04E−34
3.13E−48
5.88E−41
1.06E−29
3.84E−43

38
2.69E−37
3.79E−48
4.21E−43
9.89E−32
5.95E−40

39
2.84E−38
3.78E−14
1.15E−05
9.70E−31
9.25E−01

40
1.88E−36
1.05E−46
3.80E−41
1.01E−30
2.77E−43

41
4.01E−36
1.78E−19
2.93E−16
1.27E−21
2.46E−10

42
5.45E−16
4.08E−18
6.25E−28
7.56E−08
6.65E−46

43
1.13E−15
5.57E−18
9.82E−28
1.16E−07
1.05E−45

44
2.55E−25
6.58E−14
7.47E−22
3.89E−16
2.18E−20

45
5.14E−35
2.41E−27
5.02E−15
4.61E−29
2.22E−12

46
1.40E−36
2.78E−33
1.06E−29
5.12E−30
2.25E−28

47
3.46E−32
1.18E−32
1.62E−32
2.49E−29
1.62E−26

48
6.74E−36
1.36E−34
2.38E−34
1.27E−25
6.79E−29

49
9.64E−20
3.40E−22
1.36E−30
8.87E−18
1.54E−42

50
1.19E−26
1.97E−18
9.42E−19
1.46E−19
1.52E−12

TABLE 11f

Data for Klebsiella, particularly K. pneumoniae (continued)

No.
GM_pv_adj
LVX_pv_adj
P/T_pv_adj
TO_pv_adj
T/S_pv_adj

1
6.24E−60
3.97E−80
7.18E−96
1.21E−19
1.12E−106

2
6.10E−67
3.76E−55
1.20E−67
2.77E−05
3.59E−83

3
6.00E−68
3.14E−50
5.58E−70
1.37E−91
3.12E−110

4
3.06E−63
4.39E−52
7.17E−70
6.65E−91
1.85E−103

5
5.29E−59
6.80E−39
4.00E−51
1.40E−82
4.16E−97

6
5.64E−09
3.19E−59
3.01E−52
7.11E−48
1.50E−31

7
1.61E−05
6.12E−48
2.20E−40
1.45E−34
2.10E−20

8
1.57E−06
6.85E−37
6.06E−35
1.79E−29
2.02E−18

9
2.46E−06
1.41E−36
1.30E−34
3.62E−29
2.62E−18

10
2.46E−06
1.41E−36
1.30E−34
3.62E−29
2.62E−18

11
2.46E−06
1.41E−36
1.30E−34
3.62E−29
2.62E−18

12
2.30E−25
1.32E−53
6.01E−52
5.28E−59
5.07E−39

13
1.61E−25
2.14E−52
1.19E−50
1.22E−58
6.30E−38

14
6.89E−05
6.38E−32
9.66E−29
7.19E−31
3.05E−15

15
1.55E−23
1.89E−48
1.36E−48
1.49E−58
1.23E−46

16
7.14E−10
1.99E−38
1.30E−34
9.13E−37
1.47E−21

17
6.27E−40
9.96E−18
4.98E−31
1.50E−43
1.65E−56

18
7.35E−05
4.57E−28
1.61E−25
2.68E−27
2.50E−15

19
1.16E−19
5.28E−36
2.83E−54
2.59E−42
9.74E−48

20
1.16E−19
5.28E−36
2.83E−54
2.59E−42
9.74E−48

21
6.44E−22
5.93E−45
3.28E−47
2.84E−54
2.84E−46

22
6.19E−20
1.49E−36
4.90E−54
5.19E−43
1.61E−47

23
4.80E−20
5.67E−36
2.19E−53
1.90E−42
7.35E−49

24
1.78E−19
5.67E−36
2.19E−53
1.90E−42
6.83E−48

25
1.71E−21
3.92E−44
2.20E−46
1.09E−52
8.26E−45

26
1.49E−20
1.39E−44
1.02E−46
1.38E−52
9.52E−46

27
9.23E−19
4.68E−44
1.13E−48
2.14E−52
7.18E−42

28
1.04E−18
2.43E−47
2.68E−42
8.73E−48
1.22E−43

29
1.81E−19
6.48E−47
5.36E−42
7.69E−49
5.28E−43

30
1.67E−04
1.19E−33
1.48E−27
1.33E−24
2.01E−19

31
2.71E−19
3.53E−46
2.81E−41
2.57E−47
3.11E−43

32
3.53E−20
6.26E−46
5.36E−42
7.69E−49
5.57E−44

33
4.08E−20
9.51E−46
1.44E−41
1.11E−48
8.48E−44

34
9.00E−16
3.30E−45
1.53E−41
3.99E−46
1.50E−39

35
4.69E−14
4.82E−45
1.45E−39
3.68E−47
5.85E−39

36
6.72E−15
8.68E−45
4.34E−42
8.00E−45
1.33E−38

37
6.72E−15
8.68E−45
4.34E−42
8.00E−45
1.33E−38

38
4.79E−19
4.19E−45
5.36E−42
3.42E−47
5.28E−43

39
1.94E−40
1.06E−10
6.27E−21
4.23E−35
2.60E−47

40
1.53E−15
3.13E−43
2.72E−42
3.02E−45
1.22E−39

41
9.94E−38
3.55E−16
4.46E−22
7.61E−44
1.24E−41

42
2.34E−02
4.47E−21
3.44E−16
3.10E−15
2.24E−09

43
2.39E−02
1.02E−20
4.32E−16
6.38E−15
3.86E−09

44
3.44E−22
5.51E−13
6.56E−18
4.39E−24
1.24E−45

45
1.36E−21
1.14E−24
2.38E−33
2.46E−45
1.53E−29

46
1.36E−19
4.39E−32
1.03E−35
9.03E−45
5.01E−44

47
1.18E−14
5.29E−30
3.76E−40
3.55E−44
5.56E−38

48
4.91E−17
8.23E−33
1.06E−40
6.11E−39
4.88E−43

49
1.35E−04
2.25E−22
1.78E−19
5.28E−22
2.63E−12

50
8.68E−26
1.45E−15
1.73E−22
6.68E−34
1.90E−42

TABLE 11g

Data for Klebsiella, particularly K. pneumoniae (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
SSON_3896
aadA
YP_312670

2
SeHA_C1580
blaT
YP_002045448

3
HMPREF9345_05066

ZP_07100147

4
KPN_pKPN5p08201

YP_001338811
plasmid pKPN5

5
Salmoentericaenterica_010100000245

ZP_02702077

6
KPN2242_07235

AEJ97365

7
KPN2242_00750

AEJ96075

8
HMPREF0484_1390
mgtA
ZP_06014374

9
Kvar_3592

YP_003440504

10
KPK_A0103

YP_002235751
plasmid pKP187

11
HMPREF0484_1392
pacL
ZP_06014376

12
HMPREF9534_04427

ZP_07188952

13
CKO_pCKO3p06155

YP_001456633
plasmid pCKO3

14
HMPREF0484_0044
vmtV
ZP_06013029

15
HMPREF0484_2697

ZP_06015679

16
HMPREF0485_04762

ZP_06552358

17
EcolB_01004576

ZP_00708527

18
HMPREF0484_0046

ZP_06013031

19
HMPREF9538_00440

ZP_08302804

20
KPN_pKPN3p05893
ptxE
YP_001338502
plasmid pKPN3

21
KPN2242_07425

AEJ97403

22
KPN_pKPN3p05890
ptxB
YP_001338499
plasmid pKPN3

23
HMPREF9538_00443

ZP_08302807

24
KPN_pKPN3p05891
ptxC
YP_001338500
plasmid pKPN3

25
HMPREF0484_2686

ZP_06015668

26
HMPREF0484_2687
gpw
ZP_06015669

27
HMPREF0484_2684

ZP_06015666

28
ECL_04426

YP_003614904

29
KPN2242_07415

AEJ97401

30
HMPREF0485_03923

ZP_06551519

31
Salmonellentericaenterica_010100016432

ZP_03412648

32
HMPREF0484_2698

ZP_06015680

33
HMPREF0484_2694
fii
ZP_06015676

34
KPN2242_07345

AEJ97387

35
KPN2242_07330

AEJ97384

36
KPN2242_07325

AEJ97383

37
HMPREF0484_2676

ZP_06015658

38
ECL_04434

YP_003614912

39
HMPREF9538_04737

ZP_08307036

40
HMPREF0484_2673

ZP_06015655

41
SeSA_B0079

YP_002112958
plasmid

pCVM19633_110

42
Kvar_2527

YP_003439449

43
Dd1591_2579

YP_003004893

44
ETAE_p041
folP
YP_003297635
plasmid pEIB202

45
STMDT12_C39340

BAJ38877

46
SC026
aph
YP_209331
plasmid pSC138

47
STMDT12_C39170

BAJ38860

48
HMPREF9538_01820

ZP_08304144

49
t1924
exo
NP_805691

50
pK2044_00525

YP_001687935
plasmid pK2044

TABLE 11h

Data for Klebsiella, particularly K. pneumoniae (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
4110458
4111246
−
640427102

2
1525960
1526820
+
642555218

3
4715
5554
−
648294624

4
34908
35255
−
640753021

5
36757
37062
+
641778223

6
1535907
1536932
−
651053122

7
159235
160521
−
651053122

8
2865
3848
−
647009817

9
3765814
3768501
−
646312028

10
67987
70674
+
643348532

11
4691
5551
−
647009817

12
2120
2368
+
648289812

13
8632
8931
+
640753081

14
12911
13663
+
647009752

15
20402
22975
+
647009874

16
93128
94558
+
647536396

17
3555
4568
+
638359041

18
14573
15328
+
647009752

19
933
1943
−
651332959

20
38514
39383
+
640753019

21
1563447
1563746
+
651053122

22
35802
36665
+
640753019

23
3648
4475
−
651332959

24
36662
37501
+
640753019

25
11204
11776
+
647009874

26
11773
12132
+
647009874

27
10265
10696
+
647009874

28
4537618
4539336
+
646564624

29
1561697
1562869
+
651053122

30
51251
51370
−
647536393

31
154
357
−
643042634

32
23022
23267
+
647009874

33
19408
19923
+
647009874

34
1552497
1552712
+
651053122

35
1551079
1551729
+
651053122

36
1550023
1551075
+
651053122

37
6165
7229
+
647009874

38
4543715
4546123
−
646564624

39
1555
2055
−
651333542

40
2380
3411
−
647009874

41
68933
70240
+
642555219

42
2637299
2637790
+
646312028

43
2932956
2933891
+
644736389

44
32101
32916
−
646311959

45
4084530
4085237
−
651053007

46
21137
21952
−
637000354

47
4067283
4067942
+
651053007

48
2070
2927
−
651333149

49
1967759
1968439
+
637000205

50
78317
81286
−
646564501

TABLE 12a

Data for Klebsiella, particularly K. pneumoniae

Scaffold.External.

No.
Accession
Scaffold.Name
best_pv

1
NC_007384

Shigella sonnei Ss046: NC_007384
1.21395823682916e−119

2
NC_011083

Salmonella enterica subsp. enterica serovar Heidelberg str. SL476:
1.70517984237646e−115

NC_011083

3
NZ_ADWV01000045

Escherichia coli MS 107-1 E_coliMS107-1-1.0.1_Cont44.1:
3.12333368944279e−110

NZ_ADWV01000045

4
NC_009651

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid pKPN5:
1.8490215255217e−103

NC_009651

5
NZ_ABFH01000001

Salmonella enterica subsp. enterica serovar Virchow str. SL491,
4.16211077482132e−97

unfinished sequence: NZ_ABFH01000001

6
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
1.34397014479151e−80

7
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
1.21342816034335e−71

8
NZ_ACZD01000070

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
4.42089689687353e−61

contig00070: NZ_ACZD01000070

9
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
8.41004168548543e−61

10
NC_011282

Klebsiella pneumoniae 342 plasmid pKP187: NC_011282
8.41004168548543e−61

11
NZ_ACZD01000070

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
8.41004168548543e−61

contig00070: NZ_ACZD01000070

12
NZ_ADTP01000323

Escherichia coli MS 69-1 E_coli69-1-1.0_Cont630.1: NZ_ADTP01000323
4.94539115664213e−60

13
NC_009793

Citrobacter koseri ATCC BAA-895 plasmid pCKO3: NC_009793
5.71878021049123e−59

14
NZ_ACZD01000005

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
1.22977045856913e−58

contig00005: NZ_ACZD01000005

15
NZ_ACZD01000127

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
1.49068550300511e−58

contig00129: NZ_ACZD01000127

16
NZ_GG745515

Klebsiella sp. 1_1_55 genomic scaffold supercont1.8: NZ_GG745515
7.09566707309011e−58

17
NZ_AAJX01000089

Escherichia coli B171, unfinished sequence: NZ_AAJX01000089
1.65409147045657e−56

18
NZ_ACZD01000005

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
7.54090407593199e−55

contig00005: NZ_ACZD01000005

19
NZ_AFBO01000042

Klebsiella sp. MS 92-3 K_spMS92-3-l.0_Cont91.1: NZ_AFBO01000042
2.8348333685311e−54

20
NC_009649

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid pKPN3:
2.8348333685311e−54

NC_009649

21
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
2.83530891190408e−54

22
NC_009649

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid pKPN3:
4.89541334527925e−54

NC_009649

23
NZ_AFBO01000042

Klebsiella sp. MS 92-3 K_spMS92-3-l.0_Cont91.1: NZ_AFBO01000042
2.18592863711471e−53

24
NC_009649

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid pKPN3:
2.18592863711471e−53

NC_009649

25
NZ_ACZD01000127

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
1.08576020331202e−52

contig00129: NZ_ACZD01000127

26
NZ_ACZD01000127

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
1.37521017661703e−52

contig00129: NZ_ACZD01000127

27
NZ_ACZD01000127

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
2.1362800317976e−52

contig00129: NZ_ACZD01000127

28
NC_014121

Enterobacter cloacae subsp. cloacae ATCC 13047 chromosome:
2.21381524453565e−51

NC_014121

29
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
6.53846908249994e−51

30
NZ_GG745512

Klebsiella sp. 1_1_55 genomic scaffold supercont1.5: NZ_GG745512
2.78992804201171e−50

31
NZ_CAAZ01000154

Salmonella enterica subsp. enterica serovar Typhi str. E98-3139,
4.10919139010377e−50

unfinished sequence: NZ_CAAZ01000154

32
NZ_ACZD01000127

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
6.10670380866266e−50

contig00129: NZ_ACZD01000127

33
NZ_ACZD01000127

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
1.00996840886331e−49

contig00129: NZ_ACZD01000127

34
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
1.33344542353295e−48

35
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
3.00269800428115e−48

36
CP002910

Klebsiella pneumoniae KCTC 2242: CP002910
3.13126971411145e−48

37
NZ_ACZD01000127

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
3.13126971411145e−48

contig00129: NZ_ACZD01000127

38
NC_014121

Enterobacter cloacae subsp. cloacae ATCC 13047 chromosome:
3.79149056816214e−48

NC_014121

39
NZ_AFBO01000625

Klebsiella sp. MS 92-3 K_spMS92-3-1.0_Cont1175.2: NZ_AFBO01000625
2.5975548233422e−47

40
NZ_ACZD01000127

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884
1.05391699509183e−46

contig00129: NZ_ACZD01000127

41
NC_011092

Salmonella enterica subsp. enterica serovar Schwarzengrund str.
4.42178242563847e−46

CVM19633 plasmid pCVM19633_110: NC_011092

42
NC_013850

Klebsiella variicola At-22 chromosome: NC_013850
6.65483065085068e−46

43
NC_012912

Dickeya zeae Ech1591: NC_012912
1.05262166415392e−45

44
NC_013509

Edwardsiella tarda EIB202 plasmid pEIB202: NC_013509
1.24074600175825e−45

45
AP011957

Salmonella enterica subsp. enterica serovar Typhimurium str.
2.46270503642371e−45

T000240 DNA: AP011957

46
NC_006856

Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-
9.02631418377704e−45

B67 plasmid pSC138: NC_006856

47
AP011957

Salmonella enterica subsp. enterica serovar Typhimurium str.
3.37821430101762e−44

T000240 DNA: AP011957

48
NZ_AFBO01000232

Klebsiella sp. MS 92-3 K_spMS92-3-1.0_Cont505.1: NZ_AFBO01000232
4.87973844618098e−43

49
NC_004631

Salmonella enterica subsp. enterica serovar Typhi Ty2: NC_004631
1.54269244019591e−42

50
NC_006625

Klebsiella pneumoniae NTUH-K2044 plasmid pK2044: NC_006625
1.89874529968327e−42

TABLE 12b

Data for Klebsiella, particularly K. pneumoniae (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
TO
aminoglycoside

CRM; ETP; GM; LVX; P/T; TO; T/S

2
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
AUG
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

3
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; ETP; GM; LVX; P/T; TO; T/S

4
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; ETP; GM; LVX; P/T; TO; T/S

5
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; ETP; GM; LVX; P/T; TO; T/S

6
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

7
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

8
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

9
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

10
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

11
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

12
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
CAZ
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

13
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
AUG
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

14
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

15
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
TO
aminoglycoside

CRM; ETP; GM; LVX; P/T; TO; T/S

16
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

17
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; ETP; GM; LVX; P/T; TO; T/S

18
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

19
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
P/T
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

20
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
P/T
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

21
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
TO
aminoglycoside

CRM; ETP; GM; LVX; P/T; TO; T/S

22
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
P/T
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

23
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
P/T
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

24
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
P/T
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

25
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
TO
aminoglycoside

CRM; ETP; GM; LVX; P/T; TO; T/S

26
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
TO
aminoglycoside

CRM; ETP; GM; LVX; P/T; TO; T/S

27
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
TO
aminoglycoside

CRM; ETP; GM; LVX; P/T; TO; T/S

28
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

CRM; ETP; GM; LVX; P/T; TO; T/S

29
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

CRM; ETP; GM; LVX; P/T; TO; T/S

30
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

31
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

CRM; ETP; GM; LVX; P/T; TO; T/S

32
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

CRM; ETP; GM; LVX; P/T; TO; T/S

33
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

CRM; ETP; GM; LVX; P/T; TO; T/S

34
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

CRM; ETP; GM; LVX; P/T; TO; T/S

35
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

CRM; ETP; GM; LVX; P/T; TO; T/S

36
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

CRM; ETP; GM; LVX; P/T; TO; T/S

37
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

CRM; ETP; GM; LVX; P/T; TO; T/S

38
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

CRM; ETP; GM; LVX; P/T; TO; T/S

39
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; GM; LVX; P/T; TO; T/S

40
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

CRM; ETP; GM; LVX; P/T; TO; T/S

41
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
AUG
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

42
AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

ETP; LVX; P/T; TO; T/S

43
AUG; AZT; CAX; CAZ; CFT; CP; CPE; CRM;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

ETP; LVX; P/T; TO; T/S

44
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; ETP; GM; LVX; P/T; TO; T/S

45
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
TO
aminoglycoside

CRM; ETP; GM; LVX; P/T; TO; T/S

46
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
TO
aminoglycoside

CRM; ETP; GM; LVX; P/T; TO; T/S

47
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
AUG
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

48
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; ETP; GM; LVX; P/T; TO; T/S

49
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
ETP
lactam

CRM; ETP; GM; LVX; P/T; TO; T/S

50
A/S; AUG; AZT; CAX; CAZ; CFT; CP; CPE;
aminoglycoside; fluoroquinolone; lactam; other
T/S
other

CRM; ETP; GM; LVX; P/T; TO; T/S

TABLE 12c

Data for Klebsiella, particularly K. pneumoniae (continued)

No.
num_aminoglycoside
num_fluoroquinolone
num_lactam
num_other

1
2
2
10
1

2
2
2
10
1

3
2
2
10
1

4
2
2
10
1

5
2
2
10
1

6
2
2
10
1

7
2
2
10
1

8
2
2
10
1

9
2
2
10
1

10
2
2
10
1

11
2
2
10
1

12
2
2
10
1

13
2
2
10
1

14
2
2
10
1

15
2
2
10
1

16
2
2
10
1

17
2
2
10
1

18
2
2
10
1

19
2
2
10
1

20
2
2
10
1

21
2
2
10
1

22
2
2
10
1

23
2
2
10
1

24
2
2
10
1

25
2
2
10
1

26
2
2
10
1

27
2
2
10
1

28
2
2
10
1

29
2
2
10
1

30
2
2
10
1

31
2
2
10
1

32
2
2
10
1

33
2
2
10
1

34
2
2
10
1

35
2
2
10
1

36
2
2
10
1

37
2
2
10
1

38
2
2
10
1

39
2
2
9
1

40
2
2
10
1

41
2
2
10
1

42
1
2
9
1

43
1
2
9
1

44
2
2
10
1

45
2
2
10
1

46
2
2
10
1

47
2
2
10
1

48
2
2
10
1

49
2
2
10
1

50
2
2
10
1

TABLE 12d

Data for Klebsiella, particularly K. pneumoniae (continued)

No.
A/S_pv_adj
AUG_pv_adj
AZT_pv_adj
CAX_pv_adj
CAZ_pv_adj

1
1.28E−76
1.24E−105
4.06E−95
3.39E−95
5.99E−93

2
1.18E−98
1.71E−115
9.09E−91
6.55E−88
1.66E−96

3
1.08E−81
5.85E−86
2.76E−94
4.16E−97
6.84E−100

4
5.55E−76
3.05E−84
1.38E−91
2.64E−96
5.33E−94

5
1.22E−70
3.41E−71
1.41E−80
1.50E−83
6.22E−90

6
7.70E−21
1.03E−41
8.20E−48
2.50E−44
2.69E−46

7
8.54E−16
4.34E−29
4.54E−38
5.50E−34
1.34E−34

8
2.62E−12
1.74E−24
1.49E−26
2.74E−25
2.84E−24

9
5.20E−12
2.50E−24
3.69E−26
7.31E−25
7.66E−24

10
5.20E−12
2.50E−24
3.69E−26
7.31E−25
7.66E−24

11
5.20E−12
2.50E−24
3.69E−26
7.31E−25
7.66E−24

12
3.32E−43
1.75E−59
1.48E−54
9.28E−55
4.95E−60

13
2.41E−43
5.72E−59
4.20E−53
2.96E−53
2.14E−58

14
2.47E−16
8.57E−27
1.49E−34
1.96E−31
8.83E−33

15
1.72E−35
6.40E−55
1.25E−44
4.12E−43
1.61E−46

16
3.04E−18
5.19E−32
4.83E−36
2.23E−35
1.91E−32

17
1.02E−47
9.19E−45
1.85E−48
9.17E−53
6.18E−56

18
3.51E−17
3.04E−23
8.29E−30
1.21E−27
9.29E−29

19
1.03E−40
7.90E−52
1.41E−37
4.81E−39
9.97E−38

20
1.03E−40
7.90E−52
1.41E−37
4.81E−39
9.97E−38

21
8.56E−34
4.84E−53
8.75E−43
2.41E−41
9.43E−45

22
5.13E−42
1.10E−52
3.02E−38
9.55E−40
3.15E−38

23
1.11E−41
3.84E−52
1.00E−37
3.11E−39
8.03E−38

24
1.11E−41
3.84E−52
1.00E−37
3.11E−39
8.03E−38

25
8.85E−33
1.54E−51
2.83E−42
1.24E−40
2.88E−44

26
1.96E−32
2.54E−52
2.98E−42
1.41E−40
3.55E−44

27
5.12E−32
6.70E−50
1.84E−40
2.34E−38
1.33E−42

28
1.65E−30
3.00E−47
1.96E−38
1.37E−36
4.94E−39

29
4.43E−31
1.45E−47
2.29E−39
1.06E−37
3.63E−40

30
6.99E−12
2.37E−26
2.77E−24
5.28E−24
2.55E−26

31
2.78E−31
7.62E−46
1.11E−38
5.40E−37
1.95E−39

32
9.62E−32
1.45E−47
2.29E−39
1.06E−37
3.63E−40

33
2.27E−31
2.28E−47
3.20E−39
1.66E−37
5.77E−40

34
9.74E−28
9.40E−43
1.44E−35
7.30E−34
3.24E−36

35
1.57E−28
2.77E−42
6.21E−36
1.59E−34
2.14E−36

36
3.41E−27
2.34E−43
7.21E−36
4.53E−33
9.07E−37

37
3.41E−27
2.34E−43
7.21E−36
4.53E−33
9.07E−37

38
2.00E−30
7.61E−47
1.00E−38
1.06E−37
3.63E−40

39
8.29E−47
2.48E−33
3.67E−37
5.57E−42
2.74E−43

40
1.53E−27
6.97E−43
2.91E−36
2.70E−35
5.96E−38

41
1.75E−44
4.42E−46
2.16E−37
1.21E−36
1.12E−42

42
4.51E−02
4.66E−12
9.77E−17
3.13E−16
9.90E−15

43
5.37E−02
5.73E−12
1.27E−16
6.11E−16
1.15E−14

44
6.65E−31
4.17E−32
1.40E−25
3.69E−27
1.78E−29

45
6.15E−34
5.78E−41
2.29E−36
9.94E−38
1.48E−38

46
3.01E−32
3.12E−38
7.22E−37
3.96E−36
6.00E−37

47
4.35E−41
3.38E−44
1.49E−30
1.42E−33
1.82E−29

48
6.41E−31
1.63E−41
3.24E−33
2.26E−36
1.97E−31

49
2.54E−11
2.61E−18
8.71E−21
1.23E−18
1.87E−19

50
2.38E−23
3.76E−29
2.21E−27
4.97E−29
1.37E−29

TABLE 12e

Data for Klebsiella, particularly K. pneumoniae (continued)

No.
CFT_pv_adj
CP_pv_adj
CPE_pv_adj
CRM_pv_adj
ETP_pv_adj

1
2.17E−99
2.40E−85
2.31E−68
1.21E−82
1.87E−58

2
2.52E−83
1.28E−61
4.61E−66
7.83E−57
8.20E−51

3
3.93E−93
2.17E−58
2.89E−43
3.32E−73
3.54E−24

4
1.52E−90
4.25E−60
1.75E−43
2.59E−71
1.63E−23

5
3.61E−77
1.76E−47
1.47E−36
5.14E−62
6.31E−21

6
2.84E−46
1.53E−54
2.89E−63
1.06E−36
1.34E−80

7
8.43E−36
1.96E−43
3.06E−55
3.95E−29
1.21E−71

8
5.55E−27
2.63E−33
6.90E−40
1.01E−20
4.42E−61

9
1.58E−26
5.49E−33
1.32E−39
2.40E−20
8.41E−61

10
1.58E−26
5.49E−33
1.32E−39
2.40E−20
8.41E−61

11
1.58E−26
5.49E−33
1.32E−39
4.98E−21
8.41E−61

12
4.39E−54
4.96E−60
1.80E−51
7.75E−50
7.02E−53

13
1.26E−52
1.35E−58
1.72E−50
4.57E−49
3.71E−52

14
1.28E−31
2.00E−30
6.27E−42
1.20E−29
1.23E−58

15
2.05E−41
2.56E−52
7.76E−46
3.74E−32
5.20E−48

16
1.52E−36
2.10E−37
5.58E−48
5.62E−28
7.10E−58

17
9.26E−49
4.16E−22
1.22E−19
9.42E−36
5.55E−05

18
6.27E−28
1.02E−25
4.83E−36
7.62E−29
7.54E−55

19
9.92E−40
2.65E−39
2.28E−41
4.71E−28
1.10E−32

20
9.92E−40
2.65E−39
2.28E−41
4.71E−28
1.10E−32

21
1.47E−40
1.18E−49
1.74E−45
2.18E−32
1.46E−46

22
2.00E−40
6.22E−40
7.04E−42
1.08E−28
5.10E−33

23
6.77E−40
2.32E−39
3.78E−41
2.22E−28
3.70E−32

24
6.77E−40
2.32E−39
3.78E−41
2.22E−28
3.70E−32

25
4.69E−40
3.62E−49
1.06E−44
1.70E−33
2.11E−45

26
4.89E−40
1.97E−49
1.88E−45
2.34E−32
8.59E−46

27
5.94E−39
1.13E−47
2.46E−43
3.44E−33
1.93E−49

28
3.32E−36
2.21E−51
1.87E−44
1.56E−31
1.83E−41

29
2.69E−37
6.54E−51
4.48E−44
2.19E−30
3.44E−41

30
1.39E−24
6.75E−31
1.12E−35
5.11E−15
2.79E−50

31
1.34E−36
4.11E−50
1.67E−43
1.45E−31
8.85E−41

32
2.69E−37
6.11E−50
4.48E−44
2.19E−30
3.44E−41

33
6.74E−37
1.01E−49
6.91E−44
1.07E−30
4.69E−41

34
3.28E−34
1.33E−48
1.41E−40
1.52E−30
7.40E−43

35
3.72E−36
3.00E−48
1.67E−40
8.05E−31
2.56E−43

36
1.04E−34
3.13E−48
5.88E−41
1.06E−29
3.84E−43

37
1.04E−34
3.13E−48
5.88E−41
1.06E−29
3.84E−43

38
2.69E−37
3.79E−48
4.21E−43
9.89E−32
5.95E−40

39
2.84E−38
3.78E−14
1.15E−05
9.70E−31
9.25E−01

40
1.88E−36
1.05E−46
3.80E−41
1.01E−30
2.77E−43

41
4.01E−36
1.78E−19
2.93E−16
1.27E−21
2.46E−10

42
5.45E−16
4.08E−18
6.25E−28
7.56E−08
6.65E−46

43
1.13E−15
5.57E−18
9.82E−28
1.16E−07
1.05E−45

44
2.55E−25
6.58E−14
7.47E−22
3.89E−16
2.18E−20

45
5.14E−35
2.41E−27
5.02E−15
4.61E−29
2.22E−12

46
1.40E−36
2.78E−33
1.06E−29
5.12E−30
2.25E−28

47
3.46E−32
1.18E−32
1.62E−32
2.49E−29
1.62E−26

48
6.74E−36
1.36E−34
2.38E−34
1.27E−25
6.79E−29

49
9.64E−20
3.40E−22
1.36E−30
8.87E−18
1.54E−42

50
1.19E−26
1.97E−18
9.42E−19
1.46E−19
1.52E−12

TABLE 12f

Data for Klebsiella, particularly K. pneumoniae (continued)

No.
GM_pv_adj
LVX_pv_adj
P/T_pv_adj
TO_pv_adj
T/S_pv_adj

1
6.24E−60
3.97E−80
7.18E−96
1.21E−119
1.12E−106

2
6.10E−67
3.76E−55
1.20E−67
2.77E−105
3.59E−83

3
6.00E−68
3.14E−50
5.58E−70
1.37E−91
3.12E−110

4
3.06E−63
4.39E−52
7.17E−70
6.65E−91
1.85E−103

5
5.29E−59
6.80E−39
4.00E−51
1.40E−82
4.16E−97

6
5.64E−09
3.19E−59
3.01E−52
7.11E−48
1.50E−31

7
1.61E−05
6.12E−48
2.20E−40
1.45E−34
2.10E−20

8
1.57E−06
6.85E−37
6.06E−35
1.79E−29
2.02E−18

9
2.46E−06
1.41E−36
1.30E−34
3.62E−29
2.62E−18

10
2.46E−06
1.41E−36
1.30E−34
3.62E−29
2.62E−18

11
2.46E−06
1.41E−36
1.30E−34
3.62E−29
2.62E−18

12
2.30E−25
1.32E−53
6.01E−52
5.28E−59
5.07E−39

13
1.61E−25
2.14E−52
1.19E−50
1.22E−58
6.30E−38

14
6.89E−05
6.38E−32
9.66E−29
7.19E−31
3.05E−15

15
1.55E−23
1.89E−48
1.36E−48
1.49E−58
1.23E−46

16
7.14E−10
1.99E−38
1.30E−34
9.13E−37
1.47E−21

17
6.27E−40
9.96E−18
4.98E−31
1.50E−43
1.65E−56

18
7.35E−05
4.57E−28
1.61E−25
2.68E−27
2.50E−15

19
1.16E−19
5.28E−36
2.83E−54
2.59E−42
9.74E−48

20
1.16E−19
5.28E−36
2.83E−54
2.59E−42
9.74E−48

21
6.44E−22
5.93E−45
3.28E−47
2.84E−54
2.84E−46

22
6.19E−20
1.49E−36
4.90E−54
5.19E−43
1.61E−47

23
4.80E−20
5.67E−36
2.19E−53
1.90E−42
7.35E−49

24
1.78E−19
5.67E−36
2.19E−53
1.90E−42
6.83E−48

25
1.71E−21
3.92E−44
2.20E−46
1.09E−52
8.26E−45

26
1.49E−20
1.39E−44
1.02E−46
1.38E−52
9.52E−46

27
9.23E−19
4.68E−44
1.13E−48
2.14E−52
7.18E−42

28
1.04E−18
2.43E−47
2.68E−42
8.73E−48
1.22E−43

29
1.81E−19
6.48E−47
5.36E−42
7.69E−49
5.28E−43

30
1.67E−04
1.19E−33
1.48E−27
1.33E−24
2.01E−19

31
2.71E−19
3.53E−46
2.81E−41
2.57E−47
3.11E−43

32
3.53E−20
6.26E−46
5.36E−42
7.69E−49
5.57E−44

33
4.08E−20
9.51E−46
1.44E−41
1.11E−48
8.48E−44

34
9.00E−16
3.30E−45
1.53E−41
3.99E−46
1.50E−39

35
4.69E−14
4.82E−45
1.45E−39
3.68E−47
5.85E−39

36
6.72E−15
8.68E−45
4.34E−42
8.00E−45
1.33E−38

37
6.72E−15
8.68E−45
4.34E−42
8.00E−45
1.33E−38

38
4.79E−19
4.19E−45
5.36E−42
3.42E−47
5.28E−43

39
1.94E−40
1.06E−10
6.27E−21
4.23E−35
2.60E−47

40
1.53E−15
3.13E−43
2.72E−42
3.02E−45
1.22E−39

41
9.94E−38
3.55E−16
4.46E−22
7.61E−44
1.24E−41

42
2.34E−02
4.47E−21
3.44E−16
3.10E−15
2.24E−09

43
2.39E−02
1.02E−20
4.32E−16
6.38E−15
3.86E−09

44
3.44E−22
5.51E−13
6.56E−18
4.39E−24
1.24E−45

45
1.36E−21
1.14E−24
2.38E−33
2.46E−45
1.53E−29

46
1.36E−19
4.39E−32
1.03E−35
9.03E−45
5.01E−44

47
1.18E−14
5.29E−30
3.76E−40
3.55E−44
5.56E−38

48
4.91E−17
8.23E−33
1.06E−40
6.11E−39
4.88E−43

49
1.35E−04
2.25E−22
1.78E−19
5.28E−22
2.63E−12

50
8.68E−26
1.45E−15
1.73E−22
6.68E−34
1.90E−42

TABLE 12g

Data for Klebsiella, particularly K. pneumoniae (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
SSON_3896
aadA
YP_312670

2
SeHA_C1580
blaT
YP_002045448

3
HMPREF9345_05066

ZP_07100147

4
KPN_pKPN5p08201

YP_001338811
plasmid pKPN5

5
Salmoentericaenterica_010100000245

ZP_02702077

6
KPN2242_07235

AEJ97365

7
KPN2242_00750

AEJ96075

8
HMPREF0484_1390
mgtA
ZP_06014374

9
Kvar_3592

YP_003440504

10
KPK_A0103

YP_002235751
plasmid pKP187

11
HMPREF0484_1392
pacL
ZP_06014376

12
HMPREF9534_04427

ZP_07188952

13
CKO_pCKO3p06155

YP_001456633
plasmid pCKO3

14
HMPREF0484_0044
vmtV
ZP_06013029

15
HMPREF0484_2697

ZP_06015679

16
HMPREF0485_04762

ZP_06552358

17
EcolB_01004576

ZP_00708527

18
HMPREF0484_0046

ZP_06013031

19
HMPREF9538_00440

ZP_08302804

20
KPN_pKPN3p05893
ptxE
YP_001338502
plasmid pKPN3

21
KPN2242_07425

AEJ97403

22
KPN_pKPN3p05890
ptxB
YP_001338499
plasmid pKPN3

23
HMPREF9538_00443

ZP_08302807

24
KPN_pKPN3p05891
ptxC
YP_001338500
plasmid pKPN3

25
HMPREF0484_2686

ZP_06015668

26
HMPREF0484_2687
gpw
ZP_06015669

27
HMPREF0484_2684

ZP_06015666

28
ECL_04426

YP_003614904

29
KPN2242_07415

AEJ97401

30
HMPREF0485_03923

ZP_06551519

31
Salmonellentericaenterica_010100016432

ZP_03412648

32
HMPREF0484_2698

ZP_06015680

33
HMPREF0484_2694
fii
ZP_06015676

34
KPN2242_07345

AEJ97387

35
KPN2242_07330

AEJ97384

36
KPN2242_07325

AEJ97383

37
HMPREF0484_2676

ZP_06015658

38
ECL_04434

YP_003614912

39
HMPREF9538_04737

ZP_08307036

40
HMPREF0484_2673

ZP_06015655

41
SeSA_B0079

YP_002112958
plasmid

pCVM19633_110

42
Kvar_2527

YP_003439449

43
Dd1591_2579

YP_003004893

44
ETAE_p041
folP
YP_003297635
plasmid pEIB202

45
STMDT12_C39340

BAJ38877

46
SC026
aph
YP_209331
plasmid pSC138

47
STMDT12_C39170

BAJ38860

48
HMPREF9538_01820

ZP_08304144

49
t1924
exo
NP_805691

50
pK2044_00525

YP_001687935
plasmid pK2044

TABLE 12h

Data for Klebsiella, particularly K. pneumoniae (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
4110458
4111246
−
640427102

2
1525960
1526820
+
642555218

3
4715
5554
−
648294624

4
34908
35255
−
640753021

5
36757
37062
+
641778223

6
1535907
1536932
−
651053122

7
159235
160521
−
651053122

8
2865
3848
−
647009817

9
3765814
3768501
−
646312028

10
67987
70674
+
643348532

11
4691
5551
−
647009817

12
2120
2368
+
648289812

13
8632
8931
+
640753081

14
12911
13663
+
647009752

15
20402
22975
+
647009874

16
93128
94558
+
647536396

17
3555
4568
+
638359041

18
14573
15328
+
647009752

19
933
1943
−
651332959

20
38514
39383
+
640753019

21
1563447
1563746
+
651053122

22
35802
36665
+
640753019

23
3648
4475
−
651332959

24
36662
37501
+
640753019

25
11204
11776
+
647009874

26
11773
12132
+
647009874

27
10265
10696
+
647009874

28
4537618
4539336
+
646564624

29
1561697
1562869
+
651053122

30
51251
51370
−
647536393

31
154
357
−
643042634

32
23022
23267
+
647009874

33
19408
19923
+
647009874

34
1552497
1552712
+
651053122

35
1551079
1551729
+
651053122

36
1550023
1551075
+
651053122

37
6165
7229
+
647009874

38
4543715
4546123
−
646564624

39
1555
2055
−
651333542

40
2380
3411
−
647009874

41
68933
70240
+
642555219

42
2637299
2637790
+
646312028

43
2932956
2933891
+
644736389

44
32101
32916
−
646311959

45
4084530
4085237
−
651053007

46
21137
21952
−
637000354

47
4067283
4067942
+
651053007

48
2070
2927
−
651333149

49
1967759
1968439
+
637000205

50
78317
81286
−
646564501

Example 7: Proteus, particularly Proteus mirabilis, Proteus penneri and/or Proteus vulgaris

The procedure was carried out as in Example 1, except that the following microorganisms were used:

Bacterial Strains

The inventors selected 582 Proteus strains from the microbiology strain collection at Siemens Healthcare Diagnostics (West Sacramento, Calif.) for susceptibility testing and whole genome sequencing.

From MetaRef, 2318 centroids of Proteus species were used as reference sequences.

The results for Proteus are shown in Tables 13 (corresponding to Table 1) and 14 (corresponding to Table 2).

TABLE 13a

Data for Proteus species

Scaffold.External.

No.
Accession
Scaffold.Name
best_pv

1
NZ_ABVP01000020

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont338: NZ_ABVP01000020
9.1377556355866E−62

2
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866E−62

3
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866E−62

4
NZ_ABVP01000023

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont336: NZ_ABVP01000023
9.1377556355866E−62

5
NZ_ABVP01000026

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont348: NZ_ABVP01000026
9.1377556355866E−62

6
NZ_ABVP01000019

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont6.1: NZ_ABVP01000019
9.1377556355866E−62

7
NZ_ABVP01000021

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont356: NZ_ABVP01000021
9.1377556355866E−62

8
NC_010554

Proteus mirabilis HI4320: NC_010554
9.1377556355866E−62

9
NZ_ABVP01000022

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont341: NZ_ABVP01000022
9.1377556355866E−62

10
NZ_ABVP01000026

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont348: NZ_ABVP01000026
9.1377556355866E−62

11
NZ_ABVP01000026

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont348: NZ_ABVP01000026
9.1377556355866E−62

12
NZ_ABVP01000014

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont350: NZ_ABVP01000014
9.1377556355866E−62

13
NZ_ABVP01000026

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont348: NZ_ABVP01000026
9.1377556355866E−62

14
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866E−62

15
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866E−62

16
NC_010554

Proteus mirabilis HI4320: NC_010554
9.1377556355866E−62

17
NZ_ABVP01000022

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont341: NZ_ABVP01000022
9.1377556355866E−62

18
NZ_ACLE01000064

Proteus mirabilis ATCC 29906 contig00088: NZ_ACLE01000064
9.1377556355866E−62

19
NZ_ABVP01000026

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont348: NZ_ABVP01000026
9.1377556355866E−62

20
NZ_ABVP01000026

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont348: NZ_ABVP01000026
9.1377556355866E−62

21
NZ_ABVP01000026

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont348: NZ_ABVP01000026
9.1377556355866E−62

22
NZ_ABVP01000022

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont341: NZ_ABVP01000022
9.1377556355866E−62

23
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866E−62

24
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866E−62

25
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866E−62

26
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866E−62

27
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866E−62

28
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866E−62

29
NC_010554

Proteus mirabilis HI4320: NC_010554
9.1377556355866E−62

30
NZ_ABVP01000021

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont356: NZ_ABVP01000021
9.1377556355866E−62

31
NZ_ABVP01000020

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont338: NZ_ABVP01000020
9.1377556355866E−62

32
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866E−62

33
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866E−62

34
NZ_ABVP01000023

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont336: NZ_ABVP01000023
9.1377556355866E−62

35
NZ_ABVP01000022

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont341: NZ_ABVP01000022
9.1377556355866E−62

36
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866E−62

37
NZ_ABVP01000024

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont334: NZ_ABVP01000024
9.1377556355866E−62

38
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866E−62

39
NC_010554

Proteus mirabilis HI4320: NC_010554
9.1377556355866E−62

40
NZ_ABVP01000019

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont6.1: NZ_ABVP01000019
9.1377556355866E−62

41
NZ_ABVP01000019

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont6.1: NZ_ABVP01000019
9.1377556355866E−62

42
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866E−62

43
NZ_ABVP01000020

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont338: NZ_ABVP01000020
9.1377556355866E−62

44
NZ_ABVP01000023

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont336: NZ_ABVP01000023
9.1377556355866E−62

45
NZ_ABVP01000026

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont348: NZ_ABVP01000026
9.1377556355866E−62

46
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866E−62

47
NZ_ABVP01000021

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont356: NZ_ABVP01000021
9.1377556355866E−62

48
NZ_ACLE01000079

Proteus mirabilis ATCC 29906 contig00105: NZ_ACLE01000079
9.1377556355866E−62

49
NC_010554

Proteus mirabilis HI4320: NC_010554
9.1377556355866E−62

50
NZ_ABVP01000023

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont336: NZ_ABVP01000023
9.1377556355866E−62

TABLE 13b

Data for Proteus species (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

2
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

3
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

4
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

5
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

6
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

7
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

8
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

9
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

10
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

11
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

12
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

13
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

14
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

15
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

16
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

17
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

18
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

19
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

20
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

21
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

22
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

23
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

24
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

25
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

26
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

27
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

28
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

29
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

30
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

31
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

32
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

33
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

34
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

35
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

36
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

37
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

38
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

39
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

40
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

41
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

42
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

43
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

44
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

45
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

46
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

47
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

48
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

49
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

50
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

TABLE 13c

Data for Proteus species (continued)

No.
num_aminoglycoside
num_fluoroquinolone
num_lactam
num_other

1
2
2
3
1

2
2
2
3
1

3
2
2
3
1

4
2
2
3
1

5
2
2
3
1

6
2
2
3
1

7
2
2
3
1

8
2
2
3
1

9
2
2
3
1

10
2
2
3
1

11
2
2
3
1

12
2
2
3
1

13
2
2
3
1

14
2
2
3
1

15
2
2
3
1

16
2
2
3
1

17
2
2
3
1

18
2
2
3
1

19
2
2
3
1

20
2
2
3
1

21
2
2
3
1

22
2
2
3
1

23
2
2
3
1

24
2
2
3
1

25
2
2
3
1

26
2
2
3
1

27
2
2
3
1

28
2
2
3
1

29
2
2
3
1

30
2
2
3
1

31
2
2
3
1

32
2
2
3
1

33
2
2
3
1

34
2
2
3
1

35
2
2
3
1

36
2
2
3
1

37
2
2
3
1

38
2
2
3
1

39
2
2
3
1

40
2
2
3
1

41
2
2
3
1

42
2
2
3
1

43
2
2
3
1

44
2
2
3
1

45
2
2
3
1

46
2
2
3
1

47
2
2
3
1

48
2
2
3
1

49
2
2
3
1

50
2
2
3
1

TABLE 13d

Data for Proteus species (continued)

No.
AM_pv_adj
A/S_pv_adj
CAX_pv_adj
CP_pv_adj
CRM_pv_adj

1
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

2
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

3
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

4
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

5
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

6
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

7
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

8
5.45E−37
9.36E−01
4.09E−17
7.21E−08
9.14E−62

9
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

10
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

11
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

12
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

13
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

14
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

15
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

16
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

17
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

18
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

19
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

20
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

21
1.07E−35
9.36E−01
8.67E−17
1.70E−08
9.14E−62

22
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

23
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

24
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

25
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

26
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

27
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

28
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

29
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

30
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

31
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

32
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

33
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

34
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

35
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

36
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

37
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

38
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

39
5.45E−37
9.36E−01
4.09E−17
6.06E−09
9.14E−62

40
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

41
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

42
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

43
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

44
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

45
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

46
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

47
1.07E−35
9.36E−01
8.67E−17
1.70E−08
9.14E−62

48
6.31E−38
5.69E−01
1.13E−16
4.44E−07
9.14E−62

49
1.56E−36
8.45E−01
2.42E−17
1.26E−07
9.14E−62

50
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

TABLE 13e

Data for Proteus species (continued)

No.
GM_pv_adj
LVX_pv_adj
TO_pv_adj
T/S_pv_adj

1
3.39E−06
1.43E−06
6.08E−05
2.82E−06

2
3.39E−06
1.43E−06
6.08E−05
2.82E−06

3
3.39E−06
1.43E−06
6.08E−05
2.82E−06

4
3.39E−06
1.43E−06
6.08E−05
2.82E−06

5
3.39E−06
1.43E−06
6.08E−05
2.82E−06

6
3.39E−06
1.43E−06
6.08E−05
2.82E−06

7
3.39E−06
1.43E−06
6.08E−05
2.82E−06

8
4.54E−05
4.64E−06
3.83E−05
1.26E−05

9
3.39E−06
1.43E−06
6.08E−05
2.82E−06

10
3.39E−06
1.43E−06
6.08E−05
2.82E−06

11
3.39E−06
1.43E−06
6.08E−05
2.82E−06

12
3.39E−06
1.43E−06
6.08E−05
2.82E−06

13
3.39E−06
1.43E−06
6.08E−05
2.82E−06

14
3.39E−06
1.43E−06
6.08E−05
2.82E−06

15
3.39E−06
1.43E−06
6.08E−05
2.82E−06

16
3.39E−06
1.43E−06
6.08E−05
2.82E−06

17
3.39E−06
1.43E−06
6.08E−05
2.82E−06

18
3.39E−06
1.43E−06
6.08E−05
2.82E−06

19
3.39E−06
1.43E−06
6.08E−05
2.82E−06

20
3.39E−06
1.43E−06
6.08E−05
2.82E−06

21
5.45E−06
1.43E−06
6.08E−05
4.40E−06

22
3.39E−06
1.43E−06
6.08E−05
2.82E−06

23
3.39E−06
1.43E−06
6.08E−05
2.82E−06

24
3.39E−06
1.43E−06
6.08E−05
2.82E−06

25
3.39E−06
1.43E−06
6.08E−05
2.82E−06

26
3.39E−06
1.43E−06
6.08E−05
2.82E−06

27
3.39E−06
1.43E−06
6.08E−05
2.82E−06

28
3.39E−06
1.43E−06
6.08E−05
2.82E−06

29
3.39E−06
1.43E−06
6.08E−05
2.82E−06

30
3.39E−06
1.43E−06
6.08E−05
2.82E−06

31
3.39E−06
1.43E−06
6.08E−05
2.82E−06

32
3.39E−06
1.43E−06
6.08E−05
2.82E−06

33
3.39E−06
1.43E−06
6.08E−05
2.82E−06

34
3.39E−06
1.43E−06
6.08E−05
2.82E−06

35
3.39E−06
1.43E−06
6.08E−05
2.82E−06

36
3.39E−06
1.43E−06
6.08E−05
2.82E−06

37
3.39E−06
1.43E−06
6.08E−05
2.82E−06

38
3.39E−06
1.43E−06
6.08E−05
2.82E−06

39
4.54E−05
8.81E−07
4.61E−04
1.26E−05

40
3.39E−06
1.43E−06
6.08E−05
2.82E−06

41
3.39E−06
1.43E−06
6.08E−05
2.82E−06

42
3.39E−06
1.43E−06
6.08E−05
2.82E−06

43
3.39E−06
1.43E−06
6.08E−05
2.82E−06

44
3.39E−06
1.43E−06
6.08E−05
2.82E−06

45
3.39E−06
1.43E−06
6.08E−05
2.82E−06

46
3.39E−06
1.43E−06
6.08E−05
2.82E−06

47
5.45E−06
1.43E−06
6.08E−05
4.40E−06

48
1.60E−03
2.08E−05
4.47E−04
7.97E−06

49
3.39E−06
7.10E−06
6.19E−05
2.82E−06

50
3.39E−06
1.43E−06
6.08E−05
2.82E−06

TABLE 13f

Data for Proteus species (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
PROPEN_00658
ZP_03802316

2
PROPEN_02821
ZP_03804437

3
PROPEN_02837
ZP_03804453

4
PROPEN_01744
ZP_03803381

5
PROPEN_04772
ZP_03806369

6
PROPEN_00566
ZP_03802226

7
PROPEN_00937
ZP_03802594

8
PMI0230
YP_002150011

9
PROPEN_01382
ZP_03803029

10
PROPEN_04308
ZP_03805908

11
PROPEN_03726
ZP_03805332

12
PROPEN_00113
ZP_03801788

13
PROPEN_04501
ZP_03806101

14
PROPEN_02952
ZP_03804567

15
PROPEN_03365
ZP_03804978

16
PMI3610
YP_002153285

17
PROPEN_01429
ZP_03803076

18
HMPREF0693_2570
ZP_03841679

19
PROPEN_04448
ZP_03806048

20
PROPEN_04169
ZP_03805774

21
PROPEN_04170
ZP_03805775

22
PROPEN_01358
ZP_03803005

23
PROPEN_02831
ZP_03804447

24
PROPEN_03253
ZP_03804866

25
PROPEN_03536
ZP_03805144

26
PROPEN_03368
ZP_03804981

27
PROPEN_03235
ZP_03804848

28
PROPEN_03484
ZP_03805093

29
PMI3521
YP_002153198

30
PROPEN_00908
ZP_03802565

31
PROPEN_00654
ZP_03802312

32
PROPEN_03299
ZP_03804912

33
PROPEN_03648
ZP_03805254

34
PROPEN_01652
ZP_03803297

35
PROPEN_01314
ZP_03802961

36
PROPEN_02647
ZP_03804265

37
PROPEN_02468
ZP_03804091

38
PROPEN_03281
ZP_03804894

39
PMI0234
YP_002150015

40
PROPEN_00544
ZP_03802209

41
PROPEN_00500
ZP_03802168

42
PROPEN_02930
ZP_03804546

43
PROPEN_00758
ZP_03802416

44
PROPEN_01810
ZP_03803447

45
PROPEN_04133
ZP_03805738

46
PROPEN_02599
ZP_03804222

47
PROPEN_01149
ZP_03802800

48
HMPREF0693_3224
ZP_03842333

49
PMI3023
YP_002152722

50
PROPEN_01623
ZP_03803268

TABLE 13g

Data for Proteus species (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
42080
42412
+
643889140

2
185454
186779
−
643889145

3
201544
202038
+
643889145

4
122639
124333
−
643889143

5
853119
853544
+
643889146

6
57621
58505
−
643889139

7
44265
45014
+
643889141

8
273673
274467
+
642555123

9
115768
116316
−
643889142

10
495434
496444
−
643889146

11
53270
53875
−
643889146

12
28708
29421
−
643889134

13
639163
640215
−
643889146

14
285467
286066
−
643889145

15
601755
602153
−
643889145

16
3948188
3948604
−
642555123

17
160792
161340
+
643889142

18
122510
123433
−
643905827

19
593048
593632
−
643889146

20
390159
391736
+
643889146

21
391736
392329
+
643889146

22
99554
100063
−
643889142

23
195059
197509
−
643889145

24
511254
511508
−
643889145

25
711617
713044
+
643889145

26
603518
605086
−
643889145

27
500249
500962
+
643889145

28
676951
677898
−
643889145

29
3840767
3841663
−
642555123

30
23566
24027
−
643889141

31
39429
39599
+
643889140

32
548639
549616
−
643889145

33
797158
797820
+
643889145

34
48570
49238
−
643889143

35
63033
63515
+
643889142

36
56690
57196
−
643889145

37
284519
287461
+
643889144

38
535246
536289
+
643889145

39
279605
281008
+
642555123

40
44077
44439
−
643889139

41
12698
14710
−
643889139

42
268387
269874
−
643889145

43
106241
106837
−
643889140

44
175312
176142
+
643889143

45
362809
363438
+
643889146

46
23652
24185
+
643889145

47
200043
201293
−
643889141

48
37235
38317
−
643905842

49
3320488
3321087
+
642555123

50
30478
31134
+
643889143

TABLE 14a

Data for Proteus species

Scaffold.External.

No.
Accession
Scaffold.Name
best_pv

1
NZ_ABVP01000020

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont338: NZ_ABVP01000020
9.1377556355866e−62

2
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866e−62

3
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866e−62

4
NZ_ABVP01000023

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont336: NZ_ABVP01000023
9.1377556355866e−62

5
NZ_ABVP01000026

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont348: NZ_ABVP01000026
9.1377556355866e−62

6
NZ_ABVP01000019

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont6.1: NZ_ABVP01000019
9.1377556355866e−62

7
NZ_ABVP01000021

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont356: NZ_ABVP01000021
9.1377556355866e−62

8
NC_010554

Proteus mirabilis HI4320: NC_010554
9.1377556355866e−62

9
NZ_ABVP01000022

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont341: NZ_ABVP01000022
9.1377556355866e−62

10
NZ_ABVP01000026

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont348: NZ_ABVP01000026
9.1377556355866e−62

11
NZ_ABVP01000026

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont348: NZ_ABVP01000026
9.1377556355866e−62

12
NZ_ABVP01000014

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont350: NZ_ABVP01000014
9.1377556355866e−62

13
NZ_ABVP01000026

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont348: NZ_ABVP01000026
9.1377556355866e−62

14
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866e−62

15
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866e−62

16
NC_010554

Proteus mirabilis HI4320: NC_010554
9.1377556355866e−62

17
NZ_ABVP01000022

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont341: NZ_ABVP01000022
9.1377556355866e−62

18
NZ_ACLE01000064

Proteus mirabilis ATCC 29906 contig00088: NZ_ACLE01000064
9.1377556355866e−62

19
NZ_ABVP01000026

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont348: NZ_ABVP01000026
9.1377556355866e−62

20
NZ_ABVP01000026

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont348: NZ_ABVP01000026
9.1377556355866e−62

21
NZ_ABVP01000026

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont348: NZ_ABVP01000026
9.1377556355866e−62

22
NZ_ABVP01000022

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont341: NZ_ABVP01000022
9.1377556355866e−62

23
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866e−62

24
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866e−62

25
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866e−62

26
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866e−62

27
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866e−62

28
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866e−62

29
NC_010554

Proteus mirabilis HI4320: NC_010554
9.1377556355866e−62

30
NZ_ABVP01000021

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont356: NZ_ABVP01000021
9.1377556355866e−62

31
NZ_ABVP01000020

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont338: NZ_ABVP01000020
9.1377556355866e−62

32
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866e−62

33
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866e−62

34
NZ_ABVP01000023

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont336: NZ_ABVP01000023
9.1377556355866e−62

35
NZ_ABVP01000022

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont341: NZ_ABVP01000022
9.1377556355866e−62

36
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866e−62

37
NZ_ABVP01000024

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont334: NZ_ABVP01000024
9.1377556355866e−62

38
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866e−62

39
NC_010554

Proteus mirabilis HI4320: NC_010554
9.1377556355866e−62

40
NZ_ABVP01000019

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont6.1: NZ_ABVP01000019
9.1377556355866e−62

41
NZ_ABVP01000019

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont6.1: NZ_ABVP01000019
9.1377556355866e−62

42
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866e−62

43
NZ_ABVP01000020

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont338: NZ_ABVP01000020
9.1377556355866e−62

44
NZ_ABVP01000023

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont336: NZ_ABVP01000023
9.1377556355866e−62

45
NZ_ABVP01000026

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont348: NZ_ABVP01000026
9.1377556355866e−62

46
NZ_ABVP01000025

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont344: NZ_ABVP01000025
9.1377556355866e−62

47
NZ_ABVP01000021

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont356: NZ_ABVP01000021
9.1377556355866e−62

48
NZ_ACLE01000079

Proteus mirabilis ATCC 29906 contig00105: NZ_ACLE01000079
9.1377556355866e−62

49
NC_010554

Proteus mirabilis HI4320: NC_010554
9.1377556355866e−62

50
NZ_ABVP01000023

Proteus penneri ATCC 35198 P_penneri-1.1.1_Cont336: NZ_ABVP01000023
9.1377556355866e−62

TABLE 14b

Data for Proteus species (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

2
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

3
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

4
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

5
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

6
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

7
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

8
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

9
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

10
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

11
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

12
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

13
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

14
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

15
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

16
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

17
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

18
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

19
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

20
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

21
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

22
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

23
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

24
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

25
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

26
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

27
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

28
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

29
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

30
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

31
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

32
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

33
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

34
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

35
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

36
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

37
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

38
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

39
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

40
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

41
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

42
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

43
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

44
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

45
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

46
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

47
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

48
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

49
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

50
AM; CAX; CP; CRM; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CRM
lactam

TABLE 14c

Data for Proteus species (continued)

No.
num_aminoglycoside
num_fluoroquinolone
num_lactam
num_other

1
2
2
3
1

2
2
2
3
1

3
2
2
3
1

4
2
2
3
1

5
2
2
3
1

6
2
2
3
1

7
2
2
3
1

8
2
2
3
1

9
2
2
3
1

10
2
2
3
1

11
2
2
3
1

12
2
2
3
1

13
2
2
3
1

14
2
2
3
1

15
2
2
3
1

16
2
2
3
1

17
2
2
3
1

18
2
2
3
1

19
2
2
3
1

20
2
2
3
1

21
2
2
3
1

22
2
2
3
1

23
2
2
3
1

24
2
2
3
1

25
2
2
3
1

26
2
2
3
1

27
2
2
3
1

28
2
2
3
1

29
2
2
3
1

30
2
2
3
1

31
2
2
3
1

32
2
2
3
1

33
2
2
3
1

34
2
2
3
1

35
2
2
3
1

36
2
2
3
1

37
2
2
3
1

38
2
2
3
1

39
2
2
3
1

40
2
2
3
1

41
2
2
3
1

42
2
2
3
1

43
2
2
3
1

44
2
2
3
1

45
2
2
3
1

46
2
2
3
1

47
2
2
3
1

48
2
2
3
1

49
2
2
3
1

50
2
2
3
1

TABLE 14d

Data for Proteus species (continued)

No.
AM_pv_adj
A/S_pv_adj
CAX_pv_adj
CP_pv_adj
CRM_pv_adj

1
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

2
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

3
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

4
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

5
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

6
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

7
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

8
5.45E−37
9.36E−01
4.09E−17
7.21E−08
9.14E−62

9
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

10
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

11
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

12
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

13
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

14
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

15
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

16
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

17
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

18
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

19
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

20
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

21
1.07E−35
9.36E−01
8.67E−17
1.70E−08
9.14E−62

22
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

23
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

24
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

25
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

26
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

27
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

28
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

29
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

30
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

31
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

32
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

33
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

34
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

35
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

36
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

37
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

38
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

39
5.45E−37
9.36E−01
4.09E−17
6.06E−09
9.14E−62

40
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

41
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

42
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

43
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

44
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

45
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

46
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

47
1.07E−35
9.36E−01
8.67E−17
1.70E−08
9.14E−62

48
6.31E−38
5.69E−01
1.13E−16
4.44E−07
9.14E−62

49
1.56E−36
8.45E−01
2.42E−17
1.26E−07
9.14E−62

50
3.94E−36
1
1.38E−16
1.03E−08
9.14E−62

TABLE 14e

Data for Proteus species (continued)

No.
GM_pv_adj
LVX_pv_adj
TO_pv_adj
T/S_pv_adj

1
3.39E−06
1.43E−06
6.08E−05
2.82E−06

2
3.39E−06
1.43E−06
6.08E−05
2.82E−06

3
3.39E−06
1.43E−06
6.08E−05
2.82E−06

4
3.39E−06
1.43E−06
6.08E−05
2.82E−06

5
3.39E−06
1.43E−06
6.08E−05
2.82E−06

6
3.39E−06
1.43E−06
6.08E−05
2.82E−06

7
3.39E−06
1.43E−06
6.08E−05
2.82E−06

8
4.54E−05
4.64E−06
3.83E−05
1.26E−05

9
3.39E−06
1.43E−06
6.08E−05
2.82E−06

10
3.39E−06
1.43E−06
6.08E−05
2.82E−06

11
3.39E−06
1.43E−06
6.08E−05
2.82E−06

12
3.39E−06
1.43E−06
6.08E−05
2.82E−06

13
3.39E−06
1.43E−06
6.08E−05
2.82E−06

14
3.39E−06
1.43E−06
6.08E−05
2.82E−06

15
3.39E−06
1.43E−06
6.08E−05
2.82E−06

16
3.39E−06
1.43E−06
6.08E−05
2.82E−06

17
3.39E−06
1.43E−06
6.08E−05
2.82E−06

18
3.39E−06
1.43E−06
6.08E−05
2.82E−06

19
3.39E−06
1.43E−06
6.08E−05
2.82E−06

20
3.39E−06
1.43E−06
6.08E−05
2.82E−06

21
5.45E−06
1.43E−06
6.08E−05
4.40E−06

22
3.39E−06
1.43E−06
6.08E−05
2.82E−06

23
3.39E−06
1.43E−06
6.08E−05
2.82E−06

24
3.39E−06
1.43E−06
6.08E−05
2.82E−06

25
3.39E−06
1.43E−06
6.08E−05
2.82E−06

26
3.39E−06
1.43E−06
6.08E−05
2.82E−06

27
3.39E−06
1.43E−06
6.08E−05
2.82E−06

28
3.39E−06
1.43E−06
6.08E−05
2.82E−06

29
3.39E−06
1.43E−06
6.08E−05
2.82E−06

30
3.39E−06
1.43E−06
6.08E−05
2.82E−06

31
3.39E−06
1.43E−06
6.08E−05
2.82E−06

32
3.39E−06
1.43E−06
6.08E−05
2.82E−06

33
3.39E−06
1.43E−06
6.08E−05
2.82E−06

34
3.39E−06
1.43E−06
6.08E−05
2.82E−06

35
3.39E−06
1.43E−06
6.08E−05
2.82E−06

36
3.39E−06
1.43E−06
6.08E−05
2.82E−06

37
3.39E−06
1.43E−06
6.08E−05
2.82E−06

38
3.39E−06
1.43E−06
6.08E−05
2.82E−06

39
4.54E−05
8.81E−07
4.61E−04
1.26E−05

40
3.39E−06
1.43E−06
6.08E−05
2.82E−06

41
3.39E−06
1.43E−06
6.08E−05
2.82E−06

42
3.39E−06
1.43E−06
6.08E−05
2.82E−06

43
3.39E−06
1.43E−06
6.08E−05
2.82E−06

44
3.39E−06
1.43E−06
6.08E−05
2.82E−06

45
3.39E−06
1.43E−06
6.08E−05
2.82E−06

46
3.39E−06
1.43E−06
6.08E−05
2.82E−06

47
5.45E−06
1.43E−06
6.08E−05
4.40E−06

48
1.60E−03
2.08E−05
4.47E−04
7.97E−06

49
3.39E−06
7.10E−06
6.19E−05
2.82E−06

50
3.39E−06
1.43E−06
6.08E−05
2.82E−06

TABLE 14f

Data for Proteus species (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
PROPEN_00658
ZP_03802316

2
PROPEN_02821
ZP_03804437

3
PROPEN_02837
ZP_03804453

4
PROPEN_01744
ZP_03803381

5
PROPEN_04772
ZP_03806369

6
PROPEN_00566
ZP_03802226

7
PROPEN_00937
ZP_03802594

8
PMI0230
YP_002150011

9
PROPEN_01382
ZP_03803029

10
PROPEN_04308
ZP_03805908

11
PROPEN_03726
ZP_03805332

12
PROPEN_00113
ZP_03801788

13
PROPEN_04501
ZP_03806101

14
PROPEN_02952
ZP_03804567

15
PROPEN_03365
ZP_03804978

16
PMI3610
YP_002153285

17
PROPEN_01429
ZP_03803076

18
HMPREF0693_2570
ZP_03841679

19
PROPEN_04448
ZP_03806048

20
PROPEN_04169
ZP_03805774

21
PROPEN_04170
ZP_03805775

22
PROPEN_01358
ZP_03803005

23
PROPEN_02831
ZP_03804447

24
PROPEN_03253
ZP_03804866

25
PROPEN_03536
ZP_03805144

26
PROPEN_03368
ZP_03804981

27
PROPEN_03235
ZP_03804848

28
PROPEN_03484
ZP_03805093

29
PMI3521
YP_002153198

30
PROPEN_00908
ZP_03802565

31
PROPEN_00654
ZP_03802312

32
PROPEN_03299
ZP_03804912

33
PROPEN_03648
ZP_03805254

34
PROPEN_01652
ZP_03803297

35
PROPEN_01314
ZP_03802961

36
PROPEN_02647
ZP_03804265

37
PROPEN_02468
ZP_03804091

38
PROPEN_03281
ZP_03804894

39
PMI0234
YP_002150015

40
PROPEN_00544
ZP_03802209

41
PROPEN_00500
ZP_03802168

42
PROPEN_02930
ZP_03804546

43
PROPEN_00758
ZP_03802416

44
PROPEN_01810
ZP_03803447

45
PROPEN_04133
ZP_03805738

46
PROPEN_02599
ZP_03804222

47
PROPEN_01149
ZP_03802800

48
HMPREF0693_3224
ZP_03842333

49
PMI3023
YP_002152722

50
PROPEN_01623
ZP_03803268

TABLE 14g

Data for Proteus species (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
42080
42412
+
643889140

2
185454
186779
−
643889145

3
201544
202038
+
643889145

4
122639
124333
−
643889143

5
853119
853544
+
643889146

6
57621
58505
−
643889139

7
44265
45014
+
643889141

8
273673
274467
+
642555123

9
115768
116316
−
643889142

10
495434
496444
−
643889146

11
53270
53875
−
643889146

12
28708
29421
−
643889134

13
639163
640215
−
643889146

14
285467
286066
−
643889145

15
601755
602153
−
643889145

16
3948188
3948604
−
642555123

17
160792
161340
+
643889142

18
122510
123433
−
643905827

19
593048
593632
−
643889146

20
390159
391736
+
643889146

21
391736
392329
+
643889146

22
99554
100063
−
643889142

23
195059
197509
−
643889145

24
511254
511508
−
643889145

25
711617
713044
+
643889145

26
603518
605086
−
643889145

27
500249
500962
+
643889145

28
676951
677898
−
643889145

29
3840767
3841663
−
642555123

30
23566
24027
−
643889141

31
39429
39599
+
643889140

32
548639
549616
−
643889145

33
797158
797820
+
643889145

34
48570
49238
−
643889143

35
63033
63515
+
643889142

36
56690
57196
−
643889145

37
284519
287461
+
643889144

38
535246
536289
+
643889145

39
279605
281008
+
642555123

40
44077
44439
−
643889139

41
12698
14710
−
643889139

42
268387
269874
−
643889145

43
106241
106837
−
643889140

44
175312
176142
+
643889143

45
362809
363438
+
643889146

46
23652
24185
+
643889145

47
200043
201293
−
643889141

48
37235
38317
−
643905842

49
3320488
3321087
+
642555123

50
30478
31134
+
643889143

Example 8

Pseudomonas, particularly P. aeruginosa

The procedure was carried out as in Example 1, except that the following microorganisms were used:

Bacterial Strains

The inventors selected 1042 Pseudomonas strains, particularly Pseudomonas aeruginosa, from the microbiology strain collection at Siemens Healthcare Diagnostics (West Sacramento, Calif.) for susceptibility testing and whole genome sequencing.

From MetaRef, 640 centroids of Pseudomonas aeruginosa were used as reference sequences.

The results for P. aeruginosa are shown in Tables 15 (corresponding to Table 1) and 16 (corresponding to Table 2).

TABLE 15a

Data for Pseudomonas, particularly Pseudomonas aeruginosa

Scaffold.External.

No.
Accession
Scaffold.Name
best_pv

1
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
4.52939243363163e−78

2
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
2.75541175953672e−58

3
NZ_AEEX01000100

Pseudomonas aeruginosa 39016 contig00116: NZ_AEEX01000100
4.23483908607088e−28

4
NC_010501

Pseudomonas putida W619: NC_010501
2.9087092265635e−26

5
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
5.61705273260437e−22

6
NC_015740

Pseudomonas stutzeri ATCC 17588 = LMG 11199 chromosome: NC_015740
5.61705273260437e−22

7
NC_015733

Pseudomonas putida S16 chromosome: NC_015733
1.91188334380809e−20

8
NZ_AEEX01000148

Pseudomonas aeruginosa 39016 contig00164: NZ_AEEX01000148
4.25099609715652e−20

9
NZ_AAKV01000030

Pseudomonas aeruginosa C3719, unfinished sequence: NZ_AAKV01000030
2.79764535555464e−19

10
NZ_AEEX01000098

Pseudomonas aeruginosa 39016 contig00114: NZ_AEEX01000098
4.15595600170243e−19

11
NZ_AEEX01000163

Pseudomonas aeruginosa 39016 contig00179: NZ_AEEX01000163
4.72113166087411e−19

12
NZ_AAKW01000042

Pseudomonas aeruginosa 2192, unfinished sequence: NZ_AAKW01000042
2.33370938002383e−17

13
NZ_AEEX01000009

Pseudomonas aeruginosa 39016 contig00011: NZ_AEEX01000009
3.60022886576205e−17

14
NZ_AAKW01000075

Pseudomonas aeruginosa 2192, unfinished sequence: NZ_AAKW01000075
1.13322970340506e−14

15
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
2.33016029331653e−14

16
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
2.33822187391836e−14

17
NZ_AEEX01000098

Pseudomonas aeruginosa 39016 contig00114: NZ_AEEX01000098
2.91419614855849e−14

18
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
5.5018212149287e−14

19
NC_010501

Pseudomonas putida W619: NC_010501
6.06970436387873e−14

20
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
7.75377932078369e−14

21
NZ_AAKW01000022

Pseudomonas aeruginosa 2192, unfinished sequence: NZ_AAKW01000022
3.34337634494896e−13

22
NZ_ABKZ01000250

Pseudomonas aeruginosa PAb1 NZ_ABKZ01000250: NZ_ABKZ01000250
6.17495854397665e−13

23
NC_008463

Pseudomonas aeruginosa UCBPP-PA14: NC_008463
6.42896969501816e−13

24
NZ_AAKW01000022

Pseudomonas aeruginosa 2192, unfinished sequence: NZ_AAKW01000022
1.20774339924326e−12

25
NZ_AAQW01000001

Pseudomonas aeruginosa PACS2, unfinished sequence: NZ_AAQW01000001
1.22221957191107e−12

26
NC_011770

Pseudomonas aeruginosa LESB58: NC_011770
1.79185026742242e−12

27
NZ_AAQW01000001

Pseudomonas aeruginosa PACS2, unfinished sequence: NZ_AAQW01000001
2.12378785336506e−12

28
NZ_AAKW01000022

Pseudomonas aeruginosa 2192, unfinished sequence: NZ_AAKW01000022
2.4812070369021e−12

29
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
3.74499379826048e−12

30
NZ_AEEX01000148

Pseudomonas aeruginosa 39016 contig00164: NZ_AEEX01000148
4.42748938639645e−12

31
NC_008463

Pseudomonas aeruginosa UCBPP-PA14: NC_008463
5.32658560222593e−12

32
NZ_AAQW01000001

Pseudomonas aeruginosa PACS2, unfinished sequence: NZ_AAQW01000001
5.99725940121888e−12

33
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
7.28057447109574e−12

34
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
7.48144363663932e−12

35
NZ_AAKW01000022

Pseudomonas aeruginosa 2192, unfinished sequence: NZ_AAKW01000022
9.72376870484031e−12

36
NZ_AEEX01000085

Pseudomonas aeruginosa 39016 contig00101: NZ_AEEX01000085
9.72376870484031e−12

37
NZ_AAQW01000001

Pseudomonas aeruginosa PACS2, unfinished sequence: NZ_AAQW01000001
9.72376870484031e−12

38
NZ_AAQW01000001

Pseudomonas aeruginosa PACS2, unfinished sequence: NZ_AAQW01000001
9.72376870484031e−12

39
NZ_AAKW01000022

Pseudomonas aeruginosa 2192, unfinished sequence: NZ_AAKW01000022
9.73896479060769e−12

40
NC_011770

Pseudomonas aeruginosa LESB58: NC_011770
9.73896479060769e−12

41
CP002622

Pseudomonas stutzeri DSM 4166: CP002622
9.73896479060769e−12

42
NZ_AAQW01000001

Pseudomonas aeruginosa PACS2, unfinished sequence: NZ_AAQW01000001
9.73896479060769e−12

43
NZ_AEEX01000149

Pseudomonas aeruginosa 39016 contig00165: NZ_AEEX01000149
1.05759735249337e−11

44
NZ_AEEX01000149

Pseudomonas aeruginosa 39016 contig00165: NZ_AEEX01000149
1.05759735249337e−11

45
NC_008463

Pseudomonas aeruginosa UCBPP-PA14: NC_008463
1.05759735249337e−11

46
NZ_AAKW01000024

Pseudomonas aeruginosa 2192, unfinished sequence: NZ_AAKW01000024
1.13412272447338e−11

47
NZ_AAKW01000022

Pseudomonas aeruginosa 2192, unfinished sequence: NZ_AAKW01000022
1.64096469464127e−11

48
NC_012560

Azotobacter vinelandii DJ: NC_012560
1.85224764530357e−11

49
NZ_AEEX01000149

Pseudomonas aeruginosa 39016 contig00165: NZ_AEEX01000149
1.86265894165925e−11

50
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
1.8721278417616e−11

TABLE 15b

Data for Pseudomonas, particularly Pseudomonas aeruginosa (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
AZT; CAZ; CP; CPE; GM; IMP; LVX; MER;
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

P/T; TO

2
AZT; CAZ; CP; CPE; GM; IMP; LVX; MER;
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

P/T; TO

3
CP; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

4
CP; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

5
CP; GM; LVX; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

6
CP; GM; LVX; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

7
CP; GM; LVX; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

8
CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

9
CAZ; CP; CPE; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

10
CP; GM; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

11
AZT; CAZ; CP; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

12
CAZ; CP; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

13
AZT; CAZ; CP; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

14
CP; GM; LVX; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

15
CAZ; CP; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

16
CP; GM; IMP; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

17
CP; GM; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

18
CAZ; CP; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

19
CP; GM; LVX; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

20
CP; GM; LVX; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

21
CAZ; CP; GM; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

22
CP; GM; IMP; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

23
CP; GM; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

24
CAZ; CP; GM; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

25
CAZ; CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

26
CAZ; CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

27
CAZ; CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

28
CP; GM; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

29
CP; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

30
CP; GM; IMP; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

31
AZT; CAZ; CP; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

32
CAZ; CP; GM; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

33
CP; GM; IMP; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

34
CAZ; CP; CPE; GM; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

35
CAZ; CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

36
CAZ; CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

37
CAZ; CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

38
CAZ; CP; GM; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

39
CAZ; CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

40
CAZ; CP; GM; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

41
CAZ; CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

42
CAZ; CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

43
CP; GM; IMP; LVX; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

44
CP; GM; IMP; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

45
CP; GM; IMP; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

46
CP; GM; IMP; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

47
CAZ; CP; GM; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

48
CP; GM; IMP; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

49
CP; GM; IMP; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

50
CP; GM; IMP; LVX; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

TABLE 15c

Data for Pseudomonas, particularly Pseudomonas aeruginosa

(continued)

No.
num_aminoglycoside
num_fluoroquinolone
num_lactam

1
2
2
6

2
2
2
6

3
2
2
2

4
2
2
2

5
2
2
0

6
2
2
0

7
2
2
0

8
2
2
2

9
2
2
4

10
2
1
0

11
2
2
4

12
2
2
3

13
2
2
4

14
2
2
0

15
2
2
3

16
2
2
2

17
2
1
0

18
2
2
3

19
2
2
0

20
2
2
0

21
2
1
3

22
2
2
2

23
2
1
0

24
2
1
3

25
2
2
3

26
2
2
3

27
2
2
3

28
2
1
0

29
2
2
2

30
2
2
2

31
2
2
4

32
2
2
2

33
2
2
2

34
2
1
3

35
2
2
3

36
2
2
3

37
2
2
3

38
2
2
2

39
2
2
3

40
2
2
2

41
2
2
3

42
2
2
3

43
2
2
1

44
2
2
2

45
2
2
2

46
2
2
2

47
2
2
2

48
2
2
2

49
2
2
2

50
2
2
1

TABLE 15d

Data for Pseudomonas, particularly Pseudomonas aeruginosa (continued)

No.
AZT_pv_adj
CAZ_pv_adj
CP_pv_adj
CPE_pv_adj
GM_pv_adj

1
4.68E−03
2.31E−09
4.27E−32
5.83E−17
1.14E−56

2
1.88E−03
1.86E−08
3.37E−28
4.30E−16
2.05E−42

3
4.88E−01
1.79E−02
4.13E−10
4.41E−04
7.91E−18

4
5.97E−01
1.23E−02
2.07E−09
2.52E−04
9.24E−17

5
5.49E−01
5.49E−01
9.07E−06
1.26E−01
1.33E−11

6
5.49E−01
5.49E−01
9.07E−06
1.26E−01
1.33E−11

7
6.66E−01
3.70E−01
9.33E−05
1.41E−01
5.53E−11

8
9.33E−01
6.81E−02
1.30E−09
3.20E−02
9.74E−12

9
2.57E−01
3.98E−05
1.63E−09
1.56E−07
6.24E−16

10
7.47E−01
4.36E−01
2.70E−04
2.27E−01
5.68E−10

11
4.31E−03
4.22E−08
3.91E−13
2.77E−09
7.84E−16

12
3.06E−02
6.75E−05
1.29E−09
9.32E−06
1.77E−14

13
2.11E−03
3.40E−07
3.34E−10
7.91E−07
4.31E−14

14
6.90E−01
3.88E−02
8.36E−06
2.05E−02
1.97E−09

15
1.08E−01
8.48E−04
2.11E−07
1.99E−04
4.46E−13

16
8.07E−01
4.16E−02
3.85E−08
3.59E−02
1.19E−09

17
6.52E−01
4.40E−01
1.90E−04
5.44E−01
1.07E−07

18
1.20E−02
1.84E−06
1.64E−08
1.64E−07
4.99E−11

19
4.08E−01
1.28E−02
2.37E−05
3.15E−02
2.20E−09

20
9.48E−01
6.78E−02
9.58E−07
3.17E−02
1.32E−09

21
5.47E−01
9.24E−03
2.24E−04
5.63E−02
4.24E−08

22
8.08E−01
1.43E−01
2.42E−06
2.48E−01
1.01E−07

23
8.44E−01
2.48E−01
4.61E−04
3.25E−01
9.75E−07

24
4.14E−01
4.37E−03
1.78E−04
5.65E−02
1.49E−07

25
3.25E−01
1.51E−03
6.15E−05
2.63E−02
9.67E−08

26
6.54E−01
5.11E−03
1.38E−05
1.82E−02
5.63E−08

27
1.63E−01
1.65E−04
7.86E−05
1.59E−02
1.34E−09

28
7.69E−01
2.48E−01
7.44E−04
3.25E−01
2.80E−06

29
4.44E−01
6.54E−02
4.51E−05
8.97E−06
1.56E−07

30
9.82E−01
1.63E−01
3.28E−06
2.73E−01
2.89E−08

31
7.11E−03
2.08E−05
1.73E−08
1.31E−06
7.90E−09

32
4.78E−01
7.49E−03
4.49E−05
2.57E−02
2.96E−07

33
6.55E−01
1.81E−01
8.24E−06
2.97E−01
2.97E−07

34
5.00E−01
5.68E−03
8.53E−03
7.20E−03
1.63E−11

35
4.77E−01
4.27E−03
6.00E−05
2.17E−02
9.67E−08

36
4.77E−01
4.27E−03
6.00E−05
2.17E−02
9.67E−08

37
4.77E−01
4.27E−03
6.00E−05
2.17E−02
9.67E−08

38
5.46E−01
9.06E−03
6.00E−05
3.01E−02
2.03E−07

39
4.78E−01
4.34E−03
1.28E−04
2.20E−02
1.35E−07

40
5.47E−01
9.22E−03
7.62E−05
3.04E−02
2.83E−07

41
4.78E−01
4.34E−03
1.28E−04
2.20E−02
1.35E−07

42
4.78E−01
4.34E−03
1.28E−04
2.20E−02
1.35E−07

43
1
1.81E−01
8.55E−06
2.01E−01
4.71E−07

44
9.49E−01
1.43E−01
2.47E−06
2.48E−01
2.19E−07

45
1
1.12E−01
4.65E−06
2.01E−01
2.19E−07

46
9.82E−01
4.90E−02
6.77E−07
7.55E−02
2.07E−07

47
4.78E−01
7.49E−03
7.54E−05
2.57E−02
2.96E−07

48
9.49E−01
1.44E−01
6.20E−06
2.48E−01
4.67E−07

49
9.82E−01
1.43E−01
2.41E−06
1.62E−01
6.60E−07

50
7.30E−01
2.71E−01
1.97E−05
4.14E−01
1.33E−06

TABLE 15e

Data for Pseudomonas, particularly Pseudomonas aeruginosa (continued)

No.
IMP_pv_adj
LVX_pv_adj
MER_pv_adj
P/T_pv_adj
TO_pv_adj

1
1.35E−04
9.50E−27
2.29E−10
3.68E−18
4.53E−78

2
3.88E−03
4.29E−23
1.88E−05
3.33E−17
2.76E−58

3
4.33E−01
1.56E−06
1.57E−01
7.34E−04
4.23E−28

4
3.93E−01
4.01E−06
1.33E−01
9.25E−04
2.91E−26

5
2.74E−01
1.86E−03
8.61E−02
3.50E−01
5.62E−22

6
2.74E−01
1.86E−03
8.61E−02
3.50E−01
5.62E−22

7
5.97E−01
7.47E−03
1.01E−01
4.09E−01
1.91E−20

8
4.04E−02
2.96E−08
8.12E−03
3.01E−03
4.25E−20

9
4.48E−01
4.75E−07
8.35E−03
1.95E−05
2.80E−19

10
8.37E−01
1.48E−02
2.27E−01
4.37E−01
4.16E−19

11
1
7.77E−10
2.74E−02
2.06E−06
4.72E−19

12
8.04E−01
2.34E−06
1.05E−01
5.83E−04
2.33E−17

13
1
1.18E−06
1.82E−01
5.92E−05
3.60E−17

14
2.13E−02
2.85E−04
4.99E−01
1.04E−02
1.13E−14

15
4.16E−01
1.60E−05
4.41E−01
1.42E−03
2.33E−14

16
1.11E−03
7.44E−05
3.68E−04
1.33E−02
2.34E−14

17
4.55E−01
3.37E−02
3.01E−01
5.40E−01
2.91E−14

18
9.48E−01
9.19E−07
1.68E−01
5.53E−05
5.50E−14

19
1
1.24E−03
2.34E−01
1.09E−01
6.07E−14

20
1.05E−02
1.87E−04
2.63E−01
3.01E−02
7.75E−14

21
1.13E−01
1.21E−02
5.24E−03
6.95E−03
3.34E−13

22
2.50E−03
3.35E−04
2.39E−03
1.14E−01
6.17E−13

23
9.76E−02
4.12E−02
1.60E−01
4.20E−01
6.43E−13

24
1.75E−01
1.21E−02
8.59E−03
4.17E−03
1.21E−12

25
1.31E−01
7.32E−03
6.68E−03
1.51E−03
1.22E−12

26
9.53E−02
5.07E−03
6.50E−03
9.57E−03
1.79E−12

27
1.89E−02
8.78E−03
1.36E−04
3.10E−04
2.12E−12

28
1.14E−01
4.77E−02
1.85E−01
4.19E−01
2.48E−12

29
3.21E−02
1.60E−05
3.06E−01
2.70E−04
3.74E−12

30
4.18E−03
1.07E−03
6.72E−03
1.01E−01
4.43E−12

31
8.38E−01
7.16E−05
2.64E−01
1.39E−03
5.33E−12

32
6.86E−02
3.50E−03
3.93E−03
1.13E−02
6.00E−12

33
5.18E−03
1.07E−03
8.59E−03
1.13E−01
7.28E−12

34
9.58E−01
1.06E−02
1.47E−01
6.26E−03
7.48E−12

35
8.10E−02
4.28E−03
4.05E−03
8.08E−03
9.72E−12

36
8.10E−02
4.28E−03
4.05E−03
8.08E−03
9.72E−12

37
8.10E−02
4.28E−03
4.05E−03
8.08E−03
9.72E−12

38
8.10E−02
4.28E−03
4.05E−03
1.56E−02
9.72E−12

39
8.13E−02
7.24E−03
5.04E−03
9.57E−03
9.74E−12

40
8.13E−02
5.09E−03
5.04E−03
1.83E−02
9.74E−12

41
8.13E−02
7.24E−03
5.04E−03
9.57E−03
9.74E−12

42
8.13E−02
7.24E−03
5.04E−03
9.57E−03
9.74E−12

43
4.13E−03
1.98E−03
1.07E−02
1.29E−01
1.06E−11

44
2.49E−03
1.32E−03
4.07E−03
1.01E−01
1.06E−11

45
2.49E−03
1.98E−03
4.07E−03
7.86E−02
1.06E−11

46
6.61E−03
1.62E−03
6.66E−03
3.47E−02
1.13E−11

47
6.86E−02
5.04E−03
3.93E−03
1.56E−02
1.64E−11

48
1.92E−03
1.62E−03
5.24E−03
1.28E−01
1.85E−11

49
3.22E−03
1.08E−03
6.76E−03
7.83E−02
1.86E−11

50
6.52E−03
4.34E−03
1.32E−02
2.40E−01
1.87E−11

TABLE 15f

Data for Pseudomonas, particularly Pseudomonas aeruginosa (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
PSPA7_5342

YP_001350673

2
PSPA7_5335

YP_001350666

3
PA39016_001160000

ZP_07794022

4
PputW619_2322

YP_001749191

5
PSPA7_0102

YP_001345498

6
PSTAB_1238
merR
YP_004713608

7
PPS_5233

YP_004704640

8
PA39016_001640030

ZP_07794960

9
PaerC_01001712

ZP_00968897

10
PA39016_001140033

ZP_07794005

11
PA39016_001790028

ZP_07795388

12
Paer2_01003738

ZP_00973073

13
PA39016_000110208

ZP_07792174

14
Paer2_01005870

ZP_00970967

15
PSPA7_0117

YP_001345513

16
PSPA7_3727

YP_001349081

17
PA39016_001140034

ZP_07794006

18
PSPA7_5254

YP_001350586

19
PputW619_2321

YP_001749190

20
PSPA7_4822

YP_001350163

21
Paer2_01002125

ZP_00974743

22
PaerPAb_010100012576

ZP_06878458

23
PA14_15470
merP
YP_789375

24
Paer2_01002118

ZP_00974736

25
PaerPA_01003088

ZP_01365958

26
PLES_26911

YP_002440283

27
PaerPA_01003092

ZP_01365962

28
Paer2_01002142

ZP_00974760

29
PSPA7_0357

YP_001345752

30
PA39016_001640027

ZP_07794957

31
PA14_49520
pyoS3A
YP_792115

32
PaerPA_01003114

ZP_01365983

33
PSPA7_3718

YP_001349072

34
PSPA7_0113
merP1
YP_001345509

35
Paer2_01002136

ZP_00974754

36
PA39016_001010047

ZP_07793693

37
PaerPA_01003095

ZP_01365965

38
PaerPA_01003132

ZP_01366001

39
Paer2_01002121

ZP_00974739

40
PLES_26591

YP_002440252

41
PSTAA_1280

AEA83190

42
PaerPA_01003094

ZP_01365964

43
PA39016_001650006

ZP_07794967

44
PA39016_001650001

ZP_07794962

45
PA14_30900

YP_790630

46
Paer2_01002387

ZP_00974497

47
Paer2_01002180

ZP_00974798

48
Avin_35690
trbE
YP_002800691

49
PA39016_001650003

ZP_07794964

50
PSPA7_3698

YP_001349052

TABLE 15g

Data for Pseudomonas, particularly Pseudomonas aeruginosa (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
5509888
5510901
+
640753026

2
5497616
5498380
−
640753026

3
269
829
+
649999021

4
2600850
2601410
−
641522670

5
112316
112732
+
640753026

6
1298354
1298788
+
650716170

7
5930458
5930823
−
650716164

8
29403
29642
−
649999069

9
9109
10122
−
638362473

10
35241
35606
−
649999019

11
25607
28270
+
649999084

12
18240
19688
−
638362609

13
212874
213821
−
649998930

14
22370
34666
+
638362642

15
122819
123664
+
640753026

16
3864574
3865185
−
640753026

17
35624
37309
−
649999019

18
5409448
5411001
−
640753026

19
2597880
2600846
−
641522670

20
4961575
4962753
−
640753026

21
167495
167935
+
638362589

22
28
241
−
647002430

23
1310460
1310735
−
639279323

24
161059
161934
+
638362589

25
3500513
3501292
+
638372930

26
2885013
2885837
−
643348637

27
3505406
3506134
+
638372930

28
182786
184474
+
638362589

29
366452
367480
−
640753026

30
26408
27688
−
649999069

31
4403159
4405534
−
639279323

32
3528459
3529049
+
638372930

33
3855983
3856195
−
640753026

34
121405
121680
−
640753026

35
179158
179895
+
638362589

36
48194
50227
+
649999006

37
3507452
3509473
+
638372930

38
3547764
3548102
+
638372930

39
163874
164434
+
638362589

40
2856655
2857038
−
643348637

41
1367161
1367601
−
651053081

42
3506732
3507172
+
638372930

43
6653
8650
−
649999070

44
2001
4451
−
649999070

45
2683111
2683836
−
639279323

46
138340
138654
−
638362591

47
214185
216386
+
638362589

48
3640230
3642680
−
643692060

49
4730
5116
−
649999070

50
3833901
3834893
−
640753026

TABLE 16a

Data for Pseudomonas, particularly Pseudomonas aeruginosa

No.
Scaffold.External.Accession
Scaffold.Name
best_pv

1
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
4.52939243363163e−78

2
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
2.75541175953672e−58

3
NZ_AEEX01000100

Pseudomonas aeruginosa 39016 contig00116: NZ_AEEX01000100
4.23483908607088e−28

4
NC_010501

Pseudomonas putida W619: NC_010501
2.9087092265635e−26

5
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
5.61705273260437e−22

6
NC_015740

Pseudomonas stutzeri ATCC 17588 = LMG 11199 chromosome: NC_015740
5.61705273260437e−22

7
NC_015733

Pseudomonas putida S16 chromosome: NC_015733
1.91188334380809e−20

8
NZ_AEEX01000148

Pseudomonas aeruginosa 39016 contig00164: NZ_AEEX01000148
4.25099609715652e−20

9
NZ_AAKV01000030

Pseudomonas aeruginosa C3719, unfinished sequence: NZ_AAKV01000030
2.79764535555464e−19

10
NZ_AEEX01000098

Pseudomonas aeruginosa 39016 contig00114: NZ_AEEX01000098
4.15595600170243e−19

11
NZ_AEEX01000163

Pseudomonas aeruginosa 39016 contig00179: NZ_AEEX01000163
4.72113166087411e−19

12
NZ_AAKW01000042

Pseudomonas aeruginosa 2192, unfinished sequence: NZ_AAKW01000042
2.33370938002383e−17

13
NZ_AEEX01000009

Pseudomonas aeruginosa 39016 contig00011: NZ_AEEX01000009
3.60022886576205e−17

14
NZ_AAKW01000075

Pseudomonas aeruginosa 2192, unfinished sequence: NZ_AAKW01000075
1.13322970340506e−14

15
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
2.33016029331653e−14

16
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
2.33822187391836e−14

17
NZ_AEEX01000098

Pseudomonas aeruginosa 39016 contig00114: NZ_AEEX01000098
2.91419614855849e−14

18
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
5.5018212149287e−14

19
NC_010501

Pseudomonas putida W619: NC_010501
6.06970436387873e−14

20
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
7.75377932078369e−14

21
NZ_AAKW01000022

Pseudomonas aeruginosa 2192, unfinished sequence: NZ_AAKW01000022
3.34337634494896e−13

22
NZ_ABKZ01000250

Pseudomonas aeruginosa PAb1 NZ_ABKZ01000250: NZ_ABKZ01000250
6.17495854397665e−13

23
NC_008463

Pseudomonas aeruginosa UCBPP-PA14: NC_008463
6.42896969501816e−13

24
NZ_AAKW01000022

Pseudomonas aeruginosa 2192, unfinished sequence: NZ_AAKW01000022
1.20774339924326e−12

25
NZ_AAQW01000001

Pseudomonas aeruginosa PACS2, unfinished sequence: NZ_AAQW01000001
1.22221957191107e−12

26
NC_011770

Pseudomonas aeruginosa LESB58: NC_011770
1.79185026742242e−12

27
NZ_AAQW01000001

Pseudomonas aeruginosa PACS2, unfinished sequence: NZ_AAQW01000001
2.12378785336506e−12

28
NZ_AAKW01000022

Pseudomonas aeruginosa 2192, unfinished sequence: NZ_AAKW01000022
2.4812070369021e−12

29
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
3.74499379826048e−12

30
NZ_AEEX01000148

Pseudomonas aeruginosa 39016 contig00164: NZ_AEEX01000148
4.42748938639645e−12

31
NC_008463

Pseudomonas aeruginosa UCBPP-PA14: NC_008463
5.32658560222593e−12

32
NZ_AAQW01000001

Pseudomonas aeruginosa PACS2, unfinished sequence: NZ_AAQW01000001
5.99725940121888e−12

33
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
7.28057447109574e−12

34
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
7.48144363663932e−12

35
NZ_AAKW01000022

Pseudomonas aeruginosa 2192, unfinished sequence: NZ_AAKW01000022
9.72376870484031e−12

36
NZ_AEEX01000085

Pseudomonas aeruginosa 39016 contig00101: NZ_AEEX01000085
9.72376870484031e−12

37
NZ_AAQW01000001

Pseudomonas aeruginosa PACS2, unfinished sequence: NZ_AAQW01000001
9.72376870484031e−12

38
NZ_AAQW01000001

Pseudomonas aeruginosa PACS2, unfinished sequence: NZ_AAQW01000001
9.72376870484031e−12

39
NZ_AAKW01000022

Pseudomonas aeruginosa 2192, unfinished sequence: NZ_AAKW01000022
9.73896479060769e−12

40
NC_011770

Pseudomonas aeruginosa LESB58: NC_011770
9.73896479060769e−12

41
CP002622

Pseudomonas stutzeri DSM 4166: CP002622
9.73896479060769e−12

42
NZ_AAQW01000001

Pseudomonas aeruginosa PACS2, unfinished sequence: NZ_AAQW01000001
9.73896479060769e−12

43
NZ_AEEX01000149

Pseudomonas aeruginosa 39016 contig00165: NZ_AEEX01000149
1.05759735249337e−11

44
NZ_AEEX01000149

Pseudomonas aeruginosa 39016 contig00165: NZ_AEEX01000149
1.05759735249337e−11

45
NC_008463

Pseudomonas aeruginosa UCBPP-PA14: NC_008463
1.05759735249337e−11

46
NZ_AAKW01000024

Pseudomonas aeruginosa 2192, unfinished sequence: NZ_AAKW01000024
1.13412272447338e−11

47
NZ_AAKW01000022

Pseudomonas aeruginosa 2192, unfinished sequence: NZ_AAKW01000022
1.64096469464127e−11

48
NC_012560

Azotobacter vinelandii DJ: NC_012560
1.85224764530357e−11

49
NZ_AEEX01000149

Pseudomonas aeruginosa 39016 contig00165: NZ_AEEX01000149
1.86265894165925e−11

50
NC_009656

Pseudomonas aeruginosa PA7: NC_009656
1.8721278417616e−11

TABLE 16b

Data for Pseudomonas, particularly Pseudomonas aeruginosa (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
AZT; CAZ; CP; CPE; GM; IMP; LVX; MER;
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

P/T; TO

2
AZT; CAZ; CP; CPE; GM; IMP; LVX; MER;
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

P/T; TO

3
CP; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

4
CP; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

5
CP; GM; LVX; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

6
CP; GM; LVX; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

7
CP; GM; LVX; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

8
CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

9
CAZ; CP; CPE; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

10
CP; GM; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

11
AZT; CAZ; CP; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

12
CAZ; CP; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

13
AZT; CAZ; CP; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

14
CP; GM; LVX; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

15
CAZ; CP; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

16
CP; GM; IMP; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

17
CP; GM; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

18
CAZ; CP; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

19
CP; GM; LVX; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

20
CP; GM; LVX; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

21
CAZ; CP; GM; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

22
CP; GM; IMP; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

23
CP; GM; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

24
CAZ; CP; GM; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

25
CAZ; CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

26
CAZ; CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

27
CAZ; CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

28
CP; GM; TO
aminoglycoside; fluoroquinolone
TO
aminoglycoside

29
CP; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

30
CP; GM; IMP; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

31
AZT; CAZ; CP; CPE; GM; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

32
CAZ; CP; GM; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

33
CP; GM; IMP; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

34
CAZ; CP; CPE; GM; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

35
CAZ; CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

36
CAZ; CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

37
CAZ; CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

38
CAZ; CP; GM; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

39
CAZ; CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

40
CAZ; CP; GM; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

41
CAZ; CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

42
CAZ; CP; GM; LVX; MER; P/T; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

43
CP; GM; IMP; LVX; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

44
CP; GM; IMP; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

45
CP; GM; IMP; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

46
CP; GM; IMP; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

47
CAZ; CP; GM; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

48
CP; GM; IMP; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

49
CP; GM; IMP; LVX; MER; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

50
CP; GM; IMP; LVX; TO
aminoglycoside; fluoroquinolone; lactam
TO
aminoglycoside

TABLE 16c

Data for Pseudomonas, particularly Pseudomonas aeruginosa (continued)

No.
num_aminoglycoside
num_fluoroquinolone
num_lactam

1
2
2
6

2
2
2
6

3
2
2
2

4
2
2
2

5
2
2
0

6
2
2
0

7
2
2
0

8
2
2
2

9
2
2
4

10
2
1
0

11
2
2
4

12
2
2
3

13
2
2
4

14
2
2
0

15
2
2
3

16
2
2
2

17
2
1
0

18
2
2
3

19
2
2
0

20
2
2
0

21
2
1
3

22
2
2
2

23
2
1
0

24
2
1
3

25
2
2
3

26
2
2
3

27
2
2
3

28
2
1
0

29
2
2
2

30
2
2
2

31
2
2
4

32
2
2
2

33
2
2
2

34
2
1
3

35
2
2
3

36
2
2
3

37
2
2
3

38
2
2
2

39
2
2
3

40
2
2
2

41
2
2
3

42
2
2
3

43
2
2
1

44
2
2
2

45
2
2
2

46
2
2
2

47
2
2
2

48
2
2
2

49
2
2
2

50
2
2
1

TABLE 16d

Data for Pseudomonas, particularly Pseudomonas aeruginosa (continued)

No.
AZT_pv_adj
CAZ_pv_adj
CP_pv_adj
CPE_pv_adj
GM_pv_adj

1
4.68E−03
2.31E−09
4.27E−32
5.83E−17
1.14E−56

2
1.88E−03
1.86E−08
3.37E−28
4.30E−16
2.05E−42

3
4.88E−01
1.79E−02
4.13E−10
4.41E−04
7.91E−18

4
5.97E−01
1.23E−02
2.07E−09
2.52E−04
9.24E−17

5
5.49E−01
5.49E−01
9.07E−06
1.26E−01
1.33E−11

6
5.49E−01
5.49E−01
9.07E−06
1.26E−01
1.33E−11

7
6.66E−01
3.70E−01
9.33E−05
1.41E−01
5.53E−11

8
9.33E−01
6.81E−02
1.30E−09
3.20E−02
9.74E−12

9
2.57E−01
3.98E−05
1.63E−09
1.56E−07
6.24E−16

10
7.47E−01
4.36E−01
2.70E−04
2.27E−01
5.68E−10

11
4.31E−03
4.22E−08
3.91E−13
2.77E−09
7.84E−16

12
3.06E−02
6.75E−05
1.29E−09
9.32E−06
1.77E−14

13
2.11E−03
3.40E−07
3.34E−10
7.91E−07
4.31E−14

14
6.90E−01
3.88E−02
8.36E−06
2.05E−02
1.97E−09

15
1.08E−01
8.48E−04
2.11E−07
1.99E−04
4.46E−13

16
8.07E−01
4.16E−02
3.85E−08
3.59E−02
1.19E−09

17
6.52E−01
4.40E−01
1.90E−04
5.44E−01
1.07E−07

18
1.20E−02
1.84E−06
1.64E−08
1.64E−07
4.99E−11

19
4.08E−01
1.28E−02
2.37E−05
3.15E−02
2.20E−09

20
9.48E−01
6.78E−02
9.58E−07
3.17E−02
1.32E−09

21
5.47E−01
9.24E−03
2.24E−04
5.63E−02
4.24E−08

22
8.08E−01
1.43E−01
2.42E−06
2.48E−01
1.01E−07

23
8.44E−01
2.48E−01
4.61E−04
3.25E−01
9.75E−07

24
4.14E−01
4.37E−03
1.78E−04
5.65E−02
1.49E−07

25
3.25E−01
1.51E−03
6.15E−05
2.63E−02
9.67E−08

26
6.54E−01
5.11E−03
1.38E−05
1.82E−02
5.63E−08

27
1.63E−01
1.65E−04
7.86E−05
1.59E−02
1.34E−09

28
7.69E−01
2.48E−01
7.44E−04
3.25E−01
2.80E−06

29
4.44E−01
6.54E−02
4.51E−05
8.97E−06
1.56E−07

30
9.82E−01
1.63E−01
3.28E−06
2.73E−01
2.89E−08

31
7.11E−03
2.08E−05
1.73E−08
1.31E−06
7.90E−09

32
4.78E−01
7.49E−03
4.49E−05
2.57E−02
2.96E−07

33
6.55E−01
1.81E−01
8.24E−06
2.97E−01
2.97E−07

34
5.00E−01
5.68E−03
8.53E−03
7.20E−03
1.63E−11

35
4.77E−01
4.27E−03
6.00E−05
2.17E−02
9.67E−08

36
4.77E−01
4.27E−03
6.00E−05
2.17E−02
9.67E−08

37
4.77E−01
4.27E−03
6.00E−05
2.17E−02
9.67E−08

38
5.46E−01
9.06E−03
6.00E−05
3.01E−02
2.03E−07

39
4.78E−01
4.34E−03
1.28E−04
2.20E−02
1.35E−07

40
5.47E−01
9.22E−03
7.62E−05
3.04E−02
2.83E−07

41
4.78E−01
4.34E−03
1.28E−04
2.20E−02
1.35E−07

42
4.78E−01
4.34E−03
1.28E−04
2.20E−02
1.35E−07

43
1
1.81E−01
8.55E−06
2.01E−01
4.71E−07

44
9.49E−01
1.43E−01
2.47E−06
2.48E−01
2.19E−07

45
1
1.12E−01
4.65E−06
2.01E−01
2.19E−07

46
9.82E−01
4.90E−02
6.77E−07
7.55E−02
2.07E−07

47
4.78E−01
7.49E−03
7.54E−05
2.57E−02
2.96E−07

48
9.49E−01
1.44E−01
6.20E−06
2.48E−01
4.67E−07

49
9.82E−01
1.43E−01
2.41E−06
1.62E−01
6.60E−07

50
7.30E−01
2.71E−01
1.97E−05
4.14E−01
1.33E−06

TABLE 16e

Data for Pseudomonas, particularly Pseudomonas aeruginosa (continued)

No.
IMP_pv_adj
LVX_pv_adj
MER_pv_adj
P/T_pv_adj
TO_pv_adj

1
1.35E−04
9.50E−27
2.29E−10
3.68E−18
4.53E−78

2
3.88E−03
4.29E−23
1.88E−05
3.33E−17
2.76E−58

3
4.33E−01
1.56E−06
1.57E−01
7.34E−04
4.23E−28

4
3.93E−01
4.01E−06
1.33E−01
9.25E−04
2.91E−26

5
2.74E−01
1.86E−03
8.61E−02
3.50E−01
5.62E−22

6
2.74E−01
1.86E−03
8.61E−02
3.50E−01
5.62E−22

7
5.97E−01
7.47E−03
1.01E−01
4.09E−01
1.91E−20

8
4.04E−02
2.96E−08
8.12E−03
3.01E−03
4.25E−20

9
4.48E−01
4.75E−07
8.35E−03
1.95E−05
2.80E−19

10
8.37E−01
1.48E−02
2.27E−01
4.37E−01
4.16E−19

11
1
7.77E−10
2.74E−02
2.06E−06
4.72E−19

12
8.04E−01
2.34E−06
1.05E−01
5.83E−04
2.33E−17

13
1
1.18E−06
1.82E−01
5.92E−05
3.60E−17

14
2.13E−02
2.85E−04
4.99E−01
1.04E−02
1.13E−14

15
4.16E−01
1.60E−05
4.41E−01
1.42E−03
2.33E−14

16
1.11E−03
7.44E−05
3.68E−04
1.33E−02
2.34E−14

17
4.55E−01
3.37E−02
3.01E−01
5.40E−01
2.91E−14

18
9.48E−01
9.19E−07
1.68E−01
5.53E−05
5.50E−14

19
1
1.24E−03
2.34E−01
1.09E−01
6.07E−14

20
1.05E−02
1.87E−04
2.63E−01
3.01E−02
7.75E−14

21
1.13E−01
1.21E−02
5.24E−03
6.95E−03
3.34E−13

22
2.50E−03
3.35E−04
2.39E−03
1.14E−01
6.17E−13

23
9.76E−02
4.12E−02
1.60E−01
4.20E−01
6.43E−13

24
1.75E−01
1.21E−02
8.59E−03
4.17E−03
1.21E−12

25
1.31E−01
7.32E−03
6.68E−03
1.51E−03
1.22E−12

26
9.53E−02
5.07E−03
6.50E−03
9.57E−03
1.79E−12

27
1.89E−02
8.78E−03
1.36E−04
3.10E−04
2.12E−12

28
1.14E−01
4.77E−02
1.85E−01
4.19E−01
2.48E−12

29
3.21E−02
1.60E−05
3.06E−01
2.70E−04
3.74E−12

30
4.18E−03
1.07E−03
6.72E−03
1.01E−01
4.43E−12

31
8.38E−01
7.16E−05
2.64E−01
1.39E−03
5.33E−12

32
6.86E−02
3.50E−03
3.93E−03
1.13E−02
6.00E−12

33
5.18E−03
1.07E−03
8.59E−03
1.13E−01
7.28E−12

34
9.58E−01
1.06E−02
1.47E−01
6.26E−03
7.48E−12

35
8.10E−02
4.28E−03
4.05E−03
8.08E−03
9.72E−12

36
8.10E−02
4.28E−03
4.05E−03
8.08E−03
9.72E−12

37
8.10E−02
4.28E−03
4.05E−03
8.08E−03
9.72E−12

38
8.10E−02
4.28E−03
4.05E−03
1.56E−02
9.72E−12

39
8.13E−02
7.24E−03
5.04E−03
9.57E−03
9.74E−12

40
8.13E−02
5.09E−03
5.04E−03
1.83E−02
9.74E−12

41
8.13E−02
7.24E−03
5.04E−03
9.57E−03
9.74E−12

42
8.13E−02
7.24E−03
5.04E−03
9.57E−03
9.74E−12

43
4.13E−03
1.98E−03
1.07E−02
1.29E−01
1.06E−11

44
2.49E−03
1.32E−03
4.07E−03
1.01E−01
1.06E−11

45
2.49E−03
1.98E−03
4.07E−03
7.86E−02
1.06E−11

46
6.61E−03
1.62E−03
6.66E−03
3.47E−02
1.13E−11

47
6.86E−02
5.04E−03
3.93E−03
1.56E−02
1.64E−11

48
1.92E−03
1.62E−03
5.24E−03
1.28E−01
1.85E−11

49
3.22E−03
1.08E−03
6.76E−03
7.83E−02
1.86E−11

50
6.52E−03
4.34E−03
1.32E−02
2.40E−01
1.87E−11

TABLE 16f

Data for Pseudomonas, particularly Pseudomonas aeruginosa (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
PSPA7_5342

YP_001350673

2
PSPA7_5335

YP_001350666

3
PA39016_001160000

ZP_07794022

4
PputW619_2322

YP_001749191

5
PSPA7_0102

YP_001345498

6
PSTAB_1238
merR
YP_004713608

7
PPS_5233

YP_004704640

8
PA39016_001640030

ZP_07794960

9
PaerC_01001712

ZP_00968897

10
PA39016_001140033

ZP_07794005

11
PA39016_001790028

ZP_07795388

12
Paer2_01003738

ZP_00973073

13
PA39016_000110208

ZP_07792174

14
Paer2_01005870

ZP_00970967

15
PSPA7_0117

YP_001345513

16
PSPA7_3727

YP_001349081

17
PA39016_001140034

ZP_07794006

18
PSPA7_5254

YP_001350586

19
PputW619_2321

YP_001749190

20
PSPA7_4822

YP_001350163

21
Paer2_01002125

ZP_00974743

22
PaerPAb_010100012576

ZP_06878458

23
PA14_15470
merP
YP_789375

24
Paer2_01002118

ZP_00974736

25
PaerPA_01003088

ZP_01365958

26
PLES_26911

YP_002440283

27
PaerPA_01003092

ZP_01365962

28
Paer2_01002142

ZP_00974760

29
PSPA7_0357

YP_001345752

30
PA39016_001640027

ZP_07794957

31
PA14_49520
pyoS3A
YP_792115

32
PaerPA_01003114

ZP_01365983

33
PSPA7_3718

YP_001349072

34
PSPA7_0113
merP1
YP_001345509

35
Paer2_01002136

ZP_00974754

36
PA39016_001010047

ZP_07793693

37
PaerPA_01003095

ZP_01365965

38
PaerPA_01003132

ZP_01366001

39
Paer2_01002121

ZP_00974739

40
PLES_26591

YP_002440252

41
PSTAA_1280

AEA83190

42
PaerPA_01003094

ZP_01365964

43
PA39016_001650006

ZP_07794967

44
PA39016_001650001

ZP_07794962

45
PA14_30900

YP_790630

46
Paer2_01002387

ZP_00974497

47
Paer2_01002180

ZP_00974798

48
Avin_35690
trbE
YP_002800691

49
PA39016_001650003

ZP_07794964

50
PSPA7_3698

YP_001349052

TABLE 16g

Data for Pseudomonas, particularly

Pseudomonas aeruginosa (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
5509888
5510901
+
640753026

2
5497616
5498380
−
640753026

3
269
829
+
649999021

4
2600850
2601410
−
641522670

5
112316
112732
+
640753026

6
1298354
1298788
+
650716170

7
5930458
5930823
−
650716164

8
29403
29642
−
649999069

9
9109
10122
−
638362473

10
35241
35606
−
649999019

11
25607
28270
+
649999084

12
18240
19688
−
638362609

13
212874
213821
−
649998930

14
22370
34666
+
638362642

15
122819
123664
+
640753026

16
3864574
3865185
−
640753026

17
35624
37309
−
649999019

18
5409448
5411001
−
640753026

19
2597880
2600846
−
641522670

20
4961575
4962753
−
640753026

21
167495
167935
+
638362589

22
28
241
−
647002430

23
1310460
1310735
−
639279323

24
161059
161934
+
638362589

25
3500513
3501292
+
638372930

26
2885013
2885837
−
643348637

27
3505406
3506134
+
638372930

28
182786
184474
+
638362589

29
366452
367480
−
640753026

30
26408
27688
−
649999069

31
4403159
4405534
−
639279323

32
3528459
3529049
+
638372930

33
3855983
3856195
−
640753026

34
121405
121680
−
640753026

35
179158
179895
+
638362589

36
48194
50227
+
649999006

37
3507452
3509473
+
638372930

38
3547764
3548102
+
638372930

39
163874
164434
+
638362589

40
2856655
2857038
−
643348637

41
1367161
1367601
−
651053081

42
3506732
3507172
+
638372930

43
6653
8650
−
649999070

44
2001
4451
−
649999070

45
2683111
2683836
−
639279323

46
138340
138654
−
638362591

47
214185
216386
+
638362589

48
3640230
3642680
−
643692060

49
4730
5116
−
649999070

50
3833901
3834893
−
640753026

Example 9

Salmonella species

The procedure was carried out as in Example 1, except that the following microorganisms were used:

Bacterial Strains

The inventors selected 634 Salmonella strains, particularly from Salmonella_choleraesuis, Salmonella_dublin, Salmonella_enterica_ssp_arizonae, Salmonella_enterica_ssp_diarizoniae, Salmonella_enteritidis, Salmonella_gallinarum, Salmonella Group_A, Salmonella_Group_B, Salmonella_Group_C, Salmonella_Group_D, Salmonella_heidelberg, Salmonella_miami, Salmonella_newport, Salmonella_panama, Salmonella_parahaemolyticus_A, Salmonella_paratyphi_A, Salmonella_paratyphi_B, Salmonella_pullorum, Salmonella_senfienberg, Salmonella species, Salmonella_species_Lac_−−,_ONPG_+, Salmonella_species_Lac_+,_ONPG_+, Salmonella subgenus_I, Salmonella_subgenus_II, Salmonella_subgenus_IV, Salmonella subgroup_I_Suc+, Salmonella_tennessee, and Salmonella_typhi, from the microbiology strain collection at Siemens Healthcare Diagnostics (West Sacramento, Calif.) for susceptibility testing and whole genome sequencing.

From MetaRef, 713 centroids of Salmonella species were used as reference sequences.

The results for Salmonella species are shown in Tables 17 (corresponding to Table 1) and 18 (corresponding to Table 2).

TABLE 17a

Data for Salmonella species

Scaffold.External.

No.
Accession
Scaffold.Name
best_pv

1
NC_011083

Salmonella enterica subsp. enterica serovar Heidelberg str. SL476:
1.09817680047592e−59

NC_011083

2
NC_011092

Salmonella enterica subsp. enterica serovar Schwarzengrund str.
3.48405564494782e−42

CVM19633 plasmid pCVM19633_110: NC_011092

3
NZ_ADUB01000261

Escherichia coli MS 175-1 E_coli175-1-1.0_Cont542.3: NZ_ADUB01000261
2.50701590062067e−24

4
NC_009651

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid pKPN5:
3.64875434048827e−22

NC_009651

5
NC_013509

Edwardsiella tarda EIB202 plasmid pEIB202: NC_013509
1.44445847616457e−21

6
NZ_ABFH01000001

Salmonella enterica subsp. enterica serovar Virchow str. SL491,
3.48310596778991e−21

unfinished sequence: NZ_ABFH01000001

7
NC_011743

Escherichia fergusonii ATCC 35469 plasmid pEFER: NC_011743
3.48310596778991e−21

8
NZ_ADWV01000045

Escherichia coli MS 107-1 E_coliMS107-1-1.0.1_Cont44.1:
1.74745925214862e−20

NZ_ADWV01000045

9
NC_013509

Edwardsiella tarda EIB202 plasmid pEIB202: NC_013509
3.3130773442785e−20

10
NZ_AAJX01000089

Escherichia coli B171, unfinished sequence: NZ_AAJX01000089
5.485221922018e−20

11
NZ_AFBO01000625

Klebsiella sp. MS 92-3 K_spMS92-3-1.0_Cont1175.2: NZ_AFBO01000625
7.41649956052229e−17

12
NZ_ADTM01000311

Escherichia coli MS 182-1 E_coli182-1-1.0_Cont460.3: NZ_ADTM01000311
8.87457605302667e−17

13
CP001383

Shigella flexneri 2002017: CP001383
5.28841759700461e−14

14
NC_007384

Shigella sonnei Ss046: NC_007384
5.8995130852235e−14

15
NZ_ADUD01000537

Escherichia coli MS 196-1 E_coli196-1-1.0_Cont1482.1:
1.65276555063276e−13

NZ_ADUD01000537

16
NZ_ABFH01000001

Salmonella enterica subsp. enterica serovar Virchow str. SL491,
1.65276555063276e−13

unfinished sequence: NZ_ABFH01000001

17
NC_009650

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid pKPN4:
3.61473686772869e−13

NC_009650

18
NZ_ABFH01000001

Salmonella enterica subsp. enterica serovar Virchow str. SL491,
5.18796174101329e−13

unfinished sequence: NZ_ABFH01000001

19
NZ_ADWV01000017

Escherichia coli MS 107-1 E_coliMS107-1-1.0.1_Cont16.1:
3.37689513091676e−12

NZ_ADWV01000017

20
NZ_ADWT01000152

Escherichia coli MS 124-1 E_coliMS124-1-1.0.1_Cont151.1:
5.32683257781776e−12

NZ_ADWT01000152

21
CP001383

Shigella flexneri 2002017: CP001383
9.59412420701724e−12

22
NC_011081

Salmonella enterica subsp. enterica serovar Heidelberg str. SL476
1.80214883490127e−11

plasmid pSL476_91: NC_011081

23
AP011957

Salmonella enterica subsp. enterica serovar Typhimurium str. T000240
2.02729069966733e−11

DNA: AP011957

24
NC_009650

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid pKPN4:
2.02729069966733e−11

NC_009650

25
NC_011092

Salmonella enterica subsp. enterica serovar Schwarzengrund str.
3.62500325966221e−11

CVM19633 plasmid pCVM19633_110: NC_011092

26
NZ_ABKX01000001

Escherichia albertii TW07627, unfinished sequence: NZ_ABKX01000001
5.50212585421897e−11

27
CP002490

Salmonella enterica subsp. enterica serovar Typhimurium str. 4/74
1.68214594408478e−10

plasmid TY474p3: CP002490

28
NC_012124

Salmonella enterica subsp. enterica serovar Paratyphi C strain
8.57828076933948e−10

RKS4594 plasmid pSPCV: NC_012124

29
NC_007385

Shigella sonnei Ss046 plasmid pSS_046: NC_007385
1.06330274297554e−09

30
NC_004851

Shigella flexneri 2a str. 301 plasmid pCP301: NC_004851
2.2269317280314e−09

31
NC_003277

Salmonella typhimurium LT2 plasmid pSLT: NC_003277
2.2269317280314e−09

32
CP001362

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
1.72272938882188e−08

plasmid: CP001362

33
NZ_ABKX01000001

Escherichia albertii TW07627, unfinished sequence: NZ_ABKX01000001
1.8184047282463e−08

34
NC_012124

Salmonella enterica subsp. enterica serovar Paratyphi C strain
3.5232749457209e−08

RKS4594 plasmid pSPCV: NC_012124

35
NC_012125

Salmonella enterica subsp. enterica serovar Paratyphi C strain
4.21301623299358e−08

RKS4594: NC_012125

36
CP002487

Salmonella enterica subsp. enterica serovar Typhimurium str. 4/74:
5.49621728459414e−08

CP002487

37
NZ_ABEL01000010

Salmonella enterica subsp. enterica serovar Heidelberg str. SL486,
9.94168564125988e−08

unfinished sequence: NZ_ABEL01000010

38
NC_012124

Salmonella enterica subsp. enterica serovar Paratyphi C strain
1.81471391611537e−07

RKS4594 plasmid pSPCV: NC_012124

39
NC_012125

Salmonella enterica subsp. enterica serovar Paratyphi C strain
1.9714526298817e−07

RKS4594: NC_012125

40
NC_003197

Salmonella typhimurium LT2: NC_003197
2.16264005553646e−07

41
CP002488

Salmonella enterica subsp. enterica serovar Typhimurium str. 4/74
2.16264005553646e−07

plasmid TY474p1: CP002488

42
NZ_ABAM01000046

Salmonella enterica subsp. enterica serovar Saintpaul str. SARA23,
2.29779633234294e−07

unfinished sequence: NZ_ABAM01000046

43
NC_010102

Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7:
3.05541326329248e−07

NC_010102

44
AP011957

Salmonella enterica subsp. enterica serovar Typhimurium str. T000240
3.48861961356893e−07

DNA: AP011957

45
NC_010067

Salmonella enterica subsp. arizonae serovar 62:z4,z23:--: NC_010067
4.35325104483177e−07

46
NC_010067

Salmonella enterica subsp. arizonae serovar 62:z4,z23:--: NC_010067
4.35325104483177e−07

47
NC_015761

Salmonella bongori NCTC 12419: NC_015761
4.35325104483177e−07

48
NZ_ABEL01000010

Salmonella enterica subsp. enterica serovar Heidelberg str. SL486,
7.61833017744037e−07

unfinished sequence: NZ_ABEL01000010

49
NC_012125

Salmonella enterica subsp. enterica serovar Paratyphi C strain
8.71713912669417e−07

RKS4594: NC_012125

50
NZ_ABEJ01000032

Salmonella enterica subsp. enterica serovar Schwarzengrund str.
8.71713912669417e−07

SL480, unfinished sequence: NZ_ABEJ01000032

TABLE 17b

Data for Salmonella species (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
AM; A/S
lactam
AM
lactam

2
AM; A/S
lactam
AM
lactam

3
AM; A/S
lactam
AM
lactam

4
AM; A/S
lactam
A/S
lactam

5
AM; A/S
lactam
AM
lactam

6
AM; A/S
lactam
A/S
lactam

7
AM; A/S
lactam
AM
lactam

8
AM; A/S
lactam
A/S
lactam

9
AM; A/S
lactam
AM
lactam

10
AM; A/S
lactam
A/S
lactam

11
AM; A/S
lactam
A/S
lactam

12
AM; A/S
lactam
A/S
lactam

13
AM; A/S
lactam
AM
lactam

14
AM; A/S
lactam
A/S
lactam

15
AM; A/S
lactam
A/S
lactam

16
AM; A/S
lactam
A/S
lactam

17
AM; A/S
lactam
A/S
lactam

18
AM; A/S
lactam
A/S
lactam

19
AM; A/S
lactam
A/S
lactam

20
AM; A/S
lactam
AM
lactam

21
AM; A/S
lactam
AM
lactam

22
AM; A/S
lactam
AM
lactam

23
AM; A/S
lactam
A/S
lactam

24
AM; A/S
lactam
A/S
lactam

25
AM; A/S
lactam
A/S
lactam

26
AM; A/S
lactam
AM
lactam

27
AM; A/S
lactam
AM
lactam

28
AM; A/S
lactam
AM
lactam

29
AM; A/S
lactam
AM
lactam

30
AM; A/S
lactam
AM
lactam

31
AM; A/S
lactam
AM
lactam

32
AM; A/S
lactam
AM
lactam

33
AM; A/S
lactam
AM
lactam

34
AM; A/S
lactam
AM
lactam

35
AM; A/S
lactam
AM
lactam

36
AM; A/S
lactam
AM
lactam

37
AM; A/S
lactam
A/S
lactam

38
AM; A/S
lactam
AM
lactam

39
AM; A/S
lactam
AM
lactam

40
AM; A/S
lactam
AM
lactam

41
AM; A/S
lactam
AM
lactam

42
AM; A/S
lactam
A/S
lactam

43
AM; A/S
lactam
AM
lactam

44
AM; A/S
lactam
A/S
lactam

45
AM; A/S
lactam
A/S
lactam

46
AM; A/S
lactam
A/S
lactam

47
AM; A/S
lactam
A/S
lactam

48
AM; A/S
lactam
A/S
lactam

49
AM; A/S
lactam
A/S
lactam

50
AM; A/S
lactam
A/S
lactam

TABLE 17c

Data for Salmonella species (continued)

No.
num_lactam
AM_pv_adj
A/S_pv_adj

1
2
1.10E−59
1.70E−55

2
2
3.48E−42
1.81E−40

3
2
2.51E−24
2.30E−22

4
2
1.08E−21
3.65E−22

5
2
1.44E−21
6.88E−20

6
2
1.05E−20
3.48E−21

7
2
3.48E−21
1.05E−20

8
2
5.22E−20
1.75E−20

9
2
3.31E−20
1.15E−19

10
2
1.65E−19
5.49E−20

11
2
1.74E−16
7.42E−17

12
2
2.98E−16
8.87E−17

13
2
5.29E−14
1.45E−13

14
2
1.45E−13
5.90E−14

15
2
3.62E−13
1.65E−13

16
2
3.62E−13
1.65E−13

17
2
6.38E−13
3.61E−13

18
2
1.10E−12
5.19E−13

19
2
6.91E−12
3.38E−12

20
2
5.33E−12
3.21E−11

21
2
9.59E−12
8.71E−10

22
2
1.80E−11
6.37E−10

23
2
3.64E−11
2.03E−11

24
2
3.64E−11
2.03E−11

25
2
6.67E−11
3.63E−11

26
2
5.50E−11
4.78E−09

27
2
1.68E−10
1.06E−09

28
2
8.58E−10
2.16E−08

29
2
1.06E−09
2.10E−08

30
2
2.23E−09
3.77E−08

31
2
2.23E−09
3.77E−08

32
2
1.72E−08
2.02E−07

33
2
1.82E−08
1.76E−06

34
2
3.52E−08
8.59E−08

35
2
4.21E−08
6.33E−08

36
2
5.50E−08
7.64E−08

37
2
1.40E−07
9.94E−08

38
2
1.81E−07
3.88E−07

39
2
1.97E−07
2.71E−07

40
2
2.16E−07
2.91E−07

41
2
2.16E−07
7.75E−07

42
2
7.51E−07
2.30E−07

43
2
3.06E−07
8.87E−07

44
2
2.22E−06
3.49E−07

45
2
1.28E−06
4.35E−07

46
2
1.28E−06
4.35E−07

47
2
1.25E−06
4.35E−07

48
2
2.83E−06
7.62E−07

49
2
1.23E−06
8.72E−07

50
2
4.30E−06
8.72E−07

TABLE 17d

Data for Salmonella species (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
SeHA_C1580
blaT
YP_002045448

2
SeSA_B0079

YP_002112958
plasmid pCVM19633_110

3
HMPREF9547_03104

ZP_07169558

4
KPN_pKPN5p08201

YP_001338811
plasmid pKPN5

5
ETAE_p041
folP
YP_003297635
plasmid pEIB202

6
Salmoentericaenterica_010100000245

ZP_02702077

7
pEFER_0049

YP_002394596
plasmid pEFER

8
HMPREF9345_05066

ZP_07100147

9
ETAE_p040

YP_003297634
plasmid pEIB202

10
EcolB_01004576

ZP_00708527

11
HMPREF9538_04737

ZP_08307036

12
HMPREF9548_03784

ZP_07141588

13
SFxv_1142

ADA73400

14
SSON_3896
aadA
YP_312670

15
HMPREF9551_04611

ZP_07191964

16
Salmoentericaenterica_010100000130

ZP_02702054

17
KPN_pKPN4p07064

YP_001338673
plasmid pKPN4

18
Salmoentericaenterica_010100000105

ZP_02702049

19
HMPREF9345_03525

ZP_07098656

20
HMPREF9347_06051

ZP_07213485

21
SFxv_1141

ADA73399

22
SeHA_A0031

YP_002043869
plasmid pSL476_91

23
STMDT12_C39390

BAJ38882

24
KPN_pKPN4p07068
merC
YP_001338677
plasmid pKPN4

25
SeSA_B0082

YP_002112961
plasmid pCVM19633_110

26
ESCAB7627_0644

ZP_02900823

27
STM474_p303
repA
ADX20580
plasmid TY474p3

28
SPC_p013
rsdB
YP_002635587
plasmid pSPCV

29
SSO_P190
traD
YP_313445
plasmid pSS_046

30
CP0245
mvpA
NP_858378
plasmid pCP301

31
PSLT105
trbH
NP_490589
plasmid pSLT

32
STM14_5622
traD
ACY86531

33
ESCAB7627_0650

ZP_02900555

34
SPC_p042
traX
YP_002635616
plasmid pSPCV

35
SPC_2707

YP_002638248

36
STM474_1038

ADX16744

37
Senterienterica_010100019467

ZP_02668762

38
SPC_p041
finO
YP_002635615
plasmid pSPCV

39
SPC_2708

YP_002638249

40
STM1046

NP_460021

41
STM474_p1093
ccdB
ADX20463
plasmid TY474p1

42
Sentent_010100022581

ZP_02341659

43
SPAB_05276

YP_001591385

44
STMDT12_C10780

BAJ36021

45
SARI_01515

YP_001570553

46
SARI_01514

YP_001570552

47
SBG_1292
malR
YP_004730162

48
Senterienterica_010100019192

ZP_02668707

49
SPC_0340

YP_002635966

50
Senteenterica_010100025269

ZP_02664569

TABLE 17e

Data for Salmonella species (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
1525960
1526820
+
642555218

2
68933
70240
+
642555219

3
3248
3841
+
648291919

4
34908
35255
−
640753021

5
32101
32916
−
646311959

6
36757
37062
+
641778223

7
48658
49503
+
643692014

8
4715
5554
−
648294624

9
31237
32040
−
646311959

10
3555
4568
+
638359041

11
1555
2055
−
651333542

12
8819
9535
+
648288593

13
1108351
1108854
−
646862363

14
4110458
4111246
−
640427102

15
97
531
−
648293053

16
19257
19691
+
641778223

17
23310
24614
−
640753020

18
16271
16636
−
641778223

19
1071
1307
−
648294596

20
812
1663
−
648294425

21
1107342
1107968
+
646862363

22
16416
17195
+
642555216

23
4088051
4088326
−
651053007

24
25970
27664
−
640753020

25
71061
71411
−
642555219

26
233492
234697
−
641784575

27
1988
2827
−
650378006

28
10060
10842
−
643692029

29
166425
168626
+
640427103

30
198117
198515
−
637000224

31
86566
87285
+
637000134

32
84297
86459
+
646862361

33
238788
239996
−
641784575

34
28413
29153
−
643692029

35
2745099
2745596
−
643692030

36
1088568
1089272
+
650378003

37
62341
62874
−
641777794

38
27795
28358
−
643692029

39
2745695
2746027
−
643692030

40
1131381
1132118
+
637000122

41
73221
73526
−
650378004

42
23575
23910
−
641746440

43
4445787
4448009
+
641228523

44
1141208
1141399
−
651053007

45
1476854
1478026
+
641228515

46
1475252
1476844
+
641228515

47
1414087
1415115
+
650716177

48
26832
28046
+
641777794

49
367421
368839
+
643692030

50
35858
36535
−
641777693

TABLE 18a

Data for Salmonella species

Scaffold.External.

No.
Accession
Scaffold.Name
best_pv

1
NC_011083

Salmonella enterica subsp. enterica serovar Heidelberg str. SL476:
1.09817680047592e−59

NC_011083

2
NC_011092

Salmonella enterica subsp. enterica serovar Schwarzengrund str.
3.48405564494782e−42

CVM19633 plasmid pCVM19633_110: NC_011092

3
NZ_ADUB01000261

Escherichia coli MS 175-1 E_coli175-1-1.0_Cont542.3: NZ_ADUB01000261
2.50701590062067e−24

4
NC_009651

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid pKPN5:
3.64875434048827e−22

NC_009651

5
NC_013509

Edwardsiella tarda EIB202 plasmid pEIB202: NC_013509
1.44445847616457e−21

6
NZ_ABFH01000001

Salmonella enterica subsp. enterica serovar Virchow str. SL491,
3.48310596778991e−21

unfinished sequence: NZ_ABFH01000001

7
NC_011743

Escherichia fergusonii ATCC 35469 plasmid pEFER: NC_011743
3.48310596778991e−21

8
NZ_ADWV01000045

Escherichia coli MS 107-1 E_coliMS107-1-1.0.1_Cont44.1:
1.74745925214862e−20

NZ_ADWV01000045

9
NC_013509

Edwardsiella tarda EIB202 plasmid pEIB202: NC_013509
3.3130773442785e−20

10
NZ_AAJX01000089

Escherichia coli B171, unfinished sequence: NZ_AAJX01000089
5.485221922018e−20

11
NZ_AFBO01000625

Klebsiella sp. MS 92-3 K_spMS92-3-1.0_Cont1175.2: NZ_AFBO01000625
7.41649956052229e−17

12
NZ_ADTM01000311

Escherichia coli MS 182-1 E_coli182-1-1.0_Cont460.3: NZ_ADTM01000311
8.87457605302667e−17

13
CP001383

Shigella flexneri 2002017: CP001383
5.28841759700461e−14

14
NC_007384

Shigella sonnei Ss046: NC_007384
5.8995130852235e−14

15
NZ_ADUD01000537

Escherichia coli MS 196-1 E_coli196-1-1.0_Cont1482.1: NZ_ADUD01000537
1.65276555063276e−13

16
NZ_ABFH01000001

Salmonella enterica subsp. enterica serovar Virchow str. SL491,
1.65276555063276e−13

unfinished sequence: NZ_ABFH01000001

17
NC_009650

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid pKPN4:
3.61473686772869e−13

NC_009650

18
NZ_ABFH01000001

Salmonella enterica subsp. enterica serovar Virchow str. SL491,
5.18796174101329e−13

unfinished sequence: NZ_ABFH01000001

19
NZ_ADWV01000017

Escherichia coli MS 107-1 E_coliMS107-1-1.0.1_Cont16.1:
3.37689513091676e−12

NZ_ADWV01000017

20
NZ_ADWT01000152

Escherichia coli MS 124-1 E_coliMS124-1-1.0.1_Cont151.1:
5.32683257781776e−12

NZ_ADWT01000152

21
CP001383

Shigella flexneri 2002017: CP001383
9.59412420701724e−12

22
NC_011081

Salmonella enterica subsp. enterica serovar Heidelberg str. SL476
1.80214883490127e−11

plasmid pSL476_91: NC_011081

23
AP011957

Salmonella enterica subsp. enterica serovar Typhimurium str. T000240
2.02729069966733e−11

DNA: AP011957

24
NC_009650

Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid pKPN4:
2.02729069966733e−11

NC_009650

25
NC_011092

Salmonella enterica subsp. enterica serovar Schwarzengrund str.
3.62500325966221e−11

CVM19633 plasmid pCVM19633_110: NC_011092

26
NZ_ABKX01000001

Escherichia albertii TW07627, unfinished sequence: NZ_ABKX01000001
5.50212585421897e−11

27
CP002490

Salmonella enterica subsp. enterica serovar Typhimurium str. 4/74
1.68214594408478e−10

plasmid TY474p3: CP002490

28
NC_012124

Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
8.57828076933948e−10

plasmid pSPCV: NC_012124

29
NC_007385

Shigella sonnei Ss046 plasmid pSS_046: NC_007385
1.06330274297554e−09

30
NC_004851

Shigella flexneri 2a str. 301 plasmid pCP301: NC_004851
2.2269317280314e−09

31
NC_003277

Salmonella typhimurium LT2 plasmid pSLT: NC_003277
2.2269317280314e−09

32
CP001362

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
1.72272938882188e−08

plasmid: CP001362

33
NZ_ABKX01000001

Escherichia albertii TW07627, unfinished sequence: NZ_ABKX01000001
1.8184047282463e−08

34
NC_012124

Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
3.5232749457209e−08

plasmid pSPCV: NC_012124

35
NC_012125

Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594:
4.21301623299358e−08

NC_012125

36
CP002487

Salmonella enterica subsp. enterica serovar Typhimurium str. 4/74:
5.49621728459414e−08

CP002487

37
NZ_ABEL01000010

Salmonella enterica subsp. enterica serovar Heidelberg str. SL486,
9.94168564125988e−08

unfinished sequence: NZ_ABEL01000010

38
NC_012124

Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
1.81471391611537e−07

plasmid pSPCV: NC_012124

39
NC_012125

Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594:
1.9714526298817e−07

NC_012125

40
NC_003197

Salmonella typhimurium LT2: NC_003197
2.16264005553646e−07

41
CP002488

Salmonella enterica subsp. enterica serovar Typhimurium str. 4/74
2.16264005553646e−07

plasmid TY474p1: CP002488

42
NZ_ABAM01000046

Salmonella enterica subsp. enterica serovar Saintpaul str. SARA23,
2.29779633234294e−07

unfinished sequence: NZ_ABAM01000046

43
NC_010102

Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7:
3.05541326329248e−07

NC_010102

44
AP011957

Salmonella enterica subsp. enterica serovar Typhimurium str. T000240
3.48861961356893e−07

DNA: AP011957

45
NC_010067

Salmonella enterica subsp. arizonae serovar 62:z4,z23:--: NC_010067
4.35325104483177e−07

46
NC_010067

Salmonella enterica subsp. arizonae serovar 62:z4,z23:--: NC_010067
4.35325104483177e−07

47
NC_015761

Salmonella bongori NCTC 12419: NC_015761
4.35325104483177e−07

48
NZ_ABEL01000010

Salmonella enterica subsp. enterica serovar Heidelberg str. SL486,
7.61833017744037e−07

unfinished sequence: NZ_ABEL01000010

49
NC_012125

Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594:
8.71713912669417e−07

NC_012125

50
NZ_ABEJ01000032

Salmonella enterica subsp. enterica serovar Schwarzengrund str. SL480,
8.71713912669417e−07

unfinished sequence: NZ_ABEJ01000032

TABLE 18b

Data for Salmonella species (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
AM; A/S
lactam
AM
lactam

2
AM; A/S
lactam
AM
lactam

3
AM; A/S
lactam
AM
lactam

4
AM; A/S
lactam
A/S
lactam

5
AM; A/S
lactam
AM
lactam

6
AM; A/S
lactam
A/S
lactam

7
AM; A/S
lactam
AM
lactam

8
AM; A/S
lactam
A/S
lactam

9
AM; A/S
lactam
AM
lactam

10
AM; A/S
lactam
A/S
lactam

11
AM; A/S
lactam
A/S
lactam

12
AM; A/S
lactam
A/S
lactam

13
AM; A/S
lactam
AM
lactam

14
AM; A/S
lactam
A/S
lactam

15
AM; A/S
lactam
A/S
lactam

16
AM; A/S
lactam
A/S
lactam

17
AM; A/S
lactam
A/S
lactam

18
AM; A/S
lactam
A/S
lactam

19
AM; A/S
lactam
A/S
lactam

20
AM; A/S
lactam
AM
lactam

21
AM; A/S
lactam
AM
lactam

22
AM; A/S
lactam
AM
lactam

23
AM; A/S
lactam
A/S
lactam

24
AM; A/S
lactam
A/S
lactam

25
AM; A/S
lactam
A/S
lactam

26
AM; A/S
lactam
AM
lactam

27
AM; A/S
lactam
AM
lactam

28
AM; A/S
lactam
AM
lactam

29
AM; A/S
lactam
AM
lactam

30
AM; A/S
lactam
AM
lactam

31
AM; A/S
lactam
AM
lactam

32
AM; A/S
lactam
AM
lactam

33
AM; A/S
lactam
AM
lactam

34
AM; A/S
lactam
AM
lactam

35
AM; A/S
lactam
AM
lactam

36
AM; A/S
lactam
AM
lactam

37
AM; A/S
lactam
A/S
lactam

38
AM; A/S
lactam
AM
lactam

39
AM; A/S
lactam
AM
lactam

40
AM; A/S
lactam
AM
lactam

41
AM; A/S
lactam
AM
lactam

42
AM; A/S
lactam
A/S
lactam

43
AM; A/S
lactam
AM
lactam

44
AM; A/S
lactam
A/S
lactam

45
AM; A/S
lactam
A/S
lactam

46
AM; A/S
lactam
A/S
lactam

47
AM; A/S
lactam
A/S
lactam

48
AM; A/S
lactam
A/S
lactam

49
AM; A/S
lactam
A/S
lactam

50
AM; A/S
lactam
A/S
lactam

TABLE 18c

Data for Salmonella species (continued)

No.
num_lactam
AM_pv_adj
A/S_pv_adj

1
2
1.10E−59
1.70E−55

2
2
3.48E−42
1.81E−40

3
2
2.51E−24
2.30E−22

4
2
1.08E−21
3.65E−22

5
2
1.44E−21
6.88E−20

6
2
1.05E−20
3.48E−21

7
2
3.48E−21
1.05E−20

8
2
5.22E−20
1.75E−20

9
2
3.31E−20
1.15E−19

10
2
1.65E−19
5.49E−20

11
2
1.74E−16
7.42E−17

12
2
2.98E−16
8.87E−17

13
2
5.29E−14
1.45E−13

14
2
1.45E−13
5.90E−14

15
2
3.62E−13
1.65E−13

16
2
3.62E−13
1.65E−13

17
2
6.38E−13
3.61E−13

18
2
1.10E−12
5.19E−13

19
2
6.91E−12
3.38E−12

20
2
5.33E−12
3.21E−11

21
2
9.59E−12
8.71E−10

22
2
1.80E−11
6.37E−10

23
2
3.64E−11
2.03E−11

24
2
3.64E−11
2.03E−11

25
2
6.67E−11
3.63E−11

26
2
5.50E−11
4.78E−09

27
2
1.68E−10
1.06E−09

28
2
8.58E−10
2.16E−08

29
2
1.06E−09
2.10E−08

30
2
2.23E−09
3.77E−08

31
2
2.23E−09
3.77E−08

32
2
1.72E−08
2.02E−07

33
2
1.82E−08
1.76E−06

34
2
3.52E−08
8.59E−08

35
2
4.21E−08
6.33E−08

36
2
5.50E−08
7.64E−08

37
2
1.40E−07
9.94E−08

38
2
1.81E−07
3.88E−07

39
2
1.97E−07
2.71E−07

40
2
2.16E−07
2.91E−07

41
2
2.16E−07
7.75E−07

42
2
7.51E−07
2.30E−07

43
2
3.06E−07
8.87E−07

44
2
2.22E−06
3.49E−07

45
2
1.28E−06
4.35E−07

46
2
1.28E−06
4.35E−07

47
2
1.25E−06
4.35E−07

48
2
2.83E−06
7.62E−07

49
2
1.23E−06
8.72E−07

50
2
4.30E−06
8.72E−07

TABLE 18d

Data for Salmonella species (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
SeHA_C1580
blaT
YP_002045448

2
SeSA_B0079

YP_002112958
plasmid pCVM19633_110

3
HMPREF9547_03104

ZP_07169558

4
KPN_pKPN5p08201

YP_001338811
plasmid pKPN5

5
ETAE_p041
folP
YP_003297635
plasmid pEIB202

6
Salmoentericaenterica_010100000245

ZP_02702077

7
pEFER_0049

YP_002394596
plasmid pEFER

8
HMPREF9345_05066

ZP_07100147

9
ETAE_p040

YP_003297634
plasmid pEIB202

10
EcolB_01004576

ZP_00708527

11
HMPREF9538_04737

ZP_08307036

12
HMPREF9548_03784

ZP_07141588

13
SFxv_1142

ADA73400

14
SSON_3896
aadA
YP_312670

15
HMPREF9551_04611

ZP_07191964

16
Salmoentericaenterica_010100000130

ZP_02702054

17
KPN_pKPN4p07064

YP_001338673
plasmid pKPN4

18
Salmoentericaenterica_010100000105

ZP_02702049

19
HMPREF9345_03525

ZP_07098656

20
HMPREF9347_06051

ZP_07213485

21
SFxv_1141

ADA73399

22
SeHA_A0031

YP_002043869
plasmid pSL476_91

23
STMDT12_C39390

BAJ38882

24
KPN_pKPN4p07068
merC
YP_001338677
plasmid pKPN4

25
SeSA_B0082

YP_002112961
plasmid pCVM19633_110

26
ESCAB7627_0644

ZP_02900823

27
STM474_p303
repA
ADX20580
plasmid TY474p3

28
SPC_p013
rsdB
YP_002635587
plasmid pSPCV

29
SSO_P190
traD
YP_313445
plasmid pSS_046

30
CP0245
mvpA
NP_858378
plasmid pCP301

31
PSLT105
trbH
NP_490589
plasmid pSLT

32
STM14_5622
traD
ACY86531

33
ESCAB7627_0650

ZP_02900555

34
SPC_p042
traX
YP_002635616
plasmid pSPCV

35
SPC_2707

YP_002638248

36
STM474_1038

ADX16744

37
Senterienterica_010100019467

ZP_02668762

38
SPC_p041
finO
YP_002635615
plasmid pSPCV

39
SPC_2708

YP_002638249

40
STM1046

NP_460021

41
STM474_p1093
ccdB
ADX20463
plasmid TY474p1

42
Sentent_010100022581

ZP_02341659

43
SPAB_05276

YP_001591385

44
STMDT12_C10780

BAJ36021

45
SARI_01515

YP_001570553

46
SARI_01514

YP_001570552

47
SBG_1292
malR
YP_004730162

48
Senterienterica_010100019192

ZP_02668707

49
SPC_0340

YP_002635966

50
Senteenterica_010100025269

ZP_02664569

TABLE 18e

Data for Salmonella species (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
1525960
1526820
+
642555218

2
68933
70240
+
642555219

3
3248
3841
+
648291919

4
34908
35255
−
640753021

5
32101
32916
−
646311959

6
36757
37062
+
641778223

7
48658
49503
+
643692014

8
4715
5554
−
648294624

9
31237
32040
−
646311959

10
3555
4568
+
638359041

11
1555
2055
−
651333542

12
8819
9535
+
648288593

13
1108351
1108854
−
646862363

14
4110458
4111246
−
640427102

15
97
531
−
648293053

16
19257
19691
+
641778223

17
23310
24614
−
640753020

18
16271
16636
−
641778223

19
1071
1307
−
648294596

20
812
1663
−
648294425

21
1107342
1107968
+
646862363

22
16416
17195
+
642555216

23
4088051
4088326
−
651053007

24
25970
27664
−
640753020

25
71061
71411
−
642555219

26
233492
234697
−
641784575

27
1988
2827
−
650378006

28
10060
10842
−
643692029

29
166425
168626
+
640427103

30
198117
198515
−
637000224

31
86566
87285
+
637000134

32
84297
86459
+
646862361

33
238788
239996
−
641784575

34
28413
29153
−
643692029

35
2745099
2745596
−
643692030

36
1088568
1089272
+
650378003

37
62341
62874
−
641777794

38
27795
28358
−
643692029

39
2745695
2746027
−
643692030

40
1131381
1132118
+
637000122

41
73221
73526
−
650378004

42
23575
23910
−
641746440

43
4445787
4448009
+
641228523

44
1141208
1141399
−
651053007

45
1476854
1478026
+
641228515

46
1475252
1476844
+
641228515

47
1414087
1415115
+
650716177

48
26832
28046
+
641777794

49
367421
368839
+
643692030

50
35858
36535
−
641777693

Example 10

Serratia, particularly Serratia marcescens

The procedure was carried out as in Example 1, except that the following microorganisms were used:

Bacterial Strains

The inventors selected 437 Serratia strains from the microbiology strain collection at Siemens Healthcare Diagnostics (West Sacramento, Calif.) for susceptibility testing and whole genome sequencing.

From MetaRef, 1671 centroids of Serratia species were used as reference sequences.

The results for Serratia are shown in Tables 19 (corresponding to Table 1) and 20 (corresponding to Table 2).

TABLE 19a

Data for Serratia, particularly Serratia marcescens

Scaffold.External.

No.
Accession
Scaffold.Name
best_pv

1
NC_009832

Serratia proteamaculans 568: NC_009832
3.70422109249874e−06

2
NZ_ADBY01000058

Serratia odorifera DSM 4582 contig00061: NZ_ADBY01000058
6.00624466630552e−06

3
NZ_ADBY01000056

Serratia odorifera DSM 4582 contig00059: NZ_ADBY01000056
6.00624466630552e−06

4
NZ_ADBY01000031

Serratia odorifera DSM 4582 contig00034: NZ_ADBY01000031
8.61505367610747e−06

5
NZ_GL636422

Serratia symbiotica str. Tucson genomic scaffold contig09350:
8.61505367610747e−06

NZ_GL636422

6
NZ_ADBX01000013

Serratia odorifera 4Rx13 SODm: NZ_ADBX01000013
8.61505367610747e−06

7
NZ_ADBX01000004

Serratia odorifera 4Rx13 SODd: NZ_ADBX01000004
1.33354783010227e−05

8
NC_009832

Serratia proteamaculans 568: NC_009832
1.37889112422256e−05

9
NZ_ADBX01000010

Serratia odorifera 4Rx13 SODj: NZ_ADBX01000010
1.55998636550055e−05

10
NZ_ADBX01000013

Serratia odorifera 4Rx13 SODm: NZ_ADBX01000013
1.55998636550055e−05

11
NZ_GL636105

Serratia symbiotica str. Tucson genomic scaffold scaffold00209:
1.55998636550055e−05

NZ_GL636105

12
NC_014837

Pantoea sp. At-9b chromosome: NC_014837
1.55998636550055e−05

13
NZ_GL636364

Serratia symbiotica str. Tucson genomic scaffold contig09039:
1.55998636550055e−05

NZ_GL636364

14
NC_009832

Serratia proteamaculans 568: NC_009832
1.55998636550055e−05

15
NZ_ADBY01000048

Serratia odorifera DSM 4582 contig00051: NZ_ADBY01000048
2.17438866604963e−05

16
NZ_ADBX01000002

Serratia odorifera 4Rx13 SODb: NZ_ADBX01000002
2.94809945975299e−05

17
NZ_ADBY01000031

Serratia odorifera DSM 4582 contig00034: NZ_ADBY01000031
3.13750499443641e−05

18
NZ_ADBY01000045

Serratia odorifera DSM 4582 contig00048: NZ_ADBY01000045
3.13750499443641e−05

19
NZ_ADBY01000031

Serratia odorifera DSM 4582 contig00034: NZ_ADBY01000031
3.13750499443641e−05

20
NZ_ADBY01000058

Serratia odorifera DSM 4582 contig00061: NZ_ADBY01000058
3.13750499443641e−05

21
NZ_ADBX01000002

Serratia odorifera 4Rx13 SODb: NZ_ADBX01000002
3.43966250408489e−05

22
NZ_ADBY01000050

Serratia odorifera DSM 4582 contig00053: NZ_ADBY01000050
3.66332257629745e−05

23
NZ_ADBY01000013

Serratia odorifera DSM 4582 contig00016: NZ_ADBY01000013
3.7147650177074e−05

24
NZ_ADBY01000056

Serratia odorifera DSM 4582 contig00059: NZ_ADBY01000056
3.7147650177074e−05

25
NZ_ADBY01000026

Serratia odorifera DSM 4582 contig00029: NZ_ADBY01000026
3.7147650177074e−05

26
NZ_ADBX01000001

Serratia odorifera 4Rx13 SODa: NZ_ADBX01000001
3.77977323028027e−05

27
NZ_ADBY01000057

Serratia odorifera DSM 4582 contig00060: NZ_ADBY01000057
4.06693999812307e−05

28
NC_009832

Serratia proteamaculans 568: NC_009832
4.06693999812307e−05

29
NZ_ADBY01000057

Serratia odorifera DSM 4582 contig00060: NZ_ADBY01000057
4.06693999812307e−05

30
NZ_ADBX01000013

Serratia odorifera 4Rx13 SODm: NZ_ADBX01000013
4.06693999812307e−05

31
NZ_ADBY01000031

Serratia odorifera DSM 4582 contig00034: NZ_ADBY01000031
4.20000578456372e−05

32
NZ_ADBX01000002

Serratia odorifera 4Rx13 SODb: NZ_ADBX01000002
5.02288669357547e−05

33
NZ_ADBX01000002

Serratia odorifera 4Rx13 SODb: NZ_ADBX01000002
5.02288669357547e−05

34
NZ_ADBX01000003

Serratia odorifera 4Rx13 SODc: NZ_ADBX01000003
5.02288669357547e−05

35
NC_009832

Serratia proteamaculans 568: NC_009832
5.02288669357547e−05

36
NC_009832

Serratia proteamaculans 568: NC_009832
5.02288669357547e−05

37
NC_009832

Serratia proteamaculans 568: NC_009832
5.02288669357547e−05

38
NZ_ADBX01000004

Serratia odorifera 4Rx13 SODd: NZ_ADBX01000004
5.02288669357547e−05

39
NZ_GG657374

Citrobacter sp. 30_2 genomic scaffold supercont1.9: NZ_GG657374
5.02288669357547e−05

40
NC_009832

Serratia proteamaculans 568: NC_009832
5.02288669357547e−05

41
NC_009832

Serratia proteamaculans 568: NC_009832
5.02288669357547e−05

42
NC_009832

Serratia proteamaculans 568: NC_009832
5.02288669357547e−05

43
NZ_ADBX01000001

Serratia odorifera 4Rx13 SODa: NZ_ADBX01000001
5.02288669357547e−05

44
NZ_ADBX01000004

Serratia odorifera 4Rx13 SODd: NZ_ADBX01000004
5.02288669357547e−05

45
NZ_ADBX01000002

Serratia odorifera 4Rx13 SODb: NZ_ADBX01000002
5.02288669357547e−05

46
NZ_ADBY01000056

Serratia odorifera DSM 4582 contig00059: NZ_ADBY01000056
5.02288669357547e−05

47
NZ_ADBY01000032

Serratia odorifera DSM 4582 contig00035: NZ_ADBY01000032
5.02288669357547e−05

48
NZ_ADBY01000013

Serratia odorifera DSM 4582 contig00016: NZ_ADBY01000013
5.88044402302405e−05

49
NC_009832

Serratia proteamaculans 568: NC_009832
6.62251962114689e−05

50
NC_009832

Serratia proteamaculans 568: NC_009832
7.15986854143193e−05

TABLE 19b

Data for Serratia, particularly Serratia marcescens (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
AZT; CAX; CAZ; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

2
CP; LVX; T/S
fluoroquinolone; other
CP
fluoroquinolone

3
AZT; CAX; CP; LVX; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

4
AZT; CAX; CFT; CP; LVX; P/T; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

5
CAX; CAZ; CFT; CP; LVX; P/T
fluoroquinolone; lactam
CP
fluoroquinolone

6
AZT; CAX; CAZ; CFT; CP; LVX; P/T
fluoroquinolone; lactam
CP
fluoroquinolone

7
CAX; CFT; CP; LVX
fluoroquinolone; lactam
LVX
fluoroquinolone

8
CAX; CFT; CP; LVX; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

9
CAX; CFT; CP; LVX; TO
aminoglycoside; fluoroquinolone; lactam
LVX
fluoroquinolone

10
AZT; CAX; CAZ; CFT; CP; LVX; P/T
fluoroquinolone; lactam
CP
fluoroquinolone

11
AZT; CAX; CAZ; CFT; CP; P/T
fluoroquinolone; lactam
CAX
lactam

12
CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

13
AZT; CAX; CAZ; CFT; CP; P/T
fluoroquinolone; lactam
CAX
lactam

14
CP; LVX
fluoroquinolone
LVX
fluoroquinolone

15
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

16
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

17
AZT; CAX; CFT; CP; LVX; P/T; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

18
CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

19
AZT; CAX; CFT; CP; LVX; P/T; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

20
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

21
CAX; CP; LVX; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

22
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

23
CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

24
AZT; CAX; CAZ; CFT; P/T
lactam
CAZ
lactam

25
CAX; CFT; CP; GM; LVX; P/T
aminoglycoside; fluoroquinolone; lactam
LVX
fluoroquinolone

26
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

27
AZT; CAZ; CFT; CP; TO
aminoglycoside; fluoroquinolone; lactam
CP
fluoroquinolone

28
CAX; CP; LVX
fluoroquinolone; lactam
LVX
fluoroquinolone

29
AZT; CAZ; CFT; CP; TO
aminoglycoside; fluoroquinolone; lactam
CP
fluoroquinolone

30
AZT; CAZ; CFT; CP; TO
aminoglycoside; fluoroquinolone; lactam
CP
fluoroquinolone

31
CAX; CFT; CP; LVX; P/T; T/S
fluoroquinolone; lactam; other
P/T
lactam

32
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

33
CAX; CFT; CP; LVX; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

34
CAX; CFT; CP; LVX; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

35
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

36
AZT; CAX; CFT; CP; LVX; T/S
fluoroquinolone; lactam; other
CP
fluoroquinolone

37
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

38
CAX; CFT; CP; LVX; P/T; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

39
CP; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; other
LVX
fluoroquinolone

40
CAX; CFT; CP; LVX; P/T; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

41
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

42
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

43
CP; LVX; P/T
fluoroquinolone; lactam
LVX
fluoroquinolone

44
CAX; CFT; CP; LVX; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

45
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

46
AZT; CAX; CAZ
lactam
CAZ
lactam

47
AZT; CAX; CFT; CP; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

48
CAX; CFT; CP; LVX; P/T
fluoroquinolone; lactam
LVX
fluoroquinolone

49
CAX; CFT; CP; LVX
fluoroquinolone; lactam
LVX
fluoroquinolone

50
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

TABLE 19c

Data for Serratia, particularly Serratia marcescens (continued)

No.
num_aminoglycoside
num_fluoroquinolone
num_lactam
num_other

1
2
2
5
1

2
0
2
0
1

3
0
2
2
1

4
0
2
4
1

5
0
2
4
0

6
0
2
5
0

7
0
2
2
0

8
0
2
2
1

9
1
2
2
0

10
0
2
5
0

11
0
1
5
0

12
2
2
3
1

13
0
1
5
0

14
0
2
0
0

15
2
2
4
1

16
2
2
4
1

17
0
2
4
1

18
2
2
3
1

19
0
2
4
1

20
2
2
4
1

21
0
2
1
1

22
2
2
4
1

23
2
2
3
1

24
0
0
5
0

25
1
2
3
0

26
2
2
4
1

27
1
1
3
0

28
0
2
1
0

29
1
1
3
0

30
1
1
3
0

31
0
2
3
1

32
2
2
4
1

33
0
2
2
1

34
0
2
2
1

35
2
2
4
1

36
0
2
3
1

37
2
2
4
1

38
0
2
3
1

39
2
2
0
1

40
0
2
3
1

41
2
2
4
1

42
2
2
4
1

43
0
2
1
0

44
0
2
2
1

45
2
2
4
1

46
0
0
3
0

47
2
2
3
1

48
0
2
3
0

49
0
2
2
0

50
2
2
4
1

TABLE 19d

Data for Serratia, particularly Serratia marcescens (continued)

No.
AZT_pv_adj
CAX_pv_adj
CAZ_pv_adj
CFT_pv_adj
CP_pv_adj

1
4.82E−04
5.24E−04
6.41E−03
7.29E−04
2.27E−05

2
1.58E−01
1.39E−01
2.26E−01
3.68E−02
6.01E−06

3
6.77E−04
8.30E−03
2.51E−02
1.65E−02
2.17E−05

4
8.92E−03
3.01E−03
3.16E−01
7.90E−03
2.95E−05

5
1.60E−02
4.77E−04
5.25E−03
1.36E−04
8.62E−06

6
1.22E−03
1.22E−03
1.24E−03
4.08E−04
8.62E−06

7
3.82E−02
3.55E−03
4.51E−02
2.17E−03
7.86E−05

8
1.48E−01
5.09E−03
6.93E−02
4.93E−03
1.10E−04

9
4.53E−02
5.02E−03
3.12E−01
2.64E−03
5.13E−04

10
6.43E−04
1.61E−04
7.67E−04
8.45E−05
1.56E−05

11
3.67E−05
1.56E−05
1.56E−05
5.02E−05
6.54E−03

12
1.44E−02
6.36E−03
4.83E−02
3.41E−03
2.36E−04

13
3.67E−05
1.56E−05
1.56E−05
5.02E−05
6.54E−03

14
4.07E−01
5.36E−02
7.62E−01
4.93E−02
5.86E−04

15
1.11E−03
7.67E−04
4.28E−02
1.04E−03
4.94E−05

16
6.43E−04
1.24E−03
2.38E−02
2.68E−03
1.82E−04

17
4.26E−03
1.84E−03
6.64E−02
4.93E−03
1.22E−04

18
1.73E−02
1.76E−04
2.04E−02
5.24E−04
6.30E−04

19
4.26E−03
1.84E−03
6.64E−02
4.93E−03
1.22E−04

20
9.20E−04
1.82E−04
2.34E−02
1.48E−04
1.69E−04

21
2.19E−02
6.70E−03
1
2.46E−02
7.82E−04

22
1.55E−03
4.30E−04
6.08E−02
5.90E−04
1.52E−04

23
4.85E−02
7.20E−04
1.01E−01
6.90E−04
3.71E−05

24
2.28E−03
2.41E−03
3.71E−05
4.23E−03
1.66E−01

25
1.01E−02
3.27E−04
5.44E−02
4.95E−04
7.62E−04

26
8.18E−04
3.20E−04
4.45E−02
3.27E−04
1.53E−04

27
5.89E−04
1.07E−02
1.19E−03
3.35E−03
4.07E−05

28
2.82E−02
6.08E−03
2.88E−01
4.51E−02
1.10E−04

29
5.89E−04
1.07E−02
1.19E−03
3.35E−03
4.07E−05

30
5.89E−04
1.07E−02
1.19E−03
3.35E−03
4.07E−05

31
5.92E−02
3.15E−04
6.50E−01
1.11E−03
6.89E−03

32
1.66E−03
6.30E−04
8.28E−02
6.43E−04
3.33E−04

33
5.14E−02
1.60E−03
5.77E−02
2.64E−03
1.17E−03

34
5.14E−02
1.60E−03
5.77E−02
2.64E−03
1.17E−03

35
1.17E−03
3.15E−04
5.90E−02
3.27E−04
3.15E−04

36
1.07E−03
3.99E−03
2.05E−02
2.84E−03
5.02E−05

37
1.16E−03
5.89E−04
5.88E−02
6.07E−04
2.32E−04

38
4.11E−02
1.55E−03
5.76E−02
2.12E−03
1.15E−03

39
2.08E−02
2.04E−02
2.72E−01
3.09E−02
3.33E−04

40
5.14E−02
1.13E−03
5.80E−02
1.53E−03
1.50E−03

41
1.17E−03
3.15E−04
5.90E−02
3.27E−04
3.15E−04

42
4.30E−03
1.43E−03
1.74E−01
2.47E−03
9.38E−04

43
8.63E−02
1.24E−02
2.31E−01
1.12E−02
7.34E−04

44
5.14E−02
2.07E−03
5.80E−02
2.73E−03
1.50E−03

45
1.17E−03
3.15E−04
5.90E−02
3.27E−04
3.15E−04

46
2.22E−03
6.95E−03
5.02E−05
1.63E−02
4.21E−01

47
7.04E−03
6.21E−03
3.82E−02
3.31E−03
1.04E−04

48
3.16E−01
1.58E−03
5.58E−01
1.57E−03
7.78E−04

49
2.46E−02
8.70E−03
2.31E−01
5.07E−03
1.80E−03

50
1.55E−03
7.82E−04
5.97E−02
8.10E−04
3.15E−04

TABLE 19e

Data for Serratia, particularly Serratia marcescens (continued)

No.
GM_pv_adj
LVX_pv_adj
P/T_pv_adj
TO_pv_adj
T/S_pv_adj

1
7.29E−04
3.70E−06
4.19E−03
5.65E−04
2.79E−04

2
3.92E−02
8.62E−06
5.32E−01
5.08E−02
9.68E−03

3
3.60E−02
6.01E−06
4.96E−02
9.86E−02
1.55E−03

4
2.38E−01
8.62E−06
4.51E−04
1.33E−01
5.10E−03

5
2.87E−01
4.05E−04
5.63E−05
3.66E−02
2.11E−02

6
9.01E−01
8.10E−04
6.41E−03
4.07E−02
1.63E−01

7
3.66E−02
1.33E−05
1.49E−02
1.15E−02
2.81E−02

8
1.16E−01
1.38E−05
1.31E−02
6.43E−02
5.52E−03

9
1.25E−02
1.56E−05
5.88E−02
1.37E−03
3.00E−02

10
2.58E−01
1.22E−04
9.05E−05
4.31E−02
3.97E−02

11
2.06E−01
3.60E−01
3.67E−05
1.87E−01
3.72E−01

12
5.33E−03
1.56E−05
6.87E−03
3.46E−03
8.20E−03

13
2.06E−01
3.60E−01
3.67E−05
1.87E−01
3.72E−01

14
4.95E−02
1.56E−05
1.34E−01
1.43E−01
2.07E−02

15
2.56E−03
2.17E−05
2.35E−03
3.96E−03
4.94E−04

16
3.89E−04
2.95E−05
1.52E−03
3.51E−03
2.43E−03

17
1.48E−01
3.14E−05
2.32E−04
8.78E−02
5.89E−04

18
3.24E−03
3.14E−05
2.41E−03
4.32E−03
4.63E−03

19
1.48E−01
3.14E−05
2.32E−04
8.78E−02
5.89E−04

20
2.78E−03
3.14E−05
1.10E−03
2.42E−03
6.75E−04

21
2.77E−02
3.44E−05
5.49E−02
1.12E−01
1.40E−03

22
5.63E−03
3.66E−05
3.16E−03
5.49E−03
3.24E−03

23
3.72E−03
4.07E−05
1.76E−03
4.82E−03
3.60E−03

24
2.22E−01
1
9.74E−03
1.18E−01
2.81E−01

25
4.82E−03
3.71E−05
7.82E−04
2.06E−02
1.08E−02

26
1.24E−03
3.78E−05
1.36E−03
2.34E−03
1.55E−03

27
6.23E−01
1.02E−02
5.43E−02
8.38E−03
8.82E−02

28
5.36E−02
4.07E−05
4.63E−02
3.92E−02
1.38E−02

29
6.23E−01
1.02E−02
5.43E−02
8.38E−03
8.82E−02

30
6.23E−01
1.02E−02
5.43E−02
8.38E−03
8.82E−02

31
1.41E−01
7.82E−04
4.20E−05
3.04E−02
5.10E−03

32
2.77E−03
5.02E−05
1.37E−03
5.69E−03
2.21E−03

33
1.47E−02
5.02E−05
1.03E−02
3.27E−02
6.75E−03

34
1.47E−02
5.02E−05
1.03E−02
3.27E−02
6.75E−03

35
1.76E−03
5.02E−05
1.07E−03
4.09E−03
2.26E−03

36
2.27E−02
3.89E−04
4.16E−02
1.11E−02
6.71E−03

37
1.76E−03
5.02E−05
1.80E−03
3.17E−03
2.24E−03

38
1.48E−02
5.02E−05
8.05E−03
2.57E−02
6.70E−03

39
2.77E−03
5.02E−05
1.42E−02
2.41E−03
2.10E−04

40
1.48E−02
5.02E−05
5.52E−03
3.27E−02
6.89E−03

41
1.76E−03
5.02E−05
1.07E−03
4.09E−03
2.26E−03

42
1.31E−03
5.02E−05
5.93E−03
3.06E−03
2.21E−03

43
3.13E−02
5.02E−05
5.52E−03
1.02E−02
9.79E−02

44
1.48E−02
5.02E−05
1.06E−02
3.27E−02
6.89E−03

45
1.76E−03
5.02E−05
1.07E−03
4.09E−03
2.26E−03

46
2.06E−01
1
7.15E−02
3.33E−01
1.57E−01

47
9.28E−04
5.02E−05
6.47E−02
2.47E−03
1.76E−03

48
1.83E−02
5.88E−05
1.62E−03
1.34E−02
1.37E−02

49
9.13E−01
6.62E−05
6.12E−02
1.22E−01
1.54E−01

50
1.80E−03
7.16E−05
2.42E−03
4.20E−03
2.34E−03

TABLE 19f

Data for Serratia, particularly Serratia marcescens (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
Spro_0657

YP_001476891

2
HMPREF0758_4528

ZP_06641192

3
HMPREF0758_4282
wrbA
ZP_06640946

4
HMPREF0758_1761

ZP_06638425

5
SSYM_0272

ZP_08040542

6
SOD_m00050

ZP_06193534

7
SOD_d02380

ZP_06191491

8
Spro_3910

YP_001480133

9
SOD_j00160

ZP_06193066

10
SOD_m00140

ZP_06193543

11
SSYM_0779

ZP_08038782

12
Pat9b_2844

YP_004116700

13
SSYM_0215

ZP_08040491

14
Spro_1286

YP_001477518

15
HMPREF0758_3087
paaY
ZP_06639751

16
SOD_b04490

ZP_06190513

17
HMPREF0758_1765

ZP_06638429

18
HMPREF0758_2630
deoR
ZP_06639294

19
HMPREF0758_1762
vtaK
ZP_06638426

20
HMPREF0758_4768
yedI
ZP_06641432

21
SOD_b01290

ZP_06190194

22
HMPREF0758_3449
mdtJ
ZP_06640113

23
HMPREF0758_0340

ZP_06637004

24
HMPREF0758_4122
dnaC
ZP_06640786

25
HMPREF0758_1641
pepE
ZP_06638305

26
SOD_a01780

ZP_06189226

27
HMPREF0758_4410

ZP_06641074

28
Spro_0998

YP_001477230

29
HMPREF0758_4409

ZP_06641073

30
SOD_m00010

ZP_06193530

31
HMPREF0758_1747

ZP_06638411

32
SOD_b01600

ZP_06190225

33
SOD_b01460

ZP_06190211

34
SOD_c02470

ZP_06190898

35
Spro_2856

YP_001479085

36
Spro_1467

YP_001477699

37
Spro_1011

YP_001477243

38
SOD_d01640

ZP_06191418

39
CSAG_04704

ZP_04558356

40
Spro_0906

YP_001477140

41
Spro_2853

YP_001479082

42
Spro_4574

YP_001480795

43
SOD_a08590

ZP_06189897

44
SOD_d03490

ZP_06191602

45
SOD_b05060

ZP_06190570

46
HMPREF0758_4124
cpaE
ZP_06640788

47
HMPREF0758_1879
yhcC
ZP_06638543

48
HMPREF0758_0325
apbE
ZP_06636989

49
Spro_2867

YP_001479096

50
Spro_0904

YP_001477138

TABLE 19g

Data for Serratia, particularly Serratia marcescens (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
721013
721786
+
640753091

2
113063
113683
+
647012891

3
196203
196802
+
647012889

4
14537
15286
+
647012864

5
1
622
+
651285392

6
5289
5756
−
647012829

7
276617
277270
−
647012820

8
4328564
4329223
+
640753091

9
10640
11029
−
647012826

10
12102
12680
−
647012829

11
54235
55095
−
651285075

12
3117915
3119003
−
649633106

13
1
203
+
651285334

14
1415512
1416153
−
640753091

15
166028
166624
−
647012881

16
563304
564224
−
647012818

17
17164
19063
+
647012864

18
1577
1921
+
647012878

19
15286
15990
+
647012864

20
357014
357931
−
647012891

21
207219
208373
−
647012818

22
144943
145311
+
647012883

23
46700
47314
−
647012846

24
40618
41358
−
647012889

25
66823
67548
+
647012859

26
183381
184292
+
647012817

27
12440
13084
−
647012890

28
1101888
1102271
+
640753091

29
11210
12427
−
647012890

30
189
1409
−
647012829

31
1316
1822
+
647012864

32
243135
244313
−
647012818

33
227360
228310
+
647012818

34
276786
277940
−
647012819

35
3134756
3135724
−
640753091

36
1599118
1600077
+
640753091

37
1112389
1113570
−
640753091

38
196893
197789
−
647012820

39
17332
17544
−
646206740

40
1005118
1006293
+
640753091

41
3131862
3132830
−
640753091

42
5048349
5049131
−
640753091

43
927700
928224
+
647012817

44
395510
396043
+
647012820

45
616091
617041
−
647012818

46
42335
42577
−
647012889

47
107941
108870
+
647012865

48
30480
31511
−
647012846

49
3146974
3147780
−
640753091

50
1003277
1004080
+
640753091

TABLE 20a

Data for Serratia, particularly Serratia marcescens

Scaffold.External.

No.
Accession
Scaffold.Name
best_pv

1
NC_009832

Serratia proteamaculans 568: NC_009832
3.70422109249874e−06

2
NZ_ADBY01000058

Serratia odorifera DSM 4582 contig00061: NZ_ADBY01000058
6.00624466630552e−06

3
NZ_ADBY01000056

Serratia odorifera DSM 4582 contig00059: NZ_ADBY01000056
6.00624466630552e−06

4
NZ_ADBY01000031

Serratia odorifera DSM 4582 contig00034: NZ_ADBY01000031
8.61505367610747e−06

5
NZ_GL636422

Serratia symbiotica str. Tucson genomic scaffold contig09350:
8.61505367610747e−06

NZ_GL636422

6
NZ_ADBX01000013

Serratia odorifera 4Rx13 SODm: NZ_ADBX01000013
8.61505367610747e−06

7
NZ_ADBX01000004

Serratia odorifera 4Rx13 SODd: NZ_ADBX01000004
1.33354783010227e−05

8
NC_009832

Serratia proteamaculans 568: NC_009832
1.37889112422256e−05

9
NZ_ADBX01000010

Serratia odorifera 4Rx13 SODj: NZ_ADBX01000010
1.55998636550055e−05

10
NZ_ADBX01000013

Serratia odorifera 4Rx13 SODm: NZ_ADBX01000013
1.55998636550055e−05

11
NZ_GL636105

Serratia symbiotica str. Tucson genomic scaffold scaffold00209:
1.55998636550055e−05

NZ_GL636105

12
NC_014837

Pantoea sp. At-9b chromosome: NC_014837
1.55998636550055e−05

13
NZ_GL636364

Serratia symbiotica str. Tucson genomic scaffold contig09039:
1.55998636550055e−05

NZ_GL636364

14
NC_009832

Serratia proteamaculans 568: NC_009832
1.55998636550055e−05

15
NZ_ADBY01000048

Serratia odorifera DSM 4582 contig00051: NZ_ADBY01000048
2.17438866604963e−05

16
NZ_ADBX01000002

Serratia odorifera 4Rx13 SODb: NZ_ADBX01000002
2.94809945975299e−05

17
NZ_ADBY01000031

Serratia odorifera DSM 4582 contig00034: NZ_ADBY01000031
3.13750499443641e−05

18
NZ_ADBY01000045

Serratia odorifera DSM 4582 contig00048: NZ_ADBY01000045
3.13750499443641e−05

19
NZ_ADBY01000031

Serratia odorifera DSM 4582 contig00034: NZ_ADBY01000031
3.13750499443641e−05

20
NZ_ADBY01000058

Serratia odorifera DSM 4582 contig00061: NZ_ADBY01000058
3.13750499443641e−05

21
NZ_ADBX01000002

Serratia odorifera 4Rx13 SODb: NZ_ADBX01000002
3.43966250408489e−05

22
NZ_ADBY01000050

Serratia odorifera DSM 4582 contig00053: NZ_ADBY01000050
3.66332257629745e−05

23
NZ_ADBY01000013

Serratia odorifera DSM 4582 contig00016: NZ_ADBY01000013
3.7147650177074e−05

24
NZ_ADBY01000056

Serratia odorifera DSM 4582 contig00059: NZ_ADBY01000056
3.7147650177074e−05

25
NZ_ADBY01000026

Serratia odorifera DSM 4582 contig00029: NZ_ADBY01000026
3.7147650177074e−05

26
NZ_ADBX01000001

Serratia odorifera 4Rx13 SODa: NZ_ADBX01000001
3.77977323028027e−05

27
NC_009832

Serratia proteamaculans 568: NC_009832
4.06693999812307e−05

28
NZ_ADBY01000031

Serratia odorifera DSM 4582 contig00034: NZ_ADBY01000031
4.20000578456372e−05

29
NZ_ADBX01000002

Serratia odorifera 4Rx13 SODb: NZ_ADBX01000002
5.02288669357547e−05

30
NZ_ADBX01000002

Serratia odorifera 4Rx13 SODb: NZ_ADBX01000002
5.02288669357547e−05

31
NZ_ADBX01000003

Serratia odorifera 4Rx13 SODc: NZ_ADBX01000003
5.02288669357547e−05

32
NC_009832

Serratia proteamaculans 568: NC_009832
5.02288669357547e−05

33
NC_009832

Serratia proteamaculans 568: NC_009832
5.02288669357547e−05

34
NC_009832

Serratia proteamaculans 568: NC_009832
5.02288669357547e−05

35
NZ_ADBX01000004

Serratia odorifera 4Rx13 SODd: NZ_ADBX01000004
5.02288669357547e−05

36
NZ_GG657374

Citrobacter sp. 30_2 genomic scaffold supercont1.9: NZ_GG657374
5.02288669357547e−05

37
NC_009832

Serratia proteamaculans 568: NC_009832
5.02288669357547e−05

38
NC_009832

Serratia proteamaculans 568: NC_009832
5.02288669357547e−05

39
NC_009832

Serratia proteamaculans 568: NC_009832
5.02288669357547e−05

40
NZ_ADBX01000001

Serratia odorifera 4Rx13 SODa: NZ_ADBX01000001
5.02288669357547e−05

41
NZ_ADBX01000004

Serratia odorifera 4Rx13 SODd: NZ_ADBX01000004
5.02288669357547e−05

42
NZ_ADBX01000002

Serratia odorifera 4Rx13 SODb: NZ_ADBX01000002
5.02288669357547e−05

43
NZ_ADBY01000032

Serratia odorifera DSM 4582 contig00035: NZ_ADBY01000032
5.02288669357547e−05

44
NZ_ADBY01000013

Serratia odorifera DSM 4582 contig00016: NZ_ADBY01000013
5.88044402302405e−05

45
NC_009832

Serratia proteamaculans 568: NC_009832
6.62251962114689e−05

46
NC_009832

Serratia proteamaculans 568: NC_009832
7.15986854143193e−05

47
NZ_ADBX01000002

Serratia odorifera 4Rx13 SODb: NZ_ADBX01000002
7.1811098690049e−05

48
NC_009832

Serratia proteamaculans 568: NC_009832
7.1811098690049e−05

49
NC_009832

Serratia proteamaculans 568: NC_009832
7.1811098690049e−05

50
NZ_ADBY01000036

Serratia odorifera DSM 4582 contig00039: NZ_ADBY01000036
7.1811098690049e−05

TABLE 20b

Data for Serratia, particularly Serratia marcescens (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
AZT; CAX; CAZ; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

2
CP; LVX; T/S
fluoroquinolone; other
CP
fluoroquinolone

3
AZT; CAX; CP; LVX; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

4
AZT; CAX; CFT; CP; LVX; P/T; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

5
CAX; CAZ; CFT; CP; LVX; P/T
fluoroquinolone; lactam
CP
fluoroquinolone

6
AZT; CAX; CAZ; CFT; CP; LVX; P/T
fluoroquinolone; lactam
CP
fluoroquinolone

7
CAX; CFT; CP; LVX
fluoroquinolone; lactam
LVX
fluoroquinolone

8
CAX; CFT; CP; LVX; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

9
CAX; CFT; CP; LVX; TO
aminoglycoside; fluoroquinolone; lactam
LVX
fluoroquinolone

10
AZT; CAX; CAZ; CFT; CP; LVX; P/T
fluoroquinolone; lactam
CP
fluoroquinolone

11
AZT; CAX; CAZ; CFT; CP; P/T
fluoroquinolone; lactam
CAX
lactam

12
CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

13
AZT; CAX; CAZ; CFT; CP; P/T
fluoroquinolone; lactam
CAX
lactam

14
CP; LVX
fluoroquinolone
LVX
fluoroquinolone

15
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

16
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

17
AZT; CAX; CFT; CP; LVX; P/T; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

18
CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

19
AZT; CAX; CFT; CP; LVX; P/T; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

20
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

21
CAX; CP; LVX; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

22
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

23
CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
CP
fluoroquinolone

24
AZT; CAX; CAZ; CFT; P/T
lactam
CAZ
lactam

25
CAX; CFT; CP; GM; LVX; P/T
aminoglycoside; fluoroquinolone; lactam
LVX
fluoroquinolone

26
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

27
CAX; CP; LVX
fluoroquinolone; lactam
LVX
fluoroquinolone

28
CAX; CFT; CP; LVX; P/T; T/S
fluoroquinolone; lactam; other
P/T
lactam

29
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

30
CAX; CFT; CP; LVX; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

31
CAX; CFT; CP; LVX; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

32
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

33
AZT; CAX; CFT; CP; LVX; T/S
fluoroquinolone; lactam; other
CP
fluoroquinolone

34
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

35
CAX; CFT; CP; LVX; P/T; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

36
CP; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; other
LVX
fluoroquinolone

37
CAX; CFT; CP; LVX; P/T; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

38
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

39
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

40
CP; LVX; P/T
fluoroquinolone; lactam
LVX
fluoroquinolone

41
CAX; CFT; CP; LVX; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

42
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

43
AZT; CAX; CFT; CP; GM; LVX; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

44
CAX; CFT; CP; LVX; P/T
fluoroquinolone; lactam
LVX
fluoroquinolone

45
CAX; CFT; CP; LVX
fluoroquinolone; lactam
LVX
fluoroquinolone

46
AZT; CAX; CFT; CP; GM; LVX; P/T; TO; T/S
aminoglycoside; fluoroquinolone; lactam; other
LVX
fluoroquinolone

47
AZT; CAX; CFT; CP; LVX; P/T; TO
aminoglycoside; fluoroquinolone; lactam
CP
fluoroquinolone

48
CAX; CFT; CP; LVX; T/S
fluoroquinolone; lactam; other
LVX
fluoroquinolone

49
CFT; CP; LVX
fluoroquinolone; lactam
LVX
fluoroquinolone

50
AZT; CAX; CFT; CP; GM; LVX; P/T
aminoglycoside; fluoroquinolone; lactam
CAX
lactam

TABLE 20c

Data for Serratia, particularly Serratia marcescens (continued)

No.
num_aminoglycoside
num_fluoroquinolone
num_lactam
num_other

1
2
2
5
1

2
0
2
0
1

3
0
2
2
1

4
0
2
4
1

5
0
2
4
0

6
0
2
5
0

7
0
2
2
0

8
0
2
2
1

9
1
2
2
0

10
0
2
5
0

11
0
1
5
0

12
2
2
3
1

13
0
1
5
0

14
0
2
0
0

15
2
2
4
1

16
2
2
4
1

17
0
2
4
1

18
2
2
3
1

19
0
2
4
1

20
2
2
4
1

21
0
2
1
1

22
2
2
4
1

23
2
2
3
1

24
0
0
5
0

25
1
2
3
0

26
2
2
4
1

27
0
2
1
0

28
0
2
3
1

29
2
2
4
1

30
0
2
2
1

31
0
2
2
1

32
2
2
4
1

33
0
2
3
1

34
2
2
4
1

35
0
2
3
1

36
2
2
0
1

37
0
2
3
1

38
2
2
4
1

39
2
2
4
1

40
0
2
1
0

41
0
2
2
1

42
2
2
4
1

43
2
2
3
1

44
0
2
3
0

45
0
2
2
0

46
2
2
4
1

47
1
2
4
0

48
0
2
2
1

49
0
2
1
0

50
1
2
4
0

TABLE 20d

Data for Serratia, particularly Serratia marcescens (continued)

No.
AZT_pv_adj
CAX_pv_adj
CAZ_pv_adj
CFT_pv_adj
CP_pv_adj

1
4.82E−04
5.24E−04
6.41E−03
7.29E−04
2.27E−05

2
1.58E−01
1.39E−01
2.26E−01
3.68E−02
6.01E−06

3
6.77E−04
8.30E−03
2.51E−02
1.65E−02
2.17E−05

4
8.92E−03
3.01E−03
3.16E−01
7.90E−03
2.95E−05

5
1.60E−02
4.77E−04
5.25E−03
1.36E−04
8.62E−06

6
1.22E−03
1.22E−03
1.24E−03
4.08E−04
8.62E−06

7
3.82E−02
3.55E−03
4.51E−02
2.17E−03
7.86E−05

8
1.48E−01
5.09E−03
6.93E−02
4.93E−03
1.10E−04

9
4.53E−02
5.02E−03
3.12E−01
2.64E−03
5.13E−04

10
6.43E−04
1.61E−04
7.67E−04
8.45E−05
1.56E−05

11
3.67E−05
1.56E−05
1.56E−05
5.02E−05
6.54E−03

12
1.44E−02
6.36E−03
4.83E−02
3.41E−03
2.36E−04

13
3.67E−05
1.56E−05
1.56E−05
5.02E−05
6.54E−03

14
4.07E−01
5.36E−02
7.62E−01
4.93E−02
5.86E−04

15
1.11E−03
7.67E−04
4.28E−02
1.04E−03
4.94E−05

16
6.43E−04
1.24E−03
2.38E−02
2.68E−03
1.82E−04

17
4.26E−03
1.84E−03
6.64E−02
4.93E−03
1.22E−04

18
1.73E−02
1.76E−04
2.04E−02
5.24E−04
6.30E−04

19
4.26E−03
1.84E−03
6.64E−02
4.93E−03
1.22E−04

20
9.20E−04
1.82E−04
2.34E−02
1.48E−04
1.69E−04

21
2.19E−02
6.70E−03
1
2.46E−02
7.82E−04

22
1.55E−03
4.30E−04
6.08E−02
5.90E−04
1.52E−04

23
4.85E−02
7.20E−04
1.01E−01
6.90E−04
3.71E−05

24
2.28E−03
2.41E−03
3.71E−05
4.23E−03
1.66E−01

25
1.01E−02
3.27E−04
5.44E−02
4.95E−04
7.62E−04

26
8.18E−04
3.20E−04
4.45E−02
3.27E−04
1.53E−04

27
2.82E−02
6.08E−03
2.88E−01
4.51E−02
1.10E−04

28
5.92E−02
3.15E−04
6.50E−01
1.11E−03
6.89E−03

29
1.66E−03
6.30E−04
8.28E−02
6.43E−04
3.33E−04

30
5.14E−02
1.60E−03
5.77E−02
2.64E−03
1.17E−03

31
5.14E−02
1.60E−03
5.77E−02
2.64E−03
1.17E−03

32
1.17E−03
3.15E−04
5.90E−02
3.27E−04
3.15E−04

33
1.07E−03
3.99E−03
2.05E−02
2.84E−03
5.02E−05

34
1.16E−03
5.89E−04
5.88E−02
6.07E−04
2.32E−04

35
4.11E−02
1.55E−03
5.76E−02
2.12E−03
1.15E−03

36
2.08E−02
2.04E−02
2.72E−01
3.09E−02
3.33E−04

37
5.14E−02
1.13E−03
5.80E−02
1.53E−03
1.50E−03

38
1.17E−03
3.15E−04
5.90E−02
3.27E−04
3.15E−04

39
4.30E−03
1.43E−03
1.74E−01
2.47E−03
9.38E−04

40
8.63E−02
1.24E−02
2.31E−01
1.12E−02
7.34E−04

41
5.14E−02
2.07E−03
5.80E−02
2.73E−03
1.50E−03

42
1.17E−03
3.15E−04
5.90E−02
3.27E−04
3.15E−04

43
7.04E−03
6.21E−03
3.82E−02
3.31E−03
1.04E−04

44
3.16E−01
1.58E−03
5.58E−01
1.57E−03
7.78E−04

45
2.46E−02
8.70E−03
2.31E−01
5.07E−03
1.80E−03

46
1.55E−03
7.82E−04
5.97E−02
8.10E−04
3.15E−04

47
2.96E−04
2.61E−03
5.49E−02
3.46E−03
7.18E−05

48
5.20E−02
2.61E−03
5.87E−02
3.46E−03
1.53E−03

49
2.15E−01
1.36E−02
2.60E−01
9.12E−03
1.92E−04

50
2.93E−03
7.18E−05
2.88E−02
7.18E−05
1.15E−03

TABLE 20e

Data for Serratia, particularly Serratia marcescens (continued)

No.
GM_pv_adj
LVX_pv_adj
P/T_pv_adj
TO_pv_adj
T/S_pv_adj

1
7.29E−04
3.70E−06
4.19E−03
5.65E−04
2.79E−04

2
3.92E−02
8.62E−06
5.32E−01
5.08E−02
9.68E−03

3
3.60E−02
6.01E−06
4.96E−02
9.86E−02
1.55E−03

4
2.38E−01
8.62E−06
4.51E−04
1.33E−01
5.10E−03

5
2.87E−01
4.05E−04
5.63E−05
3.66E−02
2.11E−02

6
9.01E−01
8.10E−04
6.41E−03
4.07E−02
1.63E−01

7
3.66E−02
1.33E−05
1.49E−02
1.15E−02
2.81E−02

8
1.16E−01
1.38E−05
1.31E−02
6.43E−02
5.52E−03

9
1.25E−02
1.56E−05
5.88E−02
1.37E−03
3.00E−02

10
2.58E−01
1.22E−04
9.05E−05
4.31E−02
3.97E−02

11
2.06E−01
3.60E−01
3.67E−05
1.87E−01
3.72E−01

12
5.33E−03
1.56E−05
6.87E−03
3.46E−03
8.20E−03

13
2.06E−01
3.60E−01
3.67E−05
1.87E−01
3.72E−01

14
4.95E−02
1.56E−05
1.34E−01
1.43E−01
2.07E−02

15
2.56E−03
2.17E−05
2.35E−03
3.96E−03
4.94E−04

16
3.89E−04
2.95E−05
1.52E−03
3.51E−03
2.43E−03

17
1.48E−01
3.14E−05
2.32E−04
8.78E−02
5.89E−04

18
3.24E−03
3.14E−05
2.41E−03
4.32E−03
4.63E−03

19
1.48E−01
3.14E−05
2.32E−04
8.78E−02
5.89E−04

20
2.78E−03
3.14E−05
1.10E−03
2.42E−03
6.75E−04

21
2.77E−02
3.44E−05
5.49E−02
1.12E−01
1.40E−03

22
5.63E−03
3.66E−05
3.16E−03
5.49E−03
3.24E−03

23
3.72E−03
4.07E−05
1.76E−03
4.82E−03
3.60E−03

24
2.22E−01
1
9.74E−03
1.18E−01
2.81E−01

25
4.82E−03
3.71E−05
7.82E−04
2.06E−02
1.08E−02

26
1.24E−03
3.78E−05
1.36E−03
2.34E−03
1.55E−03

27
5.36E−02
4.07E−05
4.63E−02
3.92E−02
1.38E−02

28
1.41E−01
7.82E−04
4.20E−05
3.04E−02
5.10E−03

29
2.77E−03
5.02E−05
1.37E−03
5.69E−03
2.21E−03

30
1.47E−02
5.02E−05
1.03E−02
3.27E−02
6.75E−03

31
1.47E−02
5.02E−05
1.03E−02
3.27E−02
6.75E−03

32
1.76E−03
5.02E−05
1.07E−03
4.09E−03
2.26E−03

33
2.27E−02
3.89E−04
4.16E−02
1.11E−02
6.71E−03

34
1.76E−03
5.02E−05
1.80E−03
3.17E−03
2.24E−03

35
1.48E−02
5.02E−05
8.05E−03
2.57E−02
6.70E−03

36
2.77E−03
5.02E−05
1.42E−02
2.41E−03
2.10E−04

37
1.48E−02
5.02E−05
5.52E−03
3.27E−02
6.89E−03

38
1.76E−03
5.02E−05
1.07E−03
4.09E−03
2.26E−03

39
1.31E−03
5.02E−05
5.93E−03
3.06E−03
2.21E−03

40
3.13E−02
5.02E−05
5.52E−03
1.02E−02
9.79E−02

41
1.48E−02
5.02E−05
1.06E−02
3.27E−02
6.89E−03

42
1.76E−03
5.02E−05
1.07E−03
4.09E−03
2.26E−03

43
9.28E−04
5.02E−05
6.47E−02
2.47E−03
1.76E−03

44
1.83E−02
5.88E−05
1.62E−03
1.34E−02
1.37E−02

45
9.13E−01
6.62E−05
6.12E−02
1.22E−01
1.54E−01

46
1.80E−03
7.16E−05
2.42E−03
4.20E−03
2.34E−03

47
4.20E−02
8.45E−05
9.22E−03
6.72E−03
1.09E−02

48
1.50E−02
7.18E−05
1.34E−02
4.14E−02
9.77E−03

49
4.30E−02
7.18E−05
3.73E−02
2.25E−02
1.57E−02

50
4.68E−03
1.51E−04
1.15E−03
2.57E−02
1.67E−02

TABLE 20f

Data for Serratia, particularly Serratia marcescens (continued)

Gene.
GenBank.

No.
Locus.Tag
Symbol
Accession
Chromosome

1
Spro_0657

YP_001476891

2
HMPREF0758_4528

ZP_06641192

3
HMPREF0758_4282
wrbA
ZP_06640946

4
HMPREF0758_1761

ZP_06638425

5
SSYM_0272

ZP_08040542

6
SOD_m00050

ZP_06193534

7
SOD_d02380

ZP_06191491

8
Spro_3910

YP_001480133

9
SOD_j00160

ZP_06193066

10
SOD_m00140

ZP_06193543

11
SSYM_0779

ZP_08038782

12
Pat9b_2844

YP_004116700

13
SSYM_0215

ZP_08040491

14
Spro_1286

YP_001477518

15
HMPREF0758_3087
paaY
ZP_06639751

16
SOD_b04490

ZP_06190513

17
HMPREF0758_1765

ZP_06638429

18
HMPREF0758_2630
deoR
ZP_06639294

19
HMPREF0758_1762
vtaK
ZP_06638426

20
HMPREF0758_4768
yedI
ZP_06641432

21
SOD_b01290

ZP_06190194

22
HMPREF0758_3449
mdtJ
ZP_06640113

23
HMPREF0758_0340

ZP_06637004

24
HMPREF0758_4122
dnaC
ZP_06640786

25
HMPREF0758_1641
pepE
ZP_06638305

26
SOD_a01780

ZP_06189226

27
Spro_0998

YP_001477230

28
HMPREF0758_1747

ZP_06638411

29
SOD_b01600

ZP_06190225

30
SOD_b01460

ZP_06190211

31
SOD_c02470

ZP_06190898

32
Spro_2856

YP_001479085

33
Spro_1467

YP_001477699

34
Spro_1011

YP_001477243

35
SOD_d01640

ZP_06191418

36
CSAG_04704

ZP_04558356

37
Spro_0906

YP_001477140

38
Spro_2853

YP_001479082

39
Spro_4574

YP_001480795

40
SOD_a08590

ZP_06189897

41
SOD_d03490

ZP_06191602

42
SOD_b05060

ZP_06190570

43
HMPREF0758_1879
yhcC
ZP_06638543

44
HMPREF0758_0325
apbE
ZP_06636989

45
Spro_2867

YP_001479096

46
Spro_0904

YP_001477138

47
SOD_b01270

ZP_06190192

48
Spro_4454

YP_001480676

49
Spro_4262

YP_001480484

50
HMPREF0758_2167
hrpB
ZP_06638831

TABLE 20g

Data for Serratia, particularly Serratia marcescens (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
721013
721786
+
640753091

2
113063
113683
+
647012891

3
196203
196802
+
647012889

4
14537
15286
+
647012864

5
1
622
+
651285392

6
5289
5756
−
647012829

7
276617
277270
−
647012820

8
4328564
4329223
+
640753091

9
10640
11029
−
647012826

10
12102
12680
−
647012829

11
54235
55095
−
651285075

12
3117915
3119003
−
649633106

13
1
203
+
651285334

14
1415512
1416153
−
640753091

15
166028
166624
−
647012881

16
563304
564224
−
647012818

17
17164
19063
+
647012864

18
1577
1921
+
647012878

19
15286
15990
+
647012864

20
357014
357931
−
647012891

21
207219
208373
−
647012818

22
144943
145311
+
647012883

23
46700
47314
−
647012846

24
40618
41358
−
647012889

25
66823
67548
+
647012859

26
183381
184292
+
647012817

27
1101888
1102271
+
640753091

28
1316
1822
+
647012864

29
243135
244313
−
647012818

30
227360
228310
+
647012818

31
276786
277940
−
647012819

32
3134756
3135724
−
640753091

33
1599118
1600077
+
640753091

34
1112389
1113570
−
640753091

35
196893
197789
−
647012820

36
17332
17544
−
646206740

37
1005118
1006293
+
640753091

38
3131862
3132830
−
640753091

39
5048349
5049131
−
640753091

40
927700
928224
+
647012817

41
395510
396043
+
647012820

42
616091
617041
−
647012818

43
107941
108870
+
647012865

44
30480
31511
−
647012846

45
3146974
3147780
−
640753091

46
1003277
1004080
+
640753091

47
202590
204044
−
647012818

48
4927194
4927727
+
640753091

49
4725710
4726606
−
640753091

50
70350
72779
+
647012869

Example 11

Shigella

The procedure was carried out as in Example 1, except that the following microorganisms were used:

Bacterial Strains

The inventors selected 442 Shigella strains, particularly Shigella boydii, Shigella dysenteriae, Shigella flexneri, Shigella sonnei and other Shigella species, from the microbiology strain collection at Siemens Healthcare Diagnostics (West Sacramento, Calif.) for susceptibility testing and whole genome sequencing.

From MetaRef, 730 centroids of Shigella species were used as reference sequences.

The results for Shigella species are shown in Tables 21 (corresponding to Table 1) and 22 (corresponding to Table 2).

TABLE 21a

Data for Shigella species

Scaffold.External.

No.
Accession
Scaffold.Name
best_pv

1
NZ_ADUB01000093

Escherichia coli MS 175-1 E_coli175-1-1.0_Cont166.1: NZ_ADUB01000093
6.86676649351252e−56

2
NZ_ADUD01000475

Escherichia coli MS 196-1 E_coli196-1-1.0_Cont1343.1: NZ_ADUD01000475
4.14817893591733e−46

3
N Z_ADWT01000006

Escherichia coli MS 124-1 E_coliMS124-1-1.0.1_Cont5.1: NZ_ADWT01000006
4.14817893591733e−46

4
AP011957

Salmonella enterica subsp. enterica serovar Typhimurium str. T000240
1.24332752332433e−44

DNA: AP011957

5
CP001383

Shigella flexneri 2002017: CP001383
5.69762827081762e−37

6
NZ_AAMJ01000001

Shigella dysenteriae 1012, unfinished sequence: NZ_AAMJ01000001
3.04086824044829e−34

7
NZ_ADUB01000227

Escherichia coli MS 175-1 E_coli175-1-1.0_Cont422.2: NZ_ADUB01000227
3.04086824044829e−34

8
NZ_AAMJ01000001

Shigella dysenteriae 1012, unfinished sequence: NZ_AAMJ01000001
5.67507153238613e−34

9
CP001383

Shigella flexneri 2002017: CP001383
1.46728061376833e−26

10
NZ_ADUB01000365

Escherichia coli MS 175-1 E_coli175-1-1.0_Cont823.2: NZ_ADUB01000365
4.97695865217724e−26

11
NZ_ADUB01000054

Escherichia coli MS 175-1 E_coli175-1-1.0_Cont100.1: NZ_ADUB01000054
1.31351033204593e−24

12
CP001383

Shigella flexneri 2002017: CP001383
1.66700615646725e−24

13
NC_013509

Edwardsiella tarda EIB202 plasmid pEIB202: NC_013509
3.081692811393e−24

14
NZ_ABKX01000001

Escherichia albertii TW07627, unfinished sequence: NZ_ABKX01000001
3.45432516278107e−24

15
NC_007384

Shigella sonnei Ss046: NC_007384
4.84345172785563e−23

16
CP001383

Shigella flexneri 2002017: CP001383
1.59570448713613e−17

17
NZ_ADUT01000002

Shigella dysenteriae 1617 gss1617.assembly.11: NZ_ADUT01000002
4.66906657298136e−17

18
NZ_ABKX01000001

Escherichia albertii TW07627, unfinished sequence: NZ_ABKX01000001
5.88113462200155e−17

19
NZ_ADTR01000390

Escherichia coli MS 21-1 E_coli21-1-1.0_Cont744.1: NZ_ADTR01000390
7.05214682414966e−16

20
NZ_ADUT01000002

Shigella dysenteriae 1617 gss1617.assembly.11: NZ_ADUT01000002
3.49647006284355e−15

21
NC_006856

Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
3.88428414470937e−13

plasmid pSC138: NC_006856

22
NC_011743

Escherichia fergusonii ATCC 35469 plasmid pEFER: NC_011743
6.18164438611072e−13

23
NZ_ADUT01000048

Shigella dysenteriae 1617 gss1617.assembly.53: NZ_ADUT01000048
6.40162543140323e−12

24
NZ_ADUT01000002

Shigella dysenteriae 1617 gss1617.assembly.11: NZ_ADUT01000002
1.53869362793954e−11

25
NC_011745

Escherichia coli ED1a: NC_011745
2.16302499579491e−11

26
NZ_ADUT01000002

Shigella dysenteriae 1617 gss1617.assembly.11: NZ_ADUT01000002
2.30761086733495e−11

27
NZ_ABKY02000005

Escherichia coli O157:H7 str. TW14588, unfinished sequence:
4.43701528503845e−11

NZ_ABKY02000005

28
NZ_ADUT01000002

Shigella dysenteriae 1617 gss1617.assembly.11: NZ_ADUT01000002
8.04473895167901e−11

29
CP002729

Escherichia coli UMNK88: CP002729
1.42165494676851e−10

30
NC_011742

Escherichia coli S88: NC_011742
2.05879614239143e−10

31
NZ_ABAK01000021

Salmonella enterica subsp. enterica serovar Kentucky str. CVM29188,
2.13757750700881e−10

unfinished sequence: NZ_ABAK01000021

32
NC_013509

Edwardsiella tarda EIB202 plasmid pEIB202: NC_013509
4.04449595701974e−10

33
NZ_ABHS01000025

Escherichia coli O157:H7 str. EC4486, unfinished sequence:
4.85503165975477e−10

NZ_ABHS01000025

34
NC_012759

Escherichia coli BW2952: NC_012759
4.85503165975477e−10

35
NZ_ADUD01000718

Escherichia coli MS 196-1 E_coli196-1-1.0_Cont2124.2: NZ_ADUD01000718
5.8673304681529e−10

36
NC_002655

Escherichia coli O157:H7 EDL933: NC_002655
7.67538561798816e−10

37
CP001509

Escherichia coli BL21(DE3): CP001509
8.69490265401296e−10

38
FP929040

Enterobacter cloacae subsp. cloacae NCTC 9394 draft genome.: FP929040
1.59741374269166e−09

39
NZ_AFBO01000392

Klebsiella sp.MS 92-3 K_spMS92-3-1.0_Cont773.2: NZ_AFBO01000392
1.59741374269166e−09

40
NZ_ADTQ01000190

Escherichia coli MS 187-1 E_coli187-1-1.0_Cont287.1: NZ_ADTQ01000190
1.59741374269166e−09

41
NZ_ACZD01000015

Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884 contig00015:
1.59741374269166e−09

NZ_ACZD01000015

42
NC_007384

Shigella sonnei Ss046: NC_007384
1.59741374269166e−09

43
NZ_ADUT01000040

Shigella dysenteriae 1617 gss1617.assembly.46: NZ_ADUT01000040
1.75588873952222e−09

44
NZ_CAAZ01000109

Salmonella enterica subsp. enterica serovar Typhi str. E98-3139,
4.20666708065652e−09

unfinished sequence: NZ_CAAZ01000109

45
NZ_AAMJ01000012

Shigella dysenteriae 1012, unfinished sequence: NZ_AAMJ01000012
5.072437403203e−09

46
NC_010658

Shigella boydii CDC 3083-94: NC_010658
8.52438957707961e−09

47
FN554766

Escherichia coli 042: FN554766
8.7610944464379e−09

48
NZ_ADTL01000219

Escherichia coli MS 115-1 E_coli115-1-1.0_Cont569.1: NZ_ADTL01000219
8.7610944464379e−09

49
NZ_ABJT01000012

Escherichia coli O157:H7 str. EC4024, unfinished sequence:
9.3358254121691e−09

NZ_ABJT01000012

50
NZ_AAJV01000016

Escherichia coli E22, unfinished sequence: NZ_AAJV01000016
1.17232056049228e−08

TABLE 21b

Data for Shigella species (continued)

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
AM; A/S; AUG; T/S
lactam; other
AUG
lactam

2
AM; A/S; AUG; T/S
lactam; other
AUG
lactam

3
AM; A/S; AUG; T/S
lactam; other
AUG
lactam

4
AM; A/S; AUG; T/S
lactam; other
AUG
lactam

5
AM; A/S; AUG
lactam
AUG
lactam

6
T/S
other
T/S
other

7
T/S
other
T/S
other

8
T/S
other
T/S
other

9
T/S
other
T/S
other

10
T/S
other
T/S
other

11
AM; A/S; AUG; T/S
lactam; other
AUG
lactam

12
AM; A/S; AUG; T/S
lactam; other
AUG
lactam

13
A/S; AUG; T/S
lactam; other
T/S
other

14
AM; A/S; AUG; T/S
lactam; other
AUG
lactam

15
AM; A/S; AUG; T/S
lactam; other
AUG
lactam

16
T/S
other
T/S
other

17
AM; A/S
lactam
A/S
lactam

18
AM; A/S; AUG
lactam
AUG
lactam

19
AM; A/S
lactam
A/S
lactam

20
AM; A/S
lactam
A/S
lactam

21
AM; A/S
lactam
A/S
lactam

22
T/S
other
T/S
other

23
AM; A/S; AUG
lactam
AUG
lactam

24
AM; A/S
lactam
A/S
lactam

25
AM; A/S; AUG; T/S
lactam; other
AM
lactam

26
AM; A/S
lactam
A/S
lactam

27
AM; A/S; AUG
lactam
A/S
lactam

28
AM; A/S
lactam
A/S
lactam

29
AUG
lactam
AUG
lactam

30
T/S
other
T/S
other

31
AM; A/S
lactam
A/S
lactam

32
T/S
other
T/S
other

33
AM; A/S
lactam
A/S
lactam

34
AM; A/S
lactam
AM
lactam

35
AM; A/S
lactam
A/S
lactam

36
AUG
lactam
AUG
lactam

37
AM; A/S
lactam
AM
lactam

38
AM; A/S
lactam
AM
lactam

39
AM; A/S
lactam
AM
lactam

40
AM; A/S
lactam
AM
lactam

41
AM; A/S
lactam
AM
lactam

42
AM; A/S
lactam
AM
lactam

43
AUG
lactam
AUG
lactam

44
AUG
lactam
AUG
lactam

45
AUG
lactam
AUG
lactam

46
AUG
lactam
AUG
lactam

47
AUG
lactam
AUG
lactam

48
AUG
lactam
AUG
lactam

49
AM; A/S
lactam
AM
lactam

50
AM; A/S; T/S
lactam; other
AM
lactam

TABLE 21c

Data for Shigella species (continued)

No.
num_lactam
num_other
AM_pv_adj
A/S_pv_adj
AUG_pv_adj
T/S_pv_adj

1
3
1
2.50E−24
2.78E−27
6.87E−56
6.43E−03

2
3
1
3.96E−18
5.18E−21
4.15E−46
3.89E−03

3
3
1
1.61E−18
1.80E−21
4.15E−46
2.75E−03

4
3
1
1.48E−18
1.80E−21
1.24E−44
5.45E−03

5
3
0
6.38E−20
1.76E−12
5.70E−37
1.36E−02

6
0
1
4.19E−01
7.59E−01
1.18E−01
3.04E−34

7
0
1
4.19E−01
7.59E−01
1.18E−01
3.04E−34

8
0
1
4.14E−01
6.88E−01
1.42E−01
5.68E−34

9
0
1
5.86E−01
9.62E−01
1.89E−01
1.47E−26

10
0
1
6.64E−01
8.98E−01
3.47E−01
4.98E−26

11
3
1
1.30E−12
6.35E−09
1.31E−24
1.10E−04

12
3
1
8.43E−13
4.07E−09
1.67E−24
3.04E−05

13
2
1
5.59E−02
5.39E−03
8.83E−03
3.08E−24

14
3
1
6.77E−13
3.67E−09
3.45E−24
4.57E−05

15
3
1
1.11E−11
1.11E−08
4.84E−23
3.29E−12

16
0
1
7.13E−01
9.56E−01
8.48E−02
1.60E−17

17
2
0
1.56E−14
4.67E−17
6.49E−01
1.06E−01

18
3
0
7.73E−05
2.34E−06
5.88E−17
9.61E−01

19
2
0
5.63E−14
7.05E−16
9.63E−01
3.40E−02

20
2
0
4.77E−14
3.50E−15
1
7.62E−02

21
2
0
3.45E−11
3.88E−13
6.47E−01
3.82E−02

22
0
1
5.80E−01
2.16E−01
2.14E−01
6.18E−13

23
3
0
5.45E−03
1.12E−03
6.40E−12
1.67E−01

24
2
0
2.67E−09
1.54E−11
4.21E−01
7.26E−02

25
3
1
2.16E−11
8.03E−10
4.80E−05
1.95E−03

26
2
0
3.72E−09
2.31E−11
5.37E−01
1.18E−01

27
3
0
2.93E−08
4.44E−11
1.86E−03
1.59E−01

28
2
0
7.34E−09
8.04E−11
6.55E−01
7.07E−02

29
1
0
2.46E−01
5.71E−02
1.42E−10
5.27E−01

30
0
1
1.01E−01
3.04E−02
5.99E−01
2.06E−10

31
2
0
7.76E−09
2.14E−10
3.71E−01
1.76E−01

32
0
1
6.37E−01
2.87E−01
2.49E−01
4.04E−10

33
2
0
5.22E−08
4.86E−10
2.71E−01
2.09E−01

34
2
0
4.86E−10
3.14E−08
5.20E−02
5.27E−01

35
2
0
1.90E−08
5.87E−10
4.20E−01
1.73E−01

36
1
0
1.02E−01
2.02E−02
7.68E−10
3.60E−01

37
2
0
8.69E−10
5.22E−08
6.38E−02
5.96E−01

38
2
0
1.60E−09
8.74E−08
6.39E−02
5.96E−01

39
2
0
1.60E−09
8.74E−08
6.39E−02
5.96E−01

40
2
0
1.60E−09
8.74E−08
6.39E−02
5.96E−01

41
2
0
1.60E−09
8.74E−08
6.39E−02
5.96E−01

42
2
0
1.60E−09
8.74E−08
6.39E−02
5.96E−01

43
1
0
4.98E−01
1.34E−01
1.76E−09
3.44E−01

44
1
0
5.00E−01
1.36E−01
4.21E−09
4.06E−01

45
1
0
3.20E−01
7.93E−02
5.07E−09
6.63E−01

46
1
0
1
5.81E−01
8.52E−09
4.31E−01

47
1
0
2.42E−01
8.26E−02
8.76E−09
5.20E−01

48
1
0
2.42E−01
8.26E−02
8.76E−09
5.20E−01

49
2
0
9.34E−09
1.80E−06
2.16E−01
7.92E−02

50
2
1
1.17E−08
4.60E−05
3.74E−02
7.92E−04

TABLE 21d

Data for Shigella species (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
HMPREF9547_01191

ZP_07167682

2
HMPREF9551_04221

ZP_07191576

3
HMPREF9347_01086

ZP_07208640

4
STMDT12_C39170

BAJ38860

5
SFxv_1168

ADA73425

6
Sdys1_01000012

ZP_00922750

7
HMPREF9547_02735

ZP_07169192

8
Sdys1_01000013

ZP_00922751

9
SFxv_4146

ADA76106

10
HMPREF9547_04432

ZP_07170853

11
HMPREF9547_00721

ZP_07167228

12
SFxv_1141

ADA73399

13
ETAE_p041
folP
YP_003297635
plasmid pEIB202

14
ESCAB7627_0644

ZP_02900823

15
SSON_3896
aadA
YP_312670

16
SFxv_4148

ADA76108

17
SD1617_0118

ZP_07678322

18
ESCAB7627_0650

ZP_02900555

19
HMPREF9530_04295

ZP_07154150

20
SD1617_0032

ZP_07678236

21
SC109
ccgA2
YP_209411
plasmid pSC138

22
pEFER_0049

YP_002394596
plasmid pEFER

23
SD1617_4863

ZP_07682961

24
SD1617_0123

ZP_07678327

25
ECED1_1050

YP_002397074

26
SD1617_0043

ZP_07678247

27
ESCCO14588_3315

ZP_03445386

28
SD1617_0122

ZP_07678326

29
UMNK88_1471

AEE56075

30
ECS88_2899
rusA
YP_002392541

31
Sente_010100023234

ZP_02563153

32
ETAE_p040

YP_003297634
plasmid pEIB202

33
EcolO157_010100025333

ZP_02795604

34
BWG_3989
fecR
YP_002929180

35
HMPREF9551_05588

ZP_07192915

36
Z1242
dmsC
NP_286773

37
ECD_04153
fecE
ACT45937

38
ENC_36610

CBK86965

39
HMPREF9538_03067

ZP_08305382

40
HMPREF9550_02956

ZP_07146070

41
HMPREF0484_0234
fecA
ZP_06013219

42
SSON_4460
fecD
YP_313172

43
SD1617_4069

ZP_07682183

44
Salmonellentericaenterica_010100012935

ZP_03412076

45
Sdys1_01002088

ZP_00921058

46
SbBS512_E0266

YP_001879059

47
EC042_2952

CBG35781

48
HMPREF9540_02755

ZP_07135552

49
EscherichcoliO157_010100012850

ZP_03082702

50
EcolE2_01002516

ZP_00729149

TABLE 21e

Data for Shigella species (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
6987
7817
+
648291751

2
10102
10662
−
648292991

3
2726
5692
−
648294279

4
4067283
4067942
+
651053007

5
1128245
1129249
+
646862363

6
12375
12701
−
638365528

7
4692
5189
−
648291885

8
14252
14776
+
638365528

9
3950954
3952570
−
646862363

10
8898
9719
−
648292023

11
5423
6016
−
648291712

12
1107342
1107968
+
646862363

13
32101
32916
−
646311959

14
233492
234697
−
641784575

15
4110458
4111246
−
640427102

16
3954100
3955767
−
646862363

17
94539
95570
+
649994652

18
238788
239996
−
641784575

19
2693
3169
+
648290614

20
9270
9803
−
649994652

21
84616
85080
−
637000354

22
48658
49503
+
643692014

23
80678
81835
−
649994698

24
98900
99016
−
649994652

25
1066134
1066832
+
643348624

26
17832
18008
+
649994652

27
383590
384330
−
642987534

28
98413
98754
−
649994652

29
1420478
1421209
−
651053088

30
2863316
2863705
−
644736332

31
17544
17792
+
641746180

32
31237
32040
−
646311959

33
65402
65668
−
641781914

34
4453522
4454475
−
644736346

35
1327
1764
−
648293234

36
1164368
1165231
+
637000062

37
4424087
4424854
−
646862369

38
3698592
3699494
−
650378029

39
2039
3037
−
651333309

40
271
792
+
648290104

41
4245
6485
+
647009762

42
4731572
4732528
−
640427102

43
500702
501520
+
649994690

44
43535
45085
+
643042589

45
19505
20209
−
638365539

46
266116
266985
−
641522725

47
3140492
3141238
−
646862421

48
1421
1912
−
648288078

49
103370
103972
+
642792886

50
35676
36281
−
638358744

TABLE 22a

Data for Shigella species

No.
Scaffold.External.Accession
Scaffold.Name
best_pv

1
NZ_ADUB01000093

Escherichia coli MS 175-1 E_coli175-1-1.0_Cont166.1: NZ_ADUB01000093
6.86676649351252e−56

2
NZ_ADUD01000475

Escherichia coli MS 196-1 E_coli196-1-1.0_Cont1343.1: NZ_ADUD01000475
4.14817893591733e−46

3
NZ_ADWT01000006

Escherichia coli MS 124-1 E_coliMS124-1-1.0.1_Cont5.1: NZ_ADWT01000006
4.14817893591733e−46

4
AP011957

Salmonella enterica subsp. enterica serovar Typhimurium str. T000240
1.24332752332433e−44

DNA: AP011957

5
CP001383

Shigella flexneri 2002017: CP001383
5.69762827081762e−37

6
NZ_AAMJ01000001

Shigella dysenteriae 1012, unfinished sequence: NZ_AAMJ01000001
3.04086824044829e−34

7
NZ_ADUB01000227

Escherichia coli MS 175-1 E_coli175-1-1.0_Cont422.2: NZ_ADUB01000227
3.04086824044829e−34

8
NZ_AAMJ01000001

Shigella dysenteriae 1012, unfinished sequence: NZ_AAMJ01000001
5.67507153238613e−34

9
CP001383

Shigella flexneri 2002017: CP001383
1.46728061376833e−26

10
NZ_ADUB01000365

Escherichia coli MS 175-1 E_coli175-1-1.0_Cont823.2: NZ_ADUB01000365
4.97695865217724e−26

11
NZ_ADUB01000054

Escherichia coli MS 175-1 E_coli175-1-1.0_Cont100.1: NZ_ADUB01000054
1.31351033204593e−24

12
CP001383

Shigella flexneri 2002017: CP001383
1.66700615646725e−24

13
NC_013509

Edwardsiella tarda EIB202 plasmid pEIB202: NC_013509
3.081692811393e−24

14
NZ_ABKX01000001

Escherichia albertii TW07627, unfinished sequence: NZ_ABKX01000001
3.45432516278107e−24

15
NC_007384

Shigella sonnei Ss046: NC_007384
4.84345172785563e−23

16
CP001383

Shigella flexneri 2002017: CP001383
1.59570448713613e−17

17
NZ_ABKX01000001

Escherichia albertii TW07627, unfinished sequence: NZ_ABKX01000001
5.88113462200155e−17

18
NC_011743

Escherichia fergusonii ATCC 35469 plasmid pEFER: NC_011743
6.18164438611072e−13

19
NZ_ADUT01000048

Shigella dysenteriae 1617 gss1617.assembly.53: NZ_ADUT01000048
6.40162543140323e−12

20
NC_011745

Escherichia coli ED1a: NC_011745
2.16302499579491e−11

21
NZ_ABKY02000005

Escherichia coli O157:H7 str. TW14588, unfinished sequence:
4.43701528503845e−11

NZ_ABKY02000005

22
NC_011742

Escherichia coli S88: NC_011742
2.05879614239143e−10

23
NC_013509

Edwardsiella tarda EIB202 plasmid pEIB202: NC_013509
4.04449595701974e−10

24
NZ_AAJV01000016

Escherichia coli E22, unfinished sequence: NZ_AAJV01000016
1.17232056049228e−08

25
NC_012731

Klebsiella pneumoniae NTUH-K2044: NC_012731
1.74593394018129e−08

26
NC_011740

Escherichia fergusonii ATCC 35469: NC_011740
2.08793524887857e−08

27
NC_011740

Escherichia fergusonii ATCC 35469: NC_011740
3.5987076197447e−08

28
NZ_GG749327

Escherichia coli B354 genomic scaffold supercont1.2: NZ_GG749327
3.5987076197447e−08

29
NZ_ADTP01000357

Escherichia coli MS 69-1 E_coli69-1-1.0_Cont727.1: NZ_ADTP01000357
3.5987076197447e−08

30
NC_008258

Shigella flexneri 5 str. 8401: NC_008258
3.5987076197447e−08

31
NC_008258

Shigella flexneri 5 str. 8401: NC_008258
3.6014669209108e−08

32
NC_011093

Salmonella enterica subsp. enterica serovar Schwarzengrund str.
4.21633659816666e−08

CVM19633 plasmid pCVM19633_4: NC_011093

33
NZ_ABWL01000002

Citrobacter youngae ATCC 29220 C_sp-1.0_Cont0.2: NZ_ABWL01000002
5.87968902033994e−08

34
NC_011740

Escherichia fergusonii ATCC 35469: NC_011740
5.87968902033994e−08

35
NZ_ADUT01000013

Shigella dysenteriae 1617 gss1617.assembly.21: NZ_ADUT01000013
5.87968902033994e−08

36
NC_010658

Shigella boydii CDC 3083-94: NC_010658
5.87968902033994e−08

37
NC_011740

Escherichia fergusonii ATCC 35469: NC_011740
5.87968902033994e−08

38
NZ_ABEJ01000032

Salmonella enterica subsp. enterica serovar Schwarzengrund str. SL480,
6.12813910192695e−08

unfinished sequence: NZ_ABEJ01000032

39
NC_009345

Shigella sonnei Ss046 plasmid pSS046_spA: NC_009345
7.76943438061442e−08

40
NC_011740

Escherichia fergusonii ATCC 35469: NC_011740
8.81464918585737e−08

41
NZ_ABKX01000001

Escherichia albertii TW07627, unfinished sequence: NZ_ABKX01000001
1.19080570281449e−07

42
CP001671

Escherichia coli ABU 83972: CP001671
1.50273530777206e−07

43
CP001637

Escherichia coli DH1: CP001637
2.0405961424353e−07

44
NC_004741

Shigella flexneri 2a str. 2457T: NC_004741
2.0405961424353e−07

45
NZ_AAKB01000013

Escherichia coli 53638, unfinished sequence: NZ_AAKB01000013
2.08917442901333e−07

46
NZ_ADUL01000041

Escherichia coli 2362-75 gec2362.assembly.47: NZ_ADUL01000041
2.54562372489639e−07

47
NZ_ABKX01000001

Escherichia albertii TW07627, unfinished sequence: NZ_ABKX01000001
3.82958267583033e−07

48
NZ_ADTR01000289

Escherichia coli MS 21-1 E_coli21-1-1.0_Cont515.2: NZ_ADTR01000289
3.97520776634592e−07

49
NC_010658

Shigella boydii CDC 3083-94: NC_010658
4.00202730594618e−07

50
NZ_GG657366

Citrobacter sp. 30_2 genomic scaffold supercont1.1: NZ_GG657366
4.18196454987758e−07

TABLE 22b

Data for Shigella species

No.
sign_phenos
sign_phenos_class
best_pheno
best_pheno_class

1
AM; A/S; AUG; T/S
lactam; other
AUG
lactam

2
AM; A/S; AUG; T/S
lactam; other
AUG
lactam

3
AM; A/S; AUG; T/S
lactam; other
AUG
lactam

4
AM; A/S; AUG; T/S
lactam; other
AUG
lactam

5
AM; A/S; AUG
lactam
AUG
lactam

6
T/S
other
T/S
other

7
T/S
other
T/S
other

8
T/S
other
T/S
other

9
T/S
other
T/S
other

10
T/S
other
T/S
other

11
AM; A/S; AUG; T/S
lactam; other
AUG
lactam

12
AM; A/S; AUG; T/S
lactam; other
AUG
lactam

13
A/S; AUG; T/S
lactam; other
T/S
other

14
AM; A/S; AUG; T/S
lactam; other
AUG
lactam

15
AM; A/S; AUG; T/S
lactam; other
AUG
lactam

16
T/S
other
T/S
other

17
AM; A/S; AUG
lactam
AUG
lactam

18
T/S
other
T/S
other

19
AM; A/S; AUG
lactam
AUG
lactam

20
AM; A/S; AUG; T/S
lactam; other
AM
lactam

21
AM; A/S; AUG
lactam
A/S
lactam

22
T/S
other
T/S
other

23
T/S
other
T/S
other

24
AM; A/S; T/S
lactam; other
AM
lactam

25
AM; A/S; T/S
lactam; other
AM
lactam

26
AM; A/S; AUG
lactam
AM
lactam

27
AM; A/S; T/S
lactam; other
AM
lactam

28
AM; A/S; T/S
lactam; other
AM
lactam

29
AM; A/S; T/S
lactam; other
AM
lactam

30
AM; A/S; T/S
lactam; other
AM
lactam

31
AM; A/S; AUG
lactam
AUG
lactam

32
AM; A/S; AUG
lactam
AM
lactam

33
AM; A/S; T/S
lactam; other
A/S
lactam

34
AM; A/S; T/S
lactam; other
A/S
lactam

35
AM; A/S; T/S
lactam; other
A/S
lactam

36
AM; A/S; T/S
lactam; other
A/S
lactam

37
AM; A/S; T/S
lactam; other
A/S
lactam

38
AM; A/S; AUG; T/S
lactam; other
T/S
other

39
AM; A/S; AUG; T/S
lactam; other
T/S
other

40
AM; A/S; AUG; T/S
lactam; other
AUG
lactam

41
AM; A/S; AUG
lactam
A/S
lactam

42
AM; A/S; T/S
lactam; other
AM
lactam

43
AM; A/S; AUG
lactam
A/S
lactam

44
AM; A/S; AUG
lactam
A/S
lactam

45
AM; A/S; AUG
lactam
AM
lactam

46
AM; A/S; AUG; T/S
lactam; other
A/S
lactam

47
AM; A/S; AUG
lactam
A/S
lactam

48
AM; A/S; T/S
lactam; other
AM
lactam

49
AM; A/S; T/S
lactam; other
T/S
other

50
AM; A/S; AUG
lactam
AM
lactam

TABLE 22c

Data for Shigella species

No .
num_lactam
num_other
AM_pv_adj
A/S_pv_adj
AUG_pv_adj
T/S_pv_adj

1
3
1
2.50E−24
2.78E−27
6.87E−56
6.43E−03

2
3
1
3.96E−18
5.18E−21
4.15E−46
3.89E−03

3
3
1
1.61E−18
1.80E−21
4.15E−46
2.75E−03

4
3
1
1.48E−18
1.80E−21
1.24E−44
5.45E−03

5
3
0
6.38E−20
1.76E−12
5.70E−37
1.36E−02

6
0
1
4.19E−01
7.59E−01
1.18E−01
3.04E−34

7
0
1
4.19E−01
7.59E−01
1.18E−01
3.04E−34

8
0
1
4.14E−01
6.88E−01
1.42E−01
5.68E−34

9
0
1
5.86E−01
9.62E−01
1.89E−01
1.47E−26

10
0
1
6.64E−01
8.98E−01
3.47E−01
4.98E−26

11
3
1
1.30E−12
6.35E−09
1.31E−24
1.10E−04

12
3
1
8.43E−13
4.07E−09
1.67E−24
3.04E−05

13
2
1
5.59E−02
5.39E−03
8.83E−03
3.08E−24

14
3
1
6.77E−13
3.67E−09
3.45E−24
4.57E−05

15
3
1
1.11E−11
1.11E−08
4.84E−23
3.29E−12

16
0
1
7.13E−01
9.56E−01
8.48E−02
1.60E−17

17
3
0
7.73E−05
2.34E−06
5.88E−17
9.61E−01

18
0
1
5.80E−01
2.16E−01
2.14E−01
6.18E−13

19
3
0
5.45E−03
1.12E−03
6.40E−12
1.67E−01

20
3
1
2.16E−11
8.03E−10
4.80E−05
1.95E−03

21
3
0
2.93E−08
4.44E−11
1.86E−03
1.59E−01

22
0
1
1.01E−01
3.04E−02
5.99E−01
2.06E−10

23
0
1
6.37E−01
2.87E−01
2.49E−01
4.04E−10

24
2
1
1.17E−08
4.60E−05
3.74E−02
7.92E−04

25
2
1
1.75E−08
3.59E−04
9.59E−02
5.74E−05

26
3
0
2.09E−08
6.13E−08
3.86E−05
4.21E−01

27
2
1
3.60E−08
2.62E−04
7.92E−02
9.64E−04

28
2
1
3.60E−08
5.37E−04
7.92E−02
1.59E−04

29
2
1
3.60E−08
2.62E−04
7.92E−02
9.64E−04

30
2
1
3.60E−08
5.37E−04
7.92E−02
1.59E−04

31
3
0
6.06E −04
1.15E−05
3.60E−08
1.18E−02

32
3
0
4.22E−08
6.96E−07
1.35E−04
3.01E−02

33
2
1
2.70E−07
5.88E−08
1.78E−01
7.31E−04

34
2
1
2.70E−07
5.88E−08
1.78E−01
7.31E−04

35
2
1
2.70E−07
5.88E−08
1.78E−01
7.31E−04

36
2
1
2.70E−07
5.88E−08
1.78E−01
7.31E−04

37
2
1
2.70E−07
5.88E−08
1.78E−01
7.31E−04

38
3
1
3.43E−04
1.83E−03
7.05E−04
6.13E−08

39
3
1
8.13E−05
5.17E−04
3.23E−04
7.77E−08

40
3
1
2.18E−04
3.33E−06
8.81E−08
1.34E−03

41
3
0
5.77E−06
1.19E−07
6.46E−03
3.28E−01

42
2
1
1.50E−07
1.17E−03
6.39E−02
1.05E−04

43
3
0
1.24E−05
2.04E−07
6.60E−03
3.27E−01

44
3
0
1.24E−05
2.04E−07
6.60E−03
3.27E−01

45
3
0
2.09E−07
1.92E−06
4.75E−05
4.59E−01

46
3
1
1.84E−04
2.55E−07
1.33E−06
3.22E−03

47
3
0
1.32E−05
3.83E−07
8.66E−03
2.79E−01

48
2
1
3.98E−07
1.01E−05
1.08E−01
3.36E−03

49
2
1
3.82E−05
1.71E−03
2.98E−01
4.00E−07

50
3
0
4.18E−07
3.44E−06
2.44E−03
1.37E−01

TABLE 22d

Data for Shigella species

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
HMPREF9547_01191

ZP_07167682

2
HMPREF9551_04221

ZP_07191576

3
HMPREF9347_01086

ZP_07208640

4
STMDT12_C39170

BAJ38860

5
SFxv_1168

ADA73425

6
Sdys1_01000012

ZP_00922750

7
HMPREF9547_02735

ZP_07169192

8
Sdys1_01000013

ZP_00922751

9
SFxv_4146

ADA76106

10
HMPREF9547_04432

ZP_07170853

11
HMPREF9547_00721

ZP_07167228

12
SFxv_1141

ADA73399

13
ETAE_p041
folP
YP_003297635
plasmid pEIB202

14
ESCAB7627_0644

ZP_02900823

15
SSON_3896
aadA
YP_312670

16
SFxv_4148

ADA76108

17
ESCAB7627_0650

ZP_02900555

18
pEFER_0049

YP_002394596
plasmid pEFER

19
SD1617_4863

ZP_07682961

20
ECED1_1050

YP_002397074

21
ESCCO14588_3315

ZP_03445386

22
ECS88_2899
rusA
YP_002392541

23
ETAE_p040

YP_003297634
plasmid pEIB202

24
EcolE2_01002516

ZP_00729149

25
KP1_1529
betB
YP_002918349

26
EFER_2751
fhiA
YP_002383857

27
EFER_1964

YP_002383093

28
ECEG_03397

ZP_06652297

29
HMPREF9534_04860

ZP_07189724

30
SFV_0325
betT
YP_687904

31
SFV_3136
tsaC
YP_690497

32
SeSA_C0004

YP_002113008
plasmid

pCVM19633_4

33
CIT292_00036

ZP_03834370

34
EFER_4022
phoU
YP_002385049

35
SD1617_0888
pstA
ZP_07679073

36
SbBS512_E4201
pstC
YP_001882442

37
EFER_4026
pstS
YP_002385053

38
Senteenterica_010100025269

ZP_02664569

39
SSON_PA02
tetA
YP_001139953
plasmid

pSS046_spA

40
EFER_4455

YP_002385453

41
ESCAB7627_0589
agaF
ZP_02900787

42
ECABU_c04070
betA
ADN45010

43
EcDH1_0571

ACX38258

44
S3383
agaV
NP_838641

45
Ecol5_01002315

ZP_00735973

46
EC236275_0400

ZP_07778877

47
ESCAB7627_0593

ZP_02900381

48
HMPREF9530_03165

ZP_07153036

49
SbBS512_E1297

YP_001879929

50
CSAG_02340

ZP_04563010

TABLE 22e

Data for Shigella species

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
6987
7817
+
648291751

2
10102
10662
−
648292991

3
2726
5692
−
648294279

4
4067283
4067942
+
651053007

5
1128245
1129249
+
646862363

6
12375
12701
−
638365528

7
4692
5189
−
648291885

8
14252
14776
+
638365528

9
3950954
3952570
−
646862363

10
8898
9719
−
648292023

11
5423
6016
−
648291712

12
1107342
1107968
+
646862363

13
32101
32916
−
646311959

14
233492
234697
−
641784575

15
4110458
4111246
−
640427102

16
3954100
3955767
−
646862363

17
238788
239996
−
641784575

18
48658
49503
+
643692014

19
80678
81835
−
649994698

20
1066134
1066832
+
643348624

21
383590
384330
−
642987534

22
2863316
2863705
−
644736332

23
31237
32040
−
646311959

24
35676
36281
−
638358744

25
1469088
1470560
−
646564530

26
2808563
2810692
+
643692013

27
2010341
2013862
−
643692013

28
167911
168516
−
647536674

29
4513
7977
−
648289846

30
342056
344089
+
637000590

31
3209986
3212835
−
637000590

32
2398
3933
−
642555220

33
7614
8387
+
643891493

34
4127070
4127795
−
643692013

35
217087
217971
−
649994663

36
3927571
3928530
+
641522725

37
4130610
4131650
−
643692013

38
35858
36535
−
641777693

39
1155
2429
+
640427123

40
4539896
4540645
+
643692013

41
182707
183141
−
641784575

42
425884
427554
−
648231700

43
602662
603063
−
646862383

44
3261857
3262366
+
637000219

45
39234
40157
−
638359205

46
26968
27516
−
649994608

47
185313
186593
−
641784575

48
5665
6162
−
648290513

49
1184368
1184799
+
641522725

50
2538496
2539857
+
646206732

Example 12

Staphylococcus, particularly S. aureus

The procedure was carried out as in Example 1, except for the following changes:

Bacterial Strains

The inventors selected 1001 specimens of S. aureus from the microbiology strain collection at Siemens Healthcare Diagnostics (West Sacramento, Calif.) for susceptibility testing and whole genome sequencing, of which 985 had an assembly, a unique Kiel NGS ID (NGS data and assembly ID, a unique resistance profile (no different resistance profiles with different outcomes, and at least one drug with non-missing resistance value, so that these were further analyzed.

From MetaRef, 754 centroids of S. aureus were used as reference sequences.

Resistance/susceptibility was determined for the following antibiotics as described below: Amoxicillin/Clavulanate, Ampicillin, Ampicillin/Sulbactam, Azithromycin, Cefalothin, Cefazolin, Cefepime, Cefotaxime, Cefoxitin, Ceftriaxone, Cefuroxime, Chloramphenicol, Ciprofloxacin, Clindamycin, Daptomycin, Ertapenem, Erythromycin, Fosfomycin, Fusidic acid, Gentamicin, Imipenem, Levofloxacin, Linezolid, Meropenem, Moxifloxacin, Mupirocin, Nitrofurantoin, Norfloxacin, Ofloxacin, Oxacillin, Penicillin G, Piperacillin/Tazobactam, Quinupristin/Dalfopristin, Rifampicin, Teicoplanin, Tetracycline, Tigecycline, Tobramycin, Trimethoprim/Sulfamethoxazole, and Vancomycin.

For testing, standard procedures were used, i.e. VITEK 2 system and AST cards (Biomerieux), Microscan system and AST panels (Beckmann Coulter).

DNA Extraction

DNA extraction and purification was carried out using the MagAttract HMW DNA Kit (Qiagen) procedure with the following changes. After up to 2×10⁹bacteria (1m1 culture) were centrifuged in a 2 ml tube (10 min, 5000 ×g) and the supernatant was discharged, it was again centrifuged 1 min and the sample was taken. The resulting pellet was dispersed in 160 μl P1, 20 μl lysozyme (100 mg/ml) and 4 μl lysostaphin were added and mixed, and the suspension was incubated at 37° C. at 900 rpm for 30 mins in a thermal mixer. Afterwards 300 μl lysis buffer and proteinase K (30 μl) (both from the blood kit for Maxwell of Promega) were added and the whole again incubated for 30 mins at 56° C. and 900 rpm. The samples as a whole (˜510 μl) were then transferred to the Maxwell cartridges for further processing, using the Tissue LEV Total RNA Kit AS1220 or the XAS1220 Custom Kit (Promega).

Next generation sequencing and data analysis was carried out as in Example 1.

The results for S. aureus are shown in Tables 23 (corresponding to Table 1) and 24 (corresponding to Table 2).

TABLE 23a

Data for Staphylococcus, particularly S. aureus

No.
Scaffold.External.Accession
Scaffold.Name
best_pv

1
NZ_ACJC01000132

Staphylococcus epidermidis W23144: NZ_ACJC01000132
9.38479881072327e−227

2
NZ_ADMU01000036

Staphylococcus epidermidis M23864: W2 (grey) contig00037:
9.38479881072327e−227

NZ_ADMU01000036

3
NZ_ADMU01000036

Staphylococcus epidermidis M23864: W2 (grey) contig00037:
2.67435403500704e−225

NZ_ADMU01000036

4
NZ_GG770515

Staphylococcus aureus subsp. aureus EMRSA16 genomic scaffold
1.77186061517335e−211

supercont1.3: NZ_GG770515

5
NZ_ACHE01000064

Staphylococcus epidermidis BCM-HMP0060: NZ_ACHE01000064
3.22333061264623e−210

6
NZ_ACKJ01000008

Staphylococcus aureus A9719: NZ_ACKJ01000008
4.28801157250818e−188

7
FN433596

Staphylococcus aureus subsp. aureus TW20: FN433596
6.72085159673615e−181

8
FN433596

Staphylococcus aureus subsp. aureus TW20: FN433596
6.72085159673615e−181

9
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
6.72085159673615e−181

10
NZ_ACKF01000035

Staphylococcus aureus A6300: NZ_ACKF01000035
8.5426103876016e−179

11
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
8.5426103876016e−179

12
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
1.81714784068785e−175

13
NZ_ADMU01000035

Staphylococcus epidermidis M23864: W2 (grey) contig00036:
3.23410033711171e−175

NZ_ADMU01000035

14
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
9.12700235375297e−175

15
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
9.12700235375297e−175

16
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
9.12700235375297e−175

17
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
9.12700235375297e−175

18
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
2.25944344923286e−173

19
NZ_ACKF01000007

Staphylococcus aureus A6300: NZ_ACKF01000007
2.40063417489507e−172

20
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
2.59802993040457e−167

21
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
3.12953724144125e−166

22
NZ_ADJJ01000031

Staphylococcus aureus A8796 cont1.31: NZ_ADJJ01000031
3.37208086862656e−166

23
NC_002745

Staphylococcus aureus subsp. aureus N315: NC_002745
3.37208086862656e−166

24
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
7.17319474297637e−161

25
NZ_ACHH01000128

Staphylococcus aureus subsp. aureus TCH70: NZ_ACHH01000128
4.16856451727179e−152

26
NZ_ACKC01000026

Staphylococcus aureus A5937: NZ_ACKC01000026
1.58751373713434e−135

27
NZ_ACKC01000026

Staphylococcus aureus A5937: NZ_ACKC01000026
1.69633422486642e−135

28
CP001844

Staphylococcus aureus 04-02981: CP001844
1.77656315889944e−134

29
FR714927

Staphylococcus aureus subsp. aureus ECT-R 2: FR714927
4.06264970457926e−133

30
CP001844

Staphylococcus aureus 04-02981: CP001844
1.01251954267327e−130

31
NC_007622

Staphylococcus aureus RF122: NC_007622
4.84169534955158e−126

32
NC_009632

Staphylococcus aureus subsp. aureus JH1: NC_009632
6.20485118760467e−122

33
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
5.75915090813908e−120

34
NZ_ACYO01000032

Staphylococcus aureus A8117 cont1.32: NZ_ACYO01000032
1.84672228386398e−116

35
FR714927

Staphylococcus aureus subsp. aureus ECT-R 2: FR714927
7.1946440374743e−116

36
NZ_ACHD01000273

Staphylococcus aureus subsp. aureus TCH130: NZ_ACHD01000273
4.22320321058421e−113

37
NZ_ACKE01000012

Staphylococcus aureus A6224: NZ_ACKE01000012
4.22320321058421e−113

38
CP002114

Staphylococcus aureus subsp. aureus JKD6159: CP002114
4.83609713640718e−112

39
NZ_GG730131

Staphylococcus aureus subsp. aureus C101 genomic scaffold
4.63942446669448e−110

supercont1.12: NZ_GG730131

40
NZ_ACKF01000014

Staphylococcus aureus A6300: NZ_ACKF01000014
5.76090691723747e−108

41
NZ_ACKK01000039

Staphylococcus aureus A9763: NZ_ACKK01000039
2.40583396327414e−107

42
NZ_ACKE01000008

Staphylococcus aureus A6224: NZ_ACKE01000008
2.99974766558167e−106

43
NZ_ACKG01000031

Staphylococcus aureus A8115: NZ_ACKG01000031
1.57559858677166e−102

44
NC_009632

Staphylococcus aureus subsp. aureus JH1: NC_009632
1.0725409335823e−101

45
NZ_ACYO01000003

Staphylococcus aureus A8117 cont1.3: NZ_ACYO01000003
1.0725409335823e−101

46
FR714929

Staphylococcus aureus subsp. aureus ECT-R 2 plasmid
5.26123840198017e−101

pLUH02: FR714929

47
CP001844

Staphylococcus aureus 04-02981: CP001844
8.01600909282956e−101

48
CP001844

Staphylococcus aureus 04-02981: CP001844
1.78546333248495e−95

49
NZ_ADJK01000020

Staphylococcus aureus A8819 cont1.20: NZ_ADJK01000020
1.80469278143707e−94

50
NZ_GL545262

Staphylococcus hominis subsp. hominis C80 genomic scaffold
2.82728623419544e−94

supercont1.11: NZ_GL545262

TABLE 23b

Data for Staphylococcus, particularly S. aureus (continued)

No.
sign_phenos

1
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tobramycin

2
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tobramycin

3
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tobramycin

4
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tobramycin

5
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tobramycin

6
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tobramycin

7
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

8
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

9
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

10
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

11
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

12
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

13
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

14
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

15
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

16
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

17
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

18
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

19
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

20
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

21
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

22
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

23
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

24
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

25
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

26
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

27
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

28
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

29
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

30
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

31
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

32
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tobramycin

33
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

34
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tobramycin

35
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

36
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

37
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

38
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

39
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

40
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

41
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

42
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

43
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

44
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

45
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

46
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

47
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

48
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

49
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

50
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

TABLE 23c

Data for Staphylococcus, particularly S. aureus (continued)

No.
sign_phenos_class
best_pheno
best_pheno_class

1
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide
Oxacillin
lactam

2
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide
Oxacillin
lactam

3
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide
Oxacillin
lactam

4
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide
Oxacillin
lactam

5
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide
Oxacillin
lactam

6
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide
Moxifloxacin
fluoroquinolone

7
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

8
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

9
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

10
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

11
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

12
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

13
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

14
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

15
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

16
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

17
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

18
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

19
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

20
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

21
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

22
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

23
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

24
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

25
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

26
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

27
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

28
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

29
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

30
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

31
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

32
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide
Moxifloxacin
fluoroquinolone

33
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

34
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide
Moxifloxacin
fluoroquinolone

35
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

36
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

37
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

38
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

39
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

40
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

41
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

42
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

43
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

44
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

45
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

46
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

47
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

48
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

49
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

50
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

TABLE 23d

Data for Staphylococcus, particularly S. aureus (continued)

No.
num_aminoglycoside
num_fluoroquinolone
num_lactam
num_lincosamide
num_macrolide
num_tetracycline

1
1
3
9
1
1
0

2
1
3
9
1
1
0

3
1
3
9
1
1
0

4
1
3
9
1
1
0

5
1
3
9
1
1
0

6
1
3
9
1
1
0

7
1
3
9
1
1
1

8
1
3
9
1
1
1

9
1
3
9
1
1
1

10
1
3
9
1
1
1

11
1
3
9
1
1
1

12
1
3
9
1
1
1

13
1
3
9
1
1
1

14
1
3
9
1
1
1

15
1
3
9
1
1
1

16
1
3
9
1
1
1

17
1
3
9
1
1
1

18
1
3
9
1
1
1

19
1
3
9
1
1
1

20
1
3
9
1
1
1

21
1
3
9
1
1
1

22
1
3
9
1
1
1

23
1
3
9
1
1
1

24
1
3
9
1
1
1

25
1
3
9
1
1
1

26
1
3
8
1
1
1

27
1
3
8
1
1
1

28
1
3
8
1
1
1

29
1
3
8
1
1
1

30
1
3
8
1
1
1

31
1
3
9
1
1
1

32
1
3
8
1
1
0

33
1
3
9
1
1
1

34
1
3
8
1
1
0

35
1
3
8
1
1
1

36
1
3
9
1
1
1

37
1
3
9
1
1
1

38
1
3
8
1
1
1

39
1
3
8
1
1
1

40
1
3
8
1
1
1

41
1
3
8
1
1
1

42
1
3
8
1
1
1

43
1
3
8
1
1
1

44
1
3
8
1
1
1

45
1
3
8
1
1
1

46
1
3
9
1
1
1

47
1
3
8
1
1
1

48
1
3
8
1
1
1

49
1
3
9
1
1
1

50
1
3
9
1
1
1

TABLE 23e

Data for Staphylococcus, particularly S. aureus (continued)

No.
Ampicillin_pv_adj
Ampicillin/Sulbactam_pv_adj
Cefepim_pv_adj
Cefotaxim_pv_adj

1
2.20E−08
5.96E−37
5.96E−37
5.96E−37

2
2.20E−08
5.96E−37
5.96E−37
5.96E−37

3
2.20E−08
5.96E−37
5.96E−37
5.96E−37

4
4.64E−08
4.55E−35
4.55E−35
4.55E−35

5
2.20E−08
2.16E−33
2.16E−33
2.16E−33

6
2.22E−09
1.64E−31
1.64E−31
1.64E−31

7
3.22E−07
2.72E−27
2.72E−27
2.72E−27

8
3.22E−07
2.72E−27
2.72E−27
2.72E−27

9
3.22E−07
2.72E−27
2.72E−27
2.72E−27

10
3.22E−07
2.72E−27
2.72E−27
2.72E−27

11
3.22E−07
2.72E−27
2.72E−27
2.72E−27

12
6.85E−07
2.72E−27
2.72E−27
2.72E−27

13
2.90E−07
1.05E−25
1.05E−25
1.05E−25

14
3.22E−07
2.72E−27
2.72E−27
2.72E−27

15
3.22E−07
2.72E−27
2.72E−27
2.72E−27

16
3.22E−07
2.72E−27
2.72E−27
2.72E−27

17
3.22E−07
2.72E−27
2.72E−27
2.72E−27

18
2.90E−07
1.05E−25
1.05E−25
1.05E−25

19
2.90E−07
1.05E−25
1.05E−25
1.05E−25

20
8.65E−04
1.18E−21
1.18E−21
1.18E−21

21
8.65E−04
1.18E−21
1.18E−21
1.18E−21

22
3.21E−03
7.21E−21
7.21E−21
7.21E−21

23
3.21E−03
7.21E−21
7.21E−21
7.21E−21

24
1.55E−03
1.27E−19
1.27E−19
1.27E−19

25
1.83E−03
2.01E−19
2.01E−19
2.01E−19

26
1.26E−02
1.32E−20
1.32E−20
1.32E−20

27
1.18E−02
7.81E−20
7.81E−20
7.81E−20

28
1.18E−02
7.81E−20
7.81E−20
7.81E−20

29
1.26E−02
7.25E−19
7.25E−19
7.25E−19

30
3.28E−02
3.76E−18
3.76E−18
3.76E−18

31
4.05E−03
1.35E−15
1.35E−15
1.35E−15

32
1.24E−02
1.13E−19
1.13E−19
1.13E−19

33
1.11E−03
1.73E−15
1.73E−15
1.73E−15

34
1.27E−02
6.35E−19
6.35E−19
6.35E−19

35
2.32E−02
3.05E−13
3.05E−13
3.05E−13

36
7.10E−03
2.03E−18
2.03E−18
2.03E−18

37
7.10E−03
2.03E−18
2.03E−18
2.03E−18

38
1.24E−02
2.91E−15
2.91E−15
2.91E−15

39
3.37E−02
1.60E−16
1.60E−16
1.60E−16

40
5.70E−02
1.88E−12
1.88E−12
1.88E−12

41
1.15E−01
1.25E−15
1.25E−15
1.25E−15

42
3.84E−02
9.78E−11
9.78E−11
9.78E−11

43
3.56E−02
5.77E−17
5.77E−17
5.77E−17

44
3.37E−02
1.60E−16
1.60E−16
1.60E−16

45
3.37E−02
1.60E−16
1.60E−16
1.60E−16

46
2.90E−07
1.61E−15
1.61E−15
1.61E−15

47
7.69E−02
7.81E−20
7.81E−20
7.81E−20

48
8.07E−02
6.08E−12
6.08E−12
6.08E−12

49
2.90E−07
1.61E−15
1.61E−15
1.61E−15

50
3.04E−06
1.82E−17
1.82E−17
1.82E−17

TABLE 23f

Data for Staphylococcus, particularly S. aureus (continued)

No.
Cefuroxim_pv_adj
Ciprofloxacin_pv_adj
Clindamycin_pv_adj
Erythromycin_pv_adj

1
1.02E−172
4.82E−131
5.41E−111
1.04E−111

2
1.02E−172
4.82E−131
5.41E−111
1.04E−111

3
1.02E−172
3.02E−132
6.31E−112
7.39E−113

4
1.19E−170
1.00E−131
5.45E−114
1.72E−111

5
9.55E−169
1.65E−131
8.55E−113
3.44E−110

6
3.09E−155
2.03E−145
7.78E−102
4.54E−100

7
2.00E−140
4.08E−138
6.00E−125
2.44E−127

8
2.00E−140
5.95E−135
7.70E−123
2.44E−127

9
2.00E−140
4.08E−138
6.00E−125
2.44E−127

10
2.29E−138
2.11E−136
1.31E−123
4.65E−126

11
2.29E−138
3.02E−133
1.67E−121
4.65E−126

12
1.01E−138
1.36E−128
4.01E−120
1.01E−123

13
2.71E−145
1.43E−135
2.49E−122
2.94E−121

14
5.87E−142
6.84E−140
7.88E−125
3.61E−124

15
5.87E−142
6.84E−140
7.88E−125
3.61E−124

16
5.87E−142
6.84E−140
7.88E−125
3.61E−124

17
5.87E−142
6.84E−140
7.88E−125
3.61E−124

18
3.15E−140
6.84E−140
1.65E−123
1.01E−122

19
3.78E−139
5.24E−139
7.90E−123
4.58E−122

20
3.99E−125
5.65E−132
3.88E−136
8.83E−140

21
5.82E−123
4.09E−130
1.24E−134
2.39E−138

22
4.30E−124
5.65E−132
7.67E−139
1.30E−142

23
4.30E−124
5.65E−132
7.67E−139
1.30E−142

24
8.70E−122
4.09E−130
4.42E−135
5.01E−139

25
1.95E−112
3.48E−117
1.09E−121
8.26E−126

26
9.99E−102
2.00E−99
7.42E−94
1.88E−93

27
9.92E−101
1.25E−100
4.84E−95
2.65E−94

28
1.08E−99
6.62E−99
5.06E−95
1.80E−94

29
4.45E−100
1.46E−101
3.05E−98
1.82E−99

30
3.62E−99
6.76E−98
4.11E−89
2.04E−88

31
5.46E−82
8.46E−90
4.95E−69
2.56E−67

32
3.45E−93
1.68E−88
1.37E−90
2.27E−88

33
7.10E−92
7.29E−86
6.57E−78
1.16E−76

34
3.46E−90
5.20E−83
1.49E−80
4.89E−80

35
9.56E−73
1.94E−83
1.78E−63
2.45E−61

36
1.95E−83
3.50E−91
5.92E−79
2.14E−84

37
1.95E−83
3.50E−91
5.92E−79
2.14E−84

38
7.71E−76
4.08E−77
6.05E−58
6.49E−57

39
3.93E−89
4.20E−78
5.89E−71
3.43E−72

40
3.54E−69
3.19E−77
4.43E−58
3.86E−57

41
8.95E−84
1.49E−77
1.71E−74
1.87E−74

42
3.77E−75
8.95E−84
6.90E−85
9.85E−84

43
6.75E−81
1.60E−81
9.46E−72
9.56E−79

44
3.58E−81
2.83E−81
9.63E−72
1.15E−78

45
4.14E−80
2.83E−81
1.29E−70
1.77E−77

46
7.59E−62
5.15E−79
7.94E−76
5.98E−76

47
6.11E−79
1.32E−73
5.43E−98
2.20E−97

48
1.16E−77
7.87E−68
1.31E−67
3.92E−67

49
5.08E−59
3.55E−74
3.25E−71
5.25E−71

50
4.13E−78
4.35E−52
2.56E−53
1.24E−51

TABLE 23g

Data for Staphylococcus, particularly S. aureus (continued)

No.
Imipenem_pv_adj
Levofloxacin_pv_adj
Moxifloxacin_pv_adj
Oxacillin_pv_adj

1
2.22E−97
8.36E−31
1.85E−167
9.38E−227

2
2.22E−97
8.36E−31
1.85E−167
9.38E−227

3
2.22E−97
8.36E−31
1.24E−168
2.67E−225

4
5.09E−91
5.82E−30
1.90E−168
1.77E−211

5
2.50E−88
1.50E−28
3.37E−166
3.22E−210

6
1.02E−75
5.49E−34
4.29E−188
2.96E−187

7
5.60E−79
1.02E−27
1.24E−168
6.72E−181

8
5.60E−79
1.02E−27
8.38E−166
6.72E−181

9
5.60E−79
1.02E−27
1.24E−168
6.72E−181

10
5.60E−79
1.02E−27
9.67E−167
8.54E−179

11
7.66E−78
1.02E−27
6.64E−164
8.54E−179

12
5.60E−79
5.41E−27
4.22E−160
1.82E−175

13
1.11E−77
1.82E−28
7.77E−170
3.23E−175

14
5.16E−79
1.02E−27
1.02E−172
9.13E−175

15
5.16E−79
1.02E−27
1.02E−172
9.13E−175

16
5.16E−79
1.02E−27
1.02E−172
9.13E−175

17
5.16E−79
1.02E−27
1.02E−172
9.13E−175

18
1.11E−77
4.43E−26
5.10E−171
2.26E−173

19
1.11E−77
4.43E−26
4.94E−170
2.40E−172

20
2.49E−65
7.88E−28
2.60E−167
1.43E−155

21
7.09E−65
7.88E−28
3.13E−166
2.33E−153

22
1.38E−64
8.83E−27
3.37E−166
1.17E−154

23
1.38E−64
8.83E−27
3.37E−166
1.17E−154

24
6.20E−63
2.26E−24
7.17E−161
3.62E−151

25
1.34E−61
1.22E−26
4.17E−152
4.81E−142

26
6.28E−51
3.77E−23
1.59E−135
2.07E−120

27
6.51E−51
2.53E−22
1.70E−135
8.40E−122

28
6.51E−51
2.53E−22
1.78E−134
8.52E−120

29
5.53E−51
1.45E−21
4.06E−133
1.84E−119

30
8.78E−49
9.16E−21
1.01E−130
3.53E−117

31
8.13E−44
1.25E−24
4.84E−126
3.22E−102

32
2.98E−44
2.87E−19
6.20E−122
5.33E−111

33
6.56E−47
5.69E−23
5.76E−120
7.13E−108

34
4.99E−46
2.00E−18
1.85E−116
2.91E−105

35
1.79E−38
1.08E−20
7.19E−116
1.17E−92

36
4.65E−43
6.88E−21
4.22E−113
2.39E−97

37
4.65E−43
6.88E−21
4.22E−113
2.39E−97

38
1.60E−42
7.01E−24
4.84E−112
7.55E−91

39
1.54E−44
3.19E−20
4.64E−110
2.85E−100

40
4.20E−36
3.14E−19
5.76E−108
5.09E−88

41
1.65E−39
8.87E−19
2.41E−107
6.05E−97

42
8.79E−40
1.09E−14
3.00E−106
3.22E−94

43
1.21E−43
1.71E−19
1.58E−102
1.41E−92

44
2.98E−44
8.40E−19
1.07E−101
4.03E−92

45
8.13E−44
8.40E−19
1.07E−101
4.03E−92

46
2.94E−31
2.14E−17
5.26E−101
5.94E−79

47
1.67E−43
1.76E−21
8.02E−101
1.17E−94

48
2.19E−35
1.61E−13
1.79E−95
4.56E−88

49
4.69E−30
2.14E−17
1.80E−94
5.69E−74

50
3.32E−41
8.45E−15
1.32E−71
2.83E−94

TABLE 23h

Data for Staphylococcus, particularly S. aureus (continued)

Penicillin

No.
G_pv_adj
Piperacillin/Tazobactam_pv_adj
Tetracyclin_pv_adj
Tobramycin_pv_adj

1
1.37E−41
1.55E−21
1.22E−01
2.16E−15

2
1.37E−41
1.55E−21
1.22E−01
2.16E−15

3
1.51E−41
1.55E−21
9.63E−02
2.16E−15

4
3.46E−40
1.17E−19
2.75E−02
6.21E−16

5
6.83E−41
2.25E−18
3.70E−02
2.16E−15

6
3.80E−41
1.59E−17
1.27E−02
1.94E−13

7
6.95E−35
3.69E−14
5.90E−03
7.81E−15

8
6.95E−35
3.69E−14
5.90E−03
7.81E−15

9
6.95E−35
3.69E−14
5.90E−03
7.81E−15

10
1.50E−34
3.69E−14
8.03E−03
7.81E−15

11
1.50E−34
3.69E−14
8.03E−03
7.81E−15

12
5.97E−34
3.69E−14
8.79E−03
7.81E−15

13
5.30E−34
5.46E−13
9.97E−04
9.71E−16

14
1.23E−34
3.69E−14
1.42E−03
7.81E−15

15
1.23E−34
3.69E−14
1.42E−03
7.81E−15

16
1.23E−34
3.69E−14
1.42E−03
7.81E−15

17
1.23E−34
3.69E−14
1.42E−03
7.81E−15

18
1.23E−34
5.46E−13
1.42E−03
3.02E−14

19
1.23E−34
5.46E−13
1.42E−03
3.02E−14

20
5.10E−21
3.04E−11
5.98E−04
7.15E−15

21
9.90E−21
3.04E−11
2.52E−04
7.15E−15

22
2.82E−20
9.29E−11
5.97E−04
2.24E−14

23
2.82E−20
9.29E−11
5.97E−04
2.24E−14

24
1.92E−20
4.28E−09
8.65E−04
4.98E−13

25
1.42E−21
6.78E−10
2.40E−03
6.71E−15

26
2.07E−10
4.04E−10
5.35E−05
4.17E−12

27
1.36E−10
1.16E−09
2.27E−05
1.33E−11

28
2.18E−10
1.16E−09
3.46E−05
1.33E−11

29
4.59E−14
1.16E−09
8.29E−05
7.56E−11

30
6.54E−10
2.97E−08
3.46E−05
2.92E−10

31
4.06E−09
7.73E−08
2.02E−05
2.25E−08

32
2.64E−11
3.31E−11
2.07E−02
6.23E−11

33
2.28E−19
2.60E−08
2.52E−06
9.88E−10

34
1.20E−07
3.78E−10
1.24E−02
9.10E−11

35
4.14E−07
1.59E−06
1.78E−06
6.53E−07

36
4.05E−13
7.74E−09
1.25E−04
1.01E−10

37
4.05E−13
7.74E−09
1.25E−04
1.01E−10

38
4.22E−06
1.49E−07
1.46E−05
5.29E−08

39
1.18E−06
8.70E−08
2.19E−04
7.09E−11

40
1.87E−06
1.59E−06
3.63E−05
1.92E−07

41
4.31E−06
6.90E−07
1.08E−04
2.74E−09

42
6.34E−11
4.80E−05
2.10E−05
6.87E−09

43
2.66E−09
4.09E−08
4.92E−04
1.94E−10

44
7.22E−09
8.70E−08
3.32E−04
6.07E−10

45
2.79E−09
8.70E−08
3.32E−04
6.07E−10

46
1.54E−26
8.34E−08
2.05E−05
1.24E−11

47
4.32E−03
1.16E−09
4.05E−06
1.33E−11

48
1.28E−06
1.86E−05
1.61E−03
1.89E−08

49
3.43E−27
8.34E−08
1.11E−03
1.24E−11

50
2.12E−15
1.05E−10
6.95E−03
1.62E−07

TABLE 23i

Data for Staphylococcus, particularly S. aureus (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
HMPREF0791_1752
mecA
ZP_04797671

2
HMPREF0794_1488
ugpQ
ZP_06614206

3
HMPREF0794_1485
mecR
ZP_06614203

4
SIAG_00762

ZP_06819251

5
HMPREF0789_1682

ZP_04825874

6
SAMG_01950

ZP_05682863

7
Missing locus_tag: FN433596.cds78.83191..82796

CBI47961

8
SATW20_00761

CBI67631

9
SERP2515

YP_190057

10
SAIG_02579

ZP_05694555

11
SERP2519
mecI
YP_190060

12
SERP2505

YP_190047

13
HMPREF0794_1451

ZP_06614169

14
SERP2490
kdeP
YP_190033

15
SERP2487
kdpA
YP_190030

16
SERP2485
kdpC
YP_190028

17
SERP2489
kdpD
YP_190032

18
SERP2486
kdpB
YP_190029

19
SAIG_01884

ZP_05693385

20
SERP1347
tnpA-2
YP_188919

21
SERP1223
tnpB-1
YP_188797

22
SLAG_02844

ZP_06930609

23
SA0049
ant(9)
NP_373289

24
SERP1342

YP_188914

25
HMPREF0773_2426
radC
ZP_04829125

26
SAFG_01021

ZP_05703394

27
SAFG_01015

ZP_05703388

28
SA2981_2149

ADC38360

29
ECTR2_1640

CBX35020

30
SA2981_1770

ADC37981

31
SAB0169

YP_415679

32
SaurJH1_0467

YP_001315613

33
SERP1345
tnpC-2
YP_188917

34
SGAG_02626

ZP_06303506

35
ECTR2_2075

CBX35404

36
HMPREF0774_2643

ZP_04869332

37
SAHG_01730

ZP_05696261

38
SAA6159_00204
coa
ADL22160

39
SARG_01832

ZP_06332611

40
SAIG_01373

ZP_05693621

41
SANG_00111

ZP_05682471

42
SAHG_02693

ZP_05696106

43
SAJG_00740

ZP_05692517

44
SaurJH1_0188

YP_001315337

45
SGAG_00714

ZP_06301594

46
ECTR2_2580

CBX35910
plasmid

pLUH02

47
SA2981_0414
lpl3
ADC36625

48
SA2981_1977
agrB
ADC38188

49
SMAG_02765

ZP_06817387

50
HMPREF0798_02109

ZP_07844597

TABLE 23j

Data for Staphylococcus, particularly S. aureus (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
1335
3341
+
645076738

2
7348
8091
−
647019109

3
3685
4599
−
647019109

4
3987
5336
−
647537018

5
1842
3491
−
645076234

6
89170
89277
−
645958292

7
82796
84130
−
646862418

8
81146
81214
−
646862418

9
2570266
2571330
+
637000098

10
6265
7374
+
645958144

11
2574428
2574799
−
637000098

12
2562107
2562424
+
637000098

13
8938
9252
+
647019108

14
2549489
2550184
+
637000098

15
2544901
2546577
−
637000098

16
2542288
2542845
−
637000098

17
2546845
2549514
+
637000098

18
2542861
2544882
−
637000098

19
76580
76657
−
645958116

20
1403752
1404837
−
637000098

21
1255425
1257317
−
637000098

22
4557
5288
−
647016972

23
56859
57641
−
637000072

24
1399547
1399606
+
637000098

25
4478
5164
−
645076413

26
277066
278082
+
645957989

27
272112
272231
−
645957989

28
2299803
2300126
−
646862390

29
1804139
1805368
−
651053129

30
1899111
1899692
+
646862390

31
209129
211012
+
637000460

32
487880
489091
+
640753011

33
1401479
1401856
−
637000098

34
245
686
−
647008393

35
2210164
2210319
−
651053129

36
16441
17124
+
645076159

37
85620
86303
+
645958072

38
242193
244169
+
648231718

39
177946
180372
+
647535981

40
38140
39216
+
645958123

41
77988
79490
−
645958383

42
5009
5929
−
645958068

43
78131
78853
+
645958189

44
221049
221729
+
640753011

45
44419
44616
+
647008364

46
12682
13458
−
651053131

47
456367
457155
+
646862390

48
2096829
2097392
+
646862390

49
14918
15697
−
647017059

50
54037
54601
+
651285048

TABLE 24a

Data for Staphylococcus, particularly S. aureus

No.
Scaffold.External.Accession
Scaffold.Name
best_pv

1
NZ_ACJC01000132

Staphylococcus epidermidis W23144: NZ_ACJC01000132
9.38479881072327e−227

2
NZ_ADMU01000036

Staphylococcus epidermidis M23864: W2 (grey) contig00037:
9.38479881072327e−227

NZ_ADMU01000036

3
NZ_ADMU01000036

Staphylococcus epidermidis M23864: W2 (grey) contig00037:
2.67435403500704e−225

NZ_ADMU01000036

4
NZ_GG770515

Staphylococcus aureus subsp. aureus EMRSA16 genomic scaffold
1.77186061517335e−211

supercont1.3: NZ_GG770515

5
NZ_ACHE01000064

Staphylococcus epidermidis BCM-HMP0060: NZ_ACHE01000064
3.22333061264623e−210

6
NZ_ACKJ01000008

Staphylococcus aureus A9719: NZ_ACKJ01000008
4.28801157250818e−188

7
FN433596

Staphylococcus aureus subsp. aureus TW20: FN433596
6.72085159673615e−181

8
FN433596

Staphylococcus aureus subsp. aureus TW20: FN433596
6.72085159673615e−181

9
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
6.72085159673615e−181

10
NZ_ACKF01000035

Staphylococcus aureus A6300: NZ_ACKF01000035
8.5426103876016e−179

11
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
8.5426103876016e−179

12
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
1.81714784068785e−175

13
NZ_ADMU01000035

Staphylococcus epidermidis M23864: W2 (grey) contig00036:
3.23410033711171e−175

NZ_ADMU01000035

14
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
9.12700235375297e−175

15
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
9.12700235375297e−175

16
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
9.12700235375297e−175

17
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
9.12700235375297e−175

18
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
2.25944344923286e−173

19
NZ_ACKF01000007

Staphylococcus aureus A6300: NZ_ACKF01000007
2.40063417489507e−172

20
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
2.59802993040457e−167

21
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
3.12953724144125e−166

22
NZ_ADJJ01000031

Staphylococcus aureus A8796 cont1.31: NZ_ADJJ01000031
3.37208086862656e−166

23
NC_002745

Staphylococcus aureus subsp. aureus N315: NC_002745
3.37208086862656e−166

24
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
7.17319474297637e−161

25
NZ_ACHH01000128

Staphylococcus aureus subsp. aureus TCH70: NZ_ACHH01000128
4.16856451727179e−152

26
NZ_ACKC01000026

Staphylococcus aureus A5937: NZ_ACKC01000026
1.58751373713434e−135

27
NZ_ACKC01000026

Staphylococcus aureus A5937: NZ_ACKC01000026
1.69633422486642e−135

28
CP001844

Staphylococcus aureus 04-02981: CP001844
1.77656315889944e−134

29
FR714927

Staphylococcus aureus subsp. aureus ECT-R 2: FR714927
4.06264970457926e−133

30
CP001844

Staphylococcus aureus 04-02981: CP001844
1.01251954267327e−130

31
NC_007622

Staphylococcus aureus RF122: NC_007622
4.84169534955158e−126

32
NC_009632

Staphylococcus aureus subsp. aureus JH1: NC_009632
6.20485118760467e−122

33
NC_002976

Staphylococcus epidermidis RP62A: NC_002976
5.75915090813908e−120

34
NZ_ACYO01000032

Staphylococcus aureus A8117 cont1.32: NZ_ACYO01000032
1.84672228386398e−116

35
FR714927

Staphylococcus aureus subsp. aureus ECT-R 2: FR714927
7.1946440374743e−116

36
NZ_ACHD01000273

Staphylococcus aureus subsp. aureus TCH130: NZ_ACHD01000273
4.22320321058421e−113

37
NZ_ACKE01000012

Staphylococcus aureus A6224: NZ_ACKE01000012
4.22320321058421e−113

38
CP002114

Staphylococcus aureus subsp. aureus JKD6159: CP002114
4.83609713640718e−112

39
NZ_GG730131

Staphylococcus aureus subsp. aureus C101 genomic scaffold
4.63942446669448e−110

supercont1.12: NZ_GG730131

40
NZ_ACKF01000014

Staphylococcus aureus A6300: NZ_ACKF01000014
5.76090691723747e−108

41
NZ_ACKK01000039

Staphylococcus aureus A9763: NZ_ACKK01000039
2.40583396327414e−107

42
NZ_ACKE01000008

Staphylococcus aureus A6224: NZ_ACKE01000008
2.99974766558167e−106

43
NZ_ACKG01000031

Staphylococcus aureus A8115: NZ_ACKG01000031
1.57559858677166e−102

44
NC_009632

Staphylococcus aureus subsp. aureus JH1: NC_009632
1.0725409335823e−101

45
NZ_ACYO01000003

Staphylococcus aureus A8117 cont1.3: NZ_ACYO01000003
1.0725409335823e−101

46
FR714929

Staphylococcus aureus subsp. aureus ECT-R 2 plasmid pLUH02:
5.26123840198017e−101

FR714929

47
CP001844

Staphylococcus aureus 04-02981: CP001844
8.01600909282956e−101

48
CP001844

Staphylococcus aureus 04-02981: CP001844
1.78546333248495e−95

49
NZ_ADJK01000020

Staphylococcus aureus A8819 cont1.20: NZ_ADJK01000020
1.80469278143707e−94

50
NZ_GL545262

Staphylococcus hominis subsp. hominis C80 genomic scaffold
2.82728623419544e−94

supercont1.11: NZ_GL545262

TABLE 24b

Data for Staphylococcus, particularly S. aureus (continued)

No.
sign_phenos

1
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tobramycin

2
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tobramycin

3
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tobramycin

4
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tobramycin

5
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tobramycin

6
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tobramycin

7
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

8
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

9
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

10
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

11
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

12
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

13
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

14
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

15
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

16
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

17
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

18
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

19
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

20
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

21
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

22
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

23
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

24
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

25
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

26
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

27
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

28
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

29
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

30
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

31
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

32
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tobramycin

33
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

34
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tobramycin

35
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

36
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

37
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

38
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

39
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

40
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

41
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

42
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

43
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

44
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

45
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

46
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

47
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

48
Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem; Levofloxacin;

Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

49
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

50
Ampicillin; Ampicillin/Sulbactam; Cefepim; Cefotaxim; Cefuroxim; Ciprofloxacin; Clindamycin; Erythromycin; Imipenem;

Levofloxacin; Moxifloxacin; Oxacillin; Penicillin G; Piperacillin/Tazobactam; Tetracyclin; Tobramycin

TABLE 24c

Data for Staphylococcus, particularly S. aureus (continued)

No.
sign_phenos_class
best_pheno
best_pheno_class

1
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide
Oxacillin
lactam

2
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide
Oxacillin
lactam

3
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide
Oxacillin
lactam

4
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide
Oxacillin
lactam

5
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide
Oxacillin
lactam

6
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide
Moxifloxacin
fluoroquinolone

7
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

8
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

9
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

10
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

11
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

12
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

13
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

14
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

15
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

16
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

17
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

18
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

19
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

20
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

21
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

22
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

23
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

24
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

25
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

26
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

27
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

28
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

29
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

30
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

31
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

32
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide
Moxifloxacin
fluoroquinolone

33
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

34
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide
Moxifloxacin
fluoroquinolone

35
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

36
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

37
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

38
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

39
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

40
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

41
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

42
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

43
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

44
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

45
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

46
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

47
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

48
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

49
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Moxifloxacin
fluoroquinolone

50
aminoglycoside; fluoroquinolone; lactam; lincosamide; macrolide; tetracycline
Oxacillin
lactam

TABLE 24d

Data for Staphylococcus, particularly S. aureus (continued)

No.
num_aminoglycoside
num_fluoroquinolone
num_lactam
num_lincosamide
num_macrolide
num_tetracycline

1
1
3
9
1
1
0

2
1
3
9
1
1
0

3
1
3
9
1
1
0

4
1
3
9
1
1
0

5
1
3
9
1
1
0

6
1
3
9
1
1
0

7
1
3
9
1
1
1

8
1
3
9
1
1
1

9
1
3
9
1
1
1

10
1
3
9
1
1
1

11
1
3
9
1
1
1

12
1
3
9
1
1
1

13
1
3
9
1
1
1

14
1
3
9
1
1
1

15
1
3
9
1
1
1

16
1
3
9
1
1
1

17
1
3
9
1
1
1

18
1
3
9
1
1
1

19
1
3
9
1
1
1

20
1
3
9
1
1
1

21
1
3
9
1
1
1

22
1
3
9
1
1
1

23
1
3
9
1
1
1

24
1
3
9
1
1
1

25
1
3
9
1
1
1

26
1
3
8
1
1
1

27
1
3
8
1
1
1

28
1
3
8
1
1
1

29
1
3
8
1
1
1

30
1
3
8
1
1
1

31
1
3
9
1
1
1

32
1
3
8
1
1
0

33
1
3
9
1
1
1

34
1
3
8
1
1
0

35
1
3
8
1
1
1

36
1
3
9
1
1
1

37
1
3
9
1
1
1

38
1
3
8
1
1
1

39
1
3
8
1
1
1

40
1
3
8
1
1
1

41
1
3
8
1
1
1

42
1
3
8
1
1
1

43
1
3
8
1
1
1

44
1
3
8
1
1
1

45
1
3
8
1
1
1

46
1
3
9
1
1
1

47
1
3
8
1
1
1

48
1
3
8
1
1
1

49
1
3
9
1
1
1

50
1
3
9
1
1
1

TABLE 24e

Data for Staphylococcus, particularly S. aureus (continued)

No.
Ampicillin_pv_adj
Ampicillin/Sulbactam_pv_adj
Cefepim_pv_adj
Cefotaxim_pv_adj

1
2.20E−08
5.96E−37
5.96E−37
5.96E−37

2
2.20E−08
5.96E−37
5.96E−37
5.96E−37

3
2.20E−08
5.96E−37
5.96E−37
5.96E−37

4
4.64E−08
4.55E−35
4.55E−35
4.55E−35

5
2.20E−08
2.16E−33
2.16E−33
2.16E−33

6
2.22E−09
1.64E−31
1.64E−31
1.64E−31

7
3.22E−07
2.72E−27
2.72E−27
2.72E−27

8
3.22E−07
2.72E−27
2.72E−27
2.72E−27

9
3.22E−07
2.72E−27
2.72E−27
2.72E−27

10
3.22E−07
2.72E−27
2.72E−27
2.72E−27

11
3.22E−07
2.72E−27
2.72E−27
2.72E−27

12
6.85E−07
2.72E−27
2.72E−27
2.72E−27

13
2.90E−07
1.05E−25
1.05E−25
1.05E−25

14
3.22E−07
2.72E−27
2.72E−27
2.72E−27

15
3.22E−07
2.72E−27
2.72E−27
2.72E−27

16
3.22E−07
2.72E−27
2.72E−27
2.72E−27

17
3.22E−07
2.72E−27
2.72E−27
2.72E−27

18
2.90E−07
1.05E−25
1.05E−25
1.05E−25

19
2.90E−07
1.05E−25
1.05E−25
1.05E−25

20
8.65E−04
1.18E−21
1.18E−21
1.18E−21

21
8.65E−04
1.18E−21
1.18E−21
1.18E−21

22
3.21E−03
7.21E−21
7.21E−21
7.21E−21

23
3.21E−03
7.21E−21
7.21E−21
7.21E−21

24
1.55E−03
1.27E−19
1.27E−19
1.27E−19

25
1.83E−03
2.01E−19
2.01E−19
2.01E−19

26
1.26E−02
1.32E−20
1.32E−20
1.32E−20

27
1.18E−02
7.81E−20
7.81E−20
7.81E−20

28
1.18E−02
7.81E−20
7.81E−20
7.81E−20

29
1.26E−02
7.25E−19
7.25E−19
7.25E−19

30
3.28E−02
3.76E−18
3.76E−18
3.76E−18

31
4.05E−03
1.35E−15
1.35E−15
1.35E−15

32
1.24E−02
1.13E−19
1.13E−19
1.13E−19

33
1.11E−03
1.73E−15
1.73E−15
1.73E−15

34
1.27E−02
6.35E−19
6.35E−19
6.35E−19

35
2.32E−02
3.05E−13
3.05E−13
3.05E−13

36
7.10E−03
2.03E−18
2.03E−18
2.03E−18

37
7.10E−03
2.03E−18
2.03E−18
2.03E−18

38
1.24E−02
2.91E−15
2.91E−15
2.91E−15

39
3.37E−02
1.60E−16
1.60E−16
1.60E−16

40
5.70E−02
1.88E−12
1.88E−12
1.88E−12

41
1.15E−01
1.25E−15
1.25E−15
1.25E−15

42
3.84E−02
9.78E−11
9.78E−11
9.78E−11

43
3.56E−02
5.77E−17
5.77E−17
5.77E−17

44
3.37E−02
1.60E−16
1.60E−16
1.60E−16

45
3.37E−02
1.60E−16
1.60E−16
1.60E−16

46
2.90E−07
1.61E−15
1.61E−15
1.61E−15

47
7.69E−02
7.81E−20
7.81E−20
7.81E−20

48
8.07E−02
6.08E−12
6.08E−12
6.08E−12

49
2.90E−07
1.61E−15
1.61E−15
1.61E−15

50
3.04E−06
1.82E−17
1.82E−17
1.82E−17

TABLE 24f

Data for Staphylococcus, particularly S. aureus (continued)

No.
Cefuroxim_pv_adj
Ciprofloxacin_pv_adj
Clindamycin_pv_adj
Erythromycin_pv_adj

1
1.02E−172
4.82E−131
5.41E−111
1.04E−111

2
1.02E−172
4.82E−131
5.41E−111
1.04E−111

3
1.02E−172
3.02E−132
6.31E−112
7.39E−113

4
1.19E−170
1.00E−131
5.45E−114
1.72E−111

5
9.55E−169
1.65E−131
8.55E−113
3.44E−110

6
3.09E−155
2.03E−145
7.78E−102
4.54E−100

7
2.00E−140
4.08E−138
6.00E−125
2.44E−127

8
2.00E−140
5.95E−135
7.70E−123
2.44E−127

9
2.00E−140
4.08E−138
6.00E−125
2.44E−127

10
2.29E−138
2.11E−136
1.31E−123
4.65E−126

11
2.29E−138
3.02E−133
1.67E−121
4.65E−126

12
1.01E−138
1.36E−128
4.01E−120
1.01E−123

13
2.71E−145
1.43E−135
2.49E−122
2.94E−121

14
5.87E−142
6.84E−140
7.88E−125
3.61E−124

15
5.87E−142
6.84E−140
7.88E−125
3.61E−124

16
5.87E−142
6.84E−140
7.88E−125
3.61E−124

17
5.87E−142
6.84E−140
7.88E−125
3.61E−124

18
3.15E−140
6.84E−140
1.65E−123
1.01E−122

19
3.78E−139
5.24E−139
7.90E−123
4.58E−122

20
3.99E−125
5.65E−132
3.88E−136
8.83E−140

21
5.82E−123
4.09E−130
1.24E−134
2.39E−138

22
4.30E−124
5.65E−132
7.67E−139
1.30E−142

23
4.30E−124
5.65E−132
7.67E−139
1.30E−142

24
8.70E−122
4.09E−130
4.42E−135
5.01E−139

25
1.95E−112
3.48E−117
1.09E−121
8.26E−126

26
9.99E−102
2.00E−99
7.42E−94
1.88E−93

27
9.92E−101
1.25E−100
4.84E−95
2.65E−94

28
1.08E−99
6.62E−99
5.06E−95
1.80E−94

29
4.45E−100
1.46E−101
3.05E−98
1.82E−99

30
3.62E−99
6.76E−98
4.11E−89
2.04E−88

31
5.46E−82
8.46E−90
4.95E−69
2.56E−67

32
3.45E−93
1.68E−88
1.37E−90
2.27E−88

33
7.10E−92
7.29E−86
6.57E−78
1.16E−76

34
3.46E−90
5.20E−83
1.49E−80
4.89E−80

35
9.56E−73
1.94E−83
1.78E−63
2.45E−61

36
1.95E−83
3.50E−91
5.92E−79
2.14E−84

37
1.95E−83
3.50E−91
5.92E−79
2.14E−84

38
7.71E−76
4.08E−77
6.05E−58
6.49E−57

39
3.93E−89
4.20E−78
5.89E−71
3.43E−72

40
3.54E−69
3.19E−77
4.43E−58
3.86E−57

41
8.95E−84
1.49E−77
1.71E−74
1.87E−74

42
3.77E−75
8.95E−84
6.90E−85
9.85E−84

43
6.75E−81
1.60E−81
9.46E−72
9.56E−79

44
3.58E−81
2.83E−81
9.63E−72
1.15E−78

45
4.14E−80
2.83E−81
1.29E−70
1.77E−77

46
7.59E−62
5.15E−79
7.94E−76
5.98E−76

47
6.11E−79
1.32E−73
5.43E−98
2.20E−97

48
1.16E−77
7.87E−68
1.31E−67
3.92E−67

49
5.08E−59
3.55E−74
3.25E−71
5.25E−71

50
4.13E−78
4.35E−52
2.56E−53
1.24E−51

TABLE 24g

Data for Staphylococcus, particularly S. aureus (continued)

No.
Imipenem_pv_adj
Levofloxacin_pv_adj
Moxifloxacin_pv_adj
Oxacillin_pv_adj

1
2.22E−97
8.36E−31
1.85E−167
9.38E−227

2
2.22E−97
8.36E−31
1.85E−167
9.38E−227

3
2.22E−97
8.36E−31
1.24E−168
2.67E−225

4
5.09E−91
5.82E−30
1.90E−168
1.77E−211

5
2.50E−88
1.50E−28
3.37E−166
3.22E−210

6
1.02E−75
5.49E−34
4.29E−188
2.96E−187

7
5.60E−79
1.02E−27
1.24E−168
6.72E−181

8
5.60E−79
1.02E−27
8.38E−166
6.72E−181

9
5.60E−79
1.02E−27
1.24E−168
6.72E−181

10
5.60E−79
1.02E−27
9.67E−167
8.54E−179

11
7.66E−78
1.02E−27
6.64E−164
8.54E−179

12
5.60E−79
5.41E−27
4.22E−160
1.82E−175

13
1.11E−77
1.82E−28
7.77E−170
3.23E−175

14
5.16E−79
1.02E−27
1.02E−172
9.13E−175

15
5.16E−79
1.02E−27
1.02E−172
9.13E−175

16
5.16E−79
1.02E−27
1.02E−172
9.13E−175

17
5.16E−79
1.02E−27
1.02E−172
9.13E−175

18
1.11E−77
4.43E−26
5.10E−171
2.26E−173

19
1.11E−77
4.43E−26
4.94E−170
2.40E−172

20
2.49E−65
7.88E−28
2.60E−167
1.43E−155

21
7.09E−65
7.88E−28
3.13E−166
2.33E−153

22
1.38E−64
8.83E−27
3.37E−166
1.17E−154

23
1.38E−64
8.83E−27
3.37E−166
1.17E−154

24
6.20E−63
2.26E−24
7.17E−161
3.62E−151

25
1.34E−61
1.22E−26
4.17E−152
4.81E−142

26
6.28E−51
3.77E−23
1.59E−135
2.07E−120

27
6.51E−51
2.53E−22
1.70E−135
8.40E−122

28
6.51E−51
2.53E−22
1.78E−134
8.52E−120

29
5.53E−51
1.45E−21
4.06E−133
1.84E−119

30
8.78E−49
9.16E−21
1.01E−130
3.53E−117

31
8.13E−44
1.25E−24
4.84E−126
3.22E−102

32
2.98E−44
2.87E−19
6.20E−122
5.33E−111

33
6.56E−47
5.69E−23
5.76E−120
7.13E−108

34
4.99E−46
2.00E−18
1.85E−116
2.91E−105

35
1.79E−38
1.08E−20
7.19E−116
1.17E−92

36
4.65E−43
6.88E−21
4.22E−113
2.39E−97

37
4.65E−43
6.88E−21
4.22E−113
2.39E−97

38
1.60E−42
7.01E−24
4.84E−112
7.55E−91

39
1.54E−44
3.19E−20
4.64E−110
2.85E−100

40
4.20E−36
3.14E−19
5.76E−108
5.09E−88

41
1.65E−39
8.87E−19
2.41E−107
6.05E−97

42
8.79E−40
1.09E−14
3.00E−106
3.22E−94

43
1.21E−43
1.71E−19
1.58E−102
1.41E−92

44
2.98E−44
8.40E−19
1.07E−101
4.03E−92

45
8.13E−44
8.40E−19
1.07E−101
4.03E−92

46
2.94E−31
2.14E−17
5.26E−101
5.94E−79

47
1.67E−43
1.76E−21
8.02E−101
1.17E−94

48
2.19E−35
1.61E−13
1.79E−95
4.56E−88

49
4.69E−30
2.14E−17
1.80E−94
5.69E−74

50
3.32E−41
8.45E−15
1.32E−71
2.83E−94

TABLE 24h

Data for Staphylococcus, particularly S. aureus (continued)

No.
Penicillin G_pv_adj
Piperacillin/Tazobactam_pv_adj
Tetracyclin_pv_adj
Tobramycin_pv_adj

1
1.37E−41
1.55E−21
1.22E−01
2.16E−15

2
1.37E−41
1.55E−21
1.22E−01
2.16E−15

3
1.51E−41
1.55E−21
9.63E−02
2.16E−15

4
3.46E−40
1.17E−19
2.75E−02
6.21E−16

5
6.83E−41
2.25E−18
3.70E−02
2.16E−15

6
3.80E−41
1.59E−17
1.27E−02
1.94E−13

7
6.95E−35
3.69E−14
5.90E−03
7.81E−15

8
6.95E−35
3.69E−14
5.90E−03
7.81E−15

9
6.95E−35
3.69E−14
5.90E−03
7.81E−15

10
1.50E−34
3.69E−14
8.03E−03
7.81E−15

11
1.50E−34
3.69E−14
8.03E−03
7.81E−15

12
5.97E−34
3.69E−14
8.79E−03
7.81E−15

13
5.30E−34
5.46E−13
9.97E−04
9.71E−16

14
1.23E−34
3.69E−14
1.42E−03
7.81E−15

15
1.23E−34
3.69E−14
1.42E−03
7.81E−15

16
1.23E−34
3.69E−14
1.42E−03
7.81E−15

17
1.23E−34
3.69E−14
1.42E−03
7.81E−15

18
1.23E−34
5.46E−13
1.42E−03
3.02E−14

19
1.23E−34
5.46E−13
1.42E−03
3.02E−14

20
5.10E−21
3.04E−11
5.98E−04
7.15E−15

21
9.90E−21
3.04E−11
2.52E−04
7.15E−15

22
2.82E−20
9.29E−11
5.97E−04
2.24E−14

23
2.82E−20
9.29E−11
5.97E−04
2.24E−14

24
1.92E−20
4.28E−09
8.65E−04
4.98E−13

25
1.42E−21
6.78E−10
2.40E−03
6.71E−15

26
2.07E−10
4.04E−10
5.35E−05
4.17E−12

27
1.36E−10
1.16E−09
2.27E−05
1.33E−11

28
2.18E−10
1.16E−09
3.46E−05
1.33E−11

29
4.59E−14
1.16E−09
8.29E−05
7.56E−11

30
6.54E−10
2.97E−08
3.46E−05
2.92E−10

31
4.06E−09
7.73E−08
2.02E−05
2.25E−08

32
2.64E−11
3.31E−11
2.07E−02
6.23E−11

33
2.28E−19
2.60E−08
2.52E−06
9.88E−10

34
1.20E−07
3.78E−10
1.24E−02
9.10E−11

35
4.14E−07
1.59E−06
1.78E−06
6.53E−07

36
4.05E−13
7.74E−09
1.25E−04
1.01E−10

37
4.05E−13
7.74E−09
1.25E−04
1.01E−10

38
4.22E−06
1.49E−07
1.46E−05
5.29E−08

39
1.18E−06
8.70E−08
2.19E−04
7.09E−11

40
1.87E−06
1.59E−06
3.63E−05
1.92E−07

41
4.31E−06
6.90E−07
1.08E−04
2.74E−09

42
6.34E−11
4.80E−05
2.10E−05
6.87E−09

43
2.66E−09
4.09E−08
4.92E−04
1.94E−10

44
7.22E−09
8.70E−08
3.32E−04
6.07E−10

45
2.79E−09
8.70E−08
3.32E−04
6.07E−10

46
1.54E−26
8.34E−08
2.05E−05
1.24E−11

47
4.32E−03
1.16E−09
4.05E−06
1.33E−11

48
1.28E−06
1.86E−05
1.61E−03
1.89E−08

49
3.43E−27
8.34E−08
1.11E−03
1.24E−11

50
2.12E−15
1.05E−10
6.95E−03
1.62E−07

TABLE 24i

Data for Staphylococcus, particularly S. aureus (continued)

No.
Locus.Tag
Gene.Symbol
GenBank.Accession
Chromosome

1
HMPREF0791_1752
mecA
ZP_04797671

2
HMPREF0794_1488
ugpQ
ZP_06614206

3
HMPREF0794_1485
mecR
ZP_06614203

4
SIAG_00762

ZP_06819251

5
HMPREF0789_1682

ZP_04825874

6
SAMG_01950

ZP_05682863

7
Missing locus_tag: FN433596.cds78.83191..82796

CBI47961

8
SATW20_00761

CBI67631

9
SERP2515

YP_190057

10
SAIG_02579

ZP_05694555

11
SERP2519
mecI
YP_190060

12
SERP2505

YP_190047

13
HMPREF0794_1451

ZP_06614169

14
SERP2490
kdeP
YP_190033

15
SERP2487
kdpA
YP_190030

16
SERP2485
kdpC
YP_190028

17
SERP2489
kdpD
YP_190032

18
SERP2486
kdpB
YP_190029

19
SAIG_01884

ZP_05693385

20
SERP1347
tnpA-2
YP_188919

21
SERP1223
tnpB-1
YP_188797

22
SLAG_02844

ZP_06930609

23
SA0049
ant(9)
NP_373289

24
SERP1342

YP_188914

25
HMPREF0773_2426
radC
ZP_04829125

26
SAFG_01021

ZP_05703394

27
SAFG_01015

ZP_05703388

28
SA2981_2149

ADC38360

29
ECTR2_1640

CBX35020

30
SA2981_1770

ADC37981

31
SAB0169

YP_415679

32
SaurJH1_0467

YP_001315613

33
SERP1345
tnpC-2
YP_188917

34
SGAG_02626

ZP_06303506

35
ECTR2_2075

CBX35404

36
HMPREF0774_2643

ZP_04869332

37
SAHG_01730

ZP_05696261

38
SAA6159_00204
coa
ADL22160

39
SARG_01832

ZP_06332611

40
SAIG_01373

ZP_05693621

41
SANG_00111

ZP_05682471

42
SAHG_02693

ZP_05696106

43
SAJG_00740

ZP_05692517

44
SaurJH1_0188

YP_001315337

45
SGAG_00714

ZP_06301594

46
ECTR2_2580

CBX35910
plasmid

pLUH02

47
SA2981_0414
lpl3
ADC36625

48
SA2981_1977
agrB
ADC38188

49
SMAG_02765

ZP_06817387

50
HMPREF0798_02109

ZP_07844597

TABLE 24j

Data for Staphylococcus, particularly S. aureus (continued)

No.
Start.Coord
End.Coord
Strand
Scaffold.ID

1
1335
3341
+
645076738

2
7348
8091
−
647019109

3
3685
4599
−
647019109

4
3987
5336
−
647537018

5
1842
3491
−
645076234

6
89170
89277
−
645958292

7
82796
84130
−
646862418

8
81146
81214
−
646862418

9
2570266
2571330
+
637000098

10
6265
7374
+
645958144

11
2574428
2574799
−
637000098

12
2562107
2562424
+
637000098

13
8938
9252
+
647019108

14
2549489
2550184
+
637000098

15
2544901
2546577
−
637000098

16
2542288
2542845
−
637000098

17
2546845
2549514
+
637000098

18
2542861
2544882
−
637000098

19
76580
76657
−
645958116

20
1403752
1404837
−
637000098

21
1255425
1257317
−
637000098

22
4557
5288
−
647016972

23
56859
57641
−
637000072

24
1399547
1399606
+
637000098

25
4478
5164
−
645076413

26
277066
278082
+
645957989

27
272112
272231
−
645957989

28
2299803
2300126
−
646862390

29
1804139
1805368
−
651053129

30
1899111
1899692
+
646862390

31
209129
211012
+
637000460

32
487880
489091
+
640753011

33
1401479
1401856
−
637000098

34
245
686
−
647008393

35
2210164
2210319
−
651053129

36
16441
17124
+
645076159

37
85620
86303
+
645958072

38
242193
244169
+
648231718

39
177946
180372
+
647535981

40
38140
39216
+
645958123

41
77988
79490
−
645958383

42
5009
5929
−
645958068

43
78131
78853
+
645958189

44
221049
221729
+
640753011

45
44419
44616
+
647008364

46
12682
13458
−
651053131

47
456367
457155
+
646862390

48
2096829
2097392
+
646862390

49
14918
15697
−
647017059

50
54037
54601
+
651285048

For examples 1-12, as well as further testes microorganisms, a consolidated list of the centroids that were found is given in the following Table 25.

TABLE 25

List of centroids in Examples

Organism
# samples
MetaRef centroids
MetaRef centroid notes

Acinetobacter baumannii

448

baumannii.1380.centroids

Citrobacter koseri

108

Citrobacter.1608.centroids
NA for C. koseri, used centroids of genus

Enterobacter aerogenes

298

aerogenes.5220.centroids

Enterobacter cloacae

397

cloacae.3734.centroids

Escherichia coli

1144

coli.318.centroids

Klebsiella oxytoca

389

Klebsiella.1640.centroids
NA for K. oxytoca, used centroids of genus

Klebsiella pneumoniae

1179

pneumoniae.1641.centroids

Morganella morganii

297
NA
NA for M. morgannii or Morganella

Proteus

582

Proteus.2318.centroids

Pseudomonas aeruginosa

1042

aeruginosa.640.centroids

Salmonella

634

Salmonella.713.centroids

Shigella

442

Shigella.730.centroids

Serratia marcescens

437

Serratia.1671.centroids
NA for S. marcescens, used centroids of

genus

Stenotrophomonas

494

Stenotrophomonas.2333.centroids
NA for S. maltophilia, used centroids of

maltophilia

genus

Staphylococcus aureus

987

aureus.754.centroids

Staphylococcus aureus

985

aureus.754.centroids

# significant centroids

before/after

annotation filtering

Organism
before
after

Acinetobacter baumannii

2859
810

Citrobacter koseri

0
0

Enterobacter aerogenes

126
56

Enterobacter cloacae

1417
763

Escherichia coli

6739
1625

Klebsiella oxytoca

951
507

Klebsiella pneumoniae

2571
908

Morganella morganii

NA
NA

Proteus

3401
1504

Pseudomonas aeruginosa

1256
315

Salmonella

2333
670

Shigella

2046
788

Serratia marcescens

537
299

Stenotrophomonas maltophilia

NA
NA

Staphylococcus aureus

1333
367

Staphylococcus aureus

1435
395

In Table 25 herein the number of significant centroids (with the respective p-values) found by the present method before and after the above filtering process is given. This shows that, while the best 50 gene sequences are given for the Examples in the odd Tables (Tables 1, 3, 5, etc.), more than those 50 gene sequences were actually found for all the examples after filtering, e.g. 810 for Acinetobacter baumannii.

As noted above, for the even Tables (Tables 2, 4, 6, etc.) the data are further processed.

As can be seen from the Examples, similarities in gene sequences can be found over all the bacterial species, showing that they form clusters, which can also be seen in the fact that for several bacteria centroids from other bacterial species are found as suitable, e.g. from E.coli.

A genetic test for the combined pathogen identification and antimicrobial susceptibility testing direct from the patient sample can reduce the time-to actionable result significantly from several days to hours, thereby enabling targeted treatment. Furthermore, this approach will not be restricted to central labs, but point of care devices can be developed that allow for respective tests. Such technology along with the present methods and computer program products could revolutionize the care, e.g. in intense care units or for admissions to hospitals in general. Furthermore, even applications like real time outbreak monitoring can be achieved using the present methods.

Compared to approaches using MALDI-TOF MS, the present approach has the advantage that it covers almost the complete genome and thus enables us to identify the potential genomic structural changes that might be related to resistance. While MALDI-TOF MS can also be used to identify point mutations in bacterial proteins, this technology only detects a subset of proteins and of these not all are equally well covered. In addition, the identification and differentiation of certain related strains is not always feasible.

The present method allows computing a best breakpoint for the separation of isolates into resistant and susceptible groups. The inventors designed a flexible software tool that allows to consider—besides the best breakpoints—also values defined by different guidelines (e.g. European and US guidelines), preparing for an application of the GAST in different countries.

The current approach enables

- a. Identification and validation of markers for genetic identification and susceptibility/resistance testing within one diagnostic test
- b. Validation of known drug targets and modes of action
- c. Detection of potentially novel resistance mechanisms leading to putative novel target/secondary target genes for new therapies

The current method is faster than classical culture-based predictions and has the potential to be faster than tests based on single bases, e.g. SNPs. Most remarkably the current method can help improve the accuracy of novel genetic tests.

With the present methods, structural variations can be detected, which particularly also include copy-number variations that can lead to gene dosage effects.

Genetic resistance prediction against antimicrobial drugs in microorganism using structural changes in the genome

Information

Publication Number

Date Filed

Date Published

Inventors

Original Assignees

CPC

International Classifications

Abstract

Description

Claims

Priority Claims (1)

PCT Information