Specific And Universal Probes And Amplification Primers To Rapidly Detect And Identify Common Bacterial Pathogens And Antibiotic Resistance Genes From Clinical Specimens For Routine Diagnosis In Microbiology Laboratories

Abstract

The present invention relates to DNA-based methods for universal bacterial detection, for specific detection of the common bacterial pathogens Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Proteus mirabilis, Streptococcus pneumoniae, Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis, Staphylococcus saprophyticus, Streptococcus pyogenes, Haemophilus influenzae and Moraxella catarrhalis as well as for specific detection of commonly encountered and clinically relevant bacterial antibiotic resistance genes directly from clinical specimens or, alternatively, from a bacterial colony. The above bacterial species can account for as much as 80% of bacterial pathogens isolated in routine microbiology laboratories. The core of this invention consists primarily of the DNA sequences from all species-specific genomic DNA fragments selected by hybridization from genomic libraries or, alternatively, selected from data banks as well as any oligonucleotide sequences derived from these sequences which can be used as probes or amplification primers for PCR or any other nucleic acid amplification methods. This invention also includes DNA sequences from the selected clinically relevant antibiotic resistance genes. With these methods, bacteria can be detected (universal primers and/or probes) and identified (species-specific primers and/or probes) directly from the clinical specimens or from an isolated bacterial colony. Bacteria are further evaluated for their putative susceptibility to antibiotics by resistance gene detection (antibiotic resistance gene specific primers and/or probes). Diagnostic kits for the detection of the presence, for the bacterial identification of the above-mentioned bacterial species and for the detection of antibiotic resistance genes are also claimed. These kits for the rapid (one hour or less) and accurate diagnosis of bacterial infections and antibiotic resistance will gradually replace conventional methods currently used in clinical microbiology laboratories for routine diagnosis. They should provide tools to clinicians to help prescribe promptly optimal treatments when necessary. Consequently, these tests should contribute to saving human lives, rationalizing treatment, reducing the development of antibiotic resistance and avoid unnecessary hospitalizations.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application is a continuation of U.S. patent application Ser. No. 10/121,120 to Bergeron et al., entitled "Specific and universal probes and amplification primers to rapidly detect and identify common bacterial pathogens and antibiotic resistance genes from clinical specimens for routine diagnosis in microbiology laboratories," filed Apr. 11, 2002, which is a continuation of U.S. patent application Ser. No. 09/452,599, filed Dec. 1, 1999, now abandoned, which is a continuation of U.S. patent application Ser. No. 08/526,840, filed Sep. 11, 1995, now U.S. Pat. No. 6,001,564, which is a continuation-in-part of U.S. patent application Ser. No. 08/304,732, filed Sep. 12, 1994, now abandoned.

REFERENCE TO SEQUENCE LISTING

[0002] The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled GENOM.046CP1CC3.TXT, created Aug. 20, 2007, which is 115 KB in size. The information in the electronic format of the Sequence Listing is incorporated herein by reference in its entirety.

BACKGROUND OF THE INVENTION

Classical Identification of Bacteria

[0003] Bacteria are classically identified by their ability to utilize different substrates as a source of carbon and nitrogen through the use of biochemical tests such as the API20E.TM. system. Susceptibility testing of Gram negative bacilli has progressed to microdilution tests. Although the API and the microdilution systems are cost-effective, at least two days are required to obtain preliminary results due to the necessity of two successive overnight incubations to isolate and identify the bacteria from the specimen. Some faster detection methods with sophisticated and expensive apparatus have been developed. For example, the fastest identification system, the autoSCAN-Walk-Away System.TM. identifies both Gram negative and Gram positive from isolated bacterial colonies in 2 hours and susceptibility patterns to antibiotics in only 7 hours. However, this system has an unacceptable margin of error, especially with bacterial species other than Enterobacteriaceae (York et al., 1992. J. Clin. Microbiol. 30:2903-2910). Nevertheless, even this fastest method requires primary isolation of the bacteria as a pure culture, a process which takes at least 18 hours if there is a pure culture or 2 to 3 days if there is a mixed culture.

Urine Specimens

[0004] A large proportion (40-50%) of specimens received in routine diagnostic microbiology laboratories for bacterial identification are urine specimens (Pezzlo, 1988, Clin. Microbiol. Rev. 1:268-280). Urinary tract infections (UTI) are extremely common and affect up to 20% of women and account for extensive morbidity and increased mortality among hospitalized patients (Johnson and Stamm, 1989; Ann. Intern. Med. 111:906-917). UTI are usually of bacterial etiology and require antimicrobial therapy. The Gram negative bacillus Escherichia coli is by far the most prevalent urinary pathogen and accounts for 50 to 60% of UTI (Pezzlo, 1988, op. cit.). The prevalence for bacterial pathogens isolated from urine specimens observed recently at the "Centre Hospitalier de l'Universit Laval (CHUL)" is given in Tables 1 and 2.

[0005] Conventional pathogen identification in urine specimens. The search for pathogens in urine specimens is so preponderant in the routine microbiology laboratory that a myriad of tests have been developed. The gold standard is still the classical semi-quantitative plate culture method in which a calibrated loop of urine is streaked on plates and incubated for 18-24 hours. Colonies are then counted to determine the total number of colony forming units (CFU) per liter of urine. A bacterial UTI is normally associated with a bacterial count of .gtoreq.10.sup.7 CFU/L in urine. However, infections with less than 10.sup.7 CFU/L in urine are possible, particularly in patients with a high incidence of diseases or those catheterized (Stark and Maki, 1984, N. Engl. J. Med. 311:560-564). Importantly, close to 80% of urine specimens tested are considered negative (<10.sup.7 CFU/L; Table 3).

[0006] Accurate and rapid urine screening methods for bacterial pathogens would allow a faster identification of negative results and a more efficient clinical investigation of the patient. Several rapid identification methods (Uriscreen.TM., UTIscreen.TM., Flash Track.TM. DNA probes and others) were recently compared to slower standard biochemical methods which are based on culture of the bacterial pathogens. Although much faster, these rapid tests showed low sensitivities and specificities as well as a high number of false negative and false positive results (Koening et al., 1992. J. Clin. Microbiol. 30:342-345; Pezzlo et al., 1992. J. Clin. Microbiol. 30:640-684).

[0007] Urine specimens found positive by culture are further characterized using standard biochemical tests to identify the bacterial pathogen and are also tested for susceptibility to antibiotics.

Any Clinical Specimens

[0008] As with urine specimen which was used here as an example, our probes and amplification primers are also applicable to any other clinical specimens. The DNA-based tests proposed in this invention are superior to standard methods currently used for routine diagnosis in terms of rapidity and accuracy. While a high percentage of urine specimens are negative, in many other clinical specimens more than 95% of cultures are negative (Table 4). These data further support the use of universal probes to screen out the negative clinical specimens. Clinical specimens from organisms other than humans (e.g. other primates, mammals, farm animals or live stocks) may also be used.

Towards the Development of Rapid DNA-Based Diagnostic

[0009] A rapid diagnostic test should have a significant impact on the management of infections. For the identification of pathogens and antibiotic resistance genes in clinical samples, DNA probe and DNA amplification technologies offer several advantages over conventional methods. There is no need for subculturing, hence the organism can be detected directly in clinical samples thereby reducing the costs and time associated with isolation of pathogens. DNA-based technologies have proven to be extremely useful for specific applications in the clinical microbiology laboratory. For example, kits for the detection of fastidious organisms based on the use of hybridization probes or DNA amplification for the direct detection of pathogens in clinical specimens are commercially available (Persing et al, 1993. Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.).

[0010] The present invention is an advantageous alternative to the conventional culture identification methods used in hospital clinical microbiology laboratories and in private clinics for routine diagnosis. Besides being much faster, DNA-based diagnostic tests are more accurate than standard biochemical tests presently used for diagnosis because the bacterial genotype (e.g. DNA level) is more stable than the bacterial phenotype (e.g. biochemical properties). The originality of this invention is that genomic DNA fragments (size of at least 100 base pairs) specific for 12 species of commonly encountered bacterial pathogens were selected from genomic libraries or from data banks. Amplification primers or oligonucleotide probes (both less than 100 nucleotides in length) which are both derived from the sequence of species-specific DNA fragments identified by hybridization from genomic libraries or from selected data bank sequences are used as a basis to develop diagnostic tests. Oligonucleotide primers and probes for the detection of commonly encountered and clinically important bacterial resistance genes are also included. For example, Annexes I and II present a list of suitable oligonucleotide probes and PCR primers which were all derived from the species-specific DNA fragments selected from genomic libraries or from data bank sequences. It is clear to the individual skilled in the art that oligonucleotide sequences appropriate for the specific detection of the above bacterial species other than those listed in Annexes 1 and 2 may be derived from the species-specific fragments or from the selected data bank sequences. For example, the oligonucleotides may be shorter or longer than the ones we have chosen and may be selected anywhere else in the identified species-specific sequences or selected data bank sequences. Alternatively, the oligonucleotides may be designed for use in amplification methods other than PCR. Consequently, the core of this invention is the identification of species-specific genomic DNA fragments from bacterial genomic DNA libraries and the selection of genomic DNA fragments from data bank sequences which are used as a source of species-specific and ubiquitous oligonucleotides. Although the selection of oligonucleotides suitable for diagnostic purposes from the sequence of the species-specific fragments or from the selected data bank sequences requires much effort it is quite possible for the individual skilled in the art to derive from our fragments or selected data bank sequences suitable oligonucleotides which are different from the ones we have selected and tested as examples (Annexes I and II).

[0011] Others have developed DNA-based tests for the detection and identification of some of the bacterial pathogens for which we have identified species-specific sequences (PCT patent application Serial No. WO 93/03186). However, their strategy was based on the amplification of the highly conserved 16S rRNA gene followed by hybridization with internal species-specific oligonucleotides. The strategy from this invention is much simpler and more rapid because it allows the direct amplification of species-specific targets using oligonucleotides derived from the species-specific bacterial genomic DNA fragments.

[0012] Since a high percentage of clinical specimens are negative, oligonucleotide primers and probes were selected from the highly conserved 16S or 23S rRNA genes to detect all bacterial pathogens possibly encountered in clinical specimens in order to determine whether a clinical specimen is infected or not. This strategy allows rapid screening out of the numerous negative clinical specimens submitted for bacteriological testing.

[0013] We are also developing other DNA-based tests, to be performed simultaneously with bacterial identification, to determine rapidly the putative bacterial susceptibility to antibiotics by targeting commonly encountered and clinically relevant bacterial resistance genes. Although the sequences from the selected antibiotic resistance genes are available and have been used to develop DNA-based tests for their detection (Ehrlich and Greenberg, 1994. PCR-based Diagnostics in Infectious Diseases, Blackwell Scientific Publications, Boston, Mass.; Persing et al, 1993. Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.), our approach is innovative as it represents major improvements over current "gold standard" diagnostic methods based on culture of the bacteria because it allows the rapid identification of the presence of a specific bacterial pathogen and evaluation of its susceptibility to antibiotics directly from the clinical specimens within one hour.

[0014] We believe that the rapid and simple diagnostic tests not based on cultivation of the bacteria that we are developing will gradually replace the slow conventional bacterial identification methods presently used in hospital clinical microbiology laboratories and in private clinics. In our opinion, these rapid DNA-based diagnostic tests for severe and common bacterial pathogens and antibiotic resistance will (i) save lives by optimizing treatment, (ii) diminish antibiotic resistance by reducing the use of broad spectrum antibiotics and (iii) decrease overall health costs by preventing or shortening hospitalizations.

SUMMARY OF THE INVENTION

[0015] In accordance with the present invention, there is provided sequence from genomic DNA fragments (size of at least 100 base pairs and all described in the sequence listing) selected either by hybridization from genomic libraries or from data banks and which are specific for the detection of commonly encountered bacterial pathogens (i.e. Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Proteus mirabilis, Streptococcus pneumoniae, Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis, Staphylococcus saprophyticus, Streptococcus pyogenes, Haemophilus influenzae and Moraxella catarrhalis) in clinical specimens. These bacterial species are associated with approximately 90% of urinary tract infections and with a high percentage of other severe infections including septicemia, meningitis, pneumonia, intraabdominal infections, skin infections and many other severe respiratory tract infections. Overall, the above bacterial species may account for up to 80% of bacterial pathogens isolated in routine microbiology laboratories.

[0016] Synthetic oligonucleotides for hybridization (probes) or DNA amplification (primers) were derived from the above species-specific DNA fragments (ranging in sizes from 0.25 to 5.0 kilobase pairs (kbp)) or from selected data bank sequences (GenBank and EMBL). Bacterial species for which some of the oligonucleotide probes and amplification primers were derived from selected data bank sequences are Escherichia coli, Enterococcus faecalis, Streptococcus pyogenes and Pseudomonas aeruginosa. The person skilled in the art understands that the important innovation in this invention is the identification of the species-specific DNA fragments selected either from bacterial genomic libraries by hybridization or from data bank sequences. The selection of oligonucleotides from these fragments suitable for diagnostic purposes is also innovative. Specific and ubiquitous oligonucleotides different from the ones tested in the practice are considered as embodiments of the present invention.

[0017] The development of hybridization (with either fragment or oligonucleotide probes) or of DNA amplification protocols for the detection of pathogens from clinical specimens renders possible a very rapid bacterial identification. This will greatly reduce the time currently required for the identification of pathogens in the clinical laboratory since these technologies can be applied for bacterial detection and identification directly from clinical specimens with minimum pretreatment of any biological specimens to release bacterial DNA. In addition to being 100% specific, probes and amplification primers allow identification of the bacterial species directly from clinical specimens or, alternatively, from an isolated colony. DNA amplification assays have the added advantages of being faster and more sensitive than hybridization assays, since they allow rapid and exponential in vitro replication of the target segment of DNA from the bacterial genome. Universal probes and amplification primers selected from the 16S or 23S rRNA genes highly conserved among bacteria, which permit the detection of any bacterial pathogens, will serve as a procedure to screen out the numerous negative clinical specimens received in diagnostic laboratories. The use of oligonucleotide probes or primers complementary to characterized bacterial genes encoding resistance to antibiotics to identify commonly encountered and clinically important resistance genes is also under the scope of this invention.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT

Development of Species-Specific DNA Probes

[0018] DNA fragment probes were developed for the following bacterial species: Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Proteus mirabilis, Streptococcus pneumoniae, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus saprophyticus, Haemophilus influenzae and Moraxella catarrhalis. (For Enterococcus faecalis and Streptococcus pyogenes, oligonucleotide sequences were exclusively derived from selected data bank sequences). These species-specific fragments were selected from bacterial genomic libraries by hybridization to DNA from a variety of Gram positive and Gram negative bacterial species (Table 5).

[0019] The chromosomal DNA from each bacterial species for which probes were seeked was isolated using standard methods. DNA was digested with a frequently cutting restriction enzyme such as Sau3AI and then ligated into the bacterial plasmid vector pGEM3Zf (Promega) linearized by appropriate restriction endonuclease digestion. Recombinant plasmids were then used to transform competent E. coli strain DH5.alpha. thereby yielding a genomic library. The plasmid content of the transformed bacterial cells was analyzed using standard methods. DNA fragments of target bacteria ranging in size from 0.25 to 5.0 kilobase pairs (kbp) were cut out from the vector by digestion of the recombinant plasmid with various restriction endonucleases. The insert was separated from the vector by agarose gel electrophoresis and purified in low melting point agarose gels. Each of the purified fragments of bacterial genomic DNA was then used as a probe for specificity tests.

[0020] For each given species, the gel-purified restriction fragments of unknown coding potential were labeled with the radioactive nucleotide .sup..alpha.32P(dATP) which was incorporated into the DNA fragment by the random priming labeling reaction. Non-radioactive modified nucleotides could also be incorporated into the DNA by this method to serve as a label.

[0021] Each DNA fragment probe (i.e. a segment of bacterial genomic DNA of at least 100 bp in length cut out from clones randomly selected from the genomic library) was then tested for its specificity by hybridization to DNAs from a variety of bacterial species (Table 5). The double-stranded labeled DNA probe was heat-denatured to yield labeled single-stranded DNA which could then hybridize to any single-stranded target DNA fixed onto a solid support or in solution. The target DNAs consisted of total cellular DNA from an array of bacterial species found in clinical samples (Table 5). Each target DNA was released from the bacterial cells and denatured by conventional methods and then irreversibly fixed onto a solid support (e.g. nylon or nitrocellulose membranes) or free in solution. The fixed single-stranded target DNAs were then hybridized with the single-stranded probe. Pre-hybridization, hybridization and post-hybridization conditions were as follows: (i) Pre-hybridization; in 1 M NaCl+10% dextran sulfate+1% SDS (sodium dodecyl sulfate)+1 .mu.g/ml salmon sperm DNA at 650.degree. C. for 15 min. (ii) Hybridization; in fresh pre-hybridization solution containing the labeled probe at 650.degree. C. overnight. (iii) Post-hybridization; washes twice in 3.times.SSC containing 1% SDS (1.times.SSC is 0.15M NaCl, 0.015M NaCitrate) and twice in 0.1.times.SSC containing 0.1% SDS; all washes were at 650.degree. C. for 15 min. Autoradiography of washed filters allowed the detection of selectively hybridized probes. Hybridization of the probe to a specific target DNA indicated a high degree of similarity between the nucleotide sequence of these two DNAs. Species-specific DNA fragments selected from various bacterial genomic libraries ranging in size from 0.25 to 5.0 kbp were isolated for 10 common bacterial pathogens (Table 6) based on hybridization to chromosomal DNAs from a variety of bacteria performed as described above. All of the bacterial species tested (66 species listed in Table 5) were likely to be pathogens associated with common infections or potential contaminants which can be isolated from clinical specimens. A DNA fragment probe was considered specific only when it hybridized solely to the pathogen from which it was isolated. DNA fragment probes found to be specific were subsequently tested for their ubiquity (i.e. ubiquitous probes recognized most isolates of the target species) by hybridization to bacterial DNAs from approximately 10 to 80 clinical isolates of the species of interest (Table 6). The DNAs were denatured, fixed onto nylon membranes and hybridized as described above.

Sequencing of the Species-Specific Fragment Probes

[0022] The nucleotide sequence of the totality or of a portion of the species-specific DNA fragments isolated (Table 6) was determined using the dideoxynucleotide termination sequencing method which was performed using Sequenase.TM. (USB Biochemicals) or T7 DNA polymerase (Pharmacia). These nucleotide sequences are shown in the sequence listing. Alternatively, sequences selected from data banks (GenBank and EMBL) were used as sources of oligonucleotides for diagnostic purposes for Escherichia coli, Enterococcus faecalis, Streptococcus pyogenes and Pseudomonas aeruginosa. For this strategy, an array of suitable oligonucleotide primers or probes derived from a variety of genomic DNA fragments (size of more than 100 bp) selected from data banks was tested for their specificity and ubiquity in PCR and hybridization assays as described later. It is important to note that the data bank sequences were selected based on their potential of being species-specific according to available sequence information. Only data bank sequences from which species-specific oligonucleotides could be derived are included in this invention.

[0023] Oligonucleotide probes and amplification primers derived from species-specific fragments selected from the genomic libraries or from data bank sequences were synthesized using an automated DNA synthesizer (Millipore). Prior to synthesis, all oligonucleotides (probes for hybridization and primers for DNA amplification) were evaluated for their suitability for hybridization or DNA amplification by polymerase chain reaction (PCR) by computer analysis using standard programs (e.g. Genetics Computer Group (GCG) and Oligo.TM. 4.0 (National Biosciences)). The potential suitability of the PCR primer pairs was also evaluated prior to the synthesis by verifying the absence of unwanted features such as long stretches of one nucleotide, a high proportion of G or C residues at the 3' end and a 3'-terminal T residue (Persing et al, 1993. Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.).

Hybridization with Oligonucleotide Probes

[0024] In hybridization experiments, oligonucleotides (size less than 100 nucleotides) have some advantages over DNA fragment probes for the detection of bacteria such as ease of preparation in large quantities, consistency in results from batch to batch and chemical stability. Briefly, for the hybridizations, oligonucleotides were 5' end-labeled with the radionucleotide .sup..gamma.32P(ATP) using T4 polynucleotide kinase (Pharmacia). The unincorporated radionucleotide was removed by passing the labeled single-stranded oligonucleotide through a Sephadex G50 column. Alternatively, oligonucleotides were labeled with biotin, either enzymatically at their 3' ends or incorporated directly during synthesis at their 5' ends, or with digoxigenin. It will be appreciated by the person skilled in the art that labeling means other than the three above labels may be used.

[0025] The target DNA was denatured, fixed onto a solid support and hybridized as previously described for the DNA fragment probes. Conditions for pre-hybridization and hybridization were as described earlier. Post-hybridization washing conditions were as follows: twice in 3.times.SSC containing 1% SDS, twice in 2.times.SSC containing 1% SDS and twice in 1.times.SSC containing 1% SDS (all of these washes were at 65.degree. C. for 15 min), and a final wash in 0.1.times.SSC containing 1% SDS at 25.degree. C. for 15 min. For probes labeled with radioactive labels the detection of hybrids was by autoradiography as described earlier. For non-radioactive labels detection may be calorimetric or by chemiluminescence.

[0026] The oligonucleotide probes may be derived from either strand of the duplex DNA. The probes may consist of the bases A, G, C, or T or analogs. The probes may be of any suitable length and may be selected anywhere within the species-specific genomic DNA fragments selected from the genomic libraries or from data bank sequences.

DNA Amplification

[0027] For DNA amplification by the widely used PCR (polymerase chain reaction) method, primer pairs were derived either from the sequenced species-specific DNA fragments or from data bank sequences or, alternatively, were shortened versions of oligonucleotide probes. Prior to synthesis, the potential primer pairs were analyzed by using the program Oligo.TM.4.0 (National Biosciences) to verify that they are likely candidates for PCR amplifications.

[0028] During DNA amplification by PCR, two oligonucleotide primers binding respectively to each strand of the denatured double-stranded target DNA from the bacterial genome are used to amplify exponentially in vitro the target DNA by successive thermal cycles allowing denaturation of the DNA, annealing of the primers and synthesis of new targets at each cycle (Persing et al, 1993. Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.). Briefly, the PCR protocols were as follows. Clinical specimens or bacterial colonies were added directly to the 50 .mu.L PCR reaction mixtures containing 50 mM KCl, 10 mM Tris-HCl pH 8.3, 2.5 mM MgCl.sub.2, 0.4 .mu.M of each of the two primers, 200 .mu.M of each of the four dNTPs and 1.25 Units of Taq DNA polymerase (Perkin Elmer). PCR reactions were then subjected to thermal cycling (3 min at 95.degree. C. followed by 30 cycles of 1 second at 95.degree. C. and 1 second at 55.degree. C.) using a Perkin Elmer 480.TM. thermal cycler and subsequently analyzed by standard ethidium bromide-stained agarose gel electrophoresis. It is clear that other methods for the detection of specific amplification products, which may be faster and more practical for routine diagnosis, may be used. Such methods may be based on the detection of fluorescence after amplification (e.g. TaqMan.TM. system from Perkin Elmer or Amplisensor.TM. from Biotronics) or liquid hybridization with an oligonucleotide probe binding to internal sequences of the specific amplification product. These novel probes can be generated from our species-specific fragment probes. Methods based on the detection of fluorescence are particularly promising for utilization in routine diagnosis as they are, very rapid and quantitative and can be automated.

[0029] To assure PCR efficiency, glycerol or dimethyl sulfoxide (DMSO) or other related solvents, can be used to increase the sensitivity of the PCR and to overcome problems associated with the amplification of target with a high GC content or with strong secondary structures. The concentration ranges for glycerol and DMSO are 5-15% (v/v) and 3-10% (v.backslash.v), respectively. For the PCR reaction mixture, the concentration ranges for the amplification primers and the MgCl.sub.2 are 0.1-1.0 .mu.M and 1.5-3.5 mM, respectively. Modifications of the standard PCR protocol using external and nested primers (i.e. nested PCR) or using more than one primer pair (i.e. multiplex PCR) may also be used (Persing et al, 1993. Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.). For more details about the PCR protocols and amplicon detection methods see examples 7 and 8.

[0030] The person skilled in the art of DNA amplification knows the existence of other rapid amplification procedures such as ligase chain reaction (LCR), transcription-based amplification systems (TAS), self-sustained sequence replication (3SR), nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA) and branched DNA (bDNA) (Persing et al, 1993. Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.). The scope of this invention is not limited to the use of amplification by PCR, but rather includes the use of any rapid nucleic acid amplification methods or any other procedures which may be used to increase rapidity and sensitivity of the tests. Any oligonucleotides suitable for the amplification of nucleic acid by approaches other than PCR and derived from the species-specific fragments and from selected antibiotic resistance gene sequences included in this document are also under the scope of this invention.

Specificity and Ubiquity Tests for Oligonucleotide Probes and Primers

[0031] The specificity of oligonucleotide probes, derived either from the sequenced species-specific fragments or from data bank sequences, was tested by hybridization to DNAs from the array of bacterial species listed in Table 5 as previously described. Oligonucleotides found to be specific were subsequently tested for their ubiquity by hybridization to bacterial DNAs from approximately 80 isolates of the target species as described for fragment probes. Probes were considered ubiquitous when they hybridized specifically with the DNA from at least 80% of the isolates. Results for specificity and ubiquity tests with the oligonucleotide probes are summarized in Table 6. The specificity and ubiquity of the amplification primer pairs were tested directly from cultures (see example 7) of the same bacterial strains. For specificity and ubiquity tests, PCR assays were performed directly from bacterial colonies of approximately 80 isolates of the target species. Results are summarized in Table 7. All specific and ubiquitous oligonucleotide probes and amplification primers for each of the 12 bacterial species investigated are listed in Annexes I and II, respectively. Divergence in the sequenced DNA fragments can occur and, insofar as the divergence of these sequences or a part thereof does not affect the specificity of the probes or amplification primers, variant bacterial DNA is under the scope of this invention.

Universal Bacterial Detection

[0032] In the routine microbiology laboratory a high percentage of clinical specimens sent for bacterial identification is negative (Table 4). For example, over a 2 year period, around 80% of urine specimens received by the laboratory at the "Centre Hospitalier de l'Universite Laval (CHUL)" were negative (i.e. <10.sup.7 CFU/L) (Table 3). Testing clinical samples with universal probes or universal amplification primers to detect the presence of bacteria prior to specific identification and screen out the numerous negative specimens is thus useful as it saves costs and may rapidly orient the clinical management of the patients. Several oligonucleotides and amplification primers were therefore synthesized from highly conserved portions of bacterial 16S or 23S ribosomal RNA gene sequences available in data banks (Annexes III and IV). In hybridization tests, a pool of seven oligonucleotides (Annex I; Table 6) hybridized strongly to DNA from all bacterial species listed in Table 5. This pool of universal probes labeled with radionucleotides or with any other modified nucleotides is consequently very useful for detection of bacteria in urine samples with a sensitivity range of .gtoreq.10.sup.7 CFU/L. These probes can also be applied for bacterial detection in other clinical samples.

[0033] Amplification primers also derived from the sequence of highly conserved ribosomal RNA genes were used as an alternative strategy for universal bacterial detection directly from clinical specimens (Annex IV; Table 7). The DNA amplification strategy was developed to increase the sensitivity and the rapidity of the test. This amplification test was ubiquitous since it specifically amplified DNA from 23 different bacterial species encountered in clinical specimens.

[0034] Well-conserved bacterial genes other than ribosomal RNA genes could also be good candidates for universal bacterial detection directly from clinical specimens. Such genes may be associated with processes essential for bacterial survival (e.g. protein synthesis, DNA synthesis, cell division or DNA repair) and could therefore be highly conserved during evolution. We are working on these candidate genes to develop new rapid tests for the universal detection of bacteria directly from clinical specimens.

Antibiotic Resistance Genes

[0035] Antimicrobial resistance complicates treatment and often leads to therapeutic failures. Furthermore, overuse of antibiotics inevitably leads to the emergence of bacterial resistance. Our goal is to provide the clinicians, within one hour, the needed information to prescribe optimal treatments. Besides the rapid identification of negative clinical specimens with DNA-based tests for universal bacterial detection and the identification of the presence of a specific pathogen in the positive specimens with DNA-based tests for specific bacterial detection, the clinicians also need timely information about the ability of the bacterial pathogen to resist antibiotic treatments. We feel that the most efficient strategy to evaluate rapidly bacterial resistance to antimicrobials is to detect directly from the clinical specimens the most common and important antibiotic resistance genes (i.e. DNA-based tests for the detection of antibiotic resistance genes). Since the sequence from the most important and common bacterial antibiotic resistance genes are available from data banks, our strategy is to use the sequence from a portion or from the entire gene to design specific oligonucleotides which will be used as a basis for the development of rapid DNA-based tests. The sequence from the bacterial antibiotic resistance genes selected on the basis of their clinical relevance (i.e. high incidence and importance) is given in the sequence listing. Table 8 summarizes some characteristics of the selected antibiotic resistance genes.

EXAMPLES

[0036] The following examples are intended to be illustrative of the various methods and compounds of the invention.

Example 1

[0037] Isolation and cloning of fragments. Genomic DNAs from Escherichia coli strain ATCC 25922, Klebsiella pneumoniae strain CK2, Pseudomonas aeruginosa strain ATCC 27853, Proteus mirabilis strain ATCC 35657, Streptococcus pneumoniae strain ATCC 27336, Staphylococcus aureus strain ATCC 25923, Staphylococcus epidermidis strain ATCC 12228, Staphylococcus saprophyticus strain ATCC 15305, Haemophilus influenzae reference strain Rd and Moraxella catarrhalis strain ATCC 53879 were prepared using standard procedures. It is understood that the bacterial genomic DNA may have been isolated from strains other than the ones mentioned above. (For Enterococcus faecalis and Streptococcus pyogenes oligonucleotide sequences were derived exclusively from data banks). Each DNA was digested with a restriction enzyme which frequently cuts DNA such as Sau3AI. The resulting DNA fragments were ligated into a plasmid vector (pGEM3Zf) to create recombinant plasmids and transformed into competent E. coli cells (DH5.alpha.). It is understood that the vectors and corresponding competent cells should not be limited to the ones herein above specifically exemplified. The objective of obtaining recombinant plasmids and transformed cells is to provide an easily reproducible source of DNA fragments useful as probes. Therefore, insofar as the inserted fragments are specific and selective for the target bacterial DNA, any recombinant plasmids and corresponding transformed host cells are under the scope of this invention. The plasmid content of the transformed bacterial cells was analyzed using standard methods. DNA fragments from target bacteria ranging in size from 0.25 to 5.0 kbp were cut out from the vector by digestion of the recombinant plasmid with various restriction endonucleases. The insert was separated from the vector by agarose gel electrophoresis and purified in a low melting point agarose gel. Each of the purified fragments was then used for specificity tests.

[0038] Labeling of DNA fragment probes. The label used was .sup..alpha.32P(dATP), a radioactive nucleotide which can be incorporated enzymatically into a double-stranded DNA molecule. The fragment of interest is first denatured by heating at 95.degree. C. for 5 min, then a mixture of random primers is allowed to anneal to the strands of the fragments. These primers, once annealed, provide a starting point for synthesis of DNA. DNA polymerase, usually the Klenow fragment, is provided along with the four nucleotides, one of which is radioactive. When the reaction is terminated, the mixture of new DNA molecules is once again denatured to provide radioactive single-stranded DNA molecules (i.e. the probe). As mentioned earlier, other modified nucleotides may be used to label the probes.

[0039] Specificity and ubiquity tests for the DNA fragment probes. Species-specific DNA fragments ranging in size from 0.25 to 5.0 kbp were isolated for 10 common bacterial pathogens (Table 6) based on hybridization to chromosomal DNAs from a variety of bacteria. Samples of whole cell DNA for each bacterial strain listed in Table 5 were transferred onto a nylon membrane using a dot blot apparatus, washed and denatured before being irreversibly fixed. Hybridization conditions were as described earlier. A DNA fragment probe was considered specific only when it hybridized solely to the pathogen from which it was isolated. Labeled DNA fragments hybridizing specifically only to target bacterial species (i.e. specific) were then tested for their ubiquity by hybridization to DNAs from approximately 10 to 80 isolates of the species of interest as described earlier. The conditions for pre-hybridization, hybridization and post-hybridization washes were as described earlier. After autoradiography (or other detection means appropriate for the non-radioactive label used), the specificity of each individual probe can be determined. Each probe found to be specific (i.e. hybridizing only to the DNA from the bacterial species from which it was isolated) and ubiquitous (i.e. hybridizing to most isolates of the target species) was kept for further experimentations.

Example 2

[0040] Same as example 1 except that testing of the strains is by colony hybridization. The bacterial strains were inoculated onto a nylon membrane placed on nutrient agar. The membranes were incubated at 37.degree. C. for two hours and then bacterial lysis and DNA denaturation were carried out according to standard procedures. DNA hybridization was performed as described earlier.

Example 3

[0041] Same as example 1 except that bacteria were detected directly from clinical samples. Any biological samples were loaded directly onto a dot blot apparatus and cells were lysed in situ for bacterial detection. Blood samples should be heparizined in order to avoid coagulation interfering with their convenient loading on a dot blot apparatus.

Example 4

[0042] Nucleotide sequencing of DNA fragments. The nucleotide sequence of the totality or a portion of each fragment found to be specific and ubiquitous (Example 1) was determined using the dideoxynucleotide termination sequencing method (Sanger et al., 1977, Proc. Natl. Acad. Sci. USA. 74:5463-5467). These DNA sequences are shown in the sequence listing. Oligonucleotide probes and amplification primers were selected from these nucleotide sequences, or alternatively, from selected data banks sequences and were then synthesized on an automated Biosearch synthesizer (Millipore.TM.) using phosphoramidite chemistry.

[0043] Labeling of oligonucleotides. Each oligonucleotide was 5' end-labeled with .sup..gamma.32P-ATP by the T4 polynucleotide kinase (Pharmacia) as described earlier. The label could also be non-radioactive.

[0044] Specificity test for oligonucleotide probes. All labeled oligonucleotide probes were tested for their specificity by hybridization to DNAs from a variety of Gram positive and Gram negative bacterial species as described earlier. Species-specific probes were those hybridizing only to DNA from the bacterial species from which it was isolated. Oligonucleotide probes found to be specific were submitted to ubiquity tests as follows.

[0045] Ubiquity test for oligonucleotide probes. Specific oligonucleotide probes were then used in ubiquity tests with approximately 80 strains of the target species. Chromosomal DNAs from the isolates were transferred onto nylon membranes and hybridized with labeled oligonucleotide probes as described for specificity tests. The batteries of approximately 80 isolates constructed for each target species contain reference ATCC strains as well as a variety of clinical isolates obtained from various sources. Ubiquitous probes were those hybridizing to at least 80% of DNAs from the battery of clinical isolates of the target species. Examples of specific and ubiquitous oligonucleotide probes are listed in Annex I.

Example 5

[0046] Same as example 4 except that a pool of specific oligonucleotide probes is used for bacterial identification (i) to increase sensitivity and assure 100% ubiquity or (ii) to identify simultaneously more than one bacterial species. Bacterial identification could be done from isolated colonies or directly from clinical specimens

Example 6

[0047] PCR amplification. The technique of PCR was used to increase sensitivity and rapidity of the tests. The PCR primers used were often shorter derivatives of the extensive sets of oligonucleotides previously developed for hybridization assays (Table 6). The sets of primers were tested in PCR assays performed directly from a bacterial colony or from a bacterial suspension (see Example 7) to determine their specificity and ubiquity (Table 7). Examples of specific and ubiquitous PCR primer pairs are listed in annex II.

[0048] Specificity and ubiquity tests for amplification primers. The specificity of all selected PCR primer pairs was tested against the battery of Gram negative and Gram positive bacteria used to test the oligonucleotide probes (Table 5). Primer pairs found specific for each species were then tested for their ubiquity to ensure that each set of primers could amplify at least 80% of DNAs from a battery of approximately 80 isolates of the target species. The batteries of isolates constructed for each species contain reference ATCC strains and various clinical isolates representative of the clinical diversity for each species.

[0049] Standard precautions to avoid false positive PCR results should be taken. Methods to inactivate PCR amplification products such as the inactivation by uracil-N-glycosylase may be used to control PCR carryover.

Example 7

[0050] Amplification directly from a bacterial colony or suspension. PCR assays were performed either directly from a bacterial colony or from a bacterial suspension, the latter being adjusted to a standard McFarland 0.5 (corresponds to 1.5 times.10.sup.8 bacteria/mL). In the case of direct amplification from a colony, a portion of the colony was transferred directly to a 50 .mu.L PCR reaction mixture (containing 50 mM KCl, 10 mM Tris pH 8.3, 2.5 mM MgCl.sub.2, 0.4 .mu.M of each of the two primers, 200 .mu.M of each of the four dNTPs and 1.25 Unit of Taq DNA polymerase (Perkin Elmer)) using a plastic rod. For the bacterial suspension, 4 .mu.L of the cell suspension was added to 46 .mu.L of the same PCR reaction mixture. For both strategies, the reaction mixture was overlaid with 50 .mu.L of mineral oil and PCR amplifications were carried out using an initial denaturation step of 3 min. at 95.degree. C. followed by 30 cycles consisting of a 1 second denaturation step at 95.degree. C. and of a 1 second annealing step at 55.degree. C. in a Perkin Elmer 480.TM. thermal cycler. PCR amplification products were then analyzed by standard agarose gel (2%) electrophoresis. Amplification products were visualized in agarose gels containing 2.5 .mu.g/mL of ethidium bromide under UV at 254 mm. The entire PCR assay can be completed in approximately one hour.

[0051] Alternatively, amplification from bacterial cultures was performed as described above but using a "hot start" protocol. In that case, an initial reaction mixture containing the target DNA, primers and dNTPs was heated at 85.degree. C. prior to the addition of the other components of the PCR reaction mixture. The final concentration of all reagents was as described above. Subsequently, the PCR reactions were submitted to thermal cycling and analysis as described above.

Example 8

[0052] Amplification directly from clinical specimens. For amplification from urine specimens, 4 .mu.L of undiluted or diluted (1:10) urine was added directly to 46 .mu.L of the above PCR reaction mixture and amplified as described earlier.

[0053] To improve bacterial cell lysis and eliminate the PCR inhibitory effects of clinical specimens, samples were routinely diluted in lysis buffer containing detergent(s). Subsequently, the lysate was added directly to the PCR reaction mixture. Heat treatments of the lysates, prior to DNA amplification, using the thermocycler or a microwave oven could also be performed to increase the efficiency of cell lysis.

[0054] Our strategy is to develop rapid and simple protocols to eliminate PCR inhibitory effects of clinical specimens and lyse bacterial cells to perform DNA amplification directly from a variety of biological samples. PCR has the advantage of being compatible with crude DNA preparations. For example, blood, cerebrospinal fluid and sera may be used directly in PCR assays after a brief heat treatment. We intend to use such rapid and simple strategies to develop fast protocols for DNA amplification from a variety of clinical specimens.

Example 9

[0055] Detection of antibiotic resistance genes. The presence of specific antibiotic resistance genes which are frequently encountered and clinically relevant is identified using the PCR amplification or hybridization protocols described in previous sections. Specific oligonucleotides used as a basis for the DNA-based tests are selected from the antibiotic resistance gene sequences. These tests can be performed either directly from clinical specimens or from a bacterial colony and should complement diagnostic tests for specific bacterial identification.

Example 10

[0056] Same as examples 7 and 8 except that assays were performed by multiplex PCR (i.e. using several pairs of primers in a single PCR reaction) to (i) reach an ubiquity of 100% for the specific target pathogen or (ii) to detect simultaneously several species of bacterial pathogens.

[0057] For example, the detection of Escherichia coli requires three pairs of PCR primers to assure a ubiquity of 100%. Therefore, a multiplex PCR assay (using the "hot-start" protocol (Example 7)) with those three primer pairs was developed. This strategy was also used for the other bacterial pathogens for which more than one primer pair was required to reach a ubiquity of 100%.

[0058] Multiplex PCR assays could also be used to (i) detect simultaneously several bacterial species or, alternatively, (ii) to simultaneously identify the bacterial pathogen and detect specific antibiotic resistance genes either directly from a clinical specimen or from a bacterial colony.

[0059] For these applications, amplicon detection methods should be adapted to differentiate the various amplicons produced. Standard agarose gel electrophoresis could be used because it discriminates the amplicons based on their sizes. Another useful strategy for this purpose would be detection using a variety of fluorochromes emitting at different wavelengths which are each coupled with a specific oligonucleotide linked to a fluorescence quencher which is degraded during amplification to release the fluorochrome (e.g. TaqMan.TM., Perkin Elmer).

Example 11

[0060] Detection of amplification Products. The person skilled in the art will appreciate that alternatives other than standard agarose gel electrophoresis (Example 7) may be used for the revelation of amplification products. Such methods may be based on the detection of fluorescence after amplification (e.g. Amplisensor.TM., Biotronics; TaqMan.TM.) or other labels such as biotin (SHARP Signal.TM. system, Digene Diagnostics). These methods are quantitative and easily automated. One of the amplification primers or an internal oligonucleotide probe specific to the amplicon(s) derived from the species-specific fragment probes is coupled with the fluorochrome or with any other label. Methods based on the detection of fluorescence are particularly suitable for diagnostic tests since they are rapid and flexible as fluorochromes emitting different wavelengths are available (Perkin Elmer).

Example 12

[0061] Species-specific, universal and antibiotic resistance gene amplification primers can be used in other rapid amplification procedures such as the ligase chain reaction (LCR), transcription-based amplification systems (TAS), self-sustained sequence replication (3SR), nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA) and branched DNA (bDNA) or any other methods to increase the sensitivity of the test. Amplifications can be performed from an isolated bacterial colony or directly from clinical specimens. The scope of this invention is therefore not limited to the use of PCR but rather includes the use of any procedures to specifically identify bacterial DNA and which may be used to increase rapidity and sensitivity of the tests.

Example 13

[0062] A test kit would contain sets of probes specific for each bacterium as well as a set of universal probes. The kit is provided in the form of test components, consisting of the set of universal probes labeled with non-radioactive labels as well as labeled specific probes for the detection of each bacterium of interest in specific clinical samples. The kit will also include test reagents necessary to perform the pre-hybridization, hybridization, washing steps and hybrid detection. Finally, test components for the detection of known antibiotic resistance genes (or derivatives therefrom) will be included. Of course, the kit will include standard samples to be used as negative and positive controls for each hybridization test.

[0063] Components to be included in the kits will be adapted to each specimen type and to detect pathogens commonly encountered in that type of specimen. Reagents for the universal detection of bacteria will also be included. Based on the sites of infection, the following kits for the specific detection of pathogens may be developed:

[0064] A kit for the universal detection of bacterial pathogens from most clinical specimens which contains sets of probes specific for highly conserved regions of the bacterial genomes.

[0065] A kit for the detection of bacterial pathogens retrieved from urine samples, which contains eight specific test components (sets of probes for the detection of Escherichia coli, Enterococcus faecalis, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa, Staphylococcus saprophyticus, Staphylococcus aureus and Staphylococcus epidermidis).

[0066] A kit for the detection of respiratory pathogens which contains seven specific test components (sets of probes for detecting Streptococcus pneumoniae, Moraxella catarrhalis, Haemophilus influenzae, Klebsiella pneumoniae, Pseudomonas aeruginosa, Streptococcus pyogenes and Staphylococcus aureus).

[0067] A kit for the detection of pathogens retrieved from blood samples, which contains eleven specific test components (sets of probes for the detection of Streptococcus pneumoniae, Moraxella catarrhalis, Haemophilus influenzae, Proteus mirabilis, Klebsiella pneumoniae, Pseudomonas aeruginosa, Escherichia coli, Enterococcus faecalis, Staphylococcus aureus, Streptococcus pyogenes and Staphylococcus epidermidis).

[0068] A kit for the detection of pathogens causing meningitis, which contains four specific test components (sets of probes for the detection of Haemophilus influenzae, Streptococcus pneumoniae, Escherichia coli and Pseudomonas aeruginosa).

[0069] A kit for the detection of clinically important antibiotic resistance genes which contains sets of probes for the specific detection of at least one of the 19 following genes associated with bacterial resistance: bla.sub.tem, bla.sub.rob, bla.sub.shv, aadB, aacC1, aacC2, aacC3, aacA4, mecA, vanA, vanH, vanX, satA, aacA-aphD, vat, vga, msrA, sul and int.

[0070] Other kits adapted for the detection of pathogens from skin, abdominal wound or any other clinically relevant kits will be developed.

Example 14

[0071] Same as example 13 except that the test kits contain all reagents and controls to perform DNA amplification assays. Diagnostic kits will be adapted for amplification by PCR (or other amplification methods) performed directly either from clinical specimens or from a bacterial colony. Components required for universal bacterial detection, bacterial identification and antibiotic resistance genes detection will be included.

[0072] Amplification assays could be performed either in tubes or in microtitration plates having multiple wells. For assays in plates, the wells will be coated with the specific amplification primers and control DNAs and the detection of amplification products will be automated. Reagents and amplification primers for universal bacterial detection will be included in kits for tests performed directly from clinical specimens. Components required for bacterial identification and antibiotic resistance gene detection will be included in kits for testing directly from colonies as well as in kits for testing directly from clinical specimens.

[0073] The kits will be adapted for use with each type of specimen as described in example 13 for hybridization-based diagnostic kits.

Example 15

[0074] It is understood that the use of the probes and amplification primers described in this invention for bacterial detection and identification is not limited to clinical microbiology applications. In fact, we feel that other sectors could also benefit from these new technologies. For example, these tests could be used by industries for quality control of food, water, pharmaceutical products or other products requiring microbiological control. These tests could also be applied to detect and identify bacteria in biological samples from organisms other than humans (e.g. other primates, mammals, farm animals and live stocks). These diagnostic tools could also be very useful for research purposes including clinical trials and epidemiological studies.

TABLE-US-00001 TABLE 1 Distribution of urinary isolates from positive urine samples (.gtoreq.10.sup.7CFU/L) at the Centre Hospitalier de l'Universite Laval (CHUL) for the 1992-1994 period % of isolates November April July January 1992 1993 1993 1994 Organisms n = 267.sup.a n = 265 n = 238 n = 281 Escherichia coli 53.2 51.7 53.8 54.1 Enterococcus faecalis 13.8 12.4 11.7 11.4 Klebsiella pneumoniae 6.4 6.4 5.5 5.3 Staphylococcus epidermidis 7.1 7.9 3.0 6.4 Proteus mirabilis 2.6 3.4 3.8 2.5 Pseudomonas aeruginosa 3.7 3.0 5.0 2.9 Staphylococcus 3.0 1.9 5.4 1.4 saprophyticus Others.sup.b 10.2 13.3 11.8 16.0 .sup.an = total number of isolates for the indicated month .sup.bSee Table 2

TABLE-US-00002 TABLE 2 Distribution of uncommon.sup.a urinary isolates from positive urine samples (.gtoreq.10.sup.7CFU/L) at the Centre Hospitalier de l'Universite Laval (CHUL) for the 1992-1994 period % of isolates November April July January Organisms 1992 1993 1993 1994 Staphylococcus aureus 0.4 1.1 1.3 1.4 Staphylococcus spp. 2.2 4.9 1.7 6.0 Micrococcus spp. 0.0 0.0 0.4 0.7 Enterococcus faecium 0.4 0.4 1.3 1.4 Citrobacter spp. 1.4 0.8 0.4 0.7 Enterobacter spp. 1.5 1.1 1.3 1.4 Klebsiella oxytoca 1.1 1.5 2.5 1.8 Serratia spp. 0.8 0.0 0.5 0.0 Proteus spp. 0.4 0.4 0.0 1.1 Moganella and 0.4 0.8 0.4 0.0 Providencia Hafania alvei 0.8 0.0 0.0 0.0 NFB.sup.b 0.0 0.4 1.3 1.1 (Stenotrophomonas, Acinetobacter Candida spp. 0.8 1.9 0.7 0.4 .sup.aUncommon urinary isolates are those identified as "Others" in Table 1. .sup.bNFB: non-fermentative bacilli

TABLE-US-00003 TABLE 3 Distribution of positive.sup.a (bacterial count .gtoreq.10.sup.7CFU/L) and negative samples (bacterial count .ltoreq.10.sup.7CFU/L) urine specimens tested at the Centre Hospitalier de l'Universite Laval (CHUL) for the 1992-1994 period Number of isolates November 1992 April 1993 July 1993 January 1994 n = 267.sup.a n = 265 n = 238 n = 281 received 53.2 51.7 53.8 54.1 positive 13.8 12.4 11.7 11.4 negative 6.4 6.4 5.5 5.3 .sup.an = total number of isolates for the indicated month

TABLE-US-00004 TABLE 4 Distribution of positive and negative clinical specimens tested in the Microbiology Laboratory of the CHUL No. of % of % of samples positive negative Clinical Specimens.sup.a tested specimens specimens Urine 17,981 19.4 80.6 Haemoclulture/marrow 10.010 6.9 93.1 Sputum 1,266 68.4 31.6 Superficial pus 1,136 72.3 27.7 Cerebrospinal fluid 553 1.0 99.0 Synovial fluid-articular 523 2.7 97.3 Bronch./Trach./Amyg/Throat 502 56.6 43.4 Deep pus 473 56.8 43.2 Ears 289 47.1 52.9 Pleural and pericardial fluid 132 1.0 99.0 Peritonial fluid 101 28.6 71.4 .sup.aSpecimens tested from February 1994 to January 1995

TABLE-US-00005 TABLE 5 Bacterial Species (66) used for testing the specificity of DNA fragment probes, oligonucleotides probes and PCR primers Number Number of of Bacterial species strains Bacterial species strains Gram negative: tested Gram negative: tested Proteus mirabilis 5 Streptococcus pneumoniae 7 Klebsiella pneumoniae 5 Streptococcus salivarius 2 Pseudomonas aeruginosa 5 Streptococcus viridans 2 Escherichia coli 5 Streptococcus pyogenes 2 Moraxella catarrhalis 5 Staphylococcus aureus 2 Proteus vulgaris 2 Staphylococcus 2 epidermidis Morganella morganii 2 Staphylococcus 5 saprophyticus Enterobater cloacae 2 Micrococcus species 2 Providencia stuartii 1 Corynebacterium species 2 Providencia spp. 1 Streptococcus group B 2 Enterobacter 2 Staphylococcus simulans 2 agglomerans Providencia rettgeri 2 Staphylococcus 1 ludgunesis Neisseria mucosa 1 Staphylococcus capitis 2 Providencia 1 Staphylococcus 2 alcalifaciens haemolyticus Providencia 1 Staphylococcus hominis 2 rustigianii Burkholderia cepacia 2 Enterococcus faecalis 2 Enterobacter aerogenes 2 Enterococcus faecium 1 Stenotrophomonas 2 Staphylococcus warneri 1 maltophilia Pseudomonas 1 Enterococcus durans 1 fluorescens Comamonas acidovorans 2 Streptococcus bovis 1 Pseudomonas putida 2 Diphteriods 2 Haemophilus 5 Lactobacillus 1 influenzae acidophilus Haemophilus 2 parainfluenzae Bordetella pertussis 2 Haemophilus 2 parahaemolyticus Haemophilus aegyptius 2 Kingella indologenes 1 Moraxella atlantae 1 Neisseria cavaie 1 Neisseria subflava 1 Moraxella urethralis 1 Shigella sonnei 1 Shigella flexneri 1 Klebsiella oxytoca 2 Serratia marcescens 2 Salmonella 1 typhimurium Yersinia 1 enterocolitica Acinetobacter 1 calcoaceticus Acinetobacter lwoffi 1 Haftnia alvei 2 Citrobacter diversus 1 Citrobacter freundii 1 Salmonella species 1

TABLE-US-00006 TABLE 6 Species-specific DNA fragment and oligonucleotide probes for hybridization Number of Number of fragment probes oligonucleotide probes Spe- Ubi- Synthe- Spe- Ubi- Organisms Tested cific quitous sized cific quitous E. coli.sup.d -- -- -- 20 12 9.sup.f E. coli 14 2 .sup. 2.sup.e -- -- -- K. pneumoniae.sup.d -- -- -- 15 1 1 K. pneumoniae 33 3 3 18 12 8 P. mirabilis.sup.d -- -- -- 3 3 2 P. mirabilis 14 3 .sup. 3.sup.e 15 8 7 P. aeruginosa.sup.d -- -- -- 26 13 9 P. aeruginosa 6 2 .sup. 2.sup.e 6 0 0 S. saprophyticus 7 4 4 20 9 7 H. influenzae.sup.d -- -- -- 16 2 2 H. influenzae 1 1 1 20 1 1 S. pneumoniae.sup.d -- -- -- 6 1 1 M. catarrhalis 2 2 2 9 8 8 S. epidermidis 62 1 1 -- -- -- S. aureus 30 1 1 -- -- -- Universal probes.sup.d -- -- -- 7 -- .sup. 7.sup.g .sup.a No DNA fragment or oligonucleotide probes were tested for E. faecalis and S. pyogenes. .sup.b Sizes of DNA fragments range from 0.25 to 5.0 kbp .sup.c A specific probe was considered ubiquitous when at least 80% of isolates of the target species (approximately 80 isolates) were recognized by each specific probe. When 2 or more probes are combined, 100% of the isolates are recognized. .sup.dThese sequences were selected from data banks. .sup.eUbiquity tested with approximately 10 isolates of the target species .sup.fA majority of probes (8/9) do not discriminate E. coli and Shigella spp. .sup.gUbiquity testes with a pool of the 7 probes detected all 66 bacterial species listed in Table 5.

TABLE-US-00007 TABLE 7 PCR amplification for bacterial pathogens commonly encountered in urine, sputum, blood, cerebrospinal fluid and other specimens DNA amplification Primer pair Amplicon from from Organism #(SEQ ID NO:) size (bp) Ubiquity.sup.b colonies.sup.c specimens.sup.d E. coli 1.sup.e (55 56) 107 75/80 + + 2.sup.e (46 47) 297 77/80 + + 3 (42 43) 102 78/80 + + 4 (131 132) 134 73/80 + + 1 + 2 + 3 + 4 -- 80/80 + + E. faecalis 1.sup.e (38 39) 200 71/80 + + 2.sup.e (40 41) 121 79/80 + + 1 + 2 -- 80/80 + + K. pneumoniae 1 (67 68) 198 76/80 + + 2 (61 62) 143 67/80 + + 3.sup.h (135 136) 148 78/80 + .sup. N.T..sup.i 4 (137 138) 116 69/80 + N.T. 1 + 2 + 3 -- 80/80 + N.T. P. mirabilis 1 (74 75) 167 73/80 + N.T. 2 (133 134) 123 8080 + N.T. P. aeruginosa 1.sup.e (83 84) 139 79/80 + N.T. 2.sup.e (85 86) 223 80/80 + N.T. S. saprophyticus 1 (98 99) 126 79/80 + + 2 (139 140) 190 80/80 + N.T. M. catarrhalis 1 (112 113) 157 79/80 + N.T. 2 (118 119) 118 80/80 + N.T. 3 (160 119) 137 80/80 + N.T. H. influenzae 1.sup.e (154 155) 217 80/80 + N.T. S. pneumoniae 1.sup.e (156 157) 134 80/80 + N.T. 2.sup.e (158 159) 197 74/80 + N.T. 3 (78 79) 175 67/80 + N.T. S. epidermidis 1 (147 148) 175 80/80 + N.T. 2 (145 146) 125 80/80 + N.T. S. aureus 1 (152 153) 108 80/80 + N.T. 2 (149 150) 151 80/80 + N.T. 3 (149 151) 176 80/80 + N.T. S. pyogenes.sup.f 1.sup.e (141 142) 213 80/80 + N.T. 2.sup.e (143 144) 157 24/24 + N.T. Universal 1.sup.e (126 127) 241 .sup. 194/195.sup.g + N.T. .sup.a All primer pairs are specific in PCR assays since no amplification was observed with DNA from 66 different species of both Gram positive and Gram negative bacteria other than the species of interest. .sup.bThe ubiquity was normally tested on 80 strains of the species of interest. All retained primer pairs amplified at least 90% of the isolates. When combinations of primers were used, a ubiquity of 100% was reached. .sup.cFor all primer pairs and multiplex combinations, PCR amplifications directly performed from a bacterial colony were 100% species specific. .sup.dPCR assays performed directly from urine specimens. .sup.ePrimer pairs derived from data bank sequences. Primer pairs with no "e" are derived from our species-specific fragments. .sup.fFor S. pyogenes, primer pair #1 is specific for Group A Streptococci (GAS). Primer pair #2 is specific for GAS-producing exotoxin A gene (SpeA) .sup.gUbiquity tested on 195 isolates from 23 species representative of bacterial pathogens commonly encountered in clinical specimens. .sup.hOptimizations are in progress to eliminate non-specific amplification observed with some bacterial species other than the target species. .sup.iN.T.: not tested.

TABLE-US-00008 TABLE 8 Selected antibiotic resistance genes for diagnostic purposes Genes Antibiotics Bacteria.sup.a SEQ ID NO: (bla.sub.tem) TEM-1 .beta.-lactams Enterobacteriaceae, 161 Pseudomonadaceae, Haemophilus, Neisseria (bla.sub.rob) ROB-1 .beta.-lactams Haemophilus, 162 Pasteurella (bla.sub.shv) SHV-1 .beta.-lactams Klebsiella and other 163 Enterobacteriaceae aadB, aacC1, Aminoglycosides Enterobacteriaceae, 164, 165, aacC2, aacC3, Pseudomonadaceae 166, 167, aacC4, aacA4 168 mecA .beta.-lactams Staphylococci 169 vanH, vanA, Vancomycin Enterococci 170 vanX satA Macrolides Enterococci 173 aacA-aphD Aminoglycosides Enterococci, 174 Staphylococci vat Macrolides Staphylococci 175 vga Macrolides Staphylococci 176 msrA Erythromycin Staphylococci 177 Int and Sul .beta.-lactams, Enterobacteriaceae 171, 172 trimethoprim conserved aminoglycosides, Pseudomonadaecae sequences antiseptic, chloramphenicol .sup.aBacteria having high incidence for the specified antibiotic resistance genes. The presence in other bacteria is not excluded.

TABLE-US-00009 ANNEX I Annex I: Specific and ubiquitous oligonucleotide probes for hybridization Originating DNA fragment SEQ ID SEQ ID Nucleotide NO: Nucleotide Sequence NO: position Bacterial species: Escherichia coli 44 5'-CAC CCG CTT GCG TGG CAA GCT GCC C 5.sup.a 213-237 45 5'-CGT TTG TGG ATT CCA GTT CCA TCC G 5.sup.a 489-513 48 5'-TGA AGC ACT GGC CGA AAT GCT GCG T 6.sup.a 759-783 49 5'-GAT GTA CAG GAT TCG TTG AAG GCT T 6.sup.a 898-922 50 5'-TAG CGA AGG CGT AGC AGA AAC TAA C 7.sup.a 1264-1288 51 5'-GCA ACC CGA ACT CAA CGC CGG ATT T 7.sup.a 1227-1251 52 5'-ATA CAC AAG GGT CGC ATC TGC GGC C 7.sup.a 1313-1337 53 5'-TGC GTA TGC ATT GCA GAC CTT GTG GC 7.sup.a 111-136 54 5'-GCT TTC ACT GGA TAT CGC GCT TGG G 7.sup.a 373-397 Bacterial species: Proteus mirabilis 70.sup.b 5'-TGG TTC ACT GAC TTT GCG ATG TTT C 12 23-47 72 5'-TCG AGG ATG GCA TGC ACT AGA AAA T 12 53-77 72.sup.b 5'-CGC TGA TTA GGT TTC GCT AAA ATC TTA TTA 12 80-109 73 5'-TTG ATC CTC ATT TTA TTA ATC ACA TGA CCA 12 174-203 76 5'-CCG CCT TTA GCA TTA ATT GGT GTT TAT AGT 13 246-275 77 5'-CCT ATT GCA GAT ACC TTA AAT GTC TTG GGC 13 291-320 80.sup.b 5'-TTG AGT GAT GAT TTC ACT GAC TCC C 14 18-42 81 5'-GTG AGA CAG TGA TGG TGA GGA CAC A 15.sup.a 1185-1203 82 5'-TGG TTG TCA TGC TGT TTG TGT GAA AAT 15.sup.a 1224-1230 Bacterial species: Klebsiella pneumoniae 57 5'-GTG GTG TCG TTC AGG GGT TTC AC 8 45-67 58 5'-GCG ATA TTC ACA CCC TAC GCA GCC A 9 161-185 59.sup.b 5'-GTC GAA AAT GCC GGA AGA GGT ATA CG 9 203-228 60.sup.b 5'-ACT GAG CTG CAG ACC GGT AAA ACT CA 9 233-258 63.sup.b 5'-CGT GAT GGA TAT TCT TAA CGA AGG GC 10 250-275 64.sup.b 5'-ACC AAA CTG TTG AGC CGC CTG GA 10 201-223 65 5'-GTG ATC GCC CCT CAT CTG CTA CT 10 77-99 66 5'-CGC CCT TCG TTA AGA ATA TCC ATC AC 10 249-274 69 5'-CAG GAA GAT GCT GCA CCG GTT GTT G 11.sup.a 296-320 Bacterial species: Pseudomonas aeruginosa 87 5'-AAT GCG GCT GTA CCT CGG CGC TGG T 18.sup.a 2985-3009 88 5'-GGC GGA GGG CCA GTT GCA CCT GCC A 18.sup.a 2929-2953 89 5'-AGC CCT GCT CCT CGG CAG CCT CTG C 18.sup.a 2821-2845 90 5'-TGG CTT TTG CAA CCG CGT TCA GGT T 18.sup.a 1079-1103 91 5'-GCG CCC GCG AGG GCA TGC TTC GAT G 19.sup.a 705-729 92 5'-ACC TGG GCG CCA ACT ACA AGT TCT A 19.sup.a 668-692 93 5'-GGC TAC GCT GCC GGG CTG CAG GCC G 19.sup.a 505-529 94 5'-CCG ATC TAG ACC ATC GAG ATG GGC G 20.sup.a 1211-1235 95 5'-GAG CGC GGC TAT GTG TTC GTC GGC T 20.sup.a 2111-2135 Bacterial species: Streptococcus pneumoniae 120 5'-TCT GTG CTA GAG ACT GCC CCA TTT C 30 423-447 121 5'-CGA TGT CTT GAT TGA GCA GGG TTA T 31.sup.a 1198-1222 Bacterial species: Staphylococcus saprophyticus 96 5'-CGT TTT TAC CCT TAC CTT TTC GTA CTA CC 21 45-73 97.sup.b 5'-TCA GGC AGA GGT AGT ACG AAA AGG TAA GGG 21 53-82 100 5'-CAC CAA GTT TGA CAC GTG AAG ATT CAT 22 89-115 101.sup.b 5'-ATG AGT GAA GCG GAG TCA GAT TAT GTG CAG 23 105-134 102 5'-CGC TCA TTA CGT ACA GTG ACA ATC G 24 20-44 103 5'-CTG GTT AGC TTG ACT CTT AAC AAT CTT GTC 24 61-90 104.sup.b 5'-GAC GCG ATT GTC ACT GTA CGT AAT GAG CGA 24 19-48 Bacterial species: Moraxella catarrhalis 108 5'-GCC CCA AAA CAA TGA AAC ATA TGG T 28 81-105 109 5'-CTG CAG ATT TTG GAA TCA TAT CGC C 28 126-130 110 5'-TGG TTT GAC CAG TAT TTA ACG CCA T 28 165-189 111 5'-CAA CGG CAC CTG ATG TAC CTT GTA C 28 232-256 114 5'-TTA CAA CCT GCA CCA CAA GTC ATC A 29 97-121 115 5'-GTA CAA ACA AGC CGT CAG CGA CTT A 29 139-163 116 5'-CAA TCT GCG TGT GTG CGT TCA CT 29 178-200 117 5'-GCT ACT TTG TCA GCT TTA GCC ATT CA 29 287312 Bacterial species: Haemophilus influenzae 105.sup.b 5'-GCG TCA GAA AAA GTA GGC GAA ATG AAA G 25 138-165 106.sup.b 5'-AGC GGC TCT ATC TTG TAA TGA CAC A 26.sup.a 770-794 107.sup.b 5'-GAA ACG TGA ACT CCC CTC TAT ATA A 27.sup.a 5184-5208 Universal probes.sup.c 122.sup.b 5'-ATC CCA CCT TAG GCG GCT GGC TCC A -- -- 123 5'-ACG TCA AGT CAT CAT GGC CCT TAC GAG TAG G -- -- 124.sup.b 5'-GTG TGA CGG GCG GTG TGT ACA AGG C -- -- 125.sup.b 5'-GAG TTG CAG ACT CCA ATC CGG ACT ACG A -- -- 128.sup.b 5'-CCC TAT ACA TCA CCT TGC GGT TTA GCA GAG AG -- -- 129 5'-GGG GGG ACC ATC CTC CA GGC TAA ATA C -- -- 130.sup.b 5'-CGT CCA CTT TCG TGT TTG CAG AGT GCT GTG TT -- -- .sup.aSequence from data banks .sup.bThese sequences are from the opposite DNA strand of the sequences given in the Sequence listing.

TABLE-US-00010 ANNEX II ANNEX II: Specific and ubiquitous primers for DNA amplification Originating DNA fragment SEQ ID SEQ ID Nucleotide NO: Nucleotide Sequence NO: position Bacterial species: Escherichia coli 42 5'-GCT TTC CAG CGT CAT ATT G 4 177-195 43.sup.b 5'-GAT CTC GAC AAA ATG GTG A 4 260-278 46 5'-TCA CCC GCT TGC GTG GC 5.sup.a 212-228 47.sup.b 5'-GGA ACT GGA ATC CAC AAA C 5.sup.a 490-508 55 5'-GCA ACC CGA ACT CAA CGC C 7.sup.a 1227-1245 56.sup.b 5'-GCA GAT GCG ACC CTT GTG T 7.sup.a 1315-1333 131 5'-CAG GAG TAC GGT GAT TTT TA 3 60-79 132.sup.b 5'-ATT TCT GGT TTG GTC ATA CA 3 174-193 Bacterial species: Enterococcus faecalis 38 5'-GCA ATA CAG GGA AAA ATG TC 1.sup.a 69-88 39.sup.b 5'-CTT CAT CAA ACA ATT AAC TC 1.sup.a 249-268 40 5'-GAA CAG AAG AAG CCA AAA AA 2.sup.a 569-588 41.sup.b 5'-GCA ATC CCA AAT AAT ACG GT 2.sup.a 670-689 Bacterial species: Klebsiella pneumoniae 61 5'-GAC AGT CAG TTC GTC AGC C 9 37-55 62.sup.b 5'-CGT AGG GTG TGA ATA TCG C 9 161-179 67 5'-TCG CCC CTC ATC TGC TAC T 10 81-99 68.sup.b 5'-GAT CGT GAT GGA TAT TCT T 10 260-278 135 5'-GCA GCG TGG TGT CGT TCA 8 40-57 136.sup.b 5'-AGC TGG CAA CGG CTG GTC 8 170-187 137 5'-ATT CAC ACC CTA CGC AGC CA 9 166-185 138.sup.b 5'-ATC CGG CAG CAT CTC TTT GT 9 262-281 Bacterial species: Proteus mirabilis 74 5'-GAA ACA TCG CAA AGT CAG T 12 23-41 75.sup.b 5'-ATA AAA TGA GGA TCA AGT TC 12 170-189 133 5'-CGG GAG TCA GTG AAA TCA TC 14 17-36 134.sup.b 5'-CTA AAA TCG CCA CAC CTC TT 14 120-139 Bacterial species: Staphylococcus saprophyticus 98 5'-CGT TTT TAC CCT TAC CTT TTC GTA CT 21 45-70 99.sup.b 5'-ATC GAT CAT CAC ATT CCA TTT GTT TTT A 21 143-170 139 5'-CTG GTT AGC TTG ACT CTT AAC AAT C 24 61-85 140.sup.b 5'-TCT TAA CGA TAG AAT GGA GCA ACT G 24 26-250 Bacterial species: Psuedomonas aeruginosa 83 5'-CGA GCG GGT GGT GTT CAT C 16.sup.a 554-572 84.sup.b 5'-CAA GTC GTG GTG GGA GGG A 16.sup.a 674-692 85 5'-TCG CTG TTC ATC AAG ACC C 17.sup.a 1423-1441 86.sup.b 5'-CCG AGA ACC AGA CTT CAT C 17.sup.a 1627-1645 Bacterial species: Moraxella catarrhalis 112 5'-GGC ACC TGA TGT ACC TTG 28 235-252 113.sup.b 5'-AAC AGC TCA CAC GCA TT 28 375-391 118 5'-TGT TTT GAG CTT TTT ATT TTT TGA 29 41-64 119 5'-CGC TGA CGG CTT GTT TGT ACC A 29 137-158 160 5'-GCT CAA ATC AGG GTC AGC 29 22-39 119.sup.b 5'-CGC TGA CGG CTT GTT TGT ACG A 29 137-158 Bacterial species: Staphylococcus epidermidis 145 5'-ATC AAA AAG TTG GCG AAC CTT TTC A 36 21-45 146 5'-CAA AAG AGC GTG GAG AAA AGT ATC A 36 121-145 147 5'-TCT CTT TTA ATT TCA TCT TCA ATT CCA TAG 36 448-477 148.sup.b 5'-AAA CAC AAT TAC AGT CTG GTT ATC CAT ATC 36 593-622 Bacterial species: Staphylococcus aureus 149.sup.b 5'-CTT CAT TTT ACG GTG ACT TCT TAG AAG ATT 37 409-438 150 5'-TCA ACT GTA GCT TCT TTA TCC ATA CGT TGA 37 288-317 149.sup.b 5'-CTT CAT TTT ACG GTG ACT TCT TAG AAG ATT 37 409-438 151 5'-ATA TTT TAG CTT TTC AGT TTC TAT ATC AAC 37 263-292 152 5'-AAT CTT TGT CGG TAC ACG ATA TTC TTC ACG 37 5-34 153.sup.b 5'-CGT AAT GAG ATT TCA GTA GAT AAT ACA ACA 37 83-112 Bacterial species: Haemophilus influenzae 154 5'-TTT AAC GAT CCT TTT ACT CCT TTT G 27.sup.a 5074-5098 155.sup.b 5'-ACT GCT GTT GTA AAG AGG TTA AAA T 27.sup.a 5266-5290 Bacterial species: Streptococcus pneumoniae 78 5'-AGT AAA ATG AAA TAA GAA CAG GAC AG 34 164-189 79.sup.b 5'-AAA ACA GGA TAG GAG AAC GGG AAA A 34 314-338 156 5'-ATT TGG TGA CGG GTG ACT TT 31.sup.a 1401-1420 157.sup.b 5'-GCT GAG GAT TTG TTC TTC TT 31a 1515-1534 158 5'-GAG CGG TTT CTA TGA TTG TA 35.sup.a 1342-1361 159.sup.b 5'-ATC TTT CCT TTC TTG TTC TT 35a 1519-1538 Bacterial species: Steptococcus pyogenes 149 5'-TGA AAA TTC TTG TAA CAG GC 32.sup.a 286-305 142.sup.b 5'-GGC CAC CAG CTT GCC CAA TA 32.sup.a 479-498 143 5'-ATA TTT TCT TTA TGA GGG TG 33.sup.a 966-985 144.sup.b 5'-ATC CTT AAA TAA AGT TGC CA 33.sup.a 1103-1122 Universal primers.sup.c 126 5'-GGA GGA AGG TGG GGA TGA CG -- -- 127.sup.b 5'-ATG GTG TGA CGG GCG GTG TG -- -- .sup.asequence from data banks .sup.bThese sequences are from the opposite DNA strand of the sequences given in the Sequence listing.

TABLE-US-00011 ANNEX III ANNEX III Selection of Universal Probes by Alignment of the Sequences of Bacterial 16S and 23S Ribosomal RNA Genes Reverse strand of TGGACGG AGCCGCCTA GGTGGGAT SEQ ID NO:122 1251 1300 Streptococcus TGAGGTAACC TTTTGGAGCC AGCCGCCTAA GGTGGGATAG ATGANNGGGG salivarius Proteus vulgaris TAGCTTAACC TTCGGGAGGG CGCTTACCAC TTTGTGATTC ATGACTGGGG Pseudomonas aeruginosa TAGTCTAACC GCAAGGGGGA CGGTTACCAC GGAGTGATTC ATGACTGGGG Neiserria gonorrhoeae TAGGGTAACC GCAAGGAGTC CGCTTACCAC GGTATGCTTC ATGACTGGGG Streptococcus lactis TTGCCTAACC GCAAGGAGGG CGCTTCCTAA GGTAAGACCG ATGACNNGGG SEQ ID NO: 123 ACGTCAAGTC ATCATGGC CCTTACGAGT AGG 1251 1300 Haemophilus influenzae GGTNGGGATG ACGTCAAGTC ..ATCATGGC CCTTACGAGT AGGGCTACAC Neiserria gonorrhoeae GGTGGGGATG ACGTCAAGTC ..CTCATGGC CCTTATGACC AGGGCTTCAC Pseudomonas cepacia GGTNGGGATG ACGTCAAGTC ..CTCATGGC CCTTATGGGT AGGGCTTCAC Serratia marcescens GGTGGGGATG ACGTCAAGTC ..CTCATGGC CCTTATGGGT AGGGCTTCAC Escherichia coli GGTGGGGATG ACGTCAAGTC ..ATCATGGC CCTTACGACC AGGGCTACAC Proteus vulgaris GGTGGGGATG ACGTTAAGTC GTATCATGGC CCTTACGAGT AGGGCTACAC Pseudomonas aeruginosa GGTGGGGATG ACGTCAAGTC ..ATCATGGC CCTTACGGCN AGGGCTACAC Clostridium pefringens GGTGGGGATG ACGTNNAATC ..ATCATGCC CNTTATGTGT AGGGCTACAC Mycoplasma hominis GGTGGGGATG ACGTCAAATC ..ATCATGCC TCTTACGAGT GGGGCCACAC Helicobacter pylori GGTGGGGACG ACGTCAAGTC ..ATCATGGC CCTTACGCCT AGGGCTACAC Mycoplasma pneumoniae GGAAGGGATG ACGTCAAATC ..ATCATGCC CCTTATGTCT AGGGCTGCAA Reverse of the probe GCCTTGTACA CACCGCCCGT CACAC SEQ ID NO:124 1451 1490 Escherichia coli ACGTTCCCGG GCCTTGTACA CACCGCCCGT CACACCATGG Neiserria ghonorrhoeae ACGTTCCCNG NNCTTGTACA CACCGCCCGT CACACCATGG Pseudomonas cepacia ACGTTCCCGG GTCTTGTACA CACNGCCCGT CACACCATGG Serratia marcescens ACGTTCCCGG GCCTTGTACA CACCGCCCGT CACACCATGG Proteus vulgaris ACGTTCCCGG GCCTTGTACA CACCGCCCGT CACACCATGG Haemophilus influenzae ACGTTCCCGG GCNTTGTACA CACCGCCCGT CACACCATGG Pseudomonas aeruginosa ACGTTCCCGG GCCTTGTACA CACCGCCCGT CACACCATGG Clostridium pefringens ACGTTCCCNG GTCTTGTACA CACCGCNCGT CACACCATGA Mycoplasma hominis ACGTTCTCGG GTCTTGTACA CACCGCCCGT CACACCATGG Helicobacter pylori ACGTTCCCGG GTCTTGTACT CACCGCCCGT CACACCATGG Mycoplasma pneumoniae ACGTTCTCGG GTCTTGTACA CACCGCCCGT CAAACTATGA Reverse strand of TCG TAGTCCGGAT TGGAGTCTGC AACTC SEQ ID NO: 125 1361 1400 Escherichia coli AAGTGCGTCG TAGTCCGGAT TGGAGTCTGC AACTCGACTC Neiserria ghonorrhoeae AAACCGATCG TAGTCCGGAT TGCACTCTGC AACTCGAGTG Pseudomonas cepacia AAACCGATCG TAGTCCGGAT TGCACTCTGC AACTCGAGTG Serratia marcescens AAGTATGTCG TAGTCCGGAT TGGAGTCTGC AACTCGACTC Proteus vulgaris AAGTCTGTCG TAGTCCGGAT TGGAGTCTGC AACTCGACTC Haemophilus influenzae AAGTACGTCT AAGTCCGGAT TGGAGTCTGC AACTCGACTC Pseudomonas aeruginosa AAACCGATCG TAGTCCGGAT CGCAGTCTGC AACTCGACTG Clostridium pefringens AAACCAGTCT CAGTTCGGAT TGTAGGCTGA AACTCGCCTA Mycoplasma hominis AAGCCGATCT CAGTTCGGAT TGGAGTCTGC AATTCGACTC Helicobacter pylori ACACC..TCT CAGTTCGGAT TGTAGGCTGC AACTCGCCTG Mycoplasma pneumoniae AAGTTGGTCT CAGTTCGGAT TGAGGGCTGC AATTCGTCTT Reverse strand of SEQ ID NO: 128 481 530 Lactobacillus lactis AAACACAGCT CTCTGCTAAA CCGCAAGGTG ATGTATAGGG GGTGACGCCT Escherichia coli AAACACAGCA CTGTGCAAAC ACGAAAGTGG ACGTATACGG TGTGACGCCT Pseudomonas aeruginosa AAACACAGCA CTCTGCAAAC ACGAAAGTGG ACGTATAGGG TGTGACGCCT Pseudomonas cepacia AAACACAGCA CTCTGCAAAC ACGAAAGTGG ACGTATAAGG TGTGACGCCT Bacillus AAACACAGGT CTCTGCGAAG TCGTAAGGCG ACGTATAGGG GCTGACACCT stearothermophilus Micrococcus luteus AAACACAGGT CCATGCGAAG TCGTAAGACG ATGTATATGG ACTGACTCCT SEQ ID NO: 129 GGGGGGACC ATCCTCCAAG GCTAAATAC 1991 2040 Escherichia coli TGTCTGAATG TGGGGGGACC ATCCTCCAAG GCTAAATACT CCTGACTGAC Pseudomonas aeruginosa TGTCTGAACA TGGGGGGACC ATCCTCCAAG GCTAAATACT ACTGACTGAC Pseudomonas cepacia TGTCTGAAGA TGGGGGGACC ATCCTCCAAG GCTAAATACT CGTGATCGAC Lactobacillus lactis AGTTTGAATC GCCCAGGACC ATCTCCCAAC CCTAAATACT CCTTAGTGAC Micrococcus luteus CGTGTGAATC TGCCAGGACC ACCTGGTAAG CCTGAATACT ACCTGTTGAC Reverse strand of AACACAGCA CTCTGCAAAC ACGAAAGTGG ACG SEQ ID NO: 130 1981 2030 Pseudomonas aeruginosa TGTTTATTAA AAACACAGCA CTCTGCAAAC ACGAAAGTGG ACGTATAGGG Escherichia coli TGTTTATTAA AAACACAGCA CTGTGGAAAC ACGAAAGTGG ACGTATACGG Bacillus TGTTTAATAA AAACACAGCA CTCTGCAAAC ACGAAAGTGG ACGTATAGGG stearothermophilus Lactobacillus lactis TGTTTATCAA AAACACAGCT CTCTGCTAAA CCACAAGGTG ATGTATAGGG Micrococcus luteus TGTTTATCAA AAACACAGGT CCATGCGAAG TCGTAAGACG ATGTATATGG SEQ ID NO: 126 GGAGGAA GGTGGGGATG ACG Reverse strand of CA CACCGCCCGT CACACCAT SEQ ID NO: 127 Escherichia coli ACTGGAGGAA GGTGGGGATG ACGTCAAGTC...GCCTTGTACA CACCGCCCGT CACACCATGG Neiserria ghonorrhoeae GCCGGAGGAA GGTGGGGATG ACGTCAAGTC...NNCTTGTACA CACCGCCCGT CACACCATGG Pseudomonas cepacia ACCGGAGGAA GGTNGGGATG ACGTCAAGTC...GTCTTGTACA CACNGCCCGT CACACCATGG Serratia marcescens ACTGGAGGAA GGTGGGGATG ACGTCAAGTC...GCCTTGTACA CACCGCCCGT CACACCATGG Proteus vulgaris ACCGGAGGAA GGTGGGGATG ACGTTAAGTC...GCCTTGTACA CACCGCCCGT CACACCATGG Haemophilus influenzae ACTGGAGGAA GGTNGGGATG ACGTCAAGTC...GCNTTGTACA CACCGCCCGT CACACCATGG Legionella pneumophila ACCGGAGGAA GGCGGGGATG ACGTCAAGTC...GCCTTGTACA CACCGCCCGT CACACCATGG Pseudomonas aeruginosa ACCGGAGGAA GGTGGGGATG ACGTCAAGTC...GCCTTGTACA CACCGCCCGT CACACCATGG Clostridium perfringens CCAGGAGGAA GGTGGGGATG ACGTNNAATC...GTCTTGTACA CACCGCNCGT CACACCATGA Mycoplasma hominis CTGGGAGGAA GGTGGGGATG ACGTCAAATC...GTCTTGTACA CACCGCCCGT CACACCATGG Helicobacter pylori GGAGGAGGAA GGTGGGGACG ACGTCAAGTC...GTCTTGTACT CACCGCCCGT CACACCATGG Mycoplasma pneumoniae ATTGGAGGAA GGAAGGGATG ACGTCAAATC...GTCTTGTACA CACCGCCCGT CAAACTATGA

Sequence CWU 1

1

17711817DNAEnterococcus faecalis 1acagtaaaaa agttgttaac gaatgaattt gttaacaact tttttgctat ggtattgagt 60tatgaggggc aatacaggga aaaatgtcgg ctgattaagg aatttagata gtgccggtta 120gtagttgtct ataatgaaaa tagcaacaaa tatttacgca gggaaagggg cggtcgttta 180acgggaaaaa ttagggagga taaagcaata cttttgttgg gaaaagaaat aaaaggaaac 240tggggaagga gttaattgtt tgatgaaggg aaataaaatt ttatacattt taggtacagg 300catctttgtt ggaagttcat gtctattttc ttcacttttt gtagccgcag aagaacaagt 360ttattcagaa agtgaagttt caacagtttt atcgaagttg gaaaaggagg caatttctga 420ggcagctgct gaacaatata cggttgtaga tcgaaaagaa gacgcgtggg ggatgaagca 480tcttaagtta gaaaagcaaa cggaaggcgt tactgttgat tcagataatg tgattattca 540tttagataaa aacggtgcag taacaagtgt tacaggaaat ccagttgatc aagttgtgaa 600aattcaatcg gttgatgcaa tcggtgaaga aggagttaaa aaaattgttg cttctgataa 660tccagaaact aaagatcttg tctttttagc tattgacaaa cgtgtaaata atgaagggca 720attattttat aaagtcagag taacttcttc accaactggt gaccccgtat cattggttta 780taaagtgaac gctacagatg gaacaattat ggaaaaacaa gatttaacgg aacatgtcgg 840tagtgaagta acgttaaaaa actcttttca agtaacgttt aatgtaccag ttgaaaaaag 900caatacggga attgctttac acggaacgga taacacaggg gtttaccatg cagtagttga 960tggcaaaaat aattattcta ttattcaagc gccatcacta gcgacattaa atcagaatgc 1020tattgacgcc tatacgcatg gaaaatttgt gaaaacatat tatgaagatc atttccaacg 1080acacagtatt gatgatcgag ggatgcccat cttgtcagtt gttgatgaac aacatccaga 1140tgcttatgac aatgcttttt gggatggaaa agcaatgcgt tatggtgaaa caagtacacc 1200aacaggaaaa acgtatgctt cctctttaga tgtagttggt catgaaatga cacatggtgt 1260gacggaacat actgccggtt tagaatattt aggacaatca ggtgccttga atgaatctta 1320ttctgatttg atgggttata ttatttcggg tgcatctaat ccagaaattg gtgcggatac 1380tcagagtgtt gaccgaaaaa caggtattcg aaatttacaa acgccaagta aacacggaca 1440accagaaacc atggctcaat acgacgatcg agcacggtat aaaggaacgc cttattatga 1500tcaaggcggt gttcattata acagtggaat tattaatcgg attggttaca ccattatcca 1560gaacttaggc attgaaaaag cacagactat tttctacagc tcgttagtaa attacttaac 1620acctaaagca caattcagtg atgctcgtga tgcgatgctt gctgctgcaa aagttcaata 1680tggcgatgaa gcagcttcag tggtgtcagc agcctttaac tctgctggaa tcggagctaa 1740agaagacatt caggtaaacc aaccaagtga atctgttctg gtcaatgaat gaaaaaaatt 1800ccccaattaa ataaaaa 181722275DNAEnterococcus faecalis 2ggtaccaaag aaaaaaacga acgccacaac caacagcctc taaagcaaca cctgcttctg 60aaattgaggg agatttagca aatgtcaatg agattctttt ggttcacgat gatcgtgtcg 120ggtcagcaac gatgggaatg aaagtcttag aagaaatttt agataaagag aaaatttcaa 180tgccgattcg aaaaattaat attaatgaat taactcaaca aacacaggct ttaattgtca 240caaaagctga actaacggaa caagcacgta aaaaagcacc gaaagcgaca cacttatcag 300taaaaagtta tggttaatcc ccaaaaatat gaaacagtgg gtttcgctct taaaagaaag 360tgcctagaga ggaagaaaac aatggaaaat cttacgaata tttcaattga attaaatcaa 420cagtttaata caaaagaaga agctattcgc ttttccggcc agaaactagt cgaggcaggc 480tgtgttgagc ccgcttatat cgaagcaatg attgaaagag accaattgct atctgcccat 540atggggaatt ttattgccat tcctcatgga acagaagaag ccaaaaaatt agtgaaaaaa 600tcaggaatct gtgtagtgca agtcccagag ggcgttaatt ttggcaccga agaagatgaa 660aaaattgcta ccgtattatt tgggattgcc ggagtcggtg aagaacattt gcaattagtc 720caacaaattg cactttattg tagtgatatg gataacgtgg tgcaacttgc cgatgcatta 780agtaaagaag aaataacaga aaatttagcc attgcttaaa ggagagaata agaatgaacg 840cagtacattt tggagcagga aatattggac gcggctttat tggcgaaatt ttagctaaaa 900cgggtttcat attaccgttt gtggatgtta atggaaacca tcatcaagcg ttaaaagaac 960gtaaaagtta tacaattgaa ttggccgatg cctcacatca acaaattaac gttgaaaatg 1020tgaccgggtt aaataacatg acagaaccag aaaaagtagt agaagcaatt gcggaagccg 1080atttagtcac gacggcaatt ggtcctaata ttttaccaag aattgctgaa ttaattgctc 1140aaggaattga tgcacgtgcc gaagcaaatt gtcaaaacgg cccgctggat attatcgctt 1200gtgaaaatat gattggtggt tcaacctttt tagcagaaga agtggccata atatttgaaa 1260aacccagctt atctgaacaa tggattggtt ttcctgatgc ggcagttgat cggattgttc 1320cattacaaaa acataaagat ccactttttg ttcaagttga gcctttttgt gaatgggtca 1380ttgatgatac caaccgaaaa gccaaagaga ttcagttaga aggcgtcatt acttgtcgat 1440tagagccgta tattgaacga aaattattta gtgtaaccag tggccatgct acagttgcct 1500atacaggggc gttgttaggc tatcaaacca ttgacgaagc gatgcaggac gccttagtgg 1560tagcgcaact caaatcagtt ttgcaggaaa ccggtaaact tttagtggcc aaatggaatt 1620ttgatgaaca agaacatgca gcctatattg aaaaaattat caaccgtttc caaaataaat 1680atatttcaga tgctattaca cgtgtagcac ggacaccaat cagaaaatta ggtgcgcaag 1740aacggtttat tcgaccaatc cgtgaattac aggaacgcaa tctagtgtcg gccgcattta 1800tagcaatgat tggtattgtc tttaattatc atgatccaga agatgaacaa agccgtcaat 1860tacaggaaat gcttgaccaa gaaagtgttg atacagtgga tcgctgaagt aacgggcatt 1920gaagatccag aaacggttaa aaatattaaa caaaacgtag aactgctatg cgcgaccaca 1980agtagcataa ttaacaaaat ccttctacca agatacttca catttcttaa ttaaagaaaa 2040aacaaccgcg cctcacctga gccgaccccc aaaagttaga cctagaaatc taacttttgg 2100aggttttttt gtatggcaaa atacagtttt gaaatttaaa cttaaacttg ttcatgacta 2160cttatatggt caaggaggtc taaggtttct cgcaaagaag tatgggttta aagatagtct 2220caaataagca aatggataaa tgcctataaa gaacttggtg aagaaggggg gatcc 22753227DNAEscherichia coli 3gatccgccat gggttgtttt ccgattgagg attttataga tggtttctgg cgacctgcac 60aggagtacgg tgatttttaa ttattgcaat tgcacaagag tcagttctcc cccaaagaca 120gcaccggtat caatataatg caggttgcca atatccacgc gatggcgcaa aggtgtatga 180ccaaaccaga aatgatcggc cacctgcatc gccagttcgc gagtcgg 2274278DNAEscherichia coli 4gatctaaatc aaattaattg gttaaagata accacagcgg ggccgacata aactctgaca 60agaagttaac aaccatataa cctgcacagg acgcgaacat gtcttctcat ccgtatgtca 120cccagcaaaa taccccgctg gcggacgaca ccactctgat gtccactacc gatctcgctt 180tccagcgtca tattggggcg cgctacgttg gggcgtgggc gtaattggtc aatcaggcgc 240ggggtcagcg gataaacatt caccattttg tcgagatc 27851596DNAEscherichia coli 5atggctgaca ttctgctgct cgataatatc gactctttta cgtacaacct ggcagatcag 60ttgcgcagca atgggcataa cgtggtgatt taccgcaacc atataccggc gcaaacctta 120attgaacgct tggcgaccat gagtaatccg gtgctgatgc tttctcctgg ccccggtgtg 180ccgagcgaag ccggttgtat gccggaactc ctcacccgct tgcgtggcaa gctgcccatt 240attggcattt gcctcggaca tcaggcgatt gtcgaagctt acgggggcta tgtcggtcag 300gcgggcgaaa ttctccacgg taaagcctcc agcattgaac atgacggtca ggcgatgttt 360gccggattaa caaacccgct gccggtggcg cgttatcact cgctggttgg cagtaacatt 420ccggccggtt taaccatcaa cgcccatttt aatggcatgg tgatggcagt acgtcacgat 480gcggatcgcg tttgtggatt ccagttccat ccggaatcca ttctcaccac ccagggcgct 540cgcctgctgg aacaaacgct ggcctgggcg cagcataaac tagagccagc caacacgctg 600caaccgattc tggaaaaact gtatcaggcg cagacgctta gccaacaaga aagccaccag 660ctgttttcag cggtggtgcg tggcgagctg aagccggaac aactggcggc ggcgctggtg 720agcatgaaaa ttcgcggtga gcacccgaac gagatcgccg gggcagcaac cgcgctactg 780gaaaacgcag cgccgttccc gcgcccggat tatctgtttg ctgatatcgt cggtactggc 840ggtgacggca gcaacagtat caatatttct accgccagtg cgtttgtcgc cgcggcctgt 900gggctgaaag tggcgaaaca cggcaaccgt agcgtctcca gtaaatctgg ttcgtccgat 960ctgctggcgg cgttcggtat taatcttgat atgaacgccg ataaatcgcg ccaggcgctg 1020gatgagttag gtgtatgttt cctctttgcg ccgaagtatc acaccggatt ccgccacgcg 1080atgccggttc gccagcaact gaaaacccgc accctgttca atgtgctggg gccattgatt 1140aacccggcgc atccgccgct ggcgttaatt ggtgtttata gtccggaact ggtgctgccg 1200attgccgaaa ccttgcgcgt gctggggtat caacgcgcgg cggtggtgca cagcggcggg 1260atggatgaag tttcattaca cgcgccgaca atcgttgccg aactgcatga cggcgaaatt 1320aaaagctatc agctcaccgc agaagacttt ggcctgacac cctaccacca ggagcaactg 1380gcaggcggaa caccggaaga aaaccgtgac attttaacac gtttgttaca aggtaaaggc 1440gacgccgccc atgaagcagc cgtcgctgcg aacgtcgcca tgttaatgcg cctgcatggc 1500catgaagatc tgcaagccaa tgcgcaaacc gttcttgagg tactgcgcag tggttccgct 1560tacgacagag tcaccgcact ggcggcacga gggtaa 159662703DNAEscherichia coli 6gacgacttag ttttgacgga atcagcatag ttaatcactt cactgtggaa aatgaggaaa 60tattattttt tttgcgcttc gtaattaatg gttataaggt cggccagaaa cctttctaat 120gcaagcgatg acgttttttt atgtgtctga atttgcactg tgtcacaatt ccaaatcttt 180attaacaact cacctaaaac gacgctgatc cagcgtgaat actggtttcc cttatgttca 240tcagattcat ttaagcaagg gtttcttctt cattcctgat gaaagtgcca tctaaaaaga 300tgatcttaat aaatctatta agaatgagat ggagcacact ggatatttta cttatgaaac 360tgtttcactc ctttacttaa tttatagagt taccttccgc tttttgaaaa tacgcaacgg 420ccattttttg cacttagata cagattttct gcgctgtatt gcattgattt gatgctaatc 480ctgtggtttg cactagcttt aagtggttga gatcacattt ccttgctcat ccccgcaact 540cctccctgcc taatcccccg caggatgagg aaggtcaaca tcgagcctgg caaactagcg 600ataacgttgt gttgaaaatc taagaaaagt ggaactccta tgtcacaacc tatttttaac 660gataagcaat ttcaggaagc gctttcacgt cagtggcagc gttatggctt aaattctgcg 720gctgaaatga ctcctcgcca gtggtggcta gcagtgagtg aagcactggc cgaaatgctg 780cgtgctcagc cattcgccaa gccggtggcg aatcagcgac atgttaacta catctcaatg 840gagtttttga ttggtcgcct gacgggcaac aacctgttga atctcggctg gtatcaggat 900gtacaggatt cgttgaaggc ttatgacatc aatctgacgg acctgctgga agaagagatc 960gacccggcgc tgggtaacgg tggtctggga cgtctggcgg cgtgcttcct cgactcaatg 1020gcaactgtcg gtcagtctgc gacgggttac ggtctgaact atcaatatgg tttgttccgc 1080cagtcttttg tcgatggcaa acaggttgaa gcgccggatg actggcatcg cagtaactac 1140ccgtggttcc gccacaacga agcactggat gtgcaggtag ggattggcgg taaagtgacg 1200aaagacggac gctgggagcc ggagtttacc attaccggtc aagcgtggga tctccccgtt 1260gtcggctatc gtaatggcgt ggcgcagccg ctgcgtctgt ggcaggcgac gcacgcgcat 1320ccgtttgatc tgactaaatt taacgacggt gatttcttgc gtgccgaaca gcagggcatc 1380aatgcggaaa aactgaccaa agttctctat ccaaacgaca accatactgc cggtaaaaag 1440ctgcgcctga tgcagcaata cttccagtgt gcctgttcgg tagcggatat tttgcgtcgc 1500catcatctgg cggggcgtga actgcacgaa ctggcggatt actaagttat tcagctgaac 1560gatacccacc caactatcgc gattccagaa ctgctgcgcg tgctgatcga tgagcaccag 1620atgagctggg atgacgcttg ggccattacc agcaaaactt tcgcttacac caaccatacc 1680ctgatgccag aagcgctgga acgctgggat gtgaaactgg tgaaaggctt actgccgcgc 1740cacatgcaga ttattaacga aattaatact cgctttaaaa cgctggtaga gaaaacctgg 1800ccgggcgatg aaaaagtgtg ggccaaactg gcggtggtgc acgacaaaca agtgcatatg 1860gcgaacctgt gtgtggttgg cggtttcgcg gtgaacggtg ttgcggcgct gcactcggat 1920ctggtggtga aagatctgtt cccggaatat caccagctat ggccgaacaa attccataac 1980gtcaccaacg gtattacccc acgtcgctgg atcaaacagt gcaacccggc actggcggct 2040ctgttggata aatcactgca aaaagagtgg gctaacgatc tcgatcagct gatcaatctg 2100gttaaattgg ctgatgatgc gaaattccgt cagctttatc gcgtgatcaa gcaggcgaat 2160aaagtccgtc tggcggagtt tgtgaaagtt cgtaccggta ttgacatcaa tccacaggcg 2220attttcgata ttcagatcaa acgtttgcac gagtacaaac gccagcacct gaatctgctg 2280cgtattctgg cgttgtacaa agaaattcgt gaaaacccgc aggctgatcg cgtaccgcgc 2340gtcttcctct tcggcgcgaa agcggcaccg ggctactacc tggctaagaa tattatcttt 2400gcgatcaaca aagtggctga cgtgatcaac aacgatccgc tggttggcga taagttgaag 2460gtggtgttcc tgccggatta ttgcgtttcg gcggcggaaa aactgatccc ggcggcggat 2520atctccgaac aaatttcgac tgcaggtaaa gaagcttccg gtaccggcaa tatgaaactg 2580gcgctcaatg gtgcgcttac tgtcggtacg ctggatgggg cgaacgttga aatcgccgag 2640aaagtcggtg aagaaaatat ctttattttt ggtcatacgg tcaaacaagt gaaggcaatc 2700gac 270371391DNAEscherichia coli 7agagaagcct gtcggcaccg tctggtttgc ttttgccact gcccgcggtg aaggcattac 60ccggcgggat gcttcagcgg cgaccgtgat gcggtgcgtc gtcaggctac tgcgtatgca 120ttgcagacct tgtggcaaca atttctacaa aacacttgat actgtatgag catacagtat 180aattgcttca acagaacata ttgactatcc ggtattaccc ggcatgacag gagtaaaaat 240ggctatcgac gaaaacaaac agaaagcgtt ggcggcagca ctgggccaga ttgagaaaca 300atttggtaaa ggctccatca tgcgcctggg tgaagaccgt tccatggatg tggaaaccat 360ctctaccggt tcgctttcac tggatatcgc gcttggggca ggtggtctgc cgatgggccg 420tatcgtcgaa atctacggac cggaatcttc cggtaaaacc acgctgacgc tgcaggtgat 480cgccgcagcg cagcgtgaag gtaaaacctg tgcgtttatc gatgctgaac acgcgctgga 540cccaatctac gcacgtaaac tgggcgtcga tatcgacaac ctgctgtgct cccagccgga 600caccggcgag caggcactgg aaatctgtga cgccctggcg cgttctggcg cagtagacgt 660tatcgtcgtt gactccgtgg cggcactgac gccgaaagcg gaaatcgaag gcgaaatcgg 720cgactctcac atgggccttg cggcacgtat gatgagccag gcgatgcgta agctggcggg 780taacctgaag cagtccaaca cgctgctgat cttcatcaac cagatccgta tgaaaattgg 840tgtgatgttc ggtaacccgg aaaccactac cggtggtaac gcgctgaaat tctacgcctc 900tgttcgtctc gacatccgtc gtatcggcgc ggtgaaagag ggcgaaaacg tggtgggtag 960cgaaacccgc gtgaaagtgg tgaagaacaa aatcgctgcg ccgtttaaac aggctgaatt 1020ccagatcctc tacggcgaag gtatcaactt ctacggcgaa ctggttgacc tgggcgtaaa 1080agagaagctg atcgagaaag caggcgcgtg gtacagctac aaaggtgaga agatcggtca 1140gggtaaagcg aatgcgactg cctggctgaa agataacccg gaaaccgcga aagagatcga 1200gaagaaagta cgtgagttgc tgctgagcaa cccgaactca acgccggatt tctctgtaga 1260tgatagcgaa ggcgtagcag aaactaacga agatttttaa tcgtcttgtt tgatacacaa 1320gggtcgcatc tgcggccctt ttgctttttt aagttgtaag gatatgccat gacagaatca 1380acatcccgtc g 13918238DNAKlebsiella pneumoniae 8tcgccaggaa ggcggcattc ggctgggtca gagtgacctg cagcgtggtg tcgttcagcg 60ctttcacccc caacgtctcg ggtccctttt gcccgagggc aatctcgcgg gcgttggcga 120tatgcatatt gccagggtag ctcgcgtagg gggaggctgt tgccggcgag accagccgtt 180gccagctcca gacgatatcc tgcgctgtaa tggccgtgcc gtcagaccag gtcagacc 2389385DNAKlebsiella pneumoniae 9cagcgtaatg cgccgcggca taacggcgcc actatcgaca gtcagttcgt cagcctgcag 60cctgggctga atctgggacc atggcgcctg ccgaactaca gcacctatag ccacagcgat 120aacaacagcc gctgggagtc ggtttactcc tatcttgccc gcgatattca caccctacgc 180agccagctgg tggtcggtaa tacgtatacc tcttccggca ttttcgacag tttgagtttt 240accggtctgc agctcagttc gacaaagaga tgctgccgga tagcctgcat gctttgcgcc 300gacgattcga gggatcgcgc gcaccaccgc ggaggtctcg gtttatcaga atggttacag 360catttataaa accaccgtcg ctacc 38510462DNAKlebsiella pneumoniae 10ctctatattc aggacgaaca tatctggacc tctggcgggg tcagttccgg ctttgatcgc 60cctgcacccg cagcgggtga tcgcccctca tctgctactg cggcgctgca acaggcgacg 120atcgatgacg ttattcctgg ccagcaaaca gcagaccaat taaggtctga tagtggctct 180cttcctccgg cgcgcgacgg tccaggcggc tcaacagttt ggtgcatagc gctttgcggt 240tgagatgacg cccttcgtta agaatatcca tcacgatctc cgtccatgga gagtagcgtt 300tattccagaa tagggttttt caggatctca tggatctgcg cctgcttatc gctattttgt 360aaccagatcg cataaagtgg acgggataac gtagcgctgt ccatgaccgt atgtaaccca 420tgcttctctt tcgcccagcg agcaggtagc caacagcagc cg 46211730DNAKlebsiella pneumoniae 11gctgaccgct aaactgggtt acccgatcac tgacgatctg gacatctaca cccgtctggg 60cggcatggtt tggcgcgctg actccaaagg caactacgct tcaaccggcg tttcccgtag 120cgaacacgac actggcgttt ccccagtatt tgctggcggc gtagagtggg ctgttactcg 180tgacatcgct acccgtctgg aataccagtg ggttaacaac atcggcgacg cgggcactgt 240gggtacccgt cctgataacg gcatgctgag cctgggcgtt tcctaccgct tcggtcagga 300agatgctgca ccggttgttg ctccggctcc ggctccggct ccggaagtgg ctaccaagca 360cttcaccctg aagtctgacg ttctgttcaa cttcaacaaa gctaccctga aaccggaagg 420tcagcaggct ctggatcagc tgtacactca gctgagcaac atggatccga aagacggttc 480cgctgttgtt ctgggctaca ccgaccgcat cggttccgaa gcttacaacc agcagctgtc 540tgagaaacgt gctcagtccg ttgttgacta cctggttgct aaaggcatcc cggctggcaa 600aatctccgct cgcggcatgg gtgaatccaa cccggttact ggcaacacct gtgacaacgt 660gaaagctcgc gctgccctga tcgattgcct ggctccggat cgtcgtgtag agatcgaagt 720taaaggtatc 73012225DNAProteus mirabilis 12cgctactgtt taaatctcat ttgaaacatc gcaaagtcag tgaaccacat attcgaggat 60ggcatgcact agaaaatatt aataagattt tagcgaaacc taatcagcgc aatatcgctt 120aattatttta ggtatgttct cttctatcct acagtcacga ggcagtgtcg aacttgatcc 180tcattttatt aatcacatga ccaatggtat aagcgtcgtc acata 22513402DNAProteus mirabilis 13acattttaaa taggaagcca cctgataaca tccccgcagt tggatcatca gatttatagc 60ggcatttggt atccgctaga taaaagcagt ccaacgatcc cgccaattgt tagatgaaat 120tggactattc tttttatttg ctccgcttta tcacagtggt tttcgctttg ccgcccctgt 180gcgccaacag ctaagaacac gcacgctctt taatgtgtta ggcccattaa ttaatccagc 240gcgttccgcc tttagcatta attggtgttt atagtcctga attattaatg cctattgcag 300ataccttaaa tgtcttgggc tacaaacgtg cggcagtggt ccatagtggt ggaatggatg 360aagtgtcatt acatgctccc acacaagtgg ctgagttaca ca 40214157DNAProteus mirabilis 14ctgaaacgca tttatgcggg agtcagtgaa atcatcactc aattttcacc cgatgtattt 60tctgttgaac aagtctttat ggcaaaaaat gcagactcag cattaaaatt aggccaagca 120agaggtgtgg cgattttagc ggcagtcaat aatgatc 157151348DNAProteus mirabilis 15tttctcttta aaatcaattc ttaaagaaat tattaataat taacttgata ctgtatgatt 60atacagtata atgagtttca acaagcaaaa tcatatacgt tttaatggta gtgacccatc 120tttatgcttc actgcccaga gggagataac atggctattg atgaaaacaa acaaaaagca 180ttggccgcag cacttggtca aattgaaaag caatttggta aaggttctat catgcgtctg 240ggcgaagacc gttccatgaa cgtagaaact atctctacag gatctttatc attagacgtt 300gctttaggtg caggtggatt gccacgtggc cgtattgttg aaatctatgg ccctgaatct 360tctggtaaaa caaccttgac tctacaagtt attgcctctg ctcagcgtga aggaaaaatt 420tgtgcattta ttgatgctga acatgcatta gacccaattt atgctcaaaa gctaggtgtc 480gatatcgata atctactctg ctctcaacct gacacaggtg aacaagctct ggaaatttgt 540gatgcattat ctcgctctgg tgcggtcgat gttattgtcg tggactccgt ggcagcatta 600acaccaaaag ctgaaattga aggtgaaatt ggtgattcac acgttggttt agccgcacgt 660atgatgagcc aagctatgcg taaactagcg ggtaacctta aaaactctaa tacactgctg 720attttcatta accaaattcg tatgaaaatc ggtgttatgt ttggtaaccc agaaaccacg 780accggtggta atgcgcttaa attctatgct tctgttcgtt tagacattcg tcgcattggc 840tctgtcaaaa atggtgatga agtcattggt agtgagactc gcgttaaagt tgttaaaaat 900aaagtggctg caccgtttaa acaagctgaa ttccaaatta tgtacggtga aggtattaat 960acctatggcg aactgattga tttaggtgtt aaacataagt tagtagagaa agcaggtgct 1020tggtatagct acaatggcga aaaaattggt caaggtaaag ctaacgcaac caattactta 1080aaagaacatc ctgaaatgta caatgagtta aacactaaat tgcgtgaaat gttgttaaat 1140catgctggtg aattcacaag tgctgcggat tttgcaggtg aagagtcaga cagtgatgct 1200gacgacacaa aagagtaatt agctggttgt catgctgttt gtgtgaaaat agaccttaaa 1260tcattggcta ttatcacgac agcatcccat agaataactt gtttgtataa attttattca 1320gatggcaaag gaagccttaa aaaagctt

1348162167DNAPseudomonas aeruginosa 16ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat 60ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac 120aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg 180aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg 240agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc 300ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg 360tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg 420agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga 480acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga 540ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa 600gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct 660acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg 720cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg 780ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg 840aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt 900acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct 960tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc 1020tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt 1080acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca 1140gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc 1200agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt 1260ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg 1320cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca 1380gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt 1440gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc 1500gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc 1560cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga 1620tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa 1680gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca 1740ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct 1800gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg 1860aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt 1920catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg 1980gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct 2040gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa 2100ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt 2160cctcgag 2167171872DNAPseudomonas aeruginosa 17gaattcccgg gagttcccga cgcagccacc cccaaaacac tgctaaggga gcgcctcgca 60gggctcctga ggagatagac catgccattt ggcaagccac tggtgggcac cttgctcgcc 120tcgctgacgc tgctgggcct ggccaccgct cacgccaagg acgacatgaa agccgccgag 180caataccagg gtgccgcttc cgccgtcgat cccgctcacg tggtgcgcac caacggcgct 240cccgacatga gtgaaagcga gttcaacgag gccaagcaga tctacttcca acgctgcgcc 300ggttgccacg gcgtcctgcg caagggcgcc accggcaagc cgctgacccc ggacatcacc 360cagcaacgcg gccagcaata cctggaagcg ctgatcacct acggcacccc gctgggcatg 420ccgaactggg gcagctccgg cgagctgagc aaggaacaga tcaccctgat ggccaagtac 480atccagcaca ccccgccgca accgccggag tggggcatgc cggagatgcg cgaatcgtgg 540aaggtgctgg tgaagccgga ggaccggccg aagaaacagc tcaacgacct cgacctgccc 600aacctgttct cggtgaccct gcgcgacgcc gggcagatcg ccctggtcga cggcgacagc 660aaaaagatcg tcaaggtcat cgataccggc tatgccgtgc atatctcgcg gatgtccgct 720tccggccgct acctgctggt gatcggccgc gacgcgcgga tcgacatgat cgacctgtgg 780gccaaggagc cgaccaaggt cgccgagatc aagatcggca tcgaggcgcg ctcggtggaa 840agctccaagt tcaagggcta cgaggaccgc tacaccatcg ccggcgccta ctggccgccg 900cagttcgcga tcatggacgg cgagaccctg gaaccgaagc agatcgtctc cacccgcggc 960atgaccgtag acacccagac ctaccacccg gaaccgcgcg tggcggcgat catcgcctcc 1020cacgagcacc ccgagttcat cgtcaacgtg aaggagaccg gcaaggtcct gctggtcaac 1080tacaaggata tcgacaacct caccgtcacc agcatcggtg cggcgccgtt cctccacgac 1140ggcggctggg acagcagcca ccgctacttc atgaccgccg ccaacaactc caacaaggtt 1200gccgtgatcg actccaagga ccgtcgcctg tcggccctgg tcgacgtcgg caagaccccg 1260cacccggggc gtggcgccaa cttcgtgcat cccaagtacg gcccggtgtg gagcaccagc 1320cacctgggcg acggcagcat ctcgctgatc ggcaccgatc cgaagaacca tccgcagtac 1380gcctggaaga aagtcgccga actacagggc cagggcggcg gctcgctgtt catcaagacc 1440catccgaagt cctcgcacct ctacgtcgac accaccttca accccgacgc caggatcagc 1500cagagcgtcg cggtgttcga cctgaagaac ctcgacgcca agtaccaggt gctgccgatc 1560gccgaatggg ccgatctcgg cgaaggcgcc aagcgggtgg tgcagcccga gtacaacaag 1620cgcggcgatg aagtctggtt ctcggtgtgg aacggcaaga acgacagctc cgcgctggtg 1680gtggtggacg acaagaccct gaagctcaag gccgtggtca aggacccgcg gctgatcacc 1740ccgaccggta agttcaacgt ctacaacacc cagcacgacg tgtactgaga cccgcgtgcg 1800gggcacgccc cgcacgctcc cccctacgag gaaccgtgat gaaaccgtac gcactgcttt 1860cgctgctcgc ca 1872183451DNAPseudomonas aeruginosa 18tcgagacggg aagccactct ctacgagaag acagaagccc ctcacagagg cctctgtcta 60cgcctactaa agctcggctt attcatatgt atttatattc tttcaataga tcactcagcg 120ctattttaag ttcaccctct gtaagttcac ctgggcgctc tttctttcct tcggtaaagc 180tgtcggccag accaaacatt aaactcaagc atctcccaag cgatgcatca tcttgggcca 240gcatccctga atcgcgcgtc ggacctccaa gtcttaaaaa attcttcgct gaaggttttc 300ccatcaatcg atgaggctaa tagcttcttt gcaatatcta tcatttccat gctcacctta 360aagcacctca tttttcatgt aaaaattgta ttgatccgtg ccagactcaa tcctccaccc 420agaaacaaac atcccatcct ctccaatgat aacaacaata ttagtcctgg cattgtaatg 480tacttttgag tttacttcgg agtggtaagt ccctttttct acggttgcag gatcagcaag 540gtgctcaaga attttatccc taaactctgc aagcgttcca ttgttggcgc ttttttcacc 600cagcccaaaa tcatatttgt ggctatcaaa ttttttctgt agttgcctcc gtgtgaagat 660accactatca agaggactac tgagcattac ataaacaggt ttgactccag aatccgccgg 720gaaaatcacg atcagatcgt ttaggtccag tagcattccc ggataggact ccgggccggt 780cttcaacggt gtgagggccg ctccctcata taccggcacc ggcttcggta tgaccggagt 840ggtactcgaa gggttctggt ttcctggagg actcgccggc gtccaagtca ggatcagtgg 900cggcgcttct gcgaccgtag agggaaccgt aacctcgtac agtcctgttg cggcgttata 960ggccccatcc ggaccggaac gctttcggaa cgctcacacc atcggtctga ccaccgaaag 1020gtcgtcgtgt tgcctcgcgc ctcgttggtc aggcgcatcg gcagatcgac ggtaccgctg 1080gcttttgcaa ccgcgttcag gtttacgctt gggggaagcc ccaatttagc ggcatccatg 1140cccagggcgt aacgaacgct atcgggcgtt tggtcctgcc attgctcggc agtccgggag 1200agtaggtcag actggcaagc cacggccatc accgaggtgc tgaagccagg accgccagga 1260cggcaatcgc atcggagatc gcttgagcaa gggatgcggc gcctgtgcga cctggatcag 1320accccgctgc ggcggtggcg cacccgctgc cattggctgg catggcataa gtattggcag 1380ccctgatcgc cgcttgacga gcgatttcct tgcgccttgc cgtttcggcg ttcagcttgt 1440ccagccgtgc ttgcaggctg gcgatttcat ccactaggta ggacatcggc gttgtaggtt 1500gccttttgtt tctccagtgc attgggtgcc ttggcaatca aggcattgtt tgcagtctgc 1560aattcttctt attgcgatcg cctgcgtaag gagttgagta gcgcgttcaa gccactgctc 1620tggcgttgga ttggtcagtt gaggcaaagc attcccagcc tggtcaagct cggactgcac 1680ttttttctcg acatttgcct tcctggcctt gtagtccgcc tccacctcag cagcggctcg 1740ctgggcttct gcttccaatg accgggcttt attctccagc tcttgagacg tttgtttcaa 1800gatagcgatt tgcgccttat agatatcggc gctgtacgct ttggccagct cactcatatg 1860gcgatccagg aactctccat agaattttcg gctggccagc aactgactct ggtacatcga 1920ctctgacttc tgaggaaagt ctgaagccgt ataaagattg gccgggcgat cctcaatgac 1980ctttagcgat tttgctttgg catccatgag tgcatcaacg atactctttt catcgcggat 2040gtcattggca ctgaccgctt tacctggcaa ccccgcttca ctcttgagtt catcaacctc 2100cttcagggtt tcatttttca ggtttttctt gagttctgaa tgggacttat caagcgtact 2160tcttagcttc ctgtactcct gcattccagt accgacatac ggacttggtc ctggtgggac 2220aaatggtgga gtaccgtagc ttgatcgagc aggaatatac tggattatgt cacgcccacc 2280accctgcaca tgtgtaataa ccatcgaacc aggttcgtaa tcattgacag ccatagatcg 2340cccctacatt aatttgaaag tgtaatgtat tgagcgactc ccacctagag aaccctctcc 2400cagtcaataa gccccaatgc atcggcaata cactgcaatc aacttcaata tcccgtgttt 2460agatgatcca gaaggtgcgc tctctcgcct cttataatcg cgcctgcgtc aaacggtcat 2520ttccttaacg cacacctcat ctaccccggc cagtcacgga agccgcatac cttcggttca 2580ttaacgaact cccactttca aaattcatcc atgccgcccc ttcgcgagct tccggacaaa 2640gccacgctga ttgcgagccc agcgtttttg attgcaagcc gctgcagctg gtcaggccgt 2700ttccgcaacg cttgaagtcc tggccgatat accggcaggg ccagccatcg ttcgacgaat 2760aaagccacct cagccatgat gccctttcca tccccagcgg aaccccgaca tggacgccaa 2820agccctgctc ctcggcagcc tctgcctggc cgccccattc gccgacgcgg cgacgctcga 2880caatgctctc tccgcctgcc tcgccgcccg gctcggtgca ccgcacacgg cggagggcca 2940gttgcacctg ccactcaccc ttgaggcccg gcgctccacc ggcgaatgcg gctgtacctc 3000ggcgctggtg cgatatcggc tgctggccag gggcgccagc gccgacagcc tcgtgcttca 3060agagggctgc tcgatagtcg ccaggacacg ccgcgcacgc tgaccctggc ggcggacgcc 3120ggcttggcga gcggccgcga actggtcgtc accctgggtt gtcaggcgcc tgactgacag 3180gccgggctgc caccaccagg ccgagatgga cgccctgcat gtatcctccg atcggcaagc 3240ctcccgttcg cacattcacc actctgcaat ccagttcata aatcccataa aagccctctt 3300ccgctccccg ccagcctccc cgcatcccgc accctagacg ccccgccgct ctccgccggc 3360tcgcccgaca agaaaaacca accgctcgat cagcctcatc cttcacccat cacaggagcc 3420atcgcgatgc acctgatacc ccattggatc c 345119744DNAPseudomonas aeruginosa 19gggttcagca agcgttcagg ggcggttcag taccctgtcc gtactctgca agccgtgaac 60gacacgactc tcgcagaacg gagaaacacc atgaaagcac tcaagactct cttcatcgcc 120accgccctgc tgggttccgc cgccggcgtc caggccgccg acaacttcgt cggcctgacc 180tggggcgaga ccagcaacaa catccagaaa tccaagtcgc tgaaccgcaa cctgaacagc 240ccgaacctcg acaaggtgat cgacaacacc ggcacctggg gcatccgcgc cggccagcag 300ttcgagcagg gccgctacta cgcgacctac gagaacatct ccgacaccag cagcggcaac 360aagctgcgcc agcagaacct gctcggcagc tacgacgcct tcctgccgat cggcgacaac 420aacaccaagc tgttcggcgg tgccaccctc ggcctggtca agctggaaca ggacggcaag 480ggcttcaagc gcgacagcga tgtcggctac gctgccgggc tgcaggccgg tatcctgcag 540gagctgagca agaatgcctc gatcgaaggc ggctatcgtt acctgcgcac caacgccagc 600accgagatga ccccgcatgg cggcaacaag ctgggctccc tggacctgca cagcagctcg 660caattctacc tgggcgccaa ctacaagttc taaatgaccg cgcagcgccc gcgagggcat 720gcttcgatgg ccgggccgga aggt 744202760DNAPseudomonas aeruginosa 20ctgcagctgg tcaggccgtt tccgcaacgc ttgaagtcct ggccgatata ccggcagggc 60cagccatcgt tcgacgaata aagccacctc agccatgatg ccctttccat ccccagcgga 120accccgacat ggacgccaaa gccctgctcc tcggcagcct ctgcctggcc gccccattcg 180ccgacgcggc gacgctcgac aatgctctct ccgcctgcct cgccgcccgg ctcggtgcac 240cgcacacggc ggagggccag ttgcacctgc cactcaccct tgaggcccgg cgctccaccg 300gcgaatgcgg ctgtacctcg gcgctggtgc gatatcggct gctggccagg ggcgccagcg 360ccgacagcct cgtgcttcaa gagggctgct cgatagtcgc caggacacgc cgcgcacgct 420gaccctggcg gcggacgccg gcttggcgag cggccgcgaa ctggtcgtca ccctgggttg 480tcaggcgcct gactgacagg ccgggctgcc accaccaggc cgagatggac gccctgcatg 540tatcctccga tcggcaagcc tcccgttcgc acattcacca ctctgcaatc cagttcataa 600atcccataaa agccctcttc cgctccccgc cagcctcccc gcatcccgca ccctagacgc 660cccgccgctc tccgccggct cgcccgacaa gaaaaaccaa ccgctcgatc agcctcatcc 720ttcacccatc acaggagcca tcgcgatgca cctgataccc cattggatcc ccctggtcgc 780cagcctcggc ctgctcgccg gcggctcgtc cgcgtccgcc gccgaggaag ccttcgacct 840ctggaacgaa tgcgccaaag cctgcgtgct cgacctcaag gacggcgtgc gttccagccg 900catgagcgtc gacccggcca tcgccgacac caacggccag ggcgtgctgc actactccat 960ggtcctggag ggcggcaacg acgcgctcaa gctggccatc gacaacgccc tcagcatcac 1020cagcgacggc ctgaccatcc gcctcgaagg cggcgtcgag ccgaacaagc cggtgcgcta 1080cagctacacg cgccaggcgc gcggcagttg gtcgctgaac tggctggtac cgatcggcca 1140cgagaagccc tcgaacatca aggtgttcat ccacgaactg aacgccggca accagctcag 1200ccacatgtcg ccgatctaca ccatcgagat gggcgacgag ttgctggcga agctggcgcg 1260cgatgccacc ttcttcgtca gggcgcacga gagcaacgag atgcagccga cgctcgccat 1320cagccatgcc ggggtcagcg tggtcatggc ccagacccag ccgcgccggg aaaagcgctg 1380gagcgaatgg gccagcggca aggtgttgtg cctgctcgac ccgctggacg gggtctacaa 1440ctacctcgcc cagcaacgct gcaacctcga cgatacctgg gaaggcaaga tctaccgggt 1500gctcgccggc aacccggcga agcatgacct ggacatcaaa cccacggtca tcagtcatcg 1560cctgcacttt cccgagggcg gcagcctggc cgcgctgacc gcgcaccagg cttgccacct 1620gccgctggag actttcaccc gtcatcgcca gccgcgcggc tgggaacaac tggagcagtg 1680cggctatccg gtgcagcggc tggtcgccct ctacctggcg gcgcggctgt cgtggaacca 1740ggtcgaccag gtgatccgca acgccctggc cagccccggc agcggcggcg acctgggcga 1800agcgatccgc gagcagccgg agcaggcccg tctggccctg accctggccg ccgccgagag 1860cgagcgcttc gtccggcagg gcaccggcaa cgacgaggcc ggcgcggcca acgccgacgt 1920ggtgagcctg acctgcccgg tcgccgccgg tgaatgcgcg ggcccggcgg acagcggcga 1980cgccctgctg gagcgcaact atcccactgg cgcggagttc ctcggcgacg gcggcgacgt 2040cagcttcagc acccgcggca cgcagaactg gacggtggag cggctgctcc aggcgcaccg 2100ccaactggag gagcgcggct atgtgttcgt cggctaccac ggcaccttcc tcgaagcggc 2160gcaaagcatc gtcttcggcg gggtgcgcgc gcgcagccag gacctcgacg cgatctggcg 2220cggtttctat atcgccggcg atccggcgct ggcctacggc tacgcccagg accaggaacc 2280cgacgcacgc ggccggatcc gcaacggtgc cctgctgcgg gtctatgtgc cgcgctcgag 2340cctgccgggc ttctaccgca ccagcctgac cctggccgcg ccggaggcgg cgggcgaggt 2400cgaacggctg atcggccatc cgctgccgct gcgcctggac gccatcaccg gccccgagga 2460ggaaggcggg cgcctggaga ccattctcgg ctggccgctg gccgagcgca ccgtggtgat 2520tccctcggcg atccccaccg acccgcgcaa cgtcggcggc gacctcgacc cgtccagcat 2580ccccgacaag gaacaggcga tcagcgccct gccggactac gccagccagc ccggcaaacc 2640gccgcgcgag gacctgaagt aactgccgcg accggccggc tcccttcgca ggagccggcc 2700ttctcggggc ctggccatac atcaggtttt cctgatgcca gcccaatcga atatgaattc 276021172DNAStaphylococcus saprophyticus 21ttgatgaaat gcatcgatta ataaattttc atgtacgatt aaaacgtttt tacccttacc 60ttttcgtact acctctgcct gaagttgacc acctttaaag tgattcgttg aaatccatta 120tgctcattat taatacgatc tataaaaaca aatggaatgt gatgatcgat ga 17222155DNAStaphylococcus saprophyticus 22gttccattga ctctgtatca cctgttgtaa cgaacatcca tatgtcctga aactccaacc 60acaggtttga ccacttccaa tttcagacca ccaagtttga cacgtgaaga ttcatcttct 120aatatttcgg aattaatatc atattattta aatag 15523145DNAStaphylococcus saprophyticus 23acatagaaaa actcaaaaga tttacttttt tcaaatggaa aataagggta cacacgatat 60ttcccgtcat cttcagttac cggtacaaca tcctctttat taacctgcac ataatctgac 120tccgcttcac tcatcaaact actaa 14524266DNAStaphylococcus saprophyticus 24tttcactgga attacatttc gctcattacg tacagtgaca atcgcgtcag atagtttctt 60ctggttagct tgactcttaa caatcttgtc taaattttgt ttaattcttt gattcgtact 120agaaatttta cttctaattc cttgtaattc ataacttgca ttatcatata aatcataagt 180atcacatttt tgatgaatac tttgatataa atctgacaat acaggcagtt gctccattct 240atcgttaaga atagggtaat taatag 26625845DNAHaemophilus influenzae 25tgttaaattt ctttaacagg gattttgtta tttaaattaa acctattatt ttgtcgcttc 60tttcactgca tctactgctt gagttgcttt ttctgaaacc gcctctttca tttcacttgc 120tttttctgat gctgcttctt tcatttcgcc tactttttct gacgctgctt ctgttgctga 180tttaattact tctttcgcat cttccacttt ctctgctact ttatttttca cgtctgtaga 240aagctgctgt gctttttcct ttacttcagt cattgtatta gctgcagcat cttttgtttc 300tgatgcgact gatgctacag tttgcttcgt atcctcaact ttttgttttg cttcttgctt 360atcaaaacaa cctgtcacga ctaaagctga acctaaaacc aatgctaatg ttaatttttt 420cattattttc tccatagaat aatttgattg ttacaaagcc ctattacttt gatgcagttt 480agtttacggg aattttcata aaaagaaaaa cagtaatagt aaaactttac ctttctttaa 540aaagattact ttataaaaaa acatctaaga tattgatttt taatagatta taaaaaacca 600ataaaaattt tattttttgt aaaaaaaaag aatagtttat tttaaataaa ttacaggaga 660tgcttgatgc atcaatattt ctgatttatt accatcccat aataattgag caatagttgc 720aggataaaat gatattggat ttcgttttcc atacagttca gcaacaattt ctcccactaa 780gggcaaatgg gaaacaatta atacagattt aacgccctcg tcttttagca cttctaaata 840atcaa 845261598DNAHaemophilus influenzae 26gaatagagtt gcactcaata gattcgggct ttataattgc ccagattttt atttataaca 60aagggttcca aatgaaaaaa tttaatcaat ctctattagc aactgcaatg ttgttggctg 120caggtggtgc aaatgcggca gcgtttcaat tggcggaagt ttctacttca ggtcttggtc 180gtgcctatgc gggtgaagcg gcgattgcag ataatgcttc tgtcgtggca actaacccag 240ctttgatgag tttatttaaa acggcacagt tttccacagg tggcgtttat attgattcta 300gaattaatat gaatggtgat gtaacttctt atgctcagat aataacaaat cagattggaa 360tgaaagcaat aaaggacggc tcagcttcac agcgtaatgt tgttcccggt gcttttgtgc 420caaatcttta tttcgttgcg ccagtgaatg ataaattcgc gctgggtgct ggaatgaatg 480tcaatttcgg tctaaaaagt gaatatgacg atagttatga tgctggtgta tttggtggaa 540aaactgactt gagtgctatc aacttaaatt taagtggtgc ttatcgagta acagaaggtt 600tgagcctagg tttaggggta aatgcggttt atgctaaagc ccaagttgaa cggaatgctg 660gtcttattgc ggatagtgtt aaggataacc aaataacaag cgcactctca acacagcaag 720aaccattcag agatcttaag aagtatttgc cctctaagga caaatctgtt gtgtcattac 780aagatagagc cgcttggggc tttggctgga atgcaggtgt aatgtatcaa tttaatgaag 840ctaacagaat tggtttagcc tatcattcta aagtggacat tgattttgct gaccgcactg 900ctactagttt agaagcaaat gtcatcaaag aaggtaaaaa aggtaattta acctttacat 960tgccagatta cttagaactt tctggtttcc atcaattaac tgacaaactt gcagtgcatt 1020atagttataa atatacccat tggagtcgtt taacaaaatt acatgccagc ttcgaagatg 1080gtaaaaaagc ttttgataaa gaattacaat acagtaataa ctctcgtgtt gcattagggg 1140caagttataa tctttatgaa aaattgacct tacgtgcggg tattgcttac gatcaagcgg 1200catctcgtca tcaccgtagt gctgcaattc cagataccga tcgcacttgg tatagtttag 1260gtgcaaccta taaattcacg ccgaatttat ctgttgatct tggctatgct tacttaaaag 1320gcaaaaaagt tcactttaaa gaagtaaaaa caataggtga caaacgtaca ttgacattga 1380atacaactgc aaattatact tctcaagcac acgcaaatct ttacggtttg aatttaaatt 1440atagtttcta atccgttaaa aaatttagca taataaagca caattccaca ctaagtgtgc 1500ttttctttta taaaacaagg cgaaaaatga ccgcacttta ttacacttat tacccctcgc 1560cagtcggacg gcttttgatt ttatctgacg gcgaaaca 1598279100DNAHaemophilus influenzae 27gtcaaaaatt gcgtgcattc tagcgaaaaa atgggctttt gggaactgtg ggatttattt 60aaaatcttag aaaatcttac cgcactttta agctataaag tgcggtgaaa tttagtggcg 120tttataatgg agaattactc

tggtgtaatc cattcgactg tccagcttcc agtaccttct 180ggaactaatg tttttgtgag ataaggcaaa atttctttca tttgggtttc taatgtccaa 240ggtggattaa ttaccaccat accgctcgca gtcattcctc gttgatcgct atctgggcga 300acggcgagtt caatttttag aatttttcta attcccgttg cttctaaacc cttaaaaata 360cgtttagttt gttggcgtaa tacaacagga taccaaatcg cataagtgcc agtggcaaaa 420cgtttatagc cctcttcaat ggctttaaca acgagatcat aatcatcttt taattcataa 480ggcggatcga tgagtactaa gcctcggcgt tcttttggcg gaagcgttgc tttgacttgt 540tgaaagccat tgtcacattt tacggtgaca tttttgtcgt cgctaaaatt attgcgaaga 600attggataat cgctaggatg aagctcggtc aatagtgcgc gatcttgtga gcgcaacaat 660tccgcggcaa ttaatggaga acccgcgtaa taacgtagtt ctttgccacc ataattgagt 720tttttgatca tttttacata acgagcaata tcttcgggta aatctgtttg atcccacagg 780cgtccaatac cttctttata ttcccccgtt ttttctgatt catttgagga taaacgataa 840cgccccacac cagagtgcgt atccaaataa aaaaagcctt tttctttgag tttaagattt 900tccaaaatga gcattaaaac aatatgtttc aagacatcgg catgattgcc agcgtgaaat 960gagtgatgat aactcagcat aatatattcc ttatatattc cttatttgtt taataacgaa 1020ggcgagccaa ttgactcgcc cgattacaca ctaaagtgcg gtcattttta gaagagttct 1080tgtggttgcg tcgctggcgt attgccttca ttatttaagc gttgctgtaa ctcagtagga 1140acataataac cacgctcttg catttccgaa agataggtac gtgtcggttc tgttcccgca 1200ataaaatatt ctttgcgccc accgtttgga gaaagcaaac ctgtcaaagt atcaatgttt 1260ttttccacaa tttttggcgg tagcgacaat ttacgttctg gcttatcact caaagccgtt 1320ttcatataag tgatccaagc aggcattgct gtttttgctc ctgcttctcc acgcccaagt 1380actcgtttgt tatcatcaaa cccgacataa gttgtggtta ctaagtttgc accaaatccc 1440gcataccaag ccacttttga actgttggta gtacctgttt taccgcctat atcgctacgt 1500ttaatgcttt gtgcaatacg ccagctggtg cctttccagt ctaaaccttg ttcgccataa 1560attgccgtat ttaaggcact acgaatgaga aaagcaagtt cgccactaat gacacgtggc 1620gcatattcta ttttcgacga agcatttttt gcagcagcca ttaaatcaat cgcatcttct 1680ttaagtgcgg tcatatttga ttgtaattct ggcagttcag gcacagtttc aggttgttga 1740tctaattctt cgccattggt gctgtcatct gttggtttta aggcattctc gcctaaagga 1800atattggcaa agccgttgat tttgtctttg gtttcgccat aaattacagg tatatcatta 1860cattcaatgc aagcaatttt agggtttgca ataaataagt ctttacccgt gttatcttga 1920attttttcaa tgatataagg ttcaatgagg aagccaccat tatcaaacac cgcataagct 1980cgcgccattt ctaatggtgt gaaagaggct gcgccaagtg ctaaggcttc actggcaaaa 2040tattgatcac gtttaaaacc aaaacgttgt aaaaattctg ctgtgaaatc aatacctgcc 2100gtttggatag cacgaatagc aattatattt ttggattgac ctaatcctac gcgtaaacgc 2160atcgggccat cataacgatc aggcgagttt ttcggttgcc acattttttg tcccggtttt 2220tgaatagaaa tcgggctgtc ttgtaatacg cttgaaagtg ttaagccttt ttctaatgct 2280gccgcgtaaa taaatggttt gatagaagaa cccacttgaa ctaaagactg tgtggctcga 2340ttgaatttac tttgttcata gctaaagcca ccgaccactg cttcaatcgc accattatct 2400gaattaagag aaactaatgc tgaatttgct gcgggaattt gtcctaattg ccattcccca 2460ttagcacgct gatgaatcca aatttgctcg ccgactttca caggattgct tctgcctgtc 2520caacgcattg cattggttga taaggtcatt ttttccccag aagcgagcaa tatatcagca 2580ccgcctttta caattccaat cactgccgca ggaataaatg gctctgaatc aggtagtttg 2640cgtagaaaac cgacaatgcg atcattgtcc caagcggctt catttttttg ccataatggc 2700gcgccaccgc gataaccgtg acgcatatcg taatcaatca agttattacg cacagctttt 2760tgggcttcag cttggtcttt tgaaagtaca gtggtaaata ctttataacc actggtgtaa 2820gcattttctt cgccaaaacg acgcaccatt tcttgacgca ccatttcagt gacataatcg 2880gctcgaaatt caaattttgc gccgtgatag ctcgccacaa tcggctcttt caatgcagca 2940tcatattctt ctttgctgat gtatttttca tctaacatac ggcttagcac cacattgcgg 3000cgttcttctg aacgttttaa agaataaagc gggttcattg ttgaaggtgc tttaggtaaa 3060ccagcaataa tcgccatttc cgataaggtc aattcattca atgatttacc gaaataggtt 3120tgtgctgccg ctgcaacacc ataagaacga tagcctaaaa agattttgtt taaataaagc 3180tctaatattt cttgtttgtt gagagtattt tcgatttcta ccgcaagcac ggcttcacga 3240gctttacgaa taatggtttt ttctgaggtt aagaaaaagt tacgcgctaa ttgttgagta 3300atcgtacttg cgccttgtga tgcaccgcca ttactcactg cgacaaacaa tgcacgggca 3360atgccgatag ggtctaatcc gtgatgatcg taaaaacgac tgtcttccgt cgctaaaaat 3420gcgtcaatta agcgttgtgg cacatcggct aatttcactg gaatacggcg ttgctcaccc 3480acttcgccaa ttaatttacc gtcagccgta taaatctgca ttggttgctg taattcaacg 3540gtttttaatg tttctactga gggcaattca gattttaagt ggaaatacaa cattccgcct 3600gctactaaac ctaaaataca taaagttaat agggtgttta atattaattt tgcgatccgc 3660atcgtaaaat tctcgcttcg ttaatgaata ttcttgtcaa gagacctatg atttggctgt 3720taagtataaa agattcagcc tttaaagaat aggaaagaat atgcaattct ccctgaaaaa 3780ttaccgcact ttacaaatcg gcattcatcg taagcagagt tattttgatt ttgtgtggtt 3840tgatgatctc gaacagccac aaagttatca aatctttgtt aatgatcgtt attttaaaaa 3900tcgtttttta caacagctaa aaacacaata tcaagggaaa acctttcctt tgcagtttgt 3960agcaagcatt cccgcccact taacttggtc gaaagtatta atgttgccac aagtgttaaa 4020tgcgcaagaa tgtcatcaac aatgtaaatt tgtgattgaa aaagagctgc ctattttttt 4080agaagaattg tggtttgatt atcgttctac cccgttaaag caaggttttc gattagaggt 4140tactgcaatt cgtaaaagta gcgctcaaac ttatttgcaa gattttcagc catttaatat 4200taatatattg gatgttgcgt caaatgctgt tttgcgtgca tttcaatatc tgttgaatga 4260acaagtgcgg tcagaaaata ccttattttt atttcaagaa gatgactatt gcttggcgat 4320ttgtgaaaga tctcagcaat cacaaatttt acaatctcac gaaaatttga ccgcacttta 4380tgaacaattt accgaacgtt ttgaaggaca acttgaacaa gtttttgttt atcaaattcc 4440ctcaagtcat acaccattac ccgaaaactg gcagcgagta gaaacagaac tcccttttat 4500tgcgctgggc aacgcgctat ggcaaaaaga tttacatcaa caaaaagtgg gtggttaaat 4560gtcgatgaat ttattgcctt ggcgtactta tcaacatcaa aagcgtttac gtcgtttagc 4620tttttatatc gctttattta tcttgcttgc tattaattta atgttggctt ttagcaattt 4680gattgaacaa cagaaacaaa atttgcaggc acagcaaaag tcgtttgaac aacttaatca 4740acagcttcat aaaactacca tgcaaattga tcagttacgc attgcggtga aagttggtga 4800agttttgaca tctattccca acgagcaagt aaaaaagagt ttacaacagc taagtgaatt 4860accttttcaa caaggagaac tgaataaatt taaacaagat gccaataact taagcttgga 4920aggtaacgcg caagatcaaa cagaatttga actgattcat caatttttaa agaaacattt 4980tcccaatgtg aaattaagtc aggttcaacc tgaacaagat acattgtttt ttcactttga 5040tgtggaacaa ggggcggaaa aatgaaagct ttttttaacg atccttttac tccttttgga 5100aaatggctaa gtcagccttt ttatgtgcac ggtttaacct ttttattgct attaagtgcg 5160gtgatttttc gccccgtttt agattatata gaggggagtt cacgtttcca tgaaattgaa 5220aatgagttag cggtgaaacg ttcagaattg ttgcatcaac agaaaatttt aacctcttta 5280caacagcagt cggaaagtcg aaaactttct ccagaactgg ctgcacaaat tattcctttg 5340aataaacaaa ttcaacgttt agctgcgcgt aacggtttat ctcagcattt acgttgggaa 5400atggggcaaa agcctatttt gcatttacag cttacaggtc attttgaaaa aacgaagaca 5460tttttatccg cacttttggc taattcgtca cagctttctg taagtcggtt gcaatttatg 5520aaacccgaag acggcccatt gcaaaccgag atcatttttc agctagataa ggaaacaaaa 5580tgaaacattg gtttttcctg attatattat tttttatgaa ttgcagttgg ggacaagatc 5640ctttcgataa aacacagcgt aaccgttctc agtttgataa cgcacaaaca gtaatggagc 5700aaacagaaat aatttcctca gatgtgccta ataatctatg cggagcggat gaaaatcgcc 5760aagcggctga aattcctttg aacgctttaa aattggtggg ggtagtgatt tctaaagata 5820aagcctttgc cttgttgcaa gatcaaggtt tgcaagttta cagcgtttta gagggcgttg 5880atgtggctca agagggctat attgtagaaa aaatcaacca aaacaatgtt caatttatgc 5940gtaagctagg agagcaatgt gatagtagtg aatggaaaaa attaagtttt taaaggaaga 6000ttatgaagaa atatttttta aagtgcggtt attttttagt atgtttttgt ttgccattaa 6060tcgtttttgc taatcctaaa acagataacg aacgtttttt tattcgttta tcgcaagcac 6120ctttagctca aacactggag caattagctt ttcaacaaga tgtgaattta gtgattggag 6180atatattgga aaacaagatc tctttgaaat taaacaatat tgatatgcca cgtttgctac 6240aaataatcgc aaaaagtaag catcttactt tgaataaaga tgatgggatt tattatttaa 6300acggcagtca atctggcaaa ggtcaggttg caggaaatct tacgacaaat gaaccgcact 6360tagtgagtca cacggtaaaa ctccattttg ctaaagcttc tgaattaatg aaatccttaa 6420caacaggaag tggctctttg ctttctcccg ctgggagcat tacctttgat gatcgcagta 6480atttgctggt tattcaggat gaacctcgtt ctgtgcaaaa tatcaaaaaa ctgattgctg 6540aaatggataa gcctattgaa cagatcgcta ttgaagcgcg aattgtgaca attacggatg 6600agagtttgaa agaacttggc gttcggtggg ggatttttaa tccaactgaa aatgcaagac 6660gagttgcggg cagccttaca ggcaatagct ttgaaaatat tgcggataat cttaatgtaa 6720attttgcgac aacgacgaca cctgctggct ctatagcatt acaagtcgcc aaaattaatg 6780ggcgattgct tgatttagaa ttgagtgcgt tggagcgtga aaataatgta gaaattattg 6840caagccctcg cttactcact accaataaga aaagtgcgag cattaaacag gggacagaaa 6900ttccttacat cgtgagtaat actcgtaacg atacgcaatc tgtggaattt cgtgaggcgg 6960tgcttggttt ggaagtgacg ccacatattt ctaaagataa caatatctta cttgatttat 7020tggtaagtca aaattcccct ggttctcgtg tcgcttatgg acaaaatgag gtggtttcta 7080ttgataaaca agaaattaat actcaggttt ttgccaaaga tggggaaacc attgtgcttg 7140gcggcgtatt tcacgataca atcacgaaaa gcgaagataa agtgccattg cttggcgata 7200tacccgttat taaacgatta tttagcaaag aaagtgaacg acatcaaaaa cgtgagctag 7260tgattttcgt cacgccacat attttaaaag caggagaaaa cgttagaggc gttgaaacaa 7320aaaagtgagg gtaaaaaata actttttaaa tgatgaattt ttttaatttt cgctgtatcc 7380actgtcgtgg caatcttcat atcgcaaaaa atgggttatg ttcaggttgc caaaaacaaa 7440ttaaatcttt tccttattgc ggtcattgtg gttcggaatt gcaatattat gcgcagcatt 7500gtgggaattg tcttaaacaa gaaccaagtt gggataagat ggtcattatt gggcattata 7560ttgaacctct ttcgatattg attcagcgtt ttaaatttca aaatcaattt tggattgacc 7620gcactttagc tcggctttta tatcttgcgg tacgtgatgc taaacgaacg catcaactta 7680aattgccaga ggcaatcatt ccagtgcctt tatatcattt tcgtcagtgg cgacggggtt 7740ataatcaggc agatttatta tctcagcaat taagtcgttg gctggatatt cctaatttga 7800acaatatcgt aaagcgtgtg aaacacacct atactcaacg tggtttgagt gcaaaagatc 7860gtcgtcagaa tttaaaaaat gccttttctc ttgctgtttc gaaaaatgaa tttccttatc 7920gtcgtgttgc gttggtggat gatgtgatta ctactggttc tacactcaat gaaatctcaa 7980aattgttgcg aaaattaggt gtggaggaga ttcaagtgtg ggggctggca cgagcttaat 8040ataaagcact ggaaaaaaaa gcgcgataag cgtattattc ccgatacttt ctctcaagta 8100tttaggacat aattatggaa caagcaaccc agcaaatcgc tatttctgat gccgcacaag 8160cgcattttcg aaaactttta gacacccaag aagaaggaac gcatattcgt attttcgcgg 8220ttaatcctgg tacgcctaat gcggaatgtg gcgtatctta ttgccccccg aatgccgtgg 8280aagaaagcga tattgaaatg aaatataata ctttttctgc atttattgat gaagtgagtt 8340tgcctttctt agaagaagca gaaattgatt atgttaccga agagcttggt gcgcaactga 8400ccttaaaagc accgaatgcc aaaatgcgta aggtggctga tgatgcgcca ttgattgaac 8460gtgttgaata tgtaattcaa actcaaatta acccacagct tgcaaatcac ggtggacgta 8520taaccttaat tgaaattact gaagatggtt acgcagtttt acaatttggt ggtggctgta 8580acggttgttc aatggtggat gttacgttaa aagatggggt agaaaaacaa cttgttagct 8640tattcccgaa tgaattaaaa ggtgcaaaag atataactga gcatcaacgt ggcgaacatt 8700cttattatta gtgagttata aaagaagatt tataatgacc gcacttttga aagtgcggtt 8760atttttatgg agaaaaaatg aaaatacttc aacaagatga ttttggttat tggttgctta 8820cacaaggttc taatctgtat ttagtgaata atgaattgcc ttttggtatc gctaaagata 8880ttgatttgga aggattgcag gcaatgcaaa ttggggaatg gaaaaattat ccgttgtggc 8940ttgtggctga gcaagaaagt gatgaacgag aatatgtgag tttgagtaac ttgctttcac 9000tgccagagga tgaattccat atattaagcc gaggtgtgga aattaatcat tttctgaaaa 9060cccataaatt ctgtggaaag tgcggtcata aaacacaaca 910028525DNAMoraxella catarrhalis 28aaaaatcgac tgccgtcatt ttcaaccacc acatagctca tattcgcaag ccaatgtatt 60gaccgttggg aataataaca gccccaaaac aatgaaacat atggtgatga gccaaacata 120ctttcctgca gattttggaa tcatatcgcc atcagcacca gtatggtttg accagtattt 180aacgccatag acatgtgtaa aaaaattaaa taacggtgca agcatgagac caacggcacc 240tgatgtacct tgtacgatga cctcacctgc tgtggcaacc ataccaagtc cattgcctgt 300gatatttttg cgaaaagaca aacttaccac acagaccaag ccgatgattg agatgacaaa 360ataaaaccaa tccaaatgcg tgtgagctgt tgtggtccaa aatccagtaa atagtgcaat 420aaatccgcaa acaaaccaaa gtagcaccca gcttgttgtc caatcttttt taccaaagcc 480tgtgatgtta tctaaaatat caattttcat cagattttcc ctaat 52529466DNAMoraxella catarrhalis 29taatgataac cagtcaagca agctcaaatc agggtcagcc tgttttgagc tttttatttt 60ttgatcatca tgcttaagat tcactctgcc atttttttac aacctgcacc acaagtcatc 120atcgcatttg caaaaatggt acaaacaagc cgtcagcgac ttaaacaaaa aaaggctcaa 180tctgcgtgtg tgcgttcact tttacaaatc accatgcacc gctttgacat tgttggtgaa 240tttcatgacc atgcacaccc ttattatatt aactcaaata aaatacgcta ctttgtcagc 300tttagccatt cagataatca agtcgctctc atcatcagct taacaccttg tgccattgac 360atagaagtta acgatattaa atacagtgtg gttgaacgat actttcatcc caatgaaatt 420tatctactta ctcaatttag ctctactgat aggcaacagc ttatta 46630631DNAStreptococcus pneumoniae 30gatctttgat tttcattgag tattactctc tcttgtcact tctttctatt ttaccataaa 60gtccagcctt tgaagaactt ttactagaag acaaggggct tctgtctcta tttgccatct 120taggcatcaa aaaagagggg tcatccctct ttacgaattc aatgctacta gggtatccaa 180atactggttg ttgatgactg ccaaaatata ggtatctgct ttcaagaggt catctggtcc 240aaattcaaca tccaatgggg aattttcctg ctctcggaaa cccaaaatat tcagattgta 300tttgccacgg aggtctaatt tacttcagac tttgacctgc ccaagactga ggaattttca 360tctccacgat agacacattt ttatccaact gaaagacatc aacactatta tgaaaagaat 420ggtctgtgct agagactgcc ccatttcata ctctggcgag ataaccgagt cagctccaat 480cttttctagc actttcttag cggtctgact tttgacctta gcaataacag tcggtacccc 540caaactctta cagtgcataa ccgcaagcac actcgactcc agattttcac ctgtcgcgac 600tacaacggta tcgcaggtat caatccctgc t 631313754DNAStreptococcus pneumoniae 31ccaatatttt ggtcagcata gtgttctttt tcagtggtaa cagcttgcaa tacttgagca 60gaaatggcag atttatcaag gaaaaagtta acgtaaggtc ctgttgcgac aactttttca 120aaggcttggc tgttcatttt ttcagccagt tcagccgcaa tcatttgtgg tgctttacgt 180tcgacttttg caagagaaaa agcagggaaa gcaatgtctc ccatttctga gtttttaggg 240gtttccagta actttaaaat agcctcttgg tccaggctat caatgatgct agataattcg 300ctagcaatca attcttttgt attcattaag agctcctttt tggacttttc tactatttta 360tcacaatttt aaagaaagaa gaaaaaattt ttgaaatctc ctgttttttt ggtataatat 420ggttataaat atagttataa atatagttat aaatatgcac gcaagaggat tttatgagaa 480aaagagatcg tcatcagtta ataaaaaaaa tgattactga ggagaaatta agtacacaaa 540aagaaattca agatcggttg gaggcgcaca atgtttgtgt gacgcagaca accttgtctc 600gtgatttgcg cgaaatcggc ttgaccaagg tcaagaaaaa tgatatggtg tattatgtac 660tagtaaatga gacagaaaag attgatttgg tggaattttt gtctcatcat ttagaaggtg 720ttgcaagagc agagtttacc ttggtgcttc ataccaaatt gggagaagcc tctgttttgg 780caaatattgt agatgtaaac aaggatgaat ggattttagg aacagttgct ggtgccaata 840ccttattggt tatttgtcga gatcagcacg ttgccaaact catggaagat cgtttgctag 900atttgatgaa agataagtaa ggtcttggga gttgctctca agacttattt ttgaaaagga 960gagacagaaa atggcgatag aaaagctatc acccggcatg caacagtatg tggatattaa 1020aaagcaatat ccagatgctt ttttgctctt tcggatgggt gatttttatg aattatttta 1080tgaggatgcg gtcaatgctg cgcagattct ggaaatttcc ttaacgagtc gcaacaagaa 1140tgccgacaat ccgatcccta tggcgggtgt tccctatcat tctgcccaac agtatatcga 1200tgtcttgatt gagcagggtt ataaggtggc tatcgcagag cagatggaag atcctaaaca 1260agcagttggg gttgttaaac gagaggttgt tcaggtcatt acgccaggga cagtggtcga 1320tagcagtaag ccggacagtc agaataattt tttggtttcc atagaccgcg aaggcaatca 1380atttggccta gcttatatgg atttggtgac gggtgacttt tatgtgacag gtcttttgga 1440tttcacgctg gtttgtgggg aaatccgtaa cctcaaggct cgagaagtgg tgttgggtta 1500tgacttgtct gaggaagaag aacaaatcct cagccgccag atgaatctgg tactctctta 1560tgaaaaagaa agctttgaag accttcattt attggatttg cgattggcaa cggtggagca 1620aacggcatct agtaagctgc tccagtatgt tcatcggact cagatgaggg aattgaacca 1680cctcaaacct gttatccgct acgaaattaa ggatttcttg cagatggatt atgcgaccaa 1740ggctagtctg gatttggttg agaatgctcg ctcaggtaag aaacaaggca gtcttttctg 1800gcttttggat gaaaccaaaa cggctatggg gatgcgtctc ttgcgttctt ggattcatcg 1860ccccttgatt gataaggaac gaatcgtcca acgtcaagaa gtagtgcagg tctttctcga 1920ccatttcttt gagcgtagtg acttgacaga cagtctcaag ggtgtttatg acattgagcg 1980cttggctagt cgtgtttctt ttggcaaaac caatccaaag gatctcttgc agttggcgac 2040taccttgtct agtgtgccac ggattcgtgc gattttagaa gggatggagc aacctactct 2100agcctatctc atcgcacaac tggatgcaat ccctgagttg gagagtttga ttagcgcagc 2160gattgctcct gaagctcctc atgtgattac agatggggga attatccgga ctggatttga 2220tgagacttta gacaagtatc gttgcgttct cagagaaggg actagctgga ttgctgagat 2280tgaggctaag gagcgagaaa actctggtat cagcacgctc aagattgact acaataaaaa 2340ggatggctac tattttcatg tgaccaattc gcaactggga aatgtgccag cccacttttt 2400ccgcaaggcg acgctgaaaa actcagaacg ctttggaacc gaagaattag cccgtatcga 2460gggagatatg cttgaggcgc gtgagaagtc agccaacctc gaatacgaaa tatttatgcg 2520cattcgtgaa gaggtcggca agtacatcca gcgtttacaa gctctagccc aaggaattgc 2580gacggttgat gtcttacaga gtctggcggt tgtggctgaa acccagcatt tgattcgacc 2640tgagtttggt gacgattcac aaattgatat ccggaaaggg cgccatgctg tcgttgaaaa 2700ggttatgggg gctcagacct atattccaaa tacgattcag atggcagaag ataccagtat 2760tcaattggtt acagggccaa acatgagtgg gaagtctacc tatatgcgtc agttagccat 2820gacggcggtt atggcccagc tgggttccta tgttcctgct gaaagcgccc atttaccgat 2880ttttgatgcg atttttaccc gtatcggagc agcagatgac ttggtttcgg gtcagtcaac 2940ctttatggtg gagatgatgg aggccaataa tgccatttcg catgcgacca agaactctct 3000cattctcttt gatgaattgg gacgtggaac tgcaacttat gacgggatgg ctcttgctca 3060gtccatcatc gaatatatcc atgagcacat cggagctaag accctctttg cgacccacta 3120ccatgagttg actagtctgg agtctagttt acaacacttg gtcaatgtcc acgtggcaac 3180tttggagcag gatgggcagg tcaccttcct tcacaagatt gaaccgggac cagctgataa 3240atcctacggt atccatgttg ccaagattgc tggcttgcca gcagaccttt tagcaagggc 3300ggataagatt ttgactcagc tagagaatca aggaacagag agtcctcctc ccatgagaca 3360aactagtgct gtcactgaac agatttcact ctttgatagg gcagaagagc atcctatcct 3420agcagaatta gctaaactgg atgtgtataa tatgacacct atgcaggtta tgaatgtctt 3480agtagagtta aaacagaaac tataaaacca agactcacta gttaatctag ctgtatcaag 3540gagacttctt tgacaattct ccactttttt gctagaataa catcacacaa acagaatgaa 3600aagggctgac gcattgtcgc tcccttttgt ctatttttta aggagaaagt atgctgattc 3660agaaaataaa aacctacaag tggcaggccc tgcttcgctc ctgatgacag gcttgatggt 3720tgctagttca cttctgcaac cgcgttatct gcag 3754321337DNAStreptococcus pyogenes 32aacaaaataa aagaacttac ctattttcca tccaaaatgt ttagcaatca tcatctgcaa 60ggcaacgtat tgcatggcat tgatgtgatg agcaactaat atgtcattag aacgttgcgt 120caaactagca tctaaataaa gatcgaaatg cagttatcaa aaatgcaagc tcctatcggc 180ccttgtttta attattactc acattgcctt aatgtattta cttgcttatt attaactttt 240ttgctaagtt agtagcgtca gttattcatt gaaaggacat tattatgaaa attcttgtaa 300caggctttga tccctttggc ggcgaagcta ttaatcctgc ccttgaagct atcaagaaat 360tgccagcaac cattcatgga gcagaaatca aatgtattga agttccaacg gtttttcaaa 420aatctgccga tgtgctccag cagcatatcg aaagctttca acctgatgca

gtcctttgta 480ttgggcaagc tggtggccgg actggactaa cgccagaacg cgttgccatt aatcaagacg 540atgctcgcat tcctgataac gaagggaatc agcctattga tacacctatt cgtgcagatg 600gtaaagcagc ttatttttca accttgccaa tcaaagcgat ggttgctgcc attcatcagg 660ctgggcttcc tgcttctgtt tctaatacag ctggtacctt tgtttgcaat catttgatgt 720atcaagccct ttacttagtg gataaatatt gtccaaatgc caaagctggg tttatgcata 780ttccctttat gatggaacag gttgttgata aacctaatac agctgccatg aacctcgatg 840atattacaag aggaattgag gctgctattt ttgccattgt cgatttcaaa gatcgttccg 900atttaaaacg tgtagggggc gctactcact gactgtgacg ctactaaacc tattttaaaa 960aaacagagat atgaactaac tctgtttttt ttgtgctaaa aatgaaagac ctagggaaac 1020ttttcatcgg tctttctcaa ttgtcatctt aatctaatac tacttctaac atcagcgggt 1080atagtttgcc agtaattaag aaacgttgtt gatctaaatg agcaatccca ttcaaaacat 1140taaggtcagg gtaatgggac ttatcaagat ttaaggcttt taacaaagga ctaatatcat 1200aggtggctac cacctttcca gaatcaggtt ggagtttgac aatagtattg gtttgccaaa 1260tattggcata gagataacca tctacatact ctaattcgtt aagcattgag atagggacac 1320tttctatagc aactagt 1337331837DNAStreptococcus pyogenes 33tcatgtttga cagcttatca tcgataagct tacttttcga atcaggtcta tccttgaaac 60aggtgcaaca tagattaggg catggagatt taccagacaa ctatgaacgt atatactcac 120atcacgcaat cggcaattga tgacattgga actaaattca atcaatttgt tactaacaag 180caactagatt gacaactaat tctcaacaaa cgttaattta acaacattca agtaactccc 240accagctcca tcaatgctta ccgtaagtaa tcataactta ctaaaacctt gttacatcaa 300ggttttttct ttttgtcttg ttcatgagtt accataactt tctatattat tgacaactaa 360attgacaact cttcaattat ttttctgtct actcaaagtt ttcttcattt gatatagtct 420aattccacca tcacttcttc cactctctct accgtcacaa cttcatcatc tctcactttt 480tcgtgtggta acacataatc aaatatcttt ccgtttttac gcactatcgc tactgtgtca 540cctaaaatat accccttatc aatcgcttct ttaaactcat ctatatataa catatttcat 600cctcctacct atctattcgt aaaaagataa aaataactat tgtttttttt gttattttat 660aataaaatta ttaatataag ttaatgtttt ttaaaaatat acaattttat tctatttata 720gttagctatt ttttcattgt tagtaatatt ggtgaattgt aataaccttt ttaaatctag 780aggagaaccc agatataaaa tggaggaata ttaatggaaa acaataaaaa agtattgaag 840aaaatggtat tttttgtttt agtgacattt cttggactaa caatctcgca agaggtattt 900gctcaacaag accccgatcc aagccaactt cacagatcta gtttagttaa aaaccttcaa 960aatatatatt ttctttatga gggtgaccct gttactcacg agaatgtgaa atctgttgat 1020caacttttat ctcacgattt aatatataat gtttcagggc caaattatga taaattaaaa 1080actgaactta agaaccaaga gatggcaact ttatttaagg ataaaaacgt tgatatttat 1140ggtgtagaat attaccatct ctgttattta tgtgaaaatg cagaaaggag tgcatgtatc 1200tacggagggg taacaaatca tgaagggaat catttagaaa ttcctaaaaa gatagtcgtt 1260aaagtatcaa tcgatggtat ccaaagccta tcatttgata ttgaaacaaa taaaaaaatg 1320gtaactgctc aagaattaga ctataaagtt agaaaatatc ttacagataa taagcaacta 1380tatactaatg gaccttctaa atatgaaact ggatatataa agttcatacc taagaataaa 1440gaaagttttt ggtttgattt tttccctgaa ccagaattta ctcaatctaa atatcttatg 1500atatataaag ataatgaaac gcttgactca aacacaagcc aaattgaagt ctacctaaca 1560accaagtaac tttttgcttt tggcaacctt acctactgct ggatttagaa attttattgc 1620aattctttta ttaatgtaaa aaccgctcat ttgatgagcg gttttgtctt atctaaagga 1680gctttacctc ctaatgctgc aaaattttaa atgttggatt tttgtatttg tctattgtat 1740ttgatgggta atcccatttt tcgacagaca tcgtcgtgcc acctctaaca ccaaaatcat 1800agacaggagc ttgtagctta gcaactattt tatcgtc 183734841DNAStreptococcus pneumoniae 34gatcaatatg tccaagaaac cacatgttcc taagacaaga gctaacagac tggccgtcaa 60taatagtatt gttctttttt tcatcattac tccttaacta gtgtttaact gattaattag 120ccagtaaata gtttatcttt atttacacta tctgttaaga tatagtaaaa tgaaataaga 180acaggacagt caaatcgatt tctaacaatg ttttagaagt agaggtatac tattctaatt 240tcaatctact atattttgca cattttcata aaaaaaatga gaactagaac tcacattctg 300ctctcatttt tcgttttccc gttctcctat cctgttttta ggagttagaa aatgctgcta 360cctttactta ctctccttta ataaagccaa tagtttttca gcttctgcca taatagtatt 420gttgtcctgg gtgccaaata gtaaattatt ttttaatcct gtgagagtct ctttggcatt 480ggacttgata attggattct ggatttttcc aagtaaatct tcagcctctc tcagttttct 540taacctttca gtctcgacct gaggttcttc tgattcctct ggtgattctt ctggtgattc 600ttcttctggt tcctctgttg gttttggaga ctctggtttc tcgctttgcg gtttctcttc 660tcgaggggtt tcttcctcag gtttttctgt ctgaggtttc tcctcgtttg gtttttccgt 720ttgattggta tcagcttgac catttttgtt tctttgaaca tggtcgctag cgttaccaaa 780accattatct gaatgcgacg ttcgtttgga tgttcgacat agtacttgac agtcgccaaa 840a 841354500DNAStreptococcus pneumoniae 35gatcaggaca gtcaaatcga tttctaacaa tgttttagaa gtagatgtgt actattctag 60tttcaatcta ttatatttat agaatttttt gttgctagat ttgtcaaatt gcttaaaata 120atttttttca gaaagcaaaa gccgatacct atcgagtagg gtagttcttg ctatcgtcag 180gcttgtctgt aggtgttaac acttttcaaa aatctcttca aacaacgtca gctttgcctt 240gccgtatata tgttactgac ttcgtcagtt ctatctgcca cctcaaaacg gtgttttgag 300ctgacttcgt cagttctatc cacaacctca aaacagtgtt ttgagctgac ttcgtcagtt 360ctatccacaa cctcaaaaca gtgttttgag ctgactttgt cagtcttatc tacaacctca 420aaacagtgtt ttgagcatca tgcggctagc ttcttagttt gctctttgat tttcattgag 480tataaaaaca gatgagtttc tgttttcttt ttatggacta taaatgttca gctgaaacta 540ctttcaagga cattattata taaaagaatt ttttgaaact aaaatctact atattacact 600atattgaaag cgttttaaaa atgaggtata ataaatttac taacacttat aaaaagtgat 660agaatctatc tttatgtata tttaaagata gattgctgta aaaatagtag tagctatgcg 720aaataacaga tagagagaag ggattgaagc ttagaaaagg ggaataatat gatatttaag 780gcattcaaga caaaaaagca gagaaaaaga caagttgaac tacttttgac agtttttttc 840gacagttttc tgattgattt atttcttcac ttatttggga ttgtcccctt taagctggat 900aagattctga ttgtgagctt gattatattt cccattattt ctacaagtat ttatgcttat 960gaaaagctat ttgaaaaagt gttcgataag gattgagcag gaagtatggt gtaaatagca 1020taagctgatg tccatcattt gcttataaag agatatttta gtttaattgc agcggtgtcc 1080tggtagataa actagattgg caggagtctg attggagaaa ggagagggga aatttggcac 1140caatttgaga tagtttgttt agttcatttt tgtcatttaa atgaactgta gtaaaagaaa 1200gttaataaaa gacaaactaa gtgcattttc tggaataaat gtcttatttc agaaatcggg 1260atatagatat agagaggaac agtatgaatc ggagtgttca agaacgtaag tgtcgttata 1320gcattaggaa actatcggta ggagcggttt ctatgattgt aggagcagtg gtatttggaa 1380cgtctcctgt tttagctcaa gaaggggcaa gtgagcaacc tctggcaaat gaaactcaac 1440tttcggggga gagctcaacc ctaactgata cagaaaagag ccagccttct tcagagactg 1500aactttctgg caataagcaa gaacaagaaa ggaaagataa gcaagaagaa aaaattccaa 1560gagattacta tgcacgagat ttggaaaatg tcgaaacagt gatagaaaaa gaagatgttg 1620aaaccaatgc ttcaaatggt cagagagttg atttatcaag tgaactagat aaactaaaga 1680aacttgaaaa cgcaacagtt cacatggagt ttaagccaga tgccaaggcc ccagcattct 1740ataatctctt ttctgtgtca agtgctacta aaaaagatga gtacttcact atggcagttt 1800acaataatac tgctactcta gaggggcgtg gttcggatgg gaaacagttt tacaataatt 1860acaacgatgc acccttaaaa gttaaaccag gtcagtggaa ttctgtgact ttcacagttg 1920aaaaaccgac agcagaacta cctaaaggcc gagtgcgcct ctacgtaaac ggggtattat 1980ctcgaacaag tctgagatct ggcaatttca ttaaagatat gccagatgta acgcatgtgc 2040aaatcggagc aaccaagcgt gccaacaata cggtttgggg gtcaaatcta cagattcgga 2100atctcactgt gtataatcgt gctttaacac cagaagaggt acaaaaacgt agtcaacttt 2160ttaaacgctc agatttagaa aaaaaactac ctgaaggagc ggctttaaca gagaaaacgg 2220acatattcga aagcgggcgt aacggtaaac caaataaaga tggaatcaag agttatcgta 2280ttccagcact tctcaagaca gataaaggaa ctttgatcgc aggtgcagat gaacgccgtc 2340tccattcgag tgactggggt gatatcggta tggtcatcag acgtagtgaa gataatggta 2400aaacttgggg tgaccgagta accattacca acttacgtga caatccaaaa gcttctgacc 2460catcgatcgg ttcaccagtg aatatcgata tggtgttggt tcaagatcct gaaaccaaac 2520gaatcttttc tatctatgac atgttcccag aagggaaggg aatctttgga atgtcttcac 2580aaaaagaaga agcctacaaa aaaatcgatg gaaaaaccta tcaaatcctc tatcgtgaag 2640gagaaaaggg agcttatacc attcgagaaa atggtactgt ctatacacca gatggtaagg 2700cgacagacta tcgcgttgtt gtagatcctg ttaaaccagc ctatagcgac aagggggatc 2760tatacaaggg taaccaatta ctaggcaata tctacttcac aacaaacaaa acttctccat 2820ttagaattgc caaggatagc tatctatgga tgtcctacag tgatgacgac gggaagacat 2880ggtcagcgcc tcaagatatt actccgatgg tcaaagccga ttggatgaaa ttcttgggtg 2940taggtcctgg aacaggaatt gtacttcgga atgggcctca caagggacgg attttgatac 3000cggtttatac gactaataat gtatctcact taaatggctc gcaatcttct cgtatcatct 3060attcagatga tcatggaaaa acttggcatg ctggagaagc ggtcaacgat aaccgtcagg 3120tagacggtca aaagatccac tcttctacga tgaacaatag acgtgcgcaa aatacagaat 3180caacggtggt acaactaaac aatggagatg ttaaactctt tatgcgtggt ttgactggag 3240atcttcaggt tgctacaagt aaagacggag gagtgacttg ggagaaggat atcaaacgtt 3300atccacaggt taaagatgtc tatgttcaaa tgtctgctat ccatacgatg cacgaaggaa 3360aagaatacat catcctcagt aatgcaggtg gaccgaaacg tgaaaatggg atggtccact 3420tggcacgtgt cgaagaaaat ggtgagttga cttggctcaa acacaatcca attcaaaaag 3480gagagtttgc ctataattcg ctccaagaat taggaaatgg ggagtatggc atcttgtatg 3540aacatactga aaaaggacaa aatgcctata ccctatcatt tagaaaattt aattgggact 3600ttttgagcaa agatctgatt tctcctaccg aagcgaaagt gaagcgaact agagagatgg 3660gcaaaggagt tattggcttg gagttcgact cagaagtatt ggtcaacaag gctccaaccc 3720ttcaattggc aaatggtaaa acagcacgct tcatgaccca gtatgataca aaaaccctcc 3780tatttacagt ggattcagag gatatgggtc aaaaagttac aggtttggca gaaggtgcaa 3840ttgaaagtat gcataattta ccagtctctg tggcgggcac taagctttcg aatggaatga 3900acggaagtga agctgctgtt catgaagtgc cagaatacac aggcccatta gggacatccg 3960gcgaagagcc agctccaaca gtcgagaagc cagaatacac aggcccacta gggacatccg 4020gcgaagagcc agccccgaca gtcgagaagc cagaatacac aggcccacta gggacagctg 4080gtgaagaagc agctccaaca gtcgagaagc cagaatttac agggggagtt aatggtacag 4140agccagctgt tcatgaaatc gcagagtata agggatctga ttcgcttgta actcttacta 4200caaaagaaga ttatacttac aaagctcctc ttgctcagca ggcacttcct gaaacaggaa 4260acaaggagag tgacctccta gcttcactag gactaacagc tttcttcctt ggtctgttta 4320cgctagggaa aaagagagaa caataagaga agaattctaa acatttgatt ttgtaaaaat 4380agaaggagat agcaggtttt caagcctgct atcttttttt gatgacattc aggctgatac 4440gaaatcataa gaggtctgaa actactttca gagtagtctg ttctataaaa tatagtagat 450036705DNAStaphylococcus epidermidis 36gatccaagct tatcgatatc atcaaaaagt tggcgaacct tttcaaattt tggttcaaat 60tcttgagatg tatagaattc aaaatattta ccatttgcat agtctgattg ctcaaagtct 120tgatactttt ctccacgctc ttttgcaatt tccattgaac gttcgatgga ataatagttc 180ataatcataa agaatatatt agcaaagtct tttgcttctt cagattcata gccaatttta 240tttttagcta gataaccatg taagttcatt actcctagtc caacagaatg tagttcacta 300ttcgcttttt ttacacctgg tgcattttga atatttgctt catcacttac aactgtaaga 360gcatccatac ctgtgaacac agaatctctg aatttacctg attccataac attcactata 420ttcaatgagc ctaagttaca tgaaatatct cttttaattt catcttcaat tccatagtcg 480ttaattactg atgtctcttg taattggaaa atttcagtac ataaattact cattttaatt 540tgcccaatat ttgaattcgc atgtactttg tttgcattat ctttaaacat aagatatgga 600taaccagact gtaattgtgt ttgtgcaatc atatttaaca tttcacgtgc gtcttttttc 660tttttatcga tttcgaaccc ggggtaccga attcctcgag tctag 70537442DNAStaphylococcus aureus 37gatcaatctt tgtcggtaca cgatattctt cacgactaaa taaacgctca ttcgcgattt 60tataaatgaa tgttgataac aatgttgtat tatctactga aatctcatta cgttgcatcg 120gaaacattgt gttctgtatg taaaagccgt cttgataatc tttagtagta ccgaagctgg 180tcatacgaga gttatatttt ccagccaaaa cgatattttt ataatcatta cgtgaaaaag 240gtttcccttc attatcacac aaatatttta gcttttcagt ttctatatca actgtagctt 300ctttatccat acgttgaata attgtacgat tctgacgcac catcttttgc acacctttaa 360tgttatttgt tttaaaagca tgaataagtt tttcaacaca acgatgtgaa tcttctaaga 420agtcaccgta aaatgaagga tc 4423820DNAEnterococcus faecalis 38gcaatacagg gaaaaatgtc 203920DNAEnterococcus faecalis 39cttcatcaaa caattaactc 204020DNAEnterococcus faecalis 40gaacagaaga agccaaaaaa 204120DNAEnterococcus faecalis 41gcaatcccaa ataatacggt 204219DNAEscherichia coli 42gctttccagc gtcatattg 194319DNAEscherichia coli 43gatctcgaca aaatggtga 194425DNAEscherichia coli 44cacccgcttg cgtggcaagc tgccc 254525DNAEscherichia coli 45cgtttgtgga ttccagttcc atccg 254617DNAEscherichia coli 46tcacccgctt gcgtggc 174719DNAEscherichia coli 47ggaactggaa tccacaaac 194825DNAEscherichia coli 48tgaagcactg gccgaaatgc tgcgt 254925DNAEscherichia coli 49gatgtacagg attcgttgaa ggctt 255025DNAEscherichia coli 50tagcgaaggc gtagcagaaa ctaac 255125DNAEscherichia coli 51gcaacccgaa ctcaacgccg gattt 255225DNAEscherichia coli 52atacacaagg gtcgcatctg cggcc 255326DNAEscherichia coli 53tgcgtatgca ttgcagacct tgtggc 265425DNAEscherichia coli 54gctttcactg gatatcgcgc ttggg 255519DNAEscherichia coli 55gcaacccgaa ctcaacgcc 195619DNAEscherichia coli 56gcagatgcga cccttgtgt 195723DNAKlebsiella pneumoniae 57gtggtgtcgt tcagcgcttt cac 235825DNAKlebsiella pneumoniae 58gcgatattca caccctacgc agcca 255926DNAKlebsiella pneumoniae 59gtcgaaaatg ccggaagagg tatacg 266026DNAKlebsiella pneumoniae 60actgagctgc agaccggtaa aactca 266119DNAKlebsiella pneumoniae 61gacagtcagt tcgtcagcc 196219DNAKlebsiella pneumoniae 62cgtagggtgt gaatatcgc 196326DNAKlebsiella pneumoniae 63cgtgatggat attcttaacg aagggc 266423DNAKlebsiella pneumoniae 64accaaactgt tgagccgcct gga 236523DNAKlebsiella pneumoniae 65gtgatcgccc ctcatctgct act 236626DNAKlebsiella pneumoniae 66cgcccttcgt taagaatatc catcac 266719DNAKlebsiella pneumoniae 67tcgcccctca tctgctact 196819DNAKlebsiella pneumoniae 68gatcgtgatg gatattctt 196925DNAKlebsiella pneumoniae 69caggaagatg ctgcaccggt tgttg 257025DNAProteus mirabilis 70tggttcactg actttgcgat gtttc 257125DNAProteus mirabilis 71tcgaggatgg catgcactag aaaat 257230DNAProteus mirabilis 72cgctgattag gtttcgctaa aatcttatta 307330DNAProteus mirabilis 73ttgatcctca ttttattaat cacatgacca 307419DNAProteus mirabilis 74gaaacatcgc aaagtcagt 197520DNAProteus mirabilis 75ataaaatgag gatcaagttc 207630DNAProteus mirabilis 76ccgcctttag cattaattgg tgtttatagt 307730DNAProteus mirabilis 77cctattgcag ataccttaaa tgtcttgggc 307826DNAStreptococcus pneumoniae 78agtaaaatga aataagaaca ggacag 267925DNAStreptococcus pneumoniae 79aaaacaggat aggagaacgg gaaaa 258025DNAProteus mirabilis 80ttgagtgatg atttcactga ctccc 258125DNAProteus mirabilis 81gtcagacagt gatgctgacg acaca 258227DNAProteus mirabilis 82tggttgtcat gctgtttgtg tgaaaat 278319DNAPseudomonas aeruginosa 83cgagcgggtg gtgttcatc 198419DNAPseudomonas aeruginosa 84caagtcgtcg tcggaggga 198519DNAPseudomonas aeruginosa 85tcgctgttca tcaagaccc 198619DNAPseudomonas aeruginosa 86ccgagaacca gacttcatc 198725DNAPseudomonas aeruginosa 87aatgcggctg tacctcggcg ctggt 258825DNAPseudomonas aeruginosa 88ggcggagggc cagttgcacc tgcca 258925DNAPseudomonas aeruginosa 89agccctgctc ctcggcagcc tctgc 259025DNAPseudomonas aeruginosa 90tggcttttgc aaccgcgttc aggtt 259125DNAPseudomonas aeruginosa 91gcgcccgcga gggcatgctt cgatg 259225DNAPseudomonas aeruginosa 92acctgggcgc caactacaag ttcta 259325DNAPseudomonas aeruginosa 93ggctacgctg ccgggctgca ggccg 259425DNAPseudomonas aeruginosa 94ccgatctaca ccatcgagat gggcg 259525DNAPseudomonas aeruginosa 95gagcgcggct atgtgttcgt cggct 259629DNAStaphylococcus saprophyticus 96cgtttttacc cttacctttt cgtactacc 299730DNAStaphylococcus saprophyticus 97tcaggcagag gtagtacgaa aaggtaaggg 309826DNAStaphylococcus saprophyticus 98cgtttttacc cttacctttt cgtact 269928DNAStaphylococcus saprophyticus 99atcgatcatc acattccatt tgttttta 2810027DNAStaphylococcus saprophyticus 100caccaagttt gacacgtgaa gattcat 2710130DNAStaphylococcus

saprophyticus 101atgagtgaag cggagtcaga ttatgtgcag 3010225DNAStaphylococcus saprophyticus 102cgctcattac gtacagtgac aatcg 2510330DNAStaphylococcus saprophyticus 103ctggttagct tgactcttaa caatcttgtc 3010430DNAStaphylococcus saprophyticus 104gacgcgattg tcactgtacg taatgagcga 3010528DNAHaemophilus influenzae 105gcgtcagaaa aagtaggcga aatgaaag 2810625DNAHaemophilus influenzae 106agcggctcta tcttgtaatg acaca 2510725DNAHaemophilus influenzae 107gaaacgtgaa ctcccctcta tataa 2510825DNAMoraxella catarrhalis 108gccccaaaac aatgaaacat atggt 2510925DNAMoraxella catarrhalis 109ctgcagattt tggaatcata tcgcc 2511025DNAMoraxella catarrhalis 110tggtttgacc agtatttaac gccat 2511125DNAMoraxella catarrhalis 111caacggcacc tgatgtacct tgtac 2511218DNAMoraxella catarrhalis 112ggcacctgat gtaccttg 1811317DNAMoraxella catarrhalis 113aacagctcac acgcatt 1711425DNAMoraxella catarrhalis 114ttacaacctg caccacaagt catca 2511525DNAMoraxella catarrhalis 115gtacaaacaa gccgtcagcg actta 2511623DNAMoraxella catarrhalis 116caatctgcgt gtgtgcgttc act 2311726DNAMoraxella catarrhalis 117gctactttgt cagctttagc cattca 2611824DNAMoraxella catarrhalis 118tgttttgagc tttttatttt ttga 2411922DNAMoraxella catarrhalis 119cgctgacggc ttgtttgtac ca 2212025DNAStreptococcus pneumoniae 120tctgtgctag agactgcccc atttc 2512125DNAStreptococcus pneumoniae 121cgatgtcttg attgagcagg gttat 2512225DNAArtificial SequenceOligonucleotide 122atcccacctt aggcggctgg ctcca 2512331DNAArtificial SequenceOligonucleotide 123acgtcaagtc atcatggccc ttacgagtag g 3112425DNAArtificial SequenceOligonucleotide 124gtgtgacggg cggtgtgtac aaggc 2512528DNAArtificial SequenceOligonucleotide 125gagttgcaga ctccaatccg gactacga 2812620DNAArtificial SequenceOligonucleotide 126ggaggaaggt ggggatgacg 2012720DNAArtificial SequenceOligonucleotide 127atggtgtgac gggcggtgtg 2012832DNAArtificial SequenceOligonucleotide 128ccctatacat caccttgcgg tttagcagag ag 3212928DNAArtificial SequenceOligonucleotide 129ggggggacca tcctccaagg ctaaatac 2813032DNAArtificial SequenceOligonucleotide 130cgtccacttt cgtgtttgca gagtgctgtg tt 3213120DNAEscherichia coli 131caggagtacg gtgattttta 2013220DNAEscherichia coli 132atttctggtt tggtcataca 2013320DNAProteus mirabilis 133cgggagtcag tgaaatcatc 2013420DNAProteus mirabilis 134ctaaaatcgc cacacctctt 2013518DNAKlebsiella pneumoniae 135gcagcgtggt gtcgttca 1813618DNAKlebsiella pneumoniae 136agctggcaac ggctggtc 1813720DNAKlebsiella pneumoniae 137attcacaccc tacgcagcca 2013820DNAKlebsiella pneumoniae 138atccggcagc atctctttgt 2013925DNAStaphylococcus saprophyticus 139ctggttagct tgactcttaa caatc 2514025DNAStaphylococcus saprophyticus 140tcttaacgat agaatggagc aactg 2514120DNAStreptococcus pyogenes 141tgaaaattct tgtaacaggc 2014220DNAStreptococcus pyogenes 142ggccaccagc ttgcccaata 2014320DNAStreptococcus pyogenes 143atattttctt tatgagggtg 2014420DNAStreptococcus pyogenes 144atccttaaat aaagttgcca 2014525DNAStaphylococcus epidermidis 145atcaaaaagt tggcgaacct tttca 2514625DNAStaphylococcus epidermidis 146caaaagagcg tggagaaaag tatca 2514730DNAStaphylococcus epidermidis 147tctcttttaa tttcatcttc aattccatag 3014830DNAStaphylococcus epidermidis 148aaacacaatt acagtctggt tatccatatc 3014930DNAStaphylococcus aureus 149cttcatttta cggtgacttc ttagaagatt 3015030DNAStaphylococcus aureus 150tcaactgtag cttctttatc catacgttga 3015130DNAStaphylococcus aureus 151atattttagc ttttcagttt ctatatcaac 3015230DNAStaphylococcus aureus 152aatctttgtc ggtacacgat attcttcacg 3015330DNAStaphylococcus aureus 153cgtaatgaga tttcagtaga taatacaaca 3015425DNAHaemophilus influenzae 154tttaacgatc cttttactcc ttttg 2515525DNAHaemophilus influenzae 155actgctgttg taaagaggtt aaaat 2515620DNAStreptococcus pneumoniae 156atttggtgac gggtgacttt 2015720DNAStreptococcus pneumoniae 157gctgaggatt tgttcttctt 2015820DNAStreptococcus pneumoniae 158gagcggtttc tatgattgta 2015920DNAStreptococcus pneumoniae 159atctttcctt tcttgttctt 2016018DNAMoraxella catarrhalis 160gctcaaatca gggtcagc 18161861DNAEscherichia coli 161atgagtattc aacatttccg tgtcgccctt attccctttt ttgcggcatt ttgccttcct 60gtttttgctc acccagaaac gctggtgaaa gtaaaagatg ctgaagatca gttgggtgca 120cgagtgggtt acatcgaact ggatctcaac agcggtaaga tccttgagag ttttcgcccc 180gaagaacgtt ttccaatgat gagcactttt aaagttctgc tatgtggcgc ggtattatcc 240cgtgttgacg ccgggcaaga gcaactcggt cgccgcatac actattctca gaatgacttg 300gttgagtact caccagtcac agaaaagcat cttacggatg gcatgacagt aagagaatta 360tgcagtgctg ccataaccat gagtgataac actgcggcca acttacttct gacaacgatc 420ggaggaccga aggagctaac cgcttttttg cacaacatgg gggatcatgt aactcgcctt 480gatcgttggg aaccggagct gaatgaagcc ataccaaacg acgagcgtga caccacgatg 540cctgcagcaa tggcaacaac gttgcgcaaa ctattaactg gcgaactact tactctagct 600tcccggcaac aattaataga ctggatggag gcggataaag ttgcaggacc acttctgcgc 660tcggcccttc cggctggctg gtttattgct gataaatctg gagccggtga gcgtgggtct 720cgcggtatca ttgcagcact ggggccagat ggtaagccct cccgtatcgt agttatctac 780acgacgggga gtcaggcaac tatggatgaa cgaaatagac agatcgctga gataggtgcc 840tcactgatta agcattggta a 861162918DNAPasteurella haemolytica 162atgttaaata agttaaaaat cggcacatta ttattgctga cattaacggc ttgttcgccc 60aattctgttc attcggtaac gtctaatccg cagcctgcta gtgcgcctgt gcaacaatca 120gccacacaag ccacctttca acagactttg gcgaatttgg aacagcagta tcaagcccga 180attggcgttt atgtatggga tacagaaacg ggacattctt tgtcttatcg tgcagatgaa 240cgctttgctt atgcgtccac tttcaaggcg ttgttggctg gggcggtgtt gcaatcgctg 300cctgaaaaag atttaaatcg taccatttca tatagccaaa aagatttggt tagttattct 360cccgaaaccc aaaaatacgt tggcaaaggc atgacgattg cccaattatg tgaagcagcc 420gtgcggttta gcgacaacag cgcgaccaat ttgctgctca aagaattggg tggcgtggaa 480caatatcaac gtattttgcg acaattaggc gataacgtaa cccataccaa tcggctagaa 540cccgatttaa atcaagccaa acccaacgat attcgtgata cgagtacacc caaacaaatg 600gcgatgaatt taaatgcgta tttattgggc aacacattaa ccgaatcgca aaaaacgatt 660ttgtggaatt ggttggacaa taacgcaaca ggcaatccat tgattcgcgc tgctacgcca 720acatcgtgga aagtgtacga taaaagcggg gcgggtaaat atggtgtacg caatgatatt 780gcggtggttc gcataccaaa tcgcaaaccg attgtgatgg caatcatgag tacgcaattt 840accgaagaag ccaaattcaa caataaatta gtagaagatg cagcaaagca agtatttcat 900actttacagc tcaactaa 918163864DNAKlebsiella pneumoniae 163atgcgttata ttcgcctgtg tattatctcc ctgttagcca ccctgccgct ggcggtacac 60gccagcccgc agccgcttga gcaaattaaa ctaagcgaaa gccagctgtc gggccgcgta 120ggcatgatag aaatggatct ggccagcggc cgcacgctga ccgcctggcg cgccgatgaa 180cgctttccca tgatgagcac ctttaaagta gtgctctgcg gcgcagtgct ggcgcgggtg 240gatgccggtg acgaacagct ggagcgaaag atccactatc gccagcagga tctggtggac 300tactcgccgg tcagcgaaaa acaccttgcc gacgcaatga cggtcggcga actctgcgcc 360gccgccatta ccatgagcga taacagcgcc gccaatctgc tactggccac cgtcggcggc 420cccgcaggat tgactgcctt tttgcgccag atcggcgaca acgtcacccg ccttgaccgc 480tgggaaacgg aactgaatga ggcgcttccc ggcgacgccc gcgacaccac taccccggcc 540agcatggccg cgaccctgcg caacgttggc ctgaccagcc agcgtctgag cgcccgttcg 600caacggcagc tgctgcagtg gatggtggac gatcgggtcg ccggaccgtt gatccgctcc 660gtgctgccgg cgggctggtt tatcgccgat aagaccggag ctggcgagcg gggtgcgcgc 720gggattgtcg ccctgcttgg cccgaataac aaagcagagc gcattgtggt gatttatctg 780cgggataccc cggcgagcat ggccgagcga aatcagcaaa tcgccgggat cggcaaggcg 840ctgtacgagc actggcaacg ctaa 864164534DNAKlebsiella pneumoniae 164atggacacaa cgcaggtcac attgatacac aaaattctag ctgcggcaga tgagcgaaat 60ctgccgctct ggatcggtgg gggctgggcg atcgatgcac ggctagggcg tgtaacacgc 120aagcacgatg atattgatct gacgtttccc ggcgagaggc gcggcgagct cgaggcaata 180gttgaaatgc tcggcgggcg cgtcatggag gagttggact atggattctt agcggagatc 240ggggatgagt tacttgactg cgaacctgct tggtgggcag acgaagcgta tgaaatcgcg 300gaggctccgc agggctcgtg cccagaggcg gctgagggcg tcatcgccgg gcggccagtc 360cgttgtaaca gctgggaggc gatcatctgg gattactttt actatgccga tgaagtacca 420ccagtggact ggcctacaaa gcacatagag tcctacaggc tcgcatgcac ctcactcggg 480gcggaaaagg ttgaggtctt gcgtgccgct ttcaggtcgc gatatgcggc ctaa 534165465DNAArtificial SequenceEnterobacteriaceae 165atgggcatca ttcgcacatg taggctcggc cctgaccaag tcaaatccat gcgggctgct 60cttgatcttt tcggtcgtga gttcggagac gtagccacct actcccaaca tcagccggac 120tccgattacc tcgggaactt gctccgtagt aagacattca tcgcgcttgc tgccttcgac 180caagaagcgg ttgttggcgc tctcgcggct tacgttctgc ccaggtttga gcagccgcgt 240agtgagatct atatctatga tctcgcagtc tccggcgagc accggaggca gggcattgcc 300accgcgctca tcaatctcct caagcatgag gccaacgcgc ttggtgctta tgtgatctac 360gtgcaagcag attacggtga cgatcccgca gtggctctct atacaaagtt gggcatacgg 420gaagaagtga tgcactttga tatcgaccca agtaccgcca cctaa 465166861DNAEscherichia coli 166atgcatacgc ggaaggcaat aacggaggcg cttcaaaaac tcggagtcca aaccggtgac 60ctattgatgg tgcatgcctc acttaaagcg attggtccgg tcgaaggagg agcggagacg 120gtcgttgccg cgttacgctc cgcggttggg ccgactggca ctgtgatggg atacgcatcg 180tgggaccgat caccctacga ggagactcgt aatggcgctc ggttggatga caaaacccgc 240cgtacctggc cgccgttcga tcccgcaacg gccgggactt accgtgggtt cggcctgctg 300aatcagtttc tggttcaagc ccccggcgcg cggcgcagcg cgcaccccga tgcatcgatg 360gtcgcggttg gtccactggc tgaaacgctg acggagcctc acaagctcgg tcacgccttg 420ggggaagggt cgcccgtcga gcggttcgtt cgccttggcg ggaaggccct gctgttgggt 480gcgccgctaa actccgttac cgcattgcac tacgccgagg cggttgccga tatccccaac 540aaacggcggg tgacgtatga gatgccgatg cttggaagca acggcgaagt cgcctggaaa 600acggcatcgg attacgattc aaacggcatt ctcgattgct ttgctatcga aggaaagccg 660gatgcggtcg aaactatagc aaatgcttac gtgaagctcg gtcgccatcg agaaggtgtc 720gtgggctttg ctcagtgcta cctgttcgac gcgcaggaca tcgtgacgtt cggcgtcacc 780tatcttgaga agcatttcgg aaccactccg atcgtgccag cacacgaagt cgccgagtgc 840tcttgcgagc cttcaggtta g 861167816DNAPseudomonas aeruginosa 167atgaccgatt tgaatatccc gcatacacac gcgcaccttg tagacgcatt tcaggcgctc 60ggcatccgcg cggggcaggc gctcatgctg cacgcatccg ttaaagcagt gggcgcggtg 120atgggcggcc ccaatgtgat cttgcaggcg ctcatggatg cgctcacgcc cgacggcacg 180ctgatgatgt atgcgggatg gcaagacatc cccgacttta tcgactcgct gccggacgcg 240ctcaaggccg tgtatcttga gcagcaccca ccctttgacc ccgccaccgc ccgcgccgtg 300cgcgaaaaca gcgtgctagc ggaatttttg cgcacatggc cgtgcgtgca tcgcagcgca 360aaccccgaag cctctatggt ggcggtaggc aggcaggccg ctttgctgac cgctaatcac 420gcgctggatt atggctacgg agtcgagtcg ccgctggcta aactggtggc aatagaagga 480tacgtgctga tgcttggcgc gccgctggat accatcacac tgctgcacca cgcggaatat 540ctggccaaga tgcgccacaa gaacgtggtc cgctacccgt gcccgattct gcgggacggg 600cgcaaagtgt gggtgaccgt tgaggactat gacaccggtg atccgcacga cgattatagt 660tttgagcaaa tcgcgcgcga ttatgtggcg cagggcggcg gcacacgcgg caaagtcggt 720gatgcggatg cttacctgtt cgccgcgcag gacctcacac ggtttgcggt gcagtggctt 780gaatcacggt tcggtgactc agcgtcatac ggatag 816168498DNAPseudomonas aeruginosa 168atgctctatg agtggctaaa tcgatctcat atcgtcgagt ggtggggcgg agaagaagca 60cgcccgacac ttgctgacgt acaggaacag tacttgccaa gcgttttagc gcaagagtcc 120gtcactccat acattgcaat gctgaatgga gagccgattg ggtatgccca gtcgtacgtt 180gctcttggaa gcggggacgg atggtgggaa gaagaaaccg atccaggagt acgcggaata 240gaccagttac tggcgaatgc atcacaactg ggcaaaggct tgggaaccaa gctggttcga 300gctctggttg agttgctgtt caatgatccc gaggtcacca agatccaaac ggacccgtcg 360ccgagcaact tgcgagcgat ccgatgctac gagaaagcgg ggtttgagag gcaaggtacc 420gtaaccaccc cagatggtcc agccgtgtac atggttcaaa cacgccaggc attcgagcga 480acacgcagtg atgcctaa 4981692007DNAStaphylococcus aureus 169atgaaaaaga taaaaattgt tccacttatt ttaatagttg tagttgtcgg gtttggtata 60tatttttatg cttcaaaaga taaagaaatt aataatacta ttgatgcaat tgaagataaa 120aatttcaaac aagtttataa agatagcagt tatatttcta aaagcgataa tggtgaagta 180gaaatgactg aacgtccgat aaaaatatat aatagtttag gcgttaaaga tataaacatt 240caggatcgta aaataaaaaa agtatctaaa aataaaaaac gagtagatgc tcaatataaa 300attaaaacaa actacggtaa cattgatcgc aacgttcaat ttaattttgt taaagaagat 360ggtatgtgga agttagattg ggatcatagc gtcattattc caggaatgca gaaagaccaa 420agcatacata ttgaaaattt aaaatcagaa cgtggtaaaa ttttagaccg aaacaatgtg 480gaattggcca atacaggaac acatatgaga ttaggcatcg ttccaaagaa tgtatctaaa 540aaagattata aagcaatcgc taaagaacta agtatttctg aagactatat caacaacaaa 600tggatcaaaa ttgggtacaa gatgatacct tcgttccact ttaaaaccgt taaaaaaatg 660gatgaatatt taagtgattt cgcaaaaaaa tttcatctta caactaatga aacagaaagt 720cgtaactatc ctctagaaaa agcgacttca catctattag gttatgttgg tcccattaac 780tctgaagaat taaaacaaaa agaatataaa ggctataaag atgatgcagt tattggtaaa 840aagggactcg aaaaacttta cgataaaaag ctccaacatg aagatggcta tcgtgtcaca 900atcgttgacg ataatagcaa tacaatcgca catacattaa tagagaaaaa gaaaaaagat 960ggcaaagata ttcaactaac tattgatgct aaagttcaaa agagtattta taacaacatg 1020aaaaatgatt atggctcagg tactgctatc caccctcaaa caggtgaatt attagcactt 1080gtaagcacac cttcatatga cgtctatcca tttatgtatg gcatgagtaa cgaagaatat 1140aataaattaa ccgaagataa aaaagaacct ctgctcaaca agttccagat tacaacttca 1200ccaggttcaa ctcaaaaaat attaacagca atgattgggt taaataacaa aacattagac 1260gataaaacaa gttataaaat cgatggtaaa ggttggcaaa aagataaatc ttggggtggt 1320tacaacgtta caagatatga agtggtaaat ggtaatatcg acttaaaaca agcaatagaa 1380tcatcagata acattttctt tgctagagta gcactcgaat taggcagtaa gaaatttgaa 1440aaaggcatga aaaaactagg tgttggtgaa gatataccaa gtgattatcc attttataat 1500gctcaaattt caaacaaaaa tttagataat gaaatattat tagctgattc aggttacgga 1560caaggtgaaa tactgattaa cccagtacag atcctttcaa tctatagcgc attagaaaat 1620aatggcaata ttaacgcacc tcacttatta aaagacacga aaaacaaagt ttggaagaaa 1680aatattattt ccaaagaaaa tatcaatcta ttaaatgatg gtatgcaaca agtcgtaaat 1740aaaacacata aagaagatat ttatagatct tatgcaaact taattggcaa atccggtact 1800gcagaactca aaatgaaaca aggagaaagt ggcagacaaa ttgggtggtt tatatcatat 1860gataaagata atccaaacat gatgatggct attaatgtta aagatgtaca agataaagga 1920atggctagct acaatgccaa aatctcaggt aaagtgtatg atgagctata tgagaacggt 1980aataaaaaat acgatataga tgaataa 20071702607DNAEnterococcus faecium 170atgaataaca tcggcattac tgtttatgga tgtgagcagg atgaggcaga tgcattccat 60gctctttcgc ctcgctttgg cgttatggca acgataatta acgccaacgt gtcggaatcc 120aacgccaaat ccgcgccttt caatcaatgt atcagtgtgg gacataaatc agagatttcc 180gcctctattc ttcttgcgct gaagagagcc ggtgtgaaat atatttctac ccgaagcatc 240ggctgcaatc atatagatac aactgctgct aagagaatgg gcatcactgt cgacaatgtg 300gcgtactcgc cggatagcgt tgccgattat actatgatgc taattcttat ggcagtacgc 360aacgtaaaat cgattgtgcg ctctgtggaa aaacatgatt tcaggttgga cagcgaccgt 420ggcaaggtac tcagcgacat gacagttggt gtggtgggaa cgggccagat aggcaaagcg 480gttattgagc ggctgcgagg atttggatgt aaagtgttgg cttatagtcg cagccgaagt 540atagaggtaa actatgtacc gtttgatgag ttgctgcaaa atagcgatat cgttacgctt 600catgtgccgc tcaatacgga tacgcactat attatcagcc acgaacaaat acagagaatg 660aagcaaggag catttcttat caatactggg cgcggtccac ttgtagatac ctatgagttg 720gttaaagcat tagaaaacgg gaaactgggc ggtgccgcat tggatgtatt ggaaggagag 780gaagagtttt tctactctga ttgcacccaa aaaccaattg ataatcaatt tttacttaaa 840cttcaaagaa tgcctaacgt gataatcaca ccgcatacgg cctattatac cgagcaagcg 900ttgcgtgata ccgttgaaaa aaccattaaa aactgtttgg attttgaaag gagacaggag 960catgaataga ataaaagttg caatactgtt tgggggttgc tcagaggagc atgacgtatc 1020ggtaaaatct gcaatagaga tagccgctaa cattaataaa gaaaaatacg agccgttata 1080cattggaatt acgaaatctg gtgtatggaa aatgtgcgaa aaaccttgcg cggaatggga

1140aaacgacaat tgctattcag ctgtactctc gccggataaa aaaatgcacg gattacttgt 1200taaaaagaac catgaatatg aaatcaacca tgttgatgta gcattttcag ctttgcatgg 1260caagtcaggt gaagatggat ccatacaagg tctgtttgaa ttgtccggta tcccttttgt 1320aggctgcgat attcaaagct cagcaatttg tatggacaaa tcgttgacat acatcgttgc 1380gaaaaatgct gggatagcta ctcccgcctt ttgggttatt aataaagatg ataggccggt 1440ggcagctacg tttacctatc ctgtttttgt taagccggcg cgttcaggct catccttcgg 1500tgtgaaaaaa gtcaatagcg cggacgaatt ggactacgca attgaatcgg caagacaata 1560tgacagcaaa atcttaattg agcaggctgt ttcgggctgt gaggtcggtt gtgcggtatt 1620gggaaacagt gccgcgttag ttgttggcga ggtggaccaa atcaggctgc agtacggaat 1680ctttcgtatt catcaggaag tcgagccgga aaaaggctct gaaaacgcag ttataaccgt 1740tcccgcagac ctttcagcag aggagcgagg acggatacag gaaacggcaa aaaaaatata 1800taaagcgctc ggctgtagag gtctagcccg tgtggatatg tttttacaag ataacggccg 1860cattgtactg aacgaagtca atactctgcc cggtttcacg tcatacagtc gttatccccg 1920tatgatggcc gctgcaggta ttgcacttcc cgaactgatt gaccgcttga tcgtattagc 1980gttaaagggg tgataagcat ggaaatagga tttacttttt tagatgaaat agtacacggt 2040gttcgttggg acgctaaata tgccacttgg gataatttca ccggaaaacc ggttgacggt 2100tatgaagtaa atcgcattgt agggacatac gagttggctg aatcgctttt gaaggcaaaa 2160gaactggctg ctacccaagg gtacggattg cttctatggg acggttaccg tcctaagcgt 2220gctgtaaact gttttatgca atgggctgca cagccggaaa ataacctgac aaaggaaagt 2280tattatccca atattgaccg aactgagatg atttcaaaag gatacgtggc ttcaaaatca 2340agccatagcc gcggcagtgc cattgatctt acgctttatc gattagacac gggtgagctt 2400gtaccaatgg ggagccgatt tgattttatg gatgaacgct ctcatcatgc ggcaaatgga 2460atatcatgca atgaagcgca aaatcgcaga cgtttgcgct ccatcatgga aaacagtggg 2520tttgaagcat atagcctcga atggtggcac tatgtattaa gagacgaacc ataccccaat 2580agctattttg atttccccgt taaataa 26071711288DNAPseudomonas aeruginosa 171ggatccatca ggcaacgacg ggctgctgcc ggccatcagc ggacgcaggg aggactttcc 60gcaaccggcc gttcgatgcg gcaccgatgg ccttcgcgca ggggtagtga atccgccagg 120attgacttgc gctgccctac ctctcactag tgaggggcgg cagcgcatca agcggtgagc 180gcactccggc accgccaact ttcagcacat gcgtgtaaat catcgtcgta gagacgtcgg 240aatggccgag cagatcctgc acggttcgaa tgtcgtaacc gctgcggagc aaggccgtcg 300cgaacgagtg gcggagggtg tgcggtgtgg cgggcttcgt gatgcctgct tgttctacgg 360cacgtttgaa ggcgcgctga aaggtctggt catacatgtg atggcgacgc acgacaccgc 420tccgtggatc ggtcgaatgc gtgtgctgcg caaaaaccca gaaccacggc caggaatgcc 480cggcgcgcgg atacttccgc tcaagggcgt cgggaagcgc aacgccgctg cggccctcgg 540cctggtcctt cagccaccat gcccgtgcac gcgacagctg ctcgcgcagg ctgggtgcca 600agctctcggg taacatcaag gcccgatcct tggagccctt gccctcccgc acgatgatcg 660tgccgtgatc gaaatccaga tccttgaccc gcagttgcaa accctcactg atccgcatgc 720ccgttccata cagaagctgg gcgaacaaac gatgctcgcc ttccagaaaa ccgaggatgc 780gaaccacttc atccggggtc agcaccaccg gcaagcgccg cgacggccga ggtcttccga 840tctcctgaag ccagggcaga tccgtgcaca gcaccttgcc gtagaagaac agcaaggccg 900ccaatgcctg acgatgcgtg gagaccgaaa ccttgcgctc gttcgccagc caggacagaa 960atgcctcgac ttcgctgctg cccaaggttg ccgggtgacg cacaccgtgg aaacggatga 1020aggcacgaac ccagtggaca taagcctgtt cggttcgtaa gctgtaatgc aagtagcgta 1080tgcgctcacg caactggtcc agaaccttga ccgaacgcag cggtggtaac ggcgcagtgg 1140cggttttcat ggcttgttat gactgttttt ttgtacagtc tatgcctcgg gcatccaagc 1200agcaagcgcg ttacgccgtg ggtcgatgtt tgatgttatg gagcagcaac gatgttacgc 1260agcagggcag tcgccctaaa acaaagtt 12881721650DNAPseudomonas aeruginosa 172gttagatgca ctaagcacat aattgctcac agccaaacta tcaggtcaag tctgctttta 60ttatttttaa gcgtgcataa taagccctac acaaattggg agatatatca tgaaaggctg 120gctttttctt gttatcgcaa tagttggcga agtaatcgca acatccgcat taaaatctag 180cgagggcttt actaagcttg ccccttccgc cgttgtcata atcggttatg gcatcgcatt 240ttattttctt tctctggttc tgaaatccat ccctgtcggt gttgcttatg cagtctggtc 300gggactcggc gtcgtcataa ttacagccat tgcctggttg cttcatgggc aaaagcttga 360tgcgtggggc tttgtaggta tggggctcat aattgctgcc tttttgctcg cccgatcccc 420atcgtggaag tcgctgcgga ggccgacgcc atggtgacgg tgttcggcat tctgaatctc 480accgaggact ccttcttcga tgagagccgg cggctagacc ccgccggcgc tgtcaccgcg 540gcgatcgaaa tgctgcgagt cggatcagac gtcgtggatg tcggaccggc cgccagccat 600ccggacgcga ggcctgtatc gccggccgat gagatcagac gtattgcgcc gctcttagac 660gccctgtccg atcagatgca ccgtgtttca atcgacagct tccaaccgga aacccagcgc 720tatgcgctca agcgcggcgt gggctacctg aacgatatcc aaggatttcc tgaccctgcg 780ctctatcccg atattgctga ggcggactgc aggctggtgg ttatgcactc agcgcagcgg 840gatggcatcg ccacccgcac cggtcacctt cgacccgaag acgcgctcga cgagattgtg 900cggttcttcg aggcgcgggt ttccgccttg cgacggagcg gggtcgctgc cgaccggctc 960atcctcgatc cggggatggg atttttcttg agccccgcac cggaaacatc gctgcacgtg 1020ctgtcgaacc ttcaaaagct gaagtcggcg ttggggcttc cgctattggt ctcggtgtcg 1080cggaaatcct tcttgggcgc caccgttggc cttcctgtaa aggatctggg tccagcgagc 1140cttgcggcgg aacttcacgc gatcggcaat ggcgctgact acgtccgcac ccacgcgcct 1200ggagatctgc gaagcgcaat caccttctcg gaaaccctcg cgaaatttcg cagtcgcgac 1260gccagagacc gagggttaga tcatgcctag cattcacctt ccggccgccc gctagcggac 1320cctggtcagg ttccgcgaag gtgggcgcag acatgctggg ctcgtcagga tcaaactgca 1380ctatgaggcg gcggttcata ccgcgccagg ggagcgaatg gacagcgagg agcctccgaa 1440cgttcgggtc gcctgctcgg gtgatatcga cgaggttgtg cggctgatgc acgacgctgc 1500ggcgtggatg tccgccaagg gaacgcccgc ctgggacgtc gcgcggatcg accggacatt 1560cgcggagacc ttcgtcctga gatccgagct cctagtcgcg agttgcagcg acggcatcgt 1620cggctgttgc accttgtcgg ccgaggatcc 1650173630DNAEnterococcus faecium 173atgggtccga atcctatgaa aatgtatcct atagaaggaa acaaatcagt acaatttatc 60aaacctattt tagaaaaatt agaaaatgtt gaggttggag aatactcata ttatgattct 120aagaatggag aaacttttga taagcaaatt ttatatcatt atccaatctt aaacgataag 180ttaaaaatag gtaaattttg ctcaatagga ccaggtgtaa ctattattat gaatggagca 240aatcatagaa tggatggctc aacatatcca tttaatttat ttggtaatgg atgggagaaa 300catatgccaa aattagatca actacctatt aagggggata caataatagg taatgatgta 360tggataggaa aagatgttgt aattatgcca ggagtaaaaa tcggggatgg tgcaatagta 420gctgctaatt ctgttgttgt aaaagatata gcgccataca tgttagctgg aggaaatcct 480gctaacgaaa taaaacaaag atttgatcaa gatacaataa atcagctgct tgatataaaa 540tggtggaatt ggccaataga cattattaat gagaatatag ataaaattct tgataatagc 600atcattagag aagtcatatg gaaaaaatga 6301741440DNAEnterococcus faecalis 174atgaatatag ttgaaaatga aatatgtata agaactttaa tagatgatga ttttcctttg 60atgttaaaat ggttaactga tgaaagagta ttagaatttt atggtggtag agataaaaaa 120tatacattag aatcattaaa aaaacattat acagagcctt gggaagatga agtttttaga 180gtaattattg aatataacaa tgttcctatt ggatatggac aaatatataa aatgtatgat 240gagttatata ctgattatca ttatccaaaa actgatgaga tagtctatgg tatggatcaa 300tttataggag agccaaatta ttggagtaaa ggaattggta caagatatat taaattgatt 360tttgaatttt tgaaaaaaga aagaaatgct aatgcagtta ttttagaccc tcataaaaat 420aatccaagag caataagggc ataccaaaaa tctggtttta gaattattga agatttgcca 480gaacatgaat tacacgaggg caaaaaagaa gattgttatt taatggaata tagatatgat 540gataatgcca caaatgttaa ggcaatgaaa tatttaattg agcattactt tgataatttc 600aaagtagata gtattgaaat aatcggtagt ggttatgata gtgtggcata tttagttaat 660aatgaataca tttttaaaac aaaatttagt actaataaga aaaaaggtta tgcaaaagaa 720aaagcaatat ataatttttt aaatacaaat ttagaaacta atgtaaaaat tcctaatatt 780gaatattcgt atattagtga tgaattatct atactaggtt ataaagaaat taaaggaact 840tttttaacac cagaaattta ttctactatg tcagaagaag aacaaaattt gttaaaacga 900gatattgcca gttttttaag acaaatgcac ggtttagatt atacagatat tagtgaatgt 960actattgata ataaacaaaa tgtattagaa gagtatatat tgttgcgtga aactatttat 1020aatgatttaa ctgatataga aaaagattat atagaaagtt ttatggaaag actaaatgca 1080acaacagttt ttgagggtaa aaagtgttta tgccataatg attttagttg taatcatcta 1140ttgttagatg gcaataatag attaactgga ataattgatt ttggagattc tggaattata 1200gatgaatatt gtgattttat atacttactt gaagatagtg aagaagaaat aggaacaaat 1260tttggagaag atatattaag aatgtatgga aatatagata ttgagaaagc aaaagaatat 1320caagatatag ttgaagaata ttatcctatt gaaactattg tttatggaat taaaaatatt 1380aaacaggaat ttatcgaaaa tggtagaaaa gaaatttata aaaggactta taaagattga 1440175660DNAStaphylococcus aureus 175ttgaatttaa acaatgacca tggacctgat cccgaaaata ttttaccgat aaaagggaat 60cggaatcttc aatttataaa acctactata acgaacgaaa acattttggt gggggaatat 120tcttattatg atagtaagcg aggagaatcc tttgaagatc aagtcttata tcattatgaa 180gtgattggag ataagttgat tataggaaga ttttgttcaa ttggtcccgg aacaacattt 240attatgaatg gtgcaaacca tcggatggat ggatcaacat atccttttca tctattcagg 300atgggttggg agaagtatat gccttcctta aaagatcttc ccttgaaagg ggacattgaa 360attggaaatg atgtatggat aggtagagat gtaaccatta tgcctggggt gaaaattggg 420gacggggcaa tcattgctgc agaagctgtt gtcacaaaga atgttgctcc ctattctatt 480gtcggtggaa atcccttaaa atttataaga aaaaggtttt ctgatggagt tatcgaagaa 540tggttagctt tacaatggtg gaatttagat atgaaaatta ttaatgaaaa tcttcccttc 600ataataaatg gagatatcga aatgctgaag agaaaaagaa aacttctaga tgacacttga 6601761569DNAStaphylococcus aureus 176atgaaaataa tgttagaggg acttaatata aaacattatg ttcaagatcg tttattgttg 60aacataaatc gcctaaagat ttatcagaat gatcgtattg gtttaattgg taaaaatgga 120agtggaaaaa caacgttact tcacatatta tataaaaaaa ttgtgcctga agaaggtatt 180gtaaaacaat tttcacattg tgaacttatt cctcaattga agctcataga atcaactaaa 240agtggtggtg aagtaacacg aaactatatt cggcaagcgc ttgataaaaa tccagaactg 300ctattagcag atgaaccaac aactaactta gataataact atatagaaaa attagaacag 360gatttaaaaa attggcatgg agcatttatt atagtttcac atgatcgcgc ttttttagat 420aacttgtgta ctactatatg ggaaattgac gagggaagaa taactgaata taaggggaat 480tatagtaact atgttgaaca aaaagaatta gaaagacatc gagaagaatt agaatatgaa 540aaatatgaaa aagaaaagaa acgattggaa aaagctataa atataaaaga acagaaagct 600caacgagcaa ctaaaaaacc gaaaaactta agtttatctg aaggcaaaat aaaaggagca 660aagccatact ttgcaggtaa gcaaaagaag ttacgaaaaa ctgtaaaatc tctagaaacc 720agactagaaa aacttgaaag cgtcgaaaag agaaacgaac ttcctccact taaaatggat 780ttagtgaact tagaaagtgt aaaaaataga actataatac gtggtgaaga tgtctcgggt 840acaattgaag gacgggtatt gtggaaagca aaaagtttta gtattcgcgg aggagacaag 900atggcaatta tcggatctaa tggtacagga aagacaacgt ttattaaaaa aattgtgcat 960gggaatcctg gtatttcatt atcgccatct gtcaaaatcg gttattttag ccaaaaaata 1020gatacattag aattagataa gagcatttta gaaaatgttc aatcttcttc acaacaaaat 1080gaaactctta ttcgaactat tctagctaga atgcattttt ttagagatga tgtttataaa 1140ccaataagtg tcttaagtgg tggagagcga gttaaagtag cactaactaa agtattctta 1200agtgaagtta atacgttggt actagatgaa ccaacaaact ttcttgatat ggaagctata 1260gaggcgtttg aatctttgtt aaaggaatat aatggcagta taatctttgt atctcacgat 1320cgtaaattta tcgaaaaagt agccactcga ataatgacaa ttgataataa agaaataaaa 1380atatttgatg gcacatatga acaatttaaa caagctgaaa agccaacaag gaatattaaa 1440gaagataaaa aacttttact tgagacaaaa attacagaag tactcagtcg attgagtatt 1500gaaccttcgg aagaattaga acaagagttt caaaacttaa taaatgaaaa aagaaatttg 1560gataaataa 15691771467DNAStaphylococcus epidermidis 177atggaacaat atacaattaa atttaaccaa atcaatcata aattgacaga tttacgatca 60cttaacatcg atcatcttta tgcttaccaa tttgaaaaaa tagcacttat tgggggtaat 120ggtactggta aaaccacatt actaaatatg attgctcaaa aaacaaaacc agaatctgga 180acagttgaaa cgaatggcga aattcaatat tttgaacagc ttaacatgga tgtggaaaat 240gattttaaca cgttagacgg tagtttaatg agtgaactcc atatacctat gcatacaacc 300gacagtatga gtggtggtga aaaagcaaaa tataaattac gtaatgtcat atcaaattat 360agtccgatat tacttttaga tgaacctaca aatcacttgg ataaaattgg taaagattat 420ctgaataata ttttaaaata ttactatggt actttaatta tagtaagtca cgatagagca 480cttatagacc aaattgctga cacaatttgg gatatacaag aagatggcac aataagagtg 540tttaaaggta attacacaca gtatcaaaat caatatgaac aagaacagtt agaacaacaa 600cgtaaatatg aacagtatat aagtgaaaaa caaagattgt cccaagccag taaagctaaa 660cgaaatcaag cgcaacaaat ggcacaagca tcatcaaaac aaaaaaataa aagtatagca 720ccagatcgtt taagtgcatc aaaagaaaaa ggcacggttg agaaggctgc tcaaaaacaa 780gctaagcata ttgaaaaaag aatggaacat ttggaagaag ttgaaaaacc acaaagttat 840catgaattca attttccaca aaataaaatt tatgatatcc ataataatta tccaatcatt 900gcacaaaatc taacattggt taaaggaagt caaaaactgc taacacaagt acgattccaa 960ataccatatg gcaaaaatat agcgctcgta ggtgcaaatg gtgtaggtaa gacaacttta 1020cttgaagcta tttaccacca aatagaggga attgattgtt ctcctaaagt gcaaatggca 1080tactatcgtc aacttgctta tgaagacatg cgtgacgttt cattattgca atatttaatg 1140gatgaaacgg attcatcaga atcattcagt agagctattt taaataactt gggtttaaat 1200gaagcacttg agcgttcttg taatgttttg agtggtgggg aaagaacgaa attatcgtta 1260gcagtattat tttcaacgaa agcgaatatg ttaattttgg atgaaccaac taatttttta 1320gatattaaaa cattagaagc attagaaatg tttatgaata aatatcctgg aatcattttg 1380tttacatcac atgatacaag gtttgttaaa catgtatcag ataaaaaatg ggaattaaca 1440ggacaatcta ttcatgatat aacttaa 1467

Claims

1. A method to detect and identify the presence of Staphylococcus aureus and at least a second and a third target bacterial species in a sample by performing an assay, comprising: simultaneously contacting a sample with a set of amplification primers comprising a plurality of at least a first, second, and third primer pair, wherein said first primer pair hybridizes solely to the nucleic acids of Staphylococcus aureus, and wherein said second and third primer pairs hybridize solely to target DNA of said second and third target bacterial species, respectively, and are ubiquitous to at least 80% to Staphylococcus aureus, and second and third target bacterial species, respectively, wherein the plurality of primer pairs are chosen to allow amplification under a single amplification protocol; amplifying target nucleic acid from said sample under said single amplification protocol; and detecting the presence or amount of amplified product(s) as an indication of the presence of Staphylococcus aureus and said second and third target bacterial species in said sample.