Method For The Detection And Identification Of Methicillin-resistant Staphylococcus Aureus

Abstract

The present invention describes novel SCCmec right extremity junction sequences for the detection of methicillin-resistant Staphylococcus aureus (MRSA). It relates to the use of these DNA sequences for diagnostic purposes.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application is a continuation of U.S. patent application Ser. No. 16/568,156, filed Sep. 11, 2019, which is a continuation of U.S. patent application Ser. No. 15/707,421, filed Sep. 18, 2017, now U.S. Pat. No. 10,577,664, which is a continuation of U.S. patent application Ser. No. 11/416,500, now U.S. Pat. No. 9,777,335, which is a continuation of U.S. patent application Ser. No. 10/479,674, now U.S. Pat. No. 7,449,289, to Huletsky, et al., "SEQUENCES FOR DETECTION AND IDENTIFICATION OF METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS," filed Sep. 7, 2004 which is a National Phase Application of International Patent Application PCT/CA02/00824, filed Jun. 4, 2002, now closed, which claims priority to Canadian Patent Application No. 2,348,042, filed Jun. 4, 2001, now abandoned.

REFERENCE TO SEQUENCE LISTING, TABLE, OR COMPUTER PROGRAM LISTING

[0002] The present application is being filed along with a sequence listing in electronic format. The sequence listing is provided as a file entitled GENOM_051C4.TXT, created Oct. 9, 2020 which is 187 KB in size. The information in the electronic format of the sequence listing is incorporated herein by reference in its entirety.

BACKGROUND OF THE INVENTION

[0003] Clinical Significance of Staphylococcus aureus

[0004] The coagulase-positive species Staphylococcus aureus is well documented as a human opportunistic pathogen. Nosocomial infections caused by S. aureus are a major cause of morbidity and mortality. Some of the most common infections caused by S. aureus involve the skin, and they include furuncles or boils, cellulitis, impetigo, and postoperative wound infections at various sites. Some of the more serious infections produced by S. aureus are bacteremia, pneumonia, osteomyelitis, acute endocarditis, myocarditis, pericarditis, cerebritis, meningitis, scalded skin syndrome, and various abcesses. Food poisoning mediated by staphylococcal enterotoxins is another important syndrome associated with S. aureus. Toxic shock syndrome, a community-acquired disease, has also been attributed to infection or colonization with toxigenic S. aureus (Murray et al. Eds, 1999, Manual of Clinical Microbiology, 7.sup.th Ed., ASM Press, Washington, D.C.).

[0005] Methicillin-resistant S. aureus (MRSA) emerged in the 1980s as a major clinical and epidemiologic problem in hospitals. MRSA are resistant to all .beta.-lactams including penicillins, cephalosporins, carbapenems, and monobactams, which are the most commonly used antibiotics to cure S. aureus infections. MRSA infections can only be treated with more toxic and more costly antibiotics, which are normally used as the last line of defence. Since MRSA can spread easily from patient to patient via personnel, hospitals over the world are confronted with the problem to control MRSA. Consequently, there is a need to develop rapid and simple screening or diagnostic tests for detection and/or identification of MRSA to reduce its dissemination and improve the diagnosis and treatment of infected patients.

[0006] Methicillin resistance in S. aureus is unique in that it is due to acquisition of DNA from other coagulase-negative staphylococci (CNS), coding for a surnumerary .beta.-lactam-resistant penicillin-binding protein (PBP), which takes over the biosynthetic functions of the normal PBPs when the cell is exposed to .beta.-lactam antibiotics. S. aureus normally contains four PBPs, of which PBPs 1, 2 and 3 are essential. The low-affinity PBP in MRSA, termed PBP 2a (or PBP2'), is encoded by the choromosomal mecA gene and functions as a .beta.-lactam-resistant transpeptidase. The mecA gene is absent from methicillin-sensitive S. aureus but is widely distributed among other species of staphylococci and is highly conserved (Ubukata et al., 1990, Antimicrob. Agents Chemother. 34:170-172).

[0007] By nucleotide sequence determination of the DNA region surrounding the mecA gene from S. aureus strain N315 (isolated in Japan in 1982), Hiramatsu et al. have found that the mecA gene is carried by a novel genetic element, designated staphylococcal cassette chromosome mec (SCCmec), inserted into the chromosome. SCCmec is a mobile genetic element characterized by the presence of terminal inverted and direct repeats, a set of site-specific recombinase genes (ccrA and ccrB), and the mecA gene complex (Ito et al., 1999, Antimicrob. Agents Chemother. 43:1449-1458; Katayama et al., 2000, Antimicrob. Agents Chemother. 44:1549-1555). The element is precisely excised from the chromosome of S. aureus strain N315 and integrates into a specific S. aureus chromosomal site in the same orientation through the function of a unique set of recombinase genes comprising ccrA and ccrB. Two novel genetic elements that shared similar structural features of SCCmec were found by cloning and sequencing the DNA region surrounding the mecA gene from MRSA strains NCTC 10442 (the first MRSA strain isolated in England in 1961) and 85/2082 (a strain from New Zealand isolated in 1985). The three SCCmec have been designated type I (NCTC 10442), type II (N315) and type III (85/2082) based on the year of isolation of the strains (Ito et al., 2001, Antimicrob. Agents Chemother. 45:1323-1336) (FIG. 1). Hiramatsu et al. have found that the SCCmec DNAs are integrated at a specific site in the methicillin-sensitive S. aureus (MSSA) chromosome. They characterized the nucleotide sequences of the regions around the left and right boundaries of SCCmec DNA (i.e. attL and attR, respectively) as well as those of the regions around the SCCmec DNA integration site (i.e. attBscc which is the bacterial chromosome attachment site for SCCmec DNA). The attBscc site was located at the 3' end of a novel open reading frame (ORF), orfX. The orfX potentially encodes a 159-amino acid polypeptide sharing identity with some previously identified polypeptides, but of unknown function (Ito et al., 1999, Antimicrob. Agents Chemother. 43:1449-1458). Recently, a new type of SCCmec (type IV) has been described by both Hiramatsu et al. (Ma et al, 2002, Antimicrob. Agents Chemother. 46:1147-1152) and Oliveira et al. (Oliveira et al, 2001, Microb. Drug Resist. 7:349-360). The sequences of the right extremity of the new type IV SCCmec from S. aureus strains CA05 and 8/6-3P published by Hiramatsu et al. (Ma et al., 2002, Antimicrob. Agents Chemother. 46:1147-1152) were nearly identical over 2000 nucleotides to that of type II SCCmec of S. aureus strain N315 (Ito et al., 2001, Antimicrob. Agents Chemother. 45:1323-1336). No sequence at the right extremity of the SCCmec type IV is available from the S. aureus strains HDE288 and PL72 described by Oliveira et al. (Oliveira et al., 2001, Microb. Drug Resist. 7:349-360).

[0008] Previous methods used to detect and identify MRSA (Saito et al., 1995, J. Clin. Microbiol. 33:2498-2500; Ubukata et al., 1992, J. Clin. Microbiol. 30:1728-1733; Murakami et al., 1991, J. Clin. Microbiol. 29:2240-2244; Hiramatsu et al., 1992, Microbiol. Immunol. 36:445-453), which are based on the detection of the mecA gene and S. aureus-specific chromosomal sequences, encountered difficulty in discriminating MRSA from methicillin-resistant coagulase-negative staphylococci (CNS) because the mecA gene is widely distributed in both S. aureus and CNS species (Suzuki et al., 1992, Antimicrob. Agents. Chemother. 36:429-434). Hiramatsu et al. (U.S. Pat. No. 6,156,507) have described a PCR assay specific for MRSA by using primers that can specifically hybridize to the right extremities of the 3 types of SCCmec DNAs in combination with a primer specific to the S. aureus chromosome, which corresponds to the nucleotide sequence on the right side of the SCCmec integration site. Since nucleotide sequences surrounding the SCCmec integration site in other staphylococcal species (such as S. epidermidis and S. haemolyticus) are different from those found in S. aureus, this PCR assay was specific for the detection of MRSA. This PCR assay also supplied information for MREP typing (standing for mec right extremity polymorphism ) of SCCmec DNA (Ito et al., 2001, Antimicrob. Agents Chemother. 45:1323-1336; Hiramatsu et al., 1996, J. Infect. Chemother. 2:117-129). This typing method takes advantage of the polymorphism at the right extremity of SCCmec DNAs adjacent to the integration site among the three types of SCCmec. Type III has a unique nucleotide sequence while type II has an insertion of 102 nucleotides to the right terminus of SCCmec type I. The MREP typing method described by Hiramatsu et al. (Ito et al., 2001, Antimicrob. Agents Chemother. 45:1323-1336; Hiramatsu et al., 1996, J. Infect. Chemother. 2:117-129) defines the SCCmec type I as MREP type i, SCCmec type II as MREP type ii and SCCmec type III as MREP type iii. It should be noted that the MREP typing method cannot differentiate the new SCCmec type IV described by Hiramatsu et al. (Ma et al., 2002, Antimicrob. Agents Chemother. 46:1147-1152) from SCCmec type II because these two SCCmec types exhibit the same nucleotide sequence to the right extremity.

[0009] The set of primers described by Hiramatsu et al. as being the optimal primer combination (SEQ ID NOs.: 22, 24, 28 in U.S. Pat. No. 6,156,507 corresponding to SEQ ID NOs.: 56, 58 and 60, respectively, in the present invention) have been used in the present invention to test by PCR a variety of MRSA and MSSA strains (FIG. 1 and Table 1). Twenty of the 39 MRSA strains tested were not amplified by the Hiramatsu et al. multiplex PCR assay (Tables 2 and 3). Hiramitsu's method indeed was successful in detecting less than 50% of the tested 39 MRSA strains.

[0010] This finding demonstrates that some MRSA strains have sequences at the right extremity of SCCmec-chromosome right extremity junction different from those identified by Hiramatsu et al. Consequently, the system developed by Hiramatsu et al. does not allow the detection of all MRSA. The present invention relates to the generation of SCCmec-chromosome right extremity junction sequence data required to detect more MRSA strains in order to improve the Hiramatsu et al. assay. There is a need for developing more ubiquitous primers and probes for the detection of most MRSA strains around the world.

SUMMARY OF THE INVENTION

[0011] It is an object of the present invention to provide a specific, ubiquitous and sensitive method using probes and/or amplification primers for determining the presence and/or amount of nucleic acids from all MRSA strains.

[0012] Ubiquity of at least 50% amongst the strains representing MRSA strains types IV to X is an objective of this invention.

[0013] Therefore, in accordance with the present invention is provided a method to detect the presence of a methicillin-resistant Staphylococcus aureus (MRSA) strain in a sample, the MRSA strain being resistant because of the presence of an SCCmec insert containing a mecA gene, said SCCmec being inserted in bacterial nucleic acids thereby generating a polymorphic right extremity junction (MREJ), the method comprising the step of annealing the nucleic acids of the sample with a plurality of probes and/or primers, characterized by:

[0014] the primers and/or probes are specific for MRSA strains and capable of annealing with polymorphic MREJ nucleic acids, the polymorphic MREJ comprising MREJ types i to x; and

[0015] the primers and/or probes altogether can anneal with at least four MREJ types selected from MREJ types i to x.

[0016] In a specific embodiment, the primers and/or probes are all chosen to anneal under common annealing conditions, and even more specifically, they are placed altogether in the same physical enclosure.

[0017] A specific method has been developed using primers and/or probes having at least 10 nucleotides in length and capable of annealing with MREJ types i to iii, defined in any one of SEQ ID NOs: 1, 20, 21, 22, 23, 24, 25, 41, 199; 2, 17, 18, 19, 26, 40, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 185, 186, 197; 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 104, 184, 198 and with one or more of MREJ types iv to ix, having SEQ ID NOs: 42, 43, 44, 45, 46, 51; 47, 48, 49, 50; 171; 165, 166; 167; 168. To be perfectly ubiquitous with the all the sequenced MREJs, the primers and/or probes altogether can anneal with said SEQ ID NOs of MREJ types i to ix.

[0018] The following specific primers and/or probes having the following sequences have been designed:

[0019] 66, 100, 101, 105, 52, 53, 54, 55, 56, 57, 64, 71, 72, 73, 74, 75, 76, 70, 103, 130, 132, 158, 159, 59, 62, 126, 127, 128, 129, 131, 200, 201, 60, 61, 63, 32, 83, 84, 160, 161, 162, 163, 164, 85, 86, 87, 88, 89, for the detection of MREJ type i

[0020] 66, 97, 99, 100, 101, 106, 117, 118, 124, 125, 52, 53, 54, 55, 56, 57 64, 71, 72, 73, 74, 75, 76, 70, 103, 130, 132, 158, 159, 59, 62, 126, 127, 128, 129, 131, 200, 201, 60, 61, 63, 32, 83, 84, 160, 161, 162, 163, 164, 85, 86, 87, 88, 89 for the detection of MREJ type ii

[0021] 67, 98, 102, 107, 108, 64, 71, 72, 73, 74, 75, 76, 70, 103, 130, 132, 158, 159, 58, 59, 62, 126, 127, 128, 129, 131, 200, 201, 60, 61, 63, 32, 83, 84, 160, 161, 162, 163, 164, 85, 86, 87, 88, 89, for the detection of MREJ type iii

[0022] 79, 77, 145, 147, 64, 71, 72, 73, 74, 75, 76, 70, 103, 130, 132, 158, 159, 59, 62, 126, 127, 128, 129, 131, 200, 201, 60, 61, 63, 68, 32, 83, 84, 160, 161, 162, 163, 164, 85, 86, 87, 88, 89, for the detection of MREJ type iv

[0023] 65, 80, 146, 154, 155, 64, 71, 72, 73, 74, 75, 76, 70, 103, 130, 132, 158, 159, 59, 62, 126, 127, 128, 129, 131, 200, 201, 60, 61, 63, 32, 83, 84, 160, 161, 162, 163, 164, 85, 86, 87, 88, 89, for the detection of MREJ type v

[0024] 202, 203, 204, 4, 71, 72, 73, 74, 75, 76, 70, 103, 130, 132, 158, 159, 59, 62, 126, 127, 128, 129, 131, 200, 201, 60, 61, 63, 32, 83, 84, 160, 161, 162, 163, 164, 85, 86, 87, 88, 89, for the detection of MREJ type vi

[0025] 112, 113, 114, 119, 120, 121, 122, 123, 150, 151, 153, 64, 71, 72, 73, 74, 75, 76, 70, 103, 130, 132, 158, 159, 59, 62, 126, 127, 128, 129, 131, 200, 201, 60, 61, 63, 32, 83, 84, 160, 161, 162, 163, 164, 85, 86, 87, 88, 89, for the detection of MREJ type vii

[0026] 115, 116, 187, 188, 207, 208, 64, 71, 72, 73, 74, 75, 76, 70, 103, 130, 132, 158, 159

[0027] 59, 62, 126, 127, 128, 129, 131, 200, 201, 60, 61, 63, 32, 83, 84, 160, 161, 162, 163, 164, 85, 86, 87, 88, 89, for the detection of MREJ type viii

[0028] 109, 148, 149, 205, 206, 64, 71, 72, 73, 74, 75, 76, 70, 103, 130, 132, 158, 159, 59, 62, 126, 127, 128, 129, 131, 200, 201, 60, 61, 63, 32, 83, 84, 160, 161, 162, 163, 164, 85, 86, 87, 88, 89, for the detection of MREJ type ix.

[0029] Amongst these, the following primer pairs having the following sequences are used:

[0030] 64/66, 64/100, 64/101; 59/52, 59/53, 59/54, 59/55, 59/56, 59/57, 60/52, 60/53, 60/54, 60/55, 60/56, 60/57, 61/52, 61/53, 61/54, 61/55, 61/56, 61/57, 62/52, 62/53, 62/54, 62/55, 62/56, 62/57, 63/52, 63/53, 63/54, 63/55, 63/56, 63/57, for the detection of type i MREJ

[0031] 64/66, 64/97, 64/99, 64/100, 64/101, 59/52, 59/53, 59/54, 59/55, 59/56, 59/57, 60/52, 60/53, 60/54, 60/55, 60/56, 60/57, 61/52, 61/53, 61/54, 61/55, 61/56, 61/57, 62/52, 62/53, 62/54, 62/55, 62/56, 62/57, 63/52, 63/53, 63/54, 63/55, 63/56, 63/57 for the detection of type ii MREJ

[0032] 64/67, 64/98, 64/102; 59/58, 60/58, 61/58, 62/58, 63/58 for the detection of type iii MREJ

[0033] 64/79 for the detection of type iv MREJ

[0034] 64/80 for the detection of type v MREJ

[0035] 64/204 for the detection of type vi MREJ

[0036] 64/112, 64/113 for the detection of type vii MREJ

[0037] 64/115, 64/116 for the detection of type viii MREJ

[0038] 64/109 for the detection of type ix MREJ

[0039] As well, amongst these, the following probes having the following sequences are used:

[0040] SEQ ID NOs: 32, 83, 84, 160, 161, 162, 163, 164 for the detection of MREJ types i to ix.

[0041] In the most preferred embodied method, the following primers and/or probes having the following nucleotide sequences are used together. The preferred combinations make use of:

[0042] SEQ ID NOs: 64, 66, 84, 163, 164 for the detection of MREJ type i

[0043] SEQ ID NOs: 64, 66, 84, 163, 164 for the detection of MREJ type ii

[0044] SEQ ID NOs: 64, 67, 84, 163, 164 for the detection of MREJ type iii

[0045] SEQ ID NOs: 64, 79, 84, 163, 164 for the detection of MREJ type iv

[0046] SEQ ID NOs: 64, 80, 84, 163, 164 for the detection of MREJ type v

[0047] SEQ ID NOs: 64, 112, 84, 163, 164 for the detection of MREJ type vii.

[0048] All these probes and primers can even be used together in the same physical enclosure.

[0049] It is another object of this invention to provide a method for typing a MREJ of a MRSA strain, which comprises the steps of: reproducing the above method with primers and/or probes specific for a determined MREJ type, and detecting an annealed probe or primer as an indication of the presence of a determined MREJ type.

[0050] It is further another object of this invention to provide a nucleic acid selected from SEQ ID NOs:

[0051] SEQ ID NOs: 42, 43, 44, 45, 46, 51 for sequence of MREJ type iv;

[0052] SEQ ID NOs: 47, 48, 49, 50 for sequence of MREJ type v;

[0053] SEQ ID NOs: 171 for sequence of MREJ type vi;

[0054] SEQ ID NOs: 165, 166 for sequence of MREJ type vii;

[0055] SEQ ID NOs: 167 for sequence of MREJ type viii;

[0056] SEQ ID NOs: 168 for sequence of MREJ type ix.

[0057] Oligonucleotides of at least 10 nucleotides in length which hybridize with any of these nucleic acids and which hybridize with one or more MREJ of types selected from iv to ix are also objects of this invention. Amongst these, primer pairs (or probes) having the following SEQ ID NOs:

[0058] 64/66, 64/100, 64/101; 59/52, 59/53, 59/54, 59/55, 59/56, 59/57, 60/52, 60/53, 60/54, 60/55, 60/56, 60/57, 61/52, 61/53, 61/54, 61/55, 61/56, 61/57, 62/52, 62/53, 62/54, 62/55, 62/56, 62/57, 63/52, 63/53, 63/54, 63/55, 63/56, 63/57 for the detection of type i MREJ

[0059] 64/66, 64/97, 64/99, 64/100, 64/101, 59/52, 59/53, 59/54, 59/55, 59/56, 59/57, 60/52, 60/53, 60/54, 60/55, 60/56, 60/57, 61/52, 61/53, 61/54, 61/55, 61/56, 61/57, 62/52, 62/53, 62/54, 62/55, 62/56, 62/57, 63/52, 63/53, 63/54, 63/55, 63/56, 63/57 for the detection of type ii MREJ

[0060] 64/67, 64/98, 64/102; 59/58, 60/58, 61/58, 62/58, 63/58 for the detection of type iii MREJ

[0061] 64/79 for the detection of type iv MREJ

[0062] 64/80 for the detection of type v MREJ

[0063] 64/204 for the detection of type vi MREJ

[0064] 64/112, 64/113 for the detection of type vii MREJ

[0065] 64/115, 64/116 for the detection of type viii MREJ

[0066] 64/109 for the detection of type ix MREJ,

[0067] are also within the scope of this invention.

[0068] Further, internal probes having nucleotide sequences defined in any one of SEQ ID NOs: 32, 83, 84, 160, 161, 162, 163, 164, are also within the scope of this invention. Compositions of matter comprising the primers and/or probes annealing or hybridizing with one or more MREJ of types selected from iv to ix as well as with the above nucleic acids, comprising or not primers and/or probes, which hybridize with one or more MREJ of types selected from i to iii, are further objects of this invention. The preferred compositions would comprise the primers having the nucleotide sequences defined in SEQ ID NOs:

[0069] 64/66, 64/100, 64/101; 59/52, 59/53, 59/54, 59/55, 59/56, 59/57, 60/52, 60/53, 60/54, 60/55, 60/56, 60/57, 61/52, 61/53, 61/54, 61/55, 61/56, 61/57, 62/52, 62/53, 62/54, 62/55, 62/56, 62/57, 63/52, 63/53, 63/54, 63/55, 63/56, 63/57, for the detection of type i MREJ

[0070] 64/66, 64/97, 64/99, 64/100, 64/101, 59/52, 59/53, 59/54, 59/55, 59/56, 59/57, 60/52, 60/53, 60/54, 60/55, 60/56, 60/57, 61/52, 61/53, 61/54, 61/55, 61/56, 61/57, 62/52, 62/53, 62/54, 62/55, 62/56, 62/57, 63/52 63/53, 63/54, 63/55, 63/56, 63/57 for the detection of type ii MREJ

[0071] 64/67, 64/98, 64/102; 59/58, 60/58, 61/58, 62/58, 63/58 for the detection of type iii MREJ

[0072] 64/79 for the detection of type iv MREJ

[0073] 64/80 for the detection of type v MREJ

[0074] 64/204 for the detection of type vi MREJ

[0075] 64/112, 64/113 for the detection of type vii MREJ

[0076] 64/115, 64/116 for the detection of type viii MREJ

[0077] 64/109 for the detection of type ix MREJ,

[0078] or probes, which SEQ ID NOs are: 32, 83, 84, 160, 161, 162, 163, 164, or both.

BRIEF DESCRIPTION OF THE DRAWINGS

[0079] FIG. 1 is a diagram illustrating the position of the primers developed by Hiramatsu et al. (U.S. Pat. No. 6,156,507) in the SCCmec-chromosome right extremity junction for detection and identification of MRSA.

[0080] FIG. 2 is a diagram illustrating the position of the primers selected in the present invention in the SCCmec-orfX right extremity junction for detection and identification of MRSA.

[0081] FIG. 3 is a diagram illustrating the position of the primers selected in the present invention to sequence new MREP types.

[0082] FIGS. 4A-4D illustrate a sequence alignment of nine MREP types.

DETAILED DESCRIPTION OF THE INVENTION

[0083] Here is particularly provided a method wherein each of MRSA nucleic acids or a variant or part thereof comprises a selected target region hybridizable with said primers or probes developed to be ubiquitous;

[0084] wherein each of said nucleic acids or a variant or part thereof comprises a selected target region hybridizable with said primers or probes;

[0085] 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 MRSA.

[0086] In the method, sequences from DNA fragments of SCCmec-chromosome right extremity junction, thereafter named MREJ standing for mec right extremity junction including sequences from SCCmec right extremity and chromosomal DNA to the right of the SCCmec integration site are used as parental sequences from which are derived the primers and/or the probes. MREJ sequences include our proprietary sequences as well as sequences obtained from public databases and from U.S. Pat. No. 6,156,507 and were selected for their capacity to sensitively, specifically, ubiquitously and rapidly detect the targeted MRSA nucleic acids.

[0087] Our proprietary DNA fragments and oligonucleotides (primers and probes) are also another object of this invention.

[0088] Compositions of matter such as diagnostic kits comprising amplification primers or probes for the detection of MRSA are also objects of the present invention.

[0089] In the above methods and kits, probes and primers are not limited to nucleic acids and may include, but are not restricted to, analogs of nucleotides. The diagnostic reagents constituted by the probes and the primers may be present in any suitable form (bound to a solid support, liquid, lyophilized, etc.).

[0090] 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 dependent signal amplification (NDSA), m) rolling circle amplification technology (RCA), n) Anchored strand displacement amplification, o) Solid-phase (immobilized) rolling circle amplification.

[0091] In the above methods and kits, detection of the nucleic acids of target genes may include real-time or post-amplification technologies. These detection technologies can include, but are not limited to fluorescence resonance energy transfer (FRET)-based methods such as adjacent hybridization of probes (including probe-probe and probe-primer methods), TaqMan probe, molecular beacon probe, Scorpion probe, nanoparticle probe and Amplifluor probe. Other detection methods include target gene nucleic acids detection via immunological methods, solid phase hybridization methods on filters, chips or any other solid support. In these systems, the hybridization can be monitored by fluorescence, chemiluminescence, potentiometry, mass spectrometry, plasmon resonance, polarimetry, colorimetry, flow cytometry or scanometry. Nucleotide sequencing, including sequencing by dideoxy termination or sequencing by hybridization (e.g. sequencing using a DNA chip) represents another method to detect and characterize the nucleic acids of target genes.

[0092] In a preferred embodiment, a PCR protocol is used for nucleic acid amplification.

[0093] A method for detection of a plurality of potential MRSA strains having different MREJ types may be conducted in separate reactions and physical enclosures, one type at the time. Alternatively, it could be conducted simultaneously for different types in separate physical enclosures, or in the same physical enclosures. In the latter scenario a multiplex PCR reaction could be conducted which would require that the oligonucleotides are all capable of annealing with a target region under common conditions. Since many probes or primers are specific for a determined MREJ type, typing a MRSA strain is a possible embodiment. When a mixture of oligonucleotides annealing together with more than one type is used in a single physical enclosure or container, different labels would be used to distinguish one type from another.

[0094] We aim at developing a DNA-based test or kit to detect and identify MRSA. Although the sequences from orfX genes and some SCCmec DNA fragments are available from public databases and have been used to develop DNA-based tests for detection of MRSA, new sequence data allowing to improve MRSA detection and identification which are object of the present invention have either never been characterized previously or were known but not shown to be located at the right extremity of SCCmec adjacent to the integration site (Table 4). These novel sequences could not have been predicted nor detected by the MRSA-specific PCR assay developed by Hiramatsu et al. (U.S. Pat. No. 6,156,507). These sequences will allow to improve current DNA-based tests for the diagnosis of MRSA because they allow the design of ubiquitous primers and probes for the detection and identification of more MRSA strains including all the major epidemic clones from around the world.

[0095] The diagnostic kits, primers and probes mentioned above can be used to detect and/or identify MRSA, whether said diagnostic kits, primers and probes are used for in vitro or in situ applications. The said samples may include but are not limited to: any clinical sample, any environmental sample, any microbial culture, any microbial colony, any tissue, and any cell line.

[0096] It is also an object of the present invention that said diagnostic kits, primers and probes can be used alone or in combination with any other assay suitable to detect and/or identify microorganisms, including but not limited to: any assay based on nucleic acids detection, any immunoassay, any enzymatic assay, any biochemical assay, any lysotypic assay, any serological assay, any differential culture medium, any enrichment culture medium, any selective culture medium, any specific assay medium, any identification culture medium, any enumeration culture medium, any cellular stain, any culture on specific cell lines, and any infectivity assay on animals.

[0097] 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 sequences have been obtained either from our proprietary sequences or from public databases (Tables 5, 6, 7, 8 and 9).

[0098] It is clear to the individual skilled in the art that oligonucleotide sequences other than those described in the present invention and which are appropriate for detection and/or identification of MRSA may also be derived from the proprietary fragment sequences or selected public database sequences. For example, the oligonucleotide primers or probes may be shorter but of a length of at least 10 nucleotides or longer than the ones chosen; they may also be selected anywhere else in the proprietary DNA fragments or in the sequences selected from public databases; they may also be variants of the same oligonucleotide. If the target DNA or a variant thereof hybridizes to a given oligonucleotide, or if the target DNA or a variant thereof can be amplified by a given oligonucleotide PCR primer pair, the converse is also true; a given target DNA may hybridize to a variant oligonucleotide probe or be amplified by a variant oligonucleotide PCR primer. Alternatively, the oligonucleotides may be designed from said DNA fragment sequences for use in amplification methods other than PCR. Consequently, the core of this invention is the detection and/or identification of MRSA by targeting genomic DNA sequences 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 require 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 Tables 5, 6, 7, 8 and 9 which are suitable for diagnostic purposes. When a proprietary fragment or a public database sequence is selected for its specificity and ubiquity, it increases the probability that subsets thereof will also be specific and ubiquitous.

[0099] The proprietary DNA fragments have been obtained as a repertory of sequences created by amplifying MRSA nucleic acids with new primers. These primers and the repertory of nucleic acids as well as the repertory of nucleotide sequences are further objects of this invention (Tables 4, 5, 6, 7, 8 and 9).

[0100] Claims therefore are in accordance with the present invention.

Sequences for Detection and Identification of MRSA

[0101] In the description of this invention, the terms nucleic acids and sequences might be used interchangeably. However, nucleic acids are chemical entities while sequences are the pieces of information encoded by these nucleic acids . Both nucleic acids and sequences are equivalently valuable sources of information for the matter pertaining to this invention.

Oligonucleotide Primers and Probes Design and Synthesis

[0102] As part of the design rules, all oligonucleotides (probes for hybridization and primers for DNA amplification by PCR) were evaluated for their suitability for hybridization or PCR amplification by computer analysis using standard programs (i.e. the GCG Wisconsin package programs, the primer analysis software Oligo.TM. 6 and MFOLD 3.0). The potential suitability of the PCR primer pairs was also evaluated prior to their synthesis by verifying the absence of unwanted features such as long stretches of one nucleotide and a high proportion of G or C residues at the 3' end (Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.). Oligonucleotide amplification primers were synthesized using an automated DNA synthesizer (Applied Biosystems). Molecular beacon designs were evaluated using criteria established by Kramer et al. (http://www.molecular-beacons.org).

[0103] The oligonucleotide sequence of 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) (Nichols et al., 1994, Nature 369:492-493). Primers and probes may also consist of nucleotide analogs such as Locked Nucleic Acids (LNA) (Koskin et al., 1998, Tetrahedron 54:3607-3630), and Peptide Nucleic Acids (PNA) (Egholm et al., 1993, Nature 365:566-568). The primers or probes may be of any suitable length and may be selected anywhere within the DNA sequences from proprietary fragments, or from selected database sequences which are suitable for the detection of MRSA.

[0104] Variants for a given target microbial gene are naturally occurring and are attributable to sequence variation within that gene during evolution (Watson et al., 1987, Molecular Biology of the Gene, 4.sup.th ed., The Benjamin/Cummings Publishing Company, Menlo Park, Calif.; Lewin, 1989, Genes IV, John Wiley & Sons, New York, N.Y.). For example, different strains of the same microbial species may have a single or more nucleotide variation(s) at the oligonucleotide hybridization site. The person skilled in the art is well aware of the existence of variant nucleic acids and/or 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 variations 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 primer hybridization site. A similar strategy may be applied to show variations at the hybridization site of a probe. Insofar as the divergence of the target nucleic acids and/or sequences or a part thereof does not affect significantly the sensitivity and/or specificity and/or ubiquity of the amplification primers or probes, variant microbial 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 target DNA.

DNA Amplification

[0105] For DNA amplification by the widely used PCR method, primer pairs were derived from our proprietary DNA fragments or from public database sequences.

[0106] During DNA amplification by PCR, two oligonucleotide primers binding respectively to each strand of the heat-denatured target DNA from the microbial 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.).

[0107] Briefly, the PCR protocols on a standard thermocycler (PTC-200 from MJ Research Inc., Watertown, Mass.) were as follows: Treated standardized bacterial suspensions or genomic DNA prepared from bacterial cultures or clinical specimens were amplified in a 20 .mu.l PCR reaction mixture. Each PCR reaction contained 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 2.5 mM MgCl.sub.2, 0.4 .mu.M of each primer, 200 .mu.M of each of the four dNTPs (Pharmacia Biotech), 3.3 .mu.g/.mu.l bovine serum albumin (BSA) (Sigma-Aldrich Canada Ltd, Oakville, Ontario, Canada) and 0.5 unit of Taq DNA polymerase (Promega Corp., Madison, Wis.) combined with the TaqStart.TM. antibody (BD Biosciences, Palo Alto, Calif.). The TaqStart.TM. antibody, which is a neutralizing monoclonal antibody to Tag DNA polymerase, was added to all PCR reactions to enhance the specificity and the sensitivity of the amplifications (Kellogg et al., 1994, Biotechniques 16:1134-1137). The treatment of bacterial cultures or of clinical specimens consists in a rapid protocol to lyse the microbial cells and eliminate or neutralize PCR inhibitors (described in co-pending application U.S. 60/306,163). For amplification from purified genomic DNA, the samples were added directly to the PCR amplification mixture. An internal control, derived from sequences not found in the target MREJ sequences or in the human genome, was used to verify the efficiency of the PCR reaction and the absence of significant PCR inhibition.

[0108] 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 a clinical specimen is higher than for detection from a microbial culture. Consequently, more sensitive PCR assays having more thermal cycles are probably required for direct detection from clinical specimens.

[0109] The person skilled in the art of nucleic acid amplification knows the existence of other rapid amplification procedures such as ligase chain reaction (LCR), reverse transcriptase PCR (RT-PCR), 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), rolling circle amplification technology (RCA), solid phase RCA, anchored SDA and nuclease dependent signal amplification (NDSA) (Lee et al., 1997, Nucleic Acid Amplification Technologies: Application to Disease Diagnosis, Eaton Publishing, Boston, Mass.; Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.; Westin et al., 2000, Nat. Biotechnol. 18:199-204). The scope of this invention is not limited to the use of amplification by PCR, but rather includes the use of any nucleic acid amplification method or any other procedure which may be used to increase the sensitivity and/or the rapidity of nucleic acid-based diagnostic tests. The scope of the present invention also covers the use of any nucleic acids amplification and detection technology including real-time or post-amplification detection technologies, any amplification technology combined with detection, any hybridization nucleic acid chips or array technologies, any amplification chips or combination of amplification and hybridization chip technologies. Detection and identification by any nucleotide sequencing method is also under the scope of the present invention.

[0110] Any oligonucleotide derived from the S. aureus MREJ DNA sequences and used with any nucleic acid amplification and/or hybridization technologies are also under the scope of this invention.

Evaluation of the MRSA Detection Method Developed by Hiramatsu et al.

[0111] According to Hiramatsu et al. (Ito et al., 1999, Antimicrob. Agents Chemother. 43:1449-1458; Katayama et al., 2000, Antimicrob. Agents Chemother. 44:1549-1555; Ito et al., 2001, Antimicrob. Agents Chemother. 45:1323-1336, Ma et al., 2002, Antimicrob. Agents Chemother. 46:1147-1152), four types of SCCmec DNA are found among MRSA strains. They have found that SCCmec DNAs are integrated at a specific site of the MSSA chromosome (named orfX). They developed a MRSA-specific multiplex PCR assay including primers that can hybridize to the right extremity of SCCmec types I, II and III (SEQ ID NOs.: 18, 19, 20, 21, 22, 23, 24 in U.S. Pat. No. 6,156,507 corresponding to SEQ ID NOs.: 52, 53, 54, 55, 56, 57, 58, respectively, in the present invention) as well as primers specific to the S. aureus chromosome to the right of the SCCmec integration site (SEQ ID NO.: 25, 28, 27, 26, 29 in U.S. Pat. No. 6,156,507 corresponding to SEQ ID NOs.: 59, 60, 61, 62, 63, respectively, in the present invention) (Table 1 and FIG. 1). The set of primers described by Hiramatsu et al. as being the optimal primer combination (SEQ ID NOs.: 22, 24 and 28 in U.S. Pat. No. 6,156,507 corresponding to SEQ ID NOs.: 56, 58 and 60 in the present invention) was used in the present invention to test by PCR a variety of MRSA, MSSA, methicillin-resistant CNS (MRCNS) and methicillin-sensitive CNS (MSCNS) strains (Table 2). A PCR assay performed using a standard thermocycler (PTC-200 from MJ Research Inc.) was used to test the ubiquity, the specificity and the sensitivity of these primers using the following protocol: one .mu.l of a treated standardized bacterial suspension or of a genomic DNA preparation purified from bacteria were amplified in a 20 .mu.l PCR reaction mixture. Each PCR reaction contained 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl.sub.2, 0.4 .mu.M of each of the SCCmec- and S. aureus chromosome-specific primers (SEQ ID NOs.: 22, 24 and 28 in U.S. Pat. No. 6,156,507 corresponding to SEQ ID NOs.: 56, 58 and 60 in the present invention), 200 .mu.M of each of the four dNTPs (Pharmacia Biotech), 3.3 .mu.g/.mu.l BSA (Sigma), and 0.5 U Taq polymerase (Promega) coupled with TaqStart.TM. Antibody (BD Biosciences).

[0112] PCR reactions were then subjected to thermal cycling 3 min at 94.degree. C. followed by 40 cycles of 60 seconds at 95.degree. C. for the denaturation step, 60 seconds at 55.degree. C. for the annealing step, and 60 seconds at 72.degree. C. for the extension step, then followed by a terminal extension of 7 minutes at 72.degree. C. using a standard thermocycler (PTC-200 from MJ Research Inc.). Detection of the PCR products was made by electrophoresis in agarose gels (2%) containing 0.25 .mu.g/ml of ethidium bromide. Twenty of the 39 MRSA strains tested were not amplified with the PCR assay developed by Hiramatsu et al. (Example 1, Tables 2 and 3).

[0113] With a view of establishing a rapid diagnostic test for MRSAs, the present inventors developed new sets of primers specific to the right extremity of SCCmec types I and II (SEQ ID NOs.: 66, 100 and 101) (Annex 1), SCCmec type II (SEQ ID NOs.: 97 and 99), SCCmec type III (SEQ ID NOs.: 67, 98 and 102) and in the S. aureus chromosome to the right of the SCCmec integration site (SEQ ID NOs.: 64, 70, 71, 72, 73, 74, 75 and 76) (Table 5). These primers, amplifying short amplicons (171 to 278 bp), are compatible for use in rapid PCR assays (Table 7). The design of these primers was based on analysis of multiple sequence alignments of orfX and SCCmec sequences described by Hiramatsu et al. (U.S. Pat. No. 6,156,507) or available from GenBank (Table 10, Annex I). These different sets of primers were used to test by PCR a variety of MRSA, MSSA, MRCNS and MSCNS strains. Several amplification primers were developed to detect all three SCCmec types (SEQ ID NOs.: 97 and 99 for SCCmec type II, SEQ ID NOs.: 66, 100 and 101 for SCCmec types I and II and SEQ ID NOs.: 67, 98 and 102 for SCCmec type III). Primers were chosen according to their specificity for MRSA strains, their analytical sensitivity in PCR and the length of the PCR product. A set of two primers was chosen for the SCCmec right extremity region (SEQ ID NO.: 66 specific to SCCmec types I and II; SEQ ID NO.: 67 specific to SCCmec type III). Of the 8 different primers designed to anneal on the S. aureus chromosome to the right of the SCCmec integration site (targeting orfX gene) (SEQ ID NOs.: 64, 70, 71, 72, 73, 74, 75 and 76), only one (SEQ ID.: 64) was found to be specific for MRSA based on testing with a variety of MRSA, MSSA, MRCNS and MSCNS strains (Table 12). Consequently, a PCR assay using the optimal set of primers (SEQ ID NOs.: 64, 66 and 67) which could amplify specifically MRSA strains containing SCCmec types I, II and III was developed (FIG. 2, Annex I). While the PCR assay developed with this novel set of primers was highly sensitive (i.e allowed the detection of 2 to 5 copies of genome for all three SCCmec types) (Table 11), it had the same shortcomings (i.e. lack of ubiquity) of the test developed by Hiramatsu et al. The 20 MRSA strains which were not amplified by the Hiramatsu et al. primers were also not detected by the set of primers comprising SEQ ID NOs.: 64, 66 and 67 (Tables 3 and 12). Clearly, diagnostic tools for achieving at least 50% ubiquity amongst the tested strains are needed.

[0114] With a view to establish a more ubiquitous (i.e. ability to detect all or most MRSA strains) detection and identification method for MRSA, we determined the sequence of the MREJ present in these 20 MRSA strains which were not amplified. This research has led to the discovery and identification of seven novel distinct MREJ target sequences which can be used for diagnostic purposes. These seven new MREJ sequences could not have been predicted nor detected with the system described in U.S. Pat. No. 6,156,507 by Hiramatsu et al. Namely, the present invention represents an improved method for the detection and identification of MRSA because it provides a more ubiquitous diagnostic method which allows for the detection of all major epidemic MRSA clones from around the world.

Sequencing of MREJ Nucleotide Sequences from MRSA Strains not Amplifiable with Primers Specific to SCCmec Types I, II and III

[0115] Since DNA from twenty MRSA strains were not amplified with the set of primers developed by Hiramatsu et al. (SEQ ID NOs.: 22, 24 and 28 in U.S. Pat. No. 6,156,507 corresponding to SEQ ID NOs.: 56, 58 and 60 in the present invention) (Tables 2 and 3) nor with the set of primers developed in the present invention based on the same three SCCmec types (I, II and III) sequences (SEQ ID NOs.: 64, 66 and 67) (Table 12), the nucleotide sequence of the MREJ was determined for sixteen of these twenty MRSA strains.

[0116] Transposase of IS431 is often associated with the insertion of resistance genes within the mec locus. The gene encoding this transposase has been described frequently in one or more copies within the right segment of SCCmec (Oliveira et al., 2000, Antimicrob. Agents Chemother. 44:1906-1910; Ito et al., 2001, Antimicrob. Agents Chemother. 45:1323-36). Therefore, in a first attempt to sequence the novel MREJ for 16 of the 20 MRSA strains described in Table 3, a primer was designed in the sequence of the gene coding for the transposase of IS431 (SEQ ID NO.: 68) and combined with an orfX-specific primer to the right of the SCCmec integration site (SEQ ID NO.: 70) (Tables 5 and 8). The strategy used to select these primers is illustrated in FIG. 3.

[0117] The MREJ fragments to be sequenced were amplified using the following amplification protocol: one .mu.L of treated cell suspension (or of a purified genomic DNA preparation) was transferred directly into 4 tubes containing 39 .mu.L of a PCR reaction mixture. Each PCR reaction contained 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl.sub.2, 1 .mu.M of each of the 2 primers (SEQ ID NOs.: 68 and 70), 200 .mu.M of each of the four dNTPs, 3.3 .mu.g/.mu.l of BSA (Sigma-Aldrich Canada Ltd) and 0.5 unit of Taq DNA polymerase (Promega) coupled with the TaqStart.TM. Antibody (BD Bisociences). PCR reactions were submitted to cycling using a standard thermocycler (PTC-200 from MJ Research Inc.) as follows: 3 min at 94.degree. C. followed by 40 cycles of 5 sec at 95.degree. C. for the denaturation step, 30 sec at 55.degree. C. for the annealing step and 2 min at 72.degree. C. for the extension step.

[0118] Subsequently, the four PCR-amplified mixtures were pooled and 10 .mu.L of the mixture were resolved by electrophoresis in a 1.2% agarose gel containing 0.25 .mu.g/mL of ethidium bromide. The amplicons were then visualized with an Alpha-Imager (Alpha Innotech Corporation, San Leandro, Calif.) by exposing to UV light at 254 nm. Amplicon size was estimated by comparison with a 1 kb molecular weight ladder (Life Technologies, Burlington, Ontario, Canada). The remaining PCR-amplified mixture (150 .mu.L, total) was also resolved by electrophoresis in a 1.2% agarose gel. The amplicons were then visualized by staining with methylene blue (Flores et al., 1992, Biotechniques, 13:203-205) Amplicon size was once again estimated by comparison with a 1 kb molecular weight ladder. Of the sixteen strains selected from the twenty described in Table 3, six were amplified using SEQ ID NOs.: 68 and 70 as primers (CCRI-178, CCRI-8895, CCRI-8903, CCRI-1324, CCRI-1331 and CCRI-9504). For these six MRSA strains, an amplification product of 1.2 kb was obtained. The band corresponding to this specific amplification product was excised from the agarose gel and purified using the QlAquick.TM. gel extraction kit (QIAGEN Inc., Chatsworth, Calif.). The gel-purified DNA fragment was then used directly in the sequencing protocol. Both strands of the MREJ amplification products were sequenced by the dideoxynucleotide chain termination sequencing method by using an Applied Biosystems automated DNA sequencer (model 377) with their Big Dye.TM. Terminator Cycle Sequencing Ready Reaction Kit (Applied Biosystems, Foster City, Calif.). The sequencing reactions were performed by using the same primers (SEQ ID NOs.: 68 and 70) and 10 ng/100 bp per reaction of the gel-purified amplicons. Sequencing of MREJ from the six MRSA strains (CCRI-178, CCRI-8895, CCRI-8903, CCRI-1324, CCRI-1331 and CCRI-9504) described in Table 3 yielded SEQ ID NOs.: 42, 43, 44, 45, 46 and 51, respectively (Table 4).

[0119] In order to ensure that the determined sequence did not contain errors attributable to the sequencing of PCR artefacts, we have sequenced two preparations of the gel-purified MREJ amplification products originating from two independent PCR amplifications. For most target fragments, the sequences determined for both amplicon preparations were identical. Furthermore, the sequences of both strands were 100% complementary thereby confirming the high accuracy of the determined sequence. The MREJ sequences determined using the above strategy are described in the Sequence Listing and in Table 4.

[0120] In order to sequence MREJ in strains for which no amplicon had been obtained using the strategy including primers specific to the transposase gene of IS431 and orfX, another strategy using primers targeting mecA and orfX sequences was used to amplify longer genomic fragments. A new PCR primer targeting mecA (SEQ ID NO.: 69) (Table 8) to be used in combination with the same primer in the orfX sequence (SEQ ID NO.: 70). The strategy used to select these primers is illustrated in FIG. 3.

[0121] The following amplification protocol was used: Purified genomic DNA (300 ng) was transferred to a final volume of 50 .mu.l of a PCR reaction mixture. Each PCR reaction contained Herculase buffer (Stratagene, La Jolla, Calif.), 0.8 .mu.M of each of the 2 primers (SEQ ID NOs.: 69 and 70), 0.56 mM of each of the four dNTPs and 5 units of Herculase (Stratagene). PCR reactions were subjected to cycling using a standard thermal cycler (PTC-200 from MJ Research Inc.) as follows: 2 min at 92.degree. C. followed by 35 or 40 cycles of 10 sec at 92.degree. C. for the denaturation step, 30 sec at 55.degree. C. for the annealing step and 30 min at 68.degree. C. for the extension step.

[0122] Subsequently, 10 .mu.L of the PCR-amplified mixture were resolved by electrophoresis in a 0.7% agarose gel containing 0.25 .mu.g/mL of ethidium bromide. The amplicons were then visualized as described above Amplicon size was estimated by comparison with a 1 kb molecular weight ladder (Life Technologies). A reamplification reaction was then performed in 2 to 5 tubes using the same protocol with 3 .mu.l of the first PCR reaction used as test sample for the second amplification. The PCR-reamplified mixtures were pooled and also resolved by electrophoresis in a 0.7% agarose gel. The amplicons were then visualized by staining with methylene blue as described above. An amplification product of approximately 12 kb was obtained using this amplification strategy for all strains tested. The band corresponding to the specific amplification product was excised from the agarose gel and purified as described above. The gel-purified DNA fragment was then used directly in the sequencing protocol as described above. The sequencing reactions were performed by using the same amplification primers (SEQ ID NOs.: 69 and 70) and 425-495 ng of the gel-purified amplicons per reaction. Subsequently, internal sequencing primers (SEQ ID NOs.: 65, 77 and 96) (Table 8) were used to obtain sequence data on both strands for a larger portion of the amplicon. Five of the 20 MRSA strains (CCRI-1331, CCRI-1263, CCRI-1377, CCRI-1311 and CCRI-2025) described in Table 3 were sequenced using this strategy, yielding SEQ ID NOs.: 46, 47, 48, 49 and 50, respectively (Table 4). Sequence within mecA gene was also obtained from the generated amplicons yielding SEQ ID NOs: 27, 28, 29, 30 and 31 from strains CCRI-2025, CCRI-1263, CCRI-1311, CCRI-1331 and CCRI-1377, respectively (Table 4). Longer sequences within the mecA gene and from downstream regions were also obtained for strains CCRI-2025, CCRI-1331, and CCRI-1377 as described below.

[0123] In order to obtain longer sequences of the orfX gene, two other strategies using primers targeting mecA and orfX sequences (at the start codon) was used to amplify longer chromosome fragments. A new PCR primer was designed in orfX (SEQ ID NO.: 132) to be used in combination with the same primer in the mecA gene (SEQ ID NO.: 69). The strategy used to select these primers is illustrated in FIG. 3. Eight S. aureus strains were amplified using primers SEQ ID NOs.: 69 and 132 (CCRI-9860, CCRI-9208, CCRI-9504, CCRI-1331, CCRI-9583, CCRI-9681, CCRI-2025 and CCRI-1377). The strategy used to select these primers is illustrated in FIG. 3.

[0124] The following amplification protocol was used: Purified genomic DNA (350 to 500 ng) was transferred to a 50 .mu.l PCR reaction mixture. Each PCR reaction contained 1.times. Herculase buffer (Stratagene), 0.8 .mu.M of each of the set of 2 primers (SEQ ID NOs.: 69 and 132), 0.56 mM of each of the four dNTPs and 7.5 units of Herculase (Stratagene) with 1 mM MgCl.sub.2. PCR reactions were subjected to thermocycling as described above.

[0125] Subsequently, 5 .mu.L of the PCR-amplified mixture were resolved by electrophoresis in a 0.8% agarose gel containing 0.25 .mu.g/mL of ethidium bromide. The amplicons were then visualized as described above. For one S. aureus strain (CCRI-9583), a reamplification was then performed by using primers SEQ ID NOs.: 96 and 158 (FIG. 3) in 4 tubes, using the same PCR protocol, with 2 .mu.l of the first PCR reaction as test sample for the second amplification. The PCR-reamplified mixtures were pooled and also resolved by electrophoresis in a 0.8% agarose gel. The amplicons were then visualized by staining with methylene blue as described above. A band of approximately 12 to 20 kb was obtained using this amplification strategy depending on the strains tested. The band corresponding to the specific amplification product was excised from the agarose gel and purified using the QlAquick.TM. gel extraction kit or QIAEX II gel extraction kit (QIAGEN Inc.). Two strains, CCRI-9583 and CCRI-9589, were also amplified with primers SEQ ID NOs.: 132 and 150, generating an amplification product of 1.5 kb. Long amplicons (12-20 kb) were sequenced using 0.6 to 1 .mu.g per reaction, while short amplicons (1.5 kb) were sequenced using 150 ng per reaction. Sequencing reactions were performed using different sets of primers for each S. aureus strain: 1) SEQ ID NOs.: 68, 70, 132, 145, 146, 147, 156, 157 and 158 for strain CCRI-9504; 2) SEQ ID NOs.: 70, 132, 154 and 155 for strain CCRI-2025; 3) SEQ ID NOs.: 70, 132, 148, 149, 158 and 159 for strain CCRI-9681; 4) SEQ ID NOs.: 70, 132, 187, and 188 for strain CCRI-9860; 5) SEQ ID NOs: 70, 132, 150 and 159 for strain CCRI-9589, 6) SEQ ID NOs.: 114, 123, 132, 150 and 158 for strain CCRI-9583; 7) SEQ ID NOs: 70, 132, 154 and 155 for strain CCRI-1377, 8) SEQ ID NOs.: 70, 132, 158 and 159 for strain CCRI-9208; 9) SEQ ID NOs: 68, 70, 132, 145, 146, 147 and 158 for strain CCRI-1331; and 10) SEQ ID NOs.: 126 and 127 for strain CCRI-9770.

[0126] In one strain (CCRI-9770), the orfX and orfSA0022 genes were shown to be totally or partially deleted based on amplification using primers specific to these genes (SEQ ID NOs: 132 and 159 and SEQ ID NOs.: 128 and 129, respectively) (Table 8). Subsequently, a new PCR primer was designed in orfSA0021 (SEQ ID NO.: 126) to be used in combination with the same primer in the mecA gene (SEQ ID NO.: 69). An amplification product of 4.5 kb was obtained with this primer set. Amplification, purification of amplicons and sequencing of amplicons were performed as described above.

[0127] To obtain the sequence of the SSCmec region containing mecA for ten of the 20 MRSA strains described in Table 3 (CCRI-9504, CCRI-2025, CCRI-9208, CCRI-1331, CCRI-9681, CCRI-9860, CCRI-9770, CCRI-9589, CCRI-9583 and CCRI-1377), the primer described above designed in mecA (SEQ ID NO.: 69) was used in combination with a primer designed in the downstream region of mecA (SEQ ID NO.: 118) (Table 8). An amplification product of 2 kb was obtained for all the strains tested. For one strain, CCRI-9583, a re-amplification with primers SEQ ID NOs.: 96 and 118 was performed with the amplicon generated with primers SEQ ID NOs.: 69 and 132 described above. The amplication, re-amplification, purification of amplicons and sequencing reactions were performed as described above. Sequencing reactions were performed with amplicons generated with SEQ ID NOs.: 69 and 132 described above or SEQ ID NOs.: 69 and 118. Different sets of sequencing primers were used for each S. aureus strain: 1) SEQ ID NOs.: 69, 96, 117, 118, 120, 151, 152 for strains CCRI-9504, CCRI-2025, CCRI-1331, CCRI-9770 and CCRI-1377; 2) SEQ ID NOs.: 69, 96, 118 and 120 for strains CCRI-9208, CCRI-9681 and CCRI-9589; 3) SEQ ID NOs.: 69, 96, 117, 118, 120 and 152 for strain CCRI-9860; and 4) SEQ ID NOs.: 96, 117, 118, 119, 120, 151 and 152 for strain CCRI-9583.

[0128] The sequences obtained for 16 of the 20 strains non-amplifiable by the Hiramatsu assay (Table 4) were then compared to the sequences available from public databases. In all cases, portions of the sequence had an identity close to 100% to publicly available sequences for orfX (SEQ ID NOs.: 42-51, 165-168 and 171) or mecA and downstream region (SEQ ID NOs.: 27-31, 189-193, 195, 197-199 and 225). However, while the orfX portion of the fragments (SEQ ID NOs.: 42-51, 165-168 and 171) shared nearly 100% identity with the orfX gene of MSSA strain NCTC 8325 described by Hiramatsu et al. (SEQ ID NO.: 3), the DNA sequence within the right extremity of SCCmec itself was shown to be very different from those of types I, II, III and IV described by Hiramatsu et al. (Table 13, FIG. 4). Six different novel sequence types were obtained.

[0129] It should be noted that Hiramatsu et al. demonstrated that SCCmec type I could be associated with MREP type i, SCCmec types II and IV are associated with MREP type ii, and SCCmec type III is associated with MREP type iii. Our MREJ sequencing data from various MRSA strains led to the discovery of 6 novel MREP types designated types iv, v vi, vii, viii, and ix. The MREJ comprising distinct MREP types were named according to the MREP numbering scheme. Hence, MREP type i is comprised within MREJ type i, MREP type ii is comprised within MREJ type ii and so on up to MREP type ix.

[0130] The sequences within the right extremity of SCCmec obtained from strains CCRI-178, CCRI-8895, CCRI-8903, CCRI-1324, CCRI-1331 and CCRI-9504 (SEQ ID NOs.: 42, 43, 44, 45, 46 and 51) were nearly identical to each other and exhibited nearly 100% identity with IS431 (GenBank accession numbers AF422691, AB037671, AF411934). However, our sequence data revealed for the first time the location of this IS431 sequence at the right extremity of SCCmec adjacent to the integration site. Therefore, as the sequences at the right extremity of SCCmec from these 6 MRSA strains were different from those of SCCmec type I from strain NCTC 10442, SCCmec type II from strain N315, SCCmec type III from strain 85/2082 and SCCmec type IV from strains CA05 and 8/6-3P described by Hiramatsu et al. (Ito et al., 2001, Antimicrob. Agents Chemother. 45:1323-1336; Ma et al., 2002, Antimicrob. Agents Chemother. 46:1147-1152), these new sequences were designated as MREP type iv (SEQ ID NOs.: 42-46 and 51). A BLAST search with the SCCmec portion of MREP type iv sequences produced significant alignments with sequences coding for portions of a variety of known transposases. For example, when compared to Genbank accession no. AB037671, MREP type iv from SEQ ID NO. 51 shared 98% identity with the putative transposase of IS431 and its downstream region; two gaps of 7 nucleotides each were also present in the alignment.

[0131] Sequences obtained from strains CCRI-1263, CCRI-1377, CCRI-1311 and CCRI-2025 (SEQ ID NOs.: 47-50) were nearly identical to each other and different from all three SCCmec types and MREP type iv and, consequently, were designated as MREP type v. When compared with Genbank sequences using BLAST, MREP type v sequences did not share any significant homology with any published sequence, except for the first 28 nucleotides. That short stretch corresponded to the last 11 coding nucleotides of orfX, followed by the 17 nucleotides downstream, including the right inverted repeat (IR-R) of SCCmec.

[0132] Sequence obtained from strain CCRI-9208 was also different from all three SCCmec types and MREP types iv and v and, consequently, was designated as MREP type vi (SEQ ID NO.: 171). Upon a BLAST search, MREP type vi was shown to be unique, exhibiting no significant homology to any published sequence.

[0133] Sequences obtained from strains CCRI-9583 and CCRI-9589 were also different from all three SCCmec types and MREP types iv to vi and were therefore designated as MREP type vii (SEQ ID NOs.: 165 and 166). Upon a BLAST search, MREP type vii was also shown to be unique, exhibiting no significant homology to any published sequence.

[0134] Sequence obtained from strain CCRI-9860 was also different from all three SCCmec types and MREP types iv to vii and was therefore designated as MREP type viii (SEQ ID NO.: 167). Sequence obtained from strain CCRI-9681 was also different from all three SCCmec types and MREP types iv to viii and was therefore designated as MREP type ix (SEQ ID NO.: 168). BLAST searches with the SCCmec portion of MREP types viii and ix sequences yielded significant alignments, but only for the first .about.150 nucleotides of each MREP type. For example, the beginning of the MREP type viii sequence had 88% identity with a portion of Genbank accession no. AB063173, but no significant homology with any published sequence was found for the rest of the sequence. In the same manner, the first .about.150 nucleotides of MREP type ix had 97% identity with the same portion of AB063173, with the rest of the sequence being unique. The short homologous portion of MREP types viii and ix corresponds in AB063173 to the last 14 coding nucleotides of orfX, the IR-R of SCCmec, and a portion of orfCM009. Although sharing resemblances, MREP types viii and ix are very different from one another; as shown in Table 13, there is only 55.2% identity between both types for the first 500 nucleotides of the SCCmec portion.

[0135] Finally, we did not obtain any sequence within SSCmec from strain CCRI-9770. However, as described in the section "Sequencing of MREJ nucleotide sequences from MRSA strains not amplifiable with primers specific to SCCmec types I, II and III", this strain has apparently a partial or total deletion of the orfX and orfSA0022 genes in the chromosomal DNA to the right of the SCCmec integration site and this would represent a new right extremity junction. We therefore designated this novel sequence as MREP type x (SEQ ID NO.: 172). Future sequencing should reveal whether this so called MREJ type x contains a novel MREP type x or if the lack of amplification is indeed caused by variation in the chromosomal part of the MREJ.

[0136] The sequences of the first 500-nucleotide portion of the right extremity of all SCCmec obtained in the present invention were compared to those of SCCmec types I, II and III using GCG programs Pileup and Gap. Table 13 depicts the identities at the nucleotide level between SCCmec right extremities of the six novel sequences with those of SCCmec types I, II and III using the GCG program Gap. While SCCmec types I and II showed nearly 79.2% identity (differing only by a 102 bp insertion present in SCCmec type II) (FIGS. 1, 2 and 4), all other MREP types showed identities varying from 40.9 to 57.1%. This explains why the right extremities of the novel MREP types iv to ix disclosed in the present invention could not have been predicted nor detected with the system described by Hiramatsu et al.

[0137] Four strains (CCRI-1312, CCRI-1325, CCRI-9773 and CCRI-9774) described in Table 3 were not sequenced but rather characterized using PCR primers. Strains CCRI-1312 and CCRI-1325 were shown to contain MREP type v using specific amplification primers described in Examples 4, 5 and 6 while strains CCRI-9773 and CCRI-9774 were shown to contain MREP type vii using specific amplification primers described in Example 7.

[0138] To obtain the complete sequence of the SCCmec present in the MRSA strains described in the present invention, primers targeting the S. aureus chromosome to the left (upstream of the mecA gene) of the SCCmec integration site were developed. Based on available public database sequences, 5 different primers were designed (SEQ ID NOs.: 85-89) (Table 9). These primers can be used in combination with S. aureus chromosome-specific primers in order to sequence the entire SCCmec or, alternatively, used in combination with a mecA-specific primer (SEQ ID NO.: 81) in order to sequence the left extremity junction of SCCmec. We have also developed several primers specific to known SCCmec sequences spread along the locus in order to obtain the complete sequence of SCCmec (Table 9). These primers will allow to assign a SCCmec type to the MRSA strains described in the present invention.

Selection of Amplification Primers from SCCmec/orfX Sequences

[0139] The MREJ sequences determined by the inventors or selected from public databases were used to select PCR primers for detection and identification of MRSA. The strategy used to select these PCR primers was based on the analysis of multiple sequence alignments of various MREJ sequences.

[0140] Upon analysis of the six new MREP types iv to ix sequence data described above, primers specific to each new MREP type sequence (SEQ ID NOs.: 79, 80, 109, 112, 113, 115, 116 and 204) were designed (FIG. 2, Table 5, Examples 3, 4, 5, 6, 7 and 8). Primers specific to MREP types iv, v and vii (SEQ ID NOs.: 79, 80 and 112) were used in multiplex with the three primers to detect SCCmec types I, II and III (SEQ ID NOs: 64, 66 and 67) and the primer specific to the S. aureus orfX (SEQ ID NO. 64) (Examples 3, 4, 5, 6 and 7). Primers specific to MREP types vi, viii and ix (SEQ ID NOs.: 204, 115, 116 and 109) were also designed and tested against their specific target (Example 8).

Detection of Amplification Products

[0141] Classically, the detection of PCR amplification products is performed by standard ethidium bromide-stained agarose gel electrophoresis as described above. It is however clear that other methods for the detection of specific amplification products, which may be faster and more practical for routine diagnosis, may be used. Examples of such methods are described in co-pending patent application WO01/23604 A2.

[0142] Amplicon detection 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 sequence from our repertory and designed to specifically hybridize to DNA amplification products which are objects of the present invention. Alternatively, amplicons can be characterized by sequencing. See co-pending patent application WO01/23604 A2 for examples of detection and sequencing methods.

[0143] In order to improve nucleic acid amplification efficiency, the composition of the reaction mixture may be modified (Chakrabarti and Schutt, 2002, Biotechniques, 32:866-874; Al-Soud and Radstrom, 2002, J. Clin. Microbiol., 38:4463-4470; Al-Soud and Radstrom, 1998, Appl. Environ. Microbiol., 64:3748-3753; Wilson, 1997, Appl. Environ. Microbiol., 63:3741-3751). Such modifications of the amplification reaction mixture include the use of various polymerases or the addition of nucleic acid amplification facilitators such as betaine, BSA, sulfoxides, protein gp32, detergents, cations, tetramethylamonium chloride and others.

[0144] In a preferred embodiment, real-time detection of PCR amplification was monitored using molecular beacon probes in a SMART CYCLER.RTM. apparatus (Cepheid, Sunnyvale, Calif.). A multiplex PCR assay containing primers specific to MREP types i to v and orfX of S. aureus (SEQ ID NOs.: 64, 66, 67, 79 and 80), a molecular beacon probe specific to the orfX sequence (SEQ ID NO. 84, see Annex II and FIG. 2) and an internal control to monitor PCR inhibition was developed. The internal control contains sequences complementary to MREP type iv- and orfX-specific primers (SEQ ID NOs. 79 and 64). The assay also contains a molecular beacon probe labeled with tetrachloro-6-carboxyfluorescein (TET) specific to sequence within DNA fragment generated during amplification of the internal control. Each PCR reaction contained 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 3.45 mM MgCl.sub.2, 0.8 .mu.M of each of the MREP-specific primers (SEQ ID NOs.: 66 and 67) and orfX-specific primer (SEQ ID NO.: 64), 0.4 .mu.M of each of the MREP-specific primers (SEQ ID NOs.: 79 and 80), 80 copies of the internal control, 0.2 .mu.M of the TET-labeled molecular beacon probe specific to the internal control, 0.2 .mu.M of the molecular beacon probe (SEQ ID NO.: 84) labeled with 6-carboxyfluorescein (FAM), 330 .mu.M of each of the four dNTPs (Pharmacia Biotech), 3.45 .mu.g/.mu.l of BSA (Sigma), and 0.875 U Taq polymerase (Promega) coupled with TaqStart.TM. Antibody (BD Biosciences). The PCR amplification on the SMART CYCLER.RTM. was performed as follows: 3 min. at 95.degree. C. for initial denaturation, then forty-eight cycles of three steps consisting of 5 seconds at 95.degree. C. for the denaturation step, 15 seconds at 60.degree. C. for the annealing step and 15 seconds at 72.degree. C. for the extension step. Sensitivity tests performed by using purified genomic DNA from one MRSA strain of each MREP type (i to v) showed a detection limit of 2 to 10 genome copies (Example 5). None of the 26 MRCNS or 10 MSCNS tested were positive with this multiplex assay. The eight MRSA strains (CCRI-9208, CCRI-9770, CCRI-9681, CCRI-9860, CCRI-9583, CCRI-9773, CCRI-9774, CCRI-9589) which harbor the new MREP types vi, viii, ix and x sequences described in the present invention remained undetectable (Example 5).

[0145] In a preferred embodiment, detection of MRSA using the real-time multiplex PCR assay on the SMART CYCLER.RTM. apparatus (Cepheid, Sunnyvale, Calif.) directly from clinical specimens was evaluated. A total of 142 nasal swabs were collected during a MRSA hospital surveillance program at the Montreal General Hospital (Montreal, Quebec, Canada). The swab samples were tested at the Centre de Recherche en Infectiologie de l'Universite Laval within 24 hours of collection. Upon receipt, the swabs were plated onto mannitol agar and then the nasal material from the same swab was prepared with a simple and rapid specimen preparation protocol described in co-pending patent application No. U.S. 60/306,163. Classical identification of MRSA was performed by standard culture methods.

[0146] The PCR assay detected 33 of the 34 samples positive for MRSA based on the culture method. As compared to culture, the PCR assay detected 8 additional MRSA positive specimens for a sensitivity of 97.1% and a specificity of 92.6% (Example 6). This multiplex PCR assay represents a rapid and powerful method for the specific detection of MRSA carriers directly from nasal specimens and can be used with any types of clinical specimens such as wounds, blood or blood culture, CSF, etc.

[0147] In a preferred embodiment, a multiplex PCR assay containing primers specific to MREP types i, ii, iii, iv, v and vi and orfX of S. aureus (SEQ ID NOs.: 66, 67, 79, 80 and 112), and three molecular beacons probes specific to orfX sequence which allowed detection of the two sequence polymorphisms identified in this region of the orfX sequence was developed. Four of the strains which were not detected with the multiplex assay for the detection of MREP types i to v were now detected with this multiplex assay while the four MRSA strains (CCRI-9208, CCRI-9770, CCRI-9681, CCRI-9860) which harbor the MREP types vi, viii, ix and x described in the present invention remained undetectable (Example 7). Primers specific to MREP types vi, viii and ix (SEQ ID NOs.: 204, 115, 116 and 109) were also designed and were shown to detect their specific target strains (Example 8). While the primers and probes derived from the teaching of Hiramatsu et al., permitted the detection of only 48.7% (19 strains out of 39) of the MRSA strains of Table 2, the primers and probes derived from the present invention enable the detection of 97.4% of the strains (38 strains out of 39) (see examples 7 and 8). Therefore it can be said that our assay has a ubiquity superior to 50% for the MRSA strains listed in Table 2.

Specificity, Ubiquity and Sensitivity Tests for Oligonucleotide Primers and Probes

[0148] The specificity of oligonucleotide primers and probes was tested by amplification of DNA or by hybridization with staphylococcal species. All of the staphylococcal 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 microbial cells using standard chemical and/or physical treatments to lyse the cells (Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2.sup.nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.) or alternatively, genomic DNA purified with the GNOME.TM. DNA kit (Qbiogene, Carlsbad, Calif.) was used. Subsequently, the DNA was subjected to amplification with the set of primers. Specific primers or probes hybridized only to the target DNA.

[0149] Oligonucleotides primers found to amplify specifically DNA from the target MRSA were subsequently tested for their ubiquity by amplification (i.e. ubiquitous primers amplified efficiently most or all isolates of MRSA). Finally, the analytical sensitivity of the PCR assays was determined by using 10-fold or 2-fold dilutions of purified genomic DNA from the targeted microorganisms. For most assays, sensitivity levels in the range of 2-10 genome copies were obtained. The specificity, ubiquity and analytical sensitivity of the PCR assays were tested either directly with bacterial cultures or with purified bacterial genomic DNA.

[0150] Molecular beacon probes were tested using the SMART CYCLER.RTM. platform as described above. A molecular beacon probe was considered specific only when it hybridized solely to DNA amplified from the MREJ of S. aureus. Molecular beacon probes found to be specific were subsequently tested for their ubiquity (i.e. ubiquitous probes detected efficiently most or all isolates of the MRSA) by hybridization to bacterial DNAs from various MRSA strains.

Bacterial Strains

[0151] The reference strains used to build proprietary SCCmec-chromosome right extremity junction sequence data subrepertories, as well as to test the amplification and hybridization assays, were obtained from (i) the American Type Culture Collection (ATCC), (ii) the Laboratoire de sante publique du Quebec (LSPQ) (Ste-Anne de Bellevue, Quebec, Canada), (iii) the Centers for Disease Control and Prevention (CDC) (Atlanta, Ga.), (iv) the Institut Pasteur (Paris, France), and V) the Harmony Collection (London, United Kingdom) (Table 14). Clinical isolates of MRSA, MSSA, MRCNS and MSCNS from various geographical areas were also used in this invention (Table 15). The identity of our MRSA strains was confirmed by phenotypic testing and reconfirmed by PCR analysis using S. aureus-specific primers and mecA-specific primers (SEQ ID NOs.: 69 and 81) (Martineau et al., 2000, Antimicrob. Agents Chemother. 44:231-238).

[0152] For sake of clarity, below is a list of the Examples, Tables, Figures and Annexes of this invention.

DESCRIPTION OF THE EXAMPLES

[0153] Example 1: Primers developed by Hiramatsu et al. can only detect MRSA strains belonging to MREP types i, ii, and iii while missing prevalent novel MREP types.

[0154] Example 2: Detection and identification of MRSA using primers specific to MREP types i, ii and iii sequences developed in the present invention.

[0155] Example 3: Development of a multiplex PCR assay on a standard thermocycler for detection and identification of MRSA based on MREP types i, ii, iii, iv and v sequences.

[0156] Example 4: Development of a real-time multiplex PCR assay on the SMART CYCLER.RTM. for detection and identification of MRSA based on MREP types i, ii, iii, iv and v sequences.

[0157] Example 5: Development of a real-time multiplex PCR assay on the SMART CYCLER.RTM. for detection and identification of MRSA based on MREP types i, ii, iii, iv and v sequences and including an internal control.

[0158] Example 6: Detection of MRSA using the real-time multiplex assay on the SMART CYCLER.RTM. based on MREP types i, ii, iii, iv and v sequences for the detection of MRSA directly from clinical specimens.

[0159] Example 7: Development of a real-time multiplex PCR assay on the SMART CYCLER.RTM. for detection and identification of MRSA based on MREP types i, ii, iii, iv, v, vi and vii sequences.

[0160] Example 8: Development of real-time PCR assays on the SMART CYCLER.RTM. for detection and identification of MRSA based on MREP types vi, viii and ix.

DESCRIPTION OF THE TABLES

[0161] Table 1 provides information about all PCR primers developed by Hiramatsu et al. in U.S. Pat. No. 6,156,507.

[0162] Table 2 is a compilation of results (ubiquity and specificity) for the detection of SCCmec-orfX right extremity junction using primers described by Hiramatsu et al. in U.S. Pat. No. 6,156,507 on a standard thermocycler.

[0163] Table 3 is a list of MRSA strains not amplifiable using primers targeting types I, II and III of SCCmec-orfX right extremity junction sequences.

[0164] Table 4 is a list of novel sequences revealed in the present invention.

[0165] Table 5 provides information about all primers developed in the present invention.

[0166] Table 6 is a list of molecular beacon probes developed in the present invention.

[0167] Table 7 shows amplicon sizes of the different primer pairs described by Hiramatsu et al. in U.S. Pat. No. 6,156,507 or developed in the present invention.

[0168] Table 8 provides information about primers developed in the present invention to sequence the SCCmec-chromosome right extremity junction.

[0169] Table 9 provides information about primers developed in the present invention to obtain sequence of the complete SCCmec.

[0170] Table 10 is a list of the sequences available from public databases (GenBank, genome projects or U.S. Pat. No. 6,156,507) used in the present invention to design primers and probes.

[0171] Table 11 gives analytical sensitivity of the PCR assay developed in the present invention using primers targeting types I, II and III of SCCmec-orfX right extremity junction sequences and performed using a standard thermocycler.

[0172] Table 12 is a compilation of results (ubiquity and specificity) for the detection of MRSA using primers developed in the present invention which target types I, II and III of SCCmec-orfX right extremity junction sequences and performed using a standard thermocycler.

[0173] Table 13 shows a comparison of sequence identities between the first 500 nucleotides of SCCmec right extremities between 9 types of MREP.

[0174] Table 14 provides information about the reference strains of MRSA, MSSA, MRCNS and MSCNS used to validate the PCR assays developed in the present invention.

[0175] Table 15 provides information about the origin of clinical strains of MRSA, MSSA, MRCNS and MSCNS used to validate the PCR assays described in the present invention.

[0176] Table 16 depicts the analytical sensitivity of the PCR assay developed in the present invention using primers targeting 5 types of MREP sequences and performed on a standard thermocycler.

[0177] Table 17 is a compilation of results (ubiquity and specificity) for the PCR assay developed in the present invention using primers targeting 5 types of MREP sequences and performed on a standard thermocycler.

[0178] Table 18 depicts the analytical sensitivity of the PCR assay developed in the present invention using the SMART CYCLER.RTM. platform for the detection of 5 types of MREP.

[0179] Table 19 is a compilation of results (ubiquity and specificity) for the PCR assay developed in the present invention using primers and a molecular beacon probe targeting 5 types of MREP sequences and performed on the SMART CYCLER.RTM. platform.

[0180] Table 20 depicts the analytical sensitivity of the PCR assay developed in the present invention using the SMART CYCLER.RTM. platform for the detection of 6 MREP types.

[0181] Table 21 is a compilation of results (ubiquity and specificity) for the PCR assay developed in the present invention using primers and a molecular beacon probe targeting 6 types of MREP sequences and performed on the SMART CYCLER.RTM. platform.

FIGURE LEGENDS

[0182] FIG. 1. Schematic organization of types I, II and III SCCmec-orfX right extremity junctions and localization of the primers (SEQ ID NOs: 52-63) described by Hiramatsu et al. for the detection and identification of MRSA. Amplicon sizes are depicted in Table 7.

[0183] FIG. 2. Schematic organization of MREP types i, ii, iii, iv, v, vi, vii, viii and ix and localization of the primers and molecular beacon targeting all MREP types (SEQ ID NOs. 20, 64, 66, 67, 79, 80, 84, 112, 115, 116, 84, 163 and 164) which were developed in the present invention. Amplicon sizes are depicted in Table 7.

[0184] FIG. 3. Schematic organization of the SCCmec-chromosome right extremity junctions and localization of the primers (SEQ ID NOs. 65, 68, 69, 70, 77, 96, 118, 126, 132, 150 and 158) developed in the present invention for the sequencing of MREP types iv, v, vi, vii, viii, ix and x.

[0185] FIG. 4. Multiple sequence alignment of representatives of nine MREP types (represented by portions of SEQ ID NOs.: 1, 2, 104, 51, 50, 171, 165, 167 and 168 for types i, iii, iv, v, vi, vii, viii and ix, respectively).

DESCRIPTION OF THE ANNEXES

[0186] The Annexes show the strategies used for the selection of primers and internal probes:

[0187] Annex I illustrates the strategy for the selection of primers from SCCmec and orfX sequences specific for SCCmec types I and II.

[0188] Annex II illustrates the strategy for the selection of specific molecular beacon probes for the real-time detection of SCCmec-orfX right extremity junctions.

[0189] As shown in these Annexes, the selected amplification primers may contain inosines and/or base ambiguities. 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 degeneracies in the amplification primers allows 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, N.Y.).

EXAMPLES

Example 1

[0190] Primers Developed by Hiramatsu et al. Can Only Detect MRSA Strains Belonging to MREP Types ii, and iii while Missing Prevalent Novel MREP Types.

[0191] As shown in FIG. 1, Hiramatsu et al. have developed various primers that can specifically hybridize to the right extremities of types I, II and III SCCmec DNAs. They combined these primers with primers specific to the S. aureus chromosome region located to the right of the SCCmec integration site for the detection of MRSA. The primer set (SEQ ID NOs.: 22, 24 and 28 in U.S. Pat. No. 6,156,507 corresponding to SEQ ID NOs.: 56, 58 and 60 in the present invention) was shown by Hiramatsu et al. to be the most specific and ubiquitous for detection of MRSA. This set of primers gives amplification products of 1.5 kb for SCCmec type I, 1.6 kb for SCCmec type II and 1.0 kb for SCCmec type III (Table 7). The ubiquity and specificity of this multiplex PCR assay was tested on 39 MRSA strains, 41 MSSA strains, 9 MRCNS strains and 11 MSCNS strains (Table 2). One .mu.L of a treated standardized bacterial suspension or of a bacterial genomic DNA preparation purified from bacteria were amplified in a 20 .mu.l PCR reaction mixture. Each PCR reaction contained 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl.sub.2, 0.4 .mu.M of each of the SCCmec- and orfX-specific primers (SEQ ID NOs.: 56, 58 and 60), 200 .mu.M of each of the four dNTPs (Pharmacia Biotech), 3.3 .mu.g/.mu.l of BSA (Sigma), and 0.5 U Taq polymerase (Promega) coupled with TaqStart.TM. Antibody (BD Biosciences).

[0192] PCR reactions were then subjected to thermal cycling: 3 min at 94.degree. C. followed by 40 cycles of 60 seconds at 95.degree. C. for the denaturation step, 60 seconds at 55.degree. C. for the annealing step, and 60 seconds at 72.degree. C. for the extension step, then followed by a terminal extension of 7 minutes at 72.degree. C. using a standard thermocycler (PTC-200 from MJ Research Inc.). Detection of the PCR products was made by electrophoresis in agarose gels (2%) containing 0.25 .mu.g/ml of ethidium bromide.

[0193] None of the MRCNS or MSCNS strains tested were detected with the set of primers detecting SCCmec types I, II and III. Twenty of the 39 MRSA strains tested were not detected with this multiplex PCR assay (Tables 2 and 3). One of these undetected MRSA strains corresponds to the highly epidemic MRSA Portuguese clone (strain CCRI-9504; De Lencastre et al., 1994. Eur. J. Clin. Microbiol. Infect. Dis. 13:64-73) and another corresponds to the highly epidemic MRSA Canadian clone CMRSA1 (strain CCRI-9589; Simor et al. CCDR 1999, 25-12, June 15). These data demonstrate that the primer set developed by Hiramatsu et al. (SEQ ID NOs.: 22, 24 and 28 in U.S. Pat. No. 6,156,507 corresponding to SEQ ID NOs.: 56, 58 and 60 in the present invention) is not ubiquitous for the detection of MRSA and suggest that some MRSA strains have sequences at the SCCmec right extremity junction which are different from those identified by Hiramatsu et al. other types of SCCmec sequences or other sequences at the right extremity of SCCmec (MREP type) are found in MRSA. A limitation of this assay is the non-specific detection of 13 MSSA strains (Table 2).

Example 2

Detection and Identification of MRSA Using Primers Specific to MREP Types i, ii and iii Sequences Developed in the Present Invention.

[0194] Based on analysis of multiple sequence alignments of orfX and SCCmec sequences described by Hiramatsu et al. or available from GenBank, a set of primers (SEQ ID NOs: 64, 66, 67) capable of amplifying short segments of types I, II and III of SCCmec-orfX right extremity junctions from MRSA strains and discriminating from MRCNS (Annex I and FIG. 2) were designed. The chosen set of primers gives amplification products of 176 bp for SCCmec type I, 278 pb for SCCmec type II and 223 bp for SCCmec type III and allows rapid PCR amplification. These primers were used in multiplex PCR to test their ubiquity and specificity using 208 MRSA strains, 252 MSSA strains, 41 MRCNS strains and 21 MRCNS strains (Table 12). The PCR amplification and detection was performed as described in Example 1. PCR reactions were then subjected to thermal cycling (3 minutes at 94.degree. C. followed by 30 or 40 cycles of 1 second at 95.degree. C. for the denaturation step and 30 seconds at 60.degree. C. for the annealing-extension step, and then followed by a terminal extension of 2 minutes at 72.degree. C.) using a standard thermocycler (PTC-200 from MJ Research Inc.). Detection of the PCR products was made as described in Examplel.

[0195] None of the MRCNS or MSCNS strains tested were detected with this set of primers (Table 12). However, the twenty MRSA strains which were not detected with the primer set developed by Hiramatsu et al. (SEQ ID NOs: 56, 58 and 60) were also not detected with the primers developed in the present invention (Tables 3 and 12). These data also demonstrate that some MRSA strains have sequences at the SCCmec-chromosome right extremity junction which are different from those identified by Hiramatsu et al. Again, as observed with the Hiramatsu primers, 13 MSSA strains were also detected non-specifically (Table 12). The clinical significance of this finding remains to be established since these apparent MSSA strains could be the result of a recent deletion in the mec locus (Deplano et al., 2000, J. Antimicrob. Chemotherapy, 46:617-619; Inglis et al., 1990, J. Gen. Microbiol., 136:2231-2239; Inglis et al., 1993, J. Infect. Dis., 167:323-328; Lawrence et al. 1996, J. Hosp. Infect., 33:49-53; Wada et al., 1991, Biochem. Biophys. Res. Comm., 176:1319-1326).

Example 3

[0196] Development of a Multiplex PCR Assay on a Standard Thermocycler for Detection and Identification of MRSA Based on MREP Types i, ii, iii, iv and v Sequences.

[0197] Upon analysis of two of the new MREP types iv and v sequence data described in the present invention, two new primers (SEQ ID NOs.: 79 and 80) were designed and used in multiplex with the three primers SEQ ID NOs.: 64, 66 and 67 described in Example 2. PCR amplification and detection of the PCR products was performed as described in Example 2. Sensitivity tests performed by using ten-fold or two-fold dilutions of purified genomic DNA from various MRSA strains of each MREP type showed a detection limit of 5 to 10 genome copies (Table 16). Specificity tests were performed using 0.1 ng of purified genomic DNA or 1 .mu.l of a standardized bacterial suspension. All MRCNS or MSCNS strains tested were negative with this multiplex assay (Table 17). Twelve of the 20 MRSA strains which were not detected with the multiplex PCR described in Examples 1 and 2 were now detected with this multiplex assay. Again, as observed with the Hiramatsu primers, 13 MSSA strains were also detected non-specifically (Table 12). The eight MRSA strains (CCRI-9208, CCRI-9583, CCRI-9773, CCRI-9774, CCRI-9589, CCRI-9860, CCRI-9681, CCRI-9770) and which harbor the new MREP types vi, vii, viii, ix and x sequences described in the present invention remained undetectable.

Example 4

[0198] Development of a Real-Time Multiplex PCR Assay on the SMART CYCLER.RTM. for Detection and Identification of MRSA Based on MREP Types i, ii, iii, iv and v Sequences.

[0199] The multiplex PCR assay described in Example 3 containing primers (SEQ ID NOs.: 64, 66, 67, 79 and 80) was adapted to the SMART CYCLER.RTM. platform (Cepheid). A molecular beacon probe specific to the orfX sequence was developed (SEQ ID NO. 84, see Annex II). Each PCR reaction contained 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 3.5 mM MgCl.sub.2, 0.4 .mu.M of each of the SCCmec- and orfX-specific primers (SEQ ID NOs.: 64, 66, 67, 79 and 80), 0.2 .mu.M of the FAM-labeled molecular beacon probe (SEQ ID NO.: 84), 200 .mu.M of each of the four dNTPs, 3.3 .mu.g/.mu.l of BSA, and 0.5 U Taq polymerase coupled with TaqStart.TM. Antibody. The PCR amplification on the SMART CYCLER.RTM. was performed as follows: 3 min. at 94.degree. C. for initial denaturation, then forty-five cycles of three steps consisting of 5 seconds at 95.degree. C. for the denaturation step, 15 seconds at 59.degree. C. for the annealing step and 10 seconds at 72.degree. C. for the extension step. Fluorescence detection was performed at the end of each annealing step. Sensitivity tests performed by using purified genomic DNA from several MRSA strains of each MREP type showed a detection limit of 2 to 10 genome copies (Table 18). None of the MRCNS or MSCNS were positive with this multiplex assay (Table 19). Again, as observed with the Hiramatsu primers, 13 MSSA strains were also detected non-specifically. Twelve of the twenty MRSA strains which were not detected with the multiplex PCR described in Examples 1 and 2 were detected by this multiplex assay. As described in Example 3, the eight MRSA strains which harbor the new MREP types vi, vii, viii, ix and x sequences described in the present invention remained undetectable.

Example 5

[0200] Development of a Real-Time Multiplex PCR Assay on the SMART CYLCER.RTM. for Detection and Identification of MRSA Based on MREP Types i, ii, iii, iv and v Sequences Including an Internal Control.

[0201] The multiplex PCR assay described in Example 4 containing primers specific to MREP types i to v and orfX of S. aureus (SEQ ID NOs.: 64, 66, 67, 79 and 80) and a molecular beacon probe specific to the orfX sequence (SEQ ID NO. 84, see Annex II) was optimized to include an internal control to monitor PCR inhibition. This internal control contains sequences complementary to MREP type iv- and orfX-specific primers (SEQ ID NOs. 79 and 64). The assay also contains a TET-labeled molecular beacon probe specific to sequence within the amplicon generated by amplification of the internal control. Each PCR reaction contained 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 3.45 mM MgCl.sub.2, 0.8 .mu.M of each of the MREP-specific primers (SEQ ID NOs.: 66 and 67) and orfX-specific primer (SEQ ID NO.: 64), 0.4 .mu.M of each of the MREP-specific primers (SEQ ID NOs.: 79 and 80), 80 copies of the internal control, 0.2 .mu.M of the TET-labeled molecular beacon probe specific to the internal control, 0.2 .mu.M of the FAM-labeled molecular beacon probe (SEQ ID NO.: 84), 330 .mu.M of each of the four dNTPs (Pharmacia Biotech), 3.45 .mu.g/.mu.l of BSA (Sigma), and 0.875 U Taq polymerase (Promega) coupled with TaqStart.TM. Antibody (BD Biosciences). The PCR amplification on the SMART CYCLER.RTM. was performed as follows: 3 min. at 95.degree. C. for initial denaturation, then forty-eight cycles of three steps consisting of 5 seconds at 95.degree. C. for the denaturation step, 15 seconds at 60.degree. C. for the annealing step and 15 seconds at 72.degree. C. for the extension step. Sensitivity tests performed by using purified genomic DNA from one MRSA strain of each MREP type (i to v) showed a detection limit of 2 to 10 genome copies. None of the 26 MRCNS or 10 MSCNS were positive with this multiplex assay. Again, as observed with the Hiramatsu primers, 13 MSSA strains were also detected non-specifically. As described in Examples 3 and 4, the eight MRSA strains which harbor the new MREP types vi to x sequences described in the present invention remained undetectable.

Example 6

[0202] Detection of MRSA Using the Real-Time Multiplex Assay on the SMART CYLCER.RTM. Based on MREP Types i, ii, iii, iv and v Sequences Directly from Clinical Specimens.

[0203] The assay described in Example 5 was adapted for detection directly from clinical specimens. A total of 142 nasal swabs collected during a MRSA hospital surveillance program at the Montreal General Hospital (Montreal, Quebec, Canada) were tested. The swab samples were tested at the Centre de Recherche en Infectiologie de l'Universite Laval within 24 hours of collection. Upon receipt, the swabs were plated onto mannitol agar and then the nasal material from the same swab was prepared with a simple and rapid specimen preparation protocol described in co-pending patent application No. U.S. 60/306,163. Classical identification of MRSA was performed by standard culture methods.

[0204] The PCR assay described in Example 5 detected 33 of the 34 samples positive for MRSA based on the culture method. As compared to culture, the PCR assay detected 8 additional MRSA positive specimens for a sensitivity of 97.1% and a specificity of 92.6%. This multiplex PCR assay represents a rapid and powerful method for the specific detection of MRSA carriers directly from nasal specimens and can be used with any type of clinical specimens such as wounds, blood or blood culture, CSF, etc.

Example 7

[0205] Development of a Real-Time Multiplex PCR Assay on the SMART CYCLER.RTM. for Detection and Identification of MRSA Based on MREP Types i, ii, iii, iv, v and vii Sequences.

[0206] Upon analysis of the new MREP type vii sequence data described in the present invention (SEQ ID NOs.:165 and 166), two new primers (SEQ ID NOs.: 112 and 113) were designed and tested in multiplex with the three primers SEQ ID NOs.: 64, 66 and 67 described in Example 2. Primer SEQ ID NO.: 112 was selected for use in the multiplex based on its sensitivity. Three molecular beacon probes specific to the orfX sequence which allowed detection of two sequence polymorphisms identified in this region of the orfX sequence, based on analysis of SEQ ID NOs.: 173-186, were also used in the multiplex (SEQ ID NOs.: 84, 163 and 164). Each PCR reaction contained 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 3.45 mM MgCl.sub.2, 0.8 .mu.M of each of the SCCmec-specific primers (SEQ ID NOs.: 66 and 67) and orfX-specific primer (SEQ ID NO.: 64), 0.4 .mu.M of each of the SCCmec-specific primers (SEQ ID NOs.: 79 and 80), 0.2 .mu.M of the FAM-labeled molecular beacon probe (SEQ ID NO.: 84), 330 .mu.M of each of the four dNTPs (Pharmacia Biotech), 3.45 .mu.g/.mu.l of BSA (Sigma), and 0.875 U of Taq polymerase (Promega) coupled with TaqStart.TM. Antibody (BD Biosciences). The PCR amplification on the SMART CYCLER.RTM. was performed as follows: 3 min. at 95.degree. C. for initial denaturation, then forty-eight cycles of three steps consisting of 5 seconds at 95.degree. C. for the denaturation step, 15 seconds at 60.degree. C. for the annealing step and 15 seconds at 72.degree. C. for the extension step. The detection of fluorescence was done at the end of each annealing step. Sensitivity tests performed by using purified genomic DNA from several MRSA strains of each MREP type showed a detection limit of 2 genome copies (Table 20). None of the 26 MRCNS or 8 MSCNS were positive with this multiplex assay. Again, as observed with the Hiramatsu primers, 13 MSSA strains were also detected non-specifically (Table 21). Four of the strains which were not detected with the multiplex assay for the detection of MREP types i to v were now detected with this multiplex assay while the four MRSA strains (CCRI-9208, CCRI-9770, CCRI-9681, CCRI-9860) which harbor the MREP types vi, viii, ix and x described in the present invention remained undetectable.

Example 8

[0207] Development of Real-Time PCR Assays on the SMART CYCLER.RTM. for Detection and Identification of MRSA Based on MREP Types vi, viii, ix.

[0208] Upon analysis of the new MREP types vi, viii and ix sequence data described in the present invention, one new primers specific to MREP type vi (SEQ ID NO.: 201), one primer specific to MREP type viii (SEQ ID NO.: 115), a primer specific to MREP type ix (SEQ ID NO.: 109) and a primer specific to both MREP types viii and ix (SEQ ID NO.: 116) were designed. Each PCR primer was used in combination with the orfX-specific primer (SEQ ID NO.: 64) and tested against its specific target strain. Each PCR reaction contained 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 3.45 mM MgCl.sub.2, 0.4 .mu.M of each of the SCCmec- and orfX-specific primers, 200 .mu.M of each of the four dNTPs, 3.4 .mu.g/.mu.l of BSA, and 0.875 U Taq polymerase coupled with TaqStart.TM. Antibody. The PCR amplification was performed as described en Example 7. Sensitivity tests performed by using genomic DNA purified from their respective MRSA target strains showed that the best primer pair combination was SEQ ID NOs.: 64 and 115 for the detection of MREP types viii and ix simultaneously. These new SCCmec-specific primers may be used in multiplex with primers specific to MREP types i, ii, ii, iv, v and vii (SEQ ID NOs.: 64, 66, 67, 79 and 80) described in previous examples to provide a more ubiquitous MRSA assay.

[0209] In conclusion, we have improved the ubiquity of detection of MRSA strains. New MREJ types iv to x have been identified. Amongst strains representative of these new types, Hiramitsu's primers and/or probes succeeded in detecting less than 50% thereof. We have therefore amply passed the bar of at least 50% ubiquity, since our primers and probes were designed to detect 100% of the strains tested as representatives of MREJ types iv to ix. Therefore, although ubiquity depends on the pool of strains and representatives that are under analysis, we know now that close to 100% ubiquity is an attainable goal, when using the sequences of the right junctions (MREJ) to derive probes and primers dealing with polymorphism in this region. Depending on how many unknown types of MREJ exist, we have a margin of maneuver going from 50% (higher than Hiramatsu's primers for the tested strains) to 100% if we sequence all the existing MREJs to derive properly the present diagnostic tools and methods, following the above teachings.

[0210] 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-US-00001 TABLE 1 PCR amplification primers reported by Hiramatsu et al. in U.S. Pat. No. 6,156,507 found in the sequence listing SEQ ID NO.: SEQ ID NO.: (present (U.S. Pat. No. invention) Target Position.sup.a,b 6,156,507) 52 MREP types i and ii 480 18 53 MREP types i and ii 758 19 54 MREP types i and ii 927 20 55 MREP types i and ii 1154 21 56 MREP types i and ii 1755 22 57 MREP types i and ii 2302 23 58 MREP type iii .sup. 295.sup.c 24 59 orfX 1664 25 60 orfSA0022.sup.d 3267 28 61 orfSA0022.sup.d 3585 27 62 orfX 1389 26 63 orfSA0022.sup.d 2957 29 .sup.aPosition refers to nucleotide position of the 5' end of primer. .sup.bNumbering for SEQ ID NOs.: 52-57 refers to SEQ ID NO.: 2; numbering for SEQ ID NO.: 58 refers to SEQ ID NO.: 4; numbering for SEQ ID NOs.: 59-63 refers to SEQ ID NO.: 3. .sup.cPrimer is reverse-complement of target sequence. .sup.dorfSA0022 refers to the open reading frame designation from GenBank accession number AP003129 (SEQ ID NO.: 231).

TABLE-US-00002 TABLE 2 Specificity and ubiquity tests performed on a standard thermocycler using the optimal set of primers described by Hiramatsu et al. (SEQ ID NOs.: 22, 24 and 28 in U.S. Pat. No. 6,156,507 corresponding to SEQ ID NOs.: 56, 58 and 60, respectively, in the present invention) for the detection of MRSA PCR results for SCCmec - orfX right extremity junction Strains Positive (%) Negative (%) MRSA - 39 strains 19 (48.7) 20 (51.2) MSSA - 41 strains 13 (31.7) 28 (68.3) MRCNS - 9 strains* 0 (0%) 9 (100%) MSCNS - 11 strains* 0 (0%) 11 (100%) *Details regarding CNS strains: MRCNS: S. caprae (1) S. cohni cohnii (1) S. epidermidis (1) S. haemolyticus (2) S. hominis (1) S. sciuri (1) S. simulans (1) S. warneri (1) MSCNS: S. cohni cohnii (1) S. epidermidis (1) S. equorum (1) S. gallinarum (1) S. haemolyticus (1) S. lentus (1) S. lugdunensis (1) S. saccharolyticus (1) S. saprophyticus (2) S. xylosus (1)

TABLE-US-00003 TABLE 3 Origin of MRSA strains not amplifiable using primers developed by Hiramatsu et al. (SEQ ID NOs.: 22, 24 and 28 in U.S. Pat. No. 6,156,507 corresponding to SEQ ID NOs.: 56, 58 and 60, respectively, in the present invention) as well as primers developed in the present invention targeting MREP types i, ii and iii (SEQ ID NOs.: 64, 66 and 67) Staphylococcus aureus strain designation: Original CCRI.sup.a Origin ATCC BAA-40.sup.b CCRI-9504 Portugal ATCC 33592 CCRI-178 USA R991282 CCRI-2025 Quebec, Canada 4508 CCRI-9208 Quebec, Canada 19121 CCRI-8895 Denmark Z109 CCRI-8903 Denmark 45302 CCRI-1263 Ontario, Canada R655 CCRI-1324 Quebec, Canada MA 50428 CCRI-1311 Quebec, Canada MA 50609 CCRI-1312 Quebec, Canada MA 51363 CCRI-1331 Quebec, Canada MA 51561 CCRI-1325 Quebec, Canada 14A0116 CCR1-9681 Poland 23 (CCUG 41787) CCRI-9860 Sweden SE26-1 CCRI-9770 Ontario, Canada SE1-1 CCRI-9583 Ontario, Canada ID-61880.sup.c CCRI-9589 Ontario, Canada SE47-1 CCRI-9773 Ontario, Canada SE49-1 CCRI-9774 Ontario, Canada 39795-2 CCRI-1377 Quebec, Canada .sup.aCCRI stands for "Collection of the Centre de Recherche en Infectiologie". .sup.bPortuguese clone. .sup.cCanadian clone EMRSA1.

TABLE-US-00004 TABLE 4 Staphylococcus aureus MREJ nucleotide sequences revealed in the present invention Staphylococcus aureus SEQ strain designation: ID NO. Original CCRI.sup.a Genetic Target 27 R991282 CCRI-2025 mecA 28 45302 CCRI-1263 mecA 29 MA 50428 CCRI-1311 mecA 30 MA 51363 CCRI-1331 mecA 31 39795-2 CCRI-1377 mecA and 1.5 kb of downstream region 42 ATCC 33592 CCRI-178 MREP type iv 43 19121 CCRI-8895 MREP type iv 44 Z109 CCRI-8903 MREP type iv 45 R655 CCRI-1324 MREP type iv 46 MA 51363 CCRI-1331 MREP type iv 47 45302 CCRI-1263 MREP type v 48 39795-2 CCRI-1377 MREP type v 49 MA 50428 CCRI-1311 MREP type v 50 R991282 CCRI-2025 MREP type v 51 ATCC BAA-40 CCRI-9504 MREP type iv 165 SE1-1 CCRI-9583 MREP type vii 166 ID-61880 CCRI-9589 MREP type vii 167 23 (CCUG 41787) CCRI-9860 MREP type viii 168 14A016 CCRI-9681 MREP type ix 171 4508 CCRI-9208 MREP type vi 172 SE26-1 CCRI-9770 orfSA0021.sup.b and 75 bp of orfSA0022.sup.b 173 26 (98/10618) CCRI-9864 MREP type ii 174 27 (98/26821) CCRI-9865 MREP type ii 175 28 (24344) CCRI-9866 MREP type ii 176 12 (62305) CCRI-9867 MREP type ii 177 22 (90/14719) CCRI-9868 MREP type ii 178 23 (98/14719) CCRI-9869 MREP type ii 179 32 (97S99) CCRI-9871 MREP type ii 180 33 (97S100) CCRI-9872 MREP type ii 181 38 (825/96) CCRI-9873 MREP type ii 182 39 (842/96) CCRI-9874 MREP type ii 183 43 (N8-892/99) CCRI-9875 MREP type ii 184 46 (9805-0137) CCRI-9876 MREP type iii 185 1 CCRI-9882 MREP type ii 186 29 CCRI-9885 MREP type ii 189 SE1-1 CCRI-9583 mecA and 2.2 kb of downstream region, including IS431mec 190 ATCC BAA-40 CCRI-9504 mecA and 1.5 kb of downstream region 191 4508 CCRI-9208 mecA and 0.9 kb of downstream region 192 ID-61880 CCRI-9589 mecA and 0.9 kb of downstream region 193 14A016 CCRI-9681 mecA and 0.9 kb of downstream region 195 SE26-1 CCRI-9770 mecA and 1.5 kb of downstream region, including IS431mec 197 ATCC 43300 CCRI-175 MREP type ii 198 R522 CCRI-1262 MREP type iii 199 13370 CCRI-8894 MREP type i 219 ATCC BAA-40 CCRI-9504 tetK Staphylococcus aureus SEQ strain designation: ID NO. Original CCRI.sup.b Genetic Target.sup.a 220 MA 51363 CCRI-1331 mecA and 1.5 kb of downstream region 221 39795-2 CCRI-1377 IS431mec and 0.6 kb of upstream region 222 R991282 CCRI-2025 mecA and 1.5 kb of downstream region 223 R991282 CCRI-2025 IS431mec and 0.6 kb of upstream region 224 23 (CCUG 41787) CCRI-9860 mecA and 1.5 kb of downstream region 225 23 (CCUG 41787) CCRI-9860 IS431mec and 0.6 kb of upstream region 233 14A016 CCRI-9681 MREP type ix .sup.aCCRI stands for "Collection of the Centre de Recherche en Infectiologie". .sup.borfSA0021 and orfSA0022 refer to the open reading frame designation from GenBank accession number AP003129 (SEQ ID NO.: 231).

TABLE-US-00005 TABLE 5 PCR primers developed in the present invention Originating DNA SEQ SEQ ID NO. Target Position.sup.a ID NO. 64 orfX 1720 3 70 orfX 1796 3 71 orfX 1712 3 72 orfX 1749 3 73 orfX 1758 3 74 orfX 1794 3 75 orfX 1797 3 76 orfX 1798 3 66 MREP types i and ii 2327 2 100 MREP types i and ii 2323 2 101 MREP types i and ii 2314 2 97 MREP type ii 2434 2 99 MREP type ii 2434 2 67 MREP type iii .sup. 207.sup.b 4 98 MREP type iii .sup. 147.sup.b 4 102 MREP type iii .sup. 251.sup.b 4 79 MREP type iv .sup. 74.sup.b 43 80 MREP type v .sup. 50.sup.b 47 109 MREP type ix .sup. 652.sup.b 168 204 MREP type vi .sup. 642.sup.b 171 112 MREP type vii .sup. 503.sup.b 165 113 MREP type vii .sup. 551.sup.b 165 115 MREP type viii .sup. 514.sup.b 167 116 MREP type viii .sup. 601.sup.b 167 .sup.aPosition refers to nucleotide position of 5' end of primer. .sup.bPrimer is reverse-complement of target sequence.

TABLE-US-00006 TABLE 6 Molecular beacon probes developed in the present invention SEQ ID NO. Target Position 32 orfX 86.sup.a.sup. 83 orfX 86.sup.a.sup. 84 orfX 34.sup.a, b 160 orfX 55.sup.a, b 161 orfX 34.sup.a, b 162 orfX 114.sup.a.sup. 163 orfX 34.sup.a, b 164 orfX 34.sup.a, b .sup.aPosition refers to nucleotide position of the 5' end of the molecular beacon's loop on SEQ ID NO.: 3. .sup.bSequence of molecular beacon's loop is reverse-complement of SEQ ID NO.: 3.

TABLE-US-00007 TABLE 7 Length of amplicons obtained with the different primer pairs which are objects of the present invention SEQ ID NO. Target.sup.d Amplicon length.sup.a 59/52.sup.b orfX/MREP type i and ii 2079 (type i); 2181 (type ii) 59/53.sup.b orfX/MREP type i and ii 1801 (type i); 1903 (type ii) 59/54.sup.b orfX/MREP type i and ii 1632 (type i); 1734 (type ii) 59/55.sup.b orfX/MREP type i and ii 1405 (type i); 1507 (type ii) 59/56.sup.b orfX/MREP type i and ii 804 (type i); 906 (type ii) 59/57.sup.b orfX/MREP type i and ii 257 (type i); 359 (type ii) 60/52.sup.b orfSA0022/MREP type i and ii 2794 (type i); 2896 (type ii) 60/53.sup.b orfSA0022/MREP type i and ii 2516 (type i); 2618 (type ii) 60/54.sup.b orfSA0022/MREP type i and ii 2347 (type i); 2449 (type ii) 60/55.sup.b orfSA0022/MREP type i and ii 2120 (type i); 2222 (type ii) 60/56.sup.b orfSA0022/MREP type i and ii 1519 (type i); 1621 (type ii) 60/57.sup.b orfSA0022/MREP type i and ii 972 (type i); 1074 (type ii) 61/52.sup.b orfSA0022/MREP type i and ii 2476 (type i); 2578 (type ii) 61/53.sup.b orfSA0022/MREP type i and ii 2198 (type i); 2300 (type ii) 61/54.sup.b orfSA0022/MREP type i and ii 2029 (type i); 2131 (type ii) 61/55.sup.b orfSA0022/MREP type i and ii 1802 (type i); 1904 (type ii) 61/56.sup.b orfSA0022/MREP type i and ii 1201 (type i); 1303 (type ii) 61/57.sup.b orfSA0022/MREP type i and ii 654 (type i); 756 (type ii) 62/52.sup.b orfX/MREP type i and ii 2354 (type i); 2456 (type ii) 62/53.sup.b orfX/MREP type i and ii 2076 (type i); 2178 (type ii) 62/54.sup.b orfX/MREP type i and ii 1907 (type i); 2009 (type ii) 62/55.sup.b orfX/MREP type i and ii 1680 (type i); 1782 (type ii) 62/56.sup.b orfX/MREP type i and ii 1079 (type i); 1181 (type ii) 62/57.sup.b orfX/MREP type i and ii 532 (type i); 634 (type ii) 63/52.sup.b orfSA0022/MREP type i and ii 3104 (type i); 3206 (type ii) 63/53.sup.b orfSA0022/MREP type i and ii 2826 (type i); 2928 (type ii) 63/54.sup.b orfSA0022/MREP type i and ii 2657 (type i); 2759 (type ii) 63/55.sup.b orfSA0022/MREP type i and ii 2430 (type i); 2532 (type ii) 63/56.sup.b orfSA0022/MREP type i and ii 1829 (type i); 1931 (type ii) 63/57.sup.b orfSA0022/MREP type i and ii 1282 (type i); 1384 (type ii) 59/58.sup.b orfX/MREP type iii 361 60/58.sup.b orfSA0022/MREP type iii 1076 61/58.sup.b orfSA0022/MREP type iii 758 62/58.sup.b orfX/MREP type iii 656 63/58.sup.b orfSA0022/MREP type iii 1386 70/66.sup. orfX/MREP type i and ii 100 (type i); 202 (type ii) 70/67.sup. orfX/MREP type iii 147 (type iii) 64/66.sup.c orfX/MREP type i and ii 176 (type i); 278 (type ii) 64/67.sup.c orfX/MREP type iii 223 64/79.sup.c orfX/MREP type iv 215 64/80.sup.c orfX/MREP type v 196 64/97.sup.c orfX/MREP type ii 171 64/98.sup.c orfX/MREP type iii 163 64/99.sup.c orfX/MREP type ii 171 64/100.sup.c orfX/MREP types i and ii 180 (type i); 282 (type ii) 64/101.sup.c orfX/MREP types i and ii 189 (type i); 291 (type ii) 64/102.sup.c orfX/MREP type iii 263 64/109.sup.c orfX/MREP type ix 369 64/204.sup.c orfX/MREP type vi 348 64/112.sup.c orfX/MREP type vii 214 64/113.sup.c orfX/MREP type vii 263 64/115.sup.c orfX/MREP type viii 227 64/116.sup.c orfX/MREP type viii 318 .sup.aAmplicon length is given in base pairs for MREP types amplified by the set of primers. .sup.bSet of primers described by Hiramatsu et al. in U.S. Pat. No. 6,156,507. .sup.cSet of primers developed in the present invention. .sup.dorfSA0022 refers to the open reading frame designation from GenBank accession number AP003129 (SEQ ID NO.: 231).

TABLE-US-00008 TABLE 8 Other primers developed in the present invention Originating DNA SEQ SEQ ID NO. Target Position.sup.a ID NO. 77 MREP type iv 993 43 65 MREP type v 636 47 70 orfX 1796 3 68 IS431 626 92 69 mecA 1059 78 96 mecA 1949 78 81 mecA 1206 78 114 MREP type vii .sup. 629.sup.b 165 117 MREP type ii 856 194 118 MREP type ii .sup. 974.sup.b 194 119 MREP type vii 404 189 120 MREP type vii .sup. 477.sup.b 189 123 MREP type vii 551 165 124 MREP type ii 584 170 125 MREP type ii .sup. 689.sup.b 170 126 orfSA0021 336 231 127 orfSA0021 563 231 128 orfSA0022.sup.d 2993 231 129 orfSA0022.sup.d 3467.sup.b.sup. 231 132 orfX 3700 231 145 MREP type iv 988 51 146 MREP type v 1386 51 147 MREP type iv .sup. 891.sup.b 51 148 MREP type ix 664 168 149 MREP type ix .sup. 849.sup.b 168 150 MREP type vii 1117.sup.b.sup. 165 151 MREP type vii 1473 189 152 IS431mec 1592.sup.b.sup. 189 154 MREP type v .sup. 996.sup.b 50 155 MREP type v 935 50 156 tetK from plasmid pT181 1169.sup.b.sup. 228 157 tetK from plasmid pT181 136 228 158 orfX 2714.sup.b.sup. 2 159 orfX 2539 2 187 MREP type viii .sup. 967.sup.b 167 188 MREP type viii 851 167 .sup.aPosition refers to nucleotide position of the 5' end of primer. .sup.bPrimer is reverse-complement of target sequence.

TABLE-US-00009 TABLE 9 Amplification and/or sequencing primers developed in the present invention Originating DNA SEQ SEQ ID NO. Target Position.sup.a ID NO. 85 S. aureus chromosome .sup. 197.sup.b 35 86 S. aureus chromosome .sup. 198.sup.b 37 87 S. aureus chromosome .sup. 197.sup.b 38 88 S. aureus chromosome 1265.sup.b.sup. 39 89 S. aureus chromosome 1892 3 103 orfX 1386 3 105 MREP type i 2335 2 106 MREP type ii 2437 2 107 MREP type iii .sup. 153.sup.b 4 108 MREP type iii .sup. 153.sup.b 4 121 MREP type vii 1150 165 122 MREP type vii 1241.sup.b.sup. 165 130 orfX 4029.sup.b.sup. 231 131 region between orfSA0022 3588 231 and orfSA0023.sup.d 133 merB from plasmid pI258 262 226 134 merB from plasmid pI258 .sup. 539.sup.b 226 135 merR from plasmid pI258 564 226 136 merR from plasmid pI258 444 227 137 merR from plasmid pI258 529 227 138 merR from plasmid pI258 .sup. 530.sup.b 227 139 rep from plasmid pUB110 796 230 140 rep from plasmid pUB110 .sup. 761.sup.b 230 141 rep from plasmid pUB110 600 230 142 aadD from plasmid pUB110 1320.sup.b.sup. 229 143 aadD from plasmid pUB110 759 229 144 aadD from plasmid pUB110 646 229 153 MREP type vii 1030 165 200 orfSA0022.sup.d .sup. 871.sup.c 231 201 orfSA0022.sup.d 1006 231 202 MREP type vi 648 171 203 MREP type vi .sup. 883.sup.b 171 205 MREP type ix 1180 168 206 MREP type ix 1311.sup.b.sup. 233 207 MREP type viii 1337 167 208 MREP type viii 1441.sup.b.sup. 167 209 ccrA 184 232 210 ccrA 385 232 211 ccrA .sup. 643.sup.b 232 212 ccrA 1282.sup.b.sup. 232 213 ccrB 1388 232 214 ccrB 1601 232 215 ccrB 2139.sup.b.sup. 232 216 ccrB 2199.sup.b.sup. 232 217 ccrB 2847.sup.b.sup. 232 218 ccrB 2946.sup.b.sup. 232 .sup.aPosition refers to nucleotide position of the 5' end of primer. .sup.bPrimer is reverse-complement of target sequence. .sup.cPrimer contains two mismatches. .sup.dorfSA0022 and orfSA0023 refer to the open reading frame designation from GenBank accession number AP003129 (SEQ ID NO.: 231).

TABLE-US-00010 TABLE 10 Origin of the nucleic acids and/or sequences available from public databases found in the sequence listing SEQ Staphylococcal Accession ID NO. strain Source number Genetic Target.sup.a, b 1 NCTC 10442 Database AB033763 SCCmec type I MREJ 2 N315 Database D86934 SCCmec type II MREJ 3 NCTC 8325 Database AB014440 MSSA chromosome 4 86/560 Database AB013471 SCCmec type III MREJ 5 86/961 Database AB013472 SCCmec type III MREJ 6 85/3907 Database AB013473 SCCmec type III MREJ 7 86/2652 Database AB013474 SCCmec type III MREJ 8 86/1340 Database AB013475 SCCmec type III MREJ 9 86/1762 Database AB013476 SCCmec type III MREJ 10 86/2082 Database AB013477 SCCmec type III MREJ 11 85/2111 Database AB013478 SCCmec type III MREJ 12 85/5495 Database AB013479 SCCmec type III MREJ 13 85/1836 Database AB013480 SCCmec type III MREJ 14 85/2147 Database AB013481 SCCmec type III MREJ 15 85/3619 Database AB013482 SCCmec type III MREJ 16 85/3566 Database AB013483 SCCmec type III MREJ 17 85/2232 Database AB014402 SCCmec type II MREJ 18 85/2235 Database AB014403 SCCmec type II MREJ 19 MR108 Database AB014404 SCCmec type II MREJ 20 85/9302 Database AB014430 SCCmec type I MREJ 21 85/9580 Database AB014431 SCCmec type I MREJ 22 85/1940 Database AB014432 SCCmec type I MREJ 23 85/6219 Database AB014433 SCCmec type I MREJ 24 64/4176 Database AB014434 SCCmec type I MREJ 25 64/3846 Database AB014435 SCCmec type I MREJ 26 HUC19 Database AF181950 SCCmec type II MREJ 33 G3 U.S. Pat. No. 6,156,507 SEQ ID NO.: 15 S. epidermidis SCCmec type II MREJ 34 SH 518 U.S. Pat. No. 6,156,507 SEQ ID NO.: 16 S. haemolyticus SCCmec type II MREJ 35 ATCC 25923 U.S. Pat. No. 6,156,507 SEQ ID NO.: 9 S. aureus chromosome 36 STP23 U.S. Pat. No. 6,156,507 SEQ ID NO.: 10 S. aureus chromosome 37 STP43 U.S. Pat. No. 6,156,507 SEQ ID NO.: 12 S. aureus chromosome 38 STP53 U.S. Pat. No. 6,156,507 SEQ ID NO.: 13 S. aureus chromosome 39 476 Genome project.sup.c S. aureus chromosome 40 252 Genome project.sup.c SCCmec type II MREJ 41 COL Genome project.sup.d SCCmec type I MREJ 78 NCTC 8325 Database X52593 mecA 82 NCTC 10442 Database AB033763 mecA 90 N315 Database D86934 mecA 91 85/2082 Database AB037671 mecA 92 NCTC 10442 Database AB033763 IS431 93 N315 Database D86934 IS431 94 HUC19 Database AF181950 IS431 95 NCTC 8325 Database X53818 IS431 104 85/2082 Database AB037671 SCCmec type III MREJ 226 unknown Database L29436 merB on plasmid pI258 227 unknown Database L29436 merR on plasmid pI258 228 unknown Database S67449 tetK on plasmid pT181 229 HUC19 Database AF181950 aadD on plasmid pUB110 230 HUC19 Database AF181950 rep on plasmid pUB110 231 N315 Database AP003129 orfSA0021, orfSA0022, orfSA0023 232 85/2082 Database AB037671 ccrA/ccrB .sup.aMREJ refers to mec right extremity junction and includes sequences from SCCmec-right extremity and chromosomal DNA to the right of SCCmec integration site. .sup.bUnless otherwise specified, all sequences were obtained from S. aureus strains. .sup.cSanger Institute genome project (http://www.sanger.ac.uk). .sup.dTIGR genome project (http://www.tigr.org).

TABLE-US-00011 TABLE 11 Analytical sensitivity of the MRSA-specific PCR assay targeting MREP types i, ii and iii on a standard thermocycler using the set of primers developed in the present invention (SEQ ID NOs.: 64, 66 and 67) Strain designation: Detection limit Original CCRI.sup.a (MREP type) (number of genome copies) 13370 CCRI-8894 (I) 5 ATCC 43300 CCRI-175 (II) 2 35290 CCRI-1262 (III) 2 .sup.aCCRI stands for "Collection of the Centre de Recherche en Infectiologie".

TABLE-US-00012 TABLE 12 Specificity and ubiquity tests performed on a standard thermocycler using the set of primers targeting MREP types i, ii and iii developed in the present invention (SEQ ID NOs.: 64, 66 and 67) for the detection of MRSA PCR results for MREJ Strains Positive (%) Negative (%) MRSA - 208 strains 188 (90.4) 20 (9.6) MSSA - 252 strains 13 (5.2) 239 (94.8) MRCNS - 41 strains* 0 42 (100) MSCNS - 21 strains* 0 21 (100) *Details regarding CNS strains: MRCNS: S. caprae (2) S. cohni cohnii (3) S. cohni urealyticum (4) S. epidermidis (8) S. haemolyticus (9) S. hominis (4) S. sciuri (4) S. sciuri sciuri (1) S. simulans (3) S. warneri (3) MSCNS: S. cohni cohnii (1) S. epidermidis (3) S. equorum (2) S. felis (1) S. gallinarum (1) S. haemolyticus (1) S. hominis (1) S. lentus (1) S. lugdunensis (1) S. saccharolyticus (1) S. saprophyticus (5) S. simulans (1) S. warneri (1) S. xylosus (1)

TABLE-US-00013 TABLE 13 Percentage of sequence identity for the first 500 nucleotides of SCCmec right extremities between all 9 types of MREP.sup.a,b MREP type i ii iii iv v vi vii viii ix i -- 79.2 42.8 42.8 41.2 44.4 44.6 42.3 42.1 ii 43.9 47.5 44.7 41.7 45.0 52.0 57.1 iii 46.8 44.5 42.9 45.0 42.8 45.2 iv 45.8 41.4 44.3 48.0 41.3 v 45.4 43.7 47.5 44.3 vi 45.1 41.1 47.2 vii 42.8 40.9 viii 55.2 ix -- .sup.a"First 500 nucleotides" refers to the 500 nucleotides within the SCCmec right extremity, starting from the integration site of SCCmec in the Staphylococcus aureus chromosome as shown on FIG. 4. .sup.bSequences were extracted from SEQ ID NOs.: 1, 2, 104, 51, 50, 171, 165, 167, and 168 for types i to ix, respectively.

TABLE-US-00014 TABLE 14 Reference strains used to test sensitivity and/or specificity and/or ubiquity of the MRSA-specific PCR assays targeting MREJ sequences Staphylococcal species Strains Source.sup.a MRSA (n = 45) 33591 ATCC 33592 ATCC 33593 ATCC BAA-38 ATCC BAA-39 ATCC BAA-40 ATCC BAA-41 ATCC BAA-42 ATCC BAA-43 ATCC BAA-44 ATCC F182 CDC 23 (CCUG 41787) HARMONY Collection ID-61880 (EMRSA1) LSPQ MA 8628 LSPQ MA 50558 LSPQ MA 50428 LSPQ MA 50609 LSPQ MA 50884 LSPQ MA 50892 LSPQ MA 50934 LSPQ MA 51015 LSPQ MA 51056 LSPQ MA 51085 LSPQ MA 51172 LSPQ MA 51222 LSPQ MA 51363 LSPQ MA 51561 LSPQ MA 52034 LSPQ MA 52306 LSPQ MA 51520 LSPQ MA 51363 LSPQ 98/10618 HARMONY Collection 98/26821 HARMONY Collection 24344 HARMONY Collection 62305 HARMONY Collection 90/10685 HARMONY Collection 98/14719 HARMONY Collection 97S99 HARMONY Collection 97S100 HARMONY Collection 825/96 HARMONY Collection 842/96 HARMONY Collection N8-890/99 HARMONY Collection 9805-01937 HARMONY Collection 1 Kreiswirth-1 29 Kreiswirth-1 MRCNS (n = 4) 29060 ATCC 35983 ATCC 35984 ATCC 2514 LSPQ MSSA (n = 28) MA 52263 LSPQ 6538 ATCC 13301 ATCC 25923 ATCC 27660 ATCC 29213 ATCC 29247 ATCC 29737 ATCC RN 11 CDC RN 3944 CDC RN 2442 CDC 7605060113 CDC BM 4611 Institut Pasteur BM 3093 Institut Pasteur 3511 LSPQ MA 5091 LSPQ MA 8849 LSPQ MA 8871 LSPQ MA 50607 LSPQ MA 50612 LSPQ MA 50848 LSPQ MA 51237 LSPQ MA 51351 LSPQ MA 52303 LSPQ MA 51828 LSPQ MA 51891 LSPQ MA 51504 LSPQ MA 52535 LSPQ MA 52783 LSPQ MSCNS (n = 17) 12228 ATCC 14953 ATCC 14990 ATCC 15305 ATCC 27836 ATCC 27848 ATCC 29070 ATCC 29970 ATCC 29974 ATCC 35539 ATCC 35552 ATCC 35844 ATCC 35982 ATCC 43809 ATCC 43867 ATCC 43958 ATCC 49168 ATCC .sup.aATCC stands for "American Type Culture Collection". LSPQ stands for "Laboratoire de Sante Publique du Quebec". CDC stands for "Center for Disease Control and Prevention".

TABLE-US-00015 TABLE 15 Clinical isolates used to test the sensitivity and/or specificity and/or ubiquity of the MRSA- specific PCR assays targeting MREJ sequences Staphylococcal Number of species strains Source MRSA (n = 177) 150 Canada 10 China 10 Denmark 9 Argentina 1 Egypt 1 Sweden 1 Poland 3 Japan 1 France MSSA (n = 224) 208 Canada 10 China 4 Japan 1 USA 1 Argentina MRCNS (n = 38) 32 Canada 3 China 1 France 1 Argentina 1 USA MSCNS (n = 17) 14 UK 3 Canada

TABLE-US-00016 TABLE 16 Analytical sensitivity of tests performed on a standard thermocycler using the set of primers targeting MREP types i, ii, iii, iv and v (SEQ ID NOs.: 64, 66, 67, 79 and 80) developed in the present invention for the detection and identification of MRSA Staphylococcus aureus strain designation: Detection limit Original CCRI.sup.a (MREP type) (number of genome copies) 13370 CCRI-8894 (i) 10 ATCC 43300 CCRI-175 (ii) 5 9191 CCRI-2086 (ii) 10 35290 CCRI-1262 (iii) 5 352 CCRI-1266 (iii) 10 19121 CCRI-8895 (iv) 5 ATCC 33592 CCRI-178 (iv) 5 MA 50428 CCRI-1311 (v) 5 R991282 CCRI-2025 (v) 5 .sup.aCCRI stands for "Collection of the Centre de Recherche en Infectiologie".

TABLE-US-00017 TABLE 17 Specificity and ubiquity tests performed on a standard thermocycler using the set of primers targeting MREP types i, ii, iii, iv and v (SEQ ID NO.: 64, 66, 67, 79 and 80) developed in the present invention for the detection and identification of MRSA PCR results for SCCmec - orfX right extremity junction Strains Positive (%) Negative (%) MRSA - 35 strains.sup.a 27 (77.1) 8 (22.9) MSSA - 44 strains 13 (29.5) 31 (70.5) MRCNS - 9 strains* 0 9 (100) MSCNS - 10 strains* 0 10 (100) .sup.aMRSA strains include the 20 strains listed in Table 3. *Details regarding CNS strains: MRCNS: S. caprae (1) S. cohni cohnii (1) S. epidermidis (1) S. haemolyticus (2) S. hominis (1) S. sciuri (1) S. simulans (1) S. warneri (1) MSCNS: S. cohni (1) S. epidermidis (1) S. equorum (1) S. haemolyticus (1) S. lentus (1) S. lugdunensis (1) S. saccharolyticus (1) S. saprophyticus (2) S. xylosus (1)

TABLE-US-00018 TABLE 18 Analytical sensitivity of tests performed on the SMART CYCLER .RTM. thermocycler using the set of primers targeting MREP types i, ii, iii, iv and v (SEQ ID NOs.: 64, 66, 67, 79 and 80) and molecular beacon probe (SEQ ID NO.: 84) developed in the present invention for the detection and identification of MRSA Staphylococcus aureus strain designation: Detection limit Original CCRI.sup.a (MREP type) (number of genome copies) 13370 CCRI-8894 (i) 2 ATCC 43300 CCRI-175 (ii) 2 9191 CCRI-2086 (ii) 10 35290 CCRI-1262 (iii) 2 352 CCRI-1266 (iii) 10 ATCC 33592 CCRI-178 (iv) 2 MA 51363 CCRI-1331 (iv) 5 19121 CCRI-8895 (iv) 10 Z109 CCRI-8903 (iv) 5 45302 CCRI-1263 (v) 10 MA 50428 CCRI-1311 (v) 5 MA 50609 CCRI-1312 (v) 5 MA 51651 CCRI-1325 (v) 10 39795-2 CCRI-1377 (v) 10 R991282 CCRI-2025 (v) 2 .sup.aCCRI stands for "Collection of the Centre de Recherche en Infectiologie".

TABLE-US-00019 TABLE 19 Specificity and ubiquity tests performed on the SMART CYCLER .RTM. thermocycler using the set of primers targeting MREP types i, ii, iii, iv and v (SEQ ID NO.: 64, 66, 67, 79 and 80) and molecular beacon probe (SEQ ID NO.: 84) developed in the present invention for the detection of MRSA PCR results for MREJ Strains Positive (%) Negative (%) MRSA - 29 strains.sup.a 21 (72.4) 8 (27.6) MSSA - 35 strains 13 (37.1) 22 (62.9) MRCNS - 14 strains 0 14 (100) MSCNS - 10 strains 0 10 (100) .sup.aMRSA strains include the 20 strains listed in Table 3. Details regarding CNS strains: MRCNS: S. epidermidis (1) S. haemolyticus (5) S. simulans (5) S. warneri (3) MSCNS: S. cohni cohnii (1) S. epidermidis (1) S. gallinarum (1) S. haemolyticus (1) S. lentus (1) S. lugdunensis (1) S. saccharolyticus (1) S. saprophyticus (2) S. xylosus (1)

TABLE-US-00020 TABLE 20 Analytical sensitivity of tests performed on the SMART CYCLER .RTM. thermocycler using the set of primers targeting MREP types i, ii, iii, iv, v and vii (SEQ ID NOs.: 64, 66, 67, 79 and 80) and molecular beacon probe (SEQ ID NO.: 84) developed in the present invention for the detection and identification of MRSA Staphylococcus aureus strain designation: Detection limit Original CCRI.sup.a (MREP type) (number of genome copies) 13370 CCRI-8894 (i) 2 ATCC 43300 CCRI-175 (ii) 2 35290 CCRI-1262 (iii) 2 ATCC 33592 CCRI-178 (iv) 2 R991282 CCRI-2025 (v) 2 SE-41-1 CCRI-9771 (vii) 2 .sup.aCCRI stands for "Collection of the Centre de Recherche en Infectiologie".

TABLE-US-00021 TABLE 21 Specificity and ubiquity tests performed on the SMART CYCLER .RTM. thermocycler using the set of primers targeting MREP types i, ii, iii, iv, vi and vii (SEQ ID NOs.: 64, 66, 67, 79 and 80) and molecular beacon probe (SEQ ID NO.: 84) developed in the present invention for the detection and identification of MRSA PCR results for MREJ Strains Positive (%) Negative (%) MRSA - 23 strains.sup.a 19 (82.6) 4 (17.4) MSSA - 25 strains 13 (52) 12 (48) MRCNS - 26 strains 0 26 (100) MSCNS - 8 strains 0 8 (100) .sup.aMRSA strains include the 20 strains listed in Table 3. Details regarding CNS strains: MRCNS: S. capitis (2) S. caprae (1) S. cohnii (1) S. epidermidis (9) S. haemolyticus (5) S. hominis (2) S. saprophyticus (1) S. sciuri (2) S. simulans (1) S. warneri (2) MSCNS: S. cohni cohnii (1) S. epidermidis (1) S. haemolyticus (1) S. lugdunensis (1) S. saccharolyticus (1) S. saprophyticus (2) S. xylosus (1)

TABLE-US-00022 ANNEX I Strategy for the selection of specific amplification primers for types i and ii MREP A. Types i and ii MREP orfX SEQ ID NO.: 2324 2358 2583 2607 2 TAT GTCAAAAATC ATGAACCTCA TTACTTATGA TA ... CCT TGTGCAGGCC GTTTGATCCG CC 1 TAT GTCAAAAATC ATGAACCTCA TTACTTATGA TA ... CCT TGTGCAGGCC GTTTGATCCG CC 17.sup.a TAT GTCAAAAATC ATGAACCTCA TTACTTATGA TA ... CCT TGTGCAGGCC GTTTGATCCG CC 18.sup.a TAT GTCAAAAATC ATGAACCTCA TTACTTATGA TA ... CCT TGTGCAGGCC GTTTGATCCG CC 19.sup.a TAT GTCAAAAATC ATGAACCTCA TTACTTATGA TA ... CCT TGTGCAGGCC GTTTGATCCG CC 20.sup.a TAT GTCAAAAATC ATGAACCTCA TTACTTATGA TA ... CCT TGTGCAGGCC GTTTGATCCG CC 21.sup.a TAT GTCAAAAATC ATGAACCTCA TTACTTATGA TA ... CCT TGTGCAGGCC GTTTGATCCG CC 22.sup.a TAT GTCAAAAATC ATGAACCTCA TTACTTATGA TA ... CCT TGTGCAGGCC GTTTGATCCG CC 23.sup.a TAT GTCAAAAATC ATGAACCTCA TTACTTATGA TA ... CCT TGTGCAGGCC GTTTGATCCG CC 24.sup.a TAT GTCAAAAATC ATGAACCTCA TTACTTATGA TA ... CCT TGTGCAGGCC GTTTGATCCG CC 25.sup.a TAT GTCAAAAATC ATGAACCTCA TTACTTATGA TA ... CCT TGTGCAGGCC GTTTGATCCG CC 26 TAT GTCAAAAATC ATGAACCTCA TTACTTATGA TA ... CCT TGTGCAGGCC GTTTGATCCG CC 33.sup.c CtT gGTGtAaaCC aTTgGAgCCa CC 34.sup.c CCT caTGCAatCC aTTTGATC Selected sequence GTCAAAAATC ATGAACCTCA TTACTTATG for type i MREP and ii primer (SEQ ID No.: 66) Selected sequence TGTGCAGGCC GTTTGATCC for orfX primer.sup.b (SEQ ID NO.: 64) The sequence positions refer to SEQ ID NO.: 2. Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the displayed sequences. .sup.aThese sequences are the reverse-complements of SEQ ID NOs.: 17-25. .sup.bThis sequence is the reverse-complement of the selected primer. .sup.cSEQ ID NOs.: 33 and 34 were obtained from CNS species.

TABLE-US-00023 ANNEX II Strategy for the selection of a specific molecular beacon probe for the real-time detection of MREJ orfX SEQ ID NO.: 327 371 165 ACAAG GACGT CTTACAACGC AGTAACTAtG CACTA 180 ACAAG GACGT CTTACAACGC AGTAACTAtG CACTA 181 ACAAG GACGT CTTACAACGC AGTAACTAtG CACTA 182 ACAAG GACGT CTTACAACGC AGTAACTAtG CACTA 183 ACAAG GACGT CTTACAACGC AGTAACTAtG CACTA 184 ACAAG GACGT CTTACAACGC AGTAACTAtG CACTA 186 ACAAG GACGT CTTACAACGC AGTAACTAtG CACTA 174 ACAAG GACGT CTTACAACGt AGTAACTACG CACTA 175 ACAAG GACGT CTTACAACGt AGTAACTACG CACTA 178 ACAAG GACGT CTTACAACGt AGTAACTACG CACTA 176 ACAAG GACGT CTTACAACGt AGTAACTACG CACTA 173 ACAAG GACGT CTTACAACGt AGTAACTACG CACTA 177 ACAAG GACGT CTTACAACGt AGTAACTACG CACTA 169 ACAAG GACGT CTTACAACGC AGTAACTACG CACTA 199 ACAAG GACGT CTTACAACGC AGTAACTACG CACTA 33.sup.a,b ACcAa GACGT CTTACAACGC AGcAACTAtG CttTA 34.sup.a,b AtgAG GACGT CTTACAACGC AGcAACTACG CACTt Selected sequence for orfX molecular beacon probes (SEQ ID NO.: 163).sup.c GACGT CTTACAACGC AGTAACTAtG (SEQ ID NO.: 164).sup.c GACGT CTTACAACGt AGTAACTACG (SEQ ID NO.: 84).sup.c GACGT CTTACAACGC AGTAACTACG Nucleotide discrepancies between the orfX sequences and SEQ ID NO.: 84 are shown in lower-case. Other entries in the sequence listing also present similar variations. The stem of the molecular beacon probes are not shown for sake of clarity. The sequence positions refer to SEQ ID NO.: 165. .sup.aThese sequences are the reverse-complements of SEQ ID NOs.: 33 and 34. .sup.bSEQ ID NOs.: 33 and 34 were obtained from CNS species. .sup.cThe sequences presented are the reverse-complement of the selected molecular beacon probes.

Sequence CWU 1

1

26913050DNAStaphylococcus aureus 1tcgtgccatt gatgcagagg gacatacatt agatatttgg ttgcgtaagc aacgagataa 60tcattcagca tatgcgttta tcaaacgtct cattaaacaa tttggtaaac ctcaaaaggt 120aattacagat caggcacctt caacgaaggt agcaatggct aaagtaatta aagcttttaa 180acttaaacct gactgtcatt gtacatcgaa atatctgaat aacctcattg agcaagatca 240ccgtcatatt aaagtaagaa agacaaggta tcaaagtatc aatacagcaa agaatacttt 300aaaaggtatt gaatgtattt acgctctata taaaaagaac cgcaggtctc ttcagatcta 360cggattttcg ccatgccacg aaattagcat catgctagca agttaagcga acactgacat 420gataaattag tggttagcta tattttttta ctttgcaaca gaaccgaaaa taatctcttc 480aatttatttt tatatgaatc ctgtgactca atgattgtaa tatctaaaga tttcagttca 540tcatagacaa tgttcttttc aacatttttt atagcaaatt gattaaataa attctctaat 600ttctcccgtt tgatttcact accatagatt atattatcat tgatatagtc aatgaataat 660gacaaattat cactcataac agtcccaacc cctttatttt gatagactaa ttatcttcat 720cattgtaaaa caaattacac cctttaaatt taactcaact taaatatcga caaattaaaa 780aacaataaaa ttacttgaat attattcata atatattaac aactttatta tactgctctt 840tatatataaa atcattaata attaaacaag ccttaaaata tttaactttt ttgtgattat 900tacacattat cttatctgct ctttatcacc ataaaaatag aaaaaacaag attcctaaag 960aatataggaa tcttgtttca gactgtggac aaactgattt tttatcagtt agcttattta 1020gaaagtttta tttaaattac agtttctatt tttattagat cacaatttta ttttagctct 1080tgttcaagta atcatttttc gccaaaaact ttatactgaa tagcttctac attaaatact 1140ttgtcaatga gatcatctac atctttaaat tcagaataat ttgcatatgg atctataaaa 1200taaaattgtg gttctttacc ggaaacatta aatattctta atattaaata tttctgctta 1260tattctttca tagcaaacat ttcatttagc gacataaaaa atggttcctc aatactagaa 1320gatgtagatg ttttaatttc aataaatttt tctacagctt tatctgtatt tgttggatca 1380aaagctacta aatcatagcc atgaccgtgt tgagagcctg gattatcatt taaaatattc 1440ctaaactgtt ctttcttatc ttcgtctatt ttattatcaa ttagctcatt aaagtaattt 1500agcgctaatt tttctccaac tttaccggtt aatttattct ctttatttga tttttcaatt 1560tctgaatcat ttttagtagt ctttgataca ccttttttat attttggaat tattccttta 1620ggtgcttcca cttccttgag tgtcttatct ttttgtgctg ttctaatttc ttcaatttcg 1680ctgtcttcct gtatttcgtc tatgctattg accaagctat cataggatgt ttttgtaact 1740tttgaagcta attcattaaa tagttctaaa aatttcttta aatcctctag catatcttct 1800tctgtgaatc cttcattcaa atcataatat ttgaatctta ttgatccatg agaatatcct 1860gatggataat cattttttaa atcataagat gaatctttat tttctgcgta ataaaatctt 1920ccagtattaa attcatttga tgtaatatat ttattgagtt cggaagataa agttaatgct 1980ctttgttttg cagcattttt atcccgcgga aacatatcac ttatctttga ccatccttga 2040ttcaaagata agtatatgcc ttctccttcc ggatgaaaaa gatataccaa ataatatcca 2100tcctttgttt cttttgttat attctcatca tatattgaaa tccaaggaac tttactatag 2160ttcccagtag caaccttccc tacaactgaa tatttatctt cttttatatg cacttttaac 2220tgcttgggta acttatcatg gactaaagtt ttatatagat cacctttatc ccaatcagat 2280tttttaacta cattattggt acgtttctct ttaattaatt taaggacctg cataaagttg 2340tctatcattt gaaattccct cctattataa aatatattat gtctcatttt cttcaatatg 2400tacttattta tattttaccg taatttacta tatttagttg cagaaagaat tttctcaaag 2460ctagaacttt gcttcactat aagtattcag tataaagaat atttcgctat tatttacttg 2520aaatgaaaga ctgcggaggc taactatgtc aaaaatcatg aacctcatta cttatgataa 2580gcttctcctc gcataatctt aaatgctctg tacacttgtt caattaacac aacccgcatc 2640atttgatgtg ggaatgtcat tttgctgaat gatagtgcgt agttactgcg ttgtaagacg 2700tccttgtgca ggccgtttga tccgccaatg acgaaaacaa agtcgctttg cccttgggtc 2760atgcgttggt tcaattcttg ggccaatcct tcggaagata gcatctttcc ttgtatttct 2820aatgtaatga ctgtggattg tggtttgatt ttggctagta ttcgttggcc ttctttttct 2880tttacttgct caatttcttt gtcactcata ttttctggtg ctttttcgtc tggaacttct 2940atgatgtcta tcttggtgta tgggcctaaa cgtttttcat attctgctat ggcttgcttc 3000caatatttct cttttagttt ccctacagct aaaatggtga ttttcatgtc 305023050DNAStaphylococcus aureus 2acctcattga gcaagatcac cgtcatatta aagtaagaaa gacaaggtat caaagtatca 60atacagcaaa gaatacttta aaaggtattg aatgtattta cgctctatat aaaaagaacc 120gcaggtctct tcagatctac ggattttcgc catgccacga aattagcatc atgctagcaa 180gttaagcgaa cactgacatg ataaattagt ggttagctat atttttttac tttgcaacag 240aaccgaaaat aatctcttca atttattttt atatgaatcc tgtgactcaa tgattgtaat 300atctaaagat ttcagttcat catagacaat gttcttttca acatttttta tagcaaattg 360attaaataaa ttctctaatt tctcccgttt gatttcacta ccatagatta tattatcatt 420gatatagtca atgaataatg acaaattatc actcataaca gtcccaaccc ctttcttttg 480atagactaat tatcttcatc attgtaaaac aaattacacc ctttaaattt aactcaactt 540aaatatcgac aaattaaaaa acaataaaat tacttgaata ttattcataa tatattaaca 600actttattat actgctcttt atatataaaa tcattaataa ttaaacaagc cttaaaatat 660ttaacttttt tgtgattatt acacattatc ttatctgctc tttatcacca taaaaataga 720aaaaacaaga ttcctaaaga atataggaat cttgtttcag actgtggaca aactgatttt 780ttatcagtta gcttatttag aaagttttat ttaaattaca gtttctattt ttattagatc 840acaattttat tttagctctt gttcaagtaa tcatttttcg ccaaaaactt tatactgaat 900agcttctaca ttaaatactt tgtcaatgag atcatctaca tctttaaatt cagaataatt 960tgcatatgga tctataaaat aaaattgtgg ttctttaccg gaaacattaa atattcttaa 1020tattaaatat ttctgcttat attctttcat agcaaacatt tcatttagcg acataaaaaa 1080tggttcctca atactagaag atgtagatgt tttaatttca ataaattttt ctacagcttt 1140atctgtattt gttggatcaa aagctactaa atcatagcca tgaccgtgtt gagagcctgg 1200attatcattt aaaatattcc taaactgttc tttcttatct tcgtctattt tattatcaat 1260tagctcatta aagtaattta gcgctaattt ttctccaact ttaccggtta atttattctc 1320tttatttgat ttttcaattt ctgaatcatt tttagtagtc tttgatacac cttttttata 1380ttttggaatt attcctttag gtgcttccac ttccttgagt gtcttatctt tttgtgctgt 1440tctaatttct tcaatttcgc tgtcttcctg tatttcgtct atgctattga ccaagctatc 1500ataggatgtt tttgtaactt ttgaagctaa ttcattaaat agttctaaaa atttctttaa 1560atcctctagc atatcttctt ctgtgaatcc ttcattcaaa tcataatatt tgaatcttat 1620tgatccatga gaatatcctg atggataatc attttttaaa tcataagatg aatctttatt 1680ttctgcgtaa taaaatcttc cagtattaaa ttcatttgat gtaatatatt tattgagttc 1740ggaagataaa gttaatgctc tttgttttgc agcattttta tcccgcggaa acatatcact 1800tatctttgac catccttgat tcaaagataa gtatatgcct tctccttccg gatgaaaaag 1860atataccaaa taatatccat cctttgtttc ttttgttata ttctcatcat atattgaaat 1920ccaaggaact ttactatagt tcccagtagc aaccttccct acaactgaat atttatcttc 1980ttttatatgc acttttaact gcttgggtaa cttatcatgg actaaagttt tatatagatc 2040acctttatcc caatcagatt ttttaactac attattggta cgtttctctt taattaattt 2100aaggacctgc ataaagttgt ctatcatttg aaattccctc ctattataaa atatattatg 2160tctcattttc ttcaatatgt acttatttat attttaccgt aatttactat atttagttgc 2220agaaagaatt ttctcaaagc tagaactttg cttcactata agtattcagt ataaagaata 2280tttcgctatt atttacttga aatgaaagac tgcggaggct aactatgtca aaaatcatga 2340acctcattac ttatgataag cttcttaaaa acataacagc aattcacata aacctcatat 2400gttctgatac attcaaaatc cctttatgaa gcggctgaaa aaaccgcatc atttatgata 2460tgcttctcca cgcataatct taaatgctct atacacttgc tcaattaaca caacccgcat 2520catttgatgt gggaatgtca ttttgctgaa tgatagtgcg tagttactgc gttgtaagac 2580gtccttgtgc aggccgtttg atccgccaat gacgaataca aagtcgcttt gcccttgggt 2640catgcgttgg ttcaattctt gggccaatcc ttcggaagat agcatctttc cttgtatttc 2700taatgtaatg actgtggatt gtggtttaat tttggctagt attcgttggc cttctttttc 2760ttttacttgc tcaatttctt tgtcgctcat attttctggt gctttttcgt ctggaacttc 2820tatgatgtct atcttggtgt atgggcctaa acgtttttca tattctgcta tggcttgctt 2880ccaatatttc tcttttagtt tccctacagc taaaatggtg attttcatgt cgtttggtcc 2940tccaaattgt tatcaacttt ccagttatcc acaagttatt aacttgttca cactgttccc 3000tcttattata ccaatatttt ttgcagtttt tgatattttc ctgacattta 305033183DNAStaphylococcus aureus 3ctgcagaggt aattattcca aacaatacca ttgatttcaa aggagaaaga gatgacgtta 60gaacgcgtga aacaaattta ggaaacgcga ttgcagatgc tatggaagcg tatggcgtta 120agaatttctc taaaaagact gactttgccg tgacaaatgg tggaggtatt cgtgcctcta 180tcgcaaaagg taaggtgaca cgctatgatt taatctcagt attaccattt ggaaatacga 240ttgcgcaaat tgatgtaaaa ggttcagacg tctggacggc tttcgaacat agtttaggcg 300caccaacaac acaaaaggac ggtaagacag tgttaacagc gaatggcggt ttactacata 360tctctgattc aatccgtgtt tactatgata taaataaacc gtctggcaaa cgaattaatg 420ctattcaaat tttaaataaa gagacaggta agtttgaaaa tattgattta aaacgtgtat 480atcacgtaac gatgaatgac ttcacagcat caggtggcga cggatatagt atgttcggtg 540gtcctagaga agaaggtatt tcattagatc aagtactagc aagttattta aaaacagcta 600acttagctaa gtatgatacg acagaaccac aacgtatgtt attaggtaaa ccagcagtaa 660gtgaacaacc agctaaagga caacaaggta gcaaaggtag taagtctggt aaagatacac 720aaccaattgg tgacgacaaa gtgatggatc cagcgaaaaa accagctcca ggtaaagttg 780ttttgttgct agcgcataga ggaactgtta gtagcggtac agaaggttct ggtcgcacaa 840tagaaggagc tactgtatca agcaagagtg ggaaacaatt ggctagaatg tcagtgccta 900aaggtagcgc gcatgagaaa cagttaccaa aaactggaac taatcaaagt tcaagcccag 960aagcgatgtt tgtattatta gcaggtatag gtttaatcgc gactgtacga cgtagaaaag 1020ctagctaaaa tatattgaaa ataatactac tgtatttctt aaataagagg tacggtagtg 1080tttttttatg aaaaaaagcg ataaccgttg ataaatatgg gatataaaaa cgaggataag 1140taataagaca tcaaggtgtt tatccacaga aatggggata gttatccaga attgtgtaca 1200atttaaagag aaatacccac aatgcccaca gagttatcca caaatacaca ggttatacac 1260taaaaatcgg gcataaatgt caggaaaata tcaaaaactg caaaaaatat tggtataata 1320agagggaaca gtgtgaacaa gttaataact tgtggataac tggaaagttg ataacaattt 1380ggaggaccaa acgacatgaa aatcaccatt ttagctgtag ggaaactaaa agagaaatat 1440tggaagcaag ccatagcaga atatgaaaaa cgtttaggcc catacaccaa gatagacatc 1500atagaagttc cagacgaaaa agcaccagaa aatatgagtg acaaagaaat tgagcaagta 1560aaagaaaaag aaggccaacg aatactagcc aaaatcaaac cacaatccac agtcattaca 1620ttagaaatac aaggaaagat gctatcttcc gaaggattgg cccaagaatt gaaccaacgc 1680atgacccaag ggcaaagcga ctttgttttc gtcattggcg gatcaaacgg cctgcacaag 1740gacgtcttac aacgcagtaa ctacgcacta tcattcagca aaatgacatt cccacatcaa 1800atgatgcggg ttgtgttaat tgaacaagtg tacagagcat ttaagattat gcgaggagag 1860gcgtatcata agtaaaacta aaaaattctg tatgaggaga taataatttg gagggtgtta 1920aatggtggac attaaatcca cgttcattca atatataaga tatatcacga taattgcgca 1980tataacttaa gtagtagcta acagttgaaa ttaggcccta tcaaattggt ttatatctaa 2040aatgattaat atagaatgct tctttttgtc cttattaaat tataaaagta actttgcaat 2100agaaacagtt atttcataat caacagtcat tgacgtagct aagtaatgat aaataatcat 2160aaataaaatt acagatattg acaaaaaata gtaaatattc caatgaagtt tcaaaagaac 2220aattccaaga aattgagaat gtaaataata aggtcaaaga attttattaa gatttgaaag 2280agtatcaatc aagaaagatg tagtttttta ataaactatt tggaaaataa ttatcataat 2340ttaaaaactg acaatttgcg agactcataa aatgtaataa tggaaataga tgtaaaatat 2400aattaagggg tgtaatatga agattaatat ttataaatct atttataatt ttcaggaaac 2460aaatacaaat tttttagaga atctagaatc tttaaatgat gacaattatg aactgcttaa 2520tgataaagaa cttgttagtg attcaaatga attaaaatta attagtaaag tttatatacg 2580taaaaaagac aaaaaactat tagattggca attattaata aagaatgtat acctagatac 2640tgaagaagat gacaatttat tttcagaatc cggtcatcat tttgatgcaa tattatttct 2700caaagaagat actacattac aaaataatgt atatattata ccttttggac aagcatatca 2760tgatataaat aatttgattg attatgactt cggaattgat tttgcagaaa gagcaatcaa 2820aaatgaagac atagttaata aaaatgttaa tttttttcaa caaaacaggc ttaaagagat 2880tgttaattat agaaggaata gtgtagatta cgttagacct tcagaatctt atatatcagt 2940ccaaggacat ccacagaatc ctcaaatttt tggaaaaaca atgacttgtg gtacaagtat 3000ttcattgcgt gtaccgaata gaaagcagca attcatagat aaaattagtg tgataatcaa 3060agaaataaac gctattatta atcttcctca aaaaattagt gaatttccta gaatagtaac 3120tttaaaagac ttgaataaaa tagaagtatt agatacttta ttgctaaaaa aactatcgaa 3180ttc 31834479DNAStaphylococcus aureus 4ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgaacaa 120gtgtacagag catttaagat tatgcgtgga gaagcgtatc ataaataaaa ctaaaaatta 180ggttgtgtat aatttaaaaa tttaatgaga tgtggaggaa ttacatatat gaaatattgg 240attatacctt gcaatatcat acgatgttta tagagtgttt aataaaccat ttttcaacta 300ttgatgatct agaatatata ataactgtac aaattatatt gattatggaa ctacaattaa 360attaagaaat tgatgatgaa attttaaatt taaactaatg gaatcaagaa agaatgaaag 420gaaatataca atgcctacga ttaataaaag gaagtttatt agattttgtg ttagaaaca 4795480DNAStaphylococcus aureus 5ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgaacaa 120gtgtacagag catttaagat tatgcgtgga gaagcgtatc ataaataaaa ctaaaaatta 180ggttgtgtat aatttaaaaa tttaatgaga tgtggaggaa ttacatatat gaaatattgg 240attatacctt gcaatatcat acgatgttta tagagtgttt aataaaccat ttttcaacta 300ttgatgatct agaatatata ataactgtac aaattatatt gattatggaa ctacaattaa 360attaagaaat tgatgatgaa attttaaatt taaactaatg gaatcaagaa agaatgaaag 420gaaatataac atgcctacga ttaataaaag gaagtttatt agattttgtg ttagaaacag 4806480DNAStaphylococcus aureus 6ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac atccccacat caaatgatgc gggttgtgtt aattgaacaa 120gtgtacagag catttaagat tatgcgtgga gaagcgtatc ataaataaaa ctaaaaatta 180ggttgtgtat aatttaaaaa tttaatgaga tgtggaggaa ttacatatat gaaatattgg 240attatacctt gcaatatcat acgatgttta tagagtgttt aataaaccat ttttcaacta 300ttgatgatct agaatatata ataactgtac aaattatatt gattatggaa ctacaattaa 360attaagaaat tgatgatgaa attttaaatt taaactaatg gaatcaagaa agaatgaaag 420gaaatataca atgcctacga ttaataaaag gaagtttatt agatttgtgt tagaaacagt 4807480DNAStaphylococcus aureus 7ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgaacaa 120gtgtacagag catttaagat tatgcgtgga gaagcgtatc ataaataaaa ctaaaaatta 180ggttgtgtat aatttaaaaa tttaatgaga tgtggaggaa ttacatatat gaaatattgg 240attatacctt gcaatatcat acgatgttta tagagtgttt aataaaccat ttttcaacta 300ttgatgatct agaatatata ataactgtac aaattatatt gattatggaa ctacaattaa 360attaagaaat tgatgatgaa attttaaatt taaactaatg gaatcaagaa agaatgaaag 420gaaatataca atgcctacga ttaataaaag gaagtttatt agattttgtg ttagaaacag 4808309DNAStaphylococcus aureusmisc_feature237n = A,T,C or G 8ggcggatcaa acggcctgca caaggacgtc ttacaacgca gtaactacgc actatcattc 60agcaaaatga cattcccaca tcaaatgatg cgggttgtgt taattgaaca agtgtacaga 120gcatttaaga ttatgcgtgg agaagcgtat cataaataaa actaaaaatt aggttgtgta 180taatttaaaa atctaatgag atgtggagga attacatata tgaaatattg gattatncct 240tgcaatatca tacgatgttt atagagtgtt taataaacca tttttcaact attgatgatc 300tacaatata 3099471DNAStaphylococcus aureus 9ttggcggatc aaacggcctg cacaaggacg tcttacaacg cagtaactac gcactatcat 60tcagcaaaat gacattccca catcaaatga tgcgggttgt gttaattgaa caagtgtaca 120gagcatttaa gattatgcgt ggagaagcgt atcataaata aaactaaaaa ttaggttgtg 180tataatttaa aaatttaatg agatgtggag gaattacata tatgaaatat tggattatac 240cttgcaatat catacgatgt ttatagagtg tttaataaac catttttcaa ctattgatga 300tctagaatat ataataactg tacaaattat attgattatg gaactacaat taaattaaga 360aattgatgat gaaattttaa atttaaacta atggaatcaa gaaagaatga aaggaaatat 420acaatgccta cgattaataa aaggaagttt attagatttt gtgttagaaa c 47110480DNAStaphylococcus aureus 10ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgaacaa 120gtgtacagag catttaagat tatgcgtgga gaagcgtatc ataaataaaa ctaaaaatta 180ggttgtgtat aatttaaaaa tttaatgaga tgtggaggaa ttacatatat gaaatattgg 240attatacctt gcaatatcat acgatgttta tagagtgttt aataaaccat ttttcaacta 300ttgatgatct agaatatata ataactgtac aaattatatt gattatggaa ctacaattaa 360attaagaaat tgatgatgaa attttaaatt taaactaatg gaatcaagaa agaatgaaag 420gaaatataca atgcctacga ttaataaaag gaagtttatt agattttgtg ttagaaacag 48011480DNAStaphylococcus aureus 11ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgaacaa 120gtgtacagag catttaagat tatgcgtgga gaagcgtatc ataaataaaa ctaaaaatta 180ggttgtgtat aatttaaaaa tttaatgaga tgtggaggaa ttacatatat gaaatattgg 240attatacctt gcaatatcat acgatgttta tagagtgttt aataaaccat ttttcaacta 300ttgatgatct agaatatata ataactgtac aaattatatt gattatggaa ctacaattaa 360attaagaaat tgatgatgaa attttaaatt taaactaatg gaatcaagaa agaatgaaag 420gaaatataca atgcctacga ttaataaaag gaagtttatt agattttgtg ttagaaacag 48012480DNAStaphylococcus aureus 12ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgaacaa 120gtgtacagag catttaagat tatgcgtgga gaagcgtatc ataaataaaa ctaaaaatta 180ggttgtgtat aatttaaaaa tttaatgaga tgtggaggaa ttacatatat gaaatattgg 240attatacctt gcaatatcat acgatgttta tagagtgttt aataaaccat ttttcaacta 300ttgatgatct agaatatata ataactgtac aaattatatt gattatggaa ctacaattaa 360attaagaaat tgatgatgaa attttaaatt taaactaatg gaatcaagaa agaatgaaag 420gaaatataca atgcctacga ttaataaaag gaagtttatt agattttgtg ttagaaacag 48013478DNAStaphylococcus aureus 13ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgaacaa 120gtgtacagag catttaagat tatgcgtgga gaagcgtatc ataaataaaa ctaaaaatta 180ggttgtgtat aatttaaaaa tttaatgaga tgtggaggaa ttacatatat gaaatattgg 240attatacctt gcaatatcat acgatgttta tagagtgttt aataaaccat ttttcaacta 300ttgatgatct agaatatata ataactgtac aaattatatt gattatggaa ctacaattaa 360attaagaaat tgatgatgaa attttaaatt taaactaatg gaatcaagaa agaatgaaag 420gaaatataca atgcctacga ttaataaaag gaagtttatt agattttgtg ttagaaac 47814479DNAStaphylococcus aureus 14ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgaacaa 120gtgtacagag catttaagat tatgcgtgga gaagcgtatc ataaataaaa ctaaaaatta 180ggttgtgtat aatttaaaaa tttaatgaga tgtggaggaa ttacatatat gaaatattgg 240attatacctt gcaatatcat acgatgttta tagagtgttt aataaaccat ttttcaacta 300ttgatgatct agaatatata ataactgtac aaattatatt gattatggaa ctacaattaa 360attaagaaat tgatgatgaa attttaaatt taaactaatg gaatcaagaa agaatgaaag 420gaaatataca atgcctacga ttaataaaag gaagtttatt agattttgtg ttagaaaca 47915480DNAStaphylococcus aureusmisc_feature406n = A,T,C or G 15ttcgtcattg gcggatcaaa cggcctgcac

aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgaacaa 120gtgtacagag catttaagat tatgcgtgga gaagcgtatc ataaataaaa ctaaaaatta 180ggttgtgtat aatttaaaaa tttaatgaga tgtggaggaa ttacatatat gaaatattgg 240attatacctt gcaatatcat acgatgttta tagagtgttt aataaaccat ttttcaacta 300ttgatgatct agaatatata ataactgtac aaattatatt gattatggaa ctacaattaa 360attaagaaat tgatgatgaa attttaaatt taaactaatg gaatcncgaa agaatgaaag 420gaaatataca atgcctacga ttaataaaag gaagtttatt agattttgtg ttagaaacag 48016480DNAStaphylococcus aureus 16ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgaacaa 120gtgtacagag catttaagat tatgcgtgga gaagcgtatc ataaataaaa ctaaaaatta 180ggttgtgtat aatttaaaaa tttaatgaga tgtggaggaa ttacatatat gaaatattgg 240attatacctt gcaatatcat acgatgttta tagagtgttt aataaaccat ttttcaacta 300ttgatgatct agaatatata ataactgtac aaattatatt gattatggaa ctacaattaa 360attaagaaat tgatgatgaa attttaaatt taaactaatg gaatcaagaa agaatgaaag 420gaaatataca atgcctacga ttaataaaag gaagtttatt agattttgtg ttagaaacag 48017480DNAStaphylococcus aureus 17ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgaacaa 120gtgtacagag catttaagat tatgcgtgga gaagcatatc ataaatgatg cggttttttc 180agccgcttca taaagggatt ttgaatgtat cagaacatat gaggtttatg tgaattgctg 240ttatgttttt aagaagctta tcataagtaa tgaggttcat gatttttgac atagttagcc 300tccgcagtct ttcatttcaa gtaaataata gcgaaatatt ctttatactg aatacttata 360gtgaagcaaa gttctagctt tgagaaaatt ctttctgcaa ctaaatatag taaattacgg 420taaaatataa ataagtacat attgaagaaa atgagacata atatatttta taataggagg 48018480DNAStaphylococcus aureus 18ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgagcaa 120gtgtatagag catttaagat tatgcgtgga gaagcatatc ataaatgatg cggttttttc 180agccgcttca taaagggatt ttgaatgtat cagaacatat gaggtttatg tgaattgctg 240ttatgttttt aagaagctta tcataagtaa tgaggttcat gatttttgac atagttagcc 300tccgcagtct ttcatttcaa gtaaataata gcgaaatatt ctttatactg aatacttata 360gtgaagcaaa gttctagctt tgagaaaatt ctttctgcaa ctaaatatag taaattacgg 420taaaatataa ataagtacat attgaagaaa atgagacata atatatttta taataggagg 48019458DNAStaphylococcus aureus 19ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgaacaa 120gtgtacagag catttaagat tatgcgtgga gaagcatatc ataaatgatg cggttttttc 180agccgcttca taaagggatt ttgaatgtat cagaacatat gaggtttatg tgaattgctg 240ttatgttttt aagaagctta tcataagtaa tgaggttcat gatttttgac atagttagcc 300tccgcagtct ttcatttcaa gtaaataata gcgaaatatt ctttatactg aatacttata 360gtgaagcaaa gttctagctt tgagaaaatt ctttctgcaa ctaaatatag taaattacgg 420taaaatataa ataagtacat attgaagaaa atgagaca 45820385DNAStaphylococcus aureus 20ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgagcaa 120gtgtatagag catttaagat tatgcgtgga gaagcttatc ataagtaatg aggttcatga 180tttttgacat agttagcctc cgcagtcttt catttcaagt aaataatagc gaaatattct 240ttatactgaa tacttatagt gaagcaaagt tctagctttg agaaaattct ttctgcaact 300aaatatagta aattacggta aaatataaat aagtacatat tgaagaaaat gagacataat 360atattttata ataggaggga atttc 38521385DNAStaphylococcus aureus 21ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgagcaa 120gtgtatagag catttaagat tatgcgtgga gaagcttatc ataagtaatg aggttcatga 180tttttgacat agttagcctc cgcagtcttt catttcaagt aaataatagc gaaatattct 240ttatactgaa tacttatagt gaagcaaagt tctagctttg agaaaattct ttctgcaact 300aaatatagta aattacggta aaatataaat aagtacatat tgaagaaaat gagacataat 360atattttata ataggaggga atttc 38522385DNAStaphylococcus aureus 22ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgagcaa 120gtgtatagag catttaagat tatgcgtgga gaagcttatc ataagtaatg aggttcatga 180tttttgacat agttagcctc cgcagtcttt catttcaagt aaataatagc gaaatattct 240ttatactgaa tacttatagt gaagcaaagt tctagctttg agaaaattct ttctgcaact 300aaatatagta aattacggta aaatataaat aagtacatat tgaagaaaat gagacataat 360atattttata ataggaggga atttc 38523385DNAStaphylococcus aureus 23ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgcg 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgaacaa 120gtgtacaaag catttaagat tatgcgagga gaagcttatc ataagtaatg aggttcatga 180tttttgacat agttagcctc cgcagtcttt catttcaagt aaataatagc gaaatattct 240ttatactgaa tacttatagt gaagcaaagt tctagctttg agaaaattct ttctgcaact 300aaatatagta aattacggta aaatataaat aagtacatat tgaagaaaat gagacataat 360atattttata ataggaggga atttc 38524340DNAStaphylococcus aureus 24cgcagtaact acgcgctatc attcagcaaa atgacattcc cacatcaaat gatgcgggtt 60gtgttagttg agcaagtgta catagcattt aagattatgc gaggagaagc ttatcataag 120taatgaggtt catgattttt gacatagtta gcctccgcag tctttcattt caagtaaata 180atagcgaaat attctttata ctgaatactt atagtgaagc aaagttctag ctttgagaaa 240attctttctg caactaaata tagtaaatta cggtaaaata taaataagta catattgaag 300aaaatgagac ataatatatt ttataatagg agggaatttc 34025369DNAStaphylococcus aureus 25caaacggcct gcacaaggac gtcttacaac gcagtaacta cgcactatca ttcagcaaaa 60tgacattccc acatcaaatg atgcgggttg tgttaattga acaagtgtac agagcattta 120agattatgcg aggagaagct tatcataagt aatgaggttc atgatttttg acatagttag 180cctccgcagt ctttcatttc aagtaaataa tagcgaaata ttctttatac tgaatactta 240tagtgaagca aagttctagc tttgagaaaa ttctttctgc aactaaatat agtaaattac 300ggtaaaatat aaataagtac atattgaaga aaatgagaca taatatattt tataatagga 360gggaatttc 369263050DNAStaphylococcus aureus 26aatttggtaa acctcaaaag gtaattacag atcaggcacc ttcaacgaag gtagcaatgg 60ctaaagtaat taaagctttt aaacttaaac ctgactgtca ttgtacatcg aaatatctga 120ataacctcat tgagcaagat caccgtcata ttaaagtaag aaagacaagg tatcaaagta 180tcaatacagc aaagaatact ttaaaaggta ttgaatgtat tcacgctcta tataaaaaga 240accgcaggtc tcttcagatc tacggatttt cgccatgcca cgaaattagc atcatgctag 300caagttaagc gaacactgac atgataaatt agtggttagc tatatttttt tactttgcaa 360cagaaccgaa aataatctct tcaatttatt tttatatgaa tcctgtgact caatgattgt 420aatatctaaa gatttcagtt catcatagac aatgttcttt tcaacatttt ttatagcaaa 480ttgattaaat aaattctcta atttctcccg tttgatttca ctaccataga ttatattatc 540attgatatag tcaatgaata atgacaaatt atcactcata acagtcccaa cccctttatt 600ttgatagact aattatcttc atcattgtaa aacaaattac accctttaaa tttaactcaa 660cttaaatatc gacaaattaa aaaacaataa aattacttga atattattca taatatatta 720acaactttat tatactgctc tttatatata aaatcattaa taattaaaca agccttaaaa 780tatttaactt ttttgtgatt attacacatt atcttatctg ctctttatca ccataaaaat 840agaaaaaaca agattcctaa agaatatagg aatcttgttt cagactgtgg acaaactgat 900tttttatcag ttagcttatt tagaaagttt tatttaaatt acagtttcta tttttattag 960atcacaattt tattttagct cttgttcaag taatcatttt tcgccaaaaa ctttatactg 1020aatagcttct acattaaata cttgtcaatg agatcatcta catctttaaa ttcagaataa 1080ttcgcatatg gatctataaa ataaaattgt ggttctttac cggaaacatt aaatattctt 1140aatattaaat atttctgctt atattctttc atagcaaaca tttcatttag cgacataaaa 1200aatggttcct caatactaga agatgtagat gttttaattt caataaattt ttctacagct 1260ttatctgtat ttgttggatc aaaagctact aaatcatagc catgaccgtg ttgagagcct 1320ggattatcat ttaaaatatt cctaaactgt tctttcttat cttcgtctat tttattatca 1380attagctcat taaagtaatt tagcgctaat ttttctccaa ctttaccggt taatttattc 1440tctttatttg atttttcaat ttctgaatca tttttagtag tctttgatac acctttttta 1500tattttggaa ttattccttt aggtgcttcc acttccttga gtgtcttatc tttttgtgct 1560gttctaattt cttcaatttc gctgtcttcc tgtatttcgt ctatgctatt gaccaagcta 1620tcataggatg tttttgtaac ttttgaagct aattcattaa atagttctaa aaatttcttt 1680aaatcctcta gcatatcttc ttctgtgaat ccttcattca aatcataata tttgaatctt 1740attgatccat gagaatatcc tgatggataa tcatttttta aatcataaga tgaatcttta 1800ttttctgcgt aataaaatct tccagtatta aattcatttg atgtaatata tttattgagt 1860tcggaagata aagttaatgc tctttgtttt gcagcatttt tatcccgcgg aaacatatca 1920cttatctttg accatccttg attcaaagat aagtatatgc cttctccttc cggatgaaaa 1980agatatacca aataatgtcc atcctttgtt tcttttgtta tattctcatc atatattgaa 2040atccaaggaa ctttactata gttcccagta gcaaccttcc ctacaactga atatttatct 2100tcttttatat gcacttttaa ctgcttgggt aacttatcat ggactaaagt tttatataga 2160tcacctttat cccaatcaga ttttttaact acattattgg tacgtttctc tttaattaat 2220ttaaggacct gcataaagtt gtctatcatt tgaaattccc tcctattata aaatatatta 2280tgtctcattt tcttcaatat gtacttattt atattttacc gtaatttact atatttagtt 2340gcagaaagaa ttttctcaaa gctagaactt tgcttcacta taagtattca gtataaagaa 2400tatttcgcta ttatttactt gaaatgaaag actgcggagg ctaactatgt caaaaatcat 2460gaacctcatt acttatgata agcttcttaa aaacataaca gcaattcaca taaacctcat 2520atgttctgat acattcaaaa tccctttatg aagcggctga aaaaaccgca tcatttatga 2580tatgcttctc ctcgcataat cttaaatgct ctgtacactt gttcaattaa cacaacccgc 2640atcatttgat gtgggaatgt cattttgctg aatgatagtg cgtagttact gcgttgtaag 2700acgtccttgt gcaggccgtt tgatccgcca atgacgaaaa caaagtcgct ttgcccttgg 2760gtcatgcgtt ggttcaattc ttgggccaat ccttcggaag atagcatctt tccttgtatt 2820tctaatgtaa tgactgtgga ttgtggtttg attttggcta gtattcgttg gccttctttt 2880tcttttactt gctcaatttc tttgtcactc atattttctg gtgctttttc gtctggaact 2940tctatgatgt ctatcttggt gtatgggcct aaacgttttt catattctgc tatggcttgc 3000ttccaatatt tctcttttag tttccctaca gctaaaatgg tgattttcat 305027657DNAStaphylococcus aureus 27ccaccttcat atgacgtcta tccatttatg tatggcatga gtaacgaaga atataataaa 60ttaaccgaag ataaaaaaga acctctgctc aacaagttcc agattacaac ttcaccaggt 120tcaactcaaa aaatattaac agcaatgatt gggttaaata acaaaacatt agacgataaa 180acaagttata aaatcgatgg taaaggttgg caaaaagata aatcttgggg tggttacaac 240gttacaagat atgaagtggt aaatggtaat atcgacttaa aacaagcaat agaatcatca 300gataacattt tctttgctag agtagcactc gaattaggca gtaagaaatt tgaaaaaggc 360atgaaaaaac taggtgttgg tgaagatata ccaagtgatt atccatttta taatgctcaa 420atttcaaaca aaaatttaga taatgaaata ttattagctg attcaggtta cggacaaggt 480gaaatactga ttaacccagt acagatcctt tcaatctata gcgcattaga aaataatggc 540aatattaacg cacctcactt attaaaagac acgaaaaaca aagtttggaa gaaaaatatt 600atttccaaag aaaatatcaa tctattaact gatggtatgc aacaagtcgt aaataaa 65728782DNAStaphylococcus aureus 28caccttcata tgacgtctat ccatttatgt atggcatgag taacgaagaa tataataaat 60taaccgaaga taaaaaagaa cctctgctca acaagttcca gattacaact tcaccaggtt 120caactcaaaa aatattaaca gcaatgattg ggttaaataa caaaacatta gacgataaaa 180caagttataa aatcgatggt aaaggttggc aaaaagataa atcttggggt ggttacaacg 240ttacaagata tgaagtggta aatggtaata tcgacttaaa acaagcaata gaatcatcag 300ataacatttt ctttgctaga gtagcactcg aattaggcag taagaaattt gaaaaaggca 360tgaaaaaact aggtgttggt gaagatatac caagtgatta tccattttat aatgctcaaa 420tttcaaacaa aaatttagat aatgaaatat tattagctga ttcaggttac ggacaaggtg 480aaatactgat taacccagta cagatccttt caatctatag cgcattagaa aataatggca 540atattaacgc acctcactta ttaaaagaca cgaaaaacaa agtttggaag aaaaatatta 600tttccaaaga aaatatcaat ctattaactg atggtatgca acaagtcgta aataaaacac 660ataaagaaga tatttataga tcttatgcaa acttaattgg caaatccggt actgcagaac 720tcaaaatgaa acaaggagaa actggcagac aaattgggtg gtttatatca tatgataaag 780at 78229744DNAStaphylococcus aureus 29tatgacgtct atccatttat gtatggcatg agtaacgaag aatataataa attaaccgaa 60gataaaaaag aacctctgct caacaagttc cagattacaa cttcaccagg ttcaactcaa 120aaaatattaa cagcaatgat tgggttaaat aacaaaacat tagacgataa aacaagttat 180aaaatcgatg gtaaaggttg gcaaaaagat aaatcttggg gtggttacaa cgttacaaga 240tatgaagtgg taaatggtaa tatcgactta aaacaagcaa tagaatcatc agataacatt 300ttctttgcta gagtagcact cgaattaggc agtaagaaat ttgaaaaagg catgaaaaaa 360ctaggtgttg gtgaagatat accaagtgat tatccatttt ataatgctca aatttcaaac 420aaaaatttag ataatgaaat attattagct gattcaggtt acggacaagg tgaaatactg 480attaacccag tacagatcct ttcaatctat agcgcattag aaaataatgg caatattaac 540gcacctcact tattaaaaga cacgaaaaac aaagtttgga agaaaaatat tatttccaaa 600gaaaatatca atctattaac tgatggtatg caacaagtcg taaataaaac acataaagaa 660gatatttata gatcttatgc aaacttaatt ggcaaatccg gtactgcaga actcaaaatg 720aaacaaggag aaactggcag acaa 74430652DNAStaphylococcus aureus 30ccaccttcat atgacgtcta tccatttatg tatggcatga gtaacgaaga atataataaa 60ttaaccgaag ataaaaaaga acctctgctc aacaagttcc agattacaac ttcaccaggt 120tcaactcaaa aaatattaac agcaatgatt gggttaaata acaaaacatt agacgataaa 180acaagttata aaatcgatgg taaaggttgg caaaaagata aatcttgggg tggttacaac 240gttacaagat atgaagtggt aaatggtaat atcgacttaa aacaagcaat agaatcatca 300gataacattt tctttgctag agtagcactc gaattaggca gtaagaaatt tgaaaaaggc 360atgaaaaaac taggtgttgg tgaagatata ccaagtgatt atccatttta taatgctcaa 420atttcaaaca aaaatttaga taatgaaata ttattagctg attcaggtta cggacaaggt 480gaaatactga ttaacccagt acagatcctt tcaatctata gcgcattaga aaataatggc 540aatattaacg cacctcactt attaaaagac acgaaaaaca aagtttggaa gaaaaatatt 600atttccaaag aaaatatcaa tctattaact gatggtatgc aacaagtcgt aa 652312436DNAStaphylococcus aureus 31ccaccttcat atgacgtcta tccatttatg tatggcatga gtaacgaaga atataataaa 60ttaaccgaag ataaaaaaga acctctgctc aacaagttcc agattacaac ttcaccaggt 120tcaactcaaa aaatattaac agcaatgatt gggttaaata acaaaacatt agacgataaa 180acaagttata aaatcgatgg taaaggttgg caaaaagata aatcttgggg tggttacaac 240gttacaagat atgaagtggt aaatggtaat atcgacttaa aacaagcaat agaatcatca 300gataacattt tctttgctag agtagcactc gaattaggca gtaagaaatt tgaaaaaggc 360atgaaaaaac taggtgttgg tgaagatata ccaagtgatt atccatttta taatgctcaa 420atttcaaaca aaaatttaga taatgaaata ttattagctg attcaggtta cggacaaggt 480gaaatactga ttaacccagt acagatcctt tcaatctata gcgcattaga aaataatggc 540aatattaacg cacctcactt attaaaagac acgaaaaaca aagtttggaa gaaaaatatt 600atttccaaag aaaatatcaa tctattaact gatggtatgc aacaagtcgt aaataaaaca 660cataaagaag atatttatag atcttatgca aacttaattg gcaaatccgg tactgcagaa 720ctcaaaatga aacaaggaga aactggcaga caaattgggt ggtttatatc atatgataaa 780gataatccaa acatgatgat ggctattaat gttaaagatg tacaagataa aggaatggct 840agctacaatg ccaaaatctc aggtaaagtg tatgatgagc tatatgagaa cggtaataaa 900aaatacgata tagatgaata acaaaacagt gaagcaatcc gtaacgatgg ttgcttcact 960gttttattat gaattattaa taagtgctgt tacttctccc ttaaatacaa tttcttcatt 1020ttcattgtat gttgaaagtg acactgtaac gagtccattt tcttttttta tggatttctt 1080atttgtaatt tcagcgataa cgtacaatgt attacctggg tatacaggtt taataaattt 1140aacgttattc atttgtgttc ctgctacaac ttcttctccg tatttacctt cttctaccca 1200taatttaaat gatattgaaa gtgtatgcat gccagatgca atgatacctt taaatctact 1260ttgttctgct ttttctttat ctatatgcat atattgagga tcaaaagttg ttgcaaattg 1320gataatttct tcttctgtaa tatgaaggct ttttgttttg aatgtttctc ctactataaa 1380atcatcgtat ttcatatatg tctctctttc ttattcaaat taatttttta gtatgtaaca 1440tgttaaaggt aagtctaccg tcactgaaac gtaagactca cctctaactt tctattgaga 1500caaatgcacc attttatctg cattgtctgt aaagatacca tcaactcccc aattagcaag 1560ttggtttgca cgtgctggtt tgtttacagt ccatacgttc aattcataac ccgcttcttt 1620taccattttt acttttgctt tagtaagttt ggcatcttca gtgtttacta ttttagcatt 1680acagtaatct aaaagtgttc tccagtcttc acgaaacgaa gttgtatgga atataactgc 1740tctgttatat tgtggcatga tttcttctgc aagtttaaca agcacaacat taaagcttga 1800aatgagcact tcttgattct gatttaagtt tgttaattgt tcttccactt gcttaaccat 1860acttttagaa agtgctagtc cattcggtcc agtaatacct tttaattcta catttaaatt 1920catattatat tcatttgcta tttttactac atcatcgaaa gttggcaaat gttcatcttt 1980gaatttttca ccaaaccaag atcctgcaga agcatcttta atttcatcat aattcaattc 2040agttatttcc ccggacatat ttgtagtccg ttctaaataa tcatcatgaa tgataatcag 2100ttgttcatct tttgtaattg caacatctaa ctccaaccag tttatacctt ctacttctga 2160agcagcttta aatgatgcaa ttgtattttc cggagcttta ctaggtaatc ctctatgtcc 2220atatacagtt agcatattac ctctccttgc atttttattt ttttaattaa cgtaactgta 2280ttatcacatt aatcgcactt ttatttccat taaaaagaga tgaatatcat aaataaagaa 2340gtcgatagat tcgtattgat tatggagtta atctacgtct catctcattt ttaaaaaatc 2400atttatgtcc caagctccat tttgtaatca agtcta 24363236DNAArtificial SequenceSynthetic nucleic acid sequence 32cgcttgccac atcaaatgat gcgggttgtg caagcg 3633336DNAStaphylococcus epidermis 33ctcattactt atgataagct tcttaaaaac ataacagcaa ttcacataaa cctcatatgt 60tctgatacat tcaaaatccc tttatgaagc ggctgaaaaa accgcatcat ttatgatatg 120cttcgcctct catgatctta aatgcgcgat aaatttgttc gatcaatatg acgcgcatat 180ttggtgtggg aaggtcatat tgctaaaaga taaagcatag ttgctgcgtt gtaagacgtc 240ttggtgtaaa ccattggagc cacctatgac aaatgtaaag tcgctttgac cttgtgtcat 300gcgtgtttgt agttctttag cgagtccttc tgaaga 33634260DNAStaphylococcus haemolyticus 34ctcattactt atgataagct tcttaaaaac ataacagcaa tccacataaa cctcatatgt 60tctgatacat tcaaaatccc tttatgaagc ggctgaaaaa accgcatcat ttatgatatg 120cttccctcgc atgattttaa atgctctgta tacttgctcg attaagacaa cgcgcatcat 180ttgatgtggg aatgtcattt tactgaatga aagtgcgtag ttgctgcgtt gtaagacgtc 240ctcatgcaat ccatttgatc 26035225DNAStaphylococcus aureus 35ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgaacaa 120gtgtacagag catttaagat tatgcgtgga gaggcgtatc acaaataaaa ctaaaaatgg 180agtaactatt aatatagtat aaattcaata tggtgataaa aacag 22536225DNAStaphylococcus aureus 36ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattca gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgaacaa

120gtgtacagag catttaagat tatgcgtgga gaggcgtatc acaaataaaa ctaaaaatgg 180agtaactatt aatatagtat aaattcaata tggtgataaa aacag 22537225DNAStaphylococcus aureus 37ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgtag taactacgca 60ctatcattca gcaaaatgac atttccacat caaatgatgc gggttgtgtt aattgaacaa 120gtgtacagag catttaagat tatgcgtgga gaggcgtatc ataagtaatg aggttcatga 180tttttgacat agttagcctc cgcagtcttt caagtaaata atatc 22538225DNAStaphylococcus aureus 38ttcgtcattg gcggatcaaa cggcctgcac aaggacgtct tacaacgcag taactacgca 60ctatcattta gcaaaatgac attcccacat caaatgatgc gggttgtgtt aattgaacaa 120gtgtatagag catttaagat tatgcgtgga gaggcgtatc ataagtgatg cttgttagaa 180tgatttttaa caatatgaaa tagctgtgga agctcaaaca tttgt 225391500DNAStaphylococcus aureus 39tgagtctggt aaagatacac aaccaattgg taaagagaaa gtgatgaatc cagcgaaaca 60accagcgaca ggtaaagttg tgttgttacc agcgcataga ggaactgtta gtagcggtac 120agaaggttct gatcgcgcat tagaaggaac tgctgtatca agtaagagtg ggaaacaatt 180ggctaacatg tcagcgccta aaggtagcgc acatgagaaa cagttaccaa aaactggaac 240tgatcaaagt tcaagcccag cagcgatgtt tgtattagta acaggtatag gtttaatcgc 300gactgtacga cgtagaaaag ctagctaaaa tatattgaaa acaatactac tgtatttctt 360aaataagagg tacggtagtg tttttttatg gaaaaaagct ataaccgttg ataaatatgg 420gatataaaaa cggggataag taataagaca tcaaggtatt tatccacaga aatggggata 480gttatccaga attgtgtaca atttaaagag aaatacccac aatgcccaca gagttatcca 540caaatacaca agttatacac tgaaaattgg gcatgaatgt cagaaaaata tcaaaaactg 600caaaaaaact tggtataata agagggaaaa gtgtgaacaa gttaataact tgtggataac 660tggaaagttg ataacaattt ggaggaccaa acgacatgaa aatcaccatt ttagctgtag 720ggaaactaaa agagaaatat tggaagcaag ccatagcaga atatgaaaaa cgtttaggcc 780catacaccaa gatagacatc atagaagtta cagacgaaaa agcaccagaa aatatgagcg 840acaaagaaat cgagcaagta aaagaaaaag aaggccaacg aatactagcc aaaatcaaac 900cacaatccac agtcattaca ttagaaatac aaggaaagat gctatcttcc gaaggattgg 960cccaagaatt gaaccaacgc atgacccaag ggcaaagcga ctttgtattc gtcattggcg 1020gatcaaacgg cctgcacaag gacgtcttac aacgtagtaa ctacgcacta tcattcagca 1080aaatgacatt tccacatcaa atgatgcggg ttgtgttaat tgaacaagtg tacagagcat 1140ttaagattat gcgtggagaa gcttatcata aatgatgcgg ttttttcttg aaaaatttaa 1200ttagatatta gaatccttta atttatttga aaatcagaag tgagtaacaa tggtaagtga 1260aatagttagt gcaataattg gaattatagg gatttattga gatgtatgga gatgcggggc 1320atttatcgag tagattacaa ttagagcatg taggtgattt gctttttcat gcaagtaaag 1380ataaactttt aaaaatccta taagaattta gaaactttag aataactaaa tattaaaaaa 1440atatcgtatg aaagtgaaat taggatgaga gaccatagct aaattaaaaa ttttagcaaa 1500401501DNAStaphylococcus aureus 40ttgcacaacc aattggtaaa gacaaagtga tggatccagc gaaacaacca gcgccaagta 60aagttgtatt gttgccagcg catagaggaa ctgttagtag tggtagagaa ggttctgatc 120gcgcattgga aggaactgct gtatcaagta agagcgggaa acaattggct agcatgtcag 180cgcctaaagg tagcacacat gagaagcagt taccaaaaac tggaactgat caaagttcaa 240gcccagcagc gatgtttgta ttagtagcag gtataggttt aattgcgact gtacgacgta 300gaaaagctag ctaaaatata ttgaaaacaa tactactgta tttcttaaac aagaggtacg 360gtagtgtttt tttatgaaaa aaagctataa ccgttgataa atatgggata taaaaacggg 420gataagtaat aagacatcaa ggtatttatc cacagaaatg gggatagtta tccagaattg 480tgtacaattt aaagagaaat acccacaatg cccacagagt tatccacaaa tacacaggtt 540atacactaaa aattgggcat gaatgtcaga aaaatatcaa aaactgcaaa gaatattggt 600ataataagag ggaacagtgt gaacaagtta ataacttgtg gataactgga aagttgataa 660caatttggag gaccaaacga catgaaaatc accattttag ctgtagggaa actaaaagag 720aaatattgga agcaagccat agcagaatat gaaaaacgtt taggcccata caccaagata 780gacatcatag aagttccaga cgaaaaagca ccagaaaata tgagcgacaa agaaattgag 840caagtaaaag aaaaagaagg ccaacgaata ctagccaaaa tcaaaccaca atcaacagtc 900attacattag aaatacaagg aaagatgcta tcttccgaag gattggccca agaattgaac 960caacgcatga cccaagggca aagcgacttt gtattcgtca ttggcggatc aaacggcctg 1020cacaaggacg tcttacaacg cagtaactac gcactatcat tcagcaaaat gacattccca 1080catcaaatga tgcgggttgt gttaattgaa caagtgtaca gagcatttaa gattatgcgt 1140ggagaagcat atcataaatg atgcggtttt ttcagccgct tcataaaggg attttgaatg 1200tatcagaaca tatgaggttt atgtgaattg ctgttatgtt tttaagaagc ttatcataag 1260taatgaggtt catgattttt gacatagtta gcctccgcag tctttcattt caagtaaata 1320atagcgaaat attctttata ctgaatactt atagtgaagc aaagttctag ctttgagaaa 1380attctttctg caactaaata tagtaaatta cggtaaaata taaataagta catattgaag 1440aaaatgagac ataatatatt ttataatagg agggaatttc aaatgataga caactttatg 1500c 1501412480DNAStaphylococcus aureus 41aaaccgtctg gcaaacgaat taatgctatt caaattttaa ataaagagac aggtaagttt 60gaaaatattg atttaaaacg tgtatatcac gtaacgatga atgacttcac agcatcaggt 120ggcgacggat atagtatgtt cggtggtcct agagaagaag gtatttcatt agatcaagta 180ctagcaagtt atttaaaaac agctaactta gctaagtatg atacgacaga accacaacgt 240atgttattag gtaaaccagc agtaagtgaa caaccagcta aaggacaaca aggtagcaaa 300ggtagtaagt ctggtaaaga tacacaacca attggtgacg acaaagtgat ggatccagcg 360aaaaaaccag ctccaggtaa agttgtattg ttgctagcgc atagaggaac tgttagtagc 420ggtacagaag gttctggtcg cacaatagaa ggagctactg tatcaagcaa gagtgggaaa 480caattggcta gaatgtcagt gcctaaaggt agcgcgcatg agaaacagtt accaaaaact 540ggaactaatc aaagttcaag cccagaagcg atgtttgtat tattagcagg tataggttta 600atcgcgactg tacgacgtag aaaagctagc taaaatatat tgaaaataat actactgtat 660ttcttaaata agaggtacgg tagtgttttt ttatgaaaaa aagcgataac cgttgataaa 720tatgggatat aaaaacgagg ataagtaata agacatcaag gtgtttatcc acagaaatgg 780ggatagttat ccagaattgt gtacaattta aagagaaata cccacaatgc ccacagagtt 840acccacaaat acacaggtta tacactaaaa atcgggcata aatgtcagga aaatatcaaa 900aactgcaaaa aatattggta taataagagg gaacagtgtg aacaagttaa taacttgtgg 960ataactggaa agttgataac aatttggagg accaaacgac atgaaaatca ccattttagc 1020tgtagggaaa ctaaaagaga aatattggaa gcaagccata gcagaatatg aaaaacgttt 1080aggcccatac accaagatag acatcataga agttccagac gaaaaagcac cagaaaatat 1140gagtgacaaa gaaattgagc aagtaaaaga aaaagaaggc caacgaatac tagccaaaat 1200caaaccacaa tccacagtca ttacattaga aatacaagga aagatgctat cttccgaagg 1260attggcccaa gaattgaacc aacgcatgac ccaagggcaa agcgactttg ttttcgtcat 1320tggcggatca aacggcctgc acaaggacgt cttacaacgc agtaactacg cactatcatt 1380cagcaaaatg acattcccac atcaaatgat gcgggttgtg ttaattgaac aagtgtacag 1440agcatttaag attatgcgag gagaagctta tcataagtaa tgaggttcat gatttttgac 1500atagttagcc tccgcagtct ttcatttcaa gtaaataata gcgaaatatt ctttatactg 1560aatacttata gtgaagcaaa gttctagctt tgagaaaatt ctttctgcaa ctaaatatag 1620taaattacgg taaaatataa ataagtacat attgaagaaa atgagacata atatatttta 1680taataggagg gaatttcaaa tgatagacaa ctttatgcag gtccttaaat taattaaaga 1740gaaacgtacc aataatgtag ttaaaaaatc tgattgggat aaaggtgatc tatataaaac 1800tttagtccat gataagttac ccaagcagtt aaaagtgcat ataaaagaag ataaatattc 1860agttgtaggg aaggttgcta ctgggaacta tagtaaagtt ccttggattt caatatatga 1920tgagaatata acaaaagaaa caaaggatgg atattatttg gtatatcttt ttcatccgga 1980aggagaaggc atatacttat ctttgaatca aggatggtca aagataagtg atatgtttcc 2040gcgggataaa aatgctgcaa aacaaagagc attaacttta tcttccgaac tcaataaata 2100tattacatca aatgaattta atactggaag attttattac gcagaaaata aagattcatc 2160ttatgattta aaaaatgatt atccatcagg atattctcat ggatcaataa gattcaaata 2220ttatgatttg aatgaaggat tcacagaaga agatatgcta gaggatttaa agaaattttt 2280agaactattt aatgaattag cttcaaaagt tacaaaaaca tcctatgata gcttggtcaa 2340tagcatagac gaaatacagg aagacagcga aattgaagaa attagaacag cacaaaaaga 2400taagacactc aaggaagtgg aagcacctaa aggaataatt ccaaaatata aaaaaggtgt 2460atcaaagact actaaaaatg 2480421045DNAStaphylococcus aureus 42ccagtttttt gtttaatgaa caaggtaaat tacgagataa tatttgaaga aaacaataaa 60gtagagatgg atttccatat cctctttagt agcggttttt atctgtaagg tttattaata 120attaaataaa taggcgggat agttatatat agcttattaa tgaaagaata tgattattaa 180tttagtatta tattttaata ttaaaaagaa gatatgaaat aattattcat accttccacc 240ttacaataat tagttttcaa tcgaatatta agattattag tagtcttaaa agttaagact 300tccttatatt aatgacctaa tttattattt gcctcatgaa ttatcttttt atttctttga 360tatgtcccaa accacatcgt gatatacact acaataaata ttatgatgaa actaataata 420ttctcaaagt tcagatggaa ccaacctgct agaatagcga gtgggaagaa taggattatc 480atcaatataa agtgaactac agtctgtttt gttatactcc aatcggtatc tgtaaatatc 540aaattaccat aagtaaacaa aattccaatc aatgcccata gtgctacaca tattagcata 600ataaccgctt cattaaagtt ttcataataa attttaccca taaaagaatc tggatatagt 660ggtacatatt tatcccttga aaaaaataag tgaagtaatg acagaaatca taagaccagt 720gaacgcacct ttttgaacag cgtggaataa ttttttcata gtgagatgga ccattccatt 780tgtttctaac ttcaagtgat caatgtaatt tagattgata atttctgatt ttgaaatacg 840cacgaatatt gaaccgacaa gctcttcaat ttggtaaagt cgctgataaa gttttaaagc 900tttattattc attgttatcg catacctgtt tatcttctac tatgaactgt gcaatttgtt 960ctagatcaat tgggtaaaca tgatggttct gttgcaaagt aaaaaaatat agctaaccac 1020taatttatca tgtcagtgtt cgctt 1045431118DNAStaphylococcus aureus 43cagagcattt aagattatgc gtggagaagc gtaccacaaa tgatgcggtt ttttatccag 60ttttttgttt aatgaacaag gtaaattacg agataatatt tgaagaaaac aataaagtag 120agatggattt ccatatcctc tttagtagcg gtttttatct gtaaggttta ttaataatta 180aataaatagg cgggatagtt atatatagct tattaatgaa agaatatgat tattaattta 240gtattatatt ttaatattaa aaagaagata tgaaataatt attcatacct tccaccttac 300aataattagt tttcaatcga atattaagat tattagtagt cttaaaagtt aagacttcct 360tatattaatg acctaattta ttatttgcct catgaattat ctttttattt ctttgatatg 420tcccaaacca catcgtgata tacactacaa taaatattat gatgaaacta ataatattct 480caaagttcag atggaaccaa cctgctagaa tagcgagtgg gaagaatagg attatcatca 540atataaagtg aactacagtc tgttttgtta tactccaatc ggtatctgta aatatcaaat 600taccataagt aaacaaaatt ccaatcaatg cccatagtgc tacacatatt agcataataa 660ccgcttcatt aaagttttca taataaattt tacccataaa agaatctgga tatagtagta 720catatttatc ccttgaaaaa aataagtgaa gtaatgacag aaatcataag accagtgaac 780gcaccttttt gaacagcgtg gaataatttt ttcatagtga gatggaccat tccatttgtt 840tctaacttca agtgatcaat gtaatttaga ttgataattt ctgattttga aatacgcacg 900aatattgaac cgacaagctc ttcaatttgg taaagtcgct gataaagttt taaagcttta 960ttattcattg ttatcgcata cctgtttatc ttctactatg aactgtgcaa tttgttctag 1020atcaattggg taaacatgat ggttctgttg caaagtaaaa aaatatagct aaccactaat 1080ttatcatgtc agtgttcgct taacttgcta gcatgatg 1118441118DNAStaphylococcus aureus 44cagagcattt aagattatgc gtggagaagc gtaccacaaa tgatgcggtt ttttatccag 60ttttttgttt aatgaacaag gtaaattacg agataatatt tgaagaaaac aataaagtag 120agatggattt ccatatcctc tttagtagcg gtttttatct gtaaggttta ttaataatta 180aataaatagg cgggatagtt atatatagct tattaatgaa agaatatgat tattaattta 240gtattatatt ttaatattaa aaagaagata tgaaataatt attcatacct tccaccttac 300aataattagt tttcaatcga atattaagat tattagtagt cttaaaagtt aagacttcct 360tatattaatg acctaattta ttatttgcct catgaattat ctttttattt ctttgatatg 420tcccaaacca catcgtgata tacactacaa taaatattat gatgaaacta ataatattct 480caaagttcag atggaaccaa cctgctagaa tagcgagtgg gaagaatagg attatcatca 540atataaagtg aactacagtc tgttttgtta tactccaatc ggtatctgta aatatcaaat 600taccataagt aaacaaaatt ccaatcaatg cccatagtgc tacacatatt agcataataa 660ccgcttcatt aaagttttca taataaattt tacccataaa agaatctgga tatagtagta 720catatttatc ccttgaaaaa aataagtgaa gtaatgacag aaatcataag accagtgaac 780gcaccttttt gaacagcgtg gaataatttt ttcatagtga gatggaccat tccatttgtt 840tctaacttca agtgatcaat gtaatttaga ttgataattt ctgattttga aatacgcacg 900aatattgaac cgacaagctc ttcaatttgg taaagtcgct gataaagttt taaagcttta 960ttattcattg ttatcgcata cctgtttatc ttctactatg aactgtgcaa tttgttctag 1020atcaattggg taaacatgat ggttctgttg caaagtaaaa aaatatagct aaccactaat 1080ttatcatgtc agtgttcgct taacttgcta gcatgatg 1118451113DNAStaphylococcus aureus 45agcatttaag attatgcgtg gagaagcgta ccacaaatga tgcggttttt tatccagttt 60tttgtttaat gaacaaggta aattacgaga taatatttga agaaaacaat aaagtagaga 120tggatttcca tatcctcttt agtagcggtt tttatctgta aggtttatta ataattaaat 180aaataggcgg gatagttata tatagcttat taatgaaaga atatgattat taatttagta 240ttatatttta atattaaaaa gaagatatga aataattatt cataccttcc accttacaat 300aattagtttt caatcgaata ttaagattat tagtagtctt aaaagttaag acttccttat 360attaatgacc taatttatta tttgcctcat gaattatctt tttatttctt tgatatgtcc 420caaaccacat cgtgatatac actacaataa atattatgat gaaactaata atattctcaa 480agttcagatg gaaccaacct gctagaatag cgagtgggaa gaataggatt atcatcaata 540taaagtgaac tacagtctgt tttgttatac tccaatcggt atctgtaaat atcaaattac 600cataagtaaa caaaattcca atcaatgccc atagtgctac acatattagc ataataaccg 660cttcattaaa gttttcataa taaattttac ccataaaaga atctggatat agtggtacat 720atttatccct tgaaaaaaat aagtgaagta atgacagaaa tcataagacc agtgaacgca 780cctttttgaa cagcgtggaa taattttttc atagtgagat ggaccattcc atttgtttct 840aacttcaagt gatcaatgta atttagattg ataatttctg attttgaaat acgcacgaat 900attgaaccga caagctcttc aatttggtaa agtcgctgat aaagttttaa agctttatta 960ttcattgtta tcgcatacct gtttatcttc tactatgaac tgtgcaattt gttctagatc 1020aattgggtaa acatgatggt tctgttgcaa agtaaaaaaa tatagctaac cactaattta 1080tcatgtcagt gttcgcttaa cttgctagca tga 1113462153DNAStaphylococcus aureus 46ctgtagggaa actaaaagag aaatactgga agcaagccat agcagaatat gaaaaacgtt 60taggcccata caccaagata gacatcatag aagttccaga cgaaaaagca ccagaaaata 120tgagcgacaa agaaatcgag caagtaaaag aaaaagaagg ccaacgaata ctagccaaaa 180tcaaaccaca atccacagtc attacattag aaatacaagg aaagatgcta tcttccgaag 240gattggccca agaattgaac caacgcatga cccaagggca aagcgacttt gtattcgtca 300ttggcggatc aaacggcctg cacaaggacg tcttacaacg cagtaactac gcactatcat 360tcagcaaaat gacattccca catcaaatga tgcgggttgt gttaattgaa caagtgtaca 420gagcatttaa gattatgcgt ggagaagcgt accacaaatg atgcggtttt ttatccagtt 480ttttgtttaa tgaacaaggt aaattacgag ataatatttg aagaaaacaa taaagtagag 540atggatttcc atatcctctt tagtagcggt ttttatctgt aaggtttatt aataattaaa 600taaataggcg ggatagttat atatagctta ttaatgaaag aatatgatta ttaatttagt 660attatatttt aatattaaaa agaagatatg aaataattat tcataccttc caccttacaa 720taattagttt tcaatcgaat attaagatta ttagtagtct taaaagttaa gacttcctta 780tattaatgac ctaatttatt atttgcctca tgaattatct ttttatttct ttgatatgtc 840ccaaaccaca tcgtgatata cactacaata aatattatga tgaaactaat aatattctca 900aagttcagat ggaaccaacc tgctagaata gcgagtggga agaataggat tatcatcaat 960ataaagtgaa ctacagtctg ttttgttata ctccaatcgg tatctgtaaa tatcaaatta 1020ccataagtaa acaaaattcc aatcaatgcc catagtgcta cacatattag cataataacc 1080gcttcattaa agttttcata ataaatttta cccataaaag aatctggata tagtggtaca 1140tatttatccc ttgaaaaaaa taagtgaagt aatgacagaa atcataagac cagtgaacgc 1200acctttttga acagcgtgga ataatttttt catagtgaga tggaccattc catttgtttc 1260taacttcaag tgatcaatgt aatttagatt gataatttct gattttgaaa tacgcacgaa 1320tattgaaccg acaagctctt caatttggta aagtcgctga taaagtttta aagctttatt 1380attcattgtt atcgcatacc tgtttatctt ctactatgaa ctgtgcaatt tgttctagat 1440caattgggta aacatgatgg ttctgttgca aagtaaaaaa atatagctaa ccactaattt 1500atcatgtcag tgttcgctta acttgctagc atgatgctaa tttcgtggca tggcgaaaat 1560ccgtagatct gatgagacct gcggttcttt ttatatagag cgtaaataca ttcaatacct 1620tttaaagtat tctttgctgt attgatactt tgataccttg tctttcttac tttaatatga 1680cggtgatctt gctcaatgag gttattcaaa tatttcgatg tacaatgaca gtcaggttta 1740agtttaaaag ctttaattac tttagccatt gctaccttcg ttgaaggtgc ctgatctgta 1800attacctttt gaggtttacc aaattgttta atgagacgtt taataaacgc atatgctgaa 1860tgattatctc gttgcttacg caaccaaata tctaatgtat gtccctctgc atcaatggca 1920cgatataaat agctccattt tccttttatt ttgatgtacg tctcatcaat acgccatttg 1980taataagctt ttttatgctt tttcttccaa atttgatata aaattggggc atattcttga 2040acccaacggt agaccgttga atgatgaacg tttacaccac gtccccttaa tatttcagat 2100atatcacgat aactcaatgc atatcttaga tagtagccaa cggctacagt gat 215347737DNAStaphylococcus aureus 47tttaagatta tgcgtggaga agcatatcat aaatgatgcg gttatttcag ccgtaatttt 60ataatataaa gcagagttta ttaaatttta atgattactt tttattaaga attaattcta 120gttgatatat tataatgtga aacacaaaat aataatttgt aattgttagt ttataggcat 180ctgtatttgg aattttttgt agactattta aaaaatagtg tatataagta ttgagttcat 240gtattaactg tcttttttca tcgttcatca agtataagga tgtagagatt tgttggataa 300tttcttcgga tgtttttaaa attatcatta aattagatgg tatctgatct tgagttttgt 360ttttagtgta tgtatatttt aaaaaatttt tgattgttgt tatttgactc tcttttaatt 420tgacaccctc atcaataaat gtgttaaata tatcttcatt tgtacttaaa tcatcaaaat 480ttgccaacaa atatttgaac gtctctaaat cattatgttt gagttccgtt ttgctattcc 540ataattccaa accatttggt agaaagccca agctgtgatt ttgatctccc catatagctg 600aatttaaatc agtgagttga ttaatttttt caacacagaa atgtaatttt ggaatgagga 660atcgaagttg ttcttctact tgctgtactt ttcttttgtt ttcaataaaa tttctacacc 720atactgttat caaaccg 737481592DNAStaphylococcus aureus 48aactaaaaga gaaatattgg aagcaagcca tagcagaata tgaaaaacgt ttaggcccat 60acaccaagat agacatcata gaagttccag acgaaaaagc accagaaaat atgagtgaca 120aagaaattga gcaagtaaaa gaaaaagaag gccaacgaat actagccaaa atcaaaccac 180aatccacagt cattacatta gaaatacaag gaaagatgct atcttccgaa ggattggccc 240aagaattgaa ccaacgcatg acccaagggc aaagcgactt tgttttcgtc attggcggat 300caaacggcct gcacaaggac gtcttacaac gcagtaacta cgcactatca ttcagcaaaa 360tgacattccc acatcaaatg atgcgggttg tgttaattga acaagtgtac agagcattta 420agattatgcg aggagaagca tatcataaat gatgcggtta tttcagccgt aattttataa 480tataaagcag agtttattaa attttaatga ttacttttta ttaagaatta attctagttg 540atatattata atgtgaaaca caaaataata atttgtaatt gttagtttat aggcatctgt 600atttggaatt ttttgtagac tatttaaaaa atagtgtata taagtattga gttcatgtat 660taactgtctt ttttcatcgt tcatcaagta taaggatgta gagatttgtt ggataatttc 720ttcggatgtt tttaaaatta tcattaaatt agatggtatc tgatcttgag ttttgttttt 780agtgtatgta tattttaaaa aatttttgat tgttgttatt tgactctctt ttaatttgac 840accctcatca ataaatgtgt taaatatatc ttcatttgta cttaaatcat caaaatttgc 900caacaaatat ttgaacgtct ctaaatcatt atgtttgagt tccgttttgc tattccataa 960ttccaaacca tttggtagaa agcccaagct gtgattttga tctccccata tagctgaatt 1020taaatcagtg agttgattaa ttttttcaac acagaaatgt aattttggaa tgaggaatcg

1080aagttgttct tctacttgct gtacttttct tttgttttca ataaaatttc tacaccatac 1140tgttatcaaa ccgccaatta ttgtgcacaa tcctccaatg attgtagata aaattgacaa 1200tatattacac acctttctta gaggtttatt aacatctatt tttgaattta aaattattac 1260tttggtagcg ttataaccta tttaacagat tagagaaaaa ttgaatgatc gattgaagaa 1320tttccaaaat accgtcccat atgcgttgaa ggagatttct attttcttct gtattcaaat 1380ctttggcttt atcctttgct ttattcaata aatcatctga gtttttttca atatttttta 1440atacatcttt ggcattttgt ttaaatactt taggatcgga agttagggca ttagagtttg 1500ccacattaat catattatta ttaatcattt gaatttgatt atctgataat atctctgata 1560acctacgctc atcgaggact ttattaacag tg 159249730DNAStaphylococcus aureus 49agcatttaag attatgcgtg gagaagcata tcataaatga tgcggttatt tcagccgtaa 60ttttataata taaagcagag tttattaaat tttaatgatt actttttatt aagaattaat 120tctagttgat atattataat gtgaaacaca aaataataat ttgtaattgt tagtttatag 180gcatctgtat ttggaatttt ttgtagacta tttaaaaaat agtgtatata agtattgagt 240tcatgtatta actgtctttt ttcatcgttc atcaagtata aggatgtaga gatttgttgg 300ataatttctt cggatgtttt taaaattatc attaaattag atggtatctg atcttgagtt 360ttgtttttag tgtatgtata ttttaaaaaa tttttgattg ttgttatttg actctctttt 420aatttgacac cctcatcaat aaatgtgtta aatatatctt catttgtact taaatcatca 480aaatttgcca acaaatattt gaacgtctct aaatcattat gtttgagttc cgttttgcta 540ttccataatt ccaaaccatt tggtagaaag cccaagctgt gattttgatc tccccatata 600gctgaattta aatcagtgag ttgattaatt ttttcaacac agaaatgtaa ttttggaatg 660aggaatcgaa gttgttcttc tacttgctgt acttttcttt tgttttcaat aaaatttcta 720caccatactg 730501696DNAStaphylococcus aureus 50aaagagaaat attggaagca agccatagca gaatatgaaa aacgtttagg cccatacacc 60aagatagaca tcatagaagt tccagacgaa aaagcaccag aaaatatgag tgacaaagaa 120attgagcaag taaaagaaaa agaaggccaa cgaatactag ccaaaatcaa accacaatcc 180acagtcatta cattagaaat acaaggaaag atgctatctt ccgaaggatt ggcccaagaa 240ttgaaccaac gcatgaccca agggcaaagc gactttgttt tcgtcattgg cggatcaaac 300ggcctgcaca aggacgtctt acaacgcagt aactacgcac tatcattcag caaaatgaca 360ttcccacatc aaatgatgcg ggttgtgtta attgaacaag tgtacagagc atttaagatt 420atgcgaggag aagcatatca taaatgatgc ggttatttca gccgtaattt tataatataa 480agcagagttt attaaatttt aatgattact ttttattaag aattaattct agttgatata 540ttataatgtg aaacacaaaa taataatttg taattgttag tttataggca tctgtatttg 600gaattttttg tagactattt aaaaaatagt gtatataagt attgagttca tgtattaact 660gtcttttttc atcgttcatc aagtataagg atgtagagat ttgttggata atttcttcgg 720atgtttttaa aattatcatt aaattagatg gtatctgatc ttgagttttg tttttagtgt 780atgtatattt taaaaaattt ttgattgttg ttatttgact ctcttttaat ttgacaccct 840catcaataaa tgtgttaaat atatcttcat ttgtacttaa atcatcaaaa tttgccaaca 900aatatttgaa cgtctctaaa tcattatgtt tgagttccgt tttgctattc cataattcca 960aaccatttgg tagaaagccc aagctgtgat tttgatctcc ccatatagct gaatttaaat 1020cagtgagttg attaattttt tcaacacaga aatgtaattt tggaatgagg aatcgaagtt 1080gttcttctac ttgctgtact tttcttttgt tttcaataaa atttctacac catactgtta 1140tcaaaccgcc aattattgtg cacaatcctc caatgattgt agataaaatt gacaatatat 1200tacacacctt tcttagaggt ttattaacat ctatttttga atttaaaatt attactttgg 1260tagcgttata acctatttaa cagattagag aaaaattgaa tgatcgattg aagaatttcc 1320aaaataccgt cccatatgcg ttgaaggaga tttctatttt cttctgtatt caaatctttg 1380gctttatcct ttgctttatt caataaatca tctgagtttt tttcaatatt ttttaataca 1440tctttggcat tttgtttaaa tactttagga tcggaagtta gggcattaga gtttgccaca 1500ttaatcatat tattattaat catttgaatt tgattatctg ataatatctc tgataaccta 1560cgctcatcga ggactttatt aacagtgtct tcaacttgtt gttgtgtgat ttgtttatct 1620tgattttgtt taatatctgc aagttgttct ttaatatctg ctatagaagc atttaaagct 1680tcatctgaat acccat 1696512122DNAStaphylococcus aureus 51ggaaactaaa agagaaatat tggaagcaag ccatagcaga atatgaaaaa cgtttaggcc 60catacaccaa gatagacatc atagaagttc cagacgaaaa agcaccagaa aatatgagcg 120acaaagaaat tgagcaagta aaagaaaaag aaggccaacg aatactagcc aaaatcaaac 180cacaatcaac agtcattaca ttagaaatac aaggaaagat gctatcttcc gaaggattgg 240cccaagaatt gaaccaacgc atgacccaag ggcaaagcga ctttgtattc gtcattggcg 300gatcaaacgg cctgcacaag gacgtcttac aacgcagtaa ctacgcacta tcattcagca 360aaatgacatt cccacatcaa atgatgcggg ttgtgttaat tgaacaagtg tacagagcat 420ttaagattat gcgtggagaa gcgtaccaca aatgatgcgg ttttttatcc agttttttgt 480ttaatgaaca aggtaaatta cgagataata tttgaagaaa acaataaagt agagatggat 540ttccatatcc tctttagtag cggtttttat ctgtaaggtt tattaataat taaataaata 600ggcgggatag ttatatatag cttattaatg aaagaatatg attattaatt tagtattata 660ttttaatatt aaaaagaaga tatgaaataa ttattcatac cttccacctt acaataatta 720gttttcaatc gaatattaag attattagta gtcttaaaag ttaagacttc cttatattaa 780tgacctaatt tattatttgc ctcatgaatt atctttttat ttctttgata tgtcccaaac 840cacatcgtga tatacactac aataaatatt atgatgaaac taataatatt ctcaaagttc 900agatggaacc aacctgctag aatagcgagt gggaagaata ggattatcat caatataaag 960tgaactacag tctgttttgt tatactccaa tcggtatctg taaatatcaa attaccataa 1020gtaaacaaaa ttccaatcaa tgcccatagt gctacacata ttagcataat aaccgcttca 1080ttaaagtttt cataataaat tttacccata aaagaatctg gatatagtgg tacatattta 1140tcccttgaaa aaaataagtg aagtaatgac agaaatcata agaccagtga acgcaccttt 1200ttgaacagcg tggaataatt ttttcatagt gagatggacc attccatttg tttctaactt 1260caagtgatca atgtaattta gattgataat ttctgatttt gaaatacgca cgaatattga 1320accgacaagc tcttcaattt ggtaaagtcg ctgataaagt tttaaagctt tattattcat 1380tgttatcgca tacctgttta tcttctacta tgaactgtgc aatttgttct agatcaattg 1440ggtaaacatg atggttctgt tgcaaagtaa aaaaatatag ctaaccacta atttatcatg 1500tcagtgttcg cttaacttgc tagcatgatg ctaatttcgt ggcatggcga aaatccgtag 1560atctgatgag acctgcggtt ctttttatat agagcgtaaa tacattcaat accttttaaa 1620gtattctttg ctgtattgat actttgatac cttgtctttc ttactttaat atgacggtga 1680tcttgctcaa tgaggttatt cagatatttc gatgtacaat gacagtcagg tttaagttta 1740aaagctttaa ttactttagc cattgctacc ttcgttgaag gtgcctgatc tgtaattacc 1800ttttgaggtt taccaaattg tttaatgaga cgtttgataa acgcatatgc tgaatgatta 1860tctcgttgct tacgcaacca aatatctaat gtatgtccct ctgcatcaat ggcacgatat 1920aaatagctcc attttccttt tattttgatg tacgtctcat caatacgcca tttgtaataa 1980gcttttttat gctttttctt ccaaatttga tacaaaattg gggcatattc ttgaacccaa 2040cggtagaccg ttgaatgatg aacgtttaca ccacgttccc ttaatatttc agatatatca 2100cgataactca atgtatatct ta 21225221DNAArtificial SequenceSynthetic nucleic acid sequence 52gatagactaa ttatcttcat c 215321DNAArtificial SequenceSynthetic nucleic acid sequence 53cagactgtgg acaaactgat t 215420DNAArtificial SequenceSynthetic nucleic acid sequence 54tgagatcatc tacatcttta 205520DNAArtificial SequenceSynthetic nucleic acid sequence 55ggatcaaaag ctactaaatc 205620DNAArtificial SequenceSynthetic nucleic acid sequence 56atgctctttg ttttgcagca 205723DNAArtificial SequenceSynthetic nucleic acid sequence 57atgaaagact gcggaggcta act 235823DNAArtificial SequenceSynthetic nucleic acid sequence 58atattctaga tcatcaatag ttg 235921DNAArtificial SequenceSynthetic nucleic acid sequence 59aagaattgaa ccaacgcatg a 216021DNAArtificial SequenceSynthetic nucleic acid sequence 60gttcaagccc agaagcgatg t 216123DNAArtificial SequenceSynthetic nucleic acid sequence 61tcgggcataa atgtcaggaa aat 236221DNAArtificial SequenceSynthetic nucleic acid sequence 62aaacgacatg aaaatcacca t 216333DNAArtificial SequenceSynthetic nucleic acid sequence 63ttattaggta aaccagcagt aagtgaacaa cca 336419DNAArtificial SequenceSynthetic nucleic acid sequence 64ggatcaaacg gcctgcaca 196526DNAArtificial SequenceSynthetic nucleic acid sequence 65cacagaaatg taattttgga atgagg 266629DNAArtificial SequenceSynthetic nucleic acid sequence 66gtcaaaaatc atgaacctca ttacttatg 296729DNAArtificial SequenceSynthetic nucleic acid sequence 67atttcatata tgtaattcct ccacatctc 296820DNAArtificial SequenceSynthetic nucleic acid sequence 68tctacggatt ttcgccatgc 206927DNAArtificial SequenceSynthetic nucleic acid sequence 69aacaggtgaa ttattagcac ttgtaag 277021DNAArtificial SequenceSynthetic nucleic acid sequence 70atcaaatgat gcgggttgtg t 217119DNAArtificial SequenceSynthetic nucleic acid sequence 71tcattggcgg atcaaacgg 197222DNAArtificial SequenceSynthetic nucleic acid sequence 72acaacgcagt aactacgcac ta 227322DNAArtificial SequenceSynthetic nucleic acid sequence 73taactacgca ctatcattca gc 227422DNAArtificial SequenceSynthetic nucleic acid sequence 74acatcaaatg atgcgggttg tg 227522DNAArtificial SequenceSynthetic nucleic acid sequence 75tcaaatgatg cgggttgtgt ta 227624DNAArtificial SequenceSynthetic nucleic acid sequence 76caaatgatgc gggttgtgtt aatt 247726DNAArtificial SequenceSynthetic nucleic acid sequence 77ctactatgaa ctgtgcaatt tgttct 26782007DNAStaphylococcus aureus 78atgaaaaaga taaaaattgt tccacttatt ttaatagttg tagttgtcgg gtttggtata 60tatttttatg cttcaaaaga taaagaaatt aataatacta ttgatgcaat tgaagataaa 120aatttcaaac aagtttataa agatagcagt tatatttcta aaagcgataa tggtgaagta 180gaaatgactg aacgtccgat aaaaatatat aatagtttag gcgttaaaga tataaacatt 240caggatcgta aaataaaaaa agtatctaaa aataaaaaac gagtagatgc tcaatataaa 300attaaaacaa actacggtaa cattgatcgc aacgttcaat ttaattttgt taaagaagat 360ggtatgtgga agttagattg ggatcatagc gtcattattc caggaatgca gaaagaccaa 420agcatacata ttgaaaattt aaaatcagaa cgtggtaaaa ttttagaccg aaacaatgtg 480gaattggcca atacaggaac acatatgaga ttaggcatcg ttccaaagaa tgtatctaaa 540aaagattata aagcaatcgc taaagaacta agtatttctg aagactatat caacaacaaa 600tggatcaaaa ttgggtacaa gatgatacct tcgttccact ttaaaaccgt taaaaaaatg 660gatgaatatt taagtgattt cgcaaaaaaa tttcatctta caactaatga aacagaaagt 720cgtaactatc ctctagaaaa agcgacttca catctattag gttatgttgg tcccattaac 780tctgaagaat taaaacaaaa agaatataaa ggctataaag atgatgcagt tattggtaaa 840aagggactcg aaaaacttta cgataaaaag ctccaacatg aagatggcta tcgtgtcaca 900atcgttgacg ataatagcaa tacaatcgca catacattaa tagagaaaaa gaaaaaagat 960ggcaaagata ttcaactaac tattgatgct aaagttcaaa agagtattta taacaacatg 1020aaaaatgatt atggctcagg tactgctatc caccctcaaa caggtgaatt attagcactt 1080gtaagcacac cttcatatga cgtctatcca tttatgtatg gcatgagtaa cgaagaatat 1140aataaattaa ccgaagataa aaaagaacct ctgctcaaca agttccagat tacaacttca 1200ccaggttcaa ctcaaaaaat attaacagca atgattgggt taaataacaa aacattagac 1260gataaaacaa gttataaaat cgatggtaaa ggttggcaaa aagataaatc ttggggtggt 1320tacaacgtta caagatatga agtggtaaat ggtaatatcg acttaaaaca agcaatagaa 1380tcatcagata acattttctt tgctagagta gcactcgaat taggcagtaa gaaatttgaa 1440aaaggcatga aaaaactagg tgttggtgaa gatataccaa gtgattatcc attttataat 1500gctcaaattt caaacaaaaa tttagataat gaaatattat tagctgattc aggttacgga 1560caaggtgaaa tactgattaa cccagtacag atcctttcaa tctatagcgc attagaaaat 1620aatggcaata ttaacgcacc tcacttatta aaagacacga aaaacaaagt ttggaagaaa 1680aatattattt ccaaagaaaa tatcaatcta ttaaatgatg gtatgcaaca agtcgtaaat 1740aaaacacata aagaagatat ttatagatct tatgcaaact taattggcaa atccggtact 1800gcagaactca aaatgaaaca aggagaaagt ggcagacaaa ttgggtggtt tatatcatat 1860gataaagata atccaaacat gatgatggct attaatgtta aagatgtaca agataaagga 1920atggctagct acaatgccaa aatctcaggt aaagtgtatg atgagctata tgagaacggt 1980aataaaaaat acgatataga tgaataa 20077929DNAArtificial SequenceSynthetic nucleic acid sequence 79caaatattat ctcgtaattt accttgttc 298029DNAArtificial SequenceSynthetic nucleic acid sequence 80ctctgcttta tattataaaa ttacggctg 298127DNAArtificial SequenceSynthetic nucleic acid sequence 81attgctgtta atattttttg agttgaa 27822007DNAStaphylococcus aureus 82atgaaaaaga taaaaattgt tccacttatt ttaatagttg tagttgtcgg gtttggtata 60tatttttatg cttcaaaaga taaagaaatt aataatacta ttgatgcaat tgaagataaa 120aatttcaaac aagtttataa agatagcagt tatatttcta aaagcgataa tggtgaagta 180gaaatgactg aacgtccgat aaaaatatat aatagtttag gcgttaaaga tataaacatt 240caggatcgta aaataaaaaa agtatctaaa aataaaaaac gagtagatgc tcaatataaa 300attaaaacaa actacggtaa cattgatcgc aacgttcaat ttaattttgt taaagaagat 360ggtatgtgga agttagattg ggatcatagc gtcattattc caggaatgca gaaagaccaa 420agcatacata ttgaaaattt aaaatcagaa cgtggtaaaa ttttagaccg aaacaatgtg 480gaattggcca atacaggaac agcatatgag ataggcatcg ttccaaagaa tgtatctaaa 540aaagattata aagcaatcgc taaagaacta agtatttctg aagactatat caaacaacaa 600atggatcaaa attgggtaca agatgatacc ttcgttccac ttaaaaccgt taaaaaaatg 660gatgaatatt taagtgattt cgcaaaaaaa tttcatctta caactaatga aacagaaagt 720cgtaactatc ctctagaaaa agcgacttca catctattag gttatgttgg tcccattaac 780tctgaagaat taaaacaaaa agaatataaa ggctataaag atgatgcagt tattggtaaa 840aagggactcg aaaaacttta cgataaaaag ctccaacatg aagatggcta tcgtgtcaca 900atcgttgacg ataatagcaa tacaatcgca catacattaa tagagaaaaa gaaaaaagat 960ggcaaagata ttcaactaac tattgatgct aaagttcaaa agagtattta taacaacatg 1020aaaaatgatt atggctcagg tactgctatc caccctcaaa caggtgaatt attagcactt 1080gtaagcacac cttcatatga cgtctatcca tttatgtatg gcatgagtaa cgaagaatat 1140aataaattaa ccgaagataa aaaagaacct ctgctcaaca agttccagat tacaacttca 1200ccaggttcaa ctcaaaaaat attaacagca atgattgggt taaataacaa aacattagac 1260gataaaacaa gttataaaat cgatggtaaa ggttggcaaa aagataaatc ttggggtggt 1320tacaacgtta caagatatga agtggtaaat ggtaatatcg acttaaaaca agcaatagaa 1380tcatcagata acattttctt tgctagagta gcactcgaat taggcagtaa gaaatttgaa 1440aaaggcatga aaaaactagg tgttggtgaa gatataccaa gtgattatcc attttataat 1500gctcaaattt caaacaaaaa tttagataat gaaatattat tagctgattc aggttacgga 1560caaggtgaaa tactgattaa cccagtacag atcctttcaa tctatagcgc attagaaaat 1620aatggcaata ttaacgcacc tcacttatta aaagacacga aaaacaaagt ttggaagaaa 1680aatattattt ccaaagaaaa tatcaatcta ttaactgatg gtatgcaaca agtcgtaaat 1740aaaacacata aagaagatat ttatagatct tatgcaaact taattggcaa atccggtact 1800gcagaactca aaatgaaaca aggagaaact ggcagacaaa ttgggtggtt tatatcatat 1860gataaagata atccaaacat gatgatggct attaatgtta aagatgtaca agataaagga 1920atggctagct acaatgccaa aatctcaggt aaagtgtatg atgagctata tgagaacggt 1980aataaaaaat acgatataga tgaataa 20078336DNAArtificial SequenceSynthetic nucleic acid sequence 83cccaccccac atcaaatgat gcgggttgtg ggtggg 368437DNAArtificial SequenceSynthetic nucleic acid sequence 84cccgcgcgta gttactgcgt tgtaagacgt ccgcggg 378527DNAArtificial SequenceSynthetic nucleic acid sequence 85gtttttatca ccatattgaa tttatac 278625DNAArtificial SequenceSynthetic nucleic acid sequence 86atttacttga aagactgcgg aggag 258724DNAArtificial SequenceSynthetic nucleic acid sequence 87tgtttgagct tccacagcta tttc 248827DNAArtificial SequenceSynthetic nucleic acid sequence 88ccctataatt ccaattattg cactaac 278925DNAArtificial SequenceSynthetic nucleic acid sequence 89atgaggagat aataatttgg agggt 25902007DNAStaphylococcus aureus 90atgaaaaaga taaaaattgt tccacttatt ttaatagttg tagttgtcgg gtttggtata 60tatttttatg cttccaaaga taaagaaatt aataatacta ttgatgcaat tgaagataaa 120aatttcaaac aagtttataa agatagcagt tatatttcta aaagcgataa tggtgaagta 180gaaatgactg aacgtccgat aaaaatatat aatagtttag gcgttaaaga tataaacatt 240caggatcgta aaataaaaaa agtatctaaa aataaaaaac gagtagatgc tcaatataaa 300attaaaacaa actacggtaa cattgatcgc aacgttcaat ttaattttgt taaagaagat 360ggtatgtgga agttagattg ggatcatagc gtcattattc caggaatgca gaaagaccaa 420agcatacata ttgaaaattt aaaatcagaa cgtggtaaaa ttttagaccg aaacaatgtg 480gaattggcca atacaggaac agcatatgag ataggcatcg ttccaaagaa tgtatctaaa 540aaagattata aagcaatcgc taaagaacta agtatttctg aagactatat caaacaacaa 600atggatcaaa attgggtaca agatgatacc ttcgttccac ttaaaaccgt taaaaaaatg 660gatgaatatt taagtgattt cgcaaaaaaa tttcatctta caactaatga aacagaaagt 720cgtaactatc ctctaggaaa agcgacttca catctattag gttatgttgg tcccattaac 780tctgaagaat taaaacaaaa agaatataaa ggctataaag atgatgcagt tattggtaaa 840aagggactcg aaaaacttta cgataaaaag ctccaacatg aagatggcta tcgtgtcaca 900atcgttgacg ataatagcaa tacaatcgca catacattaa tagagaaaaa gaaaaaagat 960ggcaaagata ttcaactaac tattgatgct aaagttcaaa agagtattta taacaacatg 1020aaaaatgatt atggctcagg tactgctatc caccctcaaa caggtgaatt attagcactt 1080gtaagcacac cttcatatga cgtctatcca tttatgtatg gcatgagtaa cgaagaatat 1140aataaattaa ccgaagataa aaaagaacct ctgctcaaca agttccagat tacaacttca 1200ccaggttcaa ctcaaaaaat attaacagca atgattgggt taaataacaa aacattagac 1260gataaaacaa gttataaaat cgatggtaaa ggttggcaaa aagataaatc ttggggtggt 1320tacaacgtta caagatatga agtggtaaat

ggtaatatcg acttaaaaca agcaatagaa 1380tcatcagata acattttctt tgctagagta gcactcgaat taggcagtaa gaaatttgaa 1440aaaggcatga aaaaactagg tgttggtgaa gatataccaa gtgattatcc attttataat 1500gctcaaattt caaacaaaaa tttagataat gaaatattat tagctgattc aggttacgga 1560caaggtgaaa tactgattaa cccagtacag atcctttcaa tctatagcgc attagaaaat 1620aatggcaata ttaacgcacc tcacttatta aaagacacga aaaacaaagt ttggaagaaa 1680aatattattt ccaaagaaaa tatcaatcta ttaactgatg gtatgcaaca agtcgtaaat 1740aaaacacata aagaagatat ttatagatct tatgcaaact taattggcaa atccggtact 1800gcagaactca aaatgaaaca aggagaaact ggcagacaaa ttgggtggtt tatatcatat 1860gataaagata atccaaacat gatgatggct attaatgtta aagatgtaca agataaagga 1920atggctagct acaatgccaa aatctcaggt aaagtgtatg atgagctata tgagaacggt 1980aataaaaaat acgatataga tgaataa 2007912007DNAStaphylococcus aureus 91atgaaaaaga taaaaattgt tccacttatt ttaatagttg tagttgtcgg gtttggtata 60tatttttatg cttcaaaaga taaagaaatt aataatacta ttgatgcaat tgaagataaa 120aatttcaaac aagtttataa agatagcagt tatatttcta aaagcgataa tggtgaagta 180gaaatgactg aacgtccgat aaaaatatat aatagtttag gcgttaaaga tataaacatt 240caggatcgta aaataaaaaa agtatctaaa aataaaaaac gagtagatgc tcaatataaa 300attaaaacaa actacggtaa cattgatcgc aacgttcaat ttaattttgt taaagaagat 360ggtatgtgga agttagattg ggatcatagc gtcattattc caggaatgca gaaagaccaa 420agcatacata ttgaaaattt aaaatcagaa cgtggtaaaa ttttagaccg aaacaatgtg 480gaattggcca atacaggaac agcatatgag ataggcatcg ttccaaagaa tgtatctaaa 540aaagattata aagcaatcgc taaagaacta agtatttctg aagactatat caaacaacaa 600atggatcaaa agtgggtaca agatgatacc ttcgttccac ttaaaaccgt taaaaaaatg 660gatgaatatt taagtgattt cgcaaaaaaa tttcatctta caactaatga aacagaaagt 720cgtaactatc ctctagaaaa agcgacttca catctattag gttatgttgg tcccattaac 780tctgaagaat taaaacaaaa agaatataaa ggctataaag atgatgcagt tattggtaaa 840aagggactcg aaaaacttta cgataaaaag ctccaacatg aagatggcta tcgtgtcaca 900atcgttgacg ataatagcaa tacaatcgca catacattaa tagagaaaaa gaaaaaagat 960ggcaaagata ttcaactaac tattgatgct aaagttcaaa agagtattta taacaacatg 1020aaaaatgatt atggctcagg tactgctatc caccctcaaa caggtgaatt attagcactt 1080gtaagcacac cttcatatga cgtctatcca tttatgtatg gcatgagtaa cgaagaatat 1140aataaattaa ccgaagataa aaaagaacct ctgctcaaca agttccagat tacaacttca 1200ccaggttcaa ctcaaaaaat attaacagca atgattgggt taaataacaa aacattagac 1260gataaaacaa gttataaaat cgatggtaaa ggttggcaaa aagataaatc ttggggtggt 1320tacaacgtta caagatatga agtggtaaat ggtaatatcg acttaaaaca agcaatagaa 1380tcatcagata acattttctt tgctagagta gcactcgaat taggcagtaa gaaatttgaa 1440aaaggcatga aaaaactagg tgttggtgaa gatataccaa gtgattatcc attttataat 1500gctcaaattt caaacaaaaa tttagataat gaaatattat tagctgattc aggttacgga 1560caaggtgaaa tactgattaa cccagtacag atcctttcaa tctatagcgc attagaaaat 1620aatggcaata ttaacgcacc tcacttatta aaagacacga aaaacaaagt ttggaagaaa 1680aatattattt ccaaagaaaa tatcaatcta ttaactgatg gtatgcaaca agtcgtaaat 1740aaaacacata aagaagatat ttatagatct tatgcaaact taattggcaa atccggtact 1800gcagaactca aaatgaaaca aggagaaact ggcagacaaa ttgggtggtt tatatcatat 1860gataaagata atccaaacat gatgatggct attaatgtta aagatgtaca agataaagga 1920atggctagct acaatgccaa aatctcaggt aaagtgtatg atgagctata tgagaacggt 1980aataaaaaat acgatataga tgaataa 200792675DNAStaphylococcus aureus 92atgaactatt tcagatataa acaatttaac aaggatgtta tcactgtagc cgttggctac 60tatctaagat atacattgag ttatcgtgat atatctgaaa tattaaggga acgtggtgta 120aacgttcatc attcaacggt ctaccgttgg gttcaagaat atgccccaat tttgtatcaa 180atttggaaga aaaagcataa aaaagcttat tacaaatggc gtattgatga gacgtacatc 240aaaataaaag gaaaatggag ctatttatat cgtgccattg atgcagaggg acatacatta 300gatatttggt tgcgtaagca acgagataat cattcagcat atgcgtttat caaacgtctc 360attaaacaat ttggtaaacc tcaaaaggta attacagatc aggcaccttc aacgaaggta 420gcaatggcta aagtaattaa agcttttaaa cttaaacctg actgtcattg tacatcgaaa 480tatctgaata acctcattga gcaagatcac cgtcatatta aagtaagaaa gacaaggtat 540caaagtatca atacagcaaa gaatacttta aaaggtattg aatgtattta cgctctatat 600aaaaagaacc gcaggtctct tcagatctac ggattttcgc catgccacga aattagcatc 660atgctagcaa gttaa 67593675DNAStaphylococcus aureus 93atgaactatt tcagatataa acaatttaac aaggatgtta tcactgtagc cgttggctac 60tatctaagat atacattgag ttatcgtgat atatctgaaa tattaaggga acgtggtgta 120aacgttcatc attcaacggt ctaccgttgg gttcaagaat atgccccaat tttgtatcaa 180atttggaaga aaaagcataa aaaagcttat tacaaatggc gtattgatga gacgtacatc 240aaaataaaag gaaaatggag ctatttatat cgtgccattg atgcagaggg acatacatta 300gatatttggt tgcgtaagca acgagataat cattcagcat atgcgtttat caaacgtctc 360attaaacaat ttggtaaacc tcaaaaggta attacagatc aggcaccttc aacgaaggta 420gcaatggcta aagtaattaa agcttttaaa cttaaacctg actgtcattg tacatcgaaa 480tatctgaata acctcattga gcaagatcac cgtcatatta aagtaagaaa gacaaggtat 540caaagtatca atacagcaaa gaatacttta aaaggtattg aatgtattta cgctctatat 600aaaaagaacc gcaggtctct tcagatctac ggattttcgc catgccacga aattagcatc 660atgctagcaa gttaa 67594675DNAStaphylococcus aureus 94atgaactatt tcagatataa acaatttaac aaggatgtta tcactgtagc cgttggctac 60tatctaagat atacattgag ttatcgtgat atatctgaaa tattaaggga acgtggtgta 120aacgttcatc attcaacggt ctaccgttgg gttcaagaat atgccccaat tttgtatcaa 180atttggaaga aaaagcataa aaaagcttat tacaaatggc gtattgatga gacgtacatc 240aaaataaaag gaaaatggag ctatttatat cgtgccattg atgcagaggg acatacatta 300gatatttggt tgcgtaagca acgagttaat cattcagcat atgcgtttat caaacgtctc 360attaaacaat ttggtaaacc tcaaaaggta attacagatc aggcaccttc aacgaaggta 420gcaatggcta aagtaattaa agcttttaaa cttaaacctg actgtcattg tacatcgaaa 480tatctgaata acctcattga gcaagatcac cgtcatatta aagtaagaaa gacaaggtat 540caaagtatca atacagcaaa gaatacttta aaaggtattg aatgtattca cgctctatat 600aaaaagaacc gcaggtctct tcagatctac ggattttcgc catgccacga aattagcatc 660atgctagcaa gttaa 67595675DNAStaphylococcus aureus 95atgaactatt tcagatataa acaatttaac aaggatgtta tcactgtagc cgttggctac 60tatctaagat atacattgag ttatcgtgat atatctgaaa tattaaggga acgtggtgta 120aacgttcatc attcaacggt ctaccgttgg gttcaagaat atgccccaat tttgtatcaa 180atttggaaga aaaagcataa aaaagcttat tacaaatggc gtattgatga gacgtacatc 240aaaataaaag gaaaatggag ctatttatat cgtgccattg atgcagaggg acatacatta 300gatatttggt tgcgtaagca acgagataat cattcagcat atgcgtttat caaacgtctc 360attaaacaat ttggtaaacc tcaaaaggta attacagatc aggcaccttc aacgaaggta 420gcaatggcta aagtaattaa agcttttaaa cttaaacctg actgtcattg tacatcgaaa 480tatctgaata acctcattga gcaagatcac cgtcatatta aagtaagaaa gacaaggtat 540caaagtatca atacagcaaa gaatacttta aaaggtattg aatgtattta cgctctatat 600aaaaagaacc gcaggtctct tcagatctac ggattttcgc catgccacga aattagcatc 660atgctagcaa gttaa 6759628DNAArtificial SequenceSynthetic nucleic acid sequence 96gtaaagtgta tgatgagcta tatgagaa 289727DNAArtificial SequenceSynthetic nucleic acid sequence 97gctgaaaaaa ccgcatcatt trtgrta 279829DNAArtificial SequenceSynthetic nucleic acid sequence 98tttagtttta tttatgatac gcttctcca 299927DNAArtificial SequenceSynthetic nucleic acid sequence 99gctgaaaaaa ccgcatcatt tatgata 2710028DNAArtificial SequenceSynthetic nucleic acid sequence 100ctatgtcaaa aatcatgaac ctcattac 2810123DNAArtificial SequenceSynthetic nucleic acid sequence 101ggaggctaac tatgtcaaaa atc 2310225DNAArtificial SequenceSynthetic nucleic acid sequence 102ctctataaac atcgtatgat attgc 2510320DNAArtificial SequenceSynthetic nucleic acid sequence 103accaaacgac atgaaaatca 201041256DNAStaphylococcus aureus 104ttcagaaaaa tgattaatgt gtttcaataa aatctctcct tctttgtgaa catattcatt 60tttatactaa ttaatataat ttccaaaaaa gtttctgttt aaaagtgaaa aatattattt 120accgtttgac ttaaatcttc aatatatagg tgtttatatg tatcattttg cgccaatttg 180aataaacggg aatcaagtct gtttctgagt ttatttcaac tttcttatag taaacattgt 240cttaatatga tgaacttcaa taaaactttc cctatgcccc ataaaatttt ctcaaaatca 300aaaataacat accttacaac ttttaccgtc gatatcaatt gctcttttct taatttagga 360ttgctttcaa attttgtact ataacgtgaa actacttttc cttctttata attaaaattt 420actaattcac aatcattttt acttccattt acaaaaacat ccactgtttc taacacaaaa 480tctaataaac ttccttttat taatcgtagg cattgtatat ttcctttcat tctttcttga 540ttccattagt ttaaatttaa aatttcatcc atcaatttct taatttaatt gtagttccat 600aatcaatata atttgtacag ttattatata ttctagatca tcaatagttg aaaaatggtt 660tattaaacac tctataaaca tcgtatgata ttgcaaggta taatccaata tttcatatat 720gtaattcctc cacatctcat taaattttta aattatacac aacctaattt ttagttttat 780ttatgatacg cttctccacg cataatctta aatgctctgt acacttgttc aattaacaca 840acccgcatca tttgatgtgg gaatgtcatt ttgctgaatg atagtgcgta gttactgcgt 900tgtaagacgt ccttgtgcag gccgtttgat ccgccaatga cgaatacaaa gtcgctttgc 960ccttgggtca tgcgttggtt caattcttgg gccaatcctt cggaagatag catctttcct 1020tgtatttcta atgtaatgac tgttgattgt ggtttgattt tggctagtat tcgttggcct 1080tctttttctt ttacttgctc aatttctttg tcgctcatat tttctggtgc tttttcgtct 1140ggaacttcta tgatgtctat cttggtgtat gggcctaaac gtttttcata ttctgctatg 1200gcttgcttcc aatatttctc ttttagtttc cctacagcta aaatggtgat tttcat 125610528DNAArtificial Sequencemisc_feature27n = inosineSynthetic nucleic acid sequence 105tcatgaacct cattacttat gataagnt 2810628DNAArtificial Sequencemisc_feature27n = inosineSynthetic nucleic acid sequence 106gaaaaaaccg catcatttat gatatgnt 2810730DNAArtificial Sequencemisc_feature29n = inosineSynthetic nucleic acid sequence 107cctaattttt agttttattt atgatacgnt 3010835DNAArtificial Sequencemisc_feature34n = inosineSynthetic nucleic acid sequence 108cacaacctaa tttttagttt tatttatgat acgnt 3510924DNAArtificial SequenceSynthetic nucleic acid sequence 109tgataagcca ttcattcacc ctaa 2411027DNAArtificial SequenceSynthetic nucleic acid sequence 110aaggactcct aatttatgtc taattcc 2711124DNAArtificial SequenceSynthetic nucleic acid sequence 111atgggagtcc ttcgctattc tgtg 2411227DNAArtificial SequenceSynthetic nucleic acid sequence 112cactttttat tcttcaaaga tttgagc 2711328DNAArtificial SequenceSynthetic nucleic acid sequence 113atggaaattc ttaatcttta cttgtacc 2811424DNAArtificial SequenceSynthetic nucleic acid sequence 114agcatcttct ttacatcgct tact 2411523DNAArtificial SequenceSynthetic nucleic acid sequence 115cagcaattcw cataaacctc ata 2311627DNAArtificial SequenceSynthetic nucleic acid sequence 116acaaactttg aggggatttt tagtaaa 2711722DNAArtificial SequenceSynthetic nucleic acid sequence 117tatattgtgg catgatttct tc 2211823DNAArtificial SequenceSynthetic nucleic acid sequence 118cgaatggact agcactttct aaa 2311921DNAArtificial SequenceSynthetic nucleic acid sequence 119ttgaggatca aaagttgttg c 2112021DNAArtificial SequenceSynthetic nucleic acid sequence 120cgatgatttt atagtaggag a 2112128DNAArtificial SequenceSynthetic nucleic acid sequence 121ttcaatctct aaatctaaat cagttttg 2812224DNAArtificial SequenceSynthetic nucleic acid sequence 122aggcgagaaa atggaacata tcaa 2412326DNAArtificial SequenceSynthetic nucleic acid sequence 123ggtacaagta aagattaaga atttcc 2612422DNAArtificial SequenceSynthetic nucleic acid sequence 124agacaacttt atgcaggtcc tt 2212522DNAArtificial SequenceSynthetic nucleic acid sequence 125taactgcttg ggtaacctta tc 2212621DNAArtificial SequenceSynthetic nucleic acid sequence 126tattgcaggt ttcgatgttg a 2112722DNAArtificial SequenceSynthetic nucleic acid sequence 127tgacccatat cgcctaaaat ac 2212822DNAArtificial SequenceSynthetic nucleic acid sequence 128aaaggacaac aaggtagcaa ag 2212922DNAArtificial SequenceSynthetic nucleic acid sequence 129tctgtggata aacaccttga tg 2213018DNAArtificial SequenceSynthetic nucleic acid sequence 130gtttgatccg ccaatgac 1813123DNAArtificial SequenceSynthetic nucleic acid sequence 131ggcataaatg tcaggaaaat atc 2313223DNAArtificial SequenceSynthetic nucleic acid sequence 132gaggaccaaa cgacatgaaa atc 2313320DNAArtificial SequenceSynthetic nucleic acid sequence 133ttcgaggttg atgggaagca 2013418DNAArtificial SequenceSynthetic nucleic acid sequence 134cgctcgactc agggtgtt 1813518DNAArtificial SequenceSynthetic nucleic acid sequence 135cgttgaagat gcctttga 1813618DNAArtificial SequenceSynthetic nucleic acid sequence 136ttttgcaaca gccattcg 1813721DNAArtificial SequenceSynthetic nucleic acid sequence 137gcacacatgt tgtaagtttg c 2113822DNAArtificial SequenceSynthetic nucleic acid sequence 138acgcaaactt acaacatgtg tg 2213922DNAArtificial SequenceSynthetic nucleic acid sequence 139cgtttgtctg atttggagga ag 2214024DNAArtificial SequenceSynthetic nucleic acid sequence 140tttcttcatc atcggtcata aaat 2414123DNAArtificial SequenceSynthetic nucleic acid sequence 141ctacgtgaat caaaaacaat gga 2314222DNAArtificial SequenceSynthetic nucleic acid sequence 142tactgcaaag tctcgttcat cc 2214324DNAArtificial SequenceSynthetic nucleic acid sequence 143cataccattt tgaacgatga cctc 2414423DNAArtificial SequenceSynthetic nucleic acid sequence 144atgtctggtc aactttccga ctc 2314525DNAArtificial SequenceSynthetic nucleic acid sequence 145caatcggtat ctgtaaatat caaat 2514624DNAArtificial SequenceSynthetic nucleic acid sequence 146tcgcatacct gtttatcttc tact 2414722DNAArtificial SequenceSynthetic nucleic acid sequence 147ttggttccat ctgaactttg ag 2214824DNAArtificial SequenceSynthetic nucleic acid sequence 148aatggcttat caaagtgaat atgc 2414924DNAArtificial SequenceSynthetic nucleic acid sequence 149taatttcctt tttttccatt cctc 2415025DNAArtificial SequenceSynthetic nucleic acid sequence 150actagaatct ccaaatgaat ccagt 2515124DNAArtificial SequenceSynthetic nucleic acid sequence 151tggagttaat ctacgtctca tctc 2415224DNAArtificial SequenceSynthetic nucleic acid sequence 152gttcatacag aagactcctt tttg 2415325DNAArtificial SequenceSynthetic nucleic acid sequence 153agttttgatt atccgaataa atgct 2515424DNAArtificial SequenceSynthetic nucleic acid sequence 154tttaaattca gctatatggg gaga 2415522DNAArtificial SequenceSynthetic nucleic acid sequence 155ttccgttttg ctattccata at 2215624DNAArtificial SequenceSynthetic nucleic acid sequence 156cctctgataa aaaacttgtg aaat 2415724DNAArtificial SequenceSynthetic nucleic acid sequence 157actactcctg gaattacaaa ctgg 2415823DNAArtificial SequenceSynthetic nucleic acid sequence 158gccaaaatta aaccacaatc cac 2315924DNAArtificial SequenceSynthetic nucleic acid sequence 159cattttgctg aatgatagtg cgta 2416048DNAArtificial SequenceSynthetic nucleic acid sequence 160cgaccggatt cccacatcaa atgatgcggg ttgtgttaat tccggtcg 4816137DNAArtificial SequenceSynthetic nucleic acid sequence 161cccgcgcrta gttactrcgt tgtaagacgt ccgcggg 3716229DNAArtificial SequenceSynthetic nucleic acid sequence 162ccccgtagtt actgcgttgt aagacgggg

2916337DNAArtificial SequenceSynthetic nucleic acid sequence 163cccgcgcata gttactgcgt tgtaagacgt ccgcggg 3716437DNAArtificial SequenceSynthetic nucleic acid sequence 164cccgcgcgta gttactacgt tgtaagacgt ccgcggg 371651282DNAStaphylococcus aureus 165accattttag ctgtagggaa actaaaagag aaatattgga agcaagccat agcagaatat 60gaaaaacgtt taggcccata caccaagata gacatcatag aagttccaga cgaaaaagca 120ccagaaaata tgagcgacaa agaaattgag caagtaaaag aaaaagaagg ccaacgaata 180ctagccaaaa tcaaaccaca atccacagtc attacattag aaatacaagg aaagatgcta 240tcttccgaag gattggccca agaattgaac caacgcatga cccaagggca aagcgacttt 300gtattcgtca ttggcggatc aaacggcctg cacaaggacg tcttacaacg cagtaactat 360gcactatcat ttagcaaaat gacattccca catcaaatga tgcgggttgt gttaattgaa 420caagtgtata gagcatttaa gattatgcgt ggagaagcgt accacaaata aaactaaaaa 480atatgagaaa attattaaat tagctcaaat ctttgaagaa taaaaagtga atattaagtt 540tgataattta ggtacaagta aagattaaga atttccatta tttaatacat ggtgtgtaaa 600tcgacttctt tttgtattag atgtttgcag taagcgatgt aaagaagatg ctaataaata 660tgtgaggaat gattacgata ctagataagc ggctaatgaa attttttaaa gtacatatat 720agacatattt ttcatttagt aaaattttga atttcacttt gctaagacta gtgtctagaa 780atttataatg atttattaac acctatttga aacttaagta taataaatga ttcggatttt 840atttttaata aagacaaact tgaacgtagc aaagtagttt ttatgataaa taataagttt 900taataatgtg acgcttttat ataagcacat tattatgaac aatgtgaatt gagcatctac 960aattacatta ataaatatat aaatgatgat ttaaattcac atatatttat aatacacata 1020ctatatgaaa gttttgatta tccgaataaa tgctaaaatt aataaaataa ttaaaggaat 1080catacttatt atacgtatac gtttagctac tgaactactg gattcatttg gagattctag 1140tagttctttt tcaatctcta aatctaaatc agttttgtaa taaccattaa ttcctaatct 1200ttcatctagc tctgtacttt tttcatcatt tttatctttg ttgatatgtt ccattttctc 1260gcctcttttt aatcaagtag aa 12821661108DNAStaphylococcus aureus 166accattttag ctgtagggaa actaaaagag aaatattgga agcaagccat agcagaatat 60gaaaaacgtt taggcccata caccaagata gacatcatag aagttccaga cgaaaaagca 120ccagaaaata tgagcgacaa agaaattgag caagtaaaag aaaaagaagg ccaacgaata 180ctagccaaaa tcaaaccaca atccacagtc attacattag aaatacaagg aaagatgcta 240tcttccgaag gattggccca agaattgaac caacgcatga cccaagggca aagcgacttt 300gtattcgtca ttggcggatc aaacggcctg cacaaggacg tcttacaacg cagtaactat 360gcactatcat ttagcaaaat gacattccca catcaaatga tgcgggttgt gttaattgaa 420caagtgtata gagcatttaa gattatgcgt ggagaagcgt accacaaata aaactaaaaa 480atatgagaaa attattaaat tagctcaaat ctttgaagaa taaaaagtga atattaagtt 540tgataattta ggtacaagta aagattaaga atttccatta tttaatacat ggtgtgtaaa 600tcgacttctt tttgtattag atgtttgcag taagcgatgt aaagaagatg ctaataaata 660tgtgaggaat gattacgata ctagataagc ggctaatgaa attttttaaa gtacatatat 720agacatattt ttcatttagt aaaattttga atttcacttt gctaagacta gtgtctagaa 780atttataatg atttattaac acctatttga aacttaagta taataaatga ttcggatttt 840atttttaata aagacaaact tgaacgtagc aaagtagttt ttatgataaa taataagttt 900taataatgtg acgcttttat ataagcacat tattatgaac aatgtgaatt gagcatctac 960aattacatta ataaatatat aaatgatgat ttaaattcac atatatttat aatacacata 1020ctatatgaaa gttttgatta tccgaataaa tgctaaaatt aataaaataa ttaaaggaat 1080catacttatt atacgtatac gtttagct 11081671530DNAStaphylococcus aureus 167ttagctgtag ggaaactaaa agagaaatat tggaagcaag ccatagcaga atatgaaaaa 60cgtttaggcc catacaccaa gatagacatc atagaagttc cagacgaaaa agcaccagaa 120aatatgagcg acaaagaaat tgagcaagta aaagaaaaag aaggccaacg aatactagcc 180aaaatcaaac cacaatccac agtcattaca ttagaaatac aaggaaagat gctatcttcc 240gaaggattgg cccaagaatt gaaccaacgc atgacccaag ggcaaagcga ctttgtattc 300gtcattggcg gatcaaacgg cctgcacaag gacgtcttac aacgcagtaa ctatgcacta 360tcatttagca aaatgacatt cccacatcaa atgatgcggg ttgtgttaat tgaacaagtg 420tatagagcat ttaagattat gcgtggagaa gcatatcata aatgatgcgg ttttttcagc 480cgcttcataa aggggggtga tcatatcgga acgtatgagg tttatgagaa ttgctgctat 540gtttttatga agcgtatcat aaatgatgca gtttttgata attttttctt tatcagagat 600tttactaaaa atcccctcaa agtttgtttt tttcaacttc aactttgaag ggaataaata 660aggaacttat ttatatttat cctttatctc attaatatct atttttttat taataatatt 720ataaatatta aattctttag aaaagtcact atcactctta ttcttcatac taaacgttat 780taatctaata atatcagcta ctatttcttt aaattctatt gcatcttctt ttttataagt 840agcgcctgta tgaacaattt tatttctcat accatagtaa tctttcatat atttttttac 900acaattttta atttcattag aattatccaa atctagatta tcaattgtct ttaataaatg 960atcattaaca acattagcat acccacatcc aagcttcttt tttatctctt catcacttaa 1020attttcatct aatttataat atctttctaa aaaatttgtg ataaaaactt ctaatgcagt 1080ctgaatttgt acaattgcta aattatagtc agatttataa aaagaacgtt caccttttct 1140catagccaaa acataaatat tgctaggatg attattgaaa atattataat tttttttaat 1200atttaataaa tcactttttt tgatagatga atactgatct tcttctatct ttccaggcat 1260gtcaatcatg aaaatactca tctcttttat atttccatct atagtatata ttatataata 1320tggaatactt aatatatccc ctaatgatag ctggtatata ttatgatact gatatttaac 1380gctaataatt ttaataagat tatttagaca attaaattgc ttattaaaaa ttttcgttag 1440actattactt ttctttgatt ccctagaagt agaatttgat ttcaattttt taaactgatt 1500gtgcttgatt attgaagtta tttcaacata 15301681256DNAStaphylococcus aureus 168gctgtaggga aactaaaaga gaaatattgg aagcaagcca tagcagaata tgaaaaacgt 60ttaggcccat acaccaagat agacatcata gaagttccag acgaaaaagc accagaaaat 120atgagcgaca aagaaattga gcaagtaaaa gaaaaagaag gccaacgaat actagccaaa 180attaaaccac aatccacagt cattacatta gaaatacaag gaaagatgct atcttccgaa 240ggattggccc aagaattgaa ccaacgcatg acccaagggc aaagcgactt tgtattcgtc 300attggcggat caaacggcct gcacaaggac gtcttacaac gcagtaacta cgcactatca 360ttcagcaaaa tgacattccc acatcaaatg atgcgggttg tgttaattga gcaagtgtat 420agagcattta agattatgcg tggagaagca tatcataaat gatgcggttt tttcagccgc 480ttcataaagg gattttgaat gtatcagaac atatgaggtt tatgtgaatt gctgttatgt 540ttttaagaag catatcataa gtgatgcggt ttttattaat tagttgctaa aaaatgaagt 600atgcaatatt aattattatt aaattttgat atatttaaag aaagattaag tttagggtga 660atgaatggct tatcaaagtg aatatgcatt agaaaatgaa gtacttcaac aacttgagga 720attgaactat gaaagagtaa atatacataa tattaaatta gaaattaatg aatatctcaa 780agaactagga gtgttgaaaa atgaataagc agacaaatac tccagaacta agatttccag 840agtttgatga ggaatggaaa aaaaggaaat taggtgaagt agtaaattat aaaaatggtg 900gttcatttga aagtttagtg aaaaaccatg gtgtatataa actcataact cttaaatctg 960ttaatacaga aggaaagttg tgtaattctg gaaaatatat cgatgataaa tgtgttgaaa 1020cattgtgtaa tgatacttta gtaatgatac tgagcgagca agcaccagga ctagttggaa 1080tgactgcaat tatacctaat aataatgagt atgtactaaa tcaacgagta gcagcactag 1140tgcctaaaca atttatagat agtcaatttc tatctaagtt aattaataga aaccagaaat 1200atttcagtgt gagatctgct ggaacaaaag tgaaaaatat ttctaaagga catgta 1256169846DNAStaphylococcus aureus 169ttacattaga aatacaagga aagatgctat cttccgaagg attggcccaa gaattgaacc 60aacgcatgac ccaagggcaa agcgactttg ttttcgtcat tggcggatca aacggcctgc 120acaaggacgt cttacaacgc agtaactacg cactatcatt cagcaaaatg acattcccac 180atcaaatgat gcgggttgtg ttaattgaac aagtgtacag agcatttaag attatgcgag 240gagaagctta tcataagtaa tgaggttcat gatttttgac atagttagcc tccgcagtct 300ttcatttcaa gtaaataata gcgaaatatt ctttatactg aatacttata gtgaagcaaa 360gttctagctt tgagaaaatt ctttctgcaa ctaaatatag taaattacgg taaaatataa 420ataagtacat attgaagaaa atgagacata atatatttta taataggagg gaatttcaaa 480tgatagacaa ctttatgcag gtccttaaat taattaaaga gaaacgtacc aataatgtag 540ttaaaaaatc tgattgggat aaaggtgatc tatataaaac tttagtccat gataagttac 600ccaagcagtt aaaagtgcat ataaaagaag ataaatattc agttgtaggg aaggttgcta 660ctgggaacta tagtaaagtt ccttggattt caatatatga tgagaatata acaaaagaaa 720caaaggatgg atattatttg gtatatcttt ttcatccgga aggagaaggc atatacttat 780ctttgaatca aggatggtca aagataagtg atatgtttcc gcgggataaa aatgctgcaa 840aacaaa 8461701270DNAStaphylococcus aureus 170cattagaaat acaaggaaag atgctatctt ccgaaggatt ggcccaagaa ttgaaccaac 60gcatgaccca agggcaaagc gactttgtat tcgtcattgg cggatcaaac ggcctgcaca 120aggacgtctt acaacgcagt aactatgcac tatcatttag caaaatgaca ttcccacatc 180aaatgatgcg ggttgtgtta attgaacaag tgtatagagc atttaagatt atgcgtggag 240aagcatatca taaatgatgc ggttttttca gccgcttcat aaagggattt tgaatgtatc 300agaacatatg aggtttatgt gaattgctgt tatgttttta agaagcttat cataagtaat 360gaggttcatg atttttgaca tagttagcct ccgcagtctt tcatttcaag taaataatag 420cgaaatattc tttatactga atacttatag tgaagcaaag ttctagcttt gagaaaattc 480tttctgcaac taaatatagt aaattacggt aaaatataaa taagtacata ttgaagaaaa 540tgagacataa tatattttat aataggaggg aatttcaaat gatagacaac tttatgcagg 600tccttaaatt aattaaagag aaacgtacca ataatgtagt taaaaaatct gattgggata 660aaggtgatct atataaaact ttagtccatg ataagttacc caagcagtta aaagtgcata 720taaaagaaga taaatattca gttgtaggga aggttgctac tgggaactat agtaaagttc 780cttggatttc aatatatgat gagaatataa caaaagaaac aaaggatgga tattatttgg 840tatatctttt tcatccggaa ggagaaggca tatacttatc tttgaatcaa ggatggtcaa 900agataagtga tatgtttccg cgggataaaa atgctgcaaa acaaagagca ttaactttat 960cttccgaact caataaatat attacatcaa atgaatttaa tactggaaga ttttattacg 1020cagaaaataa agattcatct tatgatttaa aaaatgatta tccatcagga tattctcatg 1080gatcaataag attcaaatat tatgatttga atgaaggatt cacagaagaa gatatgctag 1140aggatttaaa gaaattttta gaactattta atgaattagc ttcaaaagtt acaaaaacat 1200cctatgatag cttggtcaat agcatagacg aaatacagga agacagcgaa attgaagaaa 1260ttagaacagc 1270171991DNAStaphylococcus aureus 171accattttag ctgtagggaa actaaaagag aaatactgga agcaagccat agcagaatat 60gaaaaacgtt taggcccata caccaagata gacatcatag aagttccaga cgaaaaagca 120ccagaaaata tgaactacaa agaaattgag caagtaaaag aaaaagaagg ccaacgaata 180ctagccaaaa tcaaaccaca atcaacagtc attacattag aaatacaagg aaagatgcta 240tcttccgaag gattggccca agaattgaac caacgcatga cccaagggca aagcgacttt 300gtattcgtca ttggcggatc aaacggcctg cacaaggacg tcttacaacg cagtaactac 360gcactatcat tcagcaaaat gacattccca catcaaatga tgcgggttgt gttaattgaa 420caagtgtaca gagcatttaa gattatgcga ggagaagcgt atcataagtg atggtaaaaa 480atatgagtaa gtagatgaag agtgaaaatc agattaatta ataataatgt atcaaattta 540aataaagggg tttttaagta tgaatttaag aggtcatgaa aatagactta aatttcatgc 600gaaatatgat gtgacaccta tatcacattt aaaattatta gaaggtcaaa agaaagacgg 660tgaaggcggc atactgacag atagctatta ctgtttttca tacagcttaa aaggtaattc 720taaaaaagtt ttaggtacgt ttaattgtgg ttatcatatt gctgaagatt tactaaaatt 780atcaaatcaa gataaattac ctttatttaa cccgtttaaa gtaattaatg aaggtaatca 840attgcagggc gtaacgaata aaggtaattt aaatattaat aggcaaagaa aacagtataa 900tgaagtggct ttacagcttt caaatgctat taatttaatc ataatttgtt atgaggataa 960tattaaagaa ccactttcaa cgataaaata c 991172748DNAStaphylococcus aureus 172atcgtttaac gtgtcacatg atgcgataga tccgcaattt tatattttcc ataataacta 60taagaagttt acgattttaa cagatacggg ttacgtgtct gatcgtatga aaggtatgat 120acgtggcagc gatgcattta tttttgagag taatcatgac gtcgatatgt tgagaatgtg 180tcgttatcca tggaagacga aacaacgcat tttaggcgat atgggtcatg tatctaatga 240ggatgcgggt catgcgatga cagacgtgat tacaggtaac acgaaacgta tttacttatc 300gcatttatca caagataata atatgaaaga tttggcgcgt atgagtgttg gccaagtatt 360gaacgaacac gatattgata cggaaaaaga agtattgcta tgtgatacgg ataaagctat 420tccaacacca atatatacaa tataaatgag agtcatccga taaagttccg cactgctgtg 480aaacgacttt atcgggtgct tttttatgtt gttggtggga aatggctgtt gttgagttga 540atcggattga ttgaaatgtg taaaataatt cgatattaaa tgtaatttat aaataattta 600cataaaatca aacattttaa tataaggatt atgataatat attggtgtat gacagttaat 660ggagggaacg aaatgaaagc tttattactt aaaacaagtg tatggctcgt tttgcttttt 720agtgtgatgg gattatggca tgtctcga 748173917DNAStaphylococcus aureus 173aaatacaagg aaagatgcta tcttccgaag gattggccca agaattgaac caacgcatga 60cccaagggca aagcgacttt gtattcgtca ttggcggatc aaacggcctg cacaaggacg 120tcttacaacg tagtaactac gcactatcat tcagcaaaat gacattccca catcaaatga 180tgcgggttgt gttaattgag caagtgtata gagcatttaa gattatgcgt ggagaagcat 240atcataaatg atgcggtttt ttcagccgct tcataaaggg attttgaatg tatcagaaca 300tatgaggttt atgtgaattg ctgttatgtt tttaagaagc ttatcataag taatgaggtt 360catgattttt gacatagtta gcctccgcag tctttcattt caagtaaata atagcgaaat 420attctttata ctgaatactt atagtgaagc aaagttctag ctttgagaaa attctttctg 480caactaaata tagtaaatta cggtaaaata taaataagta catattgaag aaaatgagac 540ataatatatt ttataatagg agggaatttc aaatgataga caactttatg caggtcctta 600aattaattaa agagaaacgt accaataatg tagttaaaaa atctgattgg gataaaggtg 660atctatataa aactttagtc catgataagt tacccaagca gttaaaagtg catataaaag 720aagataaata ttcagttgta gggaaggttg ctactgggaa ctatagtaaa gttccttgga 780tttcaatata tgatgagaat ataacaaaag aaacaaagga tggatattat ttggtatatc 840tttttcatcc ggaaggagaa ggcatatact tatctttgaa tcaaggatgg tcaaagataa 900gtgatatgtt tccgcgg 9171741132DNAStaphylococcus aureus 174gctgtaggga aactaaaaga gaaatattgg aagcaagcca tagcagaata tgaaaaacgt 60ttaggcccat acaccaagat agacatcata gaagttccag acgaaaaagc accagaaaat 120atgagcgaca aagaaattga gcaagtaaaa gaaaaagaag gccaacgaat actagccaaa 180atcaaaccac aatcaacagt cattacatta gaaatacaag gaaagatgct atcttccgaa 240ggattggccc aagaattgaa ccaacgcatg acccaagggc aaagcgactt tgtattcgtc 300attggcggat caaacggcct gcacaaggac gtcttacaac gtagtaacta cgcactatca 360ttcagcaaaa tgacattccc acatcaaatg atgcgggttg tgttaattga gcaagtgtat 420agagcattta agattatgcg tggagaagca tatcataaat gatgcggttt tttcagccgc 480ttcataaagg gattttgaat gtatcagaac atatgaggtt tatgtgaatt gctgttatgt 540ttttaagaag cttatcataa gtaatgaggt tcatgatttt tgacatagtt agcctccgca 600gtctttcatt tcaagtaaat aatagcgaaa tattctttat actgaatact tatagtgaag 660caaagttcta gctttgagaa aattctttct gcaactaaat atagtaaatt acggtaaaat 720ataaataagt acatattgaa gaaaatgaga cataatatat tttataatag gagggaattt 780caaatgatag acaactttat gcaggtcctt aaattaatta aagagaaacg taccaataat 840gtagttaaaa aatctgattg ggataaaggt gatctatata aaactttagt ccatgataag 900ttacccaagc agttaaaagt gcatataaaa gaagataaat attcagttgt agggaaggtt 960gctactggga actatagtaa agttccttgg atttcaatat atgatgagaa tataacaaaa 1020gaaacaaagg atggatatta tttggtatat ctttttcatc cggaaggaga aggcatatac 1080ttatctttga atcaaggatg gtcaaagata agtgatatgt ttccgcggga ta 11321751133DNAStaphylococcus aureus 175agctgtaggg aaactaaaag agaaatattg gaagcaagcc atagcagaat atgaaaaacg 60tttaggccca tacaccaaga tagacatcat agaagttcca gacgaaaaag caccagaaaa 120tatgagcgac aaagaaattg agcaagtaaa agaaaaagaa ggccaacgaa tactagccaa 180aatcaaacca caatcaacag tcattacatt agaaatacaa ggaaagatgc tatcttccga 240aggattggcc caagaattga accaacgcat gacccaaggg caaagcgact ttgtattcgt 300cattggcgga tcaaacggcc tgcacaagga cgtcttacaa cgtagtaact acgcactatc 360attcagcaaa atgacattcc cacatcaaat gatgcgggtt gtgttaattg agcaagtgta 420tagagcattt aagattatgc gtggagaagc atatcataaa tgatgcggtt ttttcagccg 480cttcataaag ggattttgaa tgtatcagaa catatgaggt ttatgtgaat tgctgttatg 540tttttaagaa gcttatcata agtaatgagg ttcatgattt ttgacatagt tagcctccgc 600agtctttcat ttcaagtaaa taatagcgaa atattcttta tactgaatac ttatagtgaa 660gcaaagttct agctttgaga aaattctttc tgcaactaaa tatagtaaat tacggtaaaa 720tataaataag tacatattga agaaaatgag acataatata ttttataata ggagggaatt 780tcaaatgata gacaacttta tgcaggtcct taaattaatt aaagagaaac gtaccaataa 840tgtagttaaa aaatctgatt gggataaagg tgatctatat aaaactttag tccatgataa 900gttacccaag cagttaaaag tgcatataaa agaagataaa tattcagttg tagggaaggt 960tgctactggg aactatagta aagttccttg gatttcaata tatgatgaga atataacaaa 1020agaaacaaag gatggatatt atttggtata tctttttcat ccggaaggag aaggcatata 1080cttatctttg aatcaaggat ggtcaaagat aagtgatatg tttccgcggg ata 11331761087DNAStaphylococcus aureus 176actaaaagag aaatattgga agcaagccat agcagaatat gaaaaacgtt taggcccata 60caccaagata gacatcatag aagttccaga cgaaaaagca ccagaaaata tgagcgacaa 120agaaattgag caagtaaaag aaaaagaagg ccaacgaata ctagccaaaa tcaaaccaca 180atcaacagtc attacattag aaatacaagg aaagatgcta tcttccgaag gattggcaca 240agaattgaac caacgcatga cccaagggca aagcgacttt gtattcgtca ttggcggatc 300aaacggcctg cacaaggacg tcttacaacg tagtaactac gcactatcat tcagcaaaat 360gacattccca catcaaatga tgcgggttgt gttaattgag caagtgtata gagcgtttaa 420gattatgcgt ggagaagcat atcataaatg atgcggtttt ttcagccgct tcataaaggg 480attttgaatg tatcagaaca tatgaggttt atgtgaattg ctgttatgtt tttaagaagc 540ttatcataag taatgaggtt catgattttt gacatagtta gcctccgcag tctttcattt 600caagtaaata atagcgaaat attctttata ctgaatactt atagtgaagc aaagttctag 660ctttgagaaa attctttctg caactaaata tagtaaatta cggtaaaata taaataagta 720catattgaag aaaatgagac ataatatatt ttataatagg agggaatttc aaatgataga 780caactttatg caggtcctta aattaattaa agagaaacgt accaataatg tagttaaaaa 840atctgattgg gataaaggtg atctatataa aactttagtc catgataagt tacccaagca 900gttaaaagtg catataaaag aagataaata ttcagttgta gggaaggttg ctactgggaa 960ctatagtaaa gttccttgga tttcaatata tgatgagaat ataacaaaag aaacaaagga 1020tggatattat ttggtatatc tttttcatcc ggaaggagaa ggcatatact tatctttgaa 1080tcaagga 1087177903DNAStaphylococcus aureus 177caaggaaaga tgctatcttc cgaaggattg gcccaagaat tgaaccaacg catgacccaa 60gggcaaagcg actttgtatt cgtcattggc ggatcaaacg gcctgcacaa ggacgtctta 120caacgtagta actacgcact atcattcagc aaaatgacat tcccacatca aatgatgcgg 180gttgtgttaa ttgagcaagt gtatagagca tttaagatta tgcgtggaga agcatatcat 240aaatgatgcg gttttttcag ccgcttcata aagggatttt gaatgtatca gaacatatga 300ggtttatgtg aattgctgtt atgtttttaa gaagcttatc ataagtaatg aggttcatga 360tttttgacat agttagcctc cgcagtcttt catttcaagt aaataatagc gaaatattct 420ttatactgaa tacttatagt gaagcaaagt tctagctttg agaaaattct ttctgcaact 480aaatatagta aattacggta aaatataaat aagtacatat tgaagaaaat gagacataat 540atattttata ataggaggga atttcaaatg atagacaact ttatgcaggt ccttaaatta 600attaaagaga aacgtaccaa taatgtagtt aaaaaatctg attgggataa aggtgatcta 660tataaaactt tagtccatga taagttaccc aagcagttaa aagtgcatat aaaagaagat 720aaatattcag ttgtagggaa ggttgctact

gggaactata gtaaagttcc ttggatttca 780atatatgatg agaatataac aaaagaaaca aaggatggat attatttggt atatcttttt 840catccggaag gagaaggcat atacttatct ttgaatcaag gatggtcaaa gataagtgat 900atg 9031781114DNAStaphylococcus aureus 178ggaaactaaa agagaaatat tggaagcaag ccatagcaga atatgaaaaa cgtttaggcc 60catacaccaa gatagacatc atagaagttc cagacgaaaa agcaccagaa aatatgagcg 120acaaagaaat tgagcaagta aaagaaaaag aaggccaacg aatactagcc aaaatcaaac 180cacaatcaac agtcattaca ttagaaatac aaggaaagat gctatcttcc gaaggattgg 240cccaagaatt gaaccaacgc atgacccaag ggcaaagcga ctttgtattc gtcattggcg 300gatcaaacgg cctgcacaag gacgtcttac aacgtagtaa ctacgcacta tcattcagca 360aaatgacatt cccacatcaa atgatgcggg ttgtgttaat tgagcaagtg tatagagcat 420ttaagattat gcgtggagaa gcatatcata aatgatgcgg ttttttcagc cgcttcataa 480agggattttg aatgtatcag aacatatgag gtttatgtga attgctgtta tgtttttaag 540aagcttatca taagtaatga ggttcatgat ttttgacata gttagcctcc gcagtctttc 600atttcaagta aataatagcg aaatattctt tatactgaat acttatagtg aagcaaagtt 660ctagctttga gaaaattctt tctgcaacta aatatagtaa attacggtaa aatataaata 720agtacatatt gaagaaaatg agacataata tattttataa taggagggaa tttcaaatga 780tagacaactt tatgcaggtc cttaaattaa ttaaagagaa acgtaccaat aatgtagtta 840aaaaatctga ttgggataaa ggtgatctat ataaaacttt agtccatgat aagttaccca 900agcagttaaa agtgcatata aaagaagata aatattcagt tgtagggaag gttgctactg 960ggaactatag taaagttcct tggatttcaa tatatgatga gaatataaca aaagaaacaa 1020aggatggata ttatttggta tatctttttc atccggaagg agaaggcata tacttatctt 1080tgaatcaagg atggtcaaag ataagtgata tgtt 11141791121DNAStaphylococcus aureus 179ggaaactaaa agagaaatat tggaagcaag ccatagcaga atatgaaaaa cgtttaggcc 60catacaccaa gatagacatc atagaagttc cagacgaaaa agcaccagaa aatatgagcg 120acaaagaaat tgagcaagta aaagaaaaag aaggccaacg aatactagcc aaaatcaaac 180cacaatccac agtcattaca ttagaaatac aaggaaagat gctatcttcc gaaggattgg 240cccaagaatt gaaccaacgc atgacccaag ggcaaagcga ctttgtattc gtcattggcg 300gatcaaacgg cctgcacaag gacgtcttac aacgcagtaa ctatgcacta tcatttagca 360aaatgacatt cccacatcaa atgatgcggg ttgtgttaat tgaacaagtg tatagagcat 420ttaagattat gcgtggagaa gcatatcata aatgatgcgg ttttttcagc cgcttcataa 480agggattttg aatgtatcag aacatatgag gtttatgtga attgctgtta tgtttttaag 540aagcttatca taagtaatga ggttcatgat ttttgacata gttagcctcc gcagtctttc 600atttcaagta aataatagcg aaatattctt tatactgaat acttatagtg aagcaaagtt 660ctagctttga gaaaattctt tctgcaacta aatatagtaa attacggtaa aatataaata 720agtacatatt gaagaaaatg agacataata tattttataa taggagggaa tttcaaatga 780tagacaactt tatgcaggtc cttaaattaa ttaaagagaa acgtaccaat aatgtagtta 840aaaaatctga ttgggataaa ggtgatctat ataaaacttt agtccatgat aagttaccca 900agcagttaaa agtgcatata aaagaagata aatattcagt tgtagggaag gttgctactg 960ggaactatag taaagttcct tggatttcaa tatatgatga gaatataaca aaagaaacaa 1020aggatggata ttatttggta tatctttttc atccggaagg agaaggcata tacttatctt 1080tgaatcaagg atggtcaaag ataagtgata tgtttccgcg g 11211801121DNAStaphylococcus aureus 180tagctgtagg gaaactaaaa gagaaatatt ggaagcaagc catagcagaa tatgaaaaac 60gtttaggccc atacaccaag atagacatca tagaagttcc agacgaaaaa gcaccagaaa 120atatgagcga caaagaaatt gagcaagtaa aagaaaaaga aggccaacga atactagcca 180aaatcaaacc acaatccaca gtcattacat tagaaataca aggaaagatg ctatcttccg 240aaggattggc ccaagaattg aaccaacgca tgacccaagg gcaaagcgac tttgtattcg 300tcattggcgg atcaaacggc ctgcacaagg acgtcttaca acgcagtaac tatgcactat 360catttagcaa aatgacattc ccacatcaaa tgatgcgggt tgtgttaatt gaacaagtgt 420atagagcatt taagattatg cgtggagaag catatcataa atgatgcggt tttttcagcc 480gcttcataaa gggattttga atgtatcaga acatatgagg tttatgtgaa ttgctgttat 540gtttttaaga agcttatcat aagtaatgag gttcatgatt tttgacatag ttagcctccg 600cagtctttca tttcaagtaa ataatagcga aatattcttt atactgaata cttatagtga 660agcaaagttc tagctttgag aaaattcttt ctgcaactaa atatagtaaa ttacggtaaa 720atataaataa gtacatattg aagaaaatga gacataatat attttataat aggagggaat 780ttcaaatgat agacaacttt atgcaggtcc ttaaattaat taaagagaaa cgtaccaata 840atgtagttaa aaaatctgat tgggataaag gtgatctata taaaacttta gtccatgata 900agttacccaa gcagttaaaa gtgcatataa aagaagataa atattcagtt gtagggaagg 960ttgctactgg gaactatagt aaagttcctt ggatttcaat atatgatgag aatataacaa 1020aagaaacaaa ggatggatat tatttggtat atctttttca tccggaagga gaaggcatat 1080acttatcttt gaatcaagga tggtcaaaga taagtgatat g 11211811131DNAStaphylococcus aureus 181ctgtagggaa actaaaagag aaatattgga agcaagccat agcagaatat gaaaaacgtt 60taggcccata caccaagata gacatcatag aagttccaga cgaaaaagca ccagaaaata 120tgagcgacaa agaaattgag caagtaaaag aaaaagaagg ccaacgaata ctagccaaaa 180tcaaaccaca atccacagtc attacattag aaatacaagg aaagatgcta tcttccgaag 240gattggccca agaattgaac caacgcatga cccaagggca aagcgacttt gtattcgtca 300ttggcggatc aaacggcctg cacaaggacg tcttacaacg cagtaactat gcactatcat 360ttagcaaaat gacattccca catcaaatga tgcgggttgt gttaattgaa caagtgtata 420gagcatttaa gattatgcgt ggagaagcat atcataaatg atgcggtttt ttcagccgct 480tcataaaggg attttgaatg tatcagaaca tatgaggttt atgtgaattg ctgttatgtt 540tttaagaagc ttatcataag taatgaggtt catgattttt gacatagtta gcctccgcag 600tctttcattt caagtaaata atagcgaaat attctttata ctgaatactt atagtgaagc 660aaagttctag ctttgagaaa attctttctg caactaaata tagtaaatta cggtaaaata 720taaataagta catattgaag aaaatgagac ataatatatt ttataatagg agggaatttc 780aaatgataga caactttatg caggtcctta aattaattaa agagaaacgt accaataatg 840tagttaaaaa atctgattgg gataaaggtg atctatataa aactttagtc catgataagt 900tacccaagca gttaaaagtg catataaaag aagataaata ttcagttgta gggaaggttg 960ctactgggaa ctatagtaaa gttccttgga tttcaatata tgatgagaat ataacaaaag 1020aaacaaagga tggatattat ttggtatatc tttttcatcc ggaaggagaa ggcatatact 1080tatctttgaa tcaaggatgg tcaaagataa gtgatatgtt tccgcgggat a 1131182896DNAStaphylococcus aureus 182cattagaaat acaaggaaag atgctatctt ccgaaggatt ggcccaagaa ttgaaccaac 60gcatgaccca agggcaaagc gactttgtat tcgtcattgg cggatcaaac ggcctgcaca 120aggacgtctt acaacgcagt aactatgcac tatcatttag caaaatgaca ttcccacatc 180aaatgatgcg ggttgtgtta attgaacaag tgtatagagc atttaagatt atgcgtggag 240aagcatatca taaatgatgc ggttttttca gccgcttcat aaagggattt tgaatgtatc 300agaacatatg aggtttatgt gaattgctgt tatgttttta agaagcttat cataagtaat 360gaggttcatg atttttgaca tagttagcct ccgcagtctt tcatttcaag taaataatag 420cgaaatattc tttatactga atacttatag tgaagcaaag ttctagcttt gagaaaattc 480tttctgcaac taaatatagt aaattacggt aaaatataaa taagtacata ttgaagaaaa 540tgagacataa tatattttat aataggaggg aatttcaaat gatagacaac tttatgcagg 600tccttaaatt aattaaagag aaacgtacca ataatgtagt taaaaaatct gattgggata 660aaggtgatct atataaaact ttagtccatg ataagttacc caagcagtta aaagtgcata 720taaaagaaga taaatattca gttgtaggga aggttgctac tgggaactat agtaaagttc 780cttggatttc aatatatgat gagaatataa caaaagaaac aaaggatgga tattatttgg 840tatatctttt tcatccggaa ggagaaggca tatacttatc tttgaatcaa ggatgg 8961831125DNAStaphylococcus aureus 183ggaaactaaa agagaaatat tggaagcaag ccatatcaga atatgaaaaa cgtttaggcc 60catacaccaa gatagacatc atagaagttc cagacgaaaa agcaccagaa aatatgagcg 120acaaagaaat cgagcaagta aaagaaaaag aaggccaacg aatactagcc aaaatcaaac 180cacaatcaac agtcattaca ttagaaatac aaggaaagat gctatcttcc gaaggattgg 240ctcaagaatt gaaccaacgc atgacccaag ggcaaagcga ctttgtattc gttattggcg 300gatcaaacgg cctgcacaag gacgtcttac aacgcagtaa ctatgcacta tcattcagca 360aaatgacatt tccacatcag atgatgcggg ttgtgttaat tgagcaagtg tatagagcat 420ttaagattat gcgtggggaa gcatatcata aatgatgcgg ttttttcagc cgcttcataa 480agggattttg aatgtatcag aacatatgag gtttatgtga attgctgtta tgtttttaag 540aagcttatca taagtaatga ggttcatgat ttttgacata gttagcctcc gcagtctttc 600atttcaagta aataatagcg aaatattctt tatactgaat acttatagtg aagcaaagtt 660ctagctttga gaaaattctt tctgcaacta aatatagtaa attacggtaa aatataaata 720agtacatatt gaagaaaatg agacataata tattttataa taggagggaa tttcaaatga 780tagacaactt tatgcaggtc cttaaattaa ttaaagagaa acgtaccaat aatgtagtta 840aaaaatctga ttgggataaa ggtgatctat ataaaacttt agtccatgat aagttaccca 900agcagttaaa agtgcatata aaagaagata aatattcagt tgtagggaag gttgctactg 960ggaactatag taaagttcct tggatttcaa tatatgatga gaatataaca aaagaaacaa 1020aggatggata ttatttggta tatctttttc atccggaagg agaaggcata tacttatctt 1080tgaatcaagg atggtcaaag ataagtgata tgtttccgcg ggata 1125184679DNAStaphylococcus aureus 184ataagaggga acagtgtgaa caagttaata acttgtggat aactggaaag ttgataacaa 60tttggaggac caaacgacat gaaaatcacc attttagctg tagggaaact aaaagagaaa 120tattggaagc aagccatagc agaatatgaa aaacgtttag gcccatacac caagatagac 180atcatagaag ttccagacga aaaagcacca gaaaatatga gcgacaaaga aattgagcaa 240gtaaaagaaa aagaaggcca acgaatacta gccaaaatca aaccacaatc cacagtcatt 300acattagaaa tacaaggaaa gatgctatct tccgaaggat tggcccaaga attgaaccaa 360cgcatgaccc aagggcaaag cgactttgta ttcgtcattg gcggatcaaa cggcctgcac 420aaggacgtct tacaacgcag taactatgca ctatcattta gcaaaatgac attcccacat 480caaatgatgc gggttgtgtt aattgaacaa gtgtatagag catttaagat tatgcgtgga 540gaggcttatc ataaataaaa ctaaaaatta gattgtgtat aatttaaaaa tttaatgaga 600tgtggaggaa ttacatatat gaaatattgg agtatacctt gcaatatcat acgatgttta 660tagagtgttt aataaacca 6791851125DNAStaphylococcus aureus 185ggaaactaaa agagaaatat tggaagcaag ccatagcaga atatgaaaaa cgtttaggcc 60catacaccaa gatagacatc atagaagttc cagacgaaaa agcaccagaa aatatgagcg 120acaaagaaat tgagcaagta aaagaaaaag aaggccaacg aatactagcc aaaatcaaac 180cacaatcaac agtcattaca ttagaaatac aaggaaagat gctatcttcc gaaggattgg 240cacaagaatt gaaccaacgc atgacccaag ggcaaagcga ctttgtattc gtcattggcg 300gatcaaacgg cctgcacaag gacgtcttac aacgtagtaa ctacgcacta tcattcagca 360aaatgacatt cccacatcaa atgatgcggg ttgtgttaat tgagcaagtg tatagagcgt 420ttaagattat gcgtggagaa gcatatcata aatgatgcgg ttttttcagc cgcttcataa 480agggattttg aatgtatcag aacatatgag gtttatgtga attgctgtta tgtttttaag 540aagcttatca taagtaatga ggttcatgat ttttgacata gttagcctcc gcagtctttc 600atttcaagta aataatagcg aaatattctt tatactgaat acttatagtg aagcaaagtt 660ctagctttga gaaaattctt tctgcaacta aatatagtaa attacggtaa aatataaata 720agtacatatt gaagaaaatg agacataata tattttataa taggagggaa tttcaaatga 780tagacaactt tatgcaggtc cttaaattaa ttaaagagaa acgtaccaat aatgtagtta 840aaaaatctga ttgggataaa ggtgatctat ataaaacttt agtccatgat aagttaccca 900agcagttaaa agtgcatata aaagaagata aatattcagt tgtagggaag gttgctactg 960ggaactatag taaagttcct tggatttcaa tatatgatga gaatataaca aaagaaacaa 1020aggatggata ttatttggta tatctttttc atccggaagg agaaggcata tacttatctt 1080tgaatcaagg atggtcaaag ataagtgata tgtttccgcg ggata 1125186926DNAStaphylococcus aureus 186tacattagaa atacaaggaa agatgctatc ttccgaagga ttggcccaag aattgaacca 60acgcatgacc caagggcaaa gcgactttgt attcgtcatt ggcggatcaa acggcctgca 120caaggacgtc ttacaacgca gtaactatgc actatcattt agcaaaatga cattcccaca 180tcaaatgatg cgggttgtgt taattgaaca agtgtataga gcatttaaga ttatgcgtgg 240agaagcatat cataaatgat gcggtttttt cagccgcttc ataaagggat tttgaatgta 300tcagaacata tgaggtttat gtgaattgct gttatgtttt taagaagctt atcataagta 360atgaggttca tgatttttga catagttagc ctccgcagtc tttcatttca agtaaataat 420agcgaaatat tctttatact gaatacttat agtgaagcaa agttctagct ttgagaaaat 480tctttctgca actaaatata gtaaattacg gtaaaatata aataagtaca tattgaagaa 540aatgagacat aatatatttt ataataggag ggaatttcaa atgatagaca actttatgca 600ggtccttaaa ttaattaaag agaaacgtac caataatgta gttaaaaaat ctgattggga 660taaaggtgat ctatataaaa ctttagtcca tgataagtta cccaagcagt taaaagtgca 720tataaaagaa gataaatatt cagttgtagg gaaggttgct actgggaact atagtaaagt 780tccttggatt tcaatatatg atgagaatat aacaaaagaa acaaaggatg gatattattt 840ggtatatctt tttcatccgg aaggagaagg catatactta tctttgaatc aaggatggtc 900aaagataagt gatatgtttc cgcggg 92618724DNAArtificial SequenceSynthetic nucleic acid sequence 187ggatgtgggt atgctaatgt tgtt 2418827DNAArtificial SequenceSynthetic nucleic acid sequence 188tgaacaattt tatttctcat accatag 271892154DNAStaphylococcus aureus 189cggtaataaa aaatacgata tagatgaata acaaaacagt gaagcaatcc gtaacgatgg 60ttgcttcact gttttattat gaattattaa taagtgctgt tacttctccc ttaaatacaa 120tttcttcatt ttcattgtat gttgaaagtg acactgtaac gagtccattt tcttttttta 180tggatttctt atttgtaatt tcagcgataa cgtacaatgt attacctggg tatacaggtt 240taataaattt aacgttattc atttgtgttc ctgctacaac ttcttctccg tatttacctt 300cttctaccca taatttaaat gatattgaaa gtgtatgcat gccagatgca atgatacctt 360taaatctact ttgttctgct ttttctttat ctatatgcat atattgagga tcaaaagttg 420ttgcaaattg gataatttct tcttctgtaa tatgaaggct ttttgttttg aatgtttctc 480ctactataaa atcatcgtat ttcatatatg tctctctttc ttattcaaat taatttttta 540gtatgtaaca tgttaaaggt aagtctaccg tcactgaaac gtaagactca cctctaactt 600tctattgaga caaatgcacc attttatctg cattgtctgt aaagatacca tcaactcccc 660aattagcaag ttggtttgca cgtgctggtt tgtttacagt ccatacgttc aattcataac 720ccgcttcttt taccattttt acttttgctt tagtaagttt ggcatcttca gtgtttacta 780ttttagcatt acagtaatct aaaagtgttc tccagtcttc acgaaacgaa gttgtatgga 840atataactgc tctgttatat tgtggcatga tttcttctgc aagtttaaca agcacaacat 900taaagcttga aatgagcact tcttgattct gatttaagtt tgttaattgt tcttccactt 960gcttaaccat acttttagaa agtgctagtc cattcggtcc agtaatacct tttaattcta 1020catttaaatt catattatat tcatttgcta tttttactac atcatcgaaa gttggcaaat 1080gttcatcttt gaatttttca ccaaaccaag atcctgcaga agcatcttta atttcatcat 1140aattcaattc agttatttcc ccggacatat ttgtagtccg ttctaaataa tcatcatgaa 1200tgataatcag ttgttcatct tttgtaattg caacatctaa ctccaaccag tttatacctt 1260ctacttctga agcagcttta aatgatgcaa ttgtattttc cggagcttta ctaggtaatc 1320ctctatgtcc atatacagtt agcatattac ctctccttgc atttttattt ttttaattaa 1380cgtaactgta ttatcacatt aatcgcactt ttatttccat taaaaagaga tgaatatcat 1440aaataaagaa gtcgatagat tcgtattgat tatggagtta atctacgtct catctcattt 1500ttaaaaaatc atttatgtcc caagctccat tttgtaatca agtctagttt ttcggttctg 1560ttgcaaagtt gaatttatag tataatttta acaaaaagga gtcttctgta tgaactattt 1620cagatataaa caatttaaca aggatgttat cactgtagcc gttggctact atctaagata 1680tacattgagt tatcgtgata tatctgaaat attaagggaa cgtggtgtaa acgttcatca 1740ttcaacggtc taccgttggg ttcaagaata tgccccaatt ttgtatcaaa tttggaagaa 1800aaagcataaa aaagcttatt acaaatggcg tattgatgag acgtacatca aaataaaagg 1860aaaatggagc tatttatatc gtgccattga tgcagaggga catacattag atatttggtt 1920gcgtaagcaa cgagataatc attcagcata tgcgtttatc aaacgtctca ttaaacaatt 1980tggtaaacct caaaaggtaa ttacagatca ggcaccttca acgaaggtag caatggctaa 2040agtaattaaa gcttttaaac ttaaacctga ctgtcattgt acatcgaaat atctgaataa 2100cctcattgag caagatcacc gtcatattaa agtaagaaag acaaggtatc aaag 21541902410DNAStaphylococcus aureus 190ccaccttcat atgacgtcta tccatttatg tatggcatga gtaacgaaga atataataaa 60ttaaccgaag ataaaaaaga acctctgctc aacaagttcc agattacaac ttcaccaggt 120tcaactcaaa aaatattaac agcaatgatt gggttaaata acaaaacatt agacgataaa 180acaagttata aaatcgatgg taaaggttgg caaaaagata aatcttgggg tggttacaac 240gttacaagat atgaagtggt aaatggtaat atcgacttaa aacaagcaat agaatcatca 300gataacattt tctttgctag agtagcactc gaattaggca gtaagaaatt tgaaaaaggc 360atgaaaaaac taggtgttgg tgaagatata ccaagtgatt atccatttta taatgctcaa 420atttcaaaca aaaatttaga taatgaaata ttattagctg attcaggtta cggacaaggt 480gaaatactga ttaacccagt acagatcctt tcaatctata gcgcattaga aaataatggc 540aatattaacg cacctcactt attaaaagac acgaaaaaca aagtttggaa gaaaaatatt 600atttccaaag aaaatatcaa tctattaact gatggtatgc aacaagtcgt aaataaaaca 660cataaagaag atatttatag atcttatgca aacttaattg gcaaatccgg tactgcagaa 720ctcaaaatga aacaaggaga aactggcaga caaattgggt ggtttatatc atatgataaa 780gataatccaa acatgatgat ggctattaat gttaaagatg tacaagataa aggaatggct 840agctacaatg ccaaaatctc aggtaaagtg tatgatgagc tatatgagaa cggtaataaa 900aaatacgata tagatgaata acaaaacagt gaagcaatcc gtaacgatgg ttgcttcact 960gttttattat gaattattaa taagtgctgt tacttctccc ttaaatacaa tttcttcatt 1020ttcattgtat gttgaaagtg acactgtaac gagtccattt tcttttttta tggatttctt 1080atttgtaatt tcagcgataa cgtacaatgt attacctggg tatacaggtt taataaattt 1140aacgttattc atttgtgttc ctgctacaac ttcttctccg tatttacctt cttctaccca 1200taatttaaat gatattgaaa gtgtatgcat gccagatgca atgatacctt taaatctact 1260ttgttctgct ttttctttat ctatatgcat atattgagga tcaaaagttg ttgcaaattg 1320gataatttct tcttctgtaa tatgaaggct ttttgttttg aatgtttctc ctactataaa 1380atcatcgtat ttcatatatg tctctctttc ttattcaaat taatttttta gtatgtaaca 1440tgttaaaggt aagtctaccg tcactgaaac gtaagactca cctctaactt tctattgaga 1500caaatgcacc attttatctg cattgtctgt aaagatacca tcaactcccc aattagcaag 1560ttggtttgca cgtgctggtt tgtttacagt ccatacgttc aattcataac ccgcttcttt 1620taccattttt acttttgctt tagtaagttt ggcatcttca gtgtttacta ttttagcatt 1680acagtaatct aaaagtgttc tccagtcttc acgaaacgaa gttgtatgga atataactgc 1740tctgttatat tgtggcatga tttcttctgc aagtttaaca agcacaacat taaagcttga 1800aatgagcact tcttgattct gatttaagtt tgttaattgt tcttccactt gcttaaccat 1860acttttagaa agtgctagtc cattcggtcc agtaatacct tttaattcta catttaaatt 1920catattatat tcatttgcta tttttactac atcatcgaaa gttggcaaat gttcatcttt 1980gaatttttca ccaaaccaag atcctgcaga agcatcttta atttcatcat aattcaattc 2040agttatttcc ccggacatat ttgtagtccg ttctaaataa tcatcatgaa tgataatcag 2100ttgttcatct tttgtaattg caacatctaa ctccaaccag tttatacctt ctacttctga 2160agcagcttta aatgatgcaa ttgtattttc cggagcttta ctaggtaatc ctctatgtcc 2220atatacagtt agcatattac ctctccttgc atttttattt ttttaattaa cgtaactgta 2280ttatcacatt aatcgcactt ttatttccat taaaaagaga tgaatatcat aaataaagaa 2340gtcgatagat tcgtattgat tatggagtta atctacgtct catctcattt ttaaaaaatc 2400atttatgtcc 24101911858DNAStaphylococcus aureus 191caccttcata tgacgtctat ccatttatgt atggcatgag taacgaagaa tataataaat 60taaccgaaga taaaaaagaa cctctgctca acaagttcca gattacaact tcaccaggtt 120caactcaaaa aatattaaca gcaatgattg ggttaaataa caaaacatta gacgataaaa 180caagttataa aatcgatggt aaaggttggc

aaaaagataa atcttggggt ggttacaacg 240ttacaagata tgaagtggta aatggtaata tcgacttaaa acaagcaata gaatcatcag 300ataacatttt ctttgctaga gtagcactcg aattaggcag taagaaattt gaaaaaggca 360tgaaaaaact aggtgttggt gaagatatac caagtgatta tccattttat aatgctcaaa 420tttcaaacaa aaatttagat aatgaaatat tattagctga ttcaggttac ggacaaggtg 480aaatactgat taacccagta cagatccttt caatctatag cgcattagaa aataatggca 540atattaacgc acctcactta ttaaaagaca cgaaaaacaa agtttggaag aaaaatatta 600tttccaaaga aaatatcaat ctattaactg atggtatgca acaagtcgta aataaaacac 660ataaagaaga tatttataga tcttatgcaa acttaattgg caaatccggt actgcagaac 720tcaaaatgaa acaaggagaa actggcagac aaattgggtg gtttatatca tatgataaag 780ataatccaaa catgatgatg gctattaatg ttaaagatgt acaagataaa ggaatggcta 840gctacaatgc caaaatctca ggtaaagtgt atgatgagct atatgagaac ggtaataaaa 900aatacgatat agatgaataa caaaacagtg aagcaatccg taacgatggt tgcttcactg 960ttttattatg aattattaat aagtgctgtt acttctccct taaatacaat ttcttcattt 1020tcattgtatg ttgaaagtga cactgtaacg agtccatttt ctttttttat ggatttctta 1080tttgtaattt cagcgataac gtacaatgta ttacctgggt atacaggttt aataaattta 1140acgttattca tttgtgttcc tgctacaact tcttctccgt atttaccttc ttctacccat 1200aatttaaatg atattgaaag tgtatgcatg ccagatgcaa tgataccttt aaatctactt 1260tgttctgctt tttctttatc tatatgcata tattgaggat caaaagttgt tgcaaattgg 1320ataatttctt cttctgtaat atgaaggctt tttgttttga atgtttctcc tactataaaa 1380tcatcgtatt tcatatatgt ctctctttct tattcaaatt aattttttag tatgtaacat 1440gttaaaggta agtctaccgt cactgaaacg taagactcac ctctaacttt ctattgagac 1500aaatgcacca ttttatctgc attgtctgta aagataccat caactcccca attagcaagt 1560tggtttgcac gtgctggttt gtttacagtc catacgttca attcataacc cgcttctttt 1620accattttta cttttgcttt agtaagtttg gcatcttcag tgtttactat tttagcatta 1680cagtaatcta aaagtgttct ccagtcttca cgaaacgaag ttgtatggaa tataactgct 1740ctgttatatt gtggcatgat ttcttctgca agtttaacaa gcacaacatt aaagcttgaa 1800atgagcactt cttgattctg atttaagttt gttaattgtt cttccacttg cttaacca 18581921861DNAStaphylococcus aureus 192ccaccttcat atgacgtcta tccatttatg tatggcatga gtaacgaaga atataataaa 60ttaaccgaag ataaaaaaga acctctgctc aacaagttcc agattacaac ttcaccaggt 120tcaactcaaa aaatattaac agcaatgatt gggttaaata acaaaacatt agacgataaa 180acaagttata aaatcgatgg taaaggttgg caaaaagata aatcttgggg tggttacaac 240gttacaagat atgaagtggt aaatggtaat atcgacttaa aacaagcaat agaatcatca 300gataacattt tctttgctag agtagcactc gaattaggca gtaagaaatt tgaaaaaggc 360atgaaaaaac taggtgttgg tgaagatata ccaagtgatt atccatttta taatgctcaa 420atttcaaaca aaaatttaga taatgaaata ttattagctg attcaggtta cggacaaggt 480gaaatactga ttaacccagt acagatcctt tcaatctata gcgcattaga aaataatggc 540aatattaacg cacctcactt attaaaagac acgaaaaaca aagtttggaa gaaaaatatt 600atttccaaag aaaatatcaa tctattaact gatggtatgc aacaagtcgt aaataaaaca 660cataaagaag atatttatag atcttatgca aacttaattg gcaaatccgg tactgcagaa 720ctcaaaatga aacaaggaga aactggcaga caaattgggt ggtttatatc atatgataaa 780gataatccaa acatgatgat ggctattaat gttaaagatg tacaagataa aggaatggct 840agctacaatg ccaaaatctc aggtaaagtg tatgatgagc tatatgagaa cggtaataaa 900aaatacgata tagatgaata acaaaacagt gaagcaatcc gtaacgatgg ttgcttcact 960gttttattat gaattattaa taagtgctgt tacttctccc ttaaatacaa tttcttcatt 1020ttcattgtat gttgaaagtg acactgtaac gagtccattt tcttttttta tggatttctt 1080atttgtaatt tcagcgataa cgtacaatgt attacctggg tatacaggtt taataaattt 1140aacgttattc atttgtgttc ctgctacaac ttcttctccg tatttacctt cttctaccca 1200taatttaaat gatattgaaa gtgtatgcat gccagatgca atgatacctt taaatctact 1260ttgttctgct ttttctttat ctatatgcat atattgagga tcaaaagttg ttgcaaattg 1320gataatttct tcttctgtaa tatgaaggct ttttgttttg aatgtttctc ctactataaa 1380atcatcgtat ttcatatatg tctctctttc ttattcaaat taatttttta gtatgtaaca 1440tgttaaaggt aagtctaccg tcactgaaac gtaagactca cctctaactt tctattgaga 1500caaatgcacc attttatctg cattgtctgt aaagatacca tcaactcccc aattagcaag 1560ttggtttgca cgtgctggtt tgtttacagt ccatacgttc aattcataac ccgcttcttt 1620taccattttt acttttgctt tagtaagttt ggcatcttca gtgtttacta ttttagcatt 1680acagtaatct aaaagtgttc tccagtcttc acgaaacgaa gttgtatgga atataactgc 1740tctgttatat tgtggcatga tttcttctgc aagtttaaca agcacaacat taaagcttga 1800aatgagcact tcttgattct gatttaagtt tgttaattgt tcttccactt gcttaaccat 1860a 18611931861DNAStaphylococcus aureus 193ccaccttcat atgacgtcta tccatttatg tatggcatga gtaacgaaga atataataaa 60ttaaccgaag ataaaaaaga acctctgctc aacaagttcc agattacaac ttcaccaggt 120tcaactcaaa aaatattaac agcaatgatt gggttaaata acaaaacatt agacgataaa 180acaagttata aaatcgatgg taaaggttgg caaaaagata aatcttgggg tggttacaac 240gttacaagat atgaagtggt aaatggtaat atcgacttaa aacaagcaat agaatcatca 300gataacattt tctttgctag agtagcactc gaattaggca gtaagaaatt tgaaaaaggc 360atgaaaaaac taggtgttgg tgaagatata ccaagtgatt atccatttta taatgctcaa 420atttcaaaca aaaatttaga taatgaaata ttattagctg attcaggtta cggacaaggt 480gaaatactga ttaacccagt acagatcctt tcaatctata gcgcattaga aaataatggc 540aatattaacg cacctcactt attaaaagac acgaaaaaca aagtttggaa gaaaaatatt 600atttccaaag aaaatatcaa tctattaact gatggtatgc aacaagtcgt aaataaaaca 660cataaagaag atatttatag atcttatgca aacttaattg gcaaatccgg tactgcagaa 720ctcaaaatga aacaaggaga aactggcaga caaattgggt ggtttatatc atatgataaa 780gataatccaa acatgatgat ggctattaat gttaaagatg tacaagataa aggaatggct 840agctacaatg ccaaaatctc aggtaaagtg tatgatgagc tatatgagaa cggtaataaa 900aaatacgata tagatgaata acaaaacagt gaagcaatcc gtaacgatgg ttgcttcact 960gttttattat gaattattaa taagtgctgt tacttctccc ttaaatacaa tttcttcatt 1020ttcattgtat gttgaaagtg acactgtaac gagtccattt tcttttttta tggatttctt 1080atttgtaatt tcagcgataa cgtacaatgt attacctggg tatacaggtt taataaattt 1140aacgttattc atttgtgttc ctgctacaac ttcttctccg tatttacctt cttctaccca 1200taatttaaat gatattgaaa gtgtatgcat gccagatgca atgatacctt taaatctact 1260ttgttctgct ttttctttat ctatatgcat atattgagga tcaaaagttg ttgcaaattg 1320gataatttct tcttctgtaa tatgaaggct ttttgttttg aatgtttctc ctactataaa 1380atcatcgtat ttcatatatg tctctctttc ttattcaaat taatttttta gtatgtaaca 1440tgttaaaggt aagtctaccg tcactgaaac gtaagactca cctctaactt tctattgaga 1500caaatgcacc attttatctg cattgtctgt aaagatacca tcaactcccc aattagcaag 1560ttggtttgca cgtgctggtt tgtttacagt ccatacgttc aattcataac ccgcttcttt 1620taccattttt acttttgctt tagtaagttt ggcatcttca gtgtttacta ttttagcatt 1680acagtaatct aaaagtgttc tccagtcttc acgaaacgaa gttgtatgga atataactgc 1740tctgttatat tgtggcatga tttcttctgc aagtttaaca agcacaacat taaagcttga 1800aatgagcact tcttgattct gatttaagtt tgttaattgt tcttccactt gcttaaccat 1860a 18611941052DNAStaphylococcus aureus 194cggtaataaa aaatacgata tagatgaata acaaaacagt gaagcaatcc gtaacgatgg 60ttgcttcact gttttattat gaattattaa taagtgctgt tacttctccc ttaaatacaa 120tttcttcatt ttcattgtat gttgaaagtg acactgtaac gagtccattt tcttttttta 180tggatttctt atttgtaatt tcagcgataa cgtacaatgt attacctggg tatacaggtt 240taataaattt aacgttattc atttgtgttc ctgctacaac ttcttctccg tatttacctt 300cttctaccca taatttaaat gatattgaaa gtgtatgcat gccagatgca atgatacctt 360taaatctact ttgttctgct ttttctttat ctatatgcat atattgagga tcaaaagttg 420ttgcaaattg gataatttct tcttctgtaa tatgaaggct ttttgttttg aatgtttctc 480ctactataaa atcatcgtat ttcatatatg tctctctttc ttattcaaat taatttttta 540gtatgtaaca tgttaaaggt aagtctaccg tcactgaaac gtaagactca cctctaactt 600tctattgaga caaatgcacc attttatctg cattgtctgt aaagatacca tcaactcccc 660aattagcaag ttggtttgca cgtgctggtt tgtttacagt ccatacgttc aattcataac 720ccgcttcttt taccattttt acttttgctt tagtaagttt ggcatcttca gtgtttacta 780ttttagcatt acagtaatct aaaagtgttc tccagtcttc acgaaacgaa gttgtatgga 840atataactgc tctgttatat tgtggcatga tttcttctgc aagtttaaca agcacaacat 900taaagcttga aatgagcact tcttgattct gatttaagtt tgttaattgt tcttccactt 960gcttaaccat acttttagaa agtgctagtc cattcggtcc agtaatacct tttaattcta 1020catttaaatt catattatat tcatttgcta tt 10521953101DNAStaphylococcus aureus 195cttcatatga cgtctatcca tttatgtatg gcatgagtaa cgaagaatat aataaattaa 60ccgaagataa aaaagaacct ctgctcaaca agttccagat tacaacttca ccaggttcaa 120ctcaaaaaat attaacagca atgattgggt taaataacaa aacattagac gataaaacaa 180gttataaaat cgatggtaaa ggttggcaaa aagataaatc ttggggtggt tacaacgtta 240caagatatga agtggtaaat ggtaatatcg acttaaaaca agcaatagaa tcatcagata 300acattttctt tgctagagta gcactcgaat taggcagtaa gaaatttgaa aaaggcatga 360aaaaactagg tgttggtgaa gatataccaa gtgattatcc attttataat gctcaaattt 420caaacaaaaa tttagataat gaaatattat tagctgattc aggttacgga caaggtgaaa 480tactgattaa cccagtacag atcctttcaa tctatagcgc attagaaaat aatggcaata 540ttaacgcacc tcacttatta aaagacacga aaaacaaagt ttggaagaaa aatattattt 600ccaaagaaaa tatcaatcta ttaactgatg gtatgcaaca agtcgtaaat aaaacacata 660aagaagatat ttatagatct tatgcaaact taattggcaa atccggtact gcagaactca 720aaatgaaaca aggagaaact ggcagacaaa ttgggtggtt tatatcatat gataaagata 780atccaaacat gatgatggct attaatgtta aagatgtaca agataaagga atggctagct 840acaatgccaa aatctcaggt aaagtgtatg atgagctata tgagaacggt aataaaaaat 900acgatataga tgaataacaa aacagtgaag caatccgtaa cgatggttgc ttcactgttt 960tattatgaat tattaataag tgctgttact tctcccttaa atacaatttc ttcattttca 1020ttgtatgttg aaagtgacac tgtaacgagt ccattttctt tttttatgga tttcttattt 1080gtaatttcag cgataacgta caatgtatta cctgggtata caggtttaat aaatttaacg 1140ttattcattt gtgttcctgc tacaacttct tctccgtatt taccttcttc tacccataat 1200ttaaatgata ttgaaagtgt atgcatgcca gatgcaatga tacctttaaa tctactttgt 1260tctgcttttt ctttatctat atgcatatat tgaggatcaa aagttgttgc aaattggata 1320atttcttctt ctgtaatatg aaggcttttt gttttgaatg tttctcctac tataaaatca 1380tcgtatttca tatatgtctc tctttcttat tcaaattaat tttttagtat gtaacatgtt 1440aaaggtaagt ctaccgtcac tgaaacgtaa gactcacctc taactttcta ttgagacaaa 1500tgcaccattt tatctgcatt gtctgtaaag ataccatcaa ctccccaatt agcaagttgg 1560tttgcacgtg ctggtttgtt tacagtccat acgttcaatt cataacccgc ttcttttacc 1620atttttactt ttgctttagt aagtttggca tcttcagtgt ttactatttt agcattacag 1680taatctaaaa gtgttctcca gtcttcacga aacgaagttg tatggaatat aactgctctg 1740ttatattgtg gcatgatttc ttctgcaagt ttaacaagca caacattaaa gcttgaaatg 1800agcacttctt gattctgatt taagtttgtt aattgttctt ccacttgctt aaccatactt 1860ttagaaagtg ctagtccatt cggtccagta atacctttta attctacatt taaattcata 1920ttatattcat ttgctatttt tactacatca tcgaaagttg gcaaatgttc atctttgaat 1980ttttcaccaa accaagatcc tgcagaagca tctttaattt catcataatt caattcagtt 2040atttccccgg acatatttgt agtccgttct aaataatcat catgaatgat aatcagttgt 2100tcatcttttg taattgcaac atctaactcc aaccagttta taccttctac ttctgaagca 2160gctttaaatg atgcaattgt attttccgga gctttactag gtaatcctct atgtccatat 2220acagttagca tattacctct ccttgcattt ttattttttt aattaacgta actgtattat 2280cacattaatc gcacttttat ttccattaaa aagagatgaa tatcataaat aaagaagtcg 2340atagattcgt attgattatg gagttaatct acgtctcatc tcatttttaa aaaatcattt 2400atgtcccaag ctccattttg taatcaagtc tagtttttcg gttctgttgc aaagttgaat 2460ttatagtata attttaacaa aaaggagtct tctgtatgaa ctatttcaga tataaacaat 2520ttaacaagga tgttatcact gtagccgttg gctactatct aagatataca ttgagttatc 2580gtgatatatc tgaaatatta agggaacgtg gtgtaaacgt tcatcattca acggtctacc 2640gttgggttca agaatatgcc ccaattttgt atcaaatttg gaagaaaaag cataaaaaag 2700cttattacaa atggcgtatt gatgagacgt acatcaaaat aaaaggaaaa tggagctatt 2760tatatcgtgc cattgatgca gagggacata cattagatat ttggttgcgt aagcaacgag 2820ataatcattc agcatatgcg tttatcaaac gtctcattaa acaatttggt aaacctcaaa 2880aggtaattac agatcaggca ccttcaacga aggtagcaat ggctaaagta attaaagctt 2940ttaaacttaa acctgactgt cattgtacat cgaaatatct gaataacctc attgagcaag 3000atcaccgtca tattaaagta agaaagacaa ggtatcaaag tatcaataca gcaaagaata 3060ctttaaaagg tattgaatgt atttacgctc tatataaaaa g 31011963506DNAStaphylococcus aureus 196ccaccttcat atgacgtcta tccatttatg tatggcatga gtaacgaaga atataataaa 60ttaaccgaag ataaaaaaga acctctgctc aacaagttcc agattacaac ttcaccaggt 120tcaactcaaa aaatattaac agcaatgatt gggttaaata acaaaacatt agacgataaa 180acaagttata aaatcgatgg taaaggttgg caaaaagata aatcttgggg tggttacaac 240gttacaagat atgaagtggt aaatggtaat atcgacttaa aacaagcaat agaatcatca 300gataacattt tctttgctag agtagcactc gaattaggca gtaagaaatt tgaaaaaggc 360atgaaaaaac taggtgttgg tgaagatata ccaagtgatt atccatttta taatgctcaa 420atttcaaaca aaaatttaga taatgaaata ttattagctg attcaggtta cggacaaggt 480gaaatactga ttaacccagt acagatcctt tcaatctata gcgcattaga aaataatggc 540aatattaacg cacctcactt attaaaagac acgaaaaaca aagtttggaa gaaaaatatt 600atttccaaag aaaatatcaa tctattaact gatggtatgc aacaagtcgt aaataaaaca 660cataaagaag atatttatag atcttatgca aacttaattg gcaaatccgg tactgcagaa 720ctcaaaatga aacaaggaga aactggcaga caaattgggt ggtttatatc atatgataaa 780gataatccaa acatgatgat ggctattaat gttaaagatg tacaagataa aggaatggct 840agctacaatg ccaaaatctc aggtaaagtg tatgatgagc tatatgagaa cggtaataaa 900aaatacgata tagatgaata acaaaacagt gaagcaatcc gtaacgatgg ttgcttcact 960gttttattat gaattattaa taagtgctgt tacttctccc ttaaatacaa tttcttcatt 1020ttcattgtat gttgaaagtg acactgtaac gagtccattt tcttttttta tggatttctt 1080atttgtaatt tcagcgataa cgtacaatgt attacctggg tatacaggtt taataaattt 1140aacgttattc atttgtgttc ctgctacaac ttcttctccg tatttacctt cttctaccca 1200taatttaaat gatattgaaa gtgtatgcat gccagatgca atgatacctt taaatctact 1260ttgttctgct ttttctttat ctatatgcat atattgagga tcaaaagttg ttgcaaattg 1320gataatttct tcttctgtaa tatgaaggct ttttgttttg aatgtttctc ctactataaa 1380atcatcgtat ttcatatatg tctctctttc ttattcaaat taatttttta gtatgtaaca 1440tgttaaaggt aagtctaccg tcactgaaac gtaagactca cctctaactt tctattgaga 1500caaatgcacc attttatctg cattgtctgt aaagatacca tcaactcccc aattagcaag 1560ttggtttgca cgtgctggtt tgtttacagt ccatacgttc aattcataac ccgcttcttt 1620taccattttt acttttgctt tagtaagttt ggcatcttca gtgtttacta ttttagcatt 1680acagtaatct aaaagtgttc tccagtcttc acgaaacgaa gttgtatgga atataactgc 1740tctgttatat tgtggcatga tttcttctgc aagtttaaca agcacaacat taaagcttga 1800aatgagcact tcttgattct gatttaagtt tgttaattgt tcttccactt gcttaaccat 1860acttttagaa agtgctagtc cattcggtcc agtaatacct tttaattcta catttaaatt 1920catattatat tcatttgcta tttttactac atcatcgaaa gttggcaaat gttcatcttt 1980gaatttttca ccaaaccaag atcctgcaga agcatcttta atttcatcat aattcaattc 2040agttatttcc ccggacatat ttgtagtccg ttctaaataa tcatcatgaa tgataatcag 2100ttgttcatct tttgtaattg caacatctaa ctccaaccag tttatacctt ctacttctga 2160agcagcttta aatgatgcaa ttgtattttc cggagcttta ctaggtaatc ctctatgtcc 2220atatacagtt agcatattac ctctccttgc atttttattt ttttaattaa cgtaactgta 2280ttatcacatt aatcgcactt ttatttccat taaaaagaga tgaatatcat aaataaagaa 2340gtcgatagat tcgtattgat tatggagtta atctacgtct catctcattt ttaaaaaatc 2400atttatgtcc caagctccat tttgtaatca agtctagttt ttctgtaccc cttatctgca 2460attttactta ggattgcttt taacttaccc cttatcagca attttactga gaactgcttt 2520taacgcacct cttatctgca attttgccta gaactgcttt taacgtacct cttatctgca 2580attttactga gaactgcttt taacttaccc cttatcagca attttgcatg gaattgcttt 2640taacgtacct cttatctgca attttactta gaactgcttt taacaaacct cttatctgca 2700attttactta gaactgcttt taacgtacct cttatctgta attttactga gaactgcttt 2760taacaaacct cttatctgca attttactta gaactgcttt taacaaacct cttatctgca 2820attttactta gaattgcttt tactattcct cttattagta taatctcagt aagaatgcgt 2880ataaaaatga aaattacaac cgattttgta agtgctgacg cctgagggaa tagtatgtgc 2940gagagactaa tggctcgagc cataccccta ggcaagcatg cacgtacaaa atcgtaagat 3000aaaaaaataa gcatatcact gtaaacttta aaaaatcagt ttagtgatat gcttatttat 3060ttcgagttag gatttatgtc ccaagctcat caagcacaat cggccactag tttatttctc 3120tatcttatat gttctgatat ggtcttctat actgtataag tatacttttg aatatggatc 3180ttgtgtcaat tcacgttcga aatcaaattc ttgattatca aatctgttaa agaatgtttc 3240gtattcttcg actgataatt gctctctaga ttctagcata tttaagtgtt tctctttatc 3300taatgctttg tcatatcctt taacgattga accactaaag atttctccta ctgctcctga 3360accataacta aatagacata ctttctcttc tggttggaat gtgtggttct gtaataacga 3420aattaaactt aagtataatg atcctgtata aatgttacca acatctctat tccataatac 3480ggttctgttg caaagttgaa tttata 3506197928DNAStaphylococcus aureus 197tacattagaa atacaaggaa agatgctatc ttccgaagga ttggcccaag aattgaacca 60acgcatgacc caagggcaaa gcgactttgt attcgtcatt ggcggatcaa acggcctgca 120caaggacgtc ttacaacgca gtaactacgc actatcattc agcaaaatga cattcccaca 180tcaaatgatg cgggttgtgt taattgaaca agtgtacaga gcatttaaga ttatgcgtgg 240agaagcatat cataaatgat gcggtttttt cagccgcttc ataaagggat tttgaatgta 300tcagaacata tgaggtttat gtgaattgct gttatgtttt taagaagctt atcataagta 360atgaggttca tgatttttga catagttagc ctccgcagtc tttcatttca agtaaataat 420agcgaaatat tctttatact gaatacttat agtgaagcaa agttctagct ttgagaaaat 480tctttctgca actaaatata gtaaattacg gtaaaatata aataagtaca tattgaagaa 540aatgagacat aatatatttt ataataggag ggaatttcaa atgatagaca actttatgca 600ggtccttaaa ttaattaaag agaaacgtac caataatgta gttaaaaaat ctgattggga 660taaaggtgat ctatataaaa ctttagtcca tgataagtta cccaagcagt taaaagtgca 720tataaaagaa gataaatatt cagttgtagg gaaggttgct actgggaact atagtaaagt 780tccttggatt tcaatatatg atgagaatat aacaaaagaa acaaaggatg gatattattt 840ggtatatctt tttcatccgg aaggagaagg catatactta tctttgaatc aaggatggtc 900aaagataagt gatatgtttc cgcgggat 928198782DNAStaphylococcus aureus 198caatgcccac agagttatcc acaaatacac aggttataca ctaaaaattg ggcatgaatg 60tcagaaaaat atcaaaaact gcaaagaata ttggtataat aagagggaac agtgtgaaca 120agttaataac ttgtggataa ctggaaagtt gataacaatt tggaggacca aacgacatga 180aaatcaccat tttagctgta gggaaactaa aagagaaata ttggaagcaa gccatagcag 240aatatgaaaa acgtttaggc ccatacacca agatagacat catagaagtt ccagacgaaa 300aagcaccaga aaatatgagc gacaaagaaa ttgagcaagt aaaagaaaaa gaaggccaac 360gaatactagc caaaatcaaa ccacaatcaa cagtcattac attagaaata caaggaaaga 420tgctatcttc cgaaggattg gcccaagaat tgaaccaacg catgacccaa gggcaaagcg 480actttgtatt cgtcattggc ggatcaaacg gcctgcacaa ggacgtctta caacgcagta 540actacgcact atcattcagc aaaatgacat tcccacatca aatgatgcgg gttgtgttaa 600ttgaacaagt gtacagagca tttaagatta tgcgtggaga agcgtatcat aaataaaact

660aaaaattagg ttgtgtataa tttaaaaatt taatgagatg tggaggaatt acatatatga 720aatattggat tataccttgc aatatcatac gatgtttata gagtgtttaa taaaccattt 780tt 782199709DNAStaphylococcus aureus 199tacattagaa atacaaggaa agatgctatc ttccgaagga ttggcccaag aattgaacca 60acgcatgacc caagggcaaa gcgactttgt tttcgtcatt ggcggatcaa acggcctgca 120caaggacgtc ttacaacgca gtaactacgc actatcattc agcaaaatga cattcccaca 180tcaaatgatg cgggttgtgt taattgaaca agtgtacaga gcatttaaga ttatgcgagg 240agaagcttat cataagtaat gaggttcatg atttttgaca tagttagcct ccgcagtctt 300tcatttcaag taaataatag cgaaatattc tttatactga atacttatag tgaagcaaag 360ttctagcttt gagaaaattc tttctgcaac taaatatagt aaattacggt aaaatataaa 420taagtacata ttgaagaaaa tgagacataa tatattttat aataggaggg aatttcaaat 480gatagacaac tttatgcagg tccttaaatt aattaaagag aaacgtacca ataatgtagt 540taaaaaatct gattgggata aaggtgatct atataaaact ttagtccatg ataagttacc 600caagcagtta aaagtgcata taaaagaaga taaatattca gttgtaggga aggttgctac 660tgggaactat agtaaagttc cttggatttc aatatatgat gagaatata 70920022DNAArtificial SequenceSynthetic nucleic acid sequence 200gtgggaaatg gctgttgttg ag 2220122DNAArtificial SequenceSynthetic nucleic acid sequence 201ttcgttccct ccattaactg tc 2220220DNAArtificial SequenceSynthetic nucleic acid sequence 202aaaagaaaga cggtgaaggc 2020325DNAArtificial SequenceSynthetic nucleic acid sequence 203cacttcatta tactgttttc tttgc 2520422DNAArtificial SequenceSynthetic nucleic acid sequence 204tcaccgtctt tcttttgacc tt 2220525DNAArtificial SequenceSynthetic nucleic acid sequence 205tgagatctgc tggaacaaaa gtgaa 2520620DNAArtificial SequenceSynthetic nucleic acid sequence 206cggtcgagtt tgctgaagaa 2020726DNAArtificial SequenceSynthetic nucleic acid sequence 207tcccctaatg atagctggta tatatt 2620827DNAArtificial SequenceSynthetic nucleic acid sequence 208tctagggaat caaagaaaag taatagt 2720932DNAArtificial SequenceSynthetic nucleic acid sequence 209caacaargrc aatgtgayrt attatgytgt ta 3221029DNAArtificial SequenceSynthetic nucleic acid sequence 210gataayatwg gmgaacaagt caraaatgg 2921135DNAArtificial SequenceSynthetic nucleic acid sequence 211ccrtattgat tgwtracacg rccacartaa ttwgg 3521232DNAArtificial Sequencemisc_feature30n = inosineSynthetic nucleic acid sequence 212atrttsartg gttcattttt gaaatagatn cc 3221332DNAArtificial SequenceSynthetic nucleic acid sequence 213acgtgtcggt atctatgtwc gtgtatcaac rg 3221430DNAArtificial SequenceSynthetic nucleic acid sequence 214tgttatgrtc tacaaaacaa accgaytagc 3021534DNAArtificial SequenceSynthetic nucleic acid sequence 215gawtaataat rggggaatgc ttaccttcag ctat 3421626DNAArtificial SequenceSynthetic nucleic acid sequence 216ggtttttgac tgacttgttt tttacg 2621729DNAArtificial SequenceSynthetic nucleic acid sequence 217tagaaytgtt ttttatgatt accrtcttt 2921826DNAArtificial SequenceSynthetic nucleic acid sequence 218ggcaaaaaya aagacgaagt gctgag 26219721DNAStaphylococcus aureus 219tgtagcttta ggtgaagggt taggtccttc aataggggga ataatagcac attatattca 60ttggtcttac ctacttatac ttcctatgat tacaatagta actatacctt ttcttattaa 120agtaatggta cctggtaaat caacaaaaaa tacattagat atcgtaggta ttgttttaat 180gtctataagt attatatgtt ttatgttatt tacgacaaat tataattgga cttttttaat 240actcttcaca atcttttttg tgatttttat taaacatatt tcaagagttt ctaacccttt 300tattaatcct aaactaggga aaaacattcc gtttatgctt ggtttgtttt ctggtgggct 360aatattttct atagtagctg gttttatatc aatggtgcct tatatgatga aaactattta 420tcatgtaaat gtagcgacaa taggtaatag tgttattttt cctggaacca tgagtgttat 480tgtttttggt tattttggtg gttttttagt ggatagaaaa ggatcattat ttgtttttat 540tttaggatca ttgtctatct ctataagttt tttaactatt gcattttttg ttgagtttag 600tatgtggttg actactttta tgtttatatt tgttatgggc ggattatctt ttactaaaac 660agttatatca aaaatagtat caagtagtct ttctgaagaa gaagttgctt ctggaagagt 720t 7212201791DNAStaphylococcus aureus 220atccggtact gcagaactca aaatgaaaca aggagaaact ggcagacaaa ttgggtggtt 60tatatcatat gataaagata atccaaacat gatgatggct attaatgtta aagatgtaca 120agataaagga atggctagct acaatgccaa aatctcaggt aaagtgtatg atgagctata 180tgagaacggt aataaaaaat acgatataga tgaataacaa aacagtgaag caatccgtaa 240cgatggttgc ttcactgttt tattatgaat tattaataag tgctgttact tctcccttaa 300atacaatttc ttcattttca ttgtatgttg aaagtgacac tgtaacgagt ccattttctt 360tttttatgga tttcttattt gtaatttcag cgataacgta caatgtatta cctgggtata 420caggtttaat aaatttaacg ttattcattt gtgttcctgc tacaacttct tctccgtatt 480taccttcttc tacccataat ttaaatgata ttgaaagtgt atgcatgcca gatgcaatga 540tacctttaaa tctactttgt tctgcttttt ctttatctat atgcatatat tgaggatcaa 600aagttgttgc aaattggata atttcttctt ctgtaatatg aaggcttttt gttttgaatg 660tttctcctac tataaaatca tcgtatttca tatatgtctc tctttcttat tcaaattaat 720tttttagtat gtaacatgtt aaaggtaagt ctaccgtcac tgaaacgtaa gactcacctc 780taactttcta ttgagacaaa tgcaccattt tatctgcatt gtctgtaaag ataccatcaa 840ctccccaatt agcaagttgg tttgcacgtg ctggtttgtt tacagtccat acgttcaatt 900cataacccgc ttcttttacc atttttactt ttgctttagt aagtttggca tcttcagtgt 960ttactatttt agcattacag taatctaaaa gtgttctcca gtcttcacga aacgaagttg 1020tatggaatat aactgctctg ttatattgtg gcatgatttc ttctgcaagt ttaacaagca 1080caacattaaa gcttgaaatg agcacttctt gattctgatt taagtttgtt aattgttctt 1140ccacttgctt aaccatactt ttagaaagtg ctagtccatt cggtccagta atacctttta 1200attctacatt taaattcata ttatattcat ttgctatttt tactacatca tcgaaagttg 1260gcaaatgttc atctttgaat ttttcaccaa accaagatcc tgcagaagca tctttaattt 1320catcataatt caattcagtt atttccccgg acatatttgt agtccgttct aaataatcat 1380catgaatgat aatcagttgt tcatcttttg taattgcaac atctaactcc aaccagttta 1440taccttctac ttctgaagca gctttaaatg atgcaattgt attttccgga gctttactag 1500gtaatcctct atgtccatat acagttagca tattacctct ccttgcattt ttattttttt 1560aattaacgta actgtattat cacattaatc gcacttttat ttccattaaa aagagatgaa 1620tatcataaat aaagaagtcg atagattcgt attgattatg gagttaatct acgtctcatc 1680tcatttttaa aaaatcattt atgtcccaag ctccattttg taatcaagtc tagtttttct 1740gtacccctta tctgcaattt tacttaggat tgcttttaac ttacccctta t 1791221600DNAStaphylococcus aureus 221aagtgctgac gcctgaggga atagtatgtg cgagagacta atggctcgag ccatacccct 60aggcaagcat gcacgtacaa aatcgtaaga taaaaaaata agcatatcac tgtaaacttt 120aaaaaatcag tttagtgata tgcttattta tttcgagtta ggatttatgt cccaagctca 180tcaagcacaa tcggccacta gtttatttct ctatcttata tgttctgata tggtcttcta 240tactgtataa gtatactttt gaatatggat cttgtgtcaa ttcacgttcg aaatcaaatt 300cttgattatc aaatctgtta aagaatgttt cgtattcttc gactgataat tgctctctag 360attctagcat atttaagtgt ttctctttat ctaatgcttt gtcatatcct ttaacgattg 420aaccactaaa gatttctcct actgctcctg aaccataact aaatagacat actttctctt 480ctggttggaa tgtgtggttc tgtaataacg aaattaaact taagtataat gatcctgtat 540aaatgttacc aacatctcta ttccataata cggttctgtt gcaaagttga atttatagta 6002221640DNAStaphylococcus aureus 222gggtggttta tatcatatga taaagataat ccaaacatga tgatggctat taatgttaaa 60gatgtacaag ataaaggaat ggctagctac aatgccaaaa tctcaggtaa agtgtatgat 120gagctatatg agaacggtaa taaaaaatac gatatagatg aataacaaaa cagtgaagca 180atccgtaacg atggttgctt cactgtttta ttatgaatta ttaataagtg ctgttacttc 240tcccttaaat acaatttctt cattttcatt gtatgttgaa agtgacactg taacgagtcc 300attttctttt tttatggatt tcttatttgt aatttcagcg ataacgtaca atgtattacc 360tgggtataca ggtttaataa atttaacgtt attcatttgt gttcctgcta caacttcttc 420tccgtattta ccttcttcta cccataattt aaatgatatt gaaagtgtat gcatgccaga 480tgcaatgata cctttaaatc tactttgttc tgctttttct ttatctatat gcatatattg 540aggatcaaaa gttgttgcaa attggataat ttcttcttct gtaatatgaa ggctttttgt 600tttgaatgtt tctcctacta taaaatcatc gtatttcata tatgtctctc tttcttattc 660aaattaattt tttagtatgt aacatgttaa aggtaagtct accgtcactg aaacgtaaga 720ctcacctcta actttctatt gagacaaatg caccatttta tctgcattgt ctgtaaagat 780accatcaact ccccaattag caagttggtt tgcacgtgct ggtttgttta cagtccatac 840gttcaattca taacccgctt cttttaccat ttttactttt gctttagtaa gtttggcatc 900ttcagtgttt actattttag cattacagta atctaaaagt gttctccagt cttcacgaaa 960cgaagttgta tggaatataa ctgctctgtt atattgtggc atgatttctt ctgcaagttt 1020aacaagcaca acattaaagc ttgaaatgag cacttcttga ttctgattta agtttgttaa 1080ttgttcttcc acttgcttaa ccatactttt agaaagtgct agtccattcg gtccagtaat 1140accttttaat tctacattta aattcatatt atattcattt gctattttta ctacatcatc 1200gaaagttggc aaatgttcat ctttgaattt ttcaccaaac caagatcctg cagaagcatc 1260tttaatttca tcataattca attcagttat ttccccggac atatttgtag tccgttctaa 1320ataatcatca tgaatgataa tcagttgttc atcttttgta attgcaacat ctaactccaa 1380ccagtttata ccttctactt ctgaagcagc tttaaatgat gcaattgtat tttccggagc 1440tttactaggt aatcctctat gtccatatac agttagcata ttacctctcc ttgcattttt 1500atttttttaa ttaacgtaac tgtattatca cattaatcgc acttttattt ccattaaaaa 1560gagatgaata tcataaataa agaagtcgat agattcgtat tgattatgga gttaatctac 1620gtctcatctc atttttaaaa 1640223592DNAStaphylococcus aureus 223aattcaactt tgcaacagaa ccgtattatg gaatagagat gttggtaaca tttatacagg 60atcattatac ttaagtttaa tttcgttatt acagaaccac acattccaac cagaagagaa 120agtatgtcta tttagttatg gttcaggagc agtaggagaa atctttagtg gttcaatcgt 180taaaggatat gacaaagcat tagataaaga gaaacactta aatatgctag aatctagaga 240gcaattatca gtcgaagaat acgaaacatt ctttaacaga tttgataatc aagaatttga 300tttcgaacgt gaattgacac aagatccata ttcaaaagta tacttataca gtatagaaga 360ccatatcaga acatataaga tagagaaata aactagtggc cgattgtgct tgatgagctt 420gggacataaa tcctaactcg aaataaataa gcatatcact aaactgattt tttaaagttt 480acagtgatat gcttattttt ttatcttacg attttgtacg tgcatgcttg cctaggggta 540tggctcgagc cattagtctc tcgcacatac tattccctca ggcgtcagca ct 5922242386DNAStaphylococcus aureus 224caccttcata tgacgtctat ccatttatgt atggcatgag taacgaagaa tataataaat 60taaccgaaga taaaaaagaa cctctgctca acaagttcca gattacaact tcaccaggtt 120caactcaaaa aatattaaca gcaatgattg ggttaaataa caaaacatta gacgataaaa 180caagttataa aatcgatggt aaaggttggc aaaaagataa atcttggggt ggttacaacg 240ttacaagata tgaagtggta aatggtaata tcgacttaaa acaagcaata gaatcatcag 300ataacatttt ctttgctaga gtagcactcg aattaggcag taagaaattt gaaaaaggca 360tgaaaaaact aggtgttggt gaagatatac caagtgatta tccattttat aatgctcaaa 420tttcaaacaa aaatttagat aatgaaatat tattagctga ttcaggttac ggacaaggtg 480aaatactgat taacccagta cagatccttt caatctatag cgcattagaa aataatggca 540atattaacgc acctcactta ttaaaagaca cgaaaaacaa agtttggaag aaaaatatta 600tttccaaaga aaatatcaat ctattaactg atggtatgca acaagtcgta aataaaacac 660ataaagaaga tatttataga tcttatgcaa acttaattgg caaatccggt actgcagaac 720tcaaaatgaa acaaggagaa actggcagac aaattgggtg gtttatatca tatgataaag 780ataatccaaa catgatgatg gctattaatg ttaaagatgt acaagataaa ggaatggcta 840gctacaatgc caaaatctca ggtaaagtgt atgatgagct atatgagaac ggtaataaaa 900aatacgatat agatgaataa caaaacagtg aagcaatccg taacgatggt tgcttcactg 960ttttattatg aattattaat aagtgctgtt acttctccct taaatacaat ttcttcattt 1020tcattgtatg ttgaaagtga cactgtaacg agtccatttt ctttttttat ggatttctta 1080tttgtaattt cagcgataac gtacaatgta ttacctgggt atacaggttt aataaattta 1140acgttattca tttgtgttcc tgctacaact tcttctccgt atttaccttc ttctacccat 1200aatttaaatg atattgaaag tgtatgcatg ccagatgcaa tgataccttt aaatctactt 1260tgttctgctt tttctttatc tatatgcata tattgaggat caaaagttgt tgcaaattgg 1320ataatttctt cttctgtaat atgaaggctt tttgttttga atgtttctcc tactataaaa 1380tcatcgtatt tcatatatgt ctctctttct tattcaaatt aattttttag tatgtaacat 1440gttaaaggta agtctaccgt cactgaaacg taagactcac ctctaacttt ctattgagac 1500aaatgcacca ttttatctgc attgtctgta aagataccat caactcccca attagcaagt 1560tggtttgcac gtgctggttt gtttacagtc catacgttca attcataacc cgcttctttt 1620accattttta cttttgcttt agtaagtttg gcatcttcag tgtttactat tttagcatta 1680cagtaatcta aaagtgttct ccagtcttca cgaaacgaag ttgtatggaa tataactgct 1740ctgttatatt gtggcatgat ttcttctgca agtttaacaa gcacaacatt aaagcttgaa 1800atgagcactt cttgattctg atttaagttt gttaattgtt cttccacttg cttaaccata 1860cttttagaaa gtgctagtcc attcggtcca gtaatacctt ttaattctac atttaaattc 1920atattatatt catttgctat ttttactaca tcatcgaaag ttggcaaatg ttcatctttg 1980aatttttcac caaaccaaga tcctgcagaa gcatctttaa tttcatcata attcaattca 2040gttatttccc cggacatatt tgtagtccgt tctaaataat catcatgaat gataatcagt 2100tgttcatctt ttgtaattgc aacatctaac tccaaccagt ttataccttc tacttctgaa 2160gcagctttaa atgatgcaat tgtattttcc ggagctttac taggtaatcc tctatgtcca 2220tatacagtta gcatattacc tctccttgca tttttatttt tttaattaac gtaactgtat 2280tatcacatta atcgcacttt tatttccatt aaaaagagat gaatatcata aataaagaag 2340tcgatagatt cgtattgatt atggagttaa tctacgtctc atctca 2386225623DNAStaphylococcus aureus 225tgaaaattac aaccgatttt gtaagtgctg acgcctgagg gaatagtatg tgcgagagac 60taatggctcg agccataccc ctaggcaagc atgcacgtac aaaatcgtaa gataaaaaaa 120taagcatatc actgtaaact ttaaaaaatc agtttagtga tatgcttatt tatttcgagt 180taggatttat gtcccaagct catcaagcac aatcggccac tagtttattt ctctatctta 240tatgttctga tatggtcttc tatactgtat aagtatactt ttgaatatgg atcttgtgtc 300aattcacgtt cgaaatcaaa ttcttgatta tcaaatctgt taaagaatgt ttcgtattct 360tcgactgata attgctctct agattctagc atatttaagt gtttctcttt atctaatgct 420ttgtcatatc ctttaacgat tgaaccacta aagatttctc ctactgctcc tgaaccataa 480ctaaatagac atactttctc ttctggttgg aatgtgtggt tctgtaataa cgaaattaaa 540cttaagtata atgatcctgt ataaatgtta ccaacatctc tattccataa tacggttctg 600ttgcaaagtt gaatttatag tat 623226651DNAStaphylococcus aureus 226atgaaaaata tttcagaatt ctcagcccaa cttgatcaaa cttttgatca aggggaagcc 60gtctctatgg agtggttatt ccgtccgttg ctaaaaatgc tggcggaggg cgatccagtc 120cccgttgagg acatcgcggc ggagaccggg aagcccgtcg aggaagttaa gcaagtccta 180cagactctac ctagtgtgga acttgatgag cagggccgtg tcgtcggtta tggcctcaca 240ctgttcccta ccccccatcg cttcgaggtt gatgggaagc aactatatgc atggtgcgcc 300cttgacacac ttatgttccc agcactcatc ggccggacgg tccacatcgc ttcgccttgt 360cacggcaccg gtaagtccgt ccggttgacg gtggaaccgg accgcgttgt aagcgtcgag 420ccttcaacag ccgttgtctc gattgttaca ccagatgaaa tggcctcggt tcggtcggcc 480ttctgtaacg acgttcactt tttcagttca ccgagtgcag cccaagactg gcttaaccaa 540caccctgagt cgagcgtttt gcccgttgaa gatgcctttg aactgggtcg ccatttggga 600gcgcgttatg aggagtcagg acctactaat gggtcctgtt gtaacattta a 651227563DNAStaphylococcus aureus 227atgaatcttg aaaaagggaa tatagaaagg aaaaaacatg gtgtccatgt taatgagtat 60ttgcaaagtg taagtaaccc gaatgtctat gcagctggag atgctgcagc aacggatggc 120ttgcccctca cacctgtagc cagtgcagat tctcatgtcg tagcatctaa tttattgaaa 180gggaacagca aaaaaattga atatcccgtg attccatctg ctgtatttac cgtacctaaa 240atggcatcgg taggtatgag cgaggaggaa gccaaaaact ctggccggaa tattaaagta 300aagcagaaaa acatctccga ctggtttacg tataaacgga caaatgagga ctttgctgcg 360tttaaagtgc tgattgacga agatcatgat caaattgttg gtgctcattt gattagtaat 420gaagccgatg aactgattaa tcattttgca acagccattc gttttgggat ttcaaccaaa 480gaattgaaac aaatgatatt tgcctatcca acggcagctt cggacattgc acacatgttg 540taagtttgcg ttttgtgaga tgt 5632281380DNAStaphylococcus aureus 228ttgtttagtt tatataaaaa atttaaaggt ttgttttata gcgttttatt ttggctttgt 60attctttcat tttttagtgt attaaatgaa atggttttaa atgtttcttt acctgatatt 120gcaaatcatt ttaatactac tcctggaatt acaaactggg taaacactgc atatatgtta 180actttttcga taggaacagc agtatatgga aaattatctg attatataaa tataaaaaaa 240ttgttaatta ttggtattag tttgagctgt cttggttcat tgattgcttt tattggtcac 300aatcactttt ttattttgat ttttggtagg ttagtacaag gagtaggatc tgctgcattc 360ccttcactga ttatggtggt tgtagctaga aatattacaa gaaaaaaaca aggcaaagcc 420tttggtttta taggatcaat tgtagcttta ggtgaagggt taggtccttc aataggggga 480ataatagcac attatattca ttggtcttac ctacttatac ttcctatgat tacaatagta 540actatacctt ttcttattaa agtaatggta cctggtaaat caacaaaaaa tacattagat 600atcgtaggta ttgttttaat gtctataagt attatatgtt ttatgttatt tacgacaaat 660tataattgga cttttttaat actcttcaca atcttttttg tgatttttat taaacatatt 720tcaagagttt ctaacccttt tattaatcct aaactaggga aaaacattcc gtttatgctt 780ggtttgtttt ctggtgggct aatattttct atagtagctg gttttatatc aatggtgcct 840tatatgatga aaactattta tcatgtaaat gtagcgacaa taggtaatag tgttattttt 900cctggaacca tgagtgttat tgtttttggt tattttggtg gttttttagt ggatagaaaa 960ggatcattat ttgtttttat tttaggatca ttgtctatct ctataagttt tttaactatt 1020gcattttttg ttgagtttag tatgtggttg actactttta tgtttatatt tgttatgggc 1080ggattatctt ttactaaaac agttatatca aaaatagtat caagtagtct ttctgaagaa 1140gaagttgctt ctggaatgag tttgctaaat ttcacaagtt ttttatcaga gggaacaggt 1200atagcaattg taggaggttt attgtcacta caattgatta atcgtaaact agttctggaa 1260tttataaatt attcttctgg agtgtatagt aatattcttg tagccatggc tatccttatt 1320attttatgtt gtcttttgac gattattgta tttaaacgtt ctgaaaagca gtttgaatag 13802291365DNAStaphylococcus aureus 229atgagaatag tgaatggacc aataataatg actagagaag aaagaatgaa gattgttcat 60gaaattaagg aacgaatatt ggataaatat ggggatgatg ttaaggctat tggtgtttat 120ggctctcttg gtcgtcagac tgatgggccc tattcggata ttgagatgat gtgtgtcatg 180tcaacagaag aagcagagtt cagccatgaa tggacaaccg gtgagtggaa ggtggaagtg 240aattttgata gcgaagagat tctactagat tatgcatctc aggtggaatc agattggcct 300cttacacatg gtcaattttt ctctattttg

ccgatttatg attcaggtgg atacttagag 360aaagtgtatc aaactgctaa atcggtagaa gcccaaacgt tccacgatgc gatttgtgcc 420cttatcgtag aagagctgtt tgaatatgca ggcaaatggc gtaatattcg tgtgcaagga 480ccgacaacat ttctaccatc cttgactgta caggtagcaa tggcaggtgc catgttgatt 540ggtctgcatc atcgcatctg ttatacgacg agcgcttcgg tcttaactga agcagttaag 600caatcagatc ttccttcagg ttatgaccat ctgtgccagt tcgtaatgtc tggtcaactt 660tccgactctg agaaacttct ggaatcgcta gagaatttct ggaatgggat tcaggagtgg 720acagaacgac acggatatat agtggatgtg tcaaaacgca taccattttg aacgatgacc 780tctaataatt gttaatcatg ttggttacgt atttattaac ttctcctagt attagtaatt 840atcatggctg tcatggcgca ttaacggaat aaagggtgtg cttaaatcgg gccattttgc 900gtaataagaa aaaggattaa ttatgagcga attgaattaa taataaggta atagatttac 960attagaaaat gaaaggggat tttatgcgtg agaatgttac agtctatccc ggcattgcca 1020gtcggggata ttaaaaagag tataggtttt tattgcgata aactaggttt cactttggtt 1080caccatgaag atggattcgc agttctaatg tgtaatgagg ttcggattca tctatgggag 1140gcaagtgatg aaggctggcg ctctcgtagt aatgattcac cggtttgtac aggtgcggag 1200tcgtttattg ctggtactgc tagttgccgc attgaagtag agggaattga tgaattatat 1260caacatatta agcctttggg cattttgcac cccaatacat cattaaaaga tcagtggtgg 1320gatgaacgag actttgcagt aattgatccc gacaacaatt tgatt 1365230831DNAStaphylococcus aureus 230atgggggttt cttttaatat tatgtgtcct aatagtagca tttattcaga tgaaaaatca 60agggttttag tggacaagac aaagagtgga aaagtgagac catggagaga aaagaaaatc 120gctaatgttg attactttga acttctgcat attcttgaat ttaaaaaggc tgaaagagta 180aaagattgtg ctgaaatatt agagtataaa caaaatcgtg aaacaggcga aagaaagttg 240tatcgagtgt ggttttgtaa atccaggctt tgtccaatgt gcaactggag gagagcaatg 300aaacatggca ttcagtcaca aaaggttgtt gctgaagtta ttaaacaaaa gccaacagtt 360cgttggttgt ttctcacatt aacagttaaa aatgtttatg atggcgaaga attaaataag 420agtttgtcag atatggctca aggatttcgc cgaatgacgc aatataaaaa aattaataaa 480aatcttgttg gttttatgcg tgcaacggaa gtgacaataa ataataaaga taattcttat 540aatcagcaca tgcatgtatt ggtatgtgtg gaaccaactt attttaagaa tacagaaaac 600tacgtgaatc aaaaacaatg gattcaattt tggaaaaagg caatgaaatt agactatgat 660ccaaatgtaa aagttcaaat gattcgaccg aaaaataaat ataaatcgga tatacaatcg 720gcaattgacg aaactgcaaa atatcctgta aaggatacgg attttatgac cgatgatgaa 780gaaaagaatt tgtaacgttt gtctgatttg gaggaaggtt tacaccgtaa a 8312314193DNAStaphylococcus aureus 231atgagccgct tgatacgcat gagtgtatta gcaagtggta gtacaggtaa cgccactttt 60gtagaaaatg aaaaaggtag tctattagtt gatgttggtt tgactggcaa gaaaatggaa 120gaattgttta gtcaaattga ccgtaatatt caagatttaa atggtatttt agtaacccat 180gaacatattg atcatattaa aggattaggt gttttggcgc gtaaatatca attgccaatt 240tatgcgaatg aaaagacttg gcaggcaatt gaaaagaaag atagtcgcat ccctatggat 300cagaaattca tttttaatcc ttatgaaaca aaatctattg caggtttcga tgttgaatcg 360tttaacgtgt cacatgatgc aatagatccg caattttata ttttccataa taactataag 420aagtttacga ttttaacgga tacgggttac gtgtctgatc gtatgaaagg tatgatacgt 480ggcagcgatg cgtttatttt tgagagtaat catgacgtcg atatgttgag aatgtgtcgt 540tatccatgga agacgaaaca acgtatttta ggcgatatgg gtcatgtatc taatgaggat 600gcgggtcatg cgatgacaga tgtgattaca ggtaacacga aacgtattta cctatcgcat 660ttatcacaag acaataacat gaaagatttg gcgcgtatga gtgttggcca agtattgaac 720gaacacgata ttgatacgga aaaagaagta ttgctatgtg atacggataa agctattcca 780acgccaatat atacaatata aatgagagtc accctataaa gttcggcact gctgtgagac 840gactttatcg ggtgcttttt tatgttattg gtgggaaatg gctgttgttg gaattaaggt 900tctatttgaa atgtaaaaaa taattcgata ttaaatgtaa tttataaata atttacataa 960aatcaatcat tttaatataa ggattatgat aatatattgg tgtatgacag ttaatggagg 1020gaacgaaatg aaagctttat tacttaaaac aagtgtatgg ctcgttttgc tttttagtgt 1080gatgggatta tggcaagtct cgaacgcggc tgagcagtat acaccaatca aagcacatgt 1140agtaacaacg atagacaaag caacaacaga taagcaacaa gtaacgccaa caaaggaagc 1200ggctcatcaa tttggtgaag aagcggcaac caacgtatca gcatcagcac agggaacagc 1260tgatgaaata aacaataaag taacatccaa cgcattttct aacaaaccat ctacagcagt 1320ttcaacaaaa gtaaacgaaa cgcacgatgt agatacacaa caagcctcaa cacaaaaacc 1380aactcaatca gcaacattca cattatcaaa tgctaaaaca gcatcacttt caccacgaat 1440gtttgctgcc aatgtaccac aaacaacaac acataaaata ttacatacaa atgatatcca 1500tggccgacta gccgaagaaa aagggcgtgt catcggtatg gctaaattaa aaacaataaa 1560agaacaagaa aagcctgatt taatgttaga cgcaggagac gccttccaag gtttaccact 1620ttcaaaccag tctaaaggtg aagaaatggc taaagcaatg aatgcagtag gttatgatgc 1680tatggcagtg ggtaaccatg aatttgactt tggatacgat cagttgaaaa agttagaggg 1740tatgttagac ttcccgatgc taagtactaa cgtttacaaa gatgggaaac gcgcgtttaa 1800gccttcaaca attgtaacga aaaatggtat tcgttatgga attattggcg taacgacacc 1860agaaacaaag acgaaaacaa gacctgaggg cattaaaggt gttgaattta gagatccatt 1920acaaagtgtg acagcagaaa tgatgcgtat ttataaagac gtagatacat ttgttgttat 1980atcacattta gggattgatc cttcaacaca agaaacatgg cgtggtgatt acttagtgaa 2040acaattaagt caaaatccac aattgaagaa acgtattaca gtcattgatg gtcattcaca 2100taccgtactt caaaatggtc aaatttataa caatgatgca ttagcacaaa caggtacagc 2160acttgcgaat atcggtaagg ttacatttaa ttaccgcaat ggagaggtat caaatattaa 2220accgtcattg attaatgtta aagacgttga aaatgtaaca ccgaacaaag cattagctga 2280acaaattaat caagctgatc aaacatttag agcacaaaca gcagaggtta ttattccaaa 2340taataccatt gatttcaaag gagaaagaga tgacgttaga acgcgtgaaa caaatttagg 2400aaacgcgatt gcagatgcta tggaagcgta tggcgttaag aatttctcta aaaagactga 2460ctttgccgtg acaaatggtg gaggtattcg tgcctctatc gcaaaaggta aggtgacacg 2520ctatgattta atctcagtat taccatttgg aaatacgatt gcgcaaattg atgtaaaagg 2580ttcagacgtc tggacagctt tcgaacatag tttaggtgca ccaacaacac aaaaagacgg 2640taagacagta ttaacagcga atggcggttt actacatatc tctgattcaa ttcgtgttta 2700ctatgatatg aataaaccgt ctggcaaacg aattaacgct attcaaattt taaataaaga 2760gacaggtaag tttgaaaata ttgatttaaa acgtgtatat catgtaacga tgaatgactt 2820cacagcatca ggtggcgacg gatatagtat gttcggtggc cctagagaag aaggtatttc 2880attagatcaa gtactagcaa gttatttaaa aacagctaac atagctaagt atgatacgac 2940agaaccacaa cgtatgttat taggtaaacc agcagtaagt gaacaaccag ctaaaggaca 3000acaaggtagc aaaggtagtg agtctggtaa agatgtacaa ccaattggtg acgacaaagc 3060gatgaatcca gcgaaacaac cagcgacagg taaagttgta ttgttaccaa cgcatagagg 3120aactgttagt agcggtacag aaggttctgg tcgcacatta gaaggagcta ctgtatcaag 3180caagagtggg aaccaattgg ttagaatgtc agtgcctaaa ggtagcgcgc atgagaaaca 3240gttaccaaaa actggaacta atcaaagctc aagcccagca gcgatgtttg tattagtagc 3300aggtataggt ttaatcgcga ctgtacgacg tagaaaagct agttaaaata tattgaaaac 3360aatactactg tatttcttaa ataagaggta cggtagtgtt tttttatgga aaaaagctat 3420aaacgttgat aaacatggga tataaaaacg gggataagta ataagacatc aaggtgttta 3480tccacagaaa tggggatagt tatccagaat tgtgtacaat ttaaagagaa atacccacaa 3540tgcccacaga gttatccaca aatacacaag ttatacacta aaaattgggc ataaatgtca 3600ggaaaatatc aaaaactgca aaaaatattg gtataataag agggaacagt gtgaacaagt 3660taataacttg tggataactg gaaagttgat aacaatttgg aggaccaaac gacatgaaaa 3720tcaccatttt agctgtaggg aaactaaaag agaaatattg gaagcaagcc atagcagaat 3780atgaaaaacg tttaggccca tacaccaaga tagacatcat agaagttcca gacgaaaaag 3840caccagaaaa tatgagcgac aaagaaattg agcaagtaaa agaaaaagaa ggccaacgaa 3900tactagccaa aattaaacca caatccacag tcattacatt agaaatacaa ggaaagatgc 3960tatcttccga aggattggcc caagaattga accaacgcat gacccaaggg caaagcgact 4020ttgtattcgt cattggcgga tcaaacggcc tgcacaagga cgtcttacaa cgcagtaact 4080acgcactatc attcagcaaa atgacattcc cacatcaaat gatgcgggtt gtgttaattg 4140agcaagtgta tagagcattt aagattatgc gtggagaagc atatcataaa tga 41932322996DNAStaphylococcus aureus 232atgaaacgag ccattggtta tttgcgccaa agtacaacga aacaacaatc actcccagct 60caaaagcaag caatagaatt attagctcca aagcacaata ttcaaaatat ccaatacatt 120agtgataagc aatcaggcag aacagataat cgaacaggct atcaacaagt caccgaacgc 180atccaacaaa gacaatgtga cgtattatgt tgttatcgct tgaatcgact tcatcgcaac 240ttgaaaaatg cattaaaact catgaaactc tgtcaaaaat atcatgttca tattctaagt 300gttcatgatg gctattttga tatggataaa gcgtttgatc gcctaaaact caatatattc 360atgagtctgg ctgaacttga atccgataat attggagaac aagtcaaaaa tggacttaga 420gaaaaggcaa aacaaggtaa actcataacg acccatgcgc ctttcggtta tcactatcaa 480aatggtactt tcatcattaa taatgatgaa tcacctaccg tcaaagctgt attcaattat 540tatcttcaag gatatggcta caagaagatt gcacaatatt tagaagacga taataaactt 600attacccgca agccttatca ggtacgaaat ataattatga acccaaatta ttgtggtcgt 660gtcatcaatc aatatggtca atataacaat atggtaccac ctattgtttc ggcaacgaaa 720tatgaacatg ctcaagcaat ccgtaataag aagcaacttc actgtatacc ttcagagaat 780cagctgaaac aaaagatcaa atgtccttgt tgtgactcaa cactgacaaa tatgacaata 840agaaaaaaac atacattgcg atattatatt tgtcctaaaa atatgaatga atctcgcttt 900gtctgttcat tcaaaggaat aaatgcacaa aaattagaag ttcaagtctt agctacatgt 960cagaacttct ttcaaaacca acagctctat tcaaaaatta ataatgcaat tcatcaacgc 1020ctcaaaaaac aaagagtgat agaagctaaa agtacgctaa ctcaagaaca actgatagat 1080aaacttgcca aaggtatgat tgatgctgaa tcattcagaa aacagactca tttgatgaat 1140caaaagcaca aaaccatatc ctccataagt gataatcagt tacaaacatc actacaaaag 1200gttatacaga aaagtttcac gttaaacatg ctgcatccct atattgatga aattcgcatt 1260acaaaaaata aagcccttgt tgggatctat ttcaaaaatg aaccattgaa cattgtgaac 1320caaacctcgc aatcatcgat tgcttaatca gaaaggatga aaaaatcatg caacaactca 1380aacaaaaacg tgtcggtatc tatgttcgtg tatcaacgga aatccaaagt actgaaggct 1440atagtatcga tggacaaatc aatcaaattc gagaatattg tgatttcaat aactttgttg 1500ttgtagatgt atacgcggat agaggtatct ctggaaaatc tatgaaccga ccagaactac 1560aacgtttgtt aaaagatgcg aacgaaggtc agattgattc tgttatggtc tacaaaacaa 1620accgactagc acgtaacact tctgacttac tcaaaattgt tgaagacctt catcgtcaaa 1680atgtcgaatt cttcagctta tctgagcgta tggaagtcaa tacaagcagt ggtaaattga 1740tgctacaaat tctagcgagt ttttcagaat ttgaaagaaa taatattgtc gaaaatgtat 1800tcatgggtca aacccgacgc gctcaagaag gctattatca aggcaatttg ccgctgggct 1860atgacaaaat accggatagc aagcatgaac tcatgataaa ccaacatgaa gcgaatattg 1920tcaaatatat atttgagtca tatgctaaag gccacggata tcgtaaaatt gcgaatgcac 1980tcaatcacaa aggatacgtg actaaaaaag gaaagccttt cagtattggt tcagtgacct 2040atatcttatc taatccattc tatgttggta aaattcaatt cgcaaagtac aaagattgga 2100atgaaaagcg tcgtaaaggg ctgaatgata aaccaataat agctgaaggt aagcattccc 2160ctattattat tcaagactta tgggataaag tccaattacg taaaaaacaa gtcagtcaaa 2220aacctcaagt ccacggtaaa ggaactaatc tattaacagg tatcgttcat tgtccacaat 2280gtggtgcacc aatggcagct agtaacacaa cgaacacatt gaaagatggt accaagaagc 2340gaatacgtta ttattcttgc agtaacttcc gaaacaaagg ctcaaaagta tgttctgcga 2400atagcgttag agctgatgtg attgagaaat acgtcatgga tcaaatactc gaaattgtca 2460aaagtgataa agtcattaac caagtcttag aacgtgtcaa tcaagaaaat aaagtcgata 2520ttggtgcatt gaaccacgat atcgcttata aacaacaaca atacgatgaa gtcagcggga 2580aactccataa tttagttaaa accattgaag ataatccgga cctaacatct gcattgaaag 2640caactattca tcaatatgaa acacaactca atgacattac aaatcaaatg aatcaactca 2700aacagcaaca aaatcaagag aaactatctt atgatacgaa acaaatcgct gccctattac 2760aacgaatatt tcaaaatata gaatcaatgg ataaagcaca actcaaagca ttatatctta 2820cagtcattga ccgtattgat attcgtaaag acggtaatca taaaaaacag ttctacgtta 2880cactaaaact caataatgaa attattaaac aacttttcaa taatacccct ctcgacgaag 2940tgctcctcag cacttcgtct ttatttttgc ctcaaacgct ctttcttcaa atctaa 29962331410DNAStaphylococcus aureus 233gctgtaggga aactaaaaga gaaatattgg aagcaagcca tagcagaata tgaaaaacgt 60ttaggcccat acaccaagat agacatcata gaagttccag acgaaaaagc accagaaaat 120atgagcgaca aagaaattga gcaagtaaaa gaaaaagaag gccaacgaat actagccaaa 180attaaaccac aatccacagt cattacatta gaaatacaag gaaagatgct atcttccgaa 240ggattggccc aagaattgaa ccaacgcatg acccaagggc aaagcgactt tgtattcgtc 300attggcggat caaacggcct gcacaaggac gtcttacaac gcagtaacta cgcactatca 360ttcagcaaaa tgacattccc acatcaaatg atgcgggttg tgttaattga gcaagtgtat 420agagcattta agattatgcg tggagaagca tatcataaat gatgcggttt tttcagccgc 480ttcataaagg gattttgaat gtatcagaac atatgaggtt tatgtgaatt gctgttatgt 540ttttaagaag catatcataa gtgatgcggt ttttattaat tagttgctaa aaaatgaagt 600atgcaatatt aattattatt aaattttgat atatttaaag aaagattaag tttagggtga 660atgaatggct tatcaaagtg aatatgcatt agaaaatgaa gtacttcaac aacttgagga 720attgaactat gaaagagtaa atatacataa tattaaatta gaaattaatg aatatctcaa 780agaactagga gtgttgaaaa atgaataagc agacaaatac tccagaacta agatttccag 840agtttgatga ggaatggaaa aaaaggaaat taggtgaagt agtaaattat aaaaatggtg 900gttcatttga aagtttagtg aaaaaccatg gtgtatataa actcataact cttaaatctg 960ttaatacaga aggaaagttg tgtaattctg gaaaatatat cgatgataaa tgtgttgaaa 1020cattgtgtaa tgatacttta gtaatgatac tgagcgagca agcaccagga ctagttggaa 1080tgactgcaat tatacctaat aataatgagt atgtactaaa tcaacgagta gcagcactag 1140tgcctaaaca atttatagat agtcaatttc tatctaagtt aattaataga aaccagaaat 1200atttcagtgt gagatctgct ggaacaaaag tgaaaaatat ttctaaagga catgtagaaa 1260actttaattt tttatctcct aattacactg aacaacaaaa aataggtaat ttcttcagca 1320aactcgaccg ccagattgag ttagaagaag agaaacttga actcttatag caacaaaagc 1380gtggatatat ttcagaagat ttttctcaag 141023460DNAStaphylococcus aureus 234tatgtcaaaa atcatgaacc tcattactta tgataccttg tgcaggccgt ttgatccgcc 6023560DNAStaphylococcus aureus 235tatgtcaaaa atcatgaacc tcattactta tgataccttg tgcaggccgt ttgatccgcc 6023660DNAStaphylococcus aureus 236tatgtcaaaa atcatgaacc tcattactta tgataccttg tgcaggccgt ttgatccgcc 6023760DNAStaphylococcus aureus 237tatgtcaaaa atcatgaacc tcattactta tgataccttg tgcaggccgt ttgatccgcc 6023860DNAStaphylococcus aureus 238tatgtcaaaa atcatgaacc tcattactta tgataccttg tgcaggccgt ttgatccgcc 6023960DNAStaphylococcus aureus 239tatgtcaaaa atcatgaacc tcattactta tgataccttg tgcaggccgt ttgatccgcc 6024060DNAStaphylococcus aureus 240tatgtcaaaa atcatgaacc tcattactta tgataccttg tgcaggccgt ttgatccgcc 6024160DNAStaphylococcus aureus 241tatgtcaaaa atcatgaacc tcattactta tgataccttg tgcaggccgt ttgatccgcc 6024260DNAStaphylococcus aureus 242tatgtcaaaa atcatgaacc tcattactta tgataccttg tgcaggccgt ttgatccgcc 6024360DNAStaphylococcus aureus 243tatgtcaaaa atcatgaacc tcattactta tgataccttg tgcaggccgt ttgatccgcc 6024460DNAStaphylococcus aureus 244tatgtcaaaa atcatgaacc tcattactta tgataccttg tgcaggccgt ttgatccgcc 6024560DNAStaphylococcus aureus 245tatgtcaaaa atcatgaacc tcattactta tgataccttg tgcaggccgt ttgatccgcc 6024625DNAStaphylococcus aureus 246cttggtgtaa accattggag ccacc 2524721DNAStaphylococcus aureus 247cctcatgcaa tccatttgat c 2124829DNAArtificial SequenceSynthetic nucleic acid sequence 248gtcaaaaatc atgaacctca ttacttatg 2924919DNAArtificial SequenceSynthetic nucleic acid sequence 249tgtgcaggcc gtttgatcc 1925035DNAStaphylococcus aureus 250acaaggacgt cttacaacgc agtaactatg cacta 3525135DNAStaphylococcus aureus 251acaaggacgt cttacaacgc agtaactatg cacta 3525235DNAStaphylococcus aureus 252acaaggacgt cttacaacgc agtaactatg cacta 3525335DNAStaphylococcus aureus 253acaaggacgt cttacaacgc agtaactatg cacta 3525435DNAStaphylococcus aureus 254acaaggacgt cttacaacgc agtaactatg cacta 3525535DNAStaphylococcus aureus 255acaaggacgt cttacaacgc agtaactatg cacta 3525635DNAStaphylococcus aureus 256acaaggacgt cttacaacgc agtaactatg cacta 3525735DNAStaphylococcus aureus 257acaaggacgt cttacaacgt agtaactacg cacta 3525835DNAStaphylococcus aureus 258acaaggacgt cttacaacgt agtaactacg cacta 3525935DNAStaphylococcus aureus 259acaaggacgt cttacaacgt agtaactacg cacta 3526035DNAStaphylococcus aureus 260acaaggacgt cttacaacgt agtaactacg cacta 3526135DNAStaphylococcus aureus 261acaaggacgt cttacaacgt agtaactacg cacta 3526235DNAStaphylococcus aureus 262acaaggacgt cttacaacgt agtaactacg cacta 3526335DNAStaphylococcus aureus 263acaaggacgt cttacaacgc agtaactacg cacta 3526435DNAStaphylococcus aureus 264acaaggacgt cttacaacgc agtaactacg cacta 3526535DNAStaphylococcus aureus 265accaagacgt cttacaacgc agcaactatg cttta 3526635DNAStaphylococcus aureus 266atgaggacgt cttacaacgc agcaactacg cactt 3526725DNAArtificial SequenceSynthetic nucleic acid sequence 267gacgtcttac aacgcagtaa ctatg 2526825DNAArtificial SequenceSynthetic nucleic acid sequence 268gacgtcttac aacgtagtaa ctacg 2526925DNAArtificial SequenceSynthetic nucleic acid sequence 269gacgtcttac aacgcagtaa ctacg 25

Claims

1. (canceled)

2. A method to detect the presence of an MREJ type ix methicillin-resistant Staphylococcus aureus (MRSA) strain nucleic acid in a sample, comprising: a) performing an amplification reaction comprising contacting a sample to be analyzed for the presence of said MREJ type ix MRSA strain nucleic acid with a first amplification primer and a second amplification primer to generate a first amplicon if said MREJ type ix MRSA strain nucleic acid is present in said sample, said MREJ type ix MRSA strain nucleic acid including a staphylococcal cassette chromosome mec (SCCmec) element containing a mecA gene inserted into chromosomal DNA, said chromosomal DNA being orfX, thereby generating a polymorphic right extremity junction (MREJ) type ix nucleic acid sequence that comprises nucleic acid sequences from both the SCCmec element right extremity and orfX adjoining said right extremity; wherein said first primer is at least 10 nucleotides in length and specifically hybridizes at least under conditions of 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl.sub.2 at 55.degree. C. with an SCCmec element right extremity of an MREJ type ix nucleic acid sequence selected from the group consisting of: SEQ ID NO: 168 and the complement thereof, wherein said second primer is at least 10 nucleotides in length and specifically hybridizes at least under conditions of 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl.sub.2 at 55.degree. C. with orfX, wherein said first amplicon generated if said MREJ type ix MRSA strain nucleic acid is present in said sample comprises polymorphic right extremity junction (MREJ) type ix sequence and orfX sequence, including the junction of the two, and is indicative of the presence of MREJ type ix MRSA strain nucleic acid in said sample; and b) detecting said first amplicon if present.

3. The method of claim 2, wherein said first amplification primer that specifically hybridizes with said SCCmec element right extremity of an MREJ type ix nucleic acid sequence comprises at least 10 consecutive residues of SEQ ID NO: 109, or the complement thereof.

4. The method of claim 3, wherein said second amplification primer comprises at least ten consecutive residues of SEQ ID NO: 64 or the complement thereof.

5. The method of claim 2, wherein said amplification reaction comprises PCR.

6. The method of claim 2, wherein said method comprises the use of at least one first or second amplification primer and/or a probe comprising a nucleic acid sequence or complement thereof selected from the group consisting of SEQ ID NOs: 109, 148, 149, 205, 206, 64, 71, 72, 73, 74, 75, 76, 70, 103, 130, 132, 158, 159, 59, 62, 32, 83, 84, 160, 161, 162, 163, and 164 for the detection of MREJ type ix nucleic acid.

7. The method of claim 2, wherein said second and first amplification primers are a primer pair consisting of SEQ ID NOs: 64 and 109, or the complements thereof.

8. The method of claim 7, further comprising the use of at least one probe having a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 32, 83, 84, 160, 161, 162, 163, 164, and the complements thereof.

9. The method of claim 2, wherein said method comprises the use of at least one first or second amplification primer and/or a probe comprising a nucleic acid sequence or complement thereof selected from the group consisting of: SEQ ID NOs: 64, 109, 84, 163, and 164, for the detection of MREJ type ix nucleic acid.

10. The method of claim 2, further comprising detecting the presence of at least one further methicillin-resistant Staphylococcus aureus (MRSA) strain nucleic acid in said sample, said at least one further MRSA strain nucleic acid including an SCCmec element containing a mecA gene inserted into chromosomal DNA, thereby generating a polymorphic right extremity junction (MREJ) type i, ii, iii, iv, v, vi, vii or viii nucleic acid sequence that comprises nucleic acid sequences from both the SCCmec element right extremity and chromosomal DNA adjoining said right extremity, wherein said method further comprises contacting said sample with at least one additional primer to generate a second amplicon if said at least one further MREJ type i, ii, iii, iv, v, vi, vii or viii MRSA strain nucleic acid is present in said sample, wherein said at least one additional primer is at least 10 nucleotides in length and specifically hybridizes at least under conditions of 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl.sub.2 at 55.degree. C. with said polymorphic nucleic acid sequences from the SCCmec element right extremity of said at least one of MREJ type i, ii, iii, iv, v, vi, vii and viii nucleic acid sequences, or complements thereof, selected from the group consisting of: a) SEQ ID NOs: 1, 20-25, and 41 for MREJ type i; b) SEQ ID NOs: 2, 17-19, 26, 40, 173-183, 185, 186 and 197 for MREJ type ii; c) SEQ ID NOs: 4-16, 104, 184 and 198 for MREJ type iii; d) SEQ ID NOs: 42-46 and 51 for MREJ type iv; e) SEQ ID NOs: 47-50 for MREJ type v; f) SEQ ID NO: 171 for MREJ type vi; g) SEQ ID NO: 165 and 166 for MREJ type vii; and h) SEQ ID NO: 167 for MREJ type viii, wherein said second amplicon generated if said at least one further MREJ type i, ii, iii, iv, v, vi, vii or viii MRSA strain nucleic acid is present in said sample comprises polymorphic right extremity junction (MREJ) type i, ii, iii, iv, v, vi, vii or viii sequence and orfX sequence, including the junction of the two, and is indicative of the presence of said at least one further MREJ type i, ii, iii, iv, v, vi, vii or viii MRSA strain nucleic acid in said sample; and detecting said second amplicon if present.

11. The method of claim 10, wherein said at least one additional primer comprises at least one primer selected from the following SEQ ID NOs or complements thereof: 66, 100, 101, 105, 52, 53, 54, 55, 56, 57, 97, 99, 106, 117, 118, 124, 125, 58, 67, 98, 102, 107, 108, 79, 77, 145, 146, 147, 65, 80, 154, 155, 202, 203, 204, 112, 113, 114, 119, 120, 121, 122, 123, 150, 151, 153, 115, 116, 187, 188, 207, and 208.

12. The method of claim 11, further comprising use of at least one second amplification primer and/or a probe selected from the following SEQ ID NOs or complements thereof: 64, 71, 72, 73, 74, 75, 76, 70, 103, 130, 132, 158, 159, 59, 62, 32, 83, 84, 160, 161, 162, 163, and 164.

13. The method of claim 10, further comprising the use of at least one primer pair selected from the following SEQ ID NOs, or the complements thereof: a) 64/66, 64/100, 64/101, 59/52, 59/53, 59/54, 59/55, 59/56, 59/57, 60/52, 60/53, 60/54, 60/55, 60/56, 60/57, 61/52, 61/53, 61/54, 61/55, 61/56, 61/57, 62/52, 62/53, 62/54, 62/55, 62/56, 62/57, 63/52, 63/53, 63/54, 63/55, 63/56 and 63/57, for the detection of type i MREJ nucleic acid; b) 64/66, 64/97, 64/99, 64/100, 64/101, 59/52, 59/53, 59/54, 59/55, 59/56, 59/57, 60/52, 60/53, 60/54, 60/55, 60/56, 60/57, 61/52, 61/53, 61/54, 61/55, 61/56, 61/57, 62/52, 62/53, 62/54, 62/55, 62/56, 62/57, 63/52, 63/53, 63/54, 63/55, 63/56 and 63/57, for the detection of type ii MREJ nucleic acid; c) 64/67, 64/98, 64/102, 59/58, 60/58, 61/58, 62/58 and 63/58, for the detection of type iii MREJ nucleic acid; d) 64/79, for the detection of type iv MREJ nucleic acid; e) 64/80, for the detection of type v MREJ nucleic acid; f) 64/204, for the detection of type vi MREJ nucleic acid; g) 64/112 and 64/113, for the detection of type vii MREJ nucleic acid; h) 64/115 and 64/116, for the detection of type viii MREJ nucleic acid.

14. The method of claim 13, comprising the use of at least one probe having a nucleic acid sequence, or the complement thereof, selected from the group consisting of: SEQ ID NOs: 32, 83, 84, 160, 161, 162, 163 and 164.

15. The method of claim 10, comprising the use of primers and probes having the following nucleic acid sequences, or the complements thereof: a) SEQ ID NOs: 64, 66, and at least one of 84, 163, 164 for the detection of MREJ type i or ii nucleic acid; b) SEQ ID NOs: 64, 67, and at least one of 84, 163, 164 for the detection of MREJ type iii nucleic acid; and c) SEQ ID NOs: 64, 79, and at least one of 84, 163, 164 for the detection of MREJ type iv nucleic acid.

16. The method of claim 10, wherein multiple primers and/or probes are used together in the same physical enclosure.

17. The method of claim 10, further comprising distinctively detecting said first amplicon as an indication of the presence of said MREJ type ix nucleic acid and said second amplicon if present as an indication of said at least one further MREJ type nucleic acid selected from MREJ types i, ii, iii, iv, v, vi, vii and viii, wherein the presence or absence of said second amplicon produced by a primer is indicative of the presence or absence, respectively, of the corresponding MREJ type i, ii, iii, iv, v, vi, vii or viii MRSA nucleic acid.

18. The method of claim 10, wherein a plurality of primers and/or probes all chosen to hybridize under the same hybridization conditions are used.

19. The method of claim 2, comprising detecting the presence or absence of at least three further MRSA strain nucleic acids in said sample, said at least three further MRSA strain nucleic acids including an SCCmec element containing a mecA gene inserted into chromosomal DNA, thereby generating a polymorphic right extremity junction (MREJ) type i, ii, iii, iv, v, vi, vii or viii nucleic acid sequence that comprises nucleic acid sequences from both the SCCmec element right extremity and chromosomal DNA adjoining said right extremity, wherein said method further comprises contacting said sample with at least three additional primers to generate a second, third or fourth amplicon if said at least three further MREJ type i, ii, iii, iv, v, vi, vii or viii MRSA strain nucleic acids are present in said sample, wherein said at least three additional primers are at least 10 nucleotides in length and each specifically hybridizes under conditions of 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl.sub.2 at 55.degree. C. with said polymorphic nucleic acid sequences from the SCCmec element right extremity of one of said at least three further MRSA strains of MREJ type i-vi, and viii-ix nucleic acid sequences, or complements thereof, selected from the group consisting of: a) SEQ ID NOs: 1, 20-25, and 41 for MREJ type i; b) SEQ ID NOs: 2, 17-19, 26, 40, 173-183, 185, 186 and 197 for MREJ type ii; c) SEQ ID NOs: 4-16, 104, 184 and 198 for MREJ type iii; d) SEQ ID NOs: 42-46 and 51 for MREJ type iv; e) SEQ ID NOs: 47-50 for MREJ type v; f) SEQ ID NO: 171 for MREJ type vi; g) SEQ ID NO: 165 and 166 for MREJ type vii; and h) SEQ ID NO: 167 for MREJ type viii, wherein said second, third and fourth amplicon generated if said at least three further MREJ type i, ii, iii, iv, v, vi, vii or viii MRSA strain nucleic acids are present in said sample comprises polymorphic right extremity junction (MREJ) type i, ii, iii, iv, v, vi, vii or viii nucleic acid sequence and orfX sequence, including the junction of the two, and said second, third and fourth amplicons are indicative of the presence of said at least three further MREJ type i, ii, iii, iv, v, vi, vii or viii MRSA strain nucleic acids in said sample; and detecting the presence or absence of each second, third and/or fourth amplicon distinctively, wherein the presence or absence of each second, third and/or fourth amplicon produced by a primer is indicative of the presence or absence, respectively, of the corresponding one of said three further MREJ type MRSA nucleic acids, thereby determining the presence or absence in a sample of at least three further MREJ types of MRSA nucleic acids.

20. The method of claim 19, for further determining the presence or absence of MREJ type i, type ii, and type iii nucleic acids.

21. The method of claim 19, for further determining the presence or absence of MREJ type i, type ii, type iii and type iv nucleic acids.

22. The method of claim 19, for further determining the presence or absence of MREJ type i, type ii, type iii, type iv, type v, type vi, type vii, and type viii nucleic acids.

23. The method of claim 2, wherein said method comprises the use of at least one second amplification primer and/or a probe specific for the S. aureus chromosome comprising a nucleic acid sequence, or the complement thereof, selected from the group consisting of SEQ ID NOs: 32, 59, 62, 70-76, 83, 84, 103, 130, 132, and 160-164.

24. The method of claim 10, wherein multiplex PCR is used.

25. The method of claim 2, comprising the use of at least one probe having a nucleic acid sequence, or the complement thereof, selected from the group consisting of SEQ ID NOs: 84, 163 and 164.

26. The method of claim 2, wherein said method comprises the use of at least one first amplification primer comprising a nucleic acid sequence or complement thereof selected from the group consisting of SEQ ID NOs: 109, 148, 149, 205 and 206, for the detection of MREJ type ix nucleic acid.

27. The method of claim 26, wherein said method further comprises the use of at least one second amplification primer and/or probe comprising a nucleic acid sequence or complement thereof selected from the group consisting of SEQ ID NOs: 64, 71, 72, 73, 74, 75, 76, 70, 103, 130, 132, 158, 159, 59, 62, 32, 83, 84, 160, 161, 162, 163, and 164.

28. A nucleic acid comprising a nucleic acid sequence selected from SEQ ID NOs: 42-46 and 51.