CA2283458A1 - Highly conserved genes and their use to generate species-specific, genus-specific, family-specific, group-specific and universal nucleic acid probes and amplification primers to rapidly detect and identify bacterial, fungal and parasitical pathogens from clinical specimens for diagnosis - Google Patents

Abstract

This invention relates to a repertory of nucleic sequences usable for the detection and/or identification of a bacterial, fungal or parasitical species, genus, family or group. This repertory is created by amplifying the nucleic acids of a plurality of given species with given primers. From this repertory are derived species-, genus-, family - or group-specific oligonucleotides used as probes or primers. Also, universal probes or primers are derived from the same repertory. All these probes or primers can be used in conjunction with probes or primers specific to the detection of any antibiot ic resistance gene and/or toxin gene, in kits or methods designed for the detection of a s et of bacteria, fungi or parasites, in association or not with antibiotic resistan ce or toxin production.

Description

s DEMANDES OU BREVETS VOLUMINEUX
LA PRESENTE PART1E DE CETTE DEMANDE OU. CE BREVET
COMPREND PLUS D'UN TOME.
CECI EST LE TOME ~ DE
NOTE: Pour les tomes additionels, veuillez contacter le Bureau canadien des brevets JUMBO APPL1CATIONS/PATENTS .
THiS SECT10N OI= THE APPLlCATION/PATENT CONTAINS MORI
THAN ONE VOLUME ~ , THIS tS VOLUME ~~- OF
' NOTE: For additional volumes-pl~ase~contact. the Canadian Patent Office .

TITLE OF THE INVENTION
HIGHLY CONSERVED GENES AN THEIR USE TO GENERATE SPECIES-SPECIFIC, GENUS-SPECIFIC, FAMILY-SPECIFIC, GROUP-SPECIFIC AND
UNIVERSAL NUCLEIC ACID PROBES AND AMPLIFICATION PRIMERS TO
RAPIDLY DETECT AND IDENTIFY BACTERIAL, FUNGAL AND PARASITICAL
PATHOGENS FROM CLINICAL SPECIMENS FOR DIAGNOSIS
BACKGROUND OF THE INVENTION
Classical methods for the identification of bacteria, fungi, and parasites 2o Bacteria and fungi 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 API20ETM 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 (i.e. the MicroScanTM system from Dade Diagnostics Corp. and 3o the Vitek system from bioMerieux) which use 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 or fungi as a pure culture, a process which takes at least 18 hours for a pure culture or 2 days for a mixed culture. Moreover, fungi other than yeasts are often difficult or very slow to cultivate from clinical specimens.
Identification must rely on labor intensive technique such as direct microscopic examination of the specimens and by direct and/or indirect immunological assays.
Cultivation of most parasites is impractical in the clinical laboratory.
Hence, microscopic examination of the specimen, a few immunological tests and clinical symptoms are often the only methods used for an identification that frequently remains presumptive.
The fastest bacterial 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 (i.e. 3.3 to 40.5%) of non-conclusive identifications with bacterial species other than Enterobacteriaceae (Croize J., 1995, Lett. Infectiol.10:109-113;
York et al., 1992, J. Clin. Microbiol. 30:2903-2910). For Enterobacteriaceae, the percentage to 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 main organisms associated with nosocomial and community-acquired human infections and are therefore considered the most clinically important.
Clinical specimens tested in clinical microbiology laboratories 2o Most clinical specimens received in clinical microbiology laboratories are urine and blood samples. At the microbiology laboratory of the Centre Hospitalier de 1'Universite Laval (CHUL), urine and blood account for approximately 55% and 30%
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 3). 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 ~L 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 4o urine. A bacterial urinary tract infection (UTI) is normally associated with a bacterial

2 count of 10? CFU/L or more in urine. However, infections with less than IO~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 80% of urine specimens tested in clinical microbiology laboratories are considered negative (i.e. bacterial count of less than 10~
CFU/L;
Table 3). 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 (UriscreenTM, UTIscreenTM, 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 et al., 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 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 3o 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 January 1995 was 93.1 % (Table 3).
Other clinical samples 4.o Upon receipt by the clinical microbiology laboratory, all body fluids other than blood and urine that are from normally sterile sites (i.e. cerebrospinal, synovial,

3 pleural, pericardial and others) are processed for direct microscopic examination and subsequent culture. Again, most clinical samples are negative for culture (Table 3). In these normally sterile site, a test for the universal detection of bacteria, fungi and parasites would be very useful.
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 or fungal 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 1o useful for the diagnosis of bacterial infections at these non sterile sites. On the other hand, DNA-based assays for species or genus or family or group 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 specimens There is an obvious need for rapid and accurate diagnostic tests for the detection and identification of bacteria, fungi and parasites directly from clinical specimens.
2o DNA-based technologies are rapid and accurate and offer a great potential to improve the diagnosis of infectious diseases (Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.). The DNA probes and amplification primers which are objects of the present invention are applicable for the detection and identification of bacteria, fungi, and parasites directly from any clinical specimens such as blood cultures, blood, urine, sputum, cerebrospinal fluid, pus and other type of specimens (Table 3).
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 these tests can be performed in one hour or less, they provide the clinicians with new diagnostic tools which should contribute to increase the efficiency of therapies with antimicrobial agents. Specimens from sources other than humans (e.g. other primates, birds, plants, mammals, farm animals, livestock, food products, water and others) may also be tested with these assays.
A high percentage of culture negative specimens Among all the clinical specimens received for routine diagnosis, approximately 80% of urine specimens and even more (around 95%) for other types of clinical 4o specimens are negative for the presence of bacterial pathogens (Table 3).
It would

4 also be desirable, in addition to identify bacteria at the species or genus or family or group level in a given specimen, to screen out the high proportion of negative clinical specimens with a test detecting the presence of any bacterium (i.e. universal bacterial detection). Such a screening test may be based on DNA amplification by PCR 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 with this assay.
Similarly, highly conserved genes of fungi and parasites could serve not only to identify particular species or genus or family or group but also to detect the presence of any fungi or 1 o parasite in the specimen.
Towards the development of rapid DNA-based diagnostic tests A rapid diagnostic test should have a significant impact on the management of infections. DNA probe and DNA amplification technologies offer several advantages over conventional methods for the identification of pathogens and antibiotic resistance genes from clinical samples (Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.; Ehrlich and Greenberg, 1994, PCR-based Diagnostics in 2o Infectious Disease, Blackwell Scientific Publications, Boston, MA). There is no need for culture of the 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 microbial identification than currently used phenotypic identification systems which are based on biochemical tests and/or microscopic examination. Commercially available DNA-based technologies are currently used in clinical microbiology laboratories, mainly for the detection and identification of fastidious bacterial pathogens such as Mycobacterium tuberculosis, Chlamydia trachomatis, Neisseria gonorrhoeae as well as for the detection of a variety of viruses (Podzorski and Persing, Molecular detection and identification of microorganisms,ln: P.
Murray et al., 1995, Manual of Clinical Microbiology, ASM press, Washington D.C.). There are also other commercially available DNA-based assays which are used for culture confirmation assays.
Others have developed DNA-based tests for the detection and identification of bacterial pathogens which are objects of the present invention for example:
Staphylococcus spp. (US patent application serial No. US 5 437 978), Neisseria spp.
(US patent application serial No. US 5 162 199 and European patent application serial No. EP 0 337 896 131) and Listeria monocytogenes (US patent applications serial Nos US 5 389 513 and US 5 089 386). However, the diagnostic tests described in these patents are based either on rRNA genes or on genetic targets different from

5 those described in the present invention. To our knowledge there are only three patents published by others mentioning the use of any of the three targets described in the present invention for diagnostic purposes (PCT international publication number WO 92/03455, European patent publication number 0 133 671 B1, and European patent publication number 0 133 288 A2). WO 92/03455 is focused on the inhibition of Candida species for therapeutic purposes. It describes antisense oligonucleotide probes hybridizing to Candida messenger RNA. Two of the numerous mRNA
proposed as target are coding for translation elongation factor 1 (tefl ) and the beta subunit of ATPase. DNA amplification or hybrization are not under the scope of their to invention and although diagnostic use is briefly mentioned in the body of the application, no specific claim are made regarding diagnostics. In the main body of the text, EP 0 133 671 B 1 describes the use of bacterial tuf sequence for diagnostics based on hybridization with bacterial RNA. To hybridize RNA, an oligonucleotide probe must be antisense. DNA amplification techniques require the use of both sense and antisense primers. Hence, claim number one from EP 0 133 671 B 1 precludes PCR or other DNA-based amplification techniques. Furthermore, EP 0 133 671 B1 makes no specific claim on the use of tuf sequences for diagnostics; only ribosomal RNA sequences are claimed. Patent EP 0 133 288 A2 describes and claims the use of bacterial tuf sequence for diagnostics based on hybridization of a tuf probe with 2o bacterial DNA. DNA amplification is not in the scope of EP 0 133 288 A2.
Nowhere, it is mentioned that multiple tuf probes could be used simultaneously. The sensitivity of the tuf hybrizations reported are, at 1x106 bacteria or 1-100 ng of DNA, much lower than those achievable by nucleic acid amplification technologies.
Although there are diagnostic kits or methods already used in clinical microbiology laboratories, there is still a need for an advantageous alternative to the conventional 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 microbial genotype (e.g. DNA level) is more 3o stable than the phenotype (e.g. physiologic level).
Knowledge of the genomic sequences of bacterial, fungal and parasitical species continuously increases as testified by the number of sequences available from public databases such as GenBank. From the sequences readily available from those public databases, there is no indication therefrom as to their potential for diagnostic purposes. For determining good candidates for diagnostic purposes, one could select sequences for DNA-based assays for (i) the species-specific detection and identification of commonly encountered bacterial, fungal and parasitical pathogens, (ii) the genus-specific detection and identification of commonly encountered bacterial, fungal or parasitical pathogens, (iii) the universal detection of bacterial, fungal or parasitical pathogens and/or (iv) the specific detection and identification of

6 antibiotic resistance genes. All of the above types of DNA-based assays may be performed directly from any type of clinical specimens or from a microbial culture.
In our co-pending U.S. (N.S. 08/526,840) and PCT (PCT/CA/95/00528 and PCT/CA97/00829) patent applications, we described DNA sequences suitable for (i) the species-specific detection and identification of clinically important bacterial pathogens, (ii) the universal detection of bacteria, and (iii) the detection of antibiotic resistance genes.
The latter co-pending application described proprietary tuf DNA sequences as well as tuf sequences selected from public databases (in both cases, fragments of at to least 100 base pairs), as well as oligonucleotide probes and amplification primers derived from these sequences. All the nucleic acid sequences described in that patent application can enter in the composition of diagnostic kits or product and methods capable of a) detecting the presence of bacteria, fungi and parasites b) detecting specifically at the species, genus, family or group levels, the presence of bacteria, fungi and parasites and antibiotic resistance genes associated with these pathogens.
However, these methods and kits need to be improved, since the ideal kit and method should be capable of diagnosing close to 100% of microbial pathogens and associated antibiotic resistance genes and toxins genes. For example, infections caused by Enterococcus faecium have become a clinical problem because of its resistance to 2o many antibiotics. Both the detection of these bacteria and the evaluation of their resistance profiles are desirable. Besides that, novel DNA sequences (probes and primers) capable of recognizing the same and other microbial pathogens or the same and additional antibiotic resistance genes are also desirable to aim at detecting more target genes and complement our earlier patent applications.
The present invention improves the co-pending application by disclosing new proprietary tuf sequences as well as describing new ways to abtain tuf sequences. In addition we disclose new proprietaryatpD and recA sequences. In addition, new uses of tuf, atpD and recA DNA sequences selected from public databases are disclosed.
Highly conserved genes for identification and diagnostics Highly conserved genes are useful for identification of microorganisms. For bacteria, the most studied genes for identification of microorganisms are the universally conserved ribosomal RNA genes (rRNA). Among those, the principal targets used for identification purposes are the small subunit (SSU) ribosomal rRNA genes (in prokaryotes) and 18S rRNA genes (in eukaryotes) (Relman and Persing, Genotyping Methods for Microbial Identification, In: D.H. Persing, 1996, PCR Protocols for Emerging Infectious Diseases, ASM Press, Washington D.C.).
The rRNA genes are also the most commonly used targets for universal identification of 4o bacteria (Chen et al., 1988, FEMS Microbiol. Lett. 57:19-24; McCabe et al., 1999, Mol. Genet. Metabol. 66:205-211 ) and fungi (Van Burik et al., 1998, J. Clin.
Microbiol. 36:1169-1175).
However, it may be difficult to discriminate between closely related species when using primers derived from the 16S rRNA. In some instances, 16S rRNA

7 sequence identity may not be sufficient to guarantee species identity (Fox et al., 1992, Int. J. Syst. Bacteriol. 42:166-170) and it has been shown that inter-operon sequence variation as well as strain to strain variation could undermine the application of 16S rRNA for identification purposes (Claytonet al., 1995, Int.
J. Syst.
Bacterio1.45:595-599).
STATEMENT OF THE INVENTION
It is an object of the present invention to provide a specific, ubiquitous and 1o sensitive method using probes and/or amplification primers for determining the presence and/or amount of nucleic acids:
- from any bacterial, fungal or parasitical species in any sample suspected of containing said nucleic acids, and optionally, - from specific microbial species or genera selected from the group consisting of the species or genera listed in Table 4 - from an antibiotic resistance gene selected from the group consisting of the genes listed in Table 5, and optionally, - from a toxin gene selected from the group consisting of the genes listed in Table 6, wherein each of said nucleic acids or a variant or part thereof comprises a selected target region hybridizable with said probe or primers;
said method comprising the steps of contacting said sample with said probes or primers and detecting the presence and/or amount of hybridized probes or amplified products as an indication of the presence and/or amount of said any microbial species, specific microbial species or genus or family or group and antibiotic resistance gene and/or toxin gene.
In a specific embodiment, a similar method directed to each specific microbial species or genus or family or group detection and identification, antibiotic resistance genes detection, toxin genes detection, and universal bacterial detection, separately, is provided.
In a more specific embodiment, the method makes use of DNA fragments from conserved genes (proprietary sequences and sequences obtained from public databases), selected for their capacity to sensitively, specifically and ubiquitously detect the targeted bacterial, fungal or parasitical 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 the present method as probes or amplification primers.
In another particularly preferred embodiment, oligonucleotides primers and 4o probes of at least 12 nucleotides in length are designed for their specificity and

8 ubiquity based upon analysis of our databases ofatpD, tuf and recA sequences.
These databases are generated using both proprietary and public databases sequence information. Altogether, these databases form a sequence repertory useful for the design of primers and probes for the detection and identification of bacterial, fungal and parasitical microorganisms. The repertory can also be subdivided into subrepertories for analysis leading to the design of primers and probes.
The atpD, tuf and recA sequences databases as a product to assist the design of oligonucleotides primers and probes for the detection and identification of bacterial, fungal and parasitical microorganisms are also an object of this invention.
1o The proprietary oligonucleotides (probes and primers) are also another object of the invention.
Diagnostic kits comprising probes or amplification primers for the detection of a microbial species or genus or family or group selected from the following list consisting of Bordetella spp., Candida albicans, Candida dubliniensis, Candida spp., Chlamydia pneumoniae, Chlamydia trachomatis, Clostridium spp., Corynebacterium spp., Cryptosporidium parvum, Entamoeba spp., Enterobacteriaceae group, Enterococcus casseliflavus-flavescens-gallinarum, Enterococcus faecalis, Enterococcus faecium, Enterococcus gallinarum, Enterococcus spp., Escherichia coli, Giardia spp., Haemophilus influenzae, Kinetoplastidae group, Leishmania spp., 2o Mycobacteriaceae family, Neisseria gonorrhoeae, platelets contaminants group, Pseudomonads group, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus saprophyticus, Staphylococcus spp., Streptococcus agalactiae, Streptococcus spp., Trypanosoma brucei, Trypanosoma cruzi, Trypanosomaspp., are also objects of the present invention.
Diagnostic kits further comprising probes or amplification primers for the detection of an antibiotic resistance gene selected from the group listed in Table 5 are also objects of this invention.
Diagnostic kits further comprising probes or amplification primers for the 3o detection of a toxin gene selected from the group listed in Table 6 are also objects of this invention.
Diagnostic kits further comprising probes or amplification primers for the detection of any bacterial, fungal or parasitical species, comprising or not comprising those for the detection of the specific microbial species or genus or family or group listed above, and further comprising or not comprising probes and primers for the antibiotic resistance genes listed above, and further comprising or not comprising probes and primers for the toxin genes listed above are also objects of this invention.
In a preferred embodiment, such a kit allows for the separate or the simultaneous detection and identification of the above-listed microbial species or

9 genus or family or group, antibiotic resistance genes, toxin genes and for the detection of any microorganism (bacteria, fungi or parasite).
In the above methods and kits, amplification reactions may include but are not restricted to: a) polymerase chain reaction (PCR), b) ligase chain reaction (LCR), c) nucleic acid sequence-based amplification (NASBA), d) self sustained sequence replication (3SR), e) strand displacement amplification (SDA), f) branched DNA
signal amplification (bDNA), g) transcription-mediated amplification (TMA), h) cycling probe technology (CPT), i) nested PCR, j) multiplex PCR, k) solid phase amplification (SPA),1) nuclease dependant signal amplification (NDSA).
In a preferred embodiment, a PCR protocol is used for nucleic acid amplification.
In a particularly preferred embodiment, a PCR protocol is provided, comprising, an initial denaturation step of 1-3 minutes at 95°C, followed by amplification cycle including a denaturation step of one seconds at 95°C and an annealing step of 30 seconds at 45-65°C, without any time allowed specifically for the elongation step. This PCR protocol has been standardized to be suitable for PCR
reactions with most 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.
2o 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 and/or parasitical species and genera and to determine rapidly the bacterial resistance to antibiotics. Although the sequences from the selected antibiotic resistance genes are available from public databases and have been used to develop DNA-based 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 3o 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 described herein below, the oligonucleotide probes and amplification primers have been derived from larger sequences (i.e. DNA
fragments of at least 100 base pairs). All DNA fragments have been obtained either from proprietary fragments or from public databases. DNA fragments selected from public databases are newly used in a method of detection according to the present invention, since they have been selected for their diagnostic potential.
In an other embodiment, the amino acid sequences translated from the repertory of atpD, tuf and recA sequences are also an object of the present invention.
It is clear to the individual skilled in the art that other oligonucleotide sequences appropriate for (i) the universal bacterial detection, (ii) the detection and identification of the above microbial species or genus or family or group, and (iii) the detection of antibiotic resistance genes, and (iv) the detection of toxin genes other l0 than those listed in Annexes I to III and XXI may also be derived from the proprietary fragments or selected public databases 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 public 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 2o from any DNA fragment sequences for use in amplification methods other than PCR.
Consequently, the core of this invention is the identification of universal, species-specific, genus-specific, resistance gene-specific, toxin 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 Annexes I to III
and XXI which are suitable for diagnostic purposes. When a proprietary fragment or a public databases 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 3), DNA fragments having a high potential for the selection of universal oligonucleotide probes or primers were selected from proprietary and public databases sequences. The amplification primers were selected from two genes highly conserved in bacteria, fungi and parasites, and are used to detect the presence of any bacterial or fungal or parasitical pathogen in clinical specimens in order to determine rapidly (less than one hour) whether it is positive or negative for bacteria, fungi or parasites. The selected genes, designated tuf, atpD and recA, encode respectively a protein (elongation factor Tu) involved in the translational process during protein 4o synthesis, a protein (beta subunit) responsible for the catalytic activity of proton pump ATPase and a protein responsible for the homologous recombination of genetic material. The tuf, atpD and recA sequence alignments used to derive the universal primers include both proprietary and public databases sequences. The universal primer strategy allows the rapid screening of the numerous negative clinical specimens (around 80% of the specimens received, see Table 3) submitted for bacteriological testing.
Table 4 provides a list of the bacterial, fungal and parasitical species for which atpD and/or tuf and/or recA sequences are revealed in the present invention.
Tables 5 and 6 provide a list of antibiotics resistance genes and toxin genes selected for diagnostic purposes. Table 7 provides the origin of tuf, atpD and recA
sequences listed in the sequence listing. Tables 8-10 provide lists or species used to test specificity and ubiquity of some assays described in examples.

DETAILED DESCRIPTION OF THE INVENTION
HIGHLY CONSERVED GENES AND THEIR USE TO GENERATE SPECIES-SPECIFIC, GENUS-SPECIFIC, FAMILY-SPECIFIC, GROUP-SPECIFIC AND
UNIVERSAL NUCLEIC ACID PROBES AND AMPLIFICATION PRIMERS TO
RAPIDLY DETECT AND IDENTIFY BACTERIAL, FUNGAL AND PARASITICAL
PATHOGENS FROM CLINICAL SPECIMENS FOR DIAGNOSIS
The present inventors compared the published Haemophilus influenzae and l0 Mycoplasma genitalium genomes and searched for the most conserved genes, which would then serve, as paradigm to develop primers and probes. This sequence comparison is highly informative as these two bacteria are distantly related and most genes present in the minimal genome of M. genitalium are likely to be present in every bacterium. Therefore genes conserved between these two bacteria are likely to be conserved in all other bacteria.
Following the genomic comparison, it was found that several protein coding genes were conserved in evolution. Highly conserved proteins included the translation elongation factor Tu (EF-Tu) and the ~i subunit of FOF 1 type ATP-synthase, and to a lesser extend, the RecA recombinase.
2o Translation elongation factor Tu is a member of a family of GTP-binding proteins which intervene in the interactions of tRNA molecules with the ribosome machinery during essential steps of protein synthesis. The role of elongation factor Tu is to facilitate the binding of aminoacylated tRNA molecules to the A site of the ribosome. The eukaryotic and archaebacterial homolog of EF-Tu is called elongation factor 1 alpha (EF-la). All protein synthesis factors originated from a common ancestor via gene duplications and fusions (Cousineau et al., 1997, J. Mol.
Evol.
45:661-670). In addition, EF-Tu is known to be the target for antibiotics belonging to the elfamycin's group as well as to other structural classes (Anborgh and Parmeggiani, 1991, EMBO J. 10:779-784; Luiten et al., 1992, European patent application serial No. EP 0 466 251 A 1 ). Interestingly, a form of the EF-Tu protein has been identified as a dominant component of the periplasm of Neisseria gonorrhoeae (Porcella et al., 1996, Microbiology 142:2481-2489), hence suggesting that at least in some bacterial species, EF-Tu might be an antigen with vaccine potential.
FOF 1 type ATP-synthase belongs to a superfamily of proton-translocating ATPases divided in three major families: P, V and F (Nelson and Taiz, 1989, TIBS
14:113-116). P-ATPases (or E,-E2 type) operate via a phosphorylated intermediate and are not evolutionarily related to the other two families. V-ATPases (or type) are present on the vacuolar and other endomembranes of eukaryotes, on the 4o plasma membrane of archaebacteria and also on the plasma membrane of some eubacteria especially, species belonging to the order Spirochaetales as well as to the Chlamydiaceae and Deinococcaceae families. F-ATPases (or FOF 1 type) are found on the plasma membrane of most eubacteria, on the inner membrane of mitochondria and on the thylakoid membrane of chloroplasts. They function mainly in ATP
synthesis. They are large multimeric enzymes sharing numerous structural and functional features with the V-ATPases. F and V-type ATPases have diverged from a common ancestor in an event preceding the appearance of eukaryotes. The (3 subunit of the F-ATPases is the catalytic subunit and it possess low but significant sequence homologies with the catalytic A subunit of V-ATPases.
The translation elongation factor Tu (EF-Tu or EF-la) and the catalytic subunit of F or V-types ATP-synthase are two highly conserved proteins sometimes used for phylogenetic analysis and their genes are also known to be highly conserved (Iwabe to et al., 1989, Proc. Natl. Acad. Sci. USA 86:9355-9359, Gogarten et al., 1989, Proc.
Natl. Acad. Sci. USA 86:6661-6665, Ludwig et al., 1993, Antonie van Leeuwenhoek 64:285-305). A recent BLAST (Altschul et al., 1997, J. Mol. Biol. 215:403-410) search performed by the present inventors on the GenBank, EMBL, DDBJ and specific genome project databases indicated that throughout bacteria, the EF-Tu and the [3 subunit of FOF 1 type ATP-synthase genes may be more conserved than other genes that are well conserved between H. influenzae and M. genitalium.
The RecA recombinase is a multifunctional protein encoded by therecA gene.
It plays a central role in homologous recombination, it is critical for the repair of DNA damage and it is involved in the regulation of the SOS system by promoting the 2o proteolytic digestion the LexA repressor. It is highly conserved in bacteria and could serve as a useful genetic marker to reconstruct bacterial phylogeny (Miller and Kokjohn, 1990, Annu. Rev. Microbiol. 44:365-394). Althought recA possess some highly conserved sequence segments that we used to design universal primers aimed at sequencing the recA fragments, it is clearly not as well conserved as tuf and atpD.
Hence, recA may not be optimal for universal detection of bacteria with high sensitivity but it was chosen as preliminary data indicated that tuf and atpD
may sometimes be too closely related to find specific primer pairs that could discriminate between certain very closely related species and genera. While RecA, like tuf and atpD, possess highly conserved regions suitable for the design of universal 3o sequencing primers, the less conserved region between primers should be divergent enough to allow species-specific and genus-specific primers in those cases.
Thus, as targets to design primers and probes for the genetic detection of microorganisms, the present inventors have concentrated on the genes encoding these three proteins: tuf, the gene for elongation factor Tu; andatpD, the gene for ~i subunit of FOF 1 type ATP-synthase; and recA the gene encoding the RecA recombinase.
In several bacterial genomes tuf is often found in two highly similar duplicated copies named tufA and tufB (Filer and Furano, 1981, J. Bacterio1.148:1006-101 l, Selaet al., 1989, J. Bacteriol. 171:581-584). In some particular cases, more divergent copies of the tuf genes can exist in some bacterial species such as some Actinomycetes (Luiten et al. European patent application publication No. EP 0 446 251 A 1; Vij genboomet al., 1994, Microbiology 140:983-998) and, as revealed as part of this invention, in several enterococcal species. The tuf, atpD and recA genes were chosen as there are well conserved in evolution and have highly conserved stretches as well as more variable segments. Moreover, these three genes have eukaryotic orthologs which are described in the present invention as targets to identify fungi and parasites.
The eukaryotic homolog of elongation factor Tu is called elongation factor 1-alpha (EF-1 a) (gene name: tef, tefl , efl , ef I or EF 1 ). In fungi, the gene for EF-1 a occurs sometimes in two or more highly similar duplicated copies (often namedtefl, tef2, tef3...). In addition, eukaryotes have a copy of elongation factor Tu which is originating from their organelle genome ancestery(gene name: tufl or tufts).
For the purpose of the current invention, the genes of these three (bacterial, eukaryotic and organellar) functionally and evolutionarily related elongation factors will hereafter be designated as «tuf sequences. The eukaryotic (mitochondrial) FpF 1 type ATP-1o synthase beta subunit gene is named atp2 in yeast. For the purpose of the current invention, the genes of catalytic subunit of either F or V-type ATP-synthase will hereafter be designated as «atpD sequences. The eukaryotic homologs of RecA
are distributed in two families, typified by the Rad51 and Dmcl proteins. For the purpose of the current invention, the genes corresponding to the latter proteins will hereafter be designated as <wecA sequences.
Analysis of multiple sequence alignments oftuf and atpD sequences present in the public databases, permitted the design of oligonucleotide primers (and probes) capable of amplifying (or hybridizing to) segments oftuf and atpD genes from a wide variety of bacterial species (see Examples 1 to 4 and Table 7). Sequencing primer 2o pairs for tuf sequences are listed in Annex I and hybridization probes are listed in Annex III. Sequencing primer pairs for atpD sequences are listed in Annex II.
Analysis of the main subdivisions of tuf and atpD sequences (see Figures 1 and 2) permitted to design sequencing primers amplifying specifically each of these subdivisions. It should be noted that these sequencing primers could also be use as universal primers. However, since some of these sequencing primers include several variable sequence (degenerated) positions, their sensitivity could be lower than that of universal primers developed for diagnostic purposes. Further subdivisions could be done on the basis of the various phyla where these genes are encountered.
Similarly, analysis of multiple sequence alignments ofrecA sequences present in 3o the public databases, permitted the design of oligonucleotide primers capable of amplifying segments of recA genes from a wide variety of bacterial species.
Sequencing primer pairs for recA sequences are listed in Annex XXI. The main subdivisions of recA sequences comprise recA, rad51 and dmcl. Further subdivisions could be done on the basis of the various phyla where these genes are encountered.
The present inventor's strategy is to get as much sequence data information from the three conserved genes (tuf, atpD and recA). This ensemble of sequence data forming a repertory (with subrepertories corresponding to each target genes and their main sequence subdivisions) and then using the sequence information of the sequence repertory (or subrepertories) to design primer pairs that could permit either universal 4o detection of bacteria or fungi or parasites, detection of a family or group of microorganism (e.g. Enterobacteriaceae), detection of a genus (e.g.Streptococcus) or finally a specific species (e.g. Staphylococcus aureus). It should be noted that for the purpose of the present invention a group of microorganisms is defined depending on the needs of the particular diagnostic test. It does not need to respect a particular taxonomical grouping or phylum. See example 12 where primers were designed to amplify a group a bacteria consisting of the 17 bacterial species most frequently encountered as platelet contaminants. Also remark that in that example, the primers' specificity is not perfect since the objective of that particular test is to be able to sensitively and rapidly detect at least the 17 most frequently encountered species but, the primers could also detect other species as well. In these circonstances the primers shown in example 12 are considered universal for platelet-contaminating bacteria.
To develop an assay specific for the latter, one or more primers or probes specific to each species could be design. Another example of primers and/or probes for group detection is given by the Pseudomonad group primers. These primers were designed to based upon alignment of tuf sequences from real Pseudomonas species as well as from former Pseudomonas species such as Stenotrophomonas maltophilia. The resulting primers are able to amplify all Pseudomonas species tested as well as several species belonging to different genera, hence we as beefing specific for a group including Pseudomonas and other species, we defined that group asPseudomonas as several members were former Pseudomonas.
For certain applications, it may be possible to develop a universal, group, family or genus-specific reaction and to proceed to species identification using sequence information within the amplicon to design species-specific internal probes or primers, or alternatively, to proceed directly by sequencing the amplicon. The various 2o strategies will be discussed further below.
The ensembles formed by public and proprietary tuf, atpD and recA sequences are used in a novel fashion so they constitute three databases containing useful information for the identification of microorganisms.
Oligonucleotide primers and probes design and synthesis The tuf, atpD and recA sequences DNA fragments sequenced by us or selected from public databases (GenBank and EMBL) were used to design oligonucleotides 3o primers and probes for diagnostic purposes. We also relied on the corresponding peptide sequence of tuf, atpD and recA sequences to facilitate the identification of regions suitable for primers and probes design. As part of the design rules, 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 (i.e. the Genetics Computer Group (GCG) programs and the primer analysis software OligoTM 5.0).
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 (Persinget al., 1993, 4o Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.). Oligonucleotide probes and amplification primers were synthesized using an automated DNA synthesizer (Perkin-Elmer Corp., Applied Biosystems Division).

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 (i) the universal detection of bacteria or fungi or parasites, (ii) the species-specific detection and identification ofCandida albicans, Candida dubliniensis, Chlamydia pneumoniae, Chlamydia trachomatis, Cryptosporidium parvum, Enterococcus faecalis, Enterococcus faecium, l0 Enterococcus gallinarum, Escherichia coli, Haemophilus influenzae, Neisseria gonorrhoeae, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus saprophyticus, Streptococcus agalactiae, Trypanosoma brucei, Trypanosoma cruzi, (iii) the genus-specific detection of Bordetella species, Candida species, Clostridium species, Corynebacterium species, Entamoeba species, Enterococcus species, Giardia species, Leishmania species, Staphylococcus species, Streptococcus species, Trypanosoma species, (iv) the family-specific detection ofEnterobacteriaceae family members, Mycobacteriaceae family members, (v) the detection of Enterococcus casseliflavus-flavescens-gallinarum group, Kinetoplastidae group, Pseudomonas extended group, Platelet contaminating bacteria group, or (vi) the detection of clinically important antibiotic resistance genes listed in Table 5, or (vii) the detection of clinically important toxin genes listed in Table 6.
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, 4t" 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 variations) 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.
Sequencing of tub sequences from a variety of bacterial, fungal and parasitical species The nucleotide sequence of a portion of tuf sequences was determined for a variety of bacterial, fungal and parasitical species. The amplification primers (SEQ
ID NOs: 107 and 108 in previous patent application PCT/CA97/00829), which 1 o amplify a tuf gene portion of approximately 890 bp, were used along with newly designed sequencing primer pairs (See Annex I for the sequencing primers fortuf sequences). Most primer pairs can amplify different copies of tuf genes (tufA
and tufB). This is not surprising since it is known that for several bacterial species these two genes are nearly identical. For example, the entire tufA and tufB genes from E.
coli differ at only 13 nucleotide positions (Neidhardtet al., 1996, Escherichia coli and Salmonella: Cellular and Molecular Biology, 2°d ed., American Society for Microbiology Press, Washington, D.C.). Similarly, some fungi are known to have two nearly identical copies of tuf sequences (EF-1 a). 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 tuf sequencing primers even sometimes amplified highly divergent copies of tuf genes (tuff) as illustrated in the case of some enterococcal species (SEQ ID NOs: 73 to 76, 614 to 618, and 621 ). To prove this we first had to clone PCR products before being able to sequence them. Using the cloned sequence data we designed new pair of sequencing primers specific to the divergent (tuff) copy of enterococci (SEQ ID NOs: 658-659 and 661) and then sequenced directly the tuff amplicons. The amplification primers (SEQ ID NOs: 543, 556, 557, 660, 664, 694, 696 and 697) could be used to amplify the tuf sequences from any bacterial 3o species. The amplification primers (SEQ ID NOs: 558, 559, 560, 653, 654, 655, 813 and 815) could be used to amplify the tuf (EF-la) genes from any fungal and parasitical species.
The tuf fragments to be sequenced were amplified using the following amplification protocol: One ~,1 of cell suspension (or of purified genomic DNA
0.1 0.5 ng/~.1) was transferred directly to 19 ~.l of a PCR reaction mixture. Each PCR
reaction contained 50 mM KC1, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl2, 1 ~M 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 PTC-200 thermal cycler (MJ Research Inc., Watertown, 4o Mass.) as follows: 3 min at 96°C followed by 30-45 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°C for the extension step. Subsequently, twenty microliters of the PCR-amplified 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-by molecular weight ladder. The band corresponding to the specific amplification product was excised from the agarose gel and purified using the QIAquickTM 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 1 o amplification product were sequenced by the dideoxynucleotide chain termination sequencing method by using an Applied Biosystems automated DNA sequencer (model 377) with their Big DyeTM Terminator Cycle Sequencing Ready Reaction Kit (Perkin-Elmer Corp., Applied Biosystems Division, Foster City, CA). The sequencing reactions were performed by using the same amplification primers and 10 ng/100 by of the gel-purified amplicon per reaction. For the sequencing of long amplicons such as those of eukaryotic tuf (EF-1 a) sequences, we designed internal sequencing primers (SEQ ID NOs: 654, 655 and 813) to be able to obtain sequence data on both strands for most of the fragment length. In order to ensure that the determined sequence did not contain errors attributable to the sequencing of PCR
2o artifacts, we have sequenced two preparations of the gel-purified tuf amplification product originating from two independent PCR amplifications. For most target microbial species, the sequences determined for both amplicon preparations were identical. In case of discrepancies, a third independant PCR amplification was sequenced. Furthermore, the sequences of both strands were 100% complementary thereby confirming the high accuracy of the determined sequence. Thetuf sequences determined using the above strategy are described in the Sequence Listing.Table 7 gives the originating microbial species and the source for eachtuf sequence in the Sequence Listing.
The alignment of the tuf sequences determined by us or selected from 3o databases reveals clearly that the length of the sequenced portion of thetuf genes is variable. There may be insertions or deletions of several amino acids. In addition, in several fungi introns were observed. Intron sequences are part oftuf sequences and could be useful in the design of species-specific primers and probes. This explains why the size of the sequenced tuf amplification product was variable from one species to another. Consequently, the nucleotide positions indicated on top of each of Annexes IV to XX do not correspond for sequences having insertions or deletions.
It should also be noted that the various tuf sequences determined by us occasionally contain degenerescences. These degenerated nucleotides correspond to sequence variations between tufA and tufB genes (or copies of EF-1 a subdivision of tuf sequences for fungi and parasite) 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 was identical and also because the sequences determined with both preparations of the gel-purified tuf amplicons were identical.
The selection of amplification primers from tuf sequences The tuf sequences determined by us or selected from public databases were used to select PCR primers for (i) the universal detection of bacteria, (ii) the genus-specific 1 o 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 and Annexes.
Sequencing of atpD and recA sequences from a variety of bacterial, fungal and parasitical species The method use to obtain atpD and recA sequences is similar to that described above 2o for tuf sequences.
The selection of amplification primers from atpD or recA
The comparison of the nucleotide sequence for the atpD or recA genes from various bacterial fungal and parasitical species allowed the selection of PCR
primers (refer to Examples 1, 2 and 6 and Annexes IV, X, XX, XXI).
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 OligoTM 5.0 software to verify that they were 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, D.C.).
Briefly, the PCR protocols were as follow: Treated clinical specimens or standardized bacterial or fungal or parasitical suspensions (see below) or purified genomic DNA from bacteria, fungi or parasites were amplified in a 20 ~l PCR
reaction mixture. Each PCR reaction contained 50 mM KCl, 10 mM Tris-HCl (pH
9.0), 2.5 mM MgCl2, 0.4 ~M of each primer, 200 ~,M of each of the four dNTPs and 0.5 unit of Taq DNA polymerise (Promega) combined with the TaqStarfM antibody (Clontech Laboratories Inc., Palo Alto, CA). The TaqStarfM antibody, which is a l0 neutralizing monoclonal antibody to Taq DNA polymerise, 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. For amplification from bacterial or fungal cultures or from purified genomic DNA, the samples were added directly to the PCR amplification mixture without any pre-treatment step. An internal control was derived from sequences not found in the target microorganisms or in the human genome. The internal control was integrated into all amplification 2o reactions to verify the efficiency of the PCR assays and to ensure that significant PCR inhibition was absent. Alternatively, an internal control derived from rRNA was also useful to monitor the efficiency of microbial lysis protocols.
PCR reactions were then subjected to thermal cycling (3 min at 95°C
followed by 30 cycles of 1 second at 95°C for the denaturation step and 30 second at 50-65°C
for the annealing-extension step) using a PTC-200 thermal cycler (MJ Research Inc.).
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 or parasitical 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.
The person skilled in the art of DNA amplification knows the existence of other rapid amplification procedures such as ligase chain reaction (LCR), transcription-mediated amplification (TMA), self sustained sequence replication (3SR), nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), branched DNA (bDNA), cycling probe technology (CPT), solid phase amplification (SPA) and nuclease dependant signal amplification (NDSA) (Leeet al., 1997, Nucleic Acid Amplification Technologies: Application to Disease Diagnosis, Eaton Publishing, Boston, MA; Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.). The scope of this invention is not limited to the use of amplification by PCR, but rather includes the use of any rapid nucleic acid amplification method or any other procedure which may be used to increase rapidity and sensitivity of the nucleic acid-based tests. Any oligonucleotide suitable for the amplification of nucleic acids by approaches other than PCR or for DNA
to hybridization and derived from the species-specific, genus-specific and universal DNA fragments as well as from selected antibiotic resistance or toxin gene sequences included in this document are also under the scope of this invention.
Detection of amplification products Classically, detection of amplification is performed by standard ethidium bromide-stained agarose gel electrophoresis. It is clear that other methods for the detection of specific amplification products, which may be faster and more practical for routine diagnosis, may be used. Such methods may be based on the detection of fluorescence after or during amplification. One simple method for monitoring amplified DNA is to measure its rate of formation by measuring the increase in fluorescence of intercalating agents such as ethidium bromide or SYBR~ Green I. If more specific detection is required, fluorescence based technologies can monitor the appearance of a specific product during the reaction. The use of dual-labeled fluorogenic probes such as in the TaqManTM system which utilizes the 5'-3' exonuclease activity of the Taq polymerase is a good example (Livak K.J.et al.
1995, PCR Methods Appl. 4:357-362). TaqManTM can be performed during amplification and this "real-time" detection can be done in a single closed tube hence eliminating post-PCR sample handling and consequently preventing the risk of amplicon 3o carryover (TaqManTM system from Perkin Elmer or AmplisensorTM from Biotronics).
Several other fluorescence-based detection methods can be performed in real-time.
Fluorescence resonance energy transfer (FRET) is the principle behind the use of adj scent hybridization probes and molecular beacons. Adj scent hybridization probes are designed to be internal to the amplification primers. The 3' end of one probe is labelled with a donor fluorophore while the 5' end of an adjacent probe is labelled with an acceptor fluorophore. When the two probes are specifically hybridized in closed proximity (spaced by 1 to 5 nucleotides) the donor fluorophore which has been excited by an external light source emits light that is absorbed by a second, acceptor that emit more fluorescence and yield FRET signal. Molecular beacons possess a 4o stem-and-loop structure where the loop is the probe and at the end of the stem a fluorescent moiety is at one end while a quenching moiety is at the other end.
The beacons undergo a fluorogenic conformational change when they hybridize to their targets hence separating the fluorochrome from its quencher. The FRET
principle is also used in an air thermal cycle with a built-in fluorometer (Wittwer, C.T.
et al.
1997. BioTechniques. 22:130-138). The amplification and detection are extremely rapid as reactions are performed in capillaries and it takes 18 min to complete 45 cycles. Those techniques are suitable, especially in the case where few pathogens are searched for. Boerhinger-Roche Inc., sells the LightCyclerTM, an apparatus capable of rapid cycle PCR combined with fluorescent SYBR~ Green I or FRET detection. We 1 o recently demonstrated in our laboratory, real-time detection of 10 CFU in less than 40 minutes using adjacent hybridization probes on the LightCyclerTM.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.
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 sequences from our repertory and designed to specifically hybridize to DNA
amplification products which are objects of the present invention.
Alternatively, the internal probes for species or genus or family or group detection and identification may be derived from the amplicons produced by a universal, family, group or genus amplification assay. The oligonucleotide probes may be labeled with biotin or with digoxigenin or with any other reporter molecules (for more details see below the section on hybrid capture). Hybrization on solid support is emendable to miniaturization.
At present the oligonucleotide nucleic acid microarray technology is appealing.
Currently, available low to medium density arrays (Heller et al., An integrated microelectronics hybridization system for genomic research and diagnostic applications. In: Harrison, D.J., and van den Berg, A., 1998, Micro total analysis systems '98, Kluwer Academic Publisher, Dordrecht.) could specifically capture 3o fluorescent-labelled amplicons. Detection methods for hybridization are not limited to fluorescence, potentiometry, colorimetry and plasmon resonance are some examples of alternative detection methods. In addition to detection by hybridization, nucleic acid microarrays could be use to perform rapid sequencing by hybrization.
Mass spectrometry could also be applicable for rapid identification of the amplicon or even for sequencing of the amplification products (Chiu and Cantor, 1999, Clinical Chemistry 45:1578; Berkenkamp et al., 1998, Science 281:260).
We also keep in mind the major challenge of molecular diagnostics tools,i.e.
integration of the major steps including sample preparation, genetic amplification, detection, data analysis and presentation (Anderson et al., Advances in integrated genetic analysis. In: Harrison, D.J., and van den Berg, A., 1998, Micro total analysis systems '98, Kluwer Academic Publisher, Dordrecht.).

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 concentration ranges for glycerol and DMSO are 5-15% (v/v) and 3-10%
(v/v), respectively. For the PCR reaction mixture, the concentration ranges for the amplification primers and MgCl2 are 0.1-1.5 ~,M and 1.0-10.0 mM, respectively.
Modifications of the standard PCR protocol using external and nested primers (i.e.
nested PCR) or using more than one primer pair (i.e. multiplex PCR) may also be used (Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.). For more details about the PCR protocols and amplicon detection methods, see Examples.
Hybrid capture and chemiluminescence detection of amplification products Hybridization and detection of amplicons by chemiluminescence were adapted from Nikiforov et al. ( 1994, PCR Methods and Applications 3:285-291 and 1995, Anal. Biochem. 227:201-209 ) and from the DIGTM system protocol of Boehringer 2o Mannheim. Briefly, 50 ~1 of a 25 picomoles solution of capture probe diluted in EDC
f 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochlorides are immobilized in each well of 96 wells plates (MicroliteTM 2, Dynex) by incubation overnight at room temperature. The next day, the plates are incubated with a solution of 1 % BSA
diluted into TNTw (10 mM Tris-HCI, pH 7.5; 150 mM NaCI; 0.05% TweenTM 20) for 1 hour at 37°C. The plates are then washed on a Wellwash AscentTM
(Labsystems) with TNTw followed by Washing Buffer (100 mM malefic acid; 150 mM NaCI; pH7.5; 0.3% TweenTM 20).
The amplicons were labelled with DIG-11-dUTP during PCR using the PCR
DIG Labelling Mix from Boehringer Mannheim according to the manufacturer's 3o instructions. Hybridization of the amplicons to the capture probes is performed in triplicate at stringent temperature (generally, probes are designed to allow hybrization at 55°C, the stringent temperature) for 30 minutes in 1.5 M NaCI; 10 mM
EDTA. It is followed by two washes in 2 X SSC; 0.1% SDS, then by four washes in O.1X SSC;
0.1% SDS at the stringent temperature (55°C). Detection with 1,2 dioxetane chemiluminescent alkaline phosphatase substrates like CSPD~ (Tropix inc.) is performed according to the manufacturer's instructions but with shorter incubations times and a different antibody concentration. The plates are agitated at each steps, the blocking incubation is performed for only 5 minutes, the anti-DIG-AP 1 is used at a 1:1000 dilution, the incubation with antibody last 15 minutes, the plates are washed 4o twice for only 5 minutes. Finally, after a 2 minutes incubation into the detection buffer, the plates are incubated 5 minutes with CSPD~ at room temperature followed by a 10 minutes incubation at 37°C without agitation. Luminous signal detection is performed on a Dynex Microtiter Plate Luminometer using RLU (Relative Light Units).
Specificity and ubiquity tests for oligonucleotide primers and probes The specificity of oligonucleotide primers and probes was tested by amplification of DNA or by hybridization with bacterial or fungal or parasitical l0 species selected from a panel comprising closely related species and species sharing the same anatomo-pathological site (see Annexes and Examples). All of the bacterial, fungal and parasitical species tested were likely to be pathogens associated with infections or potential contaminants which can be isolated from clinical specimens.
Each target DNA could be released from bacterial cells using standard chemical and/or physical 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) or alternatively, genomic DNA purified with the GNOMETM
DNA kit (Bio101, Vista, CA) was used. Subsequently, the DNA was subjected to amplification with the primer pairs.
Oligonucleotides primers found to amplify specifically the target species, genus, family or group were subsequently tested for their ubiquity by amplification (i.e.
ubiquitous primers amplified most or all isolates of the target species or genus or family or group). The specificity and ubiquity of the PCR assays using the selected amplification primer pairs were tested either directly from cultures of microbial species or from purified microbial genomic DNA.
Probes were tested in hybrid capture assays as described above. An oligonucleotide probe was considered specific only when it hybridized solely to DNA
from the species or genus or family or group from which it was selected.
Oligonucleotide probes found to be specific were subsequently tested for their 3o ubiquity (i.e. ubiquitous probes recognized most or all isolates of the target species or genus or family or group) by hybridization to microbial DNAs from different clinical isolates of the species or genus or family or group of interest including ATCC
reference strains. Similarly, oligonucleotide primers and probes could be derived from antibiotic resistance or toxin genes which are objects of the present invention.
Reference strains The reference strains used to built proprietarytuf, atpD and recA sequence data repertory, as well as to test the amplification and hybridization assays were obtained from (i) the American Type Culture Collection (ATCC), (ii) the Laboratoire de same publique du Quebec (LSPQ), (iii) the Centers for Disease Control and Prevention (CDC), (iv) the National Culture Type Collection (NCTC) and (v) several other reference laboratories throughout the world. The identity of our reference strains was confirmed by phenotypic testing and reconfirmed by analysis oftuf, atpD and recA
sequences (see example 13).
Antibiotic resistance genes Antimicrobial resistance complicates treatment and often leads to therapeutic 1 o 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 species- and/or genus- and/or family- and/or group-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 (i.e. DNA-2o 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 public databases, our strategy is 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 list of each of the bacterial antibiotic resistance genes selected on the basis of their clinical relevance (i.e. high incidence and importance) is given in the Table S. Our approach is unique because the antibiotic resistance genes detection and the bacterial detection and identification can be performed simultaneously in multiplex assays under uniform PCR amplification conditions .
Toxin genes Toxin identification is often very important 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 species- and/or genus- and/or family-and/or group-specific DNA-based tests, clinicians sometimes need timely information about the ability of certain bacterial pathogen to produce toxins. Since the sequence from the most important and common bacterial toxin genes are available from public 4o databases, our strategy is to use the sequence from a portion or from the entire toxin gene to design specific oligonucleotide primers or probes which will be used as a basis for the development of rapid DNA-based tests. The list of each of the bacterial toxin genes selected on the basis of their clinical relevance (i.e. high incidence and importance) is given in the Table 6. Our approach is unique because the toxin genes detection and the bacterial detection and identification can be performed simultaneously in multiplex assays under uniform PCR amplification conditions .
Universal bacterial detection to In the routine microbiology laboratory, a high percentage of clinical specimens sent for bacterial identification are negative by culture. Testing clinical samples with universal amplification primers or universal probes to detect the presence of bacteria prior to specific identification and screen out the numerous negative specimens is thus useful as it saves costs and may rapidly orient the clinical management of the patients. Several amplification primers and probes were therefore synthesized from highly conserved portions of bacterial sequences from the tuf and atpD
sequences.
The universal primers selection was based on a multiple sequence alignment constructed with sequences from our repertory.
2o All computer analysis of amino acid and nucleotide sequences were performed by using the GCG programs. Subsequently, optimal PCR primers for the universal amplification of bacteria were selected with the help of the OligoTM program.
The selected primers are degenerated at several nucleotide positions and contain several inosines in order to allow the amplification of all clinically relevant bacterial species (Annex I). 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 are very similar to those used for the species- and genus-specific amplification assays except that the annealing temperature is slightly lower. The original universal PCR assay described in our co-pending PCT (PCT/CA97/00829)(SEQ ID NO. 23-24 of the latter application) 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 as well as genomic DNA from Leishmania donovani, Saccharomyces cerevisiae and human lymphocytes. None of the above eukaryotic 4o DNA preparations could be amplified by the universal assay, thereby suggesting that this test is specific for bacteria. The ubiquity of the universal assay was verified by amplifying genomic DNAs from 116 reference strains which represent 95 of the most clinically relevant bacterial species. These species have been selected from the bacterial species listed in Table 4. We found that at least 104 of these species could be amplified. However, the assay could be improved since bacterial species which could not be amplified with the original tuf sequences-based assay included species belonging to the following genera: Corynebacterium ( 11 species) and Stenotrophomonas (1 species). Sequencing of the tuf genes from these bacterial species and other has been performed in the scope of the present invention in order 1o to improve the universal assay. This sequencing data has been used to select new universal primers which may be more ubiquitous. Also, we improved our primer and probes design strategy by taking into consideration the phylogeny observed in analysing our repertory of tuf, atpD and recA sequences. Data from each of the main subrepertory (tuf, atpD and recA) was subjected to a basic phylogenic analysis using the Pileup command from version 10 of the GCG package (Genetics Computer Group, inc.). This analysis indicated the main branches or phyla reflecting the relationships between sequences. Instead of trying to design primers or probes able to hybridize to all phyla, we designed primers or probes able to hybridize to the main phyla while trying to use the largest phylum possible. This strategy should allow less degenerated primers hence improving sensitivity and by combining primers in a mutiplex assay, improve ubiquity. Universal primers SEQ ID NO. 643-645 based on tuf sequences have been designed to amplify most pathogenic bacteria except Actinomyceteae, Clostridiaceae and the Cytophaga, Flexibacter and Bacteroides phylum (pathogenic bacteria of this phylum include mostly Bacteroides, Porphyromonas and Prevotella species). Primers to fill these gaps have been designed for Actinomyceteae (SEQ ID NO. 646-648), Clostridiaceae (SEQ ID NO.
796-797, 808-811 ), and the Cytophaga, Flexibacter and Bacteroides phylum (SEQ
ID NO. 649-651 ). These primers sets could be used alone or in conjuction to render the universal assay more ubiquitous. These primers are in the process of being tested.
Universal primers derived from atpD sequences include SEQ ID NO. 562-565.
Combination of these primers does not amplified human DNA but should amplify almost all pathogenic bacterial species except proteobacteria belonging to the epsilon subdivision (Campylobacter and Helicobacter), the bacteria from the Cytophaga, Flexibacter and Bacteroides group and some actinomycetes and corynebacteria.
By analysing atpD sequences from the latter species, primers and probes to specifically fill these gaps could be designed and used in conjuction with primers SEQ ID
NO.
562-565. These primers are in the process of being tested.
In addition, universality of the assay could be expanded by mixing atpD
sequences-derived primers with tuf sequences-derived primers. Ultimately, evenrecA
4o sequences-derived primers could be added to fill some gaps in the universal assay.

It is important to note that the 95 bacterial species selected 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.
Amino acid sequences derived from atpD, tuf and recA sequences The amino acid sequences translated from the repertory of atpD, tuf and recA
sequences are also an object of the present invention. The amino acid sequence data 1o will be particularly useful for homology modeling of three-dimensional (3D) structure of the elongation factor-Tu, Atpase subunit beta and RecA
recombinase. For all three proteins, at least one structure model as been published using X-ray diffraction data from crystals. Based on those structural informations it is possible to use computer sofwares to build model 3D structures for any other proteins having peptide sequence homologies with the known structure (Green 1991, Methods in Enzymology, 202:239-252, Taylor, 1994, Sali, 1995, Curr. Opin.
Biotechno1.6:437-451, Sanchez and Sali, 1997, Curr. Opin. Struct. Biol. 7:206-214, Fischer and Eisenberg, 1999, Curr. Opin. Struct. Biol. 9:208-211, Guex et al., 1999, Trends Biochem. Sci. 24: 364-367). Model structures of target proteins are used for the design or to predict the behavior of ligands and inhibitors such as antibiotics. Since EF-Tu is already known as an antibiotic target (see above) and since the beta subunit of ATPase and RecA recombinase are essential to the survival of the microbial cells in natural conditions of infection, all three proteins could be considered antibiotic targets. Sequence data, especially the new data generated by us could be very useful to assist the creation of new antibiotic molecules with desired spectrum of activity. In addition, model structures could be used to improved protein function for commercial purposes such as improving antibiotic production by microbial strains or increasing biomass.

BRIEF SUMMARY OF THE INVENTION
Three highly conserved genes, encoding translation elongation factor Tu, the catalytic subunit of proton-translocating ATPase and the RecA recombinase, are used to 1o generate species-specific, genus-specific, group-specific and universal nucleic acid probes and amplification primers to rapidly detect and identify bacterial, fungal and parasitical pathogens from clinical specimens for diagnosis. The concomittant detection of associated antibiotic resistance and toxin genes are also under the scope of the present invention.

DESCRIPTION OF THE DRAWINGS
Figures 1 and 2 illustrate the principal subdivisions of theatpD and tuf sequences repertories, respectively. For the design of primers and probes, depending on the needs, one may want to use the complete data set illustrated on the top of the pyramid or use only a subset illustrated by the different branching points. Smaller subdivisions, representing groups, families, genus and species, could even be made to 3o extend the bottom of the pyramid. Because the atpD and tuf sequences are highly conserved and evolved with each species, the design of primers and probes does not need to include all the sequences within the database or its subdivisions. As illustrated, in Annexes IV to XX, depending on the use, sequences from a limited number of species can be carefully selected to represent: i) only the main phylogenetic branches from which the intended probes and primers need to be differentiating, and ii) only the species for which they need to be matching.
However, for ubiquity purposes, and especially for primers and probes identifying large groups of species (genus, family, group or universal, or sequencing primers), the more data is included into the sequence analysis, the better the probes and primers will be suitable 4o for each particular intented use. Similarly, for specificity purposes, a larger data set (or repertory) ensures optimal primers and probes design by reducing the chance of employing nonspecific oligonucleotides.

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 atpD sequences or from the recA
sequences:
(i) Annex I illustrates the amplification primers used fortuf sequences. (ii) Annex II
l0 illustrates the amplification primers used for atpD sequences. (iii) Annex III shows the probes for hybridization with tuf sequences. (iv) Annex IV illustrates the strategy used for the selection of the amplification primers specific foratpD sequences of the F-type. (v) Annex V illustrates the strategy used for the selection of the amplification primers specific for atpD sequences of the V-type. (vi) Annex VI illustrates the strategy used for the selection of the amplification primers specific for the tuf sequences of organelle lineage (M, the letter M is used to indicate that in most case, the organelle is the mitochondria). (vii) Annexes VII illustrates the strategy used for the selection of the amplification primers specific for thetuf sequences of eukaryotes (ef 1 ). (viii) Annex VIII illustrates the strategy for the selection ofStreptococcus agalactiae-specific amplification primers from tuf sequences. (ix) Annex IX
illustrates the strategy for the selection of Streptococcus agalactiae-specific hybridization probes from tuf sequences. (x) Annex X illustrates the strategy for the selection of Streptococcus agalactiae-specific amplification primers from atpD
sequences. (xi) Annex XI illustrates the Strategy for the selection fromtuf sequences of Candida albicansldubliniensis-specific amplification primers, Candida albicans-specific hybridization probe and Candida dubliniensis-specific hybridization probe.
(xii) Annex XII illustrates the strategy for the selection ofStaphylococcus-specific amplification primers from tuf sequences. (xiii) Annex XIII illustrates the Strategy for the selection of the Staphylococcus genus-specific hybridization probe from tuf sequences. (xiv) Annex XIV illustrates the strategy for the selection of Staphylococcus saprophyticus-specific and ofStaphylococcus haemolyticus-specific hybridization probes from tuf sequences. (xv) Annex XV illustrates the strategy for the selection of Staphylococcus aureus-specific and of Staphylococcus epidermidis-specific hybridization probes from tuf sequences. (xvi) Annex XVI illustrates the strategy for the selection of the Staphylococcus hominis-specific hybridization probe from tuf sequences. (xvii) Annex XVII illustrates the strategy for the selection from tuf sequences of the amplification primers specific for the genus Enterococcus.
(xviii) Annex XVIII illustrates the strategy for the selection of the Enterococcus faecalis-specific hybridization probe, of the Enterococcus faecium-specific hybridization probe and of the Enterococcus casseliflavus-flavescens-gallinarum group-specific hybridization probe from tuf sequences. (xix) Annex XIX
illustrates the strategy for the selection of primers from tuf sequences for the identification of platelets contaminants. (xx) Annex XX illustrates the strategy for the selection of the universal amplification primers from atpD sequences. (xxi) Annex XXI
illustrates the amplification primers used for DNA amplification from recA sequences.
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 or T. Alternatively, 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
EXAMPLE 1:
Sequencing of bacterial atpD (F-type) gene fragments. As shown in Annex IV, the comparison of publicly available atpD (F-type) sequences from a variety of bacterial species revealed conserved regions allowing the design of PCR primers able to amplify atpD sequences from a wide range of bacterial species. Using primers pairs SEQ ID NO. 566 and 567, 566 and 814, 568 and 567, 570 and 567, 572 and 567, and 567, 571 and 567, and 700 and 567, it was possible to amplify and sequenceatpD
3o sequences SEQ ID NO. 242-270, 272-398, 673-674, 737-767, and 866-867.
EXAMPLE 2:
Sequencing of eukaryotic atpD (F-type) gene fragments. The comparison of publicly available atpD (F-type) sequences from a variety of fungal and parasitical species revealed conserved regions allowing the design of PCR primers able to amplifyatpD
sequences from a wide range of fungal and parasitical species. Using primers pairs SEQ ID NO. 568 and 573, 574 and 573, and 574 and 708, it was possible to amplify and sequence atpD sequences SEQ ID NO. 458-497, 530-538, 663, 667, 676, 678 680, 768-778, 856-862, and 889-896.
EXAMPLE 3:

Sequencing of eukaryotic tuf (ef 1 ) gene fragments. As shown in Annex VII, the comparison of publicly available tuf (ef 1 ) sequences from a variety of fungal and parasitical species revealed conserved regions allowing the design of PCR
primers able to amplify tuf sequences from a wide range of fungal and parasitical species.
Using primers pairs SEQ ID NO. 558 and 559, 813 and 559, 558 and 815, 560 and 559, 653 and 559, 558 and 655, and 654 and 559, it was possible to amplify and sequence tuf sequences SEQ ID NO. 399-457, 509-529, 622-624, 677, 779-790, 840-842, 865, and 897-903.
l0 EXAMPLE 4:
Sequencing of eukaryotic tuf (organelle origin, M) gene fragments. As shown in Annex VI, the comparison of publicly available tuf (organelle origin, M) sequences from a variety of fungal and parasitical organelles revealed conserved regions allowing the design of PCR primers able to amplify tuf sequences of several organelles belonging to a wide range fungal and parasitical species. Using primers pairs SEQ ID NO. 664 and 652, 664 and 561, 911 and 914, 912 and 914, 913 and 915, 916 and 561, and 664 and 917, it was possible to amplify and sequencetuf sequences SEQ ID NO. 498-508, 791-792, 843-855, and 904-910.
EXAMPLE 5:
Specific identification of Streptococcus agalactiae using tuf sequences. As shown in annex VIII, the comparison of tuf sequences from a variety of bacterial species allowed the selection of PCR primers specific forS. agalactiae. The strategy used to design the PCR primers was based on the analysis of a multiple sequence alignment of various tuf sequences. The multiple sequence alignment include thetuf sequences of four bacterial strains from the target species as well as tuf sequences from other species and bacterial genera especially, representative of closely related species. A
careful analysis of this alignment allowed the selection of oligonucleotide sequences which are conserved within the target species but which discriminate sequences from other species and genera, especially from the closely related species, thereby permitting the species-specific and ubiquitous detection and identification of the target bacterial species.
The chosen primer pair, oligos TSag340 (SEQ ID NO. 549) and TSag552 (SEQ ID
NO. S50), gives an amplification product of 252 bp. Standard PCR was carried out using 0.4 ~,M of each primers, 2.5 mM MgCl2, BSA 0.05 mM, 1X Taq Buffer (Promega), dNTP 0.2 mM (Pharmacia), 1 ~.1 Taq DNA polymerase (Promega) 0.025 4o U/~1 combined with TaqStart 5 ng/~,1 (Clontech Laboratories Inc., Palo Alto), 1 ~,l of genomic DNA sample in a final volume of 20 ~1 using a PTC-200 thermocycler (MJ
Research Inc.). The optimal cycling conditions for maximum sensitivity and specificity were 3 minutes at 95°C for initial denaturation, thenforty cycles of two steps consisting of 1 second at 95°C and 30 seconds at 62°C, followed by terminal extension at 72°C for 2 minutes. Amplification was monitored on agarose gel electrophoresis by staining the DNA with ethidium bromide.
Specificity of the assay was tested by adding into the PCR reactions, 0.1 ng of genomic DNA from each of the bacterial species listed in Table 8. Strong amplification was observed only for the 5 S. agalactiae strains listed. Of the other bacterial species, including 32 species representative of the vaginal flora and 27 other to streptococcal species, only S. acidominimus yielded amplification. The signal for 0,1 ng of S. acidominimus genomic DNA was weak and the detection limit for this species was 10 pg (corresponding to more than 4000 genome copies) while the detection limit for S. agalactiae was 2.5 fg (corresponding to one genome copy) of genomic DNA.
To increase the specificity of the assay, internal probes were designed for FRET
(Fluorescence Resonance Energy Transfer) detection using the LightCycler (Idaho Technology). As illustrated in annex IX, a multiple sequence alignment of streptococcal tuf sequence fragments corresponding the 252 by region amplified by 2o primers TSag340 (SEQ ID NO. 549) and TSag552 (SEQ ID NO. 550), was used for the design of internal probes TSagHF436 (SEQ ID NO. 582) and TSagHF465 (SEQ
ID NO. 583). The region of the amplicon selected for internal probes contained sequences unique and specific to S. agalactiae. TSagHF465 (SEQ ID NO. 583), the more specific probe is labelled with fluorescein in 3' while TSagHF436 (SEQ ID
NO. 582), the less discriminant probe is labelled with CYS in 5' and blocked in 3' with a phosphate group. However, since the FRET signal is only emitted if both probes are adjacently hybridized on the same target amplicon, detection is highly specific.
Real-time detection of PCR products using the LightCyclerTM was carried out using 0.4 ~,M of each primers (SEQ ID NO. 549-550), 0,2 ~M of each probes (SEQ ID
NO.
582-583), 2.5 mM MgCl2, BSA 450 ~,g/ml, 1X PC2 Buffer (AB Peptides, St-Louis, MO), dNTP 0.2 mM (Pharmacia), KlenTaq 1 TM DNA polymerise 0.5 U (AB
Peptides) 0.025 U/~1 combined with TaqStart (Clontech Laboratories Inc., Palo Alto), 0.7 ~l of genomic DNA sample in a final volume of 7 ~1 using a LightCycler thermocycler (Idaho Technology). The optimal cycling conditions for maximum sensitivity and specificity were 3 minutes at 94°C for initial denaturation, thenforty cycles of three steps consisting of 0 second (this setting meaning the LightCycler will reach the target temperature and stay at it for its minimal amount of time) at 94°C, 10 seconds at 64°C, 20 seconds at 72°C. Amplification was monitored during each annealing steps using the fluorescence ratio. The streptococcal species having close sequence homologies with the tuf sequence of S. agalactiae (S. acidominimus, S.
anginosus, S. bovis, S. dysgalactiae, S. equi, S. ferus, S. gordonii, S.
intermedius, S.
parasanguis, S. parauberis, S. salivarius, S. sanguis, S. suis, and of course S.
agalactiae) were tested in the LightCycler with 0.07 ng of genomic DNA per reaction. This time, only S. agalactiae yielded an amplification signal, hence demonstrating that the assay is species-specific. With the LightCycler assay using the internal FRET probes, the detection limit for S. agalactiae was 12.5 fg (corresponding to five genome copies) of genomic DNA.
EXAMPLE 6:
Specific identification of Streptococcus agalactiae using atpD sequences. As shown in Annex XIV, the comparison of atpD sequences from a variety of bacterial species allowed the selection of PCR primers specific for S. agalactiae. The primer design strategy is similar the strategy described in the preceeding example except that atpD
sequences were used in the alignment (see Annex X).
Four primers were selected, ASag42 (SEQ ID NO. 627), ASag52 (SEQ ID NO. 628), 2o ASag206 (SEQ ID NO. 625) and ASag371 (SEQ ID NO. 626). The following combinations of these four primers give four amplicons; SEQ ID NO. 627 + SEQ
ID
NO. 625 = 190 bp, SEQ ID NO. 628 + SEQ ID NO. 625 = 180 bp, SEQ ID NO. 627 + SEQ ID NO. 626 = 355 bp, and SEQ ID NO. 628 + SEQ ID NO. 626 = 345 bp.
Standard PCR was carried out on PTC-200 thermocyclers (MJ Research Inc) using 0.4 ~M of each primers pairs, 2.5 mM MgCl2, BSA 0.05 mM, 1X Taq Buffer (Promega), dNTP 0.2 mM (Pharmacia), 1 ~,1 Taq DNA polymerase (Promega) 0.025 U/~1 combined with TaqStart 5 ng/~,l (Clontech Laboratories Inc., Palo Alto), 1 ~,1 of genomic DNA sample in a final volume of 20 ~,l using a PTC-200 thermocycler (MJ
Research Inc.). The optimal cycling conditions for maximum sensitivity and specificity were adjusted for each primer pairs. Three minutes at 95°C
for initial denaturation, then forty cycles of two steps consisting of 1 second at 95°C and 30 seconds at the optimal temperature specified below, followed by terminal extension at 72°C for 2 minutes. Amplification was monitored on agarose gel electrophoresis by staining the DNA with ethidium bromide. Since atpD sequences are relatively more specific than tuf sequences, only the more closely related species namely, the steptococcal species listed in table 9, were tested.
All four primer pairs only amplified the six S. agalactiae strains. With an annealing temperature of 63°C, the primer pair SEQ ID NO. 627 + SEQ ID NO. 625 had a sensitivity of 1-5 fg (equivalent to 1-2 genome copies). At 55°C, the primer pair SEQ
ID NO. 628 + SEQ ID NO. 625 had a sensitivity of 2.5 fg (equivalent to 1 genome copy). At 60°C, the primer pair SEQ ID NO. 627 + SEQ ID NO. 626 had a sensitivity of 10 fg (equivalent to 4 genome copies). At 58°C, the primer pair SEQ
ID NO. 628 + SEQ ID NO. 626 had a sensitivity of 2.5-5 fg (equivalent to 1-2 genome copies).
This proves that all four primer pairs can detect S. agalactiae with high specificity and sensitivity. Together with example 5, this example demonstrate that bothtuf and atpD sequences are suitable targets for the identification of microorganisms at the species level.
to EXAMPLE 7:
Development of a PCR Assay for Detection and Identification of Staphylococci at Genus and Species Levels.
Material and Methods Bacterial strains. The specificity of the PCR assay was verified by using a panel of ATCC (America Type Culture Collection) and DSMZ (Deutsche Sammlung von Mikroorganismen and Zellkulturen GmbH ; German Collection of Microorganisms and Cell Cultures) ( reference strains consisting of 33 gram-negative and 47 gram-positive bacterial species (Table 11 ). An additional 295 clinical isolates of different species of staphylococci from the microbiology laboratory of the Centre Hospitalier Universitaire de Quebec, Pavilion Centre Hospitalier de 1'Universite Laval (CHUL) (Ste-Foy, Quebec, Canada) were also tested to further validate the Staphylococcus-specific PCR assay. These strains were all identified by using (i) conventional methods or (ii) the automated MicroScan Autoscan-4 system equipped with the Positive BP Combo Panel Type 6 (Dade Diagnostics, Mississauga, Ontario, 3o Canada). Bacterial strains were grown from frozen stocks kept at -80°C in brain heart infusion (BHI) broth containing 10% glycerol and cultured on sheep blood agar or in BHI broth (Quelab Laboratories Inc, Montreal, Quebec, Canada).
PCR primers and internal probes. Based on multiple sequence alignments, regions of the tuf gene unique to staphylococci were identified. Staphylococcus genus-specific PCR primers TStaG422 (SEQ ID NO. 553) and TStaG765 (SEQ ID NO. 575) were derived from these regions (Annex XII). These PCR primers are displaced by two nucleotide positions compared to original Staphylococcus genus-specific PCR
primers described in previous patent application WO 98/20157 (SEQ ID NO. 17 and 20 in the 4o said patent application). These modifications were done to ensure specificity and ubiquity of the primer pair, in the light of newtuf sequence data revealed in the present patent application for several additional streptococcal species and strains.

Similarly, sequence alignments analysis were performed to design genus and species-specific internal probes. Two internal probes for Staphylococcus-genus (SEQ
ID NO. 605-606), five for S. aureus (SEQ ID NO. 584-588), five for S.
epidermidis (SEQ ID NO. 589-593), two for S. haemolyticus (SEQ ID NO. 594-595), three for S.
hominis (SEQ ID NO. 596-598), four for S. saprophyticus (SEQ ID NO. 599-601 and 695) were designed. The range of mismatches between Staphylococcus-specific 371-by amplicon and each of the 20-mer species-specific internal probes was from 1 to 5, in the middle of the probe when possible. No mismatches were present in the two l0 Staphylococcus-genus probes for the 11 species analyzed;S. aureus, S.
auricularis, S.
capitis, S. cohnii, S. epidermidis, S. haemolyticus, S. hominis, S.
lugdunensis, S.
saprophyticus, S. simulans and S. warneri.In order to verify the infra-specific sequence conservation of the nucleotide sequence, sequences were obtained for the 371-by amplicon from five unrelated ATCC and clinical strains for each of the species S.
aureus, S. epidermidis, S. haemolyticus, S. hominisand S. saprophyticus. The OligoTM
(version 5.0) primer analysis software (National Biosciences, Plymouth, Minn.) was used to confirm the absence of self complementary regions within and between the primers or probes. When required, the primers contained inosines or degenerated nucleotides at one or more variable positions. Oligonucleotide primers and probes were 2o synthesized on a model 394 DNA synthesizer (Perkin-Elmer Corp., Applied Biosystems Division, Mississauga, Ontario, Canada). Detection of the hybridization was performed with the DIG-labeled dUTP incorporated during theamplification with the Staphylococcus-specific PCR assay and hybridization signal was detected with a luminometer (Dynex Technologies) as described above in the section on luminescent detection of amplification products. Annexes XIV to XVII illustrate the internal probes which are more specific and/or have the best signal to background ratio.
PCR amplification. For all bacterial species, amplification was performed from purified genomic DNA or from a bacterial suspension whose turbidity was adjusted to that of a 0.5 McFarland standard, which corresponds to approximately 1.5 x 10g bacteria per ml. One nanogram of genomic DNA or 1 ~.1 of the standardized bacterial suspension was transferred directly to a 19 ~,l PCR mixture. Each PCR reaction contained 50 mM KCI, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl2, 0.2 ~M (each) of the two Staphylococcus genus-specific primers (TStaG-422 and TStaG-765, SEQ ID NO. 553 and 575), 200 ~,M (each) of the four deoxynucleoside triphosphates (Pharmacia Biotech), 3.3 ~g/~.1 bovine serum albumin (BSA) (Sigma-Aldrich Canada Ltd, Oakville, Ontario, Canada), and 0.5 U Taq polymerase (Promega) coupled with TaqStartTM Antibody (Clontech). The PCR amplification and the agarose 4o gel analysis of the amplified products were performed as previously described.

For determination of the sensitivities of the PCR assays, two-fold dilutions of purified genomic DNA were used to determine the minimal number of genome copies which can be detected.
Results Amplifications with the Staphylococcus-specific PCR assay. The specificity of the assay was assessed by performing 30-cycle and 40-cycle PCR amplifications with the panel of gram-positive (47 species from 8 genera) and gram-negative (37 species from 22 genera) bacterial species listed in Table 11. The PCR assay was able to detect 27 of 27 staphylococcal species tested in both 30-cycle and 40-cycle regimens. For 30-cycle PCR, all bacterial species tested other than staphylococci were negative. For 40-cycle PCR, Enterococcus faecalis, Lactobacillus acidophilus, Lactococcus lactis, Macrococcus caseolyticus, Streptocuccus agalactiae and S. mutans were slightly positive for the Staphylococcus-specific PCR assay. The other species tested remained negative. Ubiquity tests performed on a collection of 295 clinical isolates provided by the microbiology laboratory of the Centre Hospitalier Universitaire de Quebec, Pavilion Centre Hospitalier de 1'Universite Laval (CHUL) including Staphylococcus aureus (n=34), S. auricularis (n=2), S. capitis (n=19), S. cohnii (n=5), S.
epidermidis (n=18), S. haemolyticus (n=21), S. hominis (n=73), S. lugdunensis (n=17), S.
saprophyticus (n=6), S. simulans (n=3), S. warneri (n=32) and Staphylococcus spp.
(n=65) showed a uniform amplification signal with the 30-cycle PCR assays and a perfect relation between the genotype and classical identification schemes.
The sensitivity of the Staphylococcus-specific assay with 30-cycle and 40-cycle PCR
protocols was determined by using purified genomic DNA from the 11 staphylococcal species previously mentioned. For PCR with 30 cycles, a detection limit of SO
copies of genomic DNA was consistently obtained. In order to enhance the sensitivity of the 3o assay, the number of cycles was increased. For 40 cycles PCR assays, the detection limit was lowered to a range of 5-10 genome copies, depending on the staphylococcal species tested.
Hybridization between Staphylococcus-specific 371-by amplicon and species-specific internal probes. Inter-species polymorphism was sufficient to generate species-specific internal probes for each of the principal species involved in humans diseases, S. aureus, S. epidermidis, S. haemolyticus, S. hominisand S.
saprophyticus.
In order to verify the infra-specific sequence conservation of the nucleotide sequence, sequences comparisons were performed on the 371-by amplicon from five unrelated 4o ATCC and clinical strains for each of 5 staphylococcal species; S. aureus, S.

epidermidis, S. haemolyticus, S. hominisand S. saprophyticus. Results showed a high level of conservation of nucleotide sequence between different unrelated strains from the same species. This sequence information allowed the development of staphylococcal species identification assays using species-specific internal probes hybridizing to the 371-by amplicon. In addition to the species-specific internal probes, the genus-specific internals probes were able to recognized most Staphylococcus species. These assays are specific and ubiquitous for those five staphylococcal species.
EXAMPLE 8:
Differentiating between the two closely related yeast species Candida albicans and Candida dubliniensis. It is often useful for the clinician to be able to differentiate between two very closely related species of microorganisms. Candida albicans is the most important cause of invasive human mycose. In the recent years, a very closely related species, Candida dubliniensis, was isolated in immunosuppressed patients.
These two species are difficult to distinguish by classic biochemical methods.
This example demonstrates the use of tuf sequences to differenciate Candida albicans and Candida dubliniensis. PCR primers TCa1528 and TCa1676 were selected for their ability to specifically amplify a tuf (elongation factor 1 alpha type) fragment from both species (see Annex XI for primer positions and previous patent application WO
98/20157 SEQ ID NO. 11-12). Within this tuf fragment, a region differentiating C.
albicans and C. dubliniensis by two nucleotides was selected and used to design two internal probes (see Annex IV for probe design, SEQ ID NO. 577 and 578) specific for each species. Amplification of genomic DNA from C. albicans and C.
dubliniensis was carried out using DIG-11-dUTP as described above in the section on luminescent detection of amplification products. Internal probes SEQ ID NO.

and 578 were immobilized on the bottom of individual microtiter plates and hybridization was carried out as described above in the above section on luminescent 3o detection of amplification products. Luminometer data showed that the amplicon from C. albicans hybridized only to probe SEQ ID NO. 577 while the amplicon from C. dubliniensis hybridized only to probe SEQ ID NO. 578, thereby demonstrating that each probes were species-specific.
EXAMPLE 9:
Specific identification of Entamoeba histolytica. Upon analysis of tuf (elongation factor 1 alpha) sequence data, it was possible to find four regions whereEntamoeba histolytica sequences remained conserved while other parasitical and eukaryotic 4o species have diverged. Primers TEntG38 (SEQ ID NO. 703), TEntG442 (SEQ ID

NO. 704), TEntG534 (SEQ ID NO. 705), and TEntG768 (SEQ ID NO. 706) were designed so that Entg3 8 could be paired with the three other primers.On PTC-thermocyclers (MJ Research), the cycling conditions for initial sensitivity and specificity testing were 3 min. at 94°C for initial denaturation, thenforty cycles of two steps consisting of 1 second at 95°C and 30 seconds at 55°C, followed by terminal extension at 72°C for 2 minutes. Amplification was monitored on agarose gel electrophoresis by staining the amplified DNA with ethidium bromide. The three primer pairs could detect the equivalent of less than 200 E. histolyticagenome copies.
Specificity was tested using 0.5 ng of purified genomic DNA from a panel of to microorganisms including Babesia bovis, Babesia microtti, Candida albicans, Crithidia fasciculata, Leishmania major, Leishmania hertigi and Neospora caninum.
Only E. histolytica DNA could be amplified. Thereby suggesting that the assay was species-specific.
EXAMPLE 10:
Sensitive identification of Chlamydia trachomatis. Upon analysis of tuf sequence data, it was possible to find two regions where Chlamydia trachomatis sequences remained conserved while other species have diverged. Primers Ctr82 (SEQ ID
NO.
554) and Ctr249 (SEQ ID NO. 555) were designed. With the PTC-200 thermocyclers (MJ Research), the optimal cycling conditions for maximum sensitivity and specificity were determined to be 3 min. at 94°C for initial denaturation, thenforty cycles of two steps consisting of 1 second at 95°C and 30 seconds at 60°C, followed by terminal extension at 72°C for 2 minutes. Amplification was monitored on agarose gel electrophoresis by staining the amplified DNA with ethidium bromide. The assay could detect the equivalent of 8 C. trachomatis genome copies. Specificity was tested on 0.1 ng of purified genomic DNA from a panel of microorganisms including 22 species commonly encountered in the vaginal flora (Bacillus subtilis, Bacteroides fragilis, Candida albicans, Clostridium difficile, Corynebacterium cervicis, 3o Corynebacterium urealyticum, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Fusobacterium nucleatum, Gardnerella vaginalis, Haemophilus influenzae, Klebsiella oxytoca, Lactobacillus acidophilus, Peptococcus niger, Peptostreptococcus prevotii, Porphyromonas asaccharolytica, Prevotella melaninogenica, Propionibacterium acnes, Staphylococcus aureus, Streptococcus acidominimus, and Streptococcus agalactiae). Only C. trachomatis DNA could be amplified. Thereby suggesting that the assay was species-specific.
EXAMPLE 11:

Genus-specific identification of Enterococci. Upon analysis of tuf sequence data and comparison with the repertory of tuf sequences, it was possible to find two regions where Enterococcus sequences remained conserved while other genera have diverged (Annex XVII). Primers Encg 313 (SEQ ID NO. 656) and Encg 596 (SEQ ID NO.
657) were tested for their specificity by using purified genomic DNA from a panel of bacteria listed in Table 10. Using the PTC-200 thermocyclers (MJ Research), the optimal cycling conditions for maximum sensitivity and specificity were determined to be 3 min. at 94°C for initial denaturation, thenforty cycles of two steps consisting of 1 second at 95°C and 30 seconds at 62°C, followed by terminal extension at 72°C
1 o for 2 minutes. Amplification was monitored on agarose gel electrophoresis by staining the amplified DNA with ethidium bromide. The 17 enterococcal species listed in Table 10 were all amplified. The only other species amplified were Abiotrophia adiacens and Gemella haemolysans, two Gram positive species. The sequence variation within the 306 by amplicon is sufficient so that nested PCR
or internal probes could be used to speciate the amplicon and differenciate enterococci from Abiotrophia adiacens and Gemella haemolysans. Sensitivity tested on several strains of the clinically important speciesE. casseliflavus, E. faecium, E.
faecalis, E.
flavescens and E. gallinarum ranged from 1 to 8 genome copies. A mismatch for all enterococcal species (except E. faecalis and E, solitarius) was introduced inadvertently in position 12 (C instead of G) of primer SEQ ID NO. 657.
Apparently, this mismatch did not significantly impaired the primer pair's sensitivity and specificity. Because of the known tolerance of PCR primers to mismatches in their middle, non-mismatch primer pair SEQ ID NO. 656 + SEQ ID NO. 271 should give specificity and sensitivity results similar to SEQ ID NO. 656 + SEQ ID NO.
657.
EXAMPLE 12:
Identification of the major bacterial platelets contaminants usingtuf sequences in a multiplex test. Blood platelets preparations need to be monitored for bacterial contaminations. The tuf sequences of 17 important bacterial contaminants of platelets were aligned. As shown in Annex XIX, analysis of these sequences allowed the design PCR primers. Since in the case of platelet contamination, detecting all species, not just the more frequently encountered ones is desirable, perfect specificity of primers was not an issue in the design. However, sensitivity is important.
That is why, to avoid having to put too much degeneracy, only the most frequent contaminants were included in primer design, knowing that the selected primers would anyway be able to amplify more species than the 17 used in the design.
Oligonucleotide sequences which are conserved in these 17 major bacterial contaminants of platelets were chosen (oligos Tplaq 769 and Tplaq 991, respectively 4o SEQ ID NO. 636 and 637) thereby permitting the detection of these bacterial species.

However, sensitivity was a bit deficient with staphylococci. To ensure maximal sensitivity in the detection of all the more frequent bacterial contaminants, a multiplex assay also including oligonucleotide primers targetting theStaphylococcus genera (oligos Stag 422, SEQ ID NO. 553; and Stag 765, SEQ ID NO. 575) was developed.
The primer pairs, oligos Tplaq 769 (SEQ ID NO. 636) and Tplaq 991 (SEQ ID NO.
637) that give an amplification product of 245 pb and oligos TStaG 422 (SEQ ID
NO. 553) and TStaG 765 (SEQ ID NO. 575) that give an amplification product of 368 pb, were used simultaneously in the multiplex PCR assay. Real-time detection of these PCR products was made on the LightCycler thermocycler (Idaho Technology) using SYBR~ Green I (Molecular Probe Inc.). SYBR~ Green I is a fluorescent dye that binds specifically to double-stranded DNA. It thus binds to DNA products as they are synthesized. The measure of SYBR°Green I fluorescence at the end of each elongation cycle indicates the amount of DNA duplex generated by specific DNA
fragment amplification and primer-dimer formation.
Real-time detection of PCR products with the LightCycler was carried out using 1.0 mM of both Tplaq primers (SEQ ID NO. 636-637) and 0.4 mM of both TStaG
2o primers (SEQ ID NO. 553 and 575), 2.5 mM MgCl2, BSA 500 mg/ml , dNTP 0.2 mM (Pharmacia), lOX PCR reaction buffer (Boerhinger Mannheim) and Taq DNA
polymerase (Boerhinger Mannheim) 0.025 U/ml combined with TaqStart 5 ng/ml (Clontech), and 0.7 ml of genomic DNA sample in a final volume of 7 ml. The optimal cycling conditions for maximum sensitivity were 1 minute at 94°C for initial denaturation, then forty-five cycles of three steps consisting of 0 second at 95°C, 5 seconds at 60°C and 9 seconds at 72°C. Amplification was monitored during each elongation cycle by measuring the level of SYBR~Green I. However, real analysis takes place after PCR. Melting curves are done for each sample and transformation of melting peak allows determination of Tm. Thus primer-dimer and specific PCR
3o product are discriminated. With this assay, all prominent bacterial contaminants of platelets listed in Annex XIX were detected. Sensitivity tests were performed on the 9 most frequent bacterial contaminants of platelets. The detection limit was less than 20 genome copies for E. cloacae, B. cereus, S. choleraesuis and S. marcescens;
less than 15 genome copies for P. aeruginosa; and 2 to 3 copies were detected for S.
aureus, S. epidermidis, E. coli and K. pneumoniae. Further refinements of assay conditions should increase sensitivity levels.
EXAMPLE 13:

The resolving power of the tuf and atpD sequences databases is comparable to the gold standard biochemical methods for bacterial identification. The present gold standard for bacterial identification is mainly based on key morphological traits and batteries of biochemical tests. Here we demonstrate that the use of tuf and atpD
sequences combined with simple phylogenetic analysis of databases formed by these sequences is comparable to the gold standard. In the process of acquiring data for the tuf sequences, we sequenced the tuf gene of a strain that was given to us labelled as Staphylococcus hominis ATCC 35982. That tuf sequence (SEQ ID NO: 192) was incorporated into the tuf sequences database and subjected to a basic phylogenic 1o analysis using the Pileup command from version 10 of the GCG package (Genetics Computer Group, inc.). This analysis indicated that SEQ ID NO: 192 is not associated with other S. hominis strains but rather with the S. warneri strains. The ATCC 35982 strain was sent to the reference laboratory of Laboratoire de Sante publique du Quebec (LSPQ). They used the classic gold standard identification scheme for staphylococci (Kloos and Schleifer, 1975., J. Clin. Microbiol.1:82-88).
Their results shown that although the colonial morphology could correspond toS.
hominis, the more precise biochemical assays did not. These assays included discriminant mannitol, mannose and ribose acidification tests as well as rapid and dense growth in deep thioglycolate agar. The LSPQ report identified strain ATCC
35982 as S. warneri which confirms our database analysis. The same thing happened for S. warneri (SEQ ID NO: 187) which had initially been identified as S.
haemolyticus by a routine clinical laboratory using a low resolving power automated system (MicroScan, AutoScan-4TM). Again, the tuf and LSPQ analysis agreed on its identification as S. warneri. In numerous other instances, in the course of acquiring tuf and atpD sequence data from various species and genera, analysis of our tuf and/or atpD sequence databases permitted the exact identification of mislabelled or erroneously identified strains. These results clearly demonstrate the usefulness and the high resolving power of our sequence-based identification assays using thetuf and atpD sequences databases.
Example 14:
Detection of group B streptococci in clinical specimens.
Introduction Streptococcus agalactiae, the group B streptococcus (GBS), is responsible for a severe illness affecting neonate infants. The bacterium is passed from the healthy carrier mother to the baby during delivery. To prevent this infection, it is recommended to treat expectant mothers susceptible of carrying GBS in their 4o anovaginal flora. Carrier status is often a transient condition and rigorous monitoring requires cultures and classic bacterial identification weeks before delivery.
To improve the diagnostic and identification of GBS we developped a rapid, specific and sensitive PCR test fast enought to be performed right at delivery.
Materials and Methods GBS Clinical Specimens. A total of 66 duplicate anovaginal swabs were collected from 41 consenting pregnant women admitted for delivery at the Centre Hospitalier Universitaire de Quebec, Pavilion Saint-Franrois d'Assise following the CDC recommendations. The samples were obtained either before or after rupture of 1o membranes. The swab samples were tested at the Centre de Recherche en Infectiologie de 1'Universite Laval within 24 hours of collection. Upon receipt, one swab was cut and then the tip of the swab was added to GNS selective broth for identification of group B streptococci (GBS) by the standard culture methods recommended by the Center for Diseases Control. The other swab was processed following the instruction of the IDI DNA extraction kit (Infectio Diagnotics (IDI) Inc.) prior to PCR amplification.
Oligonucleotides. PCR primers, Tsag340 (SEQ ID NO. 549) and Tsag552 (SEQ ID NO. 550) complementary to the regions of the tuf gene unique for GBS were designed based upon multiple sequence alignment using our repertory of tuf sequences. Oligo primer analysis software (version 5.0) (National Biosciences) was used to analyse primers annealing temperature, secondary structure potential as well as mispriming and dimerization potential. The primers were synthesized using a model 391 DNA synthesizer (Perkin-Elmer).
A pair of fluorescently labeled adjacent hybridization probes Sag465-F (SEQ ID
NO. 583) and Sag436-C (SEQ ID NO. 582) were synthesized and purified by Operon Technologies. They were designed to meet the recommendations of the manufacturer (Idaho Technology) and based upon multiple sequence alignment analysis using our repertory of tuf sequences to be specific and ubiquitous for GBS. These adjacent probes, which are separated by one nucleotide, allowing fluorescence resonance 3o energy transfer (FRET) to generate an increased fluorescence signal when both hybridized simultaneously to their target sequences. The probes Sag465-F was labeled with FITC in 3 prime while Sag436-C was labeled with Cy5 in 5 prime.
The Cy5-labeled probes contained a 3'-blocking phosphate group to prevent extension of the probes during the PCR reactions.
PCR Amplification. Conventional amplifications were performed either from 2 ~,l of a purified genomic DNA preparation or cell lysates of anovaginal specimens.
The 20-~1 PCR mixture contained 0.4 ~,M each GBS-specific primer (Sag465-F/Sag436), 200 wM each deoxyribonucleotide (Pharmacia Biotech), 10 mM Tris-HCl (pH 9.0), 50 mM KCI, 0.1% Triton X-100, 2.5 mM MgCl2, 3.3 mgml bovine serum albumin (BSA) (Sigma), and 0.5 U of Taq polymerase (Promega) combined with the TaqStart antibody (Clontech). The TaqStart antibody, which is a neutralizing monoclonal antibody of Taq DNA polymerise, was added to all PCR reactions to enhance the efficiency of the amplification. The PCR mixtures were subjected to thermal cycling (3 min at 95°C and then 40 cycles of 1 s at 95°C, and 30 s at 62°C
with a 2-min final extension at 72°C) with a PTC-200 DNA Engine thermocycler (MJ
research). The PCR-amplified reaction mixture was resolved by agarose gel electrophoresis.
The LightCyclerTM PCR amplifications were performed with 1 ~1 of the same preparation as described above. The 101 amplification mixture consisted of 0.4 wM
1o each GBS-specific primer (Sag465-F/Sag436), 200 ~M each dNTP, 0.2 wM each fluorescently labeled probe (Sag465-F and Sag436-C), 300~,gim1 BSA (Sigma), and 1 wl of 1 Ox PC2 buffer (containing 50 mM Tris-HCl (pH 9.1 ), 16 mM ammonium sulfate, 3.5 mM Mg2+, and 150 ~giml BSA) and 0.5 U KlenTaqlTM (AB Peptides) coupled with TaqStartTM antibody (Clontech). KlenTaq 1 TM is a highly active and more heat-stable DNA polymerise without 5'-exonuclease activity. This prevents hydrolysis of hybridized probes by the 5' to 3' exonuclease activity. A volume of 7~1 of the PCR mixture was transferred into a composite capillary tube (Idaho Technology). The tubes were then centrifuged to move the reaction mixture to the tips of the capillaries and then cleaned with optical-grade methanol.
Subsequently the 2o capillaries were loaded into the carousel of a LC32 LightCycler''M (Idaho Technology), an instruments that combine rapid-cycle PCR with fluorescence analysis for continuous monitoring during amplification. The PCR reaction mixtures were subjected to a denaturation step at 9~C for 3 min followed by 45 cycles of 0 s at 94~C, 20 s at 64°C and 10 s at 72°C with a temperature transition rate of 2(~Cis.
Fluorescence signals were obtained at each cycle by sequentially positioning each capillary on the carousel at the focus of optics affiliated to the built-in fluorimeter for 100 millisecond. Complete amplification and analysis required about 35 min.
Specificity And Sensitivity Tests. The specificity of the conventional and LightCyclerTM PCR assay was verified by using purified genomic DNA (0.1 ng/reaction) from a battery of ATCC reference strains representing 35 clinically relevent gram-positive species (Abiotrophia defectivaATCC 49176, Bifidobacterium breve ATCC 15700, Clostridium difficileATCC 9689, Corynebacterium urealyticum ATCC 43042, Enterococcus casseliflavusATCC 25788, Enterococcus durans ATCC
19432, Enterococcus faecalis ATCC 29212, Enterococcus faecium ATCC 19434, Enterococcus gallinarum ATCC 49573, Enterococcus raffinosus ATCC 49427, Lactobacillus reuteri ATCC 23273, Lactococcus lactis ATCC 19435, Listeria monocytogenes ATCC 15313, Peptococcus niger ATCC 27731, Peptostreptococcus anaerobius ATCC 27337, Peptostreptococcus prevotii ATCC 9321, Staphylococcus aureus ATCC 25923, Staphylococcus epidermidis ATCC 14990, Staphylococcus haemolyticus ATCC 29970, Staphylococcus saprophyticus ATCC 15305, Streptococcus agalactiae ATCC 27591, Streptococcus anginosus ATCC 33397, Streptococcus bovis ATCC 33317, Streptococcus constellatus ATCC 27823, Streptococcus dysgalactiae ATCC 43078, Streptococcus gordonii ATCC 10558, Streptococcus mitis ATCC 33399, Streptococcus mutans ATCC 25175, Streptococcus oralis ATCC 35037, Streptococcus parauberis ATCC 6631, Streptococcus pneumoniae ATCC 6303, Streptococcus pyogenes ATCC 19615, Streptococcus salivarius ATCC 7073, Streptococcus sanguis ATCC 10556, Streptococcus uberis ATCC 19436). These microbial species included 15 species of streptococci and many members of the normal vaginal and anal floras. In addition, 40 l0 GBS isolates of human origins confirm by Latex agglutination test (Streptex, Murex) were also used to evaluate the ubiquity of the assay.
For determination of the sensitivities (i.e., the minimal number of genome copies that could be detected) for conventional and LightCyclerTM PCR assays, serial

10-fold or 2-fold dilutions of purified genomic DNA from 5 GBS ATCC strains were used.
Results Evaluation of the GBS-specific conventional and LightCyclerTM PCR assay.
The specificity of the two assays demonstrated that only DNAs from GBS strains could be amplified. Both PCR assays did not amplify DNAs from any other bacterial 2o species tested including 14 streptococcal species other than GBS as well as phylogenetically related species belonging to the genus Enterococcus, Peptostreptococcus andLactococcus. Important members of the vaginal or anal flora, including coagulase-negative staphylococci,Lactobacillus spp., and Bacteriodes spp.
were also negative with the GBS-specific PCR assay. The LightCyclerTM PCR
assays detected only GBS DNA by producing an increased fluorescence signal which was interpreted as a positive PCR result. Both PCR methods were able to amplify all of 40 GBS clinical isolates, showing a perfect correlation with the phenotypic identification methods.
The sensitivity of the assay was determined by using purified genomic DNA
from the 5 ATCC strains of GBS. The detection limit for all of these 5 strains was one genome copy of GBS. The detection limit of the assay with the LightCyclerTM
was 3.5 fg of genomic DNA (corresponding to 1-2 genome copies of GBS). These results confirmed the high sensitivity of our GBS-specific PCR assay.
Direct Detection of GBS from anovaginal specimens. Among 66 anovaginal specimens tested, 12 were positive for GBS by culture. 11 of them were also identified by both PCR assays. The sensitivity of both PCR methods with vaginal/anal specimens for identifying colonization status in pregnant women at delivery was 91.7% when compared to culture results. Specificity and positive predictive value were both 100% and negative predictive value was 97.8%. The time for obtaining results was approximately 50 min for LightCyclerTM PCR, approximately 100 min for conventional PCR and 48 hours for culture.
Conclusion We have developed two PCR assays (conventional and LightCyclerTM) for the detection of GBS which are specific (i.e., no amplification of DNA from a variety of bacterial species other than GBS) and sensitive (i.e., able to detect around 1 genome copy for several reference ATCC strains of GBS). Both PCR assays are able to detect GBS directly from anovaginal specimens in a very short turnaround time. Using the 1o real-time PCR assay on LightCyclerTM, we can detect GBS carriage in pregnant women at delivery within 50 minutes.
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.

Table 1. Distribution (%) of nosocomial pathogens for various human infections in USA
(1990-1992) .
Pathogen UTIz SS13 BS14 Pneumonia CSFS

Escherichia coli 27 9 5 4 2 Staphylococcus aureus 2 21 17 21 2 Staphylococcus epidermidis2 6 20 0 1 Enterococcus faecalis 16 12 9 2 0 Enterococcus faecium 1 1 0 0 0 Pseudomonas aeruginosa 12 9 3 18 0 Klebsiella pneumoniae 7 3 4 9 0 Proteus mirabilis 5 3 1 2 0 Streptococcus pneumoniae0 0 3 1 18 Group B Streptococci 1 1 2 1 6 Other Streptococci 3 5 2 1 3 Haemophilus influenzae 0 0 0 6 45 Neisseria meningitides 0 0 0 0 14 Listeria monocytogenes 0 0 0 0 3 Other Enterococci 1 1 0 0 0 Other Staphylococci 2 8 13 2 0 Candida albicans 9 3 5 5 0 Other Candida 2 1 3 1 0 Enterobacter spp. 5 7 4 12 2 Acinetobacter spp. 1 1 2 4 2 Citrobacter spp. 2 1 1 1 0 Serratia marcescens 1 1 1 3 1 Other Klebsiella 1 1 1 2 1 Others 0 6 4 5 0 Data recorded by the osocomial rveillance National N Infections (NNIS) Su from 80 hospitals (Emori and Gaynes, 1993, Clin.
Microbiol. Rev., 6:428-442).

z Urinary tract infection.

3 Surgical site infection.

Bloodstream infection.

s Cerebrospinal fluid.

Table 2. Distribution (%) of bloodstream infection pathogens in Quebec (1995), Canada (1992), UK (1969-1988) and USA (1990-1992).
Organism Quebec Canada2 UK3 USA4 Community- Hospital-Hospital-acquired acquiredacquired E. coli 15.6 53.8 24.8 20.3 5.0 S. epidermidis and s other CONS 25.8 - 0.5 7.2 31.0 S. aureus 9.6 - 9.7 19.4 16.0 S. pneumoniae 6.3 - 22.5 2.2 -E. faecalis 3.0 - 1.0 4.2 -E. faecium 2.6 - 0.2 0.5 -Enterococcus spp. - - - - g,0 H. influenzae 1.5 - 3.4 0.4 -P. aeruginosa 1.5 8.2 1.0 8.2 3.0 K. pneumoniae 3.0 11.2 3.0 9.2 4.0 P. mirabilis - 3.9 2.8 5.3 1.0 S. pyogenes - - 1.9 0.9 Enterobacter spp. 4.1 5.5 0.5 2.3 4.0 Candida spp. 8.5 - - 1.0 8.0 Others 18.5 17.4 28.7 18.9 19.0 Data obtained for 270 isolates collected at the Centre Hospitalier de I'Universite Laval (CHUL) during a 5 month period (May to October 1995).

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

3 Data from a 20-year study (1969-1988)0 isolates. 90, J. Antimicrob.
for nearly 400 (Eykyn et al., Chemother., Suppl. C, 25:41-58).

Data recorded by the National Nosocomial Infections Surveillance (NNIS) from 80 hospitals (Emori and Gaynes, 1993, Clin. Microbiol.
Rev., 6:428-442).

Coagulase-negative staphylococci.

Table 3. Distribution of positive and negative clinical specimens tested at the microbiology laboratory of the CHUL (February 1994 - January 1995).
Clinical specimens No. of samples % of positive % of negative and/or sites tested (%) specimens specimens Urine 17,981 (54.5) 19.4 80.6 Blood culture/marrow 10,010 (30.4) 6.9 93.1 Sputum 1,266 (3.8) 68.4 31.6 Superficial pus 1,136 (3.5) 72.3 27.7 Cerebrospinal fluid 553 (1.7) 1.0 99.0 Synovial fluid 523 (1.6) 2.7 97.3 Respiratory tract 502 (1.5) 56.6 43.4 Deep pus 473 (1.4) 56.8 43.2 Ears 289 (0.9) 47.1 52.9 Pleural and pericardial 132 (0.4) 1.0 99.0 fluid Peritoneal fluid 101 (0.3) 28.6 71.4 Total: 32,966 (100.0) 20.0 80.0 Table 4. Non limitating example of microbial species for which atpD andlor tut and/or recA
sequences are used in the present invention Bacterial species Achromobacter xylosoxidans subsp. Chlamydia trachomatis denitrificans Acetobacterium woodi Chlorobium vibrioforme Acetobacter aceti 65 Chlorotlexus aurantiacus Acetobacter altoacetigenes Chryseobacterium meningosepficum Acetobacter polyoxogenes Citrobacter amalonaticus Acholeplasma laidlawii Citrobacter braakii Acidiphilum facilis Citrobacter farmeri Acinetobacter baumannii 70 Citrobacter freundii Acinetobacter calcoaceticus Citrobacter koseri Acinetobacter Iwoffii Citrobacter sedlakii Actinomyces meyeri Citrobacter werkmanii Aerococcus viridans Citrobacter youngae Aeromonas salmonicida 75 Clostridium acefobutylicum Agrobacterium tumefaciens Clostridium beijerincki Alcaligenes faecalis Clostridium bifermentans Allochromatium vinosum Clostridium botulinum Anabaena variabilis Clostridium difticile Anacystis nidulans 80 Clostridium innocuum Anaerorhabdus furcosus Clostridium histolyticum Aquifex aeolicus Clostridium novyi Aquifex pyrophilus Clostridium septicum Azotobacter vinelandii Clostridium perfringens Bacillus anthracis 85 Clostridium ramosum Bacillus caldotenax Clostridium sordellii Bacillus cereus Clostridium fertium Bacillus firmus Clostridium tetani Bacillus halodurans Comamonas acidovorans Bacillus megaterium 90 Corynebacterium bovis Bacillus stearothermophilus Corynebacterium cervicis Bacillus subtilis Corynebacterium diphtheriae Bacteroides distasonis Corynebacterium flavescens Bacteroides fragilis Corynebacterium glutamicum Bacteroides ovatus 95 Corynebacterium kutscheri Bacteroides vulgatus Corynebacterium minutissimum Bartonella henselae Corynebacterium mycetoides Bi>idobacterium adolescentis Corynebacterium pseudodiphtheriticum Bifidobacterium breve Corynebacterium pseudogenitalium Bifidobacterium denfium 100 Corynebacterium pseudotuberculosis Bi~dobacterium longum Corynebacterium renale Blastochloris viridis Corynebacterium ulcerans Borrelia burgdorferi Corynebacterium urealyticum Bordetella pertussis Corynebacterium xerosis Bordetella bronchiseptica 105 Coxiella burnetii Branhamella catarrhalis Cytophaga lytica Brucella abon'us Deinococcus radiodurans Brevibacterium linens Deinonema spp.

Brevibacterium flavum Edwardsiella hoshinae Buchnera aphidicola 110 Edwardsiella tarda Burkholderia cepacia Ehrlichia canis S Burkholderia mallei Ehrlichia risticii Burkholderia pseudomallei Eikenella corrodens Campylobacter jejuni Enterobacter aerogenes Cedecea davisae 115 Enterobacter agglomerans Cedecea lapagei Enterobacter amnigenus Cedecea neteri Enterobacter asburiae Chlamydia pneumoniae Enterobacter cancerogenus Chlamydia psittaci Enterobacter cloacae Table 4. Non limitating example of microbial species for which atpD andlor tut andlor recA
sequences are used in the present invention (continued) Bacterial species (continued) Enterobacter gergoviae Herpetoshiphon aurantiacus Enterobacter hormaechei 65 Kingella kingae Enterobacter sakazakii Klebsiella ornithinolytica Enterococcus avium Klebsiella oxytoca Enterococcus casseliflavus Klebsiella planticola Enterococcus cecorum Klebsiella pneumoniae subsp.
ozaenae Enterococcus dispar 70 Klebsiella pneumoniae subsp.
pneumoniae Enterococcus durans Klebsiella pneumoniae subsp.
rhinoscleromatis Enterococcus faecalis Kluyvera ascorbata Enterococcus faecium Kluyvera cryocrescens Enterococcus flavescens Kluyvera georgiana Enferococcus gallinarum 75 Lactobacillus acidophilus Enterococcus hirae Lactobacillus garvieae Enterococcus malodoratus Lactobacillus paracasei Enterococcus mundtii Lactobacillus casei subsp.
casei Enterococcus pseudoavium Lactococcus lactis subsp. lactis Enterococcus ra~nosus 80 Leclercia adecarboxylata Enterococcus saccharolyticus Legionella micdadei Enterococcus solitarius Legionella pneumophila subsp.
pneumophila Enferococcus sulfureus Leminorella grimontii Erwinia carotovora Leminorella richardii Escherichia coli 85 Lepfospira biflexa Escherichia fergusonii Lepfospira interrogans Escherichia hermannii Listeria monocytogenes Escherichia vulneris Magnetospirillum magnetotacticum Eubacterium lentum Megamonas hypermegale Eubacterium nodatum 90 Methanobacterium thermoautotrophicum Ewingella americana Methanococcus jannaschii Francisella tularensis Methanococcus vannielii Frankia alni Methanosarcina barkeri Fervidobacterium islandicum Mefhanosarcina jannaschii Fibrobacter succinogenes 95 Methylobacillus flagellatum Flavobacterium ferrigeneum Methylomonas clara Flexistipes sinusarabici Micrococcus luteus Fusobacterium gonidiaformans Micrococcus lylae Fusobacterium necrophorum subsp. Mifsuokella multacida necrophorum Fusobacterium nucleatum subsp. 100 Mobiluncus curtisii subsp.
polymorphum holmesii Gardnerella vaginalis Moellerella thermoacetica Gemella haemolysans Moellerella rvisconsensis Gemella morbillorum Moraxella osloensis Gloeobacter violaceus Morganella morganii subsp.
morganii Gloeothece spp. 105 Mycobacterium avium Gluconobacter oxydans Mycobacterium bovis SO Haemophilus actinomycetemcomitans Mycobacterium leprae Haemophilus aphrophilus Mycobacterium fuberculosis Haemophilus ducreyi Mycoplasma capricolum Haemophilus haemolyticus 110 Mycoplasma gallisepticum Haemophilus influenzae Mycoplasma genitalium Haemophilus parahaemolyticus Mycoplasma hominis Haemophilus parainfluenzae Mycoplasma pirum Haemophilus paraphrophilus Mycoplasma mycetoides Haemophilus segnis 115 Mycoplasma pneumoniae Hafnia alvei Mycoplasma pulmonis Haloarcula marismortui Mycoplasma salivarium Halobacterium salinarum Myxococcus xanthus Haloferax volcanii Neisseria animalis Helicobacter pylori 120 Neisseria canis Table 4. Non limitating example of microbial species for which atpD andlor tuf andlor recA
sequences are used in the present invention (continued) Bacterial species (continued) Neisseria cinerea Salmonella choleraesuis subsp choleraesuis Neisseria cuniculi 65 Salmonella choleraesuis subsp.
diarizonae Neisseria elongafa subsp. elongata Salmonella choleraesuis subsp.
houtenae 10Neisseria elongata subsp. intermedia Salmonella choleraesuiriai~ima Neisseria flavescens Salmonella choleraesuis subsp.
salamae Neisseria gonorrhoeae Serpulina hyodysenteriae Neisseria lactamica 70 Serratia ficaria Neisseria meningitides Serratia fonticola 15Neisseria mucosa Serratia grimesii Neisseria perflava Serratia liquefaciens Neisseria pharynges Serratia marcescens Neisseria polysaccharea 75 Serratia odorifera Neisseria sicca Serratia plymuthica 20Neisseria subflava Serratia rubidaea Neisseria weaveri Shewanella putida Ochrobactrum anthropi Shewanella putrefaciens Pantoea agglomerans 80 Shigella boydii Panfoea dispersa Shigella dysenferiae 25Paracoccus denitrificans Shigella flexneri Pasteurella multocida Shigella sonnei Pectinatus frisingensis Spirochaeta aurantia Peptococcus niger 85 Staphylococcus aureus Peptostrepfococcus anaerobius Staphylococcus auricularis 30Peptostreptococcus asaccharolyticus Staphylococcus capitis subsp.
capitis Pepfostreptococcus prevotii Staphylococcus caseolyticus Phormidium ectocarpi Staphylococcus cohnii Pirellula marina 90 Staphylococcus epidermidis Planobispora roses Staphylococcus haemolyficus 35Plectonema boryanum Staphylococcus hominis Porphyromonas asaccharolytica Staphylococcus lugdunensis Porphyromonas gingivalis Staphylococcus saprophyticus Pragia fonfium 95 Staphylococcus sciuri subsp.
sciuri Prevotella melaninogenica Staphylococcus simulans 40Prevotella oralis Staphylococcus warneri Prevotella ruminocola Stigmatella aurantiaca Prochlorofhrix hollandica Stenotrophomonas maltophilia Propionibacterium acnes 100 Streptococcus acidominimus Propionigenium modestum Streptococcus agalactiae 45Proteus mirabilis Streptococcus anginosus Proteus penneri Streptococcus bovis Proteus vulgaris Streptococcus cricetus Providencia alcalifaciens 105 Streptococcus crisfatus Providencia retfgeri Streptococcus downei 50Providencia rustigianii Streptococcus dysgalacfiae Providencia stuartii Streptococcus equi subsp.
equi Pseudomonas aeruginosa Streptococcus ferus Pseudomonas fluorescens 110 Streptococcus gordonii Pseudomonas stutzeri Streptococcus macacae 55Psychrobacter phenylpyruvicus Streptococcus mutans Rahnella aquatilis Streptococcus oralis Rickettsia prowazekii Streptococcus parasanguinis Rhodobacfer capsulatus 115 Streptococcus pneumoniae Rhodobacter sphaerolides Streptococcus pyogenes 60Rhodospirillum rubrum Streptococcus rafti Ruminococcus albus Streptococcus salivarius Salmonella bongori Streptococcus salivarius subsp.
thermophilus Salmonella choleraesuis subsp.120 Streptococcus sanguinis arizonae Table 4. Non limitating example of microbial species for which atpD and/or tuf andlor recA
sequences are used in the present invention (continued) Bacterial species (continued) Streptococcus sobrinus Trabulsiella guamensis Streptococcus suis 30 Treponema pallidum Streptococcus uberis Streptococcus vestibularis Ureaplasma urealyticum Streptomyces anbofaciens Veillonella parvula Streptomyces aureofaciens Vibrio alginolyticus Streptomyces cinnamoneus Vibrio anguillarum Streptomyces coelicolor 35 Vibrio cholerae Streptomyces collinus INolinella succinogenes Streptomyces lividans Xanthomonas citri Streptomyces ramocissimus Xanthomonas oryzae Streptomyces rimosus Xenorhabdus bovieni Streptomyces venezuelae 40 Xenorhabdus nematophilus Synechococcus spp. Yersinia bercovieri Synechocystis spp. Yersinia enterocolitica Tatumella pfyseos Yersinia frederikensii Taxeobacter occealus Yersinia intermedia Thermoplasma acidophilum 45 Yersinia pestis Thermotoga maritime Yersinia pseudotuberculosis Thermus aquaticus Yersinia rohdei Thermus thermophilus Yokenella regensburgei Thiobacillus cuprinus Zoogloea ramigera Thiobacillus ferrooxydans Fungal species Absidia corymbifera 85 Coccidioides immifis Absidia glauca Coprinus cinereus 55Alternaria alternate Cryptococcus albidus Arxula adeninivorans Cryptococcus neoformans Aspergillus oryzae Cunninghamella bertholletiae Aspergillus flavus 90 Curvularia lunata Aspergillus fumigatus Emericella nidulans 60Aspergillus niger Exophiala jeanselmei Aureobasidium pullulans Eremothecium gossypii Bipolaris hawaiiensis Fonsecaea pedrosoi Blastoschizomyces capitatus95 Fusarium oxysporum Candida albicans Geotrichum spp.

65Candida catenulata Histoplasma capsulatum Candida dubliniensis Issatchenkia orientalis kudrjanzev Candida famata Kluyveromyces lactis Candida glabrata 100 Malassezia furfur Candida guilliermondii Malassezia pachydermafis 70Candida haemulonii Malbranchea filamentosa Candida inconspicua Metschnikowia pulcherrima Candida kefyr Microsporum audouinii Candida krusei 105 Mucor circinelloides Candida lambica Neurospora crassa 75Candida lusitaniae Paecilomyces lilacinus Candida norvegensis Paracoccidioides brasiliensis Candida parapsilosis Penicillium marneffei Candida rugosa 110 Phialaphora verrucosa Candida sphaerica Pichia anomala 80Candida tropicalis Piedraia hortai Candida utilis Podospora anserina Candida viswanathii Puccinia graminis Candida zeylanoides 115 Pseudallescheria boydii Cladophialophora carrionii Rhizomucor racemosus Table 4. Non limitating example of microbial species for which atpD and/or tuf andlor recA
sequences are used in the present invention (continued) Fungal species (continued) Rhizopus oryzae Syncephalastrum racemosum Rhodotorula minuta Trichoderma reesei Rhodotorula mucilaginosa Saccharomyces cerevisiae Trichophyton mentagrophytes Saksenaea vasiformis Trichophyton tonsurans Schizosaccharomyces pombe 20 Trichosporon cutaneum Scopulariopsis koningii Ustilago maydis Sporobolomyces salmonicolor Wangiella dermatitidis Sporothrix schenckii Yarrorvia lipolytica 1 S Stephanoascus ciferrii 25 Parasitical species Babesia bigemina Leishmania hertigi subsp. hertigi Babesia bovis 45 Leishmania major Babesia microtti Leishmania mexicana 30 Blastocystis hominis Leishmania tarentolae Crithidia fasciculata Leishmania tropica Cryptosporidium parvum Neospora caninum Entamoeba histolytica 50 Onchocerca volvulus Giardia lamblia Plasmodium berghei 35 Kentrophoros spp. Plasmodium falciparum Leishmania aethiopica Plasmodium knowlesi Leishmania amazonensis Porphyra purpurea Leishmania braziliensis 55 Toxoplasma gondii Leishmania donovani subsp. donovaniTreponema pallidum 40 Leishmania donovani subsp. Trichomonas vaginalis infantum Leishmania enriettii Trypanosoma brucei subsp. brucei Leishmania gerbilli Trypanosoma congolense Leishmania guyanensis 60 Trypanosoma cruzi Table 5. Antibiotic resistance genes selected for diagnostic purposes Genes Antibiotics Bacterial ACCESSION SEQ ID
NO. NO.

(genes) aac(3)-lb 2 AminoglycosidesEnterobacteriaceaeL06157 Pseudomonads aac(3)-Ilb AminoglycosidesEnterobacteriaceae,M97172 Pseudomonads aac(3)-!Va AminoglycosidesEnterobacteriaceaeX01385 aac(3)-Vla AminoglycosidesEnterobacteriaceae,M88012 Pseudomonads aac(2)-1a 2 AminoglycosidesEnterobacteriaceae,X04555 Pseudomonads aac(6')-aph(2')AminoglycosidesEnterococcus spp., 83-86 Staphylococcus spp.

aac(6)-la, AminoglycosidesEnterobacteriaceae,M18967 Pseudomonads aac(6)-Ic 2 AminoglycosidesEnterobacteriaceae,M94066 Pseudomonads aac(6')-lla AminoglycosidesPseudomonads 112 4 aad8 [ant(2')-laAminoglycosidesEnterobacteriaceae 53-54 2] 3 aacC1 (aac(3)-laAminoglycosidesPseudomonads 55-56 2] 3 aacC2 [aac(3)-IlaAminoglycosidesPseudomonads 57-58 2] 3 aacC3 [aac(3)-IIIAminoglycosidesPseudomonads 59-60 2] 3 aacA4 [aac(6)-IbAminoglycosidesPseudomonads 65-66 2] 3 ant(3')-la AminoglycosidesEnterobacteriaceae,X02340 Enterococcus spp.,M10241 Staphylococcus spp.

anf(4')-la AminoglycosidesStaphylococcus V01282 2 spp.

aph(3)-la 2 AminoglycosidesEnterobacteriaceae,J01839 Pseudomonads aph(3)-Ila AminoglycosidesEnterobacteriaceae,V00618 Pseudomonads aph(3)-Ills AminoglycosidesEnterococcus spp.,V01547 Staphylococcus spp.

aph(3)-Vla AminoglycosidesEnterobacteriaceae,X07753 Pseudomonads rrs 2 StreptomycinM. tuberculosis L15307 rpsL 2 StreptomycinM. tuberculosis, X80120 M. avium complex U14749 bIaOXA 5'6 f~-lactams Enterobacteriaceae, 110 4 Pseudomonads bIaR08 5 f3-lactams Haemophilus spp. 45-48 Pasteurella spp.

bIaSL.IV 5'6 f3-lactams Enferobacteriacea, 41-44 Pseudomonas aeruginosa bIaTEM 5'6 f3-lactams Enterobacteriaceae, 37-40 Neisseria spp., Haemophilus spp.

bIaCARB 5 f3-lactams Pseudomodas spp.,J05162 EnterobacteriaceaeS46063 Table Antibiotic 5. resistance genes selected for diagnostic purposes (continued) Genes Antibiotics Bacterial ACCESSION NO. SEQ
ID
NO.

(genes) blaC~ f3-lactams Enterobacteriaceae X92506 blaC~ f3-lactams Enterobacteriaceae X92507 bIaCMY f3-lactams Enterobacteriaceae X91840 blapER-15f3-lactams Enterobacteriaceae, 221957 Pseudomodanaceae bIapER-27f3-lactams Enterobacteriaceae X93314 blalMp f3-lactams Enterobacteriaceae, AJ223604 Pseudomonas aeruginosa blaZ 12 f3-lactams Enterococcus spp., 111 Staphylococcus spp.

mecA 12 f3-lactams Staphylococcus spp. 97-9g penA 13 f3-lactams Neisseria gonorrhoeaeX54021 pbpla f3-lactams Streptococcus pneumoniaeM90527 xs786s pbp2b f3-lactams Streptococcus pneumoniaeX16022 U2oo72 Table Antibiotic resistance 5. genes selected for diagnostic purposes (continued) Genes Antibiotics Bacterial ACCESSION NO. SEO
ID
NO.

(genes) pbp2b (3-lactams Streptococcus pneumoniae020083 U2ooso pbp2x f3-lactams Streptococcus pneumoniaeX16367 ABO112oo int a -lactams, Enterobacteriaceae, 99-102 trimethoprim sul aminoglycosides, Pseudomonads 103-106 antiseptic, chloramphenicol ermA Macrolides, Staphylococcus 113 14 spp. 4 lincosamides, streptogramin B

erm8 Macrolides, Enferobacferiaceae, 114 Sfaphylococcus spp.

lincosamides, Enterococcus spp.

streptogramin B Sfreptococcus spp.

Table 5. Antibiotic resistance genes selected for diagnostic purposes (continued) Genes Antibiotics Bacterial ACCESSION NO. SEQ ID
NO.

(genes) ermC 14 Macrolides, Enferobacteriaceae, 115 4 lincosamides,Sfaphylococcus spp.

streptogramin B

ereA 12 Macrolides Enterobacteriaceae,M11277 Staphylococcus spp.

ere812 Macrolides EnterobacteriaceaeA15097 Staphylococcus spp.

15msrA 12 Macrolides Staphylococcus 77-80 spp. 3 mtr 8 Macrolides Neisseria gonorrhoeaeS42418 mefA, mefE Macrolides Streptococcus U70055 8 spp.

30mphA 8 Macrolides Enterobacferiaceae,D16251 Sfaphylococcus spp.

IinAlIinA' Lincosamides Staphylococcus J03947 9 spp.

IinB 10 Lincosamides Enterococcus faeciumAF110130 35rrna 11 Macrolides Mycobacterium U74494 avium complex vga 15 StreptrograminStaphylococcus 89-90 spp. 3 vgb 15 StreptrograminStaphylococcus M36022 spp.

vat 15 StreptrograminStaphylococcus 87-88 spp. 3 40vat8 15 StreptrograminStaphylococcus U19456 spp.

satA 15 StreptrograminEnferococcus faecium 81-82 ileS 12 Mupirocin Staphylococcus X74219 aureus mupA 12 Mupirocin Staphylococcus X75439 aureus 45gyrA 16 Quinolones Gram positive X95718 and gram-negative X06744 bacteria parClgrIA Quinolones Gram-positive AB005036 16 and gram-negative AF056287 bacteria Table 5. Antibiotic resistance genes selected for diagnostic purposes (continued) Genes Antibiotics Bacterial ACCESSION SEQ ID NO.
NO.

(genes) parElgrlB Quinolones Gram-positive bacteriaX95717 norA 16 Quinolones Staphylococcus D90119 spp.

mexR (nalB) Quinolones Pseudomonas aeruginosa023763 nfxB 16 Quinolones Pseudomonas aeruginosaX65646 cat 12 ChloramphenicolGram-positive and M55620 gram-negative bacteriaX15100 Ms2822 rpo8 17 Rifampin Mycobacterium tuberculosisAF055891 inhA 17 Isoniazid Mycobacterium tuberculosisAF106077 35kafG 17 Isoniazid Mycobacterium tuberculosis040593 ahpC 17 Isoniazid Mycobacterium tuberculosis043812 embB 17 Ethambutol Mycobacterium tuberculosis068480 pncA 17 Pyrazinamide Mycobacterium tuberculosis059967 50vanA 12 Vancomycin Enterococcus spp. 67-70 3 vanB 12 Vancomycin Enferococcus spp. 116 4 vanC1 12 Vancomycin Enterococcus gallinarum 117 4 vanC212 Vancomycin Enferococcus casseliflavus094521 Table 5. Antibiotic resistance genes selected for diagnostic purposes (continued) Genes Antibiotics Bacterial ACCESSION NO. SEO ID NO.
(genes) vanC3 12 Vancomycin Enterococcus flavescensL29639 vanD 18 Vancomycin Enterococcus faeciumAF130997 10tet8 19 Tetracycline Gram-negative bacteriaJ01830 tetM 19 Tetracycline Gram-negative and X52632 gram-positive bacteria sulll 20 Sulfonamides Gram-negative bacteriaD37827 dhfrla 20 Trimethoprim Gram-negative bacteriaAJ238350 dhfrlb 20 Trimethoprim Gram-negative bacteria250805 dhfrV 20 Trimethoprim Gram-negative bacteriaX12868 dhfrVll Trimethoprim Gram-negative bacteriaU31119 dhfrV11120 Trimethoprim Gram-negative bacteriaU10186 dhfrlX 20 Trimethoprim Gram-negative bacteriaX57730 25dhfrXll Trimethoprim Gram-negative bacteria221672 dfrA 20 Trimethoprim Staphylococcus spp.AF045472 1 Bacteria having high incidence for the specified antibiotic resistance gene.
The presence of the antibiotic resistance genes in other bacteria is not excluded.
2 Shaw, K. J., P. N. Rather, R. S. Hare, and G. H. Miller. 1993. Molecular genetics of aminoglycoside resistance genes and familial relationships of the aminoglycoside-modifying enzymes. Microbiol. Rev.
57:138-163.
3 Antibiotic resistance genes from our co-pending US (N.S. 08/526840) and PCT
(PCT/CA/95/00528) patent applications for which we have selected PCR primer pairs.
4 These SEQ ID NO. refer to a previous patent (application WO 98/20157).
5 Bush, K., G.A. Jacoby and A. Medeiros. 1995. A functional classification scheme for f3-lactamase and its correlation with molecular structure. Antimicrob. Agents. Chemother. 39:1211-1233.
6 Nucleotide mutations in bIaSHV, bIaTEM, and bIaOXA, are associated with extended-spectrum f3-lactamase or inhibitor-resistant f3-lactamase.
7 Bauerfeind, A., Y. Chong, and K. Lee. 1998. Plasmid-encoded AmpC beta-lactamases: how far have we gone 10 ears after discovery? Yonsei Med. J. 39:520-525.
8 Sutcliffe, J., T. Grebe, A. Tait-Kamradt, and L. Wondrack. 1996. Detection of erythromycin-resistant determinants by PCR. Antimicrob. Agent Chemother. 40:2562-2566.
9 Leclerc, R., A., Brisson-Noel, J. Duval, and P. Courvalin. 1991. Phenotypic expression and genetic heterogeneity of lincosamide inactivation in Staphylococcus spp. Antimicrob.
Agents. Chemother.
31:1887-1891.
10 gozdogan, B., L. Berrezouga, M.-S. Kuo, D. A. Yurek, K. A. Farley, B. J.
Stockman, and R. Leclercq.
1999. A new gene, IinB, conferring resistance to lincosamides by nucleotidylation in Enterococcus faecium HM1025. Antimicrob. Agents. Chemother. 43:925-929.

11 Cockerill III, F.R. 1999. Genetic methods for assessing antimicrobial resistance. Antimicrob. Agents.
Chemother. 43:199-212

12 Tenover, F. C., T. Popovic, and O Olsvik. 1996. Genetic methods for detecting antibacterial resistance genes. pp. 1368-1378. In Murray, P. R., E. J. Baron, M. A. Pfaller, F. C.
Tenover, R. H. Yolken (eds).
Manual of clinical microbiology. 6th ed., ASM Press, Washington, D.C. USA

13 powson, C. G., T. J. Tracey, and B. G. Spratt. 1994. Origin and molecular epidemiology of penicillin-binding-protein-mediated resistance to f3-lactam antibiotics. Trends Molec.
Microbiol.2: 361-366.

14 Jensen, L. B., N. Frimodt-Moller, F. M. Aarestrup. 1999. Presence of erm gene classes in Gam-positive bacteria of animal and human origin in Denmark. FEMS Microbiol. 170:151-158.

15 Thal, L. A., and M. J. Zervos. 1999. Occurrence and epidemiology of resistance to virginimycin and streptrogramins. J. Antimicrob. Chemother. 43:171-176

16 Martinez J. L., A. Alonso, J. M. Gomez-Gomez, and F. Baquero. 1998.
Quinolone resistance by mutations in chromosomal gyrase genes. Just the tip of the iceberg? J. Antimicrob.
Chemother. 42:683-688

17 Cockerill III, F.R. 1999. Genetic methods for assessing antimicrobial resistance. Antimicrob. Agents.
Chemother. 43:199-212.

18 Casadewall, B. and P. Courvalin. 999 Characterization of the vanD
glycopeptide resistance gene cluster from Enterococcus faecium BM 4339. J. Bacteriol. 181:3644-3648.

19 Roberts, M.C. 1999. Genetic mobility and distribution of tetracycline resistance determinants.Ciba Found.
Symp. 207:206-222.
Huovinen, P., L. Sundstrom, G. Swedberg, and O. Skold. 1995. Trimethoprim and sulfonamide resistance.Antimicrob. Agent Chemother. 39:279-289.

Table 6. List of bacterial toxin selected for diagnostic purposes Organism Toxin Accession number Actinobacillus actinomycetemcomitansCytolethal distending AF006830 toxin (cdtA, cdtB, cdtC) Leukotoxin (ItxA) M27399 Actinomyces pyogenes Hemolysin (pyolysin) 084782 Aeromonas hydrophila Aerolysin M16495 1 Bacillus anthracis Anthrax toxin (cya) M23179 ~

Bacillus cereus Enterotoxin (bceT) D17312 8acteroides fragilis Metalloprotease toxin-3 AF056297 Metalloprotease toxin-2 090931 15 Bordetella bronchisepticaAdenylate cyclase hemolysin237112, (cyaA) 022953 Dermonecrotic toxin (dnt) 059687 8ordetella pertussis Pertussis toxin (S1 subunit,AJ006151 tox) Patent: AJ006155 EP0322533-A 2 05ju189 AJ006157 EP0322115-A 5 28jun89 AJ006159 EP0396964-A 1 l4nov90 AJ007363 JP1987228286-A 1 7oct87 M14378, $

Adenyl cyclase (cya) 18323 Dermonecrotic toxin (dnt)010527 3~ Campylobacterjejuni Cytolethal distending 051121 toxin (cdtA, cdtB, cdtC) Citrobacter freundii Shiga-like toxin (slt-IIcA)X67514, Clostridium botulinum Botulism toxin (BoNT) X52066, The A,B,E and F serotypesM30196 are 35 neurotoxic for human X70814 The other serotypes have X71343 not be considered Partial sequences (<200 X70817 bp) have 4~ not be considered M81186 45 s7s74s Table 6. List of bacterial toxin selected for diagnostic purposes (continued) Organism Toxin Accession number Clostridium difficile A toxin (enterotoxin) AB012304 (tcdA) $ AF053400 1~ B (cytotoxin) (toxB) 223277 Clostridium perfringens Alpha (phospholipase L43545 C) (cpa) 1$ L43548 Beta (dermonecrotic L13198 protein) (cpb) Enterotoxin (cpe) Pseudogene(notexpressed)AF037328 $

Epsilon toxin (etxD) M80837 Iota (la et Ib) X73562 Lambda (metalloprotease)D45904 Theta (perfringolysin M36704 O) Clostridium tetani Tetanos toxin X06214 Corynebacterium diphtheriaeDiphtheriae toxin X00703 3 Patent:
$

JP 1985227681-All Corynebacterium pseudotuberculosisPhospholipase C A21336 Patent: WO 9011351-A

Enterobacter cloacae Shiga-like toxin II 250754, U33502 4~ Escherichia coli (EHEC) Hemolysin toxin (hlyA AF043471 and ehxA) 4$ AF074613 Shiga-like (Vero cytotoxin)X81418 (stx) Contain the sequences M10133 for both the A and B subunits M12863 $0 Patent:JP 1995008280-A/1X81417 $ L04539 $

6$

Table 6. List of bacterial toxin selected for diagnostic purposes (continued) Organism Toxin Accession number Escherichia coli (ETEC)Enterotoxin (heat-labile) M17874 (eltB) Patent: EP 0145486-A 5 M17873 Enterotoxin (heat-stable) L11241 (astA) (estA1) Escherichia coli(other)Cytolethal-distending toxin 003293 15 (cdt) (3 genes) 004208 Cytotoxic necrotizing factor 042629 1 (cnf1 ) Microcin 24 (mtPS) 047048 Autotransporter enterotoxin AF056581 (Pet) (cytotoxin) Haemophilus ducreyi Cytolethal distending toxin 053215 (cdtA, cdtB, cdtC) Helicobacter pylori Vacuolating toxin (vacA) 007145 Pasteurella multocida Mitogenic toxin (dermonecroticX57775, toxin) 228388 Pseudomonas aeruginosa Cytotoxin (Enterotoxin A) X14956 Shigella dysenteriae Shiga toxin (2 subunits) X07903, type 1 M32511 (stxA et stxB) M19437 M24352, 35 Staphylococcus aureus Gamma-hemolysin (hlg2) D42143 Enterotoxin 093688 Enterotoxin C1 (entC1) X05815 Enterotoxin H (seh) 011702 Exfoliative toxin A (ETA) M17347 (Epidermolytic toxin A) M17357 L25372, Exfoliative toxin B (ETB) M17348, Leukocidin R (F and S component,X64389, IukF and IukS) S53213 4$ (Hemolysin B and C) X72700 Toxic shock syndrome toxin X01645 1 (TSST-1 ) (alpha toxin) M90536 (alpha hemolysin) J02615 Staphylococcus epidermidisDelta toxin (hld) AF068634 Staphylococcus intermediusLeukocidin R (F and S component,X79188 IukF and IukS) (synergohymenotropic toxin) Streptococcus pneumoniaePneumolysin X52474 SS Streptococcus pyogenes Streptococcal pyrogenic exotoxinX61560 A (speA) (et 19 autres) 040453, Pyrogenic exotoxin B (spell) 063134 6l) M86905, Table 6. List of bacterial toxin selected for diagnostic purposes (continued) Organism Toxin Accession number Vibrio cholerae Cholerae toxin (ctxA et X00171 ctxB subunits) Patent: X76390 EP 0368819-A 12 (ctxB) X58785, S55782 WO 9313202-A 45 (ctxA) D30052 ~

Accessory cholera enterotoxin222569 (ace) Zonula occludens toxin, M83563 (zot) Vibrio parahaemolyticusThermostable direct hemolysinS67841 (tdh) Vibrio vulnificus Cytolysin (vvhA) M34670 I Yersinia enterocoliticaHeat-stable enterotoxin D63578 5 (ystC) Yersinia pestis Toxin X92727 Table 7. Origin of the sequences in the sequence listing.
SEQ ID NO. Bacterial,fungal or parasitical species Source Comments*
1 Acinetobacterbaumannii This patent tuf 2 Acfinomyces meyeri This patent fuf 3 Aerococcus viridans This patent tuf 4 Achromobacter xylosoxidans subsp. This patent tuf denifrificans 5 Anaerorhabdus furcosus This patent tuf 6 Bacillus anthracis This patent tuf 7 Bacillus cereus This patent tuf 8 Bacteroides distasonis This patent tuf 9 Enterococcus casseliflavus This patent tuf 10 Staphylococcus saprophyticus This patent tuf 1 11 Bacferoides vulgates This patent tuf S

12 Bartonella henselae This patent tuf 13 Bifidobacterium adolescentis This patent tuf 14 Bifidobacterium dentium This patent tuf Brucella abortus This patent tuf 16 Burkholderia cepacia This patent tuf 17 Cedecea davisae This patent tuf 18 Cedecea neteri This patent tuf 19 Cedecea lapagei This patent tuf

20 Chlamydia pneumoniae This patent tuf

21 Chlamydia psittaci This patent tuf

22 Chlamydia trachomatis This patent tuf

23 Chryseobacferium meningosepticum This patent tuf

24 Citrobacter amalonaticus This patent tuf

25 Citrobacter braakii This patent tuf

26 Cifrobacferkoseri This patent tuf

27 Cifrobacfer farmeri This patent tuf

28 Cifrobacter freundii This patent tuf

29 Cifrobacter sedlakii This patent tuf

30 Cifrobacter werkmanii This patent tuf

31 Citrobacferyoungae This patent tuf

32 Clostridium perfringens This patent tuf

33 Comamonas acidovorans This patent tuf

34 Corynebacferium bovis This patent tuf

35 Corynebacferium cervicis This patent tuf

36 Corynebacferium flavescens This patent tuf

37 Corynebacferium kutscheri This patent tuf

38 Corynebacterium minutissimum This patent tuf

39 Corynebacterium mycetoides This patent tuf

40 Corynebacterium pseudogenitalium This patent fuf

41 Corynebacterium renale This patent fuf

42 Corynebacferium ulcerans This patent fuf

43 Corynebacter7um urealyticum This patent fuf

44 Corynebacferium xerosis This patent tuf

45 Coxiella burnefii This patent tuf

46 Edwardsiella hoshinae This patent tuf

47 Edwardsiella tarda This patent tuf

48 Eikenella corrodens This patent tuf

49 Enterobacter aerogenes This patent tuf

50 Enferobacter agglomerans This patent tuf

51 Enterobacferamnigenus This patent fuf

52 Enterobacfer asburiae This patent fuf

53 Enterobacfer cancerogenus This patent tuf

54 Enterobacter cloacae This patent tuf

55 Enterobacter gergoviae This patent tuf

56 Enterobacter hormaechei This patent tuf

57 Enterobacter sakazakii This patent tuf

58 Enterococcus casseliflavus This patent tuf

59 Enterococcus cecorum This patent tuf

60 Enterococcus dispar This patent tuf

61 Enterococcus durans This patent tuf Table 7. Origin of the sequences in the sequence listing. (continued) SEQ ID NO. Bacterial,fungal or parasitical species Source Comments*
S 62 Enterococcus faecalis This patent tut 63 Enterococcus faecalis This patent tut 64 Enterococcus faecium This patent tut 65 Enterococcus flavescens This patent tut 66 Enterococcus gallinarum This patent tut 67 Enterococcus hirae This patent tut 68 Enterococcus mundtii This patent tut 69 Enterococcus pseudoavium This patent fuf 70 Enterococcus raffinosus This patent tut 71 Enterococcus saccharolyticus This patent fuf 72 Enterococcus solitarius This patent tut 73 Enterococcus casseliflavus This patent tut (C) 74 Enterococcus faecium This patent tut (C) 75 Enterococcus flavescens This patent tut (C) 76 Enterococcus gallinarum This patent tut (C) 77 Ehrlichia canis This patent tut 78 Escherichia coli This patent tut 79 Escherichia fergusonii This patent fuf 80 Escherichia hermannii This patent tut 81 Escherichia vulneris This patent tut 82 Eubacterium lentum This patent tut 83 Eubacterium nodafum This patent tut 84 Ewingella americana This patent tut 85 Francisella tularensis This patent tut 86 Fusobacterium nucleatum subsp. polymorphumThis patent tut 87 Gemella haemolysans This patent tut 88 Gemella morbillorum This patent tut 89 Haemophilus actinomycetemcomitans This patent tut 90 Haemophilus aphrophilus This patent tut 91 Haemophilus ducreyi This patent tut 92 Haemophilus haemolyticus This patent tut 93 Haemophilus parahaemolyticus This patent tut 94 Haemophilus parainfluenzae This patent tut 95 Haemophilus paraphrophilus This patent tut 96 Haemophilus segnis This patent tut 97 Hafnia alvei This patent tut 98 Kingella kingae This patent tut 99 Klebsiella omithinolytica This patent tut 100 Klebsiella oxytoca This patent tut 101 Klebsiella planticola This patent tut 102 Klebsiella pneumoniae subsp. ozaenae This patent tut 103 Klebsiella pneumoniae subsp. pneumoniaeThis patent tut 104 Klebsiella pneumoniae subsp. rhinoscleromatisThis patent tut 105 Kluyvera ascorbata This patent tut 106 Kluyvera cryocrescens This patent tut 107 Kluyvera georgiana This patent tut 108 Lactobacillus casei subsp. casei This patent tut 109 Lactococcus lactis subsp. lactis This patent tut 110 Leclercia adecarboxylata This patent tut 111 Legionella micdadei This patent tut 112 Legionella pneumophila subsp. pneumophilaThis patent tut ' 113 Leminorella grimonfii This patent tut 114 Leminorella richardii This patent tut 115 Leptospira interrogans This patent tut 116 Megamonas hypermegale This patent tut 117 Mitsuokella multacida This patent tut 118 Mobiluncus curtisii subsp. holmesii This patent tut 119 Moellerella wisconsensis This patent tut 120 Branhamella catarrhalis This patent tut 121 Morganella morganii subsp. morganii This patent tut 122 Mycobacterium tuberculosis This patent tut Table 7. Origin of the sequences in the sequence listing. (continued) SEQ ID NO. Bacterial,fungal or parasitical species Source Comments*
123 Neisseria cinerea This patenttuf 124 Neisseria elongata subsp. elongata This patenttuf 125 Neisseria flavescens This patenttuf 126 Neisseria gonorrhoeae This patenttuf 127 Neisseria lactamica This patenttuf 128 Neisseria meningitides This patenttuf 129 Neisseria mucosa This patentfuf 130 Neisseria sicca This patentfuf 131 Neisseria subflava This patenttuf 132 Neisseria weaveri This patentfuf 133 Ochrobactrum anthropi This patenttuf 134 Pantoea agglomerans This patentfuf 135 Pantoea dispersa This patenttuf 136 Pasteurella mulfocida This patenttuf 137 Pepfostreptococcus anaerobius This patenttuf 138 Pepfostreptococcus asaccharolyticus This patenttuf 139 Peptostreptococcus prevotii This patenttuf 140 Porphyromonas asaccharolytica This patenttuf 141 Porphyromonas gingivalis This patenttuf 142 Pragia fontium This patenttuf 143 Prevotella melaninogenica This patenttuf 144 Prevotella oralis This patenttuf 145 Propionibacterium acnes This patenttuf 146 Proteus mirabilis This patenttuf 147 Proteus penneri This patenttuf 148 Proteus vulgaris This patenttuf 149 Providencia alcalifaciens This patenttuf 150 Providencia rettgeri This patenttuf 151 Providencia rustigianii This patenttuf 152 Providencia sfuartii This patenttuf 153 Pseudomonas aeruginosa This patenttuf 154 Pseudomonas fluorescens This patenttuf 155 Pseudomonas stutzeri This patenttuf 156 Psychrobacter phenylpyruvicus This patenttuf 157 Rahnella aquatilis This patenttuf 158 Salmonella choleraesuis subsp.arizonae This patenttuf 159 Salmonella choleraesuis subsp. choleraesuisThis patenttuf serotype choleraesuis 160 Salmonella choleraesuis subsp. diarizonae This patenttuf 161 Salmonella choleraesuis subsp. choleraesuisThis patenttuf serotype heidelberg 162 Salmonella choleraesuis subsp. houtenae This patenttuf 163 Salmonella choleraesuis subsp. indica This patenttuf 164 Salmonella choleraesuis subsp. salamae This patenttuf 165 Salmonella choleraesuis subsp. choleraesuisThis patenttuf serotype typhi 166 Serratia fonticola This patenttuf 167 Serratia liquefaciens This patenttuf 168 Serratia marcescens This patenttuf 169 Serratia odorifera This patenttuf 170 Serratia plymuthica This patentfuf 171 Serratia rubidaea This patenttuf 172 Shigella boydii This patenttuf 173 Shigella dysenteriae This patenttuf 174 Shigella flexneri This patenttuf 175 Shigella sonnei This patenttuf 176 Staphylococcus aureus This patenttuf 177 Staphylococcus aureus This patenttuf 178 Staphylococcus aureus This patenttuf 179 Staphylococcus aureus This patenttuf 180 Staphylococcus aureus subsp. aureus This patenttuf 181 Staphylococcus auricularis This patenttuf 182 Staphylococcus capitis subsp. capitis This patenttuf 183 Staphylococcus caseolyticus This patenttuf Table 7. Origin of the sequences in the sequence listing. (continued) SEQ ID NO. Bacterial,fungal or parasitical species Source Comments*
184 Staphylococcus cohnii This patent tut 185 Staphylococcus epidermidis This patent tut 186 Staphylococcus haemolyticus This patent tut 187 Staphylococcus warneri This patent tut 188 Staphylococcus haemolyticus This patent tut 189 Staphylococcus haemolyticus This patent fuf 190 Staphylococcus haemolyticus This patent tut 191 Staphylococcus hominis subsp. hominisThis patent tut 192 Staphylococcus warneri This patent tut 193 Staphylococcus hominis This patent fuf 194 Staphylococcus hominis This patent tut 195 Staphylococcus hominis This patent tut 196 Staphylococcus hominis This patent tut 197 Staphylococcus lugdunensis This patent tut 198 Staphylococcus saprophyticus This patent tut 199 Staphylococcus saprophyticus This patent tut 200 Staphylococcus saprophyticus This patent tut 201 Staphylococcus sciuri subsp. sciuri This patent fuf 202 Staphylococcus warneri This patent tut 203 Staphylococcus warneri This patent tut 204 Bifidobacterium longum This patent tut 205 Stenotrophomonas maltophilia This patent tut 206 Streptococcus acidominimus This patent tut 207 Streptococcus agalactiae This patent tut 208 Streptococcus agalactiae This patent tut 209 Streptococcus agalactiae This patent fuf 210 Streptococcus agalactiae This patent fuf 211 Streptococcus anginosus This patent tut 212 Streptococcus bovis This patent tut 213 Streptococcus anginosus This patent tut 214 Streptococcus cricetus This patent tut 215 Streptococcus cristatus This patent tut 216 Streptococcus downei This patent tut 217 Streptococcus dysgalactiae This patent tut 218 Streptococcus equi subsp. equi This patent tut 219 Streptococcus ferns This patent tut 220 Streptococcus gordonii This patent tut 221 Streptococcus anginosus This patent tut 222 Streptococcus macacae This patent tut 223 Streptococcus gordonii This patent tut 224 Streptococcus mutans This patent tut 225 Streptococcus parasanguinis This patent tut 226 Streptococcus ratti This patent tut 227 Streptococcus sanguinis This patent tut 228 Streptococcus sobrinus This patent tut 229 Streptococcus suis This patent fuf 230 Streptococcus uberis This patent tut 231 Streptococcus vestibularis This patent tut 232 Tafumella ptyseos This patent tut 233 Trabulsiella guamensis This patent tut 234 Veillonella parvula This patent tut 235 Yersinia enterocolitica This patent tut 236 Yersinia frederiksenii This patent fuf 237 Yersinia intermedia This patent fuf 238 Yersinia pestis This patent tut 239 Yersinia pseudotuberculosis This patent tut 240 Yersinia rohdei This patent tut 241 Yokenella regensburgei This patent tut 242 Achromobacterxylosoxidans subsp. denitrificansThis patent atpD

243 Acinetobacfer baumannii This patent atpD

244 Acinetobacferlwoffii This patent atpD

Table 7. Origin of the sequences in the sequence listing. (continued) SEQ ID NO. Bacterial,fungal or parasitical species Source Comments*
245 Sfaphylococcus saprophyticus This patent atpD

246 Alcaligenes faecalis This patent atpD

247 Bacillus anthracis This patent atpD

248 Bacillus cereus This patent atpD

249 Bacteroides distasonis This patent atpD

250 Bacteroides ovatus This patent atpD

251 Leclercia adecarboxylata This patent atpD

252 Sfenotrophomonas maltophilia This patent atpD

253 Bartonella henselae This patent atpD

254 Bifidobacterium adolescentis This patent atpD

255 Brucella abortus This patent atpD

256 Cedecea davisae This patent atpD

257 Cedecea lapagei This patent atpD

258 Cedecea neteri This patent atpD

259 Chryseobacterium meningosepficum This patent atpD

260 Citrobacter amalonaticus This patent atpD

261 Citrobacter braakii This patent atpD

262 Citrobacter koseri This patent afpD

263 Citrobacter farmeri This patent atpD

264 Citrobacter freundii This patent atpD

265 Citrobacterkoseri This patent atpD

266 Citrobactersedlakii This patent atpD

267 Citrobacter werkmanii This patent atpD

268 Cifrobacter youngae This patent atpD

269 Closfridium innocuum This patent atpD

270 Clostridium perfringens This patent atpD

272 Corynebacterium diphtheriae This patent atpD

273 Corynebacterium pseudodiphtheriticum This patent atpD

274 Corynebacterium ulcerans This patent atpD

275 Corynebacterium urealyticum This patent atpD

276 Coxiella burnefii This patent atpD

277 Edwardsiella hoshinae This patent atpD

278 Edwardsiella tarda This patent afpD

279 Eikenella corrodens This patent atpD

280 Enterobacter agglomerans This patent atpD

281 Enterobacfer amnigenus This patent atpD

282 Enterobacfer asburiae This patent atpD

283 Enterobacter cancerogenus This patent atpD

284 Enterobacfer cloacae This patent atpD

285 Enterobacter gergoviae This patent atpD

286 Enterobacter hormaechei This patent afpD

287 Enterobacter sakasakii This patent atpD

288 Enterococcus avium This patent atpD

289 Enterococcus casseliflavus This patent atpD

290 Enterococcus durans This patent atpD

SO 291 Enterococcus faecalis This patent atpD

292 Enterococcus faecium This patent atpD

293 Enterococcus gallinarum This patent atpD

294 Enterococcus saccharolyticus This patent atpD

295 Escherichia fergusonii This patent atpD

296 Escherichia hermannii This patent atpD

297 Escherichia vulneris This patent atpD

298 Eubacterium lentum This patent atpD

299 Ewingella americana This patent atpD

300 Francisella tularensis This patent atpD

301 Fusobacterium gonidiaformans This patent atpD

302 Fusobacterium necrophorum subsp. necrophorumThis patent afpD

303 Fusobacterium nucleatum subsp. polymorphumThis patent atpD

304 Gardnerella vaginalis This patent atpD

305 Gemella haemolysans This patent afpD

306 Gemella morbillorum This patent atpD

Table 7. Origin of the sequences in the sequence listing. (continued) SEQ ID NO. Bacterial,fungal or parasitical species Source Comments*
307 Haemophilus ducreyi This patentafpD

308 Haemophilus haemolyticus This patentafpD

309 Haemophilus parahaemolyticus This patentatpD

310 Haemophilus parainfluenzae This patentafpD

311 Hafnia alvei This patentafpD

312 Kingella kingae This patentafpD

313 Klebsiella pneumoniae subsp. ozaenae This patentafpD

314 Klebsiella omithinolytica This patentatpD

315 Klebsiella oxytoca This patentafpD

316 Klebsiella planticola This patentafpD

317 Klebsiella pneumoniae subsp. pneumoniae This patentatpD

318 Kluyvera ascorbata This patentafpD

319 Kluyvera cryocrescens This patentafpD

320 Kluyvera georgiana This patentatpD

321 Lactobacillus acidophilus This patentatpD

322 Legionella pneumophila subsp. pneumophila This patentatpD

323 Leminorella grimontii This patentatpD

324 Lisferia monocytogenes This patentatpD

325 Micrococcus lylae This patentatpD

326 Moellerella wisconsensis This patentatpD

327 Branhamella catarrhalis This patentatpD

328 Moraxella osloensis This patentatpD

329 Morganella morganii subsp. morganii This patentatpD

330 Pantoea agglomerans This patentatpD

331 Pantoea dispersa This patentatpD

332 Pasteurella multocida This patentafpD

333 Pragia fontium This patentafpD

334 Proteus mirabilis This patentafpD

335 Proteus vulgaris This patentatpD

336 Providencia alcalifaciens This patentatpD

337 Providencia rettgeri This patentafpD

338 Providencia rustigianii This patentatpD

339 Providencia sfuartii This patentatpD

340 Psychrobacfer phenylpyruvicus This patentatpD

341 Rahnella aquafilis This patentatpD

342 Salmonella choleraesuis subsp. arizonae This patentatpD

343 Salmonella choleraesuis subsp. choleraesuisThis patentatpD
serotype choleraesuis 344 Salmonella choleraesuis subsp. diarizonae This patentatpD

345 Salmonella choleraesuis subsp. houtenae This patentafpD

346 Salmonella choleraesuis subsp. indica This patentatpD

347 Salmonella choleraesuis subsp. choleraesuisThis patentafpD
serotype paratyphi A

348 Salmonella choleraesuis subsp. choleraesuisThis patentatpD
serotype paratyphi B

349 Salmonella choleraesuis subsp. salamae This patentatpD

350 Salmonella choleraesuis subsp. choleraesuisThis patentatpD
serotype typhi 351 Salmonella choleraesuis subsp. choleraesuisThis patentatpD
serotype typhimurium 352 Salmonella choleraesuis subsp. choleraesuisThis patentatpD
serotype virchow 353 Serratia ficaria This patentatpD

354 Serratia fonticola This patentatpD

355 Serratia grimesii This patentatpD

356 Serratia liquefaciens This patentatpD

357 Serratia marcescens This patentatpD

358 Serratia odorifera This patentatpD

359 Serratia plymufhica This patentafpD

360 Serratia rubidaea This patentafpD

361 Shewanella putida This patentatpD

362 Shigella boydii This patentatpD

363 Shigella dysenteriae This patentatpD

364 Shigella flexneri This patentatpD

365 Shigella sonnei This patentatpD

366 Sfaphylococcus aureus This patentatpD

367 Sfaphylococcus auricularis This patentatpD

Table 7. Origin of the sequences in the sequence listing. (continued) SEQ ID NO. Bacterial,fungal or parasitical species Source Comments*
368 Staphylococcus capitis subsp. capitisThis patent atpD

369 Staphylococcus cohnii This patent afpD

370 Staphylococcus epidermidis This patent atpD

371 Staphylococcus haemolyticus This patent atpD

372 Staphylococcus hominis subsp. hominisThis patent atpD

373 Staphylococcus hominis This patent atpD

374 Staphylococcus lugdunensis This patent atpD

375 Staphylococcus saprophyticus This patent atpD

376 Staphylococcus simulans This patent atpD

377 Staphylococcus warneri This patent atpD

378 Streptococcus acidominimus This patent afpD

379 Streptococcus agalactiae This patent atpD

380 Streptococcus agalactiae This patent atpD

381 Streptococcus agalactiae This patent atpD

382 Streptococcus agalacfiae This patent afpD

383 Streptococcus agalactiae This patent atpD

384 Streptococcus dysgalactiae This patent atpD

385 Streptococcus equi subsp. equi This patent afpD

386 Streptococcus anginosus This patent afpD

387 Streptococcus salivarius This patent afpD

388 Streptococcus suis This patent afpD

389 Streptococcus uberis This patent atpD

390 Tatumella ptyseos This patent atpD

391 Trabulsiella guamensis This patent atpD

392 Yersinia bercovieri This patent atpD

393 Yersinia enterocolitica This patent atpD

394 Yersinia frederiksenii This patent atpD

395 Yersinia intermedia This patent atpD

396 Yersinia pseudotuberculosis This patent atpD

397 Yersinia rohdei This patent atpD

398 Yokenella regensburgei This patent atpD

399 Yarrowia lipolytica This patent tuf (ef-1 ) 400 Absidia corymbifera This patent tuf (ef-1 ) 401 Alternaria altemata This patent tuf (ef-1 ) 402 Aspergillus flavus This patent tuf (ef-1 ) 403 Aspergillus fumigafus This patent tuf (ef-1 ) 404 Aspergillus fumigafus This patent tut (ef-1 ) 405 Aspergillus niger This patent tuf (ef-1 ) 406 Blastoschizomyces capitatus This patent tuf (ef-1 ) 407 Candida albicans This patent tuf (ef-1 ) 408 Candida albicans This patent tuf (ef-1 ) 409 Candida albicans This patent tuf (ef-1 ) 410 Candida albicans This patent tuf (ef-1 ) 411 Candida albicans This patent tuf (ef-1 ) 412 Candida dubliniensis This patent tuf (ef-1 ) SO 413 Candida catenulata This patent tuf (ef-1 ) 414 Candida dubliniensis This patent tuf (ef-1 ) 415 Candida dubliniensis This patent tuf (ef-1 ) 416 Candida famafa This patent fuf (ef-1 ) 417 Candida glabrata This patent tuf (ef-1 ) 418 Candida guilliermondii This patent tuf (ef-1 ) 419 Candida haemulonii This patent tut (ef-1 ) 420 Candida inconspicua This patent tuf (ef-1 ) 421 Candida kefyr This patent tuf (ef-1 ) 422 Candida krusei This patent tuf (ef-1 ) 423 Candida lambica This patent tuf (ef-1 ) 424 Candida lusitaniae This patent tuf (ef-1 ) 425 Candida norvegensis This patent tuf (ef-1 ) 426 Candida parapsilosis This patent tuf (ef-1 ) 427 Candida rugosa This patent tuf (ef-1 ) 428 Candida sphaerica This patent tuf (ef-1 ) Table 7. Origin of the sequences in the sequence listing. (continued) SEQ ID NO. Bacterial,fungal or parasitical species Source Comments*
429 Candida tropicalis This patent tuf (ef-1 ) 430 Candida utilis This patent fuf (ef-1 ) 431 Candida viswanathii This patent fuf (ef-1 ) 432 Candida zeylanoides This patent fuf (ef-1 ) 433 Coccidioides immitis This patent tuf (ef-1 ) 434 Cryptococcus albidus This patent tuf (ef-1 ) 435 Exophiala jeanselmei This patent tuf (ef-1 ) 436 Fusarium oxysporum This patent tuf (ef-1 ) 437 Geotrichum spp. This patent tuf (ef-1 ) 438 Histoplasma capsulatum This patent tuf (ef-1 ) 439 Issatchenkia orientalis kudrjanzevThis patent tuf (ef-1 ) 440 Malassezia furfur This patent tuf (ef-1 ) 441 Malassezia pachydermatis This patent tuf (ef-1 ) 442 Malbranchea filamenfosa This patent fuf (ef-1 ) 443 Metschnikowia pulcherrima This patent fuf (ef-1 ) 444 Paecilomyces lilacinus This patent tuf (ef-1 ) 445 Paracoccidioides brasiliensis This patent tuf (ef-1 ) 446 Penicillium marneffei This patent tuf (ef-1 ) 447 Pichia anomala This patent fuf (ef-1 ) 448 Pichia anomala This patent fuf (ef-1 ) 449 Pseudallescheria boydii This patent tuf (ef-1 ) 450 Rhizopus oryzae This patent fuf (ef-1 ) 451 Rhodotorula minuta This patent tuf (ef-1 ) 452 Sporobolomyces salmonicolor This patent tuf (ef-1 ) 453 Sporothrix schenckii This patent tuf (ef-1 ) 454 Stephanoascus ciferrii This patent tuf (ef-1 ) 455 Trichophyton mentagrophytes This patent tuf (ef-1 ) 456 Trichosporon cutaneum This patent tuf (ef-1 ) 457 hVangiella dermatitidis This patent tuf (ef-1 ) 458 Aspergillus fumigatus This patent atpD

459 Blastoschizomyces capitafus This patent atpD

460 Candida albicans This patent atpD

461 Candida dubliniensis This patent atpD

462 Candida famata This patent atpD

463 Candida glabrata This patent afpD

464 Candida guilliermondii This patent atpD

465 Candida haemulonii This patent atpD

466 Candida inconspicua This patent atpD

467 Candida kefyr This patent atpD

468 Candida krusei This patent atpD

469 Candida lambica This patent atpD

470 Candida lusitaniae This patent atpD

471 Candida norvegensis This patent atpD

472 Candida parapsilosis This patent atpD

473 Candida rugosa This patent atpD

474 Candida sphaerica This patent atpD

475 Candida tropicalis This patent atpD

476 Candida utilis This patent atpD

477 Candida viswanathii This patent atpD

478 Candida zeylanoides This patent atpD

SS 479 Coccidioides immitis This patent atpD

480 Cryptococcus albidus This patent atpD

481 Fusarium oxysporum This patent atpD

482 Geotrichum spp. This patent atpD

483 Histoplasma capsulatum This patent afpD

484 Malassezia furfur This patent afpD

485 Malassezia pachydermatis This patent atpD

486 Metschnikowia pulcherrima This patent atpD

487 Penicillium marneffei This patent atpD

488 Pichia anomala This patent atpD

489 Pichia anomala This patent afpD

Table 7. Origin of the sequences in the sequence listing. (continued) SEQ ID NO. Bacterial,fungal or parasitical species Source Comments*
490 Rhodotorula minute This patentatpD

491 Rhodotorula mucilaginosa This patentatpD

492 Sporobolomyces salmonicolor This patentatpD

493 Sporothrix schenckii This patentatpD

494 Stephanoascus ciferrii This patentatpD

495 Trichophyton mentagrophytes This patentafpD

496 Wangiella dermatitidis This patentatpD

497 Yarrowia lipolytica This patentafpD

498 Aspergillus fumigatus This patenttuf (M) 499 Blastoschizomyces capitatus This patenttuf (M) 500 Candida rugosa This patenttuf (M) 501 Coccidioides immifis This patenttuf (M) 502 Fusarium oxysporum This patenttuf (M) 503 Hisfoplasma capsulatum This patenttuf (M) 504 Paracoccidioides brasiliensis This patenttuf (M) 505 Penicillium marneffei This patenttuf (M) 506 Pichia anomala This patenttuf (M) 507 Trichophyton mentagrophytes This patenttuf (M) 508 Yarrowia lipolytica This patentfuf (M) 509 Babesia bigemina This patenttuf (ef-1 ) 510 Babesia bovis This patenttuf (ef-1 ) 511 Crithidia fasciculata This patenttuf (ef-1 ) 512 Enfamoeba histolytica This patenttuf (ef-1 ) 513 Giardia lamblia This patenttuf (ef-1 ) 514 Leishmania tropics This patenttuf (ef-1 ) 515 Leishmania aefhiopica This patenttuf (ef-1 ) 516 Leishmania tropics This patenttuf (ef-1 ) 517 Leishmania donovani subsp. donovani This patenttuf (ef-1 518 Leishmania donovani subsp. infantum This patenttuf (ef-1 ) 519 Leishmania enriettii This patenttuf (ef-1 ) 520 Leishmania gerbilli This patenttuf (ef-1 ) 521 Leishmania hertigi subsp. hertigi This patentfuf (ef-1 ) 522 Leishmania major This patenttuf (ef-1 ) 523 Leishmania amazonensis This patenttuf (ef-1 ) 524 Leishmania mexicana This patenttuf (ef-1 ) 525 Leishmania tarentolae This patenttuf (ef-1 ) 526 Leishmania fropica This patenttuf (ef-1 ) 527 Neospora caninum This patenttuf (ef-1 ) 528 Trichomonas vaginalis This patenttuf (ef-1 ) 529 Trypanosome brucei subsp. brucei This patenttuf (ef-1 ) 530 Crithidia fasciculata This patentatpD

531 Leishmania fropica This patentatpD

532 Leishmania aefhiopica This patentatpD

533 Leishmania donovani subsp. donovani This patentatpD

534 Leishmania donovani subsp. infantum This patentatpD

535 Leishmania gerbilli This patentatpD

536 Leishmania hertigi subsp. hertigi This patentatpD

537 Leishmania major This patentatpD

538 Leishmania amazonensis This patentatpD

607 Enferococcus faecalis WO 98!20157tuf 608 Enterococcus faecium WO 98/20157tuf 609 Enterococcus gallinarum WO 98/20157tuf 610 Haemophilus influenzae Database fuf 611 Staphylococcus epidermidis WO 98/20157tuf 612 Salmonella choleraesuis subsp. choleraesuisThis patentfuf serotype parafyphi A

613 Serrafia ficaria This patenttuf 614 Enterococcus malodorafus This patenttuf (C) 615 Enterococcus durans This patenttuf (C) 616 Enterococcus pseudoavium This patenttuf (C) 617 Enterococcus dispar This patenttuf (C) 618 Enterococcus avium This patenttuf (C) Table 7. Origin of the sequences in the sequence listing. (continued) SEQ ID NO. Bacterial,fungal or parasitical species Source Comments*
619 Saccharomyces cerevisiae Database tuf (M) 621 Enterococcus faecium This patenttuf (C) 622 Saccharomyces cerevisiae This patenttuf (ef-1 ) 623 Cryptococcus neoformans This patentfuf (ef-1 ) 624 Candida albicans This patentfuf (ef-1 ) 662 Corynebacferium diphfheriae WO 98/20157fuf 663 Candida catenulata This patentatpD

665 Saccharomyces cerevisiae Database tuf (ef-1 ) 666 Saccharomyces cerevisiae Database atpD

667 Trypanosoma cruzi This patentatpD

668 Corynebacterium glutamicum Database tuf 669 Escherichia coli Database atpD

670 Helicobacfer pylori Database atpD

671 Clostridium acetobutylicum Database atpD

672 Cytophaga lytica Database atpD

673 Ehrlichia risticii This patentatpD

674 Vibrio cholerae This patentatpD

675 Vibrio cholerae This patenttuf 676 Leishmania enrieftii This patentatpD

677 Babesia microtti This patenttuf (ef-1 ) 678 Cryptococcus neoformans This patentatpD

679 Cryptococcus neoformans This patentatpD

680 Cunninghamella berthollefiae This patentatpD

684 Candida tropicalis Database atpD
(V) 685 Enterococcus hirae Database atpD
(V) 686 Chlamydia pneumoniae Database atpD
(V) 687 Halobacterium salinarum Database afpD
(V) 688 Human Database atpD
(V) 689 Plasmodium falciparum Database afpD
(V) 690 Saccharomyces cerevisiae Database atpD
(V) 691 Schizosaccharomyces pombe Database atpD
(V) 692 Trypanosoma congolense Database atpD
(V) 693 Thermus thermophilus Database atpD
(V) 698 Escherichia coli Database tuf 709 Borrelia burgdorferi genome atpD
project (V) 710 Treponema pallidum genome atpD
project (V) 711 Chlamydia frachomatis genome atpD
project (V) 712 Enterococcus faecalis genome atpD
project (V) 713 Mefhanosarcina barkeri Database atpD
(V) 714 Methanosarcina jannaschii Database atpD
(V) 715 Porphyromonas gingivalis genome atpD
project (V) 716 Streptococcus pneumoniae genome afpD
project (V) 717 Burkholderia mallei This patenttuf 718 Burkholderia pseudomallei This patenttuf 719 Clostridium beijerincki This patenttuf 720 Clostridium innocuum This patenttuf 721 Clostridium novyi This patenttuf 722 Clostridium septicum This patenttuf 723 Clostridium tertium This patentfuf 724 Clostridium tetani This patentfuf 725 Enterococcus malodoratus This patenttut 726 Enterococcus sulfureus This patenttuf 727 Lactococcus ganrieae This patenttuf 728 Mycoplasma pirum This patenttuf 729 Mycoplasma salivarium This patenttuf 730 Neisseria polysaccharea This patenttuf 731 Salmonella choleraesuis subsp. choleraesuisThis patentfuf serotype enteritidis 732 Salmonella choleraesuis subsp. choleraesuisThis patenttuf serotype gallinarum 733 Salmonella choleraesuis subsp. choleraesuisThis patenttuf serotype paratyphi 8 734 Salmonella choleraesuis subsp. choleraesuisThis patenttuf serotype virchow 735 Serrafia grimesii This patenttuf 736 Clostridium difficile This patenttuf 737 Burkholderia pseudomallei This patentafpD

Table 7. Origin of the sequences in the sequence listing. (continued) SEQ ID NO. Bacterial,fungal or parasitical species Source Comments*
738 Clostridium bifermentans This patentafpD

739 Clostridium beijerinckii This patentatpD

740 Clostridium difficile This patentatpD

741 Clostridium ramosum This patentatpD

742 Clostridium septicum This patentatpD

743 Clostridium tertium This patentatpD

744 Comamonas acidovorans This patentatpD

745 Klebsiella pneumoniae subsp. rhinoscleromafisThis patentatpD

746 Neisseria canis This patentatpD

747 Neisseria cinerea This patentatpD

748 Neisseria cuniculi This patentatpD

749 Neisseria elongata subsp. elongata This patentatpD

750 Neisseria flavescens This patentatpD

751 Neisseria gonorrhoeae This patentatpD

752 Neisseria gonorrhoeae This patentatpD

753 Neisseria lacfamica This patentatpD

754 Neisseria meningitidis This patentatpD

755 Neisseria mucosa This patentafpD

756 Neisseria subflava This patentatpD

757 Neisseria weaveri This patentafpD

758 Neisseria animalis This patentatpD

759 Proteus penneri This patentatpD

760 Salmonella choleraesuis subsp. choleraesuisThis patentatpD
serotype enteritidis 761 Yersinia pestis This patentatpD

762 Burkholderia mallei This patentatpD

763 Clostridium sordellii This patentatpD

764 Closfridium novyi This patentatpD

765 Clostridium botulinum This patentatpD

766 Clostridium histolyticum This patentatpD

767 Peptostreptococcus prevotii This patentatpD

768 Absidia corymbifera This patentatpD

769 Alternaria altemafa This patentatpD

770 Aspergillus flavus This patentatpD

771 Mucor circinelloides This patentatpD

772 Piedraia hortai This patentatpD

773 Pseudallescheria boydii This patentatpD

774 Rhizopus oryzae This patentatpD

775 Scopulariopsis koningii This patentatpD

776 Trichophyton mentagrophytes This patentatpD

777 Trichophyton tonsurans This patentatpD

778 Trichosporon cutaneum This patentatpD

779 Cladophialophora carrionii This patenttuf (ef-1 ) 780 Cunninghamella berthollefiae This patenttuf (ef-1 ) 781 Curvularia lunafa This patenttuf (ef-1 ) 782 Fonsecaea pedrosoi This patenttuf (ef-1 ) 783 Microsporum audouinii This patenttuf (ef-1 ) 784 Mucor circinelloides This patenttuf (ef-1 ) 785 Phialaphora verrucosa This patenttuf (ef-1 ) 786 Saksenaea vasiformis This patenttuf (ef-1 ) 787 Syncephalastrum racemosum This patentfuf (ef-1 ) 788 Trichophyton tonsurans This patenttuf (ef-1 ) 789 Trichophyton mentagrophytes This patenttuf (ef-1 ) 790 Bipolaris hawaiiensis This patenttuf (ef-1 ) 791 Aspergillus fumigates This patentfuf (M) 792 Trichophyton mentagrophytes This patentfuf (M) 827 Clostridium novyi This patentatpD
(V) 828 Clostridium difficile This patentatpD
(V) 829 Clostridium septicum This patentafpD
(V) 830 Clostridium botulinum This patentafpD
(V) 831 Clostridium perfringens This patentafpD
(V) 832 Closfridium tetani This patentafpD
(V) Table 7. Origin of the sequences in the sequence listing. (continued) SEQ ID NO. Bacterial,fungal or parasitical species Source Comments*
833 Streptococcus pyogenes Database atpD
(V) 834 Babesia bovis This patent atpD
(V) 835 Cryptosporidium parvum This patent atpD
(V) 836 Leishmania donovani subsp. infantumThis patent atpD
(V) 837 Leishmania major This patent atpD
(V) 838 Leishmania farentolae This patent atpD
(V) 839 Trypanosoma brucei This patent atpD
(V) 840 Trypanosoma cruzi This patent tuf (ef-1 ) 841 Trypanosoma cruzi This patent tuf (ef-1 ) 842 Trypanosoma cruzi This patent tuf (ef-1 ) 843 Babesia bovis This patent tuf (M) 844 Leishmania aethiopica This patent tuf (M) 845 Leishmania amazonensis This patent fuf (M) 846 Leishmania donovani subsp. donovaniThis patent tuf (M) 847 Leishmania donovani subsp. infantumThis patent fuf (M) 848 Leishmania enriettii This patent tuf (M) 849 Leishmania gerbilli This patent tuf (M) 850 Leishmania major This patent tuf (M) 851 Leishmania mexicana This patent tuf (M) 852 Leishmania tarentolae This patent tuf (M) 853 Trypanosoma cruzi This patent tuf (M) 854 Trypanosoma cruzi This patent fuf (M) 855 Trypanosoma cruzi This patent fuf (M) 856 Babesia bigemina This patent atpD

857 Babesia bovis This patent atpD

858 Babesia microfti This patent atpD

859 Leishmania guyanensis This patent atpD

860 Leishmania mexicana This patent atpD

861 Leishmania fropica This patent atpD

862 Leishmania fropica This patent atpD

863 Bordetella pertussis Database tuf 864 Trypanosoma brucei Database tuf (ef-1 ) 865 Cryptosporidium parvum This patent tuf (ef-1 ) 866 Staphylococcus saprophyticus This patent atpD

867 Zoogloea ramigera This patent atpD

868 Staphylococcus saprophyticus This patent tuf 869 Enterococcus casseliflavus This patent tuf 870 Enterococcus casseliflavus This patent tuf 871 Enterococcus flavescens This patent tuf 872 Enterococcus gallinarum This patent tuf 873 Enterococcus gallinarum This patent tuf 874 Staphylococcus haemolyticus This patent tuf 875 Staphylococcus epidermidis This patent tuf 876 Staphylococcus epidermidis This patent fuf SO 877 Staphylococcus epidermidis This patent fuf 878 Sfaphylococcus epidermidis This patent fuf 879 Enterococcus gallinarum This patent fuf 880 Pseudomonas aeruginosa This patent tuf 881 Enterococcus casseliflavus This patent tuf 882 Enterococcus casseliflavus This patent tuf 883 Enterococcus faecalis This patent tuf 884 Enterococcus faecalis This patent tuf 885 Enterococcus faecium This patent tuf 886 Enterococcus faecium This patent tuf 887 Zoogloea ramigera This patent tuf 888 Enterococcus faecalis This patent tuf 889 Aspergillus fumigatus This patent afpD

890 Penicillium marneffei This patent afpD

891 Paecilomyces lilacinus This patent atpD

892 Penicillium marneifei This patent atpD

893 Sporothrix schenckii This patent atpD

Table 7. Origin of the sequences in the sequence listing. (continued) SEQ ID NO. Bacterial,fungal or parasitical species Source Comments*
894 Malbranchea filamentosa This patent atpD

895 Paecilomyces lilacinus This patent atpD

896 Aspergillus niger This patent afpD

897 Aspergillus fumigatus This patent tuf (ef-1 ) 898 Penicillium marneffei This patent tuf (ef-1 ) 899 Piedraia hortai This patent tuf (ef-1 ) 900 Paecilomyces lilacinus This patent tuf (ef-1 ) 901 Paracoccidioides brasiliensis This patent tuf (ef-1 ) 902 Sporothrix schenckii This patent tuf (ef-1 ) 903 Penicillium marneffei This patent tuf (ef-1 ) 904 Curvularia lunata This patent tuf (M) 905 Aspergillus niger This patent tuf (M) 906 Bipolaris hawaiiensis This patent tuf (M) 907 Aspergillus flavus This patent tuf (M) 908 Alternaria altemata This patent tuf (M) 909 Penicillium marneffei This patent tuf (M) 910 Penicillium marneffei This patent tuf (M) 918 Escherichia coli Database recA

929 Bacteroides fragilis This patent atpD
(V) 930 Bacteroides distasonis This patent atpD
(V) 931 Porphyromonas asaccharolytica This patent atpD
(V) 932 Listeria monocytogenes This patent tuf 939 Saccharomyces cerevisiae Database rad51 940 Saccharomyces cerevisiae Database dmc1 * atpD indicates atpD sequences of the F-type atpD (V) indicates atpD sequences of the V-Type tuf indicates tuf sequences tuf (C) indicates tuf sequences divergent from main (usually A and B) copies of the elongation factor-Tu tuf (ef-1 ) indicates tuf sequences of the eukaryotic type (elongation factor 1 a) tuf (M) indicates tuf sequences from organellar (mostly mitochondrial) origin recA indicates recA sequences, Rad51 indicates Rad51 sequences or rad51 homologs and dmcl indicates dmc1 sequences or dmcl homologs Table 8. Bacterial species used to test the specificity of the Streptococcus agalactiae-specific amplification primers from tut sequence.
Strain Reference number Strain Reference number Streptococcus acidominimusATCC 51726 Bacteroides caccae ATCC 43185 Streptococcus agalactiaeATCC 12403 Bacteroides vulgafus ATCC 8482 Streptococcus agalactiaeATCC 12973 Bacferoides fragilis ATCC 25285 Streptococcus agalactiaeATCC 13813 Candida albicans ATCC 11006 Streptococcus agalactiaeATCC 27591 Clostridium innoculum ATCC 14501 Streptococcus agalactiaeCDCs 1073 Clostridium ramosum ATCC 25582 Streptococcus anginosusATCC 27335 Lactobacillus casei ATCC 393 subsp. casei Streptococcus anginosusATCC 33397 Clostridium septicum ATCC 12464 Streptococcus bovis ATCC 33317 Corynebacterium cervicisNCTC 10604 Streptococcus anginosusATCC 27823 Corynebacterium genitaliumATCC 33031 Streptococcus cricetus ATCC 19642 Corynebacterium urealyficumATCC 43042 Streptococcus cristatusATCC 51100 Enterococcus faecalis ATCC 29212 Streptococcus downei ATCC 33748 Enterococcus faecium ATCC 19434 Streptococcus dysgalactiaeATCC 43078 Eubacterium lentum ATCC 43055 Streptococcus equi subspATCC 9528 Eubacterium nodutum ATCC 33099 equi Streptococcus ferus ATCC 33477 Gardnerella vaginalis ATCC 14018 Streptococcus gordonii ATCC 10558 Lactobacillus acidophilusATCC 4356 Streptococcus macacae ATCC 35911 Lactobacillus crispatusATCC 33820 Streptococcus mitis ATCC 49456 Lactobacillus gasseri ATCC 33323 Streptococcus mutans ATCC 25175 Lactobacillus johnsoniiATCC 33200 Streptococcus oralis ATCC 35037 Lactococcus lactis subsp.ATCC 19435 lactis Streptococcus parasanguinisATCC 15912 Lactococcus lactis subsp.ATCC 11454 lactis Streptococcus parauberisDSM 6631 Listeria innocua ATCC 33090 Streptococcus pneumoniaeATCC 27336 Micrococcus luteus ATCC 9341 Streptococcus pyogenes ATCC 19615 Escherichia coli ATCC 25922 Streptococcus ratti ATCC 19645 Micrococcus lylae ATCC 27566 Streptococcus salivariusATCC 7073 Porphyromonas asaccharolyticaATCC 25260 Streptococcus sanguinisATCC 10556 Prevotella corporis ATCC 33547 Streptococcus sobrinus ATCC 27352 Prevotella melanogenicaATCC 25845 Streptococcus suis ATCC 43765 Staphylococcus aureus subsp. aureusATCC 13301 Streptococcus uberis ATCC 19436 Staphylococcus epidermidisATCC 14990 Streptococcus vestubularisATCC 49124 Staphylococcus saprophyticusATCC 15305 Table 9. Bacterial species used to test the specificity of the Streptococcus agalactiae-specific amplification primers from atpD sequence.
Strain Reference number Strain Reference number Streptococcus acidominimusATCC 51726 Streptococcus gordoniiATCC 10558 Streptococcus agalactiae ATCC 12400 Streptococcus macacae ATCC 35911 Streptococcus agalactiae ATCC 12403 Streptococcus mitis ATCC 49456 Streptococcus agalactiaeATCC 12973 Streptococcus mutans ATCC 25175 Streptococcus agalactiae ATCC 13813 Streptococcus oralis ATCC 35037 Streptococcus agalactiae ATCC 27591 Streptococcus parasanguinisATCC 15912 Streptococcus agalactiae CDCs-1073 Streptococcus parauberisDSM 6631 Streptococcus anginosus ATCC 27335 Streptococcus pneumoniaeATCC 27336 1 S Streptococcus anginosusATCC 27823 Streptococcus pyogenesATCC 19615 Streptococcus bovis ATCC 33317 Streptococcus ratti ATCC 19645 Streptococcus cricetus ATCC 19642 Streptococcus salivariusATCC 7073 Streptococcus cristatus ATCC 51100 Streptococcus sanguinisATCC 10556 Streptococcus downei ATCC 33748 Streptococcus sobrinusATCC 27352 Streptococcus dysgalactiaeATCC 43078 Streptococcus suis ATCC 43765 Streptococcus equi subsp. ATCC Streptococcus uberis ATCC 19436 equi 9528 Streptococcus ferus ATCC 33477 Streptococcus vesfibularisATCC 49124 Table 10. Bacterial species used to test the specificity of the Enterococcus genus-specific amplification primers from tuf sequence.
Strain Reference number PCR result Abiotrophia adjacens ATCC 49175 positive Abiotrophia defective ATCC 49176 negative Acinetobacter baumannii ATCC 19606 negative Bordefella pertussis ATCC 9797 negative Branhamella catarrhalis ATCC 43628 negative Bulkholderia cepacia LSPQ 2217 negative Citrobacter freundii ATCC 8090 negative Corynebacterium aquaficus ATCC 14665 negative Enterobacter cloacae ATCC 13047 negative Enterococcus avium ATCC 14025 positive Enterococcus casseliflavus ATCC 25788 positive Enterococcus casseliflavus 8689 positive Enterococcus casselitlavus 8754 positive Enterococcus casseliflavus 8763 positive Enterococcus cecorum ATCC 43198 positive Enferococcus columbae ATCC 51263 positive Enterococcus dispar ATCC 51266 positive Enterococcus durans ATCC 19432 positive Enterococcus faecalis ATCC 51299 positive Enterococcus faecalis 8422 positive Enterococcus faecalis 8485 positive Enterococcus faecalis 8498 positive Enterococcus faecalis 8503 positive Enterococcus faecalis 8575 positive Enterococcus faecalis 8577 positive Enterococcus faecalis 8610 positive Enterococcus faecalis 8617 positive Enterococcus faecalis ATCC 29212 positive Enterococcus faecium ATCC 19434 positive Enterococcus faecium ATCC 19434 positive Enterococcus faecium ATCC 700221 positive Enterococcus faecium 8421 positive Enterococcus faecium 8446 positive Enterococcus faecium 8448 positive Enterococcus faecium 8449 positive Enterococcus faecium 8450 positive Enterococcus faecium 8481 positive Enterococcus faecium 8482 positive Enterococcus faecium 8494 positive Enterococcus faecium 8648 positive Enterococcus flavescens ATCC 49996 positive Enterococcus flavescens 8758 positive Enterococcus flavescens 8760 positive Enterococcus gallinarum ATCC 49573 positive Enterococcus gallinarum LSPQ 3364 positive Enterococcus gallinarum 8420 positive Enterococcus gallinarum 8431 positive Enterococcus gallinarum 8432 positive Enterococcus gallinarum 8631 positive Enterococcus gallinarum 8684 positive Enterococcus gallinarum 8691 positive Enterococcus gallinarum 8757 positive Enterococcus gallinarum 8764 positive Table 10. Bacterial species used to test the specificity of the Enterococcus genus-specific amplification primers from tufsequence (continued).
Strain Reference number PCR result Enferococcus hirae ATCC 8043 positive Enterococcus malodoratus ATCC 43197 positive Enterococcus mundtii ATCC 43186 positive Enterococcus pseudoavium ATCC 49372 positive Enterococcus rafhnosus ATCC 49427 positive Enterococcus saccharolyticus ATCC 43076 positive Enterococcus solitarius ATCC 49428 positive Escherichia coli ATCC 25922 negative Gemella haemolysans ATCC 10379 positive Haemophilus influenzae ATCC 9007 negative Hafnia alvei ATCC 13337 negative Kingella kingae ATCC 23330 negative Klebsiella oxytoca ATCC 13182 negative Lactobacillus acidophilus ATCC 4356 negative Listeria grayi ATCC 19120 negative Listeria innocua ATCC 33090 negative Listeria ivanovii ATCC 19119 negative Listeria monocytogenes ATCC 15313 negative Listeria monocytogenes ATCC 35152 negative Listeria monocytogenes BD1427 negative Listeria monocytogenes L 279 negative Listeria monocytogenes L 374 negative Listeria monocytogenes L9 negative Listeria monocytogenes LSPQ 5093202 negative Listeria monocytogenes SS2 negative Listeria seeligeri ATCC 35967 negative Micrococcus luteus ATCC 9341 negative Morganella morganii subsp. morganiiATCC 25830 negative Neisseria meningitidis ATCC 13077 negative Pasteurella aerogenes ATCC 27883 negative Proteus vulgaris ATCC 13315 negative Providencia alcalifaciens ATCC 9886 negative Providencia rettgeri ATCC 9250 negative Pseudomonas aeruginosa ATCC 27853 negative Salmonella typhimurium ATCC 14028 negative Serratia marcescens ATCC 13880 negative Shigella flexneri ATCC 12022 negative Shigella sonnei ATCC 29930 negative Staphylococcus aureus subsp. aureusATCC 43300 negative Staphylococcus capitis subsp.capifisATCC 27840 negative Staphylococcus epidermidis ATCC 14990 negative Staphylococcus haemolyticus ATCC 29970 negative Staphylococcus hominis subsp. ATCC 27844 negative hominis Staphylococcus lugdunensis ATCC 43809 negative Staphylococcus saprophyticus ATCC 15305 negative Staphylococcus simulans ATCC 27848 negative Staphylococcus uvarneri ATCC 27836 negative Streptococcus anginosus ATCC 27335 negative Streptococcus anginosus ATCC 27823 negative Streptococcus anginosus ATCC 33397 negative Streptococcus bovis ATCC 33317 negative Streptococcus cristatus ATCC 51100 negative Streptococcus mitis ATCC49456 negative Streptococcus mutans ATCC 25175 negative Table 10. Bacterial species used to test the specificity of the Enterococcus genus-specific amplification primers from tufsequence (continued).
Strain Reference number PCR result Streptococcus parasanguinis ATCC 15912 negative Streptococcus pneumoniae ATCC 27736 negative Streptococcus pneumoniae ATCC 6303 negative Streptococcus pyogenes ATCC 19615 negative Streptococcus salivarius ATCC 7073 negative Streptococcus sanguinis ATCC 10556 negative Streptococcus suis ATCC 43765 negative Yersinia enterocolitica ATCC 9610 negative Table 11. Microbial species for which atpD andlor tuf andlor recA andlor Rad51 andlor dmcl sequences are available in public databases Species Strain Accession number Coding gene*
Bacteria Agrobacterium tumefaciens X99673 tuf Agrobacterium tumefaciens X99674 tuf Anacystis nidulans PCC 6301 X17442 fuf Aquifex aeolicus VF5 AE000669 tuf Aquifex pyrophilus Y15787 tuf Bacillus halodurans C-125 AB017508 tuf Bacillus stearothermophilusCCM 2184 AJ000260 tuf Bacillus subtilis DSM 10 299104 tuf Bacillus subtilis 168 D64127 tuf Bacteroides fragilis DSM 1151 -' tuf Bordefella bronchisepficaRB50 Genome project2 tuf Bordetella pertussis Tohama 1 Genome project2 tuf Borrelia burdorgferi B31 U78193 tuf Brevibacferium linens DSM 20425 X76863 tuf Buchnera aphidicola Ap Y12307 tuf Campylobacter jejuni NCTC 11168 Y17167 tuf Chlamydia pneumoniae CWL029 AE001592 tuf Chlamydia trachomatis F/IC-Cal-13 L22216 tuf Chlamydia trachomatis D/WW-3/CX AE001305 tuf Chlamydia trachomatis M74221 tuf Chlorobium vibrioforme DSM 263 X77033 tuf Chloroflexus aurantiacusDSM 636 X76865 tuf Clostridium acetobutylicumATCC 824 Genome project2 tuf Clostridium difficile 630 Genome project2 tuf Corynebacterium glutamicumASO 19 X77034 tuf Cytophaga lytica DSM 2039 X77035 tuf Deinonema spp. -' tuf Eikenella corrodens ATCC 23834 212610 tuf Escherichia coli J01690 fuf Escherichia coli K-12 MG1655 U00096 fuf Escherichia coli J01717 fuf Escherichia coli K-12 MG1655 U00006 fuf Escherichia coli X57091 fuf Fervidobacterium islandicumDSM 5733 Y15788 tuf Fibrobacter succinogenesS85 X76866 tuf Flavobacterium ferrigeneumDSM 13524 X76867 tuf Flexistipes sinusarabici X59461 tuf Gloeobacter violaceus PCC 7421 U09433 tuf Gloeothece spp. PCC 6501 U09434 tuf Haemophilus HK1651 Genome project2 tuf actinomycetemcomitans Haemophilus influenzae RD L42023 tuf Haloarcula marismortui X16677 tuf Helicobacter pylori 26695 AE000511 tuf Helicobacter pylori J99 AE001541 tuf Herpetosiphon aurantiacusHpga1 X76868 fuf Lactobacillus paracasei E13922 fuf Methanobacferium delta H AE000877 fuf thermoautrophicum Methanococcus jannaschiiATCC 43067 U67486 tuf Methanococcus vannielii X05698 tuf Table 11. Microbial species for which atpD andlor tuf andlor recA andlor Rad51 andlor dmcl sequences are available in public databases (continued) Species Strain Accession number Coding gene*
Micrococcus luteus IFO 3333 M17788 tuf Mycobacterium avium 104 Genome project2 tuf Mycobacterium bovis AF2122/97 Genome project2 tuf Mycobacterium leprae Thai 53 D13869 tuf Mycobacterium leprae 214314 tuf Mycobacterium leprae L13276 tuf Mycobacterium tuberculosisH37Rv 284395 tuf Mycobacterium tuberculosisErdmann S40925 tuf Mycobacterium tuberculosis AD000005 tuf Mycoplasma capricolum PG-31 X16462 tuf Mycoplasma genitalium G37 039732 tuf Mycoplasma hominis X57136 tuf Mycoplasma hominis PG21 M57675 fuf Mycoplasma pneumoniae M 129 AE000019 tuf Neisseria gonorrhoeae MS11 L36380 fuf Neisseria meningitidis22491 Genome project2 tuf Peptococcus niger DSM 20745 X76869 tuf Phophyromonas gingivalisW83 Genome project2 tuf Phormidium ectocarpi PCC 7375 009443 tuf Planobispora rosea ATCC 53773 067308 tuf Plectonema boryanum PCC 73110 009444 tuf Prochlorothrix hollandica 009445 tuf Pseudomonas aeruginosaPAO-1 Genome project2 tuf Rickettsia prowazekii Madrid E AJ235272 tuf Salmonella typhimuriumLT2 trpE91 X55116 tuf Salmonella typhimuriumLT2 trpE91 X55117 tuf Serratia marcescens AF058451 tuf Serpulina hyodysenteriae8204 051635 tuf Shewanella putida Genome project2 tuf Shewanella putrefaciensDSM 50426 -' tuf Shewanella putrefaciensMR-1 Genome project2 tuf Spirochaeta aurantia DSM 1902 X76874 tuf Stigmatella aurantiacaDW4 X82820 tuf Stigmatella aurantiacaSg a1 X76870 tuf Streptococcus mutans UA8159 Genome project2 tuf Streptococcus mutans GS-5 Kuramitsu 075481 tuf Streptococcus oralis NTCC 11427 P331701 tuf Streptococcus pyogenesM1-GAS Genome projectz tuf Streptomyces aureofaciensATCC 10762 AF007125 tuf Streptomyces cinnamoneusTue89 X98831 tuf Streptomyces coelicolorM 145 X77039 tuf Streptomyces collinus BSM 40733 S79408 tuf Streptomyces ramocissimus X67057 tuf Streptomyces ramocissimus X67058 tuf Synechocystis spp. PCC 6803 D90913 tuf Taxeobacter occealus Myx 2105 X77036 tuf Thermoplasma acidophilumDSM 1728 X53866 tuf Thermotoga maritima M27479 tuf Thermus aquaticus EP 00276 X66322 tuf Thermus thermophilus HB8 X06657 tuf Thermus thermophilus HB8 X05977 tuf Thiobacillus cuprinus Hoes X76871 tuf Thiobacillus cuprinus DSM 5495 078300 tuf Table 11. Microbial species for which atpD andlor tuf andlor recA andlor Rad51 andlor dmcl sequences are available in public databases (continued) Species Strain Accession number Coding gene*
Treponema pallidum AE001202 tuf Ureaplasma urealyticum ATCC 33697 234275 tuf Vibrio cholerae N16961 TIGR2 fuf Wolinella succinogenes DSM 1740 X76872 tuf Yersinia pestis CO-92 Genome projectz tuf Fungi Saccharomyces cerevisiae K00428 tuf (M) 15Absidia glauca CBS 101.48 X54730 tuf (ef-1 ) Arxula adeninivorans Ls3 247379 tuf (ef-1 ) Aspergillus oryzae KBN616 AB007770 tuf (ef-1 ) Aureobasidium pullulans 8106 U 19723 tuf (ef-1 ) Candida albicans SC5314 M29935 tuf (ef-1 ) 20Candida albicans SC5314 M29934 tuf (ef-1 ) Cryptococcus neoformans 83501 081803 tuf (ef-1 ) Cryptococcus neoformans M1-106 081804 tuf (ef-1 ) Eremothecium gossypii ATCC 10895 X73978 tuf (ef-1 ) Fusarium oxysporum NRRL 26037 AF008498 tuf (ef-1 ) 25Histoplasma capsulatum 186AS U 14100 tuf (ef-1 ) Podospora anserina X74799 fuf (ef-1 ) Puccinia graminis race 32 X73529 fuf (ef-1 ) Rhizomucor racemosus ATCC 1216B J02605 fuf (ef-1 ) Rhizomucor racemosus ATCC 1216B X17476 tuf (ef-1 ) 30Rhizomucor racemosus ATCC 1216B X17475 tuf (ef-1 ) Rhodotorula mucilaginosa AF016239 tuf (ef-1 ) Saccharomyces cerevisiae X01638 tuf (ef-1 ) Saccharomyces cerevisiae X00779 tuf (ef-1 ) Schizosaccharomyces pombe 042189 tuf (ef-1 ) 35Trichoderma reesei QM9414 223012 tuf (ef-1 ) Yarrowia lipolytica AF054510 tuf (ef-1 ) Parasites 40 Blastocystis hominis HE87-1 D64080 tuf (ef-1 ) Giardia lamblia D14342 tuf (ef-1 ) Kentrophoros spp. AF056101 tuf (ef-1 ) Leishmania amazonensis I FLA/BR/67/PH8 M92653 tuf (ef-1 ) Leishmania braziliensis 072244 tuf (ef-1 ) 45 Onchocerca volvulus M64333 tuf (ef-1 ) Porphyra purpurea Avonport 008844 tuf (ef-1 ) Plasmodium berghei ANKA AJ224150 tuf (ef-1 ) Plasmodium falciparum K1 X60488 tuf (ef-1 ) Plasmodium knowlesi line H AJ224153 tuf (ef-1 ) 50 Toxoplasma gondii RH Y11431 tuf (ef-1 ) Trypanosoma cruzi Y L76077 tuf (ef-1 ) Trypanosoma brucei LVH/75/ U 10562 tuf (ef-1 ) Table 11. Microbial species for which afpD and/or tuf andlor recA andlor Rad51 andlor dmcl sequences are available in public databases (continued) Species Strain Accession number Coding gene*
Bacteria Acetobacterium woodi DSM 1030 010505 atpD

Bacillus caldotenax D38058 atpD

Bacillus firmus OF4 M60117 atpD

Bacillus megaterium QM B1551 M20255 atpD

Bacillus stearothermophilusIF01035 D38060 atpD

Bacillus subtilis 168 228592 atpD

Bacteroides fragilis DSM 2151 M22247 atpD

Bordetella bronchisepticaRB50 Genome projectz atpD

Bordetella pertussis Tohama 1 Genome project? atpD

Borrelia burgdorferi Genome projeotz atpD (V) Burkholderia cepacia DSM50181 X76877 atpD

Brevibacterium flavum MJ-233 E09634 atpD

Campylobacter jejuni NCTC 11168 Genome projectz atpD

Chlamydia pneumoniae Genome projectz atpD (V) Chlamydia trachomatis MoPn Genome projectz atpD (V) Chlorobium vibrioforme DSM 263 X76873 atpD

Citrobacter freundii JE0503 AF037156 atpD

Clostridium acetobutylicumATCC 824 Genome projectz atpD

Clostridium acetobutylicumDSM 792 AF101055 afpD

Clostridium difficile 630 Genome project2 atpD

Corynebacterium glutamicumASO 19 X76875 afpD

Corynebacterium glutamicumDSM 792 AF101055 atpD

Cytophaga lytica DSM 2039 M22535 atpD

Enterobacter aerogenes DSM 30053 3 atpD

Enterococcus faecalis M90060 atpD

Enterococcus faecalis V583 Genome projectz atpD (V) Enterococcus hirae ATCC 9790 D17462 atpD (V) Escherichia colt V00267 atpD

Escherichia colt J01594 atpD

Escherichia colt K12 MG1655 L10328 atpD

Escherichia colt V00311 atpD

Escherichia colt M25464 atpD

Flavobacterium ferrugineumDSM 73524 -3 atpD

Haemophilus Genome project2 atpD

actinomycefemcomitans Haemophilus influenzae Rd 032730 atpD

Halobacterium salinarum S56356 atpD (V) Haloferax volcanii WR 340 X79516 atpD

Helicobacter pylori NCTC 11638 AF004014 atpD

Lactobacillus casei DSM 20021 X64542 atpD

Methanococcus jannaschiiDSM 2661 067477 atpD (V) Methanosarcina barkeri DSM 800 J04836 afpD (V) Moorella thermoacetica ATCC 39073 064318 atpD

Mycobacterium avium 104 Genome projectz atpD

Mycobacterium bouts AF2122/97 Genome projects atpD

Mycobacterium leprae U 15186 atpD

Mycobacterium tuberculosisH37Rv 273419 atpD

Mycoplasma gallisepticum X64256 atpD

Table 11. Microbial species for which atpD andlor tuf andlor recA andlor Rad51 andlor dmc1 sequences are available in public databases (continued) Species Strain Accession number Coding gene*
Mycoplasma genitalium G37 U39725 atpD

Mycoplasma pneumoniae M 129 U43738 ' atpD

Neisseria gonorrhoeae FA 1090 Genome projectz atpD

Neisseria meningitidis 22491 Genome projectz atpD

Peptococcus niger DSM 20475 X76878 atpD

Pectinatus frisingensis DSM 20465 X64543 atpD

Pirellula marina IFAM 1313 X57204 atpD

Porphyromonas gingivalis W83 Genome projectz atpD (V) Propionigenium modestum DSM 2376 X58461 atpD

1 Pseudomonas aeruginosa PA01 Genome projectz atpD
S

Rhodobacter capsulatus 8100 X99599 atpD

Rhodospirillum rubrum X02499 atpD

Rickettsia prowazekii F-12 AF036246 atpD

Ruminococcus albus 7ATCC AB006151 atpD

Salmonella choleraesuis S83769 AF037146 atpD

subsp. arizonae Salmonella choleraesuis u24 AF037147 atpD

subsp. arizonae Salmonella bongori JE04162 AF037155 atpD

Salmonella bongori BR1859 AF037154 afpD

Salmonella choleraesuis DS210/89 AF037149 atpD

subsp. diarizonae Salmonella choleraesuis JE0307 AF037148 atpD

subsp. diarizonae Salmonella choleraesuis S109671 AF037150 atpD

subsp. diarizonae Salmonella choleraesuis K228 AF037140 atpD
subsp.

choleraesuis serotype dublin Salmonella choleraesuis K771 AF037139 atpD
subsp.

choleraesuis serotype dublin Salmonella choleraesuis S84366 AF037151 atpD

subsp. houtenae Salmonella choleraesuis S84098 AF037152 atpD

subsp. houtenae Salmonella choleraesuis BR2047 AF037153 atpD

subsp. indica Salmonella choleraesuis Div36-86 AF037142 atpD
subsp.

choleraesuis serotype infantis Salmonella choleraesuis NSC72 AF037144 atpD

subsp. salamae Salmonella choleraesuis S114655 AF037145 atpD

subsp. salamae Salmonella choleraesuis Div95-86 AF037143 atpD
subsp.

choleraesuis serotype tennessee Salmonella choleraesuis LT2 AF037141 atpD
subsp.

choleraesuis serotype typhimurium Shewanella putida Genome projectz atpD

Shewanella putrefaciens MR-1 Genome projectz atpD

Stigmatella aurantiaca Sga1 X76879 atpD

Streptococcus bovis JB-1 AB009314 atpD

Table 11. Microbial species for which atpD andlor tuf andlor recA andlor Rad51 andlor dmc1 sequences are available in public databases (continued) Species Strain Accession number Coding gene*
Streptococcus mutans GS-5 031170 atpD

Streptococcus mutans UAB159 Genome projectz atpD

Streptococcus pneumoniae type 4 TIGRZ atpD

Streptococcus pneumoniae Type 4 Genome projectz atpD (V) Streptococcus pyogenes M1-GAS Genome projectz atpD

Streptococcus pyogenes Genome projectz . atpD
(V) Streptococcus sanguis 10904 AF001955 atpD

Streptomyces lividans 1326 222606 atpD

Thermus thermophilus HB8 D63799 atpD (V) Thiobacillus ferrooxidansATCC 33020 M81087 atpD

Treponema pallidum Nichols AE001228 atpD (V) Vibrio alginolyticus X16050 atpD

Vibrio cholerae N 16961 Genome projectz atpD

INolinella succinogenes DSM 1470 X76880 atpD

Yersinia enterocoliticaNCTC 10460 AF037157 atpD

Yersinia pestis CO-92 Genome projectz atpD

Fungi Candida tropicalis M64984 atpD (V) Kluyveromyces lactis 2359/152 037764 atpD

Neurospora crassa X53720 atpD

Saccharomyces cerevisiae M 12082 afpD

Saccharomyces cerevisiae X2180-1A J05409 atpD (V) Schizosaccharomyces pombe 972 h- S47814 atpD (V) Schizosaccharomyces pombe 972 h- M57956 atpD

Parasites Giardia lamblia WB 018938 atpD
Plasmodium falciparum 3D7 L08200 atpD (V) Trypanosoma congolense IL3000 225814 atpD (V) Human and plants Arabidopsis thaliana Columbia X89227 tuf (ef-1 ) Glycine max Ceresia X89058 tuf (ef-1 ) Glycine max Ceresia Y15107 tuf (ef-1 ) Glycine max Ceresia Y15108 tuf (ef-1 ) Glycine max Maple Arrow X66062 tuf (ef-1 ) Pyramimonas disomata AB008010 tuf Homo sapiens L09234 atpD (V) Homo sapiens M27132 atpD

Homo sapiens X03558 tuf (ef-1 ) Table 11. Microbial species for which atpD andlor tuf andlor recA andlor Rad51 andlor dmc1 sequences are available in public databases (continued) Species Strain Accession number Coding gene*
Bacteria Acetobacter aceti D13184 recA

Acetobacfer aceti S60630 recA

Acetobacter altoacetigenesMH-24 E05290 recA

Acetobacter polyoxogenes NBI 1028 D13183 recA

Acidiphilium facilis ATCC 35904 D16538 recA

Acinetobacfer calcoaceticusBD413/ADP1 L26100 recA

Acholeplasma laidlawii 8195 M81465 recA

Aeromonas salmonicida A449 083688 recA

Agrobacterium tumefaciens C58 L07902 recA

Allochromatium vinosum AJ000677 recA

Anabaena variabilis ATCC 29413 M29680 recA

Aquifex pyrophilus KolSa L23135 recA

Azotobacter vinelandii S96898 recA

Bacillus subtilis PB1831 087792 recA

Bacteroides fragilis M63029 recA

Bifidobacterium breve NCFB 2258 AF094756 recA

Blastochloris viridis DSM 133 AF022175 recA

Bordetella pertussis 165 X53457 recA

Borrelia burgdorferi Sh-2-82 023457 recA

Brevibacterium flavum MJ-233 E10390 recA

Brucella abortus 2308 L00679 recA

Burkholderia cepacia ATCC 17616 070431 recA

Campylobacter jejuni 81-176 003121 recA

Chlamydia trachomatis L2 U 16739 recA

Chloroflexus aurantiacus J-10-fl AF037259 recA

Clostridium perfringens 13 061497 recA

Corynebacterium glutamicumAS019 U 14965 recA

Corynebacterium glutamicumAS019 X77384 recA

Corynebacterium pseudotuberculosis 030387 recA

Deinococcus radiodurans KD8301 AB005471 recA

Enterobacter agglomerans 339 L03291 recA

Enterococcus faecalis OGIX M81466 recA

Erwinia carotovora X55554 recA

Escherichia coli J01672 recA

Escherichia coli X55552 recA

Escherichia coli K-12 AE000354 recA

Frankia alni Arl3 AJ006707 recA

Gluconobacter oxydans 021001 recA

Haemophilus influenzae Rd 032687 recA

Haemophilus influenzae Rd 032741 recA

Haemophilus influenzae Rd L07529 recA

Helicobacter pylori 69A 235478 recA

SO Lactococcus lactis ML3 M88106 recA

Legionella pneumophila X55453 recA

Leptospira biflexa serovar patoc032625 recA

Leptospira interrogans serovar pomona029169 recA

Magnetospirillum magnetotacticumMS-1 X17371 recA

SS Methylobacillus flagellatumMFK1 M35325 recA

Table 11. Microbial species for which atpD andlor tuf andlor recA andlor Rad51 andlor dmcl sequences are available in public databases (continued) Species Strain Accession number Coding gene*
Methylomonas clara ATCC 31226 X59514 recA

Mycobacterium leprae X73822 recA

Mycobacterium tuberculosisH37Rv X58485 recA

Mycoplasma genitalium G37 039717 recA

Mycoplasma mycoides GM9 L22073 recA

Mycoplasma pulmonis KD735 L22074 recA

Myxococcus xanthus L40368 recA

Neisseria animalis NCTC 10212 057910 recA

Neisseria cinerea LCDC 81-176 AJ223869 recA

Neisseria cinerea LNP 1646 057906 recA

Neisseria cinerea NCTC 10294 AJ223871 recA

Neisseria cinerea Vedros M601 AJ223870 recA

Neisseria elongate CCUG 2131 AJ223882 recA

Neisseria elongate CCUG 4165A AJ223880 recA

Neisseria elongate CCUG 4557 AJ223879 recA

subsp. intermedia Neisseria elongate NCTC 10660 AJ223881 recA

Neisseria elongate NCTC 11050 AJ223878 recA

Neisseria elongate NHITCC 2376 AJ223877 recA

Neisseria flava Bangor 9 AJ223873 recA

Neisseria flavescens LNP 444 057907 recA

Neisseria gonorrhoeae CH95 057902 recA

Neisseria gonorrhoeae FA19 X64842 recA

Neisseria gonorrhoeae MS11 X17374 recA

Neisseria lactamica CCUC 7757 AJ223866 recA

Neisseria lactamica CCUG 7852 Y11819 recA

Neisseria lactamica LCDC 77-143 Y11818 recA

Neisseria lactamica LCDC 80-111 AJ223864 recA

Neisseria lactamica LCDC 845 AJ223865 recA

Neisseria lactamica NCTC 10617 057905 recA

Neisseria lactamica NCTC 10618 AJ223863 recA

Neisseria meningitides 44/46 X64849 recA

Neisseria meningitides Bangor 13 AJ223868 recA

Neisseria meningitides HF116 X64848 recA

Neisseria meningitides H F 130 X64844 recA

Neisseria meningitides H F46 X64847 recA

Neisseria meningitides M470 X64850 recA

Neisseria meningitides N9411 X64846 recA

Neisseria meningitides NCTC 8249 AJ223867 recA

Neisseria meningitides P63 X64845 recA

Neisseria meningitides S3446 057903 recA

Neisseria meningitides S3446 X64843 recA

Neisseria mucosa LNP 405 057908 recA

Neisseria mucosa Vedros M1801 AJ223875 recA

Neisseria perflava CCUG 17915 AJ223876 recA

Neisseria pen'lava LCDC 85402 AJ223862 recA

Neisseria pharynges NCTC 4590 057909 recA

Neisseria polysacchareaCCUG 18031 Y11815 recA

Neisseria polysacchareaCCUG 24845 Y11816 recA

Neisseria polysacchareaCCUG 24846 Y11814 recA

Table 11. Microbial species for which atpD andlor tuf andlor recA andlor Rad51 andlor dmc1 sequences are available in public databases (continued) Species Strain Accession number Coding gene*
Neisseria polysacchareaINS MA 3008 Y11817 recA

Neisseria polysacchareaNCTC 11858 057904 recA

Neisseria sicca NRL 30016 AJ223872 recA

Neisseria subflava NRL 30017 AJ223874 recA

Paracoccus denitrificansDSM 413 059631 recA

Pasteurella multocida X99324 recA

Porphyromonas gingivalisW83 070054 recA

Prevotella ruminicola JCM 8958 061227 recA

Proteus mirabilis pG1300 X14870 recA

Proteus vulgaris X55555 recA

Pseudomonas aeruginosa X05691 recA

Pseudomonas aeruginosa PAM 7 X52261 recA

Pseudomonas aeruginosa PA012 D13090 recA

Pseudomonas cepacia D90120 recA

Pseudomonas fluorescensOE 28.3 M96558 recA

Pseudomonas putida L12684 recA

Pseudomonas putida PpS145 070864 recA

Rickettsia prowazekii Madrid E AJ235273 recA

Rickettsia prowazekii Madrid E 001959 recA

Rhizobium leguminosarumVF39 X59956 recA

biovar viciae Rhizobium phaseoli CNPAF512 X62479 recA

Rhodobacter capsulatus J50 X82183 recA

Rhodobacter sphaeroides2.4.1 X72705 recA

Serratia marcescens M22935 recA

Sinorhizobium meliloti 2011 X59957 recA

Shigella flexneri X55553 recA

Shigella sonnei KNIH104S AF101227 recA

Staphylococcus aureus L25893 recA

Streptococcus gordonii Challis V288 L20574 recA

Streptococcus mutans UA96 M81468 recA

Streptococcus pneumoniae 217307 recA

Streptococcus pneumoniae8800 234303 recA

Streptococcus pyogenes NZ131 021934 recA

Streptococcus salivarius M94062 recA

subsp. thermophilus Streptomyces ambofaciensDSM 40697 230324 recA

Streptomyces coelicolorA3(2) AL020958 recA

Streptomyces lividans TK24 X76076 recA

Streptomyces rimosus R6 X94233 recA

Streptomyces venezuelaeATCC10712 004837 recA

Synechococcus spp. PR6 M29495 recA

Thermotoga maritime L23425 recA

Thermus aquaticus L20095 recA

Thermus thermophilus HB8 D17392 recA

Thiobacillus ferrooxidans M26933 recA

Vibrio anguillarum M80525 recA

Vibrio cholerae 017 X71969 recA

Vibrio cholerae 2740-80 U 10162 recA

S Vibrio cholerae 5698 L42384 recA
S

Table 11. Microbial species for which atpD andlor tuf and/or recA andlor Rad51 andlor dmcl sequences are available in public databases (continued) Species Strain Accession number Coding gene*
Vibrio cholerae M549 AF117881 recA

Vibrio cholerae M553 AF117882 recA

Vibrio cholerae M645 AF117883 recA

Vibrio cholerae M793 AF117878 recA

Vibrio cholerae M794 AF117880 recA

Vibrio cholerae M967 AF117879 recA

Xanthomonas citri XW47 AF006590 recA

Xanthomonas oryzae AF013600 recA

Xenorhabdus bovieni T228/1 U87924 recA

Xenorhabdus nematophilusAN6 AF127333 recA

Yersinia pestis 231 X75336 recA

Fungi, parasites, human and plants Arabidopsis thaliana U43652 Rad51 Coprinus cinereus Okayama-7 U21905 Rad51 Emericella nidulans 280341 Rad51 Gallus gallus L09655 Rad51 Homo sapiens D13804 Rad51 Leishmania major Friedlin AF062379 Rad51 Neurospora crassa 74-OR23-1A D29638 Rad51 Saccharomyces cerevisiae D10023 Rad51 Schizosaccharomyces pombe 222691 Rad51 Tetrahymena thermophila PB9R AF064516 Rad51 Trypanosoma brucei stock 427 Y13144 Rad51 Ustilago maydis U62484 Rad51 Xenopus laevis D38488 Rad51 Xenopus laevis D38489 Rad51 Candida albicans U39808 dmcl Homo sapiens D63882 dmcl Leishmania major Friedlin AF062380 dmcl Mus musculus D58419 dmcl Schizosaccharomyces pombe 972h- AL021817 dmcl * atpD indicates atpD sequences of the F-type afpD (V) indicates atpD sequences of the V-Type tuf indicates tuf sequences tuf (C) indicates tuf sequences divergent from main (usually A and B) copies of the elongation factor-Tu tuf (ef-1 ) indicates tuf sequences of the eukaryotic type (elongation factor 1 a) tuf (M) indicates tufsequences from organellar (mostly mitochondrial) origin recA indicates recA sequences, Rad51 indicates Rad51 sequences or rad51 homologs and dmcl indicates dmcl sequences or dmc1 homologs ' Nucleotides sequences published in Arch. Microbiol. 1990 153:241-247 2 These sequences are from TIGR database (http://www.tigr.org/tdb/tdb.html) 3 Nucleotides sequences published in FEMS Microbiology Letters 1988 50:101-106 Annex I: Specific and ubiquitous primers for DNA amplification (tuf sequences) Originating DNA fragment SEQ ID NO. Nucleotide sequence SEQ ID Nucleotide NO. position R~ rial e=ecies: Chlamydia pneumoniae 630 5'-CGG AGCTAT CCT CGT A 20 2- 23 AGT TTC

629a 5'-AAG TTCCAT CTC AAG AAT A 20 146 -170 AAC GTC

1$ Bacte_ri_al_er~ecie~: Chlamydia trachomatis 554 5'-GTT CCTTAC ATC GTT CTC 22 82- 105 GTT TTT

555a 5'-TCT CGAACT TTC ATG GCA 22 249 -272 TCT TAT

paraeitical yecie~ : Cryptosporidium parvum 798 5'-TGG TTGTCC CAG ATC T 865 158 -179 CCG GTT

804a 5'-CCT GGGACG GCC GGC 865 664 -683 TCT AT

2$ 799 5'-ACC TGTGAA TAC CAA 865 280 -300 AAG TCT

805a 5'-CTC TTGTCC ATC GCA 865 895 -914 TTA GT

800 5'-GAT GAAATC TTC GAA GAT 865 307 -330 AAC GTT

806a 5'-AGC ATCACC AGA GAT 865 946 -966 CTT AAG

801 5'-ACA ACACCG AGA TCC 865 353 -372 AGA CA

803a 5'-ACT TCAGTG GTA CCA 865 616 -635 ACA GC

802 5'-TTG CCATTT CTG TCG 865 377 -396 GTT TT

3$ 807a 5'-AAA GTGGCT TCA GTT 865 981-1000 AAG GC

Bacterial species: Neisseria gonorrhoeae 551 5'-GAA GAA AAA ATC TTC GAA CTG GCT A 126 256-280 552a 5'-TAC ACG GCC GGT GAC TAC G 126 378-396 Bacterial species: Streptococcus agalactiae 549 5'-GAA CGT GAT ACT GAC AAA CCT TTA 207-210b 308-331c 4$ 550a 5'-GAA GAA GAA CAC CAA CGT TG 207-210b 520-539c $0 a These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.
b These sequences were aligned to derive the corresponding primer.
c The nucleotide positions refer to the S. agalactiae tuf sequence fragment $$ (SEQ ID NO. 209) .

Annex I: Specific and ubiquitous primers for DNA amplification (tuf sequences) (continued) OriginatingDNA fragment SEQ ID NO. Nucleotide sequence SEQ ID Nucleotide NO. position Pa_raSi_ a1 yec,_'~: Trypanosoma brucei i ~

820 5'-GAA GGAGGT GTC TGC TTA 864 513-533 CAC

821a 5'-GGC GCAAAC GTC ACC ACA 864 789-809 TCA

820 5'-GAA GGAGGT GTC TGC TTA 864 513-533 CAC

822a 5'-CGG CGGATG TCC TTA ACA 864 909-929 GAA

Pa_ra~i a~ mP.r;~~: Trypanosoma cruzi i.

794 5'-GAC GACAAG TCG GTG AAC 840-842b 281-300c TT

795a 5'-ACT TGCACG CGA TGT GGC 840-842b 874-893c AG

Bacter,'_a1_ate: Bordetella spp.

2$ 825 5'-ATG AGCARC GSA ACC ATC CAG 863 1-26 GTT TG

826 5'-TCG ATCGTG CCG ACC ATG AAC 863 1342-1367 TAG GC

Fpn~a1 qe ~: Candida spp.

576 5'-AAC TTCRTC AAG AAG GTY TAC 407-426, 332-357d GGT AA

428-432b 632a 5'-CCC TTTGGT GGR TCS TKC GA 407-426, 791-813d TTG

428-432b 631 5'-CAG ACCAAC YGA IAA RCC RAG 407-426, 523-5484 ATT AT

428-432b 632a 5'-CCC TTTGGT GGR TCS TKC GA 407-426, 791-8134 TTG

428-432b 633 5'-CAG ACCAAC YGA IAA RCC RAG 407-426, 523-5484 ITT AT

428-432b 632a 5'-CCC TTTGGT GGR TCS TKC GA 407-426, 791-8134 TTG

428-432b a These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.
b These sequences were aligned to derive the corresponding primer.
c The nucleotide positions refer to the T. cruzi tuf sequence fragment (SEQ ID
NO. 842) .
d The nucleotide positions refer to the C. albicans tuf(ef-1) sequence fragment (SEQ ID NO. 408).

Annex I: Specific and ubiquitous primers for DNA amplification (tuf sequences) (continued) Originating DNA fragment SEQ ID NO. Nucleotide sequence SEQ ID Nucleotide NO. position Bacte_r;al ~~nLS: Clostridium spp.
796 5'-GGT CCA ATG CAA ACW AGA 32,719- 32-52b CCW

724,736a 797c 5'-CAT TAA GAA YTT ATC TGT SKC 32,719- 320-346b TGG TCT

IS 724,736a 808 5'-GCI TTA IWR TTA GAA RAY CCA 32,719- 224-247b GCA

724,736a 8090 5'-TCT TCC TGT AAC TGT TCC TCT 32,719- 337-360b WGC

724,736a 810 5'-AGA GMW ACA GAT AAR SCA TTC TTA 32,719- 320-343b 724,736a 811c 5'-TRA ART AGA ATT GTG GTC TRT ATC C 32,719- 686-710b 724,736a Bacter,'al =~nLS Corynebacterium spp.
545 5'-TAC ATC GTY CTI AAC AAG 34-44,662a 89-1144 CTB GCI TG

546c 5'-CCR CGI GTR GTG AAG AT 34-44,662a 350-3724 CCG ATG

Pa_ras,_'t;_cal_ qen~e: Entamoeba spp.

703 5'-TAT GGA TCG CAT CT 512 38-57 AAT AAA

704c 5'-AGT GCT ATT GTT GG 512 442-461 CCA AAT

703 5'-TAT GGA TCG CAT CT 512 38-57 AAT AAA

705c 5'-GTA CAG CAA CTG AA 512 534-553 TTC TAC

703 5'-TAT GGA TCG CAT CT 512 38-57 AAT AAA

7060 5'-TGA AAT CAC CAA CA 512 768-787 CTT ATC

793 5'-TTA TTG CTG GTA CT 512 149-168 TTG CTG

704c 5'-AGT GCT ATT GTT GG 512 442-461 CCA AAT

a These sequences were aligned to derive the corresponding primer.
b The nucleotide positions refer to the C. perfringens tuf sequence fragment (SEQ ID NO. 32).
c These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.
d The nucleotide positions refer to the C. diphtheriae tuf sequence fragment (SEQ ID NO. 662).

Annex I: Specific and ubiquitous primers for DNA amplification (tuf sequences) (continued) Originating DNA fragment SEQ ID NO. Nucleotide sequence SEQ ID Nucleotide NO. position Para~i i a1 a _n_L~ : Trypanosoma spp.
823 5'-GAG CGG TAT GAY GAG ATT GT 529,840- 493-512b 842,864a 824c 5'-GGC TTC TGC GGC ACC ATG CG 529,840- 1171-1190b 1S 842,864a Mycobacter3aceae 539 5'-CCI TACATC CTBGTYGCI CTIAACAAG 122 85-111 540c 5'-GGD GCITCY TCRTCGWAI TCCTG 122 181-203 Ba r;a~ ~_roLp: Enterobac teriaceae group 933 5'-CAT CATCGT ITTCMTGAA CAARTG78,103,146, 390-4134 2$ 168,238,698a 934c 5'-TCA CGYTTR RTACCACGC AGIAGA78,103,146, 831-8544 168,238,698a Pa_ras,'_t,'_cal c~~_oup: Kinetoplastidae group 923 5'-GAC GCI GCC ATC CTG ATG ATC 511,514-526, 166-188e 529,840-842, 864a 924c 5'-ACC TCA GTC GTC ACG TTG GCG 511,514-526, 648-668e 529,840-842, 864a 925 5'-AAG CAG ATG GTT GTG TGC TG 511,514-526, 274-293e 529,840-842, 864a 926c 5'-CAG CTG CTC GTG GTG CAT CTC GAT 511,514-526, 676-699e 529,840-842, 864a a These sequences were aligned to derive the corresponding primer.
b The nucleotide positions refer to the T. brucei tuf sequence fragment (SEQ
ID
NO. 864).
c These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.
d The nucleotide positions refer to the E. coli tuf sequence fragment (SEQ ID
NO. 698).
a The nucleotide positions refer to the L. tropica tuf sequence fragment (SEQ
ID NO. 526).

Annex I: Specific and ubiquitous primers for DNA amplification (tuf sequences) (continued) Originating DNA fragment SEQ ID NO. Nucleotide sequence SEQ ID Nucleotide NO. position ara~i i.a1 yrou~: Kinetoplastidae group (continued) 927 5'-ACG CGG AGA AGG TGC GCT T 511,514-526, 389-407b 529,840-842, 864a 1$ 928c 5'-GGT CGT TCT TCG AGT CAC CGC A 511,514-526, 778-799b 529,840-842, 864a Bacte_r,'_a1 groL~: Pseudomonads group 541 5'-GTK GAA ATG TTC CGC AAG CTG CT 153-155a 476-4984 542c 5'-CGG AAR TAG AAC TGS GGA CGG TAG 153-155a 679-702d 541 5'-GTK GAA TTCCGCAAG CTGCT 153-155a 476-498d ATG

544c 5'-AYG TTG TCGCCMGGCATT MCCAT 153-155a 749-7714 Universal primers 636 5'-ACT GGY GTTGAIATGTTC CGYAA 7,54,78, 470-492e 100,103,159, 209,224,227b 637a 5'-ACG TCA GTIGTACGGAAR TAGAA 7,54,78, 692-714e 100,103,159, 209,224,227b 638 5'-CCA ATG CCACAAACICGT GARCACAT 7,54,78, 35-60f 100,103,159, 209,224,227b 639a 5'-TTT ACG GAACATTTCWAC ACCWGTIAC A 7,54,78, 469-496f 100,103,159, 209,224,227b a These sequences were aligned to derive the corresponding primer.
b The nucleotide positions refer to the L. tropica tuf sequence fragment (SEQ
4$ ID NO. 526).
c These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.
d The nucleotide positions refer to the P. aeruginosa tuf sequence fragment (SEQ ID NO. 153).
a The nucleotide positions refer to the E. coli tuf sequence fragment (SEQ ID
NO. 78) .
f The nucleotide positions refer to the B. cereus tuf sequence fragment (SEQ
ID
No. 7).

Annex I: Specific and ubiquitous primers for DNA amplification (tuf sequences) (continued) Originating DNA fragment SEQ ID N0. Nucleotide sequence SEQ ID Nucleotide NO. position 643 5'-ACT GGI GTI GAR ATG TTC CGY AA 1,3,4,7,12, 470-492b 13,16,49,54, 72,78,85,88, 91,94,98,103, 108,112,115, 116,120,121, 126,128,134, 136,146,154, 159,179,186, 205,209,212, 224,238a 644c 5'-ACG TCI GTI GTI CKG AAR TAG AA 1,3,4,7,12, 692-714b 13,16,49,54, 72,78,85,88, 91,94,98,103, 108,112,115, 116,120,121, 126,128,134, 136,146,154, 159, 179, 186, 205,209,212, 224,238a 3$ a These sequences were aligned to derive the corresponding primer.
b The nucleotide positions refer to the E. coli tuf sequence fragment (SEQ ID
NO. 78) .
c These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.

Annex I: Specific and ubiquitous primers for DNA amplification (tuf sequences) (continued) Originating DNA fragment S
SEQ ID NO. Nucleotide sequence SEQ ID Nucleotide N0. position l~ 643 5'-ACT GGIGTI GARATGTTC CGYAA 1,3,4,7,12, 470-492b 13,16,49,54, 72,78,85,88, 91,94,98,103, 108,112,115, 1$ 116,120,121, 126,128,134, 136,146,154, 159,179,186, 205,209,212, 224,238a 645c 5'-ACG TCIGTI GTICKGAAR TARAA 1,3,4,7,12, 692-714b 13,16,49,54, 72,78,85,88, 91,94,98,103, 25 108,112,115, 116,120,121, 126,128,134, 136, 146, 154, 159,179,186, 205,209,212, 224,238a 646 5'-ATC GACAAG CCITTCYTI ATGSC 2,13,82 317-339d 122,145a 3S 647c 5'-ACG TCCGTS GTRCGGAAG TAGAAC 2,13,82 686-7114 TG

122,145a 646 5'-ATC GACAAG CCITTCYTI ATGSC 2,13,82 317-339d 122,145a 40 648c 5'-ACG TCSGTS GTRCGGAAG TAGAAC 2,13,82 686-711d TG

122,145a a These sequences were aligned to derive the corresponding primer.
b The nucleotide positions refer to the E. coli tuf sequence fragment (SEQ ID
NO. 78).
c These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.
d The nucleotide positions refer to the A. meyeri tuf sequence fragment (SEQ
ID
NO. 2) Annex I: Specific and ubiquitous primers for DNA amplification (tuf sequences) (continued) Originating DNA fragment SEQ ID NO. Nucleotide sequence SEQ ID Nucleotide NO. position Universal primers (continued) 649 5'-GTC CTA TGCCTCARACWC GIGAGC 8,86,141,143a33- 58b AC

6500 5'-TTA CGG AACATYTCAACA CCIGT 8,86,141,143a473-495b 1S 636 5'-ACT GGY GTTGAIATGTTC CGYAA 8,86,141,143a473-495b 6510 5'-TGA CGA CCACCITCYTCY TTYTTC 8,86,141,143a639-663b A

Sequencing rimers p 556 5'-CGG CGC NATCYTSGTTGT TGC 6684 306 -326 557c 5'-CCM AGG CATRACCATCTC GGTG 6684 1047-1068 694 5'-CGG CGC IATCYTSGTTGT TGC 6684 306 -326 557c 5'-CCM AGG CATRACCATCTC GGTG 6684 1047-1068 664 5'-AAY ATGATI ACIGGIGCI GCICAR ATG 619d 604-632 GA

652c 5'-CCW AYAGTI YKICCICCY TCYCTI ATA 6194 1482-1508 664 5'-AAY ATGATI ACIGGIGCI GCICAR ATG 6194 604-632 GA

561c 5'-ACI GTICGG CCRCCCTCA CGGAT 6194 1483-1505 543 5'-ATC TTAGTA GTTTCTGCT GCTGA 607 8-30 660c 5'-GTA GAATTG AGGACGGTA GTTAG 607 678-700 3$ 658 5'-GAT YTAGTC GATGATGAA GAATT 621 116-138 659c 5'-GCT TTTTGI GTTTCWGGT TTRAT 621 443-465 658 5'-GAT YTAGTC GATGATGAA GAATT 621 116-138 661c 5'-GTA GAAYTG TGGWCGATA RTTRT 621 678-700 558 5'-TCI TTYAAR TAYGCITGG GT 665d 157-176 559c 5'-CCG ACRGCR AYIGTYTGI CKCAT 6654 1279-1301 813 5'-AAT CYGTYG AAATGCAYC ACGA 6654 687-708 559c 5'-CCG ACRGCR AYIGTYTGI CKCAT 6654 1279-1301 a These sequences aligned to primer.
were derive the corresponding b The refer to the B. distasonisuf sequence nucleotide t fragment positions SO (SEQ ID NO. 8).

c These sequences fromthe complementary the are DNA sequence strand of of the originating given Sequence fragment in Listing.
the d Sequences .
from data banks Annex I: Specific and ubiquitous primers for DNA amplification (tuf sequences) (continued) Originating DNA fragment SEQ ID NO. Nucleotide sequence SEQ ID Nucleotide NO. position Sequencing primers (continued) 558 5'-TCI TTY AAR TAY GCI TGG GT 665a 157-176 815b 5'-TGG TGC ATY TCK ACR GAC TT 665a 686-705 1$ 560 5'-GAY TTC ATY AAR AAY ATG ATY AC 665a 289-311 559b 5'-CCG ACR GCR AYI GTY TGI CKC AT 665a 1279-1301 653 5'-GAY TTC ATI AAR AAY ATG AT 665a 289-308 559b 5'-CCG ACR GCR AYI GTY TGI CKC AT 665a 1279-1301 558 5'-TCI TTYAAR TAYGCITGG GT 665a 157-176 655b 5'-CCR ATACCI CMRATYTTG TA 665a 754-773 654 5'-TAC AARATY KGIGGTATY GG 665a 754-773 2S 559b 5'-CCG ACRGCR AYIGTYTGI CKCAT 665a 1279-1301 696 5'-ATI GGICAY RTIGAYCAY GGIAAR AC 698a 52-77 697b 5'-CCI ACIGTI CKICCRCCY TCRCG 698a 1132-1154 911 5'-GAC GGMKKC ATGCCGCAR AC 853 22-41 914b 5'-GAA RAGCTG CGGRCGRTA GTG 853 700-720 912 5'-GAC GGCGKC ATGCCGCAR AC 846 20-39 914b 5'-GAA RAGCTG CGGRCGRTA GTG 846 692-712 913 5'-GAC GGYSYC ATGCCKCAG AC 843 251-270 915b 5'-AAA CGCCTG AGGRCGGTA GTT 843 905-925 916 5'-GCC GAGCTG GCCGGCTTC AG 846 422-441 561b 5'-ACI GTICGG CCRCCCTCA CGGAT 619a 1483-1505 664 5'-AAY ATGATI ACIGGIGCI GCICAR ATG 619a 604-632 GA

917b 5'-TCG TGCTAC CCGTYGCCG CCAT 846 593-614 a Sequences from data banks.
b These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.

Annex II: Specific and ubiquitous primers for DNA amplification (atpD sequences) Originating DNA fragment SEQ ID NO. Nucleotide sequence SEQ ID Nucleotide NO. position Ba r;al s=PCies: Streptococcus agalactiae 627 5'-ATT GTCTAT AAA GGC GATAAGTC 379-383a 42-67b AAT

625c 5'-CGT TGAAGA CAC CCA AAGTATCC 379-383a 206-231b GAC

628 5'-AAA ATGGCG ATA CAC AAAAAGTA 379-383a 52-77b AGT

625c 5'-CGT TGAAGA CAC CCA AAGTATCC 379-383a 206-231b GAC

627 5'-ATT GTCTAT AAA GGC GATAAGTC 379-383a 42-67b AAT

626c 5'-TAC CACCTT TTA AAG GTGCTAAT 379-383a 371-396b AGT

628 5'-AAA ATGGCG ATA CAC AAAAAGTA 379-383a 52-77b AGT

626c 5'-TAC CACCTT TTA AAG GTGCTAAT 379-383a 371-396b AGT

Bacte_r,'_a1_~~enLS Candida pp.
s 634 5'-AAC ACYGTC AGR ATT GCYATGGA 460-472, 101-1264 RCI

474-478a 635c 5'-AAA CCRGTI ARR ACT CTIGCTCT 460-472, 617-6424 GCR

474-478a a These sequences were aligned to derive the corresponding primer.
b The nucleotide positions refer to the S. agalactiae atpD sequence fragment (SEQ ID NO. 380).
c These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.
d The nucleotide positions refer to the C. albicans atpD sequence fragment (SEQ
ID NO. 460).

Annex II: Specific and ubiquitous primers for DNA amplification (atpD sequences) (continued) S -- Originating DNA fragment SEQ ID NO. Nucleotide sequence SEQ ID Nucleotide NO. position Universal primers 562 5'-CAR ATG RAY CCICCI GGI GYI MGI ATG 243,244,262,528-557b GAR

264,280,284, 291,297,309, 1S 311,315,317, 324,329,332, 334-336,339, 342,343,351, 356,357,364-366,370,375, 379,393a 563c 5'-GGY TGR TAI ACIGCI GAI GGC AT 243,244,262, 687-712b CCI

264,280,284, 291,297,309, 2S 311,315,317, 324,329,332, 334-336,339, 342,343,351, 356,357,364-30 366,370,375, 379,393a 564 5'-TAY GGI CAR AAYGAR CCI CCI GGI AA 243,244,262, 522-550b ATG

264,280,284, 3S 291,297,309, 311,315,317, 324,329,332, 334-336,339, 342,343,351, 356,357,364-366,370,375, 379,393a 565c 5'-GGY TGR TAI ACIGCI GAI GGD AT 243,244,262, 687-712b CCI

264,280,284, 4S 291,297,309, 311,315,317, 324,329,332, 334-336,339, 342,343,351, S~ 356,357,364-366,370,375, 379,393a a These sequences were aligned to derive the corresponding primer.

b The refer nucleotide to positions the K.
pneumoniae atpD
sequence fragment SS (SEQ ID NO. 317).

c These sequences are thecomplementary DNA strand of the from sequence of the originating the Sequence Listing.
fragment given in Annex II: Specific and ubiquitous primers for DNA amplification (atpD sequences) (continued) Originating DNA fragment SEQ ID NO. Nucleotide sequence SEQ ID Nucleotide N0. position Universal primers (continued) 640 5'-TCC ATG GTITWY CARATG AA 248,284,315, 513-535b GGI

317,343,357, 366,370,379,393a 6410 5'-TGA TAA CCWACI GAIGGC ATA 248,284,315, 684-709b GCI CG

317,343,357, 366,370,379,393a 642 5'-GGC GTI GGIGAR ACICGT GA 248,284,315, 438-460b CGI

317,343,357, 366,370,379,393a 641c 5'-TGA TAA CCWACI GAIGGC ATA 248,284,315, 684-709b GCI CG

317,343,357, 366,370,379,393a Sequencing primers 566 5'-TTY GGI GGIGCI GTIGGI AAR 6694 445-470 GGI AC

567c 5'-TCR TCI GCIGGI TAIAYI GCY 6694 883-908 ACR TG

566 5'-TTY GGI GGIGCI GTIGGI AAR 6694 445-470 GGI AC

814 5'-GCI GGC ACGTAC GCCTG 666d 901-920 ACI

568 5'-RTI ATI GGIGCI RTIGAY GT 669d 25-47 GTI

567c 5'-TCR TCI GCIGGI TAIAYI GCY 669d 883-908 ACR TG

570 5'-RTI RYIGGICCI GTIRTIGAY GT 672d 31-53 567c 5'-TCR TCIGCIGGI ACRTAIAYI GCYTG 6694 883-908 572 5'-RTI RTIGGISCI GTIRTIGA 6694 25-44 567c 5'-TCR TCIGCIGGI ACRTAIAYI GCYTG 6694 883-908 569 5'-RTI RTIGGISCI GTIRTIGAT AT 6714 31-53 567c 5'-TCR TCIGCIGGI ACRTAIAYI GCYTG 669d 883-908 571 5'-RTI RTIGGICCI GTIRTIGAT GT 670d 31-53 567c 5'-TCR TCIGCIGGI ACRTAIAYI GCYTG 6694 883-908 a These sequences were aligned to derive the corresponding primer.
b The nucleotide positions refer to the K. pneumoniae atpD sequence fragment SO (SEQ ID NO. 317).
c These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.
d Sequences from data banks.

Annex II: Specific and ubiquitous primers for DNA amplification (atpD sequences) (continued) OriginatingDNA fragment SEQ ID NO. Nucleotide sequence SEQ ID Nucleotide NO. position Sequencing (continued) primers 700 5' -TIRTIGAYG TCGARTTCC CTCARG 669a 38-61 567b 5' -TCRTCIGCI GGIACRTAI AYIGCYTG 669a 883-908 1S 568 5' -RTIATIGGI GCIGTIRTI GAYGT 669a 25-47 573b 5' -CCICCIACC ATRTARAAI GC 666a 1465-1484 574 5' -ATIGCIATG GAYGGIACI GARGG 666a 283-305 573b 5' -CCICCIACC ATRTARAAI GC 666a 1465-1484 574 5' -ATIGCIATG GAYGGIACI GARGG 666a 283-305 708b 5' -TCRTCCATI CCIARIATI GCIATIAT 666a 1258-1283 681 5' -GGISSITTY GGIISIGGI AARAC 685 694-716 682b 5' -GTIACIGGY TCYTCRAAR TTICCICC 686 1177-1202 681 5' -GGISSITTY GGIISIGGI AARAC 685 694-716 683b 5' -GTIACIGGI TCISWIAWR TCICCICC 685 1180-1205 681 5' -GGISSITTY GGIISIGGI AARAC 685 694-716 699 5' -GTIACIGGY TCYTYRARR TTICCICC 686 1177-1202 681 5' -GGISSITTY GGIISIGGI AARAC 685 694-716 812b 5' -GTIACIGGI TCYTYRARR TTICCICC 685 1180-1205 a Sequences from data banks.
b These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.

Annex III: Specific and ubiquitous probes for hybridization (tuf sequences) Originating DNA fragment SEQ ID NO. Nucleotide sequence SEQ ID Nucleotide NO. position Ba r; 1 S=ue Candida albicans 577 5'-CAT GAT TGA ACC ATC CAC CA 407-411a 406-425b Ba r;a1 ~=Pr;P~: Candida dubliniensis 578 5'-CAT GAT TGA AGC TTC CAC CA 412,414-415a 418-437c Bacterialenec,_'es: Enterococcus faecalis 580 5'-GCT AAA CCA GCT ACA ATC ACT CCA C 62-63,607a 584-608d 603 5'-GGT ATT AAA GAC GAA ACA TC 62-63,607a 440-459d Ba ri 1 ~= eC'; P~ : Enterococcus faecium 602 5'-AAG TTG AAG TTG TTG GTA TT 64,608a 426-445e Bacter,'a1 y ec,'_e~: Enterococcus gallinarum 604 5'-GGT GAT GAA GTA GAA ATC GT 66,609a 419-438f Ba ; l = r; ~ Escherichia coli 579 5'-GAA GGC CGT GCT GGT GAG AA 78 503-522 a These sequences were aligned to derive the corresponding primer.
b The nucleotide positions refer to the C. albicans tuf(ef-1) sequence fragment (SEQ ID N0. 408) .
c The nucleotide positions refer to the C. dubliniensis tuf(ef-1) sequence fragment (SEQ ID NO. 414).
d The nucleotide positions refer to the E. faecalis tuf sequence fragment (SEQ
ID NO. 607).
a The nucleotide positions refer to the E. faecium tuf sequence fragment (SEQ
ID N0. 608).
f The nucleotide positions refer to the E. gallinarum tuf sequence fragment (SEQ ID NO. 609) .

Annex III: Specific and ubiquitous probes for hybridization (tuf sequences) (continued) Originating DNA fragment SEQ ID NO. Nucleotide sequence SEQ ID Nucleotide NO. position Bacte_r,'_al ,y ec,_'c~: Haemophilus 3nfluenzae 581 5'-ACA TCG GTG CAT TAT TAC GTG G 610a 551-572b Bactcrialy ec,_'es: Staphylococcus aureus 584 5'-ACA TGACACATC TAA AA 176-180c 369-3884 AAC

585 5'-ACC ACATACTGA ATTCAAAG 176-180c 525-5444 586 5'-CAG AAGTATACG TATTATCA 176-180c 545-5644 587 5'-CGT ATTATCAAA AGACGAAG 176-180c 555-5744 588 5'-TCT TCTCAAACT ATCGTCCA 176-180c 593-6124 Bacter;a,~l ~pec,_'es: Staphylococcus epidermidis 589 5'-GCA CGA TTC TAA AA 185, 611c 445-464e AAC AAC

2S 590 5'-TAT ACG TAT CTA AT 185, 611c 627-646e TAT AAG

591 5'-TCC TGG TAT TAC AC 185, 611c 586-605e TTC ACC

592 5'-CAA AGC AGT ATA AT 185, 611c 616-635e TGA CGT

593 5'-TTC ACT TAT CGC CA 185, 611c 671-690e AAC CCA

Ba ri 1 ~z P('!; P~ : Staphylococcus haemolyticus 594 5'-ATT GGT ATC CAT GAC ACT TC 186,188-190c 437-456f 595 5'-TTA AAG CAG ACG TAT ACG TT 186,188-190c 615-634f Bact rial ncc,_'es; Staphylococcus hominis 596 5'-GAA ATT ATT GGT ATC AAA GA 191,193-196c 431-4508 597 5'-ATT GGT ATC AAA GAA ACT TC 191,193-196c 437-4568 598 5'-AAT TAC ACC TCA CAC AAA AT 191,193-1960 595-6148 a Sequences from data banks.
b The nucleotide positions refer to the H. influenzae tuf sequence fragment (SEQ ID NO. 610).
C These sequences were aligned to derive the corresponding probe.
d The nucleotide positions refer to the S. aureus tuf sequence fragment (SEQ
ID
NO. 179) .
a The nucleotide positions refer to the S. epidermidis tuf sequence fragment (SEQ ID NO. 611).
f The nucleotide positions refer to the S. haemolyticus tuf sequence fragment (SEQ ID NO. 186).
g The nucleotide positions refer to the S. hominis tuf sequence fragment (SEQ
ID NO. 191).

Annex III: Specific and ubiquitous probes for hybridization (tuf sequences) (continued) Originating DNA fragment SEQ ID NO. Nucleotide sequence SEQ ID Nucleotide NO. position Ba ;a1 zeciee: Staphylococcus saprophyticus 599 5'-CGG TGA AGA CGA CA 198-200a 406-425b AAT AAT

600 5'-ATG CAA GAA TCA AA 198-200a 431-450b GAA AGC

601 5'-GTT TCA CGT GAT CA 198-200a 536-555b GAT GTA

1$ 695 5'-GTT TCA CGT GAC CA 198-200a 563-582b GAT GTA

Ba.. r;a1 necies: Streptococcus agalactiae 582c 5'-TTT CAA CTT CGT CGT TGA CAC GAA CAG T 207-210a 404-4314 5830 5'-CAA CTG CTT TTT GGA TAT CTT CTT TAA TAC CAA CG 207-210a 433-4674 Bacterial = roan; Enterococcus casseliflavus-flavescens-gallinarum group 620 5'-ATT GGT GCA TTG CTA CGT 58,65,66a 527-544e Bacterial~~enLS Staphylococcus spp.
605 5'-GAA ATG TTC CGT AAA TTA TT 176-203a 403-422f 606 5'-ATT AGA CTA CGC TGA AGC TG 176-203a 420-439f a These sequences were aligned to derive the corresponding primer.
b The nucleotide positions refer to the S. saprophyticus tuf sequence fragment (SEQ ID NO. 198).
c These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.
d The nucleotide positions refer to the S. agalactiae tuf sequence fragment (SEQ ID NO. 209).
a The nucleotide positions refer to the E. flavescens tuf 'sequence fragment (SEQ ID NO. 65).
f The nucleotide positions refer to the S. aureus tuf sequence fragment (SEQ
ID
NO. 179).

z 61 N ~-i OD
O O
N

,-i l0 r I I ~O l0 I I I r I I r r I r I l0 r r l0 l0 l0 l0 N _ ~-I
l0 l0 N 1-I
N
~
tn ~
tf7 a o 0 w U E E CJ
U U E
E E E
U E E

H U U
U U U
U U U
U H U
U U U

N S-I

U U U ~, O O
H H U U
U U H
H H H
H U

U ~

~ H ~ O N N
U +~ 'Q
~
~ ~
~
~ U H

U U
U U U U 'L3 U U ~
U U
U U U
U U U
U U U
' ~ ~ ~
~ ~

U U H U +
E ~ ~ H ~ =
~ ~ H O
H
H H H
H H H
H H H
H N H
H H

9 ~

h U U

C
C
C
C
C
C
C
C
C

~ ~C ~ ~ ~ +~ ~
~ H

HHHHHHHHHHHHHH H .-.~~-I"fir U' U' H p~~ ' E-~
~~~UUUHHH~UU' W O

H H H H H
H H H ~
H
H
H
H
H
H
N
' U' U' ~ C4 ~ . Sa ~I
U' U' U' U' C7 U U' U
U' H
U
U' , Q .
~ O ~
~ ~ O

~ fC ~ ~ ~
~
~t ~C

,~~r~~~c~~~c~c~c~c~c~c~c~ ~ z ~ a~ s-I
ago m U U (~ ~ O
U FC t]'' .~

C7 r.~

H

o~ E H H N
H H H
E H H
H H H
H H E

N : : : '~ ~ m : : : a 4-I
: : : a : : :
: :

W ~-1 C/7 ~ ~
O

N C7 U , U U U

C7 U' ~

r U U
U U U
C
E r.~
U FC
C
C
C
C~

U U U U
U U U a~ +~
U U U ~ N
U U U
U U

~ ~ ~ ~ ~
~ Wd ~ ~t ~ ~ ~
~ ~ ~

~

C9 C7 x t9 C4 Q U

H H N ~
H 1~

~ U
~ C9 ~ rb b ~ ~ U ~ Z3 .-i ~ ~
~ ~

~~

U ~ ~HHH~ H y.~ ..~
U ' ~
N

H H H H ~ ~ U H
H H H ~rl H H H cn H H H
H H

UUUEE U O
U' U
U
~~~HEU

C I-I-J i C

U' U' N U 3 O
' b -rl ' ' U
' ' ' ' U' U C u1 C7 U J U G
U
C

U
U
U
C
J
H U U
U U U
U U U
U
H E

U H ~ ~ a ~ ~
~
~
~
~
~
~
~
~
~~
~
~~

c c q ~ ~,.u c c t t t t c t t uc c u c~~~~~~~~~~~~~~~ ~ ~'~ ~w .~

U U H H 21 W +~
U U U ' u~ +~
U H H u7 u7 H N U
' ' ' ' ' ' ' ' ' U U w-I ~ O
U '~
U
U
U
C
U
U
U
C
U
' ' ' U' U' U' p, O C7 U' '~ ~-i U ~
C7 U' U' U' U' U' U
U' U
U U U
U U U
U U H
H U U
H H

~ ~ ro ,H
H H H H O +~ p H H H
H H H
H H H
H H

Q ~
m H H H U U ~ p H H H
H H H
H H H
H H H

a C7 C7 N
C7 C~

H C~
~C C~

O ~ H H ro ~r-I
H H H ,H (0 H H H
H H H
H H H

'1"I~ . . .
. . .
. . .
;

a~ U U U
O U U C~ "

U E Ch rrr r.~
r.~ C7 ' ' V U C7 U H '~I ' C7 C7 H ~
E E U H

~ U

U
H H H
H H H
H H H
H H H
E H

~

O ~ U H U ~
U U U ~
U U H N
N N E H
H E

r~O
~I r1 S~

O ~ U U' U H H H H (n Q O
H H H H a.J U Q
H U U
~ U U' H ~

H H H H H H H W +
H H H H
H H H
H H H
H H

C9 ~ U PG P4 !x PG H ~ FC

~ U U
~ C9 HUU' ~HU' H
U' UU' H
H~H~U' H
H
H

O ~ H' F -F' H
H H
H F
H H' ' H
H H
H

F
F
H H

9 f 7 ri~ f c ~ ~ '~
) C C ~ 0 t C

C U' J C H
J C H

U U U H
U ~ ~
H ~

. . U U U U U U O G O W
.. U U U U U U
U U U U U 'b U U
U ~

U ~ O u1 I
v1 u1 U

H H ' T3 '~ ,~
' N

~ ~ ~ U
U

U
U

O O H E H H S-I
H ~ E H CI) A,' H b -ri U H ~I
H

U

Yi 1 ~ m 3 H
H
H

4-1~ ~ ~ ~ a~ .~
'~ ~ G4 b o ~ ~ (x b ~ ~ ~ w +~ oG
H H H H
H H H H
H
H
H

~ U
b~ b~ H
H H H H
H H H H
H H H
H H H

H
H H U' H ~
U' U' P4 U' U' L1G
U' U' C4 U' U' P4 lY

m c~ c7 CT
t7 C7 H
C7 c~ S-I
c7 C7 N ~C FC ~
~C FC O
FC U
r.~ FC
FC ~

l ~

O ~-I H !~
w-I
O

U t1 -i r~ N ~ U x p N ~, p N
N
N

i~ N N
N

U ~n U U W
~ U

~1~N -~-r G rl W -1 w-i G ~
C
C
C
G
G

ro ro N ~
+~ N
~ N
v N
N
~
N

ro ~ U u _ H ~ ~ O T3 ~n ~7 ~
N N U ~
O J ~
~
~
' "
' ' ' ' ' .. , ro b 7 +- W ~
w-10 OUro~I~a~w-i b ~Nb b"
tJ
tS
tt CJ
b NNNNNNN

ro ~ ~ cn N '~ r6 N
.C ro tn U
w-I a ~n W a C m u~
u~
rn w m w ~ .,~ ~ cn H sa o .,~ +~
+~ U m H ro w .~
o w s U a b~ TS CS" - '~
a ~ ~ 'Li +~ tn ~ w U 'O 'Q
W O ~ 'O
~ 'b ' 'b '~

ro a a ~ ~ O ~ cn -H o ~ ~
si ro v v O, v w a~
Lt +~ a~
a o a~

~a O ~

s-y., U LY .1.-~
O U C U H
J, U
N N O U
O .C U
a U
U

U Cl, N -i .
O ro U N = u7 0~ .t~ N c E-~
ro .u v V-i ~i N
3 ro N
f1 (.~, N

~-I ~ U
H N
.-a ~I
~t ,-i rl a a s W W W c H z m o W 2 ~ n b ~ ~ W cn U ~ U n ~ ~ ui c ui ~
n ~1 O ~n ~n O O

~' -~ N M
N M

m ro O H

~

U ~ ~ N

f~ M OO N O1 y.1 O O
l0 ' m ~ O1 OD 01 G t0 C7 a0 N U

mo ~o ~o ~ ~ -,~ C
U

a O
O U

' +~
N

O ~

~ FC ~C FC U ~ ro cn U U FC

o U U U FC E-~ ,~ w r6 ~C U N

U U U U U U
U

U U U z 'L3 U ~

H H H , ~ ~
H U O

H H H H H H H U U
H H

H U U ,n ~n H ~ U

C7 U U ~ H ~ UU ~ ~ ~ .
UUU U H ~ ' E U . E-a -~

U ~ w ~ ~
~ U U ~ ~

.-w ~ Ch C L4 t S-i 'J H o P;

.3 z m o o z -~
~ H ~
w U U U ~ U U V ~ v m 7 U ~ ~-.~ N Sa 1 ~ N
t ~
f J
!
!

.L L G7 O -d a O
y H v7 .
a..
;
.~
~

I U U tT U H U W --y H O, b w H H ~
.,~

H H H H H H H U U W p~
H +, cd H b H H H H O~ d ~ ~ N m H ~ E-, E-~ p w H U U U U H ~ W W ~ ~ C "O
U > H ~ O

~, ~ r~ ~' ~ U~ M ,~ N G
~' C~ C7 b~ b~ b~ b~ I C7 C~ C ~ a~
b~ ~ ~ .rou CU7 ~ ~ ~ ~-' ~
~

.~ U
, o H H H H i-- m-.i Sa H ~
a ~

t~ U' ~ ~ "O
~
~

C7 C7 y. U
~ .~
.

Q t E-~ U C7 U H
r~ FC

U U U U U U U ~ U E-~ O
U ~ -~-1 ~--i H U U U ~ O -~I ~
U U C7 ,S~

, d, p ~

~ p N ~ C7 N U
N
~
E
U
~

C p 7 C ~' 7 C ~
7 C ~

-~
~ U
U
C

C O ~ t1, H U +-~
E-m U U

ro -~
o N

~1 ~ ~ ~ ~ .U +-~ ro ~ w ~ ~ ~ ,~
-~
+~

Q ~ ~ ~ ~ ~ FC ro o ~ ~
~' ~ b~

H ~ W

~ -C O r-I .~
~o -U

' ~
U O

U C7 U v1 O z t7 Ch ~

C7H HHHC7 H zH U ~ Ox +~
N

~ ~

U' C7 L7 p ~ ~ O
O

Q Q H U U U H H ~ pi v H ~

H H H H H H H W ~, N .-I C
H H ~
~

H H H H H H H v~ ~ a~ N
H E-~ O
U U

U U H i W ~ N

N N U 7 ~ U O ~ ~C
~ ~ U u U ~

\ +~~ ~' 0.~
U' C7 ~ ~
~1 co -~
O

~i ~ U H O

~C C7 H H O N '-I
FC

Q ~ ~ '~ ' a ~

~ U U U U U b , Q -~ U U

~ U U U U U ~ .-O c ~ cn U U ~ U

r0 -ri 1d N a~ =
.u m 3 s~

V Q ~ ~ -w U

-rlU

N

4.1-riN ~' - can ~
~
~

rI '~ , 3 .. .
-rl O +-~
N
U

E-a iNW G~ ~ C u~
l -.-i N +W r -rl ~

UI ~ U cn ~ O ~ O
O c ~
~7 ~ N W

N G ~ U U
C

~ a ro ~ -~ a~
~ m .. ~ -~ ~ S-~ -.-IN ~ U U ' t3' tn N ro ~ m ~ C -~ _ O N

r0 N
~' ~

v ~ -o 'o ~ ~
o ' a ~

ro'~~ b,Ua U Ucn b"NU

Q ~ H a~ ~ ~i +~ +~ a~ _ a~ sa ~

ro 'H ro .C ~ O U U cn ro ~ N
~n ~
U ~H C

t0 N N O ~ m H
1, E~

x a ~ H

E-. 0., U c R, W ~ E, n ~n O v~ O ~n O

N N M

°' ~ H
p .; _ s~ s~
z o 0 0 I lfl I I I I 1 I I I ~ I U U U
U h f~
a z ~ o o ~
cn . ro s~ ~ ~
~o H E-~ E-~ E-~ U U U U U U U U ~ ~ O ~ cn c~ ~ ~ ~ ~ ~ ~ c~ ~ ~ r~ c~ ~ o w ro a~
N U E-~ C7 E-mC ~C U U FC FC E-a FC a _r . +~ 'C7 U U U U ~ ~ CU9 E~-~ ~ can '~ ~ O
H U N H H H H b~ ~ ~ H H ~ r~ -,~ -,~ ro ~n a~
H H H H H H H H H H H H H I--I E-~ p ~ ~, -a - .-I
U' C7 U' U' C7 Ch t9 U' ~ 1 ~ I C7 C7 O4 U' E-mC i-I o U H N b H H U U H H H b H H U C7 . O
N U U U U U U U U U U U U U U ~ C7 pl ~ ,~ - E-~ s~
I I I I I I ~I SCI I ~I I 1 ~ H ~ U a~ U rx ,~ H H H H H N E-~ ,-I r.~ ~ ~ ~ - ~I s~
~i ~I~I~IACI~I~IC7 C7 IU' O4 U' u~~
UI UI UI UI I I U ~I I HI I HI H ~ ~ U ~ U ~ ~ ~ 'L7 I I I H U oU o~ ~ w r~o40-I+~~
N +~+~+~.aJ ~~c9~I~I~t~It~7c9 p~-IpU ~ro _ U U ~ ~ 1 I I CU7 U I U I I CU7 ~ CU-7 ~,~'_, ~ -~ ~ 'z~ O
,~.a a H a U O .~ ~ b~ ~ >, ~IC9 CJ ~I~IU' C7 ~I~I~,~I~ICa'~C7 AFC ~H tTb,p '~ m ro U ~I U U ~I ~I U U ~I ~I CSI ~I ~' U ~ C7 ~ N c O
U C7I H I H H U U H t-I U ~C i--t -O ~I 3 +~
,".y HHHHHHHHHHHHHH 3 U ~~~ roc bd bd bd bd ~ ~ ~ ~ ~ ~C ~C +~ I ~ ~ U r~C -- O +, 'C3 a~
~ U H H H H H H H H U H U ro .~ ~~ G U
~ U U U U U U U U U U U w N U U E-y -rl f~
c~ c~ c~ c~ c~ c~ ~ c~ t~ ~ ~ a ,~, .,~ -~I ~ a~
f-I O ~ U U H H H H U U E-~ E-~ U H
v .. .,~ ro a~
O C7 C7 C7 c~ C7 C7 C7 C7 C7 c7 C7 C7 ,ro O O ~ C7 U cn ,~ E-~ H H E-~ C7 C7 C7 U' C7 U' C7 C~ ~ ~ O i-I +~ ~N
~UUUUUUUUHE-~HE-~ ~ .pro v H H H H H
O -ri ~i a '~ ~ ~C ~ ~ ~ ~ ~ ~ ~ ~ FC ~ N O ~ N ~ b ~
U U U U U U U U U U U U U ~ U V ~ z Oi ~0 -~ ~ rC0 N
~, N CO ~ +' i~ 1.1 i.~ ~ C9 C4 ~ C7 p p~-~ H .-i N ~ -F'~ 'CS
U H H H U H U U H H I-I O I--I ~ O a ~-I +~ .1 -~I w V -rl U U U ~ U U U U U Z U ro ~ W N U U ~ +~ O
ro ~ ~a ro ~ c~ ~
O V H H H U H H H H p H V .~ ~ ~ ,~ ~ U U
O O ~ C7 Ch c~ ro !-, O ~ ~ a~ O U N
U H ~ ~ U U U U ~ H U H hl y-I ~ ~ ~ . O ~ ~ r.~ ~ N
U U U U U U U U U U ~ U
N N -rl ~ H ~ N ~ ~ ~ ~ H H N H N ~ ~ N N ~ O b-~ ~I ro C~
H H H H H H H H H H H H H E-~ ~ ~ U N -- G -can 40-Ima o .i.1 W -ri ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ o a~ +W' ~ a~ a~ -~I U
~~1 O O H H ~ H H H H H ~ ~ ~ ~ ~ ~C ~ +' ~ i ~H ~H ~ ~ U cOn H ~ ~ ~ ~ ~ H H H H >I ~, ~ o .~ w a a cn ro -~I N
O -~
O +~ ~ O ~ .u c +-~ ,~ O
O ~ ~ ,~ . O O
s.~ ro m +~ -a +~ ~ - a~ s~
,~ U r~ ~ ~ U ro ro ~ s~
m cn m a~ -~I m -~ a~
d1 -rl N
-~ G U ~ 40-I 4-O-I ~ H G
~1 -rl b '~ S i U _ 1'-~I ~ ~ ~ .. ~ .~ ~ S-1 S'I S-I ' S'I -r-I
U U m cn ~ 3 O ~ f~ f~ N ~ ~ o O N N c O O
Cl~ ron N N ~ ~ 5 ~ C ~ ~ C C ~ _ U 4-a C
ro ro w ro .~ z~ -~ ~ a~ ~ o ~ a~ ~
ro w ro v.~ w ro ro s~ a U m.~ ~,~~u-~ wo~
.. ~ c~ a .q .p ro ro .p cn ~ cn E.-I ~ -~ .~ ~ N ~ ~ -H -H ro a~ a~ ro zs ~ a~ a~ - ro a~
O ~ ~ p0 W U O ~I w-i ~ w-I 'O '~ u7 ~ +~ N ~ u7 u7 ?~ m +~ cn 4-r N 5 -H N 47 'ZS v ~i N N ~' -~ +-~ ~ cn c~ - '~ ~n o s~ ~ ro x x H ~r ~ >~ s~ ro +~ +~ s~ a~ oa ro a~ a~ o ~ ro ro o a a~ o v .~ U U a~ ~n ro U ;~ .~ .~ ix .i~ i-~ .~
>~ U b ro a~ ~ v ro ~ o~ ti +~ ~ o ~ v 41 a~ ,-I ,-a -r-I ~ -o E-~ H E-~ c cn c H
p ~ a ~ ~ a~ a~ s~ .~ ~ s~

U Ul O ~ U' U' W U7 W C-W1 '~C u7 ~ GL H -rl -.-i m ~ v -o a~
~n O V~ O ~n O ~n ~' ~--~ N N M M

m o a~

H

a~ >.~

U

z N C~
U
U' Sa O ~ ~ O
O
U

4a ~ I I I I I I I I I I I I ~ O
I I

O
~ G
m a p w ro o w z . +~
. ~o ~, m ~n -~, O U ~
N +~

M
N

............... a~.~ ~

. . . . . . . . . . . . . w tr ~
. . o ~ a~ H
a~

~
~~c~c~c~c~c~~~c~~~~c~~~ a -I C7 C7 U' C7 U' C7 C~ C~ U _ C7 C7 C~ U' C7 C7 C7 ~I
Sa M H U' H U H C7 H r.>; U
r.~ H U U C7 U

U U U U U U U U U U U U U U U
U U

E~~~H~~N~~ ~ ~ b'~' .~~Cw ~ ~
HH~~

-I H H y E , H H H H H H H H H H H H H H H
H H

O ~ ~ S-i +~
U .,~ O
.>~

H H H H H H H H H H H H H
H H

H H o H M
H ~

H ~ ~ ~ ~ ~ ~ E~-I H H ~ ~ ~ w '~ G
~ ~ ~ ~ ~ '~
~ o t o C7 C7 C7 C7 C7 C7 U' U' C7 ~ cx ~ o '~
C9 C7 Ch ~ c~ > m ro l N
~

y a -O

H H H H H H H H H H H H ~ ~ ro H H H O ' H H H H

~ ,~ ~ U aVaU _ ,~
~I~~~
~~~~

, I 4~10o U
I H H H H U

H H H H H H H H H H H H H v1 H
v7 H a 'n ~
-~

b H H H H H H H H H H H H H H H H H ' H H
H
H

. U ?r~ Y~

O

N a~ .. m .~ ~7 ro O U

I c~ ~

~ ~ H r~ r.~ r.~ U H r.~
U H C~ H U r~
' ' J C
J C7 C7 C7 C~ C~ C~ C7 C~
C~ C'J
V
; U
C
;C
~ ~

rr c H ~
U r U U ~ U U
F
U U U

N "~
+~

, ' . . . . M ~
~ OI
u7 . . . . . . . . U W O
~ H H H H H H H H H H H H ~ G
H H H O
!1 I~ H U H U H U U H U H H U u7 ~
H H H U

~IHC7UHUUUUC7r~HC7HUH
O

N H H H H H H H H H H H H H H H
H H

j ~ U ~ ~ o ~ x N

V o~ C
's H H ~
HNH H
N
E
E
HHHU
N
N
H

C I
'J -I U
C +~

.7UC

C

U
' ~ ~ ~ O
~

Ch U .. U ~ ~

U U U U H U H H U H H U U ~ O Y
U U U ~ ~-I
~ r-I
I

~ ~ ~ ~ rC ~C ~ ~ ~ ~C ~C ~ z r~ - o ~ ~ ~ ~ ro O O
H H H H H H H H H U

H H H H H H H H ~

C7 C7 Ch C9 C
C

~
~ ~ ~

H ~ a ~ +~ .~
H

H H H H H H H H H H H H H H v7 H U
H H

H H H H H H H H H H H H H H H
H H

H U H H U U U U H H U H H I-I I--i ~
~

U U U U U U
U U U U
b~ b~ U U U

H H H H H H H H H H (U b H H ~ M
H H H ~

H U H H r.~ U r.~ U C7 U O .
H ~ H H H

~ O ~
W C7 C~ C~ U C7 U' ~ C7 U 4-I tn C
C
C

~
O ~I G

~ O~ -ri m ~ U 3 - ~

t0b +-~ _ S -S-a H
N

u7u1r0 O TS -rl ~I

U

U U -rl N _~
O
~-I

G s~W U ~ N ~
O O

.. ro -H Q7O -rl C ~ ~.I U
rl W

v m U ~ v~ ro ~ ~ ,-~ rv ro ' ro t~ -H a t~ U ts'b~C~ ~ N ~, ~
H - sa cn ~ m ro +~ a a~ m w w a~a~~ ~ U m -,t~

m ~n ~ ~ ~ ro ro w a -~ m ~nm b a~ s~ ~I
+~

-H w ro s~ ~ w ~ H .~ v a~ cn a~ ro ~., ~

~ t~ U O O H a w a .~ ~I y3~ TJ ~ -a ~
v -H ~ ~ m +~

N w w-i ~H a .-Q v~ N 5 b~ N N N u1 b" -rl -3 -Q N O +~

O s~ ~ .-Q o ~n ~ t~, ro H +~+~+~ ~ a~ c~
~ o ar a Q, ru N O ~I N --I ro ro s~ ~ O U U U N cW 0 N G O ~-I -~I U ~
U
C ro U
C ~

a - N N N a~ U -rl ~ -I
N -Q
C Q, U ~-i .R

Ai ~ a1 U U W C7 ~ x N O W W vUU~~ H
~ H S-r ~ -~

7 7 U - ro l Cl~

O ~n O V1 O v7 ~~ ~ N N M M

v .

m o ~a H

N U

H

O O
U 5a z a ~ U
c~

H

O O O
U

z ~ ' ~o ~

o ~
cn z ~s +-b ~=
o a .~, cn U

N

H C

~r H H H H
(~ H t H H H
H H H H H
H
O

' ' ' ' . r.~ U
a C G O
U

C7 r~ C7 r~
r.~ C7 rr U
' n O

~ t H H U
U H H H U
E-~

~ ~ ~

~j t U

U U +~ +~ U U U
.1~ t U b~ U
U ~ U U U

N N N H H H H '.4 " 2 H N H N H
H H H

r ~ C7 C9 C9 C7 Ch U',la j C7 i C7 C7 U' U
C7 U' CJ
CJ U' ' H U U U U H ~ ~ N m t H b~ U
U N U U U
N

b ~ ~ O -U N H H ~
H H U

N H O' ~ ~
' H H H ? N N H ~ U
H H H H H
N H H

--~
G

'''~~ H H U U U H H ' t U U U
~ ~ ~ ~ ~
~

~i. U U U U U U Ca t U ~.u U
U

~ ~

~ ~~ ~ ~
~
~
~
~

t~ ~c~ a c~
i t~

~.I~.' ~ ~ ~ ~ ~ ~ ~ t7~ a ~' ~ ~a '-, i ~ ~ ~ ~ C4 v UU' ~

td ~ ~ ~ U : ~ rC '-' 3 O w ~ ~ U ~ ~ ~ G
~ U U U

x ~ ~~~~~ t ~~~~~~~~~ ~ ~ ~~ ~~ ' ~

H H H H H H U ro a H H H H ' N H H H H

V ~~~~~~ ~ ~~~~~~~~~ ECU U O N+~ w C .
~

N ~ p0 J ~ ~1-~
FC ~C FC FC ~ 4-I
t FC FC ~C ,~
FC FC FC
~C ~C ~C
' ' ' ' ' ' '-I U -r-I
C7 I 1~

U
C~ U

~ p0 O U U U U
U U U U U U O R' U U U U U N it U ri ~ FC FC ~C
~C FC FC
FC ~C r-C
~ FC ~C FC
C7 U H U ~

H H H U U
~

r0 N

H 'J~i~ C'J ~ N
'L3 H H H H H H E-~ ,S~
N H H H H H 'b H H N H H ~

~' ~' ~' ~' ~Cc uo ~ ~ -fC b~ ~ ~ FC H -'~
~ ~' ~ ~
~ ~' ~' rly.~ H H H H H H ~o ~ ro ~ U O
U H H H H H ~ ~ o H N H H H ~

~ H H ~ U '~ ~ N +~
O

O O ro N O N
1-~ U
~

C7 Y ~ U ~ ~ ~ ~C
' C

E N N ~ ~
H H E H
N H
N
H
N
H

H H U
H H ' n ' t~ c~ ~ ~ ~ f ~ ~ n o gi c~ c~ ~ -~ -~ , ~ ~
~ ~ ~ ~ ~
~
~

c w o a a c O O

41f-1 ~ ~ ~ ~ ~C ~ FC U ~ N = ~ cn ~ ~ R' ~ U
~C ~ ~ ~
~ ~

H H H N N H H U
H H N H H
N H N H N

H C7 E-~ U
H U C~ U
C7 H r.~
r.>; H C7 U

U7 E-~ H H .~ O
H H H H H
H H H E-~
H H H

C~ C~ C7 C7 O ~ G ' S-~

C7 U' C~
C~ C7 C7 O S~I ~ ~ ro U o ~ ~

b~ _ N
-r-I -rl +~ - cn O G I--i~ ' 1~
-rl ~ O
.~-I
~
H

_ rt1+~ N N
Cl, ~ ' ~i.~~-I o -~-1 ~ -~ ~ _~,' ~ ~ ya ~7 ~ W ~ N - O
U G

.. rd -H N -rl G ~ U W U
G -rl a~ ~n v -a ~ v o ro ro ~ w ~ R~ a~ ~ ~
H - ~ o m ~ m ro +~ a~~ U ~n " v c~ -~ tr +~
-.-~

~n v~ ~ ~ m b ~ ~ ~ ~ t~' ~ ro ro w a~ ro a -~ m +~

-~ ~H ro ~ ~n a~
~ w ~ ~ H r~
a~ a~ ~ U

ro -~ -H w -~
~
Q v~ N 5 s c~ N o O . ~ ~ t~
.. +~m -~
s +~ ~
. ~ a~
~t ~ .~ o c~, ~ ~ a, ro G
~, ~ o ~
~ cy vo~vwroroC~o~~os~'N U UN ~N.~-Ib= -.-i ~ x v v .

. ~ ~ ~ r .~ ~ ~' ~ ~
ro ~-c ,~x Q,o~

- ~ -_ _ ~1 W U U W n ~ H
C7 ~ x N
O W W ~ F, >-, c C1, -~n O v1 O ~n O

N N M M

a~

c~ H
ro O

z ' ~' ~' O O

U t~ ~ ~ .
OJ b ro 01 +~ C7 ~
rl N
M
V~
~
pp N
~
N
~
~

O f~ -O I
O
rl rl N
~-i N
N
I
N
N
I
I
lD
N
~
H
'~

lp ~ , y~
N
N
N
N
N
N
N
N
N
N
N

pi U O O
U

w O

O G u C7 U' rn U' U' U' U' U' U"

U' ~r U
H H
H
H
H
H
H
H
H
H
H
H
H
U
H
U
H
~
H

m m -~

C7 C~ ~' 'Z3 C7 C7 a ~

C~
C.'J
C~

C~
U

C~

fd U U U C7 ~ = o U U U ' U U U
U U
U N
U U
U
U
U
U
U
U

H b~ U ~ H .-H H rt , ro ~
H H H o H U
H U
H tT
H
H
H
H
U
H

H H H H
H H H n ~ U
H H H
H H
H H
H H
H
H
H
H
H
H

U U U ' ~
U U +~ C7 U U U
U U
U U
U U
U
U
U
U
U
U

U H b~ H 'n z ' H b~ b U
H H N
H H
H U
H b~
H
H
U
H
H
H

H H H
H H H
H H H
H H
H H
H H
H
H
H
H
H
H

.
H H U N
H b H
H U
H b E H
H b H
U
H
U
b b ~ ~ b O U ~ ro o ~ ~
~

rt1 H H z U p o H U
H H
H
H
H
H
H
H
H
H
H
H
H
U
H
H
H

~ . ~
Ch U ~ FC w, U' C7 .. v 'o C7 Ch U' Ch U' U' U' Ch U' b U
Ch U
+~
Ch H H H U o 3 0 H H ~
H H
H
~
H
H
H
H
H
H
H
H
H
H
i0 H

U~ ~ ~~~ d~ z ro~~
~
~
( ~
~
~
~
~
~
~C~7~~~~~~~~~~~~~CU7~~

H H W C7 >, ~ m, H H a H H
H
N
rd H
N
H
N
N
H
H
N
H
H
H
N

H H UH ~ .~ ~ -d V ' H b~ H o H H
H H
H
H
H
H
H
H
H
H
H
H

C9 b rtb C7 +~ C7 c9 Ch t7 th c9 ch t7 Ch Ch U (l1 U U UU CJ W ~ b~
U U U rd >, U i.~
U U
U
U
U
~
+~
U
U
U
U
U

~ ~ ~ ~ '~ m rya ~ ~ ~
~ ~ ~
~ ~
~
~
~
~
~
~
~
~
~
~

U U ~ o U +~ C~
U U N b ~
U U O
U
~
~
+~
+~
.N
.4~
U
+~
U
U
U
U
!T
b~

-~
~ +

-W7 C7 ~ C ra C7 ~ "
c-'7 C'7 c-'J

c-7 c7 C~

~7 U C
(J +.~ N
C7 ~
U' G U

t~
~
C~
rd N
U' ~
U
+~
+~
U
~
-I~

w t~

ro d' b~ C u~ 3 H a O G b-H
H
H
H
H
H
H
H
H
H
H
b~
t5~
~
U
rtf b~
--> H ~ ~ O

1 H ~
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
~''~
U
U
U
U
U
U
U
U
U
U
U
U
~
~

U rti + +
~
U
+-U

1T U rl; v., a b~ U o b~ ry w b~
U
tT
b~
b~
U
U
U
U
U
U

s.~ +~

H H H ~
H H
H H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H

H H H
H H
H H
H
H
H
H
H
U
H
H
H
H
H
H
H
H
H

H b H ro H r0 H H
H
b td N
N
b~
N
N
N
b~
H
N
b H
b~

U U U
U U
U U
U
U
U
U
U
U
U
U
U
U
U
U
U
U
U

U U U U U ro U U U U ~ 0 0 U U U
U U
U U

~ ~ ~ U ~
~ ~ ~ ~ N +~ N
~ ~ ~ r0 ~
~
~
~

U U U U U U ' U p, ~ -~
U ' ' U ' ' ' O ro o U ' ' U
' ' ' ' ' ' r-1~-I ~~~ ~ A~ ~ ~ ~~ ~ FC ro~'ox ~ ~ ~~ ~~~
~ ~~~

N N th C9 C7 C4 Ch C7 th Ch U' th t7 Ch H U H q H v a, v H H H ~ ..
H H H
H
H
H
H
H
H
H
H
H
H
H
H

U U U U i.~ U v ro ~
U U 1~ U U o U U +~ U
U U
U U
U +~
i~
U

H H E N E a a ~ ~
E ~ H N ~ ~
E N ~ H
~ E b~
~ H ~
E b ~ E s~
-~

C9 ~ 9 ~ ~ ~
~ C ~ ~ ' o ~
~ ~ ~ U ~
~ ~
~
h C U I
iZ
-H U U H v H H H
H U H
H U
H H
H rt H H
H
H
H
U

Ch Ch Ch t4 Ch Ch Ch Ch Ch S-IO U U U ~
U U
U U
U
U
U
U
U
U
U
U
U
U
U
U
U
rd U

~ ~
~ ~
~
~
U
~
~
~
~

Id ~ ;
-' '~
a ~
U ~ FC .~
FC FC ~
~
FC
FC
FC
FC
FC
~C
~
FC
FC
~C
~
+~
FC
FC
r.C
FC

o U
U U
U
U
U
U
U
U
U
U
U
U
U
U
U
U
U
U
U

M U
U U
U
U
U
U
U
U
U
U
U
U
U
U
U
U
U
U
U

,~ W to ~ '~
N

b r~ w ~

~ G
' ~IQ1 ~ _ ~ - w a~
ro ro - m ~ .~

U1 ~ H
~' p N I " ~ ~ -rl m ~
--i a t .. ~ N ~ ~.' O
S-~
v c n N ~ -rl O U
~1 U

ro m v ~ ~
ro ~ ~ ~ G
m ro ~n ~n ro ~n -ro -a -H 'H ~ ~ C ~' ~
-H a~ s~ m -H a~
-H
~
a ~H
-H
-H
~n ~n ~n s~
ro -a ~i cn a~ o =
~ m b" ~
-a +-~
v~
v~
H
~
~
a ro 'H
-H
N
~

U ro , U ~n U
U
O
O
>~
~1 O
'N
~
~H
~
~
.~
o ro ~ zs c ra a~
ro ~ u~
ro -~
ro ~
~
~n o ~
~
~
-H
o -H
-~I
-a .~
' ~i -H ~ a~ ~ ~
H N m +~
~i a~ m ~i -~I
~H
-H
t~
ro a b~
N
ro b, +~
.C
U
-~

ro o, .N
ro ~
ro +~
ro b, tr, s~
-a v ~
.~
c2, ro .R
s~, ro ~

~
~
ro ro ro ro ro ro ~
b ~
~
v ~
~
~

~ ~ ~ ~ ~ ~ i~
, ro ~ H .~
. ~
~
'~

~i . '~ '~ ~ ~ =
. -'--~ u1 :
. H
.
.
.

. N ~ ~ .C T~
. C~ cn ~
. ~ f H -. tn ~
.
.
.
.
~

coq p0 U
U
W

. .

~n ~n O
O
~n O

N N M M

a ro ro n.

o ro z v q ~o a~
r o m ,-i ,~
N
c~
vmn ~
r m o~
o N
c~
v~
W
o r ao o~
o ,-I

H -rl O
O
I
O
~
O
.-I
N
.-I
~
rl r-I
rl .-I
rl ~-I
N
N
N
N
I
N
I
I
N
I
N
N
N
cv7 M
N
N
N

N
U N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
a U

N

df o p ~C
FC
FC
FC
FC
FC
FC
FC
~C
r~
~C
FC
FC
FC
FC
FC
FC
~
~C
FC
FC
~C
FC
FC
FC
FC
~C
~C
FC
FC
~C

O t~
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
~

H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H

U' U' t7 U' H H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H

C t9 C9 t9 C7 o C C7 f9 C9 Ch z o M

H
~ ~ U U b W
' " N U ~
' H HH H H H
V H H U H U
H H H H
H H H U
H H

H H H

U
H
H
H
H
U
H

v U ~ ~~ ~~~~ ~~~~~ ~ ~ ~ ~
ro .1~ ~ ~ b' b~ ~ b~ b~ b~ b~ a~ 'N
,l d' b~ ~ ~~ ~ ~ ~ ~ cn E ro Oi ~ ~ ~ ~
~
~

H U U H H v H E U
H H H
H H U
H H H
U H H
U
H
H
H
H
H
H
H
H

H H H C
O H ' H ~
H A .
H v H N
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
~'~~~AC~'~~~~~'~'~'~C~~'~'~~~~'~~~~

U~
'~
U~
U

. , v H H U
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H

U ~' ~
b' O N g 9 ~ ui c~~t9cF7CH'JtF
7CF7c9CH'JCH'JCH'JCH
hC4CF'JC
9CH'J

F' Ha F' F' H
g H
H
F' F
H' H

. c. ~~
. U
. U
C
C
C
Jt C
Jt C
lc .7c.
t .7c JC.
c Jt .9 t HH
U
HEHH
HHH
U
HEHHHHHHHH
U
U
U

HH
E
-~
H
C
-~
EC--~HHHE
-~C-~ H

H
~

.N~ C7 U ro C7 v t7 U' U' (9 U' U' CJ

U' U
U' U' H b' H ~
H O
H ro H ~
H
H
H
H
H
H
U
H
U
U
H
U
H
U
H
U
U
U
U
H
H
U
H
U
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H

H H H ,ta H H
H H
H H
H
H
H
H
H

1~ a t~

N ~ N

N ~~ ~ U O
F:
+~

~ z H
U
U
U
U
U
U
U
U
~
+~
U
U
U
U
U
.4i 1~
U
U
U
+~
U
U
i~
J.~
U
U
U
U
+~
U

V ~ L1 U ~
C

ro N H H
H H
H
H
H
H

H H H C

H H H
H H H
H H H
H H
H H
H H
H H
H H
H
~~
n n c ~c~~ncn~n~n c~~nc~~cncn~nc~~c~ c~~~~n~n a U
~
~ H b~ a~
c H H ~
~c~cn~n~c~c~ b N
H
H
H
H
H
N
b ~d b b~

b b~ tT W H H
U1 ro c~ ro rt H ~n c~ ~n b H
c~ c~ H H
~n ~ ro H H
c~ b ro c~ H ~
ro b ~
ro H ~
ro N ~
ro ro ro rt ro ~
c~
ro ~
ro ~n ro H
O ~ b U ~i b b U ' U U U rt U
U b b b U
U U U
U U U
U ~0 b U
b b N U
b b b H
H
H
H
H
H
H
H
H
H

O H r.~ a-H U
H p H
H
b H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H

H r.~ O
H C
H U
H ~' H v H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H

U' c7 U' U' C!

U' U' U' t9 ' C U v U ~

N
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
U
H
U
H
H
H
U
H
H
H
U
H
H
H
H

H H m U H ~
U H b' U s~
U ~' U v U
U
U
U
U
U
U
U
U
U
U
J.~
U
+~
U
U
+~
.tJ
U
U
+~
+~
U
U
U
.N
U
~
bW
~
~
b~
~
~
~
~
b~
~

v O U .-i H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H

b ~

tT
U

C
N
y, ~ tn I N
u1 -ri N N I N

U U U1 -rl tU
~ C N 'O C
v U
'"I
~
C

.. v ~ ~ a ,.
v v v v ~ro ~
v ~n ~
~

w b' v .p v ro m o ro ro ro ro m ~n m m +~
-H
a ro a cn ro b~
~
-H
w w ~H
w a a a ~n a U
a --H v Q, >, U
H v +y, b, w ~n ~H
w m H
v .
u u ~, u u r ' H rn cn G
. .C ..Q v .
.
.
~
~
u~
a .u ro b w d7 W
C
C
v SH
C
a a m U
U
U
U
U
O
O
O
+~
ro W
~
v U

I p C -~ ~ U U
ro f C

~
ro O
C
ro w-I
C
~n ..Q
O
ro ro ro ro ro C
C
~
C
N
-~-~
N
ro ~
O
U
O
C
w-I
~n it v W
~
a ~..i -.-I
~.y ~
' O ..~ ~
O ~i v v -~ ro ~I O. b"
~i U
~I
~i w-i ~.a w-I
w U
~n C
b, -H
a "d ro "p ro ~I
ro a CT
~
~H
CT
sa u1 ~, a v -~-i ro f C

b ~

ro +~ t-~ N
ro W .~
ro i C .~
ro U U - ro T ~
~
~
W
"i n a y S~
U
sa .u ro ~
N
O
~
~I
C
..Q
'i N
~
.1.~
U
b~
b~
O, b~
b~
C
C
O
C
~
~
O
J, a'' v O
ro O
a S-i ro C
~
ro ro ro o a .Q
v U

ro . a ro ~ v U H
ro O
ro ro ro ro ro ro U
U
'b TS
v 4~
p~
~
~
~
p (~
~
p, yi t~
c~
v~
try a ~
v rl .-~ ~ ~
U -.~ N

V1 ~ M ~ H
(l1 ro ~
M
~

M
~

M
~
~
(n M
~1 ~
~
~

M
~
M
M

(n rn (n M
~
~
M
~
tn m V7 O ~n O
~
O
~n O
V~

N
N
M
M

o a N M
r r ao N M ~
c io 0 H O oo r o~ m m i oo i i i i i c a~ o~
o~ o~
i N ~o r z M M M
M M M
N N N
N N M
M M

a b M ~

~ ~ U
H H H H U ~
H H H
H H H
H H H
H H ~
H H H
~
U
U
U
~
~

U' rn ' ' ' C

~

H H H H rt H
H H H
H H H
H H H
H H H
H U ~
H H H

U' U' U' ~o C7 t2, U' U' rti U' C7 U' U' U' U' U' U' U' U' U' U' U' U' U' ~ C9 ~ U' C9 t9 C9 E ~ z r1 U

H H H H b p H
O H U U b ' U U U H
U U H
U U U U U
U U U b~
U U U H
y J~ b b H
~
~
U
~

U H N
fCa'a'aCfC~fCa'~~a'fC J. H U
H H U 'U
J. G
U
U
U
a'~~a'a.'+~Ha'rCa' H H E H H F
H H H H
H H H H
H
H
H
U
H
H
H

E H H E ~ a H H H J..~ ~ U
H H U H
H H H H
H b H H
H b O U U U U U
U U U U
U U U U
U V U
U U U
U U

C

U

U U U U ,~ U
U ~ U ~
.N ~ U
1~ ~ +~
U U U U
U U b U U U U U
~ r.C
H
U' U' U' U' U' U' U' U' +~
U U' U' U' WC 1~ A~, H
A J~ ~ ~
~ +~ J~

~ ~ b1 b~ ~ ~
~
H H H H
H H H

H H H H
H H H ' H H H N
H H H
H

~ ~ JJ
IT ~ 1.~
y1 bi ~ A', A,' by' N,' b~
H ~ ~
EC

U

o~ H H O
H H H b H H H
H H H
H H H
H H H
H
H H

H H H H
H U H M
U U U
U U H
H H H
H U H
H
M U U U
U U U
U U U
U U U
U U i~
~ U U
.1-~
U

: : : :
: : :
: : :
: : :
: ~

O d' U U U O
U U U 'z U U 1~
U +~ .t~
U 1-~
J.~ U
U J.~
U U' U
U

M H H H ., H H H
H H b H H H
N b b b H b b b N H H H U
~I H H H
I H H H
H H H
H H H
H H H
y H H
U' U' U' U' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' - i H H
U
U
U
U
U
U
U
U
U
U
U
U
U
U

.~ U E
U U U U
U J~ U
U +~ U
~ .N U
U U i U i~ U
U

g ~ a~
g ~~ro~~~

H H H E
H H H
H E

O H H E U
O E b ~ b U
U U U U
V
b~
~
~

H H H H W
H U
E H H H
H H H H
H H H
H H H

'r'I H H E E
H E H
F U U
b H H E U
b F H
U E b H

O ~ p C9 C9 U' U' U' z U b~-.i U C9 C9 U U' U' U' U' f9 C9 C9 C9 (9 U' E H H H H H q U
H H ~ U U
~ b E ~
U E H H
b b H

U ~
~
U

C ~ ~ b 9 U ~
' U
' C

9 H ~
~

F ~ ~
H E
H H
H U
H H
H
E E H

H H H H
H H U
H H U
U U U
U H U
H U H
U E

H H U N
H H N
E b b b b H
b H b H H
U U U U
U U U
U U U
U U U
U U U
U
~

U H bi V a~saaa U ~ .~
I a U w,~
U
~aa~
~c - H H H H H U a U
(~ H E H b O ~~ b~ ~
~ b ~ H
~ ~~
~~

U c ~~ ~ a c ~ ~ v c ~
c c~ c~ ~
~ m c ro+
ro ro ~a ~
ro ~ ro ro ro ro H
a~
U

~ ~ ro ~

: H H , . y, . a~

. v . . . .
. . . ro : : : ~
: : :
: ' v o FC AC w r.C r.C ~ a r.C b~ C
tT U U
U U +~
~ ~ ~
~ ~ o, +, a ~

m H H H H ro H H H U v H H H U
H H H U
U U H ro H H H ro c~ O ~
O c~ c~
c~ O ~
O ~ O
b ro c~
c~ O O
' ' ' O ~ A ,~ r.C
, a ,~ H ro Q1 A ,~ ~' , ~ U U H
U U U H
U +W i' H
A', J~ ~
~ A~' b~
H H H H
H H H
H H H
H H H
H H H
H H

U' U' U' U U
U' U' +~
~ O U U' U' U' U' ~

v~ O
tn ro U U U .i.~
1~ U U
.C U +~
.N
1~ +~
~ ro ~ ~

c ro U ~ .t-~
b~ b U U
U U ~ rt ~ ~ U
b~ fi ~ ~ ~
b U ~
U U ~

H H H H b .. ~ W
H H H b ~ O Ll b H U
b H
N
N
b b N
b U
N
b~
H
H

c~ ~ c~ ro H z , o ~ c~ ~ +~ c~ v c~ c~ ~ a ~
~a ~a a ro a ~
~a ~a ~a ro ~a a~
m ~
ro ~
b ~
c~
~

~
~

~
~
~a ~a H H b~ H
~ U
H
U' H
H
H
b ~
~

~C ~ ~ .C N ~
~ ~C ~ ~
~
b~
~
~C
~
ro ~
~
.C

a sr v O U' U' U' to C7 N
I U' U' W C7 O
U' U U' U' U' U' U' U' U' U' U' U' N U' U' U' U' U' U U U U N ~ H u7 .~ N
U b U ~u N U
i~ U +~ o N
U U U U
U U

U' c~
c~ ~a ro ~ ~a ro c~
m ro ro ro . ro ~ c~ c~ ~ ro O
~ ~ c~ a ~
c~ c~ dt ro c~ ~
c~ c~ c~
ro b c~ c~
c~
HHHHH
H
H

~ H ~ O
~~I ~ b~ HH C
~ E~HHH~~~H c ' 1 d' b~ b Ca ~ o y ~ ~ ~
b~ ~ ~
b~ ~
U
~

O '~' ~ d ~ 1-i N
V U N
U

H H H H ~ U
H H H
U H H
H H U
U H U
H H ~
bi H H
' ~C ~ ~ ~ H
~ ~ ~ a' ~ ~ ~
.C .C
b~ b~
a,' ~
~ a~ U
+~ a~
H H H H
H H H
H

H H H H ~ C7 b b H H
H H U
~ b~ b U U U U
U ~ +~
U J~ U
U i~ p~
N 1~ i~
1~ y b y b U H
E H H H
E H H
H E H
H H b N H H
H U N
b H H
N H N E ~
N H U
U E b b U b b H U
U
~

E H C
E U v ~
~
~
~

C ~I ,.C, 'J C
'7 C
7 ~ C~7 b U~ F
~ ~ ~

N i~
O~ H H U1 H H H
H H H
H H H
H H H
H H H
~0 H b M H H H
H H H
H U H
U U H
b~ tr~
H H H
H try tr~ U

.. v v N

m ..~ v v v v v v v m v U
~ v -'-~

~ U
ro ro ro ~ -~ O
ro ro a ro ~n ~n cn a p, ~

U
-H -H -~ w -H -~
-~ -H
~n a -H
-~ ~, ~n o -H

~ +i .N a A.
.u .u H G v cn C U
~ ro 'H
.u E
U

U U U U
ro O C
O wl p ro tp a ~ H
>., t~
to O ro ro ro T7 U
ro ro N
~n 5 ~
v G a C N a --i -H
ro U a WO N

~i H ~r N ~.a b' v -a ~y U U
-H -y a 0~ w O~ ro .C N U
~i U -H
O N 2f N U
ro ro ro ro ro a ~ v o o ~ ~
~ s -~ ~ ,-, v m - w a w ~ v ~ v U -,-i ~n ~ v ~
, c ~ -~
,~ ~
O, O, 0~
b~ b, o ro G
>, q ro a ~ v ro ro ro o o a Q, U
N

ro ro ro v U
ro ro a .0 ~n 41, C1, ro ~n ~ ro U
w b~ w U ~ ro v ~ ~

-i b' ~ N N -.-I
~' N

~n ~7 v1 a ~ C~-~ H
~n ~7 ~ -~
~7 ~n ~n tn cn ~n v7 W W
W W W
W N ~n v1 can ~

V'1 O V7 O V7 ' O ~!1 N N M M

.r, f H C01O1~ODNV'lnl~N.-iN d.M1001C ~N ro q p.~' i N O .-1 O O .-I .-I '-1 .-a ri N U
N N N N N O I ~, N f .~ H V -.1 W z io ~ c e c rr c c~ ~ c~ v c a, sa 3 U to a~ v cr ~y, io ~ 0 w a~
O
.-i H H H H H H H H H H H H H U H N _ 'tf'riya H FC U H H H ~0 m cn ,~
C7 C7 C7 C7 C7 C~ Ch C~ C7 C7 C7 H
-~ FC C7 U C7 C7 U C7 FC C7 H ~ w rO H H H H H H H H H H H H H H H H H N
U H H H H a' ~ ~- 'd r~ U U U U U U U U U ~ U U U U U ~ U U U ~ ~-I +~
O b~ ~ ~ ~ U
U QI U U U U U U U U U U U U U U U U U ~ ' O rn I
U U U U U ~
~ ' ~= ,-I
U w ~ ~ ~ ~ ~ ~d ~a ~a ~ ~a ~a ~ ~ ~a ~ H ~ ~ H
~ ~a ~a ~a C9 H H H H H H H H H H H H H H H H H r.~'UU p qG
O ~ UU' CU9 C9 C7 CU9 CU'l C9 C9 CU9 U O N u1 U' CU'J F ~ O ~ ~
O H
H H H H H H H H b~ U b~ b~ U ~ U H r0 O
V 'rI U H H N bl b~ H W
U U U U U U U U U U U U U U cU_7~
p r-I aaaaaaaa~~~~~~aa~~~~~a ~
H H H H H H H E N H H N H 0o N u7 H H H H H H H H H U H H U U H H H o +=
N ~ U U H H H ~ ~ w U'CJU'U'U'U'U'U'U'1~U'U'1~11U'U'U'U'U'C7U'U' ~ ro cn o ~ JU.~ ,~ U .+ A', J~.) ~C ~ ~ JU.I -~ b b J.u~ 'U C u7 _ H H H E E E N H E E N H E H H H ~ -rl 3 ~ E H H E U U ~ ~ O c N
~ ~ d ~0 ~ W O
U U U U U U U U a~ ~ +W E ~ .I~ a~ U co U ~ ~ b' U' G
O a~ U J-~ .u U a~ U ~O
Gi 47 .
N H H H E E E E b~ b~ Ot b~ H H b~ 'nEU-~~EU-~ ~ AEU Uw (~ b~ ~ b~ b~ b~ bl N FC p U O U ~ w ~ O
ro o ~ ~ ~ ~ ~ 2UZC~ U 'd rt r.~ R, U ~ N p, N U U U U U U U U V U U U U U H U U H H w ~ .~I p U
H U U U plH d H ,~ w +~
O ~ ~ ~ N ~ 'U N NN
. . . . . . . . . . . . . . . . . U V ~ O r0 U
. . . . ''~ ~' .~ m a a a~ o.
O N H H H H H H H H U' H U' H H H H ~ U
H H r-C H C7 rr; c~ ' la .rlr0 N U U U U U U U U U U U U U C7 U ~ ~ ~" ~
U U U U U U ro -~ N . NN
~ 'b E .~
U ~ ~ ~ ~

HH,~HHEEEH tUEE bHE bHEE ~H b bEE

IU ~ ~ ~ U U U U U U ~ ~ b ~ U U
~ ~ U U ~ HU
UIUUUU b~b~ U O~U b~UUU UUC7 H H H H H H H N H H H H H bl H H
H b~ H H H H H
H H H H H H H H H H H H H H H H H
H H H H H N
E H E

o~a~a~aa~~a~a~aa~~a~aa~~a~a~a~a~aa~a~a~aa <r U U U U U U U U U U U U U U U
U U U H U H

~~~c~c~c~~~~~c~~c~~~c~c~~c~c~c~~
H H H H H H H H H H E H H H H E U
r.~ H H U
~ U

U~~~ bb ~U' O Caw N O U U U U U U U U U U U U U U U U U U 'L1 ~
U U U U U U ~N S.I p C p C
-rIf-/U U U U U U U U U U U U U U U U U U .~ w .Q U U U U U ~ O ~ ~ w b ~N
O U U U U U U U U U U U U U U U U U ~ ro r U
.~O U U U U U F '~ ~ ro ~ +p~ a H ~
w~J ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~C ~ ~t ~ ~ 'n C G >~ U .-i ~ -~~ ~ ~C ~C +~ d C7 t7~ rd 'CJ u7 , H H H H H H H H H H H H H H H H H
E H H H H EH-~~n rn -~-I '~ O
N H H H H H H H H H H H H H H E U ~ O G N .Q U
CIA U H H H H ~ w fa .-a ~ -~i c~~c~~r'r'c~~c~~c~c~c~~~n~~cnc~c~~cn ro ~ ~
~ ~ ~ rn ~ ~n- U .Q a U' U' U' U' U CJ U' C7 C7 U' U U U ' ~ +~ a~ ~
U' U' C7 CJ U' U' C7 C7 U' U' V U Sa N
w b u!.4N H E E E H H H E E H H H E E E N ''~ U
H H E H N a~ _w ~ ~ FC tT N
~ .~
t~c~u~c~c~c~c~c~c~c~c~c~c~c~~uc~t~
~~~ut~c~ l.~a v a~ v b _ v-, ~' o N -~ x ro U t~ a U U U U U U U U U U U U U U U U U O -d ~
J~ U U U U -'~ -.-i~ f1 G N f~ _ 'b t~ H H H H H H H H H H H H En H H +~ N ~ U
H H H H H H w c''~ V U U U U U U U U U U U U U U .U G w 'i ~ t0 U U U U H H U -.~-~ ~ N
a w v O ~ U .1~ .1.~
.~ ~ ~' -.iro ~
a O. W G ~-i SO-i ~n ~n ~n m TS ~n G N _ U O U b"
W w W -H ~ W ~p ~n +~
U7 ~n m U7 O N ~n ~n ~7 N ~ .U
~ ~ G ~ it ro ~ O wi p ro C3' N 'C~ N ~ ~ ro Y' ro ~ tn N N N N ro ~I W ro ~I ~I ~ ai -O m a -~I N C1 v -.~ tr' ~ ~ ~
'. ~ C G -H -,y .H .H .N N C ~ w ro N
ro .u ro ~n ~n m .~.mO ~ N r _ -ro ro ro ro ~ C ~ ~ ro wi w-I ro C .rl N t~ U ro ~f w-1 U -.i u1 .C ~7 U U U U wi ~n ~-t -nl N ~I N Q7 a.~ ~~u ~~'. ~H roUH
O t2,'~I O~ ro ~ N TS 'O v >, .~ O O
w ~H ~H ~H -I ~i ~I -I .0 -I >, u~ cn ,~ H y z ro ~H W ro Iy w 8 N .0 a~ v a v .Q .Q ..Q .L~ .Q .0 .Q .Q ro '~I
W a tn O N O ~ O N ~ +~ +~
H ~I H ~I a a a a ~i a N N a N ro H a C C N O U U
rorororo2s~~-cso,a3,xx~-Icy-I-~w~roc>cy~
~

U U U U U U U U U U U U U U U U ~
x 0., cn cn u~ cn v7 O ~n O N OM

a a _ o .a U
U -ri O ~ a 3 'r'I ~ O
in -~
b U

U1 'O m V o v a o sa .rl z ~ +
a~ ~

-~I , .

q O1 l0 f~
O ri N M
C ~
l0 O~

.-I
M V~
~ l0 L~
OD

O r-I
f~
N N

'PI H f~ O
f~ .-1 f~
N O~
CO
CO

OD
I OO
OD
CO

O O
OD

O I
~ I

O
.-I
c-W
--I
rl ,-i .-1 rl rl rl rl .-I
~-i rl r-I
.-I
.-r rl n-I
.-I
rl N N
.-i rl N

~ w rl of U cn , Q

z .

~

; ~

a o in V

~
-~I H
'-r-i ~
O

w N U

U U
U U
U t U U
i t U U

U U
i U
U U
t t U U
U U

~ C7 z ~ C
U' ~

U i U' O

E t n E E-n E ~ b O
E- E-n t ~ t i ~
t E E E E
E E E E
H 7 r E
~ 2 ~ i E ~ t ~ E-~
r E
~ E
~ ~
t ~
t t ~ A'' ~
~
t t ~
~

r H H r ~ m t H
H t H H
r H
t H
t t H
H

u1 U
H r H H H r H E E d H H r H r v ~ i H H H H
~ H H H
~~ t H
~ r r ~ H r i~ H
~ H
~ H
~ H
H
~
~
~

t ~ ~ ~ ~w c ~
c ut t u i uc i t~c 5t~
i t~c~
u i uc~t~
i i t~
ut~t~~ut~i H t H H
H H
H H
t H
H t H H
H r H H
H t H H
H t r H
H H
H H
H
~
~ ~
~ ~
~ ~
~ ~
~ ~

V 7 t t H
~
t ~
~
~
t ~
~
~
t ~
~
~
~

t b E r0 C7 t C7 CJ C7 C9 r U o v ~ b O C7 t C7 C9 U -~ E

C7 t C7 Ch U t C7 U' t U' t U' H t H H r N H ~ U ~ ~ , H H t H H H U ~ , b H H H H
H H b t b t H
H
H
H
t H
b ~
U t U U r ~r U ~ r~ CT ~
U U t U U U a U U ~ U U U ro ~
U U ' U O
t U t AC r U
~~~~~ U
t ~ U
U
r U
+t t ~ t bi~AC~ E ..E ro S-I
~ ~~ ~~~ .
t ~~~~
r ~
b~

U U U

H ~ t ~~ ~~~ t ' ~~~ z ~cz~ 4-I ~~
~ U' C t U
U' 9 U' U C
4C7U' t CU7U' U' t t t Ll U Ll C ~ ~
t U ' ~ t ~ H H
i Z N

. r t ~- C ~ H
, ~

r r r U ~ r ~ ~
~ ~ ~ ~ ~
~ ~
~ ~
t ~
~
~
~
~
~
~
~
~

r t W U r~ tn ~ O
U U U U U U U V.a rn U U U U U U
U U t t U
U U
U U
U U
U
U
U
U
U
U
U
t U
U
U

t ~ ~ ~CFC a v r~
~ t ~ +~ ~o ~ ~ ~
~ .N
~C bs ~ +
Wt ~
~
~
t ~
~
~

E E H 3 I'~ U
N H ro ~ '~I
N E
H H

E E
E H
N N
H H
H t E H
H E
t H
U U
U N
H

UU E.~- , U , .
UU
UUUUUUUUUU
U

~ ~ O~rl ~~ O O
~ ~
U ?
?
U
U

rt~
N

O r~ ~ ~.~4'-I
r~~ a v ~
~
U
voUUUUr.~r~r~~
i ~~~
t ~~~U
t UU

r.C v tr' . .
. .
. .
. .
. .
. .
. .
. .
. .
. .
.

. . ~ v u7 . . S~ U
. . U
.

N o ~
t7 w o ~ ~ ro c~
~ c~
~ ~
~ c~
~ c~
c~
~ c~
c~
~ ~
c~
c~
c~
c~
~ c~
c~
~ ~
~

M

~i c w E ~ v in O

~
w O b E

N H H H N M E j ~ ~, E H H ~ y H H H
b H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
b H
b i ~
U

~ .77 H H H U H C ro v H H H H E ~
H H H
H H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
U

w ~
O ~ U U U U U U ~ p U U U U
U U U
U
U
U
U
U
U
U
U
U
U
U
U
U
U
U
U
U

O U +~ O U
r0 4J ~ C ~
v w ~

q U +

H H C ~ .
H H -~ U ~ ~
H H
H H
H H
H H
H H
H H
H H
H H
H H
H H
H H
b N
H N

, b H H ~ ,~
H H v ' WO
H H TJ
H H G
H

H H d E
H H
H H
H H
H H
H H
H H
H H
H H
H H
H

O O C7 C7 W U ~ ~ ~
C7 C ~

(9 CJ
U' U' CH7 F 4 ~ E

9 F' 4 ' F
H
H

H
F

C C C C

. C 9 C C

C C
C C

C C
C C

C

C

C
C

C

U U U U U 'O
U U U U
U U U U
U U U
U U
U U
U U
U U
U
U
U
U
U
U
U

U U +~ U ~ I ~
b U U ~ ~ c U
~ U
~ U
+~
b ~

U
~C FC C w in _ rC 7 _ FC C

~C t rC
aC
~
~C
FC
FC
~
FC
FC
FC
~C
FC
FC
FC
FC
FC
~C
FC
FC
E
U
E

~ a O S"~o U cn U U ro U U
U U
U U
U U
U U
U U
U U
U U
U U
U U
U U
U U
U U

v v v GI M p : ' C S ~ 5 I U
~ ~

r.
FC ~C - +
~C +
~C
FC
~ FC
~C
FC
FC
~C
~C
FC
FC
t;C
~C
FC
FC
~C
FC
~C
FC
FC
~C
FC
FC
FC
FC

CT N
r-I b O
O

U G (J) (~ .-i N

.1..1y.l w .,~ _ U .~ ~C
~ ro ~

- v ro v a, o . x W 7 tO N
C ~1 ~ a1 'H
~ U

a m I v >~ ~ v H sn -~ c m m m ..~
o a a a s., v G
v m a u m s a ~ U O U
a a T3 v7 U 1~
U o a ~
v ~ w-I ~ C'", O U C
U ~.-I v ' C
w-I O
U U
U O
w-I
wi ~.1 w-i w-1 v ~
' ' a sa ~ v U ~ v -~-i ~I ~ ro 6 v t7 --i ~-I
w ~C
~n ~ +~
a U
0~
tT

ro ro ~
a~ _ -H +~
w a rl a a s~
c ro c -~
c '~ , ~
v . a, tr~ ti . v, U
.
-~ ..~
.~, -~ m ~ ~
~ ~
~ ~
sn m m m ~n ~;
i i ~
-n ro b rn Y~
n m -a H -I
H N
~ -I
H H
w w w w w C
C1, ~ ~
w sa ~ s-~
~I
a a a a o a o w v v o 0 o c a c c >~
a o 0 o sa v v v ~~
v ~ " ~
v v ~
v v ~~
~~
v c 't~
v ~
~ ~
w ~~
~~
~~
~~
~ s-~
sa ~ a ~ -~ ~ v N c a~ b~ ~ro H o ro v >~sass.,~rym-c~~vvv~~~~~b~cya -~s s ~

~ +~ a t~ U -~
a U N ~ -.Q~~+~
,~
a a a a a ro ro O
Cl, Cl, ro ro ro O O
O O
O a ro ro ro U ro ro ro a O
O U

ro ro N
ro ~ E
ro -.-i ro E-' U U
U v N -C
.C
-C
-C
-C
.C
-C
.C
-i ~ p tn rn 3 t~
U f~
N

rl r-I- N .
~ ul cn l G-n T3 ~1 t!1 ~ ~n ~ V7 ~ t~
t~
tn tn ~ ~n in ~ V7 ~ ~
v1 W W
N cUn , E ~-I
f U m .4 -V~
O v~
O 'n N N
M M

Annex XIII: Strategy for the selection of the Staphylococcus genus-specific hybridization probe from tuf sequences.
400 425 SEQ ID NO:

S. aureus G TTGAAATGTT CCGTAAATTA TTAGA 179 S. aureus G TTGAAATGTT CCGTAAATTA TTAGA 176 S. aureus G TTGAAATGTT CCGTAAATTA TTAGA 177 S. aureus G TTGAAATGTT CCGTAAATTA TTAGA 178 S. aureus aureus G TTGAAATGTT CCGTAAATTA TTAGA 180 S. auricularis G TAGAAATGTT CCGTAAATTA TTAGA 181 S. capitis capitis G TAGAAATGTT CCGTAAATTA TTAGA 182 S. caseolyticus G TAGAAATGTT CCGTAAATTA TTAGA 183 S. cohnii G TAGAAATGTT CCGTAAATTA TTAGA 184 S. epidermidis G TAGAAATGTT CCGTAAATTA TTAGA 185 S. haemolyticus G TAGAAATGTT CCGTAAATTA TTAGA 186 S. haemolyticus G TAGAAATGTT CCGTAAATTA TTAGA 189 S. haemolyticus G TAGAAATGTT CCGTAAATTA TTAGA 190 S. haemolyticus G TAGAAATGTT CCGTAAATTA TTAGA 188 S. hominis G TAGAAATGTT CCGTAAATTA TTAGA 196 S. hominis G TAGAAATGTT CCGTAAATTA TTAGA 194 S. hominis hominis G TAGAAATGTT CCGTAAATTA TTAGA 191 S. hominis G TAGAAATGTT CCGTAAATTA TTAGA 193 S. hominis G TAGAAATGTT CCGTAAATTA TTAGA 195 S. lugdunensis G TAGAAATGTT CCGTAAATTA TTAGA 197 S. saprophyticus G TAGAAATGTT CCGTAAATTA TTAGA 198 S. saprophyticus G TAGAAATGTT CCGTAAATTA TTAGA 200 S. saprophyticus G TAGAAATGTT CCGTAAATTA TTAGA 199 S. sciuri sciuri G TTGAAATGTT CCGTAAATTA TTAGA 201 S. warneri G TAGAAATGTT CCGTAAgTTA TTAGA 187 S. warneri G TAGAAATGTT CCGTAAgTTA TTAGA 192 S. warneri G TAGAAATGTT CCGTAAgTTA TTAGA 202 S. warneri G TAGAAATGTT CCGTAAgTTA TTAGA 203 B. subtilis G TTGAAATGTT CCGTAAgcTt cTTGA -E, coli G TTGAAATGTT CCGcAAAcTg cTGGA 78 L. monocytogenes G TAGAAATGTT CCGTAAATTA cTAGA -Selected GAAATGTT CCGTAAATTA TT
sequence Selected SEQ ID N0:
genus-specific 605 hybridization GAAATGTT CCGTAAATTA TT
probe:

The sequence numbering refers to the Staphylococcus aureus tuf gene fragment (SEQ ID N0: 179). Nucleotides in capitals are identical to the selected sequence or match that sequence. Mismatches are indicated by lower cases.

Annex XIV: Strategy for the selection of Staphylococcus saprophyticus-specific and of Staphylococcus haemolyticus-specific hybridization probes from tuf sequences.
339 383 SEQ ID NO:
S. aureus AG TtGGTGAAGA AgTtGAAATCATcGGTtTaC ATGACACaTCTAA 179 S. aureus AG TtGGTGAAGA AgTtGAAATCATcGGTtTaC ATGACACaTCTAA 176 l~ S. aureus AG TtGGTGAAGA AgTtGAAATCATcGGTtTaC ATGACACaTCTAA 177 S. aureus AG TtGGTGAAGA AgTtGAAATCATcGGTtTaC ATGACACaTCTAA 178 S. aureus aureus AG TtGGTGAAGA AgTtGAAATCATcGGTtTaC ATGACACaTCTAA 180 S. auricularis AG TCGGTGAAGA AgTtGAAATCATcGGTATga AaGACggTTCAAA 181 S. capitis capitisAG TtGGTGAAGA AgTtGAAATCATcGGTATCC AcGAaACTTCTAA 182 I$ S. caseolyticus AG TtGGTGAAGA AgTtGAAATCATTGGTtTaa cTGAagaacCAAA 183 S. cohnii AG TCGGTGAAGA AgTtGAAATCATcGGTATgC AaGAagaTTCCAA 189 S. epidermidis AG TtGGTGAAGA AgTtGAAATCATcGGTATgC AcGAaACTTCTAA 185 S. haemolyticus AG TtGGTGAAGA AgTtGAAATCATTGGTATCC ATGACACTTCTAA 186 S. haemolyticus AG TtGGTGAAGA AgTtGAAATCATTGGTATCC ATGACACTTCTAA 189 S. haemolyticus AG TtGGTGAAGA AgTtGAAATCATTGGTATCC ATGACACTTCTAA 190 S. haemolyticus AG TtGGTGAAGA AgTtGAAATtATTGGTATCa AaGAaACTTCTAA 188 S. hominis AG TtGGTGAAGA AgTtGAAATtATTGGTATCa AaGAaACTTCTAA 194 S. hominis hominisAG TtGGTGAAGA AgTtGAAATtATTGGTATCa AaGAaACTTCTAA 191 S. hominis AG TtGGTGAAGA AgTtGAAATtATTGGTATCa AaGAaACTTCTAA 193 2$ S. hominis AG TtGGTGAAGA AgTtGAAATtATTGGTATCa AaGAaACTTCTAA 195 S. hominis AG TtGGTGAAGA AgTtGAAATtATTGGTATCa AaGAtACTTCTAA 196 S. lugdunensis AG TCGGTGAAGA AgTtGAAATtATTGGTATCC AcGAtACTaCTAA 197 S. saprophyticus AG TCGGTGAAGA AATCGAAATCATcGGTATgC AaGAagaaTCCAA 198 S. saprophyticus AG TCGGTGAAGA AATCGAAATCATcGGTATgC AaGAagaaTCCAA 200 3~ S. saprophyticus AG TCGGTGAAGA AATCGAAATCATcGGTATgC AaGAagaaTCCAA 199 S. sciuri sciuri TG TtGGTGAAGA AgTtGAAATCATcGGTtTaa cTGAagaaTCTAA 201 S. warneri AG TtGGTGAAGA AgTtGAAATCATcGGTtTaC ATGACACTTCTAA 187 S. warneri AG TtGGTGAAGA AgTtGAAATCATcGGTtTaC ATGACACTTCTAA 192 S. warneri AG TtGGTGAAGA AgTtGAAATCATcGGTtTaC ATGACACTTCTAA 202 3S S. warneri AG TtGGTGAAGA AgTtGAAATCATcGGTtTaC ATGACACTTCTAA 203 B. subtilis AG TCGGTGAcGA AgTtGAAATCATcGGTcTtC AaGAagagagAAA -E. coli AG TtGGTGAAGA AgTtGAAATCgTTGGTATCa AaGAgACTcaGAA 78 L. monocytogenes AG TtGGTGAcGA AgTaGAAgTtATcGGTATCg AaGAagaaagAAA -Selected ATTGGTATCC ATGACACTTC
sequences Selected species- SEQ ID N0: 594 specific hybridization ATTGGTATCC ATGACACTTC
45 probes: SEQ ID N0: 599 CGGTGAAGA AATCGAAATC A
The sequence numbering refers to the Staphylococcus aureus tuf gene fragment (SEQ
$~ ID N0: 179). Nucleotides in capitals are identical to the selected sequence or match that sequence. Mismatches are indicated by lower cases.

Annex XV: Strategy for the selection of Staphylococcus aureus-specific and of Staphylococcus epidermidis-specific hybridization probes from tuf sequences.
SEQ ID
N0:

S. aureus TACACCACATACTGAATTC AAAGCAG...TTCTTCtCa AACTATCGtCCACAATT179 S. aureus TACACCACATACTGAATTC AAAGCAG...TTCTTCtC~ ~~~~~~~~~~~~~~~~~17g S. aureus TACACCACATACTGAATTC AAAGCAG...TTCTTCtCa AACTATCGtCCACAATT176 S. aureus TACACCACATACTGAATTC AAAGCAG...TTCTTCtCa AACTATCGtCCACAATT177 S. aureus aureus TACACCACATACTGAATTC AAAGCAG...TTCTTCtCa AACTATCGtCCACAATT180 S. auricularis TACACCACAcACTaAATTC ActGCAG...TTCTTCtCT AACTAcCGtCCACAATT181 IS S. capitis capitisCACACCACAcACTaAATTC AAAGCGG...TTCTTCAgT
AACTAcCGCCCACAATT182 S. caseolyticus TACtCCACATACTaAATTC AAAGCTG...TTCTTCACT AACTAcCGCCCtCAGTT183 S. cohnii TACACCACAcACaaAcTTt AAAGCGG...TTCTTCAgT AACTATCGCCCACAATT184 S. epidermidis TACACCACAcACaaAATTC AAAGCTG...TTCTTCACT AACTATCGCCCACAATT185 S. haemolyticus CACACCtCAcACaaAATTt AAAGCAG...TTCTTCACa AACTATCGtCCACAATT186 2~ S. haemolyticus CACACCtCAcACaaAATTt AAAGCAG...TTCTTCACa AACTATCGtCCACAATT189 S. haemolyticus CACACCtCAcACaaAATTt AAAGCAG...TTCTTCACa AACTATCGtCCACAATT190 S. haemolyticus TACACCtCAcACaaAATTC AAAGCAG...TTCTTCACT AACTATCGtCCACAATT188 S. hominis CACACCtCAcACaaAATTC AAAGCAG...TTCTTCACT AACTATCGtCCACAATT195 S. hominis TACACCtCAcACaaAATTC AAAGCAG...TTCTTGACT AACTATCGtCCACAATT196 25 S. hominis hominisTACACCtCAcACaaAATTC AAAGCAG...TTCTTCtCT
AACTATCGtCCACAATT191 S. hominis TACACCtCAcACaaAATTC AAAGCAG...TTCTTCtCT AACTATCGtCCACAATT193 S. hominis TACACCtCAcACaaAATTC AAAGCAG...TTCTTCtCT AACTATCGtCCACAATT194 S. lugdunensis TACACCtCAcACTaAP.TTt AAAGCTG...TTCTTCtCa AACTAcCGCCCACAATT197 S. saprophyticus TACACCACATACaaAATTC AAAGCGG...TTCTTCACT AACTAcCGCCCACAATT198 3O S. saprophyticus TACACCACATACaaAATTC AAAGCGG...TTCTTCACT
AACTAcCGCCCACAATT199 S. saprophyticus TACACCACATACaaAATTC AAAGCGG...TTCTTCACT AACTAcCGCCCACAATT200 S. sciuri sciuri CACACCtCAcACTaAATTC AAAGCTG...TTCTTCACa AACTAcCGCCCACAATT201 S. warneri TACACCACATACaaAATTC AAAGCGG...~~~~~~~~ ~~~~~~~~~~~~~~~~~192 S. warneri TACACCACATACaaAATTC AAAGCGG...TTCTTCAgT AACTAcCGCCCACAATT187 35 S. warneri TACACCACATACaaAATTC AAAGCGG...TTCTTCAgT
AACTAcCGCCCACAATT202 S. warneri TACACCACATACaaAATTC AAAGCGG...TTCTTCAgT AACTAcCGCCCACAATT203 B. subtilis CACtCCACAcAgcaAATTC AAAGCTG...TTCTTCtCT AACTAcCGtCCtCAGTT-E. coli CAAgCCgCAcACcaAgTTC gAAtCTG...TTCTTCAaa ggCTAcCGtCCgCAGTT78 L. monocytogenes TACtCCACAcACTaAcTTC AAAGCTG...TTCTTCAac AACTAcCGCCCACAATT-Selected ACCACA TACTGAATTC AAAG TTCACT AACTATCGCC CACA

sequences Selected SEQ ID NO: 585 SEQ ID NO: 593 species-specific ACCACA TACTGAATTC AAAG TTCACT AACTATCGCC CACA
hybridi-45 zation probes:

The sequence numbering refers to the Staphylococcus aureus tuf gene fragment (SEQ
ID NO: 179). Nucleotides in capitals are identical to the selected sequence or SD match that sequence. Mismatches are indicated by lower cases. "~" indicate incomplete sequence data.

Annex XVI:Strategy for the selection of the Staphylococcus hominis-specific hybridization probe from tuf sequences .
358 383 SEQ ID NO:

S. aureus ATC ATcGGTtTac AtGAcACaTCTAA 179 S. aureus ATC ATcGGTtTac AtGAcACaTCTAA 176 S. aureus ATC ATeGGTtTac AtGAcACaTCTAA 177 1~ S. aureus ATC ATcGGTtTac AtGAcACaTCTAA 178 S. aureus aureus ATC ATcGGTtTac AtGAcACaTCTAA 180 S. auricularis ATC ATcGGTATgA AAGAcggTTCAAA 181 S. capitis capitis ATC ATcGGTATCc AcGAAACTTCTAA 182 S. caseolyticus ATC ATTGGTtTaA ctGAAgaacCAAA 183 1$ S. cohnii ATC ATcGGTATgc AAGAAgaTTCCAA 184 S. epidermidis ATC ATcGGTATgc AcGAAACTTCTAA 185 S. haemolyticus ATC ATTGGTATCc AtGAcACTTCTAA 186 S. haemolyticus ATC ATTGGTATCc AtGAcACTTCTAA 189 S. haemolyticus ATC ATTGGTATCc AtGAcACTTCTAA 190 S. haemolyticus ATT ATTGGTATCA AAGAAACTTCTAA 188 S. hominis ATT ATTGGTATCA AAGAtACTTCTAA 196 S. hominis ATT ATTGGTATCA AAGAAACTTCTAA 194 S. hominis hominis ATT ATTGGTATCA AAGAAACTTCTAA 191 S. hominis ATT ATTGGTATCA AAGAAACTTCTAA 193 2$ S, hominis ATT ATTGGTATCA AAGAAACTTCTAA 195 S. lugdunensis ATT ATTGGTATCc AcGAtACTaCTAA 197 S. saprophyticus ATC ATcGGTATgc AAGAAgaaTCCAA 198 S. saprophyticus ATC ATeGGTATgc AAGAAgaaTCCAA 200 S. saprophyticus ATC ATcGGTATgc AAGAAgaaTCCAA 199 S. sciuri sciuri ATC ATcGGTtTaA ctGAAgaaTCTAA 201 S. warneri ATC ATcGGTtTac AtGAcACTTCTAA 187 S. warneri ATC ATcGGTtTac AtGAcACTTCTAA 192 S. warneri ATC ATcGGTtTac AtGAcACTTCTAA 202 S. warneri ATC ATcGGTtTac AtGAcACTTCTAA 203 3$ B. su.btilis ATC ATcGGTcTtc AAGAAgagagAAA -E. coli ATC gTTGGTATCA AAGAgACTcaGAA 78 h. monocytogenes GTT ATcGGTATCg AAGAAgaaagAAA -Selected ATTGGTATCA AAGAAACTTC
sequence 40 Selected SEQ ID NO: 597 species-specific hybridization ATTGGTATCA AAGAAACTTC
probe:

The sequence numbering refers to the Staphylococcus aureus tuf gene fragment 4$ (SEQ ID NO: 179). Nucleotides in capitals are identical to the selected sequence or match that sequence. Mismatches are indicated by lower cases.

s~
v o 0 ~ U c~
'~ a ~
O O U
m N
OJ 01 O rl Q ~ Ln ~ t~ a0 01 O c-~ N N l0 ~ OJ N
H ~ t1~ l0 l0 ~ ~ l0 ~ l0 l0 lfl f l'~ f~ ~ ~ rl ~ ~ ( t~ ~ N O ~ 4-I N v +~ ~
V1 cWn .-o ~_ o U
tn U
.-i N N ~
N U tr ~ ~ H G
O FC r.~ r.~ r.~ H ~ H ~ ~ H H r.~ ~ r.~ r.~ E-~ H H r.~ r~ H r.~ E-~ H O U ~
O
~ H H H H H H H H H H H H H H H H H H H H H H H H Z O
~ C7 C7 U C~ C7 C~ C7 C~ C7 U C~ C~ C'J C7 U U C7 C7 C7 C~ C7 C7 C~ C~ O ro v O ry ~ +~ U U ~ -,~ +~ O .C
W +~t+~~I +'I +~I UI+~I UI~I+~I ~I~ ,~ H .~ H W
(Il C7 U' U' ~ ~ U ,~ U rn U N v m W
O N H H H H H H H H H H H H H H H H H H H H H H H (OI H H ~ ~ N ~ v ro ~ N ~ O
U ',~' C7 C9 CJ C7 C7 C7 C9 Ch Ch U C7 C7 C7 U U' CJ C7 C7 C7 U C7 CJ CJ U C7 U' H H +y ~ b~ t0 w U U U U U U U U U U U U U U U U U U U U U U U NI U U .. FC ~~ r~ ~ v +~

1 I ~ I I I~ ~H off ro,~.o ~~+~
O U U U U U U U U U U U U U U U .NIA bIU U U U U U
U! ~ ~~~~~~'~~~~~~~~~~ b'Ib~IbdbVHHHH ~~ ~ pIU dU '~-~'° ~ .~ ~~~
U
H H H H H U U U U I 1 I I H ~ y-i W r.~ W r.~ ~ ~ U U E-~ -~-i G
W ~ ~ ~ ~U ~U ~.O~~ .~ h N ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ +~1~ UI~ ~ ~ ~I~ UI UI ~ ~ H H ~,~ ~ 3 O ~ t~~
c~c~c~~~~c~c~c~c~c~c~~c~c~~ ro~~~c~~~ ~~~
H H H H H H H H H H H H H H H UIH H H H H H
cn t~ c~ ~ c~ c~ c7 ~ ~7 ~ ~ ~ t~ c7 c7 c~ c~ ~ ~ c~ ~ c~ t7 p ~ -~ o rt a O U 'n U U U U U U U U U U U U U U U U U U U U U U ~ ~ ~ z +~ w ,~ a E-~ H H r.~ r~ ~ H H ~ r.~ ~ r.~ H E-~ U' U C~ H H r.~ ~ U H ~ ~-1 -rl . . . . . . . . . . . . . . . . . . . . . . . .
~ FC FC FC FC FC FC ~C FC FC ~C FC FC FC FC FC U FC FC ~ FC FC FC C~ ~ 'ZS a ~. U' rya r°, :°
~i U N H H H H H H H H H H E-~ H H H ~ H U C7 H C~ U' H H ~ ~ ~ ~ t~
b b ~ fd C~'J U N L
U U U U U U U U U U U U H U H H U U H H H H H H >r ~ U U F i O x v a-' V c~c~t~~t~t~c~c~c~c~t~~t~t~c~~~t~~~t~c~c~t~ c~ ~~ v ~o~
O N HHHHHHHHHHHHHHH UH ZT10HH b~H U H ,nH p ~W U ~~+~ O
H H H H H H H H H H H H H H H b~H H H H H H H H H ~ H
~ C7 U' C7 C7 C7 C7 U' U' CJ C7 ~ ~ C7 C7 ~ ~ b~ ~ b~ U U ~ U ~ O FC ~ ~ p v O
U v W ~~
N N H H H H H H H H H H H H H H H b~ b~ U b H U U N b H ~ H v +~ v ~ -~ o E~
CU7 ~C~7 C~7 ~ ~~~~ U~~~~ ~ ~ U .~ U v ~~ rt R, H H H H H H H H H H H H H H H H H U H H H U H H H a H O ~ ~ N ~ -~ U
O
H H N H N N H H N H H H N E U U U U H U E U U ~ N E'H''~ ~ ~ ~ ~ 3 U ~~~~~~~~~~~~~~~C~~ tn~~~~~~ ~ ,.~a v o . ~ v I~ ~ C7 FC ~C H FC H C7 C~ H H FC FC U C7 U C7 C~7 FC U C7 C7 C~ ~C U Sa +~ ~
N H H H E-~ H H H H H H H H H H H H r.~ E-~ H H H E-~ H C~ ~ ~ ,.~ ~ _ _ -rtf r6 ~ . ~ O +-~
(d rI -~-I -~-I U U H G
cn u1 v v +~ 1a U U ~ ~ E~ N 3 x O S-i UI ~ ~ U
a UJ ~ v v W U ~ -~ ,~ U W U
ro ~n ~ a ~n ~. ~n ro v -H ~ ~ ~ C
~i ~ a -H a H a -H ~n ro +~ b~ b~ C v v v ~ ~ o ~ ~
cn v ~ 5 ~n o -~ s~ -~ ~n -H v~ ro v v v ~ U s.a .t:
-H ~ U ro -H ro O ~ s~ v H ro -H ~ -~~ w G b"
H a ~ ~n .-i a ~n ~ -H o ~ ro ro .~ ro -H ~n ~ o H p '~ cn is ~ b -o b v v ~ ro ~ ro -H v -~ a~ .u ~s -~ .~ +~ " ~ m a cn O C~, ro U U ~ ~ ro 'b a 4-a U -~~ .~ -H ro N ~ a -~ -O, U ~
-H ~1 U cn ~ v N ro ~i s~ ~ N ~N U ~I Q, b~ (~, N -Q N ~-i ro ro +~ +~ 1-~ S-a N rW 0 ~ c -rl ro N -~ a ro ro ~r ro -H a rn ro ro o -~ ro v a a ~ O s~ s~ U U U v m ~ U
ro U U TS '~S ~N ~N ~H b~ -C ~ CZ, ~ ~ ~ 'Zf 5 U ro ~ Cl, U ~H 1-~ N N N ~ -.-i -rl rl .-W-i -~-I N f~ 'CS = tn c H
W W W W W W W W W W W W W W W U C~ rb ~ rz~ va W ~p U cvn cn cans oa H U -~
~n O v7 O N O O

a o .a U

U -.-i a 3 O
ro ro ro Ll J-~
N rl O
.-i N
~
tW
~
I~
cD

O

N
N
~O
~

v b N
N N ~
H ~
~
~
l0 l0 l0 ~
l0 ~
l0 l0 l0 f~
1~
l~
~
~
rl ~
~
~
f~
~
N

U 1.i ~ ~' w w a =

cn -.~
:o ~n I

~l.H

'HU

H N
o m U H ~ ' ~
-~ H

N U U ~ o' W

~ O W

U U rI ~E'E'E'F'HHHC7C~HHHHC~HUHUHHHHHH
--.U

~ C7 r, ~1U 0 U C7 ' o C~

C~
C~

C~
C~
C~
C~

t7 C~

C~

C~

~nt~c~~c7~nc~t~~t~c~c7~c~t~t~c~~t~c7c7~c~c~~ H H
O u H H ~
H
H
H
H
H
H
H
H
H
H
H
H
H
H
U
H
U
H
H
H
b o N
U' ' U' U' c~
U' C7 U' U' U U' U' U' U' U' U' U' U' U' U' U' U' U' U U U U U U O
U U
U U
U
U
U
U
U
U
U
U
U
U
U
U
U
U
U
b : y~
~ U A',~C O H
U ~
b~
~
~
+~
b~
ii U

W
O ~I~r I H H ~ H z -H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H H

W t~ ~ ( U
~
~
C7~
ro ro ro ro ro~u~
ro ro ro ro ro~~~~
~~~~
U
' b C
O I~ ' U 9 ~ HHHHHHHHHHHHHHHHHHHHHHHHH H

, H H U
H
H
H
H
H
H
H
H
H
H
H
H
H
U
U
U
H
U
U

H O H Oi U
~ ~ U z U w ~ H ~
U ~ a ~ ~
~ 1, ~
+' +' ~
V
~
~

N W .~i~I~ U c ~ ~ ~ n ~ ~ b r ~ ~ n O
~
~

'I') ~'~tTN H C-U-~
~ ~
H E
N
~ H
E
N
H
E E
N
E
b N U ~nc~cncn~n~n~ncnc~~nc~~n~~n~cn~ncn~nc~~~c~c~~n W ~ ~ ~ UN ~ ~~
UNE U
UENHHH
UE
UHEHNHHU
b bEN

N C N
-~

O H H
H
~
~
~
H
H
H
~
~
H
H
H
~
~
U
~N
~
~
~H~
~~

cr ~
~
~
U
U
U
~
~
~
U
U
~
~
~
U
U
~
U
~
U
U
U
U
H

rti N r0 . O

Id 'HN . .
.
.
:
.
.
.
.
.
.
:
.
.
.
.
:
: :

.
. .
. .

O GlGl H 4I ~~ tr v~ ro vv~
~
~
~
~
~
~
~~
~
~~~
~
~
~
~
~
~

a , a ;~w a ~
a a a a a a a a a a a a a a ~iO O ~ I'~ U U b b 3 U U ~ ~
U
U
U
U
U
U U
U
~
b ~
U
N
~

U U .
U cn b U ~

H ~ ~ ~ H a ~
~ H
~
~
~
~~
~
U
~H
U
~
~

U U
+~ ~
U
~ U
U
U
~~U
U
~
U

~iO U o U .1 U
~~~~ ~~
~
~

N O O U tN ~ ~ ' ~
~c ~
~

~

i~~c~c~c~c~~c~~c~~c~~ ~~c~c~~'~~ c~'~~ z :~

N b b ~ ~ .4~ J U+1 +~ Ca ~n .1.1 .yJ~U bi U a ~
yJ U U ~ '~
+~ U H 'N
11 q~' ~ ,~
~ tT
.a b~
U U .
U ~
U
U
U
'~

N N N O tn b~b~ a ~ a b tn tr~ ' ~' b~ b~ ~ b' ~' b~ U ~ o b~ U
b~
tn tn U

O .~,.~.~ ~ ~ H U U U tT d H H U ,~
U H H
U U b~
H H H
H U H
H H
H
U
H H
H
H

,,~ H H W H H O u,~
V ~ ~ H a U
H U
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
~~~~'~'~~~~~'~'~~~~~'+~~'J~
U~~i~
U~
' ~ ~r~ FC O,~
E H H H ~
H ro H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H

N N v1~ ~~~~~~~cncn~ncncnc~~n~ncnc~cncn~nc~~n~nc~c~~n c~o~ ~
~~ ~

~n~c~~n~cn~~n~cncncncn~~~ncncn~ncn~cn~n~nc~~
~.oc~ ~,~
O 4-'~' b H H U H C ~
H U
b U
H H
H H
H U
H U
H H
H H N
H H
b H
b H
H H
H H
U H
H H H
H
H
H
E
H
H
H
H
H
H
H
H
H
H

H W
C7 ' U' 7 C7 ' C7 ' U' ' U' U' U' U' U' U' b b N'I~ir~i U U C
b rt U b U U
H U U
U U
U U U
U U
U U
U
U
U
H
U

~ ~ U U Z H N O
H H U
H b~
H H
H H
H
H
H
H
H
H
H
H
H
H
H

H H H
~ ~ ~ ~ H H o c7 +' ~ H H
H H
~ cs ' is U U H N ~ ~ ~
'~ '''1rl ~ ~ ~ ~ ~ ~ ~ '~
~ ~ ro ' t t c c~ a +
t ~ ~
x U

H H H N
N
H
N
N
H
H
H
E
E
N
H
H
E
H
E
F
N
E
E
E
E
E
H

C f.
N U U 0 ~ ~cncn~n~~n~~n~cn -~ -i ~
I ro~n~ncn n~~

i-IN N ~1. ~ 'n ~l ~
~

. +~ U
+i +~
J~
a , M C7 --i S-1 C7 N b U
U

U
U' U' U
U' U' U

CJ

U' U' O O
N U 4-i y U '~
U
U
U
U
U
U
H
U
U
U
U
U
H

U
U
U
H
+-~
~' ~C
C
C
C
C
C
C

F wl a U
F .
F
F
F
~
FC
FC
FC
FC
~C
FC
FC
~C
FC
U
r.C
FC
FC
FC

U

s, ro a ' m m m o N cn N N , ~ x U U ~ . b u~ ~n N
C C ~ N
N

ro -U ~ C +.~
~ ~
~
~
t~1 ~., ro ro N
~-i ~
~

H ~ a~ a~ a~ o a _~
-H ro a H
a -~
m ro ~
tr tr~
~
~

H O. ~ U +~
n N
~

~n O
w N
-H
cn w-1 <n ro N
N

rn U
w-I ~
F
'~I
~
U
ro w-I
ro O
~-1 ~
N
~i ro w-I
C, ~1 p ~
r7 -i ~ N rl a ~
fr1 a ~
C
wi o S"., ro ro -C
ro w-1 ~~
o ~~
i ' ~
N ~
--O TJ tn ~ c6 ~ N
W
N
+.
~
ro ~
ro .-i -C
+-~
.u C
U
a W
~
W
.C
'O
'b a c ' ~

~ O N tJ' !~, U ' ro - b U
U

H
ro O a H U

.C
w-i ro N
.u a -.-I
b~
U
N
N
w-i ~1 O
tn N
N
N
ro -i N
C
N
~H
U
~~
i1 t ~

~ t-W n ~ .,~
, U a~ -~, N m +~
.4 ~ ..
N u~
~i ro ro 1-~
1.~
5 ro v ~H
a ro ro ~i ro w a cn ro ro o w ro a~
a a ~
O
s~
~
U
U
ro U
U
'O
'O
~H
'H
W
by -C
~
ly ~
~n t~
TS
~
U
ro ~n tl U 4-i .u N
N

, ,p W W cUn C1. E~-~
W ~ m W
W
W
W
W
W
W
W
W
W
W
W
U

p0 ~
W
~
W
p0 U
cUn can v7 O ~n O
N p N M '~t r3' M

c~
H

~, s~, z M 01 d1 H ao ~ U
C~ ~ O O M W 17 ~ C7 H f~ I ~ r , O O O ~ O I W -~I l0 Sa r-I rl N I I N M H ~I
a H N f-I l0 rl N ~ O
w N N H ~o O
~ c7 a~ U
O +~ 4-I
~n ~
U U V V U U U U U U U U U U ~ ~n V U U U U U ~
. .C~ b ,.o ~i t~ C~-7 C~7 U C-~-~U ~C
C~-7 C~7 ~ C~7 C~7 H S-i O
H H H H H H O ~ U
H H H H H H H H H M ~ u7 C7 C7 C7 C9 H H H H OG g W
C7 C7 C7 C7 C7 C7 C9 ~ rd O U U U U U U' C7 C7 C7 C7 U C7 ,~ N
~ U Ch c~

H H H H H U U +~ U C~ ~., U7 ~.I H U Z ~ ~ri ~NG H H H H H H H U ,p 'O N
H H H H H H H fa ~ +~
rl U U 7~ H '~ ~
H H H I--y7~ t~7 C7 C7 U' C7 U U U U U H I-I ~i N
C7 Ch E a U +~ ~
O U U U U U C7 C7 C7 U' C7 H E-~ U =
U U U' U' C7 C7 u7 ~-I
U U U U U U CJ C7 ~ m t5' U U U U U U U U U FC U
H H H H H U U U yi V ~
H U U U U U U U U E-~ ''~ P4 N
H H H H H U U U U 0o E-i rl H H H H H H H H H C7 ~C v s~ ~
~ U U U U U H H H
U H H H H H H H H U .. O
H H H ~ -1-~
(V H H H H H U U H U H U U U U y O O r~o U H U U U H v .>~
N H H H H H Z v rl E H H H H H H H H t7 ~ v ~ .~
O c-H7CH7~CH_7~CH_7H H H H C7 4-I +~
FC FC FC r~ H H H H H H H H ~ p ~
FC FC H H N M U -I~
O U U U V V cH7 HCH7HCH7HH~CH7(H7U U H ~
N U ~ ~ ~C ~ ~C ~ ~ H b ~ !~
~ ~C ~C H ~U OI~ 'I-I N
.1-~O ~n H E-~ E-~ U U V U U U U U C~.7E-~ ~
H H H U V V C7 H -'i ~ L~
U O ~ b 4 O ~ ~ . . ~ ~7 ~, ~ i H r.~ E-~ E~ H ~ . v N
4~ro C7 C7 C7 C7 H r.>; rl; ~ r.>; E-~ +~ u1 V U' C7 H q ~ C ~I
V V ~ U ~ V U U ~C ~ '~ v I~ U U U U U U
~ U v OIC7 ~ ro .C
UUUUUU C7 C7 Ch U' U' W =
O H H H H H U' C7 C7 C7 C7 E-~ ~
H U' u7 y~ ~ u7 .. HHHHHH S~ E-~ v '~
C7 C7 C7 C7 U U U U U U U U c~7 b -ri ' Ch t9 U U U ~ c~ ~,x H ~-1 H H H H H UUUUUUUUUUU U ~ .~ N
H H H H H H H H H H ~ ~C 4~ .C U
H H H b~ a ~I
,'se', U' UU' U' HHHHHHHHHHH N ,~ 3 U' U' Ch C9 C9 C7 C7 tn -a O N
C7 C7 C7 CJ C9 ~ U s~
b H H H H C7 v -I
H H H H H H H H H ~ t~ v H H H H H H H H +~ O
H ~ ~ ~ U U tn ~EUUUU' v ri Sa m C9 C7 C7 C7 C7 C7 U o O
U U U U U C7 C9 U' C9 C7 tn 'O
U C7 ,~ b~
~ H H H H N H H H 4-I v O-~
I"' FC H H H H H U G
E-~ H E-i H H H H H H H H -rl ~ O
~ E-~ E-~ H H H !~ ~
U' C7 C7 UHHUH~~HHHU rl O v+.~
C~ C~ C7 v N ro ~ c~ c~ H U U U U U U U U c1 ~ '~
H H H U U U ~ ~ ~
~ ~ ~ ~C ~ ~ ~ ~ ~ G
-~ ~C ~ ~ ~ CT' -d -rl U E-~ H E-~ E-~ rb s~ ~
H E-i E-~ En E-~ N v +-~
O H cn v =
C~ H E-~ C7 H U' +, O
v H H E-~ E-a C7 a~ x H c~ c~ H c~ H ~n v N
1?, ~ ~ ~ ~ E ~ O~ U
sa ~
v U ~ G
ro v rl V
~7 wi ro v N v -~ v ro s~ ~ ,p ~
~ ~I ro U +' ~-I
o ~ '"I N
a w U o ~ ~ O
v ~ ro ~H -rl ~ .U 1-~ U
aJ a f~
~ .s~ o ~ ro v a -H ~n v~ . tr~
~ v w v ~
v a '-I o ~n ro m Ts t~ a ro ~o ~C tr cn -I U ~
U ~ U U O O -ri v -N N U7 U 'i-I
ty -1 wi O ~ ~n ~ +~ ro ~ U v ~ -rl ,~
~ U v v -ri U ~1 ~ ~ ~ +~ -'~
cn t~ ro -~I o '~
b~ ro a v v v ~ b~ .C
v 5 a v =
a -I v ~I 'ts o v C
ro b~ -~ b~ v ~o U
s~ ro ~ o w s~ m m ~ o ~I ~ ~ -~I ro v 0~ a .~ pa ro ..~
a >., ro ro ~ v .u ro ro ro U v ~ v .~
:r s~, m c~ v .o _ m _ ~
H
G
~
-~
O
~
-O
U
4-a c0 ~

-'~
~
_ ~
~
H

v v x ~ ~L V1 ~1 ~ V7 ~ U7 s.~ ~I ro U7 ~ ~ X17 ~ U7 E-~ p Cl, cd N N M

O
z W ,~ o v~ ~ M ~ v~ o~ ,-I r r m o H I I 01 ~ I N ~ d' I ~ Oo ~O i11 r-I ~ Ol I I I f~ I
N l'7 ('7 l-~ N N N l0 M M M (~-7 l0 ~-I O .~
W O +~
~ U
S-I O
S-I O .~
N Ur~ U Ur~ U U U U U U U U U U U U U U U U U U C ~ W
m~U~~C~'J HC~7C~-7HC~-7C~~C~7 C~'JC~-7 UH -rl u1 . u7 N
U U U U U U U U U U U U U U U U U U U U U U U H H ~ ~ ~
~~~~~~~~~ n~~~~~~~~a~~ a a A
O ~ ~ R', ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ Ri ~ ~ ~ (I1 FC rt1 F(,' .1 ~-. U ~
U
H H H H H H H H H H H H H H H H H H H H H H H ~ C7 cn C7 U ~ c C7 H H H A,' R' A,' a', A,' a,' A', R,' A,' A,' A,' A,' H H .. H .. H . ~ ~ -D
f-I
U H H H H H H H H H H H H H H H H H H H H H H H O U O U ~ ~ ~ N O cn ~ ~ c~ ~ ~ c~ c~ c~ ~ ~ ~ ~ ~ ~ t~ c~ c~ c~ ~ ~ c~ c~ c~
~~v~~~ V t~t~c~i~c~U~ ~~u~~ ~ H a~ O,~ o~-°
H EU' H H N ~ V ~ V ~ U U U U ~ ~ U ~ ~ ~ U U U ~ C~-7 ~ ~ ~ ~' U U U U U U U U U U U U U U U U U U U U U U U H H H ~ '~
b~ b~ tT b~ b~ b~ b~ b~ b~ b~ b~ b~ b~ b~ b~ b~ b~ bt b~ U I b~ ~C U' ~ ?~ a ~
~ ro co O

C7 C7 ~ ~ ~ v ~ -~
~ U U U U U U U U U U U U U U U U U U U U U ~ ~ ~ .~ O
N C O -~ 3 .. w ,5 : : : : : : : : : : : : : : : : : : : : : v ~
_ ~ ~n -~I
t~ U H C7 H E-~ E-~ H U U E-~ U U U U U U U H C7 U r.>; ro ~ ~ U s~ Sa '~
~i ir7 C~ C7 C7 C7 C~ C7 C7 C7 C7 C7 C~ C~ C~ C7 C7 C7 C7 C7 C~ U U ~ ~ G O O
G
;j ~ U U U U U U U U U U U U U U U U U U U U E-i y-I ~ ~ N -rl rd C7 C7 C7 C9 C7 C9 C4 N U U U C9 C7 C9 C9 C9 U ro C7 .1..~ ~ U C7 ~ M b' -~ m H ~ ~ ~ a ~ U U U U U U U U U JH.~ H b~ ~ ~ ~ ~ ~ m O O
CH7 CH'J C4 C4 iE7 C9 C4 CH7 CH7 CH'J C4 C9 HU' HU' C9 tH7 LH'J C4 CH'J ~ bmn q O~ ~-I _H
U U H t7 U U U U U U U U U U U H H +~ -b ~
HUIUCjC3UC5rororororororororororoUUU ~ >~ ~'O~ ro-~
p . c~~ ro ~~c~~c~~~~~n~ ro ro ro ro ro ro ro ro ro ro ro ~~~~ ~ c~ ~ ~ ~ ro ~, +~ ~u rri .
H H H H H H U H H H H N H H -H q ~ ~ ~ can sa N ~~~ c~.7~~ c~~t'~ t~ c~ c~ ~ °~ ~ oo,.. -° ~- ° o O U H H H H H H H U W O r0 ~ x E-~
~rl /~., ~ U ~ ~ U ~ U ~ ~ U ~ U U U ~ ~ U ~ ~ ~ U U U .. U U ~ z C = c7 U ~ U U ~ U U U E ~ U ~ ~ ~ U U ~ U U U U U U p U ~ U ro v U ~ ~ U ~ ~ ~ U U ~ U U U ~ ~ U ~ U ~ U U U Z U ~ U .~ U ~ ~ ~ U ~ U
t~~~~c~c~~t~~~u~tUat~~~c~u~~u~~t~~ oUG oU4 ~~ o~ -~ ~°w' o o~ow°r~
r-I N
t~c~~c~t~c~c~c~t~c~~~c~c~c~c~t~~c~c~~ t~ c~ °'~ z~ .~ ~'~ +~ ~~ ~ ~
H U U H U U H U U U U U U U U H U U U H U ~ ~I ~ ~ ~1 ~~
n W ~ ~'~' ~ c w .id iJ H H H H H H H H H H H H H H H H H H H H H H H E-~ W E-~ ~ ~, ~ rl x o O
~ ~C ~C ~C ,-, U °
O O H U U E U H H U U U U U U U U U H H ~ U U H U H ~ ~ ro ~ ro ~ " s~
'"
U U U H U U U U H H U H H U U H U H H H U >-I ?a ~ ~, ~ N c ~ ~-I O
d1 U~ HI HIHIHIHIHIHIH N H H N N H H H H N HIN HI H C-~-~ ~ ° . N _ = O

N I-1 ~ H H H H H H E-~ H H H H H H E-~ H H H H H C~ H Sa +~ c~ ~ _~ ~ H' O ~ U C'J C~ C7 C~ U C~ C~ C7 C~ C~ C~ O C~ C~ C~ C~ C7 C7 E~ C~ U, r-i ~ ~ +~
C rd rt3 -~-I U U a--~ 3 O ~ W
.11 .~ " ~ -'~ cn U O °
ro N N N u7 C 47 x N G
~n N -H C G 1-I U ~ b O
U W '~
-H ~ v tr 1~ N N N G G -rl ~
.. ~ ~n v v ro a v cn -~ v v ~ ~ ~ v ~ o ro o, -H v -~ ro ~ ~I ro ro tr tr -~ ~ v v >.
U ~i ~n -r-I ~n O -~-I O -ri ~ -~-i v O N -~-I ~1 ~ N s~ b' U S-I . C~
-H ~ -H +~ -.-I -a ~ .C -H v ~ ~ U U rtf ~ ~ -~ cn <n ~ N G ~ ~ - b t~
U ~ U ~-I ~, ~n t~ s~ TS ro a~ O ~n o -~ v O -~ H rn ro ~ ro ro -H U a ro ~ C U -~--I ~ v ~ U a a~ sa -N T) '° TS ~ tn N ~
_>' +~ - -~-i a v U H a O v ~ O ~ rt1 w -C ~ U N ~U ~-I ~ O b~ N N N u~ t3' ~-I +~ - cn C1 .
O ~i ~ ~tf b~ ~ O ~ ~tf O S-I ~i O ~ ~ ~tf sr v C sr ~., ~ U U U N tn i-~ U --ri _ f~
b~ a ~N rt1 U1 ~ 21 -Q O~ W U U ~ (~, ~ N U -~-1 ~. ~ ~ N ~ N ~ -ri -r-I .~ f~ ~ ~ N
-1 rl r-I -.-i N C1, 'D H c - C7 U
U ~ W ~ W N ~ ~C ~ U W W ~ ~ ~ ~ W ~ ~ ~ W can ii can CI. H U -~ b A
~' ~-~ N N M M

Annex XXI:Specific and ubiquitous primers for DNA amplification (recA sequences) Originating DNA fragment SEQ ID NO. Nucleotide sequence SEQ ID Nucleotide NO. position 0 Universal primers (recA) 919 5'-GGI CCI GAR TCI GGI AC 918 437-459 TMI AAR

920c 5'-TCI CCV ATI TCI TCI TC 918 701-723 CCI AIY

$ 921 5'-TIY RTI GAY GCI CAI 918 515-534 GAR GC

922c 5'-TAR AAY TTI ARI YKI CC 918 872-894 GCI CCI

Universal primers (rad51) 0 935 5'-GGI AAR WSI CAR TGY AC 939 568-590 YTI CAY

936 5'-TCI SIY TCI GGI CAI 939 1126-1145 ARR GG

Universal primers (dmcl) $ 937 5'-ATI ACI GAR GYI GGI TT 940 1038-1060 TTY GAR

938 5'-CYI GTI GYI SWI TGI 940 1554-1573 GCR GC

SEQUENCE LISTING
(1)GENERAL INFORMATION:
(i) APPLICANTS: BERGERON, Michel G.1, Quebec City BOISSINOT, Mauricel, St-Augustin-de-Desmaures HULETSKY, Annl, Sillery, MENARD, Christians, St-Lambert-de-Levis OUELLETTE, Marcl, Quebec City PICARD, Fran~ois J.1, Cap-Rouge ROY, Paul H.2, Loretteville l:Canadian citizenship 2:American citizenship (ii) TITLE OF THE INVENTION: HIGHLY CONSERVED GENES AN THEIR USE
TO GENERATE SPECIES-SPECIFIC, GENUS-SPECIFIC AND UNIVERSAL
NUCLEIC ACID PROBES AND AMPLIFICATION PRIMERS TO RAPIDLY
DETECT AND IDENTIFY BACTERIAL, FUNGAL AND PARASITICAL
PATHOGENS FROM CLINICAL SPECIMENS FOR DIAGNOSIS
(iii) NUMBER OF SEQUENCES: 940 (iv) CORRESPONDENCE ADDRESS:
(A) ADDRESSEE:

(B) STREET:

(C) CITY:

(D) STATE:

(E) COUNTRY:

(F) ZIP:

(v) COMPUTER
READABLE:

(A) MEDIUM TYPE:
(B) COMPUTER:
(C) OPERATING:
(D) SOFTWARE:
(vi) CURRENT APPLICATION DATA:
(A) APPLICATION:
(B) FILING DATE:
(C) CLASSIFICATION:
(vii) PRIOR APPLICATION DATA:
(A) APPLICATION:
(B) FILING DATE:

(viii) ATTORNEY/AGENT INFORMATION:
(A) NAME:
(B) REGISTRATION NUMBER:
(ix) TELECOMMUNICATION INFORMATION:
(A) TELEPHONE:
(B) TELEFAX:

2)INFORMATION FOR SEQ ID NO: 1 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 750 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi ) ORIGINAL SOURCE
(A) ORGANISM: Acinetobacter baurnannii (B) STRAIN: ATCC 19606 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 1 2)INFORMATION FOR SEQ ID NO: 2 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 826 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Actinomyces meyeri (B) STRAIN: ATCC 35568 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 2 2)INFORMATION FOR SEQ ID NO: 3 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 835 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Aerococcus viridans (B) STRAIN: ATCC 11563 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 3 2)INFORMATION FOR SEQ ID NO: 4 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 827 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Achromobacter xylosoxidans subsp.
deni trificans (B) STRAIN: ATCC 15173 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 4 2)INFORMATION FOR SEQ ID NO: 5 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 823 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Anaerorhabdus furcosus (B) STRAIN: ATCC 25662 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 5 GGTTATGCCT GGAGACAACA TCGAA.ATGATCGTTGAATTA ATCGCTCCAA 800 2)INFORMATION FOR SEQ ID NO: 6 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 825 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Bacillus anthracis (B) STRAIN: 4229 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 6 2)INFORMATION FOR SEQ ID NO: 7 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Bacillus cereus (B) STRAIN: ATCC 14579 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 7 AGAAA.ATGCT TCTACAACTG TAACTGGTGT AGAGATGTTC CGTAAACTTC 500 2)INFORMATION FOR SEQ ID NO: 8 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 818 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Bacteroides distasonis (B) STRAIN: ATCC 8503 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 8 2)INFORMATION FOR SEQ ID NO: 9 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 639 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus casseliflavus (B) STRAIN: 8763 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 9 2)INFORMATION FOR SEQ ID NO: 10 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 692 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus saprophyticus (B) STRAIN: CSG 197 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 10 AA.ATGGAAGT TCGTGACTTA TTAAGCGAAT ATGACTTCCC AGGTGACGAT 150 2)INFORMATION FOR SEQ ID NO: 11 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 808 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Bacteroides vulgatus (B) STRAIN: ATCC 8482 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 11 2)INFORMATION FOR SEQ ID NO: 12 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 838 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Bartonella henselae (B) STRAIN: ATCC 49882 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 12 2)INFORMATION FOR SEQ ID NO: 13 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 839 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Bifidobacterium adolescentis (B) STRAIN: ATCC 15703 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 13 2)INFORMATION FOR SEQ ID NO: 14 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 839 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Bifidobacterium dentium (B) STRAIN: ATCC 27534 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 14 2)INFORMATION FOR SEQ ID NO: 15 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 838 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Brucella a~bortus (B) STRAIN: 52308 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 15 2)INFORMATION FOR SEQ ID NO: 16 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 771 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Burkholderia cepacia (B) STRAIN: LSPQ 2217 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 16 2)INFORMATION FOR SEQ ID NO: 17 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Cedecea davisae (B) STRAIN: ATCC 33431 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 17 GCGGTATCAT CAA.AGTTGGTGAAGAAGTTG AAATCGTTGG TATCAAAGAT 450 2)INFORMATION FOR SEQ ID NO: 18 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 824 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Cedecea neteri (B) STRAIN: ATCC 33855 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 18 TGCGAAATCT ACCTGTACCG GCGTTGAA.ATGTTCCGCAAA CTGCTGGACG 500 2)INFORMATION FOR SEQ ID NO: 19 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 827 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Cedecea lapagei (B) STRAIN: ATCC 33432 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 19 2)INFORMATION FOR SEQ ID NO: 20 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 831 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Chlamydia pneumoniae (B) STRAIN: CLW 029 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 20 2)INFORMATION FOR SEQ ID NO: 21 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 826 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Chlamydia psittaci (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 21 AGCTACGTTG AAAA.A.ATTCGCGAGTTAATG CAAGCAGTGG ATGATAACAT 300 2)INFORMATION FOR SEQ ID NO: 22 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 822 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Chlamydia trachomatis (B) STRAIN: LGV 12 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 22 2)INFORMATION FOR SEQ ID NO: 23 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 835 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Chryseobacterium meningosepticum (B) STRAIN: CDC B7681 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 23 2)INFORMATION FOR SEQ ID NO: 24 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 816 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Citrobacter amalonaticus (B) STRAIN: ATCC 25405 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 24 2)INFORMATION FOR SEQ ID NO: 25 (i)SEQUENCE CHARACTERISTICS:
(A)_ LENGTH: 825 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Citrobacter braakii (B) STRAIN: ATCC 43162 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 25 2)INFORMATION FOR SEQ ID NO: 26 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA

(vi)ORIGINAL SOURCE:
(A) ORGANISM: Citrobacter koseri (B) STRAIN: ATCC 27156 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 26 CGTGAAGAA.A TCGAACGTGG TCAGGTACTG GCTAAGCCGG GYTCCATCAA 600 2)INFORMATION FOR SEQ ID NO: 27 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 827 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Citrobacter farmeri (B) STRAIN: ATCC 51112 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 27 CGATGGACGA CGGTCTGCGT TTCGCAA g27 2)INFORMATION FOR SEQ ID NO: 28 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 797 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Citrobacter freundii (B) STRAIN: ATCC 8090 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 28 2)INFORMATION FOR SEQ ID NO: 29 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 826 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Citrobacter sedlakii (B) STRAIN: ATCC 51115 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 29 CGTGAAGAA.A TCGAACGTGG TCAGGTACTG GCGAAGCCGG GCACCATCAA 600 GGTAATGCCG GGCGACAACA TCAAA.ATGGTTGTTACCCTG ATCCACCCGA 800 2)INFORMATION FOR SEQ ID NO: 30 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 823 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Citrobacter werkmanii (B) STRAIN: ATCC 51114 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 30 2)INFORMATION FOR SEQ ID NO: 31 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 826 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA

(vi)ORIGINAL SOURCE:
(A) ORGANISM: Citrobacter youngae (B) STRAIN: ATCC 29935 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 31 2)INFORMATION FOR SEQ ID NO: 32 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 841 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Clostridium perfringens (B) STRAIN: ATCC 13124 (xi)SEQUENCE DESCRIPTION: SEQ ID N0:32 2)INFORMATION FOR SEQ ID NO: 33 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 822 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Comamonas acidovorans (B) STRAIN: ATCC 15668 (xi)SEQUENCE DESCRIPTION: SEQ ID N0: 33 2)INFORMATION FOR SEQ ID NO: 34 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 702 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Corynebacterium bovis (B) STRAIN: ATCC 7715 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 34 CAAGTTCCTC GACACGGCCG.AGGCCGGCGA CAACGCCGCC CTGCTGCTCC 500 2)INFORMATION FOR SEQ ID NO: 35 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 689 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi ) ORIGINAL SOURCE
(A) ORGANISM: Corynebacterium cervicis (B) STRAIN: NCTC 10604 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 35 2)INFORMATION FOR SEQ ID NO: 36 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 804 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi ) ORIGINAL SOURCE
(A) ORGANISM: Corynebacterium flavescens (B) STRAIN: ATCC 10340 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 36 2)INFORMATION FOR SEQ ID NO: 37 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 692 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Corynehacterium kutscheri (B) STRAIN: ATCC 15677 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 37 2)INFORMATION FOR SEQ ID NO: 38 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 797 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Corynebacterium minutissimum (B) STRAIN: ATCC 23348 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 38 2)INFORMATION FOR SEQ ID NO: 39 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 702 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Corynebacterium mycetoides (B) STRAIN: ATCC 21134 (xi)SEQUENCE DESCRIPTION: SEQ ID N0: 39 2)INFORMATION FOR SEQ ID NO: 40 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 674 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Corynebacterium pseudogenitalium (B) STRAIN: ATCC 33038 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 40 2)INFORMATION FOR SEQ ID NO: 41 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 694 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Corynebacterium renale (B) STRAIN: ATCC 19412 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 41 2)INFORMATION FOR SEQ ID NO: 42 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 687 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Corynebacterium ulcerans (B) STRAIN: NCTC 8665 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 42 2)INFORMATION FOR SEQ ID NO: 43 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 778 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Corynebacterium urealyticurn (B) STRAIN: ATCC 43042 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 43 2)INFORMATION FOR SEQ ID NO: 44 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 703 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Corynebacterium xerosis (B) STRAIN: ATCC 373 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 44 2)INFORMATION FOR SEQ ID NO: 45 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 832 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA

(vi)ORIGINAL SOURCE:
(A) ORGANISM: Coxiella ~burnetii (B) STRAIN: Nine Mile phase II
(xi)SEQUENCE DESCRIPTION: SEQ ID NO: 45 2)INFORMATION FOR SEQ ID NO: 46 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 816 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Edwardsiella hoshinae (B) STRAIN: ATCC 33379 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 46 2)INFORMATION FOR SEQ ID NO: 47 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 821 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Edwardsiella tarda (B) STRAIN: ATCC 15947 (xi)SEQUENCE DESCRIPTION: SEQ ID N0: 47 2)INFORMATION FOR SEQ ID NO: 48 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 830 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Eikenella corrodens (B) STRAIN: ATCC 23834 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 48 2)INFORMATION FOR SEQ ID NO: 49 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 808 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterobacter aerogenes (B) STRAIN: ATCC 13048 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 49 CGCGATGG gOg 2)INFORMATION FOR SEQ ID NO: 50 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 828 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA

(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterobacter agglomerans (B) STRAIN: ATCC 27989 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 50 TCGCGATGGA CGACGGTCTG CGTTCGCA g2g 2)INFORMATION FOR SEQ ID NO: 51 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 825 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterobacter amnigenus (B) STRAIN: ATCC 33072 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 51 2)INFORMATION FOR SEQ ID NO: 52 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 822 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterobacter asburiae (B) STRAIN: ATCC 35953 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 52 2)INFORMATION FOR SEQ ID NO: 53 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 826 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterobacter cancerogenus (B) STRAIN: ATCC 35317 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 53 GAGTGGGAAG CAA.AAATCATCGAACTGGCT GGCTTCCTGG ATTCTTACAT 300 TACTGCKA.A.A TCTACCTGTA CTGGCGTTGA AATGTTCCGC AAACTGCTGG 500 2)INFORMATION FOR SEQ ID NO: 54 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 806 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Entero~bacter cloacae (B) STRAIN: ATCC 13047 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 54 2)INFORMATION FOR SEQ ID NO: 55 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 826 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA

(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterobacter gergoviae (B) STRAIN: ATCC 33028 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 55 2)INFORMATION FOR SEQ ID NO: 56 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi ) ORIGINAL SOURCE
(A) ORGANISM: Enterobacter hormaechei (B) STRAIN: ATCC 49162 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 56 CGCGATGGAC GACGGTCTGC GTTTCGCAA g29 2)INFORMATION FOR SEQ ID NO: 57 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 831 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterobacter sakazakii (B) STRAIN: ATCC 29544 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 57 2)INFORMATION FOR SEQ ID NO: 58 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 835 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus casseliflavus (B) STRAIN: ATCC 25788 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 58 2)INFORMATION FOR SEQ ID NO: 59 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 826 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus cecorum (B) STRAIN: ATCC 43198 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 59 2)INFORMATION FOR SEQ ID NO: 60 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 835 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA

(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus dispar (B) STRAIN: ATCC 51266 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 60 TCATATGAAG AAA.AAATCTTAGAATTAATG GCTGCAGTTG ACGAATATAT 300 2)INFORMATION FOR SEQ ID NO: 61 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 835 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus durans (B) STRAIN: ATCC 19432 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 61 AGAAACAGCT CAA.ACAACAGTTACTGGTGT TGAAATGTTC CGTAAATTAT 500 2)INFORMATION FOR SEQ ID NO: 62 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 680 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus faecalis (B) STRAIN: 8610 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 62 2)INFORMATION FOR SEQ ID NO: 63 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 680 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus faecalis (B) STRAIN: 8487 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 63 2)INFORMATION FOR SEQ ID NO: 64 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 685 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
2 0 (vi ) ORIGINAL SOURCE
(A) ORGANISM: Enterococcus faecium (B) STRAIN: 8482 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 64 2)INFORMATION FOR SEQ ID NO: 65 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 825 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus flavescens (B) STRAIN: ATCC 49996 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 65 TCATACGAAG AA.AAAATCATGGAATTAATG GCTGCAGTTG ACGAATACGT 300 CACACCTCAT ACAA.AATTTAAAGCTGAAGT TTACGTTTTA ACAAAAGAAG 650 2)INFORMATION FOR SEQ ID NO: 66 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 636 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus gallinarum (B) STRAIN: 8420 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 66 2)INFORMATION FOR SEQ ID NO: 67 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 835 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA

(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus hirae (B) STRAIN: ATCC 8043 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 67 TCATACGAAG AA.AAP.ATCCTTGAATTGATG GCTGCAGTTG ACGAATATAT 300 2)INFORMATION FOR SEQ ID NO: 68 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 835 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus mundtii (B) STRAIN: ATCC 43186 (xi)SEQUENCE DESCRIPTION: SEQ ID N0: 68 2)INFORMATION FOR SEQ ID NO: 69 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 836 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus pseudoavium (B) STRAIN: ATCC 49372 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 69 TCATACRAAG AAA.AAATCTTAGAATTAATG SCTGCTGTTG ACGAATACAT 300 AGAAACTGCT AA.AACAACTGTTACAGGTGT TGAAATGTTC CGTAAATTGT 500 2)INFORMATION FOR SEQ ID NO: 70 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 835 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus raffinosus (B) STRAIN: ATCC 49427 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 70 6 0 TCATACGAAG AA.A.A.A.ATCTTAGAATTAATG GCTGCTGTTG ATGAATACAT 3 0 2)INFORMATION FOR SEQ ID NO: 71 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 835 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus saccharolyticus (B) STRAIN: ATCC 43076 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 71 GTTTACGAAG AA.A.AAATCTTCGAATTAATG GCTGCAGTTG ACGAATATAT 300 CCCAACTCCA GAACGTGATA CTGAAA.AACCATTCATGATG CCAGTTGAGG 350 CACTCCTCAT ACAA.AATTCGTAGCTGAAGT TTACGTTTTA ACTAAAGAAG 650 2)INFORMATION FOR SEQ ID NO: 72 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 823 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA

(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus solitarius (B) STRAIN: ATCC 49428 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 72 ACGTTAA.AAA GACAACAGTT ACTGGTGTAG AAATGTTCCG TAAATTGTTG 500 2)INFORMATION FOR SEQ ID NO: 73 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 665 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus casseliflavus (B) STRAIN: ATCC 25788 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 73 ACACAA.AA.AG CAGTCGTGAC AGGGGTAGAA ATGTTCCGCA AAACGATGGA 500 2)INFORMATION FOR SEQ ID NO: 74 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 664 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi ) ORIGINAL SOURCE
(A) ORGANISM: Enterococcus faecium (B) STRAIN: ATCC 19434 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 74 2)INFORMATION FOR SEQ ID NO: 75 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 666 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus flavescens (B) STRAIN: ATCC 49996 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 75 2)INFORMATION FOR SEQ ID NO: 76 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 667 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus gallinarum (B) STRAIN: ATCC 49573 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 76 2)INFORMATION FOR SEQ ID NO: 77 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 834 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Ehrlichia canis (B) STRAIN: Florida (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 77 GGCTCAGGTG TGTGGAGTGA AA.AAATAATGGAATTGATGA ATGCTTTAGA 300 AT~~A.A.AA.AAG AAGATGTAGA AAGAGGGCAA GTATTGAGTG CACCTGGACA 6 0 GATACATTCA TATAAGAGAT TTAAGGCAGA GGTATATATA TTGAA.A.AA.AG650 2)INFORMATION FOR SEQ ID NO: 78 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 817 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Escherichia coli (B) STRAIN: ATCC 23511 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 78 2)INFORMATION FOR SEQ ID NO: 79 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 825 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA

(vi)ORIGINAL SOURCE:
(A) ORGANISM: Escherichia fergusonii (B) STRAIN: ATCC 35469 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 79 2)INFORMATION FOR SEQ ID NO: 80 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Escherichia hermannii (B) STRAIN: ATCC 33650 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 80 2)INFORMATION FOR SEQ ID NO: 81 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 816 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Escherichia vulneris (B) STRAIN: ATCC 33821 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 81 GGTAATGCCG GGCGACAACA TCAA.AATGGTTGTTACCCTG ATCCATCCGA 800 2)INFORMATION FOR SEQ ID NO: 82 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 828 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Eubacterium lentum (B) STRAIN: ATCC 43055 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 82 2)INFORMATION FOR SEQ ID NO: 83 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 835 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Eu~bacterium nodatum (B) STRAIN: ATCC 33099 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 83 2)INFORMATION FOR SEQ ID NO: 84 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 826 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA

(vi)ORIGINAL SOURCE:
(A) ORGANISM: Ewingella americana (B) STRAIN: ATCC 33852 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 84 2)INFORMATION FOR SEQ ID NO: 85 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 828 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi ) ORIGINAL SOURCE
(A) ORGANISM: Francisella tularensis (B) STRAIN: LVS
(xi)SEQUENCE DESCRIPTION: SEQ ID NO: 85 AACTCAAA.AA ACTACAGTAA CTGGTGTGGA AATGTTCCGT AAGCTTTTAG 500 2)INFORMATION FOR SEQ ID NO: 86 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi ) ORIGINAL SOURCE
(A) ORGANISM: Fusobacterium nucleatum subsp. polymorphum (B) STRAIN: ATCC 10953 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 86 GTGGTCGTCA CACTCCGTTC CACAACAAAT ACCGTCCTCA GTTCTATCTG 700 ' 2)INFORMATION FOR SEQ ID N0: 87 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 828 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Gemella haemolysans (B) STRAIN: ATCC 10379 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 87 2)INFORMATION FOR SEQ ID NO: 88 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 823 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Gemella morbillorum (B) STRAIN: ATCC 27824 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 88 AAA.AGCTATC ATCGAATTAA TGGAAACAGT TGACGAGTAC ATCCCAACTC 300 2)INFORMATION FOR SEQ ID NO: 89 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA

(vi)ORIGINAL SOURCE:
(A) ORGANISM: Haemophilus actinomycetemcomitans (B) STRAIN: ATCC 33384 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 89 GCAAA.AACCA CCGTAACCGG TGTTGAAATG TTCCGTAAAT TACTTGACGA 500 2)INFORMATION FOR SEQ ID NO: 90 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 833 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi ) ORIGINAL SOURCE
(A) ORGANISM: Haemophilus aphrophilus (B) STRAIN: ATCC 33389 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 90 2)INFORMATION FOR SEQ ID NO: 91 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 815 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Haemophilus ducreyi (B) STRAIN: DSM 8925 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 91 AACGACA.AA.AACAACAGTAA CCGGTGTTGA GATGTTCCGT AAACTATTAG 500 2)INFORMATION FOR SEQ ID NO: 92 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 830 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Haemophilus haemolyticus (B) STRAIN: ATCC 33390 (xi)SEQUENCE DESCRIPTION: SEQ ID N0: 92 TTCTTAA.ACA AATGCGACAT GGTAGATGAC GAAGAGTTAT TAGAATTAGT 150 2)INFORMATION FOR SEQ ID NO: 93 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 824 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Haemophilus parahaemolyticus (B) STRAIN: ATCC 10014 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 93 AGAAAA.A.ATT CTTGAATTAG CAAACCACTT AGATACATAC ATCCCAGAGC 300 CAGGCGATAA CATCAAA.ATGACAGTATCAT TAATCCACCC AATCGCGATG 800 2)INFORMATION FOR SEQ ID NO: 94 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 833 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA

(vi ) ORIGINAL SOURCE
(A) ORGANISM: Haemophilus parainfluenzae (B) STRAIN: ATCC 7901 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 94 2)INFORMATION FOR SEQ ID NO: 95 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 824 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Haemophilus paraphrophilus (B) STRAIN: ATCC 29241 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 95 TGAA.ATGGAA GTTCGTGAAC TTCTTTCTCA ATATGACTTC CCGGGTGACG 200 GGTAATGCCT GGCGATAACA TCAA.A.ATGACCGTATCCTTA ATCCACCCAA 800 2)INFORMATION FOR SEQ ID N0: 96 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 818 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Haemophilus segnis (B) STRAIN: ATCC 33393 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 96 2)INFORMATION FOR SEQ ID NO: 97 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 763 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Hafnia alvei (B) STRAIN: ATCC 13337 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 97 2)INFORMATION FOR SEQ ID N0: 98 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 828 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Kingella kingae (B) STRAIN: ATCC 23330 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 98 CACGCAA.A.AAACCACTTGTA CTGGCGTGGA AATGTTCCGC AAATTGTTGG 500 2)INFORMATION FOR SEQ ID NO: 99 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 828 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:

(A) ORGANISM: Klebsiella ornithinolytica (B) STRAIN: ATCC 31898 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 99 2)INFORMATION FOR SEQ ID NO: 100 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 749 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Klebsiella oxytoca (B) STRAIN: ATCC 33496 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 100 2)INFORMATION FOR SEQ ID NO: 101 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 830 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Kle~bsiella planticola (B) STRAIN: ATCC 33531 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 101 2)INFORMATION FOR SEQ ID N0: 102 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 806 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Klebsiella pneumoniae subsp. ozaenae (B) STRAIN: ATCC 11296 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 102 GCGAAA.ATCA TCGAACTGGC TGGCCACCTG GATACCTATA TCCCGGAACC 300 2)INFORMATION FOR SEQ ID N0: 103 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 743 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Klebsiella pneumoniae subsp. pneumoniae (B) STRAIN: ATCC 13883 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 103 2)INFORMATION FOR SEQ ID NO: 104 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 819 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Klebsiella pneumoniae subsp. rhinoscleromatis (B) STRAIN: ATCC 13884 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 104 2)INFORMATION FOR SEQ ID NO: 105 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 832 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Kluyvera ascorbata (B) STRAIN: ATCC 33433 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 105 GAGTGGGAAG CGAA.A.ATCATCGAACTGGCT GGCTTCCTGG ATTCTTACAT 300 2)INFORMATION FOR SEQ ID NO: 106 (i)SEQUENCE CHARACTERISTICS:

(A) LENGTH: 830 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Kluyvera cryocrescens (B) STRAIN: ATCC 33435 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 106 2)INFORMATION FOR SEQ ID NO: 107 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 826 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Kluyvera georgiana (B) STRAIN: ATCC 51603 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 107 2)INFORMATION FOR SEQ ID NO: 108 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 803 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Lactobacillus casei subsp. casei (B) STRAIN: ATCC 393 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 108 2)INFORMATION FOR SEQ ID NO: 109 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 825 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi ) ORIGINAL SOURCE
(A) ORGANISM: Lactococcus lactis subsp. lactis (B) STRAIN: ATCC 19435 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 109 2)INFORMATION FOR SEQ ID NO: 110 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 824 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Leclercia adecar~boxylata (B) STRAIN: ATCC 23216 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 110 2)INFORMATION FOR SEQ ID NO: 111 (i)SEQUENCE CHARACTERISTICS:

(A) LENGTH: 838 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Legionella micdadei (B) STRAIN: ATCC 33218 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 111 2)INFORMATION FOR SEQ ID NO: 112 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 838 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Legionella pneumophila subsp. pneumophila (B) STRAIN: ATCC 33152 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 112 2)INFORMATION FOR SEQ ID NO: 113 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 828 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Leminorella grimontii (B) STRAIN: ATCC 33999 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 113 2)INFORMATION FOR SEQ ID NO: 114 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 826 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Leminorella richardii (B) STRAIN: ATCC 33998 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 114 2)INFORMATION FOR SEQ ID NO: 115 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 843 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Leptospira interrogans (B) STRAIN: ATCC 23581 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 115 TATCGGTATC CGCCCAACAA CAA.AAACTGTTGTTACCGGT ATCGAAATGT 500 TCAGAA.AACT TCTCGATCAA GCGGAAGCTG GCGACAACAT CGGCGCTCTT 550 CTTCGTGGAA CTAAAAP~AGAAGAAATCGAA AGAGGGCAAG TTCTTGCGAA 600 GCCAGGTTCT ATCACTCCTC ACAAAA.AGTTTGCCGCTGAG GTGTATGTAT 650 2)INFORMATION FOR SEQ ID NO: 116 (i)SEQUENCE CHARACTERISTICS:

(A) LENGTH: 832 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi ) ORIGINAL SOURCE
(A) ORGANISM: Megamonas hypermegale (B) STRAIN: ATCC 25560 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 116 2)INFORMATION FOR SEQ ID NO: 117 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 820 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Mitsuokella multacida (B) STRAIN: ATCC 27723 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 117 2)INFORMATION FOR SEQ ID NO: 118 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 831 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Mo~biluncus curtisii subsp. holmesii (B) STRAIN: ATCC 35242 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 118 2)INFORMATION FOR SEQ ID NO: 119 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 825 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Moellerella wisconsensis (B) STRAIN: ATCC 35017 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 119 ACCGTGAA.AA CAACATGTAC TGGCGTTGAA ATGTTCCGTA AACTGCTGGA 500 2)INFORMATION FOR SEQ ID N0:120 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 827 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Branhamella catarrhalis (B) STRAIN: ATCC 43628 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 120 2)INFORMATION FOR SEQ ID NO: 121 (i)SEQUENCE CHARACTERISTICS:

(A) LENGTH: 806 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Morganella morganii subsp. morganii (B) STRAIN: ATCC 25830 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 121 2)INFORMATION FOR SEQ ID NO: 122 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 825 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Mycobacterium tuberculosis (B) STRAIN: TB 299 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 122 2)INFORMATION FOR SEQ ID NO: 123 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 806 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Neisseria cinerea (B) STRAIN: ATCC 14685 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 123 AACTCAAAA.A ACCACTTGTA CCGGTGTTGA AATGTTCCGC AAACTGCTGG 500 2)INFORMATION FOR SEQ ID NO: 124 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 822 bases (B) TYPE: Nucleic acid _ (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi ) ORIGINAL SOURCE
(A) ORGANISM: Neisseria elongata subsp. elongata (B) STRAIN: ATCC 25295 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 124 GCTTACGAAG AAAA.AATCTTCGAACTGGCT GCTGCATTGG ACAGCTACAT 300 2)INFORMATION FOR SEQ ID NO: 125 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 820 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Neisseria flavescens (B) STRAIN: ATCC 13120 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 125 2)INFORMATION FOR SEQ ID NO: 126 (i)SEQUENCE CHARACTERISTICS:

(A) LENGTH: 830 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Neisseria gonorrhoeae (B) STRAIN: ATCC 49226 (xi)SEQUENCE DESCRIPTION: SEQ ID N0: 126 CTTACGAAGA AA.A.AATCTTCGAACTGGCTA CCGCATTGGA CAGCTACATC 300 2)INFORMATION FOR SEQ ID NO: 127 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 816 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Neisseria lactamica (B) STRAIN: ATCC 23970 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 127 AACCCAA.A.AA ACCACCTGTA CCGGTGTCGA GATGTTCCGC AAACTGCTGG 500 2)INFORMATION FOR SEQ ID NO: 128 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 831 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Neisseria meningitides (B) STRAIN: ATCC 13077 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 128 GCTTACGAAG P~AAAAATCTTCGAATTGGCT GCTGCATTGG ACAGCTACAT 300 2)INFORMATION FOR SEQ ID NO: 129 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 815 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Neisseria mucosa (B) STRAIN: ATCC 19696 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 129 AACCCAAAA.A ACCACATGTA CCGGTGTTGA AATGTTCCGC AAACTGCTGG 500 2)INFORMATION FOR SEQ ID NO: 130 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Neisseria sicca (B) STRAIN: ATCC 9913 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 130 CTTACGAAGA AAAA.ATCTTCGAACTGGCTG CTGCATTGGA CAGCTACATC 300 2)INFORMATION FOR SEQ ID NO: 131 (i)SEQUENCE CHARACTERISTICS:

(A) LENGTH: 814 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi ) ORIGINAL SOURCE
(A) ORGANISM: Neisseria subflava (B) STRAIN: ATCC 14221 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 131 ACCCAAA.AAA CCACTTGTAC CGGCGTTGAA ATGTTCCGCA AACTGCTGGA 500 2)INFORMATION FOR SEQ ID NO: 132 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 818 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Neisseria weaveri (B) STRAIN: ATCC 51223 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 132 CAA.A.A.AACTA CTTGTACCGG CGTTGAAATG TTCCGTAAAT TGCTGGATSA 500 2)TNFORMATION FOR SEQ ID NO: 133 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 836 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Ochrobactrum anthropi (B) STRAIN: ATCC 49188 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 133 2)INFORMATION FOR SEQ ID NO: 134 (i)SEQUENCE CHARACTERISTICS: .
(A) LENGTH: 805 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Pantoea agglomerans (B) STRAIN: ATCC 27155 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 134 GCAAAA.ATCG TTGAGCTGGC TGAACACCTG GACAACTACA TCCCGGATCC 300 2)INFORMATION FOR SEQ ID NO: 135 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 825 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Pantoea dispersa (B) STRAIN: ATCC 14589 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 135 2)INFORMATION FOR SEQ ID NO: 136 (i)SEQUENCE CHARACTERISTICS:

(A) LENGTH: 762 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Pasteurella multocida (B) STRAIN: NCTC 10322 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 136 GGYGTAGCTG AGTGGGAAGA GAA.A.ATTCTTGAGTTAGCCA ACCACTTAGA 250 2)INFORMATION FOR SEQ ID NO: 137 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 832 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Peptostreptococcus anaero~bius (B) STRAIN: ATCC 27337 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 137 2)INFORMATION FOR SEQ ID NO: 138 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 823 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Peptostreptococcus asaccharolyticus (B) STRAIN: LSPQ 2639 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 138 2)INFORMATION FOR SEQ ID NO: 139 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 832 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Peptostreptococcus prevotii (B) STRAIN: ATCC 9321 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 139 CACATCCTAC TAGCAAGACA AGTAGGCGTT CCAAA.A.ATCGCAGTATTCCT 100 TAA.ACCCACA CACAGAATTC GAAGGTCAAG TATACGTACT AACAAAAGAA 650 2)INFORMATION FOR SEQ ID NO: 140 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 831 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Porphyromonas asaccharolytica (B) STRAIN: ATCC 25260 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 140 2)INFORMATION FOR SEQ ID NO: 141 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 818 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Porphyromonas gingivalis (B) STRAIN: ATCC 33277 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 141 2)INFORMATION FOR SEQ ID NO: 142 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 830 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Pragia fontium (B) STRAIN: ATCC 49100 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 142 2)INFORMATION FOR SEQ ID NO: 143 (i)SEQUENCE,CHARACTERISTICS:
(A) LENGTH: 821 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Prevotella melaninogenica (B) STRAIN: ATCC 25845 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 143 CTCCTATTAT TCGTGGTTCT GCACTCGGTG CTTTGAACGG TGTTGAG~1AG 250 2)INFORMATION FOR SEQ ID NO: 144 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 827 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Prevotella oralis (B) STRAIN: ATCC 33269 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 144 2)INFORMATION FOR SEQ ID NO: 145 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 833 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Propionibacterium acnes (B) STRAIN: ATCC 6919 (xi)SEQUENCE DESCRIPTION: SEQ ID N0: 145 2)INFORMATION FOR SEQ ID NO: 146 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 745 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Proteus mirabilis (B) STRAIN: ATCC 35659 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 146 GGCGAAGCAG AGTGGGAAGC AA.AAATTGTTGAATTAGCAG AAGCACTGGA 250 2)INFORMATION FOR SEQ ID NO: 147 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Proteus penneri (B) STRAIN: ATCC 33519 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 147 AGTGGGAAGC AAA.AATTGTTGAATTAGCAG AAGCACTGGA TTCATACATC 300 GTGGCGTAAT CAA.AGTTGGTGAAGAAGTTG AAATCGTTGG TATTAAACCA 450 ACAGCGAA.AA CAACTTGTAC TGGCGTTGAA ATGTTCCGTA AATTACTTGA 500 2)INFORMATION FOR SEQ ID NO: 148 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 824 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Proteus vulgaris (B) STRAIN: ATCC 13315 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 148 2)INFORMATION FOR SEQ ID NO: 149 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 745 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Providencia alcalifaciens (B) STRAIN: ATCC 9886 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 149 2)INFORMATION FOR SEQ ID NO: 150 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 830 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Providencia rettgeri (B) STRAIN: ATCC 9250 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 150 GCCACACACT AA.ATTCGAATCAGAAGTCTA TATTCTGAGC AAAGATGAAG 650 2)INFORMATION FOR SEQ ID N0: 151 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 826 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Providencia rustigianii (B) STRAIN: ATCC 33673 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 151 2)INFORMATION FOR SEQ ID NO: 152 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 830 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Providencia stuartii (B) STRAIN: ATCC 33672 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 152 2)INFORMATION FOR SEQ ID NO: 153 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 827 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Pseudomonas aeruginosa (B) STRAIN: ATCC 35554 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 153 2)INFORMATION FOR SEQ ID NO: 154 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 841 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Pseudomonas fluorescens (B) STRAIN: ATCC 13525 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 154 CGTTGAAATG GTTATGCCAG GCGACAACAT CAAA.ATGGTTGTTACCCTGA 800 TCAA.A.ACCAT CGCAATGGAA GACGGTCTGC GTTTCGCTAT T 841 2)INFORMATION FOR SEQ ID NO: 155 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 841 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Pseudomonas stutzeri (B) STRAIN: ATCC 17588 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 155 2)INFORMATION FOR SEQ ID NO: 156 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 833 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA

(vi)ORIGINAL SOURCE:
(A) ORGANISM: Psychrohacter phenylpyruvicus (B) STRAIN: ATCC 23333 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 156 2)INFORMATION FOR SEQ ID NO: 157 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 825 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Rahnella aquatilis (B) STRAIN: ATCC 33071 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 157 2)INFORMATION FOR SEQ ID NO: 158 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 830 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Salmonella choleraesuis subsp. arizonae (B) STRAIN: ATCC 13314 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 158 GCCGCACACC AAGTTCGAAT CTGAAGTGTA CATTCTGTCC AAAGATGAAG 650.

2)INFORMATION FOR SEQ ID NO: 159 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 832 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Salmonella choleraesuis subsp. choleraesuis serotype choleraesuis (B) STRAIN: ATCC 7001 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 159 2)INFORMATION FOR SEQ ID NO: 160 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 807 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Salmonella choleraesuis subsp. diarizonae (B) STRAIN: ATCC 43973 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 160 2)INFORMATION FOR SEQ ID NO: 161 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 832 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Salmonella choleraesuis subsp. choleraesuis serotype heidelberg (B) STRAIN: ATCC 8326 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 161 2)INFORMATION FOR SEQ ID NO: 162 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 807 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Salmonella choleraesuis subsp. houtenae (B) STRAIN: ATCC 43974 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 162 2)INFORMATION FOR SEQ ID NO: 163 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 827 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Salmonella choleraesuis subsp. indica (B) STRAIN: ATCC 43976 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 163 2)INFORMATION FOR SEQ ID NO: 164 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 807 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Salmonella choleraesuis subsp. salamae (B) STRAIN: ATCC 43972 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 164 2)INFORMATION FOR SEQ ID NO: 165 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 832 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Salmonella choleraesuis subsp. choleraesuis serotype typhi (B) STRAIN: ATCC 10749 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 165 2)INFORMATION FOR SEQ ID NO: 166 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 817 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Serratia fonticola (B) STRAIN: DSM 4576 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 166 2)INFORMATION FOR SEQ ID NO: 167 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 787 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Serratia liquefaciens (B) STRAIN: ATCC 27592 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 167 2)INFORMATION FOR SEQ ID NO: 168 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 745 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Serratia marcescens (B) STRAIN: ATCC 13880 (xi)SEQUENCE DESCRIPTION: SEQ ID N0: 168 2)INFORMATION FOR SEQ ID NO: 169 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Serratia odorifera (B) STRAIN: ATCC 33077 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 169 2)INFORMATION FOR SEQ ID NO: 170 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 830 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Serratia plymuthica (B) STRAIN: DSM 4540 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 170 2)INFORMATION FOR SEQ ID NO: 171 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA

(vi)ORIGINAL SOURCE:
(A) ORGANISM: Serratia ru~bidaea (B) STRAIN: ATCC 27593 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 171 2)INFORMATION FOR SEQ ID NO: 172 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 826 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Shigella ~boydii (B) STRAIN: ATCC 9207 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 172 2)INFORMATION FOR SEQ ID NO: 173 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 818 bases (B) TYPE: Nucleic acid (C) STRAIaTDEDNESS : Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Shigella dysenteriae (B) STRAIN: ATCC 11835 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 173 CAA.AGTTGGT GAAGAAGTTG AAATCGTTGG TATCAAAGAG ACYCAGAAGT 450 2)INFORMATION FOR SEQ ID NO: 174 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 806 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi ) ORIGINAL SOURCE
(A) ORGANISM: Shigella flexneri (B) STRAIN: ATCC 12022 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 174 2)INFORMATION FOR SEQ ID NO: 175 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 832 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Shigella sonnei (B) STRAIN: ATCC 29930 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 175 2)INFORMATION FOR SEQ ID NO: 176 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 716 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA

(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus aureus (B) STRAIN: ATCC 13301 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 176 TTCAGCATTA AAAGCTTTAG AAGGCGATGC TCAATACGAA GAA.A.A.A.ATCT2 5 TCTGACAA.AC CATTCATGAT GCCAGTTGAG GACGTATTCT CAATCACTGG 350 2)INFORMATION FOR SEQ ID NO: 177 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 719 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus aureus (B) STRAIN: ATCC 29247 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 177 GAAA.AAATCT TAGAATTAAT GGAAGCTGTA GATACTTACA TTCCAACTCC 250 TGAATTCAA.A GCAGAAGTAT ACGTATTATC AAAAGACGAA GGTGGACGTC 600 2)INFORMATION FOR SEQ ID NO: 178 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 625 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus aureus (B) STRAIN: ATCC 33591 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 178 2)INFORMATION FOR SEQ ID N0: 179 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 704 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus aureus (B) STRAIN: ATCC 43300 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 179 2)INFORMATION FOR SEQ ID NO: 180 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 730 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus aureus subsp. aureus (B) STRAIN: ATCC 6538 (xi)SEQUENCE DESCRIPTION: SEQ ID N0: 180 2)INFORMATION FOR SEQ ID NO: 181 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 834 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus auricularis (B) STRAIN: ATCC 33753 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 181 GAATACGAAC AAAA.AATCTTAGACTTAATG CAACAAGTTG ACGATTACAT 300 2)INFORMATION FOR SEQ ID NO: 182 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 835 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus capitis subsp. capitis (B) STRAIN: ATCC 27840 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 182 2)INFORMATION FOR SEQ ID NO: 183 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 804 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA

(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus caseolyticus (B) STRAIN: ATCC 13548 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 183 2)INFORMATION FOR SEQ ID NO: 184 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 832 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus cohnii (B) STRAIN: DSM 20260 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 184 2)INFORMATION FOR SEQ ID NO: 185 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 699 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus epidermidis (B) STRAIN: CSG 269 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 185 2)INFORMATION FOR SEQ ID NO: 186 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus haemolyticus (B) STRAIN: ATCC 29970 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 186 CAATACGAAG AP.AA.AATCTTAGAATTAATG CAAGCAGTTG ATGACTACAT 300 2)INFORMATION FOR SEQ ID NO: 187 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 705 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus warneri (B) STRAIN: CSG 123 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 187 GGCGACGAAA AATACGAAGA AA.AAATCTTAGAATTAATGC AAGCAGTTGA 250 2)INFORMATION FOR SEQ ID NO: 188 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 678 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus haemolyticus (B) STRAIN: CSG 23 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 188 2)INFORMATION FOR SEQ ID NO: 189 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 668 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus haemolyticus (B) STRAIN: CSG 33 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 189 2)INFORMATION FOR SEQ ID NO: 190 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 593 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus haemolyticus (B) STRAIN: CSG 8 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 190 GAAAAA.ATCT TAGAATTAAT GCAAGCAGTT GATGATTACA TTCCAACTCC 200 AA.AATTTAAA GCAGACGTAT ACGTTTTATC TAAAGACGAA GGTGGACGTC 550 2)INFORMATION FOR SEQ ID NO: 191 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 828 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus hominis subsp. hominis (B) STRAIN: ATCC 27844 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 191 CAATACGAAG AAAA.AATCTTAGAATTAATG CAAGCAGTTG ATGATTATAT 300 ACCTCACACA AAATTCAA.AGCAGACGTATA CGTTTTATCA AAAGATGAAG 650 2)INFORMATION FOR SEQ ID NO: 192 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 620 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus warneri (B) STRAIN: ATCC 35982 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 192 AAAGCTTTAG AAGGCGACGA AAAATACGAA GAAAA.A.ATCTTAGAATTAAT 250 2)INFORMATION FOR SEQ ID NO: 193 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 692 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus hominis (B) STRAIN: CSG 170 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 193 TATCAA.AAGA TGAAGGTGGA CGTCATACTC CATTCTTCTC TAACTATCGT 600 TCGCGATTGA AGACGGTACT CGTTTC

2)INFORMATION FOR SEQ ID NO: 194 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 684 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus hominis (B) STRAIN: CSG 36 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 194 AAA.ACAACTG TTACTGGTGT AGAAATGTTC CGTAAATTAT TAGACTACGC 450 2)INFORMATION FOR SEQ ID NO: 195 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 685 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus hominis (B) STRAIN: CSG 6 (xi)SEQUENCE DESCRIPTION: SEQ ID N0: 195 2)INFORMATION FOR SEQ ID NO: 196 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 611 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus hominis (B) STRAIN: CSG 62 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 196 2)INFORMATION FOR SEQ ID NO: 197 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 828 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus lugdunensis (B) STRAIN: ATCC 43809 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 197 2)INFORMATION FOR SEQ ID NO: 198 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 690 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus saprophyticus (B) STRAIN: ATCC 35552 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 198 2)INFORMATION FOR SEQ ID NO: 199 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 723 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus saprophyticus (B) STRAIN: CSG 83 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 199 TCCGTAA.ATT ATTAGACTAC GCTGAAGCTG GTGACAACAT TGGTGCATTA 450 2)INFORMATION FOR SEQ ID NO: 200 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 697 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus saprophyticus (B) STRAIN: CSsa 18 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 200 GGTGTAGAA.A TGTTCCGTAA ATTATTAGAC TACGCTGAAG CTGGTGACAA 450 2)INFORMATION FOR SEQ ID NO: 201 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 835 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus sciuri subsp. sciuri (B) STRAIN: ATCC 29060 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 201 2)INFORMATION FOR SEQ ID NO: 202 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 831 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus warneri (B) STRAIN: ATCC 27836 (xi)SEQUENCE DESCRIPTION: SEQ ID N0: 202 TTCTTAA.ACA AAGTTGATAT GGTAGACGAC GAAGAATTAT TAGAATTAGT 150 AAATACGAAG F~AAAAATCTTAGAATTAATG CAAGCAGTTG ATGACTACAT 300 CGTGGTCAA.A TCAAAGTTGG TGAAGAAGTT GAAATCATCG GTTTACATGA 450 2)INFORMATION FOR SEQ ID NO: 203 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus warneri (B) STRAIN: CSG 50 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 203 2)INFORMATION FOR SEQ ID NO: 204 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 839 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Bifidobacterium Iongum (B) STRAIN: ATCC 15707 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 204 2)INFORMATION FOR SEQ ID NO: 205 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 754 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Stenotrophomonas maltophilia (B) STRAIN: CDC F3338 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 205 2)INFORMATION FOR SEQ ID NO: 206 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 835 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus acidominimus (B) STRAIN: ATCC 51726 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 206 GTGAGCACAT CCTTCTTTCA CGTCAAGTTG GTGTTAAAA.ACCTTATCGTT 100 2)INFORMATION FOR SEQ ID NO: 207 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 819 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus agalactiae (B) STRAIN: ATCC 12403 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 207 2)INFORMATION FOR SEQ ID NO: 208 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 819 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus agalactiae (B) STRAIN: ATCC 12973 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 208 CCAGTTATCC AAGGTTCAGC TCTTAAAGCA CTTGAAGGCG ATGAAA.A.ATA 250 TCCAA.AAAGC AGTTGTTACT GGTGTTGAAA TGTTCCGTAA ACAACTTGAC 500 2)INFORMATION FOR SEQ ID NO: 209 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 822 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus agalactiae (B) STRAIN: ATCC 13813 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 209 2)INFORMATION FOR SEQ ID NO: 210 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 825 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus agalactiae (B) STRAIN: CDC 1073 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 210 2)INFORMATION FOR SEQ ID NO: 211 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 826 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus anginosus (B) STRAIN: ATCC 33397 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 211 2)INFORMATION FOR SEQ ID NO: 212 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 827 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus bovis (B) STRAIN: ATCC 33317 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 212 AA.ATCCCTGT AATCCAAGGT TCAGCTCTTA AAGCCCTTGA AGGTGACACT 250 2)INFORMATION FOR SEQ ID NO: 213 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 821 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi ) ORIGINAL SOURCE
(A) ORGANISM: Streptococcus anginosus (deposited as Streptococcus constellatus) (B) STRAIN: ATCC 27823 (xi)SEQUENCE DESCRIPTION: SEQ ID N0: 213 CCCAGTTATC CAAGGTTCAG CTCTTAAAGC TCTTGAAGGT GATGAA.A.A.AT250 2)INFORMATION FOR SEQ ID NO: 214 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 821 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus cricetus (B) STRAIN: ATCC 19642 CGTGGTACTG TTAAAGTCAA CGACG

(xi)SEQUENCE DESCRIPTION: SEQ ID NO: 214 2)INFORMATION FOR SEQ ID NO: 215 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 821 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus cristatus (B) STRAIN: ATCC 51100 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 215 2)INFORMATION FOR SEQ ID NO: 216 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 792 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus downei (B) STRAIN: ATCC 33748 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 216 GTCAACGACG AAGTTGAAAT CGTTGGTATC AAGGACGAAA TCCAA.A.A.AGC450 2)INFORMATION FOR SEQ ID NO: 217 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 795 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus dysgalactiae (B) STRAIN: ATCC 43078 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 217 2)INFORMATION FOR SEQ ID NO: 218 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 828 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus equi subsp. equi (B) STRAIN: ATCC 9528 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 218 2)INFORMATION FOR SEQ ID NO: 219 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 825 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus ferus (B) STRAIN: ATCC 33477 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 219 2)INFORMATION FOR SEQ ID NO: 220 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 826 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus gordonii (B) STRAIN: ATCC 10558 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 220 2)INFORMATION FOR SEQ ID NO: 221 (i)SEQUENCE CHARACTERISTICS:

(A) LENGTH: 799 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus anginosus (B) STRAIN: ATCC 27335 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 221 2)INFORMATION FOR SEQ ID NO: 222 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 825 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus macacae (B) STRAIN: ATCC 35911 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 222 2)INFORMATION FOR SEQ ID NO: 223 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 822 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi ) ORIGINAL SOURCE
(A) ORGANISM: Streptococcus gordonii (deposited as Streptococcus mitis) (B) STRAIN: ATCC 33399 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 223 CTCAAA.A.AGCAGTTGTTACT GGTGTTGAAA TGTTCCGTAA ACAACTTGAC 500 2)INFORMATION FOR SEQ ID NO: 224 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 827 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus mutans (B) STRAIN: ATCC 25175 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 224 TGATGACATT CAAAA.AGCTGTTGTTACTGG TGTTGAAATG TTCCGTAAAC 500 2)INFORMATION FOR SEQ ID NO: 225 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 824 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus parasanguinis (B) STRAIN: ATCC 15912 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 225 2)INFORMATION FOR SEQ ID NO: 226 (i)SEQUENCE CHARACTERISTICS:

(A) LENGTH: 824 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus ratti (B) STRAIN: ATCC 19645 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 226 2)INFORMATION FOR SEQ ID NO: 227 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 795 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus sanguinis (B) STRAIN: ATCC 10556 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 227 2)INFORMATION FOR SEQ ID NO: 228 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 795 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus sobrinus (B) STRAIN: ATCC 33478 (xi)SEQUENCE DESCRIPTION: SEQ ID N0: 228 2)INFORMATION FOR SEQ ID NO: 229 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 797 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus suis (B) STRAIN: ATCC 43765 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 229 2)INFORMATION FOR SEQ ID NO: 230 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 793 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus uberis (B) STRAIN: ATCC 19436 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 230 2)INFORMATION FOR SEQ ID NO: 231 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 798 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Streptococcus vestibularis (B) STRAIN: ATCC 49124 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 231 2)INFORMATION FOR SEQ ID NO: 232 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Tatumella ptyseos (B) STRAIN: ATCC 33301 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 232 2)INFORMATION FOR SEQ ID NO: 233 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Trabulsiella guamensis (B) STRAIN: ATCC 49490 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 233 2)INFORMATION FOR SEQ ID NO: 234 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 825 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi ) ORIGINAL SOURCE
(A) ORGANISM: Veillonella parvula (B) STRAIN: ATCC 10790 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 234 2)INFORMATION FOR SEQ ID NO: 235 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 825 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Yersinia enterocolitica (B) STRAIN: ATCC 9610 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 235 2)INFORMATION FOR SEQ ID NO: 236 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 828 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DN A
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Yersinia frederiksenii (B) STRAIN: ATCC 33641 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 236 2)INFORMATION FOR SEQ ID NO: 237 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 813 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Yersinia intermedia (B) STRAIN: ATCC 29909 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 237 GCAAAA.ATTA TCGAATTAGC TGAGGCGCTG GATAGTTATA TTCCACAGCC 300 2)INFORMATION FOR SEQ ID NO: 238 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Yersinia pestis (B) STRAIN: KIM D27 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 238 2)INFORMATION FOR SEQ ID NO: 239 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 817 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi ) ORIGINAL SOURCE
(A) ORGANISM: Yersinia pseudotu~berculosis (B) STRAIN: ATCC 29833 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 239 2)INFORMATION FOR SEQ ID NO: 240 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Yersinia rohdei (B) STRAIN: ATCC 43380 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 240 2)INFORMATION FOR SEQ ID NO: 241 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 804 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Yokenella regensburgei (B) STRAIN: ATCC 35313 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 241 2)INFORMATION FOR SEQ ID NO: 242 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 849 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Achromobacter xylosoxidans subsp.
denitrificans (B) STRAIN: ATCC 15173 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 242 2)INFORMATION FOR SEQ ID NO: 243 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 787 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Acinetobacter baumannii (B) STRAIN: ATCC 19606 (xi)SEQUENCE DESCRIPTION: SEQ ID N0: 243 GCGTTAACTG GTTTGACTAT GGCTGAATAC TTCCGTGATG AAA.AAGACGA 600 2)INFORMATION FOR SEQ ID NO: 244 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 825 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Acinetobacter lwoffii (B) STRAIN: CDCF 3697 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 244 2)INFORMATION FOR SEQ ID NO: 245 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 837 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Staphylococcus saprophyticus (B) STRAIN: CSG-197 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 245 2)INFORMATION FOR SEQ ID NO: 246 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 851 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Alcaligenes faecalis (B) STRAIN: ATCC 15554 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 246 2)INFORMATION FOR SEQ ID NO: 247 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 846 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Bacillus anthracis (B) STRAIN: 4229 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 247 2)INFORMATION FOR SEQ ID NO: 248 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 810 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Bacillus cereus (B) STRAIN: ATCC 14579 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 248 2)INFORMATION FOR SEQ ID NO: 249 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 944 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Bacteroides distasonis (B) STRAIN: ATCC 8503 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 249 2)INFORMATION FOR SEQ ID NO: 250 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 939 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Bacteroides ovatus (B) STRAIN: ATCC 8483 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 250 2)INFORMATION FOR SEQ ID NO: 251 (i) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 833 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii) MOLECULE TYPE: DNA
(vi ) ORIGINAL SOURCE
(A) ORGANISM: Leclercia adecarboxylata (B) STRAIN: ATCC 23216 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 251 2)INFORMATION FOR SEQ ID NO: 252 (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 819 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii) MOLECULE TYPE: Genomic DNA
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Stenotrophomonas maltophilia (B) STRAIN: CDC F3338 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 252 2)INFORMATION FOR SEQ ID NO: 253 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 864 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Bartonella henselae (B) STRAIN: ATCC 49882 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 253 GAATCCAA.AA GACAACAATG GTTCAACAGA AGGATCAAAA TGTGCACTCG 600 2)INFORMATION FOR SEQ ID NO: 254 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 866 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Bifidobacterium adolescentis (B) STRAIN: ATCC 15703 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 254 2)INFORMATION FOR SEQ ID NO: 255 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 842 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Brucella abortus (B) STRAIN: 52308 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 255 2)INFORMATION FOR SEQ ID NO: 256 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 833 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Cedecea davisae (B) STRAIN: ATCC 33431 (xi)SEQUENCE
DESCRIPTION:
SEQ ID NO:

2)INFORMATION FOR SEQ ID NO: 257 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Cedecea lapagei (B) STRAIN: ATCC 33432 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 257 2)INFORMATION FOR SEQ ID NO: 258 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 830 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Cedecea neteri (B) STRAIN: ATCC 33855 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 258 TGCGCGTAGC GCTGACCGGT CTGACCATCG CGGAAA.AATTCCGTGACGAA 650 2)INFORMATION FOR SEQ ID NO: 259 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 931 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Chryseobacterium meningosepticum (B) STRAIN: CDC B7681 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 259 2)INFORMATION FOR SEQ ID N0:260 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 726 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Citrobacter amalonaticus (B) STRAIN: ATCC 25405 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 260 2)INFORMATION FOR SEQ ID NO: 261 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 812 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Citrobacter braakii (B) STRAIN: ATCC 43162 (xi)SEQUENCE
DESCRIPTION:
SEQ ID NO:

2)INFORMATION FOR SEQ ID NO: 262 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 811 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Citrobacter koseri (B) STRAIN: ATCC 27156 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 262 2)INFORMATION FOR SEQ ID NO: 263 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 816 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Citrobacter farmeri (B) STRAIN: ATCC 51112 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 263 2)INFORMATION FOR SEQ ID NO: 264 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 819 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Citrobacter freundii (B) STRAIN: ATCC 8090 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 264 2)INFORMATION FOR SEQ ID NO: 265 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 822 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Citrobacter koseri (B) STRAIN: ATCC 27028 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 265 TAACGACTTC TACCACGAA.ATGACCGACTC CAACGTTATC GACAAAGTAT 550 2)INFORMATION FOR SEQ ID N0:266 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 820 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Citrobacter sedlakii (B) STRAIN: ATCC 51115 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 266 2)INFORMATION FOR SEQ ID NO: 267 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 806 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Citrobacter werkmanii (B) STRAIN: ATCC 51114 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 267 2)INFORMATION FOR SEQ ID NO: 268 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 810 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Citro~bacter youngae (B) STRAIN: ATCC 29935 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 268 2)INFORMATION FOR SEQ ID NO: 269 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 827 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Clostridium innocuum (B) STRAIN: ATCC 14501 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 269 2)INFORMATION FOR SEQ ID NO: 270 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Clostridium perfringens (B) STRAIN: ATCC 13124 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 270 CGACCTTTTA GCACCTTACC AAAGAGGGGG AAA.AATCGGTCTATTTGGAG 400 2)INFORMATION FOR SEQ ID NO: 271 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(xi)SEQUENCE DESCRIPTION: SEQ ID NO: 271 2)INFORMATION FOR SEQ ID NO: 272 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 818 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Corynebacterium diphtheriae (B) STRAIN: ATCC 27010 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 272 GCGACGTTGT TAA.AGGCCACGTTTTCAACG CACTGGGCGA TTGCTTGGAT 250 AGGAGCGTAT TACCTCTA glg 2)INFORMATION FOR SEQ ID NO: 273 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 833 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA

(vi)ORIGINAL SOURCE:
(A) ORGANISM: Corynebacterium pseudodiphtheriticum (B) STRAIN: ATCC 10700 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 273 2)INFORMATION FOR SEQ ID NO: 274 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 417 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Corynebacterium ulcerans (B) STRAIN: NCTC 8665 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 274 2)INFORMATION FOR SEQ ID NO: 275 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 835 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Corynebacterium urealyticum (B) STRAIN: ATCC 43042 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 275 2)INFORMATION FOR SEQ ID NO: 276 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 818 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Coxiella burnetii (B) STRAIN: Nine Mile phase II
(xi)SEQUENCE DESCRIPTION: SEQ ID N0: 276 AATTGCCATG GGCAGCACTG AGGGCTTAAA ACGCGATATC GCCGTAA.A.A.A150 AAAAGAA.AAA CTCCCTATTC ATCGTCCTGC GCCGAGCTTT ATTGAGCAAT 300 2)INFORMATION FOR SEQ ID NO: 277 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Edwardsiella hoshinae (B) STRAIN: ATCC 33379 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 277 2)INFORMATION FOR SEQ ID NO: 278 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 809 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Edwardsiella tarda (B) STRAIN: ATCC 15947 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 278 2)INFORMATION FOR SEQ ID NO: 279 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 840 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Eikenella corrodens (B) STRAIN: ATCC 23834 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 279 GTTGCTCTAA CTGGTTTGTC GATGGCTGAA TACTTCCGTG ACGAA.AAAGA 650 2)INFORMATION FOR SEQ ID NO: 280 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 803 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterobacter agglomerans (B) STRAIN: ATCC 27989 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 280 2)INFORMATION FOR SEQ ID NO: 281 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 833 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterobacter amnigenus (B) STRAIN: ATCC 33072 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 281 CTGGATAA.AG TATCCCTGGT TTATGGCCAG ATGAACGAGC CACCAGGAAA 600 2)INFORMATION FOR SEQ ID NO: 282 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 810 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterobacter asburiae (B) STRAIN: ATCC 35953 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 282 2)INFORMATION FOR SEQ ID NO: 283 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 811 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterobacter cancerogenus (B) STRAIN: ATCC 35317 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 283 2)INFORMATION FOR SEQ ID NO: 284 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 817 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterobacter cloacae (B) STRAIN: ATCC 13047 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 284 2)INFORMATION FOR SEQ ID NO: 285 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 766 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterobacter gergoviae (B) STRAIN: ATCC 33028 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 285 2)INFORMATION FOR SEQ ID NO: 286 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 805 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterobacter hormaechei (B) STRAIN: ATCC 49162 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 286 2)INFORMATION FOR SEQ ID NO: 287 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 791 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Entero~bacter sakasakii (B) STRAIN: ATCC 29544 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 287 2)INFORMATION FOR SEQ ID NO: 288 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 839 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus avium (B) STRAIN: ATCC 14025 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 288 AGCACCTTTT CCAGAAGATG CAGAAAGAAG CGGCATTCAT AAA.A.AGGCGC 300 2)INFORMATION FOR SEQ ID NO: 289 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 847 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus casseliflavus (B) STRAIN: ATCC 25788 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 289 2)INFORMATION FOR SEQ ID NO: 290 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 845 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus durans (B) STRAIN: ATCC 19432 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 290 AAA.A.ATGATGAGAAGAAATC GAAAGTTGTT CTTGAAACAG CGCTAGAATT 100 TTACAAGAAC GGATCACTTC AACGAAAA.AAGGTTCAATCA CTTCA 845 2)INFORMATION FOR SEQ ID NO: 291 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 840 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus faecalis (B) STRAIN: ATCC 29212 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 291 GCGTTATTGA AA.A.A.ACAGCCATGGTTTTTG GTCAAATGAA CGAACCGCCA 600 2)INFORMATION FOR SEQ ID NO: 292 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 831 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus faecium (B) STRAIN: ATCC 19434 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 292 2)INFORMATION FOR SEQ ID NO: 293 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 826 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus gallinarum (B) STRAIN: ATCC 49573 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 293 CCTTACCAGA TATCAACAAT GCGTTGATCG TTTACAAA.A.A AGACGAGAAA 50 CCCAGAAGAT GCCAAACGTA GTGGCATCCA CAAA.AAAGCCCCAGATTTCG 300 2)INFORMATION FOR SEQ ID NO: 294 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 846 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Enterococcus saccharolyticus (B) STRAIN: ATCC 43076 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 294 AAAAAGAATG ATGAA.AAA.ACAAAAGTGGTA CTTGAAACAG CTTTAGAACT 100 TTACAAGAAC GTATTACGTC AACGAAAAP,AGGCTCAATTA CATCAA 846 2)INFORMATION FOR SEQ ID NO: 295 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 803 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Escherichia fergusonii (B) STRAIN: ATCC 35469 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 295 2)INFORMATION FOR SEQ ID NO: 296 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 822 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Escherichia hermannii (B) STRAIN: ATCC 33650 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 296 2)INFORMATION FOR SEQ ID NO: 297 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 808 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Escherichia vulneris (B) STRAIN: ATCC 33821 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 297 TATCACCT gOg 2)INFORMATION FOR SEQ ID NO: 298 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 843 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Eubacterium lentum (B) STRAIN: ATCC 43055 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 298 2)INFORMATION FOR SEQ ID NO: 299 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 829 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Ewingella americana (B) STRAIN: ATCC 33852 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 299 TCTACCAAAA GTGGTTCTAT CACCTCCGT g2g 2)INFORMATION FOR SEQ ID NO: 300 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 805 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Francisella tularensis (B) STRAIN: LVS
(xi)SEQUENCE DESCRIPTION: SEQ ID NO: 300 TATTA g05 2)INFORMATION FOR SEQ ID NO: 301 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 825 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Fusobacterium gonidiaformans (B) STRAIN: ATCC 25563 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 301 GACGAATTGC CAA.AAATATACAATGCATTA AAGGTGCAAG TTGGAGAAAA 50 AATATTGAAT GTTTTGGGAG AGCCTGTGGA TCAA.AAAGGGCCTGTGGAAA 250 AAAATCAGGA TCTATCACTT CGGTA g25 2)INFORMATION FOR SEQ ID NO: 302 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 806 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Fuso~bacterium necrophorum subsp. necrophorum (B) STRAIN: ATCC 25286 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 302 GGAAAAACAG GCCTATTCGG AGGAGCCGGA GTAGGAAAA.ACCGTTTTGAT 400 TATGGAACTG ATCAATAATA TTGCAAA.AGGTCATGGAGGA ATTTCTGTTT 450 2)INFORMATION FOR SEQ ID NO: 303 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 821 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Fusobacterium nucleatum subsp. polymorphum (B) STRAIN: ATCC 10953 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 303 AGCACCATAT ATTAAAGGTG GAAAA.ATAGGATTATTTGGT GGAGCTGGAG 400 TAGGAA.AAAC AGTTTTAATA ATGGAACTTA TCAACAACAT TGCAAAAGGA 450 TAGAGACTTA TATGGTGAAA TGACTGAATC AGGAGTTATC ACAAAA.ACAG 550 2)INFORMATION FOR SEQ ID NO: 304 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 864 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Gardnerella vaginalis (B) STRAIN: ATCC 49145 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 304 ATTCTATTAC GTCG ' 864 2)INFORMATION FOR SEQ ID NO: 305 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 848 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Gemella haemolysans (B) STRAIN: ATCC 10379 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 305 GAA.AAAGGCG ATGGGAAAA.AAGAAA.A.ATTAGTTCTTGAAG TTTCTCTTGA 10 2)INFORMATION FOR SEQ ID NO: 306 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 848 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Gemella mor~billorum (B) STRAIN: ATCC 27824 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 306 GAAA.A.AGGCG ATGGAA.AA.AAAGAAAAATTA GTTCTTGAAG TTTCTCTTGA 10 TGACCACGGA GAAGAAGCTG GAGCAGAAGT TCAAAA.AGAATCTATTCATA 300 2)INFORMATION FOR SEQ ID NO: 307 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 813 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Haemophilus ducreyi (B) STRAIN: DSM 8925 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 307 2)INFORMATION FOR SEQ ID NO: 308 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 826 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Haemophilus haemolyticus (B) STRAIN: ATCC 33390 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 308 2)INFORMATION FOR SEQ ID NO: 309 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 809 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Haemophilus parahaemolyticus (B) STRAIN: ATCC 10014 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 309 CGTATTGGGT GAGCCGATTG ACGAA.AAAGGTCCTATCGGT GAAGAAGCAC 250 2)INFORMATION FOR SEQ ID NO: 310 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 824 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Haemophilus parainfluenzae (B) STRAIN: ATCC 7901 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 310 2)INFORMATION FOR SEQ ID NO: 311 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 811 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Hafnia alvei (B) STRAIN: ATCC 13337 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 311 2)INFORMATION FOR SEQ ID NO: 312 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 831 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Kingella kingae (B) STRAIN: ATCC 23330 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 312 2)INFORMATION FOR SEQ ID NO: 313 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 812 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Klebsiella pneumoniae subsp. ozaenae (B) STRAIN: ATCC 11296 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 313 2)INFORMATION FOR SEQ ID NO: 314 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 812 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Klebsiella ornithinolytica (B) STRAIN: ATCC 31898 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 314 2) INFORMATION FOR SEQ ID NO: 315 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 813 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Kle~bsiella oxytoca (B) STRAIN: ATCC 33496 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 315 2)INFORMATION FOR SEQ ID NO: 316 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 822 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Klehsiella planticola (B) STRAIN: ATCC 33531 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 316 2)INFORMATION FOR SEQ ID NO: 317 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 785 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Kle~bsiella pneumoniae subsp. pneumoniae (B) STRAIN: ATCC 13883 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 317 TCACCTCCAC CAA.A.ACCGGTTCTATCACCT CCGTA 785 2)INFORMATION FOR SEQ ID NO: 318 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 759 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Kluyvera ascor~bata (B) STRAIN: ATCC 33433 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 318 TAAA.ACCGTA AACATGATGG AGCTGATCCG TAACATCGCG ATCGAGCACT 400 2)INFORMATION FOR SEQ ID NO: 319 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 831 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Kluyvera cryocrescens (B) STRAIN: ATCC 33435 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 319 2)INFORMATION FOR SEQ ID NO: 320 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 810 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Kluyvera georgiana (B) STRAIN: ATCC 51603 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 320 2)INFORMATION FOR SEQ ID NO: 321 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 834 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Lactobacillus acidophilus (B) STRAIN: ATCC 4356 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 321 2)INFORMATION FOR SEQ ID NO: 322 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 824 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Legionella pneumophila subsp. pneumophila (B) STRAIN: ATCC 33152 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 322 2)INFORMATION FOR SEQ ID NO: 323 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 818 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Leminorella grimontii (B) STRAIN: ATCC 33999 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 323 2)INFORMATION FOR SEQ ID NO: 324 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 835 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Listeria monocytogenes (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 324 2)INFORMATION FOR SEQ ID NO: 325 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 828 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA

(vi)ORIGINAL SOURCE:
(A) ORGANISM: Micrococcus lylae (B) STRAIN: ATCC 27566 (xi)SEQUENCE DESCRIPTION: SEQ ID N0: 325 2)INFORMATION FOR SEQ ID NO: 326 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 822 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Moellerella wisconsensis (B) STRAIN: ATCC 35017 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 326 2)INFORMATION FOR SEQ ID NO: 327 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 854 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Branhamella catarrhalis (B) STRAIN: ATCC 43628 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 327 2)INFORMATION FOR SEQ ID NO: 328 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 831 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Moraxella osloensis (B) STRAIN: ATCC 19976 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 328 2)INFORMATION FOR SEQ ID NO: 329 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 835 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear (ii)MOLECULE TYPE: Genomic DNA
(vi)ORIGINAL SOURCE:
(A) ORGANISM: Morganella morganii subsp. morganii (B) STRAIN: ATCC 25830 (xi)SEQUENCE DESCRIPTION: SEQ ID NO: 329 2)INFORMATION FOR SEQ ID NO: 330 (i)SEQUENCE CHARACTERISTICS:
(A) LENGTH: 824 bases (B) TYPE: Nucleic acid (C) STRANDEDNESS: Double (D) TOPOLOGY: Linear DEMANDES OU BREVETS VOLUMINEUX
LA PRESENTS PARTIE DE CETTE DEMANDS OU CE BREVET
COMPREND PLUS D'UN TOME.
CECI EST LE TOME ~ DE
NOTE: Pour les tomes additionels, veuillez contacter le Bureau canadien des brevets JUMBO APP~ICA'I'IONS/PA~'EtIITS
THIS SECT10N OF THE APP~ICAT10N/PATENT CONTAINS MORE
THAN ONE VOLUME
. THIS IS VOLUME OI=
NOTE: For additional volumes-phase contact the Canadian Patent Ofific~ . ~'

Claims (11)

What is claimed is:

1. A repertory of nucleic acid sequences used for the detection and/or identification of a bacterial, fungal or parasitical species, genus, family or group, which repertory is created by amplifying the nucleic acids of a plurality of determined bacterial, fungal and parasitical species with any combination of the primer pairs shown in annex I, annex II and annex XXI.

2. A nucleic acid used for universal detection of any bacterium, fungus or parasite which is derived from the repertory of claim 1.

A nucleic acid used for universal detection as set forth in claim 2, which has a nucleic acid sequence of at least 12 nucleotides capable of hybridizing with said any bacterium, fungus or parasite and with any one of SEQ ID NOs: 543, 556-574, 636-655, 658-661, 664, 681-683, 694, 696-697, 699-700, 708, 812-815, 911-917, 919-922.

4. A nucleic acid used for the specific and ubiquitous detection and for identification of a bacterial, fungal or parasital species, genus, family or group, which is derived from the repertory of claim 1.

5. A nucleic acid as set forth in claim 4, which has a nucleic acid sequence of at least 12 nucleotides capable of hybridizing with the nucleic acids of said bacterial, fungal or parasitical species, genus, family or group and with any one of:
SEQ ID NOs:
630, 629 for the detection and/or identification of Chlamydia pneumoniae 554, 555 for the detection and/or identification of Chlamydia trachomatis 551, 552 for the detection and/or identification of Neisseria gonorrhoeae 549, 550, 627, 625, 628, 626, 582, 583 for the detection and/or identification of Streptococcus agalactiae 576, 632, 631, 633, 634, 635 for the detection and/or identification of Candida spp.
545, 546 for the detection and/or identification of Corynebacterium spp.
656, 657, 271 for the detection and/or identification of Enterococcus spp.
541, 542, 544 for the detection and/or identification of Pseudomonads group 553, 575, 707, 605, 606 for the detection and/or identification of Staphylococcus spp.

547, 548 for the detection and/or identification of Streptococcus spp.

539, 540 for the detection and/or identification of Mycobacteriaceae family 577 for the detection and/or identification of Candida albicans 578 for the detection and/or identification of Candida dubliniensis 580, 603 for the detection and/or identification of Enterococcus faecalis 602 for the detection and/or identification of Enterococcus faecium 604 for the detection and/or identification of Enterococcus gallinarum 579 for the detection and/or identification of Escherichia coli 581 for the detection and/or identification of Haemophilus influenzae 584, 585, 586, 587, 588 for the detection and/or identification of Staphylococcus aureus 589, 590, 591, 592, 593 for the detection and/or identification of Staphylococcus epidermidis 594, 595 for the detection and/or identification of Staphylococcus haemolyticus 596, 597, 598 for the detection and/or identification of Staphylococcus hominis 599, 600, 601, 695 for the detection and/or identification of Staphylococcus saprophyticus for the detection and/or identification of Enterococcus casseliflavus-flavescens-gallinarum 820, 821, 822 for the detection and/or identification of Trypanosoma brucei 794, 795 for the detection and/or identification of Trypanosoma cruzi 798, 799, 800, 801, 802, 803, 804, 805, 806, 807 for the detection and/or identification of Cryptosporidium parvum 825, 826 for the detection and/or identification of Bordetella spp.

796, 797, 808 809, 810, 811 for the detection and/or identification of Clostridium spp.

703, 704, 705, 706, 793 for the detection and/or identification of Entamoeba spp.

816, 817, 818, 819 for the detection and/or identification of Giardia spp.

701, 702 for the detection and/or identification of Leishmania spp.

823, 824 for the detection and/or identification of Trypanosoma spp.

923, 924, 925, 926, 927, 928 for the detection and/or identification of Kinetoplastidae group 933, 934 for the detection and/or identification of Enterobacteriaceae group

6. A method for the specific detection or identification of a bacterial, fungal or parasitical species, genus, family or group in a sample, using a panel of probes or amplification primers or both, each individual probe or primer being derived from a nucleic acid as defined in claim 4, the method comprising the step of contacting the nucleic acids of the sample with said primers or probes under suitable conditions of hybridization or of amplification and detecting the presence of hybridized probes or amplified products as an indication of the presence of said specific bacterial, fungal or parasitical species, genus, family or group.

7. A method as set forth in claim 6, which is for the detection or identification of bacterial species, genus, family or group.

8. A method as set forth in claim 7, which further comprises probes or primers, or both, for the detection of at least one of the antibiotic resistance genes listed in Table 5.

9. A method as set forth in claim 7 or 8, which further comprises probes or primers, or both, for the detection of at least one of the toxin genes listed in Table 6.

A method as defined in claim 6, which further comprises the universal detection of any species, genus, family or group of bacteria, fungi or parasites.

11. A method as defined in any one of claims 7 to 9, which further comprises the universal detection of any species, genus, family or group of bacteria.