AU775763B2 - 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: Actual Inventors: Infectio Diagnostic Inc.

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 T M 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.

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 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.

-2- 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 (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' CFU/L; Table Urine specimens found positive by culture are further characterized using standard biochemical tests to identify the bacterial pathogen and are also tested for susceptibility to antibiotics. 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 UTIscreen

T

M, 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 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 specimens There is an obvious need for rapid and accurate diagnostic tests for bacterial detection and identification directly from clinical specimens. DNA-based technologies are rapid and accurate and offer a great potential to improve the diagnosis of infectious diseases (Persing et 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 -4.

there tests ars performed in around only one hour. they provide the clinicians with new diagnostic tools which should contribute to increase the efficiency of therapies with antimicrobial atlents. Clinical specimens from organisms other than humans other primates, birds, plants, mammals, farm animals, livestock and others) may aiso be tested with thv:ee assaya.

A high glercenitage of culture negativespecimeng Amonp all the clinical specimens received for routine diagnosis, approximately of urine specimens and even more (around 95%) for other types of clinical specimens arti, negative for the presence of bacteria! pathogens (Table It would also be desirable, in addition to identify bacteria at the species or genus level in a given specime:1, to screen out the high proportion of negative clinical specimens with a test detectin .l the presence of any bactenium unlversal bacterial detection). Such e screening teil may be based on the DNA 21mplification by POR of a highly conserved genetic target.. 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 wrth this assay.

Towards th8. devlopment -of rapid DNA-basad dingnostic tgsts A ,apicl diagnostic test should have a significant impact on the management of irifections. DNA probe and DNA amplification technologies offer several advantages *20 over conventicnal methods for the identfication of pathogens and antibiotic resistance *.genes. frorn clinical samples (Paraing of af., 1993, Diagnostic Molecular Microbiology- Principles an,: Applications, American Society for Microbiology, Washington, D.C., Ehrlich and Greenberg, 1994, PC R-based. Diagnostics in Infectious Disease, Blackwell Scientific Pulilications, Boston, MA). There Is no need for culture or the bacterial pathogens, hence 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 bacteria! identification than currently used phenotypic identIfIcatIon systems which are based on biochemical tests.

Colmmercially available DNA-based technologies are currently usead in clinical 3) microbiology laboratories, mainly for the detection and identification of fastidious bacterial pathiogens such as Mycobacterium tuberculosis, Chiamydia trachomatis, Neisseria gonorrtioeae as well as for the detection of a variety of viruses (Podzorski and Prming, Molecular detection and identification of microorganisms. In P. Murray et al., 1995, Manual of Clinical Microbiology, ASM press, Washington There are also other coimmercially available DNA-based assays which are used for culture confirmation Iiissays.

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

(US patent No. US 5 437 978), Neisseria spp. (US patent No. US 5 162 19 and- \4 0 Europp~an pat.ent publication No. EP 0 337 090 131) and isteria monocytoganfls (Us patents No's--i389*513 anid 5i 089 386). However, the diagniostic tests oe.*-inribed 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 clinica! microbiology laboratories, there is still a need for an advantageous alternative to the 6 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 me sequences readily available from oatabases, there is no indication therrfrom 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 aetection and identification cf commonly encountered bacterial or fungal pathogens, (iii) the universal detection of I:acterial 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 Le performed directly from any type of clinical specimens or from a microbial cultu;re.

In WO 36/08502 patent publication, we described DNA sequences suitable for the species-specific detection and identification of 12 clinically important bacterial pathogens, the universal detection of bacteria, and (III) 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 wel as oligonucleotide probes and amplification primers derived from these sequences. 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 Enterococ,:us faecium have become a clinical problem because of its resistance to many antibiotics. Both the detection of these bacteria and the evaluation of their resistance pirfiles 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 otthr microbial pathogens or the same and additional antibiotic resistance genes are als o desirable to aim at detecting more taigei genes'aind complement our patent 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 blaem, blarob, blashv, blaoxa, blaZ, aadB, aacC1, aacC2, aacC3, aacA4, aac6'-Ha, 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 tuf or 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 an-r existing 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 S" 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) i.: cycling probe technology (CPT) i) nested PCR, orj) multiplex PCR.

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

oe 20 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 suitable for PCR reactions with all selected primer pairs, which greatly facilitates the 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 15 fragments have been derived either from proprietary fragments or from databases.

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

It is clear to the individual skilled in the art that other oligonucleotide 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 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 o -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 soecies-specific, aenus-specific, universal and antibiotic resistance gene-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 universal detection of bacteria, the database sequences (GenBank, EMBL and Swiss- Prot) were chosen based on their potential for diagnostic purposes according to esequence 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 synthesis 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 S".i 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 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 al., 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, 4" 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 tuf genes from any fungal species.

The tufgenes were amplified directly from bacterial or yeast cultures using the following amplification protocol: One PL of cell suspension was transferred directly to -12- 19 gL 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 /M 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*C for the denaturation step, 1 min at 30-50°C for the annealing step and 1 min at 72 0 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 QIAquick T 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 tuf genes amplification product were sequenced by the dideoxynucleotide chain termination sequencing method by using an Applied Biosystems automated DNA sequencer (model 373A) with their PRISMTM 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 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 tuf seauences 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 Staphlococcus 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).

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 vL of the standardized bacterial suspension was transferred directly to 19 pL of a PCR reaction mixture containing 50 mM KCI, 10 mM Tris-HCI (pH 0.1% Triton X-100, 2.5 mM MgCI 2 -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 0 C for the annealing step and 1 min at 72 0 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 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 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 ML PCR reaction mixture containing 50 mM KCI, 10 mM Tris-HCI (pH 2.5 mM MgCI 2 'o 0.4 pM of each primer, 200 pM of each of the four dNTPs and 0.5 unit of Taq DNA polymerase (Promega) combined with the TaqStart TM antibody (Clontech Laboratories Inc., Palo Alto, CA). The TaqStart T M antibody, which is a neutralizing monoclonal S 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 55C 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 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 intemal 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 pM 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 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.

Hybridization assays with oligonucleotide 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 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.AIIl 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, 2' d 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, 2" ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY). Prehybridization conditions were in 1 M NaCI 10% dextran sulfate 1% SDS 100 pig/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 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.

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 ubiquity tests for oliaonucleotide 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 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 .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, S 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. weaven. 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. schleifer, 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. crista, 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 I 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 laboratories throughout the world: These reference strains are representative of S. 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 genes Antimicrobial resistance complicates treatment and often leads to therapeutic S 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 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 S, 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 S 20 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 tufsequences 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 Oligo

T

M 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 15 annealing temperature was 50 0 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 *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 S"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: Corynebactenum (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"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 tuf sequences 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) 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 is a nucleotide analog able to specifically bind to any of the four nucleotides A, C, G Sor 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 rimers 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 tufsequences 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 seuences. As shown in Annexes 2 and 3, the comparison of tuf sequences 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 tuf sequences of four representative bacterial species selected from each target genus as well as tuf sequences from species of other closely related bacterial genera. A careful analysis of those alignments allowed the selection of oligonucleotide sequences which are conserved within the target genus but which S. discriminate sequences from other closely related genera, thereby permitting the 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 tuf sequences used in the alignment were either sequenced by us or selected from databases. The analysis of this Ssequence 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 S 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 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.

sciur) 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 orimers specific for Candida albicans. 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 tufsequences 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 tuf sequences 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 Candida albicans strains tested were efficiently amplified and there was no S: 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 Streptococcus-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 seauencing of DNA fragments The nucleotide sequence of a portion of the tufgenes 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 sequenber (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 tufgenes. 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-_ 2 p (dATP) by the T4 polynucleotide kinase (Pharmacia) as 15 described earlier. The label could also be non-radioactive.

Specificitv 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 S. 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 ,L PCR reaction mixture containing 50 mM KCI, 10 mM Tris-HCI (pH 0.1% Triton X-100, 2.5 mM MgCI 2 0.4 pM of each primer, 200 /M 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 pL of the cell suspension was added to 19 pL 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 McFarand 0.5 for bacterial cells.

-28- PCR reactions were then subjected to thermal cycling (3 min at 95°C followed by 30 cycles of 1 second at 95 0 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 pg/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 intemal 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.

EXAMPLE 11: Amplification directly from urine sDecimens. For PCR amplification performed *directly from urine specimens, 1 /L 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 Sadded directly to 19 AL 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,, 0.4 .M of each primer, 200 AM of each of the four dNTPs. In addition, each 25 j

A

L reaction contained 0.5 unit of Taq DNA polymerase (Promega) combined with the TaqStartT 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 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.

Se e Amplisensor

T

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 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 for the universal detection of bacteria will also be included. Based on the sites of S- 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,,, blaZ, aadB, aacC1, 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.

32 Table 1. DIstribution of nosocomial pathogens for various human Infections in USA (1990.1992)1.

Pathogen UT1 2 SS1 3 BSI' Pneumonia Escherichia coi Staphylococcus aureus Staphylococcus epoidermidis Enterococcus (aecalis Enterococcus faecium Pseudomonas aeruginose Kiebsiella pneumoniae Proteus mirabilis Streptococcus pneumoniae Group B Streptococci Other Streptococci Haemophilus influenzae Neisseria meningitidis Listeria monocyto genes Other Enterococci Other Staphylococci Candida albicans Other Candida Enterobacter spp.

Acinetobacter spp.

Citrobacter spp.

Serratia marcescens Other Kiebsiella Others 9 5 21 17 6 20 12 9 1 0 9 3 3 4 3 1 0 3 1 2 5 2 o 0 o 0 o 0 1 0 8 3 5 1 7 4 1 2 6 1

CSF

2 2 1 0 0 0 0 0 18 6 3 14 3 0 0 2 2 0 1 1 0 6 4 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.

3 Surgical 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 1 Canada 2 UK' 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 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 S. pyogenes NR NI 1.9 0.9 NR Enterobacter spp. 4.1 5.5 0.5 2.3 Candida spp. 8.5 NI NR 1.0 Others 18.5 17.4" 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 al., 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 1994 January 1995).

Clinical specimens and/or sites Urine Blood culture/marrow Sputum Superficial pus Cerebrospinal fluid Synovial fluid Respiratory tract Deep pus Ears 15 Pleural and pericardial fluid Peritoneal fluid No. of samples tested 17,981 (54.5) 10,010 (30.4) 1,266 (3.8) 1,136 (3.5) 553 (1.7) 523 (1.6) 502 (1.5) 473 (1.4) 289 (0.9) 132(0.4) 101(0.3) 32,966 (100.0) of positive specimens 19.4 6.9 68.4 72.3 1.0 2.7 56.6 56.8 47.1 1.0 28.6 20.0 of negative specimens 80.6 93.1 31.6 27.7 99.0 97.3 43.4 43.2 52.9 99.0 71.4 80.0 r r Total: 20.0 80.0 Table 4. Gram-negative bacterial species (90) used to test the specificity of PCR primers and DNA probes (continues on next page).

Bacterial species Acinetobacter baumannil Acinetobacter Iwo ff1 Actinobacillus Iignieresii Alcali genes faecalis Alcali genes odorans Alcaligenes xylosoxydans subsp. denitrificans Sactemoides distasonis Bacteraides fra gills Bacteroides ovatus Bacteroides thetaiotaomicron Bactemoides vulgatus Bordetella bronchiseptica Bordetella pare pertussis 20 Bordetella pertussis Burkholderia cepacia Citrabacter amalonaticus Citrobacter diversus subsp. koseri Citrobacter freundii Comamonas acidovorans Enterobacter aero genes Entemobacter agglomerans Enterobacter cloace Escherichia coi Escherichia fergusonii Number of reference strains tested 9 1 3 1 1 Moraxella phenylpyruvica Morganella morganii Neisseria animalis Neisseria canis 1 Neisseria caviae Neisseria cinerea 1 Neisseria cuniculi 1 Neisseria elongata subsp. elan gata 1 Neisseria elan gata subsp. glycaytica 1 Neisseria flavescens 1 Neisseria flavescens Branham 1 Neisseria gonorrhoeae I Neisseria lactamica Bacterial species Number of reference strains testeda 1 1 18 1 1 1 3 3 1 1 Neisseria meningitidis Neisseria mucosa Neisseria polysaccharea Neisseria sicca Neisseria sub flava Neisseria weaveri Ochrobactrum antropi Pasteurella aero genes Pasteurella multocida Prevotella melaninogenica Proteus mirabilis Proteus vulgaris 36 Bacterial species Number of reference strains testeda Bacterial species V Escherichia hermannii Eschenichia vulneris Flavobacterium meningosepticum Flavobacterium indolo genes Flavobacterium odoratum Fusobacterium necropho rum Gardnerella vaginelis Haemnophilus haemolyticus Haemnophllus influenzae Haemophilus parahaemolyticus Haemophilus parainfluenzae Hafnia a/ye, Kin gella indolo genes subsp. suttonella Kin gella kin gae Kiebsiella omithinolytica Kiebsiella oxytoca Kiebsiella pneumoniae Moraxella atlantae Moraxella catarrhalis Moraxella lacunata Moraxella osloensis 1 Providencia stuarii 1 Pseudomonas aeruginosa 2 Pseudomonas fluorescens 1 Pseudomonas stutzeri 1 Salmonella arizonae 12 Salmonella choleraesuis 1 Salmonella gallinarum 2 Salmonella typhimunium Providencia alcalifaciens Providencia rettgeni Providencia rustigianh Number of reference strains testeda 14 2 3 Serratia liquefaciens Serratia marcescens Shewanella putida Shigella, boydli Shigella dysenteniae Shigella flexneni Shigella, sonnel Stenotrophomnonas malto philia Yersinia enterocolitica aMost reference strains were obtained from the American Type Culture Collection (ATCC). The other reference strains were obtained from the Laboratoire de Sant Publique du Quebec (LSPQ), (ii) the Center for Disease Control and Prevention (CDC) and (iii) the National Culture Type Collection (NCTC).

37- Table S. 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 aqua ticum Corynebacterium bovis Coiynebacterium ceivicis Corynebacterium diphteniae Corynebacterium flavescens Corynebacterium genitalium Corynebacterium jeikeium Corynebacterium kutcheri Corynebacterium mat ruchotii Corynebactenium minutissimum Corynebacterium mycetoides Corynebacterium pseudodiphtheriticum Corynebactenium pseudo genitalium Car ynebacterium renale Corynebacterium striatum Corynebacterium ulcerans Number of reference strains tested' I Micrococcus knistinae Micrococcus luteus Micrococcus Iylae Micrococcus roseus Micrococcus varians Peptococcus niger 1 Peptostreptococcus anaerobius 1 Peptostreptococcus asaccharolyticus 6 Staphylococcus aureus 1 Staphylococcus auricularis 6 Staphylococcus capitis subsp. urealyticus 1 Staphylococcus cohnii 1 Staphylococcus epidermidis 1 Staphylococcus haemolyicus I Staphylococcus hominis 1 Staphylococcus lugdunensis 1 Staphylococcus saprophyticus 6 Staphylococcus schielffen Bacterial species Number of reference strains testeda 1

I

1 1 1 2 2 2 3 Staphylococcus sciuni Staph ylococcus simulans Staphylococcus wamre -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 solitarius Eubacterium lentum Gemella haemolysans Gemella morbillorum Lactobacillus acidophilus Listeria innocua Listeria ivanovii Listeria grayi Listeria monocytogenes Listeria murrayi Listeria seeligeri Listeria welshimeri Number of reference strains testeda 1 1 1 3 1 1 1 6 3 1 3 1 1 1 1 1 1 1 1 1 1 i 1 3 1 1 1 Bacterial species Staphylococcus xylosus Streptococcus agalactiae Streptococcus anginosus Streptococcus bovis Streptococcus constellatus Streptococcus crista Streptococcus dysgalactiae Streptococcus equi Streptococcus gordonii Group C Streptococci Group D Streptococci Group E Streptococci Group F Streptococci Group G Streptococci Streptococcus intermedius Streptococcus mitis Streptococcus mutans Streptococcus oralis Streptococcus parasanguis Streptococcus pneumoniae Streptococcus pyogenes Streptococcus salivarius Streptococcus sanguis Streptococcus sobrinus Streptococcus suis Streptococcus uberis Streptococcus vestibularis Number of reference strains testeda 1 6 2 2 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 1 6 3 2 2 1 1 1 1 SMost reference strains were obtained from the American Type Culture Collection (ATCC). The other reference strains were obtained from the Laboratoire de Sant& Publique du Quebec (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 Candida albicans Candida glabrata Candida guilliermondil Candida kefyr Candida krusei Candida Iusitaniae Candida parapsilosis Candida tropoicalis Rhodotorula glutinis Rhodotorula minuta Rhodotorula rubra Saccharomyces cerevisiae Number of reference strains tested' 12 3 2 1 2 3 a Most reference strains were obtained from the American Type Culture Collection (ATCC) and (ii) the Laboratoire de Sante Publique du Quebec (LSPQ). 20 Table 7. PCR assays developed for several clinically important bacterial and fungal pathogens (continues on next page).

Organism Primer Pair" Amplicon Ubiquityb DNA amplification from SEQ ID NO size (bp) culturec specimens" Enterococcus faecium 1-2 216 79/80 Listeria monocytogenes 3-4 130 164/168" Neisseria meningitidis 5-6 177 258/258 Staphylococcus 7-8 149 245/260 NT saprophyticus Streptococcus 9-10 154 29/29 agalactiae Candida albicans 11-12 149 88/88 NT Enterococcus 13-14 112 87/87 NT spp. (11 species)' Neisseria spp. 15-16 103 321/321 (12 species)' Staphylococcus spp. 17-18 192 13/14 NT (14 species) 19-20 221 13/14 NT Streptococcus spp. 21-22 153 210/214' (22 species)' Universal detection" 23-24 309 104/ 116' species)' a 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 (MacFariand) or from a colony were all specific and ubiquitous.

d PCR assays performed directly from blood cultures, urine specimens or -41cerebrospinal fluid. NT, not tested.

SThe 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.

9 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 15 Stenotrophomonas (1 species).

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

S

S

S

*S.S

Microorganisms Candida albicans Enterococcus faecium Gene Listena monocytogenes Neisseria meningitidis Streptococcus agalactiae Staphylococcus saprophyticus Enterococcus spp.

Neisseria spp.

Staphylococcus spp.

Streptococcus spp.

Universal detection tuf ddl actA omp cAMP unknown Protein encoded translation elongation factor EF-Tu D-alanine:D-alanine ligase actin-assembly inducing protein outer membrane protein cAMP factor unknown tuf translation elongation factor EF-Tu asd ASA-dehydrogenase tuf translation elongation factor EF-Tu recA RecA protein 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 bla 0 8 49-50 110 fP-lactams Enterobacteniaceae, Pseudomorpadaceae blaZ 51-52 i11 J-actams Enterococcus spp.

aac6-Ia 61-64 112 Aminoglycosides Pseudomonadaceae ermA 91-92 113 Macrolides Staphylococcus spp.

ermnB 93-94 114 Macrolides Staphylococcus spp.

ermC 95-96 115 Macrolides Staphylococcus spp.

vanB 71-74 116 Vancomycin Enterococcus spp.

vanC 75-76 117 Vancomycin Enterococcus spp.

aad(6') 173-174 Streptomycin Enterococcus spp.

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

S

4 55050

C

0@ S S S *5 eq S 4 SS *5 0 4@Se eCCe 0*

C

S

0

S

0485

C

Ce..

S.

Ce..

**ee 0 OC@e -43- Table 10. Antibiotic resistance genes from our co-pending US (N.S.

081526840) and PCT (PCT1CA195100528) patent applications for which we have selected PCR primer pairs.

Genes SEQ ID NOs Antibiotics Bacteria-' of selected primers bla,,, 37-40 1-lactamns blaob blasm, aadB aacCl aacC2 15 aacC3 aacA4 mecA vanA satA aac(6')-aph(2") vat vga msrA int 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 99-102 103-1 06 P-actamns D-Iactamns Aminoglycosides J-lactamns Vancomycin Macrolides Aminoglycasides Macrolides Macrolides Erythromycin P -Iactams, trimeth opnm, aminoglycosides, antiseptic, -chloramphenicol Enterobacteriaceae, Pseudomonadaceae, Haemophllus spp., Neisseria spp.

Haemophllus spp., Pasteurella spp.

Kiebsiella spp.

and other Enterobacteriaceae Enterobacteriaceae, Pseudomonadaceae Staphylococcus spp.

Enterococcus spp.

Enterococcus spp.

Enterococcus spp., Staphylococcus spp.

Staphylococcus spp.

Staphylococcus spp.

Staphylococcus spp.

Enterobacteriaceae, Pseudomonadaceae SBacteria 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 Oxacillin Phenotype blaZ mecA Disk diffusion (Kirby-Bauer)b PCR Resistant Intermediate Sensitive 165 0 0 0 0 31 51 11 4 Gentamycin Erythromycin aac(6')aph(2") 128 6 148 0 0 ermA ermB ermC msrA The 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. wamern (5 strains), for a total of 196 strains.

b Susceptibility 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'.

Antibiotic Phenotype PCR Disk diffusion (Kirby-Bauer)b Resistant Sensitive 0 2 blaZ Ampicillin Gentamycin Streptomycin aac(6')aph(2") aad(6') Vancomycin vanA vanB The Enterococcus strains studied include E. faecalis (33 strains) and E. faecium (69 strains), for a total of 102 strains.

b Susceptibility 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).

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 r Statg fo th seecio fro tu e e of th unvra.mlfcto primers (cnine on pae 49 to Annex I t Abiotrophia adiacens Ablotrophia defecti va Agrobacteri ur turefaciens Ba cill us subtilis Bacteroides fragilis is Borrella burgdorferi Brevibacteri ur lin ens Burkhol deria cepacia Chlamydia trachona ti s 491L CA ACTGTAA

CTACCQMU

CGACTGTTAC

CAA920TAC CAGT9MMC

CGACTG;TCAC

CGACCTGC

CGAT=A~

517 776 CGGTC;TTGA. ATGTTCC. AAAI CGGCGTTOA ATGTTCC AAAMGGT AGGTGTTGAA. ATGTTCC.. .AA&TfGI AGGTGTTG A &MCC. AA&Tg= TO-TGTTGAT AAAGX CGCXATCGAG ATGTTCC AGATGGT QWCGTTGA ATGTTCC AAAG.

TGGGGTGATA AGATGGT 1&1GCCAGGC

ZATGCCTGGA

CATGCCCGGC

CATGCCGGG

802

GATAA=GAA

GACAACG AC

GACAACGTCA

GATAACACTG

9&ThLATGTAG

GACACCACCG

GACAACGTGT

QATA.ACG TG SEQ To

NO

118 119 147 Corynebacteri ur diphteriae CACCGTTA COTTCA ATTCC. AGTG A(CG; GACAACGTC( 4 4* 4 *4 4 Corynebac teriurn genltallun Corynebacten urn jel ke urn Enterococcus fa eca 115 En terococcu s faeci ur Escheri chia coli Fibrobac ter succinogenes Flavobacteri ur ferrugin eurn Gardnerella vaginalls Haerophilus influenzae Helicobac ten pylori Li steria monocytogenes MI crococcuS luteus Mycobacterium? tuberculosis ccCaCC=l CTCCAZQGAg A=ICA. AGTG TATGC-CGCMC QACAACOTTG TATGCCG4(3C CCACCfl&K

CAACYGTTAC

CA Ch

CTACCTGTAC

ACGTgAZCAC cTAC99=hC CCACgrTCAC MCmaxmch 9rC.ACAQ ATOTCA AGA=G

TGGCGTTGAA

AGOTGTTGAG

r.CATC

GGTGTA&A

ATGTTCC.. .AAATGQ AATGCCTQ;GT ATGTTCC... .AAAG CATGCCCOGT ATGTTCC... .AGATGGT AATGCCGGGC ATGTTCC .AAATGGT TCTGG ATOTTCC... AAAZGITCTGGT ACC=ZCC AAAZI TCGCG ATGTTCC. .AAJM AATGCCAGGC .AA&TQM TAOCT

GACAACGTTG

GATAACGTTG

GACAACGT..

GACAACICA

GACACGGTCA

GATAACACCA

QATCAQCAA.

GATA.ACATCA

9AjAATGTGA CGA&T7GM-h-A CGGTTA TATgT&AC TGGAGTAGAA ATGTTCC. AAA=G AAYCCTG GATAACATTG &=CC AGMW CATGrccCGC GACAACACCG CCCCTC CGGTGTGGAG AGTOTATOCCCGGT GACAACCA Mycoplasma genltallun ?Jeisserla gonorrhoea e Rlckettsia prowazekii Salmonella typhimuri ur Shewanel Ia putida Stigma tella auran tiaca Staphylococcus a ureu s Staphylococcus epidermidls Streptococcus agal1act ia e Streptococcus pneumoniae Streptococcus pyo genes Thiobacillus cuprinfu s Treponena pallidun CAT9 *gqATA AAA X. A= aX(C Cbtjg* .diGi~ S .AT AA-COO 9&&.9 CGAGTTA AGTGA ATGTT... AGATG TACTG(; GAThACTA CTg~M TGGCOXTGAA ATGTTCC. AGATGGT XATGCCGGGC GACAACATCA CAACqqT~AC TGGTOTAGA ATGTTCC. AGTL AATG;CCAGGC GAAC& CGGTCAlg&C GGGGGTGGAG C AGATGGT GATGCCGGG AC ACACG CAACMTACh AGGTGTTGAA AAATG MIAIC Q GTTG CAACgTTjAC TGGTGTAGAA ATTC TATGCCTGGC GACAACGTTG CAGTT~A= TGOTrGTTr. A~rTC AAA=~ TATOCCTGGT gATA&MTA CAGTQGAC TGGTQTTGA ATGTTCC AAA=~ ATCCTGQT GAACGC CTGTIZfl&C TGTTTA AT C AAAJ= TATGCCTCMT GATAACGTGA CCAC=WAC CGGCOTOGAA TC.. AAA=~ CILTGCCCGGC QATAATGTCA CAGTOGIAhC TGrAflGA &TGTA. AC= GlACG CATAACACCA 140 141 144 145 167 168 169 4 4 4 4 4 4 4 4 *4 4 4 4 9 4 4 4 *9 **4 Ureaplasma urea lyti cwn Wolinella succinogenes Candida albi cans Schi zo saccharornyces pal Human Selected' equences" CTOTTMflC A99AX=M AITA. ATrkM~ ThTGC&I CATGOTTG (hCqCTAAC TGGCGTOAG AGUMG TAGCGTGCAGT GTGTACAC TAGTCA&B TCCGITG AGRAATT 9GAAGA&AI CCAAAATICG GTGTCACTC C9A9CAA TCTGrG... AGAjA ![GAG gATC~ CCGT itbe TG9C9T

ACXXUAC

2MAGA9TC CACA.AGA. *..AGAA9AGC;TGCCATG CC9GGG2AGG ATGOGT IATGCCIGGI GAIAAYRT SEQ ID NO: 2 4 b AYRTT ITCICCIGGC ATIACCAT Selected universal is primer sequences": SEQ ID NO:23 ACIKKIAC IGGIGTIGAR ATGTT The sequence numbering refers to the E. coli tuf gene fragment. Underlined nucleotides are identical to the selected sequence or match that sequence.

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

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

Annex 11 t Bacillus Statg fo th seecio fro tu seuece of th amlfcto prmr peii o th geu .neoccu (cnine on pae 53 an 54). 31 34 401 43 SEQ NO. CGGA& AMCT C*GA .C .TGA. .GG .CAM A .C9MP .LO 14 subtills Bacteroides fragills Burkhol deria cepacia Chlamydia trachomatis Corynebac teriuzr diphteriae gnterococcug En terococcu s En terococcu s faeIim En terococcus

CGCGAIGTIG

CGTGCAQTIQG

AGAGAMTL

CGTGAGASCG

CGTGA&M

CGTGAT=~

CGTGAC&AACg CGTGAT&U-0 AGGCGPGfl

ACAAACCATT

ACAAACCATT

CCTGAT CCG

CTIA&TGCCT

-CCAMCCT

CATGATGCCA

CATGATGCCA

GTAGA ACTGG GTGGA. .CGCGG ATTGA. CGTGG ATCGA. CGTGG GTCGA. CGTGG GTCGA CGTGG GTTGA. .CGTGG GTCGA. .CGTGG

TGTTAZCPAT

CATC91CAAG

AATTMTAAA

CTCCCTGAAG

ACAATZ9G

ACA.AGTTCGC

ACAAGTTCGC

GTA99GAT9 MACGAAAT CTCGGCGAAG AAATCGAAAT GTTTCC9ATA A.GTCAGTT 9CAACGAGO ACOCGAGAT C;T;QQC A~GAAAT GTTGGTGACG AAIGTAAAT GTG;TA A=GAAGT qGTGTG&TQ A69AGAAAT 126 131 132 133 134 Escherichia coi CGTGCGAT!g &CAAG-GTj CMCT-CCG ATCGA CGCGG TATCAIJCAAA GTMTGAA9 ALLTGAAAT Gardnerel la vaginal is Haeniophil1us influenza e Hellcobacter pylori Li steri a monocytogenes Microcaccus luteus Mycobacteriurn tuberculosis Mycoplasma genltaliwn Neisserla gonorrhoeae Salmonella typhimuri ur Shewanell1a putlda Staphylococcus aureus Staphylococcus epi derrnidi s Staphylococcus saprophyti cus

CACGA-CTTM

CGTGCGATTM

AGAGACM

CGTGAI9T- CGCGACAAG9

CGCGAG&C-CG

CGTGAAGTAQ

CGTGCCGTG9 CGTGCG&kTlI(

CGTGACATCG(

CGTGAITCTO

.AAGCATIf.TGATGCCA ATCGA CGTGG TAAGCI.CCCA A.!CAACAC.CC CAGGAGAT

LCCM-CGII

ACAAACCATT

ACAG=GT

ACAAACCATT

~AGPGT

!9CjTC7TCCA

ACCG

CATGATGCCA

CC19ATOCCG

CCTQATOCCG

CTIATTAGCA

9;ClgClCCT

CCTGCTGCCG

_CCIACTOCCA

CATGATGCCA

CATGATGCCA

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

ATCGA...CGCGG

ATCGA... .CGTGG GTTGA .CGTGG GTTGA .CGTGG

TATTATCMT

CGTGGTGAAA

ACAAMAAA

CACCCTGAAG

CGTGATCAA9

TGAACT-CAAA

TAT AICAP

TATCATCAAA

TATT2AC

TCAAATCAAA

ACAGGTQATG

GTAQ;GCGATO

GTTGOGACG

AICAACTCQG

GTGAACGAGO

PTAr--C!AA

GTTGGTOACG

GTGGGCQAAG

9ACCQACG gTTGGTG.-A

MAGTAGAAAT

AMGGGAAAT

M~GTAGAAGT

AG9-TCGAGAT

~A=IGAGAT

AA=IGAAAT

ALGAT-TGAAAT

AAGTTGAAAT

~A=GAAAT

AAGAAAT

LLA=GAAAT

135 157 158 138 159 160 CGTGAITCTG AC&&AIT TCAAAICAAA 92XWGGTAA9 CGTGATMI ACAAACCATT CATOATOCCA GTTGA CGTGG TCAAATCAAA C-GGTQ;AA9 AACGARAT Streptococcus a galac t ia e Streptococcus pneumonlae Streptococcus pyogen es Ureaplasma urealyticum Selected sequences CGTGAChAM CGCGAC~qTG

CGTAGTACTG

ThCIG 9&**Cj *CTXTC CGG .A~ZIG 9-CAA 9A GAA ACAAACC17T CI-TCZTCCA GTCGA... CGTGG TACTTCT gTCAACAC MAflGAAAT ACAAACCATT CTj!ATj!AGCA ATTGA CGTGG TGTATTAAAA GTTAATQATG AGGTTGAAAT ACAAACCATT CATCATO GTTCGC GTTGGTGACG AAGTT 144 145 167 170 Selected SEQ ID NO: 13 SEQ ID NO: 14' genus-specific primer TACTO ACAAACCATT 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.

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

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

S

S S *5

S

9

S**

S S S S

S

S 55 S S S *5* :1 01 .9 :90 *55 Annex III: Bacillus sub tilis Bacteroldes fragl 1s Burkhol derla cepacia Chlarnydia trachoma ti a Corynebacteriwi diph terlae Enterococcus faecalis Enterococcus faecl ur Escherl chia col Gardnerella 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

TGGCGTGA G QACCEGA_ GIC CGG TGCT ~C TACAATCAT CCACACAGCA 148 AGGTMA.IC gW&C=.QG TTATCCATGT AGO..TTT GTAAACCGGQ TCAGATTAA_4 CCTCACTCTA 149 =GTGGC g&GgCGCA TCGTGAAGGT CGG..TGG CGAAGWGG MIGAZTCACG CCCAACC TGGACGTAI gGCgTGGAA TTGT~GT TTC..TTT GCTTG99AAA _QGZGZTAAA =TCAT CAC 153

D

n ccGGcQa~

AGGAGT(;T

AGGTCgg!GT CGGT-CgGTA

CGGTQIQT

2AG99MrGCT CCCIGAAGGT QAC-GT AnGTCGCGT gMQGg~ MGnTCGCGT g&rCGGTA TCATAMGT gGgGGTA AGCTSCCAAT

CAA..TTG.

TGG..TAG

TGG..TAG

TGG... TOG CAA... TOG TTAAOrAI CG=AA9C CTAAA9C IAA&&Tg CTAAACCAGG TACWACACA6 CTAAG=GG CACAW CTCCC9 TTCGXGACT -CC-T A CC G

CCAACAA

=CRACALA

&CAACJCCA

126 132 133 154 135 q 9 9 .9 9 9 9 9** 9 9 9 9 9 9 9 *9 9 9 *99 9 9 9 9 9 *9 *99 **9 Haemophil1us Influenza e liel icobacter pylori Listeria monocytogenes Micrococcus luteus Mycoba cteriumn tuberculosis Mycop a sma genitallum, Neisseria gonorrhoea e Salmonella typhimurium She wanel la pu tida Srarihy ococcus air staphvI ococcue star'hvliococcus Stap~hylococcus AGGTCGTGTA GA MA TTATCCQTAC AGGTAGGAT GAAGAGGCO TGGIGAA.GT TGGA=T 9M-IA AMGZTTGT CGGTOCgCC QAGCCCA CCC0BAGAT CGGA=GI 9AGQCQ9CG TGj~CGT AGGAArzA 9AgAMG AACTkAAGT CGG9=A 2AGMA99A TC&AgCACGT CGGTIOIA PAGMCMA TCATCAAAGT AGGT9=I 9AOCGTGGTA TTGTACGCGT

AGO..TAG

AGO..TAT

TGG..TAG

CAA...TG

GAA..TCA

AGO..TAG

TGG..TGG

GGG GG

AGO..TAG

TGG..TAG

CGAAACCAGO

GCAAACZCAGO

CAA=AM

TGGAGCCGW

CCAAGCC

CAAAACCAgaG

CCAAACGGGG

CTAAGZ-Gg CGAAG9CAGG

CTGCTCCTGG

CTPQgCTCCG

CTGCTCCTGG

CA99CCCGG

TTCAATCACAL

CTCCTCACC

CACCACCACG

CTCTTTAAA

TTCTATTAC

TACTATC!ACA

CTCTATTACT

CCACAC CTG

=CA-CAGA

CCACACACTA

9CG9LCCCA 9 GCACCCG ~gKCACA.AGA ggTCACCCA 9CCCACCA

CCACACACTA

CCA-CATACTG

CCACACACAA

CCACATACAA

CCAACAA

158 138 159 160 161 162 164 165 140 141 142

AGGCCGTQT

AGGCCOTOTI

AGGCGT=

GAACG;TG;TC AAATCAAAGT GAACGTGGTC A&CMGT

WGG..TAG

CG..TAG

COG..TAG

@9 0 00 9 9 99C88.9.9* Streptococcus AGGAMAZTC 9CC& GGTA CTGITCGTGT CAA..TTG CTAAA9 Zj9&&TCAC C&AACCTA 144 agalact ia e Streptococcus AGGAMGAIC gACCgg=QA TCGTAGT CAA..TCG CTAAACCAGG I=AMIC&AC CCP.CAC CTA 145 pneumoniae Ureapla sma TGGA Z QOAACGTGGTG TAT-SAM&GT TAA..TTG TAAAAggAgG A~&ZTA ggTCCGTA 170 urea lyti cuin Selected CCGTGT~T GAACGTGGTC AMTC&A GCTCCTGG YWWT~- CCACAY sequences* Selected SEQ ID NO: 17 SEQ ID NO: 1 8 b genus-specific primer CCG'IGTT GA.ACGTGGTC AAATCA.A TRTGTGGT GTRATWGWRC CAGGAGC sequences'-

L

The sequence numbering refers to the S.aureus tuf gene fragment. Underlined nucleotides are identical to the selected sequence or match that sequence.

and designate nucleotide positions which are degenerated. I"Rn 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.

0 600 0 ~e 0 SOS S 0

S

500

S

0@ S

S

S

S

*5 S S S S S S 005 555* S 5 0 0 555005 00 @5 0 S S 55** S 0 0 S 5 0 *5 S See 505 OS.

Annex IVt Strategy for the selection from tuf oequenceo of the amplification primers specific for the species Candida albicana (continues on pages 59 and Candida albi cans Candlda glabrata Candi da kr-usei Candida Parapsilosis Candida troplcalis Schizosaccha roniyces Human Chlamydia trachoma ti s CorynebacteriL2 diph eeriae En terococcus faecalis Escheri chi a coi CGTC&&&&AO G=GGTTACA ACCCUAGC CAT9AAG.AAG aCGGTTACA CATCAAGAAO QTTGGTTAC CGTCA.AGA.AG GTTGGTTACA CGTCAAqAAg GTTGGTTAC CATMAGIAAQ 9MQTT pombe GGAGATCCGG gAGCTGCT GGAGCTGCGC GAGCTGCT un GGAGATCCRT GAGCTGCTCG GGAAGTTCGT GACTTATTAT GGAAGTTCGT gAACTICTGT ACCCAAAG C

ACCCAAAGAC

ACCCTAAAGC

ACCCTALC

CCGAGTTTGG

GCAAGTACGG

CTGACCAGGA

CAGA&T&CO;A

CTC-AGTACGA

181 TGT. .CAA TOT. CAA TGT... .CAA TGT... .TAA TOT CAA COT. .CAA

GTT

.CAA

.GAA

TTT..

CTT..

GGCTGGTGTC

GGCAGGTGTT

AGCTGGTAAG

WgGQTAAG

AGGCCTGAAG

OTGOACCCAG

T9AAGA

GGPAAGCG

213 GTTACTOT &GACCTTGTT GTCAAGGGM AGAYCTTGTT GTAAGGGTA AGACCTTATT GTTACCGGTA AACCGTT GTTACCGThAAG TITOrr gCAAQM AQACTCTTTT TCTGTGCAGA AGCTACTGGA S. ThTTCTGG A9CTGATGAA TCC&TCATCO ACCTCATGCA AAAATCTTAG MATTAATGGC AAAATCCTGG AACTGGCTGG SEQ ID NO 120 121 122 123 124 153 126 132 154

V.

V V V V 0 V V V. *VV **V Flavobacteri ur ferrugineum Gardnerella vaginalis Haemophilus influenzae Listerla moflocytogefles Mi crococcus Iuteus Nel sseri a gol2orrhoeae Salmonella typhiniuri ur Staphylococcus aureu s Streptococcus pneurnoniae Treponema pallidum CGAGGTCGC GAAgAACTG,& AQAGGTCCGT 9ACCTCCTCG GGAACTTCGT 9AACTXCTAT GGAAATTCGT _qAICTAITA& GGAAGTCCGT GAGTTGCTGG GGAAMTCCGC 9ACCTOCTGT GGAAGTTCGC QAACTGCTGT G43AAQTTCOT GOkCT-TATTAA GGAAATCCGT GACCTATTGT CTAAACaCOO

AMGAAACGG

CT-CA&TATOA

CTGMA~TTGA

CTGCCCAGGA

CCAGCTACGA

CTf-AGTACGA OCCA&TATaA

CAGAATACQA

TTh.

CTT. CTT.

ATT.

ATT.

CTT.

CTT.

.GGGTThAA CAA GjGG9TAGAG;

.GGGAAGAA

.GGGAAGCT

.CAA GTGGGTCGAG

.ACGAAGA

.GG2AAGCG rAAGQM

CGAAGAC

QAATTAAA ACCTQKTGGA ACCGTCAAGG &ACTCATGAA AAAATCCTIG AGTTAGCAAA AAAATMACO AOTTAATGGA TCT:GTCACAC LTTGATGGA AAAATCTTCG AACTGQCTAC AAALATCATCQ AACTGGCTGG AAAATCTTAG JATTAATGGA ATCGTIATOG MPTTGATGAA

CTT..

CTT..

164 140 145 AGAGGTQCGT GATCGCTTO CTGGATATGG GTT. GGA GGAT9CAGCT TGTATX9AGQ AACTOCTTGC 0 0 0 *0 0 0 0 0 *0* Selected sequences CAAGAAQ GTXGGII&CA ACCAA ATCCGGT GTTACxGGTA AGACCT Selected species-specific primer sequences: SEQ ID NO: 11 CAAGAAG GTTGGTTACA ACCCAAAGA 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.

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

C. C

C

C a C C. *CC **C Annex V: Bordecella pertussi s Burkholderla cepacl a Cainpyiobac ter lo jejunl chlaniydia trachoma tis Clostridiumn perfringens cor-ynebacteriU pseudo tubercul En terobac ter aggi omerains En terococcus faecium Escherichia coli Strategy for the selection from the recA gene of the amplification primers specific for the genus Streptococcusl (continues on pages 62 and 63).

415 449 540 574 SE ID N CTCg&GAICA CCGACGCGCT GGTGCGCTCG GGCTC. GGCCC GCCTGATGAG Cr-AGGCGCM OQCGCTGA CTCGAAICA CCGATGCGCT GGTGCGCTCG GGCTC. GGCCC GCCTGATGTC GCAGGCGCTG CGCAAGCTGA TTAG&&AMMG TagAAACTAX AGCAAGAAGT GGCG AGCAA GACTTATGTC TCAAGCTCI!A AGAAAACTTA TTGAGTAT M&AraCTCII AGCGCGTTCT GGAGC AGCTC GCATgATGTC GgAGGCTCTA _qCAATTAA TTAOAAATAA CAGAAGCTII AG=~AGATCA GGAGC. AGCTA GATZAAI'C ACAAGCCTTZA AGkAAGTTAA m CTGPAGTTO CAATTGCX TGMCGCTCT GGAGC AGCGC GTTTGATGAG TCAGGCGCI9 CTGATGA CTGGA&&ZCT GTgAZGCGCI OACCCGTTCA GGCGC AGCTC GThITGAG CC9-C~ CGTGCTTG TTAgAGATTG gCCgAj(CCLI AGTTCAAGT GGTGC AGCTC GACIALTTC T ACTA 99LAATTAT CTGQAAATCT GTgAgGCCCI 9GCGCGTTCT GGCGC GGCAC GThTGATOA CCA~G&I2 V_(AGCTGG

Q

0 Ha emuophil us influenzae Mel icobacter pyl orli Lactococcus lactis Legionella pneurnophlla Mycopi a sna genltaIiwn Neisseria gonorrhoea e Proteus mirabilis Pseudomonas aeruginosa Serra tia marcescens Shi gel la flexneri Staphylococcus a ureu s Streptococcus crQrdoni Streptococcus mutns GCGAACAGAA GAATAG&&fl TTAATGCATT TTAAM= T~gAACGA7I CACCAGAAGC CTTCAM=T CTGAAA=Af 9=ACTTCT CTGGAAATTA CTGATTCI 9GXGCGTTCT TTTGCTC=A TCGAATCAT AAT-TAAACA TTGGAAATCT GC9CACGC-T CGTCCGTTCG CTGAAIIT GT-GAGC ATCICGCTCT CTGGAAA CA -qCgACATGCT 0GGXGCGCTCC CTGGAAATCT GTGAiGCQCIT 2CCCGCTCC CTGGAAATCT GTOGACCCCI 9GCGCGTTCT CTTAAC9 9CP AG TGMAGAAGT TTAGAMATTG CAGAA GATTGACTCT CTTAAAT CAGGGAMTT 9MMQTTCT ACCGC. .GACCT GGAGG.. .AGCAA GGAGC... .AGCAC GCAGC GGCAA

AACAA...TGCAA

GGCGG... .GGCGC GGTGC CGCAC AACGC... .GGCAC GGCGC. .GGCGC GGCGC. .GGCAC GGTGC... .AGCTC GGGGC GGCGC. .AGCAC GTGAgTITAC

GGCITTATGAG

GTATGATGTC

GATTGATGTC

GAATCATGTC

GCCTGATGAG

GTATGATGAG

GCCTGATOTC

GCATGATGAG

GTATQATQAQ

G~aGCTr-

CCATGCGTIA

ACAAGCCATG

GCAAGCCCTG

AAAGGTTTC

TCAGGCTT2M

CCAAGCTT_

CCAGOCGCTO

CCgq(gCG&~r

CCAGGCGATG

AGACATTAAA

AgAAAATCA 99ZA-ACTTG 99ATTGA

CCGAAGAATAC

CGCAAACTGA

P-GIWCTAG

MCAGATCA

CGTAAGCTGG

CG AGCTGG GTTT&AZGTC ACA(;GTTA CgX-ACTTT GCAT(;ATGAG TCA.AGCQT C-ILAAATTAT 3 3 a a a a.

a aaa stre~tacoccus gtentcoc Vibri 0 cholera e Yersinia Pestls Selected sequences' CT~&gA(;T PGGAA=.~ CTTAA&T2 CAGTAZT CTCQAAATTG CAGGTAAG;CI CTGAMATT GT9Aj!GCACT CTGGAAATZT GTGATGCGCI GAAATTG CAGGIAAATT GATTG CTCA

GATGATTCT

GATTG CTCT 9GCTCGCTCT

GACTCGCTCT

GATTGA

GGTGC... .GGCTC GGTGC .ACCAC GGTGC .AGCGC GGTGC .AGCGC GGTGC.. CGCGC GTATgAXGIAG

GTATGATGA~

GTAT9ATGAG

GTAITTZTC

GTATGATGAG

ATGATGAG

CCAGGCCALTG

TCAGGCCATG;

TCAAGCCATG

GAA&

CCAGGCTI

TCAIGCCATG

CQTAAACTTG

9GTAAATTAT

C-QXAACTTT

99j"CTGA

CGTAAGCTGG

CGTAA

I

Selected SEQ ID NO: 21 SEQ ID NO: 22 genus-specific primer GAAATTG; CACGXAAATT CATT13A TTACQCAT GGCITGACTC ATCAT sequen~ces': The sequence numbering refers. to the S.pneumonlae recA sequence. Underlined nucleotides are identical to the selected sequence or match that sequence.

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- Annex 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 1. 51-TGC TTT AGC AAC AGC CTA TCA G 266 273-294 2b 5'-TAA ACT TCT TCC GGC ACT TCG 261 468-488 Sacteprial1 snecies: Llntex-ja monocyteogenes 3 51-TGC GGC TAT AAA TGA AGA GGC 27& 339-359 4 b 51-ATC CGA TGA TGC TAT GGC TTT 274 448-468 Bacterial s~ecies: Melsocria meningilIdIs 5'-CCA GCG GTA TTG TTT GGT GGT 281 56-76 6b 51-CAG GCG GCC TTT AAT AAT TTC 28a 212-232 Bacterial secies: Staphylococcus gwaprophyticus 7 2 5: AGA TCG AAT TCC ACA TGA AGG TTA TTA TGA 2 9c 290-319 8 b 5 TG TTCTCCC CA AATCA AAC TAT CCT 29 c 409-438 Bacterial-secies; Streptococcus agalactlae *9 5' -TTT CAC CAG CTG TAT TAG AAG TA 30* 59-81 lo* 1 b 51-GTT CCC TGA ACA TTA TC2T TTG AT 30& 190-212 :8Fungxal necies: Candida albicans 11 51 -CAA GAA GGT TGG TTA CAA CCC ~AAGA 120c 61-86 1 2 b 5 '-AGG TCT TAC CAG TAA CTT TAC CGG AT 120c 184-209 Sequences from databases.

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

CSequences determined by our group.

65 An~nex VI: Specific and ubiquitous primers for DNA amplification (continues on next page) SEQ ID NO Nucleotide sequence Originating DNA fragment SEQ ID Nucleotide NO position Bacterial genlus; EnterococcuB 13 51-TAC TGA CAA ACC ATT CAT GAT G 131-1 34 &b 319-340c .14d 51-AAC TTC GTC ACC AAC GCG AAC 1 3 1 1 3 4 .b 410-.430c Bacterial genus* Neisse-za 51-CTG GCG CGG TAT GGT CGG TT 3le 21-40' 16d 51-GCC GAC OTT GGA AGT GOT AAA G 31e 102-123c B3acterial genuse Staphylococcus 17 51-CCG TGT TGA ACG TGG TCA AAT CAA A 1 4 0 1 4 3 b 39 1 4 1 5 9 led 51-TRT GTG GTG TRA TWG WRC CAG GAG C 1 4 0 1 4 3 ab 58 4 -6 0 9 19 51-ACA ACG TGG WCA AGT WTT AGC WGC T 1 4 0 1 4 3 0,b 562-5839 208 51-ACC ATT TCW GTA CCT TCT GOT AAG T 1 4 0-1 43 729-7539 Bacterial genus: Streptococcus 21 51-GAA ATT GCA G01 AAA TTG ATT GA 32-36e 41-01 22d 51-TTA CGC ATG GCI TGA CTC ATC AT 32-36e 547-569h~ Universal primers 23 51-ACI KKI ACI GGI OTI GAR ARO TT 1 1 8 1 4 6 a~b 493-515i 24d 51-AYR TTI TCI CCI GGC ATI ACC AT 1 1 8 1 4 6 9b 778-800' *These sequences were aligned to derive the corresponding primer.

b tuf 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.

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

66 9 The nucleotide positions refer to the S. aureus tuf gene fragment (SEQ ID NO: 14 0).

h The nucleotide positions refer to the S. pneumoniae rer-A gene (SEQ ID NO: 34).

The nucleotide positions refer to the E. coil 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 Antibiotic resistance 37 SI-CTA TGT GCC 38 51-CGC ACT CTT 39 5'-CTG AAT GAA 51-ATC AGC AAT Antibiotic resistance 41 51-TTA CCA TGA 42 5'-CTC ATT CAG 43 51-CAG CTG CTG 44 51-CGC TCT GCT Antibiotic resistance 5'-TAC GCC AAC 46 5'-TTG AAT TTG 47 51-GGG ATA CAG 48 51-TAA ATC TTT Antibiotic resistance 49 S'-CAT GGT TTG 30 5 0 b 51-AAT TTA GTG Antibiotic resistance 51 5'-ACT TCA ACA 35 52 b 5'TG CCA CTT Antibiotic resistance 53 51-GGC AAT AGT 54 5S-CAG CTG TTA Antibiotic resistance 51-TCT ATO ATC 56 5I-ATC GTC ACC ciene: bla,_ GCG GTA TTA TC ATC ACT CAT GG GCC ATA CCA AA AAA CCA GCC AG GCG ATA ACA CC TTC CGT TTC CC CAG TGG ATG GT TTG TTA TTC GG .gn: bla.,.

ATC GTG GAA AG GCT TCT TCG GT AAA CGG GAC AT TTC AGG CAG CG gene: bla.

AAG dCT TTA TTA TGT TTA GAA TGG blaZ CCT GCT GCT TTC TTA TCA GCA ACC *gene aadB TGA AAT C CG CAA CGG ACT GG gene: aacC1 TCG CAG TCT CC GTA ATC TGC TT position 6B06-710 8 02-826 511-531 66 3-683 TAA G 110' TGA T 110, 1111 ilia *Sequences from databases.

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

-68- Annex VI: specific and ubiquitous primers for DNA amplification SEQ ID NO Nucleotide sequence Originating DNA fragment SEQ ID Nucleotide NO position Antibiotic renigtance grene: aacC 2 57 S'-CAT TCT CGA TTG CTT TGC TA 0000 000.

0 58 5'-CCG AAA TGC TTC Antibiotic rpsi-stanne arene 59 51-CTG GAT TAT GGC 51-AGC AGT GTG ATG Antibiotic resistance arene 61 51-GAC TCT TGA TGA 6 2 b 51-CTG GTC TAT TCC 63 51-TAT GAG AAG GCA 6 4 b 51-GCT TTC TCT CGA Antibiotic resistance gene 51-GAG TTG CTG TTC 66 5'-GTG TTT GAA CCA Antibiot-ic-resistance gene 173 51-TCT TTA GCA GAA 174 5'-GAA TAA TTC ATA Antibiotic resistance gene 67 51-TGT AGA GGT CTA 68 51-ACG GGG ATA ACG 69 51-ATA AAG ATG ATA 51-TGC TGT CAT ATT Antibiotic resistance gene 71 51-ATT ATC TTC GGC 7 2 b 51-GAC TAT CGG CTT 73 51-CGA TAG AAG CAG 7 4 5'-CrG ATG GAT GCc TCA AGA TA :aacC3 TAC GGA CT GTA TCC AG :aac6l-I~a AGT GCT GG TCG CAC TC GGA TTC GT AGG CTT GT :aac-A4 AAT GAT CC TGT ACA CG :aad(6') CAG CAT GAA TCC TCC G VaMA GCC CGT GT ACT GTA TG GGC CGG TG GTC TTG CC :vanB GGT TGC TC CCC ATT CC CAG GAC AA GAA CAT AC 112a 112a 1126 112a 116, 116a 116a 12 3-142 284 -303 44 5-464 522-54 1 22-41 171- 190 575 -594 *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 Nucleotide NO position a. a a a *aa.

Antibiotic resistance 51-GCC TTA TOT 7 6 b 51-GTG ACT TTW Antibiotic resistance 77 51-TCC AAT CAT 7B 51-AAT TCC CTC 79 51-TCC CAA GCC 80 5S-TGG TTTrTTC Antibintic resistance 81 51-TCA TAG AAT 82 51-AGC TAC TAT Antibiotic resistance 83 51-CAA TAA GGG 84 51-CCT TAA CAT 51-TTG GGA AGA 86 51-CCT TTA CTC 30 Antibiotic resiStance 87 5'-TTT CAT CTA 88 51-GGA GCA ACA Antibintic resistance 89 51-TGT GCC TGA 90 5'-CGT GTT ACT Antibiotic resistance ciene: vanC ATG AAC AAA TGG GTG ATC CCT Trr GA .gene: marA TGC ACA AAA TC TAT TTG GTG 07 AGT AAA OCT AA AAC TTC TTC CA cyne satA GGA TGG CTC AA TGC ACC ATC CC CAT ACC AAA AAT C TTG TGG CAT TAT C TGA AGT TTT TAG A CAA TAA TTT GGC T crene: vat TTC AGG ATG GO TTC TTT GTG AC crne vga AGA AGG TAT TO TICA CCA CCA CT Ciel~ ermcA 1171 373-393 541- 56 3 91 5'-TAT CTT ATC OTT GAG AAG GGA TT 9 2 b 51-CTA CAC TTG GCT TAG OAT GAA A 113' 113a 370-392 4B87-508 Sequences from databases.

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

Annex VI: Specific and ubiquitous primers for DNA amplification SEQ ID NO Nucleotide sequence Originating DNA fragment SEQ Mucleotide ID No position Antibiotic resistapnce arefe: ermB 93 51-CTA TCT GAT TGT TGA AGA AGG ATT 1146 366-389 9 4 b 5'-GTT TAC TCT TGG TTT AGO ATG AAA 1140 484-507 Antibiot-ic resistance aene: ernC 5'-CTT GTT GAT 9 6 b 5'-ATC TTT TAG Antibiotic resistance

CAC

CAA

6* 6 97 51-AAC AGO TGA ATT 98 51-ATT OCT GTT AAT Antibiotic resistance Sene 99 51-GTG ATC GAA ATC 100 5'-ATC CTC GGT TTT 101 51-CTG GTC ATA CAT 25 102 51-GAT GTT ACC CGA Antibiotic rPsistance cene 103 51-TTA AGC CTO CAT 104 51-TTG CGA TTA CTT 105 51-TTT ACT AAG CTT 106 51-AAA AGG CAC CAA GAT AAT TTC C ACC CGT Arr C :mecA ATT AGC ACT TC ATr TTT TGA G' In CAG ATC C CTG GAA G GTG ATG G GAG CTT G ul AAT AAG CC CGC CAA CT GCC CCT TC TTA TGA GC 1156 1155 ;T AAG

~TGAA

214-235 382 -403 a Sequences from databases.

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

EDITORIAL NOTE APPLICATION NUMBER 54221/01 The following Sequence Listing pages 71 to 155 are part of the description. The claims pages follow on pages 156 to 158.

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 S(D) STATE: QUEBEC COUNTRY: CANADA POSTAL CODE (ZIP): G1Y 1A1 NAME: OUELLETTE, MARC STREET: 1035 DE PLOERMEL CITY: SILLERY STATE: QUEBEC COUNTRY: CANADA POSTAL CODE (ZIP): GIS 3S1 NAME: ROY, PAUL H.

STREET: 28, RUE CHARLES GARNIER CITY: LORETTEVILLE o. STATE: QUEBEC COUNTRY:

CANADA

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) 0 (vi) ORIGINAL SOURCE: ORGANISM: Neisseria meningitidis (xi) SEQUENCE DESCRIPTION: SEQ ID NO: CCAGCGGTAT TGTTTGGTGG T 21 INFORMATION FOR SEQ ID NO: 6: j &0*0 SEQUENCE CHARACTERISTICS: LENGTH: 21 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear cee (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 saprophycicus (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 8: TCGCTTCTCC CTCAACAATC AAACTATCCT INFORMATION FOR SEQ ID NO: 9: i) SEQUENCE CHARACTERISTICS: LENGTH: 23 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear e** (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 STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Candida albicans (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 12: i* 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 S(ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 16: GCCGACGTTG GAAGTGGTAA AG 22 S INFORMATION FOR SEQ ID NO: 17: SEQUENCE CHARACTERISTICS: eeo 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 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: 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: (i).SEQUENCE CHARACTERISTICS: LENGTH: 23 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (ix) FEATURE: NAME/KEY: miscfeature LOCATION:12 OTHER INFORMATION:/note- "n inosine" (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 21: GAAATTGCAG GNAAATTGAT TGA 23 78 INFORMATION FOR SEQ ID NO: 22: Wi SEQUENCE CHARACTERISTICS: LENGTH: 23 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genornic) (ix) FEATURE: NAME/KEY: misc-feature LOCATION:12 OTHER INFORMATION:/note= On inosine" (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 22: TTACGCATGG CNTGACTCAT CAT 23 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)

FEATURE:

NAME/KEY: misc-feature (B3) LOCATION:3 OTHER INFORMATION:/note= O m n inosinelf (ix) FEATURE: NAME/KEY: misc-feature LOCATION:6 =ioie OTHER INFORMATION:/note=on isne (ix) FEATURE: NAME/KEY: misc-feature LOCATION:9 OTHER INFORMATION:/note= On =inosineO (ix) FEATURE: NAME/KEY: misc-feature LOCATION:12 CD) OTHER INFORMATION:/note= 'In inosine"l (ix) FEATURE: NAME/KEY: misc-feature LOCATION:lS OTHER INFORMATION:/flote= 'n iriosine" (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 23: 79 r r

O

r r r ACNKKNACNG GNGTNGARAT GTT 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: miscfeature 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 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 faeciun (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 26: TTCTTAGAGA CATTGAATAT GCCTTATGTC GGCGCAGGCG

ATGGATAAAA

GTACCAGTAC

GGTTCTTTGC

ACAAAGGCAG

TCTCGAGCAA

AATGAAGATG

TATGAAGCCA

GAAGTTTATC

TCATGACCAA

TTAAGAATCA

TTTATCCGAT

AAAACCGAGA

TCGTTGAACA

TTCGGACGAC

AATATATCAA

AAAAAGCGCA

GTATATTTTA

ATGGAAAGAA

GTTTGTCAAA

AGAGCTGCAA

AGGAATTGAA

TTTGCCTGGC

TAATAAAATC

AGAGTACGCG

CAAGCTGCTG

AATCCTAAAA

CCTGCGAATA

AATGCTTTAG

GCGCGCGAAA

GAAGTCGTAA

GAAATGCAGA

AAGTTAGCTT

TATTGACCAG

GTGTGCCGCA

AAGTATTTGA

TGGGTTCTAG

CAACAGCCTA

TCGA.AGTTGC

AAGACGTAGC

TTCCAGCCGA

ACACGATG'1r TGCATGTGcC

AGTTCCTTAT

TCAATGTGAA

TGTCGGCATT

TCAGTATGAT

TGTATTAGGA

ATTCTATGAT

AGTGCCGGAA

AGGTGGAAGC

GGATTGAGCC GGTGCGAT1'T CTTTTTGACA AATAAAAATG AATTATTCCT GAATGAXTTA INFORMATION FOR SEQ ID NO: 27: Wi SEQUENCE CHARACTERISTICS: LENGTH: 1920 base pairs TYPE: nucleic acid STR.ANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Listeria monocytogenes (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 27: GTGGGATTAA ACAGATT'rAT GCGTGCGATG ATGGTGGTTT TCATTACTGC ACGATTAACC CCGAC-ATAAT ATTTGCAGCG ACAGATAGCG AAGATTCTAG GATGAATGGG AAGAAGAA AACAGAAGAG CAACCAAGCG AGGTAAATAC TACGAAACTG CACGTGAAGT AAGTTCACGT GATATTAAAG AACTAGAAAA GTGAGAAATA CGAACAAAGC AGACCTAATA GCAATGTTGA AAGAAAAAGC CCAAATATCA ATAATAACAA CAGTGAACAA ACTGAGAATG CGGCTATAAA 120 180 240 300 360 420 480 540 600 120 160 240 300 360

CAATTGCATT

TCTAAACACA

GGGACCAAGA

ATCGAATAAA

AGAAAAAGGT

TGAAGAGGCT

81

TCAGGAGCCG

AGCGCAGCGG

AGCCTTACTT

GTTGCGGATG

CCACAACCTT

GATGCGGGGA

GTTGATAAAA

AATGCTTCGG

ACACCAATGC

CCACCACCAC

GGTTTTAATG

GAAGATGAAC

GGGGATTTAG

CCACCAATCC

TTTAGTTCGC

GAAATTGATC

GGT TTTTAC

TCGAAAATAA

CCATCACAGC

CCAACCCCTG

ACCGTACTTA

TCAATTAATA

GAAATGAAAC

AACGGAAAAA

GACGAAAAAG

ACCGACCAGC

AAATTAAAAA

ATCCGGATAA

CTTCTGAAAG

TAAAAGCAAA

AATGGGTACG

GTGCAGGGT2

ACTTCCCGCC

TTCTTGGTTT

CTACGGATGA

CTCCTGCTAC

TAGAAATCAT

CTAGTTTGAG

CAACAGAAGA

TGAATAGTGG

GCCTAGCTGA

CATTAAATCC

GCGACCGGGC

CATTAAATGT

TAAAGACCGC

GGGAAAATAA

TGCCGAGCCT

CACAAACCGA

ATCGTTCTGC

CGAAGGAAGA

TATACAAGTG

AAGAAGGAAA

ACCAACAAAA

TGACTTAGAT

CCAACAACCA

TGATAAAATC

AATTGACCAA

ACCACCTACG

TAATGCTCCT

AGAGTTAAGA

ATCGGAACCG

CCGGGAAACA

AAATGCTATT

AGAGTTGAAC

TGATTTTACA

TTTAAGAGAT

GTTTGCTAGC

TCTGATAAGT

GTTTAATA.AA

ACCAAAGCTA

AACACCCTTT

ACCAGTAATC

GGAAAAAATG

TGGCATTGAA

ACCAGGGAAC

GTAAATAAGA

TCTAGCATGC

TTTTTC!CCTA

GACGAAAATC

TTATTAACCA

GATGAAGAGT

GCTACATCAG

CTTGCTTX'GC

AGCTCGTTCG

GCATCCTCGC

AATCGCCATA

GGGAGAGGCG

GATGACGAAA

AGAGGAACAG

AGCCCGGTTC

AA.AAAGTGGC

AGTCAGCAGA

AAGTATTTAA

CTGAAGTAAA

AAAACAAAAG

TAAGACT'TGC

AACCGAGCTC

CAGAGACGCC

AATTTCCACC

TAGATTCTAG

GTCAAAATTT

GTAGACCAAC

ACAGCGAGAC

GAAAACACTC

CTTCGTTAAG

GAGCGTCGTC ATCCAGQATT GCCATAGCAT CATCGGATAG

GCCATCGGAT

TGAGCTTGAA

GAAAGAGTCA

TGAGTCTTCA

AAAAATAAAA

GAAAGCGATT

TGAAGAGGTA

TTTGCCAGAG

ATTCGAATTT

AATGCTTCTT

GCCTCCAACA

TTTTACAAGA

CTCTGATTTC

ATCTGAAGAA

AACAGAAGAA

AAGAAATGCG

TCCAAAGGTA

ATTTAAGAAT

GACTAAAAAA

ACCACAAGAA

AAACAAGCAG

CGATAAAGAG

TAATAACGCA

AAGTGCAGAA

AATGTTAGCT

420 480 540 600 660 720 780 840 900 960 1020 1080 1140 1200 1260 1320 1380 1440 1500 1560 1620 1680 1740 1800 1860 1920 GACATAACTA AAAAAACGCC AAAACTACAA CGAAAACAGT GCAGAACTTC CTGCCACAAA ATAGAAAAAC AAGCAGAAAC CAAAAAGAAG CTACAGAGAG GTAGAGGAAA GCGAATCAGC GAAGGAAAAC TAATTGCTAA CATACOACOT TAATTCTTGC ATTGGCGTGT TCTCTTTAGG GGCGTTTATC AAAATTATTC AATTAAGAAA AAATAATTAA INFORM41TIoN FOR SEQ ID NO: 28: Mi SEQUENCE CHARACTERISTICS: LENGTH: 415 base pairs 82 TYPE: nucleic acid STR.ANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genoniic) (vi) ORIGINAL SOURCE: ORGANISM: Neisseria meningitidis (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 26: TACCGGTACG CTAAATATTG GTGATGTATT GGATATTATG ATTTGGGAAG CGCCGCCAGC GGTATIGTTT GGTGGTGGCC TTTCITCGAT GGGCTCGGGT AGTGCGCAAC AAACCAAGTT 120* GCCGGAGCAA CTGGTGACGG CACGTGGTAC GGTTTCTGTG CCGTTTGTTG GCGATATTTC 180 GGTGGTCGGT AAAACGCCTG GTCAGGTTCA GGAAATTATT AAAGGCCGCC TGAAAAAAAT 240 GGCCAATCAG CCGCAAGTGA TGGTGCGCTT GGTGCAGAAT AATGCGGCAA ATGTATCGGT 300 GATTCGCGCA GGCAATAGTG TGCGTATGCC GTTGACGGCA GCCGGTGAGC GTGTGTTGGA 360 TGCGGTGGCT GCGGTAGGTG GTTCAACGGC AAATGTGCAG GATACGAATG TGCAG 415 INFORMATION FOR SEQ ID NO: 29: SEQUENCE CHARACTERISTICS: A) LENGTH: 438 basepar TYPE: nucleic acid STRANqDEDNESS: double TOPOLOGY: linear (iMOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Staphylococcus saprophyticu s (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 29: TCGCTTCTCC AGAAGAAATT TTAGAAACAT ATCTAGAAAA TCCCAAATTA GATAAACCGT TTATATTATG TGAATACGCA CATGCAATGG GAAATTCACC AGGAGATCTT AATGCATATC 120 AAACATTAAT TGAA!AAATAT GATAGTTTTA TTGGCGGTTT TGTTTGGGAA TGGTGTGATC 180 ATAGCATTCA GGTTGGGATA AAGGAAGGTA AACCAATTTT TAGATATGGT GGAGATTTTG 240 GTGAGGCCTT ACATGACGGT AATTTTTGTG TTGATGGTAT TGTTTCGCCA GATCGAATTC 300 CACATGAAGG TTATTATGAG TTTAAACATG AACATAGACC rrTGAGATTG GTTAACGAAG 360 AGGATTATCG GTTTACATTG AAGAATCAAT TTGATTTTAC AAATGCGA GATAGTITGA 420 TTGTTGAG4GG AGAAGCGA 438 83 INFORMATION FOR SEQ ID NO: Wi SEQUENCE CHARACTERISTICS: LENGTH: 766 base pairs TYPE: nucleic acid STRAkNDEDNESS: double TOPOLOGY. linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Streptococcus agalactiae (xi) SEQUENCE DESCRIPTION: SEQ ID NO: ATGAACGTTA CACATATGAT GTATCTATCT GGAACTCTAG

TCACCAGCTG

GTAAATAGTA

TTGAGAAATA

ATTACTAGCG

T1'GAATTCTA

TCAACTCAAC

ACTAAGCTAG

GTTAACGATG

GATAGAGCTA

ACTAGAGATA

GCAATCACAC

TATTAGAAGT

ATAATCAAGC

TCAAAGATAA

TGGAAAAATT

TTGGTAGTCG

ATTTAACAAA

TTATTCGCAT

TAAAGGCATT

CCATCTATAC

AAAAAGTACT

ATGCTGTTGG

ACATGCTGAT

CCAGCAAATG

TGTTCAGGGA

AAPLGACTTCA

TGTAGAAGCC

TAAGGTTAGT

TTTAGATCCA

AGAACAAAAA

AAAATCAAA

TAACGTCAAA

AGTTCAGTTG

CAAGTGACAA

GCTCAAAAGC

ACAGATTATG

TTGCGTGCC.A

TTAACAGATG

CAAGCAAATA

TTTGCTTC.AG

GTTTTAACTT

CTTGATAAGG

GA.ATTTAAAG

AATCCAAATG

TGGCTGGTGC

CTCCACAAGT

TTGATCAAGA

AAAAACCGGT

ACCCTGAGAC

TGATTGAAGC

TTGATATGGG

TTGATTCAAT

ATCCTGATT

AA.ATCTGGAA

TTTACAATAC

TACGGTACA

ATTGTTATTT

GGTAAATCAT

TAGCATTCAG

TAATGAGGCT

AGTrTATGAT

AATCACTTTT

ATTTGGGATA

TAAAGCTCAA

AAAACCAACT

TACACGCTTT

TTTAAATAA.A

ACAAGTTGAT

120 180 240 300 360 420 480 540 600 660 720 768 CAAGAGATTG TAACATTACA AGCAGCACTT CAAACAGCAT TAAA.ATAA 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 menlngitidis (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 31: 84 ATGAAAGTAG GTTTCGTCGG C TGGCGCGGT ATGGTCGGTT CGGTTTTGAT GCAGCGTATG AAAGAAGAAA ACGACTTCGC CCACATTCCC GAAGCGTTTT TCTTTACCAC TTCCAACGTC 120 GGCGGCGCAC GCCCTGATTT CGGTCAGGCG GCTAAAACAT TATTGGACGC GAACAACGTT 180 GCCGAGCTGG CAAAAATGGA CATCATCGTT ACCTGCCAAG GCGGCGACTA CACCAAATCC 240 GTCTTCCAAG CCCTGCGCGA CAGCGGCTGG AACGGCTACT GGATTGACGC GGCATCCTCG 300 CTGCGTATGA AAGACGACGC GATTATCGTC CTCGACCCC!G TCAACCGCAA CGTCATCGAC 360 AACGGCCTCA AAAACGGCGT GAAAAACTAC ATCGGCGGCA ACTGTACCGT TTCCCTGATG 420 C 421 INFORMATION FOR SEQ ID NO: 32: Wi SEQUENCE CHARACTERISTICS: LENGTH: 213 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Streptococcus gordonii (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 32: TTCATAGACG CTGAGCACGC TTTGGATCCA TCTTACGCGG CTGCTCTAGG TGTAAATATT GATGAGCTGT TGCTATCTCA ACCAGATTCT GGTGAGCAAG GTTTAGAAAT TGCAGGAAAA 120 TI'GATTGACT CTGGGGCAGT TGATTTrAGTT GTCATCGACT CTGTI'GCAGC TCTTGTACCA 180 CGTGCGGAAA TCGATGGAGA TATCGGTGAT AGC 213 INFORMATION FOR SEQ ID NO: 33: Wi SEQUENCE CHARACTERISTICS: LENGTH: 692 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Str-eptococcus mutans (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 33: GGGCCGGAAT CTTCTGGTAA GACAACTGTC GCT~CTATG3 CTGCTGCTCA GGCGCAAAAA as

GATGGCGG.TA

GCTCTTGGCG

CTTGAAATTG

GTGGCAGCTT

TTACAAGCAC

AAAACCATTG

CCAGAAACAA

CGCGGCAATA

ACCAAAATTA

ATTATATATG

TTGCCGCU 1 1

TTAATATTGA

CAGGGAAATT

TAGTACCACG

GCATGATGAG

CTATTTTTAT

CCCCTGGCGG

CTCAAATTAA

AAGTTGTTAA

GTGAAGGCAT

CATTGATGCA

TGAGCTTTTG

GATTGATTCT

TGCGGAGATT

TCAAGCGATG

TAATCAATTG

GCGTGCCTTG

AGGAACCGGG

AAATAAAGTT

TTCTCGTACA

GAACATGCCC

CTTTCACAAC

GGCGCTGTTG

GACGGAGATA

CGTAAATTAT

CGGGAAAAAG

AAGT17TTATT

GAACAAAAAG

GCTCCACCAT

GGTGAATTAG

TC

TTGATCCAGC

CAGATTCAGG

ATTTAGTTGT

TTGGTA.ATAG

CAGCTTCAAT

TTGGTATTAT

CTTCTGTGCG

ACAGCAATAT

TTAAGGAAGC

TTAAGATTGC

CTATGCTGCT

AGAACAGGGT

TGTTGACTCA

TCATGTTGGC

CAATAAAACA

GTTTGGTAAT

TCTTGATGTC

TGGTAAAGAG

TTTTGTAGAA

CAGTGATTTG

120 180 240 300 360 420 480 540 600 660 692 GGAATTATCC AAAAAGCTGG AGCTTGGTAC INFORMATION FOR SEQ ID NO: 34: Wi SEQUENCE CHARACTERISTICS: LENGTH: 1204 -base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (i)MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Streptococcus pneuznoniae (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 34: ATGGCGAAAA AACCAAAAAA ATTAGAAGAA ATTTCAAAAA AATTTGGGGC

AAGGCCTTGA.

CTTGGGTO3

GACATTGCC

GAGTCATCTG

CGGATTGCTG

GGTGTCAATA

ATTGCGGGAA

GCCCTTGTTc

GCTCGTATGA

ATGACGCTCT

AACGTGCGGA

TTGGCTCAGG

GTAAGACAAC

CCTTTATCGA

TTGACGAATT

AATTGATTGA

CTCGTGCGGA

TGAGCCAGGC

TAAATTGATT

GCAAAAGGTG

TGGTT.ATCCT

GTTGCCCTT

TGCGGAACAT

GCTCTTGTC T

CTCAGGTGCA

AATTGATGGA

CATGCGTzAJA

GAGAAAGACT

CAAGTGATGA

AAGGGACGTA

CATGCAGTTG

GCCCTTGATC

CAACCAGACT

GTTGATCM~

GATATCGGAG

CTTrGGCGCCT

TTGGTAAAGG

GCTCAGGT1'C

TCATCGAAAT

CACAAGCGCA

CAGCTTATGC

CAGGAGAGCA

TCGTAGTCGA

ATAGCCATGT

CTATCAATAA

AGAACGTGAA

ATCAATCATG

TTTAGCTCTT

CTATGGCCCA

AAAAGAAGGT

TGCGGCCCTT

AGGTCTTGAG

CTCAGTTGCT

TGGTTTGCAG

AACCAAAAcA 86 ATTGCCATTT TTATCAACCA ATTGCGTGAA

ACAACACCGG

AATACACAAA

ATTAAGGTTG

TACGGAGAAG

ATCAAAAAAG

AATGCTAAGA

CGTTCTAAAT

AAAGATGAGC

GAACTTGAAA

TCGA

GCGGA.CGTGC

TTAAGGGAAC

TAAAAAATAA

GAATTTrCTAA

CAGGGGCTTG

AATACTTGGC

TTGGCTTGAT

CAAAGAXAGA

TCGAAATTGA

TTTGAAATTC

TGGTGATCAA

GGTAGCTCCA

GACTGGTGAG

GTATTCTTAC

AGAGCACCCA

TGATGGAGAA

AGAAGCAGTG

AGAATAAGCT

AAAGTTGGAG TGATGTTTGG TATGCTTCAG TCCGCTTGGA AAAGAAACCA ATGTCGGTAA CCGTTTAAGG A.AGCCGTAGT CTTTTGAAGA TTGCAAGCGA AAAGATGAAAk AAATTGGGCA GAAATCTTTG ATGAAATTGA GAAGTTTCAG AACAAGATAC AATGAAGAAG TTCCGCTTGA GTTAAAGCAG TGGAGAAATC

AAATCCAGAA

TGTTCGTGGT

AGAAACTAAG

TGAAATTATG

TTTGGATATT

AGGTTCTGAG

TAAGCAAGTC

TGAAAACAAA

CTTAGGCGAT

CGCTACTTTT

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

CGTATCATCG

GTAGCACAAG

GATCCAGCTT

GATTCTGGAG

CTGGTTGTTG

GGCGATAGCC

GCTTCTATTA

GGTGTGATGT

TCTGTTCGGC

AAATCTATGG

CTCAAAAAGA

ATGCTGCTGC

AACAAGGACT

TCGATTCAGT

ATGTCGGATT

ATAAAACAAA

TTGGAAATCC

TGGATGTGCG

TCCAGAGTCT

AGGTGGAATC

GCTTGGGGTT

TGAAATTGCA

AGCAGCTTTA

GCAAGCACGT

AACTATCGCA

TGAAACAACA

TGGAAACAAC

TCCGGTAAAA

GCAGCCTTTA

AATATTGATO

GGTAAATTGA

GTGCCACGTG

ATGATGAGTC

ATCTTTATCA

CCAGGTGG3TC

CAAATTAAAG

CGACTGTGGC TTTACATGCT TCGATGCCGA GCATGCGCTT AACTTCTCTT GTCTCAACCA TTGATTCTGG TGCGGTTGAC CTGAAATrGA TGGTGATATT .AGGCCATGCG TAAATTATCA ACCAATTGCG TGAAAAAGTT GAGCTTTGAA ATTCTATGCT GAACTGGTGA CCAAAAGATA 120 180 240 300 360 420 480 540 600 87 GCCAGCATTG GTAAGGAGAC CAAAATCAAG GTTGTTAAAA ACAA( AAGGTAGCAG AAGTTGAAAT CATGTATGGG GAAGGTATTT CTCG AAAATTGCTT CTGATTTGGA CATTATCCAA AAAGCAGGTG CTTG( GAGAAGATTG GCCAAGGTTC TGAAAATGCT AAGCGTTArr TGGC( TTTGATGAAA TCGACCGTAA AGTACGTGTT AAATTTGGTT TGCT1.

GAATCTGCTA TGGCAGTAGC ATCAGAAGAA ACCGATGATC TTGC GGTATTGAAA TTGAAGATTA A INFORMATION FOR SEQ ID NO: 36: Wi SEQUENCE CHARACTERISTICS: LENGTH: 312 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genornic) (vi) ORIGINAL SOURCE: ORGANISM: Streptococcus salivarlus (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 36: GCGTATGCAC GAGCTCTAGG TGTTAATATC GATGAGCTTC TTTT( GGTGAGCAAG GTCTCGAAAT TGCAGGTAAG CTGATTGACT CTGG GTTGTTGACT CAGTTGCGGC CTTCGTACCA CGTGCAGAAA TTGAV AGTCATGTAG GACTrCAAGC GCGTATGATG AGTCAAGCCA TGCG ATTAATAA&A CAAAAACGAT TGCTATCTTT ATTAACCAGT TGCG' ATGTT'rGGTA AC 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: CTATGTGGCG CGGTATTATc INFORMATION FOR SEQ ID NO: 38:

GTCGC

TACAGG

3TTCTC

CGATCA

FGAAGA

rTTAGA

TCCGCCATTT

GGAGCTTGTG

TTATAATGGT

TCCACAATTG

AAGCGAAGAA

TTTAGATAAT

660 720 780 840 900 960 981 120 180 240 300 312 ;TCGCA GCCTGATTCT TGCAGT GGATTTAGTT LGGAGA TAGTGGTGAC FAAACT TCTGCATCT I'GAAAA AGTTGGTATC 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: 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) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 43: CAGCTGCTGC AGTGGATGGT 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: 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: S 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 o INFORMATION FOR SEQ ID NO: 52: o. SEQUENCE CHARACTERISTICS: LENGTH: 21 base pairs TYPE: nucleic acid oo.; STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 52: TGACCACTTT TATCAGCAAC C 21 INFORMATION FOR SEQ ID NO: 53: **eO 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: S TCTATGATCT CGCAGTCTCC INFORMATION FOR SEQ ID NO: 56: o• SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs S, 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: CTGGATTATG GCTACGGAGT 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 S: INFORMATION FOR SEQ ID NO: 64: 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: 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 (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 68: ACGGGGATAA CGACTGTATG 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 (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 76: GTGACTTTWG TGATCCCTTT TGA 23 INFORMATION FOR SEQ ID NO: 77: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs S 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) (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 S INFORMATION FOR SEQ ID NO: e e SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid 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: 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: S* CAATAAGGGC ATACCAAAAA TC 22 S INFORMATION FOR SEQ ID NO: 84: SEQUENCE CHARACTERISTICS: LENGTH: 22 base pairs TYPE: nucleic acid 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 e INFORMATION FOR SEQ ID NO: 88: SEQUENCE CHARACTERISTICS: S. LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear **o*oe S(ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 88: 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 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 INFORMATION FOR SEQ ID NO: 96: SEQUENCE CHARACTERISTICS: LENGTH: 22 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 96: ATCTTTTAGC AAACCCGTAT TC 22 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 INFORMATION FOR SEQ ID NO: 100: SEQUENCE CHARACTERISTICS: LENGTH: 19 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear ooeeo: MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 100: ATCCTCGGTT TTCTGGAAG 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 S INFORMATION FOR SEQ ID NO: 104: SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) *e (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 *5 S S

S

SEQUENCE CHARACTERISTICS: LENGTH: 20 base pairs TYPE: nucleic acid STRANDEDNESS: 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 inosinel (ix) FEATURE: NAME/KEY: misc-feature LOCATION:12 OTHER INFORMATION: /note= 'n inosine" (ix) FEATURE: NAME/KEY: misc-feature OTHER INFORMATION: /note- 'In -inosines (ix) FEATURE: NAME/KEY: misc-feature LOCATION:18 OTHER INFORMATION: /note= 'n inosinet" (ix) FEATURE: NAME/KEY: misc-feature (B3) LOCATION:21 OTHER INFORMATION:/note= 'In inosine.0 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 107: AAYATGATNA CNGGNGCNGC NCARATGGA INFORMATION FOR SEQ ID NO: 108: SEQUENCE CHARACTERISTICS: LENGTH: 23 base pairs TYPE: nucleic acid 106 STRANDEDNESS: single CD) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (ix) FEATURE: NAME/KEY: misc feature LOCATION.3 CD) OTHER INFORMATION: /note= 'In inosine" (ix) FEATURE: NAME/KEY: misc-feature LOCATION:6 OTHER INFORMATION: /note= 'In inosine" (ix) FEATURE: CA) NAME/KEY: misc-feature CB) LOCATION:9 OTHER INFORMATION: /note= 'In inosine" (ix) FEATURE:.

NAME/KEY: misc-feature LOCATION:12 CD) OTHER INFORMATION: /note= 'In inosine" (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 108: CCNACNGTNC KNCCRCCYTC RCG 23 INFORMATION FOR SEQ ID NO: 109: C)SEQUENCE CHARACTERISTICS: CA) LENGTH: 29 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear Ci)MOLECULE TPE: DNA (genomic) Cix) FEATURE: NAME/KEY: misc-feature LOCATION:6 OTHER INFORMATION: /note= "ni inosine", (ix) FEATURE: NAME/KEY: misc feature LOCATION:12 OTHER INFORMATION: /note= 'In inosine" Cix) FEATURE: NAME/KEY: misc-feature OTHER INFORMATION: /note= "n inosine," (ix) FEATURE: NAME/KEY: misc feature 107 LOCATION:18 OTHER INFORMATION:/note= 'In =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 STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 110: ATGAAAAACA CAATACATAT CAACTTCGCT ATTTTTTTAA TAATTGCAAA TATTATCTAC 4OS..O

S

S

*5 S. 0O 5* 0

OSS@

0@

S

S

*SSO

0

@ISS

S

S5e*

S

0SB@

AGCAGCGCCA

GAAGGTTGTT

GCAAAGTGTG

GCATTTGATG

GGAATGGAGA

TGGGTTTCGC

GATTTTGATT

GAAGCATGGC

AAAATTATTA

ATGTATCTAC

AC.AGCAAATA

CATAAATATG

GTGCATCAAC

TTTTACTTTA

CAACGCAAAT

CGGAAATAAT

TCTGGAACAG

AAGAAATAAC

ATGGAAATCA

TCGAAAGTAG

ATCACAATCT

AAGATCTGGA

GAACCTTACA

TTTTTGTGTC

AGATATCTCT

CGATGCATCC

GGCACCAGAT

AGATCAGAAA.

CAATCATACA

CCAAAAAATT

AGACTTCTCT

CTTAAAAATT

CCCAGTTAAA

TAATAGTACA

AAACGGATGG

CGCACTTACA

ACTGTTGCAT

ACAP.ACGCTG

TCAACTTTCA

ACCATATTCA

CCAAAGACGT

AGATTAAATA

GGAGATAAAG

TCACCAGAAG

AACTCAGCCA

AAACTGTATG

TTTGAAGGGT

GGAAACTTGG

CTAAACACAC

CTCCATTATT

AAATTGCTCA

AGATCGCATT

AATGGGATAA

GGATGCAATT

AAATCAAGAA

AAAGAAACAA

AACAAATTCA

TAGAAAACAC

GGAAAACTGG

TTATTATAAG

GGTCGAATTT

TAAATTTATA

TGAAGGAACT

ATTCAATAAA

ATCACTTATG

AACCCCCAAA

TTCTGTTGTT

TTATCTCAAA

CGGATTAACA

ATTCCTGCGT

CATAGAGAAC

TGCAGGATTC

CAAATCAGGA

AACATCAAGC

A

29 120 180 240 300 360 420 480 540 600 660 720 780 831 ATAAAAGCCA AGAAAAATGC GATCACCATT INFORMATION FOR SEQ ID NO: 111: Wi SEQUENCE CHARACTERISTICS: LENGTH: 846 base pairs CE) TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) 108 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: Ill: TTGAAAAAGT TAATATTTTT AATTGTAATT GCTTTAGTTT TAAGTGCATG

AGTTCACATG

TATGCTrTAG

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

TATCACTTTA

TAAAATTATA

AGATAAAGTA

CAAAAAAGAT

TGGAAA.ATTA

CGGAGATACT

TCAAGCAATA

TGAACCTATT

TAAGTTGATA

GAAAAAAAAT

GTAAAATTTA

GCTATTTTGT

GATGATATAG

AAAGCACTTA

AAAGAAATCG

ACAAATCCAG

ACTTCAACAC

AGCAAAGAAA

TTAATTAAAG

ACATATGCTT

GTTTTAGTCA

AGTGAAACCG

ATAATGCTCA

ATTCAGATAA

TAGAACAAGT

TTGCTTATTC

TTGAGGCTrC

GTOGAATCAA

TTAGATATGA

CTGCTGCTrr ACAAAAAATr

ACGGTGTTCC

CTAGAAATGA

TTTTTACGAA

CCAAGAGTGT

TAATTCAAAC

TATTGGTGTT

GAGATTTGCC

ACCTTATAAT

TCCTATTTrA

AATGACATAT

AAAAGTTAAA

GATAGAATTA

CGGTA.AGACT

CTTACTTGAT

AAAAGACTAT

TGT1'GCTTTT

TAAAGACAAT

AATGAAGGAA

120 180 240 300 360 420 480 540 600 660 720 780 840 0 0 INFORMATION FOR SEQ ID NO: 112: Ci) 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 CTTGAG-TGGT GGGGTGGCGA CCGACTCTTG ATGAAGTGCT GGAACACTAC CTGCCCAGAG CGATGGCGGA ACACCOTACA TCGCAATGCT GGGCGAGGAA CCGATCGGCT ATGCTCAGTC CTCGGAAGCG GTGATGGCTG GTGGGAAGAT GAAACTGATC CAGGAGTGCG CAGTCTCTGG, CTGACCCGAC ACAGTTGAAC AAAGGCCTAG GAACAAGCT

CCTGCCGATG

CGAAGAGCGA

AGAGTCCGTA

GTACGTCGCG

AGGAATAGAC

TGTCCGCGCT

120 IS0 240 300 360 109 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 (geflomic) (xi) SEQUENCE DESCRIPTION: SEQ, ID NO: 113: ATGAACCAGA AAAACCCTAA AGACACGCAA AATTTTATTA CTTCTAAAAA GCATGTAAAA

C

GAAATATTGA

AAAGGACATT

GATGGAGGCT

ATTCAAACGG

AATATTCCTT

AAATATAGCT

GCTTTGGGTT

CTATATTTTC

CCATTGATTT

CGTGAATATC

GTCACTAATA

ATCACACGAA

TTACCAAAGA

TATGTCAAGT

ATATTCTAAA

ATAACATCAG

ATCTTATCGT

TACTATTAAT

ATCCTAAGC C CAAAGAAG4GA

GTGTTCTTTT

TAATAAACT

TATCAGTAAA

GCTAGTCAAA

GACTAAAGAA

ATTTTCCTTC

TACGGATATT

TGAGAAGGGA

GGTGGAGATG

AAGTGTAGAC

CTACAAAAAG

CACTAAAAAC

ATCGAAGGAA

CAAGACAACG

ATGAGTCGAT

GCGGTAAACC

CCAAAACATA

GTCAAAAGAA

TTTGCGAAAA

GATATAAAAA

TCTGTATTGA

TATCGATCTT

CAATTCCGAC

CA.ATTTCTTT

TAATAGAAAT

CAGOTTACTGC

CCTCTGAGAA

TAAACTATAA

TTACCTTTGA

GATTGCAAAA

TGCTCAAAAA

TTGTTCTTGA

TTGTTTATAA

AGGCTTTGAA

CTATTTTCAA

CGGATCAGGA

TATAGAAATT

TATAAAAGTG

GATATATGGT

AAGTCAGGCT

TCTGCAACGA

AGTACCACCA

ACGACATCAA

GTGGGTAAAC

GCATGCAAAT

TAGTTACAAA

420 480 540 555 120 180 240 300 360 420 480 540 600 660 720 732 TTGTTTCACT AA INFORMATION FOR SEQ ID NO: 114: CW SEQUENCE CHARACTERISTICS: 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 TTCTCAAAC TTTTAACGA

ATAATAAAAC

GGGCATTTAA

AGTCATCTAT

CACCAAGATA

ATTCCTTACC

GACATCTATC

CTAGGGTTGC

TGCTTTCATC

GATGTTCCAG

GAPLTATCGTC

AACAATTTAA

AATTGAATTT

CGACGAAACT

TCAACTTATC

TTCTACAG7T

ATTTAAGCAC

TGATTGTTGA

TCTTGCACAC

CTAAACCAAG

ATAAATATTG

AACTGTTTAC

GTACCGTTAC

AAAAGAAACC

GGCTAAAATA

GTCAGAAAAA

TCAATTCCCT

ACAAATTATT

AGAAGGATTC

TCAAGTCTCG

AGTAAACAGT

GAAGCTATAT

TAAAAATCAG

TTATGAGCAA

GATACCGTTT

AGTAAACAGG

TTAAAATCGA

AACAAACAGA

AAAAAAGTGG

TACAAGCGTA

ATTCAGCAAT

GTCTTAATAA

ACGTACTTTG

TTTCATCAAG

GTATTGTCTA

GTGAAAAAGT

ACGAAATTGG

TAACGTCTAT

ATAC TCGTGT

GGTATAAAAT

TTTTTGAAAG

CCTTGGATAT

TGCTTAAGCT

AACTTACCCG

TTTCAAAATG

CAATGAAACA

TT TTTAATAG

ACTCAACCAA

AACAGGTAAA

TGAATTAGAC

CACTTTAATT

TGTTGGGAAT

CCATGCGTCT

TCACCGAACA

GCCAGCGGAA

CCATACCACA

GGTCAATCGA

CGCCAAAGTA

TTATCTATTA

120 180 240 300 360 420 480 540 600 660 720 TTTAACGGGA GAAATAA INFORMATION FOR SEQ ID NO: 115: i)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 AACTTTATTA CTTCAAAACA AAAATAATGA CAAATATAAG ATTAAATGAA CATGATAATA TCTTTGAAAT AAAGGGCATT TTACCCTTGA ATTArn2ACAG AGGTGTAATT TCGTAACTGC GACCATAAAT TATGCAAAAC TACAGAAAAT AAACTTGTTG ATCACGATAA TTAAACAAGG ATATATTGCA GTTTAAATTT CCTAAAAACC AATCCTATAA AATATACCTT ATAACATAAG TACGGATATA ATACGCAAAA TTGTTrGA GATGAGATTT ATTTAATCGT GGAATACGGG TTTGC!TAAAA GATTATTAAA TCATTGGCAT TATTTTTAAT GGCAGAAGTT GATATTTCTA TATTAAGTAT

TAATATAGAT

CGGCTCAGGA

CATTGAAATA

TTTCCA.AGTT

AATATTTGGT

TAGTATAGCT

TACAAAACGC

GGTTCCAAGA

120 180 240 300 360 420 480 ill GAATATTTTC ATCCTAAACC TAGAGTGAAT AGCTCACTTA TCAGA'I7AAA TAGAAAAAAA TCAAGAATAT CACACAAAGA TAAACAGAAG TATAATTATT TCGTTATGAA ATGGGTTAAC AAAGAATACA AGAAAATATT TACAAAAAAT CAATTTAACA ATTCCTTAAA ACATGCAGGA ATTGACGATT TAAACAATAT TAGCTTTGAA CAAtTCTTAT CTCTTTTCAA TAG CTATAAA TTATTTAATA. AGTAA INFORMATION FOR SEQ ID NO: 116: SEQUENCE CHARACTERISTICS: LENGTH: 1029 base pairs (B3) TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 116: ATGAATAAAA TA.AA.AGTCGC AATTATCTTC GGCGGTTGCT CGGAGGAACA

GTAAAATCCG

ATCGGAATTA

GCCGATAGTC

AAAGAAAGAG

TGCGGGGAGG

TGCGATATTC

AATGCGGGCA

AGGACGCTTA

ACCAAAGTAA

GGAAAAATCT

AACGAGGATG

CGCATCCATC

GCAGACATTC

GTGCTTGGAT

GTTCTAAACG

GCGGCTGCCG

CAATAGAAAT

CAAAAAACG

TCCCCGCCAT

AATACGAAAC

ATGGTGCGAT

AAAGCTCCGC

TCGCCGTCCC

CCTACCCTGT

ACAGTACGGA

TAATTGAGCA

ATTTGATTGT

AGGAAAACGA

CGGTCGAGGA

GCAGAGGGCT

AGGTCAATAC

CAGGAATCAC

TGCTGCGAAC

CGTATGGAAG

ATTCTCCCCG

TCGGCGTATT

ACAGGGTCTG

AGCTTGCATG

CGAATTTCA.A

CTTTGTGA.AG

AGAACTAAAC

AGCGATTTCG

CGGCGAAGTG

GCCGGAAAAA

ACGAAATCGG

TGCTCGTGTT

CCTGCCCGGT

GCTTCCCGCA

ATTAATACTG

CTATGCAAGA

GATAGGAAAA

GACGTGGCTT

TTTGAATTGT

GACAAATCAC

ATGATTGAAA

CCGGCACGGT

GCTGCGATAG

GGCTGTGAGG

GATCAAATCC

GGCTCAGAGA

GTGCAAGAAA

GATCTTTTrT

T=ACATCGT

CTAATTGACA

AAAAATTCGA

AGCCATGTAC

CGCATGGTCT

TCCCGGTTTT

CTGGTATCCC

TGGCCTAC-AT

AAGGTGACAA

CAGGTTCGTC

AAGCAGCAGG

TCGGCTGCGC

GGTTGAGCCA

ATGCGATGAT

CGGCAAAGAA

TGCAGGAGGA

ACAGCCGCTA

GCCTGATTAC

TGATGTGTCG

TCCGCACTAC

GGAATGGGAA

GCTTGTCATG

GCATGGCAA.A

CTATGTAGGC

TCT TACA.AAA

ACCGGAGGCG

CTTTGGCGTA

ACAATATGAT

GGTCATGGGA

CGGTATCTTC

TATCGTTCCA

AGTATATCGG

TGGCGGCATC

TCCACGCATG

ATTGGCGATA

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

GAGAGGTGA

INFORMATION 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: 1029

C

ATGAAAAAAA

TCAGCAGCAA

ATCGCACCAA

ACTTGGCTAG

TTAGGAGAAA

GAGGATGGCT

GTCGCTGCCT

GGAATCGCTA

GATCGTTTTA

TCAAAAGGGA

TTTGCTTACG

GGCATCTTAG

GGTTTTTTTG

CCATTGCCTC

TTGGGATTGA

TTAAACGAAA

GCGGAAGTCG

TTGCCGTTTT

GTGTGATCCA

CAATGGATTG

AAGATCACAA

AACGAATCGT

GTATCCAAGG

CCGCATTATG

GTGCTCCCAC

TTCAAGACCA

TCACAAAAGT

GTTCTACTGT

GAAATGAGCA

ATTTTGAAGA

TCGCGCTTGA

CGGGTCTGGC

TCAACACCAT

GGTTATCCTA

AGCTATTGAC

GTATTGGTAT

AAACT.GTCAC

CCCTGATGTC

ACTGCTTGAA

TATGAACAAA

TTTGCTTTA

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

AAAACGATCC

AGCCGAATGA

AATCTGCATT

CGGGTATTGA

ATGCGATTTC

CCACGATCAC

CACAGCTGCT

CCAATCAAGG

CCCGCTACCC

TGATTGCACT

GACCATTGGC

TCGCAATGAT

AGGATTTATA

GAAGTATGGC

TGGTTGCCAT

TGATACCATG

TGCCACAATC

AGCCGGTTCT

AACGACTGCT

AATTGGCTGC

TCTTGTCGAC

TGTCCCAGCA

TTATCGAAAC

AGCGATTTAT

AGCTATGATG

GGCAGAGGAG

ATTTGGAGGG AATTCTCCAG AATACTCAGT GTCACTAACC 120 1830 240 300 360 420 480 540 600 660 720 780 840 900 960 1020 1031 GACAAACGAT G INFORMATION FOR SEQ ID NO: 118: Ci) SEQUENCE CHARACTERISTICS: LENGTH: 809 base pairs TYPE: nucleic acid STRANDEDNESS: double 113 TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genornic) (vi) ORIGINAL, SOURCE: ORGANISM: Abiotrophia adiacens (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 118: TGGTGCTATC TTAGTAGTAT CTGCAGCTGA TGGTCCAATG CCTCAAACAC GTGAACACAT

CTTATTATCA

GGTTGACGAT

ATACGATTrc

AGGCGACGCT

TCCAACTCCA

AATCACAGGT

TGACGAAGTT

TGAAATGTTC

ACGTGGTGTT

CACTCCACAT

TCATACTCCA

TGGTGTTTGT

CGTCAAGTAG

GAAGAATTAT

CCAGGCGATG

TCATACRAAG

GAACGYGACG

CGTGGTACTG

GAAATCGTTG

CGTAAATTGT

ACACGTGACA

ACTAAATTCA

TTCTTCTCTA

GTGTTACCAG

GTGTTCCTTA

TAGAATTAGT

ACACTCCAGT

AAAAAATCTT

TTGACAA.ACC

TTGCTACAGG

GTATTTCAGA

TAGACTACGC

ACATCGAACG

AAGCTGAAGT

ACTACCGTCC

AAGGCGTTGA

CATCGTTGTA

AGAAATGGAA

TGTTGCAGGT

AGAATTAATG

ATTCATGATG

TCGTGTTGAA

AGAAACTTCA

TGAAGCAGGG

TGGACAAGTT

TTACGTATTA

TCAATTCTAC

AATGGTAATG

TTCTTAAACA

GTTCGTGACT

TCTGCTTTAC

GCTGCTGTTG

CCAG7TGAAG

CGTGGACAAG

AAAACAACTG

GATAACATTG

CTTGCTAAAC

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: Wj 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 CGGCCCA.ATG CCACAAACTC GTGAACACAT CCTCTTGTCT CGTCAAGTTG GTGTTCCTTA CATCGTAGTA TTCTTGAACA AAGTTGACAT 114 GGTTGACGAC GAAGAATTGC TCGAATTAGT TGAA.ATGGAA GTTCGTGACC TCTTGTCTGA

ATACGACTTC

AGGCGACGCT

TCCAGAACCA

TATCACTGGT

TGACGAAGTT

TGAAATGTTC

ACGTGGTGTA

CACTCCGYAC

TCACACTCCA

TGGTGTTGTT

CCAGGCGACG

AACTACGAAG

GAACGTGACA

CGTGGTACTG

GAAATCGTTG

CGTAAGTTAT

ACTCGTGACC

ACTAAGTTCG

TTCTTCTCTA

ACTTTACCAG

ACACTCCAGT

CTAAAGTTTT

CTGACAAGCC

TTGCAACTGG

GTATCGAAGA

TGGATTACGC

AAATCCAACG

AAGCTGAAGT

ACTACCGTCC

AAGGTACTGA

TATCGCTGGT

AGAATTGATG

ATTCATGATG

TCGTGTTGAA

AGAAACTTCT

TGAAGCTGGG

TGGTCAAGTA

GTACGTATTG

ACAATTCTAC

AATGGTTATG

TCAGCTTTGA

GAACAAGTTG

CCAGTCGAAG

CGTGGTCAAG

AAGACTACCG

GACAACGTTG

TTATCTAAAC

TCTAAAGAAG

TI'CCGTACAA

CCAGGCGACA

AAGCTTTAGA

ATGCTTACAT

ACGTATTCTC

TTCGCGTTGG

TTACCGGTCT

GTACCTTGTT

CAGGTTCAAT

AAGGTGGTCG

CTGACGTAAC

ACGTACAAAT

240 300 360 420 480 540 600 660 720.

780 817 GGTTGTTGAA TTGATCCACC CAATCGCGAT CGAAGAA a

C

INFORMATION FOR SEQ ID NO: 120: SEQUENCE CHARACTERISTICS: LENGTH: 754 base pairs TYPE: nucleic acid STR.ANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Candida albicans (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 120: CTCTGTCAAA TGGGACAAAA ACAGATTTGA AGAAATCATC AAGGAAACCT CAAGAAGGTT GGTTACAACC CAAAGACTGT TCCATTCGTT CCAATCTCTG TGACAACWTG ATTGAAS CAT CCACCAACTG TCCATGGTAC AAGGGTTGGG CAAATCCGGT AAAGTTACTG GTAAGACCTT GTTAGAAGCT ATTGACGCTA AACCAGACCA ACCGACAAAC CATTGAGATT GCCATTRCAA GATGTTTACA TATTGGTACT GTGCCAGTCG GTAGAGTTGA AACTGGTATC ATCAAAGCCG TACTTTCGCC CCAGCTGGTG TTACCACTGA AGTCAA1RTCC GTTGAAATGC ATTGGCTGAA GGTGTTCCAG GTGACAATGT TRGTTTCAAC GTTAAGAACR AGAAATTAGA AGAGGTAACG TTGTGGTGA CTCCAAGAAC GATCCACCAA

CCAACTTCGT

GTTGGAATGG

AAAAGGAAAC

TTGAACCACC

AGATCGGTGG

GTATGGTWGT

ATCACGAACA

TTTCCGTTAA

AGGGTTGTGA

120 180 240 300 360 420 480 540 115 CTC=rCAAT GCCCAAGTCA TTGTTTTGAA CCATCCAGGT CAAATCTCTG CTGGTTACTC TCCAGTCTTG GATTGTCACR CTGCCCACAT TGCTTGTAAA TTCGACRCTTI TGGTTGAAAA GATTGACAGA AGAACTGGTA AGRAATTGGA AGAAAATCCA A).ATTCGTCA 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 (genornic) (vi) ORIGINAL SOURCE: ORGANISM: Candida glabrat~a (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 121: TCTGTCAAGT GGGATGAATC CAGATTCGCT GAAATCGTTA AGGAA.ACCTC CAACTTCATC 600 660 720 754 120 180 240 300 360 420 480 540 600 660 720 a.

a

AAGAAGGTCG

GACAACATGA

AAGGCTGGTG

ACCAGACCAA

ATCGGTACGG

ACCTTCGCCC

TTGACTGAAG

GAAATCAGAA

TCTTTCAACG

CCAGTTTTGG

AACGACAGAA

GTTACAACCC

TTGAAGCCAC

TCGTCAAGGG

CTGACAAGCC

TGCCAGTCGG

CAGCTGGTGT

GTTTGCCAGG

GAGGTAATGT

CTACCGTCAT

ACTGTCACAC

GATCCGGTAA

AAAGACTGTT

CACCAACGCT

TAAGACCTTG

ATTGAGATTG

TAGAGTCGAA

TACCACTGAA

TGACAACGTT

CTGTGGTGAC

TGTCTTGAAC

CGCCCACATT

GAAGTTGGAA

CCATTCGTCC

TCCTGGTACA

TTGGAAGCCA

CCATTGCAAG

ACCGGTGTCA

GTCAAGTCCG

GGTTTCAACG

TCCAAGAACG

CACCCAGGTC

GCTTGTAAGT

GACTCTCCAA

CAATCTCTGG

AGGGTTGGGA

TTGACGCTAT

ATGTCTACAA

TCAAGCCAGG

?1'GAAATGCA

TTAAGAACGT

ACCCACCAAA

AAATCTCTGC

TCGAAGAATT

AGTTCTTGAA

TTGGAACGGT

AAAGGAAACC

CGAACCACCA

GATCGGTGGT

TATGGTTGTT

CCACGAACAA

TTCCGTTAAG

GGCTGCTGCT

TGGTTACTCT

GTTGGAAAAG

GTCCGGTGAC

GCTGCTTTGG TTAAGTTCGT TCCATCCAAG CCA INFORMATION FOR SEQ ID NO: 122: Wi SEQUENCE CHARACTERISTICS: LENGTH: 752 base pairs TYPE: nucleic acid STR.ANDEDNESS: double TOPOLOGY: linear 116 (ii) MOLECULE TYPE: DNA (geriomic) (vi) ORIGINAL SOURCE: ORGANISM: Candida krusei (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 122: CCGTTAAGTG GGATGAAAAC AGATTTGAAG AAATTGTCAA GGAAACCCAA AACTTCATCA

AGAAGGTTGG

ACAACATGAT

AGGCAGGTGT

TCAGACCAAC

TTGGTACTGT

CTTTTGCTCC

TAGAACAAGG

ATATCAAGAG

CTTTCAATGC

C-AGTCTTGGA

TTGACAGAAG

TTACAACCCA

TGAAGCATCC

TGTTAAGGGT

CGAAAAGCCA

GCCACTCGGT

AGCAGGTGTC

TGTTCCAGGT

AGGTAACGTT

TCAAGTCATT

*[TGTCACACT

AACTGGTAAG

AAGACTGTTC

ACCAACTGTC

AAGACCTTAT

TTAAGATTAC

AGAGTCGAAA

ACCACCGAAG

GATAACGTTG

TGTGGTGACT

GTCTTGAACC

GCCCACATTG

TCTGTTGAAG

CATTCGTTCC

CATGGTACAA

TAGAAGCAAT

CATACAAGA

CCGGTGTCAT

TCAAATCCGT

GTTTCAACGT

CCAAGAACGA

ACCCTGGTCA

CATGTAAGTT

ACCATCCAAA

AATCTCTGGT

GGGTTGGACT

CGATGCTATT

TGTTTACAAG

TAAGCCAGGT

TGAAATGCAC

TAAGAACGTY

CCCACCAATG

A.ATTTCCGCT

CGACGAATTA

GTCYGTCAAG

TGGAATGGTG

AAGGAAACCA

GAACCACCTG

ATTGGTGGTA

ATGGTTGTCA

CATGAACAAT

TCTGTCAAGG

GGTGCAGC?1T

GGTTACTCTC

ATCGAAAAGA

TCTGGTGATG

CAGCTATCGT CAAGATGGTC CCAACCAAGC CA INFORMATION FOR SEQ ID NO: 123: i)SEQUENCE CHARACTERISTICS: CA) LENGTH: 754 base pairs TYPE: nucleic acid STRANqDEDNESS: double TOPOLOGY: linear MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Candida parapsailosis (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 123: CTCAGTCAAA TGGGACAAGA RCAGATACGA AGAAATTGTC AAGGAAACTT CCAACTTCGT CAAGAAGGTT GGTTACAACC CTAAAGCTGT CCCATTCGTC CCAATCTCTG GTTGGAACGG TGACAATATG ATTGAACCAT CAACCAACTG TCCATGGTAC AAGGGTTGGG AAAAGGAAAC TAAAGCTGGT AAGGTTACCG GTAAGACCTT GTTGGAAGCT ATCGATGCTA TCGARCCACC 120 180 240 300 360 420 480 540 600 660 '720 752 120 190 240 117

AACCAGACCA

TATTGGAACT

TACTTTTGCC

ATTGACTGAA

GGAAATCAGA

YTCCTTCAAT

ACCAGTCTTG

GATTOACAGA

ACTGACAAGC

GTGCCAGTTG

CCAGCTGGTG

GGTGTCCCAG

AGAGGTAACG

GCTCAAGTTA

GATTGTCACA

AGAACCGGTA

CATTGAGATT

GTAGAGTTGA

TTACCACTGA

GTGACAATGT

TYTGTGGTGA

TTGTCTTGAA

CTGCCCACAT

AGAAATTGGA

GCCAT'rGCAA

AACCGGTATC

AGTCAAGTCC

TGGTTTCAAC

CTCCAAGAAC

CCACCCAGGT

TGCTTGTAAA

AGWTGAACCA

GATGTCTACA

ATCAAGGCTG

GTTGAAATGC

GTCAAGAACG

GATCCACCAA

CAAATCTCTG

TTCGACACTT

AAATTCATCA

AGATTGGTGG

GTATGGTTGT

ACCACGAACA

TTTCAGTTAA

AGGGATGTGA

CTGGTTACTC

TGATTGAAAA

AGTCCGGTGA

300 360 420 480 540 600 660 720 754 a. a TGCTGCYATC GTCAAGATGG TCCCAACCAA GCCA INFORMATION 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: TCTGTTAAAT GGGACAARAA CAGATTTGAA GAAATTATCA AGGAAACYTC TAACTTCGTC

AAGAAGGTTG

GACAACATGA

AAGGCTGGTA

TCAAGACCAA

ATTGGTACTG

ACTTTYGCCC

TTGGCTGAAG

GAAATTAGAA

TCTTTCAACG

CCAGTCTTGG

ATTGACAGAA

GTTACAACCC

TTGAAGCTTC

AGGTTACCGG

CTGACAAGCC

TGCCAGTCGG

CAGCTGGTGT

GTGTCCCAGG

GAGGTAACGT

CTCAAGTTAT

ATTGTCACAC

GAACTGGTAA

TAAGGCTGTT

TACCAACTGT

TAAGACTTTG

ATTGAGATrG

TAGAGTTGAA

TACCACTGAA

TGACAATGTT

TTGTGGTGAC

TGTCTTGAAC

TGCTCATATT

GAAATTGGAA

CCATTCGTTC

CCATGGTACA

TTGGAAGCCA

CCATTGCAAG

ACTGGTGTCA

GTCAAATCCG

GGTTTCAACG

TCCAAGAACG

CACCCAGGTC

GCTTGTAAAT

GAAAATCCAA

CADLTCTCWGG

AGGGTTGGGA

T]TGATGCTAT

ATGTTTACAA

TCAAAGCCGG

TYGAAATGCA

TTAAGAACGT

ATCCACCAAA

A.AATYTCTGC

TCGACACCTT

AATTCGTCAA

TTGGAATGGT

AAAAGAAACC

TGAACCACCT

GATTGGTGGT

TATGGTTGTT

CCACGAACAA

TTCTGTTAAA

GGGTTGTGAC

TGGTTACTCT

GGTTGAAAAG

ATCCGGTGAT

120 180 240 300 360 420 480 540 600 660 720 118 GCTGCTATTG TCAAGATGGT TCCAACCAAA CCA INFORMATION FOR SEQ ID NO: 125: Wi SEQUENCE CHARACTERISTICS: LENGTH: 814 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: CA) ORGANISM: Corynebacteriun accolens (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 125: CGGCGCTATC CTGGTTGTTG CTGCAACCGA TGGCCCGATG CCGCAGACCC GCGAGCACGT TCTGC'rTGCT

GGTTGATGAT

GCAGGACTAC

TGACGAGAAG

TGATCCGGAG

TACCGGCCGC

GGACGTTGAG

GATGTTCCGC

TGGTACCAAG

CCCTCACACC

CACCCCGYTC

CGCCAGGTTG

GAGGAAATCA

GATGAGGAAG

TGGGTACAGT

CGCGCTACCG

GGTACCGTTG

ATCATCGGTA

AAGATGATGG

CGTGAGGACG

AAGTTCGAGG

ATGAACAACT

GCGTTCCTTA

TCGAGCTCGT

CTCCTATCGT

CCATCGTTGA

ATCAGCCGTT

TTACCGGCCG

TCCAGGAGAA

ACTACACCGA

TGAGCGTGG

GTTCCGTCTA

ACCGTCCTCA

GCACCGAGAT

CATCCTCGTT

GGAGATGGAG

TCACATCTCC

CCTGATGGAT

CTTGATGCCT

TGTTGAGCGT

GTCCCAGAAC

GGCTGGCGAC

CCAGGTTGTT

CGTCCTGAAG

GTTCTACTTC

GGTTATGCCT

GCACTGAACA

ATCTCCGAGC

GCTCTGAAGG

GCCTGCGACA.

ATCGAGGACA

GGTCGTCTGA

ACCACCGTTA

AACTGTGGTC

ATCAAGCCGG

AAGGAAGAGG

CGCACCACCG

GGCGACAACG

AGTGCGACAT

TGCTCGCAGA

CACTCGAGGG

ACTCCATCCC

TCTTCACCAT

ACGTCAACGA

CCGGTATCGA

TGCTTCTGCG

GCGCTTACAC

GCGGCCGCCA

ACGTTACCGG

TTGAGATGTC

753 120 180 240 300 360 420 480 540 600 660 720 780 TGTTGTGAAC CTGCCTGAGG TGTTGAGCTC ATCCAGCCTG TTGCTATGGA COAG INFORMATION FOP 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: Coryziebaeter~un diphteriae (xi) SEQUENCE DESCRIPTION; SEQ ID NO: 126: CGGCGCAATC CTCGTTGTTG CTGCCACCGA CGGCCCAATG CCTCAGACCC

TCTGCTCGCT

GGTrGATGAT

GCAGGATTAC

CGACGAGAAG

AGACCCAGAG

CACCGGCCGC

GGACGTCGAG

GATGTTCCGT

TGGCGTTAAG

CCCTCACACC

CACCCCArrC

TGTTGTGAAG

CGCCAGGTCG

GAGGAAATCA

GACGAAGAGG

TGGACCCAGT

CGTGAGACCG

GGTACCGTTG

ATCATCGGTA

AAGCTTCTCG

CGCGAAGACG

GAGTTCGAGG

TTCGACAACT

CTTCCTGAGG

GCGTTCC TTA

TCGAGCTCGT

CTCCAATCAT

CCATCATCGA

ACAAGCCATT

TTACCGGCCG

TCCGCGAGAA

ACTACACCGA

TTGAGCGTGG

GCTCTGTCTA

ACCGCCCACA

GCACCGAGAT

CATCCTCGTT

CGAGATGGAG

CCACATCTCC

CCTCATGCAG

CCTCATGCCT

TGTTGAGCGT

KGCTACCACC

GGCTGGCGAC

CCAGGTTGTT

CGTTC TGTCC

GTTCTACTTC

GGTCATGCCT

GCTCTGAACA

ATCCRTGAGC

GCACTGAAGG

GCTTGCKATG

ATCGAGGACA

GGCTCCCTGA

ACCACCGTTA

AACTGTGGTC

GTTAAGCCAG

AAGGACGAGG

CGCACCACCG

GGCGACAAC!G

GTGAGCACGT

AGTGCGACAT

TGCTCGCTGA

CTCTTGAGGG

ATTCCATCCC

TCTTCACCAT

AGGTCAACGA

CCGGTATCGA

TGCTTC!TCCG

GCGCTTACAC

GTGGCCGCCA

ACGTTACCGG

TCGACATGTC

0 0 0.

120 180 240 300 360 420 480 540 600 660 720 780 814 120 180 240 300 CGTCACCCTG ATCCAGCCTG TCGCTATGGA TGAG INFORMATION FOR SEQ ID NO: 127: Wi SEQUENCE CHARACTERISTICS: LENGTH: 814 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Corynebacteriun genitallwn (xi) SEQUENCE DESCR.IPTION: SEQW ID NO: 127: CGGCGCCATC CTGGTTGTTG CTGCAACCGA TGGCCCGATG CCGCAGACCC GTGAGCACGT TC TGC TGGCT CGCCAGGTTG GCGTTCCGTA CATCCTAGTT GCACTGAACA AGTGCGACAT GGTTGATGAT GAGGAGCTGC TGGAGCTCGT CGAGATGGAG GTCCGCGAGC TGCTGGCTGA GCAGGACTTC GACGAGGAAG CACCTGTTGT TCACATCTCC GCACTGAAGG CCCTGGAGGG CGACGAGAAG TGGGCTAAGC AGATCC TGGA GCTCATGGAG GCTTGCGACA ACTCCATCCC 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 CGTTCTGTCC AAGGACGAGG CACCCCGTTC TTCGACAACT ACCGTCCGC.A 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) ORIGINAL SOURCE: ORGANISM: Corynebacteriui jeikewn (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 128:

TCTTCACCAT

ACCTGAACGA

CCTCCATCGA

TGCTGCTGCG

GCGAGTACAC

GTGGCCGCCA

ACGTTACCGG

TTGACATGTC

360 420 480 540 600 660 720 780 814 V-0 CGGCGCCATC CTGGTTGTTG CCGCAACCGA TGGCCCGATG CCGCAGACCC GCGAGCACGT

TCTGCTGGCY

GGTTGACGAT

GCAGGACTTC

CGACGAGAAG

GGATCCGGAG

TACCGGTCGC

CGAGGTTGAG

GATGTTCAAC

TGGTCTGAAG

CCCGCACACC

CGCCAGGTTG

GAGGAGCTGC

GACGAGGAAG

TGG43CTAACC

CGCGAGACCG

GGTACCGTTG

ATCCTGGGTA

AAGCTGCTGG

CGCGAGGACG

GAGTTCGAGG

GCGTTCCGTA

TGGAGCTCGT

CTCCGGTTGT

AGATTCTCGA

ACAAGCCGTT

TTACCGGCCG

TCCGCGAGA.A

ACACCGCAGA

T TGAGCGTGG

GCTCCGTCTA

CATCCTGGTT

CGAGATGGAG

TCACATCTCC

GCTGATGCAG

CCTGATGCCG

TGTTGAGCGT

GTCCCAGAAG

GGCTGGCRAC

CCAGATCATC

CGTTCTGTCC

GCACTGAACA

GTCCGCGAGC

GCACTGAAGG

GC TTGCGAC!G

GTTGWGGACA

GGCATCCTGA

ACCACCGTTA

AACGCTGCAC

GCTAAGCCGG

AAGGACGAGG

AGTGTGACAT

TGCTGGCTGA

CCCTGGAGGG

AGTCTATCCC

TCTTCACCAT

ACCTGAACGA

CCTCCATCGA

TGCTGCTGCG

GCGAGTAcAC

GCGGCCGCCA

120 180 240 300 360 420 480 540 600 660 720 CACCCCGTTC TTCGACAACT ACCGTCCGCA GTTCTAC TTC COCACCACCO ACGTTACCG 121 TGTTGTGAAG CTGCCTGAGG GCACCGAGAT GGTTATGCCG GGCGACAACG TYGACATGTC CGTCACCCTG ATCCAGCCGG TTGCTATGGA CGAG INFORMATION FOR SEQ ID NO: 129: Mi SEQUENCE CHARACTERISTICS: LEN GTH 748 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Corynebacterium pseudodiphteriticum (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 129: 780 814 CGGCGCTATC TTGGTTGTTG CAGCTACCGA CGGCCCAATG CCACAGACTC

TCTGCTGGCT

GGTTGACGAC

CCAGGAATTC

CGAAGAGAGG

TGATCCAGAC

TACCGGTCGT

AGAAGTC!GAG

AATGTTCCGC

CGGTACCAAG

CACCCACAAG

CACCCCGTTC

CGCCAGGTTG

GAGGAAATCC

GACGAAGAAG

TGGGTTAACG

CGTGCTACCG

GGCACCGTTG

ATCATCGGCA

AAGATGCTGG

CGTGAAGACG

AAGTTCGAAG

GCGTTCCTTA

TCGAGCTCGT

CTCCAATCGT

CCATCGTTGA

ACAAGCCATT

TTACGGGTCG

TCAAGGAAAA

ACTACACCGA

CATCCTGGTT

CGAGATGGAG

TCACATCTCC

ACTGATGGAT

CCTGATGCCT

TGTTGAGCGT

GTCCCAGAAG

GGCCGGCGAC

GCACTAAACA

ATCCGCGAAT

GCAGTCGGCG

GCTTGTGACG

ATCGAGGACA

GGTTCCCTGA

ACCACCATCA

AACGCTGGTC

GTTGCTCCAG

GCGAGCACGT

AGTGCGACAT

TGCTGGCTGA.

CCTTGGAAGG

AGTCGATCCC

TC'IrCACCAT

AGGTCAACGA

CCGGTATCGA

TGCTGCTTCG

GTGCTTACAG

GCGGCCGCCA

ACGTTACCGG

120 180 240 300 360 420 480 540 600 660 720 TTGAGCGTGG ACAGGTTATC GTTCCGTCTA CGTTCTTTiCC AAGGACGAGG TTCGACAACT ACCGTCCTCA GTTCTACTTC CGCACCACCG TGTTGTTACC CTGCCTGAGG GCACCGAG INFORMATION FOR SEQ ID NO: 130: (i)SEQUENCE CHARACTERISTICS: LENGTH: 813 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: 122 ORGANISM: Corynebacterun stratun (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 130: GGCGCTATCT TGGTTGTTGC TGCAACCGAT GGCCCGRTGC CGCAGACCCG CGAGCACGTT

CTTCTGGCTC

GTTGACGACG

CAGGACTACG

GRCGAGAAGT

GATC!CGGAGC

ACC GGCCGCG

GACGTTGAGA

ATGYTCCGCA

GGTACCAAGC

CCTCACACCC

ACCCCGTTCA

GTCATCAAGC

GTCGAGCTGA

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

CTGATGCAGG

CTGATGCCAA

GTTGAGCGTG

TCCATCTCCA

GCTGGCGACA

CAGGTTGTTA

GTCCTGAAGA

TTCTACTTCC

GTTATGCCTG

CACTGAACAA

TCCGCGAACT

CTCTGAAGGC

CTTGCGATGA

TCGAGGACAT

GCTCCCTGAA

CCACCGTTAC

ACTGTGGTCT

TTAAGCCGGG

AGGAAGAGGG

GCACCACCGA

GCGACAACGT

GTGCGACATG

GCTCGCAGAG

TCTTGAGGGC

CTCCATCCCG

CTTCACCATC

CGTCAACGAG

CGGTATCGAG

GCTTCTGCGT

CGCTTACACC

CGGCCGCCAC

CGTTACCGGC

CGAGATGTCY

120 180 240 3*00 360 42'0 480 54D 600 660 720 780 .o TCCAGCCGGT CGCTATGGAC GAG INFORMATION FOR SEQ ID NO: 131: Ci) SEQUENCE CHARACTERISTICS: LENGTH: 817 base pairs TYPE: nucleic acid C(C) STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINL SOURCE: C(A) ORGANISM: Enterococcus aviuni Cxi).SEQUENCE DESCRIPTION: SEQ ID NO: 131: CGGAGCTATC TTAGTAGTAT CTGCTGCTGA TGGCCCTATG CCTCAAACTC GTOAACACAT CTTGTTATCT CGTAACGTTG GTGTTCCTTA CATCGTTGTA TCTAAACA AAATGGATAT GGTTGACGAT GAAGAATTAC TTGAATTAGT TGAAATGGAA GTTCGTGACT TATTAACTGA ATACGACTTC CCAGGCGACG ACACTCCAGT TATCGCAGGT TC-AGCGT'rGA AAGCTTTAGA AGGCGACGCT TCATACGAAG AAAAAATCTT AGAATTAATG GCTGCTGTTG ACGAATATAT 123 CCCAACACCA GTTCGTGATA CTGACAAACC ATTCATGATG CCAGTCGAAG AATCACTGGT CGTGGTACTG TTGCAACTGG TCGTGTTGAA CGTGGACAAG TGACGAAGTT GAAATCGTAG GTATCGCTGA CGAAACTGCT AAAACAACTG TGAAATGI-rC CGTAAATTCT TAGACTACGC TGAAGCAGGT GACAACATCG ACGTGGTGTT GCACGTGAAG ATATCCAACG TGGACAAGTA TTGGCTAAAC CACTCCACAT ACAAAATTCT CTGCAGAAGT TTATGTTCTA ACTAAA.GAAG TCATACTCCA TTCTTCACTA ACTACCGTCC TCAGTTCTAC TTCCGTACAA TGGTGTAGTT GATCTACCAG AAGGTACTGA AATGGTWATG CCTGGGGATA GGAAGTTGAA TTGATYCACC CAATYGCGGT AGAAGAC INFO RM'ATION FOR SEQ ID NO: 132: Wi SEQUENCE CHARACTERISTICS: LENGTH: 817 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Enterococcus faecalls (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 132:

ACGTATTCTC

TTCGCGTTGG

TTACAGGTGT

GTGCTTTGTT

CAGCTTCAAT

AAGGTGGACG

CTGACGTAAC

ACGTAACTAT

360 420 480 540 600 660 720 780 817 CGGAGCTATC TTAGTAGTTT CTGCTGCTGA TGGTCCTATG CCTCAAACAC GTGAACATAT

CTTATTATCA.

GGTTGATGAC

ATACGATTTC

AGGCGACGAG

CCCAACTCCA

AATCACTGGA

TGACGAAGTT

TGAAATGTTC

ACGTGGTGTA

CACTCCACAC

CGTAACGTTG

GAAGAATTAT

CCAGGCGATG

TCTTATGAAG

GAACGTGATA

CGTGGTACTG

GAAATCGTTG

CGTAAATTAT

GCACGTGAAG

ACAAAATTCA

OTOTACCATA

TAGAATTAGT

ATGTTCCAGT

AAAAAATCTT

CTGACAAACC

TTGLCTACAGrG

GTATTAAAGA

TAGACTACGC

ATATCGAACG

AAGCTGAAGT

CATCGTTGTA TTCTTAAACA AGAAATGGAA GTTCGTGACT TATCGCAGGT TCTGCTTTGA AGAATTAATG GCTGCAGTTG ATTCATGATG CCAGTCGAAG ACGT=TTGAA CGTGGTGAAG, CGAAACATCT AAAACAACYG TGAAGCAGGC GACAACMTCG TGGACAAGTA TTAGCTAAAC ATACGTATTA TCAAAAGAAG

AAATGGATAT

TATTATCAGA

AAGCTTTAGA

ACGAATATAT

ACGTATTCTC

TTCGCGTTGG

TTACAGGTGT

GTGCTTTATT

CAGCTACAAT

AAGGCGGACG

120 1SO 240 300 360 420 480 540 600 660 TCACACTCCA 'rrCTTCACTA ACTACCGTCC TCAATTCTAC TTCCGTACAA CAGACGTTAC 124 TGGTGTTGTA GAATTGCCAG AAGGTACTGA AATGGTAATG CCTGGTGATA ACGTTGCTAT GGACGTTGAA TTAATTCACC CAATCGCTAT CGAAGAC INFORM4ATION 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 faecaium (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 133: CGGAGCTATC TTGGTAGTTT CTGCTGCTGA CGGCCCAATG CCTCAAACTC GTGAACACAT a

CCTATTGTCT

GGTTGATGAC

ATACRAATTC

AGGCGACGCT

CCCAACTCCA

AATTACTGGA

TGACGAAGTT

TGA.AATGT'C

ACGTGGTGTT

CACACCTCRT

TCATACTCCA

CGTCAAGTTG

GAAGAATrTAC

CCTGGTGRCG

TCATACGAAG

GAACGTGACA

CGTGGTACTG

GAAGTTGTTG

CGTAAATTGT

GCACGTGAAG

ACAAAATTCT

TTCTTCACTA

GTGTTCCTTA

TAGAATTAGT

ATGTTCCTGT

AAAAAATTCT

ACGACAAACC

TTGCTACAGG

GTATTGCTGA

TAGACYACGC

ACATCCAACG

CTGCAGAAGT

ACTACCGTCC

CATCGTTGTA

TGAAATGGAA

AGTTGCTGGA

TGAATTAATG

ATTCATGATG

TCGTGTTGAA

AGAAACTTCA

TGAAGC TGGA

TGGACAAGTT

ATACGTGTTG

ACAATTCTAC

TTCTTGAACA

GTTCGTGACC

TCAGCTTTGA

GCTGCAGTTG

CCAGTTGAAG

CGTGGACAAG

AAAACAACAG

GACRACATTG

T'TAGCTAAAC

ACAAAAGAAG

TTCCGTACAA

AAGTAGACAT

TATTAACAGA

AAGCTCTAGA

ACGAATACAT

ACGTGTTCTC

TTCGCGTTGG

TTACTGGTGT

GTGCTTTACT

CAGGTACAAT

AAGGTGGACG

CTGACGTAAC

780 817 120 180 240 300 360 420 480 540 600 660 720 AGGTGTTGTT GAATTACCAG AAGGAACTGA AATGGTCATG CCCGGTGACA ACGT INFORMATION FOR SEQ ID NO: 134: SEQUENCE CHARACTERISTICS: LENGTH: 809 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: 125 ORGANISM: Enterococcus gallinarun (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 134: CGGTGCGATC TTAGTAGTAT CTOCTGCTGA CGGTCCTATG CC'rCAAACTC GTGAACACAT

CTT=TATCA

GGTTGAYGAC

ATATGACTTC

AGGAGATCCT

TCCAACTCCA

AATCACTGGA

TGATGAAGTA

TGAAATGTTC

ACGTGGGGTT

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

CCGTGTTGA.A

CGAAACTGCT

TGAAGCAGGG

TGGACAAGTA

TTATGTTTTG

TCAGTTCTAC

AATGGTGATG

TTCTTGAACA

GTTCGTGACC

TCTGCTTTGA

GCTGCAGTTG

CCAGTCGAAG

CGTGGACAAG

AAAACAACTG

GATAACATTG

TTGGCTAAAG

ACAAAAGAAG

T=CGTACAA

CCTGGCGACA

AAATGGATAT

TATTGTCTGA

AAGCTCTTGA

ACGAATACGT

ACGTATTCTC

TTCGCGTTGG

TAACAGGTGT

GTGCATTGCT

CTGGTACAAT

AAGGTGGACG

CTGACGTAAC

ACGTGACCAT

S

120 180 240 300 360 420 480 540 600 660 720 780 809 120 240 300 CGACGTTGAA TTGATRCACC CAATCGCTC INFORMATION FOR SEQ ID NO: 135: SEQUENCE CHARACTERISTICS: LENGTH: 823 base pairs TYPE: nucleic acid STR7ANDEDNESS: double TOPOLOGY: linear (ii) MOLaECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Gardnex-ella vaginalls (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 135: TGGCGCAATC CTCGTGGTTG CTGCTACCGA CGGTCCAATG GCTCAGACCC GTGAACACGT CTTGCTTGCT AAGCAGGTCG GCGTTCCAA.A AATTCTTGTT GCTTTGAACA AGTGCGATAT GGTTGACGAC GAAGAGCTTA TCGATCTCGT TGAAGAAGAG GTCCGTGACC TCCTCGAAGA AAACGGCTTC GATCGCGATT GCCCAGTCYT CCGTACTTCC GCTTACGGCG CIT1'GCATGA TGACGCTCCA GACCACGACA AGTGGGTAGA GACCGTCAAG GAACTCATGA AGGCTGTTGA 126 CGAGTACATC CCAACCCCAA CTCACGATCT TGACAAGCCA TTCTTGATGC TGTGTTCACC ATCTCCGGTC GTGGTYCCGT TGTCACCGGT CGTGTTGAGC CCCAATCAAC ACCCCAGTTG AGATCGTTGG TTTGCGCGAT ACCCAGACCA CTCTATCGAG ACCTTCCACA AGCAGATGGA TGAGGCAGAG GCTGGCGATA TCTTCTCCGC GGTATCAACC GTACCGACGT TGAGCGTGGT CAGGTTGTGG TTCTGTGACT CCACACACCA. AGTTCGAAGG CGAAGTTTAC GTCTTGACCA TGGCCGTCAC TCGCCATTCT TCTCCAACTA CCGTCCACAG TTCTACTTCC TGTTACTGGC GTTATCACCT TGCCAGACGG CATCGAAATG GTTCAGCCAG AACCTTCACT GTTGAGTTGA TCCAGGCTAT CGCAATGGA), GAG INFORMATION FOR SEQ ID NO: 136: SEQUENCE CHARACTERISTICS: LENGTH: 817 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (Vi) ORIGINAL SOURCE: ORGANISM: Listeria innocua (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 136:

CAATCGAAGA

GTGGTAAGCT

CCACCGTCAC

ACACTGGTCT

CTGCTCCAGG

AGGACGAAGG

GTACCACCGA

GCGATCAC!GC

360 420 480 540 600 660 720 780 823 0 Je S I 0 *0 0*

S.

*5 S 0 CGGAGCTATC TTAGTAGTAT CTGCTGCTGA TGGCCCA.ATG CCACAAACTC GTGAACATAT

S

0@*e CTTACTTT CA

GGTTGACGAT

ATATGAATTC

AGGTGAAGCT

TCCAACTCCA

AATCACTGGT

TGACGAAGTA

AGA.AATGTTC

ACGTGGTGTT

TACTCCACAC

TCACACTCCA

CGTCAAGTTG

GAAGAATTAC

CCTGGCGATG

GACTGGGAAG

GAACGTGATA

CGTGGA.ACAr,

GAAGTTATCG

CGTAAATTAC

GCTCGTGAAG

ACTAACTTCA

TTCTTCAACA

GTGTTCCATA

TAGAATTAGT

ACATTCCTGT

CTAAAATTGA

CTGACAAACC

TTGCAAC-TG

GTATTGAAGA.

TAGACTACGC

ATATCCAACG

AAGCTGAAAC

ACTACCGCCC

CATCGTTGTA

TGAAATGGAA

AATCAAAGGT

CGAGTTA.ATG

ATTCATGATG

ACGTGTrGAA

AGAAAGCAAA

TGAAGCTGGC

TGGTCAAGTA

TTATGTTTTA

ACAATTCTAT

TTCATGAACA

ATTCGTGATC

TCAGCTCTTA

GAAGCTGTAG

CCAGTTGAGG

CGTGGACAAG

AAACGTAGTAG

GACAACATTG

TTAL3CTAAAC

ACTAAAGAAG,

TTCCGTACTA

AATGTGACAT

TATTAACTGA

AACCACTTCA

ATTCTTACAT

ATGTATTCTC

TrAAAGTTGG

TAACTGGAGT

GCGCACTTCT

CAGGTTCGAT

AAGGTGGACG

CTGACGTAAC

120 180 240 300 360 4 480 540 600 660 720 127 TGGTATTG=r ACACTTCCAG AAGGTACTGA AATGGTA.ATG CCTGGTGATA ACATTGAGCT TGCAGTTGAA CTAATTGCAC CAATCGCTAT CGAAGAC INFORMATION FOR SEQ, ID NO: 137: SEQUENCE CHARACTERISTICS: LENGTH: 818 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Listeria ivanovii (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 137: CGGAGCTATC TTAGTAGTAT CTGCTGCTGA TGGTCCAATG CCACAAACTC GTGAACATAT see* 0. 0 0* 006 000 0 00

TCTTACTTTC

TGGTTGACGA

AATATGAATT

AAGGTGAAGC

TTCCAACTCC

CAA6TCACTGG GTGACGAAGTr

TAGAAATGT

TACGTGGTGT

TTACTCCACA

GTCATACTCC

CTGGTATTGT

ACGTCAAGTT

TGAAGAATTA

CCCTGGCGAC

TGATTGGGAA

AGAACGTGAT

TCGTGGAACA

AGAAGTTATC

CCGTAAATTA

TGCTCGTGAA

TACTAACTTC

ATTCTTCAAC

TACACTTCCA

GGTGTTCCAT

CTTGAATTAG

GACA'I7CCTG

GCTAAAATTG

ACTGACAAAC

GTTGCAACTG

GGTATTGAAG

CTAGACTACG

GATATCCAAC

AAAGCTGAAA

AACTACCGCC

GAAGGTACTG

ACATCGTTGT

TTGA.AATGGA

TAATCAAAGG

ACGAGTTAAT

CATTCATGAT

GACGTGTTGA

AAGAAAGCAA

CT'GAAGCTGG

GTGGTCAAGT

CTTATGTTTT

CACAATTCTA

AAATGGTAAT

TCGAAGAC

ATTCATGAAC

AATTCGTGAT

TTCAGCTCTT

GGAAGCTGTA

GCCAGTTGAG

ACGTGGACAA

AAAAGTAGTA

CGACAACATT

A77AGCTAAA

AACTAAAGAA

TTCCGTACT

GCCTGGTGAT

AAATGTGAC.A

CTATTAACTG

AAAGCACTTC

GArrCTTACA

GATGTATTCT

GTTAAAGT'G

GTAACTGGAG

GGCGCACTTC

CCAGGTTCGA

GAAGGTGGAC

ACTGACGTAA

AACATTGAGC

780 817 120 180 240 300 360 420 480 540 600 660 720 780 ale TTGCAGTTGA ACTAATTGCA CCAATCGCTA INFORMATION FOR SEQ ID NO: 138: CW SEQUENCE CHARACTERISTICS: LENGTH: 817 base pairs TYPE: nucleic acid STRAN4DEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) 128 (vi) ORIGINAL SOURCE: ORGANISM: Listeria monocytogenes (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 138: CGGAGCTATC TTAGTAGTAT CTGCTGCTGA TGGCCCAATG CCACAAACTC GTGAACATAT

CTTACTTTCA

GGTTGACGAT

ATATGAATTC

AGGTGAAGCT

TCCAACTCCW

AATCACTGGT

TGACGAAGTA

AGAAATGTTC

ACGTGGTGTT

TACTCCACAC

TCACACTCCA

TGGTATTGTT

TGCAGTTGAA

CGTCAAGTTG

GAAGAATTAC

CCTGGCGATG

GACTGGGAAG

GAACGTGATA

CGTGGAACAG

GAAGTTATCG

CGTAAATTAC

GCTCGTGAAG

ACTAACTTCA

TrCTTCAACA

ACACTTCCAG

CTAATTGCAC

GTGTTCCATA

TAGAATTAGT

ACATTCCTGT

CTAAAATTGA

CTGACAAACC

TTGCAACTGG

GTATCGAAGA

TAGACTACGC

ATATCCAACR

AAGCTGAAAC

ACTACCGCCCC

AAGGTACTGA

CATCGTTGTA

TGAAATGGAA

AATCAAAGGT

CGAGTTAATG

ATTCATGATG

ACGTGTTGAA,

AGAAAGCAAA

TGAAGCTGGC

TGGTCAAGTA

TTATGTTTTA

ACAATTCTAT

AATGGTAAYG

TTCATGAACA

ATTCGTGATC

TCAGCTCTTA

GAAGCTGTAG

CCAGTTGAGG

CGTGGACAAG

AAAGTAGTAG

GACAACATTG

TTAGCTAAAC

ACTAAAGAAG

TTCCGTACTA

CCTGGTGATA

AATGTGACAT

TATTAACTGA

AAGCACTTCA

ATTCTTACAT

ATGTATTCTC

TTAAAGTTGG

TAACTGGAGT

GCGCACTTCT

CAGGTTCGAT

AAGGTGGACG

CTGACGTAAC

ACATTGAGCT

120 180 240 300 360 420 480 540 600 660 720 780 817 120 180 240 CAATCGCTAT CGAAGAC INFORMATION FOR SEQ ID NO: 139: SEQUENCE CHARACTERISTICS: LENGTH: 817 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (geflomic) (vi) ORIGINAL SOURCE: ORGANISM: Listeria seeligeri (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 139: CGGAGCTATC TTAGTAGTAT CTGC TGCTGA TGGCCCAATG CCACAAACTC GTGAACATAT CTTACTTTCA CGTC.AAGTTG GTGTTCCATA CATCGTTGTA TTCATGAACA AATGTGACAT GGTTGACGAT GAAGAATTAC TTGAATTAGT TGAAATGGA ATTCGTGATC TATTAACTGA ATATGAATTC CCTCGTGATG 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

GTATTGAAGA

TAGACTACGC

ATATCCAACG

AAGCTGAAAC

ACTACCGCCC

AAGGTACTGA

CGAGTTAATG GAAGCTGTAG ATTCATGATG CCAGTTGAGG ACGTGTTGAA CGTGGACAAG AGAAAGCAAA AAAGTAATAG TGAAGCTGGC GACAACATTG TGGTCAALGTA TTAGCTAAAC TTATGTTTTA ACTAAAGAAG ACAATTCTAT TTCCGTACTA AATGGTAATG CCTGGTGATA

ATTCTTACAT

ATGTATTCTC

TTAAAGTTGG

TAACTGGAGT

GCGCACTTCT

CAGGTTCGAT

AAGGTGGACG

CTGACGTAAC

ACATTGAGCT

TGCAGTTGAA CTAATTGCAC CAATCGCTAT CGAAGAC INFORMATION FOR SEQ ID NO: 140: Wi SEQUENCE CHARACTERISTICS: CA) LENGTH: 814 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (geriomic) (vi) ORIGINA.L SOURCE: CA) ORGANISM: Staphylococcus aureus (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 140: CGGTCGTATC TTAGTAGTAT CTCCTGCTGA CGGTCCAATG CCACAAACTC GTGAACACAT

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

ATTAGTAGTA TTCTTAAACA AGAAATGGAA GTTCGTGACT AATCGCTGGT TCAGCATTAR AGAATTARTG GAAGCTGTAG ATTCATGATG CCAGTTGAGG CCGTGTTGAA CGTGGTCAAA CACATCTAAA ACAAcTGTrA AGCTGGTGAC AACATTGGTG TCAAGTATTA GCTGCTCCTG CGTATTATCA AAAGACGAAG

AAGTTGACAT

TATTAAGCGA

AAGCTTTAGA

ATACTTACAT

ACGTATTCTC

TCAAAGTTGG

CAGGTGTrTGA

CATTATTACG

GTTCAATTAC

GTGGACGTCA

120 180 240 300 360 420 480 540 600 660 130 CACTCCATTC TTCTCAAACT ATCGTCCACA ATTCTATTTC CGTACTACTG ACGTAACTGG TGTTGTTCAC TTACCAGAAG GTACTGAAAT GGTAATGCCT GGTGATAACG TTGAAATGAC AGTAGAATTA ATCGCTCCAA TCGCGATTGA AGAC INFORMATION FOR SEQ ID NO: 141: SEQUENCE CHARACTERISTICS: LENGTH: 814 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Staphylococcus epiderrnidis (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 141: 720 780 814- CGGCGGTATC TTAGTTGTAT CTGCTGCTGA CGGTCCI4ATG CCACAAACTC

CTTATTATCA

GGTAGACGAC

ATATGACTTC

AGGCGATGCT

TCCAACTCCA

AATCACTGGT

TGAAGAAGTT

AATGTTCCGT

TGGTGTTGCA

ACCACACACA.

CACTCCATTC

TGTI'GTAAAC

CGTAACGTTG

GAAGAATTAT

CCAGGTGACG

GAATACGAAC

GAACGTGATT

CGTGGTACTG

GAAATCATCG

AAATTATTAG

CGTGAAGACG

AAATTCAAAG

'I7CACTAACT

TTACCAGAAG

GTGTACCAGC

TAGAATTAGT

ATGTACCTGT

AAAAAATCTT

CTGACAAACC

TTGCTACAGG

GTATGCACGA

ACTACGCTGA

TACAACGTGG

CTGAAGTATA

ATCGCCCACA

GTACAGAAAT

ATTAGTTGTA TTCTTAAACA TGAAATGGAA GTTCGTGACT AATCGCTGGT TCTGCATTAA AGACTTAATG CAAGCAGTTG ATTCATGATG CCAGTTGAGG CCGTGTTGAA CGTGGTCAAA AA CTT CTAAA ACAA.CTGTTA AGCTGGTGAC AACATCGGTG TCAAGTATTA GCTGCTCCTG CGTATTATCT AAAGATGAAG ATTCTATTTC CRTACTACTG GGTTATGCCT GGI'GAI~.ACG

GTGAIACACAT

AAGTTGACAT

TATTAAGCGA

AAGCATTAGA

ATGATTACAT

ACGTATTCTC

TCAAAGTWGG

CTGGTGTAGA

CTTTATTACG

GTTCTATTAC

GTGGACGTCA

ACGTAACTGG

TTGAPAPT=A

120 180 240 300 360 420 480 540 600 660 720 '780 814 AGT=GAATTA ATCGCTCCAA TCGCTATCGA. AGAC INFORMATION FOR SEQ ID NO: 142: SEQUENCE CHARACTERISTICS: LENGTH: 817 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear 131 (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Staphylococcus saprophytaicus (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 142: CGGAGCTATC TTAGTAGTAT CTGCTGCTGA TGGCCCAATG CCACAAACTC GTGAACACAT

TCTTTTATCA

GGTTGACGAY

ATATGACTTC

AGGCGACGCT

TCCAACACCA

AATCACTGGT

TGAAGAAATC

AGAAATGTTC

ACGTGGTGTT

CACACCACAT

TCATACGCCA

TGGTGTTGTT

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

AGAAATGGAA

AATCTCTGGT

AGACTTAATG

ATTCATGATG

CCGTGTTGAA

AGAATCAAGC

TGAAGCTGGT

TGGTCAAGTT

TACGTTTTA

ACAATTCTAT

AATGGTTATG

TTCTTAAACA AAGTTGACAT GTTCGTGRCT TATTAAGCGA TCTGCATTAP, AAGCTTTAGA CAAGCTGTTG ATGACTYCAT CCAGTTGAGG ACGTATTCTC CGTGGTCAAA TCAAAGTCGG AAAACAACTG TTACTGGTGT GACAACATTG GTGCATTATT TTAGC TGCTC CTGGTACTAT TCTAAAGATG AAGGTGGTCG TTCCGTACTA CTGACGTAAC CCTGGCGATA ACGTTGAAAT 120 180 240 300 360 420 480 540 600 660 720 780 817 120 180 GGATGTTGAA TTAATTTCTC CAATCGCTAT TGAAGAC INFORMATION FOR SEQ ID NO: 143: Wi SEQUENCE CHARACTERISTICS: LENGTH: 817 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (geriomic) (vi) ORIGINAL SOURCE: ORGANISM: Staphylococcus simulans (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 143: CGGCGGTATC TTAGTAGTAT CTGCTGCAGA TGGTCCAATG CCACAAACTC GTGAACACAT CTTATTATCA CGTAACGTTG GTGTACCAGC TTTAGTTGTA T1TCTTAAACA AAGCTGACAT GGTTGACGAC GAAGAATTAT TAGAATTAGT TGAAATGGAA GTTCGTGACT TATTATCTGA 132

ATACGACTTC

AGGCGACCCA

CCCAACTCCA

AATCACTGGT

TGAAGAAGTT

AGAAATGTTC

ACGTGGTGTT

TACTCCACAC

TCATACTCCA

TGGCGTTGTT

GACTGTTGAA

CCTGGTGACG

GAATACGAAC

GAACGTGACI'

CGTGGTACTG

GAAATCATCG

CGTAAATTAT

GCACGTGAAG

ACAAAATTCA

TTCTTCACTA

CACTTACCAG

ATGTACCAGT

AAAAAATCTT

CTGATAAACC

TAG CAACAGG

GTATCACTGA

TAGACTACGC

ACGTACAACG

AAGCTGATGT

ACTACCGCCC

AAGGTACTGA

TATCGTTGGT

AGACTTAATG

ATTCATGATG

CCGTGTTGAA

AGAAAGCAAG

TGAAGCTGGT

TGGACAAGTA

TTACGTTTrA

ACAATTCTAC

A.ATGGTTATG

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 TTGATCGCTC CAATCGCGAT INFORMATION FOR SEQ ID NO: 144: SEQUENCE CHARACTERISTICS: LENGTH: 817 base pairs TYPE: nucleic acid STR.ANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Streptococcus agalactiae (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 144: CGGAGCTATC CTTGTAGTTG CTTCAACTGA TGGACCAATG CCACAAACTC GTGAGCACAT CCTTCTTTcA

TGTTGATGAT

ATACGACTTC

AGGCGACGAA

TCCAGAACCA

AATCACTGGA

CGACGAAGTT

TGAAATarrC

TCGTGGTGT

CGTCAAGTTG

GAAGAATTGC

CCAGGTGATG

AAATACGAAr,

GAACGTGATA

CGTGGTACAG

GAAATCGTTG

CGTAAACAAC

CAACGTGATG

GTGTTAAACA

TI'GAATTGGT

ACCTTCCAGT

ACATCATCAT

CTGACAAACC

TTGCTTCAGG

GTATTAAAGA

TTGACGAAGG

AAATCGAACG

CCTTATCCTA

TGAAATGGAA

TATCCAAGGr GGAA7"TGATC

TTTACTTCTT

ACGTATCGAC

AGATATCCAA

TC TTGCAGGG

TGGTCAAGTT

TTCATGAACA AAGTTGACCT ATTCGTGACC TTCTTTCAGA TCAGCTCTTA AAGCACTTGA ACCACTOTTC ATGAGTACAT CCAGTTGAAG ATGTATTCTC CGTGGTACTG TTC!GTGTCA.A AAAGCAGTTG TTACTGGTGT GACAACGTTG GTGTTCTTCT CTTGCTAAAc cAGGTTCAAT 120 180 240 300 360 420 480 540 600 133 CAACCCACAC ACTAAATTTA AAGGTGAAGT TTACATCCTT TCTAAAGAAG AAGGTGGACG TCATACTCCA TTCTTCAACA ACTACCGTCC ACAATTCTAC TTCCGTACAA CTGACGTAAC AGGTTCAATC GAACTTCCAG CAGGAACAGA AATGGTTATG CCTGGTGATA ACOTTACTAT CGAAGTTGAA TTGATTCACC CAATCGCCGT AGAACAA INFORMATION FOR SEQ ID NO: 145: SEQUENCE CHARACTERISTICS: LENGTH: 817 base pairs TYPE: nucleic acid STRAINDEDNESS: 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 CCTTCTTTr.LCA

GGTTGACGAC

ATACGACTTC

AGGTGACTCT

CCCAGAACCA

AATCACTGGA

CGACGAAATC

TGAAATGTTC

TCGTGGTGTr

CAACCCACAC

TCACACTCCA

AGGTTCAATC

CGTCAGGTTG

GAAGAATTGC

CCAGGTGACG

AAATACGAAG

GAACGTGACA

CGTGGTACAG

GAAATCGTTG

CGTAAACAAC

CAACGTGATG

ACTAAATTCA

TTCTTCAACA

GAACTTCCAG

GTGTTAAACA CCTTXJ TTGAATTGGT TGAAA1 ATCTTCCAGT TATCC ACATCGTTAT GGAATJ] CTGACAAACC ATTGCI TTGCTTCAGG ACGTAI GTATCAAAGA AGAAA( TTGACGAAGG TCTTG( AAATCGAACG TGGAC AAGGTGAAGT CTACA, ACTACCGTCC ACAAT CAGGTACTGA AATGG'

~CGTC

~GGAA

AGGT

'GATG

TCTT

~CGAC

.TCRA

:TGGA

=.ATT

FCCTT

rcTAc

TTCATGAACA

ATCCGTGACC

TCAGCACTTA

AACACAGTTG

CCAGTCGAGG

CGTGGTATCG

AAAGCAGTTG

GATAACGTAG

ATCGCTAAAC

ACTAAAGAAG

TTCCGTACTA

AAGTTGACTT

TATTGTCAGA

AAGCTCTTGA

ATGAGTATAT

ACGTATTCTC

TTAAAGTCAA

TTACTGGTGT

GTGTCCTTCT

CAGGTTCAAT

AAGGTGGACG

CTGACGTTAC

660 720 780 817 120 180 240 300 360 420 480 540 600 660 720 780 817 TAATG CCTGGTGATA ACGTGACAAT CGACGTTGAG TTGATTCACC CAATCGCCGT AGAACAA 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 salivar-ius (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 146: CGGTGCGATC CTTGTAGTAG CATCTACTGA CGGACCAATG CCACAAACTC GTGAGCACAT

CCTTCTTTCA

GGTTGACGAT

ATACGATTTC

AGGTGATTCT

CCCAGAACCA

AATCACTGGT

TGACGAAGTT

TGAAATGTTC

TCGTGGTATC

CAACCCACAC

TCACACTCCA

AGGTTCAATC

CGTCAGGTTG

GAAGAATTGC

CCAGGTGATG

AAATACGAAG

GAACGTGACA

CGTGGTACTG

GAAATCGTTG

CGTAAACAAC

CAACGTGATG

ACTAAATTCA

TTCTTCAACA

GAACTTCCTG

GTGTTAAAC-A

TTGAATTGGT

ACATTCCAGT

ACATCATCAT

CTGACAAACC

TTGCT TCAGG

GTCTTAP.AGA

TTGACGRAGG

AAATCGAACG

AAGGTGAAGT

ACTACCGTCC

CAGGTACTGA

CCTTATC!GTC

TGAAATGGAA

TATCCAAGGT

GGACTTGATG

ATTGTTGCTT

ACGTATCGAC

AGACATCCAA

TATI'GCCGGA

TG4GTCAAGTA

TTACATCC!TT

ACAGTTCTAC

AATGGTTATG

TGAACAA

TTCATGAACA

ATCCGTGACC

TCAGCTCTTA

AACACTGTTG

C!CAGTCGAAG

CGTGGTGTTG

AAAGCAGTTG

GATAACGTCG

TTGGCTGCAC

TCTAAAGAAG

TTCCGTACAA

CCTGGTGATA

AAGTTGACTT

TTCTTTCAGA

AAGCTCTTGA

ACGAATACAT

ACGTATTCTC

TTCGTGTCAA

TTACTGGTGT

GTGTTC TTCT

CTGGTTCAAT

AAGGTGGACO

CTGACGTAAC

ACGTGACTAT

*o.

0..

120 180 240 300 360 420 480 540 600 660 720 780 817 120 CGACGT'GAG TTGATCCACC CAATCGCCGT INFORMATION 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: Agrobacteriui tuznefaciens (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 147: AACATGATCA CCGGTGCTGC CGAGATGGAC GGCGCGATCC TGGTTTGCTC GGCTGCCGAC GGCCCGATGC CACAGACCCG CGAGCACATC CTGCTGCCC G.TCAGGTGGG CGTTCCGGCC 135

ATCGTCGTGT

GAGCTTGAAG

ATCAAGGGTT

ATCCGCGAGC

CAGCCGTTCC

ACGGGTCGCG

CGTCCGACCT

GGCCAGGCCG

CGTGGTCAGA

GCCTACATCC

CCGCAGTTCT

GAAATGGTTA

TCCTCAACAA

TTCGCGAACT

CGGCACTTGC

TGATGGCTGC

TGATGCCGAT

TTGAGCGCGG

CGAAGACGAC

GCCACAACAT

TCCTGTGCAA

TGACGAAGGA

ACTTCCGTAC

TGCCTGGCGA

GGTCGACCAG

TCTGTCGTCC

TGCTCTTGAA

TGTCGACGCC

CGAAGACGTG

TATCGTCAAG

TGTTACCGGC

CGGTGCACTC

GCCGGGTTCG

AGAAGGCGGC

GACTGACGTT

CAACGTCACT

CTTGACGACG

TACGACTTCC

GATTCTGACA

TACATCCCGA

TTCTCGATCT

GTTGGTGAAG

GTTGAAATGT

GTTCGCGGCG

GTCAAGCCGC

CGTCATACC

ACCGGTATCG

GTTGAAGTCG

CCGAGCTTCT

CGGGCGACGA

AGAAGATCGG

CGCCTGAGCG

CGGGTCGTGG

AAGTCGAAAT

TCCGCAAGCT

TTACCCGTGA

ACAAGAAGTT

CGTTCTTCAC

TTTCGCTTCC

AGCTGATCGT

CGAGCTCCTC

TATCCCGATC

TGAAGACGCG

TCCGATCGAC

TACGGTTGTG

CGTCGGCATC

GCTCGACCAG

CGGCGTCGAG

CATGGCAGAA

GAACTACCGT

TGAAGGCACG

TCCGATCGCG

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 (genonmic) (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 GACTTCCC TG GTGATGATGT AAAGGTTCTG CTCTTAAAGC TCTTGAAGGA GACGCTGAGT GGGAAGCTAA CTTATGGATG CGG1-rGATGA 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 AGGTGTTGAA ATGTTCCGTA AGCTTCTrGA GCTGGTGACA ACATTGGTGC CCTTCTTCGC GGTGTATCTC GTGAAGAAAT CAAGTACTTG CTAAACCAGG TACAATCACT CCACACAGCA AATTCAAAGC GTTCTTTCTA AAGAAGAGGG TGGACGTCAT ACTCCATTCT TCTCTAACTA 'ITCTACTTCC 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 gilis (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 149:

TTACGCTGAA.

CCAACGTGGT

TGAAGTTTAC

CCGTCCTCAG

CGTAGAAATG

CGCTATCGAA

540 600 660 720 780 840 ATGGTTACTG GTGCTGCTCA GATGGACGGT GCTATCATTG TAGTTGCTGC TACTGATGGT

CCGATGCCTC

GTTGTATTCA

ATGGAAATGA

CAGGGTTCTG

CTGATGGAAG

TTGATGCCGG

ATCGAAACTG

AAGAAATCAG

GGTGACAACG

GTTCTTTGTA

CTGAAGAAAG

TACCTGCGTA

ATGCCGGGTG

AGACTCGTGA

TGAACAAGTG

GAGAATTGCT

CTCTTGGTGC

CTGTTGATAC

TAGAAGACGT

GTGTTATCCA

TTGTAACAGG

TAGGTCTGTT

AACCGGGTCA

AAGAAGGTGG

CTATGGACTG

ATAACGTAAC

GCACATCCTT

CGATATGGTT

TTCATTCTAT

ATTGAACGGC

TTGGATTCCA

GTTCTCTATC

TGTAGGTGAT

TGTTGAAATG

GCTTCGTGGT

GATTAAACCT

TCGTCACACT

TACAGGTGAA

TATCACTGTA

TTGGCTC!GTC

GAAGATGCTG

GATTTCGACC

GTAGAAAAAT

CTGCCTCCGC

ACAGGTCGTG

GAAATCGAAA

TTCCGCAAAC

GTTGACAAGA

CACTCTAAAT

CCATTCCATA

ATCACTCT-C

GAGTTGATCT

AGGTAAACGT

AGATGTTGGA

GTGACAATAC

GGGAAGACAA

GCGATGTTGA

GTACTGTAGC

TCCTCGGTI

TTCTGGATCA

ACGAAATCAA

TCAAAGCAGA

ACAAATATCG

CGGAAGGAAC

ATCCGGMTC

TCCGAAGCTG

ACTTGTTGAA

TCCGATCATT

AGTAPLTGGAA

TAAACCTTTC

TACAGGTCGT

GGGTGAAGAT

GGGTGAAGCT

ACGTGGTATG

GGTTTATATC

TCCTCAGTTC

TGAAATGGTA

ACTGAACATC

120 180 240 300 360 420 480 540 600 660 720 780 840 137 GGTCT'rCGTT TCGCTATCCG CGAAGGTGGA CGTACAGTAG GT INFORMATION FOR SEQ ID NO: 150: SEQUENCE CHARACTERISTICS: LENGTH: 886 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Borrelia burgdorferi (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 150: AATATGATTA CAGGAGCAGC TCAAATGGAT GCAGCGATAC TTTTAGTTGC TGCTGATAGT

GGTGCTGAGC

ATAATAGTTT

GTTGAAGTTT

GGTTCAGCTT

GAACTTCTTG

TTTTTGCTTG

CGTATTGAAA

ACCAGAAAAA

GCAGGGGATA

CAAGTTTTGT

TGTTTGACTA

TTCTTTTTTA

ATGCCTGGTG

CTCAAACAAA

TTTTAAATAA

TAGAACTTGT

TTGGGGCTAT

AATCTATGGA

CTGTTGAAGA

GAGGTATTAT

CTACTGTTAC

ATGTTrGGTCT

CAGCTCCAGG

AAGAAGAAGG

GAACAACCGA

ATAATGTTGA

AGAGCATTTG

ATTGGACTTA

TGAAAAATAT

GTCAAATCCA

TAATTATTTT

TGTATTTTCT

TAAAGTTGGT

TGGTGTTGAA

TCTTTTGAGA

TACAATTACT

CGGTAGGCAC

TGTTAC!TGGA

TATTATTGTT

CTTCTTGCTC AAAGAATGGG GCAGATCCTG AACTTGTTGA GGCTTTTC.AG CTGATACTCC GAAGATCCTG AATCTACAAA GATCTTCCAG AAAGAGATAT ATTTCAGGAA GAGGCACTGT CAAGAAGTTG AAATAGTIGG ATGTTCCAGA. AAATTCTTGA GGCGTTGATA AAAAAGACAT CCACACAAGA AATTTAAAGC AAGCCATTTT TCCCAGGGTA GTTGTTGC'rT TAGAGGGCAA GAG CTGATCT CTTCAATAGC

AATAAAGAAA

GCTTGTTGA.A

AATAATCAAA

ATGCGTTA.AA

TGACAAGCCA

TGCTACTGGG

AA77AAAGAA

GCAAGGTCAA

TGAGAGGGGG

TTCAATTTAT

TAGACCACAG

AGAAATGGTT

TATGGATAAG

882 120 180 240 300 360 420 480 540 600 660 720 760 840 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: Brevibacterui linens (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 151: AACATGATCA CCGGTGCCGC TCAGATGGAC GGTGCGATCC TCGTCGTCGC CGCTACCGAC

GGACCGATGC

ATCGTCGTGG

GAATTCGAGG

ATTCCGGTGT

GATCTCATGG

TTCCTCATGC

CGTGTCGAGC

AAGTCGTCCA

CGTGCAGGTG

GGTCAGGTCA

TACATCCTGA

CAGTTCTACT

ATGGTCATGC

CCCAGACCCG

CTCTGAACAA

TCCGCGACCT

CCGCTCTCAA

CTGCCGTCGA

CCGTCGAGGA

GCGGCGTGCT

AGACGACTGT

AGAACGTCGG

TCGTGAAGCC

GCAAGGACGA

TCCGGACCAC

CCGGCGACAA

TGAGCACGTG

GTCCGACATG

GCTCTCGAGC

GGCGCTGGAA

TGACAACGTT

CGTCTTCACG

CCTGCCTAAC

CACCGCTATC

TCTGCTCCTC

GGGTTCGATC

GGGCGGACGT

GGACGTCACC

CACCGATATG

CTGCTCGCGC

GTCGATGACG

CAGGACTTCG

GGCGACGAGA

CCGGAGCCGG

ATCACCGGTC

GACGAAATCG

GAGATGTTCC

CGCGGCACCA

ACCCCGCACA

CACAACCCGT

GGTGTCATCA

TCGGTCGAGC

GTCAGGTCGG

AGGAGCTCCT

ACGGAGACAA

AGTGGGTCAA

AGCGCGATST

GTGGAACCGT

AAATCGTCGG

GCAAGACCCT

AGCGCGAGGA

CCAAGTTCGA

TCTACTCGAA

CGCTGCCCGA

TCATCCAGCC

CGTTCCCTAC

CGAGCTCGTC

CGCTCCGGTC

GAGCGTTCAG

CGACAAGCCG

CGTCACCGGT

CATCAhGGAG

GCCGGATGCC

TGTTGAGCGC

GGCTCAGGTC

CTACCGTCCG

GGGCACCGAG

GATCGCTATG

120 240 300 360 420 480 540 600 660 720 780 840 SOS SOS 0 4* 0 S 4* SO S S

S.

*S*

S.

S. 0*O S *55500

S

S

9* 55..

S

*055 GAGGACCGCC TCCGCTTCGC AATCCGCGAA GGTGGCCGCA CCGTCGGCGC CGGT INFORMATION FOR SEQ ID NO: 152: Wi SEQUENCE CHARACTERISTICS: LENGTH: 888 base pairs TYPE: nucleic acid STR.ANDEDNESS: 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 AGCAGACGGC CCGATGCCGC AAACGCGTGA GCACATCCTG CTGGCGCGTC AGGTTGGTGT TCCGTACATC ATCGTGTTCC TGAACAAGTG CGACAGTGTG GACGACGCTG AACTGCTCGA GCTGGTCGAG 139

ATGGAAGTTC

AAGGGTTCGG

ATGAGCCTGG

GCGTTCCTGA

GGTCGTGTCG

CCGACGGTGA

CAGGCAGGCG

GGCCAGGTTC

TACGTGCTGA

CAGTTCTACT

ATGGTGATGC

GCGAACTCCT

CCAAGCTGGC

CAGACGCGCT

TGCCGGTGGA

AGCGCGGCAT

AGACGACCTG

ACAACGTCGG

TGGCGAAGC C

GCAAGGACGA

TCCGTACGAC

CGGGCGACAA

GTCGA.AGTAC

GCTGGAAGGC

GGACACGTAC

AGACGTGTTC

CGTGAAGGTC

CACGGGCGTT

TATCCTGCTG

GGGTTCGATC

AGGCGGCCGT

GGACGTGACG

CGTGTCGATC

GACTTCCCGG GCGACGACAC GACACGGGCG AGCTGGGCGA ATCCCGACGC CGGAGCGTGC TCGATCTCGG GCCGTGGTAC GGCGAAGAAA TC!GAAATCGT GAAATGTTCC GCAAGCTGCI CGCGGCACGA AGCGTGAAGA ACGCCGCACA CGCACTrCAC CACACGCCGT TCTTCAACAA GGCTCGATCG AGCTGCCGAA ACGGTGAAGC TGATTGCTCC 4* GAAGAAGGTC TGCGCTTCGC AATCCGTGAA GGCGGCCGTA CGGTCGGC INFORMATION FOR SEQ ID, NO: 153: SEQUENCE CHARACTERISTICS: LENGTH: 891 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Chlaznydia trachomatis (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 153: AACATGATCA CCGGTGCGGC TCAAATGGAC GGGGCTATTC TAGTAGrTTC GGAGCTATGC CTCAAACTAA AGAGCATATT CTTTTGGCAA GACAAGTTGG ATCGTrGI-rT TTCTCAATAA AATTGACATG ATTTCCGAAG AAGACGCTGA TTGGTTGAGA TGGAGTTGGC TGAGCTTCTT GAAGAGAAAG GATACAAAGG ATCAGAGGTT CTGCTCTGAA AGCTTTGGAA GGAGATGCTG CATACATAGA GAGCTAATGC AAGCCGTCGA TGATAATATC CCTACTCCAG AAAGAGAAAT TTCTTAATGC CTATTGAGGA CGTGTTCTCT ATCTCCGGAC GAGGAACTGT CGTATTGAGC GTGGAATTGT TAAAGTTTCC GATAAAGTTC AGTTGGTCGG ACTAAAGAAA CGATTGTTAC TGGGGTTGAA ATGTTCAGAA AAGAACTCCC

GCCGATCGTG

AGTGGCGATC

AGTTGACGGC

GGTGGTGACG

CGGTATCAAG

GGACCAAGGT

CGTGGAGCGT

GGCTGAAGTG

CTACCGTCCG

GGACAAGGAA

GATCGCGATG

TGCAACAGAC

GGTTCCTTAC

ATTGGTCGAC

GTGTCCAATC

GAAAGTTCGA

TGACAAGCCT

AGTAACTGGA

TCTTAGAGAT

AGAAGGTCGT

240 300 360 420 480 540 600 660 720 780 840 PCT/CA97/00829 140 GCAGGAGAGA ACGTTGGATT GCTCCTCAGA GGTATTGGTA AGAACGATGT ATGGTTGTTT GCTTGCCAAA CAGTGTTAAA CCTCATACAC AGTTTAAGTG GTTCTGCAAA AAGAAGAAGG TGGACGACAT AAGCCTTTCT TCACAGGATA TTCTTCTTCC GTACAACAGA CGTTACAGGT GTGGTAACTC TGCC'rGAGGG GTCATGCCTG GGGATAACGT TGAGTTTGAA GTGCAATTGA TTAGCCCTGT GAAGGTATGA GA TTT GCGAT TCGTGAAGGT GGTCGTACAA TCGGTGCTGG INFORMATION FOR SEQ ID NO: 154: SEQUENCE CHARACTERISTICS: LENGTH: 891 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Escherichia coli (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 154:

GGAAAGAGGA

TGCTGTTTAC

TAGACCTCAA

AGTTGAGATG

GGCTTTAGAA

A

0* 0 *.0.0 AACATGATCA CCGGTGCTGC GCAGATGGAC GGCGCGATCC TGGTAGTTGC TGCGACTGAC

GGCCCGATGC

ATCATCGTGT

GAAATGGAAG

GTTCGTGGTT

GAACTGGCTG

TCCTGCTGC

CGTr3TAGAAC

ACTCAGAAGT

GCTGGTGAGA

CAGGTACTGG

ATTCTGTCCA

TTCTACTTCC

GTAATGCCGG

CGCAGACTCG

TCCTGAACAA

TTCGTGAACT

CTGCTCTGAA

GCTTCCTGGA.

CGATCGAAGA

GCGGTATCAT

CTACCTGTAC

ACGTAGGTGT

CTAAGCCGGG

AAGATGAAGG

GTACTACTGA.

GCGACAACAT

TGAGCACATC

ATGCGACATG

TCTGTCTCAG

AGCGCTGGAA

TTCTTACATT

CGTATTCTCC

CAAAGTTGGT

TGGCGTTGAA.

TCTGCTGCGT

CACCATCAAG

CGGCCGTCAT

CGTGACTGGT

CAAAATGGTT

CTGCTGGGTC

GTTGATGACG

TACGACTTCC

GGCGACGCAG

CCGGAACCAG

ATCTCCGGTC

GAAGAAGTTG

ATGTTCCGCA

GGTATCAAAC

CCGCACACCA

ACTCCGTTCT

ACCATCGAAC

GTCAGGTAGG

AAGAGCTGCT

CGGGCGACGA

AGTGGGAAGC

AGCGTGCGAT

GTGGTACCGT

AAATCGTTGG

AACTGCTGGA

GTGAAGAAAT

AGTTCGAATC

TCAAAGGCTA

TGCCGGAAGG

CGTTCCGTAC

GGAACTGGTT

CACTCCGATC

GAAAATCCTG

TGACAAGCCG

TGTTACCGGT

TATCAAAGAG

CGAAGGCCGT

CGAACGTGGT

TGAAGTGTAC

CCGTCCGCAG

CGTAGAGATG

GTTACCCTGA TCCACCCGAT CGCGATGGAC GACGGTCTGC GTTCGCAAT CCGTGAAGGC GGCCGTACCG TTGGCGCGGG C 141 INFORMATION FOR SEQ ID NO: 155: Wi SEQUENCE CHARACTERISTICS: LENGTH: 891 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Fibrobacter succmnogenes (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 155: AACATGGTGA CTGGTGCTGC TCAGATGGAC GGCGCTATCC TCGTTGTTGC CGCTACTGAC

GGTCCGATGC

ATCGTCGTGT

GAAATGGAAG

ATCCGTGGTT

GAACTCATGA

TTCCTCATGC

CGTATCGAAC

ACCACCGAAT

GCAGGTGACA

ATGGTTCTCG

GTTCTCACGA

TTCTACTTCC

GTTACTCCGG

CGCAGACTCG

TCATGAACAA

TTCGCGAACT

CCGCTCTCAA

ACGCTTGCGA

CGATCGAAGA

GCGGTGTCGT

ACGTCATCAC

ACGTTGGTCT

CAGCTCCGAA

AGGACGAAGG

GCACCACCGA

GTGACACGGT

CGAACACATC

GTGCGACATG

CCTCTCCAAG

GGCCCTCGAA

CGAATACATC

CGTGTTCACG

TCGCTTGAAC

CGGTGTTGAA

CCTCCTCCGT

GTCTGTCACT

TGGCCGTCAC

CGTTACTGGT

CACGATCCAC

CTTCTCGCTC

GTTGACGATG

TATGACTTCG

GGCGATCCGG

CCGCTCCCGC

ATTACTGGCC

GACAAGGTTG

ATGTTCCGTA

GGTGCTGAAA

CCGCACACCG

ACGCCGTTCA

ACGATCCAGC

GTGAACCTCA

ACCAGGTTGG

CTGAAATTCT

ACGGTGACAA

AATACCAGGA

AGCGCGATAC

GCGGCACTGT

AACGTATCGG

AGCTCCTCGA

AGAAGGACAT

A.ATTTAAGGC

TGAATGGCTA

TCCCGGAAGG

TCGCTCCGAT

CGTGCCGAAG

CGACCTCGTC

CACCCCGATC

CAAGGTCATG

CGACAAGCCG

CGCTACTGGC

TCTCGGTGAA

CGACGCTCAG

CGTCCGTGGC

TGAAATCTAC

CCGTCCGCAG

TGTCGA.AATG

CGCTATGGAA

AAGCAGCTCC GCTTCGCTAT CCGTGAAGGT GGACGTACTG TTGGTGCTGG C INFORMATION FOR SEQ ID NO: 156: SEQUENCE CHARACTERISTICS: LENGTH: 894 base pairs TYPE: nucleic acid STRANDEDNESS: double CD) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: 142 ORGANISM: Flavobacterium ferruginewn (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 156: AACATGATCA CCGGTGCTGC CCAGATGGAC GGTGCTATCT TAGTTGTGGC TGCATCAGAC

GGTCCTATGC

ATGGTTGTGT

GAGATCGAGG

ATCAAAGGTT

AACCTGATGG

TTCCTGATGA

CGTATCGAGC

TCTCCCCTGA

GAAGCTGGTG

GGTATGGTAA

TACGTACTGA

CAAI'CTACT

ATGGTTATGC

GAAAAAGGTC

CTCAAACAAA

TTCTGAATAA

TTCGCGAAGA

CCGCTACAGG

ACGCTGTTGA

GCGTAGAGGA

GTGGCCGTAT

AC'rCTACCGT

ATAACGCCGG

TCGTTAAACC

GCAAAGACGA

TCCGTACAAC

CTGGTGATAA

AGAACACATC

AGTTGACCTC

ACTGACTAAA

CGCCCTCGCT

CAGCTACATC

CGTATTCTCT

CAAAGTTGGT

TACAGGTGTT

TCTCCTCCTC

CGGTTCCATC

AGGTGGCCGT

TGACGTTACA

CACCAACCTG

CTGCI'TGC TG

GTTGACGACG

CGCGGTTTCG

GGTGAAGAAI4

CCACTGCCTC

ATCACTGGTC

GAGCCTGTTG

GAGATGTTCC

CGTGGTGTTG

ACTCCGCACA

CACACTCCAT

GGTGAAGTAG

ACCGTTAAAC

CCCAGGTAGG

AAGAGCTCCT

ACGGCGACAA

AGTGGGTTAA

CTCGTCCGGT

GTGGTACTGT

AGATCGTAGG

GCAAACTCCT

AAAAAACACA

CGGACTTCAA

TCTTCAACAA

AACTGAACGC

TGATCCAACC

TGTACCTAAA

GGAGCTGGTT

CACTCCAATC

AGAAATTGAA

TGATCTGCCG

TGCTACCGGT

TCTGCAGGAG

CGACGAAGGT

GATCCGTCGC

AGGCGAAGTT

ATACCGTCCT

AGGAACAGAA

GATCGCTATG

120 180 240 300 360 420 480 540 600 660 720 780 840 694 120 160 240 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: Haeniophailus influenzae (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 157: AATATGATTA CTGGTGCGGC ACAAATGGAT GGTGCTATTT TAGTAGTAGC AGCAACAGAT GGTCCTATGC CACAAACTCG TGAACACATC TTATTAGGTC GCCAAGTAGG TGTTCCATAC ATCATCGTAT TCTTAAACAA ATGCQACATG GTAGATGACG AAGAGTTATT AGAATTAGTC GAAATGGAAG TTCGTGAACT TCTATCTCAA TATGACTTCC CAGGTGACGA TACACCAATc 143

GTACGTGGTT

GAGTTAGCAA

TTCCTTCTTC

CGTGTAGAAC

ACAGCGAAAA

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

CCACACACTG

ACTCCATTCT

ACAATCGAAT

GTAAGCTTAA

GOCCCTACAG

AATGGGAAGA

AACGTGCGAT

GTGGTACTGT

AAATCGTCGG

AATTACTTGA

GTGAAGAAAT

ACTTCGAATC

TCAAAGGTTA

TACCAGAAGG

TCCACCCAAT

TAGGTGCAGG

AAAAATCCT

TGACCAACCG

AGTAACAGGT

TATCAA)AGAT

CGAAGGTCGT

CGAACGTGGT

AGAAGTGTAC

CCGTCCACAA

CGTGGAAATG

TGCGATGGAT

C

300 360 420 480 540 600 660 720 780 840 891 GTTTCGCAAT CCGTGAAGGT INFORMATION FOR SEQ ID NO: 158: Wi SEQUENCE CHARACTERISTICS: LENGTH: 906 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DINA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Helicobacter, pylori (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 158: AACATGATCA CCGGTGCGGC GCAAATGGAC GGAGCGATTT TGGTTGTTTC TGCAGCTGAT

GGCCCTATGC

ATCGTTGTTT

GAAATGGAAG

GTAGCGGGTT

GGTGAAAAAG

GACACTGAAA

ACTTGGTrA

GTTGCTATCA

TTGGAAAAAG

CTCAAACTAG

TCTTAAACAA

TGCGCGAATT

CAGCTTTAAG

TGCTTAAACT

AAACTTTCTT

CAGGTAGGAT

GACCTACACA

GTGAAGCcGG

GGAGCATATC

ACAAGACATG

GTTGAGCGCG

AGCTTTAGAA

TATGGCTGAA

GATGCCGGTT

TGAAAGAGGC

AAAAACGACT

CGATAATGTG

TTATTGTCTC

GTAGATGACC

TATGAATTTC

GAAGCAAAGG

GTGGATGCCT

GAAGATGTGT

GTGGTGAAAG

GTAACCGGTG

GGCGTGCTTT

GTCAAGTAGG

AAGAATTGTr

C!TGGCGATGA

C!TGGTAATGT

ATATCCCTAC

TC'TCTATTGC

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 TCTGCGCACA ACTGATGTGA CTGGCTCTAT CACCCTTCCT GAAGGCGTAG AAATGGTTAT GCCTGGCGAT AATGTGAAAA TCACTGTAGA GTTGATrAGC CCTGTTGCGT TAGAGTTGGG AACTAAATTT GCGATTCGTG A.AGGCGGTAG GACCGTTGGT

GCTGGT

INFORMATION FOR SEQ ID NO: 159: Wi SEQUENCE CHARACTERISTICS: LENGTH: 891 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Hicrococcus 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 G43CCCGATGG

CTGCTCGTGG

GAGATGGAGG

ATCCGCACCT

GACCTCATGG

TTCCTGATGC

CGCGCCGAGC

GTGCAGAAGA

GCCGGCGAGA

C.AGGTGCTGG

ATCCTGTCCA

TTCTACTTCC

GTCATGCCCG

CCCAGACCCG

CCCTGAACAA

TCCGGCAGCT

CCGCTCTGAA

ATGCCGTGGA

CGATCGAGGA

GCGGCACCCT

CCACTGTCAC

ACTGCGGTCT

TGGAGCCGGG

AGGACGAGGG

GCACCACCGA

GCGACACCAC

TGAGCACGTG

GTCGGACATG

GCTGTCCTCC

GGCCCTCGAG

CGAGTACATC

CGTCTTCACG

GAAGATCAAC

CGGCATCGAG

GCTCGTGCGC

CTCCATCACC

TGGGCGTCAC

CGTCACCGGC

CGAGATGTCG

CTCCTGGCCC

GTGGAGGACG

AGGAGCTTCG

GGCGACCCCC

CCGGACCCGG

ATCACCGGCC

TCCGAGGTCG

ATGTTCCACA

GGTCTGA.AGC

CCGCACACCA

ACCCCGTTCT

GTCATCACGC

GTCGAGCTCA

GCCAGGTCGG

AGGAGCTCCT

ACGTCGACGA

AGTGGGTCAA

TGCGCGACAA

GTGGCACCGT

AGATCGTCGG

AGCAGCTCGA

GCGACGACGT

ACTTCGAGGC

ACTCGAACTA

TGCCCGAGGG

TCCAGCCGAT

CGTGCCGGCC

CGAGCGTGTC

GGCCCCGGTC

GTCCGTCGAG

GGACAAGCCG

GGTGACCGGT

CATCCGCGAC

CGAGGCCTGG

CGAGCGCGGC

GAACGTCTAC

CCGCGCGCAG

CACCGAGATG

CGCCATGGAG

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: mycobacteriumi tuberculosis (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 160: AACATGATCA CCGGCGCCGC GCAGATGGAC GGTGCGATCC TGGTGGTCGC CGCCACCGAC 0

GGCCCGATGC

ATCCTGGTAG

GAGATGGAGG

CGGGTCTCGG

CTGATGAACG

CTGATGCCGG

GTGGAGCGCG

ACCACCAAGA

GCGGGCGACA

CAGGTTGTCA

ATCCTGTCCA

TTCTACTTCC

GTGATGCCCG

CCCAGACCCG

CGCTGAACAA

TCCGCGAGCT

CGCTCAAGGC

CGGTCGACGA

TCGAGGACGT

GCGTGATCAA

CCACCGTCAC

ACGTTGGTTT

CCAAGCCCGG

AGGACGAGOG

GCACCACCGA

GTGACAACAC

CGAGCACGTT

GGCCGACGCA

GCTGGCTGCC

GCTCGAGGGT

GTCGATTCCG

CTTCACCATT

CGTGAACGAG

CGGTGTGGAG

GCTGCTGCGG

CACCACCACG

CGGCCGGCAC

CGTGACCGGT

CAACATCTCG

CTGCTGGCGC

GTGGACGACG

CAGGAATTCG

GACGCGA6AGT

GACCCGGTCC

ACCGGCCGCG

GAAGTTGAGA

ATGTTCCGCA

GGCGTCA.AGC

CCGCACACCG

ACGCCGTTCT

GTGGTGACAC

GTGAAGTTGA

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 GAAGGTCTGC GTTTCGCGAT CCGCGAGGGT GGCCGCACCG TGGGCGCCGG C INFORM'ATION 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 genicaliwn (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 161:

AATATGATCA

AGTGTGATGC

ATGGTAGTTT

GCTGAAGAAG

ATT TATGGCT

GATTTGATTA

TTCTTATTAG

AGAGTTGAAA

ATTAGAAAAG

GCTGGTGACA

CAAGTTTTAG

GCTTTAAAGA

TTCTATTTCC

GTTCTACCTG

CAGGTGCTGC ACAAATGGAT GGAGCTATTC TAGTTGTTTC AGCAACTGAT

CCCAAACCCG

TTCAAACAA

TACGTGATCT

CAGCTTTAAA

AAGCAGTTGA

CAATTGAAGA

GAGGTGAACT

CAGTTGTTAC

ATGCTGGGGT

CAAAACCAGG

AAGAAGAAGG

GTACCACTGA

GTGATAATGC

CGAGCACATC

GTGTGATATT

GTTAACTTCC

AGCATTGGAA

TGAATGGATT

TACGATGACC

CAAAGTAGGT

TGGAATTGAA

ATTATTACGT

CTCTATTAAA

TGGTAGACAC

TGTAACTGGT

TTCTATTACT

TTACTTGCCC GCCAAGTAGG GCTAGTGATG AAGAGGTACA TATGGTTTTG ATGGTA.AGAA GGTGATCCAA AGTGGGAGGC CCAACTCCTA CACGTGAAGT ATTACTGGTA GAGGTACAGT CAAGAAGTTG AAATTGTTGG ATGTTCAAAA AGGAACTTGA GGTGTTGAAC GTAAAGAAGT CCGCACAAGA AATTTAAAGC ACTGGTTTTT TAAACGGTTA TCTATTGCTT TAGCTGAAAA GTTGAGTTA.A TTGCTCCTAT

GGTTCCTAAA

AGAACTTGTT

CACTCCTATT

TAAGATCCAT

AGATAAACCT

TGTTACAGGA

TTTAAAACCA

TTCAGCAATG

TGAAAGAGGT

TGAGATCTAT

CCGTCCTCAA

TACTGAAATG

CGCTTGTGAA

120 180 240 300 360 420 480 540 600 660 720 780 840 891 120 180 240 AAAGGTAGTA AGTTCTCAAT TCGTGAAGGT GGTAGAACTG TAGGGGCAGG C INFORMATION FOR SEQ ID NO: 162: SEQUENCE CHARACTERISTICS: LENGTH: 891 base pairs TYPE: nucleic acid STRJNDEDNESS: 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 GGTGCAA.TCC TGGTATGTTC TGCTGCCGAC GGCCCTATGC CGCAAACCCG CGAACACATC CTGCTGGCCC GTCAAGTAGG CGTACCTTAC ATCATCGTGT TCATGAACAA ATGCGACATG GTCGACGATG CCGAGCTGTT CCAACTGGTT GAAATGGAAA TCCGCGACCT GCTGTCCAGC TACGACTTCC CCGGCGACGA CTGCCCGATC 147

GTACAAGGTT

GAACTGGCTA

TTCCTGCTGC

CGTGTAGAGC

ACCCAAAAAA

GCGGGCGACA

CAGGTATTGG

GTATTGAGCA

TCTACTTCC

GTAATGCCGG

CCGCACTGAA

CCGCATTGGA

CTATCGAAGA

GAGGTATCAT

CCACCTGTAC

ACGTAGGCGT

CCAAACGGGG

AAGAAGAGGG

GTACCACTGA

GTGAGAACGT

AGCCTTGGAA

CAGATACATC

CGTGTTCTCC

CCACGTTGGT

CGGCGTTGAA

ATTGCTGCGC

TACTATCACT

CGGCCCCCAT

CGTAACCGGC

AACCATTACT

GGCGATGCCG CTTACGAAGA CCGACTCCCG AGCGTGCCGT ATTTCCGGCC GCGGTACCGT GACGAGAT TG AAATCGTCGG ATGTTCCGCA AACTGCTGGA GGTACCAAAC GTGAAGACGT CCTCACACCA AGTTCAAAGC ACCCCGTTTT TCGCCAACTA ACGATTACTT TGGAAAAAGG GTAGAACTGA TTGCGCCTAT GGCCGTACCG TGGGTGCCGG

AAAAATCTTC

GGACAAACCA

AGTCACCGGC

TCTGAAAGAA

CGAAGGTCAG

AGAACGCGGT

AGAAGTGTAC

CCGTCCCCAA

TGTGGAAATG

CGCTATGGAA

C

GAAGGTCTGC GCTTTGCGAT TCGCGAAGGC INFORMATION FOR SEQ ID NO: 163: Wi SEQUENCE CHARACTERISTICS: LENGTH: 891 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: i ORGANISM: Rickettsia prowazekii SEQUENCE DESCRIPTION: SEQ ID NO: 163: AATATGATAA CTGGTGCCGC TCAGATGGAT GGTGCTATAT TAGTAGTTflC TGCTGCTGAT

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

TTACTGGCAA AACAGGTAGG GTAGATGATC CTGACCTAI-r TATGGTTTCC CTGGTAATGA GGAAAACCTG AAGGTGAAAA CCTCAGCCTA TAGAGCTACA ATT TCAGGCA GAGGTACCGT GAAGAAATTG AAATAGTAGG ATGTTCAGAA AATrACTTGA GGTACAAAAA GAGAAGAAGT

TGTACCTGCT

AGAATTAGTT

AATACCTATT

AGCTATTAAT

AGATAAACCT

TGTAACTGG'T

TCTAAAAAAT

TGAAGGACAA

AGA.AAGAGGA

120 180 240 300 360 420 480 540 600 148 CAAGTACTTG CAAAACCTGG GAG CATAAAA 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 STR.ANDEDNESS: double TOPOLOGY: linear (iMOLECULE TYPE. DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Salmionella typhimurium (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 164: AACATGATCA CCGGTGCTGC TCAGATGGAC GGCGCGATCC TGGTTGTTGC TGCGACTGAC

GGCCCGATGC

ATCATCGTGT

GAGATGGAAG

GTTCGTGGTT

GAACTGGCTG

TTCCTGCTGC

CGTGTAGAGC

ACTCAGAAGT

GCCGGTGAGA

CAGGTACTGG

ATTCTGTCCA

TTCTACTTCC

GTAATGCCGG

CGCAGACCCG

TCCTGAACAA

TTCGCGAACT

CTGCTCTGAA

GCTTCCTGGA

CGATCGAAGA

GCGGTATCAT

CTACCTGTAC

ACGTAGGTGT

CTAAGCCGGG

AAGATGAAGG

GTACTACTGA

GCGACAACAT

TGAGCACATC

ATGCGACATG

GCTGTCTCAG

AGCGCTGGAA

TTCTTATATT

CGTATTCTCC

CAAAGTGGGC

TGGCGTTGAA

TCTGCTGCGT

CACCATCAAG

CGGCCGTCAT

CGTGACTGGT

CAAAATG4GTT

CTGCTGGGTC

GTTGATGACG

TACGACTTCC

GGCGACGCAG

CCGGAACCAG

ATCTCCGGTC

GAAGAAGTTG

ATGTTCCGCA

GGTATCAAAC

CCGCACACCA

ACTCCGTTCT

ACCATCGAAC

GTTACCCTGA

GTCAGGTAGG CGTTCCGTAC AAGAGCTGCT GGAACTGGTT

CGGGCGACGA

AGTGGGAAGC

AGCGTGCGAT

GTGGTACCGT

AAATCGTTGG

AACTGCTGGA

GTGAAGAAAT

AGTTCGAATC

TCAAAGGCTA

TGCCGGAAGG

TCCACCCGAT

CACTCCGATC

GAAAATCATC

TGACAAGCCG

TGTTACCGGT

TATCAAAGAG

CGAAGGCCGT

CGAACGTGGT

TGAAGTGTAC

CCGTCCGCAG

CGTAGAGATG

CGCGATGGAC

120 180 240 300 360 420 480 540 600 660 720 780 840 GACGGTCTGC GTTTCGCAAT CCGTGAAGGC GGCCOTACCG TTGGCGCGGG C INFORMATION FOR SEQ ID NO: 165: 149 SEQUENCE CHARACTERISTICS: LENGTH: 681 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genornic) (vi) ORIGINAL SOURCE: ORGANISM: Shewanella putida (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 165: ATGATCACTG GTGCTGCACA GATGGACGGC GCGATTCTGG TAGTCGCTTC AACAGACGGT 4*4*e* 0 9* 0 00 9 .4 4

OS

0@

S

90*0 0040 0*0 0 0 e0.

0 0* 0*64

S

4606

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

TACATTCCA

ATTCTCAATT

CGTAGGCGAC

TGTAGAAATG

GTTACGTGGT

AATCAACCCA

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 AGTTTACGTA AAGGCTACCG TCCACAG'rrC CAGAAGGCGT AGAGATGGTA GCCCAATCGC GATGGACGAA 120 180 240 300 360 420 480 540 600 660 720 760 840 881 GGTTTACGCT TCGCAATCCG TGAAGGCGGT CGTACAGTGG T INFORMATION FOR SEQ ID NO: 166: SEQUENCE CHARACTERISTICS: LENGTH: 897 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: -Stiginatella aurantiaCa 150 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 166: AACATGATCA CGGGCGCGGC GCAGATGGAC GGAGCGATTC

GGCCCGATGC

ATCGTCGTCT

GAGATGGAGG

ATCCC TGGCA

ATCCTGAAGC

AAGCCGTTCC

ACGGGCCGAG

CGTCCGACGC

GGCATGGCGG

CGTGGGCAGG

GTGTACCTGC

CCGCAGTTCT

GAGATGGTGA.

CCCAGACGCG

TCCTGAACAA

TGCGCGACCT

GCGCGCTCAA

TGATGGCGGC

TGAT GCCGGT

TGGAGCGCGG

AGAAGACGGT

GAGACAACAT

TGCTGGCGAA

TGTCGAAGGA

ACTTCCGGAC

TGCCGGGAGA

TGAGCACATC

GGTGGACATG

GCTCAAGAAG

GGCGCTGGAG

GGTGGACGAG

GGAAGACGTG

CAAGATCAAG

CATCACGGGG

CGGAGCGC TG

CTGGGGGAGC

AGAGGGAGGG

GACGGACGTG

CAACATCGCC

CTGCTGGCCA

CTGGACGATC

TACGAGTTCC

GGAGACACCA

TACATCCCGA

TTCTCCATCG

GTGGGCGAGG

GTGGAGATGT

CTGCGAGGCC

TGGTGGTGTC CGCGGCCGAC GGCAGGTGGG CGTGCCCTAc CGGAGCTGCG CGAGCTGGTG CGGGCGACAG CATCCCCATC GCGACATCGG CGAGGGAGCG CGCCGC!AGCG TGCGACGGAC CAGGCC!GAGG AACGGTGGCG AAGTGGAGAT CGTGGGGATC TCCGCAAGCT GCTGGACGAG TGAAGCGCGA GGACCTGGAG 120 180 240 300 360 420 480 540 600 660 720 780 840 ATCAACCCGC ACACGAAGTT CGGCACACGC CGTTCTTCAA ACCGGAACGG TGAAGCTGCC ATCGAGGTGG AGCTCAT TAC

CAAGGCGCAG

GGGATACCGG

GGACAACGTG

TCCGGTCGCC

ATGGAGAAGG AGCTGCCGTT CGCCATCCGT GAGGGTGGCC GCACGGTGGG CGCCGGC INFORMATION FOR SEQ ID NO: 167: Wi SEQUENCE CHARACTERISTICS: LENGTH: 894 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Streptococcus pyogenes (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 167: AACATGATCA CTGGTGCCGC TCAAATGGAC GGAGCTATCC TTGTAGTTGC TTCAACTGAT GGACCAATGC CACAAACTCG TGAGCACATC CTTCTTTCIAC GTCAGGTTGG TGTTAAAC-AC CTTATCGTGT TCATGAACAA AGTTGACCTT GTTGATGACG AAGAGTTGCT TGAATTAGTT GAGATGGAAA TTCGTGACCT TCTTTCAGAA TACGATTTCC CAGGTGATGA CCTTCCAGTT ATCCAAGGTT CAGCTC TTAA AGCTCTTGAA GGCGACACTA AATTTGAAGA CATCATCATG 151

GAATTGATGG

TTGCTTCTTC

CGTATCGACC

GAA.ACTAAAA

CTTGCAGGAG

GGTCAAGTTA

TATATCCTTT

CAATTCTACT

ATGGTTATGC

ATACTGTTGA

CAGTCGAAGA

GTGGTACTGT

AAGCTGTTGT

ACAACGTAGG

TTGCTAAACC

CTAAAGACGA

TCCGTACAAC

CTGGTGATA.A

TTCATACATT

CGTATTCTCA

TCGTGTCAAC

TACTGGTGTr

TATCCTTCT

AAGTTCAATC

AGGTGGACGT

TGACGTAACA

CGTGACAATC

CCAGAACCAG

ATTACAGGTC

GACGAAATCG

GAAATGTTCC

CGTGGTGTTC

AACCCACACA

CACACTCCAT

GGTTCAATCG

AACGTTGAGT

AACGCGACAC TGACAAACCA GTGGTACAGT TGCTTCAGGA AAATCGTTGG TATCAAAGAA GTAAACAACT TGACGAAGGT AACGTGACGA AATCGAACGT CTAAATTCAA AGGTGAAGTA TCTTCAACAA CTACCGTCCA AACTTCCAGC AGGTACAGAA TGATCCACCC AATCGCCGTA 360 420 480 540 600 660 720 780 840 GAACAAGGTA CTACTTTCTC 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 (genouuic) (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

T GCTGTGCAA

CGAGCACATC

GTGCGACATG

GCTGTCCAAG

GGCCCTCGAA

CCTGGACACC

GGAAGACGTG

CATCATCAAG

CTGCACCGGC

CGGCATCTTG

ACCCGGCTCG

CTGCTGGCGC

GTCGACGACG

TACGACTTCC

GGCGACAAGG

TACATCCCCA

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 CCTTCTTCAA CAACTACCGC CCGCAGTTCT ACTTCCGCAC CACCGACGTC ACCGGCGCCA TCGAACTGCC CAAGGACAAG GAAATGGTCA. TGCCCGGCGA TAATGTGAGC ATCACCGTCA AGCTCATCGC CCCCATCGCC ATGGAAGAAG GCCTGCGCTT CGCCATCCGC GAAGGCGGCC GCACCGTCGG CGCCGGC INFORMATION FOR SEQ ID NO: 169: SEQUENCE CHARACTERISTICS: LENGTH: 894 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Treponema pal lidum (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 169: 720 780 840 897 AATATGATCA CGGGTGCTGC GCAGATGGAC

GGCGTTATGC

ATCATTGTTT

GAAGAAGAGG

AAGGGGTCTG

GAGGAACTGC

CCTT TCTTGC

GGGCGCATCG

CCCACTAAGA

ATTGCAGGTG

GGTCAGGTGC

TACGTGCTCT

CAGITTTTATT

ATGGTGAAGC

CACAGACGAA

TTTTGAACAA

TGCGTGATGC

CGTTTAAAGC

TTGCGGCCAT

TCTCTATCGA

AATGTGGGGT

AAACAGTGGT

ATAACGTGGG

TTTCTA.AGCC

CTAAGGAAGA

TTAGAACTAC

CGGGGGATAA

GGAGCATCTT

GGTTGATTTG

GCTTGCTGGA

TCTGCAGGAT

GGATTCCTAC

GGATGTGTAC

AATTAGTCTG

TACTGGCATT

GCTGCTTTTG

CGGT1'CTATT

GGGTGGCCGT

TGACATTACC

CACCAAGATT

GTTGATGATC

TATGGG7=r

GGCGCTTCCC

TTTGAAGACC

ACTATTTCTG

AATGAAGAGG

GAGATGTTTA

CGCGGGGTGG

AAGCCACACA

CACAGTCCTT

GGTACGATTT

ATAGGTGAGC

CTGAGTTGCT

CGCGTGAGAC

CGGAGGATGC

CALGTGCGTGA

GGCGTGGTAC

TCGAGATCGT

ATAAGTTGCT

ATAAAAAAGA

CCAAGTTTGA

TTL-1TTCAAGG

CTCTTCCTGA

TCATCCACCC

GGTGGTATTC TCGTCGTGTC CTGCTCGCCC GTCAGGTTGG

TGCGCCTGAC

TGTTCCCTCC

AGAGCTGGTG

GCCTATCGTC

AGCTTGTATT

CGACGCAAGA

CGTTGTCACG

CGGGATTAAG

TGATCAGGGA

GGTTGAGCGC

GGCGCAGATC

TTATCGTCCG

AGGGGTAGAC

GATAGCTATG

120 180 240 300 360 420 480 540 600 660 720 780 840 GACAAGGGTC TGAAGCTTGC GATTCGTGAA GGGGGGCGCA CTATTGCTTC TGGT INFORMATION FOR SEQ ID NO: 170: SEQUENCE CHARACTERISTICS: 1S3 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 GGAGCAATrI TAGTTATTGC

GGGGTTATGG

ATCCTTCTTT

GAAATGGAAG

ATTCGTGGTT

GAATTAATGC

TTCTTATTAG

CGTGTTGAAC

ACTCAAAAA.A

GCTGGTGATA

CAAGTACTTG

ATTCTTAAAA

TTCTATTTTA

GTTATGCCAG

CTCAAACTAA

TCTTAAACAA.

TTCGTGAATT

CAGGTCTTAA

ACGCAGTTGA

CAATTGAAGA

GTGGTGTATT

CTGTTGTTAC

ATGCTGGTAT

TAAAACCAGG

AAGAAGAAGG

GAACAACAGA

GTGATGACGT

AGAACATATT

ATGTGATTTC

ATTATCTAAA

GGCTTTAGAA

TTCATGAATT

TGTATTCACA

AAAAGTTAAT

AGGAATTGAA

TTTATTACGT

ATCAATTAAA

TGGACGTCAT

TGTAACAGGT

TGAAATGACT

TTATTAGCAC

ATGACAGATC

TATGGATTTG

GGAGATCCAG

CCATTACCAG

ATTTCAGGAC

GATGAGGTTG

ATGTTTAGAA

GGTATTAAAA

CCTCACCGTA

ACACCTATTG

GC-TATTTCAT

GTAGAATTAA

GTCAAGTTGG

CAGATATGCA

ATGGCGATAA

TTTGAGAAGC

AACGTAGTAC

GTGGTACAGT

AAATTGTTGG

AATCATTAGA

AAGAAGATGT

CTTTTACTGC

TTTCAGGATA

TACCTGCTGG

TTGCTCCAGT

TGCATCTGAT

TGTTCCAAAA

AGATCTTGTT

CACACCAGTT

AAAAATTGAT

TGACAAACCA

AGTAACTGGA

TCTAAAAGAC

TCAAGCTGAA

TGAACGTGGT

TAAAGTflTAT

CCGTCCACAA

TGTTGATTTG

TGCGATI'GAA

120 240 300 360 420 480 540 600 660 720 780 840 891 GATGGATCTA AATTCTCAAT CCGTGAAGGT GGTAAAACTG TAGGTCATGG T INFORMATION FOR SEQ ID NO: 171: SEQUENCE CHARACTERISTICS: LENGTH: 909 base pairs TYPE: nucleic acid STRANDEDNESS: double TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (vi) ORIGINAL SOURCE: ORGANISM: Wolinella succinogenes (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 171: 154 AACATGATTA CAGGTGCTGC TCA.AATGGAZT GGCGCGATTC TTGTTGTI-rC TGCGGCGGAT

GGCCCCATGC

ATCGTGGTTT

GAAATGGAAG

GTTGCAGGTT

TGGGGCGAGA

CGAGATGTGG

GGAACCGTTG

ATCCTTGGTA

GAGCTCGACA

GAAGATGTTG

TTTGAAGCTG

AATGGATACc

CCTGAGGGCG

GCTCCTGTAG

GGTGCGGGT

CCCAAACTAG

TCTTGAACAA

TTAGAGAACT

CCGCTCTTAA

AAGTATTGAA

ATAAGCCTTT

TGACAGGAAG

TCCGAAACAC

AGGGTGAGGC

AGAGAGGTAT

AAGTTTACGT

GACCTCAGTT

TAGAGATGGT

CCC'rCGAAGA

GGAGCACATT

AGAAGATATG

TCTTAGCAAC

AGCTCTTGAA

GCTTATGGCT

CCTTATGCC T

AATTGAAAGA

ACAAAAAACA

GGGTGACAAC

GGTTCTTTGT

TCT TTCCAAA

CTATGTTAGA

TATGCCTGGT

GGGAACACGA

CTTCTTTCTC

GTTGATGACG

TACGACTTCC

GAGGCTAACG

GAGGTTGACC

GTTGAAGACG

GGCGTGGTTA

ACCGTAACTG

GTTGGTCTrTC

AAAATAGGTT

GAGGAAGGCG

ACTACAGACG

GACAACGTTA

TTCGCGATCC

GACAAGTAGG

CTGAGCTTCT

CTGGAGATGA

ACCAGGAAAA

GATATATTCC

TATTCTCCAT

AAGTCGGTGA

GCGTTGAGAT

TTTTGAGAGG

CTATCACTCC

GACGACACAC

TTACCGGTTC

CGTTCC TTAC

TGAGCTTGTT

CACTCCTATC

TGTTGGCGAG

TACGCCTGAG

CGCGGGTCGT

CGAAGTAGAA

GTTCCG.AAAA.

CACCAAGAAA

TCACACTAAC

TCCATTCT TC

TATCTCTCTT

120 180 240 300 360 420 480 540 -600 660 720 780 .840 900 AGATCAATGT TGAGCTTATC GTGAAGGTGG TCGAACCGTT INFORMATION FOR SEQ ID NO: 172: SEQUENCE CHARACTERISTICS: LENGTH: 26 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (ix) FEATURE: NAI4E/KEY: misc-feature LOCATION:6 OTHER INFORMATION:/note= (ix) FEATURE: NAME/KEY: misc-feature LOCATION:12 OTHER INFORMATION:/note= (ix) FEATURE: NAME/KEY: misc-feature LOCATION:18 OTHER INFORMATION:/note..

inosine" inosine" iflosine~l 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 21 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 (5)

1. 2. A method for obtaining tuf nucleic acids from any funigus 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 synthesizing an extension product of each of said prinmers, said extension product containing the target seq" 0 encc, and amplifying to obtain amplified nucleic acids. S *30 A method for obtaining tuf sequences from any bacteria which comprises the steps of reiterating steps a) and b) of the method of claima 1 and adding the following steps: c) sequencing the amplified nucleic acids, and COMS ID No: SBMI-00808349 Received by IP Australia: Time 10:23 Date 2004-06-29 29/06 '04 10:28 FAX 61 7 3229 3384 CULLEN CO. Q~006 157 d) assigning a sequence Of Step c) to a given bacterial species.
2. 4. A method for obtaining luf sequences from any fungus which comprises the steps of reiterating steps a) and b) of the mnethod of claimn 2 and adding the following steps: c) sequencing the amplified nucleic acids, and d) assigning a sequence of step c) to a given furlgal species. A method for generating sequences of probes, or primers, or both, useful for the specific detection of a micerobial species, a microbial genus or substantially all microbial species of a group comprising bacterial or fuingal species, which comprises the steps of: reproducing the method of claims 3 or 4, and adding the steps of: aligning said nucleic acid sequences, 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 deriving consenisus nucleic acid sequences useful as probes or primers from said consecutive nucleotides.
3. 6. A bank of nucleic acids comprising nucleic acids obtained from the method of claims 1 or 2.
4. 7. A bank of nucleic acid sequences comprising the sequences obtained from the method of claims 3 or 4. 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 5 and adding the step of synthesising said probes or primers upon the consensus nucleic acid sequences thereof. COMS ID No: SBMI-00808349 Received by IP Australia: Time 10:23 Date 2004-06-29 29/06 '04 10:26 FAX 61 7 3229 3384 CULLEN CO. Z007 -158
5. 9. A method for identification of a microorganism in a test sample, comprising the steps of: S obtaining a nucleic acid sequence for a tufand/or recA genes of said microorganism, and comparing said nucleic acid sequence with the nucleic acid sequences of a bank as defined in claim 7, 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 29' day of June 2004 Infectio Diagnostic Inc. By their Patent Attorneys CULLEN CO. *I e COMS ID No: SBMI-00808349 Received by IP Australia: Time 10:23 Date 2004-06-29