BACKGROUND OF THE INVENTION
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Classical identification of bacteria [0001]
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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™ 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 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 [0002] 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.
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Urine specimens [0003]
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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 [0004] 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'Université Laval (CHUL)” is given in Tables 1 and 2.
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Conventional pathoaen 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 ≧10[0005] 7 CFU/L in urine. However, infections with less than 107 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 (<107 CFU/L; Table 3).
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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™, UTIscreen™, Flash Track™ 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). [0006]
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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. [0007]
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Any clinical specimens [0008]
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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. [0009]
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Towards the development of rapid DNA-based diagnostic tests [0010]
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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.). [0011]
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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). [0012]
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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 Ser. 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. [0013]
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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. [0014]
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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 approch 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. [0015]
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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. [0016]
SUMMARY OF THE INVENTION
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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. [0017] 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.
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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 [0018] Escherichia coli, Enterococcus faecalls, 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 embodiements of the present invention.
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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.[0019]
DETAILED DESCRIPTION OF THE INVENTION
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Development of species-specific DNA probes [0020]
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DNA fragment probes were developed for the following bacterial species: [0021] 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).
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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 [0022] E. coli strain DH5α 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.
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For each given species, the gel-purified restriction fragments of unknown coding potential were labeled with the radioactive nucleotide α-[0023] 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.
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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 μg/ml salmon sperm DNA at 65° C. for 15 min. (ii) Hybridization; in fresh pre-hybridization solution containing the labeled probe at 65° C. overnight. (iii) Post-hybridization; washes twice in 3×SSC containing 1% SDS (1× SSC is 0.15M NaCl, 0.015M NaCitrate) and twice in 0.1×SSC containing 0.1% SDS; all washes were at 65° 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. [0024]
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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. [0025]
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Sequencing of the species-specific fragment probes [0026]
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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 (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 [0027] 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.
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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™ 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.). [0028]
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Hybridization with oligonucleotide probes [0029]
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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 γ[0030] 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.
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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× SSC containing 1% SDS, twice in 2× SSC containing 1% SDS and twice in 1× SSC containing 1% SDS (all of these washes were at 65° C. for 15 min ), and a final wash in 0.1× SSC containing 1% SDS at 25° 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 colorimetric or by chemiluminescence. [0031]
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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. [0032]
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DNA amplification [0033]
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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™ 4.0 (National Biosciences) to verify that they are likely candidates for PCR amplifications. [0034]
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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 μL PCR reaction mixtures containing 50 mM KCl, 10 mM Tris-HCl pH 8.3, 2.5 mM MgCl[0035] 2, 0.4 μm of each of the two primers, 200 μM 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° C. followed by 30 cycles of 1 second at 95° C. and 1 second at 55° C.) using a Perkin Elmer 480™ 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™ system from Perkin Elmer or Amplisensor™ 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.
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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\v), respectively. For the PCR reaction mixture, the concentration ranges for the amplification primers and the MgCl[0036] 2 are 0.1-1.0 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.
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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. [0037]
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Specificity and ubiquity tests for oligonucleotide probes and primers [0038]
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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. [0039]
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Universal bacterial detection [0040]
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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'Université Laval (CHUL)” were negative (i.e. <10[0041] 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 ≧107 CFU/L. These probes can also be applied for bacterial detection in other clinical samples.
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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. [0042]
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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. [0043]
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Antibiotic resistance genes [0044]
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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 resitance 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. [0045]
EXAMPLES
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The following examples are intended to be illustrative of the various methods and compounds of the invention. [0046]
Example 1
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Isolation and cloning of fragments. Genomic DNAs from [0047] 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 (DH5α). It is understood that the vectors and corresponding competent cells should not be limited to the ones herein above specifically examplified. 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.
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Labeling of DNA fragment probes. The label used was α[0048] 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° 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.
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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. [0049]
Example 2
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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° 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. [0050]
Example 3
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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. [0051]
Example 4
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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™) using phosphoramidite chemistry. [0052]
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Labeling of oligonucleotides. Each oligonucleotide was 5′ end-labeled with γ[0053] 32P-ATP by the T4 polynucleotide kinase (Pharmacia) as described earlier. The label could also be non-radioactive.
-
Specificity test for oliqonucleotide 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. [0054]
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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 1. [0055]
Example 5
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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. [0056]
Example 6
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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. [0057]
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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. [0058]
-
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. [0059]
Example 7
-
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 1.5×10[0060] 8 bacteria/mL). In the case of direct amplification from a colony, a portion of the colony was transferred directly to a 50 μL PCR reaction mixture (containing 50 mM KCl, 10 mM Tris pH 8.3, 2.5 MM MgCl2, 0.4 μM of each of the two primers, 200 μM 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 μL of the cell suspension was added to 46 μL of the same PCR reaction mixture. For both strategies, the reaction mixture was overlaid with 50 μL of mineral oil and PCR amplifications were carried out using an initial denaturation step of 3 min. at 95° C. followed by 30 cycles consisting of a 1 second denaturation step at 95° C. and of a 1 second annealing step at 55° C. in a Perkin Elmer 480™ thermal cycler. PCR amplification products were then analyzed by standard agarose gel (2%) electrophoresis. Amplification products were visualized in agarose gels containing 2.5 μg/mL of ethidium bromide under UV at 254 nm. The entire PCR assay can be completed in approximately one hour.
-
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° 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. [0061]
Example 8
-
Amplification directly from clinical specimens. For amplification from urine specimens, 4 μL of undiluted or diluted (1:10) urine was added directly to 46 μL of the above PCR reaction mixture and amplified as described earlier. [0062]
-
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. [0063]
-
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. [0064]
Example 9
-
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. [0065]
Example 10
-
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. [0066]
-
For example, the detection of [0067] 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 an ubiquity of 100%.
-
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. [0068]
-
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™, Perkin Elmer). [0069]
Example 11
-
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™, Biotronics; TaqMan™) or other labels such as biotin (SHARP Signal™ 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). [0070]
Example 12
-
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. [0071]
Example 13
-
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. [0072]
-
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: [0073]
-
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. [0074]
-
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 [0075] Escherichia coli, Enterococcus faecalis, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa, Staphylococcus saprophyticus, Staphylococcus aureus and Staphylococcus epidermidis).
-
A kit for the detection of respiratory pathogens which contains seven specific test components (sets of probes for detecting [0076] Streptococcus pneumoniae, Moraxella catarrhalis, Haemophilus influenzae, Klebsiella pneumoniae, Pseudomonas aeruginosa, Streptococcus pyogenes and Staphylococcus aureus).
-
A kit for the detection of pathogens retrieved from blood samples, which contains eleven specific test components (sets of probes for the detection of [0077] Streptococcus pneumoniae, Moraxella catarrhalis, Haemophilus influenzae, Proteus mirabilis, Klebsiella pneumoniae, Pseudomonas aeruginosa, Escherichia coli, Enterococcus faecalis, Staphylococcus aureus, Streptococcus pyogenes and Staphylococcus epidermidis).
-
A kit for the detection of pathogens causing meningitis, which contains four specific test components (sets of probes for the detection of [0078] Haemophilus influenzae, Streptococcus pneumoniae, Escherichia coli and Pseudomonas aeruginosa).
-
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[0079] tem, blarob, blashv, aadb, aacC1, aacC2, aacC3, aacA4, mecA, vanA, vanH, vanX, satA, aacA-aphD, vat, vga, msrA, sul and int.
-
Other kits adapted for the detection of pathogens from skin, abdominal wound or any other clinically relevant kits will be developed. [0080]
Example 14
-
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. [0081]
-
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. [0082]
-
The kits will be adapted for use with each type of specimen as described in example 13 for hybridization-based diagnostic kits. [0083]
Example 15
-
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.
[0084] TABLE 1 |
|
|
Distribution of urinary isolates from positive urine samples (≧107 CFU/L) |
at the Centre Hospitalier de l'Université Laval (CHUL) for the |
1992-1994 period. |
| Nov 92 | April 93 | July 93 | Jan 94 |
Organisms | n = 267a | 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 saprophyticus | 3.0 | 1.9 | 5.4 | 1.4 |
Othersb | 10.2 | 13.3 | 11.8 | 16.0 |
|
|
|
-
[0085] TABLE 2 |
|
|
Distribution of uncommona urinary isolates from positive urine samples |
(≧107 CFU/L) at the Centre Hospitalier de l'Université Laval (CHUL) |
for the 1992-1994 period. |
Organismsa | Nov 92 | April 93 | July 93 | Jan 94 |
|
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 |
Morganella and Providencia | 0.4 | 0.8 | 0.4 | 0.0 |
Hafnia alvei | 0.8 | 0.0 | 0.0 | 0.0 |
NFBb (Stenotrophomonas, | 0.0 | 0.4 | 1.3 | 1.1 |
Acinetobacter) |
Candida spp. | 0.8 | 1.9 | 0.7 | 0.4 |
|
|
|
-
[0086] TABLE 3 |
|
|
Distribution of positivea (bacterial count ≧107 CFU/L) and negative |
(bacterial count <107 CFU/L) urine specimens tested at the Centre |
Hospitalier de l'Université Laval (CHUL) for the 1992-1994 period. |
Specimens | Nov 92 | April 93 | July 93 | Jan 94 |
|
received: | 1383(100) | 1338(100) | 1139(100) | 1345(100) |
positive: | 267(19.3) | 265(19.8) | 238(20.9) | 281(20.9) |
negative: | 1116(80.7) | 1073(80.2) | 901(79.1) | 1064(79.1) |
|
|
-
[0087] TABLE 4 |
|
|
Distribution of positive and negative clinical specimens tested in the |
Microbiology Laboratory of the CHUL. |
| | | % of |
| No. of samples | % of positive | negative |
Clinical specimensa | tested | specimens | specimens |
|
Urine | 17,981 | 19.4 | 80.6 |
Haemoculture/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 |
|
|
-
[0088] TABLE 5 |
|
|
Bacterial species (66) used for testing the specificity of DNA fragment |
probes, oligonucleotide probes and PCR primers. |
| Number of strains | | Number of strains |
Bacterial species | tested | Bacterial species | tested |
|
Gram negative: | | Gram positive: | |
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 epidermidis | 2 |
Morganella morganii | 2 | Staphylococcus saprophyticus | 5 |
Enterobacter cloacae | 2 | Micrococcus species | 2 |
Providencia stuartii | 1 | Corynebacteriun species | 2 |
Providencia species | 1 | Streptococcus groupe B | 2 |
Enterobacter agglomerans | 2 | Staphylococcus simulans | 2 |
Providencia rettgeri | 2 | Staphylococcus ludgunensis | 1 |
Neisseria mucosa | 1 | Staphylococcus capitis | 2 |
Providencia alcalifaciens | 1 | Staphylococcus haemolyticus | 2 |
Providencia rustigianii | 1 | Staphylococcus hominis | 2 |
Burkholderia cepacia | 2 | Enterococcus faecalis | 2 |
Enterobacter aerogenes | 2 | Enterococcus faecium | 1 |
Stenotrophomonas maltophilia | 2 | Staphylococcus warneri | 1 |
Pseudomonas fluorescens | 1 | Enterococcus durans | 1 |
Comamonas acidovorans | 2 | Streptococcus bovis | 1 |
Pseudomonas putida | 2 | Diphteroids | 2 |
Haemophilus influenzae | 5 | Lactobacillus acidophilus | 1 |
Haemophilus parainfluenzae | 2 |
Bordetella pertussis | 2 |
Haemophilus parahaemolyticus | 2 |
Haemophilus haemolyticus | 2 |
Haemophilus aegyptius | 1 |
Kingella indologenes | 1 |
Moraxella atlantae | 1 |
Neisseria caviae | 1 |
Neisseria subflava | 1 |
Moraxella urethralis | 1 |
Shigella sonnei | 1 |
Shigella flexneri | 1 |
Klebsiella oxytoca | 2 |
Serratia marcescens | 2 |
Salmonella typhimurium | 1 |
Yersinia enterocolitica | 1 |
Acinetobacter calcoaceticus | 1 |
Acinetobacter lwoffi | 1 |
Hafnia alvei | 2 |
Citrobacter diversus | 1 |
Citrobacter freundii | 1 |
Salmonella species | 1 |
|
-
[0089] TABLE 6 |
|
|
Species-specific DNA fragment and oligonucleotide probes for hybridization. |
| Number of fragment probesb | Number of oligonucleotide probes |
Organismsa | Tested | Specific | Ubiquitousc | Synthesized | Specific | Ubiquitousc |
|
E. coli d | — | — | — | 20 | 12 | 9f |
E. coli | 14 | 2 | 2e | — | — | — |
K. pneumoniae d | — | — | — | 15 | 1 | 1 |
K. pneumoniae | 33 | 3 | 3 | 18 | 12 | 8 |
P. mirabilis d | — | — | — | 3 | 3 | 2 |
P. mirabilis | 14 | 3 | 3e | 15 | 8 | 7 |
P. aeruginosa d | — | — | — | 26 | 13 | 9 |
P. aeruginosa | 6 | 2 | 2e | 6 | 0 | 0 |
S. saprophyticus | 7 | 4 | 4 | 20 | 9 | 7 |
H. influenzae d | — | — | — | 16 | 2 | 2 |
H. influenzae | 1 | 1 | 1 | 20 | 1 | 1 |
S. pneumoniae d | — | — | — | 6 | 1 | 1 |
S. pneumoniae | 19 | 2 | 2 | 4 | 1 | 1 |
M. catarrhalis | 2 | 2 | 2 | 9 | 8 | 8 |
S. epidermidis | 62 | 1 | 1 | — | — | — |
S. aureus | 30 | 1 | 1 | — | — | — |
Universal probesd | — | — | — | 7 | — | 7g |
|
|
|
|
|
|
|
|
-
[0090] TABLE 7 |
|
|
PCR amplification for bacterial pathogens commonly encountered in |
urine, sputum, blood, cerebrospinal fluid and other specimens. |
| Primer paira | Amplicon | | DNA amplification |
Organism | # (SEQ ID NO) | size (bp) | Ubiquityb | from coloniesc | from specimensd |
|
E. coli | 1e (55-56) | 107 | 75/80 | + | + |
| 2e (46-47) | 297 | 77/80 | + | + |
| 3 (42-43) | 102 | 78/80 | + | + |
| 4 (131-132) | 134 | 73/80 | + | + |
| 1 + 3 + 4 | — | 80/80 | + | + |
E. faecalis | 1e (38-39) | 200 | 71/80 | + | + |
| 2e (40-41) | 121 | 79/80 | + | + |
| 1 + 2 | — | 80/80 | + | + |
K. pneumoniae | 1 (67-68) | 198 | 76/80 | + | + |
| 2 (61-62) | 143 | 67/80 | + | + |
| 3h (135-136) | 148 | 78/80 | + | + |
| 4 (137-138) | 116 | 69/80 | + | N.T.i |
| 1 + 2 + 3 | — | 80/80 | + | N.T. |
P. mirabilis | 1 (74-75) | 167 | 73/80 | + | N.T. |
| 2 (133-134) | 123 | 80/80 | + | N.T. |
P. aeruginosa | 1e (83-84) | 139 | 79/80 | + | N.T. |
| 2e (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 | 1e (154-155) | 217 | 80/80 | + | N.T. |
S. pneumoniae | 1e (156-157) | 134 | 80/80 | + | N.T. |
| 2e (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 f | 1e (141-142) | 213 | 80/80 | + | N.T. |
| 2e (143-144) | 157 | 24/24 | + | N.T. |
Universal | 1e (126-127) | 241 | 194/195g | + | + |
|
|
|
|
|
|
|
|
|
|
-
[0091] TABLE 8 |
|
|
Selected antibiotic resistance genes for diagnostic purposes. |
Genes | Antibiotics | Bacteriaa | SEQ ID NO |
|
(blatem) TEM-1 | β-lactams | Enterobacteriaceae, | 161 |
| | Pseudomonadaceae, |
| | Haemophilus, Neisseria |
(blarob) ROB-1 | β-lactams | Haemophilus, Pasteurella | 162 |
(blashv) SHV-1 | β-lactams | Klebsiella and other | 163 |
| | Enterobacteriaceae |
aadB, aacC1, aacC2, | Aminoglycosides | Enterobacteriaceae, | 164, 165, 166 |
aacC3, aacA4 | | Pseudomonadaceae | 167, 168 |
mecA | β-lactams | Staphylococci | 169 |
vanH, vanA, vanX | Vancomycin | Enterococci | 170 |
satA | Macrolides | Enterococci | 173 |
aacA-aphD | Aminoglycosides | Enterococci, Staphylococci | 174 |
vat | Macrolides | Staphylococci | 175 |
vga | Macrolides | Staphylococci | 176 |
msrA | Erythromycin | Staphylococci | 177 |
Int and Sul | β-lactams, trimethoprim, | Enterobacteriaceae, | 171, 172 |
conserved sequences | aminoglycosides, antiseptic, | Pseudomonadaceae |
| chloramphenicol |
|
|
-
[0092]
-
1
177
1
1817
DNA
Enterococcus faecalis
1
acagtaaaaa agttgttaac gaatgaattt gttaacaact tttttgctat ggtattgagt 60
tatgaggggc aatacaggga aaaatgtcgg ctgattaagg aatttagata gtgccggtta 120
gtagttgtct ataatgaaaa tagcaacaaa tatttacgca gggaaagggg cggtcgttta 180
acgggaaaaa ttagggagga taaagcaata cttttgttgg gaaaagaaat aaaaggaaac 240
tggggaagga gttaattgtt tgatgaaggg aaataaaatt ttatacattt taggtacagg 300
catctttgtt ggaagttcat gtctattttc ttcacttttt gtagccgcag aagaacaagt 360
ttattcagaa agtgaagttt caacagtttt atcgaagttg gaaaaggagg caatttctga 420
ggcagctgct gaacaatata cggttgtaga tcgaaaagaa gacgcgtggg ggatgaagca 480
tcttaagtta gaaaagcaaa cggaaggcgt tactgttgat tcagataatg tgattattca 540
tttagataaa aacggtgcag taacaagtgt tacaggaaat ccagttgatc aagttgtgaa 600
aattcaatcg gttgatgcaa tcggtgaaga aggagttaaa aaaattgttg cttctgataa 660
tccagaaact aaagatcttg tctttttagc tattgacaaa cgtgtaaata atgaagggca 720
attattttat aaagtcagag taacttcttc accaactggt gaccccgtat cattggttta 780
taaagtgaac gctacagatg gaacaattat ggaaaaacaa gatttaacgg aacatgtcgg 840
tagtgaagta acgttaaaaa actcttttca agtaacgttt aatgtaccag ttgaaaaaag 900
caatacggga attgctttac acggaacgga taacacaggg gtttaccatg cagtagttga 960
tggcaaaaat aattattcta ttattcaagc gccatcacta gcgacattaa atcagaatgc 1020
tattgacgcc tatacgcatg gaaaatttgt gaaaacatat tatgaagatc atttccaacg 1080
acacagtatt gatgatcgag ggatgcccat cttgtcagtt gttgatgaac aacatccaga 1140
tgcttatgac aatgcttttt gggatggaaa agcaatgcgt tatggtgaaa caagtacacc 1200
aacaggaaaa acgtatgctt cctctttaga tgtagttggt catgaaatga cacatggtgt 1260
gacggaacat actgccggtt tagaatattt aggacaatca ggtgccttga atgaatctta 1320
ttctgatttg atgggttata ttatttcggg tgcatctaat ccagaaattg gtgcggatac 1380
tcagagtgtt gaccgaaaaa caggtattcg aaatttacaa acgccaagta aacacggaca 1440
accagaaacc atggctcaat acgacgatcg agcacggtat aaaggaacgc cttattatga 1500
tcaaggcggt gttcattata acagtggaat tattaatcgg attggttaca ccattatcca 1560
gaacttaggc attgaaaaag cacagactat tttctacagc tcgttagtaa attacttaac 1620
acctaaagca caattcagtg atgctcgtga tgcgatgctt gctgctgcaa aagttcaata 1680
tggcgatgaa gcagcttcag tggtgtcagc agcctttaac tctgctggaa tcggagctaa 1740
agaagacatt caggtaaacc aaccaagtga atctgttctg gtcaatgaat gaaaaaaatt 1800
ccccaattaa ataaaaa 1817
2
2275
DNA
Enterococcus faecalis
2
ggtaccaaag aaaaaaacga acgccacaac caacagcctc taaagcaaca cctgcttctg 60
aaattgaggg agatttagca aatgtcaatg agattctttt ggttcacgat gatcgtgtcg 120
ggtcagcaac gatgggaatg aaagtcttag aagaaatttt agataaagag aaaatttcaa 180
tgccgattcg aaaaattaat attaatgaat taactcaaca aacacaggct ttaattgtca 240
caaaagctga actaacggaa caagcacgta aaaaagcacc gaaagcgaca cacttatcag 300
taaaaagtta tggttaatcc ccaaaaatat gaaacagtgg gtttcgctct taaaagaaag 360
tgcctagaga ggaagaaaac aatggaaaat cttacgaata tttcaattga attaaatcaa 420
cagtttaata caaaagaaga agctattcgc ttttccggcc agaaactagt cgaggcaggc 480
tgtgttgagc ccgcttatat cgaagcaatg attgaaagag accaattgct atctgcccat 540
atggggaatt ttattgccat tcctcatgga acagaagaag ccaaaaaatt agtgaaaaaa 600
tcaggaatct gtgtagtgca agtcccagag ggcgttaatt ttggcaccga agaagatgaa 660
aaaattgcta ccgtattatt tgggattgcc ggagtcggtg aagaacattt gcaattagtc 720
caacaaattg cactttattg tagtgatatg gataacgtgg tgcaacttgc cgatgcatta 780
agtaaagaag aaataacaga aaatttagcc attgcttaaa ggagagaata agaatgaacg 840
cagtacattt tggagcagga aatattggac gcggctttat tggcgaaatt ttagctaaaa 900
cgggtttcat attaccgttt gtggatgtta atggaaacca tcatcaagcg ttaaaagaac 960
gtaaaagtta tacaattgaa ttggccgatg cctcacatca acaaattaac gttgaaaatg 1020
tgaccgggtt aaataacatg acagaaccag aaaaagtagt agaagcaatt gcggaagccg 1080
atttagtcac gacggcaatt ggtcctaata ttttaccaag aattgctgaa ttaattgctc 1140
aaggaattga tgcacgtgcc gaagcaaatt gtcaaaacgg cccgctggat attatcgctt 1200
gtgaaaatat gattggtggt tcaacctttt tagcagaaga agtggccata atatttgaaa 1260
aacccagctt atctgaacaa tggattggtt ttcctgatgc ggcagttgat cggattgttc 1320
cattacaaaa acataaagat ccactttttg ttcaagttga gcctttttgt gaatgggtca 1380
ttgatgatac caaccgaaaa gccaaagaga ttcagttaga aggcgtcatt acttgtcgat 1440
tagagccgta tattgaacga aaattattta gtgtaaccag tggccatgct acagttgcct 1500
atacaggggc gttgttaggc tatcaaacca ttgacgaagc gatgcaggac gccttagtgg 1560
tagcgcaact caaatcagtt ttgcaggaaa ccggtaaact tttagtggcc aaatggaatt 1620
ttgatgaaca agaacatgca gcctatattg aaaaaattat caaccgtttc caaaataaat 1680
atatttcaga tgctattaca cgtgtagcac ggacaccaat cagaaaatta ggtgcgcaag 1740
aacggtttat tcgaccaatc cgtgaattac aggaacgcaa tctagtgtcg gccgcattta 1800
tagcaatgat tggtattgtc tttaattatc atgatccaga agatgaacaa agccgtcaat 1860
tacaggaaat gcttgaccaa gaaagtgttg atacagtgga tcgctgaagt aacgggcatt 1920
gaagatccag aaacggttaa aaatattaaa caaaacgtag aactgctatg cgcgaccaca 1980
agtagcataa ttaacaaaat ccttctacca agatacttca catttcttaa ttaaagaaaa 2040
aacaaccgcg cctcacctga gccgaccccc aaaagttaga cctagaaatc taacttttgg 2100
aggttttttt gtatggcaaa atacagtttt gaaatttaaa cttaaacttg ttcatgacta 2160
cttatatggt caaggaggtc taaggtttct cgcaaagaag tatgggttta aagatagtct 2220
caaataagca aatggataaa tgcctataaa gaacttggtg aagaaggggg gatcc 2275
3
227
DNA
Escherichia coli
3
gatccgccat gggttgtttt ccgattgagg attttataga tggtttctgg cgacctgcac 60
aggagtacgg tgatttttaa ttattgcaat tgcacaagag tcagttctcc cccaaagaca 120
gcaccggtat caatataatg caggttgcca atatccacgc gatggcgcaa aggtgtatga 180
ccaaaccaga aatgatcggc cacctgcatc gccagttcgc gagtcgg 227
4
278
DNA
Escherichia coli
4
gatctaaatc aaattaattg gttaaagata accacagcgg ggccgacata aactctgaca 60
agaagttaac aaccatataa cctgcacagg acgcgaacat gtcttctcat ccgtatgtca 120
cccagcaaaa taccccgctg gcggacgaca ccactctgat gtccactacc gatctcgctt 180
tccagcgtca tattggggcg cgctacgttg gggcgtgggc gtaattggtc aatcaggcgc 240
ggggtcagcg gataaacatt caccattttg tcgagatc 278
5
1596
DNA
Escherichia coli
5
atggctgaca ttctgctgct cgataatatc gactctttta cgtacaacct ggcagatcag 60
ttgcgcagca atgggcataa cgtggtgatt taccgcaacc atataccggc gcaaacctta 120
attgaacgct tggcgaccat gagtaatccg gtgctgatgc tttctcctgg ccccggtgtg 180
ccgagcgaag ccggttgtat gccggaactc ctcacccgct tgcgtggcaa gctgcccatt 240
attggcattt gcctcggaca tcaggcgatt gtcgaagctt acgggggcta tgtcggtcag 300
gcgggcgaaa ttctccacgg taaagcctcc agcattgaac atgacggtca ggcgatgttt 360
gccggattaa caaacccgct gccggtggcg cgttatcact cgctggttgg cagtaacatt 420
ccggccggtt taaccatcaa cgcccatttt aatggcatgg tgatggcagt acgtcacgat 480
gcggatcgcg tttgtggatt ccagttccat ccggaatcca ttctcaccac ccagggcgct 540
cgcctgctgg aacaaacgct ggcctgggcg cagcataaac tagagccagc caacacgctg 600
caaccgattc tggaaaaact gtatcaggcg cagacgctta gccaacaaga aagccaccag 660
ctgttttcag cggtggtgcg tggcgagctg aagccggaac aactggcggc ggcgctggtg 720
agcatgaaaa ttcgcggtga gcacccgaac gagatcgccg gggcagcaac cgcgctactg 780
gaaaacgcag cgccgttccc gcgcccggat tatctgtttg ctgatatcgt cggtactggc 840
ggtgacggca gcaacagtat caatatttct accgccagtg cgtttgtcgc cgcggcctgt 900
gggctgaaag tggcgaaaca cggcaaccgt agcgtctcca gtaaatctgg ttcgtccgat 960
ctgctggcgg cgttcggtat taatcttgat atgaacgccg ataaatcgcg ccaggcgctg 1020
gatgagttag gtgtatgttt cctctttgcg ccgaagtatc acaccggatt ccgccacgcg 1080
atgccggttc gccagcaact gaaaacccgc accctgttca atgtgctggg gccattgatt 1140
aacccggcgc atccgccgct ggcgttaatt ggtgtttata gtccggaact ggtgctgccg 1200
attgccgaaa ccttgcgcgt gctggggtat caacgcgcgg cggtggtgca cagcggcggg 1260
atggatgaag tttcattaca cgcgccgaca atcgttgccg aactgcatga cggcgaaatt 1320
aaaagctatc agctcaccgc agaagacttt ggcctgacac cctaccacca ggagcaactg 1380
gcaggcggaa caccggaaga aaaccgtgac attttaacac gtttgttaca aggtaaaggc 1440
gacgccgccc atgaagcagc cgtcgctgcg aacgtcgcca tgttaatgcg cctgcatggc 1500
catgaagatc tgcaagccaa tgcgcaaacc gttcttgagg tactgcgcag tggttccgct 1560
tacgacagag tcaccgcact ggcggcacga gggtaa 1596
6
2703
DNA
Escherichia coli
6
gacgacttag ttttgacgga atcagcatag ttaatcactt cactgtggaa aatgaggaaa 60
tattattttt tttgcgcttc gtaattaatg gttataaggt cggccagaaa cctttctaat 120
gcaagcgatg acgttttttt atgtgtctga atttgcactg tgtcacaatt ccaaatcttt 180
attaacaact cacctaaaac gacgctgatc cagcgtgaat actggtttcc cttatgttca 240
tcagattcat ttaagcaagg gtttcttctt cattcctgat gaaagtgcca tctaaaaaga 300
tgatcttaat aaatctatta agaatgagat ggagcacact ggatatttta cttatgaaac 360
tgtttcactc ctttacttaa tttatagagt taccttccgc tttttgaaaa tacgcaacgg 420
ccattttttg cacttagata cagattttct gcgctgtatt gcattgattt gatgctaatc 480
ctgtggtttg cactagcttt aagtggttga gatcacattt ccttgctcat ccccgcaact 540
cctccctgcc taatcccccg caggatgagg aaggtcaaca tcgagcctgg caaactagcg 600
ataacgttgt gttgaaaatc taagaaaagt ggaactccta tgtcacaacc tatttttaac 660
gataagcaat ttcaggaagc gctttcacgt cagtggcagc gttatggctt aaattctgcg 720
gctgaaatga ctcctcgcca gtggtggcta gcagtgagtg aagcactggc cgaaatgctg 780
cgtgctcagc cattcgccaa gccggtggcg aatcagcgac atgttaacta catctcaatg 840
gagtttttga ttggtcgcct gacgggcaac aacctgttga atctcggctg gtatcaggat 900
gtacaggatt cgttgaaggc ttatgacatc aatctgacgg acctgctgga agaagagatc 960
gacccggcgc tgggtaacgg tggtctggga cgtctggcgg cgtgcttcct cgactcaatg 1020
gcaactgtcg gtcagtctgc gacgggttac ggtctgaact atcaatatgg tttgttccgc 1080
cagtcttttg tcgatggcaa acaggttgaa gcgccggatg actggcatcg cagtaactac 1140
ccgtggttcc gccacaacga agcactggat gtgcaggtag ggattggcgg taaagtgacg 1200
aaagacggac gctgggagcc ggagtttacc attaccggtc aagcgtggga tctccccgtt 1260
gtcggctatc gtaatggcgt ggcgcagccg ctgcgtctgt ggcaggcgac gcacgcgcat 1320
ccgtttgatc tgactaaatt taacgacggt gatttcttgc gtgccgaaca gcagggcatc 1380
aatgcggaaa aactgaccaa agttctctat ccaaacgaca accatactgc cggtaaaaag 1440
ctgcgcctga tgcagcaata cttccagtgt gcctgttcgg tagcggatat tttgcgtcgc 1500
catcatctgg cggggcgtga actgcacgaa ctggcggatt actaagttat tcagctgaac 1560
gatacccacc caactatcgc gattccagaa ctgctgcgcg tgctgatcga tgagcaccag 1620
atgagctggg atgacgcttg ggccattacc agcaaaactt tcgcttacac caaccatacc 1680
ctgatgccag aagcgctgga acgctgggat gtgaaactgg tgaaaggctt actgccgcgc 1740
cacatgcaga ttattaacga aattaatact cgctttaaaa cgctggtaga gaaaacctgg 1800
ccgggcgatg aaaaagtgtg ggccaaactg gcggtggtgc acgacaaaca agtgcatatg 1860
gcgaacctgt gtgtggttgg cggtttcgcg gtgaacggtg ttgcggcgct gcactcggat 1920
ctggtggtga aagatctgtt cccggaatat caccagctat ggccgaacaa attccataac 1980
gtcaccaacg gtattacccc acgtcgctgg atcaaacagt gcaacccggc actggcggct 2040
ctgttggata aatcactgca aaaagagtgg gctaacgatc tcgatcagct gatcaatctg 2100
gttaaattgg ctgatgatgc gaaattccgt cagctttatc gcgtgatcaa gcaggcgaat 2160
aaagtccgtc tggcggagtt tgtgaaagtt cgtaccggta ttgacatcaa tccacaggcg 2220
attttcgata ttcagatcaa acgtttgcac gagtacaaac gccagcacct gaatctgctg 2280
cgtattctgg cgttgtacaa agaaattcgt gaaaacccgc aggctgatcg cgtaccgcgc 2340
gtcttcctct tcggcgcgaa agcggcaccg ggctactacc tggctaagaa tattatcttt 2400
gcgatcaaca aagtggctga cgtgatcaac aacgatccgc tggttggcga taagttgaag 2460
gtggtgttcc tgccggatta ttgcgtttcg gcggcggaaa aactgatccc ggcggcggat 2520
atctccgaac aaatttcgac tgcaggtaaa gaagcttccg gtaccggcaa tatgaaactg 2580
gcgctcaatg gtgcgcttac tgtcggtacg ctggatgggg cgaacgttga aatcgccgag 2640
aaagtcggtg aagaaaatat ctttattttt ggtcatacgg tcaaacaagt gaaggcaatc 2700
gac 2703
7
1391
DNA
Escherichia coli
7
agagaagcct gtcggcaccg tctggtttgc ttttgccact gcccgcggtg aaggcattac 60
ccggcgggat gcttcagcgg cgaccgtgat gcggtgcgtc gtcaggctac tgcgtatgca 120
ttgcagacct tgtggcaaca atttctacaa aacacttgat actgtatgag catacagtat 180
aattgcttca acagaacata ttgactatcc ggtattaccc ggcatgacag gagtaaaaat 240
ggctatcgac gaaaacaaac agaaagcgtt ggcggcagca ctgggccaga ttgagaaaca 300
atttggtaaa ggctccatca tgcgcctggg tgaagaccgt tccatggatg tggaaaccat 360
ctctaccggt tcgctttcac tggatatcgc gcttggggca ggtggtctgc cgatgggccg 420
tatcgtcgaa atctacggac cggaatcttc cggtaaaacc acgctgacgc tgcaggtgat 480
cgccgcagcg cagcgtgaag gtaaaacctg tgcgtttatc gatgctgaac acgcgctgga 540
cccaatctac gcacgtaaac tgggcgtcga tatcgacaac ctgctgtgct cccagccgga 600
caccggcgag caggcactgg aaatctgtga cgccctggcg cgttctggcg cagtagacgt 660
tatcgtcgtt gactccgtgg cggcactgac gccgaaagcg gaaatcgaag gcgaaatcgg 720
cgactctcac atgggccttg cggcacgtat gatgagccag gcgatgcgta agctggcggg 780
taacctgaag cagtccaaca cgctgctgat cttcatcaac cagatccgta tgaaaattgg 840
tgtgatgttc ggtaacccgg aaaccactac cggtggtaac gcgctgaaat tctacgcctc 900
tgttcgtctc gacatccgtc gtatcggcgc ggtgaaagag ggcgaaaacg tggtgggtag 960
cgaaacccgc gtgaaagtgg tgaagaacaa aatcgctgcg ccgtttaaac aggctgaatt 1020
ccagatcctc tacggcgaag gtatcaactt ctacggcgaa ctggttgacc tgggcgtaaa 1080
agagaagctg atcgagaaag caggcgcgtg gtacagctac aaaggtgaga agatcggtca 1140
gggtaaagcg aatgcgactg cctggctgaa agataacccg gaaaccgcga aagagatcga 1200
gaagaaagta cgtgagttgc tgctgagcaa cccgaactca acgccggatt tctctgtaga 1260
tgatagcgaa ggcgtagcag aaactaacga agatttttaa tcgtcttgtt tgatacacaa 1320
gggtcgcatc tgcggccctt ttgctttttt aagttgtaag gatatgccat gacagaatca 1380
acatcccgtc g 1391
8
238
DNA
Klebsiella pneumoniae
8
tcgccaggaa ggcggcattc ggctgggtca gagtgacctg cagcgtggtg tcgttcagcg 60
ctttcacccc caacgtctcg ggtccctttt gcccgagggc aatctcgcgg gcgttggcga 120
tatgcatatt gccagggtag ctcgcgtagg gggaggctgt tgccggcgag accagccgtt 180
gccagctcca gacgatatcc tgcgctgtaa tggccgtgcc gtcagaccag gtcagacc 238
9
385
DNA
Klebsiella pneumoniae
9
cagcgtaatg cgccgcggca taacggcgcc actatcgaca gtcagttcgt cagcctgcag 60
cctgggctga atctgggacc atggcgcctg ccgaactaca gcacctatag ccacagcgat 120
aacaacagcc gctgggagtc ggtttactcc tatcttgccc gcgatattca caccctacgc 180
agccagctgg tggtcggtaa tacgtatacc tcttccggca ttttcgacag tttgagtttt 240
accggtctgc agctcagttc gacaaagaga tgctgccgga tagcctgcat gctttgcgcc 300
gacgattcga gggatcgcgc gcaccaccgc ggaggtctcg gtttatcaga atggttacag 360
catttataaa accaccgtcg ctacc 385
10
462
DNA
Klebsiella pneumoniae
10
ctctatattc aggacgaaca tatctggacc tctggcgggg tcagttccgg ctttgatcgc 60
cctgcacccg cagcgggtga tcgcccctca tctgctactg cggcgctgca acaggcgacg 120
atcgatgacg ttattcctgg ccagcaaaca gcagaccaat taaggtctga tagtggctct 180
cttcctccgg cgcgcgacgg tccaggcggc tcaacagttt ggtgcatagc gctttgcggt 240
tgagatgacg cccttcgtta agaatatcca tcacgatctc cgtccatgga gagtagcgtt 300
tattccagaa tagggttttt caggatctca tggatctgcg cctgcttatc gctattttgt 360
aaccagatcg cataaagtgg acgggataac gtagcgctgt ccatgaccgt atgtaaccca 420
tgcttctctt tcgcccagcg agcaggtagc caacagcagc cg 462
11
730
DNA
Klebsiella pneumoniae
11
gctgaccgct aaactgggtt acccgatcac tgacgatctg gacatctaca cccgtctggg 60
cggcatggtt tggcgcgctg actccaaagg caactacgct tcaaccggcg tttcccgtag 120
cgaacacgac actggcgttt ccccagtatt tgctggcggc gtagagtggg ctgttactcg 180
tgacatcgct acccgtctgg aataccagtg ggttaacaac atcggcgacg cgggcactgt 240
gggtacccgt cctgataacg gcatgctgag cctgggcgtt tcctaccgct tcggtcagga 300
agatgctgca ccggttgttg ctccggctcc ggctccggct ccggaagtgg ctaccaagca 360
cttcaccctg aagtctgacg ttctgttcaa cttcaacaaa gctaccctga aaccggaagg 420
tcagcaggct ctggatcagc tgtacactca gctgagcaac atggatccga aagacggttc 480
cgctgttgtt ctgggctaca ccgaccgcat cggttccgaa gcttacaacc agcagctgtc 540
tgagaaacgt gctcagtccg ttgttgacta cctggttgct aaaggcatcc cggctggcaa 600
aatctccgct cgcggcatgg gtgaatccaa cccggttact ggcaacacct gtgacaacgt 660
gaaagctcgc gctgccctga tcgattgcct ggctccggat cgtcgtgtag agatcgaagt 720
taaaggtatc 730
12
225
DNA
Proteus mirabilis
12
cgctactgtt taaatctcat ttgaaacatc gcaaagtcag tgaaccacat attcgaggat 60
ggcatgcact agaaaatatt aataagattt tagcgaaacc taatcagcgc aatatcgctt 120
aattatttta ggtatgttct cttctatcct acagtcacga ggcagtgtcg aacttgatcc 180
tcattttatt aatcacatga ccaatggtat aagcgtcgtc acata 225
13
402
DNA
Proteus mirabilis
13
acattttaaa taggaagcca cctgataaca tccccgcagt tggatcatca gatttatagc 60
ggcatttggt atccgctaga taaaagcagt ccaacgatcc cgccaattgt tagatgaaat 120
tggactattc tttttatttg ctccgcttta tcacagtggt tttcgctttg ccgcccctgt 180
gcgccaacag ctaagaacac gcacgctctt taatgtgtta ggcccattaa ttaatccagc 240
gcgttccgcc tttagcatta attggtgttt atagtcctga attattaatg cctattgcag 300
ataccttaaa tgtcttgggc tacaaacgtg cggcagtggt ccatagtggt ggaatggatg 360
aagtgtcatt acatgctccc acacaagtgg ctgagttaca ca 402
14
157
DNA
Proteus mirabilis
14
ctgaaacgca tttatgcggg agtcagtgaa atcatcactc aattttcacc cgatgtattt 60
tctgttgaac aagtctttat ggcaaaaaat gcagactcag cattaaaatt aggccaagca 120
agaggtgtgg cgattttagc ggcagtcaat aatgatc 157
15
1348
DNA
Proteus mirabilis
15
tttctcttta aaatcaattc ttaaagaaat tattaataat taacttgata ctgtatgatt 60
atacagtata atgagtttca acaagcaaaa tcatatacgt tttaatggta gtgacccatc 120
tttatgcttc actgcccaga gggagataac atggctattg atgaaaacaa acaaaaagca 180
ttggccgcag cacttggtca aattgaaaag caatttggta aaggttctat catgcgtctg 240
ggcgaagacc gttccatgaa cgtagaaact atctctacag gatctttatc attagacgtt 300
gctttaggtg caggtggatt gccacgtggc cgtattgttg aaatctatgg ccctgaatct 360
tctggtaaaa caaccttgac tctacaagtt attgcctctg ctcagcgtga aggaaaaatt 420
tgtgcattta ttgatgctga acatgcatta gacccaattt atgctcaaaa gctaggtgtc 480
gatatcgata atctactctg ctctcaacct gacacaggtg aacaagctct ggaaatttgt 540
gatgcattat ctcgctctgg tgcggtcgat gttattgtcg tggactccgt ggcagcatta 600
acaccaaaag ctgaaattga aggtgaaatt ggtgattcac acgttggttt agccgcacgt 660
atgatgagcc aagctatgcg taaactagcg ggtaacctta aaaactctaa tacactgctg 720
attttcatta accaaattcg tatgaaaatc ggtgttatgt ttggtaaccc agaaaccacg 780
accggtggta atgcgcttaa attctatgct tctgttcgtt tagacattcg tcgcattggc 840
tctgtcaaaa atggtgatga agtcattggt agtgagactc gcgttaaagt tgttaaaaat 900
aaagtggctg caccgtttaa acaagctgaa ttccaaatta tgtacggtga aggtattaat 960
acctatggcg aactgattga tttaggtgtt aaacataagt tagtagagaa agcaggtgct 1020
tggtatagct acaatggcga aaaaattggt caaggtaaag ctaacgcaac caattactta 1080
aaagaacatc ctgaaatgta caatgagtta aacactaaat tgcgtgaaat gttgttaaat 1140
catgctggtg aattcacaag tgctgcggat tttgcaggtg aagagtcaga cagtgatgct 1200
gacgacacaa aagagtaatt agctggttgt catgctgttt gtgtgaaaat agaccttaaa 1260
tcattggcta ttatcacgac agcatcccat agaataactt gtttgtataa attttattca 1320
gatggcaaag gaagccttaa aaaagctt 1348
16
2167
DNA
Pseudomonas aeruginosa
16
ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat 60
ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac 120
aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg 180
aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg 240
agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc 300
ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg 360
tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg 420
agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga 480
acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga 540
ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa 600
gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct 660
acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg 720
cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg 780
ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg 840
aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt 900
acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct 960
tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc 1020
tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt 1080
acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca 1140
gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc 1200
agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt 1260
ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg 1320
cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca 1380
gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt 1440
gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc 1500
gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc 1560
cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga 1620
tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa 1680
gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca 1740
ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct 1800
gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg 1860
aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt 1920
catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg 1980
gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct 2040
gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa 2100
ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt 2160
cctcgag 2167
17
1872
DNA
Pseudomonas aeruginosa
17
gaattcccgg gagttcccga cgcagccacc cccaaaacac tgctaaggga gcgcctcgca 60
gggctcctga ggagatagac catgccattt ggcaagccac tggtgggcac cttgctcgcc 120
tcgctgacgc tgctgggcct ggccaccgct cacgccaagg acgacatgaa agccgccgag 180
caataccagg gtgccgcttc cgccgtcgat cccgctcacg tggtgcgcac caacggcgct 240
cccgacatga gtgaaagcga gttcaacgag gccaagcaga tctacttcca acgctgcgcc 300
ggttgccacg gcgtcctgcg caagggcgcc accggcaagc cgctgacccc ggacatcacc 360
cagcaacgcg gccagcaata cctggaagcg ctgatcacct acggcacccc gctgggcatg 420
ccgaactggg gcagctccgg cgagctgagc aaggaacaga tcaccctgat ggccaagtac 480
atccagcaca ccccgccgca accgccggag tggggcatgc cggagatgcg cgaatcgtgg 540
aaggtgctgg tgaagccgga ggaccggccg aagaaacagc tcaacgacct cgacctgccc 600
aacctgttct cggtgaccct gcgcgacgcc gggcagatcg ccctggtcga cggcgacagc 660
aaaaagatcg tcaaggtcat cgataccggc tatgccgtgc atatctcgcg gatgtccgct 720
tccggccgct acctgctggt gatcggccgc gacgcgcgga tcgacatgat cgacctgtgg 780
gccaaggagc cgaccaaggt cgccgagatc aagatcggca tcgaggcgcg ctcggtggaa 840
agctccaagt tcaagggcta cgaggaccgc tacaccatcg ccggcgccta ctggccgccg 900
cagttcgcga tcatggacgg cgagaccctg gaaccgaagc agatcgtctc cacccgcggc 960
atgaccgtag acacccagac ctaccacccg gaaccgcgcg tggcggcgat catcgcctcc 1020
cacgagcacc ccgagttcat cgtcaacgtg aaggagaccg gcaaggtcct gctggtcaac 1080
tacaaggata tcgacaacct caccgtcacc agcatcggtg cggcgccgtt cctccacgac 1140
ggcggctggg acagcagcca ccgctacttc atgaccgccg ccaacaactc caacaaggtt 1200
gccgtgatcg actccaagga ccgtcgcctg tcggccctgg tcgacgtcgg caagaccccg 1260
cacccggggc gtggcgccaa cttcgtgcat cccaagtacg gcccggtgtg gagcaccagc 1320
cacctgggcg acggcagcat ctcgctgatc ggcaccgatc cgaagaacca tccgcagtac 1380
gcctggaaga aagtcgccga actacagggc cagggcggcg gctcgctgtt catcaagacc 1440
catccgaagt cctcgcacct ctacgtcgac accaccttca accccgacgc caggatcagc 1500
cagagcgtcg cggtgttcga cctgaagaac ctcgacgcca agtaccaggt gctgccgatc 1560
gccgaatggg ccgatctcgg cgaaggcgcc aagcgggtgg tgcagcccga gtacaacaag 1620
cgcggcgatg aagtctggtt ctcggtgtgg aacggcaaga acgacagctc cgcgctggtg 1680
gtggtggacg acaagaccct gaagctcaag gccgtggtca aggacccgcg gctgatcacc 1740
ccgaccggta agttcaacgt ctacaacacc cagcacgacg tgtactgaga cccgcgtgcg 1800
gggcacgccc cgcacgctcc cccctacgag gaaccgtgat gaaaccgtac gcactgcttt 1860
cgctgctcgc ca 1872
18
3451
DNA
Pseudomonas aeruginosa
18
tcgagacggg aagccactct ctacgagaag acagaagccc ctcacagagg cctctgtcta 60
cgcctactaa agctcggctt attcatatgt atttatattc tttcaataga tcactcagcg 120
ctattttaag ttcaccctct gtaagttcac ctgggcgctc tttctttcct tcggtaaagc 180
tgtcggccag accaaacatt aaactcaagc atctcccaag cgatgcatca tcttgggcca 240
gcatccctga atcgcgcgtc ggacctccaa gtcttaaaaa attcttcgct gaaggttttc 300
ccatcaatcg atgaggctaa tagcttcttt gcaatatcta tcatttccat gctcacctta 360
aagcacctca tttttcatgt aaaaattgta ttgatccgtg ccagactcaa tcctccaccc 420
agaaacaaac atcccatcct ctccaatgat aacaacaata ttagtcctgg cattgtaatg 480
tacttttgag tttacttcgg agtggtaagt ccctttttct acggttgcag gatcagcaag 540
gtgctcaaga attttatccc taaactctgc aagcgttcca ttgttggcgc ttttttcacc 600
cagcccaaaa tcatatttgt ggctatcaaa ttttttctgt agttgcctcc gtgtgaagat 660
accactatca agaggactac tgagcattac ataaacaggt ttgactccag aatccgccgg 720
gaaaatcacg atcagatcgt ttaggtccag tagcattccc ggataggact ccgggccggt 780
cttcaacggt gtgagggccg ctccctcata taccggcacc ggcttcggta tgaccggagt 840
ggtactcgaa gggttctggt ttcctggagg actcgccggc gtccaagtca ggatcagtgg 900
cggcgcttct gcgaccgtag agggaaccgt aacctcgtac agtcctgttg cggcgttata 960
ggccccatcc ggaccggaac gctttcggaa cgctcacacc atcggtctga ccaccgaaag 1020
gtcgtcgtgt tgcctcgcgc ctcgttggtc aggcgcatcg gcagatcgac ggtaccgctg 1080
gcttttgcaa ccgcgttcag gtttacgctt gggggaagcc ccaatttagc ggcatccatg 1140
cccagggcgt aacgaacgct atcgggcgtt tggtcctgcc attgctcggc agtccgggag 1200
agtaggtcag actggcaagc cacggccatc accgaggtgc tgaagccagg accgccagga 1260
cggcaatcgc atcggagatc gcttgagcaa gggatgcggc gcctgtgcga cctggatcag 1320
accccgctgc ggcggtggcg cacccgctgc cattggctgg catggcataa gtattggcag 1380
ccctgatcgc cgcttgacga gcgatttcct tgcgccttgc cgtttcggcg ttcagcttgt 1440
ccagccgtgc ttgcaggctg gcgatttcat ccactaggta ggacatcggc gttgtaggtt 1500
gccttttgtt tctccagtgc attgggtgcc ttggcaatca aggcattgtt tgcagtctgc 1560
aattcttctt attgcgatcg cctgcgtaag gagttgagta gcgcgttcaa gccactgctc 1620
tggcgttgga ttggtcagtt gaggcaaagc attcccagcc tggtcaagct cggactgcac 1680
ttttttctcg acatttgcct tcctggcctt gtagtccgcc tccacctcag cagcggctcg 1740
ctgggcttct gcttccaatg accgggcttt attctccagc tcttgagacg tttgtttcaa 1800
gatagcgatt tgcgccttat agatatcggc gctgtacgct ttggccagct cactcatatg 1860
gcgatccagg aactctccat agaattttcg gctggccagc aactgactct ggtacatcga 1920
ctctgacttc tgaggaaagt ctgaagccgt ataaagattg gccgggcgat cctcaatgac 1980
ctttagcgat tttgctttgg catccatgag tgcatcaacg atactctttt catcgcggat 2040
gtcattggca ctgaccgctt tacctggcaa ccccgcttca ctcttgagtt catcaacctc 2100
cttcagggtt tcatttttca ggtttttctt gagttctgaa tgggacttat caagcgtact 2160
tcttagcttc ctgtactcct gcattccagt accgacatac ggacttggtc ctggtgggac 2220
aaatggtgga gtaccgtagc ttgatcgagc aggaatatac tggattatgt cacgcccacc 2280
accctgcaca tgtgtaataa ccatcgaacc aggttcgtaa tcattgacag ccatagatcg 2340
cccctacatt aatttgaaag tgtaatgtat tgagcgactc ccacctagag aaccctctcc 2400
cagtcaataa gccccaatgc atcggcaata cactgcaatc aacttcaata tcccgtgttt 2460
agatgatcca gaaggtgcgc tctctcgcct cttataatcg cgcctgcgtc aaacggtcat 2520
ttccttaacg cacacctcat ctaccccggc cagtcacgga agccgcatac cttcggttca 2580
ttaacgaact cccactttca aaattcatcc atgccgcccc ttcgcgagct tccggacaaa 2640
gccacgctga ttgcgagccc agcgtttttg attgcaagcc gctgcagctg gtcaggccgt 2700
ttccgcaacg cttgaagtcc tggccgatat accggcaggg ccagccatcg ttcgacgaat 2760
aaagccacct cagccatgat gccctttcca tccccagcgg aaccccgaca tggacgccaa 2820
agccctgctc ctcggcagcc tctgcctggc cgccccattc gccgacgcgg cgacgctcga 2880
caatgctctc tccgcctgcc tcgccgcccg gctcggtgca ccgcacacgg cggagggcca 2940
gttgcacctg ccactcaccc ttgaggcccg gcgctccacc ggcgaatgcg gctgtacctc 3000
ggcgctggtg cgatatcggc tgctggccag gggcgccagc gccgacagcc tcgtgcttca 3060
agagggctgc tcgatagtcg ccaggacacg ccgcgcacgc tgaccctggc ggcggacgcc 3120
ggcttggcga gcggccgcga actggtcgtc accctgggtt gtcaggcgcc tgactgacag 3180
gccgggctgc caccaccagg ccgagatgga cgccctgcat gtatcctccg atcggcaagc 3240
ctcccgttcg cacattcacc actctgcaat ccagttcata aatcccataa aagccctctt 3300
ccgctccccg ccagcctccc cgcatcccgc accctagacg ccccgccgct ctccgccggc 3360
tcgcccgaca agaaaaacca accgctcgat cagcctcatc cttcacccat cacaggagcc 3420
atcgcgatgc acctgatacc ccattggatc c 3451
19
744
DNA
Pseudomonas aeruginosa
19
gggttcagca agcgttcagg ggcggttcag taccctgtcc gtactctgca agccgtgaac 60
gacacgactc tcgcagaacg gagaaacacc atgaaagcac tcaagactct cttcatcgcc 120
accgccctgc tgggttccgc cgccggcgtc caggccgccg acaacttcgt cggcctgacc 180
tggggcgaga ccagcaacaa catccagaaa tccaagtcgc tgaaccgcaa cctgaacagc 240
ccgaacctcg acaaggtgat cgacaacacc ggcacctggg gcatccgcgc cggccagcag 300
ttcgagcagg gccgctacta cgcgacctac gagaacatct ccgacaccag cagcggcaac 360
aagctgcgcc agcagaacct gctcggcagc tacgacgcct tcctgccgat cggcgacaac 420
aacaccaagc tgttcggcgg tgccaccctc ggcctggtca agctggaaca ggacggcaag 480
ggcttcaagc gcgacagcga tgtcggctac gctgccgggc tgcaggccgg tatcctgcag 540
gagctgagca agaatgcctc gatcgaaggc ggctatcgtt acctgcgcac caacgccagc 600
accgagatga ccccgcatgg cggcaacaag ctgggctccc tggacctgca cagcagctcg 660
caattctacc tgggcgccaa ctacaagttc taaatgaccg cgcagcgccc gcgagggcat 720
gcttcgatgg ccgggccgga aggt 744
20
2760
DNA
Pseudomonas aeruginosa
20
ctgcagctgg tcaggccgtt tccgcaacgc ttgaagtcct ggccgatata ccggcagggc 60
cagccatcgt tcgacgaata aagccacctc agccatgatg ccctttccat ccccagcgga 120
accccgacat ggacgccaaa gccctgctcc tcggcagcct ctgcctggcc gccccattcg 180
ccgacgcggc gacgctcgac aatgctctct ccgcctgcct cgccgcccgg ctcggtgcac 240
cgcacacggc ggagggccag ttgcacctgc cactcaccct tgaggcccgg cgctccaccg 300
gcgaatgcgg ctgtacctcg gcgctggtgc gatatcggct gctggccagg ggcgccagcg 360
ccgacagcct cgtgcttcaa gagggctgct cgatagtcgc caggacacgc cgcgcacgct 420
gaccctggcg gcggacgccg gcttggcgag cggccgcgaa ctggtcgtca ccctgggttg 480
tcaggcgcct gactgacagg ccgggctgcc accaccaggc cgagatggac gccctgcatg 540
tatcctccga tcggcaagcc tcccgttcgc acattcacca ctctgcaatc cagttcataa 600
atcccataaa agccctcttc cgctccccgc cagcctcccc gcatcccgca ccctagacgc 660
cccgccgctc tccgccggct cgcccgacaa gaaaaaccaa ccgctcgatc agcctcatcc 720
ttcacccatc acaggagcca tcgcgatgca cctgataccc cattggatcc ccctggtcgc 780
cagcctcggc ctgctcgccg gcggctcgtc cgcgtccgcc gccgaggaag ccttcgacct 840
ctggaacgaa tgcgccaaag cctgcgtgct cgacctcaag gacggcgtgc gttccagccg 900
catgagcgtc gacccggcca tcgccgacac caacggccag ggcgtgctgc actactccat 960
ggtcctggag ggcggcaacg acgcgctcaa gctggccatc gacaacgccc tcagcatcac 1020
cagcgacggc ctgaccatcc gcctcgaagg cggcgtcgag ccgaacaagc cggtgcgcta 1080
cagctacacg cgccaggcgc gcggcagttg gtcgctgaac tggctggtac cgatcggcca 1140
cgagaagccc tcgaacatca aggtgttcat ccacgaactg aacgccggca accagctcag 1200
ccacatgtcg ccgatctaca ccatcgagat gggcgacgag ttgctggcga agctggcgcg 1260
cgatgccacc ttcttcgtca gggcgcacga gagcaacgag atgcagccga cgctcgccat 1320
cagccatgcc ggggtcagcg tggtcatggc ccagacccag ccgcgccggg aaaagcgctg 1380
gagcgaatgg gccagcggca aggtgttgtg cctgctcgac ccgctggacg gggtctacaa 1440
ctacctcgcc cagcaacgct gcaacctcga cgatacctgg gaaggcaaga tctaccgggt 1500
gctcgccggc aacccggcga agcatgacct ggacatcaaa cccacggtca tcagtcatcg 1560
cctgcacttt cccgagggcg gcagcctggc cgcgctgacc gcgcaccagg cttgccacct 1620
gccgctggag actttcaccc gtcatcgcca gccgcgcggc tgggaacaac tggagcagtg 1680
cggctatccg gtgcagcggc tggtcgccct ctacctggcg gcgcggctgt cgtggaacca 1740
ggtcgaccag gtgatccgca acgccctggc cagccccggc agcggcggcg acctgggcga 1800
agcgatccgc gagcagccgg agcaggcccg tctggccctg accctggccg ccgccgagag 1860
cgagcgcttc gtccggcagg gcaccggcaa cgacgaggcc ggcgcggcca acgccgacgt 1920
ggtgagcctg acctgcccgg tcgccgccgg tgaatgcgcg ggcccggcgg acagcggcga 1980
cgccctgctg gagcgcaact atcccactgg cgcggagttc ctcggcgacg gcggcgacgt 2040
cagcttcagc acccgcggca cgcagaactg gacggtggag cggctgctcc aggcgcaccg 2100
ccaactggag gagcgcggct atgtgttcgt cggctaccac ggcaccttcc tcgaagcggc 2160
gcaaagcatc gtcttcggcg gggtgcgcgc gcgcagccag gacctcgacg cgatctggcg 2220
cggtttctat atcgccggcg atccggcgct ggcctacggc tacgcccagg accaggaacc 2280
cgacgcacgc ggccggatcc gcaacggtgc cctgctgcgg gtctatgtgc cgcgctcgag 2340
cctgccgggc ttctaccgca ccagcctgac cctggccgcg ccggaggcgg cgggcgaggt 2400
cgaacggctg atcggccatc cgctgccgct gcgcctggac gccatcaccg gccccgagga 2460
ggaaggcggg cgcctggaga ccattctcgg ctggccgctg gccgagcgca ccgtggtgat 2520
tccctcggcg atccccaccg acccgcgcaa cgtcggcggc gacctcgacc cgtccagcat 2580
ccccgacaag gaacaggcga tcagcgccct gccggactac gccagccagc ccggcaaacc 2640
gccgcgcgag gacctgaagt aactgccgcg accggccggc tcccttcgca ggagccggcc 2700
ttctcggggc ctggccatac atcaggtttt cctgatgcca gcccaatcga atatgaattc 2760
21
172
DNA
Staphylococcus saprophyticus
21
ttgatgaaat gcatcgatta ataaattttc atgtacgatt aaaacgtttt tacccttacc 60
ttttcgtact acctctgcct gaagttgacc acctttaaag tgattcgttg aaatccatta 120
tgctcattat taatacgatc tataaaaaca aatggaatgt gatgatcgat ga 172
22
155
DNA
Staphylococcus saprophyticus
22
gttccattga ctctgtatca cctgttgtaa cgaacatcca tatgtcctga aactccaacc 60
acaggtttga ccacttccaa tttcagacca ccaagtttga cacgtgaaga ttcatcttct 120
aatatttcgg aattaatatc atattattta aatag 155
23
145
DNA
Staphylococcus saprophyticus
23
acatagaaaa actcaaaaga tttacttttt tcaaatggaa aataagggta cacacgatat 60
ttcccgtcat cttcagttac cggtacaaca tcctctttat taacctgcac ataatctgac 120
tccgcttcac tcatcaaact actaa 145
24
266
DNA
Staphylococcus saprophyticus
24
tttcactgga attacatttc gctcattacg tacagtgaca atcgcgtcag atagtttctt 60
ctggttagct tgactcttaa caatcttgtc taaattttgt ttaattcttt gattcgtact 120
agaaatttta cttctaattc cttgtaattc ataacttgca ttatcatata aatcataagt 180
atcacatttt tgatgaatac tttgatataa atctgacaat acaggcagtt gctccattct 240
atcgttaaga atagggtaat taatag 266
25
845
DNA
Haemophilus influenzae
25
tgttaaattt ctttaacagg gattttgtta tttaaattaa acctattatt ttgtcgcttc 60
tttcactgca tctactgctt gagttgcttt ttctgaaacc gcctctttca tttcacttgc 120
tttttctgat gctgcttctt tcatttcgcc tactttttct gacgctgctt ctgttgctga 180
tttaattact tctttcgcat cttccacttt ctctgctact ttatttttca cgtctgtaga 240
aagctgctgt gctttttcct ttacttcagt cattgtatta gctgcagcat cttttgtttc 300
tgatgcgact gatgctacag tttgcttcgt atcctcaact ttttgttttg cttcttgctt 360
atcaaaacaa cctgtcacga ctaaagctga acctaaaacc aatgctaatg ttaatttttt 420
cattattttc tccatagaat aatttgattg ttacaaagcc ctattacttt gatgcagttt 480
agtttacggg aattttcata aaaagaaaaa cagtaatagt aaaactttac ctttctttaa 540
aaagattact ttataaaaaa acatctaaga tattgatttt taatagatta taaaaaacca 600
ataaaaattt tattttttgt aaaaaaaaag aatagtttat tttaaataaa ttacaggaga 660
tgcttgatgc atcaatattt ctgatttatt accatcccat aataattgag caatagttgc 720
aggataaaat gatattggat ttcgttttcc atacagttca gcaacaattt ctcccactaa 780
gggcaaatgg gaaacaatta atacagattt aacgccctcg tcttttagca cttctaaata 840
atcaa 845
26
1598
DNA
Haemophilus influenzae
26
gaatagagtt gcactcaata gattcgggct ttataattgc ccagattttt atttataaca 60
aagggttcca aatgaaaaaa tttaatcaat ctctattagc aactgcaatg ttgttggctg 120
caggtggtgc aaatgcggca gcgtttcaat tggcggaagt ttctacttca ggtcttggtc 180
gtgcctatgc gggtgaagcg gcgattgcag ataatgcttc tgtcgtggca actaacccag 240
ctttgatgag tttatttaaa acggcacagt tttccacagg tggcgtttat attgattcta 300
gaattaatat gaatggtgat gtaacttctt atgctcagat aataacaaat cagattggaa 360
tgaaagcaat aaaggacggc tcagcttcac agcgtaatgt tgttcccggt gcttttgtgc 420
caaatcttta tttcgttgcg ccagtgaatg ataaattcgc gctgggtgct ggaatgaatg 480
tcaatttcgg tctaaaaagt gaatatgacg atagttatga tgctggtgta tttggtggaa 540
aaactgactt gagtgctatc aacttaaatt taagtggtgc ttatcgagta acagaaggtt 600
tgagcctagg tttaggggta aatgcggttt atgctaaagc ccaagttgaa cggaatgctg 660
gtcttattgc ggatagtgtt aaggataacc aaataacaag cgcactctca acacagcaag 720
aaccattcag agatcttaag aagtatttgc cctctaagga caaatctgtt gtgtcattac 780
aagatagagc cgcttggggc tttggctgga atgcaggtgt aatgtatcaa tttaatgaag 840
ctaacagaat tggtttagcc tatcattcta aagtggacat tgattttgct gaccgcactg 900
ctactagttt agaagcaaat gtcatcaaag aaggtaaaaa aggtaattta acctttacat 960
tgccagatta cttagaactt tctggtttcc atcaattaac tgacaaactt gcagtgcatt 1020
atagttataa atatacccat tggagtcgtt taacaaaatt acatgccagc ttcgaagatg 1080
gtaaaaaagc ttttgataaa gaattacaat acagtaataa ctctcgtgtt gcattagggg 1140
caagttataa tctttatgaa aaattgacct tacgtgcggg tattgcttac gatcaagcgg 1200
catctcgtca tcaccgtagt gctgcaattc cagataccga tcgcacttgg tatagtttag 1260
gtgcaaccta taaattcacg ccgaatttat ctgttgatct tggctatgct tacttaaaag 1320
gcaaaaaagt tcactttaaa gaagtaaaaa caataggtga caaacgtaca ttgacattga 1380
atacaactgc aaattatact tctcaagcac acgcaaatct ttacggtttg aatttaaatt 1440
atagtttcta atccgttaaa aaatttagca taataaagca caattccaca ctaagtgtgc 1500
ttttctttta taaaacaagg cgaaaaatga ccgcacttta ttacacttat tacccctcgc 1560
cagtcggacg gcttttgatt ttatctgacg gcgaaaca 1598
27
9100
DNA
Haemophilus influenzae
27
gtcaaaaatt gcgtgcattc tagcgaaaaa atgggctttt gggaactgtg ggatttattt 60
aaaatcttag aaaatcttac cgcactttta agctataaag tgcggtgaaa tttagtggcg 120
tttataatgg agaattactc tggtgtaatc cattcgactg tccagcttcc agtaccttct 180
ggaactaatg tttttgtgag ataaggcaaa atttctttca tttgggtttc taatgtccaa 240
ggtggattaa ttaccaccat accgctcgca gtcattcctc gttgatcgct atctgggcga 300
acggcgagtt caatttttag aatttttcta attcccgttg cttctaaacc cttaaaaata 360
cgtttagttt gttggcgtaa tacaacagga taccaaatcg cataagtgcc agtggcaaaa 420
cgtttatagc cctcttcaat ggctttaaca acgagatcat aatcatcttt taattcataa 480
ggcggatcga tgagtactaa gcctcggcgt tcttttggcg gaagcgttgc tttgacttgt 540
tgaaagccat tgtcacattt tacggtgaca tttttgtcgt cgctaaaatt attgcgaaga 600
attggataat cgctaggatg aagctcggtc aatagtgcgc gatcttgtga gcgcaacaat 660
tccgcggcaa ttaatggaga acccgcgtaa taacgtagtt ctttgccacc ataattgagt 720
tttttgatca tttttacata acgagcaata tcttcgggta aatctgtttg atcccacagg 780
cgtccaatac cttctttata ttcccccgtt ttttctgatt catttgagga taaacgataa 840
cgccccacac cagagtgcgt atccaaataa aaaaagcctt tttctttgag tttaagattt 900
tccaaaatga gcattaaaac aatatgtttc aagacatcgg catgattgcc agcgtgaaat 960
gagtgatgat aactcagcat aatatattcc ttatatattc cttatttgtt taataacgaa 1020
ggcgagccaa ttgactcgcc cgattacaca ctaaagtgcg gtcattttta gaagagttct 1080
tgtggttgcg tcgctggcgt attgccttca ttatttaagc gttgctgtaa ctcagtagga 1140
acataataac cacgctcttg catttccgaa agataggtac gtgtcggttc tgttcccgca 1200
ataaaatatt ctttgcgccc accgtttgga gaaagcaaac ctgtcaaagt atcaatgttt 1260
ttttccacaa tttttggcgg tagcgacaat ttacgttctg gcttatcact caaagccgtt 1320
ttcatataag tgatccaagc aggcattgct gtttttgctc ctgcttctcc acgcccaagt 1380
actcgtttgt tatcatcaaa cccgacataa gttgtggtta ctaagtttgc accaaatccc 1440
gcataccaag ccacttttga actgttggta gtacctgttt taccgcctat atcgctacgt 1500
ttaatgcttt gtgcaatacg ccagctggtg cctttccagt ctaaaccttg ttcgccataa 1560
attgccgtat ttaaggcact acgaatgaga aaagcaagtt cgccactaat gacacgtggc 1620
gcatattcta ttttcgacga agcatttttt gcagcagcca ttaaatcaat cgcatcttct 1680
ttaagtgcgg tcatatttga ttgtaattct ggcagttcag gcacagtttc aggttgttga 1740
tctaattctt cgccattggt gctgtcatct gttggtttta aggcattctc gcctaaagga 1800
atattggcaa agccgttgat tttgtctttg gtttcgccat aaattacagg tatatcatta 1860
cattcaatgc aagcaatttt agggtttgca ataaataagt ctttacccgt gttatcttga 1920
attttttcaa tgatataagg ttcaatgagg aagccaccat tatcaaacac cgcataagct 1980
cgcgccattt ctaatggtgt gaaagaggct gcgccaagtg ctaaggcttc actggcaaaa 2040
tattgatcac gtttaaaacc aaaacgttgt aaaaattctg ctgtgaaatc aatacctgcc 2100
gtttggatag cacgaatagc aattatattt ttggattgac ctaatcctac gcgtaaacgc 2160
atcgggccat cataacgatc aggcgagttt ttcggttgcc acattttttg tcccggtttt 2220
tgaatagaaa tcgggctgtc ttgtaatacg cttgaaagtg ttaagccttt ttctaatgct 2280
gccgcgtaaa taaatggttt gatagaagaa cccacttgaa ctaaagactg tgtggctcga 2340
ttgaatttac tttgttcata gctaaagcca ccgaccactg cttcaatcgc accattatct 2400
gaattaagag aaactaatgc tgaatttgct gcgggaattt gtcctaattg ccattcccca 2460
ttagcacgct gatgaatcca aatttgctcg ccgactttca caggattgct tctgcctgtc 2520
caacgcattg cattggttga taaggtcatt ttttccccag aagcgagcaa tatatcagca 2580
ccgcctttta caattccaat cactgccgca ggaataaatg gctctgaatc aggtagtttg 2640
cgtagaaaac cgacaatgcg atcattgtcc caagcggctt catttttttg ccataatggc 2700
gcgccaccgc gataaccgtg acgcatatcg taatcaatca agttattacg cacagctttt 2760
tgggcttcag cttggtcttt tgaaagtaca gtggtaaata ctttataacc actggtgtaa 2820
gcattttctt cgccaaaacg acgcaccatt tcttgacgca ccatttcagt gacataatcg 2880
gctcgaaatt caaattttgc gccgtgatag ctcgccacaa tcggctcttt caatgcagca 2940
tcatattctt ctttgctgat gtatttttca tctaacatac ggcttagcac cacattgcgg 3000
cgttcttctg aacgttttaa agaataaagc gggttcattg ttgaaggtgc tttaggtaaa 3060
ccagcaataa tcgccatttc cgataaggtc aattcattca atgatttacc gaaataggtt 3120
tgtgctgccg ctgcaacacc ataagaacga tagcctaaaa agattttgtt taaataaagc 3180
tctaatattt cttgtttgtt gagagtattt tcgatttcta ccgcaagcac ggcttcacga 3240
gctttacgaa taatggtttt ttctgaggtt aagaaaaagt tacgcgctaa ttgttgagta 3300
atcgtacttg cgccttgtga tgcaccgcca ttactcactg cgacaaacaa tgcacgggca 3360
atgccgatag ggtctaatcc gtgatgatcg taaaaacgac tgtcttccgt cgctaaaaat 3420
gcgtcaatta agcgttgtgg cacatcggct aatttcactg gaatacggcg ttgctcaccc 3480
acttcgccaa ttaatttacc gtcagccgta taaatctgca ttggttgctg taattcaacg 3540
gtttttaatg tttctactga gggcaattca gattttaagt ggaaatacaa cattccgcct 3600
gctactaaac ctaaaataca taaagttaat agggtgttta atattaattt tgcgatccgc 3660
atcgtaaaat tctcgcttcg ttaatgaata ttcttgtcaa gagacctatg atttggctgt 3720
taagtataaa agattcagcc tttaaagaat aggaaagaat atgcaattct ccctgaaaaa 3780
ttaccgcact ttacaaatcg gcattcatcg taagcagagt tattttgatt ttgtgtggtt 3840
tgatgatctc gaacagccac aaagttatca aatctttgtt aatgatcgtt attttaaaaa 3900
tcgtttttta caacagctaa aaacacaata tcaagggaaa acctttcctt tgcagtttgt 3960
agcaagcatt cccgcccact taacttggtc gaaagtatta atgttgccac aagtgttaaa 4020
tgcgcaagaa tgtcatcaac aatgtaaatt tgtgattgaa aaagagctgc ctattttttt 4080
agaagaattg tggtttgatt atcgttctac cccgttaaag caaggttttc gattagaggt 4140
tactgcaatt cgtaaaagta gcgctcaaac ttatttgcaa gattttcagc catttaatat 4200
taatatattg gatgttgcgt caaatgctgt tttgcgtgca tttcaatatc tgttgaatga 4260
acaagtgcgg tcagaaaata ccttattttt atttcaagaa gatgactatt gcttggcgat 4320
ttgtgaaaga tctcagcaat cacaaatttt acaatctcac gaaaatttga ccgcacttta 4380
tgaacaattt accgaacgtt ttgaaggaca acttgaacaa gtttttgttt atcaaattcc 4440
ctcaagtcat acaccattac ccgaaaactg gcagcgagta gaaacagaac tcccttttat 4500
tgcgctgggc aacgcgctat ggcaaaaaga tttacatcaa caaaaagtgg gtggttaaat 4560
gtcgatgaat ttattgcctt ggcgtactta tcaacatcaa aagcgtttac gtcgtttagc 4620
tttttatatc gctttattta tcttgcttgc tattaattta atgttggctt ttagcaattt 4680
gattgaacaa cagaaacaaa atttgcaggc acagcaaaag tcgtttgaac aacttaatca 4740
acagcttcat aaaactacca tgcaaattga tcagttacgc attgcggtga aagttggtga 4800
agttttgaca tctattccca acgagcaagt aaaaaagagt ttacaacagc taagtgaatt 4860
accttttcaa caaggagaac tgaataaatt taaacaagat gccaataact taagcttgga 4920
aggtaacgcg caagatcaaa cagaatttga actgattcat caatttttaa agaaacattt 4980
tcccaatgtg aaattaagtc aggttcaacc tgaacaagat acattgtttt ttcactttga 5040
tgtggaacaa ggggcggaaa aatgaaagct ttttttaacg atccttttac tccttttgga 5100
aaatggctaa gtcagccttt ttatgtgcac ggtttaacct ttttattgct attaagtgcg 5160
gtgatttttc gccccgtttt agattatata gaggggagtt cacgtttcca tgaaattgaa 5220
aatgagttag cggtgaaacg ttcagaattg ttgcatcaac agaaaatttt aacctcttta 5280
caacagcagt cggaaagtcg aaaactttct ccagaactgg ctgcacaaat tattcctttg 5340
aataaacaaa ttcaacgttt agctgcgcgt aacggtttat ctcagcattt acgttgggaa 5400
atggggcaaa agcctatttt gcatttacag cttacaggtc attttgaaaa aacgaagaca 5460
tttttatccg cacttttggc taattcgtca cagctttctg taagtcggtt gcaatttatg 5520
aaacccgaag acggcccatt gcaaaccgag atcatttttc agctagataa ggaaacaaaa 5580
tgaaacattg gtttttcctg attatattat tttttatgaa ttgcagttgg ggacaagatc 5640
ctttcgataa aacacagcgt aaccgttctc agtttgataa cgcacaaaca gtaatggagc 5700
aaacagaaat aatttcctca gatgtgccta ataatctatg cggagcggat gaaaatcgcc 5760
aagcggctga aattcctttg aacgctttaa aattggtggg ggtagtgatt tctaaagata 5820
aagcctttgc cttgttgcaa gatcaaggtt tgcaagttta cagcgtttta gagggcgttg 5880
atgtggctca agagggctat attgtagaaa aaatcaacca aaacaatgtt caatttatgc 5940
gtaagctagg agagcaatgt gatagtagtg aatggaaaaa attaagtttt taaaggaaga 6000
ttatgaagaa atatttttta aagtgcggtt attttttagt atgtttttgt ttgccattaa 6060
tcgtttttgc taatcctaaa acagataacg aacgtttttt tattcgttta tcgcaagcac 6120
ctttagctca aacactggag caattagctt ttcaacaaga tgtgaattta gtgattggag 6180
atatattgga aaacaagatc tctttgaaat taaacaatat tgatatgcca cgtttgctac 6240
aaataatcgc aaaaagtaag catcttactt tgaataaaga tgatgggatt tattatttaa 6300
acggcagtca atctggcaaa ggtcaggttg caggaaatct tacgacaaat gaaccgcact 6360
tagtgagtca cacggtaaaa ctccattttg ctaaagcttc tgaattaatg aaatccttaa 6420
caacaggaag tggctctttg ctttctcccg ctgggagcat tacctttgat gatcgcagta 6480
atttgctggt tattcaggat gaacctcgtt ctgtgcaaaa tatcaaaaaa ctgattgctg 6540
aaatggataa gcctattgaa cagatcgcta ttgaagcgcg aattgtgaca attacggatg 6600
agagtttgaa agaacttggc gttcggtggg ggatttttaa tccaactgaa aatgcaagac 6660
gagttgcggg cagccttaca ggcaatagct ttgaaaatat tgcggataat cttaatgtaa 6720
attttgcgac aacgacgaca cctgctggct ctatagcatt acaagtcgcc aaaattaatg 6780
ggcgattgct tgatttagaa ttgagtgcgt tggagcgtga aaataatgta gaaattattg 6840
caagccctcg cttactcact accaataaga aaagtgcgag cattaaacag gggacagaaa 6900
ttccttacat cgtgagtaat actcgtaacg atacgcaatc tgtggaattt cgtgaggcgg 6960
tgcttggttt ggaagtgacg ccacatattt ctaaagataa caatatctta cttgatttat 7020
tggtaagtca aaattcccct ggttctcgtg tcgcttatgg acaaaatgag gtggtttcta 7080
ttgataaaca agaaattaat actcaggttt ttgccaaaga tggggaaacc attgtgcttg 7140
gcggcgtatt tcacgataca atcacgaaaa gcgaagataa agtgccattg cttggcgata 7200
tacccgttat taaacgatta tttagcaaag aaagtgaacg acatcaaaaa cgtgagctag 7260
tgattttcgt cacgccacat attttaaaag caggagaaaa cgttagaggc gttgaaacaa 7320
aaaagtgagg gtaaaaaata actttttaaa tgatgaattt ttttaatttt cgctgtatcc 7380
actgtcgtgg caatcttcat atcgcaaaaa atgggttatg ttcaggttgc caaaaacaaa 7440
ttaaatcttt tccttattgc ggtcattgtg gttcggaatt gcaatattat gcgcagcatt 7500
gtgggaattg tcttaaacaa gaaccaagtt gggataagat ggtcattatt gggcattata 7560
ttgaacctct ttcgatattg attcagcgtt ttaaatttca aaatcaattt tggattgacc 7620
gcactttagc tcggctttta tatcttgcgg tacgtgatgc taaacgaacg catcaactta 7680
aattgccaga ggcaatcatt ccagtgcctt tatatcattt tcgtcagtgg cgacggggtt 7740
ataatcaggc agatttatta tctcagcaat taagtcgttg gctggatatt cctaatttga 7800
acaatatcgt aaagcgtgtg aaacacacct atactcaacg tggtttgagt gcaaaagatc 7860
gtcgtcagaa tttaaaaaat gccttttctc ttgctgtttc gaaaaatgaa tttccttatc 7920
gtcgtgttgc gttggtggat gatgtgatta ctactggttc tacactcaat gaaatctcaa 7980
aattgttgcg aaaattaggt gtggaggaga ttcaagtgtg ggggctggca cgagcttaat 8040
ataaagcact ggaaaaaaaa gcgcgataag cgtattattc ccgatacttt ctctcaagta 8100
tttaggacat aattatggaa caagcaaccc agcaaatcgc tatttctgat gccgcacaag 8160
cgcattttcg aaaactttta gacacccaag aagaaggaac gcatattcgt attttcgcgg 8220
ttaatcctgg tacgcctaat gcggaatgtg gcgtatctta ttgccccccg aatgccgtgg 8280
aagaaagcga tattgaaatg aaatataata ctttttctgc atttattgat gaagtgagtt 8340
tgcctttctt agaagaagca gaaattgatt atgttaccga agagcttggt gcgcaactga 8400
ccttaaaagc accgaatgcc aaaatgcgta aggtggctga tgatgcgcca ttgattgaac 8460
gtgttgaata tgtaattcaa actcaaatta acccacagct tgcaaatcac ggtggacgta 8520
taaccttaat tgaaattact gaagatggtt acgcagtttt acaatttggt ggtggctgta 8580
acggttgttc aatggtggat gttacgttaa aagatggggt agaaaaacaa cttgttagct 8640
tattcccgaa tgaattaaaa ggtgcaaaag atataactga gcatcaacgt ggcgaacatt 8700
cttattatta gtgagttata aaagaagatt tataatgacc gcacttttga aagtgcggtt 8760
atttttatgg agaaaaaatg aaaatacttc aacaagatga ttttggttat tggttgctta 8820
cacaaggttc taatctgtat ttagtgaata atgaattgcc ttttggtatc gctaaagata 8880
ttgatttgga aggattgcag gcaatgcaaa ttggggaatg gaaaaattat ccgttgtggc 8940
ttgtggctga gcaagaaagt gatgaacgag aatatgtgag tttgagtaac ttgctttcac 9000
tgccagagga tgaattccat atattaagcc gaggtgtgga aattaatcat tttctgaaaa 9060
cccataaatt ctgtggaaag tgcggtcata aaacacaaca 9100
28
525
DNA
Moraxella catarrhalis
28
aaaaatcgac tgccgtcatt ttcaaccacc acatagctca tattcgcaag ccaatgtatt 60
gaccgttggg aataataaca gccccaaaac aatgaaacat atggtgatga gccaaacata 120
ctttcctgca gattttggaa tcatatcgcc atcagcacca gtatggtttg accagtattt 180
aacgccatag acatgtgtaa aaaaattaaa taacggtgca agcatgagac caacggcacc 240
tgatgtacct tgtacgatga cctcacctgc tgtggcaacc ataccaagtc cattgcctgt 300
gatatttttg cgaaaagaca aacttaccac acagaccaag ccgatgattg agatgacaaa 360
ataaaaccaa tccaaatgcg tgtgagctgt tgtggtccaa aatccagtaa atagtgcaat 420
aaatccgcaa acaaaccaaa gtagcaccca gcttgttgtc caatcttttt taccaaagcc 480
tgtgatgtta tctaaaatat caattttcat cagattttcc ctaat 525
29
466
DNA
Moraxella catarrhalis
29
taatgataac cagtcaagca agctcaaatc agggtcagcc tgttttgagc tttttatttt 60
ttgatcatca tgcttaagat tcactctgcc atttttttac aacctgcacc acaagtcatc 120
atcgcatttg caaaaatggt acaaacaagc cgtcagcgac ttaaacaaaa aaaggctcaa 180
tctgcgtgtg tgcgttcact tttacaaatc accatgcacc gctttgacat tgttggtgaa 240
tttcatgacc atgcacaccc ttattatatt aactcaaata aaatacgcta ctttgtcagc 300
tttagccatt cagataatca agtcgctctc atcatcagct taacaccttg tgccattgac 360
atagaagtta acgatattaa atacagtgtg gttgaacgat actttcatcc caatgaaatt 420
tatctactta ctcaatttag ctctactgat aggcaacagc ttatta 466
30
631
DNA
Streptococcus pneumoniae
30
gatctttgat tttcattgag tattactctc tcttgtcact tctttctatt ttaccataaa 60
gtccagcctt tgaagaactt ttactagaag acaaggggct tctgtctcta tttgccatct 120
taggcatcaa aaaagagggg tcatccctct ttacgaattc aatgctacta gggtatccaa 180
atactggttg ttgatgactg ccaaaatata ggtatctgct ttcaagaggt catctggtcc 240
aaattcaaca tccaatgggg aattttcctg ctctcggaaa cccaaaatat tcagattgta 300
tttgccacgg aggtctaatt tacttcagac tttgacctgc ccaagactga ggaattttca 360
tctccacgat agacacattt ttatccaact gaaagacatc aacactatta tgaaaagaat 420
ggtctgtgct agagactgcc ccatttcata ctctggcgag ataaccgagt cagctccaat 480
cttttctagc actttcttag cggtctgact tttgacctta gcaataacag tcggtacccc 540
caaactctta cagtgcataa ccgcaagcac actcgactcc agattttcac ctgtcgcgac 600
tacaacggta tcgcaggtat caatccctgc t 631
31
3754
DNA
Streptococcus pneumoniae
31
ccaatatttt ggtcagcata gtgttctttt tcagtggtaa cagcttgcaa tacttgagca 60
gaaatggcag atttatcaag gaaaaagtta acgtaaggtc ctgttgcgac aactttttca 120
aaggcttggc tgttcatttt ttcagccagt tcagccgcaa tcatttgtgg tgctttacgt 180
tcgacttttg caagagaaaa agcagggaaa gcaatgtctc ccatttctga gtttttaggg 240
gtttccagta actttaaaat agcctcttgg tccaggctat caatgatgct agataattcg 300
ctagcaatca attcttttgt attcattaag agctcctttt tggacttttc tactatttta 360
tcacaatttt aaagaaagaa gaaaaaattt ttgaaatctc ctgttttttt ggtataatat 420
ggttataaat atagttataa atatagttat aaatatgcac gcaagaggat tttatgagaa 480
aaagagatcg tcatcagtta ataaaaaaaa tgattactga ggagaaatta agtacacaaa 540
aagaaattca agatcggttg gaggcgcaca atgtttgtgt gacgcagaca accttgtctc 600
gtgatttgcg cgaaatcggc ttgaccaagg tcaagaaaaa tgatatggtg tattatgtac 660
tagtaaatga gacagaaaag attgatttgg tggaattttt gtctcatcat ttagaaggtg 720
ttgcaagagc agagtttacc ttggtgcttc ataccaaatt gggagaagcc tctgttttgg 780
caaatattgt agatgtaaac aaggatgaat ggattttagg aacagttgct ggtgccaata 840
ccttattggt tatttgtcga gatcagcacg ttgccaaact catggaagat cgtttgctag 900
atttgatgaa agataagtaa ggtcttggga gttgctctca agacttattt ttgaaaagga 960
gagacagaaa atggcgatag aaaagctatc acccggcatg caacagtatg tggatattaa 1020
aaagcaatat ccagatgctt ttttgctctt tcggatgggt gatttttatg aattatttta 1080
tgaggatgcg gtcaatgctg cgcagattct ggaaatttcc ttaacgagtc gcaacaagaa 1140
tgccgacaat ccgatcccta tggcgggtgt tccctatcat tctgcccaac agtatatcga 1200
tgtcttgatt gagcagggtt ataaggtggc tatcgcagag cagatggaag atcctaaaca 1260
agcagttggg gttgttaaac gagaggttgt tcaggtcatt acgccaggga cagtggtcga 1320
tagcagtaag ccggacagtc agaataattt tttggtttcc atagaccgcg aaggcaatca 1380
atttggccta gcttatatgg atttggtgac gggtgacttt tatgtgacag gtcttttgga 1440
tttcacgctg gtttgtgggg aaatccgtaa cctcaaggct cgagaagtgg tgttgggtta 1500
tgacttgtct gaggaagaag aacaaatcct cagccgccag atgaatctgg tactctctta 1560
tgaaaaagaa agctttgaag accttcattt attggatttg cgattggcaa cggtggagca 1620
aacggcatct agtaagctgc tccagtatgt tcatcggact cagatgaggg aattgaacca 1680
cctcaaacct gttatccgct acgaaattaa ggatttcttg cagatggatt atgcgaccaa 1740
ggctagtctg gatttggttg agaatgctcg ctcaggtaag aaacaaggca gtcttttctg 1800
gcttttggat gaaaccaaaa cggctatggg gatgcgtctc ttgcgttctt ggattcatcg 1860
ccccttgatt gataaggaac gaatcgtcca acgtcaagaa gtagtgcagg tctttctcga 1920
ccatttcttt gagcgtagtg acttgacaga cagtctcaag ggtgtttatg acattgagcg 1980
cttggctagt cgtgtttctt ttggcaaaac caatccaaag gatctcttgc agttggcgac 2040
taccttgtct agtgtgccac ggattcgtgc gattttagaa gggatggagc aacctactct 2100
agcctatctc atcgcacaac tggatgcaat ccctgagttg gagagtttga ttagcgcagc 2160
gattgctcct gaagctcctc atgtgattac agatggggga attatccgga ctggatttga 2220
tgagacttta gacaagtatc gttgcgttct cagagaaggg actagctgga ttgctgagat 2280
tgaggctaag gagcgagaaa actctggtat cagcacgctc aagattgact acaataaaaa 2340
ggatggctac tattttcatg tgaccaattc gcaactggga aatgtgccag cccacttttt 2400
ccgcaaggcg acgctgaaaa actcagaacg ctttggaacc gaagaattag cccgtatcga 2460
gggagatatg cttgaggcgc gtgagaagtc agccaacctc gaatacgaaa tatttatgcg 2520
cattcgtgaa gaggtcggca agtacatcca gcgtttacaa gctctagccc aaggaattgc 2580
gacggttgat gtcttacaga gtctggcggt tgtggctgaa acccagcatt tgattcgacc 2640
tgagtttggt gacgattcac aaattgatat ccggaaaggg cgccatgctg tcgttgaaaa 2700
ggttatgggg gctcagacct atattccaaa tacgattcag atggcagaag ataccagtat 2760
tcaattggtt acagggccaa acatgagtgg gaagtctacc tatatgcgtc agttagccat 2820
gacggcggtt atggcccagc tgggttccta tgttcctgct gaaagcgccc atttaccgat 2880
ttttgatgcg atttttaccc gtatcggagc agcagatgac ttggtttcgg gtcagtcaac 2940
ctttatggtg gagatgatgg aggccaataa tgccatttcg catgcgacca agaactctct 3000
cattctcttt gatgaattgg gacgtggaac tgcaacttat gacgggatgg ctcttgctca 3060
gtccatcatc gaatatatcc atgagcacat cggagctaag accctctttg cgacccacta 3120
ccatgagttg actagtctgg agtctagttt acaacacttg gtcaatgtcc acgtggcaac 3180
tttggagcag gatgggcagg tcaccttcct tcacaagatt gaaccgggac cagctgataa 3240
atcctacggt atccatgttg ccaagattgc tggcttgcca gcagaccttt tagcaagggc 3300
ggataagatt ttgactcagc tagagaatca aggaacagag agtcctcctc ccatgagaca 3360
aactagtgct gtcactgaac agatttcact ctttgatagg gcagaagagc atcctatcct 3420
agcagaatta gctaaactgg atgtgtataa tatgacacct atgcaggtta tgaatgtctt 3480
agtagagtta aaacagaaac tataaaacca agactcacta gttaatctag ctgtatcaag 3540
gagacttctt tgacaattct ccactttttt gctagaataa catcacacaa acagaatgaa 3600
aagggctgac gcattgtcgc tcccttttgt ctatttttta aggagaaagt atgctgattc 3660
agaaaataaa aacctacaag tggcaggccc tgcttcgctc ctgatgacag gcttgatggt 3720
tgctagttca cttctgcaac cgcgttatct gcag 3754
32
1337
DNA
Streptococcus pyogenes
32
aacaaaataa aagaacttac ctattttcca tccaaaatgt ttagcaatca tcatctgcaa 60
ggcaacgtat tgcatggcat tgatgtgatg agcaactaat atgtcattag aacgttgcgt 120
caaactagca tctaaataaa gatcgaaatg cagttatcaa aaatgcaagc tcctatcggc 180
ccttgtttta attattactc acattgcctt aatgtattta cttgcttatt attaactttt 240
ttgctaagtt agtagcgtca gttattcatt gaaaggacat tattatgaaa attcttgtaa 300
caggctttga tccctttggc ggcgaagcta ttaatcctgc ccttgaagct atcaagaaat 360
tgccagcaac cattcatgga gcagaaatca aatgtattga agttccaacg gtttttcaaa 420
aatctgccga tgtgctccag cagcatatcg aaagctttca acctgatgca gtcctttgta 480
ttgggcaagc tggtggccgg actggactaa cgccagaacg cgttgccatt aatcaagacg 540
atgctcgcat tcctgataac gaagggaatc agcctattga tacacctatt cgtgcagatg 600
gtaaagcagc ttatttttca accttgccaa tcaaagcgat ggttgctgcc attcatcagg 660
ctgggcttcc tgcttctgtt tctaatacag ctggtacctt tgtttgcaat catttgatgt 720
atcaagccct ttacttagtg gataaatatt gtccaaatgc caaagctggg tttatgcata 780
ttccctttat gatggaacag gttgttgata aacctaatac agctgccatg aacctcgatg 840
atattacaag aggaattgag gctgctattt ttgccattgt cgatttcaaa gatcgttccg 900
atttaaaacg tgtagggggc gctactcact gactgtgacg ctactaaacc tattttaaaa 960
aaacagagat atgaactaac tctgtttttt ttgtgctaaa aatgaaagac ctagggaaac 1020
ttttcatcgg tctttctcaa ttgtcatctt aatctaatac tacttctaac atcagcgggt 1080
atagtttgcc agtaattaag aaacgttgtt gatctaaatg agcaatccca ttcaaaacat 1140
taaggtcagg gtaatgggac ttatcaagat ttaaggcttt taacaaagga ctaatatcat 1200
aggtggctac cacctttcca gaatcaggtt ggagtttgac aatagtattg gtttgccaaa 1260
tattggcata gagataacca tctacatact ctaattcgtt aagcattgag atagggacac 1320
tttctatagc aactagt 1337
33
1837
DNA
Streptococcus pyogenes
33
tcatgtttga cagcttatca tcgataagct tacttttcga atcaggtcta tccttgaaac 60
aggtgcaaca tagattaggg catggagatt taccagacaa ctatgaacgt atatactcac 120
atcacgcaat cggcaattga tgacattgga actaaattca atcaatttgt tactaacaag 180
caactagatt gacaactaat tctcaacaaa cgttaattta acaacattca agtaactccc 240
accagctcca tcaatgctta ccgtaagtaa tcataactta ctaaaacctt gttacatcaa 300
ggttttttct ttttgtcttg ttcatgagtt accataactt tctatattat tgacaactaa 360
attgacaact cttcaattat ttttctgtct actcaaagtt ttcttcattt gatatagtct 420
aattccacca tcacttcttc cactctctct accgtcacaa cttcatcatc tctcactttt 480
tcgtgtggta acacataatc aaatatcttt ccgtttttac gcactatcgc tactgtgtca 540
cctaaaatat accccttatc aatcgcttct ttaaactcat ctatatataa catatttcat 600
cctcctacct atctattcgt aaaaagataa aaataactat tgtttttttt gttattttat 660
aataaaatta ttaatataag ttaatgtttt ttaaaaatat acaattttat tctatttata 720
gttagctatt ttttcattgt tagtaatatt ggtgaattgt aataaccttt ttaaatctag 780
aggagaaccc agatataaaa tggaggaata ttaatggaaa acaataaaaa agtattgaag 840
aaaatggtat tttttgtttt agtgacattt cttggactaa caatctcgca agaggtattt 900
gctcaacaag accccgatcc aagccaactt cacagatcta gtttagttaa aaaccttcaa 960
aatatatatt ttctttatga gggtgaccct gttactcacg agaatgtgaa atctgttgat 1020
caacttttat ctcacgattt aatatataat gtttcagggc caaattatga taaattaaaa 1080
actgaactta agaaccaaga gatggcaact ttatttaagg ataaaaacgt tgatatttat 1140
ggtgtagaat attaccatct ctgttattta tgtgaaaatg cagaaaggag tgcatgtatc 1200
tacggagggg taacaaatca tgaagggaat catttagaaa ttcctaaaaa gatagtcgtt 1260
aaagtatcaa tcgatggtat ccaaagccta tcatttgata ttgaaacaaa taaaaaaatg 1320
gtaactgctc aagaattaga ctataaagtt agaaaatatc ttacagataa taagcaacta 1380
tatactaatg gaccttctaa atatgaaact ggatatataa agttcatacc taagaataaa 1440
gaaagttttt ggtttgattt tttccctgaa ccagaattta ctcaatctaa atatcttatg 1500
atatataaag ataatgaaac gcttgactca aacacaagcc aaattgaagt ctacctaaca 1560
accaagtaac tttttgcttt tggcaacctt acctactgct ggatttagaa attttattgc 1620
aattctttta ttaatgtaaa aaccgctcat ttgatgagcg gttttgtctt atctaaagga 1680
gctttacctc ctaatgctgc aaaattttaa atgttggatt tttgtatttg tctattgtat 1740
ttgatgggta atcccatttt tcgacagaca tcgtcgtgcc acctctaaca ccaaaatcat 1800
agacaggagc ttgtagctta gcaactattt tatcgtc 1837
34
841
DNA
Streptococcus pneumoniae
34
gatcaatatg tccaagaaac cacatgttcc taagacaaga gctaacagac tggccgtcaa 60
taatagtatt gttctttttt tcatcattac tccttaacta gtgtttaact gattaattag 120
ccagtaaata gtttatcttt atttacacta tctgttaaga tatagtaaaa tgaaataaga 180
acaggacagt caaatcgatt tctaacaatg ttttagaagt agaggtatac tattctaatt 240
tcaatctact atattttgca cattttcata aaaaaaatga gaactagaac tcacattctg 300
ctctcatttt tcgttttccc gttctcctat cctgttttta ggagttagaa aatgctgcta 360
cctttactta ctctccttta ataaagccaa tagtttttca gcttctgcca taatagtatt 420
gttgtcctgg gtgccaaata gtaaattatt ttttaatcct gtgagagtct ctttggcatt 480
ggacttgata attggattct ggatttttcc aagtaaatct tcagcctctc tcagttttct 540
taacctttca gtctcgacct gaggttcttc tgattcctct ggtgattctt ctggtgattc 600
ttcttctggt tcctctgttg gttttggaga ctctggtttc tcgctttgcg gtttctcttc 660
tcgaggggtt tcttcctcag gtttttctgt ctgaggtttc tcctcgtttg gtttttccgt 720
ttgattggta tcagcttgac catttttgtt tctttgaaca tggtcgctag cgttaccaaa 780
accattatct gaatgcgacg ttcgtttgga tgttcgacat agtacttgac agtcgccaaa 840
a 841
35
4500
DNA
Streptococcus pneumoniae
35
gatcaggaca gtcaaatcga tttctaacaa tgttttagaa gtagatgtgt actattctag 60
tttcaatcta ttatatttat agaatttttt gttgctagat ttgtcaaatt gcttaaaata 120
atttttttca gaaagcaaaa gccgatacct atcgagtagg gtagttcttg ctatcgtcag 180
gcttgtctgt aggtgttaac acttttcaaa aatctcttca aacaacgtca gctttgcctt 240
gccgtatata tgttactgac ttcgtcagtt ctatctgcca cctcaaaacg gtgttttgag 300
ctgacttcgt cagttctatc cacaacctca aaacagtgtt ttgagctgac ttcgtcagtt 360
ctatccacaa cctcaaaaca gtgttttgag ctgactttgt cagtcttatc tacaacctca 420
aaacagtgtt ttgagcatca tgcggctagc ttcttagttt gctctttgat tttcattgag 480
tataaaaaca gatgagtttc tgttttcttt ttatggacta taaatgttca gctgaaacta 540
ctttcaagga cattattata taaaagaatt ttttgaaact aaaatctact atattacact 600
atattgaaag cgttttaaaa atgaggtata ataaatttac taacacttat aaaaagtgat 660
agaatctatc tttatgtata tttaaagata gattgctgta aaaatagtag tagctatgcg 720
aaataacaga tagagagaag ggattgaagc ttagaaaagg ggaataatat gatatttaag 780
gcattcaaga caaaaaagca gagaaaaaga caagttgaac tacttttgac agtttttttc 840
gacagttttc tgattgattt atttcttcac ttatttggga ttgtcccctt taagctggat 900
aagattctga ttgtgagctt gattatattt cccattattt ctacaagtat ttatgcttat 960
gaaaagctat ttgaaaaagt gttcgataag gattgagcag gaagtatggt gtaaatagca 1020
taagctgatg tccatcattt gcttataaag agatatttta gtttaattgc agcggtgtcc 1080
tggtagataa actagattgg caggagtctg attggagaaa ggagagggga aatttggcac 1140
caatttgaga tagtttgttt agttcatttt tgtcatttaa atgaactgta gtaaaagaaa 1200
gttaataaaa gacaaactaa gtgcattttc tggaataaat gtcttatttc agaaatcggg 1260
atatagatat agagaggaac agtatgaatc ggagtgttca agaacgtaag tgtcgttata 1320
gcattaggaa actatcggta ggagcggttt ctatgattgt aggagcagtg gtatttggaa 1380
cgtctcctgt tttagctcaa gaaggggcaa gtgagcaacc tctggcaaat gaaactcaac 1440
tttcggggga gagctcaacc ctaactgata cagaaaagag ccagccttct tcagagactg 1500
aactttctgg caataagcaa gaacaagaaa ggaaagataa gcaagaagaa aaaattccaa 1560
gagattacta tgcacgagat ttggaaaatg tcgaaacagt gatagaaaaa gaagatgttg 1620
aaaccaatgc ttcaaatggt cagagagttg atttatcaag tgaactagat aaactaaaga 1680
aacttgaaaa cgcaacagtt cacatggagt ttaagccaga tgccaaggcc ccagcattct 1740
ataatctctt ttctgtgtca agtgctacta aaaaagatga gtacttcact atggcagttt 1800
acaataatac tgctactcta gaggggcgtg gttcggatgg gaaacagttt tacaataatt 1860
acaacgatgc acccttaaaa gttaaaccag gtcagtggaa ttctgtgact ttcacagttg 1920
aaaaaccgac agcagaacta cctaaaggcc gagtgcgcct ctacgtaaac ggggtattat 1980
ctcgaacaag tctgagatct ggcaatttca ttaaagatat gccagatgta acgcatgtgc 2040
aaatcggagc aaccaagcgt gccaacaata cggtttgggg gtcaaatcta cagattcgga 2100
atctcactgt gtataatcgt gctttaacac cagaagaggt acaaaaacgt agtcaacttt 2160
ttaaacgctc agatttagaa aaaaaactac ctgaaggagc ggctttaaca gagaaaacgg 2220
acatattcga aagcgggcgt aacggtaaac caaataaaga tggaatcaag agttatcgta 2280
ttccagcact tctcaagaca gataaaggaa ctttgatcgc aggtgcagat gaacgccgtc 2340
tccattcgag tgactggggt gatatcggta tggtcatcag acgtagtgaa gataatggta 2400
aaacttgggg tgaccgagta accattacca acttacgtga caatccaaaa gcttctgacc 2460
catcgatcgg ttcaccagtg aatatcgata tggtgttggt tcaagatcct gaaaccaaac 2520
gaatcttttc tatctatgac atgttcccag aagggaaggg aatctttgga atgtcttcac 2580
aaaaagaaga agcctacaaa aaaatcgatg gaaaaaccta tcaaatcctc tatcgtgaag 2640
gagaaaaggg agcttatacc attcgagaaa atggtactgt ctatacacca gatggtaagg 2700
cgacagacta tcgcgttgtt gtagatcctg ttaaaccagc ctatagcgac aagggggatc 2760
tatacaaggg taaccaatta ctaggcaata tctacttcac aacaaacaaa acttctccat 2820
ttagaattgc caaggatagc tatctatgga tgtcctacag tgatgacgac gggaagacat 2880
ggtcagcgcc tcaagatatt actccgatgg tcaaagccga ttggatgaaa ttcttgggtg 2940
taggtcctgg aacaggaatt gtacttcgga atgggcctca caagggacgg attttgatac 3000
cggtttatac gactaataat gtatctcact taaatggctc gcaatcttct cgtatcatct 3060
attcagatga tcatggaaaa acttggcatg ctggagaagc ggtcaacgat aaccgtcagg 3120
tagacggtca aaagatccac tcttctacga tgaacaatag acgtgcgcaa aatacagaat 3180
caacggtggt acaactaaac aatggagatg ttaaactctt tatgcgtggt ttgactggag 3240
atcttcaggt tgctacaagt aaagacggag gagtgacttg ggagaaggat atcaaacgtt 3300
atccacaggt taaagatgtc tatgttcaaa tgtctgctat ccatacgatg cacgaaggaa 3360
aagaatacat catcctcagt aatgcaggtg gaccgaaacg tgaaaatggg atggtccact 3420
tggcacgtgt cgaagaaaat ggtgagttga cttggctcaa acacaatcca attcaaaaag 3480
gagagtttgc ctataattcg ctccaagaat taggaaatgg ggagtatggc atcttgtatg 3540
aacatactga aaaaggacaa aatgcctata ccctatcatt tagaaaattt aattgggact 3600
ttttgagcaa agatctgatt tctcctaccg aagcgaaagt gaagcgaact agagagatgg 3660
gcaaaggagt tattggcttg gagttcgact cagaagtatt ggtcaacaag gctccaaccc 3720
ttcaattggc aaatggtaaa acagcacgct tcatgaccca gtatgataca aaaaccctcc 3780
tatttacagt ggattcagag gatatgggtc aaaaagttac aggtttggca gaaggtgcaa 3840
ttgaaagtat gcataattta ccagtctctg tggcgggcac taagctttcg aatggaatga 3900
acggaagtga agctgctgtt catgaagtgc cagaatacac aggcccatta gggacatccg 3960
gcgaagagcc agctccaaca gtcgagaagc cagaatacac aggcccacta gggacatccg 4020
gcgaagagcc agccccgaca gtcgagaagc cagaatacac aggcccacta gggacagctg 4080
gtgaagaagc agctccaaca gtcgagaagc cagaatttac agggggagtt aatggtacag 4140
agccagctgt tcatgaaatc gcagagtata agggatctga ttcgcttgta actcttacta 4200
caaaagaaga ttatacttac aaagctcctc ttgctcagca ggcacttcct gaaacaggaa 4260
acaaggagag tgacctccta gcttcactag gactaacagc tttcttcctt ggtctgttta 4320
cgctagggaa aaagagagaa caataagaga agaattctaa acatttgatt ttgtaaaaat 4380
agaaggagat agcaggtttt caagcctgct atcttttttt gatgacattc aggctgatac 4440
gaaatcataa gaggtctgaa actactttca gagtagtctg ttctataaaa tatagtagat 4500
36
705
DNA
Staphylococcus epidermidis
36
gatccaagct tatcgatatc atcaaaaagt tggcgaacct tttcaaattt tggttcaaat 60
tcttgagatg tatagaattc aaaatattta ccatttgcat agtctgattg ctcaaagtct 120
tgatactttt ctccacgctc ttttgcaatt tccattgaac gttcgatgga ataatagttc 180
ataatcataa agaatatatt agcaaagtct tttgcttctt cagattcata gccaatttta 240
tttttagcta gataaccatg taagttcatt actcctagtc caacagaatg tagttcacta 300
ttcgcttttt ttacacctgg tgcattttga atatttgctt catcacttac aactgtaaga 360
gcatccatac ctgtgaacac agaatctctg aatttacctg attccataac attcactata 420
ttcaatgagc ctaagttaca tgaaatatct cttttaattt catcttcaat tccatagtcg 480
ttaattactg atgtctcttg taattggaaa atttcagtac ataaattact cattttaatt 540
tgcccaatat ttgaattcgc atgtactttg tttgcattat ctttaaacat aagatatgga 600
taaccagact gtaattgtgt ttgtgcaatc atatttaaca tttcacgtgc gtcttttttc 660
tttttatcga tttcgaaccc ggggtaccga attcctcgag tctag 705
37
442
DNA
Staphylococcus aureus
37
gatcaatctt tgtcggtaca cgatattctt cacgactaaa taaacgctca ttcgcgattt 60
tataaatgaa tgttgataac aatgttgtat tatctactga aatctcatta cgttgcatcg 120
gaaacattgt gttctgtatg taaaagccgt cttgataatc tttagtagta ccgaagctgg 180
tcatacgaga gttatatttt ccagccaaaa cgatattttt ataatcatta cgtgaaaaag 240
gtttcccttc attatcacac aaatatttta gcttttcagt ttctatatca actgtagctt 300
ctttatccat acgttgaata attgtacgat tctgacgcac catcttttgc acacctttaa 360
tgttatttgt tttaaaagca tgaataagtt tttcaacaca acgatgtgaa tcttctaaga 420
agtcaccgta aaatgaagga tc 442
38
20
DNA
Enterococcus faecalis
38
gcaatacagg gaaaaatgtc 20
39
20
DNA
Enterococcus faecalis
39
cttcatcaaa caattaactc 20
40
20
DNA
Enterococcus faecalis
40
gaacagaaga agccaaaaaa 20
41
20
DNA
Enterococcus faecalis
41
gcaatcccaa ataatacggt 20
42
19
DNA
Escherichia coli
42
gctttccagc gtcatattg 19
43
19
DNA
Escherichia coli
43
gatctcgaca aaatggtga 19
44
25
DNA
Escherichia coli
44
cacccgcttg cgtggcaagc tgccc 25
45
25
DNA
Escherichia coli
45
cgtttgtgga ttccagttcc atccg 25
46
17
DNA
Escherichia coli
46
tcacccgctt gcgtggc 17
47
19
DNA
Escherichia coli
47
ggaactggaa tccacaaac 19
48
25
DNA
Escherichia coli
48
tgaagcactg gccgaaatgc tgcgt 25
49
25
DNA
Escherichia coli
49
gatgtacagg attcgttgaa ggctt 25
50
25
DNA
Escherichia coli
50
tagcgaaggc gtagcagaaa ctaac 25
51
25
DNA
Escherichia coli
51
gcaacccgaa ctcaacgccg gattt 25
52
25
DNA
Escherichia coli
52
atacacaagg gtcgcatctg cggcc 25
53
26
DNA
Escherichia coli
53
tgcgtatgca ttgcagacct tgtggc 26
54
25
DNA
Escherichia coli
54
gctttcactg gatatcgcgc ttggg 25
55
19
DNA
Escherichia coli
55
gcaacccgaa ctcaacgcc 19
56
19
DNA
Escherichia coli
56
gcagatgcga cccttgtgt 19
57
23
DNA
Klebsiella pneumoniae
57
gtggtgtcgt tcagcgcttt cac 23
58
25
DNA
Klebsiella pneumoniae
58
gcgatattca caccctacgc agcca 25
59
26
DNA
Klebsiella pneumoniae
59
gtcgaaaatg ccggaagagg tatacg 26
60
26
DNA
Klebsiella pneumoniae
60
actgagctgc agaccggtaa aactca 26
61
19
DNA
Klebsiella pneumoniae
61
gacagtcagt tcgtcagcc 19
62
19
DNA
Klebsiella pneumoniae
62
cgtagggtgt gaatatcgc 19
63
26
DNA
Klebsiella pneumoniae
63
cgtgatggat attcttaacg aagggc 26
64
23
DNA
Klebsiella pneumoniae
64
accaaactgt tgagccgcct gga 23
65
23
DNA
Klebsiella pneumoniae
65
gtgatcgccc ctcatctgct act 23
66
26
DNA
Klebsiella pneumoniae
66
cgcccttcgt taagaatatc catcac 26
67
19
DNA
Klebsiella pneumoniae
67
tcgcccctca tctgctact 19
68
19
DNA
Klebsiella pneumoniae
68
gatcgtgatg gatattctt 19
69
25
DNA
Klebsiella pneumoniae
69
caggaagatg ctgcaccggt tgttg 25
70
25
DNA
Proteus mirabilis
70
tggttcactg actttgcgat gtttc 25
71
25
DNA
Proteus mirabilis
71
tcgaggatgg catgcactag aaaat 25
72
30
DNA
Proteus mirabilis
72
cgctgattag gtttcgctaa aatcttatta 30
73
30
DNA
Proteus mirabilis
73
ttgatcctca ttttattaat cacatgacca 30
74
19
DNA
Proteus mirabilis
74
gaaacatcgc aaagtcagt 19
75
20
DNA
Proteus mirabilis
75
ataaaatgag gatcaagttc 20
76
30
DNA
Proteus mirabilis
76
ccgcctttag cattaattgg tgtttatagt 30
77
30
DNA
Proteus mirabilis
77
cctattgcag ataccttaaa tgtcttgggc 30
78
26
DNA
Streptococcus pneumoniae
78
agtaaaatga aataagaaca ggacag 26
79
25
DNA
Streptococcus pneumoniae
79
aaaacaggat aggagaacgg gaaaa 25
80
25
DNA
Proteus mirabilis
80
ttgagtgatg atttcactga ctccc 25
81
25
DNA
Proteus mirabilis
81
gtcagacagt gatgctgacg acaca 25
82
27
DNA
Proteus mirabilis
82
tggttgtcat gctgtttgtg tgaaaat 27
83
19
DNA
Pseudomonas aeruginosa
83
cgagcgggtg gtgttcatc 19
84
19
DNA
Pseudomonas aeruginosa
84
caagtcgtcg tcggaggga 19
85
19
DNA
Pseudomonas aeruginosa
85
tcgctgttca tcaagaccc 19
86
19
DNA
Pseudomonas aeruginosa
86
ccgagaacca gacttcatc 19
87
25
DNA
Pseudomonas aeruginosa
87
aatgcggctg tacctcggcg ctggt 25
88
25
DNA
Pseudomonas aeruginosa
88
ggcggagggc cagttgcacc tgcca 25
89
25
DNA
Pseudomonas aeruginosa
89
agccctgctc ctcggcagcc tctgc 25
90
25
DNA
Pseudomonas aeruginosa
90
tggcttttgc aaccgcgttc aggtt 25
91
25
DNA
Pseudomonas aeruginosa
91
gcgcccgcga gggcatgctt cgatg 25
92
25
DNA
Pseudomonas aeruginosa
92
acctgggcgc caactacaag ttcta 25
93
25
DNA
Pseudomonas aeruginosa
93
ggctacgctg ccgggctgca ggccg 25
94
25
DNA
Pseudomonas aeruginosa
94
ccgatctaca ccatcgagat gggcg 25
95
25
DNA
Pseudomonas aeruginosa
95
gagcgcggct atgtgttcgt cggct 25
96
29
DNA
Staphylococcus saprophyticus
96
cgtttttacc cttacctttt cgtactacc 29
97
30
DNA
Staphylococcus saprophyticus
97
tcaggcagag gtagtacgaa aaggtaaggg 30
98
26
DNA
Staphylococcus saprophyticus
98
cgtttttacc cttacctttt cgtact 26
99
28
DNA
Staphylococcus saprophyticus
99
atcgatcatc acattccatt tgttttta 28
100
27
DNA
Staphylococcus saprophyticus
100
caccaagttt gacacgtgaa gattcat 27
101
30
DNA
Staphylococcus saprophyticus
101
atgagtgaag cggagtcaga ttatgtgcag 30
102
25
DNA
Staphylococcus saprophyticus
102
cgctcattac gtacagtgac aatcg 25
103
30
DNA
Staphylococcus saprophyticus
103
ctggttagct tgactcttaa caatcttgtc 30
104
30
DNA
Staphylococcus saprophyticus
104
gacgcgattg tcactgtacg taatgagcga 30
105
28
DNA
Haemophilus influenzae
105
gcgtcagaaa aagtaggcga aatgaaag 28
106
25
DNA
Haemophilus influenzae
106
agcggctcta tcttgtaatg acaca 25
107
25
DNA
Haemophilus influenzae
107
gaaacgtgaa ctcccctcta tataa 25
108
25
DNA
Moraxella catarrhalis
108
gccccaaaac aatgaaacat atggt 25
109
25
DNA
Moraxella catarrhalis
109
ctgcagattt tggaatcata tcgcc 25
110
25
DNA
Moraxella catarrhalis
110
tggtttgacc agtatttaac gccat 25
111
25
DNA
Moraxella catarrhalis
111
caacggcacc tgatgtacct tgtac 25
112
18
DNA
Moraxella catarrhalis
112
ggcacctgat gtaccttg 18
113
17
DNA
Moraxella catarrhalis
113
aacagctcac acgcatt 17
114
25
DNA
Moraxella catarrhalis
114
ttacaacctg caccacaagt catca 25
115
25
DNA
Moraxella catarrhalis
115
gtacaaacaa gccgtcagcg actta 25
116
23
DNA
Moraxella catarrhalis
116
caatctgcgt gtgtgcgttc act 23
117
26
DNA
Moraxella catarrhalis
117
gctactttgt cagctttagc cattca 26
118
24
DNA
Moraxella catarrhalis
118
tgttttgagc tttttatttt ttga 24
119
22
DNA
Moraxella catarrhalis
119
cgctgacggc ttgtttgtac ca 22
120
25
DNA
Streptococcus pneumoniae
120
tctgtgctag agactgcccc atttc 25
121
25
DNA
Streptococcus pneumoniae
121
cgatgtcttg attgagcagg gttat 25
122
25
DNA
Artificial Sequence
Description of Artificial Sequence
Oligonucleotide
122
atcccacctt aggcggctgg ctcca 25
123
31
DNA
Artificial Sequence
Description of Artificial Sequence
Oligonucleotide
123
acgtcaagtc atcatggccc ttacgagtag g 31
124
25
DNA
Artificial Sequence
Description of Artificial Sequence
Oligonucleotide
124
gtgtgacggg cggtgtgtac aaggc 25
125
28
DNA
Artificial Sequence
Description of Artificial Sequence
Oligonucleotide
125
gagttgcaga ctccaatccg gactacga 28
126
20
DNA
Artificial Sequence
Description of Artificial Sequence
Oligonucleotide
126
ggaggaaggt ggggatgacg 20
127
20
DNA
Artificial Sequence
Description of Artificial Sequence
Oligonucleotide
127
atggtgtgac gggcggtgtg 20
128
32
DNA
Artificial Sequence
Description of Artificial Sequence
Oligonucleotide
128
ccctatacat caccttgcgg tttagcagag ag 32
129
28
DNA
Artificial Sequence
Description of Artificial Sequence
Oligonucleotide
129
ggggggacca tcctccaagg ctaaatac 28
130
32
DNA
Artificial Sequence
Description of Artificial Sequence
Oligonucleotide
130
cgtccacttt cgtgtttgca gagtgctgtg tt 32
131
20
DNA
Escherichia coli
131
caggagtacg gtgattttta 20
132
20
DNA
Escherichia coli
132
atttctggtt tggtcataca 20
133
20
DNA
Proteus mirabilis
133
cgggagtcag tgaaatcatc 20
134
20
DNA
Proteus mirabilis
134
ctaaaatcgc cacacctctt 20
135
18
DNA
Klebsiella pneumoniae
135
gcagcgtggt gtcgttca 18
136
18
DNA
Klebsiella pneumoniae
136
agctggcaac ggctggtc 18
137
20
DNA
Klebsiella pneumoniae
137
attcacaccc tacgcagcca 20
138
20
DNA
Klebsiella pneumoniae
138
atccggcagc atctctttgt 20
139
25
DNA
Staphylococcus saprophyticus
139
ctggttagct tgactcttaa caatc 25
140
25
DNA
Staphylococcus saprophyticus
140
tcttaacgat agaatggagc aactg 25
141
20
DNA
Streptococcus pyogenes
141
tgaaaattct tgtaacaggc 20
142
20
DNA
Streptococcus pyogenes
142
ggccaccagc ttgcccaata 20
143
20
DNA
Streptococcus pyogenes
143
atattttctt tatgagggtg 20
144
20
DNA
Streptococcus pyogenes
144
atccttaaat aaagttgcca 20
145
25
DNA
Staphylococcus epidermidis
145
atcaaaaagt tggcgaacct tttca 25
146
25
DNA
Staphylococcus epidermidis
146
caaaagagcg tggagaaaag tatca 25
147
30
DNA
Staphylococcus epidermidis
147
tctcttttaa tttcatcttc aattccatag 30
148
30
DNA
Staphylococcus epidermidis
148
aaacacaatt acagtctggt tatccatatc 30
149
30
DNA
Staphylococcus aureus
149
cttcatttta cggtgacttc ttagaagatt 30
150
30
DNA
Staphylococcus aureus
150
tcaactgtag cttctttatc catacgttga 30
151
30
DNA
Staphylococcus aureus
151
atattttagc ttttcagttt ctatatcaac 30
152
30
DNA
Staphylococcus aureus
152
aatctttgtc ggtacacgat attcttcacg 30
153
30
DNA
Staphylococcus aureus
153
cgtaatgaga tttcagtaga taatacaaca 30
154
25
DNA
Haemophilus influenzae
154
tttaacgatc cttttactcc ttttg 25
155
25
DNA
Haemophilus influenzae
155
actgctgttg taaagaggtt aaaat 25
156
20
DNA
Streptococcus pneumoniae
156
atttggtgac gggtgacttt 20
157
20
DNA
Streptococcus pneumoniae
157
gctgaggatt tgttcttctt 20
158
20
DNA
Streptococcus pneumoniae
158
gagcggtttc tatgattgta 20
159
20
DNA
Streptococcus pneumoniae
159
atctttcctt tcttgttctt 20
160
18
DNA
Moraxella catarrhalis
160
gctcaaatca gggtcagc 18
161
861
DNA
Escherichia coli
161
atgagtattc aacatttccg tgtcgccctt attccctttt ttgcggcatt ttgccttcct 60
gtttttgctc acccagaaac gctggtgaaa gtaaaagatg ctgaagatca gttgggtgca 120
cgagtgggtt acatcgaact ggatctcaac agcggtaaga tccttgagag ttttcgcccc 180
gaagaacgtt ttccaatgat gagcactttt aaagttctgc tatgtggcgc ggtattatcc 240
cgtgttgacg ccgggcaaga gcaactcggt cgccgcatac actattctca gaatgacttg 300
gttgagtact caccagtcac agaaaagcat cttacggatg gcatgacagt aagagaatta 360
tgcagtgctg ccataaccat gagtgataac actgcggcca acttacttct gacaacgatc 420
ggaggaccga aggagctaac cgcttttttg cacaacatgg gggatcatgt aactcgcctt 480
gatcgttggg aaccggagct gaatgaagcc ataccaaacg acgagcgtga caccacgatg 540
cctgcagcaa tggcaacaac gttgcgcaaa ctattaactg gcgaactact tactctagct 600
tcccggcaac aattaataga ctggatggag gcggataaag ttgcaggacc acttctgcgc 660
tcggcccttc cggctggctg gtttattgct gataaatctg gagccggtga gcgtgggtct 720
cgcggtatca ttgcagcact ggggccagat ggtaagccct cccgtatcgt agttatctac 780
acgacgggga gtcaggcaac tatggatgaa cgaaatagac agatcgctga gataggtgcc 840
tcactgatta agcattggta a 861
162
918
DNA
Pasteurella haemolytica
162
atgttaaata agttaaaaat cggcacatta ttattgctga cattaacggc ttgttcgccc 60
aattctgttc attcggtaac gtctaatccg cagcctgcta gtgcgcctgt gcaacaatca 120
gccacacaag ccacctttca acagactttg gcgaatttgg aacagcagta tcaagcccga 180
attggcgttt atgtatggga tacagaaacg ggacattctt tgtcttatcg tgcagatgaa 240
cgctttgctt atgcgtccac tttcaaggcg ttgttggctg gggcggtgtt gcaatcgctg 300
cctgaaaaag atttaaatcg taccatttca tatagccaaa aagatttggt tagttattct 360
cccgaaaccc aaaaatacgt tggcaaaggc atgacgattg cccaattatg tgaagcagcc 420
gtgcggttta gcgacaacag cgcgaccaat ttgctgctca aagaattggg tggcgtggaa 480
caatatcaac gtattttgcg acaattaggc gataacgtaa cccataccaa tcggctagaa 540
cccgatttaa atcaagccaa acccaacgat attcgtgata cgagtacacc caaacaaatg 600
gcgatgaatt taaatgcgta tttattgggc aacacattaa ccgaatcgca aaaaacgatt 660
ttgtggaatt ggttggacaa taacgcaaca ggcaatccat tgattcgcgc tgctacgcca 720
acatcgtgga aagtgtacga taaaagcggg gcgggtaaat atggtgtacg caatgatatt 780
gcggtggttc gcataccaaa tcgcaaaccg attgtgatgg caatcatgag tacgcaattt 840
accgaagaag ccaaattcaa caataaatta gtagaagatg cagcaaagca agtatttcat 900
actttacagc tcaactaa 918
163
864
DNA
Klebsiella pneumoniae
163
atgcgttata ttcgcctgtg tattatctcc ctgttagcca ccctgccgct ggcggtacac 60
gccagcccgc agccgcttga gcaaattaaa ctaagcgaaa gccagctgtc gggccgcgta 120
ggcatgatag aaatggatct ggccagcggc cgcacgctga ccgcctggcg cgccgatgaa 180
cgctttccca tgatgagcac ctttaaagta gtgctctgcg gcgcagtgct ggcgcgggtg 240
gatgccggtg acgaacagct ggagcgaaag atccactatc gccagcagga tctggtggac 300
tactcgccgg tcagcgaaaa acaccttgcc gacgcaatga cggtcggcga actctgcgcc 360
gccgccatta ccatgagcga taacagcgcc gccaatctgc tactggccac cgtcggcggc 420
cccgcaggat tgactgcctt tttgcgccag atcggcgaca acgtcacccg ccttgaccgc 480
tgggaaacgg aactgaatga ggcgcttccc ggcgacgccc gcgacaccac taccccggcc 540
agcatggccg cgaccctgcg caacgttggc ctgaccagcc agcgtctgag cgcccgttcg 600
caacggcagc tgctgcagtg gatggtggac gatcgggtcg ccggaccgtt gatccgctcc 660
gtgctgccgg cgggctggtt tatcgccgat aagaccggag ctggcgagcg gggtgcgcgc 720
gggattgtcg ccctgcttgg cccgaataac aaagcagagc gcattgtggt gatttatctg 780
cgggataccc cggcgagcat ggccgagcga aatcagcaaa tcgccgggat cggcaaggcg 840
ctgtacgagc actggcaacg ctaa 864
164
534
DNA
Klebsiella pneumoniae
164
atggacacaa cgcaggtcac attgatacac aaaattctag ctgcggcaga tgagcgaaat 60
ctgccgctct ggatcggtgg gggctgggcg atcgatgcac ggctagggcg tgtaacacgc 120
aagcacgatg atattgatct gacgtttccc ggcgagaggc gcggcgagct cgaggcaata 180
gttgaaatgc tcggcgggcg cgtcatggag gagttggact atggattctt agcggagatc 240
ggggatgagt tacttgactg cgaacctgct tggtgggcag acgaagcgta tgaaatcgcg 300
gaggctccgc agggctcgtg cccagaggcg gctgagggcg tcatcgccgg gcggccagtc 360
cgttgtaaca gctgggaggc gatcatctgg gattactttt actatgccga tgaagtacca 420
ccagtggact ggcctacaaa gcacatagag tcctacaggc tcgcatgcac ctcactcggg 480
gcggaaaagg ttgaggtctt gcgtgccgct ttcaggtcgc gatatgcggc ctaa 534
165
465
DNA
Unknown Organism
Description of Unknown Organism
Enterobacteriaceae
165
atgggcatca ttcgcacatg taggctcggc cctgaccaag tcaaatccat gcgggctgct 60
cttgatcttt tcggtcgtga gttcggagac gtagccacct actcccaaca tcagccggac 120
tccgattacc tcgggaactt gctccgtagt aagacattca tcgcgcttgc tgccttcgac 180
caagaagcgg ttgttggcgc tctcgcggct tacgttctgc ccaggtttga gcagccgcgt 240
agtgagatct atatctatga tctcgcagtc tccggcgagc accggaggca gggcattgcc 300
accgcgctca tcaatctcct caagcatgag gccaacgcgc ttggtgctta tgtgatctac 360
gtgcaagcag attacggtga cgatcccgca gtggctctct atacaaagtt gggcatacgg 420
gaagaagtga tgcactttga tatcgaccca agtaccgcca cctaa 465
166
861
DNA
Escherichia coli
166
atgcatacgc ggaaggcaat aacggaggcg cttcaaaaac tcggagtcca aaccggtgac 60
ctattgatgg tgcatgcctc acttaaagcg attggtccgg tcgaaggagg agcggagacg 120
gtcgttgccg cgttacgctc cgcggttggg ccgactggca ctgtgatggg atacgcatcg 180
tgggaccgat caccctacga ggagactcgt aatggcgctc ggttggatga caaaacccgc 240
cgtacctggc cgccgttcga tcccgcaacg gccgggactt accgtgggtt cggcctgctg 300
aatcagtttc tggttcaagc ccccggcgcg cggcgcagcg cgcaccccga tgcatcgatg 360
gtcgcggttg gtccactggc tgaaacgctg acggagcctc acaagctcgg tcacgccttg 420
ggggaagggt cgcccgtcga gcggttcgtt cgccttggcg ggaaggccct gctgttgggt 480
gcgccgctaa actccgttac cgcattgcac tacgccgagg cggttgccga tatccccaac 540
aaacggcggg tgacgtatga gatgccgatg cttggaagca acggcgaagt cgcctggaaa 600
acggcatcgg attacgattc aaacggcatt ctcgattgct ttgctatcga aggaaagccg 660
gatgcggtcg aaactatagc aaatgcttac gtgaagctcg gtcgccatcg agaaggtgtc 720
gtgggctttg ctcagtgcta cctgttcgac gcgcaggaca tcgtgacgtt cggcgtcacc 780
tatcttgaga agcatttcgg aaccactccg atcgtgccag cacacgaagt cgccgagtgc 840
tcttgcgagc cttcaggtta g 861
167
816
DNA
Pseudomonas aeruginosa
167
atgaccgatt tgaatatccc gcatacacac gcgcaccttg tagacgcatt tcaggcgctc 60
ggcatccgcg cggggcaggc gctcatgctg cacgcatccg ttaaagcagt gggcgcggtg 120
atgggcggcc ccaatgtgat cttgcaggcg ctcatggatg cgctcacgcc cgacggcacg 180
ctgatgatgt atgcgggatg gcaagacatc cccgacttta tcgactcgct gccggacgcg 240
ctcaaggccg tgtatcttga gcagcaccca ccctttgacc ccgccaccgc ccgcgccgtg 300
cgcgaaaaca gcgtgctagc ggaatttttg cgcacatggc cgtgcgtgca tcgcagcgca 360
aaccccgaag cctctatggt ggcggtaggc aggcaggccg ctttgctgac cgctaatcac 420
gcgctggatt atggctacgg agtcgagtcg ccgctggcta aactggtggc aatagaagga 480
tacgtgctga tgcttggcgc gccgctggat accatcacac tgctgcacca cgcggaatat 540
ctggccaaga tgcgccacaa gaacgtggtc cgctacccgt gcccgattct gcgggacggg 600
cgcaaagtgt gggtgaccgt tgaggactat gacaccggtg atccgcacga cgattatagt 660
tttgagcaaa tcgcgcgcga ttatgtggcg cagggcggcg gcacacgcgg caaagtcggt 720
gatgcggatg cttacctgtt cgccgcgcag gacctcacac ggtttgcggt gcagtggctt 780
gaatcacggt tcggtgactc agcgtcatac ggatag 816
168
498
DNA
Pseudomonas aeruginosa
168
atgctctatg agtggctaaa tcgatctcat atcgtcgagt ggtggggcgg agaagaagca 60
cgcccgacac ttgctgacgt acaggaacag tacttgccaa gcgttttagc gcaagagtcc 120
gtcactccat acattgcaat gctgaatgga gagccgattg ggtatgccca gtcgtacgtt 180
gctcttggaa gcggggacgg atggtgggaa gaagaaaccg atccaggagt acgcggaata 240
gaccagttac tggcgaatgc atcacaactg ggcaaaggct tgggaaccaa gctggttcga 300
gctctggttg agttgctgtt caatgatccc gaggtcacca agatccaaac ggacccgtcg 360
ccgagcaact tgcgagcgat ccgatgctac gagaaagcgg ggtttgagag gcaaggtacc 420
gtaaccaccc cagatggtcc agccgtgtac atggttcaaa cacgccaggc attcgagcga 480
acacgcagtg atgcctaa 498
169
2007
DNA
Staphylococcus aureus
169
atgaaaaaga taaaaattgt tccacttatt ttaatagttg tagttgtcgg gtttggtata 60
tatttttatg cttcaaaaga taaagaaatt aataatacta ttgatgcaat tgaagataaa 120
aatttcaaac aagtttataa agatagcagt tatatttcta aaagcgataa tggtgaagta 180
gaaatgactg aacgtccgat aaaaatatat aatagtttag gcgttaaaga tataaacatt 240
caggatcgta aaataaaaaa agtatctaaa aataaaaaac gagtagatgc tcaatataaa 300
attaaaacaa actacggtaa cattgatcgc aacgttcaat ttaattttgt taaagaagat 360
ggtatgtgga agttagattg ggatcatagc gtcattattc caggaatgca gaaagaccaa 420
agcatacata ttgaaaattt aaaatcagaa cgtggtaaaa ttttagaccg aaacaatgtg 480
gaattggcca atacaggaac acatatgaga ttaggcatcg ttccaaagaa tgtatctaaa 540
aaagattata aagcaatcgc taaagaacta agtatttctg aagactatat caacaacaaa 600
tggatcaaaa ttgggtacaa gatgatacct tcgttccact ttaaaaccgt taaaaaaatg 660
gatgaatatt taagtgattt cgcaaaaaaa tttcatctta caactaatga aacagaaagt 720
cgtaactatc ctctagaaaa agcgacttca catctattag gttatgttgg tcccattaac 780
tctgaagaat taaaacaaaa agaatataaa ggctataaag atgatgcagt tattggtaaa 840
aagggactcg aaaaacttta cgataaaaag ctccaacatg aagatggcta tcgtgtcaca 900
atcgttgacg ataatagcaa tacaatcgca catacattaa tagagaaaaa gaaaaaagat 960
ggcaaagata ttcaactaac tattgatgct aaagttcaaa agagtattta taacaacatg 1020
aaaaatgatt atggctcagg tactgctatc caccctcaaa caggtgaatt attagcactt 1080
gtaagcacac cttcatatga cgtctatcca tttatgtatg gcatgagtaa cgaagaatat 1140
aataaattaa ccgaagataa aaaagaacct ctgctcaaca agttccagat tacaacttca 1200
ccaggttcaa ctcaaaaaat attaacagca atgattgggt taaataacaa aacattagac 1260
gataaaacaa gttataaaat cgatggtaaa ggttggcaaa aagataaatc ttggggtggt 1320
tacaacgtta caagatatga agtggtaaat ggtaatatcg acttaaaaca agcaatagaa 1380
tcatcagata acattttctt tgctagagta gcactcgaat taggcagtaa gaaatttgaa 1440
aaaggcatga aaaaactagg tgttggtgaa gatataccaa gtgattatcc attttataat 1500
gctcaaattt caaacaaaaa tttagataat gaaatattat tagctgattc aggttacgga 1560
caaggtgaaa tactgattaa cccagtacag atcctttcaa tctatagcgc attagaaaat 1620
aatggcaata ttaacgcacc tcacttatta aaagacacga aaaacaaagt ttggaagaaa 1680
aatattattt ccaaagaaaa tatcaatcta ttaaatgatg gtatgcaaca agtcgtaaat 1740
aaaacacata aagaagatat ttatagatct tatgcaaact taattggcaa atccggtact 1800
gcagaactca aaatgaaaca aggagaaagt ggcagacaaa ttgggtggtt tatatcatat 1860
gataaagata atccaaacat gatgatggct attaatgtta aagatgtaca agataaagga 1920
atggctagct acaatgccaa aatctcaggt aaagtgtatg atgagctata tgagaacggt 1980
aataaaaaat acgatataga tgaataa 2007
170
2607
DNA
Enterococcus faecium
170
atgaataaca tcggcattac tgtttatgga tgtgagcagg atgaggcaga tgcattccat 60
gctctttcgc ctcgctttgg cgttatggca acgataatta acgccaacgt gtcggaatcc 120
aacgccaaat ccgcgccttt caatcaatgt atcagtgtgg gacataaatc agagatttcc 180
gcctctattc ttcttgcgct gaagagagcc ggtgtgaaat atatttctac ccgaagcatc 240
ggctgcaatc atatagatac aactgctgct aagagaatgg gcatcactgt cgacaatgtg 300
gcgtactcgc cggatagcgt tgccgattat actatgatgc taattcttat ggcagtacgc 360
aacgtaaaat cgattgtgcg ctctgtggaa aaacatgatt tcaggttgga cagcgaccgt 420
ggcaaggtac tcagcgacat gacagttggt gtggtgggaa cgggccagat aggcaaagcg 480
gttattgagc ggctgcgagg atttggatgt aaagtgttgg cttatagtcg cagccgaagt 540
atagaggtaa actatgtacc gtttgatgag ttgctgcaaa atagcgatat cgttacgctt 600
catgtgccgc tcaatacgga tacgcactat attatcagcc acgaacaaat acagagaatg 660
aagcaaggag catttcttat caatactggg cgcggtccac ttgtagatac ctatgagttg 720
gttaaagcat tagaaaacgg gaaactgggc ggtgccgcat tggatgtatt ggaaggagag 780
gaagagtttt tctactctga ttgcacccaa aaaccaattg ataatcaatt tttacttaaa 840
cttcaaagaa tgcctaacgt gataatcaca ccgcatacgg cctattatac cgagcaagcg 900
ttgcgtgata ccgttgaaaa aaccattaaa aactgtttgg attttgaaag gagacaggag 960
catgaataga ataaaagttg caatactgtt tgggggttgc tcagaggagc atgacgtatc 1020
ggtaaaatct gcaatagaga tagccgctaa cattaataaa gaaaaatacg agccgttata 1080
cattggaatt acgaaatctg gtgtatggaa aatgtgcgaa aaaccttgcg cggaatggga 1140
aaacgacaat tgctattcag ctgtactctc gccggataaa aaaatgcacg gattacttgt 1200
taaaaagaac catgaatatg aaatcaacca tgttgatgta gcattttcag ctttgcatgg 1260
caagtcaggt gaagatggat ccatacaagg tctgtttgaa ttgtccggta tcccttttgt 1320
aggctgcgat attcaaagct cagcaatttg tatggacaaa tcgttgacat acatcgttgc 1380
gaaaaatgct gggatagcta ctcccgcctt ttgggttatt aataaagatg ataggccggt 1440
ggcagctacg tttacctatc ctgtttttgt taagccggcg cgttcaggct catccttcgg 1500
tgtgaaaaaa gtcaatagcg cggacgaatt ggactacgca attgaatcgg caagacaata 1560
tgacagcaaa atcttaattg agcaggctgt ttcgggctgt gaggtcggtt gtgcggtatt 1620
gggaaacagt gccgcgttag ttgttggcga ggtggaccaa atcaggctgc agtacggaat 1680
ctttcgtatt catcaggaag tcgagccgga aaaaggctct gaaaacgcag ttataaccgt 1740
tcccgcagac ctttcagcag aggagcgagg acggatacag gaaacggcaa aaaaaatata 1800
taaagcgctc ggctgtagag gtctagcccg tgtggatatg tttttacaag ataacggccg 1860
cattgtactg aacgaagtca atactctgcc cggtttcacg tcatacagtc gttatccccg 1920
tatgatggcc gctgcaggta ttgcacttcc cgaactgatt gaccgcttga tcgtattagc 1980
gttaaagggg tgataagcat ggaaatagga tttacttttt tagatgaaat agtacacggt 2040
gttcgttggg acgctaaata tgccacttgg gataatttca ccggaaaacc ggttgacggt 2100
tatgaagtaa atcgcattgt agggacatac gagttggctg aatcgctttt gaaggcaaaa 2160
gaactggctg ctacccaagg gtacggattg cttctatggg acggttaccg tcctaagcgt 2220
gctgtaaact gttttatgca atgggctgca cagccggaaa ataacctgac aaaggaaagt 2280
tattatccca atattgaccg aactgagatg atttcaaaag gatacgtggc ttcaaaatca 2340
agccatagcc gcggcagtgc cattgatctt acgctttatc gattagacac gggtgagctt 2400
gtaccaatgg ggagccgatt tgattttatg gatgaacgct ctcatcatgc ggcaaatgga 2460
atatcatgca atgaagcgca aaatcgcaga cgtttgcgct ccatcatgga aaacagtggg 2520
tttgaagcat atagcctcga atggtggcac tatgtattaa gagacgaacc ataccccaat 2580
agctattttg atttccccgt taaataa 2607
171
1288
DNA
Pseudomonas aeruginosa
171
ggatccatca ggcaacgacg ggctgctgcc ggccatcagc ggacgcaggg aggactttcc 60
gcaaccggcc gttcgatgcg gcaccgatgg ccttcgcgca ggggtagtga atccgccagg 120
attgacttgc gctgccctac ctctcactag tgaggggcgg cagcgcatca agcggtgagc 180
gcactccggc accgccaact ttcagcacat gcgtgtaaat catcgtcgta gagacgtcgg 240
aatggccgag cagatcctgc acggttcgaa tgtcgtaacc gctgcggagc aaggccgtcg 300
cgaacgagtg gcggagggtg tgcggtgtgg cgggcttcgt gatgcctgct tgttctacgg 360
cacgtttgaa ggcgcgctga aaggtctggt catacatgtg atggcgacgc acgacaccgc 420
tccgtggatc ggtcgaatgc gtgtgctgcg caaaaaccca gaaccacggc caggaatgcc 480
cggcgcgcgg atacttccgc tcaagggcgt cgggaagcgc aacgccgctg cggccctcgg 540
cctggtcctt cagccaccat gcccgtgcac gcgacagctg ctcgcgcagg ctgggtgcca 600
agctctcggg taacatcaag gcccgatcct tggagccctt gccctcccgc acgatgatcg 660
tgccgtgatc gaaatccaga tccttgaccc gcagttgcaa accctcactg atccgcatgc 720
ccgttccata cagaagctgg gcgaacaaac gatgctcgcc ttccagaaaa ccgaggatgc 780
gaaccacttc atccggggtc agcaccaccg gcaagcgccg cgacggccga ggtcttccga 840
tctcctgaag ccagggcaga tccgtgcaca gcaccttgcc gtagaagaac agcaaggccg 900
ccaatgcctg acgatgcgtg gagaccgaaa ccttgcgctc gttcgccagc caggacagaa 960
atgcctcgac ttcgctgctg cccaaggttg ccgggtgacg cacaccgtgg aaacggatga 1020
aggcacgaac ccagtggaca taagcctgtt cggttcgtaa gctgtaatgc aagtagcgta 1080
tgcgctcacg caactggtcc agaaccttga ccgaacgcag cggtggtaac ggcgcagtgg 1140
cggttttcat ggcttgttat gactgttttt ttgtacagtc tatgcctcgg gcatccaagc 1200
agcaagcgcg ttacgccgtg ggtcgatgtt tgatgttatg gagcagcaac gatgttacgc 1260
agcagggcag tcgccctaaa acaaagtt 1288
172
1650
DNA
Pseudomonas aeruginosa
172
gttagatgca ctaagcacat aattgctcac agccaaacta tcaggtcaag tctgctttta 60
ttatttttaa gcgtgcataa taagccctac acaaattggg agatatatca tgaaaggctg 120
gctttttctt gttatcgcaa tagttggcga agtaatcgca acatccgcat taaaatctag 180
cgagggcttt actaagcttg ccccttccgc cgttgtcata atcggttatg gcatcgcatt 240
ttattttctt tctctggttc tgaaatccat ccctgtcggt gttgcttatg cagtctggtc 300
gggactcggc gtcgtcataa ttacagccat tgcctggttg cttcatgggc aaaagcttga 360
tgcgtggggc tttgtaggta tggggctcat aattgctgcc tttttgctcg cccgatcccc 420
atcgtggaag tcgctgcgga ggccgacgcc atggtgacgg tgttcggcat tctgaatctc 480
accgaggact ccttcttcga tgagagccgg cggctagacc ccgccggcgc tgtcaccgcg 540
gcgatcgaaa tgctgcgagt cggatcagac gtcgtggatg tcggaccggc cgccagccat 600
ccggacgcga ggcctgtatc gccggccgat gagatcagac gtattgcgcc gctcttagac 660
gccctgtccg atcagatgca ccgtgtttca atcgacagct tccaaccgga aacccagcgc 720
tatgcgctca agcgcggcgt gggctacctg aacgatatcc aaggatttcc tgaccctgcg 780
ctctatcccg atattgctga ggcggactgc aggctggtgg ttatgcactc agcgcagcgg 840
gatggcatcg ccacccgcac cggtcacctt cgacccgaag acgcgctcga cgagattgtg 900
cggttcttcg aggcgcgggt ttccgccttg cgacggagcg gggtcgctgc cgaccggctc 960
atcctcgatc cggggatggg atttttcttg agccccgcac cggaaacatc gctgcacgtg 1020
ctgtcgaacc ttcaaaagct gaagtcggcg ttggggcttc cgctattggt ctcggtgtcg 1080
cggaaatcct tcttgggcgc caccgttggc cttcctgtaa aggatctggg tccagcgagc 1140
cttgcggcgg aacttcacgc gatcggcaat ggcgctgact acgtccgcac ccacgcgcct 1200
ggagatctgc gaagcgcaat caccttctcg gaaaccctcg cgaaatttcg cagtcgcgac 1260
gccagagacc gagggttaga tcatgcctag cattcacctt ccggccgccc gctagcggac 1320
cctggtcagg ttccgcgaag gtgggcgcag acatgctggg ctcgtcagga tcaaactgca 1380
ctatgaggcg gcggttcata ccgcgccagg ggagcgaatg gacagcgagg agcctccgaa 1440
cgttcgggtc gcctgctcgg gtgatatcga cgaggttgtg cggctgatgc acgacgctgc 1500
ggcgtggatg tccgccaagg gaacgcccgc ctgggacgtc gcgcggatcg accggacatt 1560
cgcggagacc ttcgtcctga gatccgagct cctagtcgcg agttgcagcg acggcatcgt 1620
cggctgttgc accttgtcgg ccgaggatcc 1650
173
630
DNA
Enterococcus faecium
173
atgggtccga atcctatgaa aatgtatcct atagaaggaa acaaatcagt acaatttatc 60
aaacctattt tagaaaaatt agaaaatgtt gaggttggag aatactcata ttatgattct 120
aagaatggag aaacttttga taagcaaatt ttatatcatt atccaatctt aaacgataag 180
ttaaaaatag gtaaattttg ctcaatagga ccaggtgtaa ctattattat gaatggagca 240
aatcatagaa tggatggctc aacatatcca tttaatttat ttggtaatgg atgggagaaa 300
catatgccaa aattagatca actacctatt aagggggata caataatagg taatgatgta 360
tggataggaa aagatgttgt aattatgcca ggagtaaaaa tcggggatgg tgcaatagta 420
gctgctaatt ctgttgttgt aaaagatata gcgccataca tgttagctgg aggaaatcct 480
gctaacgaaa taaaacaaag atttgatcaa gatacaataa atcagctgct tgatataaaa 540
tggtggaatt ggccaataga cattattaat gagaatatag ataaaattct tgataatagc 600
atcattagag aagtcatatg gaaaaaatga 630
174
1440
DNA
Enterococcus faecalis
174
atgaatatag ttgaaaatga aatatgtata agaactttaa tagatgatga ttttcctttg 60
atgttaaaat ggttaactga tgaaagagta ttagaatttt atggtggtag agataaaaaa 120
tatacattag aatcattaaa aaaacattat acagagcctt gggaagatga agtttttaga 180
gtaattattg aatataacaa tgttcctatt ggatatggac aaatatataa aatgtatgat 240
gagttatata ctgattatca ttatccaaaa actgatgaga tagtctatgg tatggatcaa 300
tttataggag agccaaatta ttggagtaaa ggaattggta caagatatat taaattgatt 360
tttgaatttt tgaaaaaaga aagaaatgct aatgcagtta ttttagaccc tcataaaaat 420
aatccaagag caataagggc ataccaaaaa tctggtttta gaattattga agatttgcca 480
gaacatgaat tacacgaggg caaaaaagaa gattgttatt taatggaata tagatatgat 540
gataatgcca caaatgttaa ggcaatgaaa tatttaattg agcattactt tgataatttc 600
aaagtagata gtattgaaat aatcggtagt ggttatgata gtgtggcata tttagttaat 660
aatgaataca tttttaaaac aaaatttagt actaataaga aaaaaggtta tgcaaaagaa 720
aaagcaatat ataatttttt aaatacaaat ttagaaacta atgtaaaaat tcctaatatt 780
gaatattcgt atattagtga tgaattatct atactaggtt ataaagaaat taaaggaact 840
tttttaacac cagaaattta ttctactatg tcagaagaag aacaaaattt gttaaaacga 900
gatattgcca gttttttaag acaaatgcac ggtttagatt atacagatat tagtgaatgt 960
actattgata ataaacaaaa tgtattagaa gagtatatat tgttgcgtga aactatttat 1020
aatgatttaa ctgatataga aaaagattat atagaaagtt ttatggaaag actaaatgca 1080
acaacagttt ttgagggtaa aaagtgttta tgccataatg attttagttg taatcatcta 1140
ttgttagatg gcaataatag attaactgga ataattgatt ttggagattc tggaattata 1200
gatgaatatt gtgattttat atacttactt gaagatagtg aagaagaaat aggaacaaat 1260
tttggagaag atatattaag aatgtatgga aatatagata ttgagaaagc aaaagaatat 1320
caagatatag ttgaagaata ttatcctatt gaaactattg tttatggaat taaaaatatt 1380
aaacaggaat ttatcgaaaa tggtagaaaa gaaatttata aaaggactta taaagattga 1440
175
660
DNA
Staphylococcus aureus
175
ttgaatttaa acaatgacca tggacctgat cccgaaaata ttttaccgat aaaagggaat 60
cggaatcttc aatttataaa acctactata acgaacgaaa acattttggt gggggaatat 120
tcttattatg atagtaagcg aggagaatcc tttgaagatc aagtcttata tcattatgaa 180
gtgattggag ataagttgat tataggaaga ttttgttcaa ttggtcccgg aacaacattt 240
attatgaatg gtgcaaacca tcggatggat ggatcaacat atccttttca tctattcagg 300
atgggttggg agaagtatat gccttcctta aaagatcttc ccttgaaagg ggacattgaa 360
attggaaatg atgtatggat aggtagagat gtaaccatta tgcctggggt gaaaattggg 420
gacggggcaa tcattgctgc agaagctgtt gtcacaaaga atgttgctcc ctattctatt 480
gtcggtggaa atcccttaaa atttataaga aaaaggtttt ctgatggagt tatcgaagaa 540
tggttagctt tacaatggtg gaatttagat atgaaaatta ttaatgaaaa tcttcccttc 600
ataataaatg gagatatcga aatgctgaag agaaaaagaa aacttctaga tgacacttga 660
176
1569
DNA
Staphylococcus aureus
176
atgaaaataa tgttagaggg acttaatata aaacattatg ttcaagatcg tttattgttg 60
aacataaatc gcctaaagat ttatcagaat gatcgtattg gtttaattgg taaaaatgga 120
agtggaaaaa caacgttact tcacatatta tataaaaaaa ttgtgcctga agaaggtatt 180
gtaaaacaat tttcacattg tgaacttatt cctcaattga agctcataga atcaactaaa 240
agtggtggtg aagtaacacg aaactatatt cggcaagcgc ttgataaaaa tccagaactg 300
ctattagcag atgaaccaac aactaactta gataataact atatagaaaa attagaacag 360
gatttaaaaa attggcatgg agcatttatt atagtttcac atgatcgcgc ttttttagat 420
aacttgtgta ctactatatg ggaaattgac gagggaagaa taactgaata taaggggaat 480
tatagtaact atgttgaaca aaaagaatta gaaagacatc gagaagaatt agaatatgaa 540
aaatatgaaa aagaaaagaa acgattggaa aaagctataa atataaaaga acagaaagct 600
caacgagcaa ctaaaaaacc gaaaaactta agtttatctg aaggcaaaat aaaaggagca 660
aagccatact ttgcaggtaa gcaaaagaag ttacgaaaaa ctgtaaaatc tctagaaacc 720
agactagaaa aacttgaaag cgtcgaaaag agaaacgaac ttcctccact taaaatggat 780
ttagtgaact tagaaagtgt aaaaaataga actataatac gtggtgaaga tgtctcgggt 840
acaattgaag gacgggtatt gtggaaagca aaaagtttta gtattcgcgg aggagacaag 900
atggcaatta tcggatctaa tggtacagga aagacaacgt ttattaaaaa aattgtgcat 960
gggaatcctg gtatttcatt atcgccatct gtcaaaatcg gttattttag ccaaaaaata 1020
gatacattag aattagataa gagcatttta gaaaatgttc aatcttcttc acaacaaaat 1080
gaaactctta ttcgaactat tctagctaga atgcattttt ttagagatga tgtttataaa 1140
ccaataagtg tcttaagtgg tggagagcga gttaaagtag cactaactaa agtattctta 1200
agtgaagtta atacgttggt actagatgaa ccaacaaact ttcttgatat ggaagctata 1260
gaggcgtttg aatctttgtt aaaggaatat aatggcagta taatctttgt atctcacgat 1320
cgtaaattta tcgaaaaagt agccactcga ataatgacaa ttgataataa agaaataaaa 1380
atatttgatg gcacatatga acaatttaaa caagctgaaa agccaacaag gaatattaaa 1440
gaagataaaa aacttttact tgagacaaaa attacagaag tactcagtcg attgagtatt 1500
gaaccttcgg aagaattaga acaagagttt caaaacttaa taaatgaaaa aagaaatttg 1560
gataaataa 1569
177
1467
DNA
Staphylococcus epidermidis
177
atggaacaat atacaattaa atttaaccaa atcaatcata aattgacaga tttacgatca 60
cttaacatcg atcatcttta tgcttaccaa tttgaaaaaa tagcacttat tgggggtaat 120
ggtactggta aaaccacatt actaaatatg attgctcaaa aaacaaaacc agaatctgga 180
acagttgaaa cgaatggcga aattcaatat tttgaacagc ttaacatgga tgtggaaaat 240
gattttaaca cgttagacgg tagtttaatg agtgaactcc atatacctat gcatacaacc 300
gacagtatga gtggtggtga aaaagcaaaa tataaattac gtaatgtcat atcaaattat 360
agtccgatat tacttttaga tgaacctaca aatcacttgg ataaaattgg taaagattat 420
ctgaataata ttttaaaata ttactatggt actttaatta tagtaagtca cgatagagca 480
cttatagacc aaattgctga cacaatttgg gatatacaag aagatggcac aataagagtg 540
tttaaaggta attacacaca gtatcaaaat caatatgaac aagaacagtt agaacaacaa 600
cgtaaatatg aacagtatat aagtgaaaaa caaagattgt cccaagccag taaagctaaa 660
cgaaatcaag cgcaacaaat ggcacaagca tcatcaaaac aaaaaaataa aagtatagca 720
ccagatcgtt taagtgcatc aaaagaaaaa ggcacggttg agaaggctgc tcaaaaacaa 780
gctaagcata ttgaaaaaag aatggaacat ttggaagaag ttgaaaaacc acaaagttat 840
catgaattca attttccaca aaataaaatt tatgatatcc ataataatta tccaatcatt 900
gcacaaaatc taacattggt taaaggaagt caaaaactgc taacacaagt acgattccaa 960
ataccatatg gcaaaaatat agcgctcgta ggtgcaaatg gtgtaggtaa gacaacttta 1020
cttgaagcta tttaccacca aatagaggga attgattgtt ctcctaaagt gcaaatggca 1080
tactatcgtc aacttgctta tgaagacatg cgtgacgttt cattattgca atatttaatg 1140
gatgaaacgg attcatcaga atcattcagt agagctattt taaataactt gggtttaaat 1200
gaagcacttg agcgttcttg taatgttttg agtggtgggg aaagaacgaa attatcgtta 1260
gcagtattat tttcaacgaa agcgaatatg ttaattttgg atgaaccaac taatttttta 1320
gatattaaaa cattagaagc attagaaatg tttatgaata aatatcctgg aatcattttg 1380
tttacatcac atgatacaag gtttgttaaa catgtatcag ataaaaaatg ggaattaaca 1440
ggacaatcta ttcatgatat aacttaa 1467