AU5422101A - Species-specific, genus-specific and universal DNA probes and amplification primers to rapidly detect and identify common bacterial and fungal pathogens and associated antibiotic resistance genes from clinical specimens for diagnosis in microbiology laboratories - Google Patents

Description

AUSTRALIA

Patents Act 1990 COMPLETE SPECIFICATION FOR A STANDARD PATENT Name of Applicant: Infectio Diagnostic Inc.

Actual Inventors: Michel G. Bergeron Frangois J: Picard Marc Ouellette Paul H. Roy CULLEN CO., Patent Trade Mark Attorneys, 239 George Street, Brisbane, QId. 4000, Australia.

Address for Service: Invention Title: Species-specific, Genus-specific and Universal DNA Probes and Amplification Primers to Rapidly Detect and Identify Common Bacterial and Fungal Pathogens and Associated Antibiotic Resistance Genes From Clinical Specimens for Diagnosis in Microbiology Laboratories The following statement is a full description of this invention, including the best method of performing it known to us: TITLE OF THE INVENTION SPECIES-SPECIFIC, GENUS-SPECIFIC AND UNIVERSAL DNA PROBES AND AMPLIFICATION PRIMERS TO RAPIDLY DETECT AND IDENTIFY COMMON BACTERIAL AND FUNGAL PATHOGENS AND ASSOCIATED

ANTIBIOTIC

RESISTANCE GENES FROM CLINICAL SPECIMENS FOR DIAGNOSIS

IN

MICROBIOLOGY LABORATORIES BACKGROUND OF THE INVENTION Classical methods for the identification and susceptibility testing of bacteria 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 system (bioMerieux). For susceptibility testing, clinical microbiology laboratories use methods including disk diffusion, agar dilution and broth microdilution.

Although identifications based on biochemical tests and antibacterial susceptibility tests are cost-effective, at least two days are required to obtain preliminary results due to the necessity of two successive overnight incubations to identify the bacteria from clinical specimens as well as to determine their susceptibility to antimicrobial agents.

S. There are some commercially available automated systems the MicroScan system from Dade Diagnostics Corp. and the Vitek system from bioMerieux) which use 20 sophisticated and expensive apparatus for faster microbial identification and susceptibility testing (Stager and Davis, 1992, Clin. Microbiol. Rev. 5:302-327). These systems require shorter incubation periods, thereby allowing most bacterial identifications and susceptibility testing to be performed in less than 6 hours.

Nevertheless, these faster systems always require the primary isolation of the bacteria as a pure culture, a process which takes at least 18 hours for a pure culture or 2 days for a mixed culture. The fastest identification system, the autoSCAN-Walk-AwayTM system (Dade Diagnostics Corp.) identifies both gram-negative and gram-positive bacterial species from standardized inoculum in as little as 2 hours and gives susceptibility patterns to most antibiotics in 5.5 hours. However, this system has a 30 particularly high percentage 3.3 to 40.5%) of non-conclusive identifications with bacterial species other than Enterobacteriaceae (Croize 1995, Lett. Infectiol.

10:109-113; York et al., 1992, J. Clin. Microbiol. 30:2903-2910). For Enterobacteriaceae, the percentage of non-conclusive identifications was 2.7 to 11.4%.

A wide variety of bacteria and fungi are routinely isolated and identified from clinical specimens in microbiology laboratories. Tables 1 and 2 give the incidence for the most commonly isolated bacterial and fungal pathogens from various types of clinical specimens. These pathogens are the most frequently associated with nosocomial and community-acquired human infections and are therefore considered the most clinically important.

Clinical specimens tested in clinical microbiology laboratories Most clinical specimens received in clinical microbiology laboratories are urine and blood samples. At the microbiology laboratory of the Centre Hospitalier de I'Universite Laval (CHUL), urine and blood account for approximately 55% and of the specimens received, respectively (Table.3). The remaining 15% of clinical specimens comprise various biological fluids including sputum, pus, cerebrospinal fluid, synovial fluid, and others (Table Infections of the urinary tract, the respiratory tract and the bloodstream are usually of bacterial etiology and require antimicrobial therapy.

In fact, all clinical samples received in the clinical microbiology laboratory are tested routinely for the identification of bacteria and susceptibility testing.

Conventional pathogen identification from clinical specimens 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. However, the gold standard remains the classical semi-quantitative plate culture method in which 1 pL 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 urinary tract infection (UTI) is normally associated with a bacterial count of CFU/L or more 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 S..(Stark and Maki, 1984, N. Engl. J. Med. 311:560-564). Importantly, approximately of urine specimens tested in clinical microbiology laboratories are considered negative bacterial count of less than 10 7 CFU/L; Table Urine specimens found positive b."y culture are further characterized using standard biochemical tests to identify the bacterial pathogen and are also tested for susceptibility to antibiotics. The biochemical and susceptibility testing normally require 18-24 hours of incubation.

Accurate and rapid urine screening methods for bacterial pathogens would allow a faster identification of negative specimens and a more efficient treatment and care management of patients. Several rapid identification methods (Uriscreen

T

30 UTIscreenm, Flash TrackTM DNA probes and others) have been 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 poor 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 eta/., 1992, J. Clin. Microbiol. 30:640- 684).

Blood specimens The blood specimens received in the microbiology laboratory are always submitted for culture. Blood culture systems may be manual, semi-automated or completely automated. The BACTEC system (from Becton Dickinson) and the -3- BacTAlert system (from Organon Teknika Corporation) are the two most widely used automated blood culture systems. These systems incubate blood culture bottles under optimal conditions for bacterial growth. Bacterial growth is monitored continuously to detect early positives by using highly sensitive bacterial growth detectors. Once growth is detected, a Gram stain is performed directly from the blood culture and then used to inoculate nutrient agar plates. Subsequently, bacterial identification and susceptibility testing are carried out from isolated bacterial colonies with automated systems as described previously. The bottles are normally reported as negative if no growth is detected after an incubation of 6 to 7 days. Normally, the vast majority of blood cultures are reported negative. For example, the percentage of negative blood cultures at the microbiology laboratory of the CHUL for the period February 1994- January 1995 was 93.1% (Table 3).

Other clinical samples Upon receipt by the clinical microbiology laboratory, all body fluids other than blood and urine that are from normally sterile sites cerebrospinal, synovial, pleural, pericardial and others) are processed for direct microscopic examination and subsequent culture. Again, most clinical samples are negative for culture (Table 3).

Regarding clinical specimens which are not from sterile sites such as sputum or stool specimens, the laboratory diagnosis by culture is more problematic because 20 of the contamination by the normal flora. The bacterial pathogens potentially associated with the infection are purified from the contaminants and then identified as described previously. Of course, the universal detection of bacteria would not be useful °for the diagnosis of bacterial infections at these non sterile sites. On the other hand, DNA-based assays for species or genus detection and identification as well as for the detection of antibiotic resistance genes from these specimens would be very useful and would offer several advantages over classical identification and susceptibility testing methods.

DNA-based assays with any clinical spDecimens There is an obvious need for rapid and accurate diagnostic tests for bacterial 30 detection and identification directly from clinical specimens. DNA-based technologies *oe.

are rapid and accurate and offer a great potential to improve the diagnosis of infectious diseases (Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, The DNA probes and amplification primers which are objects of the present invention are applicable for bacterial or fungal detection and identification directly from any clinical specimens such as blood cultures, blood, urine, sputum, cerebrospinal fluid, pus and other type of specimens (Table The DNA-based tests proposed in this invention are superior in terms of both rapidity and accuracy to standard biochemical methods currently used for routine diagnosis from any clinical specimens in microbiology laboratories. Since -4these toctc arcs performed in around only one hour, they provide the clinicians with new diagnostic toois which should contribute to increase the efficiency of therapies with antimicrobial agjents. Clinical specimens from organisms other than humans other primates, birds 1 plants, mammals, farm animals, livestock and others) may also be tested with thts8e assays.

A higlinrc[Ittana-of culture noptlvo soeclmens Among all the clinical specimens received for routine diagnosis, approximately of urine specimens and even more (around 05%) for other types of clinical specimens ariii negative for the presence of bacteria! pathogens (Table It wouid also be desira~ble, in addition to identify bacteria at the species or genus level in a given specimel, to screen out the high proportion of negative clinical specimens with a test detectinl the presence of any bactenum universal bacterial detection). Such a screening teii may b~e based on the DNA amplification by PCR of a highly conserved genetic targez found in all bacteria. Specimens negative for bacteria would not be amplified by this assay. On the other hand, those that are positive for bacteria would give a positive amplification signal with this assay.

Towarstrh&.evllament of rapid QNA-basad dingorti tents A i'apicl diagnostic test should have a significant impact on the management of 20 infections. DNA probe and DNA amplification technologies offer several advantages conventional methods for the identfication of pathogens and antibiotic resistance genes from clinical samples (Persing at 1093, Diagnostic Molecular Microbiology.

Principles and Applications, American Society for Microbiology, Washington, D.C.; Ehrlich and Greenberg, 1994, PC R-based. Diagnostics in Infectious Disease, Blackwell Scientific PuI'ications, Boston, MA). There is no need for culture of the, bacterial pathogens, he3nce the organisms can be detected directly from clinical samples, thereby reducing the time associated with the isolation and identification of pathogens.

Furthermore, DNA-based assays are more accurate for bacterial identification than currently used phtenotypic identification systems whIch are based on blochemlcal tests.

Commercially available DNA-based technologies are cuirrently used in clinical microbiology laboratories. mainly for the detection and identification of fastidious bacterial pathogens such as Mycobacteriumn tuberculosis, Chiamydia tra6chomnatis, Neisseria gonorrhoeae as well as for the detection of a variety of viruses (Podzorski and'Persing, Moalecular detection and identification of microorganisms. In: P Murray et al., 1995, M'anual of Clinical Microbiology, ASM press, Washington There are also other commercially available DNA-based assays which are used for culture confirmation aissays.

-Othier' have developed DNA-based tests for the detection and identification of bacterial pathogens which are objects of the present invention: Staphylococcus s PP.

(US patent No.'US 5 437 978), Neisseria app. (US patent No. US 5 162 199 s~d- ,Europs~zn patant publication No. EP 0 337 890 131) and isterra monoCytogaflOs (US patents Nos"5389-513 and 5*089 386). However, the diagniostic test~s LI -ibed in these patents are based either on rRNA genes or on genetic targets different from those described in the present invention.

Although there are diagnostic kits or methods already used in clinical microbiology laboratories, there is still a need for an advantageous alternative to the conventional culture identification methods in order to improve the accuracy and the speed of the diagnosis of commonly encountered bacterial infections. Besides being much faster, DNA-based diagnostic tests are more accurate than standard biochemical tests presently used for diagnosis because the bacterial genotype DNA level) is more stable than the bacterial phenotype metabolic level).

Knowledge of the genomic sequences of bacterial and fungal species continuously increases as testified by the number of sequences available from databases. From the sequences readily available from .atabases, there is no indication thersfrom as to their potential for diagnostic purposes. For determining good candidates for diagnostic purposes, one could select sequences for DNA-based assays for the species-specific detection and identification of commonly encountered bacterial or fungal pathogens, (II) the genus-specific detection and identification cf commonly encountered bacterial or fungal pathogens, (iii) the universal detection of bacterial or fungal pathogens and/or (iv) the specific detection and identification of antibiotic resistance genes. All of the above types of DNA-based 20 assays may lbe performed directly from any type of clinical specimens or from a microbial cultuire.

In WO @6/08502 patent publication, we described DNA sequences suitable for the speciesi-specific detection and identification of 12 clinically important bacterial pathogens, ()11 the universal detection of bacteria, and (11l) the detection of 17 antibiotic resistance genes. This co-pending application described proprietary DNA sequences and DNA sequences selected from databases (in both cases, fragments of at least 100 base pairs), as well as oligonucleotide probes and amplification primers derived from these sequen::es. All the nucleic acid sequences described in this patent application enter the cormposition of diagnostic kits and methods capable of a) detecting the 30 presence of bacteria, b) detecting specifically the presence of 12 bacterial species and 17 antibiotic resistance genes. However, these methods and kits need to be improved, since the Ideal kit and method snould be capable of diagnosing close to 100% of microbial pathogens and antibiotic resistance genes. For example. infections caused by Enterococus faecium have become a clinical problem because of its resistance to many antibiolics. Both the detection of these bacteria and the evaluation of their resistance profiles are desirable. It is worthwhile noting that the French patent publication FR-A-2.699.539 discloses the sequence of vancomycin B gene, which gene may be derived from Enterococcus faecium strains resistant to this antibiotic.

"Besides that, novel DNA sequences (probes and primers) capable of recognizing the same and othe.r microbial pathogens or the same and additional antibiotic resistance genes are also, desirable to aim at detecting more taieti genebsaiiid complement our -6patent application.

STATEMENT OF THE INVENTION It is an object of the present invention to provide a method by which specific, ubiquitous and sensitive probes and/or amplification primers are obtained for determining the presence and/or amount of nucleic acids: from specific microbial species or genera selected from the group consisting of Streptococcus species, Streptococcus agalactiae, Staphylococcus species, Staphylococcus saprophyticus, Enterococcus species, Enterococcus faecium, Neisseria species, Neisseria meningitidis, Listeria monocytogenes, Candida species and Candida albicans alone or in combination with an antibiotic resistance gene selected from the group consisting of blatem, blarob, blashv, blaoxa, blaZ, aadB, aacCI, aacC2, aacC3, aacA4, aac6'-IIa, ermA, ermB, ermC, mecA, vanA, vanB, vanC, satA, aac(6')-aph(2"), aad(6'), vat, vga, msrA, sul and int, and from any bacterial or fungal species in any sample suspected of containing said nucleic acids.

In a more specific embodiment, the method leads to the obtention of DNA fragments (proprietary fragments and fragments derived from databases) which, upon alignment, lead to the selection of primers or probes for their capacity to sensitively, specifically and ubiquitously detect the targeted bacterial or fungal nucleic acids.

In a particularly preferred embodiment, oligonucleotides of at least 12 nucleotides in length have been derived from the longer DNA fragments, and are used in a diagnostic method as probes or amplification primers.

All the probes or primers for the specific detection of microbial species or genus are derived from DNA genes which are conserved amongst the microbial species. These genes include tufor recA genes. These two genes have been used to construct a novel gene bank, or to complete an existing gene bank; each gene sequence is species-specific. All the sequences can be aligned, which alignment leads to the selection of consensus oligonucleotide sequences for the universal detection or the specific detection of a microbial species or genus (fungal or bacterial).

The novel gene bank is created by using conserved primers capable of priming the amplification of genes of any bacterial or fungal species. The target conserved genes include tuf and recA genes. The new primers generated a new gene bank, the sequences of which can be aligned to select the primers or the probes suitable for the species- or genus-specific detection, or the universal detection of bacteria or fungi.

The new primers for generating a new gene bank may comprise the primers capable of hybridizing with the nucleic acids of all the microbial species of a group and with SEQ ID NO: 107 and 108, for the group of bacterial species, or with SEQ ID NO: 109 and 172, for the group of fungal species. All the nucleic acids amplified by these primers constitute a new gene bank or complement anrexisting gene bank. The primer or probe sequences that are derived from this new gene bank are used directly to identify a given species alignment resulting in 100% homology or match), or indirectly by providing information upon which probes or primers are synthetised as diagnostic tools.

In the above method, amplification reactions may include a) polymerase chain reaction (PCR), b) ligase chain reaction, c) nucleic acid sequence-based amplification, d) self-sustained sequence replication, e) strand displacement amplification, f) branched DNA signal amplification, g) transcription-mediated amplification, h) cycling probe technology (CPT) i) nested PCR, orj) multiplex PCR.

In a preferred embodiment, a PCR protocol is used as an amplification reaction.

In a particularly preferred embodiment, a PCR protocol is provided, comprising, for each amplification cycle, an annealing step of 30 seconds at 45-55 0

C

and a denaturation step of only one second at 95C, without any time allowed specifically for the elongation step. This PCR protocol has been standardized to be o.:i suitable for PCR reactions with all selected primer pairs, which greatly facilitates the *o testing because each clinical sample can be tested with universal, species-specific, genus-specific and antibiotic resistance gene PCR primers under uniform cycling conditions. Furthermore, various combinations of primer pairs may be used in multiplex PCR assays.

We aim at developing a rapid test or kit to discard rapidly all the samples which are negative for bacterial cells and to subsequently detect and identify the above bacterial and/or fungal species and genera and to determine rapidly the bacterial resistance to antibiotics. Although the sequences from the selected antibiotic resistance genes are available from databases and have been used to develop DNA- -8based tests for their detection, our approach is unique because it represents a major improvement over current gold standard diagnostic methods based on bacterial cultures. Using an amplification method for the simultaneous bacterial detection and identification and antibiotic resistance genes detection, there is no need for culturing the clinical sample prior to testing. Moreover, a modified PCR protocol has been developed to detect all target DNA sequences in approximately one hour under uniform amplification conditions. This procedure will save lives by optimizing treatment, will diminish antibiotic resistance because less antibiotics will be prescribed, will reduce the use of broad spectrum antibiotics which are expensive, decrease overall health care costs by preventing or shortening hospitalizations, and decrease the time and costs associated with clinical laboratory testing.

In the methods and kits derived from the present method of obtaining a variety of sequences, the oligonucleotide probes and amplification primers have been derived S" from larger sequences DNA fragments of at least 100 base pairs). All DNA fragments have been derived either from proprietary fragments or from databases.

DNA fragments derived from databases are newly used in a method of detection *ooo according to the present invention, since they have been selected for their diagnostic potential.

o *It is clear to the individual skilled in the art that other oligonucleotide 20 sequences appropriate for the universal bacterial detection, (ii) the detection and identification of the above microbial species or genus and (iii) the detection of antibiotic resistance genes other than those listed in Annex VI may also be derived from the proprietary fragments or selected database sequences. For example, the oligonucleotide primers or probes may be shorter or longer than the ones we have 25 chosen; they may also be selected anywhere else in the proprietary DNA fragments or in the sequences selected from databases; they may be also variants of the same oligonucleotide. If the target DNA or a variant thereof hybridizes to a given oligonucleotide, or if the target DNA or a variant thereof can be amplified by a given oligonucleotide PCR primer pair, the converse is also true; a given target DNA may hybridize to a variant oligonucleotide probe or be amplified by a variant oligonucleotide PCR primer. Alternatively, the oligonucleotides may be designed from any DNA fragment sequences for use in amplification methods other than PCR.

Consequently, the core of this invention is the identification of universal, -8aspecies-specific, genus-specific and resistance gene-specific genomic or non-genomic DNA fragments which are used as a source of specific and ubiquitous oligonucleotide probes and/or amplification primers. Although the selection and evaluation of oligonucleotides suitable for diagnostic purposes requires much effort, it is quite possible for the individual skilled in the art to derive, from the selected DNA fragments, oligonucleotides other than the ones listed in Annex VI which are suitable for diagnostic purposes. When a proprietary fragment or a database sequence is selected for its specificity and ubiquity, it increases the probability that subsets thereof will also be specific and ubiquitous.

Since a high percentage of clinical specimens are negative for bacteria (Table 4* -9- DNA fragments having a high potential for the selection of universal oligonucleotide probes or primers were selected from proprietary and database sequences. The amplification primers were selected from a gene highly conserved in bacteria and fungi, and are used to detect the presence of any bacterial pathogen in clinical specimens in order to determine rapidly (approximately one hour) whether it is positive or negative for bacteria. The selected gene, designated tuf, encodes a protein (EF-Tu) involved in the translational process during protein synthesis. The tuf gene sequence alignments used to derive the universal primers include both proprietary and database sequences (Example 1 and Annex This strategy allows the rapid screening of the numerous negative clinical specimens (around 80% of the specimens received, see Table 3) submitted for bacteriological testing. Tables 4, 5 and 6 provide a list of the bacterial or fungal species used to test the specificity of PCR primers and DNA probes.

Table 7 gives a brief description of each species-specific, genus-specific and universal amplification assays which are objects of the present invention. Tables 8, 9 and provide some relevant information about the proprietary and database sequences selected for diagnostic puposes.

DETAILED DESCRIPTION OF THE INVENTION :Development of species-sDecific. aenus-specific. universal and antibiotic resistance aene-specific DNA probes and amplification primers for microorganisms Selection from databases of sequences suitable for diagnostic purposes In order to select sequences which are suitable for species-specific or genusspecific detection and identification of bacteria or fungi or, alternatively, for the 25 universal detection of bacteria, the database sequences (GenBank, EMBL and Swiss- Prot) were chosen based on their potential for diagnostic purposes according to sequence information and computer analysis performed with these sequences. Initially, .all sequence data available for the targeted microbial species or genus were carefully analyzed. The gene sequences which appeared the most promising for diagnostic 30 purposes based on sequence information and on sequence comparisons with the corresponding gene in other microbial species or genera performed with the Genetics Computer Group (GCG, Wisconsin) programs were selected for testing by PCR.

Optimal PCR amplification primers were chosen from the selected database sequences with the help of the Oligo" 4.0 primer analysis software (National Biosciences Inc., Plymouth, Minn.). The chosen primers were tested in PCR assays for their specificity and ubiquity for the target microbial species or genus. In general, the identification of database sequences from which amplification primers suitable for species-specific or genus-specific detection and identification were selected involved the computer analysis and PCR testing of several candidate gene sequences-before obtaining a primer pair which is specific and ubiquitous for the target microbial species or genus. Annex VI provides a list of selected specific and ubiquitous PCR primer pairs. Annexes I to V and Examples 1 to 4 illustrate the strategy used to select genusspecific, species-specific and universal PCR primers from tufsequences or from the recA gene.

Oligonucleotide primers and probes design and synthei The DNA fragments sequenced by us or selected from databases (GenBank and EMBL) were used as sources of oligonucleotides for diagnostic purposes. 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 databases were tested for their specificity and ubiquity in PCR and hybridization assays as described later. It is important to note that the database sequences were selected based on their potential for being species-specific, genus-specific or universal for the detection of bacteria or fungi according to available sequence information and extensive analysis and that, in general, several candidate database sequences had to be tested in order to obtain the desired specificity, ubiquity and sensitivity.

Oligonucleotide probes and amplification primers derived from species-specific fragments selected from database sequences were synthesized using an automated DNA synthesizer (Perkin-Elmer Corp., Applied Biosystems Division). Prior to synthesis, 20 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 the Genetics Computer Group (GCG) programs and the primer analysis software Oligo T M 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 and a high proportion of G or C residues at the 3' end (Persing et 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, The oligonucleotide primers or probes may be derived from either strand of the duplex DNA. The primers or probes may consist of the bases A, G, C, or T or analogs and they may be degenerated at one or more chosen nucleotide position(s). The primers or probes may be of any suitable length and may be selected anywhere within the DNA sequences from proprietary fragments or from selected database sequences which are suitable for the universal detection of bacteria, (ii) the species-specific detection and identification of Enterococcus faecium, Listeria monocytogenes, Neisseria meningitidis, Staphylococcus saprophyticus, Streptococcus agalactiae and Candida albicans (iii) the genus-specific detection of Streptococcus species, Enterococcus species, Staphylococcus species and Neisseria species or (iv) the detection of the 26 above-mentioned clinically important antibiotic resistance genes.

-11 Variants for a given target bacterial gene are naturally occurring and are attributable to sequence variation within that gene during evolution (Watson et al., 1987, Molecular Biology of the Gene, ed., The Benjamin/Cummings Publishing Company, Menlo Park, CA; Lewin, 1989, Genes IV, John Wiley Sons, New York, NY). For example, different strains of the same bacterial species may have a single or more nucleotide variation(s) at the oligonucleotide hybridization site. The person skilled in the art is well aware of the existence of variant bacterial or fungal DNA sequences for a specific gene and that the frequency of sequence variations depends on the selective pressure during evolution on a given gene product. The detection of a variant sequence for a region between two PCR primers may be demonstrated by sequencing the amplification product. In order to show the presence of sequence variants at the primer hybridization site, one has to amplify a larger DNA target with PCR primers outside that hybridization site. Sequencing of this larger fragment will allow the detection of sequence variation at this site. A similar strategy may be applied to show variants at the hybridization site of a probe. Insofar as the divergence of the target sequences or a part thereof does not affect the specificity and ubiquity of the amplification primers or probes, variant bacterial DNA is under the scope of this invention. Variants of the selected primers or probes may also be used to amplify or hybridize to a variant DNA.

20 Sequencing of tufsequences from a variety of bacterial and fungal species The nucleotide sequence of a portion of tuf genes was determined for a variety of bacterial and fungal species. The amplification primers SEQ ID NOs: 107 and 108, which amplify a tuf gene portion of approximately 890 bp, were used for the sequencing of bacterial tuf sequences. The amplification primers SEQ ID NOs: 109 and 172, which amplify a tuf gene portion of approximately 830 bp, were used for the sequencing of fungal tuf sequences. Both primer pairs can amplify tufA and tufB genes. This is not surprising because these two genes are nearly identical. For example, the entire tufA and tufB genes from E. coli differ at only 13 nucleotide positions (Neidhardt et al., 1996, Escherichia coli and Salmonella: Cellular and 30 Molecular Biology, ed., American Society for Microbiology Press, Washington, These amplification primers are degenerated at several nucleotide positions and contain inosines in order to allow the amplification of a wide range of tuf sequences.

The strategy used to select these amplification primers is similar to that illustrated in Annex I for the selection of universal primers. The amplification primers SEQ ID NOs: 107 and 108 could be used to amplify the tufgenes from any bacterial species. The amplification primers SEQ ID NOs: 109 and 172 could be used to amplify the tufgenes from any fungal species.

The tufgenes were amplified directly from bacterial or yeast cultures using the following amplification protocol: One AL of cell suspension was transferred directly to -12- 19 ,L of a PCR reaction mixture containing 50 mM KCI, 10 mM Tris-HCI (pH 0.1% Triton X-100, 2.5 mM MgCI,, 1 uM of each of the 2 primers, 200 pM of each of the four dNTPs, 0.5 unit of Taq DNA polymerase (Promega Corp., Madison, WI). PCR reactions were subjected to cycling using a MJ Research PTC-200 thermal cycler (MJ Research Inc., Watertown, Mass.) as follows: 3 min at 96 C followed by 30-35 cycles of 1 min at 95 0 C for the denaturation step, 1 min at 30-50°C for the annealing step and 1 min at 72°C for the extension step. Subsequently, twenty microliters of the PCRamplified mixture were resolved by electrophoresis in a 1.5% agarose gel. The gel was then visualized by staining with methylene blue (Flores et al., 1992, Biotechniques, 13:203-205). The size of the amplification products was estimated by comparison with a 100-bp molecular weight ladder. The band corresponding to the specific amplification product approximately 890 or 830 bp for bacterial or fungal tuf sequences, respectively) was excised from the agarose gel and purified using the QIAquickT M gel extraction kit (QIAGEN Inc., Chatsworth, CA). The gel-purified DNA fragment was then used directly in the sequencing protocol. Both strands of the tufgenes amplification product were sequenced by the dideoxynucleotide chain termination sequencing method by using an Applied Biosystems automated DNA sequencer (model 373A) with their PRISM T Sequenase® Terminator Double-stranded DNA Sequencing Kit (Perkin- Elmer Corp., Applied Biosystems Division, Foster City, CA). The sequencing reactions 20 were all performed by using the amplification primers (SEQ ID NOs: 107 to 109 and S. 172) and 100 ng per reaction of the gel-purified amplicon. In order to ensure that the determined sequence did not contain errors attributable to the sequencing of PCR artefacts, we have sequenced two preparations of the gel-purified tuf amplification product originating from two independent PCR amplifications. For all target microbial species, the sequences determined for both amplicon preparations were identical.

Furthermore, the sequences of both strands were 100% complementary thereby confirming the high accuracy of the determined sequence. The tuf sequences determined using the above strategy are all in the Sequence Listing SEQ ID NOs:118 to 146). Table 13 gives the originating microbial species and the source for each tufsequence in the Sequence Listing.

The alignment of the tuf sequences determined by us or selected from databases reveals clearly that the length of the sequenced portion of the tuf genes is variable. There may be insertions or deletions of several amino acids. This explains why the size of the sequenced tuf amplification product was variable for both bacterial and fungal species. Among the tuf sequences determined by our group, we found insertions and deletions adding up to 5 amino acids or 15 nucleotides. Consequently, the nucleotide positions indicated on top of each of Annexes I to V do not correspond for tuf sequences having insertions or deletions.

It should also be noted that the various tuf sequences determined by us -13occasionally contain degenerescences. These degenerated nucleotides correspond to sequence variations between tufA and tufB genes because the amplification primers amplify both tuf genes. These nucleotide variations were not attributable to nucleotide misincorporations by the taq DNA polymerase because the sequence of both strands were identical and also because the sequences determined with both preparations of the gel-purified tufamplicons were identical.

The selection of amplification primers from fuf sequences The tuf sequences determined by us or selected from databases were used to select PCR primers for the universal detection of bacteria, (ii) the genus-specific detection and identification of Enterococcus spp. and Staphylococcus spp. and (iii) the species-specific detection and identification of Candida albicans. The strategy used to select these PCR primers was based on the analysis of multiple sequence alignments of various tuf sequences. For more details about the selection of PCR primers from tuf sequences, please refer to Examples 1 to 3 and Annexes I to IV.

The selection of amplification primers from recA The comparison of the nucleotide sequence for the recA gene from various bacterial species including 5 species of streptococci allowed the selection of Streptococcus-specific PCR primers. For more details about the selection of PCR primers from recA, please refer to Example 4 and Annex V.

20 DNA fragment isolation from Staphylococcus saprophyticus by arbitrarily primed PCR DNA sequences of unknown coding potential for the species-specific detection and identification of Staphylococcus saprophyticus were obtained by the method of arbitrarily primed PCR (AP-PCR).

.o AP-PCR is a method which can be used to generate specific DNA probes for microorganisms (Fani et al., 1993, Mol. Ecol. 2:243-250). A description of the AP-PCR protocol used to isolate a species-specific genomic DNA fragment from Staphylococcus saprophyticus follows. Twenty different oligonucleotide primers of nucleotides in length (all included in the AP-PCR kit OPAD (Operon Technologies, Inc., Alameda, CA)) were tested systematically with DNAs from 3 bacterial strains of Staphylococcus saprophyticus (all obtained from the American Type Culture Collection (ATCC): numbers 15305, 35552 and 43867) as well as with DNA from four other staphylococcal species (Staphylococcus aureus ATCC 25923, Staphylococcus epidermidis ATCC 14990, Staphylococcus haemolyticus ATCC 29970 and Staphylococcus hominis ATCC 35982). For all bacterial species, amplification was performed from a bacterial suspension adjusted to a standard 0.5 McFarland which corresponds to approximately 1.5 x 108 bacteria/mL. One gL of the standardized bacterial suspension was transferred directly to 19 wL of a PCR reaction mixture containing 50 mM KCI, 10 mM Tris-HCI (pH 0.1% Triton X-100, 2.5 mM MgCI,, -14- 1.2 pM of only one of the 20 different AP-PCR primers OPAD, 200 pM of each of the four dNTPs and 0.5 unit of Taq DNA polymerase (Promega Corp., Madison, Wi). PCR reactions were subjected to cycling using a MJ Research PTC-200 thermal cycler (MJ Research Inc.) as follows: 3 min at 96°C followed by 35 cycles of 1 min at 95 0 C for the denaturation step, 1 min at 32*C for the annealing step and 1 min at 72"C for the extension step. A final extension step of 7 min at 72"C was made after the 35 cycles to ensure complete extension of PCR products. Subsequently, twenty microliters of the PCR amplified mixture were resolved by electrophoresis in a 2% agarose gel containing 0.25 pg/mL of ethidium bromide. The size of the amplification products was estimated by comparison with a 50-bp molecular weight ladder.

Amplification patterns specific for Staphylococcus saprophyticus were observed with the AP-PCR primer OPAD-9 (SEQ ID NO: 25). Amplification with this primer consistently showed a band corresponding to a DNA fragment of approximately 450 bp for all Staphylococcus saprophyticus strains tested but not for any of the four other staphylococcal species tested. This species-specific pattern was confirmed by testing more clinical isolates of S. saprophyticus selected from the culture collection of the microbiology laboratory of the CHUL as well as strains selected from the gram-positive bacterial species listed in Table The band corresponding to the approximately 450 bp amplicon which was 20 specific and ubiquitous for S. saprophyticus based on AP-PCR was excised from the agarose gel and purified using the QIAquick T M gel extraction kit (QIAGEN Inc.). The gel-purified DNA fragment was cloned into the T/A cloning site of the pCR 2.1TM plasmid vector (Invitrogen Inc.) using T4 DNA ligase (New England BioLabs).

Recombinant plasmids were transformed into E. coli DH5a competent cells using standard procedures. Plasmid DNA isolation was done by the method of Bimboim and Doly (Nucleic Acids Res. 7:1513-1523) for small-scale preparations. All plasmid DNA preparations were digested with the EcoRI restriction endonuclease to ensure the presence of the approximately 450 bp AP-PCR insert into the recombinant plasmids.

Subsequently, a large-scale and highly purified plasmid DNA preparation was 30 performed from two selected clones shown to carry the AP-PCR insert by using the QIAGEN plasmid purification kit. These plasmid preparations were used for automated DNA sequencing.

Both strands of the AP-PCR insert from the two selected clones were sequenced by the dideoxynucleotide chain termination sequencing method with SP6 and T7 sequencing primers, by using an Applied Biosystems automated DNA sequencer as described previously. The analysis of the obtained sequences revealed that the DNA sequences for both strands from each clone were 100% complementary.

Furthermore, it showed that the entire sequence determined for each clone were both identical. These sequencing data confirm the 100% accuracy for the determined 438 bp sequence (SEQ ID NO: 29). Optimal amplification primers have been selected from the sequenced AP-PCR Staphylococcus saprophyticus DNA fragment with the help of the primer analysis software OligoTM 4.0. The selected primer sequences have been tested in PCR assays to verify their specificity and ubiquity (Table These PCR primers were specific since there was no amplification with DNA from bacterial species other than S. saprophyticus selected from Tables 4 and 5. Furthermore, this assay was ubiquitous since 245 of 260 strains of S. saprophyticus were efficiently amplified with this PCR assay. When used in combination with another S. saprophyticus-specific PCR assay, which is an object of our co-pending U.S. 08/526,840) and PCT (PCT/CA/95/00528) patent applications, the ubiquity reaches 100% for these 260 strains.

DNA amplification For DNA amplification by the widely used PCR (polymerase chain reaction) method, primer pairs were derived from proprietary DNA fragments or from database sequences. Prior to synthesis, the potential primer pairs were analyzed by using the Oligo T M 4.0 software to verify that they are good candidates for PCR amplification.

During DNA amplification by PCR, two oligonucleotide primers binding respectively to each strand of the heat-denatured 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, Briefly, the PCR protocols were as follow: Treated clinical specimens or standardized bacterial or fungal suspensions (see below) were amplified in a 20 ,L PCR reaction mixture containing 50 mM KCI, 10 mM Tris-HCI (pH 2.5 mM MgCI 2 0.4 MM of each primer, 200 IM of each of the four dNTPs and 0.5 unit of Taq DNA o" polymerase (Promega) combined with the TaqStartTM antibody (Clontech Laboratories Inc., Palo Alto, CA). The TaqStart T M antibody, which is a neutralizing monoclonal 30 antibody to Taq DNA polymerase, was added to all PCR reactions to enhance the specificity and the sensitivity of the amplifications (Kellogg et al., 1994, Biotechniques 16:1134-1137). The treatment of the clinical specimens varies with the type of specimen tested, since the composition and the sensitivity level required are different for each specimen type. It consists in a rapid protocol to lyse the bacterial cells and eliminate the PCR inhibitory effects (see example 11 for urine specimen preparation).

For amplification from bacterial or fungal cultures, the samples were added directly to the PCR amplification mixture without any pre-treatment step (see example 10). Primer sequences derived from highly conserved regions of the bacterial 16S ribosomal RNA gene were used to provide an internal control for all PCR reactions. Alternatively, the -16internal control was derived from sequences not found in microorganisms or in the human genome. The internal control was integrated into all amplification reactions to verify the efficiency of the PCR assays and to ensure that significant PCR inhibition was absent. The internal control derived from rRNA was also useful to monitor the efficiency of bacterial lysis protocols.

PCR reactions were then subjected to thermal cycling (3 min at 95°C followed by 30 cycles of 1 second at 95C for the denaturation step and 30 second at 55 0 C for the annealing-extension step) using a PTC-200 thermal cycler (MJ Research Inc.) and subsequently analyzed by standard ethidium bromide-stained agarose gel electrophoresis. The number of cycles performed for the PCR assays varies according to the sensitivity level required. For example, the sensitivity level required for microbial detection directly from clinical specimens is higher for blood specimens than for urine specimens because the concentration of microorganisms associated with a septicemia can be much lower than that associated with a urinary tract infection. Consequently, more sensitive PCR assays having more thermal cycles are required for direct detection from blood specimens. Similarly, PCR assays performed directly from bacterial or fungal cultures may be less sensitive than PCR assays performed directly *i from clinical specimens because the number of target organisms is normally much lower in clinical specimens than in microbial cultures.

20 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.

TaqManTM system from Perkin Elmer or Amplisensor T M from Biotronics). Methods based on the detection of fluorescence are particularly promising for utilization in routine diagnosis as they are very rapid, quantitative and can be automated (Example 14).

Microbial pathogens detection and identification may also be performed by solid support or liquid hybridization using species-specific internal DNA probes hybridizing to an amplification product. Such probes may be generated from any species-specific or genus-specific DNA amplification products which are objects of the present invention. Alternatively, the internal probes for species or genus detection and identification may be derived from the amplicons produced by the universal amplification assay. The oligonucleotide probes may be labeled with biotin or with digoxigenin or with any other reporter molecules.

To assure PCR efficiency, glycerol, 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 a target DNA having a high GC content or forming strong secondary structures (Dieffenbach and Dveksler, 1995, PCR Primer A Laboratory Manual, Cold Spring Harbor Laboratory Press, Plainview, New York). The -17concentration ranges for glycerol and DMSO are 5-15% and 3-10% respectively. For the PCR reaction mixture, the concentration ranges for the amplification primers and MgCI, are 0.1-1.5 uM 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 multiplex PCR) may also be used (Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, For more details about the PCR protocols and amplicon detection methods, see Examples 9 to 14.

The person skilled in the art of DNA amplification knows the existence of other rapid amplification procedures such as ligase chain reaction (LCR), transcriptionmediated amplification (TMA), self-sustained sequence replication (3SR), nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), branched DNA (bDNA) and cycling probe technology (CPT) (Lee et al., 1997, Nucleic Acid Amplification Technologies: Application to Disease Diagnosis, Eaton Publishing, Boston, MA Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, 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 method or any other procedure which may be used to increase rapidity and sensitivity of the tests. Any oligonucleotide suitable for 20 the amplification of nucleic acids by approaches other than PCR and derived from the species-specific, genus-specific and universal DNA fragments as well as from selected antibiotic resistance gene sequences included in this document are also under the scope of this invention.

.o Hybridization assays with oliqonucleotide probes In hybridization experiments, single-stranded oligonucleotides (size less than 100 nucleotides) have some advantages over DNA fragment probes for the detection of bacteria, such as ease of synthesis 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 y-" 3 P(dATP) using T4 polynucleotide 30 kinase (Pharmacia) (Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2"d ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY). The unincorporated radionucleotide was removed by passing the labeled oligonucleotide through a Sephadex G-50TM 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.

Each oligonucleotide probe was then tested for its specificity by hybridization to DNAs from a variety of bacterial and fungal species selected from Tables 4, 5 and 6. All of the bacterial or fungal species tested were likely to be pathogens associated -18with common infections or potential contaminants which can be isolated from clinical specimens. Each target DNA was released from bacterial cells using standard chemical treatments to lyse the cells (Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY). Subsequently, the DNA was denatured by conventional methods and then irreversibly fixed onto a solid support nylon or nitrocellulose membranes) or free in solution. The fixed single-stranded target DNAs were then hybridized with the oligonucleotide probe cells (Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY). Prehybridization conditions were in 1 M NaCI 10% dextran sulfate 1% SDS 100 /Sg/mL salmon sperm DNA at 65"C for 15 min. Hybridization was performed in fresh pre-hybridization solution containing the labeled probe at 65'C overnight. Posthybridization washing conditions were as follows: twice in 3X SSC containing 1% SDS, twice in 2X SSC containing 1% SDS and twice in 1X SSC containing 1% SDS (all of 15 these washes were at 65'C for 15 min), and a final wash in 0.1X SSC containing 1% SDS at 25'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 because of the high stringency of.the washes.

20 An oligonucleotide probe was considered specific only when it hybridized solely to DNA from the species or genus from which it was isolated. Oligonucleotide probes found to be specific were subsequently tested for their ubiquity ubiquitous probes recognized most or all isolates of the target species or genus) by hybridization to microbial DNAs from clinical isolates of the species or genus of interest including 25 ATCC strains. The DNAs from strains of the target species or genus were denatured, fixed onto nylon membranes and hybridized as described above. Probes were considered ubiquitous when they hybridized specifically with the DNA from at least 80% of the isolates of the target species or genus.

Specificity and ubiauity tests for oliqonucleotide primers and probes The specificity of oligonucleotide primers and probes, derived either from the DNA fragments sequenced by us or selected from databases, was tested by amplification of DNA or by hybridization with bacterial or fungal species selected from those listed in Tables 4, 5 and 6, as described in the two previous sections.

Oligonucleotides found to be specific were subsequently tested for their ubiquity by amplification (for primers) or by hybridization (for probes) with bacterial DNAs from isolates of the target species or genus. Results for specificity and ubiquity tests with the oligonucleotide primers are summarized in Table 7. The specificity and ubiquity of the PCR assays using the selected amplification primer pairs were tested directly from cultures (see Examples 9 and 10) of bacterial or fungal species.

-19- The various species-specific and genus-specific PCR assays which are objects of the present invention are all specific. For the PCR assays specific to bacterial species or genus, this means that DNA isolated from a wide variety of bacterial species, other than that from the target species or genus and selected from Tables 4 and 5, could not be amplified. For the PCR assay specific to Candida albicans, it means there was no amplification with genomic DNA from the fungal species listed in Table 6 as well as with a variety of bacterial species selected from Tables 4 and The various species-specific and genus-specific PCR assays which are objects of the present invention are also all ubiquitous (Table The species-specific

PCR

assays for E. faecium, L. monocytogenes, S. saprophyticus, S. agalactiae and C.

albicans amplified genomic DNA from all or most strains of the target species tested, which were obtained from various sources and which are representative of the diversity within each target species (Table The species identification of all of these strains was based on classical biochemical methods which are routinely used in clinical 15 microbiology laboratories. (ii) The genus-specific PCR assays specific for Enterococcus spp., Staphylococcus spp., Streptococcus spp. and Neisseria spp.

amplified genomic DNA from all or most strains of the target genus tested, which represent all clinically important bacterial species for each target genus. These strains 0 were obtained from various sources and are representative of the diversity within each target genus. Again, the species identification of all of these strains was based on classical biochemical methods which are routinely used in clinical microbiology laboratories. More specifically, the four genus-specific PCR assays amplified the following species: The Enterococcus-specific assay amplified efficiently DNA from all of the 11 enterococcal species tested including E. avium, E. casseliflavus, E. dispar, *oe. 25 E. durans, E. faecalis, E. faecium, E flavescens, E. gallinarum, E. hirae, E. mundtii and E. raffinosus. The Neisseria-specific assay amplified efficiently DNA from all of the 12 neisserial species tested including N. canis, N. cinerea, N. elongata, N.

flavescens, N. gonorrhoeae, N. lactamica, N. meningitidis, N. mucosa, N.

polysaccharea, N. sicca, N. subflava and N. weaved. The Staphylococcus-specific assay amplified efficiently DNA from 13 of the 14 staphylococcal species tested including S. aureus, S. auricularis, S. capitis, S. cohnii, S. epidermidis, S.

haemolyticus, S. hominis, S. lugdunensis, S. saprophyticus, S. schleiferi, S. simulans, S. wameri and S. xylosus. The staphylococcal species which could not be amplified is S. sciuri. Finally, the Streptococcus-specific assay amplified efficiently DNA from all of the 22 streptococcal species tested including S. agalactiae, S. anginosus, S.

bovis, S. constellatus, S. crsta, S. dysgalactiae, S. equi, S. gordonii, S. intermedius, S. mitis, S. mutans, S. oralis, S. parasanguis, S. pneumoniae, S. pyogenes, S.

salivarius, S. sanguis, S. sabrinus, S. suis, S. uberis, S. vestibularis and S. viridans.

On the other hand, the Streptococcus-specific assay did not amplify 3 out of 9 strains of S. mutans and 1 out of 23 strains of S. salivarius, thereby showing a slight lack of ubiquity for these two streptococcal species.

All specific and ubiquitous amplification primers for each target microbial species or genus or antibiotic resistance gene investigated are listed in Annex VI.

Divergence in the sequenced DNA fragments can occur, 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.

The PCR amplification primers listed in Annex VI were all tested for their specificity and ubiquity using reference strains as well as clinical isolates from various geographical locations. The 351 reference strains used to test the amplification and hybridization assays (Tables 4, 5 and 6) were obtained from the American Type Culture Collection (ATCC): 85%, (ii) the Laboratoire de sante publique du Quebec (LSPQ): 10%, (iii) the Centers for Disease Control and Prevention (CDC): 3% (iv) the National Culture Type Collection (NCTC): 1% and several other reference 15 laboratories throughout the world: These reference strains are representative of 90 gram-negative bacterial species (169 strains; Table (ii) 97 gram-positive :bacterial species (154 strains; Table 5) and (iii) 12 fungal species (28 strains; Table 6).

Antibiotic resistance g'enes e• Antimicrobial resistance complicates treatment and often leads to therapeutic o 20 failures. Furthermore, overuse of antibiotics inevitably leads to the emergence of bacterial resistance. Our goal is to provide clinicians, in approximately one hour, the 0 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 25 species- and/or genus-specific DNA-based tests, 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 clinically important antibiotic resistance genes DNA-based tests for the detection of antibiotic resistance genes). Since the sequence from the most important and common bacterial antibiotic resistance genes are available from databases, our strategy was to use the sequence from a portion or from the entire resistance gene to design specific oligonucleotide primers or probes which will be used as a basis for the development of rapid DNA-based tests. The sequence from each of the bacterial antibiotic resistance genes selected on the basis of their clinical relevance high incidence and importance) is given in the Sequence Listing. Tables 9 and summarize some characteristics of the selected antibiotic resistance genes. Our approach is unique because the antibiotic resistance genes detection and the bacterial detection and identification are performed simultaneously in multiplex assays under -21uniform PCR amplification conditions (Example 13).

Annex VI provides a list of all amplification primers selected from 26 clinically important antibiotic resistance genes which were tested in PCR assays. The various PCR assays for antibiotic resistance genes detection and identification were validated by testing several resistant bacterial isolates known to carry the targeted gene and obtained from various countries. The testing of a large number of strains which do not carry the targeted resistance gene was also performed to ensure that all assays were specific. So far, all PCR assays for antibiotic resistance genes are highly specific and have detected all control resistant bacterial strains known to carry the targeted gene.

The results of some clinical studies to validate the array of PCR assays for the detection and identification of antibiotic resistance genes and correlate these DNAbased assays with standard antimicrobials susceptibility testing methods are presented in Tables 11 and 12.

Universal bacterial detection In the routine microbiology laboratory, a high percentage of clinical specimens sent for bacterial identification are negative by culture (Table Testing clinical samples with universal amplification primers or universal probes 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 amplification primers and probes were therefore synthesized from highly conserved portions of bacterial sequences from the tuf genes (Table The universal primer selection was based on a multiple sequence alignment constructed with sequences determined by us or selected from available database sequences as described in Example 1 and Annex I.

25 For the identification of database sequences suitable for the universal detection of bacteria, we took advantage of the fact that the complete genome sequences for two distant microorganisms Mycoplasma genitalium and Haemophilus influenzae) are available. A comparison of the amino acid sequence for all proteins encoded by the genome of these two distant microorganisms led to the identification of highly homologous proteins. An analysis of these homologous proteins allowed to select some promising candidates for the development of universal DNA-based assays for the detection of bacteria. Since the complete nucleotide sequence of several other microbial genomes are presently available in databases, a person skilled in the art could arrive to the same conclusions by comparing genomes sequences other than those of Mycoplasma genitalium and Haemophilus influenzae. The selected tuf gene encodes a protein (EF-Tu) involved in the translation process during protein synthesis.

Subsequently, an extensive nucleotide sequence analysis was performed with the tuf gene sequences available in databases as well as with novel tuf sequences which we have determined as described previously. All computer analysis of amino acid and -22nucleotide sequences were performed by using the GCG programs. Subsequently, optimal PCR primers for the universal amplification of bacteria were selected with the help of the OligoTM program. The selected primers are degenerated at several nucleotide positions and contain several inosines in order to allow the amplification of all clinically relevant bacterial species (Annex Inosine is a nucleotide analog able to specifically bind to any of the four nucleotides A, C, G or T. Degenerated oligonucleotides consist of an oligonucleotide mix having two or more of the four nucleotides A, C, G or T at the site of mismatches. The inclusion of inosine and/or of degenerescences in the amplification primers allow mismatch tolerance thereby permitting the amplification of a wider array of target nucleotide sequences (Dieffenbach and Dveksler, 1995 PCR Primer: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Plainview,

NY).

The amplification conditions with the universal primers were identical to those used for the species- and genus-specific amplification assays except that the annealing temperature was 50°C instead of 55"C. This universal PCR assay was specific and nearly ubiquitous for the detection of bacteria. The specificity for bacteria was verified by amplifying genomic DNA isolated from the 12 fungal species listed in Table 6 as well as genomic DNA from Leishmania donovani, Saccharomyces cerevisiae and human lymphocytes. None of the above eukaryotic DNA preparations S 20 could be amplified by the universal assay, thereby suggesting that this test is specific for bacteria. The ubiquity of the universal assay was verified by amplifying genomic DNAs from 116 reference strains which represent 95 of the most clinically relevant bacterial species. These species have been selected from the bacterial species listed in Tables 4 and 5. We found that 104 of these 116 strains could be amplified. The 25 bacterial species which could not be amplified belong to the following genera: Corynebacterium (11 species) and Stenotrophomonas (1 species). Sequencing of the tufgenes from these bacterial species has been recently performed. This sequencing data has been used to select new universal primers which may be more ubiquitous.

These primers are in the process of being tested. We also observed that for several species the annealing temperature had to be reduced to 45 0 C in order to get an efficient amplification. These bacterial species include Gemella morbilbrum, Listeria spp. (3 species) and Gardnerella vaginalis. It is important to note that the 95 bacterial species selected from Tables 4 and 5 to test the ubiquity of the universal assay include all of the most clinically relevant bacterial species associated with a variety of human infections acquired in the community or in hospitals (nosocomial infections). The most clinically important bacterial and fungal pathogens are listed in Tables 1 and 2.

-23- EXAMPLES AND ANNEXES The following examples and annexes are intended to be illustrative of the various methods and compounds of the invention, rather than limiting the scope thereof.

The various annexes show the strategies used for the selection of amplification primers from tufsequences or from the recA gene: Annex I illustrates the strategy used for the selection of the universal amplification primers from tuf sequences. (ii) Annex II shows the strategy used for the selection of the amplification primers specific for the genus Enterococcus from tuf sequences. (iii) Annex III illustrates the strategy used for the selection of the amplification primers specific for the genus Staphylococcus from tuf sequences. (iv) Annex IV shows the strategy used for the selection of the amplification primers specific for the species Candida albicans from tuf sequences. Annex V illustrates the strategy used for the selection of the amplification primers specific for the genus Streptococcus from recA sequences. (vi) 15 Annex VI gives a list of all selected primer pairs. As shown in these annexes, the selected amplification primers may contain inosines and/or degenerescences. Inosine S: is a nucleotide analog able to specifically bind to any of the four nucleotides A, C, G or T. Altematively, degenerated oligonucleotides which consist of an oligonucleotide mix having two or more of the four nucleotides A, C, G or T at the site of mismatches were used. The inclusion of inosine and/or of degenerescences in the amplification primers allow mismatch tolerance thereby permitting the amplification of a wider array °of target nucleotide sequences (Dieffenbach and Dveksler, 1995 PCR Primer: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Plainview, New York).

EXAMPLES

25 EXAMPLE 1 Selection of universal PCR primers from tuf sequences. As shown in Annex I, the comparison of tuf sequences from a variety of bacterial and eukaryotic species allowed the selection of PCR primers which are universal for the detection of bacteria.

The strategy used to design the PCR primers was based on the analysis of a multiple sequence alignment of various tuf sequences. This multiple sequence alignment includes tuf sequences from 38 bacterial species and 3 eukaryotic species either determined by us or selected from databases (Table 13). A careful analysis of this multiple sequence alignment allowed the selection of primer sequences which are conserved within eubacteria but which discriminate sequences from eukaryotes, thereby permitting the universal detection of bacteria. As shown in Annex I, the selected primers contain several inosines and degenerescences. This was necessary because there is a relatively high polymorphism among bacterial tuf sequences despite the fact that this gene is highly conserved. In fact, among the tuf sequences that we determined, we found many nucleotide variations as well as some deletions and/or -24insertions of amino acids. The selected universal primers were specific and ubiquitous for bacteria (Table Of the 95 most clinically important bacterial species tested, 12 were not amplified. These species belong to the genera Corynebacterium (11 species) and Stenotrophomonas (1 species). The universal primers did not amplify DNA of nonbacterial origin, including human and other types of eukaryotic DNA.

EXAMPLE 2: Selection of genus-specific PCR primers from tuf sequences. As shown in Annexes 2 and 3, the comparison of tufsequences from a variety of bacterial species allowed the selection of PCR primers specific for Enterococcus spp. or for Staphylococcus spp. The strategy used to design the PCR primers was based on the analysis of a multiple sequence alignment of various tuf sequences. These multiple sequence alignments include the tufsequences of four representative bacterial species selected from each target genus as well as tufsequences from species of other closely related bacterial genera. A careful analysis of those alignments allowed the selection 15 of oligonucleotide sequences which are conserved within the target genus but which discriminate sequences from other closely related genera, thereby permitting the S. genus-specific and ubiquitous detection and identification of the target bacterial genus.

For the selection of primers specific for Enterococcus spp. (Annex II), we have sequenced a portion of approximately 890 bp of the tuf genes for Enterococcus avium, E. faecalis, E. faecium and E. gallinarum. All other tufsequences used in the alignment were either sequenced by us or selected from databases. The analysis of this sequence alignment led to the selection of a primer pair specific and ubiquitous for Enterococcus spp. (Table All of the 11 enterococcal species tested were efficiently amplified and there was no amplification with genomic DNA from bacterial species of 25 other genera.

For the selection of primers specific for Staphylococcus spp. (Annex III), we have also sequenced a portion of approximately 890 bp of the tuf genes for :i Staphylococcus aureus, S. epidermidis, S. saprophyticus and S. simulans. All other tuf sequences used in the alignment were either sequenced by us or selected from databases. The analysis of this sequence alignment led to the selection of two primer pairs specific and ubiquitous for Staphylococcus spp. (Table Annex III shows the strategy used to select one of these two PCR primer pairs. The same strategy was used to select the other primer pair. Of the 14 staphylococcal species tested, one (S.

sciun) could not be amplified by the Staphylococcus-specific PCR assays using either one of these two primer pairs. For PCR assays using either one of these two primer pairs, there was no amplification with DNA from species of other bacterial genera.

EXAMPLE 3: Selection from tufsequences of PCR primers secific for Cand lbican As shown in Annex IV, the comparison of tufsequences from a variety of bacterial and eukaryotic species allowed the selection of PCR primers specific for Candida albicans.

The strategy used to design the PCR primers was based on the analysis of a multiple sequence alignment of various tuf sequences. This multiple sequence alignment includes tuf sequences of five representative fungal species selected from the genus Candida which were determined by our group C. albicans, C. glabrata, C. krusei, C. parapsilosis and C. tropicalis) as well as tufsequences from other closely related fungal species, tuf sequences from various bacterial species were also included. A careful analysis of this sequence alignment allowed the selection of primers from the C. albicans tuf sequence; these primers discriminate sequences from other closely related Candida species and other fungal species, thereby permitting the speciesspecific and ubiquitous detection and identification of C. albicans (Table All of 88 S 15 Candida albicans strains tested were efficiently amplified and there was no amplification with genomic DNA from other fungal or bacterial species.

EXAMPLE 4: Selection of PCR primers specific for Streptococcus from recA. As shown in Annex V, the comparison of the various bacterial recA gene sequences available from databases (GenBank and EMBL) was used as a basis for the selection of PCR primers which are specific and ubiquitous for the bacterial genus Streptococcus. Since sequences of the recA gene are available for many bacterial species including five species of streptococci, it was possible to choose sequences well conserved within the genus Streptococcus but distinct from the recA sequences for other bacterial genera.

25 When there were mismatches between the recA gene sequences from the five Streptococcus species, an inosine residue was incorporated into the primer (Annex V).

The selected primers, each containing one inosine and no degenerescence, were specific and ubiquitous for Streptococcus species (Table This PCR assay amplified all of the 22 streptococcal species tested. However, the Streptoococcus-specific assay did not amplify DNA from 3 out of 9 strains of S. mutans and 1 out of 3 strains of S.

salivarius. There was no amplification with genomic DNA from other bacterial genera (Table 7).

EXAMPLE Nucleotide sequencing of DNA fraqments The nucleotide sequence of a portion of the tuf genes from a variety of bacterial or fungal species was determined by using the dideoxynucleotide chain termination sequencing method (Sanger et al., 1977, Proc. Natl. Acad. Sci. USA. 74:5463-5467). The sequencing was performed by using an Applied Biosystems automated DNA sequen'cer (model 373A) with their PRISM

M

Sequenase* Terminator Double-stranded DNA Sequencing Kit (Perkin-Elmer Corp., -26- Applied Biosystems Division, Foster City, CA). The sequencing strategy does not discriminate tufA and tufB genes because the sequencing primers hybridize efficiently to both bacterial tuf genes. These DNA sequences are shown in the sequence listing (SEQ ID Nos: 118 to 146). The presence of several degenerated nucleotides in the various tuf sequences determined by our group (Table 13) corresponds to sequence variations between tufA and tufB.

Oliqonucleotide primers and probes selection. Oligonucleotide probes and amplification primers were selected from the given proprietary DNA fragments or database sequences using the OligoTM program and were synthesized with an automated ABI DNA synthesizer (Model 391, Perkin-Elmer Corp., Applied Biosystems Division) using phosphoramidite chemistry.

EXAMPLE 6: Labeling of oliqonucleotides for hybridization assays. Each oligonucleotide was end-labeled with y- 32 P (dATP) by the T4 polynucleotide kinase (Pharmacia) as 15 described earlier. The label could also be non-radioactive.

Specificity test for oligonucleotide probes. All labeled oligonucleotide probes were tested for their specificity by hybridization to DNAs from a variety of bacterial and fungal species selected from Tables 4, 5 and 6 as described earlier. Species-specific or genus-specific probes were those hybridizing only to DNA from the microbial species or genus from which it was isolated. Oligonucleotide probes found to be specific were submitted to ubiquity tests as follows.

Ubiquity test for oliaonucleotide probes. Specific oligonucleotide probes were then used in ubiquity tests with strains of the target species or genus including reference strains and other strains obtained from various countries and which are 25 representative of the diversity within each target species or genus. Chromosomal DNAs from the isolates were transferred onto nylon membranes and hybridized with labeled oligonucleotide probes as described for specificity tests. The batteries of •isolates constructed for each target species or genus 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 or genus.

EXAMPLE 7: Same as example 6 except that a pool of specific oligonucleotide probes is used for microbial identification to increase sensitivity and assure 100% ubiquity or (ii) to identify simultaneously more than one microbial species and/or genus. Microbial identification could be performed from microbial cultures or directly from any clinical specimen.

-27- EXAMPLE 8: Same as example 6 except that bacteria or fungi were detected directly from clinical samples. Any biological sample was loaded directly onto a dot blot apparatus and cells were lysed in situ for bacterial or fungal detection and identification. Blood samples should be heparizined in order to avoid coagulation interfering with their convenient loading on a dot blot apparatus.

EXAMPLE 9: PCR amplification. The technique of PCR was used to increase the sensitivity and the rapidity of the assays. The sets of primers were tested in PCR assays performed directly from bacterial colonies or from a standardized bacterial suspension (see Example 10) to determine their specificity and ubiquity (Table Examples of specific and ubiquitous PCR primer pairs are listed in Annex VI.

Specificity and ubiquity tests for amplification primers. The specificity of all selected PCR primer pairs was tested against DNAs from a variety of bacterial and 15 fungal species selected from Tables 4, 5 and 6 as described earlier. Primer pairs found specific for each species or genus were then tested for their ubiquity to ensure that each set of primers could amplify at least 90% of DNAs from a battery of isolates of the target species or genus. The batteries of isolates constructed for each species contain reference ATCC strains and various clinical isolates from around the world which are representative of the diversity within each species or genus.

Standard precautions to avoid false positive PCR results should be taken (Kwok and Higuchi, 1989, Nature, 239:237-238). Methods to inactivate PCR amplification products such as the inactivation by uracil-N-glycosylase may be used to control PCR carryover.

25 EXAMPLE Amplification directly from bacterial or yeast cultures. 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 approximately x 10' bacteria/mL). In the case of direct amplification from a colony, a portion of a colony was transferred using a plastic rod directly into a 20 PL PCR reaction mixture containing 50 mM KCI, 10 mM Tris-HCI (pH 0.1% Triton X-100, 2.5 mM MgCI,, 0.4 j.M of each primer, 200 gM of each of the four dNTPs and 0.5 unit of Taq DNA polymerase (Promega) combined with the TaqStart

T

M antibody (Clontech Laboratories Inc.). For the bacterial suspension, 1 gL of the cell suspension was added to 19 ,L of the same PCR reaction mixture. For the identification from yeast cultures, 1 pL of a standard McFarland 1.0 (corresponds to approximately 3.0 x 108 bacteria/mL) concentrated 100 times by centrifugation was added directly to the PCR reaction. This concentration step for yeast cells was performed because a McFarland 0.5 for yeast cells has approximately 200 times fewer cells than a McFarland 0.5 for bacterial cells.

-28- PCR reactions were then subjected to thermal cycling (3 min at 95 0 C followed by 30 cycles of 1 second at 95*C for the denaturation step and 30 seconds at for the annealing-extension step) using a PTC-200 thermal cycler. PCR amplification products were then analyzed by standard agarose gel electrophoresis.

Amplification products were visualized in agarose gels containing 0.25 sg/mL of ethidium bromide under UV at 254 nm. The entire PCR assay can be completed in approximately one hour.

Primer sequences derived from highly conserved regions of the bacterial 16S ribosomal RNA gene were used to provide an internal control for all PCR reactions.

Alternatively, the internal control was derived from sequences not found in microorganisms or in the human genome. The internal control was integrated into all amplification reactions to verify the efficiency of the PCR assays and to ensure that significant PCR inhibition was absent. The internal control derived from rRNA was also useful to monitor the efficiency of the bacterial lysis protocols. The internal control and 15 the species-specific or genus-specific amplifications were performed simultaneously in multiplex PCR assays.

S. EXAMPLE 11: Amplification directly from urine specimens. For PCR amplification performed .directly from urine specimens, 1 pL of urine was mixed with 4 /L of a lysis solution containing 500 mM KCI, 100 mM tris-HCI (pH 1% triton X-100. After incubation for at least 15 minutes at room temperature, 1 uL of the treated urine specimen was added directly to 19 ML of the PCR reaction mixture. The final concentration of the PCR reagents was 50 mM KCI, 10 mM Tris (pH 0.1% Triton X-100, 2.5 mM MgCI 2 0.4 MM of each primer, 200 MM of each of the four dNTPs. In addition, each 25 jL reaction contained 0.5 unit of Taq DNA polymerase (Promega) combined with the TaqStartTM antibody (Clontech Laboratories Inc.).

Strategies for the internal control, PCR amplification and agarose gel detection of the amplicons are as previously described in example EXAMPLE 12: 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 previously. Specific oligonucleotides used as a basis for the DNA-based tests are selected from the antibiotic resistance gene sequences. These tests, which allow the rapid evaluation of bacterial resistance to antimicrobial agents, can be performed either directly from clinical specimens, from a standardized bacterial suspension or from a bacterial colony and should complement diagnostic tests for the universal detection of bacteria as well as for the species-specific and genus-specific microbial detection and identification.

-29- EXAMPLE 13: Same as examples 10 and 11 except that assays were performed by multiplex PCR using several pairs of primers in a single PCR reaction) to reach an ubiquity of 100% for the specific targeted pathogen(s). For more heterogeneous microbial species or genus, a combination of PCR primer pairs may be required to detect and identify all representatives of the target species or genus.

Multiplex PCR assays could also be used to detect simultaneously several microbial species and/or genera or, alternatively, (ii) to simultaneously detect and identify bacterial and/or fungal pathogens and detect specific antibiotic resistance genes either directly from a clinical specimen or from bacterial cultures.

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 fluorescent dyes 15 emitting at different wavelengths. The fluorescent dyes can be each coupled with a i specific oligonucleotide linked to a fluorescence quencher which is degraded during amplification to release the fluorescent dyes TaqMan

T

Perkin Elmer).

EXAMPLE 14: Detection of amplification products. The person skilled in the art will appreciate that alternatives other than standard agarose gel electrophoresis (Example 10) may be used for the revelation of amplification products. Such methods may be based on fluorescence polarization or on the detection of fluorescence after amplification (e.g.

AmplisensorTM, Biotronics; TaqMan T M Perkin-Elmer Corp.) or other labels such as biotin (SHARP SignalT system, Digene Diagnostics). These methods are quantitative 25 and may be automated. One of the amplification primers or an internal oligonucleotide probe specific to the amplicon(s) derived from the species-specific, genus-specific or universal DNA fragments is coupled with the fluorescent dyes 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 fluorescent dyes emitting at different wavelengths are available.

EXAMPLE Species-specific, genus-specific,. universal and antibiotic resistance gene amplification primers can be used in other rapid amplification procedures such as the ligase chain reaction (LCR), transcription-mediated amplification (TMA), self-sustained sequence replication (3SR), nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), cycling probe technology (CPT) and branched DNA (bDNA) or any other methods to increase the sensitivity of the test.

Amplifications can be performed from isolated bacterial cultures or directly from any clinical specimen. The scope of this invention is therefore not limited to the use of the 30 DNA sequences from the enclosed Sequence Listing for PCR only but rather includes the use of any procedures to specifically detect bacterial DNA and which may be used to increase rapidity and sensitivity of the tests.

EXAMPLE 16: A test kit would contain sets of probes specific for each microbial species or genus 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 species- or genus-specific probes for the detection of each pathogen of interest in specific types of 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.

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 i 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: A kit for the universal detection of bacterial or fungal pathogens from all clinical 20 specimens which contains sets of probes specific for highly conserved regions of the microbial genomes.

A kit for the detection of microbial pathogens retrieved from urine samples, which contains 5 specific test components (sets of probes for the detection of Enterococcus faecium, Enteroccus species, Staphylococcus saprophyticus, 25 Staphylococcus species and Candida albicans).

A kit for the detection of respiratory pathogens which contains 3 specific test components (sets of probes for the detection of Staphylococcus species, Enterococcus species and Candida albicans).

A kit for the detection of pathogens retrieved from blood samples, which contains 10 specific test components (sets of probes for the detection of Streptococcus species, Streptococcus agalactiae, Staphylococcus species, Staphylococcus saprophyticus, Enterococcus species, Enterococcus faecium, Neisseria species, Neisseria meningitidis, Listeria monocytogenes and Candida albicans). This kit can also be applied for direct detection and identification from blood cultures.

A kit for the detection of pathogens causing meningitis, which contains specific test components (sets of probes for the detection of Streptococcus species, Listeria monocytogenes, Neisseria meningitidis, Neisseria species and Staphylococcus species).

-31 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 26 following genes associated with antibiotic resistance: bla,, bla,,, bla,, bla 0 blaZ, aadB, aacCl, aacC2, aacC3, aacA4, aac6'-lla, ermA, ermB, ermC, mecA, vanA, vanB, vanC, satA, aac(6)-aph(2"), aad(6'), vat, vga, msrA, sul and int.

Other kits adapted for the detection of pathogens from skin, abdominal wound or any other clinically relevant infections may also be developed.

EXAMPLE 17: Same as example 16 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 microbial cultures. Components required for universal bacterial detection, (ii) species-specific and genus-specific bacterial and/or fungal detection and identification and (iii) detection of antibiotic resistance genes will be included.

Amplification assays could be performed either in tubes or in microtitration plates having multiple wells. For assays in plates, the wells will contain 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 20 required for species-specific and genus-specific bacterial and/or fungal detection and identification as well as for the simultaneous antibiotic resistance genes detection will be included in kits for testing directly from bacterial or fungal cultures as well as in kits for testing directly from any type of clinical specimen.

The kits will be adapted for use with each type of specimen as described in 25 example 16 for hybridization-based diagnostic kits.

EXAMPLE 18: It is understood that the use of the probes and amplification primers described in.this invention for bacterial and/or fungal 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, air, pharmaceutical products or other products requiring microbiological control. These tests could also be applied to detect and identify bacteria or fungi in biological samples from organisms other than humans other primates, birds, plants, mammals, farm animals, livestock and others). These diagnostic tools could also be very useful for research purposes including clinical trials and epidemiological studies.

This invention has been described herein above, and it is readily apparent that modifications can be made thereto without departing from the spirit of this invention. These modifications are under the scope of this invention, as defined in the appended claims.

Page(s) t -S3are claims pages They appear after the table c 8 32 Table 1. DIstribution of nosocomial pathogens for various human Infections in USA (1990-1992)~.

Pathogen UT1 2

SSI

3 BSI' Pneumonia CSF Escherichia coli 27 9 5 4 2 Staphylococcus aureus 2 Staphylococcus epidermidis 2 Enterococcus (aecalis 16 Enterococcus (aecium 1 Pseudomonas aeruginosa 12 Kiebsiella pneumoniae 7 Proteus mirabilis 5 Streptococcus pneumoniae 0 Group B Streptococci 1 15 Other Streptococci 3 Haemophllus influenzae 0 Neisseria meningitidis 0 Listenia monocyto genes 0 Other Enterococci 1 Other Staphylococci 2 Candida albicans 9 Other Candida 2 Enterobacter spp. 5 Acinetobacter spp. 1 Citrobacter spp. 2 Serratia marcescens 1 Other Klebsiella 1 Others 0 21 17 6 12 9 1 0 9 3 3 4 3 1 0 3 1 2 5 2 0 0 o 0 o 0 1 0 8 3 1 7 4 1 2 1 1 Data recorded by the National Nosocomial Infections Surveillance (NN IS) from hospitals (Emori and Gaynes, 1993, Clin. Microbiol. Rev., 6:428-442).

2 Urinary tract infection.

3Surgical site infection.

4 Bloodstream infection.

5 Cerebrospinal fluid.

-33- Table 2. Distribution of bloodstream infection pathogens in Quebec (1995), Canada (1992), UK (1969-1988) and USA (1990-1992).

Organism Quebec' Canada 2

UK

3

USA

4 Community- Hospital- Hospitalacquired acquired acquired E. coli 15.6 53.8 24.8 20.3 S. epidermidis 25.8 NI 6 0.5 7.2 31.0 and other CoNS

S

S. aureus 9.6 NI 9.7 19.4 16.0 S. pneumoniae 6.3 NI 22.5 2.2 NR 7 E. faecalis 3.0 NI 1.0 4.2 NR E. faecium 2.6 NI 0.2 0.5 NR Enterococcus NR NI NR NR 15 spp.

H. influenzae 1.5 NR 3.4 0.4 NR P. aeruginosa 1.5 8.2 1.0 8.2 K. pneumoniae 3.0 11.2 3.0 9.2 P. mirabilis NR 3.9 2.8 5.3 20 S. pyogenes NR NI 1.9 0.9 NR Enterobacterspp. 4.1 5.5 0.5 2.3 Candida spp. 8.5 NI NR 1.0 Others 18.5 17.48 28.7 18.9 19.0 1 Data obtained for 270 isolates collected at the Centre Hospitalier de I'Universit6 Laval (CHUL) during a 5 month period (May to October 1995).

2 Data from 10 hospitals throughout Canada representing 941 gram-negative bacterial isolates. (Chamberland et 1992, Clin. Infect. Dis., 15:615-628).

3 Data from a 20-year study (1969-1988) for nearly 4000 isolates (Eykyn et al., 1990, J. Antimicrob. Chemother., Suppl. C, 25:41-58).

4 Data recorded by the National Nosocomial Infections Surveillance (NNIS) from hospitals (Emori and Gaynes, 1993, Clin. Microbiol. Rev., 6:428-442).

s Coagulase-negative staphylococci.

6 NI, not included. This survey included only gram-negative species.

7 NR, incidence not reported for these species or genera.

8 In this case, 17.4 stands for other gram-negative bacterial species.

-34- Table 3. Distribution of positive and negative clinical specimens tested at the microbiology laboratory of the CHUL (February 1 9 9 4 January 1995).

Clinical specimens No. of samples of positive of negative and/or sites tested specimens specimens Urine 17,981 (54.5) 19.4 80.6 Blood culture/marrow 10,010 (30.4) 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 523 2.7 97.3 Respiratory tract 502 56.6 43.4 Deep pus 473 56.8 43.2 Ears 289 47.1 52.9 15 Pleural and pericardial 132(0.4) 1.0 99.0 fluid Peritoneal fluid 101(0.3) 28.6 71.4 Total: 32,966 (100.0) 20.0 80.0 35 Table 4. Gram-negative bacterial species (90) used to test the specificity of PCR primers and DNA probes (continues on next page).

Bacterial species Number of Bacterial species Number of reference reference strains strains testeda testeda Acinetobacter baumannii Acinetabacter Iwo ffl1 Actinobacillus lignieresil Alcaligenes faecalis Alcaligenes odorans Alcaligenes xylosoxydans subsp. denitrificans Bactemoides distasonis Bacteroides fra gills Bacteroides ovatus Bacteroides thetaiotaomicron Bacteroides vulgetus Bordetella bronchiseptica Bordetella parapertussis 20 Bordetella pertussis Burkholderia cepacia Citrobacter amalonaticus Citrobacter diversus subsp. koseri Citrobacter freundli Comamonas acidovorans Enterobacter aero genes Enterobacter agglomerans Enterobacter cloacae Escherichia coi Escherichia fergusonii 1 Moraxella phenylpyruvica 3 Morganella morganji 1 Neisseria animalis I Neisseria canis 1 Neisseria caviae Neisseria cinerea 1 Neisseria cuniculi 1 Neisseria elongata subsp. elongata 1 Neisseria elongata subsp. glycoytica 1 Neisseria flavescens 1 Neisseria flavescens Branham 1 Neisseria gonorrhoeae 1 Neisseria Iactamica 1 Neisseria meningitidis 2 Neisseria mucosa 1 Neisseria, polysaccharea 1 Neisseria sicca 2 Neisseria sub flava Neisseria weavedi Ochrobactrum antropi Pasteurella aero genes Paste urella multocida Prevotella melaninogenica Proteus mirabilis Proteus vulgaris -36- Bacterial species Number of Bacterial species Number of reference reference strains strains testeda tested 8 0 0 Escherichia hermannii Escherichia vuin ens Flavobacterium meningosepticum Flavobactenium indolo genes Flavobacterium odoratum Fusobacterium necrophorum Gardnerella vaginalis Haemnophiius haemnolyticus l-aemnophilus influenzae Haemophilus 15 parahaemolyticus Haemophllus parainfluenzae Hafnia alvel Kin gella indolo genes subsp. suttonella Kin gella kin gae Kiebsiella omnithinolytica Kiebsiella oxytoca Kiebsiella pneumnoniae Moraxella atlantae Moraxella catarrhalis Moraxella lacunata Moraxella osloensis I Providencia stuartfi 1 Pseudomonas aeruginosa 2 Pseudomonas fluorescens I Pseudomonas stutzeri 1 Salmonella anzonae 12 Salmonella choleraesuis I Salmonella gallinarum 2 Salmonella typhimunium Providencia alcalifaciens Providencia rettgeri Providencia rustigianli Serratia liquefaciens Serratia marcescens Shewanella, putida Shigella boydi Shigella dysenteniae Shigella flexneri Shigella sonnel Stenotrophomonas maltophilia Yersinia enterocolitica 8Most reference strains were obtained from the American Type Culture Collection (ATCC). The other reference strains were obtained from the Laboratoire de Sant6 Publique du Quebec (LSPQ), (Hi) the Center for Disease Control and Prevention (CDC) and (iii) the National Culture Type Collection (NCTC).

37 Table 5. Gram-positive bacterial species (97) used to test the specificity of PCR primers and DNA probes (continues on next page).

Bacterial species Abiotrophia adiacens Abiotrophia defectiva Actinomyces israelii Clostridium perfringens Corynebacterium accolens Corynebacterium aquaticum Corynebacterium bovis Number of reference strains tested' 1 Bacterial species Micrococcus knlstinae Micrococcus luteus Micrococcus Iylae Micrococcus rosous Micrococcus vanians Pep tococcus niger a Corynebactenium cervicis Corynebacterium 15 diphteniae Corynebacterium flavescens Corynebacterium genitalium 20 Car ynebacterium jeikeium C orynebacteriurn kutcheri Corynebactenium ma truchotii Corynebacterium minutissimum Corynebacterium mycetoides Corynebacterium pseudodiphtheriticum Corynebacterium pseudo genitalium Corynebacterium renale Corynebacterium striatum Corynebacterium ulcerans 1 Peptostreptococcus anaerobius 1 Peptostreptococcus asaccharolyticus 6 Staphylococcus aureus 1 Staphylococcus auricularis 6 Staphylococcus capitis subsp. urealyticus 1 Staphylococcus cohnii 1 Staphylococcus epidermidis I Staphylococcus haemolyicus 1 Staphylococcus hominis 1 Staphylococcus Iugdunernsis 1 Staphylococcus saprophyticus 6 Staphylococcus schiferi Number of reference strains testeda 1 1 1* 1 1 2* 3 1 1 2 1 Staphylococcus sciuri Staphylococcus simulans Staphylococcus warned 38 Bacterial species Corynebacterium urealyticum Corynebacterium xerosis Enterococcus avium Enterococcus casseliflavus Enterococcus cecorum Enterococcus dispar Enterococcus durans Enterococcus faecalis Enterococcus faecium Enterococcus flavescens Enterococcus gallinarum Enterococcus hirae 15 Enterococcus mundtii Enterococcus pseudoavium Enterococcus raffinosus Enterococcus saccharolyticus Enterococcus solitatius Eubacterium lentum Gemella haemolysans Gemella morbillorum Lactobacillus acidophilus Listeria innocua Listeria ivenovii Listeria grayi Listeria monocytogenes Listeria murrayi Listeria seeligeri Listeria welshimerin Number of reference strains testeda Bacterial species Number of reference strains testeda 1 Staphylococcus xylosus 1 Streptococcus agalactiae 1 Streptococcus anginosus 1 Streptococcus bovis 1 Streptococcus constellatus 1 Streptococcus crista 1 Streptococcus dysgalactiae 6 Streptococcus equi 3 Streptococcus gordonii 1 Group C Streptococci 3 Group D Streptococci 1 Group E Streptococci 1 Group F Streptococci 1 Group G Streptococci 1 Streptococcus intermedius 1 Streptococcus mitis 1 Streptococcus mutans 1 Streptococcus oralis 1 Streptococcus parasanguis 1 Streptococcus pneumoniae 1 Streptococcus pyogenes 1 Streptococcus salivarius 1 Streptococcus sanguis 1 Streptococcus sobrinus 3 Streptococcus suis 1 Streptococcus uberis 1 Streptococcus vestibularis 1 Most reference strains were obtained from the American Type Culture Collection (ATCC). The other reference strains were obtained from the Laboratoire de Sant& Publique du Qubbec (LSPQ), (ii) the Center for Disease Control and Prevention (CDC) and (iii) the National Culture Type Collection (NCTC).

39 Table 6. Fungal species (12) used to test the specificity of PCR primers and DNA probes.

Fungal species Number of reference strains tested' Candida albicans 12 Candida glabrata 1 Candida guilliermondli 1 Candida kefyr 3 Candida krusei 2 Candida Iusitaniae 1 Candida parapsilosis 2 Candida tropicalis 3 Rhodotorula glutinis 1 15 Rhodotorula minuta 1 Rhodotorula rubra 1 Saccharomyces cerevisiae 1 a Most reference strains were obtained from the American Type Culture Collection (ATCC) and (ii) the Laboratoire de Sante Publique du Quebec (LSPQ).

20 0 Table 7. PCR assays developed for several clinically important bacterial and fungal pathogens (continues on next page).

Organism Primer Pair" SEQ ID NO Amplicon size (bp) Enterococcus faecium Listeria monocytogenes Neisseria meningitidis Staphylococcus saprophyticus Streptococcus agalactiae Candida albicans Enterococcus

S

spp. (11 species)' Neisseria spp.

(12 species)' Staphylococcus spp.

(14 species) 1-2 3-4 5-6 7-8 9-10 11-12 13-14 15-16 17-18 19-20 21-22 23-24 154 29/29 149 88/88 112 87/87 103 321/321 192 13/14 216 130 177 149 Ubiquity DNA amplification from culturec specimensd 79/80 164/168 e 258/258 245/260

NT

221 153 13/14 210/2141 Streptococcus spp.

20 (22 species)' Universal detection" 309 104/ 116' species)' All primer pairs are specific in PCR assays since no amplification was observed with DNA from the bacterial and fungal species other than the species of interest listed in Tables 4, 5 and 6.

b Ubiquity was tested by using reference strains as well as strains from throughout the world, which are representatite of the diversity within each target species or genus.

c For all primer pairs, PCR amplifications performed directly from a standardized microbial suspension (MacFarland) or from a colony were all specific and ubiquitous.

d PCR assays performed directly from blood cultures, urine specimens or -41r

C

cerebrospinal fluid. NT, not tested.

The four L. monocytogenes strains undetected are not clinical isolates. These strains were isolated from food and are not associated with a human infection.

The bacterial species tested include all those clinically relevant for each genus (Tables 4 and All of these species were efficiently amplified by their respective genus-specific PCR assay, except for the Staphylococcus-specific assay, which does not amplify S. sciuri.

The Streptococcus-specific PCR assay did not amplify 3 out of 9 strains of S.

mutans and 1 out of 3 strains of S. salivarius.

h The primers selected for universal bacterial detection do not amplify DNA of nonbacterial origin, including human and other types of eukaryotic genomic DNA.

For the universal amplification, the 95 bacterial species tested represent the most clinically important bacterial species listed in Tables 4 and 5. The 12 strains not amplified are representatives of genera Corynebacterium (11 species) and Stenotrophomonas (1 species).

Table 8. Target genes for the various genus-specific, species-specific and universal amplification assays.

Microorganisms Gene Protein encoded Candida albicans tuf translation elongation factor EF-Tu Enterococcus faecium ddl D-alanine:D-alanine ligase Listeria monocytogenes actA actin-assembly inducing protein Neisseria meningitidis omp outer membrane protein Streptococcus agalactiae cAMP cAMP factor Staphylococcus unknown unknown saprophyticus Enterococcus spp. tuf translation elongation factor EF-Tu Neisseria spp. asd ASA-dehydrogenase Staphylococcus spp. tuf translation elongation factor EF-Tu Streptococcus spp. recA RecA protein Universal detection tuf translation elongation factor EF-Tu -42 Table 9. Antibiotic resistance genes selected for diagnostic purposes.

Genes SEQ ID NOs Antibiotics Bacteria" selected originating primers fragment Nlamx 49-50 110 Il-la ctams Enterobacteriaceae, b/aZ aac6'-Ila ermA ermB ermC vanB vanC aad(6) 51-52 61-64 91-92 93-94 95-96 7 1-74 75-76 173-1 74 il1 112 113 114 115 116 117 P-lactams Aminog lycosides Macro lides Macrolides Macrolides Vancomycin Vancomycin Streptomycin Pseudomonadaceae Enterococcus spp.

Pseudomonadaceae Staphylococcus spp.

Staphylococcus spp.

Staphylococcus spp.

Enterococcus spp.

Entero coccus spp.

0 15 0 0 0 0 00 Bacteria having high incidence for the specified antibiotic resistance genes. The presence of these antibiotic resistance genes in other bacteria is not excluded.

S

@OSSOS

@5* 0 5- Seep

OSSS

0

SOS.

-43 Table 10. Antibiotic resistance genes from our co-pending US (N.S.

081526840) and PCT (PCTICA195/00528) patent applications for which we have selected PCR primer pairs.

Genes SEQ ID NOs of selected primers Antibiotics bla,..

blam,, bla, aadB aacC 1 aacC2 15 aacC3 aacA4 mecA vanA satA 20 aac(6')-aph(2") vat vga msrA int 37-40 45-48 41-44 53-54 55-56 57-58 59-60 65-66 97-98 67-70 81-82 83-86 -87-88 89-90 77-80 99-1 02 1-lactamns J-lactams I-actams Aminoglycosides P-Iactamns Vancomycin Macro lid es Aminoglycosides Macrolides Macrolides Erythromycin P3-actamns, trimethoprim, aminoglycosides, antiseptic, -chioramphenicol Bacteria-, Enterobacteriaceae, Pseudomonadaceae, Haemophilus s pp., Neisseria spp.

Haemophllus spp., Pasteurella app.

Kiebsiella spp.

and other Enterobacteriaceae Enterobacteriaceae, Pseudomonadaceae Staphylococcus spp.

Enterococcus spp.

Enterococcus spp.

Enterococcus app., Staphylococcus spp.

Staphylococcus app.

Staphylococcus app.

Staphylococcus app.

Enterobacteriaceae, Pseudomonadaceae 103-1 06 Bacteria having high incidence for the specified antibiotic resistance genes. The presence of these antibiotic resistance genes in other bacteria is not excluded.

-44 Table 11. Correlation between disk diffusion and PCR amplification of antibiotic resistance genes in Staphylococcus species'.

Antibiotic Penicillin Phenotype blaZ

PCR

Disk diffusion (Kirby-Bauer)b Resistant Intermediate Sensitive 165 0 0 Oxacillin Gentamycin Erythromycin mecA aac(6')aph(2") 31 4 128 6 148 0 0 0 0 ermA ermnB ermC msrA aThe Staphylococcus strains studied include S. aureus (82 strains), S. epidermidis (83 strains), S. hominis (2 strains), S. capitis (3 strains), S. haemolyticus (9 20 strains), S. simulans (12 strains) and S. wameri (5 strains), for a total of 196 strains.

bSusceptibility testing was performed by the method of Kirby-Bauer according to the protocol reccommended by the National Committee of Clinical Laboratory Standards (NCCLS).

Table 12. Correlation between disk diffusion profiles and PCR amplification of antibiotic resistance genes in Enterococcus species'.

Disk diffusion (Kirby-Bauer)b Antibiotic Phenotype PCR Resistant Sensitive blaZ 0 2 Ampicillin Gentamycin Streptomycin aac(6')aph(2") aad(6') Vancomycin vanA vanB 0%.

SThe Enterococcus strains studied include E faeca (is (33 strains) and E. faecium (69 strains), for a total of 102 strains.

bSusceptibility testing was performed by the method of Kirby-Bauer according to the protocol reccommended by the National Committee of Clinical Laboratory Standards (NCCLS).

-46- Table 13. Origin of tufsequences in the Sequence Listing (continues on next page).

0 *r 00.0.

:0..0 000..

SEQ ID NO 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 Bacterial or fungal species Abiotrophia adiacens Abiotrophia defectiva Candida albicans Candida glabrata Candida krusei Candida parapsilosis Candida tropicalis Corynebacterium accolens Corynebacterium diphteriae Corynebacterium genitalium Corynebacterium jeikeium Corynebacterium pseudotuberculosis Corynebacterium striatum Enterococcus avium Enterococcus faecalis Enterococcus faecium Enterococcus gallinarum Gardnerella vaginalis Listeria innocua Listeria ivanovii Listeria monocytogenes Listeria seeligeri Staphylococcus aureus Staphylococcus epidermidis Staphylococcus saprophyticus Staphylococcus simulans Streptococcus agalactiae Streptococcus pneumoniae Source This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent This patent -47- SEQ ID NO 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 Bacterial or fungal species Streptococcus salivarius Agrobacterium tumefaciens Bacillus subtilis Bacteroides fragilis Borrelia burgdorferi Brevibacterium linens Burkholderia cepacia Chlamydia trachomatis Escherichia coli Fibrobacter succinogenes Flavobacterium ferrugineum Haemophilus influenzae Helicobacter pylori Micrococcus luteus Mycobacterium tuberculosis Mycoplasma genitalium Neisseria gonorrhoeae Rickettsia prowazekii Salmonella typhimurium Shewanella putida Stigmatella aurantiaca Streptococcus pyogenes Thiobacillus cuprinus Treponema pallidum Ureaplasma urealyticum Wolinella succinogenes Source This patent Database Database Database Database Database Database Database Database Database Database Database Database Database Database Database Database Database Database Database Database Database Database Database Database Database r St atg fo th seecio fro t se uece of th unvra aml f ct o primers (cnine on pae 49 to 52. Annex I t Ablotrophia adiacens Ablotrophia defecti va Agrobacteriurn turnefaciens Bacillus subril1.s Bacteroides fra gilis Borrella burgdorferi Brevibacteriurn linens Burkhol deria cepacla.

Chlarnydia trachona ti a 491 517.. .776 802 CAA TGTAAC TGGTGTTQA ATGTTCC AAATG &&gfJ GAZAAMGAA CTACCGTTAC CQGTGTTGA ATGTTCC AA=~ TAT~cc!AGGC GACAACGTAC CGACTGTTAC CGGCGTTGA ATG;TTCC. AAA3~ IATgCCTGac GACAACGTCA CAACTGTTAC AGGTGTTQAA ATGTTCC AATIqI TATg~CCTGG;A GATAACACTG CAGTTGTAAC AGGTGTTGAA AT CC. AAAM &T9GGGT GATAACGT AA CTACTTAC TGOTOTTO AT CC AAAX-q~ TATGCCTGGT 9ATAATGTTG CGACTG;TCAC QCTA~gA ATGT AGAI ATG CCCCGg C C GACACCACCG CGAa9CTgCAC GWGCGTT A =C AAATGG=T 9ATGCCGGC GAcAAcraTGT CGATTGTTAC TGGGGTTr-AA AGTG CATGCTGc GATAACC TG CCAq9C0TTAC CGGACGA A&ITCC. AGJW CA(;CrGG GCACGT SEQ ID

NO

118 119 147 148 149 is' 152 153 Corynebac teriurn diphteriae 9.9 9 99 9 9..

9*9 9 9 9* 9 9 99 99 9 9 9 9 9 9 9 9 9 9 99999 9. *9 9 9 9 999 9 9 9 9 9 9 9 9* 9 9.9 999 *9.

Corynebacteri ur genitalium Corynebacteri ur Jelkelun Enterococcus faecalis En terococcu s faeciurn Escheri chia coli Fibrobacter succinogenes Fiavobacteri ur ferrugin eurn Gardnerella vaginaii s Haeniophilus ifl uenzae Ieiicobacter pylori Li steri a monocytogenes MI crococcus luteus Mycobacteriumf tuberculosis CCACCgfl CTCCAZGAG ATTCA AGTGOT TATOCCGGGC GACAACG TG CCACCg=AlC CAAMYqTTAC

CAACAGTTC

CTACCTGTAC

ACGTCATCAC

CTACggTTAC CCA9CGTCAC

CT&CIIAA

CGACTG7AAC TAG;ThGTAAC CTC--A~gAG TTCA AGATGT TATCCCQOaC OACA.ACGTTG AG;GTG ATGTCC AAATQQGT AATGCCTGG3T GATAACGTTG

TGGTGTTGAA

TGGCGTTGAA

CGGTGTTGAA

AGOTOTTGAG

CTCIACAG

GGGTGTTA&

CGGTGTAGA

TGGAGTAGA

99-ATCAG ATGTTCC .AAA-TAGT ATQTTCC... .AGATGGT AITGTTCC .AAATGGT ATGTTCC AAA~ ACCflCC AAATGGT ATGTTCC AA-AM-9 &ITgIA AAT;G AGTCC AAA99 &I=fCC..AA-O

CATGCCCGGT

AATGCCGGGC

TCTGCCGGGT

XTCAGCCAGGC

AATGCCAGGC

TAGCCTGT

CATGCCCGGC

GACAACGT..

GACACGGTCA

GATAACACCA

GATC~rr-CAA gAACAMCA gAjAATG GA

GATAACATTG

GACAACACCG

135 157 158 138 159 CCACCGTCAC CGGTGTGGAG AG4T-MT aAOCCG GAA C Mycoplasma geni tallum Nel sserla gonorrhoea e Rickettsia prowazekii Salmionel la typhimuri ur ShewanellIa putida Stigma tella auran tiaca Staphylococcus a ureu s Staphylococcus epidex-midis Streptococcus agal1act ia e Streptococcus prnewfloliae Streptococcus pyogenes Thiobacillus cuprinus 2S Treponemfa pallidum r-*TgA CA~gGX4CA TGGCOTTGAA S S AT=C AAA XS C Q kTd~cc AAA=G AA(rqq ATOTTCA AGZG TATQ3CCTGGA ATTTCC .AG&TGGT AATGCCG.GGC

QATA.ATGCTT

GAGACTAA

GATAATGCTA

CAACgTGTAC TGGTGTAGA ATGTTCC.. GAG AATGCCAGGC GAAA C CGG7TCA-Tg&C GGG(GTGOAQ ATGTCC.. .AGATGGT GATGCCGGG ACA AC CAACTGTTAC AGGTGTTGAA &TgTTCC... AAATGGT MITGCCTGI GATMACGTTG CAACTTCTGGAA ATGTTCC AAA=~ TATGCCTGGC GACAACGTTG CAG;TTGZI TGGT(;TTrAA ATGTTCC AA-AM91 TATGCCTGOT GATAACGTTA CAQTZGZ=A TGGTOTTGA ATGTTCC AAAMGGT AATGCCTGGT GATAACGTGA CTGTqTT GTGTT GAC IICC& AAA=~ TATGCCTGGT (MTACTC CCACCTGCAC CGGCOTGG ATA AAA=~ CATGCCCGQC QATAATGTGA CAGTagTA& TGGCATTGAG &1T2TTA ACATGM gAQCGG GATAACCA 164 165 166 140 141 144 145 167 168 169 9 9 9..

9 *9* 9 9 9 9 9 9* 9 9 9 9 9 *9* 9 9 9 9 9 99 99 9 *99 9 9 9* 9*9 999 *99 Ureaplasma urealyti cum Wolinella succinogenes Candida al1bI cans Schizosaccharornyces Human Selected' equences' Selected universal is primer sequences': CTOTTTIAC A9AZ~ ATGTTTA ATTTM TThCCG GTGCTG CAACCQhA TGGCGTTGAG AfLTCC AGATGM TATOCCTOOT GAACGT GTGTIACCAC MAGTCAAM TCCGZTG AGRAATT GGAAGAWAA CCAAAATICG

GTGT-CAC-TAC

pombe TGA9&GGC-AT

ACXKKIAC

CAAGZCAAg TCTGITG AGAAGA-I TGAGGAgTCQ CCTAAGTTTG MQAGATOTTC CACAAGA AGM.GAGCZTG9ATG CCCGGGGAGG IGGIGITTGAR A-flT ATGGT IATGCCIGGI GAIAAYRT SEQ ID NO:23 ACIKKIAC IGGIGTIGAR ATGTT SEQ ID NO: 2 4 b AYRTT ITCICCIGGC ATIACCAT The sequence numbering refers to the E. coli tuf gene fragment. Underlined nucleotides are identical to the selected sequence or match that sequence.

"1I" stands for inosine which is a nucleotide analog that can bind to any of the four nucleotides A, C, G or T. "IKI, "IR- and "Y-1 designate nucleotide positions which are degenerated. "IK" stands for T or G; "IR" stands for A or G; stands for C or T.

b This sequence is the reverse complement of the above tuf sequence.

Statg fo th seecio fro tu seuece of th amlfcto prmr peii o th geu Eneo.cu (cnine on pae S3 an 54). Annex 11: Bacillus subtills Bacteroides Era gills Burkhol deria cepacia Chlamydia trachona ti s Corzyneba cteriurn diphteriae EnterOCoCCOUg Enterococcus En terococcus 314

CGCGAC&MI

CGCGATGTTG

CGTGCAC7IM

AGAGAAT

CGTGAGACC G

CGTGAZLCZG-

CGTGAAM!

CGTGACAACG

CGTGAZACg-L3 AAAAAC=AZ CATGAT CCA A&-C7 T- CTTGATGCCG AGGCGgGZ2 CCTOATOCCG ACAAGCCTT CTAA CCT ACAXACCATT CATOATGCCA ACACCT CATGATGCCA ACAAACCATT CATGATGCCA 348 401 GTTG.A.. CGCGG ACAAMAAA GTAGA... ACTGG TGTTAMCCAT GTGGA... CGCGG CATCP2GAAG ATTGA CGTGG AATTGTTAIA ATCGA... CGTGG CTCCCTGAAG GTCGA CGTGG ACAAgTTCGC GTCGA CGTGG TGAATTC GTTGA.. CGTGG ACAAGTTCOC GTCGA CGTGG ACAAGTTCGC 435 ~CCOTGACC AAqTffGAAAT CTAGG~TCATO AAATCGAAAT CGTCGGCGAA AkLATCGAAAT GTTTCCGATA AAGTTCAGTT QCACOAGG AC-OCGAGAT GTTG42TQACG &A=GAAAT GTTGGTGACG &AGTTGAAGT GTTGC;TGATC M=IGAAGT 149 152 153 126 131

SEQ

ID NO 148 Escherichia col i CGTGCGT9 AAGCCGTT CTGCTGCCG ATCGA CGCGG TATCA.ICAAA 0GTTGGTGAA9 AA9flGAAAT S 55 5** S S

SSS

S S S S S S *5

S

S. S S S S S @SS** 55 5* S 555 S S S S *5 5 555 555 555 Gardnerel la CACGAZCTTM &MC CTTqAMCCA ATCGA CGTGG TAAGCT-C-CA ATCAACAC-CC CA=GAGAT vaginal is Haexnophilus influenzae Helicobacter pylori Li steri a ronocytogenes Mi crococcus luteus Mlycobacteriumi tub~erculosis Mycoplasma geni taliun Neisseria gqonorrhoeae Salmonella typhimrnuiurn Shewanella putida Staphylococcus aureus Staphylococcus epi dertnidi s Staphylococcus saprophyti cus CGTGCG;ATTG ACMC- CCTTCTTCCA AGAGACACg- AAAAAACMf CGTGA149TIG ACAAACCATT CGCGACMAGg AAGCCGTT CGCGAG&-CG ACAGG= CGTGAAGTA9 CGTGCCGTGG ACAAACCATT CGTGCGATM LAACCGTT CGTGACATC9 ATMOCCOM CGTGATCT ACAAACCATT CGTGAITCTG ACAAACCA-TT CGTGAITMI ACAAACAT gT&g=CCG

-CA-TGATGCCA

CC.XGATGCCG

9CTGATOCCG

CTIATIAGCA

~CCGCCT

CCT(c;aCCG

-CACT(CCA

CATGATGCCA

CATGATGCCA

CATQATGCCA

ATCGA CGAGG GTTGA.. AGAGG GTTGA CGTGG ATCGA... CGCGG GTCGA CGCGG ATTGA... AGAGG ATCGA... CGAGG ATCGA... CGCGG ATCGA CGTGG GTTGA CGTGG GTTGA... .CGTGG GTTGA .CGTGG

TATTATCCGT

CGTGQTGAA

ACAAGTTA)A

CACCCTQAAG

CGTGATCAA-C

TGAACTCAAA

TATCATC9;Ag

TATCAICALAA

TATT2TACOC

TCAAAT!CAAA

TCAAATCAAA

TCAAAT.CAAA

ACAGGATr

GTAGGCAT-

GTTGGTGACG

ATCAACTCQG

QTGAACGAGG

GTAGGTCAAG

GTGGTGACG

9TG2CQ9A2 9TA9CCGACC; GTTGGTG3AA9

AG-TAGAAAT

MAGGGAAAT

LXGTAGAAGT

AGGTCGAGAT

LL=AGAGAT

=GAA.AT

AGATTGAAAT

AAGTTGAAAT

AA~aTTGAAAT A~LeTGAAAT 157 158 138 159 160 161 162 164 165 140 141 142 gTGGTGAAg AAGTTGAAAT gTCGGTrQAAQ2 AACGARAT Streptococcus a gal ac tia e Streptococcus pneumoniae Streptococcus pyogenes Ureaplasma urealyticum Selected sequences too. 0 964:,* a 0. 0 0 0 to to..ee C S CGTGATACZG ACAACCTTT ACTCTCCA GTTGA. CGTGG TACTgTGT gTCAACgACG; A~gTGAAAT C GTGACqT AAACCA GCTCCCA GTCGA CGTGG TATCg=AAA cAcgC~ AAATCGAAAT CGCGACACTG ACAA.ACCATT CITCXTCCA GTCGA CGTGG TACTGTTCGT GTACAC~ &AATCGAAAT CGTAGTACTG ACAALACCATT CTTATTAGCA ATTGA CGTGG TGTATTAAAA GTTAATGOATG AGGTTGAAAT TACTO ACAAACCATT CATGATG GTTCGC GTTGGTGACG AAGTT 144 145 167 170 Selected SEQ ID NO: 13 SEQ ID NO: 14' genus -specific primer TACTG ACAA.ACCATT CATGATG AACTTC GTCACCAACG CGAAC sequences: The sequence numbering refers to the E. faecalis tuf gene fragment. Underlined nucleotides are identical to the selected sequence or match that sequence.

This sequence is the reverse complement of the above tuf sequence.

NOTE: The above primers also amplify tuf sequences from Abiotrophia species; this genus has recently been related to the Enterococcus genus by 16S rRNA analysis.

S

S

9 959 9 9**

S

9 9 9 5 9 9 9 S S S S S S S S 55 S. 55 5 5 5 S S S S S *5 555 5.9 .55 Annex III: Bacillus subtiiis Bacteroldes fragl is Burkhol derla cepacia Chiarnydia trachoma ti s Corynebacteri u diphteriae Enterococcus faecaiis Enterococcus faeci ur Escheri chia coli Ga rdnerell1a vaginalis Strategy for the selection from tuf sequences of the amplification primers specific for the genus Staphylococcus (continues on pages 56 and 57).

385 420..579 611 SEQ I

NO

TGGCMG-.A GAACGCGGAg MGjTAAAGT CGG..TTG CTAAAggh TACAATCACT CCAACGCA 148 AGGTCG;TATC gAAAC=ZG TTATCCATGT AGG..TTT GTAA.ACCGGG TCAGATTAAA CCTCACTCTA 149 GGGTCG C GAGCGCGGCA TCGTGAAGGT CGG..TGG CGAAGZGGG =GTCg gGCACACGC 152 TGA~l~TGGA GGA -TTIT GT TTC..TTT GCTTG99MAA GXTGITAAA OTCATACAC 153 12 CGCCQT A GCCT CCCXGAAGGT CAA..TTG TTAAGPSAgg CGZTAjC C_ T~ CCG 126 AGGAGTGT gAACGTGGTG AGTCGCGT TGG..TAG CTAAA CAGC TACAATCACT CCCACAA 132 AGGTCGTGTT gAqACgTGA AAG;TTCGCGT TGG..TAG CTAAACCAGG TACAATCACA =.RTACAA 133 CGGTCg~TGTA g&LCCGGA TC~A G G CTGACcTPA CCA 154 CGGTCGTGTT gGggGGTA LkC=CCAAT CAA..TGG CTgL -ASIZ~ ~CCA 135

D

S

94 9 09 9 009 9 9 *9* 9 9 9 9

SS

9 5 5 9 5 9 9 9 99*O*e .9 99 9 9 9 9 9 9 9 9 9 *99 liaernophil1us Influenza e flel icobacter pylori Llsteria manocytogenes Mlcrococcus luteus M~ycobacteriumn tuberculosis Mycopi a sna gernltallun Neisseria gonorrhoeae Salmonella typhimurium She wanel la putida staphvl ococcus aue S tahyl ococcus egoidernnidi s simulan's AGGTCGTGTA GAACGAGGTA TT"TCTAC AG TAG CGAAACCAGO TTCAATCACA CCACACACTG AGGTAgGATT 9AAAGAGOCG; TGGTGAAAGT AGG. TAT GCAAACC=AgG TTCTATCACT =GCA-CAGA

TGGA~GT

CGGTrMC9CC

CGGAC=~G

AGGAAA

CGG9CGTTA.

CGGT-IMA

AGGTCGTGT

AGGCG-GT

AGCCTOI

AGGCCGTGTT

AGGCCGTGTT

gAACGTG;GAC 9AG-C9CA 9AG99C9CG hA-qAMG 2AG;CAMA 9GICC9GTA EA(gCGTGGTA

GAACGTGGTC

MAGITAAAGT TGG..TAG CCCITGMGAT CAA..TGG TG~AMCGT GAA..TCA AMCICAAGT AGG..TAG TCA=CACGT TG..TGG TCATCAAAGT GG..TGG TTGTACGCGT AGG..TAG AM~gAGT TGG..TAG

CTAXACCAM

TGGAGCCGGCG

CCAAGgCqGG

CAAAACCAG

CCA.AACGGGG

CTAAGCCGG

CGAACCCAGG

CTGCTCCTGG

TTCGZ~TC

CTCCATC

CACCACCACG

gjgCATAAA

TACTATCACT

TCACATCAA

CCAACCTA

CCGCACCCA

CCGCA CCG

!CG-CACALAGA

CCTCACACCA

CCG-CACACCA

CCACACTA

CCACATACTG

157 158 138 159 160 161 162 164 165 140 GAACG.TGGTC A&&TCkAAGT GAACGGTC AAATCAAAGT tAACGTGGTC AA&TPAGT WG..TAG CTG9CCTGG TTCTATTACA& CCACACACAA

CG..TAG

CGG..TAG

CTGTCCGGTACTATCAC CCACATACAA CAQM~.TG gTTA2IC M&CAA.

8

S@

0 48 8 088 0 0 8e* S S 8 4 #8 8 8 0 8 8** 8 8 4 *8 88 8 8 8 80* 0 8 8 S 8 8 8 08 8 050 8.8 *85 Streptococcus aga lact ia e streptococcus pneumoniae Ureaplasma urealyti cum Selected sequences' Selected genus-specific primer sequences': AGGAMAI!C gCCGTQGTA CTGTTCGTGT CAA..TTG CTAAAC TTCALATCAAC CCACACACTA AGGACQTC GACCGTGGTA TCGTTAAAGT CAA..TCG CTAAACCA9GQ T AAC CCACACACTA TGGACGTG=G GAACGTGGTG TATTAAAAGT TAA..TTG TAA.AACCAG ATCAATTAAA _TACCGTA CCGTGTT OAACGTOt2TC AAATCAA GCTCCTGG Yh IA YACA CCACAYA SEQ ID NO: 17 CCGTGTT GA.ACGTGGTC AA.ATCAAA SEQ ID NO: 1 8 b TRTGTGGT GTRATWGWRC CAGGAGC The sequence numbering refers to the Saureus tuf gene fragment. Underlined nucleotides are identical to the selected sequence or match that sequence.

"RIO, 'IW" and ,yn designate nucleotide positions which are degenerated. "IR" stands for A or G; for A or T; for C or T.

2 0 b This sequence is the reverse complement of the above tuf sequence.

0 0S 0 oS 6 640 0 .00 00 0 0 0 0 0 6 0 0 00 0 S S 0 0 0 0~0 *6G 00 0 0 S 06 00' 0 0 00 6 0 0 Annex IV: Strategy for the selection from tuf sequences of the amplification primers specific for the species Candida aibicana (continues on pages 59 and 58 90 181 CGTCM&&A GTTI;GIACA ACCC&MA&C TGT CAA ATCCGGTA GTTACTGT 213 SEQ &GACCTTGTT Candida albi cans Can dida gilabrata Can dida krusei Candida parapsilosis Candida tropl calls Schizosaccharomyces pombe Human Chlamydia tz-achoma tis Corynebacterium diph teriae Enterococcus faecalis Escherichia coli cATCAAGAAG GTCggTTACA -AAG TGT CAA

CATCAAGAAG

CGTCA.A GAAG CGTg&&gAA2 CATC&.ACAAt2

GGAGATCCGGC

G3GAGCTGCGC

GGAQATCCRT

GGAAGTTCG;T

GGAAGTTCGT

GTTGGTTAC

GTTGGTTACA

GTTGGTTACA

gXCCjTTTrCA gAGCTOCTA 9AGCTGCTCA

GAGCTGCTCG

9ACTTATTAT gAACTXCTGT

ACCCAAAGAC

ACCCTAAAC

ACCCT&LWC

ACCCCA&LAC

CCGAGTTTGG

GCAAGTACGG

CTGAGCAGGA

CAGAATACGA

CT~rAGTACGA TGT... .CAA TGT... .TAA TGT... .CAA CT. CAA CTA GTT CTT. CAA TTA. GAA

TTT..

GGCTgGTGTC

GGCAGGTGTT

AGC!TGGTAAG

GGCTGGTAAG;

OGT=GTC

AGGCCTGAAG

A~G

GTGQACCCAG

TGAAGAA

GTCAAGGGTA

GTTAAGCCGTA

GTTACC(;T

GTTACCGQTA

GTCAAG-092

TCTGTGCAGA

.TATICTGG

TCCATCATCG

AGAYCTTGTT

AGACCTTATT

AGACCTTGTT

AGACTTTGTT

&AATCTTTT

AGCTACTGGA

AGCTGATGAA

ACCTCATGCA

ID NO 120 121 122 123 124 153 126 132 154 GG9AAGCQ AAAATCTTAG MATTAATGGC AAM.TCCTGG AACTGGCTGG

S..

S

S S S a S S. S 555 Flavobacteri ur ferrugineum Gardnerella vaginal is Haeniophilus influenza e Li st era rnonocytogenes Mi crococcus luteus Neisseria gonorrhoeae Salmonella typhimuri ur Staphylococcus aureus Streptococcus pneurnoniae Treponena pallidum CGAGGTCCC 9AA-QAACTOA CTAAACGCOG GGGTTAAA rAAATZOAAA ACCTGATGGA AGAGGTCCQT !gACCTCCTCG; AAQAAAACGG GGAAGTTCGT 9AACTICTAT GGAAATTCGT GATCTATTAA GGAAG;TCCG;T 9AGTTGCTGG GGAAATCCGC GACCTGCTGT GGAAGTTCGC PAACTGCTGT GGAAQ;TTCGT 9kCTTA-TTAAk GGAAATCCGT GACCTATTGT CTrA&ATATGA

CTGA&TATGA

CTGCCCAGGA

CCAGCTACGA

CTCAGTACGA

GCGATATGA

CTT CAA GIQG.GTAGAG

GGOAAGA-A

GGGAAGCT

ATT. CAA GTGGGTCGAG

ACGAAGAA

GG9AAGCG

CGAAGAA

ACCGTCAAGG AACT.CATGAA AAAATCCTIG ATTAGCAAA AA.AAT19ACG AOTTAATGGA TCTGTCACAC -ATTGATGGA AAAATCTTCG AACTCQCTAC AAA.ATCATCG AACTGGCTGG AAAATCTTAa A.ATTAATGGA 135 157 138 159 162 CAGAATACQA CGA.AGAC ATCGTTATGG AATTGATGAA AGAGGTgCGT GATCCGCTTO CTGGATATGG GTT. GGA GGAT!!CAGCT TGMTTAGG AkACTGCTTGC 169 a. a Selected sequences CAAGAAG GTTQGTTACA ACCA ATCCGGTAA GTTACITGZ AGACC Selected species-specific primer sequences: SEQ ID NO: 11 CAAGAAG GTTGGTTACA ACCCA.AAGA SEQ ID NO: 12' AGGTCTTACC AGTAACTTTAC CGGAT The sequence numbering refers to the Candida albicans. tuf gene fragment. Underlined nucleotides are identical to the selected sequence or match that sequence.

a This sequence is the reverse -complement of the above tuf sequence.

0 0 a Annex V: Bordetella pertussi s Burkholderl a cepaci a Campylobacter jejunl Chlaniydia trachoma tis Clostridiumi perfrl ngen s is Cox-ynebacteriui pseudo tubercul Enterobacter aggi omerans Entferococcus faeciun Escherichia col i Strategy for the selection from the recA gene of the amplification primers specific for the genus Streptococcus (continues on pages 62 and 63).

415 449. .540 574 SE ID NC CTC9&G~ICA CCGACG;CGCT GGTGCGCTCG GGCTC GGCCC GCCTGATGAG CCAGGCGC" CGCAAGCTGA CTCGAAATCA _CCGATGCGCT GGTGCGCTCG GGCTC. GGCCC GCCTGATGTC GCAGGCGCTG CGCAAGCTGA TTAAAITT T~gAACTAX. AGCAAGAAGT GGCGC. AGCAA GACTTATGTC TCAAGCTC2:A AGAAAACTTA TTGAGTATTG CAGACTCfl AGCGCGTTCT GGAGC AGCTC GCATgATGTC GCAGGCTCTA CAAATTAA TTAGAAATAA CAG&GCTTI AGTTAGATCA GGAGC AGCTA GATTAATGTC A CCTTA AGAAAGTTA CTGP-&G=r CAATTGCIT TGTTCGCTCT GGAGC. AGCGC GTTTGATGAG T AGCCTG CGGATGA Osis CTGGAICT GTGAZGCGCT OCCCGTTCA GGCGC. .AGCTC GTATgATGAG C99CA CIG CTTG TTGGATTG CCQAGCCfl AGTTTCAAGT GGTGC AGCTC GACTA T-GTC IC AGCACTA 99-AATTAT CTGqAAATCT GTGACGCCCI gGCGCGTTCT GGCGC. .GGCAC GTA19ATqAG CrAGGT 99-TAGCTGG

Q

9 9 9 9 9 9 9 9. 9 9 9 9 9 Jaemophil us ifl uenzae Hel icobacter pyl orli S Lactococcus lactis Legionella pneumophila Mycoplasma genltalium Neisseria gonorrhoea e Proteus mirabilis Pseudomonas aeruginosa Serra tia marcescens Shigella flexneri Staphylococcus a ureus Streptococcus gzrdQl Streptococcus GCGAACAGAA GLAAGMTT TTAATGCATT ACCGC. GACCT GTGAGTTTAC G-CAMG-TIG AGACATTAA-A TTA9A=T TAACGAI. CACCAGAAGC CTTCAAATT. CTAA&I 9=ACTTCT CTGaAAATTA

TTTOCTCZTA

TTGGAAATCT

CTGGAALATTT

CTGGAAATCA

CTGG;AAATCT

CTGGAAACT

CTTgAAATC~g

TTA-GAAATTG;

gTgATATGCC

TCGAATCATT

GCGACACGCT

GTGAGCM

CC.GACATGCT

GTGATGCGCT

GTGACGCCCI

CAGGAAA.ATT

GG;TGCGTTCT

AATTAAAACA

CGTCCGTTCG

ATCICGCTCT

gGXGCOCTCC

GACCCGCTCC

gGCGCGTTCT

TGTTAGAAGT

GGAGG... .AGCAA GGAGCC.. .AGCAC GCAGC. GGCAA AACAA. .TGCAA GGCGG... GGCGC GGTGC CGCAC AACGC... .GGCAC GGCGC... .GGCGC GGCGC. .GGCAC GGTGC. .AGCTC GGC7.TATGAG

GTATGATGTC

GATTCATGTC

GA.ATGATGTC

GCCTGATGAG

GTATGATGAG

GCCTGATGTC

GCATGATGAG

GTATGATGAG

CCATGCGTTA

ACAAGCCATG

GCkAACCCT(3

AAAAGGTTTG

TCAGGCTTO

CCAAGCTATG

CCACGCCCTG

CCAGGCOATG

CCAGGGATG

AGAA.AAATCA

CGTAACTTG

COTAATTGA

CAAGAATAC

CGCAAACTGA

CC-A-ACTAG

CGCAAGATCA

gCGTAAGCTGG

CGTAAGCTGG

GTTTA-ATGTC Ag&&-GTTA 99MA-ACTTT 32 GATTGACTCT GGGGC CTTGAAATT CAGGGAAflT 9AITTCT GGCGC. AGCAC GCaTGATQ;AG-TCAAGCGT CkTAATTAT 3 3 0 0 a a a a.

V, %G aaa Streptacoccus Stre~tococcus Str-entococcus Vibri o cholerae Yersi n ia pestis Selected sequences*

CTTAGM

CTT9AAATTG

CTCOAAATTG

CTGGAAATTT

CTGGAPIATTT

GAAATTG

CGGGAAAATT

CAOCTAAATT

CAGGTAAGCT

GTGATGCACT.

GTgPITGCGCT!

CAGGIAAATT

GATTGACTCA GGTGC. GGCTC 9ATTGATTCT GGTGC... .AGCAC GATTGACTCT GGTGC. .AGCGC 9GCTCGCTCT GGTGC. .AGCGC GACTCGCTCT GGTGC. CGCGC

GATTGA

GTATGATGAXG CCAGGCCATG GTATGATCAG TCAGGCCATCQ GTAT-GATGAG TCAAGCCATG GTATGTZGTC GCAAAM2 GTATGATGAG C-CAGGCTATG ATGATGAG TCAIGCCATG CGTAAACTTG 3 4 CGTAAATTAT 3 C AACTTT 36 C91AAACTGA

CGTAAGCTGG

CGTAA

Selected SEQ ID NO: 21 SEQ ID NO: 2 2 b genus-specific primer GAPJATTQ; CAGGIAAATT GATTGA TTACGCAT CCCITGACTC ATCAT sequences* The sequence numbering refersto the S.pneumoniae recA sequence. Underlined nucleotides are identical to the selected sequence or match that sequence.

a stands for inosine, which is a nucleotide analog that can bind to any of the four nucleotides A, C, G or T.

b This sequence is the reverse complement of the above recA sequence.

-64- AnneOx VI: Specific and ubiquitous primers for DNA amplification SEQ ID NO Nucleotide sequence Originating DNA fragment SEQ ID Nucleotide NO Position Bacterial species: Enterococcus faecium TTT AGC AAC AGC CTA TCA G ACT TCT TCC GGC ACT TCG 273-294 468- 488 Bacterial Snecies: Listeria monocytogenes GGC TAT AAA TGA AGA GGC CGA TGA TGC TAT GGC TTT 339-359 448- 468 Bacterial Species: Helaseria meningliIi GCG GTA TTG TTT GGT GGT S'-CAG GCG 0CC TTT AAT AAT TTC 56-76 212- 232 a Bacterial species: Staphylococcus saprophyticug 7 AGA TCG AAT TCC ACA TGA AGG TTA TTA TGA 8b TCG CTT CTC CCT CAA CAA TCA AAC TAT CCT Bacterial species: Streptococcus agalactlae 9 5' -TTT CAC CAG CTG TAT TAG AAG TA Job 5' -GTT CCC TGA ACA TTA TCT TTG AT Funcral species: Candida albicann 290-3 19 409-4 38 59-81 190-212 11 5'-CAA GAA GOT TGG TTA CAA CCC AAA GA 1 2 b 5-AGG TCT TAC CAG TAA CTT TAC COG AT 120Oc 61-86 12 0 c 184-209 *Sequences f rom databases.

b These sequences are from the opposite DNA strand of the sequence of the originating fragment given in the Sequence Listing.

C Sequences determined by our group.

Annex VI: Specific and ubiquitous primers for DNA amplification (continues on next page) SEQ ID NO Nucleotide sequence Bacterial Qenus: Enterococcus 13 5'-TAC TGA CAA ACC ATT CAT GAT G 14 d 5'-AAC TTC GTC ACC AAC GCG AAC Originating DNA fragment SEQ ID Nucleotide NO position 131-1 3 4 6'b 319-340 c 1 3 1 1 3 4 ab 410-430c Bacterial genus: Neisseria 5'-CTG GCG CGG TAT GGT CGG TT 16d 5'-GCC GAC GTT GGA AGT GGT AAA G Bacterial genus: Staphylococcus 21-40' 102-123 c

TGT

GTG

ACG

5'-ACC ATT TGA ACG TGG TCA GTG TRA TWG WRC TGG WCA AGT WTT TCW GTA CCT TCT

AAT

CAG

AGC

GGT

140-143', b 140-143 a b 140-143", b 140-1431 b 391-415 9 58 4 6 08g 562-5839 729-7539 Bacterial genus: Streptococcus 21 5'-GAA ATT GCA GGI AAA TTG ATT 22 d 5'-TTA CGC ATG GCI TGA CTC ATC 32-36e 32-36 e 418-440" 547-569" Universal primers 23 5'-ACI KKI ACI GGI GTI GAR ARG TT 24 d 5'-AYR TTI TCI CCI GGC ATI ACC AT 118- 1 4 6 a, 147-1714.e 118-146'.b 147-171-" 4 9 3 5 1 5 i 778-800 1 These sequences were aligned to derive the corresponding primer.

b Cuf sequences determined by our group.

c The nucleotide positions refer to the E. faecalis tuf gene fragment (SEQ ID NO: 132).

d These sequences are from the opposite DNA strand of the sequence of the originating fragment given in the Sequence Listing.

Sequences from databases.

SThe nucleotide positions refer to the N. meningitidis asd gene fragment (SEQ ID NO: 31).

66 gThe nucleotide positions refer to the S. aureus tuf gene fragment (SEQ ID NO: 140).

SThe nucleotide positions refer to the S. pneumoniae recA gene (SEQ ID NO: 34).

nucleotide positions refer to the E. coi tuf gene fragment (SEQ ID NO: 154) -67 Annex VI: Specific and ubiquitous primers for DNA amplification SEQ ID NO Nucleotide sequence Originating DNA fragment SEQ ID Nucleotide NO Position Antibiotic resistance Qrene: bia~, 37 51-CTA TGT GGC GCG GTA TTA TC 38 51-CGC ACT GTT ATC ACT CAT GG 39 51-CTG AAT GAA CCC ATA CCA AA 51-ATC AGC AAT AAA CCA GCC AG Antibiotic resistance gene: bla,,~ 41 51-TTA CCA TGA C ATA ACA C 42 51-CTC ATT CAG TTC COT TTC CC 43 5'-CAG CTG CTG CAG TOG ATO CT 44 5'-CGC TCT OCT TTG TTA TTC CC Antibiotic-resistance azene:- bla., 51-TAC GCC AAC ATC GTG GAA AG 46 51-TTG AAT TTG GCT TCT TCG GT 47 51-GGG ATA CAG AAA CGG GAC AT 25 48 51-TAA ATC TTT TTC AGO CAG CG Antibiotic resistance arene: bla,.

49 S'-GAT OCT TTG AAG GT TTA TTJ 50 b 5'-AAT TTA GTG TGT TTA CAA TG(

S

S

k. TAA G 3 TGA T 110, 110a 686-710 8 02-826 51 53 54 otic resistance acne: bi aZ 5'-ACT TCA ACA CCT GCT GCT TTC 5'-TGA CCA CTT TTA TCA GCA ACC otic resistance ene: aadB 51-GGC AAT AGT TGA AAT OCT CG 51-CAG CTO TTA CAA COG ACT GG otic-resistance ene: aacC1 51-TCT ATG ATC TCG CAG TCT CC 51-ATC GTC ACC GTA ATC TGC TT ilia ilia 5 11-531 66 3-683 56 aSequences from databases.

b These sequences are from the opposite DNA strand of the sequence of the originating fragment given in the sequence Listing.

-68- Annex Vz: Specific and ubiquitous primers for DNA amplification SEQ ID NO Nucleotide sequence Originating DNA fragment SEQ ID Nucleotide No Position Antibiotir ritance ee: aacC 2 57 51-CAT TCT CGA TTG CTT TGC TA 58 51-CCG AAA TGC TTC TCA AGA TA Antibiotic resistance arene: aacC 3 59 51-CTG GAT TAT GGC TAC GGA GT 51-AGC AGT GTG ATG GTA TCC AG Ant ibiotic rezsstance crene: aac6 -I~a 61 51-GAC TCT TGA TGA AGT GCT GG 1128 123-142 6 2 b 51-CTG GTC TAT TCC TCG CAC TC 112a 284-303 63 5'-TAT GAG AAG GCA GGA TTC GT 1126 445-464 64b 5'-GCT TTC TCT CGA AGG CTT GT 112a 522-541 *0 Antibiotic resistance cene: aacA4 9*:65 51-GAG TTG CTG TTC AAT GAT CC 25 66 51-GTG TTT GAA CCA TGT ACA CG *Antibiotic reistance g~ene: aad(G') *173 5'-TCT TTA GCA GAA CAG GAT GAA 174 5'-GAA TAA TrCATA TCC TCC G Antibiotic resistance aCene: vanA 67 51-TGT AGA GGT CTA GCC CGT GT 68 51-ACG GGG ATA ACG ACT GTA TG 69 51-ATA AAG ATG ATA GGC CGG TG 51-TGC TGT CAT ATT GTC TTG CC 40 Antibiotic resistance gene: vanB 71 5'-ATT ATC TTC GGC GGT TGC TC 116a 22-41 7 2 b 51-GAC TAT CGO CTT CCC ATT CC 116a 171-190 73 51-CGA TAG AAG CAG CAG GAC AA 116a 575-594 7 4 b 51-CTG ATG GAT GCG GAA GAT AC 1168 713-732 *Sequences from databases.

bThese sequences are from the opposite DNA strand of the sequence of the originating fragment given in the Sequence Listing.

-69- Annex VI: Specific and ubiquitous primers for DNA amplification SEQ ID NO Nucleotide sequence Originating DNA fragment SEQ ID

NO

Nucleotide Position Ar i hi in t- r~ 0 i Vanc UyUA!-. 51-GCC TTA TGT 7 6 b 5' -GTG ACT 1'TW ATG AAC AAA TGG GTG ATC CCT TTT GA 117' 1178 373-393 541-563 Antibiotic resistance giene: morA 51-TCC AAT CAT TOC CTC TGC ACA AAA TC TAT TTG GTG GT 79 80 5'-TCC CAA GCC AGT AAA GCT AA 5'-TGG TTT TTC AAC TTC TTC CA Antibiotic resistance crene: aatA 81 82 5'-TCA TAG AAT 5'-AGC TAC TAT GGA TGG CTC AA TGC ACC ATC CC 8 8 *8 *8 8 8 8 Antibiotic resistance giene: aac(6')-aph(211) 83 25 84 5 m -CAA TAA GG 5'-CCT TAA CAT CAT ACC AAA AAT C TTG TGG CAT TAT C 5'-TTG OGA AGA TGA AGT TTT TAG A 86 5'-CCT TTA CTC CAA TAA TTT GOC T 30 Antibiotic resistance giene: vat 87 5'-TTT CAT CTA TTC AGG ATG GG B8 5'-GGA GCA ACA TTC TTT GTG AC Antibiotin resistance giene: vga 89 51-TGT GCC TGA AGA AGG TAT TG 51-CGT GTT ACT TCA CCA CCA CT Antibiotic resistance crene: ezmnA 91 51-TAT CTT ATC GTT GAG AAG GGA TT 9 2 b 51-CTA CAC TTG GCT TAG GAT GAA A 113* 370-392 113a 487-508 11 457- ~ne *Sequences from databases.

b These sequences are from the opposite DNA strand of the sequence of the Originating fragment given in the Sequence Listing.

Annex VI: Specific and ubiquitous Pr~imers for DNA amplification SEQ in NO Nucleotide sequence Originating

DNA

fragment SEQ Nucleotide ID UNo Antibiotic resistance caene: ermB 93 51-CTA TCT GAT TGT TGA AGA AGG ATT 1148 9 4 b 5 GTT TAC TCT TGG TTT AGG ATG, AAA 1146 Antibiotic resistancegcene: ermC 5'-CTT OTT GAT CAC GAT AAT TTC C 1158 9 6 b 51 -ATC TTT TAG CAA ACC CGT Arr C 15 Antibiotic resistance gene; mecA 97 5' -AAC AGO TGA ATT ATT AGC ACT TGT AAG 98 S -ATr OCT GTT AAT ATT TTT TGA GTT GAA Antibiotic resistance crene: Int 99 51-GTG ATC GAA ATC CAG ATC C 100 5 1-ATC CTC GGT TTT CTG GAA G 101 51-CTG GTC ATA CAT GTG ATG G 25 102 5'-GAT GTT ACC CGA GAG CTT G Antibioti c resistance gne: sul 103 51-TTA AGC GTG CAT AAT AAG CC 104 51-TTG CGA TTA CTT CGC CAA CT 105 51-TTT ACT AAG CTT GCC CCT TC 106 51-AAA AGO CAG CAA TTA TOA GC kVJ. 1- onJ 366-389 484-507 214-235 382-403 8* a Sequences from databases.

bThese sequences are from the opposite DNA strand of the sequence of the originating fragment given in the Sequence Listing.

,VA

71 SEQUENCE LISTING GENERAL INFORMATION:

APPLICANT:

NAME: INFECTIO DIAGNOSTIC

INC.

STREET: 2050, BOULEVARD RENE LEVESQUE OUEST, 4E ETAGE CITY: STE-FOY STATE: QUEBEC COUNTRY: CANADA POSTAL CODE (ZIP): G1V 2K8 TELEPHONE: (418) 681-4343 TELEFAX: (418) 681-5254 NAME: BERGERON, MICHEL G.

STREET: 2069 RUE BRULARD CITY: SILLERY STATE: QUEBEC COUNTRY: CANADA POSTAL CODE (ZIP): GIT 1G2 NAME: PICARD, FRANCOIS J.

STREET: 1245, RUE DE LA SAPINIERE CITY: CAP-ROUGE STATE: QUEBEC COUNTRY: CANADA S" POSTAL CODE (ZIP): G1Y 1A1 NAME: OUELLETTE, MARC STREET: 1035 DE PLOERMEL CITY: SILLERY STATE: QUEBEC COUNTRY: CANADA POSTAL CODE (ZIP) GlS 3S1 9 NAME: ROY, PAUL H.

STREET: 28, RUE CHARLES GARNIER CITY: LORETTEVILLE STATE: QUEBEC COUNTRY: CANADA 0. POSTAL CODE (ZIP): G2A 3S1 (ii) TITLE OF INVENTION: SPECIES-SPECIFIC, GENIUS-SPECIFIC AND UNIVERSAL DNA PROBES AND AMPLIFICATION PRIMERS TO RAPIDLY DETECT AND IDENTIFY COMMON BACTERIAL AND FUNGAL PATHOGENS AND ASSOCIATED ANTIBIOTIC RESISTANCE GENES (iii) NUMBER OF SEQUENCES: 174 (iv) COMPUTER READABLE FORM: MEDIUM TYPE: Floppy disk COMPUTER: IBM PC compatible OPERATING SYSTEM: PC-DOS/MS-DOS SOFTWARE: PatentIn Release Version #1.30 (EPO) (vi) PRIOR APPLICATION DATA: 72 APPLICATION NUMBER: US 08/743,637 FILING DATE: 04-NOV-1996 INFORMATION FOR SEQ ID NO: 1: SEQUENCE CHARACTERISTICS: LENGTH: 22 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Enterococcus faecium (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 1: TGCTTTAGCA ACAGCCTATC AG 22 INFORMATION FOR SEQ ID NO: 2: SEQUENCE CHARACTERISTICS: LENGTH: 21 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Enterococcus faecium (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 2: TAAACTTCTT CCGGCACTTC G 21 INFORMATION FOR SEQ ID NO: 3: SEQUENCE CHARACTERISTICS: LENGTH: 21 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Listeria monocytogenes (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 3: TGCGGCTATA AATGAAGAGG C 21 INFORMATION FOR SEQ ID NO: 4: 73 SEQUENCE CHARACTERISTICS: LENGTH: 21 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Listeria monocytogenes (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 4: ATCCGATGAT GCTATGGCTT T 21 INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 21 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Neisseria meningitidis oo, (xi) SEQUENCE DESCRIPTION: SEQ ID NO: CCAGCGGTAT TGTTTGGTGG T 21 INFORMATION FOR SEQ ID NO: 6: SEQUENCE CHARACTERISTICS: LENGTH: 21 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Neisseria meningitidis (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 6: CAGGCGGCCT TTAATAATTT C 21 INFORMATION FOR SEQ ID NO: 7: SEQUENCE CHARACTERISTICS: LENGTH: 30 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear 74 (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Staphylococcus saprophyticus (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 7: AGATCGAATT CCACATGAAG GTTATTATGA INFORMATION FOR SEQ ID NO: 8: SEQUENCE CHARACTERISTICS: LENGTH: 30 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Staphylococcus saprophyticus o* (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 8: TCGCTTCTCC CTCAACAATC AAACTATCCT 30 0 INFORMATION FOR SEQ ID NO: 9: SEQUENCE CHARACTERISTICS: LENGTH: 23 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL

SOURCE:

ORGANISM: Streptococcus agalacciae (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 9: TTTCACCAGC TGTATTAGAA GTA 23 INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 23 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Streptococcus agalactiae 75 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: GTTCCCTGAA CATTATCTTT GAT 23 INFORMATION FOR SEQ ID NO: 11: SEQUENCE CHARACTERISTICS: LENGTH: 26 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Candida albicans (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 11: CAAGAAGGTT GGTTACAACC CAAAGA 26 INFORMATION FOR SEQ ID NO: 12: SEQUENCE CHARACTERISTICS: LENGTH: 26 base pairs TYPE: nucleic acid o(C) STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Candida albicans (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 12: AGGTCTTACC AGTAACTTTA CCGGAT 26 INFORMATION FOR SEQ ID NO: 13: SEQUENCE CHARACTERISTICS: LENGTH: 22 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 13: TACTGACAAA CCATTCATGA TG 22 INFORMATION FOR SEQ ID NO: 14: SEQUENCE CHARACTERISTICS: LENGTH: 21 base pairs 76 TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 14: AACTTCGTCA CCAACGCGAA C 21 INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: CTGGCGCGGT ATGGTCGGTT INFORMATION FOR SEQ ID NO: 16: SEQUENCE CHARACTERISTICS: LENGTH: 22 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) a (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 16: GCCGACGTTG GAAGTGGTAA AG 22 INFORMATION FOR SEQ ID NO: 17: SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 17: CCGTGTTGAA CGTGGTCAAA TCAAA INFORMATION FOR SEQ ID NO: 18: SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs 1. .4 77 TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 18: TRTGTGGTGT RATWGWRCCA GGAGC INFORMATION FOR SEQ ID NO: 19: SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 19: ACAACGTGGW CAAGTWTTAG CWGCT INFORMATION FOR SEQ ID NO: S(i) SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: ACCATTTCWG TACCTTCTGG TAAGT INFORMATION FOR SEQ ID NO: 21: -SEQUENCE CHARACTERISTICS: LENGTH: 23 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (ix) FEATURE: NAME/KEY: misc_feature LOCATION:12 OTHER INFORMATION:/note- "n inosine" (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 21: GAAATTGCAG GNAAATTGAT TGA

C.

C.

78 INFORMATION FOR SEQ ID NO: 22: Ci) SEQUENCE CHARACTERISTICS: LENGTH: 23 base pairs TYPE: nucleic acid STRAINDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (ix) FEATURE: NAME/KEY: misc-feature LOCATION:12 OTHER INFORMATION: /note= 'n inosine"l (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 22: TTACGCATGG CNTGACTCAT CAT INFORMATION FOR SEQ ID NO: 23: Ci) SEQUENCE CHARACTERISTICS: LENGTH: 23 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (ix) FEATURE: NAME/KEY: misc-feature LOCATION:3 OTHER INFORMATION:/note- On =inosine"f (ix) FEATURE: NAME/KEY: misc-feature LOCATION:6 OTHER INFORMATION:/note= On inosinell (ix) FEATURE: NAME/KEY: misc-feature LOCATION:9 OTHER INFORMATION:/note= "n inosixe" (ix) FEATURE: NAME/KEY: misc-feature LOCATION:12 OTHER INFOR.MATION:-/note= 'In inosinell (ix) FEATURE: NAME/KEY: misc-feature LOCATION:lS OTHER INFORMATION:/notea 'In Im inosine" (xSEQUENCE DESCRIPTION: SEQ ID NO: 23: 79 ACNKKNACNG GNGTNGARAT GTT 23 INFORMATION FOR SEQ ID NO: 24: SEQUENCE CHARACTERISTICS: LENGTH: 23 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (ix) FEATURE: NAME/KEY: miscfeature LOCATION:6 OTHER INFORMATION:/note= "n inosine" (ix) FEATURE: NAME/KEY: misc_feature LOCATION:9 OTHER INFORMATION:/note= "n inosine" (ix) FEATURE: NAME/KEY: miscfeature LOCATION:12 OTHER INFORMATION:/note= "n inosine" (ix) FEATURE: NAME/KEY: misc feature LOCATION:18 OTHER INFORMATION:/note= "n inosine" (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 24: AYRTTNTCNC CNGGCATNAC CAT 23 INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 10 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: TCGCTTCTCC INFORMATION FOR SEQ ID NO: 26: SEQUENCE CHARACTERISTICS: LENGTH: 600 base pairs TYPE: nucleic acid STRANDEDNESS: double 80 TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Enterococcus faecium (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 26: TTCTTAGAGA

CATTGAATAT

ATGGATAAAA

GTACCAGTAC

GGTTCTTTGC

ACAAAGGCAG

TCTCGAGCA.

AATGAAGATG

TATGAAGCCA

GAAGTTTATC

GGATTGAGCC

TCATGACCAA

TTAAGAATCA

TTTATCCGAT

AAAACCGAGA

TCGTTGA.ACA

TTCGGACGAC

AATATATCAA

AAAAAGCGCA

GCCTTATGTC GGCGCAGGC!G TATTGACCAG GTATATTTTA CAAGCTGCTG GTGTGCCGCA ATGGAAAGAA AATCCTAAAA AAGTATTTGA GTTTGTCAAA CCTGCGAATA. TGGGTTCTAG AGAGCTGCAA AATGCTTTAG CAACAGCCTA AGGAATTGAA GCGCGCGAAA TCGAAGTTGC TTTGCCTGGC GAAGTCGTAA AAGACGTAGC TAATAAAATC GAAATGCAGA TTCCAGCCGA AGAGTACGCG AAGTTAGCTT ACACGATGTT

TGCATGTGCC

AGTTCCTTAT

TCAATGTGAA

TGTCGGCATT

TCAGTATGAT

TGTATTAGGA

ATTCTATGAT

AGTGCCGGA.A

AGGTGGAAGC

GGTGCGXT CTTTTTGACA AATAAAAATG AATTATTCCT GAATGAATTA INFORMATION FOR SEQ ID NO: 27: Wi SEQUENCE CHARACTERISTICS: LENGTH: 1920 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genornic) (vi) ORIGINAL SOURCE: ORGANISM: Listeria monocytogenes (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 27: GTGGGATTAA ACAGATTTAT GCGTGCGATG ATGGTGGTTT TCATTAC-TGC CAATTGCATT ACGATTAACC CCGACATAAT ATTTGCAGCG ACAGATAGCG AAGATTCTAG TCTAAACACA GATGAATGGG AAGAAGAAAA AACAGAAGAG CAACCAAGCG AGGTAAATAC GGGACCAAGA, TACGAAACTG CACGTGAAGT AAGTTCACGT GATATTAAAG AACTAGAAAA ATCGAATAAA GTGAGAAATA CGAACAAAGC AGACCTAATA GCAATGTTGA AAGAAAAAGC

AGAAAAAGGT

CCAAATATCA ATAATAACAA CAGTGAACAA ACTGAGAATG CGGCTATAAA TGAAGAGC 81 a

SS~

TCAGGAGCCG

AGCGCAGCGG

AGCCTTACTT

GTTGCGGATG

CCACAACCTT

GATGCGGGGA

GTTGATAAAA

AATGCTTCGG

ACACCAATGC

CCACCACCAC

GGTTTTAATG

GAAGATGAAC

GGGGATTTAG

CCACCAATCC

TTTAGTTCGC

GAAATTGATC

GGTTTTTTAC

TCGAAAATAA

CCATCACAGC

CCAACCCCTG

ACCGTACTTA

TCAATTAATA

GAAATGAAAC

AACGGAAAAA

GACGAAAAAG

ACCGACCAGC TATACAAGTG AAATTAAAAA AAGAAGGAAA ATCCGGATAA ACCAACAAAA CTTCTGAAAG TGACTTAGAT

TAAAAGCAAA

AATGGGTACG

GTGCAGGGTT

ACTTCCCGCC

TTCTTGGTTT

CTACGGATGA

CTCCTGCTAC

TAGAAATCAT

CTAGTTTGAG

CAACAGAAGA

TGAATAGTGG

GCCTAGCTGA

CATTAAATCC

GCGACCGGGC

CATTAAATGT

TAAAGACCGC

GGGAAAATAR

TGCCGAGCCT

CACAAACCGA

ATCGTTCTGC

CGAAGGAAGA

CCAACAACCA

TGATAAAATC

AATTGACCAA

ACCACCTACG

TAATGCTCCT

AGAGTTAAGA

ATCGGAACCG

CCGGGAAACA

AAATGCTATT

AGAGTTGAAC

TGATTTTACA

TTTAAGAGAT

GTTTGCTAGC

TCTGATAAGT

GTTTAATAAA

ACCAAAGCTA

AACACCCT1TT

ACCAGTAATC

GGAAAAAATG

TGGCATTGAA

ACCAGGGAAC

GATGAAGAGT

GCTACATCAG

CTTGCTTTGC

AGCTCGTTCG

GCATCCTCGC

AATCGCCATA

GGGAGAGGCG

GATGACGAAA

AGAGGAACAG

AGCCCGGTTC

GACATAACTA

AAAACTACAA

GCAGAACTTC

ATAGAAAAAC

CAAAAAGAAG

GTAGAGGAAA

GAAGGAAAAC

CATACGACGT

TAAGACTTGC

AACCGAGCTC

CAGAGACGCC

AATTTCCACC

TAGATTCTAG

GTCAAAATT

GTAGACCAAC

ACAGCGAGAC

GAAAACACTC

CTTCGTTAAG

AAAAAACGCC

CGAAAAC-AGT

CTGCCACAAA

AAGCAGAAAC

CTACAGAGAG

GCGAATCAC

TAATTGCTAA

TAATTCTTGC

GAGCGTCGTC ATCCAGGATT GCCATAGCAT CATCGGATAG GTAAATAAGA AAAAAGTGGC TCTAGCATGC AGTCAGCAGA TTTTTCCCTA. AAGTATTTAA GACGAAAAfrC CTGAAGTAAA TTATTAACCA AAAAGAAAAG

GCCATCGGAT

TGAGCTTGAA

GAAAGAGTCA

TGAGTCTTCA

AAAAATAAAA

GAAAGCGATT

TGAAGAGGTA

TTTGCCAGAG

ATTCGAATTT

AATCCTTCTT

GCCTCCAACA

TTTTACAAGA

CTCTGATTTC

ATCTGAAGAA

AACAGAAGAA

AAGAAATGCG

TCCAA.AGGTA

ATTTAAGAAT

GACTAAAAAA

ACCACAAGAA

AAACAAGCAG

CGATAAAGAG

TAATAACCCA

AAGTGCAGAA

AATGTTAGCT

420 480 600 660 720 780 840 900 960 1020 1080 1140 1200 1260 1320 1380 1440 1500' 1560 1620 1680 1740 1800 1860 1920 ATTGGCGTGT TCTCTTTAGG GGCGTTTATC AAAATTATTc AATTAAGAAA AAATAATTAA INFORMATION FOR SEQ ID NO: 28: Mi SEQUENCE CHARACTERISTICS: LENGTH: 415 base pairs 82

C.

TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Nelaseria merlingitidis (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 28: TACCGGTACG CTAAATATTG GTGATGTATT GGATATTATG ATTTGGGAAG GGTATTGTTT GGTGGTGGCC TTTCTTCGAT GGGCTCGGGT AGTGCGCAAC GCCGGAGCAA CTGGTGACGG CACGTGGTAC GGTTTCTGTG CCGTTTGTTG GGTGGTCGGT AAAACGCCTG GTCAGGTTCA GGAAATTATT AAAGGCCCCC GGCCAATCAG CCGCAAGTGA TGGTGCGCTT GGTGCAGAAT AATGCGGCAA GATTCGCGCA GGCAATAGTG TGCGTATGCC GTTGACGGCA GCCGGTGAGC TGCGGTGGCT GCGGTAGGTG GTTCAACGGC AAATGTGCAG GATACGAATG INFORMATION FOR SEQ ID NO: 29: Wi SEQUENCE CHARACTERISTICS: LENGTH: 438 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Staphylococcus saprophyti cus (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 29: TCGCTTCTCC AGAAGAAATT TTAGAAACAT ATCTAGAAAA TCCCAAATTA TTATATTATG TGAATACGCA CATGCAATGG GAAATTCACC AGGAGATCTT AAACATTAAT TGAAAAATAT GATAGTTTTA TTGGCGGTTT TGTTTGGGAA ATAGCATTCA GGTTGGGATA AAGGAAGGTA AACCAATTTT TAGATATGGT GTGAGGCCTT ACATGACGGT AATTTTTGTG TTGATGGTAT TGTTTCGCCA CACATGAAGG TTATTATGAG TTTAAACATG AACATAGACC TTTGAGATTG AGGATTATCG GTTTACATTG AAGAATCAAT TTGATTTTAC AAATGCGGAG TTGTTGAGGG

AGAAGCGA

CGCCGCCAGC

AAACCAAGTT

GCGATATTTC

TGAAAAAAAT

ATGTATCGGT

GTGTGTTGGA

TGCAG

GATAAACCGT

AATGCATATC

TGGTGTGATC

GGAGATTTTG

GATCGAATTC

GTTAACGAAG

GATAGTTI'GA

120 160 240 300 360 415 120 180 240 300 360 420 438 83 C2) INFORMATION FOR SEQ ID NO: WI SEQUENCE CHARACTERISTICS: LENGTH: 768 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Streptococcus agalactiae (xi) SEQUENCE DESCRIPTION: SEQ ID NO: ATGAACGTrA CACATATGAT GTATCTATCT GGAACTCTAG TGGCTGGTGC ATTGTTATTT 4* 4

TCACCAGCTG

GTAAATAGTA

TTGAGAAATA

ATTACTAGCG

TTGAATTCTA

TCAACTCAAC

ACTAAGCTAG

GTTAACGATG

GATAGAGCTA

ACTAGAGATA

GCAATCACAC

TATTAGAAGT

ATAATCAAGC

TCAAAGATAA

TGGAAAAATT

TTGGTAGTCG

ATTTAACAAA

TTATTCGCAT

TAAAGGCATT

CCATCTATAC

AAAAAGTACT

ATGCTGTTGG

ACATGCTGAT

CCAGCAAATG

TGTTCAGGGA

AAAGACTTCA

TGTAGAAGCC

TAAGGTTAGT

TTTAGATCCA

AGAACAAAAA

AAAATCAAAA

TAACGTCAAA

AGTTCAGTTG

CAAGTGACAA

GCTCAAAAC

ACAGATTATG

TTGCGTGCCA.

TTAACAGATG

CAAGCAAATA

TTTGCTTCAG

GTTTTAAC!TT

CTTGATAAGG

GAATTTAAAG

AATCCAAA.TG

CTCCACAAGT

TTGATCAAGA

AAAAACCGGT

ACCCTGAGAC

TGATTGAAGC

TTGATATGGG

TTGATTCAAT

ATCCTGATTT

AAATCTGGAA

TTTACAATAC

TTACGGTACA

GGTAAATCAT

TAGCATTCAG

TAATGAGGCT

AGTTTATGAT

AATCACTTTT

ATTTGGGATA

TAAAGCTCAA

AAAACCAACT

TACACGCTTT

TTTAAATAA.A

ACAAGTTGAT

120 180 240 300 360 420 480 540 600 660 720 CAAGAGATTG TAACATTAC.A AGCAGCACTT CAAACAGCAT TAAAATAA INFORMATION FOR SEQ ID NO: 31: Wi SEQUENCE CHARACTERISTICS: LENGTH: 421 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Neisserla meningitidis (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 31: 84

ATGAAAGTAG

AAAGAAGAAA

GGCGGCGCAC

GCCGAGCTGG

GTCTTCCAAG

CTGCGTATGA

AACGGCCTCA

GTTTCGTCGG

ACGACTTCGC

GCCCTGATTT

CAAAAATGGA

CCCTGCGCGA

AAGACGACGC

AAAACGGCGT

C TGGCGCGGT

CCACATTCCC

CGGTCAGGCG

CATCATCGTT

CAGCGGCTGG

GATTATCGTC

GAAAAACTAC

ATGGTCGGTT CGGTTTTGAT GAAGCGTTTT TCTTTACCAC GCTAAAACAT TATTGGACGC ACCTGCCAAG GCGGCGACTA AACGGCTACT GGATTGACGC CTCGACCCCG TCAACCGCAA ATCGGCGGCA ACTGTACCGT

GCAGCGTATG

TTCCAACGTC

GAACAACGTT

CACCAAATCC

GGCATCCTCG

CGTCATCGAC

TTCCCTGATG

120 180 240 300 360.

420 421 INFORMATION FOR SEQ ID NO: 32: Wi SEQUENCE CHARACTERISTICS: LENGTH: 213 base pairs TYPE: nucleic acid STR.ANDEDNESS: double TOPOLOGY: linear (iMOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Streptococcus gordonli (Xi) SEQUENCE DESCRIPTION: SEQ ID NO: 32: TTCATAGACG CTGAGCACGC TTTGGATCCA TCTTACGCGG CTGCTCTAGG TGTAAATATT GATGAGCTGT TGCTATCTCA ACCAGATTCT GGTGAGCAAG GTTTAGAAAT TGCAGGAAAA TTGATTGACT CTGGGGCAGT TGATTTAGTT GTCATCGACT CTGTTGCAGC TCTTGTACCA.

CGTGCGGAAA TCGATGGAGA TATCGGTGAT AGC INFORMATION FOR SEQ ID NO: 33: Wi SEQUENCE CHARACTERISTICS: LENGTH: 692 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genotnic) (vi) ORIGINAL SOURCE: ORGANISM: Streptococcus mutans (xi) SEQUENCE DESCRIPTIO1N: SEQ ID NO: 33: GGGCCGGAAT CTTCTGGTAA GACAACTGTC GCTCTTCATG CTGCTGCTCA GGCGCAAAAA 85

GATGGCGGTA

GCTCTTGGCG

CTTGAA.ATTG

GTGGCAGCTT

TTACAAGCAC

AAAACCATTG

CCAGAAAcAA,

CGCGGCAATA

ACCAAAATTA

ATTATATATG

TTGCCGCTTT

TTAATATTGA

CAGGGAAATT

TAGTACCACG

GCATGATGAG

CTATTTTTAT

CCCCTGGCGG

CTCAAATTAA

AAGTTGTTAA

GTGAAGGCAT

CATTGATGCA

TGAGCTTTTG

GATTGATTCT

TGCGGAGATT

TCAAGCGATG

TAATCAATTG

GCGTGCCTTG

AGGAACCGGG

AAATAA.AGTT

TTCTCGTACA

GAACATG CCC CTTTCACAAc

GGCGCTGTTG

GACGGAGATA

CGTAAATTAT

CGGGAAAAAG

AAGTTTTATT

GAACAAAAAG

GCTCCACCAT

GGTGAATTAG

TTGATCCAGC

CAGATTCAGG

ATTTAGTTGT

TTGGTA.ATAG

CAGCTTCAAT

TTGGTATT'AT

CTTCTGTGCG

ACAGCAATAT

TTAAGG;AAGC

TTAAGATTGC

CTATGCTGCT

AGAACAGGGT

TGTTGACTCA

TCATGTTGGC

CAATAAAACA

GTTTGGTAAT

TCTTGATGTC

TGGTAAAGAG

TTTTGTAGAA

CAGTGATTTG

120 180 240 300 360 420 480 540 600 660 GGAATTATCC AAAAAGCTGG AGCTTGGTAC TC INFORMATION FOR SEQ ID NO0: 34: Wi SEQUENCE CHARACTERISTICS: LENGTH: 1204-base pairs TYPE: nucleic acid STRANDfEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Streptococcus pnewnoniae SEQUENCE D)ESCRIPTION: SEQ ID NO0: 34: ATGGCGAAAA AACCAAAA ATTAGAAGAA. ATTTCAAAAA AATTTGGGGC

AAGGCCTTGA

CGTTTGGGTG

GACATTGCC

GAGTCATCTG

GGGATTGCTG

GGTGTCAATA

ATTGCGGGAA

GCCCTTGTTC

ATGACGCTCT TAAATTGATT AACGTGCGGA GCAAAAGGTG TTGGCTCAGG TGGTTATCCT GTAAGACAC GGTTGCCCTT CCTTTATCGA TGCGGAACAT TTGACGAATT GCTCTTGTCT AATTGATTGA CTCAGGTGCA CTCGTGCGGA

AATTGATGGA

GAGAAAGACT

CAAGTGATGA

AAGGGACGTA

CATGCAGTTG

GCCCTTGATC

CAACCAGACT

GTTGATCTTG

GATATCGGAG

TTGGTAAAGG

GCTCAGGTTC

TCATCGAAAT

C!ACAAGCGCA

CAGCTTATGC

CAGGAGACCA

TCGTAGTCGA

ATAGCC!ATGT

AGAACGTGAA

ATCAATCATG

TTTAGCTCT

CTATGGCCCA

AAAAGAAGGT

TGCGGCCCTT

AGGTCTTGAG

CTCAGTTGCT

TGGTTTGCAG

120 180 240 300 360 420 480 540 GCTCGTATGA TGAGCCAGGC CATGCGTA CTTGGCGCCT CTATCAATAA AACCAAAACA 86 ATTGCCATT'r

ACAACACCGG

AATACACAAA

ATTAAGGTTG

TACGGAGAAG

ATCAAAAAAG

AATGCTAAGA

CGTTCTAAAT

AAAGATGAC

GAACTTGA;A

TCGA

TTATCAACCA

GCGGACGTGC

TTAAGGGAAC

TAAAAAATAA

GAATTTCTAA

CAGGGGCTTG

AATACTTGGC

TTGGCTTGAT

CAAAGAAAGA

TCGAAATTGA

ATTGCGTGAA

TTTGAAATTC

TGGTGATCAA

GGTAGCTCCA

GACTGGTGAG

GTATTCTTAC

AGAGCACCCA

TGATGGAGAA

AGAAGCAGTG

AGAATAAGCT

AAAGTTGGAG

TATGCTTCAG

AAAGAAACCA

CCGTTTAAGG

CTTTTGAAGA

AAAGATGAAA

GAAATCTTTG

GAAGTTTCAG

AATGAAGAAG

GTTAAAGCAG

TGATGTTTGG

TCCOCTTGGA

ATGTCGGTAA

AAGCCGTAGT

TTGCAAGCGA

AAATTGGGCA

ATGAXATTGA

AACAAGATAC

TTCCGCTGA

TGGAGAAATC

AAATCCAGAA

TGTTCGTGGT

AGAAACTAAG

TGAAATTATG

TTTGGATATT

AGGTTCTGAG

TAAGCAAGTC

TGAAAACAAA

CTTAGGCGAT

CGCTACTTTT

660 720 780 840 900 960 1020 1080 1140 1200 1204 INFORMATION FOR SEQ ID NO: Wi SEQUENCE CHARACTERISTICS: LENGTH: 981 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genornic) (vi) ORIGINAL SOURCE: ORGANISM: Streptococcus pyogenes (xi) SEQUENCE DESCRIPTION: SEQ ID NO: ATGCGTTCAG GAAGTCTAGC TCTTGATATT GCTTGGATAG CTGGTGGTTA TCCTAAAGGA

CGTATCATCG

GTAGCACAAG

GATCCAGCTT

GATTCTGGAG

CTGGTTCTTG

GGCGATAGCC

GCTTCTATTA

GGTGTGATGT

TCTGTTCGGC

AAATCTATGG

CTCAAAAAGA

ATGCTGCTGC

AACAAGGACT

TCGATTCAGT

ATGTCGGATT

ATAAAACAAA

TTGGAAATCC

TGGATGTGCG

TCCAGAGTCT

AGGTGGAATC

GCTTGGGGTT

TGAAATTGCA

AGCAGCTTTA

GCAAGCACGT

AACTATCGCA

TGAAACAACA

TGGAAACAAC

TCCGGTA.AAA CGACTGTGGC GCAGCC?1'TA TCGATGCCGA AATATTGATG AACTTCTCTT GGTAAATTGA TTGATTCTGG GTGCCACGTG CTGAXATTGA ATGATGAGTC AGGCC!ATGCG ATCTTTATCA ACCAATTGCG CCAGGTGGTC GAGCTTTGAA CAAATTAAAG GAACTGGTGA

TTTACATGCT

GCATGCGCTT

GTCTCAACCA

TGCGGTTGAC

TGGTGATATT

TAAATTATCA

TGAAAAAGTT

ATTCTATGCT

CCAAAAGATA

87 GCCAGCATTG GTAAGGAGAC CAAAATCAAG GTTGTTAAAA ACAAGGTCGC TCCGCCATTT 660 AAGGTAGCAG AAGTTGAAAT CATGTATGGG GAAGGTATTT CTCGTACAGG GGAGCTTGTG 720 AAAATTGCTT CTGATTTGGA CATTATCCAA AAAGCAGGTG CTTGGTTCTC TTATAATGGT 780 GAGAAGATTG GCCAAGGTTC TGAAAATGCT AAGCGTTATT TGGCCGATCA TCCACAATTG 840 TTTGATGAAA TCGACCGTAA AGTACGTGTT AAATTTGGTT TGCTTGAAGA AAGCGAAGAA 900 GAATCTGCTA TGGCAGTAGC ATCAGAAGAA ACCGATGATC TTGCTTTAGA TTTAGATAAT 960 GGTATTGAAA TTGAAGATTA A 981 INFORMATION FOR SEQ ID NO: 36: Wi SEQUENCE CHARACTERISTICS: LENGTH: 312 base pairs TYPE: nucleic acid STRA1NDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Streptococcus salivarius (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 36: GCGTATGCAC GAGCTCTAGG TGTTAATATC GATGAGCTTC TTTTGTCGCA. GCCTGATTCT GGTGAGCAAG GTCTCGAAAT TGCAGGTAAG CTGATTGACT CTGGTGCAGT GGATTTAGTT 120 GTTGTTGACT CAGTTGCGGC CTTCGTACCA CGTGCAGAAA TTGATGGAGA TAGTGGTGAC 180 AGTCATGTAG GACTTCAAGC GCGTATGATG AGTCAAGCCA TGCGTAAACT TCTGCATCT 240 ATTAATAAAA CAAAAACGAT TGCTATCTTT AT1'AACCAGT TGCGTGAAAA AGTTGGTATC 300 ATGTTTGGTA AC 312 INFORMATION FOR SEQ ID NO: 37: Ci) SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 37: CTATGTGGC!G CGGTATTATc INFORMATION FOR SEQ ID NO: 38: 88 SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 38: CGCAGTGTTA TCACTCATGG INFORMATION FOR SEQ ID NO: 39: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 39: e S CTGAATGAAG CCATACCAAA INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: ATCAGCAATA AACCAGCCAG INFORMATION FOR SEQ ID NO: 41: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 41: TTACCATGAG CGATAACAGC INFORMATION FOR SEQ ID NO: 42: 89 SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 42: CTCATTCAGT TCCGTTTCCC INFORMATION FOR SEQ ID NO: 43: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) SEQUENCE DESCRIPTION: SEQ ID NO: 43: CAGCTGCTGC AGTGGATGGT 9 S INFORMATION FOR SEQ ID NO: 44: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 44: *9 CGCTCTGCTT TGTTATTCGG INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: TACGCCAACA TCGTGGAAAG INFORMATION FOR SEQ ID NO: 46: 90 SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 46: TTGAATTTGG CTTCTTCGGT INFORMATION FOR SEQ ID NO: 47: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 47: GGGATACAGA AACGGGACAT INFORMATION FOR SEQ ID NO: 48: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 48: TAAATCTTTT TCAGGCAGCG INFORMATION FOR SEQ ID NO: 49: SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 49: GATGGTTTGA AGGGTTTATT ATAAG INFORMATION FOR SEQ ID NO: 91 SEQUENCE CHARACTERISTICS: LENGTH: 25 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: AATTTAGTGT GTTTAGAATG GTGAT INFORMATION FOR SEQ ID NO: 51: SEQUENCE CHARACTERISTICS: LENGTH: 21 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 51: ACTTCAACAC CTGCTGCTTT C 21 INFORMATION FOR SEQ ID NO: 52: SEQUENCE CHARACTERISTICS: LENGTH: 21 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 52: 0*00o0 TGACCACTTT TATCAGCAAC C 21 INFORMATION FOR SEQ ID NO: 53: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 53: GGCAATAGTT GAAATGCTCG INFORMATION FOR SEQ ID NO: 54: 92 SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 54; CAGCTGTTAC AACGGACTGG INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: TCTATGATCT CGCAGTCTCC INFORMATION FOR SEQ ID NO: 56: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) .SEQUENCE DESCRIPTION: SEQ ID NO: 56: ATCGTCACCG TAATCTGCTT INFORMATION FOR SEQ ID NO: 57: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 57: CATTCTCGAT TGCTTTGCTA INFORMATION FOR SEQ ID NO: 58: 93 SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 58: CCGAAATGCT TCTCAAGATA INFORMATION FOR SEQ ID NO: 59: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 59: S CTGGATTATG GCTACGGAGT S. INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: AGCAGTGTGA TGGTATCCAG INFORMATION FOR SEQ ID NO: 61: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 61: GACTCTTGAT GAAGTGCTGG INFORMATION FOR SEQ ID NO: 62: 94 SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 62: CTGGTCTATT CCTCGCACTC INFORMATION FOR SEQ ID NO: 63: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 63: S TATGAGAAGG CAGGATTCGT INFORMATION FOR SEQ ID NO: 64: :o SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 64: S GCTTTCTCTC GAAGGCTTGT INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: GAGTTGCTGT TCAATGATCC INFORMATION FOR SEQ ID NO: 66: f 95 SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 66: GTGTTTGAAC CATGTACACG INFORMATION FOR SEQ ID NO: 67: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 67: TGTAGAGGTC TAGCCCGTGT INFORMATION FOR SEQ ID NO: 68: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear S(ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 68: ACGGGGATAA CGACTGTATG

C

INFORMATION FOR SEQ ID NO: 69: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 69: ATAAAGATGA TAGGCCGGTG INFORMATION FOR SEQ ID NO: 96 SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: TGCTGTCATA TTGTCTTGCC INFORMATION FOR SEQ ID NO: 71: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 71: S ATTATCTTCG GCGGTTGCTC INFORMATION FOR SEQ ID NO: 72: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 72: GACTATCGGC TTCCCATTCC INFORMATION FOR SEQ ID NO: 73: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 73: CGATAGAAGC AGCAGGACAA INFORMATION FOR SEQ ID NO: 74: 97 SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 74: CTGATGGATG CGGAAGATAC INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 21 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: GCCTTATGTA TGAACAAATG G 21 S INFORMATION FOR SEQ ID NO: 76: SEQUENCE CHARACTERISTICS: LENGTH: 23 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 76: SGTGACTTTWG TGATCCCTTT TGA 23 INFORMATION FOR SEQ ID NO: 77: i) SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 77: TCCAATCATT GCACAAAATC INFORMATION FOR SEQ ID NO: 78: 98 SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) 9 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 78: AATTCCCTCT ATTTGGTGGT INFORMATION FOR SEQ ID NO: 79: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 79: TCCCAAGCCA GTAAAGCTAA INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs (BI TVPE. nlepic arid STRANDEDNESS: single TOPOLOGY: linear (ii).MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: S TGGTTTTTCA ACTTCTTCCA INFORMATION FOR SEQ ID NO: 81: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 81: TCATAGAATG GATGGCTCAA INFORMATION FOR SEQ ID NO: 82: 0 99 SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 82: AGCTACTATT GCACCATCCC INFORMATION FOR SEQ ID NO: 83: SEQUENCE CHARACTERISTICS: LENGTH: 22 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 83: CAATAAGGGC ATACCAAAAA TC 22 INFORMATION FOR SEQ ID NO: 84: SEQUENCE CHARACTERISTICS: .o LENGTH: 22 base pairs I) T C *A licA a c JA STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 84: S CCTTAACATT TGTGGCATTA TC 22 INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 22 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: TTGGGAAGAT GAAGTTTTTA GA 22 INFORMATION FOR SEQ ID NO: 86: 100 SEQUENCE CHARACTERISTICS: LENGTH: 22 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 86: CCTTTACTCC AATAATTTGG CT 22 INFORMATION FOR SEQ ID NO: 87: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 87: S TTTCATCTAT TCAGGATGGG S INFORMATION FOR SEQ ID NO: 88: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 88: S GGAGCAACAT TCTTTGTGAC INFORMATION FOR SEQ ID NO: 89: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 89: TGTGCCTGAA GAAGGTATTG INFORMATION FOR SEQ ID NO: 101 SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: CGTGTTACTT CACCACCACT INFORMATION FOR SEQ ID NO: 91: SEQUENCE CHARACTERISTICS: LENGTH: 23 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 91: TATCTTATCG TTGAGAAGGG ATT 23 S INFORMATION FOR SEQ ID NO: 92: SEQUENCE CHARACTERISTICS: LENGTH: 22 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 92: CTACACTTGG CTTAGGATGA AA 22 S INFORMATION FOR SEQ ID NO: 93: SEQUENCE CHARACTERISTICS: LENGTH: 24 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 93: CTATCTGATT GTTGAAGAAG GATT 24 INFORMATION FOR SEQ ID NO: 94: 102 SEQUENCE CHARACTERISTICS: LENGTH: 24 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 94: GTTTACTCTT GGTTTAGGAT GAAA 24 INFORMATION FOR SEQ ID NO: SEQUENCE CHARACTERISTICS: LENGTH: 22 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: CTTGTTGATC ACGATAATTT CC 22 S INFORMATION FOR SEQ ID NO: 96: oo SEQUENCE CHARACTERISTICS: LENGTH: 22 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear S(ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 96: ATCTTTTAGC AAACCCGTAT TC 22 oo INFORMATION FOR SEQ ID NO: 97: SEQUENCE CHARACTERISTICS: LENGTH: 27 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 97: AACAGGTGAA TTATTAGCAC TTGTAAG 27 INFORMATION FOR SEQ ID. NO: 98: 103 SEQUENCE CHARACTERISTICS: (A)'LENGTH: 27 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 98: ATTGCTGTTA ATATTTTTTG AGTTGAA 27 INFORMATION FOR SEQ ID NO: 99: SEQUENCE CHARACTERISTICS: LENGTH: 19 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 99: GTGATCGAAA TCCAGATCC 19 S INFORMATION FOR SEQ ID NO: 100: SEQUENCE CHARACTERISTICS: LENGTH: 19 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear S(ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 100: ATCCTCGGTT TTCTGGAAG 19 19 INFORMATION FOR SEQ ID NO: 101: SEQUENCE CHARACTERISTICS: LENGTH: 19 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 101: CTGGTCATAC ATGTGATGG 19 INFORMATION FOR SEQ ID NO: 102: 104 SEQUENCE CHARACTERISTICS: LENGTH: 19 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 102: GATGTTACCC GAGAGCTTG 19 INFORMATION FOR SEQ ID NO: 103: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 103: TTAAGCGTGC ATAATAAGCC INFORMATION FOR SEQ ID NO: 104: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear S(ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 104: TTGCGATTAC TTCGCCAACT INFORMATION FOR SEQ ID NO: 105: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 105: TTTACTAAGC TTGCCCCTTC INFORMATION FOR SEQ ID NO: 106: 105 SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRAN~DEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 106: AAAAGGCAGC AATTATGAGC INFORMATION FOR SEQ ID NO: 107: SEQUENCE CHARACTERISTICS: LENGTH: 29 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (ix) FEATURE: NAME/KEY: misc-feature LOCATION:9 OTHER INFORMATION:/note= 'In =inosinell (ix) FEATURE: NAME/KEY: misc-feature LOCATION:12 OTHR INFORMATION: /note=~ 'n inosine"I (ix) FEATURE: NAME/KEY: misc-feature OTHER INFORMATION: /note= 'n inosine" (ix) FEATURE: NAME/KEY: misc feature LOCATION:18 OTHER INFORMATION: /note= 'In inosinet"

FEATURE:

NAME/KEY: misc feature LOCATION:21 OTHER INFORMATION: /note= 'In inosinel" (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 107:.

AAYATGATNA CNGGNGCNGC NCARATGGA 29 INFORMATION FOR SEQ ID NO: 108: Wi SEQUENCE CHARACTERISTICS: LENGTH: 23 bas-e pairs TYPE: nucleic acid 106 C. S C

C.

C.

C.

S C LC*

C

C

C..

C

*9

C*@C

STRAINDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (ix) FEATURE: NAME/KEY: misc feature LOCATION:3 OTHER INFORMATION: /note= 'n inosine"l (ix) FEATURE: NAME/KEY: misc-feature LOCATION:6 OTHER INFORMATION: /note= 'In inosine"l Cix) FEATURE: NAME/KEY: misc-feature LOCATION:9 OTHER INFORMATION:/note= 'In inosine"l (ix) FEATURE: NAME/KEY: misc-feature LOCATION.12 OTHER INFORMATION: /note= 'In inosine"l (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 108: CCNACNGTNC 1ONCCRCCYTC RCG INFORMATION FOR SEQ ID NO: 109: SEQUENCE CHARACTERISTICS: LENGTH: 29 base pairs TYPE: nucleic acid STRP&NDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (geriomic) Cix) FEATURE: NAME/KEY: misc-feature LOCATION:6 OTHER INFORMATION: /note= 'In inosine" (ix) FEATURE: NAME/KEY: misc feature LOCATION:12 OTHER INFORMATION: /note= 'In iflosine" (ix) FEATURE: NAME/KEY: misc-feature OTHER INFORMATION: /note= 'n iflosinell (ix) FEATURE: CA) NAME/KEY: misc feature 107 LOCATION:18 OTHER INFORMATION:/note= 'n =inosine' (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 109: CARYTNATHG TNGCNGTNAA YAARATGGA INFORMATION FOR SEQ ID NO: 110: SEQUENCE CHARACTERISTICS: LENGTH: 831 base pairs TYPE: nucleic acid C) STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 110: ATGAAAAACA CAATACATAT CAACTTCGCT ATTTTTTTA.A TAATTGCAA.A TATTATCTAC 4so so 0.

0* 0 0 *too ego*

AGCAGCGCCA

GAAGGTTGTT

GCAAAGTGTG

GCATTTGATG

GGAATGGAGA

TGGGTTTCGC

GATTTTGATT

GAAGCATGGC

AAAATTATTA

ATGTATCTAC

ACAGCAAATA

CATAAATATG

GTGCATCAAC

TTTTACTTTA

CAACGCAAAT

CGGAAATAAT

TCTGGAACAG

AAGAAATAAC

ATGGAAATCA

TCGAAAGTAG

ATCACAATCT

AAGATCTGGA

GAACCTTACA

TTTTTGTGTC

CGATGCATCC.

GGCACCAGAT

AGATCAGAAA

CAATCATACA

CCAAAAAATT

AGACTTCTCT

CTTAAAAATT

CCCAGTTAAA

TAATAGTACA

AAACGGATGG

CGCACTTACA

ACAAACGCTG

TCAACTTTCA

ACCATATTCA

CCAAAGACGT

AGATTAAATA

GGAGATAAAG

TCACCAGAAG

AACTCAGCCA

AAACTGTATG,

TTTGAAGGGT

GGAAACTTGG

AGATATCTCT ACTGTTGCAT

CTCCATTATT

AAATTGCTCA

AGATCGCATT

AATGGGATAA

GGATGCAATT

AAATCAAGAA

AAAGAAACAA

AACAAATTCA

TAGAAAACAC

GGAAAACTGG

TTATTATAAG

GGTCGAATTT

TGAAGGAACT

ATTCAATAAA

ATCACTTATG

AACCCCCAAA

TTCTGTTGTT

TTATCTCAAA

CGGATTAACA

ATTCCTGCGT

CATAGAGAAC

TGCAGGATTC

CAAATCAGGA

AACATCAAGC

120 180 240 300 360 420 480 540 600 660 720 780 ATAAAAGCCA AGAAAA.ATGC GATCACCATT CTAAACACAC TAAATTTATA A INFORMATION POP, SEQ ID NO: 111: SEQUENCE CHARACTERISTICS: LENGTH: 846 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) 108 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 111: TTGAAAAAGT TAATATTTTT AATTGTAATT GCTTTAGTTT TAAGTGCATG TAATTCAAAC

AGTTCACATG

TATGCTTTAG

TATGCTTCAA~

AAGTTAAATA

GAAAAATATG

AGTGATAATA

CAACGTCTAA

AATTACTATT

TTAAATAAAC

TTAATGTTAA

AAGGTTGCTG

GTTTATCCTA

AAAAGTGATA

TTTTAA

CCAAAGAGTT

ATACTAAAAG

CTTCAAAAGC

AAAAAGTACA

TAGGAAAAGA

CAGCAAACAA

AAGAACTAGG

CACCAAAGAG

TTATCGCAAA

ATAATAAAAG

ATAAAAGTGG

AGGGCCAATC

AGCCAAATGA

AAATGATTTA

TGGTAAGGAA

GATAAATAGT

TATTAACAAA

TATCACTTA

TAAAATTATA

AGATAAAGTA

CAAAAAAGAT

TGGAA.AATTA

CGGAGATACT

TCAAGCAATA

TGAACCTATT

TAAGTTGATA

GAAAAAAAAT

GTAAAATTTA

GCTATTTTGT

GATGATATAG

AAAGCACTTA

AAAGAAATCG

ACAAATCCAG

ACTTCAACAC

AGCAAAGAAA

TTAATTAAAG

ACATATGCTT

GTTTTAGTCA

AGTGAAACCG

ATAATGCTCA

ATTCAGATAA

TAGAACAAGT

TTGCTTATTC

TTGAGGCTTC

GTGGAATCAA

TTAGATATGA

CTGCTGCTTT

ACAAAAAATT

ACGGTGTTCC

CTAGAAATGA

TTTTTACGAA

CCAAGAGTGT

TATTGGTGTT

GAGATTTGCC

ACCTTATAAT

TCCTATTTTA

AATGACATAT

AAAAGTTAAA

GATAGAATTA

CGGTAAGACT

CTTACTTGAT

AAAAGACTAT

TGTTGCTTTT

TAAAGACAAT

AATGAAGGAA

120 180 240 300 360 420 480 540 600 660 720 780 840 0 INFORMATION FOR SEQ ID NO: 112: SEQUENCE CHARACTERISTICS: LENGTH: 555 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 112: ATGTCCGCGA GCACCCCCCC CATAACTCTT CGCCTCATGA CCGAGCGCGA CTCCATGACT GGCTCAACCG GCCGCACATC GTGAGTGGT GGGGTGGCGA CCGACTCTTG ATGAAGTGCT GGAACACTAC CTGCCCAGAG CGATGGCGGA ACACCGTACA TCGCAATGCT GGGCGAGGAA CCGATCGGCT ATGCTCAGTC CTCGGAAGCG GTGATGGCTG GTGGGAAGAT GAAACTGATC CAGGAGTGCG CAGTCTCTGG CTGACCCGAC ACAGTTGAAC AAAGGCCTAG GAACAAGGCT

CCTGCCGATG

CGAAGAGCGA

AGAGTCCGTA

GTACGTCGCG

AGGAATAGAC

TGTCCGCGCT

109 CTCGTTGAAC TACTGTTCTC GGACCCCACC GTGACGAAGA TTCAGACCGA CCCGACTCCG AACAACCATC GAGCCATACG CTGCTATGAG AAGGCAGGAT TCGTGCGGGA GAAGATCATC ACCACGCCTG ACGGGCCGGC GGTTTACATG GTTCAAACAC GACAAGCCTT CGAGAGAAAG CGCGGTGTTG CCTAA INFORMATION FOR SEQ ID NO: 113: Ci) SEQUENCE CHARACTERISTICS: LENGTH: 732 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 113: ATGAACCAGA AAAACCCTAA AGACACGCAA AATTTTATTA CTTCTAAAAA GCATGTAAA.A 9.

GAAATATTGA

AAAGGACATT

GATGGAGGCT

ATTCAAACGG

AATATTCCTT

AAATATAGCT

GCTTTGGGTT

CTATATTTTC

CCATTGATTT

CGTGAATATC

GTCACTAATA

ATCACACGAA

TTACCAAAGA

TATGTCAAGT

ATATTCTAAA

ATAACATCAG

ATCTTATCGT

TACTATTAAT

ATCCTAAG CC

CAAAGAAGGA

GTGTTCrTT

TTAATAAACT

TATCAGTAAA

GCTAGTCAAA

GACTAAAGAA

ATTTTCCTTC

TACGGATATT

TGAGAAGGGA

GGTGGAGATG

AAGTGTAGAC

CTACAAAAAG

CACTAAAAAC

CAAGACAACG

ATGAGTCGAT

GCGGTAAACC

CCAAAACATA

GTCAAAAGAA

TTTGCGAAAA

GATATAARAA

TCTGTATTGA

TATCGATCTT

CAATTCCGAC

TAATAGAAAT

CAGTTACTGC

CCTCTGAGAA

TAAACTATAA

TTACCTTTGA

GATTGCAAAA

TGCTCAAAAA

TTGTTCTTGA

CGGATCAGGA

TATAGAAATT

TATAAAAGTG

GATATATGGT

AAGTCAGGCT

TCTGCAACGA

AGTACCACCA

ACGACATCAA

420 480 540 555 120 180 240 300 360 420 480 540 600 660 720 TTGTTTATAA GTGGGTAAAC AGGCTTTGAA GCATGCAAAT ATCGAAGGAA CAATTTCTTT CTATTTTCAA TAGTTACAAA TTGTTTCACT AA 732 INFORMATION FOR SEQ ID NO: 114: Wi SEQUENCE CHAR.ACTERISTICS: LENGTH: 738 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) 110 (Xi) SEQUENCE DESCRIPTION: SEQ ID NO: 114: ATGAACAAAA ATATAAAATA TTCTCAAAAC TTTTTAACGA GTGAAAAAGT ACTCAACCAA ATAATAAAAC AATTGAATTT GGGCATTTAA CGACGAAACT AGTCATCTAT TCAACTTATC CACCAAGATA

TTCTACAGTT

ATTCCTTAcc ATTTAAGCAC GACATCTATC TGATTGTTGA CTAGGGTTGC TCTTGCACAC TGCTTTCATC CTAAACCAAG GATGTTCCAG; ATAAATATTG GAATATCGTC AACTGTTTAC AACAAT'rA-A GTACCGTTAC TTTAACGGGA. GGAAATAA

AAAAGAAACC

GGCTAAAATA

GTCAGAAAAA

TCAATTCCCT

ACAAATTATT

AGAAGGATTC

TCAAGTCTCG

AGTAAACAGT

GAAGCTATAT

TAAAAATCAG

TTATGAGCAA

GATACCGTTT ACGAAATTGG

AGTAAACAGG

TTAAAATCGA

AACAAACAGA

AAAAAAGTGG

TACAAGCGTA

ATTCAGCAAT

GTCTTAATAA

ACGTACTTTG

TTTCATCAAG

GTATTGTCTA

TAACGTCTAT

ATACTCGTGT

GGTATAAAAT

TTTTTGAAAG

CCTTGGATAT

TGCTTAAGCT

AACTTACCCG

TTTCAAAATG

CAATGAAACA

TTTTTAATAG

INFORMATION FOR SEQ ID NO: 115:.

SEQUENCE CHARACTERISTICS: LENGTH: 735 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 115: ATGAACGAGA AAAATATAAA ACACAGTCAA AACTTTAT1'A CTTCAAAACA AAAATAATGA CAAATATAAG ATTAAATGAA CATGATAATA TCTTTGAAAT AAAGGGCATT TTACCCTTGA ATTAGTACAG AGGTGTAATT TCGTAACTGC GACCATAAAT TATGCAAAAC TACAGAAAAT AAACTTGTTG ATCACGATAA TTAAACAAGG ATATATTGCA GTTTAAATTT CCTAAAAACC AATCCTATA AATATACCTT ATAACATAAG TACGGATATA ATACGCAAAA TTGT TTTTGA GATGAGATTT ATTTAATCGT GGAATACGGG TTTGCTAAAA GATTATTAA TcATTGGCAT TATTTTTAAT GGCAGAAGTT GATATTTCTA TATTAAGTAT

AACAGGTAAA

TGAATTAGAC

CACTTTAATT

TGTTGGGAAT

CCATGCGTCT

TCACCGAACA

GCCAGCGGAA

CCATACCACA

GGTCAATCGA

CGCCAAAGTA

TTATCTATTA

TAATATAGAT

CGGCTCAGGA

CATTGAAATA

TTTCCAAGTT

AATATTTGGT

TAGTATAGCT

TACAAAACGC

GGTTCCAAGA

120 180 240 300 360 420 480 540 600 660 720 738 120 180 240 300 360 420 480 ill GAATATTTC ATCCTAAACC TAGAGTGAAT AGCTCACTTA TCAGATTAAA TAGAAAAAAA TCAAGAATAT CACACAAAGA TAAACAGAA~G TATAATTATT TCGTTATGAA ATGGGTTAAC AAAGAATACA AGAAAATATT TACAAAAJ'AT CAATTTAACA ATTCCTTAAA ACATGCAGGA ATTGACGATT TAAACAATAT TAGCTTTGAA CAATTCTTAT C TCTTTTCAA TAGCTATAAA TTATTTAATA AGTAA INFORMATION FOR SEQ ID NO: 116: SEQUENCE CHARACTERISTICS: LENGTH: 1029 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 116: ATGAATAAAA TAAAAGTCGC AATTATCTTC GGCGGTTGCT CGGAGGAACA TGATGTGTCG

GTAAAATCCG

ATCGGAATTA

GCCGATAGTC

AAAGAAAGAG

TGCGGGGAGG

TGCGATATTC

AATGCGGGCA

AGGACGCTTA

ACCAAAGTAA

GGAAAAATCT

AACGAGGATG

CGCATCCATC

GCAGACATTC

GTGCTTGGAT

GTTCTA.AACG

GCGGCTGCCG

CAATAGAAAT

CAAAAAACGG

TCCCCGCCAT

AATACGAAAC

ATGGTGCGAT

AAAGCTCCGC

TCGCCGTCCC

CCTACCCTGT

ACAGTACGGA

TAATTGAGCA

ATTTGATTGT

AGGAAAACGA

CGGTCGAGGA

GCAGAGGGCT

AGGTCAATAC

CAGGAATCAC

TGCTGCGAAC

CGTATGGAAG

ATTCTCCCCG

TCGGCGTATT

ACAGGGTCTG

AGCTTGCATG

CGAATTTCrA

CTTTGTGA.AG

AGAACTAAAC

AGCGATTTCG

CGGCGAAGTG

GCCGGAAAAA

ACGAAATCGG

TGCTCGTGTT

CCTGCCCGGT

GCTTCCCGCA

ATTAATACTG

CTATGCAAGA

GATAGGAAAA

GACGTGGCTT

TTTGAATTGT

GACAAATCAC

ATGATTGAAA

CCGGCACGGT

GCTGCGATAG

GGCTGTGAGG

GATCAAATCC

GGCTCAGAGA

GTGCAAGAAA

GATCTTTTT

TTTACATCGT

CTAATTGACA

AAAAATTCGA

AGCCATGTAC

CGCATGGTCT

TCCCGGTTTT

CTGGTATCCC

TGGCCTACAT

AAGGTGACAA

CAGGTTCGTC

AAGCAGCAGG

TCGGCTGCGC

GGTTGAGCCA

ATGCGATGAT

CGGCAAAGAA

TGCAGGAGGA

ACAGCCGCTA

GCCTGATTAC

TCCGCACTAC

GGAATGGGAA

GCTTGTCATG,

GCATGGCAAA

CTATGTAGGC

TCTTACAAAA

ACCGGAGGCG

CTTTGGCGTA

ACAATATGAT

GGTCATGGGA

CGGTATCTTC

TATCGTTCCA

AGTATATCGG

TGGCGGCATC

TCCACGCATG

ATTGGCGATA

540 600 660 720 735 120 180 240 300 360 420 480 540 600 660 720 780 840 900 960 1020 112

GAGAGGTGA

INFORM'ATION FOR SEQ ID NO: 117: SEQUENCE CHARACTERISTICS: LENGTH: 1031 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 117: ATGAAAAAAA TTGCCGTTTT ATTTGGAGGG AATTCTCCAG AATACTCAGT GTCACTAACC

TCAGCAGCAA

ATCGCACCAA

ACTTGGCTAG

TTAGGAGAAA

GAGGATGGCT

GTCGCTGCCT

GGAATCGCTA

GATCGTTTTA

TCAAAAGGGA

TTTGCTTACG

GGCATCTTAG

GGTTTTTTTG

CCATTGCCTC

TTGGGATTGA

TTAAACGAAA

GCGGAAGTCG

GTGTGATCCA

CAATGGATTG

AAGATCACAA

AACGAATCGT

GTATCCAAGG

CCGCATTATG

GTGCTCCCAC

TTCAAGACCA

TCACAAAAGT

GTTCTACTGT

GAAATGAGCA

ATTTTGAAGA

TCGCGCTTGA

CGGGTCTGGC

TCAACACCAT

GGTTATCCTA

AGCTATTGAC

GTATTGGTAT

AAACTGTCAC

CCCTGATGTC

ACTGCTTGAA

TATGAACAAA

TTTGCTTTTA.

TGGATTCCCG

AACTGACAAA

GTTGATCCAA

ATTGACGATT

GAAATACCAA

ATCACAGATC

TCGAATCGAT

GCCGGGATTT

CGAAATATTA

CCGCTGAAAT

CAAGGAAACC

CAGCTGACTT

CTCTTTCCAG

CTAATGAACC

TGGCTCTTGC

TCCCGCTATG

ATCTTTATCA

ACAGCGCTCC

AAGGCGATAG

GGTGCTTGTG

TTAATCAGCG

AAGGAGCAGG

TTTTTCGTCA

ACTGGGCACT

GTAGAGCAAT

ATGAAGTAAT

TCGCGAATGT

TTTCTAGCCA

TCTTGCATGG

TGCCTTATGT

ATCAACTTGC

AAALACGATCC

AGCCGAATGA

AATCTGCATT

CGGGTATTGA

ATGCGATTTC

CCACGATCAC

CACAGCTGCT

CCAATCAAGG

CCCGCTACCC

TGATTGCACT

GACCATTGGC

TCGCAATGAT

AGGATTTATA

GAAGTATGGC

TGGTTGCCAT

TGATACCATG

TGCCACAPLTC

AGCCGGTTCT

AACGACTGCT

AATTGGCTGC

TCTTGTCGAC

TGTCCCAGCA

TTATCGAAAC

AGCGATTTAT

AGCTATGATG

GGCAGAGGAG

1029 120 180 240 300 360 420 480 540 600 660 720 780 840 900 960 1020 1031 GACAAACGAT G INFORMATION FOR SEQ ID NO: 118: Wi SEQUENCE CHARACTERISTICS: LENGTH: 809 base pairs TYPE: nucleic acid STRANDEDNESS: double 113 TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Abiotrophia adiacens (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 118: TGGTGCTATC TTAGTAGTAT CTGCAGCTGA TGGTCCAATG CCTCAAACAC GTGAACACAT 0 a 0.aa 0

CTTATTATCA

GGTTGACGAT

ATACGATTTc

AGGCGACGCT

TCCAACTCCA

AATCACAGGT

TGACGAAGTT

TGAAATGTTC

ACGTGGTGTT

CACTCCACAT

TCATACTCCA

TGGTGTTTGT

CGTCAAGTAG

GAAGAATTAT

CCAGGCGATG

TCATACRAAG

GAACGYGACG

CGTGGTACTG

GAAATCGTTG

CGTAAATTGT

ACACGTGACA

ACTAAATTCA

TTCTTCTCTA

GTGTTACCAG

GTGTTCCTTA

TAGAATTAGT

ACACTCCAGT

AAA.AAATCTT

TTGACAAACC

TTGCTACAGG

GTATTTCAGA

TAGACTACGC

ACATCGAACG

AAGCTGAAGT

ACTACCGTCC

AAGGCGTTGA

CATCGTTGTA

AGAAATGGAA

TGTTGCAGGT

AGAATTAATG

ATTCATGATG

TCGTGTTGAA

AGAAACTTCA

TGAAGCAGGG

TGGACAAGTT

TTACGTATTA

TCAATTCTAC

AATGGTAATG;

TTCTTAAACA

GTTCGTGACT

TCTGCTTTAC

GCTGCTGTTG

CCAGTTGAAG

CGTGGACAAG

AAAACAACTG

GATAACATTG

CTGCTAAAC

ACTAAAGAAG.

TTCCGTACAA

CCTGGTGATA

AAGTTGACAT

TATTATCAGA

GCGCTTTAGA

ACGAATACAT

ACGTGTTCTC

TTCGTGTTGG

TAACTGGTGT

GTACATTATT

CAGGAACAAT

AAGGTGGACG

CAGACATCAC

ACGTAACTAT

120 180 240 300 360 420 480 540 600 660 720 780 809 120 GGAAGTTGAA TTAATTCACC CAGTAGCGA INFORMATION FOR SEQ ID NO: 119: Wi SEQUENCE CHARACTERISTICS: LENGTH: 817 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY; linear (iMOLECULE TYPE: DNA (genomic) (vi) 'ORIGINAL SOURCE: ORGANISM: Abiotrophia defectiva (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 119: CGGCGCGATC CTCGTTGTAT CTGCTGCTGA. CGGCCCAATG CCACAAACTC GTGAACACAT CCTCTTGTCT CGTCAAGTTG GTGTTCCTTA CATCGTAGTA TTCTTGAACA AAGTTGACAT 114 GGTTGACGAC GAAGAATTGC TCGAATTAGT

ATACGACTTC

AGGCGACGCT

TCCAGAACCA

TATCACTGGT

TGACGAAGTT

TGAAATGTTC

ACGTGGTGTA

CACTCCGYAC

TCACACTCCA

TGGTGTTGTT

GGTTGTTGAA

CCAGGCGACG

AACTACGAAG

GAACGTGACA

CGTGGTACTG

GAAATCGTTG

CGTAAGrrAT

ACTCGTGACC

ACTAAGTTCG

TTCTTCTCTA

ACTTTACCAG

ACACTCCAGT

CTAA.AGTTTT

CTGACAAGCC

TTGCAACTGG

GTATCGAAGA

TGGATTACGC

AAATCCAACG

AAGCTGAAGT

ACTACCGTCC

AAGGTACTGA

TGAAATGGAA

TATCGCTGGT

AGAATTGATG

ATTCATGATG

TCGTGTTGAA

AGAAACTTCT

TGA.AGCTGGG

TGGTCAAGTA

GTACGTATTG

ACAATTCTAC

AATGGTTATG

GTTCGTGACC

TCAGCTTTGA

GAACAAGTTG

CCAGTCGAAG

CGTGGTCAAG

AAGACTACCG

GACAACGTTG

TTATCTAAAC

TCTAAAGAAG

TTCCGTACAA

CCAGGCGACA

TCTTGTCTGA

AAGCTTTAGA

ATGCTTACAT

ACGTATTCTC

TTCGCGTTGG

TTACCGGTGT

GTACCTTGTT

CAGGTTCAAT

AAGGTGGTCG

CTGACGTAAC

ACGTACAAAT

180 240 300 360 420 480 540 600 660 720.

780 TTGATCCACC CAATCGCGAT CGA.AGAA

S

C

INFORMATION FOR SEQ ID NO: 120: SEQUENCE CHARACTERISTICS: LENGTH: 754 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Candida albi cans (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 120: CTCTGTCAAA TGGGACAAAA ACAGATTTGA AGAAATCATC! AAGGAAACCT CCAACTTCGT CAAGAAGGTT GGTTACAACC CAAAGACTGT TCCATTCGTT CCAATCTCTG GTTGGAATGG TGACAACWTG ATTGAAS CAT CCACCAACTG TCCATGGTAC AAGGGTTGGG AAAAGGAAAC CAAATCCGGT AAAGTTACTG GTAAGACCTT GTTAGAAGCT ATTGACGCTA TTGAACCACC AACCAGACCA ACCGACAAAC CATTGAGATT GCCATTRCAA GATGTTTACA AGATCGGTGG TATTGGTACT GTGCCAGTCG GTAGAGTTGA AACTGGTATC ATCAAAGCCG GTATGGTWGT TACTTTCGCC CCAGCTGGTG TTACCACTGA AGTCAARTCC GTTGAAATGC ATCACGAACA ATTGGCTGAA GGTGTTCCAG GTGACAATGT TRGTTTCAAC GTTAAGAACR TTTC!CGTTAA AGAAATTAGA AGAGGTAACG TTTGTGGTGA CTCCAAGAAC GATCCACCAA AGGGTTGTGA 120 180 240 300 360 420 480 540 115 CTCTrTCAAT GCCCAAGTCA TTGTTTTGAA CCATCCAGGT CAAATCTCTG CTGGTTACTC TCCAGTCTTG GATTGTCACR CTGCCCACAT TGCTTGTAAA TTCGACRCTT TGGTTGAAAA GATTGACAGA AGAACTGGTA AGP.AATTGGA AGAAAATCCA AALATTCGTCA AATCCGGTGA TGCTGCTATC GTCAAGATGG TCCCAACCAA ACCA INFORMATION FOR SEQ ID NO: 121; ()SEQUENCE CHARACTERISTICS: LENGTH: 753 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL, SOURCE: ORGANISM: Candida glabrata (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 121: a.

a TCTGTCAAGT GGGATGAATC CAGATTCGCT

AAGAAGGTCG

GACAACATGA

AAGGCTGGTG

ACCAGACCAA

ATCGGTACGG

ACCTTCGCCC

TTGACTGAAG

GAAATCAGAA

TCTTT ICAACG

CCAGTTTTGG

AACGACAGAA

GTTACAACCC

TTGAAGCCAC

TCGTCAAGGG

CTGACAAGCC

TGCCAGTCGG

CAGCTGGTGT

GTTTGCCAGG

GAGGTAATGT

CTACCGTCAT

ACTGTCACAC

GATCCGGTAA

AAAGACTGTT

CACCAACGCT

TAAGACCTTG

ATTGAGATTG

TAGAGTCGAA

TACCACTGAA

TGACAACGTT

CTGTGGTGAC

TGTCTTGAAC

CGCCCACATT

GAAGTTGGAA

GAAATCGTTA AGGAAACCTC CCATTCGTCC CA.ATCTCTGG TCCTGGTACA AGGGTTGGGA TTGGAAGCCA TTGACGCTAT CCATTGCAAG ATGTCTACAA ACCGGTGTCA TCAAGCCAGG GTCAAGTCCG TTGAAATGCA GGTTTCAACG TTAAGAACGT TCCAAGAACG ACCCACCAAA CACCCAGGTC AAATCTCTGC GCTTGTAAGT TCGAAGAATT

CAACTTCATC

TTGGAACGGT

AAAGGAAACC

CGAACCACCA

GATCGGTGGT

TATGGTTGTT

CCACGAACAA

TTCCGTTAAG

GGCTGCTGCT

TGGTTACTCT

GTTGGAAAAG

600 660 720 754 120 180 240 300 360 420 480 540 600 660 720 GACTCTCCAA AGTTCTTGAA GTCCGGTGAC GCTGCTTTGG TTAAGTTCGT TCCATCCAAG CCA INFORMATION FOR SEQ ID NO: 122: Wi SEQUENCE CHARACTERISTICS: LENGTH: 752 base pairs TYPE: nucleic acid STRANDEDNESS; double CD) TOPOLOGY: linear 116 (ii) MOLECULE TYPE: DNA (geriomic) (vi) ORIGINAL SOURCE: ORGANISM: Candjda krusei (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 122: CCGTTAAGTG GGATGAAAAC AGATTTGAAG AAATTGTCAA GGAAACCCAA

AGAAGGTTGG

ACAACATGAT

AGGCAGGTGT

TCAGACCAAC

TTGGTACTGT

CTTTTGCTCC

TAGAACAAGG

ATATCAAGAG

CTTTCAATGC

CAGTCTTGGA

TTGACAGAAG

TTACAACCCA

TGAAGCATCC

TGTTAAGGGT

CGAAAAGCCA

GCCACTCGGT

AGCAGGTGTc

TGTTCCAGGT

AGGTAACGTT

TCAAGTCATT

TTGTCACACT

AACTGGTAAG

AAGACTGTTC

ACCAACTGTC

AAGACCTTAT

TTAAGATTAC

AGAGTCGAAA

ACCACCGAAG

GATAACGTTG

TGTGGTGACT

GTCTTGAACC

GCCCACATTG

TCTGTTGAAG

CATTCGTTCC

CATGGTACAA

TAGAAGCAAT

CATTACAAGA

CCGGTGTCAT

TCAAATCCGT

GTTTCAACGT

CCAAGAACGA

ACCCTGGTCA

CATGTAAGTT

ACCATCCAAA

AATCTCTGGT

GGGTTGGACT

C!GATGCTATT

TGTTTACAAG

TAAGCCAGGT

TGAAATGCAC

TAAGAACGTY

C!CCACCAATG

AATTTCCGCT

CGACGAATTA

GTCYGTCAAG

AACTTCATCA

TGGAATGGTG

AAGGAAACCA

GAACCACCTG

ATTGGTGGTA

ATGGTTGTCA

CATGAACAAT

TCTGTCAAGG

GGTGCAGCTT

GGTTACTCTC

ATCGAAAAGA

TCTGGTGATG

120 180 240 300 360 420 480 540 600 660 '720 e..

C

CAGCTATCGT CAAGATGGTC CCAACCAAGC CA INFORM'ATION FOR SEQ ID NO: 123: i)SEQUENCE CHARACTERISTICS: LENGTH: 754 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear MOLECULE TYPE: DNA (geriomic) (vi) ORIGINAL SOURCE- ORGANISM: Candida parapsilosis (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 123: CTCAGTCAAA TGGGACAAGA RCAGATACGA AGAAATTGTC AAGGAAACTT CCAACTTCGT CAAGAAGGTT GGTTACAACC CTAAAGCTGT CCCATTCGTC CCAATCTCTG GTTGGAACGG TGACAATATG ATTGAAC CAT CAACCAACTG TCCATGGTAC AAGGGTTGGG AAAAGGAAAC TAAAGCTGGT AAGGTTACCG GTAAGACCTT GTTGGAAGCT ATCGATGCTA TCGARCCACC 117 AACCAGACCA ACTGACAAGC CAT'rGAGATT GCCATTGCAA

GATGTCTACA

TATTGGAACT GTGCCAGTTG GTAGAGTTGA AACCGGTATC

ATCAAGGCTG

TACTTTTGCC CCAGCTGGTG TTACCACTGA AGTCAAGTCC

GTTGAAATGC

ATTGACTGA GGTGTCCCAG GTGACAATGT TGGTTTCAAC

GTCAAGAACG

GGAAATCAGA AGAGGTAACG TYTGTGGTGA CTCCAAGAAC

GATCCACCAA

YTCCTTCAAT GCTCAAGTTA TTGTCTTGAA CCACCCAGGT

CAAATCTCTG

ACCAGTCTTG GATTGTCACA CTGCCCACAT TGCTTGTAAA T'rCGACACTT GATTGACAGA AGAACCGGTA AGAAATTGGA AGWTGAACCA

AAATTCATCA

TGCTGC YATC GTCAAGATGG TCCCAACCAA

GCCA

INFORM4ATION FOR SEQ ID NO: 124: SEQUENCE

CHARACTERISTICS:

LENGTH: 753 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Candida tropicalis (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 124: AGATrGGTGG

GTATGGTTGT

ACCACGAACA

TTTCAGTTAA

AGGGATGTGA

CTGGTTACTC

TGATTGAAAA

AGTCCGGTGA

300 360 420 480 540 600 660 720 754 TCTGTTAAAT GGGACAAIUAA CAGATTTGAA GAAATTATCA AGGAAACYTC TAACTTCGTC 4 *4*

AAGAAGGTTG

GACAACATGA

AAGGCTGGTA

TCAAGACCAA

ATTGGTACTG

ACTTTYGCCC

TTGGCTGAAG

GAAATTAGAA

TCTTTCAACG

CCAGTC!TTGG

ATTGACAGAA

GTTACAACCC

TTGAAGCTTC

AGGTTACCGG

CTGACAAGCC

TGCCAGTCGG

CAGCTGGTGT

GTGTCCCAGG

GAGGTAACGT

CTCAAGTTAT

ATTGTCACAC

GAACTGGTAA

TAAGGCTGTT

TACCAACTGT

TAAGACTTTG

ATTGAGATTG

TAGAGTTGAA

TACCACTGAA

TGACAATGTT

TTGTGGTGAC

TGTCTTGAAC

TGCTCATATT

GAAATTGGAA

CCATTCGTTC

CCATGGTACA

TTGGAAGCCA

CCATTGCAAG

ACTGGTGTCA

GTCAAATCCG

GGTTTCAACG

TCCAAGAACG

CACCCAGGTC

GCTTGTAAAT

GAA.AATCCAA

CAATCTCWGG

AGGGTTG=G

TTGATGCTAT

ATGTTTACAA

TCAAAGCCGG

TYGAAATGCA

TTAAGAACGT

ATCCACCAAA

AAATYTCTGC

TCGACACCTT

AATTCGTCAA

TTGGAATGGT

AAAAGAAACC

TGAACCACCT

GATTGGTGGT

TATGGTTGTT

CCACGAACAA

TTCTGTTAAA

GGGTTGTGAC

TGGTTACTCT

GGTTGAAAAG

ATCCGGTGAT

120 160 240 300 360 420 480 540 600 660 720 118 GCTGCTATTG TCAAGATGGT TCCAACCAAA CCA INFORMATION FOR SEQ ID NO; 125: SEQUENCE CHARACTERISTICS: LENGTH: 814 base pairs TYPE: nucleic acid STRAflDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: CA) ORGANISM: Corynebacteriun accol ens (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 125: CGGCGCTATC CTGGTTGTTG CTGCA.ACCGA TGGCCCGATG CCGCAGACCC GCGAGCACGT TCTGCTTGCT CGCCAGGTTG GGTTGATGAT GAGGAAATCA GCAGGACTAC GATGAGGAAG TGACGAGAAG TGGGTACAGT TGATCCGGAG CGCGCTACCG TACCGGCCGC GGTACCGTTG GGACGTTGAG ATCATCGGTA GATGTTCCGC AAGATGATGG TGGTACCAAG CGTGAGGACG

CCCTCACACC'AAGTTCGAGG

CACCCCGYTC ATGAACAACT TGTTGTGAAC CTGCCTGAGG GCGTTCCTTA CATi TCGAGCTCCT GGAI CTCCTATCGT TCA CCATCGTTGA CCT' ATCAGCCGTT CTT' TTACCGGCCG TGT TCCAGGAGAA GTC' ACTACACCGA GGC TTGAGCGTGG CCA, GTTCCGTCTA CGT ACCGTCCTCA GTT GCACCGAGAT GGT

CCTCGTT

~ATGGAG

=ATCTCC

GATGGAT

GATGCCT

TGAGCGT

CCAGAAC

TGGCGAC!

GGTTGTT

CCTGAAG

CTACTTC

GCACTGAACA

ATCTCCGAGC

GCTCTGAAGG

GCCTGCGACA

ATCGAGGACA

GGTCGTCTGA

ACCACCGTTA

AACTGTGGTC

ATCAAGCCGG

AAGGAAGAGG

CGCACCACCG

AGTGCGACAT

TGCTCGCAGA

CACTCGAGGG

ACTCCATCCC

TCTTCACCAT

ACGTCAACGA

CCGGTATCGA

TGCTTCTGCG

GCG3CTTACAC

GCGGCCGCCA

ACGTTACCGG

753 120 180 240 300 360 420 480 540 600 660 720 780 TATGCCT GGCGACAACG TTGAGATGTC TGTTGAGCTC ATCCAGCCTG TTGCTATGGA CGAG INFORMATION FOR SEQ ID NO: 126: Wi SEQUENCE CHARACTERISTICS: LENGTH: 814 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: 119 ORGANISM: Corynebacterium diphteriae (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 126: CGGCGCAATC CTCGTTGTTG CTGCCACCGA CGGCCCAATG CCTCAGACCC GTGAGCACGT

TCTGCTCGCT

GGTTGATGAT

GCAGGATTAC

CGACGAGAAG

AGACCCAGAG

CACCGGCCGC

GGACGTCGAG

GATGTTCCGT

TGGCGTTAAG

CCCTCACACC

CACCCCATTC

TGTTGTGAAG

CGCCAGGTCG

GAGGAAATCA

GACGAAGAGG

TGGACCCAGT

CGTGAGACCG

GGTACCGTTG

ATCATCGGTA

AAGCTTCTCG

CGCGAAGACG

GAGTTCGAGG

TTCGACAACT

CTTCCTGAGG

GCGTTCCTTA

TCGAGCTCGT

CTCCAATCAT

CCATCATCGA

ACAAGCCATT

TTACCGGCCG

TCCGCGAGAA

ACTACACCGA

TTGAGCGTGG

GCTCTGTCTA

ACCGCCCACA

GCACCGAGAT

CATCCTCGTT

CGAGATGGAG

CCACATCTCC

CCTCATGCAG

CCTCATGCCT

TGTTGAGCGT

KGCTACCACC

GGCTGGCGAC

CCAGGTTGTT

CGTTCTGTCC

GTTCTACTTC

GGTCATGCCT

GCTCTGAACA

ATCCRTGAGC

GCACTGAAGG

GCTTGCKATG

ATCGAGGACA

GGCTCCCTGA

ACCACCGTTA

A.ACTGTGGTC

GTTAAGCCAG

AAGGACGAGG

CGCACCACCG

GGCGACAACG

AGTGCGACAT

TGCTCGCTGA

CTCTTGAGGG

ATTCCATCCC

TCTTCACCAT

AGGTCAACGA

CCGGTATCGA

TGCTTCTCCG

GCGCTTACAC

GTGGCCGCCA

ACGTTACCGG

TCGACATGTC

a. a.

a *aa..a CGTCACCCTG ATCCAGCCTG TCGCTATGGA TGAG INFORMATION FOR SEQ ID NO: 127: Wi SEQUENCE CHARACTERISTICS: LENGTH: 814 base pairs TYPE: nucleic acid STRA~NDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (gerlomic) (vi) ORIGINAL SOURCE: ORGANISM: Corynebacterum genitallun (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 127: CGGCGCCATC CTGGTTGTTG CTGCAACCGA TGGCCCGATG CCGCAGACCC GTGAGCACGT TCTGC TGGCT CGCCAGGTTG GCGTTCCGTA CATCCTAGTT GCACTGAACA AGTGCGACAT GGTTQATGAT GAGGAGCTGC TGGAGCTCGT CGAGATGGAG GTCCGCGAGC TGCTGGCTGA GCAGGACTTC GACGAGGAAG CACCrGTTGT TCACATCTCC GCACTGAAGG CCCTGGAGGG CGACGAGAAG TGGGCTAAGC AGATCCTGGA G.CTCATGGAG GCTTGCGACA ACTCCATCCC 120 180 240 300 360 420 480 540 600 660 720 780 814 120 240 300 120 GGATCCGGAG CGCGAGACCG ACAAGCCGTT CCTGATGCCG GTTGRGGACA TACCGGCCGC GGTACCGTTG TTACCGGCCG TGTTGAGCGT GGCGTCCTGA CGAGGTCGAG ATCCTGGGCA TCCGCGAGAA GTCCACCAAG ACCACCGTTA GATGTTCAAC AAGCTGCTGG ACACCGCAGA GGCTGGCGAC AACGCCGCAC TGGCCTGAAG CGCGAAGATG TTGAGCGTGG TCAGATCGTT GCTAAGCCGG CCCGCACACC GAGTTCGAGG GCTCCGTCTA. CGTTC'TGTCC AAGGACGAGG CACCCCGTTC TTCGACAACT ACCGTCCGCA GTTCTATTTC

CGCACCACCG

TGTTGTGAAG CTGCCGGAGG GCACCGAGAT GGTTATGCCG GGCGACAACG CGTCACCCTG ATCCAGCCGG TTGCTATGGA

CGAG

INFORMATION FOR SEQ ID NO: 128: SEQUENCE CHARACTERISTICS: LENGTH: 814 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORINAL SOURCE: ORGANISM: Coryn2ebacteriui jeikeiuw (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 128:

TCTTCACCAT

ACC'rGAACGA

CCTCCATCGA

TGCTGCTGCG

GCGAGTACAC

GTGGCCGCCA

ACGTTACCGG

TTGACATGTC

360 420 480 540 600 660 720 780 814

S

a CGGCGCCATC CTGGTTGTTG CCGCAACCGA TGGCCCGATG

*SS*

S

TCTGCTGGCY

GGTTGACGAT

GCAGGACTTC

CGACGAGAAG

GGATCCGGAG

TACCGGTCGC

CGAGGTTGAG

GATGTTCAAC

TGGTCTGAAG

CCCGCACACC

CGCCAGGTTG

GAGGAGCTGC

GACGAGGAAG

TGGGCTAACC

CGCGAGACCG

GGTACCGTTG

ATCCTGGGTA

AAGCTGCTGG

CGCGAGGACG

GAGTTCGAGG

GCGTTCCGTA

TGGAGCTCGT

CTCCGGTTGT

AGATTCTCGA

ACAAGCCGTT

TTACCGGCCG

TCCGCGAGAA

ACACCGCAGA

TTGAGCGTGG

GCTCCGTCT.A

CATCCTGGTT

CGAGATGGAG

TCACATCTCC

GCTGATGCAG

CCTGATGCCG

TGTTGAGCGT

GTCCCAGAAG

GGCTGGCRAC

CCAGATCATC

CGTTCTGTCC

CCGCAGACCC GCGAGCACGT GCACTGAACA AGTGTGACAT GTCCGCGAGC TGCTGGCTGA GCACTGAAGG

CCCTGGAGGG

GCTTGCGACG AGTCTATCCC GTTGWGGACA TCTTCACCAT GGCATCCTGA ACCTGAJACGA ACCACCGTTA

CCTCCATCGA

AACGCTGCAC

TGCTGCTGCG

GCTAAGCCGG GCGAGTACAC AAGGACGAGG GCGGCCGCA 2.20 180 240 300 360 420 480 540 600 660 CACCCCGTTC TTCGACAACT ACCGTCCGCA GTTCTACTTC CGCACCACCG

ACGTTACCOG

121 TGTTGTGAAG CTGCCTGAGG GCACCGAGAT GGTTATGCCG GGCGACAACG TYGACATGTC CGTCACCCTG ATCCAGCCGG TTGCTATGGA

CGAG

INFORMATION FOR SEQ ID NO: 129: SEQUENCE CHARACTERISTICS: LENGTH: 748 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Corynebacte-rium pseudodiphteriticun (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 129: CGGCGCTATC TTGGTTGTTG CAGCTACCGA CGGCCCAATG CCACAGACTC

S

S

S

*5S*,

S

TCTGCTGGCT

GGTTGACGAC

CCAGGAATTC

CGAAGAGAGG

TGATCCAGAC

TACCGGTCGT

AGAAGTCGAG

AATGTTC!CGC

CGGTACCAAG

CACCCACAAG

CGCCAGGTTG

GAGGAAATCC

GACGAAGAAG

TGGGTTAACG

CGTGCTACCG

GGCACCGTTG

ATCATCGGCA

AAGATGCTGG

CGTGAAGACG

AAGTTCGAAG

GCGTTCCTTA.

TCGAGCTCGT

CTCCAATCGT

CCATCGTTGA

ACAAGCCATT

TTACGGGTCG

TCAAGGAAAA

ACTACACCGA

TTGAGCGTGG.

GTTCCGTCTA

CATCCTGGTT

CGAGATGGAG

TCACATCTCC

ACTGATGGAT

CCTGATGCCT

TGTTGAGCGT

GTCCCAGAAG

GGCCGGCGAC

ACAGGTTATC

CGTTCTTTCC

GTTCTACTTC

GCACTAAACA

ATCCGCGAAT

GC.AGTCGGCG

GCTTGTGAC!G

ATCGAGGACA

GGTTCCCTGA

ACCACCATCA

AACGCTGGTC

GTTGCTCCAG

AAGGACGAGG

CGCACCACCG

GCGAGCACGT

AGTGCGACAT

TGCTGGCTGA

CCTTGGAAGG

AGTCGATCCC

TCTTCACCAT

AGGTCAACGA

CCGGTATCGA

TGCTGCTTCG

GTGCTTACAG

GCGGCCGCCA

ACGTTACCGG

CACCCCGTTC TTCGACAACT. ACCGTCCTCA TGTTGTTACC-CTGCCTGAGG

GACA

INFORMATION FOR SEQ ID NO: 130: (i)SEQUENCE CHARACTERISTICS- LENGTH: 813 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear "MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: 122 ORGANISM: Corynebacteriun stra-jatumn (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 130: GGCGCTATCT TGGTTGTTGC TGCAACCGAT GGCCCGRTGC CGrCAGACCCG

CTTCTGGCTC

GTTGACGACG

CAGGACTACG

GRCGAGAAGT

GATCCGGAGC

ACCGGCCGCG

GACGTTGAGA

ATGYTCCGCA

GGTACCAAGC

CCTCACACCC

ACCCCGTTCA

GTCATCAAGC

GTCGAGC TGA

GCCAGGTTGG

AGGAAATTAT

ATGAGGAAGC

GGGTACAGGC

GCGAGCTGGA

GTACCGTTGT

TCATCGGTAT

AGATGATGGA

GTGAAGAGGT

AGTTCGAGGG

TGGACAACTA

TGCCTGAGGG

CGTTCCTTAC

CGAGCTCGTC

TCCGATCGTT

TATCGTTGAC

CAAGCCGTTC

TACTGGCCGT

CCAGGACARG

CTACACCGAG

TGAGCGCGGC

TTCCGTCTAC!

CCGTCCGCAG

CACCGAGATG

ATCCTCGTTG

GAGATGGAGA

CACATCTCTG

CTCATGCAGG

CTGATGCCAA

GTTGAGCGTG

TCCATCTCCA

GC TGGCGACA.

CAGGTTGTTA

GTCCTGA.AGA

TTCTACTTCC

GTTATGCCTG

CACTGAACAA~

TCCGCGAACT

CTCTGAAGGC

CTTGC!GATGA

TCGAGGACAT

GCTCCCTGAA

CCACCGTTAC

ACTGTGGTCT

TTAAGCCGGG

AGGAAGAGGG

GCACCACCGA

GCGACAACGT

CGAGCACGTr

GTGCGACATG

GCTCGCAGAG

TCTTGAGGGC

CTCCATCCCG

CTTCACCATC

CGTCAACGAG

CGGTATCGAG

GCTTCTGCGT

CGCTTACACC

CGGCCGCCAC

CGTTACCGGC

CGAGATGTCY

a a TCCAGCCGGT CGCTATGGAC GAG 120 180 240 3'00 360- 42'0 480 540 600 660 720 780 813 120 180 240 300 INFORMATION-FOR SEQ ID NO: 131: SEQUECE

CHARACTERISTICS:

LENGTH: 817 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Enter-ococcus avium (xi).SEQUENCE DESCRIPTION: SEQ ID NO: 131: CGGAGCTATC TTAGTAGTAT CTGCTGCTGA TGGCCCTATG CCTCAAACTC

GTGAACACAT

CTTGTTATCT CGTAACGTTG GTGTTCCTTA CATCGTTGTA TTCTTAAACA

AAATGGATAT

GGTTGACGAT GAAGAATTAC TTGAATTAGT TGAAATGGAA GTTCGTGACT

TATTAACTGA

ATACGACTTC CCAGGCGACG ACACTCCAGT TATCGCAGGT TCAGCGTTGA

AAGCTTTAGA

AGGCGACGCT TCATACGAAG AAAAAATCTT AGAATTA.ATG GCTGCTGTTG

ACGAATATAT

123 CCCAACACCA GTTCGTGATA CTGACAAACC ATTCATGATG CCAGTCGAAG AATCACTGGT CGTGGTACTG TTGCAACTGG TCGTGTTGAA CGTGGACAAG TGACGAAGTT GAAATCGTAG GTATCGCTGA CGAAACTGCT AAAACAACTG TGAAATGTTC CGTAAATTGT TAGACTACGC TGAAGCAGGT GACAACATCG ACGTGGTGTT GCACGTGAAG ATATCCAACG TGGACAAGTA TTGGCTAAAC CACTCCACAT ACAAAATTCT CTGCAGAAGT TTATGT'rCTA ACTAAAGAAG TCATACTCCA TTCTTCACTA ACTACCGTCC TCAGTTCTAC TTCCGTACA.A TGGTGTAGTT GATCTACCAG AAGGTACTGA AATGGTWATG CCTGGGGATA GGAAGTTGAA TTGATYCACC CAATYGCGGT AGAAGAC INFO RMATION FOR SEQ ID NO: 132: SEQUENCE CHARACTERISTICS: LENGTH: 817 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Enterococcus faecalis (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 132: CGGAGCTATC TTAGTAGTTT CTGCTGCTGA TGGTCCTATG CCTCAAACAC

ACGTATTCTC

TTCGCGTTGG

TTACAGGTGT

GTGCTTTGTT

CAGCTTCAAT

AAGGTGGACG

CTGACGTAAC

ACGTAACTAT

GTGAACATAT

AAATGGATAT

TATTATCAGA

AAGCTTTAGA

ACGAATATAT

ACGTATTCTC

TTCGCGTTGG

TTACAGGTGT

GTGCTTTATT

CAGCTACAAT

AAGGCGGACG

360 420 480 540 600 660 720 780 817 120 180 240 300 360 420 480 540 600 660

CTTATTATCA

GGTTGATGAC

ATACGATTTC

AGGCGACGAG

CCCAACTCCA

AATCACTGGA

TGACGAAGTT

TGAAATGTTC

ACGTGGTGTA

CACTCCACAC

CGTAACGTTG

GAAGAATTAT

CCAGGCGATG

TCTTATGAAG

GAACGTGATA

CGTGGTACTG

GAAATCGTTG

CGTAAATTAT

GCACGTGAAG

ACAAAATTCA

GTGTACCATA

TAGAATTAGT

ATGTTCCAGT

AAAAAATCTT

CTGACAAACC

TTGCTACAGG

GTATTAAAGA

TAGACTACGC

ATATCGAACG

AAGCTGAAGT

CATCGTTGTA TTCTTA.AACA AGAAATGGAA GTTCGTGACT TATCGCAGGT TCTGCTTTGA AGAATTAATG GCTGCAGTTG ATTCATGATG CCAGTCGAAG ACGTGTTGAA CGTGGTGAAG CGAAACATCT AAAACAACYG TGAAGCAGGC GACAACMTCG TGGACAAGTA TTAGCTAAALC ATACGTATTA TCAAAAGAAG TCACACTCCA TTCT1'CACTA ACTACCGTCC TCAATTCTAC TTCCGTACAA CAGACGTTAC 124 TGGTGTTGTA GAATTGCCAG AAGGTACTGA AATGGTAATG CCTGGTGATA ACGTTGCTAT GGACGTTGAIA TTAATTCACC CAATCGCTAT CGAAGAC INFORMATION FOR SEQ ID NO: 133: Wi SEQUENCE CHARACTERISTICS: LENGTH: 774 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Enterococcus faecium (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 133: CGGAGCTATC TTGGTAGTTT CTGCTGCTGA CGGCCCAATG CCTCAAACTC

GTGAACACAT

V00.

9

CCTATTGTCT

GGTTGATGAC

ATACRAATTC

AGGCGACGCT

CCCAACTCCA

AATTACTGGA

TGACGAAGTT

TGAAATGTTC

ACGTGGTGTT

CACACCTCRT

TCATACTCCA

CGTCAAGTTG

GAAGAATTAC

CCTGGTGRCG

TCATACGAAG

GAACGTGACA

CGTGGTACTC

GAAGTTGTTG

CGTAAATTGT

GCACGTGAAG

ACAAAATTCT

TTCTTCACTA

GTGTTCCTTA

TAGAATTAGT

ATGTTtCTGT

AAAAAATTCT

ACGACAAACC

TTGCTACAGG

GTATTGCTGA

TAGACYACGC

ACATCCAACG

CTGCAGAAGT

ACTACCGTCC

CATCGTTGTA

TGAAATGGAA

AGTTdCTGGA

TGAATTAATG

ATTCATGATG

TCGTGTTGAA

AGAAACTTCA

TGAAGCTGGA

TGGACAAGTT

ATACGTGTTG

ACAATTCTAC

TTCTTGAACA AAGTAGACAT GTTCGTGACC TATTAACAGA 780 817 120 180 240 300 360 420 480 540 600 660 720

TCAGCTTTGA

GCTGCAGTTG

CCAGTTGAAG

CGTGGACAAG

AAAACAACAG

GACRACATTG

T'TAGCTAAAC

ACAAAAGAAG

TTCCGTACAA

AAGCTCTAGA

ACGAATACAT

ACGTGTTCTC

TTCGCGTTGG

TTACTGGTGT

GTGCTTTACT

CAGGTACAAT

AAGGTGGACG

CTGACGTAAC

AGGTGTTGTT GAATTACCAG AAGGAACTGA AATGGTCATG CCCGGTGACA ACGT INFORMATION FOR SEQ ID NO: 134: SEQUENCE CHARACTERISTICS: LENGTH: 809 base pairs TYPE: nucleic acid STRANDEJNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: 125 ORGANISM: E-nterococcus gallinarum (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 134: CGGTGCGATC TTAGTAGTAT CTGCTGCTGA CGGTCCTATG CCTCAAACTC GTGAACACAT

CTTGTTATCA

GGTTGAYGAC

ATATGACTTC

AGGAGATCCT

TCCAACTCCA

AATCACTGGA

TGATGAAGTA

TGAAATGTTC

AC!GTGGGGTT

CACACCTCAT

TCACACTCCA

TGGTGTTGTT

CGTAACGTTG

GAAGAATTGC

CCAGGCGACG

TCATACGAAG

GAACGTGATA

CGTGGTACTG

GAAATCGTTG

CGTAAATTGT

GCTCGTGAAG,

ACAAAATTCA

TTCTTCACTA

GAATTACCAG

GCGTACCATA

TAGAATTAGT

ATGTTCCTGT

AAAAAATCAT

CTGACAAACC

TTGCTACAGG

GTATTGCTGA

TAGACTATGC

ACATCCAACG

AAGCTGAAGT

ACTACCGTCC

AAGGAACTGA

CATCGTTGTT

TGAAATGGAA

AATCGCCGGT

GGAATTGATG

ATTCATGATG

CCGTGTTGAA

CGAAACTGCT

TGAAGCAGGG

TGGACAAGTA

TTATGTTTTG

TCAGTTCTAC

AATGGTGATG

TTCTTGAACA

GTTCGTGACC

TCTGCTTTGA

GCTGCAGTTG

C!CAGTCGAAG

CGTGGACAAG

AAAACAACTG

GATAACATTG

TTGGCTAA.AG

ACAAAAGAAG

TTCCGTACAA

C!CTGGCGACA

AAATGGATAT

TATTGTCTGA

AAGCTCTTGA

ACGAATACGT

ACGTATTCTC

TTCGCGTTGG

TAACAGGTGT

GTGCATTGCT

CTGGTACAAT

AAGGTGGACG

CTGACGTAAC

ACGTGACCAT

0 00** 0 120 180 240 300 360 420 480 540 600 660 720 780 809 120 180 240 300 CGACGTTGAA TTGATRCACC CAATCGCTC INFORMATION FOR SEQ ID NO: 135: (i.SEQUENCE CHARACTERISTICS: LENGTH: 823 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (i)MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Gardnerella vaginalis (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 135: TGGCGCAATC CTCGTGGTTG CTGCTAC!CGA CGGTCCAATG GCTCAGACCC GTGAACACGT CTTGCTTGCT AAGCAGGTCG GCGTTCCAA.A AATTCTTGTT GCTTTGAACA AGTGCGATAT GGTTGACGAC GAAGAGCTTA TCGATCTCGT TGAAGAAGAG GTCCGTGACC TCCTCGAAGA.

AAACGGCTTC GATCGCGATT GCCCAGTCYT CCGTACTTCC GCTTACGGCG CTTTGCATGA TGACGCTCCA GACCACGACA AGTGGGTAGA GACCGTCAAG GAACTCATGA AGGCTGTTA 126 CGAGTACATC CCAACCCCAA CTCACGATCT TGACAAGCCA

TTCTTGATGC

TGTGTTcACC ATCTCCGGTC GTGGTYCCGT TGTCACCGGT CGTGTTGAGC CCCAATAC ACCCCAGTTG AGATCGTTGG TTTGCGCGAT ACCCAGACCA CTCTATCGAG ACC'rTCCACA AGCAGATGGA TGAGGCAGAG GCTGGCGATA TCTTCTCC!GC GGTATCAACC GTACCGACGT TGAGCGTGGT CAGGTTGTGG TTCTGTGACT CCACACACCA AGTTCGAAGG CGAAGTTTAC GTCTTGACCA TGGCCGTCAC TCGCCATTCT TCTCCAACTA CCGTCCACAG TTCTACTTCC TGTTACTGGC GTTATCACCT TGCCAGACGG CATCGAAATG GTTCAGCCAG AACCTTCACT GTTGAGTTGA TCCAGGCTAT CGCA.ATGGAA GAG INFORM4ATION FOR SEQ ID NO: 136.

Wi SEQUENCE CHARACTERISTICS: LENGTH: 817 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genoznic) (vi) ORIGINAL SOURCE: ORGANISM: Listeria innocua (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 136:

CAATCGAAGA

GTGGTAAGCT

CCACCGTCAC

ACACTGGTCT

CTGCTCCAGG

AGGACGAAGG

GTACCACCGA

GCGATCACGC

360 420 480 540 600 660 720 780 823 seeS

S

0066 *0*446 CGGAGCTATC TTAGTAGTAT CTGCTGCTGA TGGCCCAATG CCACA.AACTC GTGAACATAT

CTTACTTTCA

GGTTGACGAT

ATATGAATTC

AGGTGAAGCT

TCCAACTCCA

AATCACTGGT

TGACGA.AGTA

AGAAATGTTC

ACGTGGTGTT

CGTCAAGTTG

GAAGAATTAC

CCTGGCGATG

GACTGGGAAG

GAACGTGATA

CGTGGAACAG

GAAGTTATCG

CGTAAATTAC

GCTCGTGAAG

GTGTTCCATA

TAGAATTAGT

ACATTCCTGT

CTAAAATTGA

CTGACAAACC

TTGCAACTGG

GTATTGAAGA

TAGACTACGC

ATATCCAACG

CATCGTTGTA

TGAAATGGAA

AATCAAAGGT

CGAGTTAATG

ATTCATGATG

ACGTGTTGAA

AGAAAGCAAA

TGAALGCTGGC

TGGTCAAGTA

TTATGTTTTA

TTCATGAAC-A

ATTCGTGATC

TCAGCTCTTA

GAAGCTGTAG

CCAGTTGAGG

CGTGGACAAG

AAAGTAGTAG

GACAACATTG

TTAfjCTAAAC

ACTAAAGAAG

AATGTGACAT

TATrAACTGA

AAGCACTTCA

ATTCTTACAT

ATGTATTCTC

TTAAAGTI'GG

TAACTGGAGT

GCGCACTTCT

CAGGTTCGAT

AAGGTGGACG

120 180 240 300 360 420 480 540 600 660 720 TACTCCACAC ACTAACTTCA AAGCTGAAAC TCACACTCCA TTC!TTCAACA ACTACCOCCCC ACAATTCTAT TTCCGTACTA CTGACGTAAC 127 TGGTATTGTT ACACTTCCAG AAGGTACTGA AATGGTAATG CCTGGTGATA ACATTGAGCT TGCAGTTGAA CTAATTGCAC CAATCGCTAT CGAAGAC INFORMATION FOR SEQ ID NO: 137: Ci) SEQUENCE CHARACTERISTICS: LENGTH: 818 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Listerja ivanovia (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 137: 780 817 CGGAGCTATC TTAGTAGTAT CTGCTGCTGA TGGTCCAATG CCACAAACTC

S

'esees

S

0S 0 e S

OS

Oe 0 0S

S.

*SSO

OS@S

S S 0*S S 0 *5500* 5

S

5005 0*

S

TCTTACTTTC

TGG;TTGACGA

AATATGAATT

AAGGTGAAGC

TTCCAACTCC

CAATCACTGG

GTGACGAAGT

TAGAAATGTT

TACGTGGTGT

TTACTCCACA

GTCATACTCC

CTGGTATTGT

ACGTCAAGTT

TGAAGAATTA

CCCTGGCGAC

TGATTGGGAA

AGAACGTGAT

TCGTGGAACA

AGAAGTTATC

CCGTAAATTA

TGCTCGTGAA

TACTAACTTC

ATTCTTCAAC

TACACTTCCA

GGTGTTCCAT

CTTGAATTAG

GACATTCCTG

GCTAAAATTG

ACTGACAAAC

GTTGCAACTG

GGTATTGAAG

CTAGACTACG

GATATCCAAC

AAAGCTGAAA

AACTACCGCC

GAAGGTACTG

ACATCGT TGT

TTGAAATGGA

TAATCAAAGG

ACGAGTTAAT

CATTCATGAT

GACGTGTTGA

AAGAAAGCAA

CTGAAGCTGG

GTGGTCAAGT

CTrATGTTTT

CACAATTCTA

AAATGGTAAT

ATTCATGAAC

AATTCGTGAT

TTCAGCTCTT

GGAAGCTGTA

GCCAGTTGAG

ACGTGG;ACAA

AAAAGTAGTA

CGACAACATT

ATTAGCTAAA

AACTAAAGAA

=~CCGTACT

GCCTGGTGAT

GTGAACATAT

AAATGTGACA

CTATTAACTG

AAAGCACTTC

GATTCTTACA

GATGTATTCT

GTTAAAGTTG

GTAACTGGAG

GGCGCACTTC

CCAGGTTCGA

GAAGGTGGAC

ACTGACGTAA

AACATTGAGC

120 180 240 300 360 420 480 540 600 660 720 780 818 TTGCAGTTGA ACTAATTGCA CCAATCGCTA TCGAAGAC INFORMATION FOR SEQ, ID NO: 138: SEQUENCE CHARACTERISTICS: LENGTH: 817 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) 128 (vi) ORIGINAL SOURCE: ORGANISM: Listeria mc'nocytogenes (Xi) SEQUENCE DESCRIPTION: SEQ ID NO: 138: CGGAGCTATC TTAGTAGTAT CTGCTGCTGA TGGCCCAATG

CTTACTTTCA

GGTTGACGAT

ATATGAATTC

AGGTGAAGCT

TCCAACTCCW

AATCACTGGT

TGACGAAGTA

AGAAATGTTC

ACGTGGTGTT

TACTCCACAC

TCACACTCCA

TGGTATTGTT

TGCAGTTGAA

CGTCAAGTTG

GAAGAATTAC

CCTGGCGATG

GACTGGGAAG

GAACGTGATA

CGTGGAACAG

GAAGTTATCG

CGTAAATTAC

GCTCGTGAAG

ACTAACTTCA

TrTCTTCAACA

ACACTTCCAG

GTGTTCCATA

TAGAATTAGT

ACATTCCTGT

CTAAAATTGA

CTGACAAACC

TTGCAACTGG

GTATCGAAGA

TAGACTACGC

ATATCCAACR

AAGCTGAAAC

ACTACCGCCC

AAGGTACTGA

CATCGTTGTA

TGAAATGGAA

AATCAAAGGT

CGAGTTAATG

ATTCATGATG

ACGTGTTGAA

AGAAAGCAAA

TGAAGCTGGC

TGGTCAAGTA

TTATGTTTTA

ACAATTCTAT

AATGGTAAYG

CGAAGAC

CCACAAACTC

TTCATGAACA

ATTCGTGATC

TCAGCTCTTA

GAAGCTGTAG

CCAGTTGAGG

CGTGGACAAG

AAAGTAGTAG

GACAACATTG

TTAGCTAAAC

ACTAAAGAAG

TTCCGTACTA

CCTGGTGATA

GTGAACATAT

AATGTGACAT

TATTAACTGA

AAGCACTTCA

ATTCTTACAT

ATGTATTCTC

TTAAAGTTGG

TAACTGGAGT

GCGCACTTCT

CAGGTTCGAT

AAGGTGGACG

CTGACGTAAC

ACATTGAGCT

120 180 240 300 360 420 480 600 660 720 780 817 120 180 240 CTAATTGCAC CAATCGCTAT INFORMATION FOR SEQ ID NO: 139: SEQUENCE CHARACTERISTICS: CA) LENGTH: 817 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Listeria seeligerj (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 139: CGGAGCTATC TTAGTAGTAT CTGCTGCTGA TGGCCCAATG CCACAAACTC

GTGAACATAT

CTTACTTTCA CGTCAAGTTG GTGTTCCATA CATCGTTGTA TTCATGAACA AATGTGACAT GGTTGACGAT GAAGAATTAC 1T'GAATTAGT TGAAATGGA ATTCGTGATC

TATTAACTGA

ATATGAATTC CCTGGTGATG ACATTCCTGT AATCAAAGGT TCAGCTCTTA AAGCACTTCA 129

AGGTGAAGCT

TCCAACTCCA

AATCACTGGT

TGACGAAGTA

AGAAATGTTC

ACGTGGTGTT

TACTCCACAT

TCACACTCCA

TGGTATTGTT

GACTGGGAAG

GAACGTGATA

CGTGGAACTG

GAAGTTATCG

CGTAAATTAC

GCTCGTGAAG

ACTAACTTCA

TTCTTCAACA

ACACTTCCAG

CTAAAATTGA

CTGACAAACC

TTGCAACTGG

GTAT1'GAAGA

TAGACTACGC

ATATCCAACG

AAGCTGAAAC

ACTACCGCCC

AAGGTACTGA

CGAGTTAATG

ATTCATGATG

ACGTGTTGAA

AGAAAGCAAA

TGAAGCTGGC

TGGTCAAGTA

TTATGTTTTA

ACAATTCTAT

AATGGTAATG

GAAGCTGTAG

CCAGTTGAGG

CGTGGACAAG

AAAGTAATAG

GACAACATTG

TTAGCTAAAC

ACTAAAGAAG

TTCCGTACTA

CCTGGTGATA

ATTCTTACAT

ATGTATTCTc

TTAAAGTTGG

TAACTGGAGT

GCGCACTTCT

CAGGTTCGAT

AAGGTGGACG

CTGACGTAAC

ACATTGAGCT

300 360 420 480 540 600 660 720 780 817 TGCAGTTGAA CTAATTGCAC CAATCGCTAT CGAAGAC INFORMA),TION FOR SEQ ID NO: 140: Wi SEQUENCE CHARACTERISTICS: LENGTH: 614 base pairs TYPE: nucleic acid STR.ANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Staphylococcus aureus (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 140: CGGTGGTATC TTAGTAGTAT CTGCTGCTGA

TCTTTTATCA

GGTTGACGAT

ATATGACTTC

AGGCGATGCT

TCCAACTCCA

AATCACTGGT

TGAAGAAGTT

AATGTTCCGT

TGGTGTTGCT

ACCACATACT

CGTAACGTTG

GAAGAATTAT

CCAGGTGACG

CAATACGAAG

GAACGTGATT

CGTGGTACTG

GAAATCATCG

AAATTATTAG

CGTGAAGACG

GAATTCAAAG

GTGTACCAGC

TAGAATTAGT

ATGTACCTGT

AAAAAATCTT

CTGACAAACC

TTGCTACAGG

GTTTACATGA

ACTACGCTGA

TACAACGTGG

CAGAAGTATA

CGGTCCAATG; CCACAAACTC ATTAGTAGTA TTCTTAAACA AGAAATGGAA GTTCGTGACT AATCGCTGGT TCAGCATTAR AGAATTARTG GAAGCTGTAG ATTCATGATG CCAGTTGAGG CCGTGTTGAA CGTGGTCAAA CACATCTAAA ACAACTGflA AGCTGGTGAC AACATTGGTG TCAAGTATTA GCTGCTCCTG CGTATTATCA AAAGJCGAAG

GTGAACACAT

AAGTTGACAT

TATTAAGCGA

AAGCTTTAGA

ATACTTACAT

ACGTATTCTC

TCAAAGTTGG

CAGGTGTTGA

CATTATTACO

GTTCAATTAC

GTGGACGTCA

120 180 240 300 360 420 480 540 600 660 130 CACTCCATTC TTCTCAAACT ATCGTCCACA ATTCTATTTC CGTACTACTG ACGTAACTG TGTTGTTCAC TTACCAGAAG GTACTGAAAT GGTAATGCCT GGTGATAACG TTGAAATGAC AGTAGAATTA ATCGCTCCAA TCGCGATTGA AGAC INFORMATION FOR SEQ ID, NO: 141: SEQUENCE CHARACTERISTICS: LENGTH: B14 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Staphylococcus epidernidis (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 141: 720 780 814- CGGCGGTATC TTAGTTGTAT CTGCTGCTGA CGGTCCAATG

CTTATTATCA

GGTAGACGAC

ATATGACTTC

AGGCGATGCT

TCCAACTCCA

AATCACTGGT

TGAAGAAGTr

AATGTTCCGT

TGGTGTTGCA

ACCACACACA.

CACTCCATTC

TGTTGTAAAC

CGTAACGTTG

GAAGAATTAT

CCAGGTGACG

GAATACGAAC

GAACGTGATT

CGTGGTACTG

GAAATCATCG

AAATTATTAG

CGTGAAGACG

AAATTCAAAG

TTCACTAACT

TTACCAGAAG

GTGTACCAGC

TAGAA'rrAGT

ATGTACCTGT

AAAAAATCTT

CTGACAAACC

TTGCTACAGG

GTATGCACGA

ACTACGCTGA

TACAACGTGG

CTGAAGTATA

ATCGCCCACA

GTACAGAAAT

ATTAGTTGTA

TGAAATGGAA

AATCGCTGGT

AGACTTAATG

ATTCATGATG

CCGTGTTGAA

AACTTCTAAA

AGCTGGTGAC

TCAAGTATTA

CGTATTATCT

ATTCTATTTC

GGTTATGCCT

CCACAAACTC GTGAACACAT TTCTTAAACA AAGTTGACAT GTTCGTGACT TATTAAGCGA TCTGCATTAA AAGCATTAGA

CAAGCAGTTG

CCAGTTGAGG

CGTGGTCAAA

ACAACTGTTA

AACATCGGTG

GCTGCTCCTG

AAAGATGAAG

CRTACTACTG

GGCGACAACG

ATGATTACAT

ACGTATTCTC

TCAAAGTWGG

CTGGTGTAGA

CTTTATTACG

GTTCTATTAC

GTGGACGTCA

ACGTAACTGG

TTGAAATGAC

120 180 240 300 360 420 480 540 600 660 720 780 AGTTGAATTA ATCGCTCCAA TCGCTATCGA AGAC INFORMATION FOR SEQ ID NO: 142: Wi SEQUENCE CHARACTERISTICS: LENGTH: 817 base pairs TYPE: nucleic acid STRA~NDEDNESS: double TOPOLOGY: linear 131 (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Staphylococcus saprophyticus (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 142: CGGAGCTATC TTAGTAGTAT CTGCTGCTGA TGGCCCAATG CCACAAACTC

TCTTTTATCA

GGTTGACGAY

ATATGACTTC

AGGCGACGCT

TCCAACACCA

AATCACTGGT

TGAAGA&ATC

AGAAATGTTC

ACGTGGTGTT

CACACCACAT

TCATACGCCA

TGGTGTTGTT

GGATGTTGAA

CGTRACGTTG

GAAGAATTAT

CCAGGTGACG

GACTATGAGC

GAACGTGATT

CGTGGTACTG

GARATCATCG

CGTAAATTAT

TCACGTGATG

ACAAAATTCA

TTCTTCACTA

AACTTACCAG

GTGYTCCAGC

TAGAATTRGT

ATGTACCTGT

AAAAAATCTT

CTGACAAACC

TTGCTACAGG

GTATGCAAGA

TAGACTACGC

ATGTACAACG

AAGCGGATGT

ACTACCGCCC

AAGGTACTGA

ATTAGTTGTA

AGAMATGGA),

AATCTCTGGT

AGACTTAATG

ATTCATGATG

CCGTGTTGAA

AGAATCAAGC

TGAAGCTGGT

TGGTCAAGTT

TTACGTTTTA

ACAATTCTAT

AATGGTTATG

TGAAGAC

TTCTTAAACA

GTTCGTGRCT

TCTGCATTAA

CAAGCTGTTG

CCAGTTGAGG

CGTGGTCAAA

AAAACAACTG

GACAACATTG

TTAGCTGCTC

TCTAAAGATG

GTGAACACAT

AAGTTGACAT

TATTAAGCGA

AAGCTT'rAGA

ATGACTYCAT

ACGTATTCTC

TCAAAGTCGG

TTACTGGTGT

GTGCATTATT

CTGGTACTAT

AAGGTGGTCG

00.

0040 TTCCGTACTA CTGACGTALC CCTGGCGATA ACGTTGAAAT TTAATTTCTC CAATCGCTAT INFORMATION FOR SEQ ID NO: 143: Ci) SEQUENCE CHARACTERISTICS: LENGTH: 817 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Staphylococcus saimulans Cxi) SEQUENCE DESCRIPTION: SEQ ID NO: 143: CGGCGGTATC TTAGTAGTAT CTGCTGCAGA TGGTCCAATG CCACAAACTC GTGAACACAT CTTATTATCA CGTAACGTTG GTGTACCAGC T1'TAGTTGTA TTCTTAAACA AAGCTGACAT GGTTGACGAC GAAGAATTAT TAGAATTAGT TGAAATGGAA GTTCGTGACT TATTATCTGA 132 ATACGACTTC CCTGGTGACG ATGTACCAGT AGGCGACCCA GAATACGAAC AAAAAATCTT CCCAACTCCA GAACGTGACT CTGATAAACC AATCACTGGT CGTGGTACTG TAGCAACAGG TGAAGAAGTT GAAATCATCG GTATCACTGA AGAAATGTTC CGTAAATTAT TAGACTACGC ACGTGGTGTT GCACGTGAAG ACGTACAACG TACTCCACAC ACAAAATTCA AAGCTGATGT TCATACTCCA TTCTTCACTA ACTACCGCCC TGGCGTTGTT CACTTACCAG A.AGGTACTGA GAcTGTTGAA TTGATCGCTC CAATCGCGAT

TATCGTTGGT

AGACTTAATG

ATTCATGATG

CCGTGTTGAA

AGAAAGCAJAG

TGAAGCTGGT

TGGACAAGTA

TTACGTTTr.A

ACAATTCTAC

AATGGTTATG

TGAAGAC

TCTGCATTAA

CAAGCTGTAG

CCAGTTGAGG

CGTGGTCAAA

AAAACAACAG

GACAACATCG

TTAGCAGCTC

TCTAAAGAAG

TTCCGTACTA

CCTGGCGATA

AAGCTTTAGA

ATGACTACAT

ACGTATTCTC

TCAAAGTCGG

TTACAGGTGT

GTGCTTTATT

CTGGCTCTAT

AAGGTGGACG

CTGACGTAAC

ACGTAGAAAT

240 300 360 420 480 540 600 660 720 780 817 INFORMATION FOR SEQ ID NO: 144: Wi SEQUENCE CHtARACTERISTICS: LENGTH: 817 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE.. DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Streptococcus agalactjae (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 144: CGGAGCTATC CTTGTAGTTG CTTCAACTGA

CCTTCTTTCA

TGTTGATGAT

ATACGACTTC

AGGCGAC!GAA

TCCAGAACCA

AATCACTGGA

CGACGAAGTT

TGAAATGTrc

TCGTGGTGT

CGTCAAG7"rG

GAAGAATTGC

CCAGGTGATG

AAATACGAAG

GAACGTGATA

CGTGGTACAG

GAAATCGTrG

CGTAAACAAC

CAACGTGATG

GTGTTAAACA

TTGAATTGGT

ACCTTCCAGT

ACATCATCAT

CTGACAAACC

TTGCTTCAGG

GTATTAAAGA

TTGACGAAGG

AAATCGAACG

TGGACCAATG

CCTTATCGTA

TGAhAATGGAA,

TATCCAAGGT

GGAATTGA'IG

TTTACTTCTT

ACGTATCGAC

AGATATCCAA

TCTTGCAGGG

TGGTCAAGTT

CCACAAACTC GTGAGCACAT TTCATGAACA AAGTTGACCT ATTCGTGACC TTCTTrCAGA TCAGCTCTTA AAGCACTTGA AGCACTGTTG ATGAGTACAT CCAGTTGAAG ATGTATTCTC CGTGGTACTG TTCGTGTCA.A AAAGCAGTTG TTACTGGTGT GACAACGTTG

GTGTTCTTCT

CTTGCTAA&C CAGGTTCAAT 120 180 240 300 360 420 460 540 600 133 CAACCCACAC ACTAAATTTA AAGGTGAAGT TTACATCCTT TCTAAAGAAG AAGGTGGACG TCATACTCCA TTCTTCAACA ACTACCGTCC ACAATTCTAC TTCCGTACAA CTGACGTAAC AGGTTCAATC GAACTTCCAG CAGGAACAGA AATGGTTATG CCTGGTGATA ACGTTACTAT CGAAGTTGAA TTGATTCACC CAATCGCCGT AGAACAA INFORMATION FOR SEQ ID NO: 145: Wi SEQUENCE CHARACTERISTICS: LENGTH: 817 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Streptococcus pneumoniae (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 145: CGGAGCTATC CTTGTAGTAG CTTCAACTGA CGGACCAATG CCACAAACTC GTGAGCACAT

CCTTCTTTCA

GGTTGACGAC

ATACGACTTC

AGGTGACTCT

CCCAGAACCA

AATCACTGGA

CGACGAAATC

TGAAATGTTC

TCGTGGTGTT

CAACCCACAC

TCACACTCCA

AGGTTCAATC

CGTCAGGTTG

GAAGAATIGC

CCAGGTGACG

AAATACGAAG

GAACGTGACA

CGTGGTACAG

GAAATCGTTG

CGTAAACAAC

CAACGTGATG

ACTAAATTCA

TTCTTCAACA

GAACTTCCAG

GTGTTAAACA

TTGAATTGGT

ATCTTCCAGT

ACATCGTTAT

CTGACAAACC

TTGCTTCAGG

GTATCAAAGA

TTGACGAAGG

AAATCGAACG

AAGGTGAAGT

ACTACCGTCC

CAGGTACTGA

CCTTATCGTC

TGAAATGGAA

TATCCAAGGT

GGAATTGATG

ATTGCT TCTT

ACGTATCGAC

AGAAACTCRA

TCTTGCTGGA

TGGACAAGTr

CTACATCCTT

ACAATTCTAC

TTCATGAACA AAGTTGACTT 660 720 780 817 120 180 240 300 360 420 480 540 600 660 720 780

ATCCGTGACC

TCAGCACTTA

AACACAGTTG

CCAGTCGAGG

CGTGGTATCG

AAAGCAGTTG

GATAACGTAG

ATCGC TAAAC

ACTAAAGAAG

TTCCGTACTA

TATTGTCAGA

AAGCTCTTGA

ATGAGTATAT

ACGTATTCTC

TTAAAGTCAA

TTACTGGTGT

GTGTCCTTCT

CAGGTTCAAT

AAGGTGGACG

CTGACGTTAC

AATGGTAATG CCTGGTGATA ACGTGACAAT COACGTTGAG TTGATTCACC CAATCGCCGT AGAACA INFORMATION FOR SEQ ID NO: 146: Wi SEQUENCE CHARACTERISTICS: LENGTH: 817 base pairs TYPE: nucleic acid 134 STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Streptococcus salivarius (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 146: CGGTGCGATC CTTGTAGTAG CATCTACTGA CGGACCAATG CC-ACAAACTC

CCTTCTTTCA

GGTTGACGAT

ATACGATTTC

AGGTCATTCT

CCCAGAACCA

AATCACTGGT

TGACGAAGTT

TGAAATGTTC

TCGTGGTATC

CAACCCACAC

TCACACTCCA

AGGTTCAATC

CGTCAGGTTG

GAAGAATTGC

CCAGGTGATG

AAATACGAAG

GAACGTGACA

CGTGGTACTG

GAAATCGTTG

CGTAAACAAC

CAACGTGATG

ACTAAATTCA

TTCTTCAACA

GAACTTCCTG

GTGTTAAACA

TTGAATTGGT

ACATTCCAGT

ACATCATCAT

CTGACAAACC

TTlGCTTCAGG

GTCTTAAAGA

TTGACGRAGG

AAATCGAACG

AAGGTGAAGT

ACTACCGTCC

CAGGTACTGA

CCTTATCGTC

TGAAATGGAA

TATCCAAGGT

GGACTTGATG

ATTGTTGCTT

ACGTATCGAC

AGAC.ATCC.AA

TATTGCCGGA

TGGTCAAGTA

TTACATCCTT

ACA.GTTCTAC

AATGGTTATG

TTCATGAACA

ATCCGTGACC

TCAGCTCTTA

AACACTGTTG

CCAGTCGAAG

CGTGGTGTTG

AAAGCAGTTG

GATAACGTCG

TTGGCTGCAC

TCTAAAGAAG

TTCCGTACAA

CCTGGTGATA

GTGAGCACAT

AAGTTGACTT

TTCTTTCAGA

AAGCTCTTGA

ACGAATACAT

ACGTATTCTC

TTCGTGTCAA

TTACTGGTGT

GTGTTCTTCT

CTGGTTCAAT

AAGGTGGACG

CTGACGTAAC

ACaTaACTAT 120 180 240 300 360 420 480 540 600 660 720 780 817 120 CGACGTTGAG TTGATCCACC CAATCGCCGT TGAACAA INFORM4ATION FOR, SEQ ID NO: 147: Wi SEQUENCE CHARACTERISTICS: LENGTH: 897 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Agrobacteriumi turnefaciens (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 147: AACATGATCA CCGGTGCTGC CGAGATGGAC GGCGCGATCC TGGTTTGCTC GGCTGCCGAC GGCCCGATGC CACAGACCCG CGAGCACATC CTGCTTGCCC GTCAGGTGGG CGTTCCGGCC 135

ATCGTCGTGT

GAGCTTGAAG

ATCAAGGGTT

ATCCGCGAGC

CAGCCGTTCC

ACGGGTCGCG

CGTC1CGACCT

GGCCAGGCCG

CGTGGTCAGA.

GCCTACATCC

CCGCAGTTCT

GAAATGGTTA

TCCTCAACAA

TTCGCGAAC!T

CGGCACTTGC

TGATGGCTGC

TGATGCCGAT

TTGAGCGCGG

CGAAGACGAC

GCGACAACAT

TCCTGTGCAA

TGACGAAGGA

ACTTCCGTAC

TGCCTGGCGA

GGTCGACCAG

TCTGTCGTCC

TGCTCTTGAA

TGTCGACGCC

CGAAGACGTG

TATCGTCAAG

TGTTACCGGC

CGGTGCACTC

GCCGGGTTCG

AGAAGGCGGC

GACTGACGTT

CAACGTCACT

GTTGACGACG

TACGACTTCC

GATTCTGACA

TACATCCCGA

TTCTCGATCT

GTTGGTGAAG

GTTGAAATGT

GTTCGCGGCG

GTCAAGCCGC

CGTCATACGC

ACCGGTATCG

GTTGAAGTCG

CCGAGCTTCT

CGGGCGACGA

AGAAGATCGG

CGCCTGAGCG

C!GGGTCGTGG

AAGTCGAAAT

TC!CGCAAGCT

TTACCCGTGA

ACAAGAAGTT

CGTTCTTCAC

TTTCGCTTCC

AGCTGATCGT

CGAGCTCGTC

TATCCCGATC

TGAAGACGCG

TCCGATCGAC

TACGGTTGTG

CGTCGGCATC

GCTCGACCAG

CGGCGTCGAG

CATGGCAGAA

GAACTACCGT

TGAAGGCACG

TCCGATCGCG

180 240 300 360 420 480 540 600 660 720 780 840 ATGGAAGAAA AGCTGCGCTT CGCTATCCGC GAAGGCGGCC GTACCGTCGG CGCCGGC INFORMATION FOR SEQ ID NO: 148: Wi SEQUENCE CHARACTERISTICS: LENGTH: 885 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Bacillus subtilis (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 148: ATGATCACTG GTGCTGCGCA AATGGACGGA GCTATCCTTG TAGTATCTGC CCAATGCCAC AAACTCGTGA GCACATCCTT CTTTCTAAAA ACGTTGGTGT GTTGTATTCT TAAACAAATG CGACATGGTA GACGACGAAG AGCTTCTTGA ATGGAAGTTC GCGATCTTCT TAGCGAATAC GACTTCCCTG GTGATGATGT AAAGGTTCTG CTCTTAAAGC TCTTGAAGGA GACGCTGAGT GGGAAGCTAA CTTATGGATG CGGTTGATGA GTACATCCCA ACTCCAGAAC GCGACACTGA ATGATGCCAG TTGAGGACGT ATTCTCAATC ACTGGTCGTG GTACAGTTGC GTAGAACGCG GACAAGTTAA AGTCGGTGAC GAAGTTGAAA TCATCGGTCT

TGCTGATGGC

ACCATACATC

ACTAGTTGAA

ACCAGTTGTT

AATCTTCGAA

AAAACCATTC

TACTGGCCGT

TCAAGAAGAG

120 180 240 300 360 420 480 136 AACAAGAAAA CAACTGTTAC AGGTGTTGA.A ATGTTCCGTA AGCTTCTTGA GCTGGTGACA ACATTGGTGC CCTTCTTCGC GGTGTATCTC GTGAAGAAAT CAAGTACTTG CTAAACCAGG TACAATCACT C-Ac:ACAGCA AATTCAAAGC GTTCTTTCTA AAGAAGAGGG TGGACGTCAT ACTCCATTCT TCTCTAACTA TTCTACTTCC GTACAACTGA CGTAACTGGT ATCATCCATC TTCCAGAAGG GTTATGCCTG GAGATAACAC TGAAATGAAC GTTGAACTTA TTTCTACAAT GAAGGAACTC GTTTCTCTAT TCGTGAAGGC GGACGTACTG TTGGT INFORMATION FOR SEQ ID NO: 149: Wi SEQUENCE CHARACTERISTICS: LENGTH: 882 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Bacteroides Era gills (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 149: ATGGTTACTG GTGCTGCTCA GATGGACGGT GCTATCATTG TAGTTGCTGC

TTACGCTGAA

CCAACGTGGT

TGAAGTTTAC

CCGTCCTCAG

CGTAGAAATG

CGCTATCGAA

TACTGATGGT

TCCGAAGCTG

ACTTG1TTGAA

TCCGATCATT

AGTAATGGAA

TAAACCTTTC

TACAGGTCGT

GGGTGAAGAT

GGGTGAAGCT

ACGTGOTATG

GGTTTATATC

TCCTCAGTTC

TGAAATGGTA

ACTGAACATC

600 660 720 780 840 885 120 180 240 300 360 420 480 540 600 660 720 780 840

CCGATGCCTC

GTTGTATTCA

ATGGAAATGA

CAGGGTTCTG

CTGATGGAAG

TTGATGCCGG

ATCGAAACTG

AAGAAATCAG

GGTGACAACG

GTTCTTTGTA

CTGAAGAAAO

TACCTGCGTA

ATGCCGGGTG

AGACTCGTGA

TGAACAAGTG

GAGAATTGCT

CTCTTGGTGC

CTGTTGATAC

TAGAAGACGT

GTGTTATCCA

TTGTAACAGG

TAGGTCTGTT

AACCGGGTCA

AAGAAGGTGG

CTATGGACTG

ATAACGTAAC

GCACATCCTT

CGATATGGT T

TTCATTCTAT

ATTGAACGGC

TTGGATTCCA

GTTCTCTATC

TGTAGGTGAT

TGTTGAAATG

GCTTCGTGGT

GAT"TAAACCT

TCGTCACACT

TTGGCTCGTC

GAAGATGCTG

GATTTCGACG

GTAGAAAAAT

CTGCCTCCGC

ACAGGTCGTG

GAAATCGAAA

TTCCGCAAAC

GTTGACAAGA

CACTCTAAAT

CCATTCCATA

AGGTAAACGT

AGATGTTGGA

GTGACAATAC

GGGAAGACAA

GCGATGTTGA

GTACTGTAGC

TCCTCGGTFT

TTCTGGATCA

ACGAAATCAA

TCAAAGCAGA

ACAAATATCG

CGGAAGGAAC

ATCCGGTTGC

TACAGGTGAA ATCACTCTTC TATCACTGTA GAGTTGATC'r 137 GGTCTTCGTT TCGCTATCCG CGAAGGTGGA CGTACAGTAG GT INFORMATION FOR SEQ ID NO: 150: SEQUENCE CHARACTERISTICS: LENGTH: 888 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Borrelia bur-gdorferi (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 150: AATATGATTA CAGGAGCAGC TCAAATGGAT GCAGCGATAC TTTTAGTTGC TGCTGATAGT 0* S S .5 *5

S

S

*SSS**

S

S

GGTGCTGAGc

ATAATAGTTT

GTTGAAGTTT

GGTTCAGCTT

GAACTTCTTG

TTTTTGCTTG

CGTATTGAAA

ACCAGAAAAA

GCAGGGGATA

CAAGTTrTGT

TGTTTGACTA

TTCTTTTTTA

ATGCCTGGTG

CTCAAACAAA

TTTTAAATAA

TAGAACTTGT

TTGGGGCTAT

AATCTATGGA

CTGTTGAAGA

GAGGTATTAT

CTACTGTTAC

ATGTTGGTCT

CAGCTCCAGG

AAGAAGAAGG

GAACAACCGA

ATAATGTTGA

AGAGCATTTG

ATTGGACTTA

TGAAAAATAT

GTCAAATCCA

TAATTATTTT

TGTATTTTCT

TAAAGTTGGT

TGGTGTTGAA

TCTTTTGAGA

TACAATTACT

CGGTAGGCAC

TGTTACTGGA

TATTATTGTT

CTTCTTGCTC

GCAGATCCTG

GGCTTTTCAG

GAAGATCCTG

GATCTTCCAG

ATTTCAGGAA

CAAGAAGTTG

ATGTTCCAGA

GGCGTTGATA

CCACACAAGA

AAGCCATTTT

GTTGTTGCTT

GAGCTGATCT

AAAGAATGGG AATAAAGAAA AACTTGTTGA GCTTGTTGAA CTGATACTCC AATAATCAAA AATCTACAAA ATGCGTTAAA AAAGAGATAT TGACAAGCCA GAGGC.ACTGT TGCTACTGGG AAATAGTTGG AATTAAAGAA AAATTCTTGA GCAAGGTCAA AAAAAGACAT TGAGAGGGGG AATTTAAAGC TTCAATTTAT TCCCAGGGTA TAGACCACAG TAGAGGGCAA AGAAATGGTT CTTCAATAGC TATGGATAAG 882 1.20 240 300 360 420 480 540 600 660 720 780 840 AATGTAGAAT TTGCTGTTCG AGAAGGTGGA AGAACCGTTG CTTCAGGA INFORMATION FOR SEQ ID NO: 151: Wi SEQUENCE CHARACTERISTICS: LENGTH: 894 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) 138 (vi) ORIGINAL SOURCE: ORGANISM: Brevibacteriun linens (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 151.

AACATGATCA CCGGTGCCGC TCAGATGGAC

GGACCGATGC

ATCGTCGTGG

GAATTCGAGG

ATTCCGGTGT

GATCTCATGG

TTCCTCATGC

CGTGTCGAGC

AAGTCGTCCA

CGTGCAGGTG

GGTCAGGTCA

TACATCCTGA

CAGTI'CTACT

ATGGTCATGC

CCCAGACCCG

CTCTGAACAA

TCCGCGACCT

CCGCTCTCAA

CTGCCGTCGA

CCGTCGAGGA

GCGGCGTGCT

AGACGACTOT

AGAACGTCGG

TCGTGAAGCC

GCAAGGACGA

TCCGGACCAC

CCGGCGACAA

TGAGCACGTG

GTCCGACATG

GCTCTCGAGc

GGCGCTGGAA

TGACAACGTT

CGTCTTCACG

CCTGCCTAAC

CACCGCTATC

TCTGCTCCTC

GGGTTCGATC

GGGCGGACGT

GGACGTCACC

CACCGATATG

GGTGCGATCC TCGTCGTCGC CTGCTCGCGC GTCAGGTCGG

GTC!GATGACG

CAGGACTTCG

GGCGACGAGA

CCGGAGCCGG

ATCACCGGTC

GACGAAATCG

GAGATGTTCC

CGCGGCACCA

ACCCCGCACA

CACAACCCGT

GGTGTCATCA

TCGGTCGAGC

AGGAGCTCCT

ACGGAGACAA

AGTGGGTCAA

AGCGCGATGT

GTGGAACCGT

AAATCGTCGG

GCAAGACCCT

AGCGCGAGGA

CCAAGTTCGA

TCTACTCGAA

CGCTGCCCGA

TCATCCAGCC

CGCTACCGAC

CGTTCCCTAC

CGAGCTCGTC

CGCTCCGGTC

GAGCGTTCAG

CGACAAGCCG

CGTCACCGGT

CATCAAGGAG

GCCGGATGCC

TGTTGAGCGC

GGCTCAGGTC

CTACCGTCCG

GGGCACCGAG

GATCGCTATG

4* 5 S S S

S.

S

S es

S

*SS

t es 0 0

S

0

S

120 180 240 300 360 420 480 540 600 660 720 780 840 894 120 GAGGACCGCC TCCGCTTCGC AATCCGCGAA GGTGGCCGCA CCGTCGGCGC CGGT INFORMATION FOR SEQ ID NO: 152: ()SEQUENCE CHARACTERISTICS: LENGTH: 888 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE:- DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Burkholderia cepacia (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 152: ATGATCACGG GCGCAGCGCA GATGGACGGC GCGATCCTGG TTTGCTCGG3C ACAGACGGC CCGATGCCGC AAACGCGTGA GCACATCCTG CTGGCGCGTC AGGTTGGTGT TCCGTACATC ATCGTGTTCC TGAACAAGTG CGACAGTGTG GACGACGCTG AACTGCTCGA GCTGGTCGAG 139

ATGGAAGTTC

AAGGGTTCGG

ATGAGCCTGG

GCGTTCCTGA

GGTCGTGTCG

CCGACGGTGA

CAGGCAGGCG

GGCCAGGTTC

TACGTGCTGA

CAGTTCTACT

ATGGTGATGC

GAAGAAGGTC

GCGAACTCCT

CC!AAGCTGGC

CAGACGCGCT

TGCCGGTGGA

AGCGCGGCAT

AGACGACCTG

ACAACGTCGG

TGGCGAAGCC

GCAAGGACGA

TCCGTACGAC

CGGGCGACAA

GTCGAAGTAC

GCTGGAAGGC

GGACACGTAC

AGACGTGTTC

CGTGAAGGTC

CACGGGCGTT

TATCCTGCTG

GGGTTCGATC

AGGCGGCCGT

GGACGTGACG

CGTGTCGATC

GACTTCCCGG GCGACGACAC GCCGATCGTG GACACGGGCG AGCTGGGCGA AGTGGCGATC

ATCCCGACGC

TCGATCTCGG

GGCGAAGAAA

GAAATGTTCC

CGCGGCACGA

ACGCCOCACA

CACACGCCGT

GGCTCGATCG

ACGGTGAAC

CGGAGCGTGc AGTTGACGGC

GCCGTGGTAC

TCGAAATCGT

GCAAGCTGCT

AGCGTGAAGA

CGCACTTCAC

TCTTCAACAA

AGCTGCCGAA

TGATTGCTCC

GGTGGTGAC!G

CGGTATCAAG

GGACCAAGGT

CCTGGAGCGT

GGCTGAAGTG

CTACCGTCCG

GGACAAGGAA

GATCGCGATG

TGCGCTTCGC AATCCGTGAA GGCGGCCGTA CGGTCGGC INFORMATION FOR SEQ ID NO: 153: Wi SEQUENCE CHARACTERISTICS: LENGTH: 891 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genornic) (vi) ORIGINAL SOURCE: ORGANISM: Chlarnydia trachomatis (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 153: AACATGATCA CCGGTGCGGC TCAAATGGAC GGGGCTATTC TAGTAGTITC GGAGCTATGC CTCAAACTAA AGAGCATATT CTTTTGGCAA GA.CAAGTTGG ATCGTTGTrT TTCTCAATA.A AATTGACATG ATTTCCGAAG AAGACGCTGA TTGGTTGAGA' TGGAGTTGGC TGAGCTTCTT GAAGAGAAAG GATACAAAGG ATCAGAGGTT CTGCTCTGAA AGCTTTGGA.A GGAGATGCTG CATACATAGA GAGCTAATGC AAGCCGTCGA TGATAATATC CCTACTCCAG AAAGAGAAAT TTCTTAATGC CTATTGAGGA CGTGTTCTCT ATCTCCGGAC GAGGAACTGT CGTATTGAGC GTGGAATTGT TAAAGTTTCC GATAAAGTTC AGTTGGTCGG ACTAAAGAAJA CGATTGTTAC TGGGGTTGAA ATGTTCAGA AAGAACTCCC 240 300 360 420 480 540 600 660 720 780 840 688 120 180 240 300 360 420 480 540

TGCAACAGAC

GGTTCCTTAC

ATTGGTCGAC

GTGTCCAATC

GAAAGTTCGA

TGACAAGCCT

AGTAACTGGA

TCTTAGAGAT

AGAAGGTCGT

PCTICA97/00829 140 GCAGGAGAGA ACGTTGGATT GCTCCTCAGA GGTATTGGTA AGAACGATGT ATGGTTGTTT GCTTGCCAAA CAGTGTTAAA CCTCATACAC AGTTTAAGTG GTTCTGCAAA AAGAAGAAGG TGGACGACAT AAGCC'rTTCT TCACAGGATA TTCTTCTTCC GTACAACAGA CGTTACAGGT GTGGTAACTC TGCCTGAGGG GTCATGCCTG GGGATAACGT TGAGTTTGAA GTGCAATTGA TTAGCCCTGT GAAGGTATGA GATTTGCGAT TCGTGAAGGT GGTCGTACAA TCGGTGCTGG INFORMATION FOR SEQ ID NO: 1-54: SEQUENCE CHARACTERISTICS: LENGTH: 891 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Escherichia coi (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 154:

GGAAAGAGGA

TGCTGTTTAC

TAGACCTCAA

AGTTGAGATG

GGCTTTAGAA

A

AACATGATCA CCGGTGCTGC GCAGATGGAC GGCGCGATCC TGGTAGTTGC TGCGACTGAC

GGCCCGATGC

ATCATCGTGT

GAAATGGAAG

GTTCGTGGTT

GAACTGGCTG

TTCCTGCTGC

CGTGTAGAAC

ACTCAGAAGT

GCTGGTGAGA

CAGGTACTGG

ATTCTGTCCA

TTCTACTTC

GTAATGCCGG

GACGGTCTGC

CGCAGACTCG

TCCTGAACAA

TTCGTGAACT

CTGCTCTGAA

GCTTCCTGGA

CGATCGAAGA

GCGGTATCAT

CTACCTGTAC

ACGTAGGTGT

CTAAGCCGGG

AAGATGAAGG

GTACTACTGA

GCGACAACAT

GTTTCGCAAT

TGAGCACATC

ATGCGACATG

TCTGTCTCAG

AGCGCTGGAA

TTCTTACATT

CGTATTCTCC

CAAAGTTGGT

TGGCGTTGAA.

TCTGCTGCGT

CACCATCAAG

CGGCCGTCAT

CGTGACTGGT

CAAAATGGTT

CCGTGAAGGC

CTGCTGGGTC

GTTGATGACG

TACGACTTCC

GGCGACGCAG

CCGGAACCAG

ATCTCCGGTC

GAAGAAGTTG

ATGTTCCGCA.

GGTATCAAAC

CCGCACACCA

ACTCCGTTCT

ACCATCGAAC

GTTACCCTGA

GGCCGTACCG

GTCAGGTAGG

AAGAGCTGCT

CGGGCGACGA

AGTGGGAAGC

AGCGTGCGAT

GTGGTACCGT

AAATCGTTGG

AACTGCTGGA

GTGAAGAAAT

AGTTCGAATC

CGTTCCGTAC

GGAACTGGTT

CACTCCGATC

GAAAATCCTG

TGACAAGCCG

TGTTACC!GGT

TATCAAAGAG

CGAAGGCCGT

CGAACGTGGT

TGAAGTGTAC

120 180 240 300 360 420 480 540 600 660 720 780 840 891 TCAAAGGCTA CCGTCCGCAG TGCCGGAAGG CGTAGAGATG TC!CACCCGAT CGCGATGGAC TTGGCGCGGG C 141 INFORMATION FOR SEQ ID NO: 155: SEQUENCE CHARACTERISTICS: LENGTH: 891 base pairs TYPE: nucleic acid STRANDEDNESS. double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Fibrobacter succinog'enes (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 155: AACATGGTGA CTGGTGCTGC TCAGATGGAC GGCGCTATCC TCGTTGTTGC CGCTACTGAC 0

GGTCCGATGC

ATCGTCGTGT

GAAATGGAAG

ATCCGTGGTT

GAACTCATGA

TTCCTCATGC

CGTATCGAAC

ACCACCGAAT

GCAGGTGACA

ATGGTTCTCG

GTTC!TCACGA

TTCTACTTCC

GTTACTCCGG

COCAGACTOG

TCATGAACAA

TTCGCGAACT

CCGCTCTCA.A

ACGCTTGCGA

CGATCGAAGA

GCGGTGTCGT

ACGTCATCAC

ACGTTGGTCT

CAGCTCCGAA

AGGACGAAGG

GCACCACCGA

GTGACACGGT

CGAACACATC CTTCTCGCTc GTGCGACATG G.TTGACGATG CCTCTCCAAG TATGACTTCG GGCCCTCGAA GGCGATCCGG CGAATACATC CCGCTCCCGC CGTGTTCACG ATTACTGGCC TCGCTTGAAC GACAAGGTTG CGGTGTTGAA ATGTTCCGTA CCTCCTCCGT GGTGCTGAAA GTCTGTCACT CCGCACACCG TGGCCGTCAC ACGCCGTTCA CGTTACTGGT ACGATCCAGC CACGATCCAC GTGAACCTCA

ACCAGGTTGG

CTGAAATTCT

ACGGTGACAA

AATACCAGGA

AGCGCGATAC

GCGGCACTGT

AACGTATCGG

AGCTCCTCGA

AGAAGGACAT

AATTTAAGGC

TGAATGGCTA

TCCCGGAAGG

TCGCTCCGAT

CGTGCCGAAG

CGACCTCGTC

CACCCCGATC

CAAGGTCATG

CGACAAGCCG

CGCTACTGGC

TCTCGGTGAA

CGACGCTCAG

CGTCCGTGGC

TGAAATCTAC

CCGTCCGCAG

TGTCGAAATG

CGCTATGGAA

120 180 240 300 360 420 480 540 600 660 720 780 840 AAGCAGCTCC GCTTCGCTAT CCGTGAAGGT GGACGTACTG TTGGTGCTGG C INFORMATION FOR SEQ ID NO: 156: Wi SEQUENCE CHARACTERISTICS: LENGTH: 894 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genornic) (Vi) ORIGINAL SOURCE.

142 ORGA.NISM: Flavobacterium ferrugineum (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 156: AACATGATCA CCGGTGCTGC CCAGATGGAC GGTGCTATCT TAGTTGTGGC

GGTCCTATGC

ATGGTTGTGT

GAGATCGAGG

ATCAAAGGTT

AACCTGATGG

TrCCTGATGA

CGTATCGAGC

TCTCCCCTGA

GAAkGCTGGTG

GGTATGGTAA

TACGTACTGA

CAATTCTACT

ATGGTTATGC

GAAAAAGGTC

CTCAAACAAA

TTCTGAATAA

TTCGCGAAGA

CCGCTACAGG

ACGCTGTTGA

GCGTAGAGGA

GTGGCCGTAT

ACTCTACCGT

ATAACGCCGG

TCGTTAAACC

GCAAAGACGA

TCCGTAC!AAC

CTGGTGATAA

AGAACACATC

AGTTGACCTC

ACTGACTAAA

CGCCCTCGCT

CAGCTACATC

CGTATTCTCT

CAAAGTTGGT

TACAGGTGTT

TCTCCTCCTC

CGGTTCCATC

AGGTGGCCGT

TGACGTTACA

CACCAACCTG

CTGCTTGCTG

GTTGACGACG

CGCGGTTTCG

GGTGAAGAAA

CCACTGCCTC

ATCACTGGTC

GAGCCTGTTG

GAGATGTTCC

CGTGGTGTTG

ACTCCGCACA

CACACTCCAT

GGTGAAGTAG

ACCGTTAAAC

CCCAGGTAGG

AAGAGCTCCT

ACGGCGACAA

AGTGGGTTAA

CTCGTCCGGT

GTGGTACTGT

AGATCGTAGG

GCAAACTCCT

AAAAAACACA,

CGGACTTCAA

TCTTCAACAA

AACTGAACGC

TGATCCAACC

TGCATCAGAC

TGTACCTAAA

GGAGCTGGTT

CACTCCAATC

AGAAATTGAA

TGATCTGCCG

TGCTAC!CGGT

TCTGCAGGAG

CGACGAAGGT

GATCCGTCGC

AGGCGAAGTT

ATACCGTCCT

AGGAACAGAA

GATCGCTATG

120 240 300 360 420 480 540 600 660 720 780 840 894 120 180 240 TGAAATTCGC GATCCGCGAA GGTGGCCGTA CCGTAGGTGC AGGA INFORMATION FOR SEQ ID NO: 157: Wi SEQUENCE CHARACTERISTICS: LENGTH: 891 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY; linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Haemophi2us influenzae (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 157: AATATGATTA CTGGTGCGGC ACAAATGGAT GGTGCTATTT TAGTAGTAGC AGCAACAGAT GGTCCTATGC CACAAACTCG TGAACACATC TTATTAGGTC GCCAAGTAGG TGTTCCATAC ATCATCGTAT TCTTAAACAA ATGCGACATG GTAGATGACG AAGAGTTATT AGAAT1TAGTC GAAATGGAAG TTCGTGAACT TCTATCTCAA TATGACTTCC CAGGTGACGA TACACCAATC 143

GTACGTGGTT

GAGTTAGCAA

TTCCTTCTTC

CGTGTAGAC

ACAGCGAAAA4

GCAGGTGAAA

CAAGTATTAG

GTATTATCAA

TTCTATTTCC

GTAATGCCAG

CAAGGTTTAC

CAGCATTACA

ACCACTTAGA

CAATCGAAGA

GAGGTATTAT

CTACTGTAAC

ACATCGGTGC

CGAAACCAGG

AAGATGAAGG

GTACAACAGA

GCGATAACAT

AGCGTTAAAC

TACTTACATC

TGTGTTCTCA

CCGTACAGGT

GGGTGTTGAA

ATTATTACGT

TTCAATCACA

TGGTCGTCAT

CGTGACTGGT

CAAGATGACA

GGCGTAGCAG

CCAGAACCAG

ATCTCAGGTC

GATGAAGTAG

ATGTTCCGTA

GGTACCAAAC

CCACACcTG

ACTCCATTCT

ACAATCGAAT

GTAAGCTTAA

AATGGGAAGA

AACGTGCGAT

GTGGTACTGT

AAATCGTCGG

AATTACTTGA

GTGAAGAAAT

ACTTCGAATc

TCAAAGGTTA

TACCAGAAGG

TCCACCCAAT

AAAAATCCTT

TGACCAACCG

AGTAACAGGT

TATCAAAGAT

CGAAGGTCGT

CGAACGTGGT

AGAAGTGTAC

CCGTCCACAA.

CGTGGAAATG

TGCGATGGAT

300 360 420 480 540 600 660 720 780 840 GTTTCGCAAT CCGTGAAGGT GGCCGTACAG TAGGTGCAGG

C

INFORMATION FOR SEQ ID NO: 158: Wi SEQUENCE CHARACTERISTICS: LENGTH: 906 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Helicobacter pylonr (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 158: AACATGATCA CCGGTGCGGC GCAAATGGAC GGAGCGATTT TGGTTGTTTC

TGCAGCTGAT

GGCCCTATGC

ATCGTTGTTT

GAAATGGAAG

GTAGCGGGTr

GGTGAAAAAG

GACACTGAAA

ACTGTGGTTA

GTTGGTATCA

TTGGAAAAAG

CTCAAACTAG

TCTTAAACAA

TGCGCGAATT

CAGCTT TAAG

TGCTTAAACT

AAACTTTCTT

CAGGTAGGAT

GACCTACACA

GTGAAGCcGG

GGAGCATATC

ACAAGACATG

GTTGAGCCC

AGCTTTAGAA

TATGGCTGAA

GATGCCGGTT

TGAAAGAGGC

AAAAACGACT

CGATAATGTG

TTATTGTcTc GTAGATGAcC

TATGAATTTC

GAAGCAAAGG

GTGGATGCCT

GAAGATGTGT

GTGGTGAAAG

GTAACCGGTG

GGCGTG=TT

GTCAAGTAGG

AAGAATTGTT

CTGGCGATGA

CTGGTAATGT

ATATCCCTAC

TCTCTATTGC

TAGGCGATGA

TAGAAATGTT

TGAGAGGAAC-

CGTGCCTCAC

AGAACTTGTA

CACTCCTATC

GGGTGAATGG

TCCAGAAAGA

GGGTAGAGGG

AGTGGAAATC

TAGGAAAGAG

TAAAAAAGAA

144 GAAGTGGAAC GCGGTATGGT TCTATGCAAA CCAGGTTCTA TCACTCCGCA CAAGAAATTT GAGGGAGAAA TTTATGTCCT TTCTAAAGAA GAAGGCGGGA GACACACTCC ATTCTTCACC AATTACCGCC CGCAATTCTA TGTGCGCACA ACTGATGTGA CTGGCTCTAT CACCCTTCCT GAAGGCGTAG AAATGGTTAT GCCTGGCGAT AATGTGAAAA TCACTGTAGA GTTGATTAGC CCTGTTGCGT TAGAGTTGGG AACTAAATTT GCGATTCGTG AAGGCGGTAG GACCGTTGGT

GCTGGT

INFORMATION FOR SEQ ID NO. 159: Wi SEQUENCE CHARACTERISTICS: LENGTH: 891 base pairs TYPE: nucleic acid STR.ANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Micrococcus lureus (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 159: AACATGATCA CCGGCGCCGC TCAGATGGAC GGCGCGATCC TCGTGGTCGC CGCTACCGAC 660 720 780 840 900 906 120 180 240 300 360 420 480 540 600 660 720 780 840

GGCCCGATGG

CTGCTCGTGG

GAGATGGAGG

ATCCGCACCT

GACCTCATGG

TTCCTGATGC

CGCGCCGAGC

GTGCAGAAGA

GCCGdCGAGA

CAGGTGCTGG

ATCCTGTCCA

TTCTACTTCC

GTCATGCCCG

CCCAGACCCG

CCCTGAACAA

TCCGGCAGCT

CCGCTCTGAA

ATGCCGTGGA

CGATCGAGGA

GCGGCACCCT

CCACTGTCAC

ACTGCGGTCT

TGGAGCCGGG

AGGACGAGGG

GCACCACCGA

GCGACACCAC

TGAGCACGTG

GTCGGAC!ATG

GCTGTCCTCC

GGCCCTCGAG

CGAGTACATC

CGTCTTCACG

GAAGATCAAC

CGGCATCGAG

GCTCGTGCGC

CTCCATCACC

TGGGCGTCAC

CGTCACCGGC

CTCCTGGCCC

GTGGAGGACG

AGGAGCTTCG

GGCGACCCCC

CCGGACCCGG

ATCACCGGCC

TCCGAGGTCG

ATGTTCCACA

GGTCTGAAGC

CCGCACACCA

ACCCCGTTCT

GTCATCACGC

GCCAGGTCGG

AGGAGCTCCT

ACGTCGACGA

AGTGGGTCAA

TGCGCGACAA

GTGGCACCGT

AGATCGTCGG

AGCA.GCTCGA

GCGACGACGT

ACTTCGAGGC

ACTCGAACTA

TGCCCGAGGG

TCCAGCCGAT

CGTGCCGGCC

CGAGCGTGTC

GGCCCCGGTC

GTCCGTCGAG

GGACAAGCCG

GGTGACCGGT

CATCCGCGAC

CGAGGCCTGG

CGAGCGCGGC

GAACGTCTAC

CCGCGCGCAG

CACCGAGATG

CGCCATGGAG

CGAGATGTCO GTCGAGCTCA GAGGGCCTCG GCTTCGCCAT CCGCGAGGGT GGCCGCACCG TGGGCTCCGG C 145 INFORMATION FOR SEQ ID NO: 160: SEQUENCE CHARACTERISTICS: LENGTH: 891 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Mycobacteriumn tuberculosis (Xi) SEQUENCE DESCRIPTION: SEQ ID NO: 160: AACATGATCA CCGGCGCCGC GCAGATGGAC GGTGCGATCC TGGTGGTCGC CGCCACCGAC GGCCCGATGC CCCAGACCCG ATCCTGGTAG CGCTGAACAA GAGATGGAGG TCCGCGAGCT CGGGTCTCGG CGCTCAAGGC CTGATGAACG CGGTCGACGA CTGATGCCGG TCGAGGACGT GTGGAGCGCG GCGTGATCAA ACCACCAAGA CCACCGTCAC GCGGGCGACA ACGTTGGTTT CAGGTTGTCA CCAAGCCCGG ATCCTGTCCA AGGACGAGGG TTCTACTTCC GCACCACCGA GTGATGCCCG GTGACAACAC

CGAGCACGTT

GGCCGACGCA

GCTGGCTGCC

GCTCGAGGGT

GTCGATTCCG

CTrCACCATT

CGTGAACGAG

CGGTGTGGAG

GCTGCTGCGG

CACCACCACG

CGGCCGGCAC

CGTGACCGGT

CTGCTGGCGC

GTGGACGACG

CAGGAATTCG

GACGCGAAGT

GACCCGGTCC

ACCGGCCGCG

GAAGTTGAGA

ATGTTCCGCA

GGCGTCAAGC

CCGCACACCG

ACGCCGTTCT

GTGGTGACAC

GTCAAGTGGG

AGGAGCTGCT

ACGAGGACGC

GGGTTGCCTC

GCGAGACCGA

GAACCGTGGT

TCGTCGGCAT

AGCTGCTCGA

GCGAGGACGT

AGTTCGAAGG

TCAACAACTA

TGCCGGAGGG

TCCAGCCCGT

TGTGCCCTAC

CGAACTCGTC

CCCGGTTGTG

TGTCGAGGAA

CAAGCCGTTC

CACCGGACGT

TCGCCCATCG

CCAGGGCCAG

CGAGCGTGGC

CCAGGTCTAC

CCGTCCGCAG

CACCGAGATG

CGCCATGGAC

120 180 240 300 360 420 480 540 600 660 720 780 840 891 CAACATCTCG GTGAALGTTGA GAAGGTCTGC GTTTCGCGAT CCGCGAGGGT GGCCGCACCG TGGGCGCCGG C INFORMATION FOR SEQ ID NO: 161:

SEQUENCE*CHARACTERISTICS:

LENGTH: 891 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: 146 ORGANISM: Mycoplasma genitalium (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 161: AATATGATCA CAGGTGCTGC ACAAATGGAT GGAGCTATTC TAGTTGTrTC AGCAACTGAT

AGTGTGATGC

ATGGTAGTTT

GCTGAAGAAG

ATTTATGGCT

GATTTGATTA

TTCTTATTAG

AGAGTTGAAA

ATTAGAAAAG

GCTGGTGACA

CAAGTTTTAG

GCTTTAAAGA

TTCTATTTCC

GTTCTACCTG

AAAGGTAGTA

CCCAAACCCG

TTCTAAACAA

TACGTGATCT

CAGCTTTAAA

AAGCAGT TGA

CAATTGAAGA

GAGGTGAACT

CAGTTGTTAC

ATGCTGGGGT

CAAAACCAGG

AAGAAGAAGG

GTACCACTGA

GTGATAATGC

CGAGCACATC

GTGTGATATT

GTTAACTTCC

AGCATTGGAA

TGAATGGATT

TACGATGACC

CAAAGTAGGT

TGGAATTGAA

ATTATTACGT

CTCTATTAAA

TGGTAGACAC

TGTAACTGGT

TTCTATTACT

TTACTTGCCC GCCAAGTAGG GGTTCCTAAA GCTAGTGATG AAGAGGTACA AGAACTTGTT TATGGTTTTG ATGGTAAGAA CACTCCTATT GGTGATCCAA AGTGGGAGGC TAAGATCCAT CCAACTCCTA CACGTGAAGT AGATAAACCT ATTACTGGTA GAGGTACAGT TGTTACAGGA CAAGAAGTTG AAATTGTTGG TTTAAAACCA ATGTTCAAAA AGGAACTTGA TTCAGCAATG GGTGTTGAAC GTAAAGAAGT TGAAAGAGGT CCGCACAAGA AATTTAAAGC TGAGATCTAT ACTGGTTTTT TAAACGGTTA CCGTCCTCA.A TCTATTGCTT TAGCTGAAAA TACTGAAATG GTTGAGTTA6A TTGCTCCTAT CGCTTGTGAA 120 180 240 300 360 42.0 480 540 600.

660 720 780 840 9* AGTTCTCAAT TCGTGAAGGT GGTAGAACTG TAGGGGCAGG C INFORMATION FOR SEQ ID NO: 162: Ci) SEQUENCE CHARACTERISTICS: LENGTH: 891 base pairs TYPE: nucleic acid STRJUDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Neisseria gonorz-heae (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 162: AACATGATTA CCGGCGCCGC ACAAATGGAC GGTGCAATCC TGGTATGTTC TGCTGCCGAC GGCCCTATGC CGCAAACCCG CGAACACATC CTGCTGGCCC GTCAAGTAGG CGTACCTTAC ATCATCGTGT TCATQAACAA ATGCGACATG GTCGACGATG CCGAGCTGTT CCAACTGGTT GAAATGGAAA TCCGCGACCT GCTGTCCAGC TACGACTTCC CCGGCGACGA CTGCCCGATC 120 180 240 147

GTACAAGGTT

GAACTGGCTA

TTCCTGCTGC

CGTGTAGAGc

ACCCAAAW

GCGGGCGACA

CAGGTATTGG

GTATTGAGCA

TTCTACTTCC

GTAATGCCGG

CCGCACTGAA

CCGCA'rTGGA

CTATCGAAGA

GAGGTATCAT

CCACCTGTAC

ACGTAGGCGT

CCAAACGGGG

AAGAAGAGGG

GTACCACTGA

GTGAGAACGT

AGCCTTGGA.A

CAGATACATC

CGTGTTCTCC

CCACGTTGGT

CGGCGTTGAA

ATTGCTGCGC

TACTATCACT

CGGCCCCCAT

CGTAACCGGC

AACCATTACT

GGCGATGCCG CTTACGAAGA CCGACTCCCG AGCGTGCCGT ATTTCCGGCC GCGGTACCGT GACGAGATTG AAATCGTCGG ATGTTCCGCA AACTGCTGGA GGTACCA)JAC GTGAAGACGT CCTCACACCA AGTTCAAAGC ACCCCGTTTT TCGCCAACTA ACGATTACTT TGGAAAAAGG GTAGAACTGA TTGCGCCTAT

AAAA.ATCTTC

GGACAAACCA

AGTCACCGGC

TCTGAAAGAA

CGAAGGTCAG3

AGAACGCGGT

AGAAGTGTAC

CCGTCCCCAA

TGTGGAAATG

CGCTATGGAA

GAAGGTCTGC GCTTTGCGAT TCGCGAAGGC GGCCGTACCG TGGGTGCCGG C INFORMATION FOR SEQ ID NO: 163: Mi SEQUENCE CHARACTERISTICS: LENGTH: 891 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Rickettsia prowazekil SEQUENCE DESCRIPTION: SEQ ID NO: 163: AATATGATAA CTGGTGCCGC TCAGATGGAT GGTGCTATAT TA 0*

GGTCCTATGC

ATGGTAGTAT

GAGATGGAAG

ATTAAAGGTT

GAGTTAATGA

TTTTTAATGC

AGAGTGGAGT

ACGCAAAAAA

TCTGGAGATA

CTCAAACTAG

TTTTGAATAA

TAAGAGAATT

CTGCACTTCA

ATGCAGTAGA

CAATAGAGGA

CAGGCATAAT

CGACTTGTAC

ATGTCGGTAT

AGAACATATA

AGTAGATATG

ATTATCAAAA

AGCTTTAGAA

TACGTATATA

TGTATTTTCT

TAAGGTGGGT

AGGTGTAGAA

ATTACTACGT

GTAGTTTC TGCTGCTGAT TTACTGGCAA AACAGGTAGG TGTACCTGCT GTAGATGATC CTGACCTATr AGAATTAGTT TATGGTTTCC CTGGTAATGA AATACCTATT GGAAAACCTG AAGGTGAAAA AGCTATTAAT CCTCAGCCTA TAGAGCTACA AGATAAACCT ATTTCAGGCA GAGGTACCGT TGTAACTGGT GAAGAAATTG AAATAGTAGG TCTAAAAAAT ATGTTCAGAA AAT1'ACTTGA TGAAGGACAA GGTACAAAAA GAGAAGAAGT AGAAAGAGGA 120 180 240 300 360 420 480 540 600 148 CAAGTACTTG CAAAACCTGG GAGCATAAAA CCGCATGATA AATTTGAAGC TGAAGTGTAT GTGCTTAGTA AAGAGGAAGG TGGACGTCAT ACCCCATTTA CTAATGATTA TCGCCCACAG TTCTATTTTA GAACAACAGA. TGTTACCGGC ACAATAAAAT TGCCTTCTGA TAAGCAGATG GTTATGCCTG GAGATAATGC TACTTTTTCA GTAGAATTAA TTAAGCCGAT TGCTATGCAA GAAGGGTTAA AATTCTCTAT ACGTGAAGGT GGTAGAACAG TAGGAGCCGG T INFORMATION FOR SEQ ID NO: 164: SEQUENCE CHARACTERISTICS: LENGTH: 891 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Salmonella typhimurium (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 164: AACATGATCA CCGGTGCTGC TCAGATGGAC GGCGCGATCC TGGTTGTTGC TGCGACTGAC 0 9* 0* 0 0* 0* 0000 00 0 0 000 0 000000 0 000 0 0000

GGCCCGATGC-

ATCATCGTGT

GAGATGGAAG

GTTCGTGGTT

GAACTGGCTG

TTCCTGCTGC

CGTGTAGAGC

ACTCAGAAGT

GCCGGTGAGA

CAGGTACTGG

ATTCTGTCCA

TTCTACTTC

GTAATGCCGG

CGCAGACCCG

TCCTGAACAA

TTCGCG.AACT

CTGCTCTGA.A

GCTTCCTGGA

CGATCGAAGA

GCGGTATCAT

CTACCTGTAC

ACGTAGGTGT

CTAAGCCGGG

AAGATGAAGG

GTACTACTGA

GCGACAACAT

TGAGCACATC

ATGCGACATG

GCTGTCTCAG

AGCGCTGGAA

TTCTTATATT

CGTATTCTCC

CAAAGTGGGC

TGGCGTTGAA

TCTGCTGCGT

CACCATCAAG

CGGCCGTCAT

CGTGACTGGT

CAAAATGGTT

CTGCTGGGTC

GTTGATGACG

TACGACTTCC

GGCGACGCAG

CCGGAACCAG

ATCTCCGGTC

GAAGAAGTTG

ATGTTCCGCA

GGTATCAAAC

CCGC.ACACCA

ACTCCGTTCT

ACCATCGAAC

GTTACCCTGA

GTCAGGTAGG CGTTCCGTAC AAGAGCTGCT GGAACTGGTT CGGGCGACGA CACTCCGATC AGTGGGAAGC GAAA.ATCATC AGCGTGCGAT TGACAAGCCG GTGGTACCGT TGTTACCGGT AAATCGTTGG TATCAAAGAG AACTGCTGGA CGAAGGCCGT GTGAAGAAAT CGAACGTGGT AGTTCGAATC TGAAGTGTAC TCAAAGGCTA CCGTCCGCAG TGCCGGAAGG CGTAGAGATG TCCACCCGAT CGCGATGGAC GACGGTCTGC GTTTCGCAAT CCGTGAAGGC GGCCGTACCG TTGGCGCGGG C INFORMATION FOR SEQ ID NO: 165: 149 Wi SEQUENCE CHARACTERISTICS: LENGTH: 681 base pairs TYPE: nucleic acid STRAINDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Shewanella putida (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 165: ATGATCACTG GTGCTGCACA GATGGACGGC GCGATTCTGG TAGTCGCTTC AACAGACGGT a*e

S

S. S 5* C p a.

8 59

S

a

S

a *9*a

CCAATGCCAC

ATCGTATTCA

ATGGAAGTGC

CAAGGTTCAG

TTAGCAGCGG

CTACTGCCAA

GTTGAGCGTG

ACTAAGACAA

GGTGAGAACT

GTATTAGCGA

CTGTCAAAAG

TACTTCCGTA

ATGCCAGGCG

AGACTCGTGA

TGAACAAATG

GTGAACTGTT

CTCTGAAAGC

CGCTGGATTC

TCGAAGACGT

GTATTGTACG

CGTGTACTGG

GTGGTATTTT

AGCCAGGTTC

AAGAAGGTGG

CAACTGACGT

ATAACATCAA

GCACATCCTG

TGACATGGTA

ATCAGAATAC

GCTAGAAGGC

TTACATTCCA

ATTCTCAATT

CGTAGGCGAC

TGTAGAAATG

GTTACGTGGT

AATCAA.CCCA

TCGTCACACG

AACCGGTACT

GATGGTAGTG

CTTTCTCGTC

GATGACGAAG

GATTTCCCAG

GAGCCAGAGT

GAACCACAAC

TCAGGCCGTG

GAAGTTGAAA

TTCCGTAAAC

ACTAAGCGTG

CACACTACTT

CCATTCTTCA

ATCGAACTGC

ACACTGATTT

AGGTTGGCGT ACCATTCATC AGCTGTTAGA. GCTAGTTGAG GTGATGACTT ACCGGTAATC GGGAAGCAAA AATCCTTGAA GTGACATCGA TAAGCCGTTC GTACAGTAGT AACAGGTCGT TCGTTGGTGT ACGTGCGACA TGCTTGACGA AGGTCGTGCA ATGACGTAGA ACGTGGTCAA TTGAATCAGA AGTT1'ACGTA AAGGCTACCC TCCACAGTTC CAGAAGGCGT AGAGATGGTA GCCCAATCGC GATGGACGAA 120 180 240 300 360 420 480 540 600 660 720 780 840 881 a a..

a OS*e GGTTTACGCT TCGCAATCCG TGAAGGCGGT CGTACAGTGG T INFORM4ATION FOR SEQ ID NO: 166: Ci) SEQUENCE CHARACTERISTICS: LENGTH: 897 base pairs TYPE: nucleic acid STR.ANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Stigmatella aurantalaca 150 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 166: AACATGATCA CGGGCGC!GGC G;CAGATGGAC

GGCCCGATGC

ATCGTCGTCT

GAGATGGAGG

ATCC!CTGGCA

ATCCTGAAC

AAGCCGTTCC

ACGGGCCGAG

CGTCCGAC!GC

GGCATGGC!GG

CGTGGGCAGG

GTGTACGTGC

CCGCAGTTCT

GAGATGGTGA

CCCAGACGCG

TCCTGAACAA

TGCGCGACCT

GCGC!GCTCAA

TGATGGC!GGC

TGATGCCGGT

TGGAGCGCGG

AGAAGACGGT

GAGACAACAT

TGC!TGGCGAA

TGTCGAAGGA

ACTTCCGGAC

TGCCGGGAGA

TGAGCACATC

GGTGGACATG

GCTCAAGAAG

GGCGC!TGGAG

GGTGGACGAG

GGAAGACGTG

CAAGATCAAG

CATCACGGGG

CGGAGCGCTG

CTGGGGGAGC

AGAGGGAGGG

GACGGACGTG

CAPLCATCGCC

GGAGCGATTC TGGTGGTGTC CTGCTGGCCA

GGCAGGTGGG

CTGGACGATC

CGGAGC!TGCG

TACGAGTTC!C CGGGCGACAG GGAGACACCA

GCGACATCGG

TACATCCCGA CGCCGCAGCG TTCTCCATCG

CAGGCCGAGG

GTGGGCGAGG AAGTGGAGAT GTGGAGATGT TCCGCAAGCT CTGCGAGGCC TGAAGCGCGA ATCAACCCGC ACACGAAGTT CGGCACACGC CGTTCTTCAA ACCGGAACGG

TGAAGCTGCC

ATCGAGGTGG AGCTCATTAC

CGCGGCCGAC

CGTGCCCTAC

CGAGCTGGTG

CATCCCCATC

CGAGGGAGCG

TGCGACGGAC

AACGGTGGCG

CGTGGGGATC

GCTGGACGAG

GGACCTGGAG

CAAGGCGCAG

GGGATACCGG

GGACAACGTG

TCCGGTCGCC

120 180 240 300 360 420 480 540 600 660 720 780 840 000.

0 ATGGAGAAGG AGCTGCCGTT CGCCATCCGT GAGGGTGGCC GCACGGTGGG

CGCCGGC

INFORMATION FOR SEQ ID NO: 167: SEQUENCE CHARACTERISTICS: LENGTH: 894 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) ORIGINAL SOURCE: ORGANISM: Streptococcus pyogenes (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 167: AACATGATCA CTGGTGCC!GC TCAAATGGAC GGAGCTATCC TTGTAGTTGC

TTCAACTGAT

GGACCAATGC CACAAACTCG TGAGCACATC CTTCTTTCAC GTCAGGTTGG TGTTAAACAC CTTATCGTGT TCATGAACAA AGTTGACCTT GTTGATGACG AAGAGTTGCT

TGAATTAGTT

GAGATGGAAA TTCGTGACCT TCTTTCAGAA TACGATTTCC CAGGTGATGA

CCTTCCAGTT

ATCCAAGGTT CAGCTCTTAA AGCTCTTGAA GGCGACACTA AATTTGAAGA CATCATC!ATG 151 GAATTGATGG ATACTGTTGA TTCATACATT CCAGAACCAG AACGCGACAC TGACAAACCA.

TTGCTTCTTC CAGTCGAAGA CGTATTCTCA CGTATCGACC GTGGTACTGT GAAACTAAAA AAGCTGTTGT CTTGCAGGAG ACAACGTAGG GGTCAAGTTA TTGCTAAACC TATATCCTTT CTAAAGACGA CAATTCTACT TCCGTACAAC ATGGTTATGC CTGGTGATAA GAACAAGGTA CTACTTTCTC

TCGTGTCAAC

TACTGGTGTT

TATCCTTCTT

AAGTTCAATC

AGGTGGACGT

TGACGTAACA

CGTGACAATC

ATTACAGGTC GTGGTACAGT GACGAAATCG AAATCGTTGG GAAATGTTCC GTAAACAACT CGTGGTGTTC AACGTGACGA AACCCACACA CTAAATTCAA CACACTCCAT TCTTCAACAA GGTTCAATCG AACTTCCAGC AACG'TTGAGT TGATCCACCC

TGCTTCAGGA

TATCAAAGAA

TGACGAAGGT

AATCGAACGT

AGGTGAAGTA

CTACCGTCCA

AGGTACAGAA

APATCGCCGTA

420 480 540 600 660 720 780 840 AATCCGTGAA GGTGGACGTA CTGTTGGTTC AGGT INFORMATION FOR SEQ ID NO: 168: Wi SEQUENCE CHARACTERISTICS: LENGTH: 897 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genornic) (vi) ORIGINAL SOURCE: ORGANISM: Thiobacillus cuprinus (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 168: AACATGATCA CCGGTGCGGC CCAGATGGAC GGCGCCATCC TGGTCGTGTC CGCCGCCGAC

GGCCCCATGC

ATCATCGTGT

GAGATGGAAG

ATCAAGGGCT

ATTCTCAAGC

GGCGCGTTCC

ACCGGGCGTG

AAGCCCACCC

GGCCAGGCCG

CGCGGCCAGG

CCCAAACCCG

TCCTCAACAA

TGCGCGAGCT

CGGCCAAGCT

TGGCCGAGGC

TCATGCCCGT

TGGAGCGCGG

TCAAGACCAC

GCGACAACGT

TGCTGTGCAA

CGAGCACATC

GTGCGACATG

GCTGTCCAAG

GGCCCTCGAA

CCTGGACACC

GGAAGACGTG

CATCATCAAG

CTGCACCGGC

CGGCATCTTG

ACCCGGCTCG

CTGCTGGCGC

GTCGACGACG

TACGACTTCC

GGCGACAAGG

TACATC CC CA

TTCTCCATCT

GTCGGCGAGG

GTGGAAATGT

CTGCGCGGCA

ATCAAGCCCC

GTCAGGTGGG

CCGAGCTGCT

CCGGTGACGA

GCGAACTGGG

CGCCCGAGCG

CCGGGCGCGG

AAATCGAGAT

TCAGGAAGCT

CCAAGCGCGA

ACACCCACTT

CGTGCCCTAC

CGAACTCGTC

CACCCCCATC

CGAAGGCGCC

GGCCGTCGAC

CACGGTGGTC

TGTCGGCCTC

GCTCGACCAG

GGAAGTCGAG

CACCGCCGAG

120 180 240 300 360 420 480 540 600 660 152 GTGTACGTGC TGAGCAAGGA CGAGGGCGGC CGCCACACCc CCTTCTTCA CAACTACCGC CCGCAGTTCT ACTTCCGCAC CACCGACGTC ACCGGCGCCA TCGAACTGCC CAAGGACAAG GAAATGGTCA TGCCCGGCGA TAATGTGAGC ATCACCGTA AGCTCATCGC

CCCCATCGCC

ATGGAAGAAG GCCTGCGCTT CGCCATCCGC GAAGGCGGCC GCACCGTCGG

CGCCGGC

INFORMATION FOR SEQ ID NO: 169: Wi SEQUENCE CHARACTERISTICS: LENGTH: 894 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Tr~eponema pallidun (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 169: AATATGATCA CGGGTGCTGC GCAGATGGAC GGTGGTATTC TCGTcG-Tr.TL

GGCGTTATGC

ATCATTGTTT

GAAGAAGAGG

AAGGGGTCTG

GAGGAACTGC

CCTTTCTTGC

GGGCGCATCG

CCCACTAAGA

ATTGCAGGTG

GGTCAGGTGC

TACGTGCTCT

CAGTTTTATT

ATGGTGAAGC

CACAGACGAA

TTTTGAACAA

TGCGTGATGC

CGTTTAAAGC

TTGCGGCCAT

TCTCTATCGA

AATGTGGGGT

AAACAGTGGT

ATAACGTGGG

TTTCTAAGCC

CTAAGGAAGA

TTAGAACTAC

CGGGGGATAA

GGAGCATCTT

GGTTGATTTG

GCTI'GCTGGA

TCTGCAGGAT

GGATTCCTAC

GGATGTGTAC

AATTAGTCTG

TACTGGCATT

GCTGCTTTTG

CGGTTCTATT

GGGTGGCCGT

TGACATTACC

CACCAAGATT

CTGCTCGCCC

GTCAGGTTGG

GTTGATGATC

CTGAGTTGCT

TATGGGTTTT CGCGTGAGAC GGCGCTTCCC

CGGAGGATGC

mTGAAGACC CAGTGCGTGA AcTATTTCTG GGCGTGGTAC AATGAAGAGG TCGAGATCGT GAGATGTTTA ATAAGTTGCT CGCGGGGTGG

ATAAAAAAGA

AAGCCACACA

CCAAGTTTGA

CACAGTCCTT TTTTTCAAGG GGTACGATTT CTCTTCCTGA ATAGGTGAGC TCATCCACCC

TGCGCCTGAC

TGTTCCCTCC

AGAGCTGGTG

GCCTATCGTC

AGCTTGTATT

CGACGCAAGA

CGTTGTCACG

CGGGATTAAG

TGATCAGGGA

GGTTGAGCGC

GGCGCAGATC

TTATCGTCCG

AGGGGTAGAC

GATAGCTATG

GACAAGGGTC TGAAGCTTGC GATTCGTGAA GGGGGGCGCA CTATTGCTTC TGGT INFORMATION FOR SEQ ID NO: 170: Wi SEQUENCE CHARACTERISTICS: 153 LENGTH: 891 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Ureaplasma urealyticwn (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 170: AATATGATTA CAGGGGCAGC ACAAATGGAT GGAGCAATT TAGTTATTGC 000..

GGGGTTATGG

ATCCTTGTTT

GAAATGGAAG

ATTCGTGGTT

GAATrAATGG

TTCTTATTAG

CGTGTTGAAC

ACTCAAAAA

GCTGGTGATA.

CAAGTACTTG

ATTCTTAAAA

TTCTATTTTA

GTTATGCCAG

CTCAAACTAA

TCTTAAACAA

TTCGTGA.ATT

CAGGTCTTAA

ACGCAGTTGA

CAATTGAAGA

GTGGTGTATT

CTGTTGTTAC

ATGCTGGTAT

TAAAACCAGG

AAGAAGAAGG

GAACAACAGA

GTGATGACGT

AGAACATATT

ATGTGATTTC

ATTATCTAAA

GGCTTTAGAA

TTCATGAATT

TGTATTCACA

AAAAGTTAAT

AGGAATTGAA

TTTATTACGT

ATCAATTAA.A

TGGACGTCAT

TGTAACAGGT

TGAAATGACT

TTATTAGCAC

ATGACAGATC

TATGGATTTG

GGAGATCCAG

CCATTACCAG

ATTTCAGGAC

GATGAGGTTG

ATGTTTAGAA

GGTATTAAAA

CCTCACCGTA

ACACCTATTG

GCTATTTCAT

GTAGAATTAA

GTCAAGTTGG

CAGATATGCA

ATGGCGATAA

TTTGAGAAGC

AACGTAGTAC

GTGGTACAGT

AAATTGTTGG

AATCATTAGA

AAGAAGATGT

CTTTTACTGC

TTTCAGGATA

TACCTGCTGG

TTGCTCCAGT

TGCATCTGAT

TGTTCCAAAA.

AGATCTTGTT

CACACCAGTT

AAAAATTGAT

TGACAAACCA

AGTAACTGGA

TCTAAAAGAC

TCAAGCTGAA

TGAACGTGGT

TAAAGTTTAT

CCGTCCACAA

TGTTGATTTG

TGCGATTGAA

120 180 240 300 360 420 480 540 600 660 720 780 040 GATGGATCTA AATTCTCAAT CCGTGA-AGGT GGTAAAACTG TAGGTCATGG T INFORMATION FOR SEQ ID NO: 171: Wi SEQUENCE CHARACTERISTICS: LENGTH: 909 base pairs TYPE: nucleic acid STRANDEDNESS; double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Wolinella succiziogenes (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 171: 154

AACATGATTA

GGCCCCATGC

ATCGTGGTrT

GAAATGGAAG

GTTGCAGGTT

TGGGGCGAGA

CGAGATGTGG

GGAACCGTTG

ATCGTTGGTA

GAGCTCGACA

GAAGATGTTG

TTTGAAGGTG

AATGGATACC

CCTGAGGGCG

CAGGTGCTGC

CCCAAACTAG

TCTTGAACAA

TTAGAGAACT

CCGCTCTTA.A

AAGTATTGAA

ATAAGCCTTT

TGACAGGAAG

TCCGAAACAC

AGGGTGAGGC

AGAGAGGTAT

AAGTTTACGT

GACCTCAGTT

TAGAGATGGT

TCAAATGGAT

GGAGCACATT

AGAAGATATG

TCTTAGCAAC

AGCTCTTGAA

GCTTATGGCT

CCTTATGCCT

AATTGAAAGA

ACAAAAAACA

GGGTGACAAC

GGTTCTTTGT

TCTTTCCA.AA

CTATGTTAGA

TATGCCTGGT

GGCGCGATTC TTGTTGTTTC TGCGGCGGAT

CTTCTTTCTC

GTTGATGACG

TACGACTcc

GAGGCTAACG

GAGGTTGACC

GTTGAAGACG

GGCGTGGTTA

ACCGTAACTG

GTTGGTGTTC

AAAATAGGTT

GAGGAAGGCG

ACTACAGACG

GACAACGTTA

GACAAGTAGG

CTGAGCTTCT

CTGGAGATGA

ACCAGGAAAA

GATATATTCC

TATTCTCCAT

AAGTCGGTGA

GCGTTGAGAT

TTTTGAGAGG

CTATCACTCC

GACGACACAC

TTACCGGTTC

AGATCAATGT

CGTTCCTTAC

TGAGCTTGTT

CACTCCTATC

TGTTGGCGAG

TACGCCTGAG

CGCGGGTCGT

CGAAGTAGAA

GTTCCGA.AAA

CACCAAGAAA

TCACACTAAC

TCCATTCTTC

TATCTCTCTT

TGAGCTTATC

120 180 240 300 360 420 480 540 -600 660 720 780 840 900 GCTCCTGTAG CCCTCGAAGA GGGAACACGA TTCGCGATCC GTGAAGGTGG .TCGAACCGTT

GGTGCGGGT

INFORMATION FOR SEQ ID NO: 172: i)SEQUENCE

CHARACTERISTICS:

LENGTH: 26 base pairs TYPE.- nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (ix) FEATURE: NAME/KEY: misc-feature LOCATION: 6 OTHER INFORMATION:/note= (ix) FEATURE: NAME/KEY: misc-feature LOCATION: 12 OTHER INFORNATION:/note= (ix) FEATURE.

NAME/KEY: misc-feature LOCATION:18 OTHER IN'FORMATION:/note- **fl iflosine" 'In1 in-osine" inasine" 155 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 172: TARTCNGTRA ANGCYTCNAC RCACAT 26 INFORMATION FOR SEQ ID NO: 173: SEQUENCE CHARACTERISTICS: LENGTH: 21 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 173: TCTTTAGCAG AACAGGATGA A INFORMATION FOR SEQ ID NO: 174: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 174: GAATAATTCC ATATCCTCCG

Claims (6)

1. A method for generating a bank of nucleic acids of tuf and/or recA genes from which are derived probes or primers, or both, useful for the specific detection of a microbial species, a microbial genus, or substantially all microbial species of a group comprising bacterial or fungal species, which comprises the step of: amplifying the nucleic acids of a plurality of determined microbial species with a primer pair which has a consensus sequence conserved amongst all microbial species of said group.

2. A method as defined in claim 1, which is for obtaining tufnucleic acids from any bacterium directly from a test sample, which comprises the following steps: a) treating said sample with an aqueous solution containing a pair of primers, each primer having a sequence having at least 12 nucleotides in length and •15 capable of hybridizing with the nucleic acids of said any bacterium and with SEQ ID NOs: 107 and 108, one of said primers being capable of hybridizing selectively with **one of the two complementary strands of said bacterial tuf gene that contains a target sequence, and the other of said primers being capable of hybridizing with the other of said strands, so as to form an extension product which contains the target sequence as a template; and b) synthesizing an extension product of each of said primers, said i "extension product containing the target sequence, and amplifying to obtain amplified o* nucleic acids. 25 3. A method as defined in claim 1 for obtaining tufnucleic acids from any fungus directly from a test sample, which comprises the following steps: a) treating said sample with an aqueous solution containing a pair of primers, each primer having a sequence having at least 12 nucleotides in length and capable of hybridizing with the nucleic acids of said any fungus and with SEQ ID NOs: 109 and 172, one of said primers being capable of hybridizing selectively with one of the two complementary strands of said fungal tuf gene that contains a target sequence, and the other of said primers being capable of hybridizing with the other of said strands, so as to form an extension product which contains the target sequence as a template; and -157- b) synthesizing an extension product of each of said primers, said extension product containing the target sequence, and amplifying to obtain amplified nucleic acids.

4. A method for obtaining tuf or recA sequences from any microbial species, which comprises the steps of reiterating the method of claim 1 and adding the steps of sequencing the amplified nucleic acids, and assigning a sequence to a given microbial species.

5. A method for obtaining tufsequences from any bacteria which comprises the steps of reiterating steps a) and b) of the method of claim 2 and adding the following steps: c) sequencing the amplified nucleic acids, and ooooo 1 6 A d) assigning a sequence of step c) to a given bacterial species. o° o: 6. A method for obtaining tuf sequences from any fungus which comprises the steps of reiterating steps a) and b) of the method of claim 3 and adding the following steps: c) sequencing the amplified nucleic acids, and d) assigning a sequence of step c) to a given fungal species.

7. A method for generating sequences of probes, or primers, or both, useful for the specific detection of a microbial species, a microbial genus or substantially all microbial species of a group comprising bacterial or fungal species, which comprises S 25 the steps of: reproducing the method of any one of claims 4, 5 or 6, and adding the steps of: 3 aligning said nucleic acid sequences, 3 locating consecutive nucleotides that are present in the nucleic acids of said species or genus, or substantially all species of said group, and not present in the nucleic acid sequences of other species, genera or groups, and 3 deriving consensus nucleic acid sequences useful as probes or primers from said consecutive nucleotides.

158- 8. A bank of nucleic acids comprising nucleic acids obtained from the method of any one of claims 1 to 3. 9. A bank of nucleic acid sequences comprising the sequences obtained from the method of any one of claims 4 to 6. A method for generating probes, or primers or both, useful for the detection of a microbial species, a microbial genus or substantially all microbial species of a group comprising bacterial or fungal species, which comprises the steps of reproducing the method of claim 7 and adding the step of synthesising said probes or primers upon the consensus nucleic acid sequences thereof. 11. A method for identification of a microorganism in a test sample, comprising the steps of: S: 15 obtaining a nucleic acid sequence for a tufand/or recA genes of said microorganism, and oo*o comparing said nucleic acid sequence with the nucleic acid sequences of a bank as defined in claim 9, said bank comprising a nucleic acid sequence obtained from the nucleic acids of said microorganism, whereby said microorganism is identified when said comparison results in a match between said sequences. DATED this 4 th day of July 2001 Infectio Diagnostic Inc. 25 By their Patent Attorneys CULLEN CO.