Patent Grant
9995751
The present invention relates to the field of microbiology. More precisely, the invention relates to the detection, by mass spectrometry, of at least one mechanism of resistance to glycopeptides of at least one microorganism obtained from a sample.
Since the discovery of microbes by Pasteur, microorganisms have been studied by microscopy and biochemical analyses. These traditional methods are often long and tedious and analytical alternatives were soon required. Thus, analysis of bacteria by mass spectrometry was begun in 1975 by J. Anhalt and C. Fenselau [1].
This preliminary work was followed by the use of gas chromatography coupled to mass spectrometry (GC-MS) for studying fatty acids of the cell wall of microorganisms [2]. This method became popular under the English name FAME for Fatty Acid Methyl Ester. It now constitutes a reference method for taxonomic studies. However, its use is still limited to certain specialized laboratories able to treat the sample by saponification, hydrolysis and derivation.
In 1996, the works of M. Claydon et al. [3] and of T. Krishnamurthy and P. Ross [4] showed that it is possible to identify various bacterial species with a mass spectrometer of the MALDI-TOF type (Matrix Assisted Laser Desorption Ionization-Time Of Flight). Analysis combines acquisition of a mass spectrum and interpretation by expert software. It is extremely simple and can be performed in a few minutes. It is currently being adopted in medical analysis laboratories [5]. Its clinical use, however, is limited to identification of bacterial species and yeasts. It is not used routinely for identifying resistance to antimicrobials.
Now, identification of resistance to antimicrobials such as antibiotics is an essential element for ensuring optimal patient management.
Other methods of mass spectrometry, notably in tandem, have been proposed for addressing these needs. As an example, we may mention the works of C. Fenselau et al., for identifying β-lactamase with a quadrupole-TOF (Q-TOF) [6]. However, these research results are not applicable to routine clinical use. They were obtained with research instruments requiring highly qualified personnel. The analysis times, often more than one hour per sample, are incompatible with the workload of a microbiological analysis laboratory.
More recently, S. Hofstadler et al. [7] proposed a method combining amplification of the microbial genome by PCR with detection of the PCR products by electrospray-TOF (ESI-TOF). This method is now fully automated [8]. However, it requires amplification by PCR with the inherent faults of molecular biology, namely extraction yield, cost of probes, etc.
In this context, the aim of the present invention is to propose a method for detecting mechanisms of resistance to glycopeptides that allows the drawbacks of the methods of the prior art to be overcome, namely to supply a low-cost method, without a reagent specific to each species, notably relative to the methods of molecular biology, giving a result in a short time, less than one hour, and usable in routine clinical practice, without requiring highly qualified personnel.
For this purpose, the invention proposes a new method of detection, for at least one microorganism contained in a sample, of at least one marker of resistance to a glycopeptide, comprising the detection, by mass spectrometry, of at least one peptide or protein of said microorganism.
Advantageously, markers of resistance to several different antimicrobials can be detected simultaneously.
Surprisingly and unexpectedly, the method of the present invention makes it possible to detect the existence of inducible mechanisms of resistance, in the absence of induction.
As indicated in application WO2011045544, markers of typing and/or of virulence of microorganisms can be detected, in the same way, by mass spectrometry, prior to or simultaneously with detection of the mechanism of resistance markers.
“Markers of resistance to at least one antimicrobial of the class of glycopeptides” means molecules of protein origin that are characteristic of said properties of resistance.
The glycopeptides are antibiotics such as vancomycin, teicoplanin, telavancin, bleomycin, ramoplanin, and decaplanin. Vancomycin is a glycopeptide proper, teicoplanin is a lipoglycopeptide. These two molecules inhibit synthesis of the bacterial wall by inhibition of the synthesis of the peptidoglycan. In fact, their pocket-shaped three-dimensional structure covers the dipeptide D-Ala D-Ala precursor of synthesis of the peptidoglycan, prevents the action of glycosyltransferases and transpeptidases and blocks elongation of the peptidoglycan. Resistance to glycopeptides is due to the presence of operons encoding enzymes catalyzing the formation of low-affinity precursors and enzymes eliminating the high-affinity precursors produced by the host bacterium. Various types of resistance are known, depending on the enzymes present in the operon. Classification of resistance to glycopeptides is based on the primary sequence of the structural genes of the resistance ligases rather than on the levels of resistance to the glycopeptides, to the extent that the minimum inhibitory concentrations (MIC) of the various types overlap. Nine types of resistance have been identified. Eight result from acquired resistance (VanA, B, D, E, G, L, M and N) and one (VanC) is a natural resistance present in E. gallinarum and to E. casseliflavus. (for a review see [9], Sujatha, S. & Praharaj, I. Glycopeptide Resistance in Gram-Positive Cocci: A Review. Interdiscip. Perspect. Infect. Dis 2012, 781679 (2012))
The VanA type of resistance is characterized by a high-level inducible resistance to vancomycin and to teicoplanin. Note that transmission of the VanA type to S. aureus has been demonstrated but is nevertheless quite rare.
The VanB type of resistance is characterized by an inducible resistance of moderate to high level to vancomycin and is sensitive to teicoplanin.
In general, the VanA and VanB phenotypes are the most important clinical cases and are frequently found in E. faecalis and in E. faecium.
The VanD type of resistance is characterized by a constitutive resistance of moderate level to vancomycin and to teicoplanin.
The types of resistance VanC, E, G, L and N are characterized by a low-level resistance to vancomycin and by sensitivity to teicoplanin.
Resistance may be expressed in the absence of antibiotic, it is then called constitutive. It may also be expressed in the presence of a certain concentration of antibiotic, it is then called inducible. Culture of the microorganism in the presence of a certain concentration of antibiotic is then called culture with induction.
Determination of resistance to at least one antimicrobial means that it is impossible to destroy the bacteria or inhibit their multiplication at a defined concentration as a function of the pharmacodynamic and pharmacokinetic parameters characteristic of each antibiotic.
Determination of a mechanism of resistance to at least one antibiotic means detecting at least one compound synthesized by the bacterium, enabling it to evade, at least partially, the action of the antibiotic, most often by modification of the structure of the antibiotic or of its metabolic target, or else by its reduced penetration into the bacterium. Preferably, said compound synthesized by the bacterium is a protein.
The method of the invention may be employed for detecting mechanisms of resistance to glycopeptides in bacteria. Thus, for example, as bacteria for which it is possible to investigate a mechanism of resistance to glycopeptides according to the method of the invention, we may mention, nonexhaustively: Enterococcus faecalis, Enterococcus faecium, Enterococcus gallinarum, Enterococcus casseliflavus, Enterococcus durans, Enterococcus avium, Enterococcus raffinosus or Staphylococcus aureus. The agents primarily responsible for infections are the Enterococci and more particularly Enterococcus faecalis and Enterococcus faecium.
Thus, the method according to the invention also makes it possible to detect a mechanism of resistance to said antibiotics.
“Sample” means a small part or small isolated amount of an entity for analysis. The sample on which the method of the invention may be implemented is any sample that may contain a target microorganism. The sample may be of biological origin, either animal, vegetable or human. It may then correspond to a sample of biological fluid (whole blood, serum, plasma, urine, cerebrospinal fluid, organic secretion, for example), a tissue sample or isolated cells. This sample may be used as it is, i.e. the markers of the mechanisms of resistance of the bacteria to glycopeptides are potentially detectable directly in the sample tested, or else it may undergo, prior to analysis, a preparation such as enrichment, extraction, concentration, purification, culture, according to methods known by a person skilled in the art.
The sample may be of industrial origin, or, according to a nonexhaustive list, a sample of air, a sample of water, a sample taken from a surface, an article or a manufactured product, a product of food origin. Among the samples of food origin, we may mention nonexhaustively a sample of a milk product (yoghurts, cheeses), of meat, of fish, of egg, of fruit, of vegetable, of water, of drink (milk, fruit juice, soda, etc.). These samples of food origin may also come from sauces or from prepared dishes. A food sample may finally be obtained from feed intended for animals, notably such as animal feed meal.
Upstream of detection by mass spectrometry, the sample to be analyzed is preferably treated beforehand to generate peptides from all of the proteins present in the sample, to fragment these proteins into peptides, for example by digestion with a proteolytic enzyme (protease), or by the action of a chemical reagent. In fact, cleavage of the proteins may be brought about by a physicochemical treatment, by a biological treatment or by a combination of both treatments. Among the treatments usable, we may mention treatment with hydroxyl radicals, notably with H2O2. Treatment with hydroxyl radicals causes cleavage of the peptide bonds, which occurs randomly on any peptide bond of the protein. The concentration of hydroxyl radicals determines the number of cleavages performed and therefore the length of the peptide fragments obtained. Other chemical treatments may also be used, such as, for example, treatment with cyanogen bromide (BrCN) which specifically cleaves the peptide bonds at the level of the carboxyl group of the methionyl residues. It is also possible to perform partial acid cleavage at the level of the aspartyl residues by heating a solution of proteins in trifluoroacetic acid at 1000° C.
Treatment of the proteins by enzymatic digestion is nevertheless preferred over physicochemical treatment as it preserves the structure of the proteins more, and is easier to control. “Enzymatic digestion” means the single or combined action of one or more enzymes in suitable reaction conditions. The enzymes performing proteolysis, called proteases, cut the proteins in specific places. Each protease generally recognizes an amino acid sequence, within which it always makes the same cut. Certain proteases recognize a single amino acid or a sequence of two amino acids between which they perform a cleavage, other proteases only recognize longer sequences. These proteases may be endoproteases or exoproteases. Among the known proteases, we may mention, as described in WO2005/098017:
Several proteases may be used simultaneously, if their modes of action are compatible, or they may be used successively. In the context of the invention, the sample is preferably digested by the action of a protease enzyme, for example trypsin.
Generation of peptides using a chemical reagent or a protease may be obtained by simple reaction in solution. It may also be carried out with a microwave oven [10], or under pressure [11], or else with an ultrasonic device [12]. In these last three cases, the protocol will be much quicker.
Among the peptides thus obtained, the specific peptides of the protein are called proteotypic peptides. These are the ones that will be determined by mass spectrometry.
According to the invention, the markers of the mechanisms of resistance of bacteria to glycopeptides are proteins of the bacterium in which the mechanisms of resistance to glycopeptides are to be investigated. In particular, said proteins are digested to peptides, preferably by an enzyme, more preferably by trypsin.
Moreover, the sample containing protein markers characterizing mechanisms of bacteria's resistance to glycopeptides may also be treated beforehand for purposes of purification. This preliminary purification treatment may be carried out before or after the step for generating peptides as described above.
The preliminary sample purification treatment is generally known by a person skilled in the art and may notably employ techniques of centrifugation, filtration, electrophoresis or chromatography. These separation techniques may be used alone or combined with one another to obtain multidimensional separation. For example, multidimensional chromatography may be used, combining separation by ion exchange chromatography with reversed-phase chromatography, as described by T. Fortin et al. [13], or H. Keshishian et al. [14]. In these works, the chromatographic medium may be in a column or in a cartridge (solid phase extraction).
The electrophoretic or chromatographic fraction (or retention time in uni- or multidimensional chromatography) of the proteotypic peptides is characteristic of each peptide and application of these techniques therefore makes it possible to select the proteotypic peptide or peptides to be determined. This fractionation of the peptides generated makes it possible to increase the specificity of subsequent determination by mass spectrometry.
An alternative to the techniques of electrophoresis or chromatography for fractionation of the peptides consists of purifying the N-glycopeptides specifically ([15] and patent application WO 2008/066629). However, purification of this kind only allows quantification of the peptides that have undergone a post-translational modification of the N-glycosylation type. Now, not all of the proteins are glycosylated, which therefore limits its use.
The mass spectrometry to be employed in the method of the invention is widely known by a person skilled in the art as a powerful tool for analysis and detection of different types of molecules. In general, any type of molecule that can be ionized can be detected as a function of its molecular weight using a mass spectrometer. Depending on the nature of the molecule to be detected, of protein origin or of metabolic origin, particular technologies of mass spectrometry may be more suitable. Nevertheless, regardless of the method of mass spectrometry used for detection, the latter comprises a step of ionization of the target molecule into so-called molecular ions, in the present case a step of ionization of the characterizing markers, and a step of separation of the molecular ions obtained as a function of their mass.
All mass spectrometers comprise:
The ionization step necessary for carrying out mass spectrometry may be performed by any method known by a person skilled in the art. The ionization source allows the molecules to be determined to be brought into an ionized gaseous state. An ionization source may be used either in positive mode for studying the positive ions, or in negative mode for studying the negative ions. There are several types of sources and they will be used depending on the result required and the molecules analyzed. We may mention, notably:
Notably, ionization may be carried out as follows: the sample containing the target molecules is introduced into an ionization source, where the molecules are ionized in the gaseous state and thus transformed into molecular ions that correspond to the initial molecules. An ionization source of the electrospray type (ESI, for electrospray ionization) allows a molecule to be ionized while converting it from a liquid state to a gaseous state. The molecular ions obtained then correspond to the molecules present in the liquid state, with, in positive mode, one, two, or even three additional protons or more and are therefore carriers of one, two, or even three charges or more. For example, when the target molecule is a protein, ionization of the proteotypic peptides obtained after fractionation of the target protein, using a source of the electrospray type operating in positive mode, leads to polypeptide ions in the gaseous state, with one, two, or even three additional protons or more and which are therefore carriers of one, two, or even three charges or more, and allows transition from a liquid state to a gaseous state [16]. This type of source is particularly suitable when the target molecules or proteotypic peptides obtained are separated beforehand by reversed-phase liquid chromatography. However, the ionization yield of the molecules present in the sample may vary as a function of the concentration and nature of the different species present. This phenomenon is reflected in a matrix effect that is well known by a person skilled in the art.
A MALDI ionization source will allow molecules to be ionized from a sample in the solid state.
The mass analyzer in which the step of separation of the ionized markers is carried out as a function of their mass/charge ratio (m/z) is any mass analyzer known by a person skilled in the art. We may mention the low-resolution analyzers, of quadrupole (Q), 3D ion trap (IT) or linear type (LIT), also called ion trap analyzers, and the high-resolution analyzers, allowing the exact mass of the analytes to be measured, and which notably use the magnetic sector coupled to an electric sector, time of flight (TOF), Fourier transform ion cyclotron resonance (FT-ICR), Orbitrap.
Separation of the molecular ions as a function of their m/z ratio may be performed once (single mass spectrometry or MS), or else several successive MS separations may be carried out. When two successive MS separations are carried out, the analysis is called MS/MS or MS2. When three successive MS separations are carried out, the analysis is called MS/MS/MS or MS3, and more generally, when n successive MS separations are performed, the analysis is called MSn.
Among the techniques employing several successive separations, SRM mode (Selected Reaction Monitoring) in the case of detection or assay of a single target molecule, or else MRM mode (Multiple Reaction Monitoring) in the case of detection or assay of several target molecules, are particular applications of MS2 separation. Similarly, the MRM3 mode is a particular application of MS/MS/MS separation. This is then called targeted mass spectrometry.
In the case of detection in single MS mode, it is the mass/charge ratio of the molecular ions obtained that is correlated with the target molecule to be detected. In the case of detection in MS/MS mode, essentially two steps are added, relative to MS determination, which are:
It is then the mass/charge ratio of the first-generation fragment ions thus obtained that is correlated with the target molecule to be detected. First-generation fragment ion means an ion derived from the precursor ion, following a fragmentation step, and whose mass-to-charge ratio m/z is different from the precursor ion.
The pairs (m/z)1 and (m/z)2 are called transitions and are representative of the characteristic ions to be detected.
The characteristic ions that are detected in order to be correlated with the target molecule are selected by a person skilled in the art according to standard methods. Selection of them will advantageously lead to assays that are the most sensitive, the most specific and the most robust as possible, in terms of reproducibility and reliability. In the methods developed for the selection of proteotypic peptides (m/z)1, and of first-generation fragment (m/z)2, the choice is essentially based on the intensity of the response. For more detail, reference may be made to V. Fusaro et al. [17]. Commercial software, such as the MIDAS and MRM Pilote software from Applied Biosystems or else MRMaid [18] will be able to be used by a person skilled in the art for predicting all the possible pairs of transitions. It will also be possible to use a database called PeptideAtlas, constructed by F. Desiere et al. [19] for compiling all the MRM transitions of peptides described by the scientific community. This PeptideAtlas database is available with free access on the Internet. For nonprotein molecules, it is also possible to use databases, for example that accessible via the Cliquid software from the company Applied Biosystems (United States of America).
An alternative approach for selecting the proteotypic peptides, (m/z)1 and (m/z)2, consists of using the MS/MS fragmentation spectra obtained in other work. This work may be, for example, the stages of discovery and identification of the biomarkers by proteome analysis. This approach was proposed by Thermo Scientific at user conferences [18]. It makes it possible to generate a list of candidate transitions from the peptides identified experimentally with the SIEVE software (Thermo Scientific). Certain criteria have been detailed by J. Mead et al. [18] for selecting the ions (m/z)1 and (m/z)2 and are detailed below:
Fragmentation of the selected precursor ions is carried out in a fragmentation cell such as the models of the triple quadrupole type [20], or ion trap type [21], or else of the time of flight (TOF) type [22], which also allow separation of the ions. The fragmentation or fragmentations will be carried out conventionally by collision with an inert gas such as argon or nitrogen, within an electric field, by photo-excitation or photodissociation using an intense light source, collision with electrons or radical species, by application of a potential difference, for example in a time-of-flight tube, or by any other method of activation. The characteristics of the electric field determine the intensity and the nature of fragmentation. Thus, the electric field applied in the presence of an inert gas, for example in a quadrupole, determines the collision energy supplied to the ions. This collision energy will be optimized, by a person skilled in the art, to increase the sensitivity of the transition to be determined. As an example, it is possible to vary the collision energy between 5 and 180 e−V in q2 in an AB SCIEX QTRAP® 5500 mass spectrometer from the company Applied Biosystems (Foster City, United States of America). Similarly, the duration of the collision step and the excitation energy within, for example, an ion trap will be optimized, by a person skilled in the art, to lead to the most sensitive determination. As an example, it is possible to vary this duration, dubbed excitation time, between 0.010 and 50 ms and the excitation energy between 0 and 1 (arbitrary unit) in Q3 in an AB SCIEX QTRAP® 5500 mass spectrometer from the company Applied Biosystems. Finally, detection of the selected characteristic ions is performed conventionally, notably using a detector and a processing system. The detector collects the ions and produces an electrical signal whose intensity depends on the quantity of ions collected. The signal obtained is then amplified for processing by computer. A data-processing computer system allows the data received by the detector to be converted to a mass spectrum.
The principle of the SRM mode, or of the MRM mode, is to select a precursor ion specifically, fragment it, and then select one of its fragment ions specifically. For such applications, devices of the triple quadrupole type or ion-trap triple quadrupole hybrids are generally used.
In the case of a triple quadrupole device (Q1q2Q3) used in MS2 mode, for determining or detecting a target protein, the first quadrupole (Q1) makes it possible to filter the molecular ions corresponding to the proteotypic peptides characteristic of the protein to be assayed, obtained in a previous digestion step, as a function of their mass-to-charge ratio (m/z). Only the peptides having the mass/charge ratio of the required proteotypic peptide, the ratio called (m/z)1, are transmitted into the second quadrupole (q2) and play the role of precursor ions for subsequent fragmentation. The q2 analyzer makes it possible to fragment the peptides of mass/charge ratio (m/z)1 into first-generation fragment ions. Fragmentation is generally obtained by collision of the precursor peptides with an inert gas, such as nitrogen or argon in q2. The first-generation fragment ions are transmitted into a third quadrupole (Q3) which filters the first-generation fragment ions as a function of a specific mass-to-charge ratio, the ratio called (m/z)2. Only the first-generation fragment ions having the mass/charge ratio of a fragment characteristic of the required proteotypic peptide (m/z)2 are transmitted into the detector to be detected, or even quantified.
This operating mode displays dual selectivity, in relation to selection of the precursor ion on the one hand and selection of the first-generation fragment ion on the other hand. Mass spectrometry in SRM or MRM mode is therefore advantageous for quantification.
When the mass spectrometry employed in the method of the invention is tandem mass spectrometry (MS2, MS3, MS4 or MS5), several mass analyzers may be coupled together. For example, a first analyzer separates the ions, a collision cell allows the ions to be fragmented, and a second analyzer separates the fragment ions. Certain analyzers, such as ion traps or FT-ICR, constitute several analyzers in one and make it possible to fragment the ions and analyze the fragments directly.
According to preferred embodiments of the invention, the method of the invention comprises one or more of the following characteristics:
Besides determination of the resistance to an antibiotic, it is appropriate to identify the microorganism or microorganisms present in the test sample.
The methods of identification of microorganisms are widely known by a person skilled in the art, as described for example by Murray P. R. et al. in Manual of Clinical Microbiology, 2007, 9th edition, and in particular in Vol. I, Section III, chapters 15 and 16 for bacteria and yeasts, Vol. II, Section VI, chapter 82 for viruses, and Vol. II, Section X, chapter 135 for protozoa. As examples of classical methods of identification, we may mention determination of the biological profile, using for example the Vitek 2 identification cards (bioMérieux™), or else using techniques of molecular biology with identification criteria based on investigation for the presence of certain genes, and investigation of their sequence. Identification may be carried out directly from the sample in which the identification is being effected, or else the microorganisms contained in the sample may be cultured by methods that are familiar to a person skilled in the art with optimal culture media and culture conditions adapted in relation to the species of microorganisms to be investigated, as described by Murray P. R. et al. in Manual of Clinical Microbiology, 2007, 9th edition, Vol. I, Section III, chapter 14, and in particular in Vol. I, Section IV, chapter 21 for bacteria, Vol. II, Section VI, chapter 81 for viruses, Vol. II, Section VIII, chapter 117 for yeasts, and Vol. II, Section X, chapter 134 for protozoa.
Thus, generally, in the case of identification of a bacterium in a sample by a biochemical method, it is first necessary to obtain it in culture pure, for example after seeding on agar. Molecular biology (PCR) may in certain cases be applied directly to the sample to be analyzed.
Instead of culturing the microorganisms, the latter may be concentrated by direct capture in the sample by means of active surfaces. Such a method has been described by W.-J. Chen et al. [10], who captured various bacterial species using magnetic beads with a surface activated with Fe3O4/TiO2. Capture by other means is also possible, such as capture by lectins [23], or by antibodies [24], or by vancomycin [25]. Capture makes it possible to concentrate the microorganisms and thus reduce or even eliminate the culture step. This results in a considerable saving of time.
Identification may also be carried out by mass spectrometry, according to the techniques described above, preferably by MS, by MS/MS, or else by MS followed by spectrometry of the MS/MS type, which constitutes one embodiment of the invention. In this case as well, the sample may be submitted beforehand to a culture step such as seeding on agar.
Use of a method of identification by MS is advantageous in that it can be carried out in a few minutes and in that it requires a mass spectrometer with a single analyzer, i.e. an instrument that is less complex than a tandem mass spectrometer used in MS/MS.
Use of a method of identification by MS followed by spectrometry of the MS/MS type is also advantageous. It provides assurance of the identity of the ions observed in MS, which increases the specificity of the analysis.
Use of a method of identification by MS/MS of the MRM type has the advantage of being more sensitive and simpler than the approaches MS then traditional MS/MS. This method does not require powerful software, which is necessary for processing information between acquisition of the MS spectrum and of the MS/MS spectrum, and does not require resetting of the machine variables, necessary for the succession of MS and then MS/MS spectra.
The method of identification by MS may be carried out with an electrospray source on a raw sample, as described by S. Vaidyanathan et al. [26] or by R. Everley et al. [27] after chromatographic separation. Different m/z ranges then allow the microorganisms to be identified. S. Vaidyanathan et al. used a window between 200 and 2000 Th, and R. Everley et al. used a window between 620 and 2450 Th. The mass spectra may also be deconvoluted to find the mass of the proteins independently of their state of charge. R. Everley et al. thus exploited masses between about 5000 and 50 000 Da. Alternatively, the method of identification by MS may also be carried out using MALDI-TOF, as described by Claydon et al. [3] and T. Krishnamurthy and P. Ross [4]. Analysis combines acquisition of a mass spectrum and interpretation by expert software. It is extremely simple and can be performed in a few minutes. This method of identification is currently being adopted in medical analysis laboratories [5].
Identification of bacteria by MS and then MS/MS via their proteins present in the sample has been widely applied by many teams. As an example, we may cite the recent works of Manes N. et al. [28], who studied the peptidome of Salmonella enterica, or the works of R. Nandakumar et al. [29] or of L. Hernychova et al. [30], who studied the proteome of bacteria after digestion of the proteins with trypsin. The classical approach consists of i) acquiring an MS spectrum, ii) successively selecting each precursor ion observed on the MS spectrum with a strong signal, iii) successively fragmenting each precursor ion and acquiring its MS/MS spectrum, iv) interrogating protein databases such as SWISS-PROT or NCBI, using software such as Mascot (Matrix Science, London, United Kingdom) or SEQUEST (Thermo Scientific, Waltham, United States of America), to identify the peptide having a high probability of corresponding to the MS/MS spectrum observed. This method may lead to identification of a microorganism if a protein or a peptide characteristic of the species is identified.
One of the advantages of using mass spectrometry is that it is particularly useful for quantifying molecules, in the present case the markers of the mechanisms of resistance of bacteria to the glycopeptides. For this purpose, the current intensity detected is used, which is proportional to the quantity of the target molecule. The current intensity thus measured can serve as a quantitative measure for determining the quantity of target molecule present, which is characterized by expression in units of the International System (Système International, SI) of the type mol/m3 or kg/m3, or by multiples or submultiples of these units, or by the usual derivatives of the SI units, including their multiples or submultiples. As a nonlimiting example, units such as ng/ml or fmol/l are units characterizing a quantitative measurement.
However, calibration is necessary so as to be able to correlate the measured peak area, corresponding to the current intensity induced by the ions detected, with the quantity of the assayed target molecule. For this, the calibrations conventionally used in mass spectrometry can be used in the context of the invention. MRM assays are conventionally calibrated using external standards or, preferably, using internal standards as described by T. Fortin et al. [13]. In the case when the target molecule is a proteotypic peptide, allowing assay of a protein of interest, the correlation between the quantitative measurement and the quantity of target proteotypic peptide, and then the protein of interest, is obtained by calibrating the measured signal relative to a standard signal for which the quantity to be assayed is known. Calibration may be performed by means of a calibration curve, for example obtained by successive injections of standard proteotypic peptide at different concentrations (external calibration), or preferably by internal calibration using a heavy peptide, as internal standard, for example according to the AQUA, QconCAT or PSAQ methods detailed below. “Heavy peptide” means a peptide corresponding to the proteotypic peptide, but in which one or more atoms of carbon 12 (12C) is (are) replaced with carbon 13 (13C), and/or one or more atoms of nitrogen 14 (14N) is (are) replaced with nitrogen 15 (15N).
The use of heavy peptides, as internal standards (AQUA), was also proposed in patent application US 2004/0229283. The principle is to synthesize proteotypic peptides artificially with amino acids comprising isotopes heavier than the usual natural isotopes. Amino acids of this kind are obtained, for example, by replacing some of the atoms of carbon 12 (12C) with carbon 13 (13C), or by replacing certain of the atoms of nitrogen 14 (14N) with nitrogen 15 (15N). The artificial peptide (AQUA) thus synthesized has strictly the same physicochemical properties as the natural peptide (except for a higher mass). It is generally added, at a given concentration, to the sample, upstream of assay by mass spectroscopy, for example between the treatment leading to cleavage of the proteins of the sample of interest and fractionation of the peptides obtained after the treatment step. Accordingly, the AQUA peptide is co-purified with the natural peptide to be assayed, during fractionation of the peptides. The two peptides are therefore injected simultaneously into the mass spectrometer, for assay. They are then subjected to the same ionization yields in the source. Comparison of the peak areas of the natural peptides and AQUA peptides, whose concentration is known, makes it possible to calculate the concentration of the natural peptide and thus arrive at the concentration of the protein to be assayed. A variant of the AQUA technique was proposed by J.-M. Pratt et al. [31] under the name QconCat. This variant is also described in patent application WO 2006/128492. It consists of concatenating various AQUA peptides and of producing the artificial polypeptide in the form of heavy recombinant protein. The recombinant protein is synthesized with amino acids comprising heavy isotopes. In this way it is possible to obtain a standard for calibrating the simultaneous assay of several proteins at lower cost. The QconCAT standard is added at the very start, upstream of the treatment leading to cleavage of the proteins and before the steps of fractionation of the proteins, denaturation, reduction and then blocking the thiol functions of the proteins, if the latter are present. The QconCAT standard therefore undergoes the same cycle of treatment leading to cleavage of the proteins as the natural protein, which makes it possible to take account of the yield of the treatment step leading to cleavage of the proteins. In fact, the treatment, notably by digestion, of the natural protein may not be complete. In this case the use of an AQUA standard would lead to underestimating the quantity of natural protein. For an absolute assay, it may therefore be important to take into account the yields of treatment leading to cleavage of the proteins. However, V. Brun et al. [33] showed that sometimes the QconQAT standards did not reproduce exactly the yield of treatment notably by digestion of the natural protein, without doubt owing to a three-dimensional conformation different from the QconCAT protein. V. Brun et al. [32] then proposed using a method dubbed PSAQ and described in patent application WO 2008/145763. In this case, the internal standard is a recombinant protein, having the same sequence as the natural protein but synthesized with heavy amino acids. The synthesis is carried out ex vivo with heavy amino acids. This standard has strictly the same physicochemical properties as the natural protein (except for a higher mass). It is added at the very start, before the step of fractionation of the proteins, when the latter is present. It is therefore co-purified with the native protein, during the step of fractionation of the proteins. It displays the same yield of treatment, notably by digestion, as the native protein. The heavy peptide obtained after cleavage is also co-purified with the natural peptide, if a step of fractionation of the peptides is carried out. The two peptides are therefore injected simultaneously into the mass spectrometer, to be assayed quantitatively. They are then subjected to the same ionization yields in the source. Comparison of the peak areas of the natural peptides and reference peptides in the PSAQ method makes it possible to calculate the concentration of the protein to be assayed taking into account all of the steps of the assay procedure.
All of these techniques, namely AQUA, QconCAT or PSAQ or any other calibration technique used in assays by mass spectrometry and in particular in MRM or MS assays, can be used for performing the calibration, in the context of the invention.
Preferably, the mass spectrometry used in the method of detection according to the invention is of the MS/MS type. More preferably, the mass spectrometry is MRM.
The method of the invention allows detection of resistances to glycopeptides, characterized by the detection of at least one peptide as resistance marker. Preferably, the method according to the invention makes it possible to detect at least one marker of resistance to vancomycin.
According to a first embodiment, the method according to the invention allows direct detection of resistance to a glycopeptide, without bringing the microorganism potentially present in the sample into contact with said glycopeptide, i.e. without a step of induction of said resistance.
According to another embodiment, the method of the invention comprises an additional step, prior to the detection step, consisting of induction of the mechanism of resistance by bringing said sample into contact with said glycopeptide(s).
Preferably, said resistance marker is a peptide derived from the proteins of the Van type, such as the respective variants of type Van A, Van B, Van C, Van D, Van E, Van G, Van L, Van M and Van N.
According to one embodiment of the invention, detection of a mechanism of resistance to glycopeptides, linked to expression of the protein VanA, is characterized by the detection of at least one peptide belonging to the protein VanA and its different variants of sequences SEQ ID No. 1 to SEQ ID No. 4.
said peptides of type VanA preferably being selected from the peptides of sequence SEQ ID No. 5 to SEQ ID No. 16 as defined below:
Advantageously, the markers of type VanA selected from the peptides of sequence SEQ ID No. 5 to SEQ ID No. 16 are detected after induction of the mechanism of resistance.
Advantageously, the markers of type VanA selected from the peptides of sequence SEQ ID No. 6, SEQ ID No. 7, SEQ ID No. 8, SEQ ID No. 11, SEQ ID No. 12, SEQ ID No. 13, SEQ ID No. 15 and SEQ ID No. 16 are detected without an induction step.
According to another embodiment of the invention, detection of a mechanism of resistance to glycopeptides, linked to expression of the protein VanB, is characterized by the detection of at least one peptide belonging to the protein VanB and its different variants of sequences SEQ ID No. 17 to SEQ ID No. 28.
said markers of type VanB preferably being selected from the peptides of sequence SEQ ID No. 29 to SEQ ID No. 35 as defined below:
Advantageously, the markers of type VanB selected from the peptides of sequence SEQ ID No. 29, SEQ ID No. 30, SEQ ID No. 32 and SEQ ID No. 33 are detected after induction of the mechanism of resistance.
According to another embodiment of the invention, detection of a mechanism of resistance to glycopeptides, linked to expression of the protein VanC, is characterized by the detection of at least one peptide belonging to the protein VanC and its different variants of sequences SEQ ID No. 36 to SEQ ID No. 58. Notably the variants VanC1 are characterized by the detection of at least one peptide belonging to the protein VanC1 and its different variants of sequences SEQ ID No. 36 to SEQ ID No. 43, the variants VanC2 or VanC3 are characterized by the detection of at least one peptide belonging to the protein VanC2 or Van C3 and its different variants of sequences SEQ ID No. 46 to SEQ ID No. 51 and SEQ ID No. 53 to SEQ ID No. 57, the variants VanC4 are characterized by the detection of at least one peptide belonging to the protein VanC4 and its different variants of sequences SEQ ID No. 44, SEQ ID No. 45, SEQ ID No. 52 and SEQ ID No. 58
said markers of type VanC preferably being selected from the peptides of sequence SEQ ID No. 59 to SEQ ID No. 71 as defined below:
According to another embodiment of the invention, detection of a mechanism of resistance to glycopeptides, linked to expression of the protein VanD, is characterized by the detection of at least one peptide belonging to the protein VanD and its different variants of sequences SEQ ID No. 72 to SEQ ID No. 79.
said peptides of type VanD preferably being selected from the peptides of sequence SEQ ID No. 80 to SEQ ID No. 83 as defined below:
Advantageously, the markers of type VanD selected from the peptides of sequence SEQ ID No. 80, SEQ ID No. 81 and SEQ ID No. 83 are detected after induction of the mechanism of resistance.
Advantageously, the markers of type VanD selected from the peptides of sequence SEQ ID No. 80, SEQ ID No. 81 and SEQ ID No. 83 are detected without an induction step.
According to another embodiment of the invention, detection of a mechanism of resistance to glycopeptides, induced by expression of the protein VanE, is characterized by the detection of at least one peptide belonging to the protein VanE of sequence SEQ ID No. 84.
said markers of type VanE preferably being selected from the peptides of sequence SEQ ID No. 85 to SEQ ID No. 91 as defined below:
Advantageously, the marker of type VanE corresponding to the peptide of sequence SEQ ID No. 89 is detected after induction of the mechanism of resistance.
According to another embodiment of the invention, detection of a mechanism of resistance to glycopeptides, linked to expression of the protein VanG, is characterized by the detection of at least one peptide belonging to the protein VanG and its different variants of sequences SEQ ID No. 92 to SEQ ID No. 94.
said markers of type VanG preferably being selected from the peptides of sequence SEQ ID No. 95 to SEQ ID No. 102 as defined below:
Advantageously, the markers of type VanG selected from the peptides of sequence SEQ ID No. 95, SEQ ID No. 96, SEQ ID No. 97, SEQ ID No. 98, SEQ ID No. 100 and SEQ ID No. 102 are detected after induction of the mechanism of resistance.
Advantageously, the markers of type VanG selected from the peptides of sequence SEQ ID No. 97 and SEQ ID No. 100 are detected without an induction step.
According to another embodiment of the invention, detection of a mechanism of resistance to glycopeptides, induced by expression of the protein VanL, is characterized by the detection of at least one peptide belonging to the protein VanL of sequence SEQ ID No. 103.
said peptides of type VanL preferably being selected from the peptides of sequence SEQ ID No. 104 to SEQ ID No. 120 as defined below:
According to another embodiment of the invention, detection of a mechanism of resistance to glycopeptides, induced by expression of the protein VanM, is characterized by the detection of at least one peptide belonging to the protein VanM of sequence SEQ ID No. 121.
said peptides of type VanM preferably being selected from the peptides of sequence SEQ ID No. 122 to SEQ ID No. 139 as defined below:
According to another embodiment of the invention, detection of a mechanism of resistance to glycopeptides, induced by expression of the protein VanN, is characterized by the detection of at least one peptide belonging to the protein VanN of sequence SEQ ID No. 140.
said peptides of type VanN preferably being selected from the peptides of sequence SEQ ID No. 141 to SEQ ID No. 154 as defined below:
The method of the invention and its advantages will become clearer from the rest of the present description, which presents several nonlimiting embodiment examples of said method.
The following protocol is carried out in 16 steps (steps 5 to 12 are optional and could be omitted if the enriched sample is treated subsequently according to example 6 and the subsequent examples):
The optimal culture media and the optimal culture conditions are different depending on the species of microorganism. By default, the sample is seeded on various media:
The sample is seeded on medium:
Identification is performed as follows:
Identification is performed as follows:
Identification is performed as follows:
The following protocol is carried out in 17 steps:
Samples Smp1 to Smp13 are identified according to one of the methods described in examples 1 to 6. Identification of the species is reported in TABLE 1.
E. faecalis
E. gallinarum
E. faecalis
E. faecalis
E. faecalis
E. faecalis
E. faecalis
E. faecium
E. faecium
E. faecalis
E. faecium
Samples Smp1 to Smp11 correspond to a species that may comprise a mechanism of resistance of the Van type. The following method is then employed for investigating such a mechanism.
The microorganism colony is obtained according to example 2, treated according to example 7, and then a volume of 50 μl of digested proteins is injected and analyzed according to the following conditions:
The transitions mentioned in TABLE 3 are detected using the parameters shown in TABLES 4 and 5.
The areas obtained for each of the transitions and for each of the microorganisms investigated were measured. When the area of a transition is greater than or equal to the positivity threshold described in TABLE 5, detection of the transition is regarded as positive and is marked “1” in TABLE 6. When the area of a transition is below the positivity threshold described in TABLE 5, detection of the transition is regarded as negative and is marked “0” in TABLE 6. When the 3 transitions of one and the same peptide are marked “1”, detection of the peptide is regarded as positive. One particular case is an exception to this rule. The peptide corresponding to the transitions with numbers 49, 50 and 51 has a transition of very low intensity. In this precise case, when transitions 49 and 50 are marked “1”, detection of this peptide will be regarded as positive.
Samples Smp1, Smp2, Smp4, Smp5, Smp7 and Smp9 do not have any peptide characteristic of resistance of the Van type. The bacteria present in samples Smp1, Smp2, Smp4, Smp5, Smp7 and Smp9 may be sensitive to the glycopeptides of the vancomycin or teicoplanin type.
Samples Smp3, Smp10 and Smp11 comprise at least one peptide characteristic of VanA. The bacteria present in samples Smp3, Smp10 and Smp11 therefore express the ligase VanA, which endows them with resistance to vancomycin and to teicoplanin.
Sample Smp6 comprises at least one peptide characteristic of VanG. The bacterium present in sample Smp6 therefore expresses the ligase VanG, which endows it with resistance to vancomycin.
Sample Smp8 comprises at least one peptide characteristic of VanD. The bacterium present in sample Smp8 therefore expresses the ligase VanD, which endows it with resistance to vancomycin and to teicoplanin.
Thus, advantageously, several mechanisms of resistance to glycopeptides are investigated simultaneously. Particularly advantageously, a mechanism of inducible resistance, such as the mechanism of resistance linked to expression of VanA, is detected without an induction phase during culture of the microorganism. This method therefore makes it possible to investigate the mechanisms of resistance to glycopeptides without a priori on their possible existence.
Samples Smp1 to Smp11 are identified according to one of the methods described in examples 1 to 6. Identification of the species is reported in TABLE 7.
E. faecalis
E. faecalis
E. faecalis
E. faecalis
E. faecalis
E. faecium
E. faecium
E. faecalis
E. faecium
Samples Smp12 to Smp20 correspond to a species that may comprise a mechanism of resistance of the Van type. The following method is then employed for investigating such a mechanism.
The microorganism colony is obtained according to example 3 and then treated according to example 7 and analyzed according to example 8.
The areas obtained for each of the transitions and for each of the microorganisms studied were measured. When the area of a transition is greater than or equal to the positivity threshold described in TABLE 5, detection of the transition is regarded as positive and is marked “1” in TABLE 8. When the area of a transition is below the positivity threshold described in TABLE 5, detection of the transition is regarded as negative and is marked “0” in TABLE 8. When the 3 transitions of one and the same peptide are marked “1”, detection of the peptide is regarded as positive. One particular case is an exception to this rule. The peptide corresponding to the transitions numbered 49, 50 and 51 has a transition of very low intensity. In this precise case, when the transitions 49 and 50 are marked “1”, detection of this peptide will be regarded as positive.
Sample Smp12 does not have any peptide characteristic of resistance of the Van type. The bacterium present in sample Smp12 may be sensitive to the glycopeptides of the vancomycin or teicoplanin type.
Samples Smp19 and Smp20 comprise at least one peptide characteristic of VanA. The bacteria present in samples Smp19 and Smp20 therefore express the ligase VanA, which endows them with resistance to vancomycin and to teicoplanin.
Samples Smp13, Smp14 and Smp18 comprise at least one peptide characteristic of VanB. The bacteria present in samples Smp13, Smp14 and Smp18 therefore express the ligase VanB, which endows them with resistance to vancomycin.
Sample Smp15 comprises at least one peptide characteristic of VanG. The bacterium present in sample Smp15 expresses the ligase VanG, which endows it with resistance to vancomycin.
Sample Smp16 comprises at least one peptide characteristic of VanE. The bacterium present in sample Smp16 expresses the ligase VanE, which endows it with resistance to vancomycin.
Sample Smp17 comprises at least one peptide characteristic of VanD. The bacterium present in sample Smp17 expresses the ligase VanD, which endows it with resistance to vancomycin and to teicoplanin.
Thus, advantageously, several mechanisms of resistance to glycopeptides may be investigated simultaneously.
The following protocol is carried out in 16 steps:
Samples Smp21 and Smp22 are identified according to one of the methods described in examples 1 to 6. Identification of the species is reported in TABLE 9.
E. faecalis
E. faecalis
Samples Smp21 and Smp22 correspond to the species Enterococcus faecalis, which may comprise a mechanism of resistance of the Van type. The following method is then employed for investigating such a mechanism.
Each sample is treated according to example 10 and analyzed according to example 8 apart from the elements mentioned below.
The areas obtained for each of the transitions and for each of the microorganisms studied were measured. When the area of a transition is greater than or equal to the positivity threshold described in TABLE 11, detection of the transition is regarded as positive and is marked “1” in TABLE 12. When the area of a transition is below the positivity threshold described in TABLE 11, detection of the transition is regarded as negative and is marked “0” in TABLE 12. When the 3 transitions of one and the same peptide are marked “1”, detection of the peptide is regarded as positive. One particular case is an exception to this rule. The peptide corresponding to the transitions numbered 49, 50 and 51 has a transition of very low intensity. In this precise case, when the transitions 49 and 50 are marked “1”, detection of this peptide will be regarded as positive.
Samples Smp21 and Smp22 comprise at least one peptide characteristic of VanA. The bacteria present in samples Smp21 and Smp22 express the ligase VanA, which endows them with resistance to vancomycin and to teicoplanin.
Thus, particularly advantageously, a mechanism of inducible resistance, such as the mechanism of resistance linked to expression of VanA, is detected without an induction phase during culture of the microorganism, after a sample preparation phase performed in less than 3 hours. This method therefore allows quick investigation of the mechanisms of resistance to glycopeptides without a priori on their possible existence.
Samples Smp23 and Smp24 are identified according to one of the methods described in examples 1 to 6. Identification of the species is reported in TABLE 13.
E. faecium
E. faecalis
E. faecium
Samples Smp23, Smp24 and Smp25 correspond to the species Enterococcus faecalis or Enterococcus faecium, which may comprise a mechanism of resistance of the Van type.
The following method is then employed for investigating such a mechanism. Each sample is treated according to example 10, with the following modifications:
Each sample is analyzed according to example 8 apart from the elements mentioned below.
The transitions mentioned in TABLE 3 are detected using the parameters shown in TABLES 4 and 11.
As in example 8, the positive areas are marked “1” in TABLE 14. The positive peptides are detected according to the rules of example 8.
Sample Smp23 comprises at least one peptide characteristic of VanB. The bacterium present in sample Smp23 expresses the ligase VanB, which endows it with resistance to vancomycin.
Sample Smp25 comprises at least one peptide characteristic of VanA. The bacterium present in sample Smp25 expresses the ligase VanA, which endows it with resistance to vancomycin and to teicoplanin.
Conversely, sample Smp24 does not have any peptide characteristic of resistance of the Van type. The bacterium present in sample Smp24 may be sensitive to the glycopeptides of the vancomycin or teicoplanin type.
Thus, particularly advantageously, a mechanism of inducible resistance, such as the mechanism of resistance linked to expression of VanB, is detected without an induction phase during culture of the microorganism, after a sample preparation phase performed in less than 3 hours. Also very advantageously, all the mechanisms of resistance to glycopeptides can be investigated and detected simultaneously. Thus, 2 mechanisms of resistance, VanB and VanA, are detected in samples Smp23 and Smp25 respectively using the same method. This method therefore allows quick investigation of the mechanisms of resistance to glycopeptides without a priori on their possible existence.
| Number | Date | Country | Kind |
|---|---|---|---|
| 12 57489 | Aug 2012 | FR | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/FR2013/051833 | 7/30/2013 | WO | 00 |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2013/051833 | 7/30/2013 | WO | A |
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| 5770361 | Arthur et al. | Jun 1998 | A |
| 6013508 | Arthur et al. | Jan 2000 | A |
| 6087106 | Arthur et al. | Jul 2000 | A |
| 6569622 | Arthur et al. | May 2003 | B1 |
| 20040229283 | Gygi et al. | Nov 2004 | A1 |
| 20120264156 | Beaulieu et al. | Oct 2012 | A1 |
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| 2005098017 | Oct 2005 | WO |
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