Patent Application
20110217703
The present invention relates to nucleic acid primers and probes to detect one or more fungal and yeast species. More specifically the invention relates to the P2, P2A and P2B gene sequences (also known as 60S acidic ribosomal protein P2, RLA-2-ASPFU, Allergen ASP f8 or Afp2), the corresponding RNA, specific probes, primers and oligonucleotides related thereto and their use in diagnostic assays to detect and/or discriminate fungal and yeast species.
Yeast and fungal infections represent a major cause of morbidity and mortality among immunocompromised patients. The number of immunocompromised patients at risk of yeast and fungal infection continues to increase each year, as does the spectrum of fungal and yeast agents causing disease. Mortality from fungal infections, particularly invasive fungal infections, is 30% or greater in certain risk groups. The array of available anti-fungal agents is growing; however, so too is the recognition of both intrinsic and emerging resistance to antifungal drugs. These factors are contributing to the increased need for cost containment in laboratory testing and have led to laboratory consolidation in testing procedures.
Invasive fungal infections are on the increase. In 2003, it was estimated that there were 9 million at risk patients of which 1.2 million developed infection. Candida spp. and Aspergillus spp. now rank as the most prominent pathogens infecting immunosupressed patients. In particular, infections are common in the urinary tract, the respiratory system and the bloodstream, at the site of insertion of stents, catheters and orthopaedic joints. Approximately, 10% of the known Candida spp. have been implicated in human infection. Invasive candidiasis occurs when candida enters the bloodstream and it is estimated to occur at a frequency of 8/100,000 population in the US with a mortality rate of 40%. Candida albicans is the 4th most common cause of bloodstream infection. Aspergillosis usually begins as a pulmonary infection that can progress to a life-threatening invasive infection in some patients and has a mortality rate of greater than 90%. Emerging mycoses agents include Fusarium, Scedosporium, Zygomycetes and Trichosporon spp. (“Stakeholder Insight: Invasive fungal infections”, Datamonitor, January 2004).
Immunocompromised patients including transplant and surgical patients, neonates, cancer patients, diabetics and those with HIV/AIDs are at high risk of developing invasive fungal infections (Datamonitor report: Stakeholder opinion—Invasive fungal infections, options outweigh replacements 2004). A large number of severe cases of sepsis are reported each year. Despite improvements in its medical management, sepsis still constitutes one of the greatest challenges in intensive care medicine. Microorganisms (bacteria, fungi and yeast) responsible for causing sepsis are traditionally detected in hospital laboratories with the aid of microbiological culture methods with poor sensitivity (25-82%), which are very time-consuming, generally taking from two to five days to complete, and up to eight days for the diagnosis of fungal infections. Definitive diagnosis of an infection caused by a yeast or fungus is usually based on either, the recovery and identification of a specific agent from clinical specimens or microscopic demonstration of fungi with distinct morphological features. However, there are numerous cases where these methods fail to provide conclusive proof as to the infecting agent. In these instances, the detection of specific host antibody responses can be used, although again this can be affected by the immune status of the patient. Time is critical in the detection and identification of bloodstream infections typically caused by bacteria and fungi. Effective treatment depends on finding the source of infection and making appropriate decisions about antibiotics or antifungals quickly and efficiently. Only after pathogens are correctly identified can targeted therapy using a specific antibiotic or anti-fungal begin. Many physicians would like to see the development of better in vitro amplification and direct detection diagnostic techniques for the early diagnosis of yeast and fungi (“Stakeholder Insight: Invasive fungal infections”, Datamonitor, January 2004). Recently Roche™ launched a real time PCR based assay (Septifast™), for the detection of bacterial, fungal and yeast DNA in clinical samples. Therefore, there is a clear need for the development of novel rapid diagnostic tests for clinically significant bacterial and fungal pathogens for bioanalysis applications in the clinical sector. This has led the current inventors to identify novel fungal and yeast nucleic acid targets for application in Nucleic Acid Diagnostics (NAD) tests. Fungal and yeast nucleic acid based diagnostics have focused heavily on the ribosomal RNA (rRNA) genes, RNA transcripts, and their associated DNA/RNA regions. The rRNA genes are highly conserved in all fungal species and they also contain divergent and distinctive intergenic transcribed spacer regions. Ribosomal rRNA comprises three genes: the large sub-unit gene (28S), the small sub-unit gene (18S) and the 5.8S gene. The 28S and 18S rRNA genes are separated by the 5.8S rRNA and two internal transcribed spacers (ITS 1 and ITS2). Because the ITS region contains a high number of sequence polymorphisms, numerous researchers have concentrated their efforts on these as targets (Atkins and Clark, 2004). rRNA genes are also multicopy genes with >10 copies within the fungal genome.
A number of groups are working on developing new assays for fungal and yeast infections. U.S. 2004044193 relates to, amongst a number of other aspects, the transcription factor CaTEC1 of Candida albicans; inhibitors thereof, and methods for the diagnosis and therapy of diseases which are connected with a Candida infection; and also diagnostic and pharmaceutical compositions which contain the nucleotide sequences, proteins, host cells and/or antibodies. WO0183824 relates to hybridization assay probes and accessory oligonucleotides for detecting ribosomal nucleic acids from Candida albicans and/or Candida dubliniensis. U.S. Pat. No. 6,017,699 and U.S. Pat. No. 5,426,026 relate to a set of DNA primers, which can be used to amplify and speciate DNA from five medically important Candida species. U.S. Pat. No. 6,747,137 discloses sequences useful for diagnosis of Candida infections. EP 0422872 and U.S. Pat. No. 5,658,726 disclose probes based on 18S rRNA genes, and U.S. Pat. No. 5,958,693 discloses probes based on 28S rRNA, for diagnosis of a range of yeast and fungal species. U.S. Pat. No. 6,017,366 describes sequences based on chitin synthase gene for use in nucleic acid based diagnostics for a range of Candida species. It is clear though, that development of faster, more accurate diagnostic methods are required, particularly in light of the selection pressure caused by modern anti-microbial treatments which give rise to increased populations of resistant virulent strains with mutated genome sequences. Methods that enable early diagnosis of microbial causes of infection enable the selection of a specific narrow spectrum antibiotic or antifungal to treat the infection (Datamonitor report: Stakeholder opinion—Invasive fungal infections, options outweigh replacements 2004; Datamonitor report: Stakeholder Opinion—Sepsis, under reaction to an overreaction, 2006).
Ribosomes are a two part organelle, composed of a large and a small subunit. The large subunit possesses a number of features which are conserved in all organisms for example the presence of a complex of a number of acidic proteins, the P proteins which form a stalk-like structure (Abramczyk et al., 2004 Tchórzewski et al., 2000; 2003). In the 60S ribosomal subunit of eukaryotes these acidic P proteins include, P0, P1 and P2 (Wool et al 1991). The complex formed by these P proteins is required for efficient translation. In yeasts, there are two isoforms of P1 (P1A and P1B) and P2 (P2A and P2B) which are encoded by four distinct single copy genes (Newton et al, 1990, Bailey-Serres et al., 1997).
This invention relates to the use of the P2A, P2B genes in yeast and the P2 gene in fungi. There are currently 65 P2B gene sequences (approx. 360 bp) available in NCBI GenBank database including 3 P2B sequences for Candida albicans and one sequence of high homology for C. glabrata. There are 329 P2 sequences available in NCBI GenBank database including annotated sequences for two Aspergillus species and presumptive P2 sequences for three species. Additional P2B sequences of representative species of Candida and P2 sequences of representative species of Aspergillus were generated by the inventors following the design of PCR primers to amplify P2B gene regions in Candida and P2 gene regions in Aspergillus spp. The published and newly generated P2B and P2 gene sequences for Candida and Aspergillus spp. respectively, were aligned and analysed using bioinformatics tools. PCR primers and species-specific DNA probes for selected species, Candida glabrata and Aspergillus fumigatus were designed and demonstrated for molecular species identification using real-time PCR. These examples demonstrate the potential of P2A/P2B and P2 genes for molecular identification of species of Candida, Aspergillus and other yeast and fungal species.
“Synthetic oligonucleotide” refers to molecules of nucleic acid polymers of 2 or more nucleotide bases that are not derived directly from genomic DNA or live organisms. The term synthetic oligonucleotide is intended to encompass DNA, RNA, and DNA/RNA hybrid molecules that have been manufactured chemically, or synthesized enzymatically in vitro.
An “oligonucleotide” is a nucleotide polymer having two or more nucleotide subunits covalently joined together. Oligonucleotides are generally about 10 to about 100 nucleotides. The sugar groups of the nucleotide subunits may be ribose, deoxyribose, or modified derivatives thereof such as OMe. The nucleotide subunits may be joined by linkages such as phosphodiester linkages, modified linkages or by non-nucleotide moieties that do not prevent hybridization of the oligonucleotide to its complementary target nucleotide sequence. Modified linkages include those in which a standard phosphodiester linkage is replaced with a different linkage, such as a phosphorothioate linkage, a methylphosphonate linkage, or a neutral peptide linkage. Nitrogenous base analogs also may be components of oligonucleotides in accordance with the invention. A “target nucleic acid” is a nucleic acid comprising a target nucleic acid sequence. A “target nucleic acid sequence,” “target nucleotide sequence” or “target sequence” is a specific deoxyribonucleotide or ribonucleotide sequence that can be hybridized to a complementary oligonucleotide.
An “oligonucleotide probe” is an oligonucleotide having a nucleotide sequence sufficiently complementary to its target nucleic acid sequence to be able to form a detectable hybrid probe:target duplex under high stringency hybridization conditions. An oligonucleotide probe is an isolated chemical species and may include additional nucleotides outside of the targeted region as long as such nucleotides do not prevent hybridization under high stringency hybridization conditions. Non-complementary sequences, such as promoter sequences, restriction endonuclease recognition sites, or sequences that confer a desired secondary or tertiary structure such as a catalytic active site can be used to facilitate detection using the invented probes. An oligonucleotide probe optionally may be labelled with a detectable moiety such as a radioisotope, a fluorescent moiety, a chemiluminescent, a nanoparticle moiety, an enzyme or a ligand, which can be used to detect or confirm probe hybridization to its target sequence. Oligonucleotide probes are preferred to be in the size range of from about 10 to about 100 nucleotides in length, although it is possible for probes to be as much as and above about 500 nucleotides in length, or below 10 nucleotides in length.
A “hybrid” or a “duplex” is a complex formed between two single-stranded nucleic acid sequences by Watson-Crick base pairings or non-canonical base pairings between the complementary bases. “Hybridization” is the process by which two complementary strands of nucleic acid combine to form a double-stranded structure (“hybrid” or “duplex”). A “fungus” or “yeast” is meant any organism of the kingdom Fungi, and preferably, is directed towards any organism of the phylum Ascomycota. “Complementarity” is a property conferred by the base sequence of a single strand of DNA or RNA which may form a hybrid or double-stranded DNA:DNA, RNA:RNA or DNA:RNA through hydrogen bonding between Watson-Crick base pairs on the respective strands. Adenine (A) ordinarily complements thymine (T) or uracil (U), while guanine (G) ordinarily complements cytosine (C).
The term “stringency” is used to describe the temperature, ionic strength and solvent composition existing during hybridization and the subsequent processing steps. Those skilled in the art will recognize that “stringency” conditions may be altered by varying those parameters either individually or together. Under high stringency conditions only highly complementary nucleic acid hybrids will form; hybrids without a sufficient degree of complementarity will not form. Accordingly, the stringency of the assay conditions determines the amount of complementarity needed between two nucleic acid strands forming a hybrid. Stringency conditions are chosen to maximize the difference in stability between the hybrid formed with the target and the non-target nucleic acid. With “high stringency” conditions, nucleic acid base pairing will occur only between nucleic acid fragments that have a high frequency of complementary base sequences (for example, hybridization under “high stringency” conditions, may occur between homologs with about 85-100% identity, preferably about 70-100% identity). With medium stringency conditions, nucleic acid base pairing will occur between nucleic acids with an intermediate frequency of complementary base sequences (for example, hybridization under “medium stringency” conditions may occur between homologs with about 50-70% identity). Thus, conditions of “weak” or “low” stringency are often required with nucleic acids that are derived from organisms that are genetically diverse, as the frequency of complementary sequences is usually less.
‘High stringency’ conditions are those equivalent to binding or hybridization at 42° C. in a solution consisting of 5×SSPE (43.8g/l NaCl, 6.9 g/l NaH2PO4H2O and 1.85 g/l EDTA, ph adjusted to 7.4 with NaOH), 0.5% SDS, 5× Denhardt's reagent and 100 μg/l denatured salmon sperm DNA followed by washing in a solution comprising 0.1×SSPE, 1.0% SDS at 42° C. when a probe of about 500 nucleotides in length is used.
‘Medium stringency’ conditions are those equivalent to binding or hybridization at 42° C. in a solution consisting of 5×SSPE (43.8 g/l NaCl, 6.9 g/l NaH2PO4H2O and 1.85 g/l EDTA, pH adjusted to 7.4 with NaOH), 0.5% SDS, 5×Denhardt's reagent and 100 μg/ml denatured salmon sperm DNA followed by washing in a solution comprising 1.0×SSPE, 1.0% SDS at 42° C., when a probe of about 500 nucleotides in length is used.
‘Low stringency’ conditions are those equivalent to binding or hybridization at 42° C. in a solution consisting of 5×SSPE (43.8 g/l NaCl, 6.9 g/l NaH2PO4H2O and 1.85 g/l EDTA, pH adjusted to 7.4 with NaOH), 0.1% SDS, 5×Denhardt's reagent [50× Denhardt's contains per 500 ml: 5 g Ficoll (Type 400, Pharamcia), 5 g BSA (Fraction V; Sigma)] and 100 μg/ml denatured salmon sperm DNA followed by washing in a solution comprising 5×SSPE, 0.1% SDS at 42° C., when a probe of about 500 nucleotides in length is used.
In the context of nucleic acid in-vitro amplification based technologies, “stringency” is achieved by applying temperature conditions and ionic buffer conditions that are particular to that in-vitro amplification technology. For example, in the context of PCR and real-time PCR, “stringency” is achieved by applying specific temperatures and ionic buffer strength for hybridisation of the oligonucleotide primers and, with regards to real-time PCR hybridisation of the probe/s, to the target nucleic acid for in-vitro amplification of the target nucleic acid.
One skilled in the art will understand that substantially corresponding probes of the invention can vary from the referred-to sequence and still hybridize to the same target nucleic acid sequence. This variation from the nucleic acid may be stated in terms of a percentage of identical bases within the sequence or the percentage of perfectly complementary bases between the probe and its target sequence. Probes of the present invention substantially correspond to a nucleic acid sequence if these percentages are from about 100% to about 80% or from 0 base mismatches in about 10 nucleotide target sequence to about 2 bases mismatched in an about 10 nucleotide target sequence. In preferred embodiments, the percentage is from about 100% to about 85%. In more preferred embodiments, this percentage is from about 90% to about 100%; in other preferred embodiments, this percentage is from about 95% to about 100%
By “sufficiently complementary” or “substantially complementary” is meant nucleic acids having a sufficient amount of contiguous complementary nucleotides to form, under high stringency hybridization conditions, a hybrid that is stable for detection. The terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (i.e., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity over a specified region, when compared and aligned for maximum correspondence over a comparison window or designated region) as measured using a BLAST or BLAST 2.0 sequence comparison algorithms with default parameters described below, or by manual alignment and visual inspection (see, e.g., NCBI web site at ncbi.nlm.nih.gov/BLAST/or the like). Such sequences are then said to be “substantially identical.” This definition also refers to, or may be applied to, the compliment of a test sequence. The definition also includes sequences that have deletions and/or additions, as well as those that have substitutions. As described below, the preferred algorithms can account for gaps and the like. Preferably, identity exists over a region that is at least about 25 amino acids or nucleotides in length, or more preferably over a region that is 50-100 amino acids or nucleotides in length.
For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Preferably, default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.
A “comparison window,” as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection (see, e.g., Current Protocols in Molecular Biology (Ausubel et al., eds. 1987-2005, Wiley Interscience)). A preferred example of algorithm that is suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., Nuc. Acids Res. 25:3389-3402 (1977) and Altschul et al., J. Mol. Biol. 215:403-410 (1990), respectively. BLAST and BLAST 2.0 are used, with the parameters described herein, to determine percent sequence identity for the nucleic acids and proteins of the invention. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=−4 and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength of 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)) alignments (B) of 50, expectation (E) of 10, M=5, N=−4, and a comparison of both strands.
“Nucleic acid” refers to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form, and complements thereof. The term encompasses nucleic acids containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides. Examples of such analogs include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs).
By “nucleic acid hybrid” or “probe:target duplex” is meant a structure that is a double-stranded, hydrogen-bonded structure, preferably about 10 to about 100 nucleotides in length, more preferably 14 to 50 nucleotides in length, although this will depend to an extent on the overall length of the oligonucleotide probe. The structure is sufficiently stable to be detected by means such as chemiluminescent or fluorescent light detection, autoradiography, electrochemical analysis or gel electrophoresis. Such hybrids include RNA:RNA, RNA:DNA, or DNA:DNA duplex molecules.
“RNA and DNA equivalents” refer to RNA and DNA molecules having the same complementary base pair hybridization properties. RNA and DNA equivalents have different sugar groups (i.e., ribose versus deoxyribose), and may differ by the presence of uracil in RNA and thymine in DNA. The difference between RNA and DNA equivalents do not contribute to differences in substantially corresponding nucleic acid sequences because the equivalents have the same degree of complementarity to a particular sequence.
By “preferentially hybridize” is meant that under high stringency hybridization conditions oligonucleotide probes can hybridize their target nucleic acids to form stable probe:target hybrids (thereby indicating the presence of the target nucleic acids) without forming stable probe:non-target hybrids (that would indicate the presence of non-target nucleic acids from other organisms). Thus, the probe hybridizes to target nucleic acid to a sufficiently greater extent than to non-target nucleic acid to enable one skilled in the art to accurately detect the presence of (for example Candida) and distinguish these species from other organisms. Preferential hybridization can be measured using techniques known in the art and described herein.
By “theranostics” is meant the use of diagnostic testing to diagnose the disease, choose the correct treatment regime and monitor the patient response to therapy. The theranostics of the invention may be based on the use of an NAD assay of this invention on samples, swabs or specimens collected from the patient.
It is an object of the current invention to provide sequences and/or diagnostic assays to detect and identify one or more yeast and fungal species. The current inventors have made use of the P2, P2A and P2B gene sequences to design primers that are specific to Candida P2B genes and to Aspergillus P2 genes. Such primers not only allow the detection of yeast and fungal species but also allow distinction between Candida and Aspergillus spp. This has an advantage over the prior art in that if one wants to identify a fungal pathogen in a sample, which contains Candida as a commensal, the approach of using universal primers may not be successful. There is a strong possibility that the Candida will out-compete the fungal pathogen in the amplification process and will be preferentially amplified, resulting in failure to detect the disease-causing pathogen. The current invention further provides for primers and probes that allow discrimination between different Candida species and among different Aspergillus species.
The present invention provides for a diagnostic kit for detection and identification of yeast and/or fungal species, comprising an oligonucleotide probe capable of binding to at least a portion of the P2, P2A or P2B gene or its corresponding mRNA. The oligonucleotide probe may have a sequence substantially homologous to or substantially complementary to a portion of the P2, P2A or P2B gene or its corresponding mRNA. It will thus be capable of binding or hybridizing with a complementary DNA or RNA molecule. The P2 gene may be a fungal P2 gene. The P2A gene may be a yeast gene. The P2B gene may be yeast P2B gene. The nucleic acid molecule may be synthetic. The oligonucleotide probe may have a sequence of SEQ ID NO 9, 10, 91-94, 105-109, or a sequence substantially homologous to or substantially complementary to those sequences, which can also act as a probe for the P2, P2A or P2B genes.
The kit may comprise more than one such probe. In particular the kit may comprise a plurality of such probes. In addition, the kit may comprise additional probes for other organisms, such as, for example, bacterial species or viruses.
The identified sequences are suitable not only for in vitro DNA/RNA amplification based detection systems but also for signal amplification based detection systems. Furthermore, the sequences of the invention identified as suitable targets provide the advantages of having significant intragenic sequence heterogeneity in some regions, which is advantageous and enables aspects of the invention to be directed towards group or species-specific targets, and also having significant sequence homogeneity in some regions, which enables aspects of the invention to be directed towards genus-specific yeast and fungal primers and probes for use in direct nucleic acid detection technologies, signal amplification nucleic acid detection technologies, and nucleic acid in vitro amplification technologies for yeast and fungal diagnostics. The P2, P2A and P2B sequences allow for multi-test capability and automation in diagnostic assays. One of the advantages of the sequences of the present invention is that the intragenic P2, P2A and P2B nucleotide sequences diversity between closely related yeast or fungal species enables specific primers and probes for use in diagnostics assays for the detection of yeast and fungi to be designed. The P2, P2A and P2B nucleotide sequences, both DNA and RNA can be used with direct detection, signal amplification detection and in vitro amplification technologies in diagnostics assays. The P2, P2A and P2B sequences allow for multi-test capability and automation in diagnostic assays.
The kit may further comprise a primer for amplification of at least a portion of the P2 and/or P2A and/or P2B genes. Suitably, the kit comprises a forward and a reverse primer for a portion of the P2, P2A and/or P2B gene.
The portion of the P2A gene may be equivalent to a portion of the region of the gene from by position 114 to by position 439 of C. albicans (AF317661.1).
The portion of the P2B gene may be equivalent to a portion of the region of the gene from base pair position 1 to position 335 in C. albicans (XM—718047.1, XM—717900.1) or position 8 to base pair position 359 of the P2B gene in C. albicans (AF317662.1). C. albicans.
Particularly preferred, are kits comprising, a probe for a portion of the P2A C. albicans gene and/or a probe for a portion of the region of the gene equivalent to base pair position 114 to by position 439 of C. albicans (AF317661.1).
Particularly preferred, are kits comprising, a probe for a portion of the P2B C. albicans gene and/or a probe for a portion of the region of the gene equivalent to base pair position 1 to position 359. Also preferred are probes for a portion of the region of the gene equivalent to base pair position 1 to position 335 in C. albicans (XM—718047.1, XM_717900.1) or position 8 to by position 359 of the P2B gene in C. albicans (AF317662.1). Equivalent base pair positioning may be found in other organisms, but not necessarily in the same position.
The portion of the P2B gene may be equivalent to a portion of the region of the gene from base pair 24 to by position 158 in C. glabrata (XM—444905.1). Particularly preferred, are kits comprising, a probe for a portion of the P2B C. glabrata gene and/or a probe for a portion of the region of the gene equivalent to base pair position 24 to base pair position 158 in C. glabrata. Sequences equivalent to base pair position 24 to base pair position 158 can be found in other organisms, but not necessarily in the same position. The kit may also comprise additional primers or probes.
The portion of the P2 gene may be equivalent to a portion of the region of the gene from base pair positions 1 to 326 in A. fumigatus. Particularly preferred, are kits comprising, a probe for a portion of the P2 A. fumigatus gene and/or a probe for a portion of the region of the gene equivalent to base pair position 1 to base pair position 326 in A. fumigatus. Equivalent sequences to base pair position 1 to base pair position 326 can be found in other organisms, but not necessarily in the same position. The kit may also comprise additional primers or probes.
The primer may have a sequence selected from the group SEQ ID NO 1-8, 85-90, 95-104, and a sequence substantially homologous to or substantially complementary to those sequences, which can also act as a primer for the P2, P2A and P2B genes. The primers may also be a primer which preferentially hybridizes to the same nucleotide sequence as is preferentially hybridized by the primers SEQ ID NO 1-8, 85-90, 95-104.
The kit may comprise at least one forward in vitro amplification primer and at least one reverse in vitro amplification primer, the forward amplification primer having a sequence selected from the group consisting of SEQ ID NO 1, 3, 7; 85-88, 95-99, and a sequence being substantially homologous or complementary thereto which can also act as a forward amplification primer for the P2A, P2B or P2 genes, and the reverse amplification primer having a sequence selected from the group consisting of SEQ ID NO 2, 4, 5, 6, 8, 89, 90, 100-104, and a sequence being substantially homologous or complementary thereto which can also act as a reverse amplification primer for the P2A, P2B or P2 genes
The diagnostic kit may be based on direct nucleic acid detection technologies, signal amplification nucleic acid detection technologies, and nucleic acid in vitro amplification technologies is selected from one or more of Polymerase Chain Reaction (PCR), Ligase Chain Reaction (LCR), Nucleic Acids Sequence Based Amplification (NASBA), Strand Displacement Amplification (SDA), Transcription Mediated Amplification (TMA), Branched DNA technology (bDNA) and Rolling Circle Amplification Technology (RCAT)), or other in vitro enzymatic amplification technologies.
The invention also provides a nucleic acid molecule selected from the group consisting of SEQ ID NO.1 to SEQ ID NO. 110 and sequences substantially homologous thereto, or substantially complementary to a portion thereof and having a function in diagnostics based on the P2 and/or P2A and P2B genes. The nucleic acid molecule may comprise an oligonucleotide having a sequence substantially homologous to or substantially complementary to a portion of a nucleic acid molecule of SEQ ID NO.1 to SEQ ID NO. 110. The invention also provides a method of detecting a target organism in a test sample comprising the steps of:
(i) Mixing the test sample with at least one oligonucleotide probe as defined above under appropriate conditions; and
(ii) hybridizing under high stringency conditions any nucleic acid that may be present in the test sample with the oligonucleotide to form a probe:target duplex; and
(iii) determining whether a probe:target duplex is present; the presence of the duplex positively identifying the presence of the target organism in the test sample.
The nucleic acid molecule and kits of the present invention may be used in a diagnostic assay to detect the presence of one or more yeast and/or fungal species, to measure yeast and/or fungal titres in a patient or in a method of assessing the efficacy of a treatment regime designed to reduce yeast and/or fungal titre in a patient or to measure yeast and/or fungal contamination in an environment. The environment may be a hospital, or it may be a food sample, an environmental sample e.g. water, an industrial sample such as an in-process sample or an end product requiring bioburden or quality assessment. The kits and the nucleic acid molecule of the invention may be used in the identification and/or characterization of one or more disruptive agents that can be used to disrupt the P2A, P2B or P2 gene function. The disruptive agent may be selected from the group consisting of antisense RNA, PNA, and siRNA.
In some embodiments of the invention, a nucleic acid molecule comprising a species-specific probe can be used to discriminate between species of the same genus. The oligonucleotides of the invention may be provided in a composition for detecting the nucleic acids of yeast and fungal target organisms. Such a composition may also comprise buffers, enzymes, detergents, salts and so on, as appropriate to the intended use of the compositions. It is also envisioned that the compositions, kits and methods of the invention, while described herein as comprising at least one synthetic oligonucleotide, may also comprise natural oligonucleotides with substantially the same sequences as the synthetic nucleotide fragments in place of, or alongside synthetic oligonucleotides.
The invention also provides for an in vitro amplification diagnostic kit for a target yeast and/or fungal organism comprising at least one forward in vitro amplification primer and at least one reverse in vitro amplification primer, the forward amplification primer being selected from the group consisting of one or more of a sequence being substantially homologous or complementary thereto which can also act as a forward amplification primer, and the reverse amplification primer being selected from the group consisting of one or more of or a sequence being substantially homologous or complementary thereto which can also act as a reverse amplification primer.
The invention also provides for a diagnostic kit for detecting the presence of candidate yeast and/or fungal species, comprising one or more DNA probes comprising a sequence substantially complementary to, or substantially homologous to the sequence of the P2A, P2B or P2 gene of the candidate yeast and/or fungal species. The present invention also provides for one or more synthetic oligonucleotides having a nucleotide sequence substantially homologous to or substantially complementary to one or more of the group consisting of the P2A, P2B gene or mRNA transcripts thereof, the yeast and or fungal P2 gene or mRNA transcript thereof, the yeast P2B gene or mRNA transcript thereof, one or more of SEQ ID NO 1-SEQ ID NO 110.
The nucleotide may comprise DNA. The nucleotide may comprise RNA. The nucleotide may comprise a mixture of DNA, RNA and PNA. The nucleotide may comprise synthetic nucleotides. The sequences of the invention (and the sequences relating to the methods, kits compositions and assays of the invention) may be selected to be substantially homologous to a portion of the coding region of the P2, P2A or P2B genes. The gene may be a gene from a target yeast or fungal organism. The sequences of the invention are preferably sufficient so as to be able form a probe:target duplex to the portion of the sequence.
The invention also provides for a diagnostic kit for a target yeast or fungal organism comprising an oligonucleotide probe substantially homologous to or substantially complementary to an oligonucleotide of the invention (which may be synthetic). It will be appreciated that sequences suitable for use as in vitro amplification primers may also be suitable for use as oligonucleotide probes: while it is preferable that amplification primers may have a complementary portion of between about 15 nucleotides and about 30 nucleotides (more preferably about 15-about 23, most preferably about 20 to about 23), oligonucleotide probes of the invention may be any suitable length. The skilled person will appreciate that different hybridization and or annealing conditions will be required depending on the length, nature & structure (eg. Hybridization probe pairs for LightCycler, Taqman 5′ exonuclease probes, hairpin loop structures etc. and sequence of the oligonucleotide probe selected.
Kits and assays of the invention may also be provided wherein the oligonucleotide probe is immobilized on a surface. Such a surface may be a bead, a membrane, a column, dipstick, a nanoparticle, the interior surface of a reaction chamber such as the well of a diagnostic plate or inside of a reaction tube, capillary or vessel or the like.
The target yeast or fungal organism may be selected from the group consisting of C. albicans, C. glabrata, C. krusei, C. parapsilosis, C. tropicalis C. dubliniensis, C. guilliermondii, C. norvegiensis, C. famata, C. haemuloni, C. kefyr, C. utilis, C. viswanathii, A. fumigatus, A. nidulans, A. clavatus, A. niger, A. terreus, A. flavus, A. versicolor and Neosartorya fischeri.
Under these circumstances, the amplification primers and oligonucleotide probes of the invention may be designed to a gene specific or genus specific region so as to be able to identify one or more, or most, or substantially all of the desired organisms of the target organism grouping.
The test sample may comprise cells of the target yeast and/or fungal organism. The method may also comprise a step for releasing nucleic acid from any cells of the target yeast or fungal organism that may be present in said test sample. Ideally, the test sample is a lysate of an obtained sample from a patient (such as a swab, or blood, urine, saliva, a bronchial lavage, dental specimen, skin specimen, scalp specimen, transplant organ biopsy, stool, mucus, or discharge sample). The test samples may be a food sample, a water sample, an environmental sample, an end product, end product or in-process industrial sample.
The invention also provides for the use of any one of SEQ ID NO.1 to SEQ ID NO.110 in a diagnostic assay for the presence of one or more yeast or fungal species. The species may be selected from the group consisting of C. albicans, C. glabrata, C. krusei, C. parapsilosis, C. tropicalis, C. dubliniensis, C. guilliermondii, C. norvegiensis, C. famata, C. haemuloni, C. kefyr, C. utilis, C. viswanathii, A. fumigatus, N. fischeri, A. clavatus, A. niger, A. terreus, A. flavus, A. versicolor and A. nidulans.
The invention also provides for kits for use in clinical diagnostics, theranostics, food safety diagnostics, industrial microbiology diagnostics, environmental monitoring, veterinary diagnostics, bio-terrorism diagnostics comprising one or more of the synthetic oligonucleotides of the invention. The kits may also comprise one or more articles selected from the group consisting of appropriate sample collecting instruments, reagent containers, buffers, labelling moieties, solutions, detergents and supplementary solutions. The invention also provides for use of the sequences, compositions, nucleotide fragments, assays, and kits of the invention in theranostics, Food safety diagnostics, Industrial microbiology diagnostics, Environmental monitoring, Veterinary diagnostics, Bio-terrorism diagnostics.
The nucleic acid molecules, composition, kits or methods may be used in a diagnostic nucleic acid based assay for the detection of yeast and/or fungal species.
The nucleic acid molecules, composition, kits or methods may be used in a diagnostic assay to measure yeast and/or fungal titres in a patient. The titres may be measured in vitro.
The nucleic acid molecules, composition, kits or methods may be used in a method of assessing the efficacy of a treatment regime designed to reduce yeast and/or fungal titre in a patient comprising assessing the yeast and/or fungal titre in the patient (by in vivo methods or in vitro methods) at one or more key stages of the treatment regime. Suitable key stages may include before treatment, during treatment and after treatment. The treatment regime may comprise an antifungal agent, such as a pharmaceutical drug. The nucleic acid molecules, composition, kits or methods may be used in a diagnostic assay to measure potential yeast and/or fungal contamination, for example, in a hospital. The nucleic acid molecules, composition, kits or methods may be used in the identification and/or characterization of one or more disruptive agents that can be used to disrupt the P2, P2A or P2B gene function. Suitable disruptive agents may be selected from the group consisting of antisense RNA, PNA, siRNA.
Candida species were cultured in Sabouraud broth (4% wt/vol glucose, 1% wt/vol peptone, 1.5% agar) for 48 hours at 37° C. in a shaking incubator. Aspergillus species were cultured in Sabouraud broth (4% wt/vol glucose, 1% wt/vol peptone, 1.5% agar) or agar for 3-4 days at 25° C.
Cells from Candida and Aspergillus spp. were pretreated with lyticase or zymolase enzymes prior to DNA isolation. DNA was isolated Candida and Apergillus spp. using the MagNA Pure System (Roche Molecular Systems) in combination with the MagNA pure Yeast and Bacterial isolation kit III.
DNA sequencing of P2B/P2 gene regions in Candida and Aspergillus spp.
The available sequences of the P2B genes of Candida and P2 genes of Aspergillus spp. were acquired from the NCBI database and aligned using Clustal W. Three annotated sequences for P2B of C. albicans (XM—718047.1, XM—717900.1 and AF317662.1) are available in the NCBI database and a sequence of high homology to P2B in C. albicans has been deposited for Candida glabrata (hypothetical protein, XM—444905.1), which is considered here to be P2B. In addition to available sequences for P2 in Aspergillus spp., three presumptive P2 sequences are deposited as hypothetical proteins for Aspergillus spp. (XM—001213622.1, XM—001397764.1, XM—658508.1). PCR Primers were designed (Table 1) and synthesized by an external company, TibMolBiol, Germany. Primer set CanP2B-F/CanP2B-R was designed to amplify a 335 by region of the P2B in Candida spp. from positions equivalent to by position 1 to position 335 in C. albicans (XM—718047.1, XM—717900.1) or position 8 to by position 342 of the P2B gene in C. albicans (AF317662.1). Primer set CanP2B-F/CanP2B-R may also in selected Candida species amplify a 326 by region of the P2A gene. Primer set CanP2B-F/CanP2B flR was designed to amplify a 352 by region of the P2B equivalent to by 8 to by 359 in C. albicans (AF317662.1). Primer set P2B-F/P2BinR1 were designed to amplify a 312 by region of the P2B gene from by position 1 to by position 312 in XM718047.1/XM 717900.1 and from by position 8 to by 319 of AF317662.1. Primer set CglabP2B-F/CglabP2B-R were designed to amplify the region in P2B equivalent to by position 24 to by position 158 in C. glabrata (XM—444905.1). Primer set AspP2-F/AspP2-R were designed to amplify a region of P2 in Aspergillus spp. from base pair positions equivalent to 1 to position 326 in A. fumigatus (XM—750250.1).
Aspergillus spp.
Candida and P2 gene region in Aspergillus spp.
The publicly available sequence information for the P2B gene in Candida spp. was aligned with the newly generated sequence information for the P2B gene in Candida spp. and analysed using bioinformatics tools. The sequence information available for the P2 gene in Aspergillus spp. was aligned with the newly generated sequence information for the P2 gene in Aspergillus spp. and analysed using bioinformatics tools. Species-specific probes were designed based on the compiled P2B and P2 sequence information for Candida glabrata and Aspergillus fumigatus respectively (Table 4).
These probes were designed as TaqMan probes and demonstrated for species detection in real-time PCR on the LightCycler using reagents and thermocycling conditions detailed in Tables 5 and 6. For the C. glabrata real-time PCR assay based on the P2B gene, PCR primers CglabP2B-F/CglabP2B-R were combined with TaqMan probe P1-Cglab-P2B. The specificity of the assay for the detection of C. glabrata was confirmed by including DNA from a range of closely related Candida species and A. fumigatus in the C. glabrata real-time PCR assay. The assay detected C. glabrata but did not detect or cross-react with DNA from any other Candida species tested or with A. fumigatus DNA.
In so far as any sequence disclosed herein differs from its counterpart in the attached sequence listing in PatentIn3.3 software, the sequences within this body of text are to be considered as the correct version.
The words “comprises/comprising” and the words “having/including” when used herein with reference to the present invention are used to specify the presence of stated features, integers, steps or components but does not preclude the presence or addition of one or more other features, integers, steps, components or groups thereof.
It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable sub-combination.
Sites of probes, oligonucleotides etc. are shown in bold and underlined. N or x=any nucleotide; w=a/t, m=a/c, r=a/g, k=g/t, s=c/g, y=c/t, h=a/t/c, v=a/g/c, d=a/g/t, b=g/t/c. In some cases, specific degeneracy options are indicated in parenthesis: e.g.: (a/g) is either A or G.
C.dubliniensis
C.dubliniensis
C.parapsilosis
C.parapsilosis
C.tropicalis
C.guilliermondii
C.guilliermondii
C.lusitanie
A.fumigatus
A.fumigatus
A.fumigatus
A.fumigatus
N.fischeri
A.clavatus
A.terreus
A.flavus
Candida albicans 60S acidic ribosomal protein
glabrata CBS138 hypothetical protein
fischeri NRRL 181 60S acidic ribosomal protein
clavatus NRRL 1 60S acidic ribosomal protein P2,
nidulans FGSC A4 chromosomel
TCGATTAAACGAGTCAACAGGCATCTCAAGATCACAGCATAAGG
A. fumigatus
A. flavus
A. niger
A. terreus
A. candidus
A. clavatus
A. glaucus
C. pulcherrima
C. pulcherrima
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| Number | Date | Country | Kind |
|---|---|---|---|
| 2008/0489 | Jun 2008 | IE | national |
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/EP2009/057338 | 6/15/2009 | WO | 00 | 5/9/2011 |
