# Patent

## Title
DNA-based methods for clone-specific identification of staphylococcus aureus

## Abstract

MRSA CC398 is a clone of S. aureus that has recently emerged in pigs and other domestic animals worldwide. As any other MRSA, the clone displays high levels of antibiotic resistance and poses a serious threat to human health because of the risk of antibiotic treatment failure in human patients. We developed a new diagnostic test for identification of MRSA CC398 using a single one-step PCR that is very easily performed within a few hours. The test is based on the principle that clonal differences within S. aureus are reflected in the sequence of a gene (sau1hsdS1) located on the chromosome of this bacterial species. Accordingly, such a gene represents an optimal target for S. aureus and MRSA identification at the clone level. The test includes detection of the gene conferring methicillin resistance (mecA), therefore allowing rapid discrimination between methicillin-susceptible and methicillin-resistant variants of the clone. A preliminary validation of the test was performed on a collection of CC398 and non-CC398 strains, resulting in 100% sensitivity and 100% specificity. The test can be combined to real-time PCR technology to further reduce simplify the test performance as well as to allow quantification of the target MRSA clone in biological specimens. The invention has important applications related to surveillance and control of MRSA CC398 in humans, animals and food products.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a national stage of International Patent Application No. PCT/DK2010/000093, filed Jun. 17, 2010, which claims the benefit of the priority of Danish Patent Application No. PA 2009 00767, filed Jun. 22, 2009, all of which are incorporated by reference herein.
FIELD OF INVENTION
The present invention relates to DNA-based methods for identification, detection and/or typing of Staphylococcus aureus strains, clones and/or lineages. Specifically, the present invention relates to DNA-based methods for detection and typing of S. aureus clonal complexes based on the sequence of the hsdS gene. More specifically the invention relates to DNA-based methods for detection and/or typing of S. aureus CC398 but can be applied to identification of any other CCs. The present invention furthermore relates to a method for simultaneous identification, detection and/or typing of a Staphylococcus aureus clonal complex and/or strain and/or lineage and for methicillin-resistant S. aureus (MRSA), wherein MRSA is determined by the presence of the mecA gene encoding methicillin resistance, thereby allowing both identification of S. aureus at the CC level and discrimination between MRSA and methicillin-susceptible S. aureus (MSSA) within any CCs.
BACKGROUND OF THE INVENTION
Staphylococcus aureus (S. aureus) is one of the most frequent causes of bacterial infections in the world. About 20% of the population is long-term carriers of S. aureus. S. aureus can cause a range of illnesses from minor skin infections, such as pimples, impetigo, boils, cellulitis folliculitis, furuncles, carbuncles, scalded skin syndrome and abscesses, to life-threatening diseases such as bacteraemia, pneumonia, meningitis, osteomyelitis, endocarditis, toxic shock syndrome (TSS), and septicaemia. Its incidence is from skin, soft tissue, respiratory, bone, joint, endovascular to wound infections. It is still one of the four most common causes of nosocomial infections, often causing postsurgical wound infections.
S. aureus may occur as a commensal on human skin; it also occurs in the nose frequently (in about a third of the population) and throat less commonly. Although the occurrence of S. aureus or MRSA under these circumstances does not indicate infection, healthy carriage of these bacteria is a major risk factor for infection, which usually manifests when normal barriers such as skin or mucosal lining have been breached. S. aureus can spread between individuals through direct contact with infected wounds, skin-to-skin contact, aerosol as well as by contact with contaminated objects such as towels, sheets, clothing, or athletic equipment. It can also colonize domestic animals such as pigs, cattle, dogs, cats and horses, and can cause various animal diseases such as mastitis in dairy cows and bumblefoot in chickens.
MRSA strains harbour the mecA gene, which confers resistance to all beta-lactam antibiotics and is often resistant to alternative antimicrobials (Chambers 1997). MRSA significantly contribute to mortality due to high risk of treatment failure, and results in an economical burden to the society due to prolonged hospitalization and recourse to more expensive antimicrobials. MRSA was originally confined to hospital and health care environments but during the last decade the incidence of community-acquired infections has increased.
Recently, MRSA belonging to a specific genetic lineage called CC398 has emerged in pigs, calves and other animals worldwide. MRSA CC398 colonizes the skin and the mucosal surfaces of healthy animals without any clinical signs. However, the emergence of this MRSA clone in animals represents a major public health problem since animal carriers may contribute to the spread of MRSA among humans. Independent studies in North America (Hanselmann et al. 2006), Holland (Wulf et al. 2006) and Denmark (Moodley et al. 2008; Wulf et al. 2008) have indicated the frequency of MRSA colonization is higher in veterinary staff and pig farmers than in the community. Two case-control studies in the Netherlands (van Loo et al. 2007) and in Denmark (Lewis et al. 2008) have shown that pig farmers are categories at risk for MRSA CC398 infection. Differently from other MRSA lineages, MRSA CC398 is likely to have animal origin and therefore is presently regarded as a zoonosis. It has been reported that the prevalence of MRSA among pig farmers was >760 times higher than that among patients admitted to Dutch hospitals (Voss et al. 2005). Typing of these MRSA indicated that they belonged to CC398 and had been transmitted from pigs to farm workers.
Recently it was established that CC398 accounted for 20% of all MRSA detected in the Netherlands (van Loo et al. 2007), highlighting the need for a fast, simple, inexpensive and reliable typing of this particular MRSA lineage. More generally, molecular typing of MRSA, in particular in hospital-acquired infections, is an important prerequisite for an effective and targeted use of infection control measures aimed at preventing further dissemination within hospitals as well as from the community to hospitals. In doing so, it is necessary to identify genetic markers allowing rapid and reliable MRSA identification at the CC level and easy communication of results between laboratories.
MRSA CC398 and more broadly any MRSA clones are currently identified using a multi-step procedure which includes: i) identification of S. aureus at the species level (Bannerman 2003); ii) detection of methicillin resistance by phenotypic and/or genotypic methods; and iii) clone identification using standard methods for S. aureus typing, namely pulsed-field gel electrophoresis (PFGE) (Murchan et al. 2003), multi-locus sequence typing (MLST) (Enright et al. 2000) and spa typing (Koreen et al. 2004). There have been attempts to merge the first two steps (Vannuffel et al. 1996). However, prior to the invention, no methods were available to cover all three steps. Recently, an restriction-modification (RM) system of S. aureus was described by Waldron et al. (2006). The RM system is composed by five genes: two hsdM (modification) genes, one hsdR (restriction) gene and two hsdS (specificity) genes. The two sau1hsdS genes (sau1hsdS1 and sau1hsdS2) were found to exhibit high sequence variation between isolates belonging to distinct CCs. This finding was subsequently used by Cockfield et al. (2008) to identify six distinct lineages (CC1, CC5, CC8, CC22, CC30 and CC45).
Due to the emerging importance of CC398 in the veterinary sector, the need for rapid methods for MRSA identification at the CC level is no longer limited to human medicine but is now extended to MRSA surveillance in living animals, farm environments and animal food products. In 2007 the EU Commission financed baseline surveys to assess the prevalence of MRSA in breeding pigs (EU Commission 2007). The EU initiative has been accompanied by a number of research and surveillance programs at the national level. This situation has determined a need for a specific method enabling rapid and accurate identification of CC398, including both MRSA and Methicillin-Sensitive S. aureus (MSSA) variants belonging to this S. aureus lineage. Therefore, the invention described herein below has important diagnostic and epidemiological applications in human medicine as well as in the veterinary sector. The invention represents a useful tool for surveillance and control of MRSA CC398 in humans, animals and food products, and more importantly, can be used for clone identification of any MRSA.



BRIEF DESCRIPTION OF DRAWINGS
FIG. 1: Example of how the invention enables identification of methicillin-susceptible (MSSA) and methicillin-resistant (MRSA) S. aureus CC398. Lane M, DNA marker (100-bp ladder); lane 1, negative control (water); lane 2, non-CC398 methicillin-susceptible S. aureus (strain ATCC 6538); lane 3, non-CC398 methicillin-resistant S. aureus (strain ATCC 33591); lane 4, CC398 methicillin-sensitive S. aureus (SSI 52615); lane 5, CC398 methicillin-resistant S. aureus (KVL 288).
FIG. 2: ST types expected to be linked to CC398. Sequence types (ST) identified to belong or associate to clonal complex 398 by eBURST analysis (www.mlst.net). Linked STs are all directly identified as belonging to CC398 whereas the CC398 unlinked isolates are identified as being double-locus variants of the directly identified STs.
FIGS. 3A-3I: Alignment of hsdS sequences. An alignment of a selection of the hsdS1 gene from various S. aureus lineages using CLCbio's Genomic Workbench v. 3.2.



SUMMARY OF THE INVENTION
The applicants herein describe a rapid and reliable identification method of S. aureus types and/or lineages and more specifically for the identification of the clone CC398, even more specifically for the detection of MRSA strains belonging to CC398. The hsdS gene has previously been found to exhibit high sequence variation between isolates belonging to distinct clonal complexes (Waldron D E et al. 2006). These genes are thus suitable for the development methods for the typing of S. aureus clonal complexes. Surprisingly the method described herein identifies S. aureus CC398 with 100% sensitivity and 100% specificity.
The present invention as described herein relates to methods using amplification primers and/or probes which are specific and sensitive for determining the presence of nucleic acid(s) from a S. aureus clonal complex, strain or lineage in any sample suspected of containing said S. aureus nucleic acid(s) thereby identifying, detecting and/or typing said S. aureus clonal complex, strain or lineage, wherein each of said nucleic acid(s) or variant(s) or part(s) thereof comprises a selected target region hybridizable with said probes or primers; said method comprising the following steps: contacting said sample with said primers, or probes and detecting the presence of amplified products or hybridized probes as an indication of the presence of said specific S. aureus clonal complex, strain or lineage thereby identifying, detecting and/or typing said S. aureus clonal complex, strain or lineage.
A specific aspect of the invention relates to detection, identification and/or typing of any S. aureus clonal complex using at least one or more amplification primers and/or probes which are specific and sensitive for determining the presence of clone-specific nucleic acid(s) from the hsdS gene which is hybridizable with said probes or primers, said method comprising the following steps: contacting a sample with said primers or probes and detecting the presence of amplified products or hybridized probes as an indication of the presence of said specific hsdS gene thereby identifying, detecting and/or typing said S. aureus clonal complex.
Another specific aspect of the invention relates to detection, identification and/or typing of any S. aureus clonal complex using at least one or more amplification primers and/or probes which are specific and sensitive for determining the presence of clone-specific nucleic acid(s) from the hsdS gene which is hybridizable with said probes or primers, said method comprising the following steps: contacting a sample with said primers or probes and detecting the presence of amplified products or hybridized probes as an indication of the presence of said specific hsdS gene thereby identifying, detecting and/or typing said S. aureus clonal complex provided that said clonal complex is not CC1, CC5, CC8, CC22, CC30 or CC45. In some embodiments it is further provided that said clonal complex may not be any one or more of: CC12, CC15, CC25, CC51, CC151, CC97, CC771, CC130, CC188, and/or CC873
Another aspect of the invention relates to a method for the detection, identification and/or typing of a S. aureus clonal complex, strain, clone or lineage, in a test sample which comprises the following steps: a) treating said sample with an aqueous solution containing at least one pair of oligonucleotide primers, one of said primers being capable of hybridizing selectively with one of the two complementary strands of said S. aureus clone-specific hsdS gene that contains a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template, said at least one primer being chosen from a nucleotide sequence within the clone-specific hsdS gene with regard to said S. aureus clonal complex, a sequence complementary thereof, and a variant thereof; b) synthesizing an extension product of each of said primers, said extension product containing the target sequence, and amplifying said target sequence, if any, to a detectable level; and c) detecting the presence and/or amount of said amplified target sequence as an indication of the presence and/or amount of said S. aureus clonal complex, in said test sample.
Preferably, the primers are the primers specified in SEQ ID NO: 2 and SEQ ID NO: 6 for the identification, detection and/or typing of S. aureus CC398 and the primers specified in SEQ ID NO: 7 and SEQ ID NO: 8 for the detection of the mecA gene.
Another aspect of the invention relates to a method for the detection, identification and/or typing of a S. aureus strain or lineage thereby identifying, detecting and/or typing said S. aureus strain or lineage, directly from a test sample or from bacterial cultures, which comprises the following steps: a) depositing and fixing on an solid support or leaving in solution the said S. aureus nucleic acid(s) of the sample or of a substantially homogeneous population of said S. aureus isolated from this sample, or inoculating said sample or said substantially homogeneous population of S. aureus isolated from this sample on an solid support, and lysing in situ said inoculated sample or said isolated S. aureus to release the said S. aureus DNA, said S. aureus DNA being made in a substantially single-stranded form; b) contacting said single-stranded DNA with a probe, said probe comprising at least one single-stranded nucleic acid which nucleotide sequence is sequence complementary to a sequence of SEQ ID NO: 1, and a variant thereof, which specifically and ubiquitously anneals with strains or lineages of S. aureus, under conditions such that the nucleic acid(s) of said probe can selectively hybridize with said S. aureus DNA, whereby a hybridization complex is formed; and c) detecting the presence of said hybridization complex on said solid support or in said solution as an indication of the presence and/or amount of said S. aureus, in said test sample.
The present invention as described herein further relates to a method for obtaining hsdS sequences from any S. aureus strain or lineage directly from a test sample or a bacterial culture, which comprises the following steps: a) treating said sample with an aqueous solution containing at least one pair of primers having a sequence selected within the nucleotide sequences defined in SEQ ID NOS: 9, 10, 11 and 12 and a variant thereof, one of said primers being capable of hybridizing selectively with one of the two complementary strands of said S. aureus hsdS gene that contains a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template; b) synthesizing an extension product of each of said primers, said extension product containing the target sequence, and amplifying said target sequence, if any, to a detectable level; and c) detecting the presence and/or amount of said amplified target sequence; and d) determining the nucleotide sequence of the said amplified target sequence by using any DNA sequencing method.
It is contemplated that said primers may not necessarily be completely within the hsdS gene, but may also hybridize to adjacent regions to said hsdS gene.
Furthermore, the present invention as described herein relates to a solid support coated with a set of probes for detection, identification or typing of any S. aureus clonal complex from an extract of its genomic DNA, each probe being able to specifically hybridize with a relevant gene or with a representative fragment thereof susceptible to be present in said genomic DNA to be tested, characterized in that said relevant genes whose presence or absence is to be determined using the set of probes comprise the following genes: a) a clone-specific hsdS gene, for identification, detection and/or typing of said S. aureus clonal complex, and b) at least one gene considered as a negative control, said gene being absent in the genome of said S. aureus species, and optionally c) a gene for antibiotic resistance. Preferably, the solid support is for detection, identification and/or typing of S. aureus CC398.
Yet another aspect of the invention relates to a DNA micro-array for identification and typing of any S. aureus clonal complex comprising the solid support of described herein below. Preferably, the DNA micro-array is for detection, identification and/or typing of S. aureus CC398.
The present invention as described herein further relates to a kit for typing any S. aureus clonal complex comprising the solid support described herein below or the DNA micro-array described herein below. Preferably, the kit is for detection, identification and/or typing of S. aureus CC398.
The present invention as described herein further relates to a kit for detection, identification and/or typing any S. aureus clonal complex, comprising any suitable combination of clone-specific primers.
The present invention as described herein further relates to a kit for detection, identification and/or typing CC398 S. aureus clonal complex, comprising any suitable combination of clone-specific primers selected from the group consisting of SEQ ID NOS: 2 and 6, sequences complementary thereof, and variants thereof.
A further aspect of the invention relates to a kit for detection, identification and/or typing S. aureus, comprising

    
    
        a. means for taking a sample from a subject
        b. means for mailing said sample to an institution for detecting, identification and/or typing of any S. aureus clonal complex and
        c. optionally means for detection of MRSA in said sample and
        d. optionally means for detection of CC398
    
    


Yet another aspect of the invention relates to a kit for detection, identification and/or typing S. aureus, comprising

    
    
        a. means for taking a sample from a subject
        b. means for, at the place where the sample is taken, detecting, identification and/or typing of any S. aureus clonal complex and optionally for detection of MRSA in said sample.
    
    


The present invention as described herein further relates to a device for the detection, identification and/or typing of any S. aureus clonal complex, wherein the device comprises means for measuring the presence of clone-specific hsdS nucleic acid(s). Preferably, the device is for identification and detection, identification and/or typing of CC398 S. aureus. 
Furthermore, the present invention as described herein relates to a device for the detection, identification and/or typing of any S. aureus clonal complex, wherein the device comprises means for measuring the presence of clone-specific hsdS nucleic acid(s) as well as the bacterial resistance gene mecA, for the detection of MRSA. Preferably, the device is for identification and detection, identification and/or typing of CC398 S. aureus. 
DEFINITIONS
Amplifying: Any process or combination of process steps that increases the number of copies of a templated molecule. Amplification of templated molecules may be carried out by any state of the art method including, but not limited to, a polymerase chain reaction to increase the copy number of each template, and using the templates for synthesising additional copies of the templated molecules comprising a sequence of functional groups resulting from the synthesis of the templated molecule being templated by the template. Any amplification reaction or combination of such reactions known in the art can be used as appropriate as readily recognized by those skilled in the art. Accordingly, templated molecules can be amplified by using the polymerase chain reaction (PCR), ligase chain reaction (LCR), in vivo amplification of cloned DNA, and the like. The amplification method should preferably result in the proportions of the amplified mixture being essentially representative of the proportions of templates of different sequences in a mixture prior to amplification.
Amplification: amplification according to the present invention is the process wherein a plurality of exact copies of a starting molecule is synthesised, without employing knowledge of the exact composition of the starting molecule. Hence a template may be amplified even though the exact composition of said template is unknown. In one preferred embodiment of the present invention amplification of a template comprises the process wherein a template is copied by a nucleic acid polymerase or polymerase homologue, for example a DNA polymerase or an RNA polymerase. For example, templates may be amplified using reverse transcription, the polymerase chain reaction (PCR), ligase chain reaction (LCR), in vivo amplification of cloned DNA, and similar procedures capable of complementing a nucleic acid sequence.
Animal: as used herein may be defined to include human beings, domestic or agricultural animals (cats, dogs, cows, sheep, llama, goat etc) or test species (mouse, rat, rabbit, etc).
Array: In the present context an array means an ordered plurality of molecules. Mostly consisting of a plurality of dsDNA or ssDNA fragments covalently attached to a slide or a similar solid support, said DNA fragments being identified by their two dimensional position in the array.
Beta-lactam antibiotics: are a broad class of antibiotics that include penicillin derivatives, cephalosporins, monobactams, carbapenems, and β-lactamase inhibitors that is, any antibiotic agent that contains a β-lactam nucleus in its molecular structure.
Biological sample: as used herein, is intended to mean a sample obtained from a subject or individual.
Clonal complex (CC): group of isolates that are genetically related based on multilocus sequence typing (MLST). They are grouped into clonal complexes by their similarity to a central allelic profile. Clonal complex and lineage can be used interchangeably herein.
Clonal complex 398/CC398/ST398: S. aureus lineage including strains that belong to MLST type ST398 and variants of this MLST type including but not limited to ST291, ST621, ST752, ST753, ST804, ST813, ST1066, ST1067, ST1112, ST1232 and ST1277. It also quite possibly includes ST140, ST580, ST601, ST727, ST810 and ST1094 as double locus variants of CC398 identified sequence types. It includes but is not limited to S. aureus strains of spa type t011, t034, t108 t567, t899, t1197, t1451, t1939, t1793, t2876, t1255 and t571.
Clone specific primers/probes or Lineage specific primers/probes: as used herein, is intended to mean primers and/or probes that target the unconserved/variable region(s) of the hsdS gene.
Complex: Templated molecule linked to the template that templated the synthesis of the templated molecule. The template can be a complementing template as defined herein that is optionally hybridised or otherwise attached to a corresponding template of linked coding elements.
Complementary or substantially complementary: Refers to the hybridization or base pairing between nucleotides or nucleic acids, such as, for instance, between the two strands of a double stranded DNA molecule or between an oligonucleotide primer and a primer binding site on a single stranded nucleic acid to be sequenced or amplified. Complementary nucleotides are, generally, A and T (or A and U), or C and G. Two single stranded RNA or DNA molecules are said to be substantially complementary when the nucleotides of one strand, optimally aligned and with appropriate nucleotide insertions or deletions, pair with at least about 80% of the nucleotides of the other strand, usually at least about 90% to 95%, and more preferably from about 98 to 100%.
Complementary DNA (cDNA): Any DNA obtained by means of reverse transcriptase acting on RNA as a substrate. Complementary DNA is also termed copy DNA.
Complementary strand: Double stranded polynucleotide contains two strands that are complementary in sequence and capable of hybridizing to one another.
Dipstick: Devices that can be dipped into a liquid to perform a chemical test or to provide a measure of quantity of the liquid. Alternatively a dry-reagent dipstick (see herein below).
dsDNA: Double stranded DNA.
hsd gene: “host specificity of DNA”, a subunit of a type I restriction system. There are three types of subunits hsdR, hsdM and hsdS.
Individual: Any species or subspecies of bird, mammal, fish, amphibian, or reptile. Preferably a human being or a domesticated animal.
Ligation: Enzymatic reaction carried out by the enzyme ligase. Ligase catalysis the covalent bonding between two nucleotides adjacent to each other. The reaction of ligase is facilitated by a complementary strand holding the two nucleotides in close proximity. The reaction is further facilitated if the two nucleotides comprises the 3′ and 5′ ends of two polynucleotides that is hold in close proximity to each other by a complementary strand leaving no gaps between the two ends. See “Hybrid oligonucleotide tag”. Even if that is the situation the reaction cannot occur if there is no phosphate group on the 5′ end or no OH group on the 3′ end or if either of the ends are blocked in any other way. Ligation can be carried out using any enzyme capable of ligating nucleotides.
Ligase Chain Reaction (LCR): In LCR, four oligonucleotides, two adjacent oligonucleotides which uniquely hybridize to one strand of target DNA, and a complementary set of adjacent oligonucleotides, which hybridize to the opposite strand are mixed and DNA ligase is added to the mixture. Provided that there is complete complementarity at the junction, ligase will covalently link each set of hybridized molecules. Importantly, in LCR, two probes are ligated together only when they base-pair with sequences in the target sample, without gaps or mismatches. Repeated cycles of denaturation, hybridization and ligation amplify a short segment of DNA.
Lineage: Clusters or groups of genetically related isolates of S. aureus. Isolates belonging to the same lineage share very similar sequence for the majority of their genome (excluding mobile genetic elements). They can also be identified by MLST that have ST types that cluster using BURST software. They can also be identified by spa typing of t types that cluster using BURP software. For S. aureus, two geographically and temporally distinct isolates can be remarkably similar because they belong to the same lineage.
Linker: Connects two moieties or groups or molecules with each other.
mecA gene: Encodes penicillin-binding protein 2a (PBP2a). The presence of mecA in a bacterium gene confers antibiotic resistance to antibiotics such as Methicillin, Penicillin, and other penicillin-like antibiotics.
Messenger RNA (mRNA): mRNA, a polynucleotide being transcribed only from genes that are actively expressed, where the expressed mRNA codes for a protein.
MRSA: Methicillin-resistant S. aureus. A bacterium displaying high levels of antibiotic resistance. It represents a serious public health concern due to increased mortality associated with treatment failure and increased costs to the healthcare system.
MSSA: Methicillin-Sensitive S. aureus, refers to all of the strains of S. aureus that are susceptible to methicillin.
MLST: Multi-locus sequence typing. A method for discriminating bacterial strains/clones belonging to the same species. The method is based on sequencing of 7 housekeeping genes present in all members of the species.
Nucleic acid: A chain or sequence of nucleotides that convey genetic information. The nucleic acid may for example be DNA, RNA, LNA, HNA, PNA, preferably the nucleic acid is DNA or RNA.
Nucleoside: A base attached to a ribose ring, as in RNA nucleosides, or a deoxyribose ring, as in DNA nucleosides.
Nucleotide: Monomer of RNA or DNA. A nucleotide is a ribose or a deoxyribose ring attached to both a base and a phosphate group. Both mono-, di-, and tri-phosphate nucleosides are referred to as nucleotides.
Oligonucleotide: The term “oligonucleotide” as used herein includes linear oligomers of natural or modified monomers or linkages, including deoxyribonucleotides, ribonucleotides, anomeric forms thereof, peptide nucleic acid monomers (PNAs), locked nucleotide acid monomers (LNA), and the like, capable of specifically binding to a single stranded polynucleotide tag by way of a regular pattern of monomer-to-monomer interactions, such as Watson-Crick type of base pairing, base stacking, Hoogsteen or reverse Hoogsteen types of base pairing, or the like. Usually monomers are linked by phosphodiester bonds or analogs thereof to form oligonucleotides ranging in size from a few monomeric units, e.g. 3-4, to several tens of monomeric units, e.g. 40-60. Whenever an oligonucleotide is represented by a sequence of letters, such as “ATGCCTG,” it will be understood that the nucleotides are in 5′→3′ order from left to right and the “A” denotes deoxyadenosine, “C” denotes deoxycytidine, “G” denotes deoxyguanosine, and “T” denotes thymidine, unless otherwise noted. Usually oligonucleotides of the invention comprise the four natural nucleotides; however, they may also comprise methylated or non-natural nucleotide analogs. When oligonucleotides are referred to as “double-stranded,” it is understood by those of skill in the art that “a pair” of oligonucleotides exist in a hydrogen-bonded, helical configuration typically associated with, for example, DNA. In addition to the 100% complementary form of double-stranded oligonucleotides, the term “double-stranded” as used herein is also meant to refer to those forms which include such structural features as bulges and loops.
PBP: Penicillin-binding proteins are membrane bound DD-peptidases that have evolved from serine proteases. PBP2a is encoded by the MecA gene and determines methicillin resistance.
PCR: The polymerase chain reaction (PCR) is a technique widely used in molecular biology. It derives its name from one of its key components, a DNA polymerase used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication.
PCR reagents: refers to the chemicals, apart from the target nucleic acid sequence, needed to perform the PCR process. These chemicals generally consist of five classes of components: (i) an aqueous buffer, (ii) a water soluble magnesium salt, (iii) at least four deoxyribonucleotide triphosphates (dNTPs), (iv) oligonucleotide primers (normally two primers for each target sequence, the sequences defining the 5′ ends of the two complementary strands of the double-stranded target sequence), and (v) a polynucleotide polymerase, preferably a DNA polymerase, more preferably a thermostable DNA polymerase, i.e., a DNA polymerase which can tolerate temperatures between 90[deg.] C. and 100[deg.] C. for a total time of at least 10 min without losing more than about half its activity [0030] The four conventional dNTPs are thymidine triphosphate (dTTP), deoxyadenosine triphosphate (dATP), deoxycitidine triphosphate (dCTP) and deoxyguanosine triphosphate (dGTP). These conventional triphosphates may be supplemented or replaced by dNTPs containing base analogues which Watson-Crick base pair like the conventional four bases, e.g., deoxyuridine triphosphate (dUTP).
RM system: Restriction modification (RM) systems are used by bacteria to protect themselves from foreign DNA.
RNA: ribonucleic acid. Different groups of ribonucleic acids exists: mRNA, tRNA, rRNA and nRNA.
sau1: A chromosomal RM system with widespread distribution in all S. aureus isolates.
Solid support: A material having a rigid or semi-rigid surface. Such materials will preferably take the form of plates or slides, small beads, pellets, disks, capillary tubes or other convenient forms, although other forms may be used. In some embodiments, at least one surface of the solid support will be substantially flat. The solid support may be biological, non-biological, organic, inorganic, or a combination of any of these, existing as particles, strands, precipitates, gels, sheets, tubing, spheres, containers, capillaries, pads, slices, films, plates, slides, etc.
Spa type: Typing method based on the sequence of a single gene called staphylococcal protein A (spa) gene. Is used for classifying different strains and/or lineages of S. aureus. A spa type is composed of various repeats, each of which represents 21 to 30 nucleotides (7-10 codons).
ssDNA: Single stranded DNA.
Staphylococcus aureus (S. aureus): Is a bacterium, frequently found in the nose and skin of a person.
Strain/isolate: A strain according to the present invention is a bacterial isolate that has initially been derived from a pure culture. A strain can also be derived from a clone. If two isolates belong to a clone it suggests that two isolates have derived from a single isolate recently. Clones may also according to the present invention derived from a strain and includes bacteria that exhibit minor changes in their genome, when compared to the initial isolate. As an example, multiple strains of the same clone can occur in one individual after some time due to a treatment which causes recombination and/or mutation events. Thus, for example, a patient could be infected by several strains that belong to the same clone that have developed from one initial infection with a single strain.
ST type: A classification system of s. aureus based on MLST typing of housekeeping genes.
T type: A classification system of s. aureus based on spa typing.
Typing: Typing according to the present invention shall mean that said strains or lineages of S. aureus are sorted into bacterial groups based on the results of the analysis as performed in the context of the present invention. Detection, identification or typing are used interchangeably herein.
vanA gene: Gene conferring vancomycin resistance.
Zoonosis (or zoonose): Any infectious disease that is able to be transmitted (in some instances, by a vector) from other animals, both wild and domestic, to humans or from humans to animals (the latter is sometimes called reverse zoonosis).
DETAILED DISCLOSURE OF THE INVENTION
The applicants herein describe a method for rapid and reliable identification of S. aureus types, clonal complexes, and/or strains and/or lineages and more specifically for the identification of clonal complex CC398.
The present invention also enables a rapid and specific identification of methicillin-resistant (MRSA) and methicillin susceptible (MSSA) variants of S. aureus by simultaneous detection of clone-specific gene sequences in the hsd RM system and of a gene for antibiotic resistance, preferably MecA.
One embodiment of the invention relates to methods using amplification primers and/or probes which are specific and sensitive for determining the presence of nucleic acid(s) from a S. aureus strain or lineage in any sample suspected of containing said S. aureus nucleic acid(s) thereby identifying, detecting and/or typing said S. aureus strain or lineage, wherein each of said nucleic acid(s) or variant(s) or part(s) thereof comprises a selected target region hybridizable with said probes or primers; said method comprising the following steps: contacting said sample with said primers, or probes and detecting the presence of amplified products or hybridized probes as an indication of the presence of said specific S. aureus strain or lineage thereby identifying, detecting and/or typing said S. aureus strain or lineage.
In a more specific embodiment the nucleic acid(s) from a S. aureus strain or lineage is a species specific restriction-modification (RM) gene, preferably a hsdS gene, even more preferably a sau1hsdS1 or sau1hsdS2 gene.
Thus in a particular embodiment the invention relates to a method for identifying, detecting and/or typing any S. aureus clonal complex using at least one or more amplification primers and/or probes which are specific and sensitive for determining the presence of clone-specific nucleic acid(s) from the hsdS gene which is hybridizable with said probes or primers, said method comprising the following steps: contacting a sample with said primers or probes and detecting the presence of amplified products or hybridized probes as an indication of the presence of said specific hsdS gene thereby identifying, detecting and/or typing said S. aureus clonal complex.
Another particular embodiment the invention relates to a method for identifying, detecting and/or typing any S. aureus clonal complex using at least one or more amplification primers and/or probes which are specific and sensitive for determining the presence of clone-specific nucleic acid(s) from the hsdS gene which is hybridizable with said probes or primers, said method comprising the following steps: contacting a sample with said primers or probes and detecting the presence of amplified products or hybridized probes as an indication of the presence of said specific hsdS gene thereby identifying, detecting and/or typing said S. aureus clonal complex provided that said clonal complex is not CC1, CC5, CC8, CC22, CC30 or CC45. In some embodiments it is further provided that said clonal complex may not be any one or more of: CC12, CC15, CC25, CC51, CC151, CC97, CC771, CC130, CC188, and/or CC873
S. aureus 
As described herein above S. aureus is one of the most frequent causes of bacterial infections in the world. About 20% of the population is long-term carriers of S. aureus. S. aureus may occur as a commensal on human skin; it also occurs in the nose frequently (in about a third of the population) and throat less commonly.
Methicillin-Resistant S. aureus (MRSA)
MRSA is by definition a strain of S. aureus that is resistant to a large group of antibiotics called the beta-lactams, which include the penicillins and the cephalosporins (see herein below). MRSA may also be referred to as multidrug-resistant S. aureus or oxacillin-resistant S. aureus (ORSA).
The organism is often sub-categorized as Community-Associated MRSA (CA-MRSA) or nosocomial infections. Nosocomial infections are also known as Health Care-Associated MRSA (HA-MRSA). Nosocomial infections are infections which are a result of treatment in a hospital or a healthcare service unit, but secondary to the patient's original condition. Infections are considered nosocomial if they first appear 48 hours or more after hospital admission or within 30 days after discharge. This type of infection is also known as a hospital-acquired infection (or more generically healthcare-associated infections).
MRSA is especially troublesome in nosocomial infections. In hospitals, patients with open wounds, invasive devices, and weakened immune systems are at greater risk for infection than the general public. Hospital staff who have not followed proper sanitary procedures may transfer bacteria from patient to patient. Visitors to patients with MRSA infections or MRSA colonization are advised to follow hospital isolation protocol by using the provided gloves, gowns, and masks if indicated. Visitors who do not follow such protocols are capable of spreading the bacteria to cafeterias, bathrooms, and elevators.
Some have defined CA-MRSA by criteria related to patients suffering from an MRSA infection while others have defined CA-MRSA by genetic characteristics of the bacteria themselves. CA-MRSA strains were first reported in the late 1980s; these cases were defined by a lack of exposure to the health care setting. In the next several years, it became clear that CA-MRSA infections were caused by strains of MRSA that differed from the older and better studied healthcare-associated strains. Both Community-Associated MRSA (CA-MRSA) and Health Care-Associated MRSA (HA-MRSA) are encompassed within the scope of the present invention.
Healthy individuals may carry MRSA asymptomatically for periods ranging from a few weeks to many years. Patients with compromised immune systems are at a significantly greater risk of symptomatic secondary infection.
The initial presentation of MRSA is small red bumps that resemble pimples, spider bites, or boils that may be accompanied by fever and occasionally rashes. Within a few days the bumps become larger, painful and eventually open into deep, pus-filled boils. About 75 percent of CA-MRSA infections are localized to skin and soft tissue and usually can be treated effectively. However CA-MRSA strains display enhanced virulence, spreading more rapidly and causing illness much more severe than traditional HA-MRSA infections and they can affect vital organs and lead to widespread infection (sepsis), toxic shock syndrome and necrotizing (“flesh-eating”) pneumonia.
Both CA-MRSA and nosocomial MRSA (HA-MRSA) are resistant to traditional anti-staphylococcal beta-lactam antibiotics (see herein below). CA-MRSA has a greater spectrum of antimicrobial susceptibility, including to sulfa drugs, tetracyclines, and clindamycin. HA-MRSA is often resistant even to these antibiotics and often is susceptible only to vancomycin.
Subjects
The subjects referred to herein are single members of a species, herein preferably a mammalian species. Any mammalian species is an object of the present invention, although any of the following species are of particular relevance: mouse, rat, guinea goat, llama, pig, hamster, rabbit, cat, dog, pig, cow, horse, sheep, monkey, and human. The subjects may in the present text also be referred to as patients or individuals.
The S. aureus nucleic acid(s), preferably clone-specific nucleic acid(s) from the hsdS gene of the present invention may be derived from strains and/or lineages of any subject, the subject being preferably persons and/or animals. In preferred embodiments the sample of S. aureus nucleic acid(s), preferably clone-specific nucleic acid(s) from the hsdS gene may be derived from strains and/or lineages from a person from an at risk population.
At risk populations include but are not limited to:

    
    
        Persons staying in a health care facility for an extended period of time
        Health care workers
        Farm workers
        Veterinarian staff
        Persons involved in sales to farms
        Persons involved in the handling of livestock
        Slaughterhouse workers
        Persons involved in post production of meat including but not limited to butchers in general
        People with weak immune systems (AIDS patients, cancer patients, severe asthmatics, etc.)
        Diabetics
        Athletes participating in contact sports or weight training
        Young children
        The elderly
        Prisoners or anyone living in confined space with other people.
        Cystic fibrosis patients
    
    


In a preferred embodiment the sample of nucleic acid(s) is derived from strains and/or lineages of persons staying in a health care facility for an extended period of time, health care workers, farm workers, veterinarian staff, persons involved in sales to farms and any person involved in the handling of livestock and/or butchery.
In a specific embodiment the sample of nucleic acid(s) is derived from strains and/or lineages of one individual patient or hospital.
In another specific embodiment several lineages and/or hospital isolates are analysed.
S. aureus is not only present in humans. It may be useful to test animals for the presence of S. aureus nucleic acid(s), preferably clone-specific nucleic acid(s) from the hsdS gene and/or for the presence of mecA nucleic acid(s).
Thus, in other embodiments the test sample may be derived from any animal, preferably any domesticated animal. In some embodiment the test sample may be derived from poultry, whereas in other embodiments the test sample may be derived from a mammal, such as a mouse, a rat, a guinea pig, a goat, a llama, a hamster, a rabbit, a cat, a dog, a pig, a cow, a horse, a sheep, a monkey, and a human being. Preferably the mammal is a human being or a domesticated animal.
In some embodiments the mammal may be selected from the group consisting of domesticated animals including but not limited to livestock such as pigs, horses and cows, sheep, goats, whereas in other embodiments the mammal may be selected from the group consisting of pet animals including but not limited to dogs and cats.
Biological Sample
A biological sample is a sample obtained from a subject. As such a biological sample may be a sample selected from the group consisting of tissue, blood, serum, plasma samples, urine, cerebrospinal fluid, synovial fluid, ascites, and saliva.
In specific embodiments of the invention the sample may be a sample selected from the group consisting of swabs from mucosal tissues including but not limited to nasal swabs, throat swabs and mouth swabs. The sample may also be a sample selected from the group consisting of swabs from the skin surface especially from hands, feet, Perineum, face and from any infectious tissue such as boils and sores.
In some specific embodiments the S. aureus nucleic acid(s) of the present invention, preferably clone-specific nucleic acid(s) from the hsdS gene may be derived from meat or any food products and any sample thereof.
Strains and Lineages
According to the present invention the S. aureus strain or lineage may be any S. aureus clonal complex, strain or lineage.
In a particular embodiment of the present invention the S. aureus strain or lineage may be any S. aureus clonal complex, strain or lineage provided that said clonal complex is not CC1, CC5, CC8, CC22, CC30 or CC45. In some embodiments it is further provided that said clonal complex may not be any one or more of: CC12, CC15, CC25, CC51, CC151, CC97, CC771, CC130, CC188, and/or CC873
In some embodiments the S. aureus clonal complex, strain or lineage is a MRSA strain or lineage, including but not limited to Community-Associated MRSA (CA-MRSA) or noncomisal MRSA (HA-MRSA).
In some embodiments, when the S. aureus clonal complex, strain or lineage is determined simultaneously with the determination of the presence of an antibiotic gene, preferably mecA, the S. aureus strain or lineage may be any S. aureus strain or lineage.
In a preferred embodiment of the present invention the S. aureus clonal complex, is CC398.
In a preferred embodiment of the present invention the S. aureus clonal complex is MRSA CC398.
In a preferred embodiment of the present invention the S. aureus strain or lineage is any CC398 lineage or strain.
In a preferred embodiment of the present invention the S. aureus strain or lineage is a MRSA CC398 lineage or strain.
Clonal Complex 398/CC398/ST398
CC398 is an S. aureus lineage that includes strains belonging to MLST type ST398 and variants of this MLST type including but not limited to ST291, ST621, ST752, ST753, ST804, ST813, ST1066, ST1067, ST1112, ST1232 and ST1277. It also quite possibly includes ST140, ST580, ST601, ST727, ST810 and ST1094 as double locus variants of CC398 identified sequence types. It includes but is not limited to S. aureus strains of spa type t011, t034, t108 t567, t899, t1197, t1451, t1939, t1793, t2876, t1255 and t571.
CC398 may also include ST140, ST580, ST601, ST727, ST810 and ST1094 as double locus variants of CC398 identified sequence types.
CC398 further includes but is not limited to S. aureus strains of spa type t011, t034, t108 t567, t899, t1197, t1451, t1939, t1793, t2876, t1255 and t571.
Preferably the CC398 strain of the present invention belongs to MLST type ST398 and variants of this MLST type including but not limited to ST291, ST621, ST752, ST753, ST804, ST813, ST1066, ST1067, ST1112, ST1232 and ST1277. It also quite possibly includes ST140, ST580, ST601, ST727, ST810 and ST1094 as double locus variants of CC398 identified sequence types. It includes but is not limited to S. aureus strains of spa type t011, t034, t108 t567, t899, t1197, t1451, t1939, t1793, t2876, t1255 and t571. but any CC398 related MLST types or spa types including as yet unidentified types are encompassed within the scope of the present invention. See FIG. 2 for a diagram of the CC398 related MLST and spa types.
Beta-Lactam Antibiotics
Beta-lactam antibiotics are a broad class of antibiotics that include penicillin derivatives, cephalosporins, monobactams, carbapenems, and β-lactamase inhibitors, that is, any antibiotic agent that contains a β-lactam nucleus in its molecular structure. They are the most widely-used group of antibiotics.
MRSA has evolved an ability to survive treatment with beta-lactamase resistant beta-lactam antibiotics, including but not limited to methicillin, dicloxacillin, nafcillin, and oxacillin.
Beta-lactam antibiotics include but are not limited to penicillins including narrow-spectrum penicillins, such as the Beta-lactamase sensitive penicillins including but not limited to benzathine penicillin, benzylpenicillin (penicillin G), phenoxymethylpenicillin (penicillin V), procaine penicillin and oxacillin; the Penicillinase-resistant penicillins including but not limited to methicillin, oxacillin, nafcillin, cloxacillin, dicloxacillin and flucloxacillin and the beta-lactamase-resistant penicillins such as temocillin. Moderate-spectrum penicillins such including but not limited to amoxycillin and ampicillin are also included as are any broad-spectrum penicillins including but not limited to co-amoxiclav (amoxicillin+clavulanic acid) as well as extended-spectrum penicillins including but not limited to azlocillin, carbenicillin, ticarcillin, mezlocillin and piperacillin.
Another class of Beta-lactam antibiotics is the cephalosporins, including first generation cephalosporins including but not limited to cephalexin, cephalothin and cefazolin as well as second generation cephalosporins including but not limited to moderate spectrum cephalosporins such as cefaclor, cefuroxime and cefamandole and second generation cephamycins including but not limited to cefotetan and cefoxitine. Third generation cephalosporins including but not limited to ceftriaxone, cefotaxime, cefpodoxime and ceftazidime are also included as are fourth generation cephalosporins including but not limited to cefepime and cefpirome.
Yet another class of Beta-lactam antibiotics is the carbapenems including but not limited to imipenem, meropenem, ertapenem, faropenem and doripenem.
Still another class of Beta-lactam antibiotics is the monobactams including but not limited to aztreonam (Azactam). The MRSA according to the present invention may be resistant to any one or more of the subgroups of betal-lactams described herein above.
Restriction Modification System (RM System)
In some embodiments of the invention the nucleic acid(s) from a S. aureus strain or lineage is a species specific restriction-modification (RM) gene, more preferably the nucleic acid(s) from a S. aureus strain or lineage is a clone specific restriction-modification (RM) gene. In a very preferred embodiment the nucleic acid(s) from a S. aureus clonal complex, strain or lineage is clone-specific nucleic acid(s) from the hsdS gene.
The restriction modification system (RM system) is used by bacteria, and perhaps other prokaryotic organisms to protect themselves from foreign DNA, such as bacteriophages. Certain bacteria strains were found to inhibit (restrict) the growth of viruses grown in previous strains. This effect was attributed to sequence-specific restriction enzymes.
Bacteria have restriction enzymes, also called restriction endonucleases, which cleave double stranded DNA at specific points into fragments, which are then degraded further by other endonucleases. This prevents infection by effectively destroying the foreign DNA introduced by an infectious agent (such as a bacteriophage). Approximately one quarter of known bacteria possess RM systems and of those about one half has more than one type of system.
Types of Restriction Modification Systems
There are three types of restriction modification systems: type I, type II and type III, all with restriction enzyme activity and a methylase activity.
Type I systems consist of three polypeptides: R (restriction), M (modification), and S (specificity). The resulting complex can both cleave and methylate DNA. The S subunit determines the specificity of both restriction and methylation. Cleavage occurs at variable distances from the recognition sequence, so discrete bands are not easily visualized by gel electrophoresis. In a preferred embodiment of the invention the RM system is a type I system.
Type II systems are the simplest and the most prevalent. Instead of working as a complex, the methytransferase and endonuclease are encoded as two separate proteins and act independently (there is no specificity protein). Both proteins recognize the same recognition site, and therefore compete for activity. The methyltransferase acts as a monomer, methylating the duplex one strand at a time. The endonuclease acts as a homodimer, which facilitates the cleavage of both strands. Cleavage occurs at a defined position close to or within the recognition sequence, thus producing discrete fragments during gel electrophoresis. For this reason, Type II systems are used in labs for DNA analysis and gene cloning. In some embodiments of the invention the RM system is a type II system. In some embodiment of the invention the RM system may be a type I system.
Type III systems have R and M proteins that form a complex of modification and cleavage. The M protein, however, can methylate on its own. Methylation also only occurs on one strand of the DNA unlike most other known mechanisms. The heterodimer formed by the R and M proteins competes with itself by modifying and restricting the same reaction. In some embodiments of the invention the RM system is a type III system. In some embodiment of the invention the RM system may be a type III system.
Type I RM Systems
In preferred embodiments of the invention the nucleic acid(s) from a S. aureus strain or lineage is a species specific restriction-modification (RM) gene of the type I of RM systems, more preferably the nucleic acid(s) from a S. aureus strain or lineage is a clone specific type I restriction-modification (RM) gene.
There are three types of type I systems, namely type IA, type IB and type IC. Type I restriction enzymes comprises three subunits which are encoded by three closely linked genes hsdR, hsdM and hsdS. The HsdM and HsdS (also known as the specificity subunit) subunits are both necessary and sufficient for methyltransferase activity. The HsdR subunit (also known as the restriction subunit) is required for restriction. The type I RM system preferably used in the present invention prevents acquisition of DNA originated from genetically unrelated S. aureus clones and other foreign DNA.
In a preferred embodiment of the invention the nucleic acid(s) from a S. aureus clonal complex, strain or lineage is one or more clone-specific hsdS nucleic acid(s).
In a very preferred embodiment of the invention the nucleic acid(s) from a S. aureus clonal complex is clone-specific nucleic acid(s) from the hsdS gene, more preferably the clone-specific nucleic acid(s) are from the sau1hsdS1 or sau1hsdS2 genes. In a most preferred embodiment of the invention the nucleic acid(s) from a S. aureus clonal complex is sau1hsdS1 (SEQ ID NO: 1) or sau1hsdS2 from CC398.
It is understood, that some hsdS sequences are found in more than one lineage of S. aureus. Further, without being bound by theory, no lineage has two identical hsdS sequences. Therefore any combination of hsdS sequences can be used to identify any specific S. aureus lineage and this is thus an embodiment of the present invention.
Also, there may within a clonal complex and/or lineage be a small variation in the sequence of the hsdS gene(s) of that particular clonal complex/lineage. The sequence variation may be too minute to distinguish the particular bacteria from other bacteria belonging to the same clonal complex/lineage and thus in the present context a clone-specific nucleic acid may in fact be of more than one specific nucleotide sequence. Thus it is an object of the present invention to detect clone-specific nucleic acid(s) from the hsdS gene(s). The difference in sequence within a clonal complex/lineage in a single hsdS gene(s) may be 1, such as 2, such as 3, such as 4, such as 5, such as 6, such as 7, such as 8, such as 9, or such as 10 nucleotides whereby it is understood that the difference may reside in a replacement of one nucleotide for another or the deletion or insertion of any of the above number of nucleotides.
Detection
It is within the general scope of the present invention to provide methods for the detection of nucleic acid(s) from S. aureus, preferably nucleic acid(s) of the RM systems described herein above even more preferably clone-specific nucleic acid(s) from the hsdS gene and optionally nucleic acid(s) of an antibiotic gene, preferably mecA.
The detection of one or more nucleic acid molecules of the RM systems described herein above even more preferably clone-specific nucleic acid(s) from the hsdS gene allows for the identification, detection and/or typing of a S. aureus clonal complex, strain and/or lineage. The identification, detection and/or typing of a S. aureus clonal complex, strain and/or lineage is of relevance both medically and scientifically and may provide important information useful for example infection control.
Any method of detection of nucleic acid(s) from S. aureus falls within the general scope of the present invention. The detection methods may be generic for the detection of nucleic acids especially DNA and/or RNA. The detection methods may be directed towards the scoring of a presence or absence of one or more nucleic acid molecules or may be useful in the detection of expression levels.
The detection methods can be divided into two categories herein referred to as in situ methods or screening methods. The term in situ method refers to the detection of nucleic acid molecules in a sample wherein the structure of the sample has been preserved. This may thus be a biopsy wherein the structure of the tissue is preserved. In situ methods are generally histological i.e. microscopic in nature and include but are not limited to methods such as: in situ hybridization techniques and in situ PCR methods. Thus nucleic acid(s) of a clone-specific hsdS gene, preferably CC398 may be detected by any of the methods described herein.
Screening methods generally employ techniques of molecular biology and most often require the preparation of the sample material in order to access the nucleic acid molecules to be detected. Screening methods include, but are not limited to methods such as: Array systems, affinity matrices, Northern blotting and PCR techniques, such as real-time quantitative RT-PCR.
An aspect of the present invention regards the detection of nucleic acid molecules by any method known in the art. In the following are given examples of various detection methods that can be employed for this purpose, and the present invention includes all the mentioned methods, but is not limited to any of these.
Amplification Methods
In specific embodiments of the invention the nucleic acid(s) of S. aureus, specifically clone-specific nucleic acid(s) from the hsdS gene are amplified. The amplification method may be any method of amplifying nucleic acid(s) and may be selected from the group consisting of polymerase chain reaction (PCR), ligase chain reaction (LCR), nucleic acid sequence-based amplification (NASBA), self-sustained sequence replication (3SR), strand displacement amplification (SDA), branched DNA signal amplification (bDNA), transcription-mediated amplification (TMA), cycling probe technology (CPT), real-time PCR, quantitative PCR, nested PCR, and multiplex PCR.
PCR
The terms “PCR reaction”, “PCR amplification”, “PCR”, “pre-PCR”, “Q-PCR”, “real-time quantitative PCR”, “nested PCR”, “multiplex PCR” and “real-time quantitative RT-PCR” are interchangeable terms used to signify use of a nucleic acid amplification system, which multiplies the target nucleic acids being detected. Examples of such systems include the polymerase chain reaction (PCR) system and the ligase chain reaction (LCR) system. Other methods recently described and known to the person of skill in the art are the nucleic acid sequence-based amplification (NASBA), self-sustained sequence replication (3SR), strand displacement amplification (SDA), branched DNA signal amplification (bDNA), transcription-mediated amplification (TMA), cycling probe technology (CPT), and Q Beta Replicase systems. The products formed by said amplification reaction may or may not be monitored in real time or only after the reaction as an end-point measurement.
Thus in one specific embodiment, the invention relates to a method for the detection, identification and/or typing of a S. aureus clonal complex, strain or lineage, in a test sample which comprises the following steps: a) treating said sample with an aqueous solution containing at least one pair of oligonucleotide primers, one of said primers being capable of hybridizing selectively with one of the two complementary strands of said S. aureus clone-specific hsdS gene that contains a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template, said at least one pair of primers being chosen from a nucleotide sequence within the clone-specific hsdS gene respectively with regard to said S. aureus clonal complex, a sequence complementary thereof, and a variant thereof; b) synthesizing an extension product of each of said primers, said extension product containing the target sequence, and amplifying said target sequence, if any, to a detectable level; and c) detecting the presence and/or amount of said amplified target sequence as an indication of the presence and/or amount of said S. aureus clonal complex, in said test sample.
In one embodiment there is provided that the clonal complex is complex is not CC1, CC5, CC8, CC22, CC30 or CC45. In some embodiments it is further provided that said clonal complex may not be any one or more of: CC12, CC15, CC25, CC51, CC151, CC97, CC771, CC130, CC188, and/or CC873
Preferably, the primers are the primers specified in SEQ ID NO: 2 and SEQ ID NO: 6 for the detection and/or identification and/or typing of CC398 S. aureus. 
Multiplex PCR
Multiplex PCR is a variant of PCR which enables simultaneous amplification of many targets of interest in one reaction by using more than one pair of primers. A Multiplex PCR assay is thus capable of screening for the presence of two or more nucleic acid(s) in a sample.
A preferred embodiment of the invention is a multiplex PCR reaction that allows the simultaneous detection of nucleic acid(s) of the RM systems described herein above and nucleic acid(s) of an antibiotic gene selected from the group consisting of mecA and vanA, preferably the antibiotic gene is mecA.
Another preferred embodiment of the invention is a multiplex PCR reaction that allows the simultaneous detection of nucleic acid(s) of the hsdS genes described herein above and nucleic acid(s) of an antibiotic gene selected from the group consisting of mecA and vanA, preferably the antibiotic gene is mecA.
A very preferred embodiment of the invention is a multiplex PCR reaction that allows the simultaneous detection of nucleic acid(s) of the hsdS genes of CC398 described herein above and nucleic acid(s) of an antibiotic gene selected from the group consisting of mecA and vanA, preferably the antibiotic gene is mecA.
Thus a very preferred embodiment of the invention the methods described herein further comprises amplification primers and/or probes which are specific and sensitive for determining the presence of nucleic acid(s) from the bacterial antibiotic resistance gene mecA in any sample suspected of containing said S. aureus nucleic acid(s) thereby determining MRSA, wherein each of said nucleic acid(s) or variant(s) or part(s) thereof comprises a selected target region hybridizable with said primers or probes; said method comprising the following steps: contacting said sample with said probes or primers and detecting the presence of amplified products or hybridized probes as an indication of the presence said specific S. aureus antibiotic resistance genes and thus MRSA.
Preferably, the primers are the primers specified in SEQ ID NO: 2 and SEQ ID NO: 6 for the identification, detection and/or typing of CC398 S. aureus and the primers specified in SEQ ID NO: 7 and SEQ ID NO: 8 for the detection of the mecA gene.
Real-Time Quantitative RT-PCR
Real-time quantitative RT-PCR is a modification of polymerase chain reaction used to rapidly measure the quantity of a product of polymerase chain reaction. It is preferably done in real-time, thus it is an indirect method for quantitatively measuring starting amounts of DNA, complementary DNA or ribonucleic acid (RNA). This is commonly used for the purpose of determining whether a genetic sequence is present or not, and if it is present the number of copies in the sample. There are 3 methods which vary in difficulty and detail. Like other forms of polymerase chain reaction, the process is used to amplify DNA samples, using thermal cycling and a thermostable DNA polymerase.
The three commonly used methods of quantitative polymerase chain reaction are through agarose gel electrophoresis, the use of SYBR Green, a double stranded DNA dye, and the fluorescent reporter probe. The latter two of these three can be analysed in real-time, constituting real-time polymerase chain reaction method.
Ligase Chain Reaction (LCR)
An aspect of the present invention regards the detection of the nucleic acid molecules by means of using LCR. In LCR, four oligonucleotides, two adjacent oligonucleotides which uniquely hybridize to one strand of target DNA, and a complementary set of adjacent oligonucleotides, which hybridize to the opposite strand are mixed and DNA ligase is added to the mixture. Provided that there is complete complementarity at the junction, ligase will covalently link each set of hybridized molecules. Importantly, in LCR, two probes are ligated together only when they base-pair with sequences in the target sample, without gaps or mismatches. Repeated cycles of denaturation, hybridization and ligation amplify a short segment of DNA.
Primers
The PCR reactions described herein requires one or more pairs of amplification primers. The single-stranded DNA primer is from about 10 to about 50 nucleotide bases in length, more preferably from about 17 to about 40 nucleotide bases in length. It can be of any sequence. The primer can have sequence redundancies reducing the occurrence of mismatches.
In preferred embodiments of the invention the amplification primers are capable of hybridizing with any clone-specific nucleic acid(s) from the hsdS gene or a sequence complementary thereto. Thus in specific embodiments the amplification primers are capable of hybridizing with sau1hsdS1 of CC398 or sau1hsdS2 of CC398 or a sequence complementary thereto. Thus is one very preferred embodiment the amplification primers are capable of hybridizing the nucleotide sequence defined in: SEQ ID NO: 1 or a sequence complementary thereto.
In is contemplated that said primers may not necessarily be completely within the hsdS gene, but may also hybridize to adjacent regions to said hsdS gene.
PCR reactions require both forward and reverse primers for the amplification of nucleic acid(s). Thus in one embodiment of the invention the PCR reaction comprises one or more forward primers and one or more reverse primers. In a preferred embodiment the PCR reaction comprises one forward and one or more reverse primers.
In one embodiment the forward primer is a non-specific primer. In a more preferred embodiment the forward primer targets the upstream conserved region of the hsdS gene. In a very preferred embodiment the forward primer (AF primer) is AGGGTTTGAAGGCGAATGGG (SEQ ID NO: 6). The non-specific AF primer is not clone specific but general to the hsdS genes of many clonal complexes and is thus not encompassed to be within the scope of the clone specific primers of the invention.
By specific is meant that the primers/probes binds to regions of the hsdS gene that are clone specific i.e. the variable/unconserved regions of the hsdS gene.
In one embodiment the one or more reverse primers are S. aureus clonal complex, strain or lineage specific primers. In a more preferred embodiment the one or more reverse primers are specific for CC398 and may be selected from the group consisting of CAGTATTAAAGAGGTGACATGACCCCT (SEQ ID NO: 2), CACCTGAATCACCGTTTAATGCC (SEQ ID NO: 3), CGAGCACCTGAATCACCGTTT (SEQ ID NO: 4) and TGGGATATGAAGTGGCATTTCC (SEQ ID NO: 5).
In a very preferred embodiment the reverse primers is the CC398 specific primer is CAGTATTAAAGAGGTGACATGACCCCT (SEQ ID NO: 2).
In one embodiment the final concentration of the each primer is in a concentration range of 0.01 μM to 10 μM, for example 0.05 μM to 5 μM, such as 0.1 to 1 μM, for example 0.5 μM. In a very preferred embodiment the final concentration of each primer is 0.2 μM.
Analysis
The detection of PCR products may be by any method including but not limited to separation by agarose gel electrophoresis followed by ethidium bromide or DNA staining, hybridization assays performed in microtitration wells, capillary electrophoresis, flow cytometry for post-PCR detection of amplification products that are fluorescently labeled or have been subjected to an oligonucleotide ligation reaction and are captured on polystyrene beads.
Flow cytometry is suitable for the development of multiplex assays. Real-time PCR methods allows continuous monitoring of the amplified fragments during PCR by a homogeneous fluorometric hybridization assay and is used widely for quantification of the fusion transcripts.
Northern Blot Analysis
An aspect of the present invention regards the detection of the nucleic acid molecules herein disclosed by the classical and to the art well-known technique of Northern blot analysis. Many variations of the protocol exist and optimizations regarding the detection of nucleic acid molecules constitute preferred embodiment s of the present invention.
Thus nucleic acid(s) of a clone-specific hsdS gene, preferably CC398 may be detected by any of the methods described herein above.
Microarray
A microarray is a microscopic, ordered array of nucleic acids, proteins, small molecules, cells or other substances that enables parallel analysis of complex biochemical samples. A DNA microarray consists of different nucleic acid probes, known as capture probes that are chemically attached to a solid support, which can be a microchip, a glass slide or a microsphere-sized bead (see herein below).
Microarrays can be fabricated using a variety of technologies, including printing with fine-pointed pins onto glass slides, photolithography using pre-made masks, photolithography using dynamic micromirror devices, ink-jet printing, or electrochemistry on microelectrode arrays.
An aspect of the present invention regards the use of microarrays for the detection of nucleic acid(s) in a S. aureus strain or lineage, thereby identifying, detecting and/or typing said S. aureus strain and/or lineage. For this purpose, total nucleic acid(s) is extracted from a sample containing S. aureus and is used directly. The nucleic acid(s) may be 3′end labelled using T4 RNA ligase and either a Cy3- or Cy5-labeled short RNA linker (f. ex. 5′-PO4-rUrUrU-Cy3/dT-3′ or 5′-PO4-rUrUrU-Cy5/dT-3′). The nucleic acid(s) samples may be labelled by incubation at 30° C. for 2 hours followed by heat inactivation of the T4 RNA ligase at 80° C. for 5 minutes. The fluorophore-labelled nucleic acid(s) complementary to the corresponding nucleic acid(s) capture probe sequences on the array will hybridize, via base pairing, to the spot at which the capture probes are affixed.
Several types of microarrays can be employed such as spotted oligonucleotide microarrays, pre-fabricated oligonucleotide microarrays or spotted long oligonucleotide arrays
In spotted oligonucleotide microarrays the capture probes are oligonucleotides complementary to nucleic acid(s) sequences of S. aureus. This type of array is typically hybridized with amplified PCR products of nucleic acid(s) sequences of S. aureus from two samples to be compared (e.g. a CC398 containing sample and a CC5 containing sample or a mecA positive and a mecA negative sample) that are labelled with two different fluorophores. Nucleic acid(s) are extracted from the abovementioned two samples and used directly, and 3′ end labeled using T4 RNA ligase and short RNA linkers labelled with two different fluorophores. The samples can be mixed and hybridized to one single microarray that is then scanned, allowing the visualization of up-regulated and down-regulated nucleic acid(s) genes in one go. Alternatively, a universal reference can be used, comprising of a large set of fluorophore-labelled oligonucleotides, complementary to the array capture probes.
In pre-fabricated oligonucleotide microarrays or single-channel microarrays, the probes are designed to match the sequences of known or predicted nucleic acid(s). There are commercially available designs that cover complete genomes from companies such as Affymetrix, or Agilent. These microarrays give estimations of the absolute value of gene expression and therefore the comparison of two conditions requires the use of two separate microarrays.
Spotted long Oligonucleotide Arrays are composed of 50 to 70-mer oligonucleotide capture probes, and are produced by either ink-jet or robotic printing. Short Oligonucleotide Arrays are composed of 20-25-mer oligonucleotide probes, and are produced by photolithographic synthesis (Affymetrix) or by robotic printing. More recently, Maskless Array Synthesis from NimbleGen Systems has combined flexibility with large numbers of probes. Arrays can contain up to 390,000 spots, from a custom array design.
The clone specific probes may be any of the probes described herein below or any probes capable of hybridizing to the variable/noncoserved region of a S. aureus clonal complex; preferably the clonal complex is CC398.
In specific embodiments the clone specific probes may be any of the probes described herein below or any probes capable of hybridizing to the variable/noncoserved region of a S. aureus clonal complex; provided that the clonal complex is complex is not CC1, CC5, CC8, CC22, CC30 or CC45. In some embodiments it is further provided that said clonal complex may not be any one or more of: CC12, CC15, CC25, CC51, CC151, CC97, CC771, CC130, CC188, and/or CC873 Preferably the clonal complex is CC398.
WO 2005056832 for example describes a microarray useful for S. aureus identification, detection and/or typing that may be useful in some embodiments of the present invention.
A preferred embodiment of the invention comprises labelling the S. aureus nucleic acid(s) in a sample or of a substantially homogeneous population of said S. aureus isolated from this sample and putting said labelled nucleic acid(s) into contact with a solid support coated with an array of probes in suitable conditions for hybridization, wherein at least one probe is able to specifically hybridize with clone-specific hsdS nucleic acid(s) or with a representative fragment thereof, susceptible to be present in said sample to be tested, so as to obtain a hybridization profile containing detectable signals characteristic for the presence or the absence of the clone-specific hsdS gene in said sample to be tested, and identification, detection and/or typing the S. aureus clonal complex relative to the characterization of the presence or absence of said clone-specific hsdS gene, wherein one or more probes optionally is able to specifically hybridize with nucleic acid(s) conferring antibiotic resistance.
In another preferred embodiment the method for determining the presence of hsdS nucleic acid(s) from a S. aureus clonal complex, strain or lineage in any sample further comprises a) depositing and fixing on an solid support or leaving in solution said S. aureus nucleic acid(s) of the sample or of a substantially homogeneous population of said S. aureus isolated from this sample, or inoculating said sample or said substantially homogeneous population of S. aureus isolated from this sample on an solid support, and lysing in situ said inoculated sample or said isolated S. aureus to release the said S. aureus hsdS nucleic acid(s), said S. aureus hsdS nucleic acid(s) being made in a substantially single-stranded form.
A preferred embodiment of the present invention thus regards the method of microarray use and analysis as described herein.
A more preferred embodiment of the present invention regards the use of a microarray method as described above for the detection of nucleic acid(s) in a S. aureus strain or lineage, thereby identifying, detecting and/or typing said S. aureus strain and/or lineage.
A most preferred embodiment of the present invention regards the use of microarrays methods as described above for the detection of nucleic acid(s) such as a hsdS gene, preferably a sau1hsdS1 or sau1hsdS2 gene from a S. aureus clonal complex.
In specific embodiments of the present invention which the clone specific probes regards the use of microarrays methods as described above for the detection of nucleic acid(s) such as a hsdS gene, preferably a sau1hsdS1 or sau1hsdS2 gene from a S. aureus clonal complex; provided that the clonal complex is complex is not CC1, CC5, CC8, CC22, CC30, or CC45. In some embodiments it is further provided that said clonal complex may not be any one or more of: CC12, CC15, CC25, CC51, CC151, CC97, CC771, CC130, CC188, and/or CC873 Preferably the clonal complex is CC398.
In a very preferred embodiment the invention regards the use of microarrays methods as described above for the detection of clone specific hsdS nucleic acid(s) such as any of sau1hsdS1 of CC398 or sau1hsdS2 of CC398 or a sequence complementary thereto. Thus is one very preferred embodiment the probes are capable of hybridizing the nucleotide sequence defined in: SEQ ID NO: 1 or a sequence complementary thereto.
In preferred embodiments of the invention the probes are capable of hybridizing with sau1hsdS1 of CC398 or sau1hsdS2 of CC398 or a sequence complementary thereto. Thus is one very preferred embodiment the probes are capable of hybridizing the nucleotide sequence defined in: SEQ ID NO: 1 or a sequence complementary thereto.
In some embodiments the probes are selected from the group consisting of CAGTATTAAAGAGGTGACATGACCCCT (SEQ ID NO: 2), CACCTGAATCACCGTTTAATGCC (SEQ ID NO: 3), CGAGCACCTGAATCACCGTTT (SEQ ID NO: 4) and TGGGATATGAAGTGGCATTTCC (SEQ ID NO: 5). Preferably, the probe is the CC398 specific primer CAGTATTAAAGAGGTGACATGACCCCT (SEQ ID NO: 2).
A specific embodiment of the invention further comprises labelling the S. aureus nucleic acid(s) in a sample or of a substantially homogeneous population of said S. aureus isolated from this sample and putting said labelled nucleic acid(s) into contact with a solid support coated with an array of probes in suitable conditions for hybridization, wherein at least one probe is able to specifically hybridize with clone-specific hsdS nucleic acid(s) or with a representative fragment thereof, susceptible to be present in said sample to be tested, so as to obtain a hybridization profile containing detectable signals characteristic for the presence or the absence of the clone-specific hsdS gene in said sample to be tested, and identifying, detecting and/or typing the S. aureus clonal complex relative to the characterization of the presence or absence of said clone-specific hsdS gene, wherein one or more probes optionally is able to specifically hybridize with nucleic acid(s) conferring antibiotic resistance.
Probe
It is an object of the present invention to provide a probe which can be used for the detection of a nucleic acid molecule as defined herein. A probe as defined herein is a specific sequence of a nucleic acid used to detect nucleic acids by hybridization. A nucleic acid is also here any nucleic acid, natural or synthetic such as DNA, RNA, LNA or PNA. A probe may be labelled, tagged or immobilized or otherwise modified according to the requirements of the detection method chosen. A label or a tag is an entity making it possible to identify a compound to which the probe is associated. It is within the scope of the present invention to employ probes that are labelled or tagged by any means known in the art such as but not limited to: radioactive labelling, fluorescent labelling and enzymatic labelling. Furthermore the probe, labelled or not, may be immobilized to facilitate detection according to the detection method of choice and this may be accomplished according to the preferred method of the particular detection method.
An aspect of the present invention relates to the use of a nucleic acid molecule as described herein as a probe, wherein the probe is a nucleotide sequence selected from the group consisting of SEQ ID NOS: 2, 3, 4, 5 and 6, and/or a nucleotide sequence which is complementary to a clone specific hsdS gene, more specifically to sau1hsdS1 of CC398 or sau1hsdS2 of CC398 and even more specifically SEQ ID NO: 1, or a fragment hereof, can hybridize under stringent condition and/or has an identity of at least 80% to any of these sequences. Most preferably the probe is either SEQ ID NO: 2 and/or a nucleotide sequence which is complementary to either sau1hsdS1 of CC398 (SEQ ID NO: 1) or sau1hsdS2 of CC398 or fragments hereof, and/or can hybridize under stringent condition and/or has an identity of at least 80% to any of these sequences. Any of the herein described probes may be modified by labelling or immobilization as mentioned above.
In Situ Hybridization
In situ hybridization (ISH) applies and extrapolates the technology of nucleic acid hybridization to the single cell level, and, in combination with the art of cytochemistry, immunocytochemistry and immunohistochemistry, permits the maintenance of morphology and the identification of cellular markers to be maintained and identified, allows the localization of sequences to specific cells within populations, such as tissues and blood samples. ISH is a type of hybridization that uses a complementary nucleic acid to localize one or more specific nucleic acid sequences in a portion or section of tissue (in situ), or, if the tissue is small enough, in the entire tissue (whole mount ISH). DNA ISH can be used to determine the structure of chromosomes and the localization of individual genes and optionally their copy numbers. Fluorescent DNA ISH (FISH) can for example be used in medical diagnostics to assess chromosomal integrity. RNA ISH is used to assay expression and gene expression patterns in a tissue/across cells.
Sample cells are treated to increase their permeability to allow the probe to enter the cells, the probe is added to the treated cells, allowed to hybridize at pertinent temperature, and then excess probe is washed away. A complementary probe is labelled with a radioactive, fluorescent or antigenic tag, so that the probe's location and quantity in the tissue can be determined using autoradiography, fluorescence microscopy or immunoassay, respectively. The sample may be any sample as herein described. The probe is likewise a probe according to any probe mentioned herein.
An embodiment of the present invention regards the method of detection by in situ hybridization as described herein.
In Situ PCR
Prior to in situ PCR, cells or tissue samples are fixed and permeabilized to preserve morphology and permit access of the PCR reagents to the intracellular sequences to be amplified. PCR amplification of target sequences is next performed either in intact cells held in suspension or directly in cytocentrifuge preparations or tissue sections on glass slides. In the former approach, fixed cells suspended in the PCR reaction mixture are thermally cycled using conventional thermal cyclers. After PCR the cells are cytocentrifugated onto glass slides with visualization of intracellular PCR products by ISH or immunohistochemistry. In situ PCR on glass slides is performed by overlaying the samples with the PCR mixture under a coverslip which is then sealed to prevent evaporation of the reaction mixture. Thermal cycling is achieved by placing the glass slides either directly on top of the heating block of a conventional or specially designed thermal cycler or by using thermal cycling ovens. Detection of intracellular PCR-products is achieved by one of two entirely different techniques. In indirect in situ PCR by ISH with PCR-product specific probes, or in direct in situ PCR without ISH through direct detection of labelled nucleotides (e.g. digoxigenin-11-dUTP, fluorescein-dUTP, 3H-CTP or biotin-16-dUTP) which have been incorporated into the PCR products during thermal cycling.
An embodiment of the present invention regards the method of in situ PCR as mentioned herein above for the detection of nucleic acid molecules as detailed herein.
The methods described herein above, may be carried out on any test sample. In preferred embodiments the test sample is a biological sample (see herein above).
In preferred embodiments of the invention is performed directly on a test sample, wherein said test sample may be a sample selected from the group consisting of swabs from mucosal tissues including but not limited to nasal swabs, throat swabs and mouth swabs. The sample may also be a sample selected from the group consisting of swabs from the skin surface especially from hands, feet, Perineum, face and any infectious tissue such as boils, sores and carbuncles. The sample may also be blood.
In some embodiments of the present invention the nucleic acid(s) are extracted from a test sample using a bacterial genomic DNA purification kit. Some embodiments further comprise culturing of the strains and/or lineages of S. aureus before the analysis.
In one embodiment of the present invention the nucleic acid(s) detection methods described herein above is performed directly from a test sample consisting of a bacterial culture or suspension.
Another aspect of the invention relates to an improved method of treatment for an infection by MRSA, using the methods described herein and performing a treatment of MRSA based, at least in part, on said identification, detection and/or typing of S. aureus. 
Another aspect of the invention relates to s method of improving the hygiene in a hospital, using the methods described herein and performing hygiene measures in said hospital based, at least in part, on said identification, detection and/or typing of S. aureus. 
The method described herein may also be used for obtaining hsdS sequences from any S. aureus clonal complex, strain or lineage directly from a test sample or a bacterial culture, which comprises the following steps: a) treating said sample with an aqueous solution containing at least one pair of primers having a sequence selected within the nucleotide sequences defined in SEQ ID NOS: 9, 10, 11 and 12, and a variant thereof, one of said primers being capable of hybridizing selectively with one of the two complementary strands of said S. aureus hsdS gene that contains a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template; b) synthesizing an extension product of each of said primers, said extension product containing the target sequence, and amplifying said target sequence, if any, to a detectable level; and c) detecting the presence and/or amount of said amplified target sequence; and d) determining the nucleotide sequence of the said amplified target sequence by using any DNA sequencing method.
In one embodiment there is provided that the clonal complex is complex is not CC1, CC5, CC8, CC22, CC30 or CC45. In some embodiments it is further provided that said clonal complex may not be any one or more of: CC12, CC15, CC25, CC51, CC151, CC97, CC771, CC130, CC188, and/or CC873
The primers used to identify the unknown sau1hsdS1 gene region may be CAATTTGTCGGTCGAGTTTGCTG (SEQ ID NO: 9), TGTGAGAAGATTTTCTGCATATAGCC (SEQ ID NO: 10), GCCTTTTTTCTGTTGTTGAAGTAATTC (SEQ ID NO: 11) and GTCGGTCGAGTTTGCTGAAG (SEQ ID NO: 12).







TABLE 1







Sequences used









SEQ




ID
Description of



No.
sequence
Sequence












1
CC398
GCGAATGGGAAGAGAAGAAGCTAGGTGAGTTTGCTGGTAAAGTTAC



consensus
CCAAAAAAATGTTGATAAAAAATATATTGAGACATTAACTAATTCAGC



sau1hsdS1
TGAGTTAGGTATCATATCTCAAAAGGATTATTTTGACAAAGAAATTTC



sequence
GAATATAGATAATATTAAAAAGTACTATGTAGTTGAAGAGAATGATTT




TGTTTATAACCCTAGAATGTCTAATTATGCTCCATTTGGACCAGTAAAT




AGAAATAAGTTAGGGAAAAAAGGGGTCATGTCACCTCTTTATACTGTG




TTTAAAATTCAAAACATTGATTTAAACTTTATTGAGTTTTATTTTAAATC




TTCAAAATGGTATAGATTTATGGCATTAAACGGTGATTCAGGTGCTCG




AGCAGATAGGTTTTCTATTAAAGATAGGACATTTATGGAAATGCCACT




TCATATCCCATGTATGGATGAACAAATAAAAATCGGTCAGTTCTTCAGC




AAACTCG


 


2
CC398-specific
CAGTATAAAGAGGTGACATGACCCCT



reverse primer




ST398 r1



 


3
CC398-specific
CACCTGAATCACCGTTTAATGCC



reverse primer




ST398 r2



 


4
CC398-specific
CGAGCACCTGAATCACCGTTT



reverse primer




ST398 r3



 


5
CC398-specific
TGGGATATGAAGTGGCATTTCC



reverse primer




ST398 r4



 


6
AF forward primer
AGGGTTTGAAGGCGAATGGG


 


7
mecup1 primer
GGGATCATAGCGTCATTATTC


 


8
mecup2 primer
AACGATTGTGACACGATAGCC


 


9
sau1hsdS1
CAATTTGTCGGTCGAGTTTGCTG



identification




primer 1



 


10
sau1hsdS1
TGTGAGAAGATTTTCTGCATATAGCC



identification




primer 2



 


11
sau1hsdS1
GCCTTTTTTCTGTTGTTGAAGTAATTC



identification




primer 3



 


12
sau1hsdS1
GTCGGTCGAGTTTGCTGAAG



identification




primer 4



 


13
CC30 isolate 507
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT



Sau1hsdS1
TTGAAGGCGAATGGGAAGAGAAGAAGGTTGGCGAGTTATTAGAATTTAA




AAATGGTTTAAATAAAGGAAAAGAATATTTTGGCTCAGGATCGTCGATTG




TTAACTTCAAAGATGTATTTAATAACAGGAGCTTAAATACAAATAATCTG




ACTGGAAAAGTTAATGTGAATAGCAAAGAACTAAAAAATTATTCTGTTGA




AAAGGGTGATGTTTTTTTTACAAGGACTAGTGAGGTAATTGGTGAAATA




GGTTATCCGTCTGTAATTTTAAATGACCCTGAAAATACTGTGTTTAGTGG




ATTTGTATTAAGAGGGCGGCCTAAATCAGGAATTGATTTAATAAATAATA




ATTTTAAAAGATATGTCTTTTTTACTAATTCATTTAGAAAAGAAATGATTA




CAAAAAGTTCTATGACAACTAGAGCTTTAACNTCAGGTAGCGCAATTAAT




AAAATGAAGGTCATATACCCTGTTTCGGCTAAAGAACAGAGAAAAATAG




GTGACTTCTTCAGCAAACTCGACCGACAAATTGAATTAGAAGAACAAAA




GCTTGAATTACTTCAACAACAAAAAAAAGGCTATATGCAGAAAATCTTCT




CACAGGAACTGCGATTCAAAGATGAGAATAGTGAAGATTATCCACATTG




GGAAAATAGCAAAATAGAAAAATATTTAAAAGAGAGAAACGAACGTTCT




GACAAAGGTCAAATGCTTTCAGTAACTATAAATAGTGGCATTATAAAATT




TAGTGAATTGGATAGAAAAGATAATTCAAGTAAAGATAAAAGTAATTATA




AAGTAGTTAGGAAAAATGATATTGCATATAATTCTATGAGAATGTGGCAA




GGGGCTAGTGGTAGATCAAATTATAATGGGATTGTTAGCCCTGCATATA




CTGTGCTTTATCCAACACAAAATACTAGCTCATTATTTATTGGATATAAG




TTTAAAACACATAGAATGATTCATAAATTTAAAATTAATTCACAAGGATTA




ACATCAGATACATGGAACTTAAAATATAAACAATTAAAAAATATAAATATA




GATATACCTGTATTGGAGGAACAAGAAAAGATAGGTGATTTCTTTAAAAA




AATGGATATATTGATTAGTAAACAGAAAATAAAAATTGAAATATTAGAAAA




AGAGAAACAATCCTTTTTACAAAAGATGTTCTTATAA


 


14
CC45 isolate
ATGAGTAATACACAAAAGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT



3067 Sau1hsdS1
TTGAAGGCGAATGGGAAGAGAAGAAGGTTGGCGAGTTATTAGAATTTAA




AAATGGTTTAAATAAAGGAAAGGAATATTTTGGCTCAGGATCGTCGATT




GTTAACTTCAAAGATGTATTTAATAACCGGAGCATAAATACAAATAATCT




GACTGGAAAAGTTAATGTGAATAGCAAAGAACTGAAGAATTATTCCGTT




GAAAAGGGTGATGTTTTTTTTACAAGGACTAGTGAGGTGATTGGTGAAA




TAGGTTATCCGTCTGTAATTTTAAATGACCCTGAAAATACTGTGTTTAGT




GGATTTGTATTAAGAGGGCGGCCTAAATCAGGAATTGATTTAATAAATAA




TAATTTTAAAAGATATGTCTTTTTTACTAATTCATTTAGAAAAGAAATGAT




TACAAAAAGTTCTATGACAACTAGAGCTTTAACATCAGGTNCCGCAATTA




ATAAAATGAAAGTCATATACCCTGTTTCTGCTAAAGAACAGAAAAAAATA




GGTGACTTCTTCAGCAAACTCGATCGACAAATTGAACTAGAAGAACAAA




AACTTGAATTACTTCAACAACAGAAAAAAGGATATATGCAGAAAATCTTC




TCACAAGAATTGCGATTCAAAGATGAGAATGGAAATGATTATCCGAATT




GGAGAACAATTGAATTAAAAAATATTTTAGAAAACATTGTGGATAATAGA




GGGAAAACACCAGATAATGCTCCTAGTGAAAAATATCCTTTATTAGAAGT




GAATGCATTAGGATATTATCGTCCAGCATATATAAAAGTAAGTAAATTTG




TTAGTGAAAACACTTATAATAACTGGTTTAGAGAACATTTAAAAGAAAAT




GATATTCTTTTTTCTACTGTAGGAAATACTGGAATAGTTAGTCTTATGGA




TAATTACAAAGCTGTAATAGCTCAAAATATCGTAGGATTAAGGGTAAATA




ATAATAACCTCCCTTCATTTATTTACTATATGCTATCGTATAAGGGAAATC




AGAAAAAAATAAAAAGAATTCAAATGGGGGCTGTACAACCAAGTGTGAA




AGTTTCTCAATTTAAGTTTATAAAATATTTAGTACCAATAAAAGATGAACA




AGAGAAGGTAGCTAAACTGTTGATTGAAATAGATAAATTAGTGAATAAAC




AATTAATAAAAATAGAATTACTTCAACAACGAAAAAAAGCCTTACTTAAAT




CGATGTTTATTTAA


 


15
CC51 isolate 3
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT



Sau1hsdS1
TTGAAGGCGAATGGGAAGAGAAGAAGTTAGAAGATATTATAAAAGTTAA




TTCTGGAAAAGATTATAAACATTTGGATAAAGGCGATATACCAGTCTATG




GTACTGGCGGTTATATGACAAGTGTTTCAGAACCACTAAGTGAAATTGA




TGCTGTTGGTATTGGGAGAAAAGGGACTATAAACAAACCATATTTGCTT




GAGGCGCCGTTTTGGACGGTGGATACATTATTTTATTGTACACCTAAAA




AAGAAACAGACATACTATTTATATTAAGTTTATTTAGAAAAATAAATTGGA




AAGTATACGATGAATCAACAGGTGTGCCAAGCTTAAGTAAACAAACCAT




TAATAAAATAAATAGATTTGTCCCTACAAATAAAGAGCAGCAAAAAATAG




GCAAGTTCTTCAGCAAACTTGACCGACAAATTGAATTAGAAGAACAAAA




ACTTGAGTTATTTCAGCAACAGAAAAAAGGCTATATGCAGAAAATCTTTT




CGCAAGAATTGCGATTCAAAGATGAGAGTGGTAATGATTATCCAGATTG




GGAAGAGAAGGAATTAGGGGAAGTAGCTGATAGAGTAATAAGGAAAAA




TAAAAACTTTGAATCGAAAAAGCCTTTAACAATATCCGGACAGTTAGGTT




TAATTGATCAAACAGAATATTTTAGTAAATCAGTTTCGTCGAAAAATCTA




GAAAATTATACACTAATAAAGAATGGAGAATTCGCGTATAATAAAAGTTA




TTCTAATGGATACCCATTAGGGGCTATTAAAAGATTAACTAGATATGAT




AGTGGTGTATTGTCCTCTTTGTATATTTGCTTTTCTATTAAAAGTGAAATG




TCTAAAGACTTCATGGAAGCATATTTTGATTCGACACACTGGTATAGAGA




AGTTTCAGGAATTGCAGTTGAGGGTGCAAGAAATCACGGATTATTAAAT




ATTTCTGTGAATGATTTTTTTACTATTCTAATTAAATATCCAAGTTTAGAA




GAGCAGAGAAAAATAGGTGACTTCTTCATCAAACTTGACCGACAAATTG




AACTAGAAGAACAAAAACTAGAATTACTTCAACAACGAAAAAAAGCCTTA




CTTAAATCGATGTTAATTTAA


 


16
CC25 isolate 16
ATGAGTAATACACAAAAGAAAAATTTGCCAGAGTTGAGATTCCCAGGGT



Sau1hsdS1
TTGAAGGCGAATGGGAAGAAAAGAAGTTAGGGAATCTTACTACCAAAAT




AGGTAGTGGAAAGACTCCCAAAGGTGGAAGTGAAAACTATACAAACAAA




GGCATACCATTTTTAAGGAGTCAAAATATTAGAAATGGTAAATTAAATCT




TAATGACTTAGTTTATATTAGTAAAGATATAGATGATGAGATGAAAAATA




GTAGAACGTACTATGGTGATGTTCTTTTAAATATTACAGGAGCATCAATA




GGTAGAACAGCCATTAATTCGATAGTTGAAACGCATGCTAATTTAAATCA




ACATGTATGTATTATTAGATTAAAAAAAGAGTATTATTATAATTTTTTTGG




ACAGTATCTATTATCAAGAAAAGGTAAAAGAAAAATTTTCCTTGCACAAA




GTGGAGGTAGTCGAGAAGGACTAAACTTCAAAGAAATTGCTAATTTAAA




AATCTTCACCCCAACTATATTTGAAGAACAACAAAAAATAGGACAATTCT




TCAGCAAACTTGACCAACAAATTGAATTAGAAGAACAAAAACTTGAATTA




CTTCAACAACAGAAAAAAGGCTATATGCAGAAAATCTTCTCACAGGAAC




TGCGATTCAAAGATGAGAATAGTGAAGATTATCCACATTGGGAAAGTAG




CAAAATAGAAAAATATTTAAAAGAGAGAAACGAACGTTCTGACAAAGGT




CAAATGCTTTCAGTAACTATAAATAGTGGCATTATAAAATTTAGTGAATT




GGATAGAAAAGATAATTCAAGTAAAGATAAAAGTAATTATAAAGTAGTTA




GGAAAAATGATATTGCATATAATTCTATGAGAATGTGGCAAGGGGCTAG




TGGTAAATCAAATTATAATGGGATTGTTAGCCCTGCATATACTGTGCTTT




ATCCAACACAAAATACTAGCTCATTATTTATTGGATATAAGTTTAAAACAC




ATAGAATGATTCATAAATTTAAAATTAATTCACAAGGATTAACATCAGATA




CATGGAACTTAAAATATAAACAATTAAAAAATATAAATATAGATATACCTG




TATTGGAGGAACAAGAAAAGATAGGTGATTTCTTTAAAAAAATGGATATA




TTGATAAGTAAACAGAAAATGAAAATTGAAATATTAGAAAAAGAGAAACA




ATCCTTTTTACAAAAAATGTTCTTATAA


 


17
CC22 isolate 720
ATGAGTAATACACAAAAGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT



Sau1hsdS1
TTGAAGGCGAATGGGAAGAGAAGAAGTTAGGGGATCTTACAGATAGAG




TAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCC




GGACAGTTAGGTTTAATTGATCAAACAGAATACTTTAGTAAATCAGTTTC




GTCGAAAAATCTAGAAAATTATACACTAATAAAGAATGGAGAATTCGCGT




ATAACAAAAGTTATTCTAATGGATACCCATTAGGGGCTATTAAAAGATTA




ACTAGATATGATAGTGGTGTATTGTCCTCTTTGTATATTTGTTTTTCTATT




AAAAGTGAAATGTCTAAAGACTTCATGGAAGCATATTTTGATTCGACACA




CTGGTATAGAGAAGTTTCTGGAATTGCAGTTGAGGGTGCAAGAAATCAC




GGATTATTAAATGTTTCTGTGAATGATTTTTTTACTATTCTAATTAAATAT




CCAAGTTTAGAAGAACAGCAAAAAATAGGCAAGTTCTTCAGCAAACTCG




ACCGACAAATTGAATTAGAAGAACAAAAGCTTGAATTACTTCAACAACAG




AAAAAAGGCTATATGCAGAAAATCTTCTCACAGGAATTGCGATTTAAGAA




TGAGAATGGTAATGATTATCCTGATTGGGAAAGAATTAAATTTTTTGATG




TAATTGATAAAGTAATAGATTTTAGAGGGAGAACACCAAAAAAATTAAAT




ATGGAATGGTCTGACGAAGGGTATTTAGCATTATCAGCAGTCAATGTAA




AAAAAGGCTATATTGATTTTAATGTAGAGGCGAAATATGGAAATCTAGAT




TTATATACTAGATGGATGAGAGGAAATGAATTATATAAGGGGCAAGTATT




ATTTACAACTGAAGCGCCAATGGGCAATGTAGCACAGGTTCCGGATAAT




AAAGGATATATATTAAGTCAAAGAACTATCGCGTTTAATTCAAATGAAAA




AATCACTGATAACTTTTTAGCATCATTGTTGAGCTCTGAAAATGTTTATAA




TGATTTATTAAAATTGTGTAGTGGTGCTACAGCAAAAGGTGTGAGTCAA




AAAAATTTAAATCGACTATACGTTACTATTCCACATTCCATATCAGAGCA




AGAAGAGATTGCTGAATTCTTTAGAAAAATTAATCAATTGGTTGAGTTGC




AAAAATATAAAATTGAACATACTAAAAGTCAAAAACAAGTGTTTTTACAAA




AGATGTTTATTTAA


 


18
CC15 isolate
ATGAGTAATAAACAAAAGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT



3150 Sau1hsdS1
TTGAAGGCGAATGGGAAGAGAAGAAGTTAGGGGAAGTAGGTACATTTA




CTTCAGGTGGGACACCCCTGAAATCAAAATCAGAGTATTGGAATGGAGA




TATTCCATGGATTACAACAGGTGATATTCATAACATAAAAAGAGAAAATA




TAACTAATTTTATAACAGAGAAAGGTTTAAATGAATCATCGGCAAAATTA




ATAACTAATGAGGCGATTTTAATAGCTATGTATGGTCAAGGTAAAACTAG




AGGAATGTCAGCAATATTGAATTTTGAGGCAACAACTAACCAAGCATGT




GCTATATATCAAACCAATCAAAATATTAATTTTGTTTTTCAATACTTTCAG




AAATTATATGAATTTTTACGCTCATTATCTAATGAAGGAAGTCAAAAGAA




TTTAAGTTTAAGCTTGTTGAAAGAAATTACTTTAAATTATCCTAATGAACA




AGAACAGAAAAAAATAGGTGATTTTTTCAGCAAACTCGACCGGCAAATT




GAATTAGAAGAACAAAAACTTGAATTGCTTCAACAACAGAAAAAAGGCT




ATATGCAGAAAATCTTCTCGCAAGAATTGCGATTTAAGGATGAGAATGG




AAATGATTATCCGGAGTGGGAAGAAACTACTATAAAAGAAATTGCTCAA




ATTAACNCTGGAAAGAAAGATACAAAAGATGCCATTACTAATGGGAGTT




ATGATTTTTACGTTAGATCTCCGATAGTTTATAAAATTAATACTTTTAGTT




ATGAAGGAGAGGCTATTTTAACTGTAGGAGATGGAGTTGGCGTAGGTA




AAGTTTTCCACTATGTAAATGGGAAATTTGATTATCATCAAAGAGTATAC




AAAATATCTGACTTTAAGAATTATTATGGACTATTGTTATTTTATTATTTTT




CACAAAACTTTTTAAAAGAAACAAAGAAATATAGTGCGAAGACATCAGTT




GATTCAGTTAGAAAAGACATGATTGCTAATATGAAAGTACCGCGTCCTA




TTTATATAGAACAAAAAAAAATCGGTCAATTCATTAAAAGAGTAGACAAC




AAAACAAAAATTCAGAAACAAGTGATTGAATTACTTAAACAACGCAAAAA




GGCATTACTTCAAAAGATGTTTATTTAA


 


19
CC12 isolate 163
ATGAGTAATACACAAAAGAAAAATGTGCCAGAGTTGAGATTCCCAGAGT



Sau1hsdS1
TTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAG




TAATTAGGAAAAATAAAAACTTAGAATCGAAAAAAGCCTTTAACAATATC




CGGACAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAAATCAGTTT




CGTCGAAAAATCTAGAAAATTATACACTAATAAAGAATGGAGAATTCGC




GTATAACAAAAGTTATTCTAATGGATACCCATTAGGGGCTATTAAAAGAT




TAACTAGATATGATAGTGGTGTATTGTCCTCTTTGTATATTTGTTTTTCTA




TTAAAAGTGAAATGTCTAAAGACTTCATGGAAGCATATTTTGATTCGACA




CACTGGTATAGAGAAGTTTCTGGAATTGCAGTTGAGGGTGCAAGAAATC




ACGGATTATTAAATGTTTCTGTGAATGATTTTTTTACTATTCTAATTAAAT




ATCCAAGTTTAGAAGAACAGCAAAAAATAGGCAAGTTCTTCAGCAAACT




CGACCGACAAATTGAATTAGAAGAACAAAAGCTTGAATTACTTCAACAA




CAGAAAAAAGGCTATATGCAGAAAATTTTCTCACAGGAACTGCGATTCA




AAGATGAGAATGGTGAAGATTATCCAGATTGGGAAAATAGCAAAATAGA




AAAATATTTAAAAGAGAGAAACGAACGTTCTGACAAAGGGCAAATGCTT




TCAGTAACTATAAATAGTGGCATTATAAAATTTAGTGAATTGGATAGAAA




AGATAATTCAAGTAAAGATAAAAGTAATTATAAAGTAGTTAGGAAAAATG




ATATTGCATATAATTCTATGAGAATGTGGCAAGGGGCTAGTGGTAAATC




AAATTATAATGGGATTGTTAGCCCTGCATATACTGTGCTTTATCCAACAC




AAAATACTAGCTCATTATTTATTGGATATAAGTTTAAAACACATAGAATGA




TTCATAAATTTAAAATTAATTCACAAGGATTAACATCAGATACATGGAACT




TAAAATATAAACAATTAAAAAATATAAATATAGATATACCTGTATTGGAGG




AACAAGAAAAGATAGGTGATTTCTTTAAAAAAATGGATATATTGATAAGT




AAACAGAAAATGAAAATTGAAATATTAGAAAAAGAGAAACAATCCTTTTT




ACAAAAAATGTTCTTATAA


 


20
CC5
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGAT



Mu50selection
TTGAGGGCGAATGGGAAGAGAAGAAGTTAGGGAATCTTACTACCAAAAT



Sau1hsdS2
AGGTAGTGGAAAGACTCCCAAAGGTGGAAGTGAAAACTATACAAACAAA




GGCATACCATTTTTAAGGAGTCAAAATATTAGAAATGGTAAATTAAATCT




TAATGACTTAGTTTATATTAGTAAAGATATAGATGATGAGATGAAAAATA




GTAGAACGTACTATGGTGATGTTCTTTTAAATATTACAGGAGCATCAATA




GGTAGAACAGCCATTAATTCGATAGTTGAAACGCATGCTAATTTAAATCA




ACATGTATGTATTATTAGATTAAAAAAAGAGTATTATTATAATTTTTTTGG




ACAGTATCTATTATCAAGAAAAGGTAAAAGAAAAATTTTCCTTGCACAAA




GTGGAGGTAGTCGAGAAGGACTAAACTTCAAAGAAATTGCTAATTTAAA




AATCTTCACCCCAACTATATTTGAAGAACAACAAAAAATAGGACAATTCT




TCAGCAAACTTGACCAACAAATTGAATTAGAAGAACAAAAACTTGAATTA




CTTCAACAACAGAAAAAATGCTATATACAGAAAATCTTCTCACAAGAATT




ACGATTCAAAGATGAAGAAGGTAATTACTATAAAGGATGGAACAAAAAG




CAATTAAAAGATGTATTAGAATTTAGTAATAAAAGAACTATTAATGAAAAT




GAATATCCTGTTTTAATATCGTCAAGACAAGGTTTAATACTTCAGTCAGA




CTACTATAAAGATAGGAAAACTTTTGCAGAGAGTAATATTGGGTATTTCA




TACTCCCTAAAAATCATATAACATACCGTTCAAGAAGCGACGATGGAATT




TTTAAGTTTAATTTAAATCTAATGATTGATGTAGGTATTATTAGTAAATAT




TACCCTGTCTTTAAAGGGATAGATGCAAATCAATATTATTTAACATTACA




CTTAAACTATCAACTGAAAAAAGAATATATTAAATATGCAACTGGTACAT




CACAATTGGTACTCTCACAAAAAGACTTGCAAAACATAAAGACTAAATTG




CCATCTTATGAAGAACAACAAAAAATCGGTGATTTTTTCAGTGAAATAGA




TAGATTGGTTGAAAAACAATCTTCAAAAGTCGGACGATTAAAAGTACGTA




AAAAAGAACTATTACAAAAAATGTTTGTTTAA


 


21
CC8 Sau1hsdS2
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGAT




TTGAGGGCGAATGGGAAGAGAAGAAGTTAGGGAATCTTACTACCAAAAT




AGGTAGTGGAAAGACTCCCAAAGGTGGAAGTGAAAACTATACAAACAAA




GGCATACCATTTTTAAGGAGTCAAAATATTAGAAATGGTAAATTAAATCT




TAATGACTTAGTTTATATTAGTAAAGATATAGATGATGAGATGAAAAATA




GTAGAACGTACTATGGTGATGTTCTTTTAAATATTACAGGAGCATCAATA




GGTAGAACAGCCATTAATTCGATAGTTGAAACGCATGCTAATTTAAATCA




ACATGTATGTATTATTAGATTAAAAAAAGAGTATTATTATAATTTTTTTGG




ACAGTATCTATTATCAAGAAAAGGTAAAAGAAAAATTTTCCTTGCACAAA




GTGGAGGTAGTCGAGAAGGACTAAACTTCAAAGAAATTGCTAATTTAAA




AATCTTCACCCCAACTATATTTGAAGAACAACAAAAAATAGGACAATTCT




TCAGCAAACTTGACCAACAAATTGAATTAGAAGAACAAAAACTTGAATTA




CTTCAACAACAGAAAAAATGCTATATACAGAAAATCTTCTCACAAGAATT




ACGATTCAAAGATGAAGAAGGTAATTACTATAAAGGATGGAACAAAAAG




CAATTAAAAGATGTATTAGAATTTAGTAATAAAAGAACTATTAATGAAAAT




GAATATCCTGTTTTAACATCGTCAAGACAAGGTTTAATACTTCAGTCAGA




CTACTATAAAGATAGGAAAACTTTTGCAGAGAGTAATATTGGGTATTTCA




TACTCCCTAAAAATCATATAACATACCGTTCAAGAAGCGACGATGGAATT




TTTAAGTTTAATTTAAATCTAATGATTGATGTAGGTATTATTAGTAAATAT




TACCCTGTCTTTAAAGGGATAGATGCAAATCAATATTATTTAACATTACA




CTTAAACTATCAACTGAAAAAAGAATATATTAAATATGCAACTGGTACAT




CACAATTGGTACTCTCACAAAAAGACTTGCAAAACATAAAGACTAAATTG




CCATCTTATGAAGAACAACAAAAAATCGGTGATTTTTTCAGTGAAATAGA




TAGATTGGTTGAAAAACAATCTTCAAAAGTCGGACGATTAAAAGTACGTA




AAAAAGAACTATTACAAAAAATGTTTGTTTAA


 


22
BF primer
CCCAAAGGTGGAAGTGAAAA


 


23
CC1 strain
atgagtaatacacaaaagaaaaatgtgccagagttgaggttcccagggtttgaaggcgaa



MSSA476
tgggaagagaagaagttaggggaccttactaccaaaataggtagtggaaagactcccaaa



SAS0395
ggtggaagtgaaaactatacaaacaaaggcataccatttttaaggagtcaaaatattaga




aatggtaaattaaatcttaatgacttagtttatattagtaaagatatagatgatgagatg




aaaaatagtagaacgtactatggtgatgttcttttaaatattacaggagcatcaataggt




agaacagccattaattcgatagttgaaatacatgctaatttaaatcaacatgtatgtatt




attagattgaaaaaagagtattattataatttttttggacagtatctattatcaagaaaa




ggtaaaaggaaaattttccttgcacaaagtggaggtagtcgagaaggactaaacttcaaa




gaaattgctaatttaaaaatcttcaccccaaaatatttgaagagcagcaaaaaataggc




gaattcatcagcaaacttgaccgacaaattgaattagaagaacaaaaacttgaattactt




cagcaacagaaaaaaggctatatgcagaaaatcttctcgcaagaattgcgattcaaagat




gaggaaggtaaagattatccagattggaaatcaaaatcaattcaagaaatatttgagaat




aagggtggcactgctctagaaacagaatttaattttgacggtaattataaagttataagt




ataggaagttattctataaatagcacttataatgatcaaaatataagagtcaataaaaat




aaaaaaactgaaaaatatattttatcaaaaggcgacttagcaatggtattaaatgataaa




acaaaagatgggaaaattataggtagaagtatatttatagataaagataatcaatatatt




tataatcaaagaactgaaagattaataccatttgctgaaaatgataataaatttttatgg




ttcttaatgaatacagatttaattagaaataaaataaaaggtatgatgcaaggagcaacc




caagtttatataaattattcatctattaaattgatatctatacaattgccacttcttgaa




gaacaacagaaaataagagggtttctagaagttttatctggaataactactaaacaattg




cacaagatagaccaattaaaagagaggaaaaaggcgtttttacagaaaatgtttatttga


 


24
CC771, isolate
atgagtaatacacaaacgaaaaatgtgccagagttgagattcccagggtttgaaggcgaa



32320
tgggaagagaagaagttaggggatcttggcctgtttcaaaaaagttattctttttcgaga




gctaaagaaggaaacggtaaaaaaaacatattcattatggtgatattcattcaaaattt




aaaacagtcttagatagtgatggtaatatccctaatataattgagaaagctgtatttgag




ttgattcaaaaaggagacattgtttttgcggatgcatcagaagattatagtgacctagga




aaagcagttatgatagatttcaaaccgaattcattgatttctggcttacatacacaccta




ttgattcaaaaaggagacattgtttttgcggatgcatcagaagattatagtgacctagga




tataaaaaattcattagacagcaaggtacaggaatatcagtacttggtatatcaaaaaaa




agtttattaaatttgaatgtattaataccacgaagtgaattagaacaacaaaaagtaggc




aagttcttcagcaaactcgaccgacaaattgaattagaagaacaaaaaatcgaattactt




caacaacagaaaaaaggctatatacagaaaatcttctcacaagaattgcgatttaaggat




gagaatggagatgattatccggagtgggaagaaactactataaaagaaattgctcaaatt




aacacaggaaagaaagatacaaaagatgccattactaatgggagttatgatttttacgtt




agatctccgatagtttataaaattaatacttttagttatgaaggagaggctattttaact




gtaggagatggagttggcgtaggtaaagttttccactatgtaaatgggaaatttgattat




catcaaagagtatacaaaatatctgactttaagaattattatggattattgttattttat




tatttttcacaaaactttttaaaagaaacaaagaaatatagtgcgaagacatcagttgat




tcagttagaaaagacatggttgctaatatgaaagtaccacgtcctatttatatagaacag




gaaaaaatcggtcaattcattaaaaaagtagacaacaaaataaaaattcagaaacaagtg




attgaattacttaaacaacgcaaaaaggcattacttcaaaagatgtttatttaa


 


25
CC97, strain
atgagtaatacacaaaagaaaaatgtgccagagttgagattcccaggatttgaaggcgaa



C01791
tgggaagagaagcagttaggggatcttactaccaaaataggtagtggaaagactcccaaa




ggtggaagtgaaaactatacaaacaaaggcataccatttttaaggagtcaaaatattaga




aatggtaaattaaatcttaatgacttagtttatattagtaaagatatagatgatgagatg




aaaaatagtagaacgtactatggtgatgttcttttaaatattacaggagcatcaataggt




agaacagccattaattcgatagttgaaacgcatgctaatttaaatcaacatgtatgtatt




attagattgaaaaaagagtattattatattttttttggacagtatctattatcaagaaaa




ggaaaaaggaaaattttccttgcacaaagtggaggtagtcgagaaggtctaaacttcaaa




gaaattgctaatttaaaaatcttcaccccaactatatttgaagaacagcaaaaaataggc




aagttcttcagcaaacttgaccgacaaattgaattagaagaacaaaaacttgaattactt




caacaacagaaaaaaggctatttgcagaaaatcttctcacaggaattgcgatttaaggat




gagaatggaaatgattatccagagtggagatttgctagatttaaggactttatgtataaa




ccaataaacatacgacctgcaataaatattagtaagtcagaattgctaactgtaaaatta




cattgtaaagggatagagaaagctaatataaatcgagtattaaaactaggagctacgaat




tattataagagatttgaaggtcaatttatttatgggaaacaaaactttttcaatggagca




tttgacatagtgccaaaaaaatttgatggactttattcatcaagtgatgtgccagcgttt




gaaataaataccgaaaagattgaacctaactattttatcagctatatctctagaccaagc




ttttataaaagtaaggaaaaatattctactggtacaggtagtaaaagaatacatgaaaat




acggtgttaaatttctctttacatttaccttgtttaaacgaacaattaaaaattgcttct




ttcgtttgttttctcaatagaaaaattgaattactagaaagaaaaatctatctaataaag




aaacaaaagcaagctttgcttcaacaaatgtttatttaa


 


26
CC130, strain
atgagtaatacacaaaagaaaaatgtgccagagttgagatttccagggtttgaaggcgaa



459J
tgggaagagaagaagttaggggaaatttttcaaataatttctggttcaacaccactaaaa




tcaaataaaaagttttatgaaaatggtaatattaattgggtcaaaacgacagatttaaat




aattctaaagttacgcatagtaaagaaaaaataactgaatatgctatgaatagtttgaaa




ttaaaattagtgcctaaaaattcagtacttatagctatgtatggtggttttaatcaaatt




ggtcgaacaggtttgttaaaaatagatgccacaataaatcaagcaatttcagccttatta




atgaatcatgaaacgaatccagaatttatacaagcatatctaaattatcaagttaagggg




tggaagagatatgcagcaagtagcagaaaagacccgaatataactaaaaaagacatagaa




caatttaaagttccttatgttagtattaatgaacagcaaaaaataggcgaattcttcagc




aagcttgaccgacaaattgagttagaagaacaaaaactagaattacttcaacaacaaaaa




aaggctatatgcagaaaatcttctcacaagaattgcgattcaaagatgagaatggtgaag




attacccggagtgggaagagaagcaacttggagaattgggagtaacatatgctggccttt




ctggtaaagctaaagaagatttcggatttggtaaagatgtgtacgtaagttatgtgaatg




ttttcaaaaacaacatagcaacattagaaatggtggaaaatgtaagtattaaacctggeg




aaaaacaaaataatgtaaaatttggagatattttatttacaacttcttcagaggttcctc




atgaggtaggtatgtcctctgtatggttatatgagaaagataatgtatatttgaatagtt




tttgttttggatttaggactacagttagttttataaaccctatatttttggctagatatc




taagaagctttgaaatgagaaaattaataacaatcttagctcagggatcaacgagattta




atatttcaaaaaaagaattgatgaaactgattgtgaaaatacctagattggatgagcaaa




atagaataataaaccttttttcaattttagatggtggtattgaattacaatccatgaagg




taaggaaadaaaaaagcgtaaacaaggattgcttcaaaaaatgtttatttaa


 


27
CC151, isolate
atgagtaatacacaaaagaaaaatgtgccagagttgagattcccagggtttgaaggcgaa



982BL
tgggaagagaagaagttaggggaaatttttcaaataatttdggttcaacaccactaaaa




tcaaataaaaagttttatgaaaatggtaatattaattgggtcaaaacgacagatttaaat




aattctaaagttacgcatagtaaagaaaaaataactgaatatgctatgaatagtttgaaa




ttaaaattagtgcctaaaaattcagtacttatagctatgtatggtggttttaatcaaatt




ggtcgaacaggtttgttaaaaatagatgccacaataaatcaagcaatttcagccttatta




atgaatcatgaaacgaatccagaatttatacaagcatatctaaattatcaagttaagggg




tggaagagatatgcagcaagtagcagaaaagacccgaatataactaaaaaagacatagaa




caatttaaagttccttatgttagtattaatgaacagcaaaaaataggcgaattcttcagc




aagcttgaccgacaaattgagttagaagaacaaaaactagaattacttcaacaacaaaaa




aaggctatatgcagaaaatcttctcacaagaattgcgattcaaagatgagaatggtgaag




attacccggagtgggaagagacaaaactccaacaaattatagaggttaaagacggtactc




atgaaagtcctaagcccactgacaatggttatttattagtaacttcaaaaaatttaaaaa




ataataaattagatttgagtgaatcttatagtatttctaaagaagattatgaaagtataa




ataaaagatctaaagacgaaaaaggcgacattttatttggaatgatagggacaataggaa




atcctattctattagaagacgaaggattcgctataaaaaatgttgctttgctaaaaacga




gttgtttacaagaaaagtattacatattgaacttcctcaaatctatagctattgctaaac




aattttataaaacgaatgctggaggaactcaaaaatttatttctttaggagttataagag




atttaaaaattgattttccatctttagaggaatcgactaaaataggaattttatttaaca




aattagatgaattgattaaaaatcaatcaataaaaattgttttattaagacggcgaaaaa




aagccttacttaaatcgatgtttatttaa


 


28
CC873, isolate
atgagtaatacacaaaagaaaaatgtgccagagttgagattcccagggtttgaaggcgaa



32326
tgggaagagaagtctattagtagttttttaaaggaaagtaaaataaaaggaagcaatgga




agtcatgctaaaaagctaactgttaagctttggggaaaaggagtagttcccaaaaaagag




acatttaaaggaagtgacaatactcagtattataaaagaaaagcagggcaattgatgtat




ggtaaadtgattttttaaattgtgcttttggtattgttcctgattcattaaataattat




gaaagtactattgattccccaagttttgattttataaatggtgattctaaattcttactt




gaaagasttaaattaaagtctttttataaaaaatttggagatattgcaaatggtagtaga




aaagcaaaacgtattaatcaagatacattcttatcattgccagtttttgcaccaaagtat




gatgaacaattaagaataggcgaattctttagcaaactcgatcgacaaattgaactacaa




aaacaaaaacttgaattacttcaacaacagaaaaaaggctatatgcagaaaattttctca




caggaactgcgattcaaagatgagaatggtgaagattatccacattgggaaaatagcaaa




atagaaaaatatttaaaagagagaaacgaacgttctgacaaaggtcaaatgctttcagta




actataaatagtggcattataaaatttagtgaattggatagaaaagataattcaagtaaa




aataaaagtaattataaagtagttaggaaaaatgatattgcatataattctatgagaatg




tggcaaggggctagtggtaaatcaaattataatgggattgttagccctgcatatactgtg




ctatatccaacacaaaataaagctcattatttattggatataagtttaaaacacataga




atgattcataaatttaaaattaattcacaaggattaacatcagatacatggaacttaaaa




tataaacaattaaaaaatataaatatagatatacctgtattggaggaacaagaaaagata




ggtgatttctttaaaaaaatggatatattgattagtaaacagaaaataaaaattgaaata




ttagaaaaagagaaacaatcctttttacaaaaaatgttcttataa


 


29
CC188, isolate
atgagtaatacacaaaagaaaaatgtgccagagttgaggttcccagggtttgaaggcgaa



818
tgggaagagaagaagttaggggaccttactaccaaaataggtagtggaaagactcccaaa




ggtggaagtgaaaactatacaaacaaaggcataccatttttaaggagtcaaaatattaga




aatggtaaattaaatcttaatgacttagtttatattagtaaagatatagatgatgagatg




aaaaatagtagaacgtactatggtgatgttcttttaaatattacaggagcatcaataggt




agaacagccattaattcgatagttgaaatacatgctaatttaaatcaacatgtatgtatt




attagattgaaaaaagagtattattataatttttttggacagtatctattatcaagaaaa




ggtaaaaggaaaattttccttgcacaaagtggaggtagtcgagaaggactaaacttcaaa




gaaattgctaatttaaaaatcttcaccccaactatatttgaagagcagcaaaaaataggc




gaattcatcagcaaacttgaccgacaaattgaattagaagaacaaaaacttgaattactt




cagcaacagaaaaaaggctatatgcagaaaatcttctcgcaagaattgcgattcaaagat




gaggaaggtaaagattatccagattggaaatcaaaatcaattcaagaaatatttgagaat




aagggtggcactgctctagaaacagaatttaattttgacggtaattataaagttataagt




ataggaagttattctataaatagcacttataatgatcaaaatataagagtcaataaaaat




aaaaaaactgaaaaatatattttatcaaaaggcgacttagcaatggtattaaatgataaa




acaaaagatgggaaaattataggtagaagtatatttatagataaagataatcaatatatt




tataatcaaagaactgaaagattaataccatttgctgaaaatgataataaatttttatgg




ttcttaatgaatacagatttaattagaaataaaataaaaggtatgatgcaaggagcaacc




caagtttatataaattattcatctattaaattgatatctatacaattgccacttcttgaa




gaacaacagaaaataagagggtttctagaagttttatctggaataactactaaacaattg




cacnagatagaccaattaaaagagaggaaaaaggcgtttttacagaaaatgtttatttga


 


30
CC72 hsds1
ATGAGTAATACACAAAAGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT



TCH130
TTGAAGGCGAATGGGAAGAGAAGAAGTTGGGGGAAGTAGCCAAAATAT




ATGATGGTACTCATCAAACTCCTAAATATACAAACGAAGGTATAAAATTT




TTGTCAGTAGAAAATATAAAAACGTTGAATTCAAGCAAGTATATTTCAGA




AGAAGCATTTGAAAAAGAGTTTAAAATCCGACCAGAATTCGGAGATATA




TTAATGACTCGAATTGGTGATATAGGTACACCAAACATAGTGAGTTCAAA




TGAAAAATTTGCTTACTATGTTAGCTTAGCATTATTAAAAACTAAGAATCT




TAATTCCTATTTTTTGAAAAATTTAATTTTATCATCATCTATCCAGAATGA




ACTATGGAGAAAAACTTTACATGTGGCATTTCCCAAAAAAATAAACAAAA




ATGAAATTGGAAAAATTAAAATTAATTACCCTAAAAAGCAAGAACAACAA




AAAATTGGTCAGTTCTTCAGCAAACTCGACCGACAAATTGAATTAGAAG




AACAAAAACTCGAATTACTTCAACAACAGAAAAAAGGCTATATGCAGAAA




ATTTTCTCACAGGAACTGAGATTTAAAGATGAGAATGGTAATGATTATCC




GGAGTGGGAAGAGAGAAGATTTGCTGATATATTTAAATTTCATAATAAAC




TAAGAAAGCCAATTAAAGAAAATTTAAGAGTAAAGGGTTCTTATCCATAT




TATGGTGCTACAGGTATTATTGATTACGTTGACGACTTTATATTTGACGG




GAATTATTTACTTATTGGAGAAGATGGTGCAAATATTATCACTAGAAGTG




CACCCCTAGTGTACTTAGTAAATGGAAAGTTTTGGGTAAATAATCATGCT




CATATATTATCTCCTTTAAATGGAAATATACAGTACTTGTATCAAGTTGCA




GAATTAGTTAATTATGAAAAATACAATACTGGAACTGCTCAGCCTAAATT




AAACATTCAAAATTTAAAAATTATTAGTGTTGTAATTTCAACGAATTTAGA




AGAACAACAAAAAATCGGAAGCTTTTTAAGTAAACTTGATCGTCAAATCG




ATTTAGAAGAACAAAAACTCGAATTACTTCAACAACGAAAAAAAGCCTTA




CTTAAATTGATGTTTGTTTAA


 


31
CC72 hsds2
ATGAGTAATACACAAAAGAAAAATGTGCCAGAGTTGAGATTCCCAGAGT



TCH130
TTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGAATATTATAAAAGTTAA




TTCTGGAAAAGATTATAAACATTTGGATAAAGGCGATATACCAGTCTATG




GTACTGGCGGTTATATGACAAGTGTTTCAGAACCACTAAGTGAAATTGA




TGCTGTTGGTATTGGGAGAAAAGGGACTATAAACAAACCATATTTGCTT




GAGGCGCCGTTTTGGACGGTGGATACATTATTTTATTGTACACCTAAAA




AAGAAACAGACATACTATTTATATTAAGTTTATTTAGAAAAATAAACTGGA




AAGTATACGATGAATCAACAGGTGTGCCAAGCTTAAGCAAACAAACCAT




TAATAAAATAAATAGATTTGTCCCTACAAATAAAGAGCAGCAAAAAATAG




GCAAGTTCTTCAGCAAACTCGACCGGCAAATTGAATTAGAAGAACAAAA




ACTTGAATTACTTCAACAACAGAAAAAAGGCTATATGCAGAAAATCTTCT




CGCAAGAATTGCGATTCAAAGATGAGAATGGTAATGATTATCCAGATTG




GACAAATGAAAGATTGGGTGAAGTTACAACTGTTACTATGGGACAAAGT




CCGAAAAGTGTAAATTATACTGATAACTCAAATGATACGGTATTAATCCA




AGGAAATGCTGATATAGAGAATGGATTAATTAATCCCCGTATTTATACAA




GGGAAGTAACCAAATTAATTCAGAAGGACGAAATTATTTTAACTGTTAGA




GCACCTGTAGGCAAATTAGCTATGGCACAAATTAATGCGTGCATTGGTA




GAGGTGTATGCTCAATTAAAGGAGATAAATTTTTATATTATTTTCTAGAAT




GGTTTGCCACTCAAAATAAATGGATCCGTTTTTCACAGGGGAGTACATT




TGAATCTATTTCAGGGAATGACATAAGAAATATACACATTAAAATACCAG




TCGAAGATGAACGTACTAAAATTATAAAATTGTTAAATAGTTTAGATGTAT




TAAATTCAAAAACAGATTTAAAAATCCAAAACCTTAAACAGAGAAAACAA




TCGCTTCTACAAAAAATATTTGTTTAA


 


32
CC425 hsds1
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGAT




TTGAAGGCGAATGGGAAGAAAAGCAGGTTGGCGAGTTATTAGAATTTAA




AAATGGTTTAAATAAAGGAAAAGAATATTTTGGCTCAGGATCGTCGATTG




TTAACTTCAAAGATGTATTTAATAACAGGAGCATAAATACAAATAATCTG




ACTGGAAAAGTTAATGTGAATAGCAAAGAACTGAAGAATTATTCCGTTG




AAAAGGGTGATGTTTTTTTTACAAGGACTAGTGAGGTAATTGGTGAAATA




GGTTATCCGTCTGTAATTTTAAATGACCCTGAAAATACTGTGTTTAGTGG




ATTTGTATTAAGAGGACGGCCTAAATCAGGAATTGATTTAATAAATAATA




ATTTTAAAAGATATGTCTTTTTTACTAATTCATTTAGAAAAGAAATGATTA




CAAAAAGTTCTATGACAACTAGAGCTTTAACATCAGGTACTGCAATTAAT




AAAATGAAGGTCATATACCCTGTTTCGGCTAAAGAACAGAAAAAAATAG




GTGACTTCTTCAGCAAACTCGATCGACAAATTGAATTAGAAGAACAAAA




ACTTGAATTGCTTCAACAACAGAAAAAAGGATATATGCAGAAAATCTTCA




CACAAGAATTGCGATTTAAGGACGAGAATGGAAATGATTATCCGGAGTG




GGAAGAAACTACTATAAAAGAAATTGCTCAAATTAACACAGGAAAGAAA




GATACAAAAGATGCCATTACTAATGGGAGTTATGATTTTTACGTTAGATC




TCCGATAGTTTATAAAATTAATACTTTTAGTTATGAAGGAGAGGCTATTTT




AACTGTAGGAGATGGAGTTGGCGTAGGTAAAGTTTTCCACTATGTAAAT




GGGAAATTTGATTATCATCAAAGAGTATACAAAATATCTGACTTTAAGAA




TTATTATGGATTATTGTTATTTTATTATTTTTACAAAACTTTTTAAAAGAA




ACAAAGAAATATAGTGCGAAGACATCAGTTGATTCAGTTAGAAAAGACA




TGGTTGCTAATATGAAAGTACCACGTCCTATTTATATAGAACAGGAAAAA




ATCGGTCAATTCATTAAAAAAGTAGACAACAAAATAAAAATTCAGAAACA




AGTGATTGAATTACTTAAACAACGCAAAAAGGCATTACTTCAAAAGATGT




TTATTTAA


 


33
MRSA9B
atgagtaatacacaaaagaaaaatgtgccagagttgagattcccagggtttgaaggcgaatgggaaga




gaagaagctaggtgagtttgctggtaaagttacccaaaaaaatgttgataaaaaatatattgagacattaa




ctaattcagctgagttaggtatcatatctcaaaaggattattttgacaaagaaatttcgaatatagataatatta




aaaagtactatgtagttgaagagaatgattttgtttataaccctagaatgtctaattatgctccatttggaccag




taaatagaaataagttagggaaaaaaggggtcatgtcacctctttatactgtgtttaaaattcaaaacattga




tttaaactttattgagttttattttaaatcttcaaaatggtatagatttatggcattaaacggtgattcaggtgctcg




agcagataggttttctattaaagataggacatttatggaaatgccacttcatatcccatgtatggatgaacaa




ataaaaatcggtcagttcttcagcaaacttgaccgacaaattgaattagaagaacaaaaacttgaattactt




caacaacagaaaaaaggctatatgcagaaaatcttctcgcaagaattgcgatttaaagatgagaatggt




aaagattatccggagtgggaagaaactactataaaagaaattgctcaaattaacactggaaagaaagat




acaaaagatgccattactaatgggagttatgatttttacgttagatctccgatagtttataaaattaatactttta




gttatgaaggagaggctattttaactgtaggagatggagttggcgtaggtaaagttttccactatgtaaatgg




gaaatttgattatcatcaaagagtatacaaaatatctgactttaagaattattatggattattgttattttattattttt




cacaaaactttttaaaagaaacaaagaaatatagtgcgaagacatcagttgattcagttagaaaagacat




gattgctaatatgaaagtaccgcgtcctatttatatagaacaaaaaaaaatcggtcaattcattaaaagagt




agacaacaaaacaaaaattcagaaacaagtgattgaattacttaaacaacgcaaaaagtcattacttca




aaagatgtttatttaag


 


34
H1374 hsds2
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT




TTGAAGGCGAATGGGAAGAGAAGAAGGTTGGCGAGTTATTAGAATTTAA




AAaTGGTTTAAATAAAGGAAAAGAATATTTTGGCTCAGGATCGTCGATTG




TTAACTTCAAAGATGTATTTAATAACAGGAGCTTAAATACAAATAATCTG




ACTGGAAAAGTTAATGTGAATAGCAAAGAACTAAAAAATTATTCTGTTGA




AAAGGGTGATGTTTTTTTTACAAGGACTAGTGAGGTAATTGGTGAAATA




GGTTATCCGTCTGTAATTTTAAATGACCCTGAAAATACTGTGTTTAGTGG




ATTTGTATTAAGAGGGCGGCCTAAATCAGGAATTGATTTAATAAATAATA




ATTTTAAAAGATATGTCTTTTTTACTAATTCATTTAGAAAAGAAATGATTA




CAAAAAGTTCTATGACAACTAGAGCTTTAACATCAGGTAGCGCAATTAAT




AAAATGAAGGTCATATACCCTGTTTCGGCTAAAGAACAGaGAAAAATAG




GTGACTTCTTCAGCAAACTCGACCGACAAATTGAATTAGAAGAACAAAA




GCTTGAATTACTTCAACAACAAAAAAAAGGCTATATGCAGAAAATCTTCT




CACAGGAACTGCGATTCAAAGATGAGAATAGTGAAGATTATCCACATTG




GGAAAATAGCAAAATAGAAAAATATTTAAAAGAGAGAAACGAACGTTCT




GACAAAGGTCAAATGCTTTCAGTAACTATAAATAGTGGCATTATAAAATT




TAGTGAATTGGATAGAAAAGATAATTCAAGTAAAGATAAAAGTAATTATA




AAGTAGTTAGGAAAAATGATATTGCATATAATTCTATGAGAATGTGGCAA




GGGGCTAGTGGTAGATCAAATTATAATGGGATTGTTAGCCCTGCATATA




CTGTGCTTTATCCAACACAAAATACTAGCTCATTATTTATTGGATATAAG




TTTAAAACACATAGAATGATTCATAAATTTAAAATTAATTCACAAGGATTA




ACATCAGATACATGGAACTTAAAATATAAACAATTAAAAAaTATAAATATA




GATATACCTGTATTGGAGGAACAAGAAAAGATAGGTGATTTCTTTAAAAA




AATGGATATATTGATTAGTAAACAGAAAATAAAAATTGAAATATTAGAAAA




aGAGAAACAATCCTTTTTACAAAaGATGTTCTTATAA


 


35
CC34 hsdS1
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT



C160
TTGAAGGCGAATGGGAAGAGAAGAAGGTTGGCGAGTTATTAGAATTTAA




AAATGGTTTAAATAAAGGAAAAGAATATTTTGGCTCAGGATCGTCGATTG




TTAACTTCAAAGATGTATTTAATAACAGGAGCTTAAATACAAATAATCTG




ACTGGAAAAGTTAATGTGAATAGCAAAGAACTAAAAAATTATTCTGTTGA




AAAGGGTGATGTTTTTTTTACAAGGACTAGTGAGGTAATTGGTGAAATA




GGTTATCCGTCTGTAATTTTAAATGACCCTGAAAATACTGTGTTTAGTGG




ATTTGTATTAAGAGGGCGGCCTAAATCAGGAATTGATTTAATAAATAATA




ATTTTAAAAGATATGTCTTTTTTACTAATTCATTTAGAAAAGAAATGATTA




CAAAAAGTTCTATGACAACTAGAGCTTTAACATCAGGTAGCGCAATTAAT




AAAATGAAGGTCATATACCCTGTTTCGGCTAAAGAACAGAGAAAAATAG




GTGACTTCTTCAGCAAACTCGACCGACAAATTGAATTAGAAGAACAAAA




GCTTGAATTACTTCAACAACAAAAAAAAGGCTATATGCAGAAAATCTTCT




CACAGGAACTGCGATTCAAAGATGAGAATAGTGAAGATTATCCACATTG




GGAAAATAGCAAAATAGAAAAATATTTAAAAGAGAGAAACGAACGTTCT




GACAAAGGTCAAATGCTTTCAGTAACTATAAATAGTGGCATTATAAAATT




TAGTGAATTGGATAGAAAAGATAATTCAAGTAAAGATAAAAGTAATTATA




AAGTAGTTAGGAAAAATGATATTGCATATAATTCTATGAGAATGTGGCAA




GGGGCTAGTGGTAGATCAAATTATAATGGGATTGTTAGCCCTGCATATA




CTGTGCTTTATCCAACACAAAATACTAGCTCATTATTTATTGGATATAAG




TTTAAAACACATAGAATGATTCATAAATTTAAAATTAATTCACAAGGATTA




ACATCAGATACATGGAACTTAAAATATAAACAATTAAAAAATATAAATATA




GATATACCTGTATTGGAGGAACAAGAAAAGATAGGTGATTTCTTTAAAAA




AATGGATATATTGATTAGTAAACAGAAAATAAAAATTGAAATATTAGAAAA




AGAGAAACAATCCTTTTTACAAAAGATGTTCTTATAA


 


36
t1333 hsds1
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT




TTGAAGGCGAATGGGAAGAGAAGAAGGTTGGCGAGTTATTAGAATTTAA




AAATGGTTTAAATAAAGGAAAAGAATATTTTGGCTCAGGATCGTCGATTG




TTAACTTCAAAGATGTATTTAATAACAGGAGCTTAAATACAAATAATCTG




ACTGGAAAAGTTAATGTGAATAGCAAAGAACTAAAAAATTATTCTGTTGA




AAAGGGTGATGTTTTTTTTACAAGGACTAGTGAGGTAATTGGTGAAATA




GGTTATCCGCCTGTAATTTTAAATGACCCTGAAAATACTGTGTTTAGTGG




ATTTGTATTAAGAGGGCGGCCTAAATCAGGAATTGATTTAATAAATAATA




ATTTTAAAAGATATGTCTTTTTTACTAATTCATTTAGAAAAGAAATGATTA




CAAAAAGTTCTATGACAACTAGAGCTTTAACATCAGGTAGCGCAATTAAT




AAAATGAAGGTCATATACCCTGTTTCGGCTAAAGAACAGAGAAAAATAG




GTGACTTCTTCAGCAAACTCGACCGACAAATTGAATTAGAAGAACAAAA




GCTTGAATTACTTCAACAACAAAAAAAAGGCTATATGCAGAAAATCTTCT




CACAGGAACTGCGATTCAAAGATGAGAATAGTGAAGATTATCCACATTG




GGAAAATAGCAAAATAGAAAAATATTTAAAAGAGAGAAACGAACGTTCT




GACAAAGGTCAAATGCTTTCAGTAACTATAAATAGTGGCATTATAAAATT




TAGTGAATTGGATAGAAAAGATAATTCAAGTAAAGATAAAAGTAATTATA




AAGTAGTTAGGAAAAATGATATTGCATATAATTCTATGAGAATGTGGCAA




GGGGCTAGTGGTAGATCAAATTATAATGGGATTGTTAGCCCTGCATATA




CTGTGCTTTATCCAACACAAAATACTAGCTCATTATTTATTGGATATAAG




TTTAAAACACATAGAATGATTCATAAATTTAAAATTAATTCACAAGGATTA




ACATCAGATACATGGAACTTAAAATATAAACAATTAAAAAATATAAATATA




GATATACCTGTATTGGAGGAACAAGAAAAGATAGGTGATTTCTTTAAAAA




AATGGATATATTGATTAGTAAACAGAAAATAAAAATTGAAATATTAGAAAA




AGAGAAACAATCCTTTTTACAAAAGATGTTCTTATAAG


 


37
CC30 hsdS2
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT



MRSA252
TTGAAGGCGAATGGGAAGAGAAAAAGTTAGGGGATCTTATAAAAGTTAA




TTCTGGAAAAGATTATAAACATTTGGAAAAAGGTGATATACCAGTCTATG




GTACTGGCGGTTATATGACAAGTGTTTCAGAACCACTAAGTGAAATTGA




TGCTGTTGGTATTGGGAGAAAAGGGACTATAAACAAACCATATTTGCTT




GAGGCGCCGTTTTGGACGGTGGATACATTATTTTATTGTACACCTAAAA




AAGAAACAGACATACTATTTATATTAAGTTTATTTAGAAAAATAAATTGGA




AAGTATACGATGAATCAACAGGTGTGCCAAGCTTAAGTAAACAAACCAT




TAATAAAATAAATAGATTTGTCCCTTCAAATAAAGAGCAGCAAAAAATAG




GCGAATTCTTCATCAAACTCGACCGACAAATTGAATTAGAAGAACAAAA




ACTTGAATTACTTCAACAACAGAAAAAAGGCTATATGCAGAAAATCTTCT




CACAGGAATTGCGATTCAAGGATGAGAATGGAAACGATTATCCGAATTG




GGAAGAGAAGAAAATAGAAGATATAGCAAGCCAAGTATATGGAGGCGG




AACACCAAATACAAAGATTAAAGAATTTTGGAATGGAGATATTCCATGGA




TTCAAAGCTCTGACGTAAAAGTAAATGATTTGATTCTACGACAATGTAAT




AAATTTATTTCCAAGAATTCAATTGAGCTTTCTTCTGCAAAACTTATTCCT




GCCAATTCAATTGCAATAGTTACAAGAGTCGGGGTTGGAAAACTGTGTT




TGGTAGAATTTGATTATGCTACAAGTCAAGATTTTTTATCATTAAGTAGT




CTTAAATATGACAAATTATACTCATTATATTCATTGCTATATACAATGAAA




AAAATTAGCGCTAATCTACAAGGAACTTCAATTAAAGGTATAACAAAAAA




AGAGTTGTTAGATAGTATAATAAAGATACCCCATAATCTAGAAGAACAGC




AAAAAATAGGTGATCTATTTTATAAAATTGATAAATATATCAGTTTTAATA




AATGTAAAATTGAGATACTTAAAAGTCTCAAACAAGGATTACTTCAAAAA




ATTTTTATATAA


 


38
CC34 hsdS2
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT



C160
TTGAAGGCGAATGGGAAGAGAAAAAGTTAGGGGATCTTATAAAAGTTAA




TTCTGGAAAAGATTATAAACATTTGGAAAAAGGTGATATACCAGTCTATG




GTACTGGCGGTTATATGACAAGTGTTTCAGAACCACTAAGTGAAATTGA




TGCTGTTGGTATTGGGAGAAAAGGGACTATAAACAAACCATATTTGCTT




GAGGCGCCGTTTTGGACGGTGGATACATTATTTTATTGTACACCTAAAA




AAGAAACAGACATACTATTTATATTAAGTTTATTTAGAAAAATAAATTGGA




AAGTATACGATGAATCAACAGGTGTGCCAAGCTTAAGTAAACAAACCAT




TAATAAAATAAATAGATTTGTCCCTTCAAATAAAGAGCAGCAAAAAATAG




GCGAATTCTTCATCAAACTCGACCGACAAATTGAATTAGAAGAACAAAA




ACTTGAATTACTTCAACAACAGAAAAAAGGCTATATGCAGAAAATCTTCT




CACAGGAATTGCGATTCAAGGATGAGAATGGAAACGATTATCCGAATTG




GGAAGAGAAGAAAATAGAAGATATAGCAAGCCAAGTATATGGAGGCGG




AACACCAAATACAAAGATTAAAGAATTTTGGAATGGAGATATTCCATGGA




TTCAAAGCTCTGACGTAAAAGTAAATGATTTGATTCTACGACAATGTAAT




AAATTTATTTCCAAGAATTCAATTGAGCTTTCTTCTGCAAAACTTATTCCT




GCCAATTCAATTGCAATAGTTACAAGAGTCGGGGTTGGAAAACTGTGTT




TGGTAGAATTTGATTATGCTACAAGTCAAGATTTTTTATCATTAAGTAGT




CTTAAATATGACAAATTATACTCATTATATTCATTGCTATATACAATGAAA




AAAATTAGCGCTAATCTACAAGGAACTTCAATTAAAGGTATAACAAAAAA




AGAGTTGTTAGATAGTATAATAAAGATACCCCATAATCTAGAAGAACAGC




AAAAAATAGGTGATCTATTTTATAAAATTGATAAATATATCAGTTTTAATA




AATGTAAAATTGAGATACTTAAAAGTCTCAAACAAGGATTACTTCAAAAA




ATTTTTATATAA


 


39
CC152 hsds2
ATGAGTAATACACAAAAGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT




TTGAAGGCGAGTGGGAAGAGAAGAAGCTAGAAGATATTATAAAAGTTAA




TTCTGGAAAAGATTATAAACATTTGGATAAAGGCGATATACCAGTCTATG




GTACTGGCGGTTATATGACAAGTGTTTCAGAACCACTGAGTGAAATTGA




TGCTGTTGGTATTGGGAGAAAAGGGACTATAAACAAACCATATGTACTT




GAGGCGCCGTTTTGGACGGTGGATACATTATTTTACTGTACACCTAAAA




AAGAAGTAGACATACTATTTATATTGAGTTTATTTAGAAAAATAAATTGGA




AGGTGTATGATGAATCAACAGGTGTGCCAAGCTTAAGTAAGCAAACCAT




TAATAAAATAATTAGATTTGTCCCTACAAATAAAGAACAACAAAAAATAG




GTAAGTTCTTCAGCAAACTTGACCGACAAATTGAATTAGAAGAACAAAAA




CTTGAATTACTTCAACAACAGAAAAAAGGCTATATGCAGAAAATCTTCTC




GCAAGAATTGCGATTTAAAGATGAGAATGGTAATGATTATCCAGATTGG




GAAGAGAAGAAAATAGAAGATATAGCAAGCCAAGTATATGGAGGAGGA




ACACCAAATACAAAAATTAAAGAATTTTGGAATGGAGATATTCCATGGAT




TCAAAGCTCTGACGTAAAAGTAAATGATTTGATTCTACAACAATGTAATA




AATTTATTTCCAAGAATTCAATTGAGCTTTCTTCTGCAAAACTTATTCCTG




CCAATTCAATTGCAATAGTTACAAGAGTCGGGGTTGGAAAACTGTGTTT




GGTAGAATTTGATTATGCTACAAGTCAAGATTTTTTATCATTAAGTAGTC




TTAAATATGACAAATTATACTCATTATATTCATTGCTATATACAATGAAAA




AAATTAGCGCTAATCTACAAGGAACTTCAATTAAAGGTATAACAAAAAAA




GAGTTGTTAGATAGTATAATAAAGATACCCCATAATCTAGAAGAACAGCA




AAAAATAGGTGAGCTATTTTATAAAATAGATAAATATATCAGTTTTAATAA




ATGTAAAATTGAGATGCTTAAAAGTCTCAAACAAGGATTACTTCAAAAAA




TGTTTATATAA


 


40
H1374_hsds1
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGGt




TTGAAGGCGAATGGGAAGAGaAAAAGtTAGGGGATCTTATAAAAGTTAAT




TCTGGAAAAGATTATAAACATTTGGAAAAAGGTGATATACCAGTCTATGG




TACTGGCGGTTATATGACAAGTGTTTCAGAACCACTAAGTGAAATTGAT




GCTGTTGGTATTGGGAGAAAAGGGACTATAAACAAACCATATTTGCTTG




AGGCGCCGTTTTGGACGGTGGATACATTATTTTATTGTACACCTaAAAAA




GAAACAGACATACTATTTATATTAAGTTTAtTTAGaAAAATaAATTGGaAAG




TATACGATGAATCAACAGGTGTGCCAAGCTTAAGTAAACAAACCATTAAT




AAAATAAATAGATTTGTCCCTTCAAATAAAGAGCAGCAAAAAATAGGCGA




ATTCTTCATCAAACTCGACCGACAAATTGAATTAGAAGAACAAAAACTTG




AATTACTTCAACAACAGAAAAAAGGCTATATGCAGAAAATCTTCTCACAG




GAATTGCGATTCAAGGATGAGAATGGAAACGATTATCCGAATTGGGAAG




AGAAGAAAATAGAAGATATAGCAAGCCAAGTATATGGAGGCGGAACAC




CAAATACAAAGATTAAAGaATTTTGGAATGGAGATATTCCATGGATTCAA




AGCTCTGACGTAAAAGTAAATGATTTGATTCTACGACAATGTAATAAATT




TATTTCCAAGAATTCAATTGAGCTTTCTTCTGCaAAACTTATTCCTGCCAA




TTCAATTGCAATAGTTACAAGAGTCGGGGTTGGAAAACTGTGTTTGGTA




GAATTTGATTATGCTACAAGTCAAGATTTTTTATCATTAAGTAGTCTTAAA




TATGACAAATTATACTCATTATATTCATTGCTATATACAATGAAAAAAATT




AGCGCTAATCTACAAGGAACTTCAATTAAAGGTATAACaAAAAAAGAGTT




GTTAGATAGTATAATAAAGATACCCCATAATCTAGAAGAACAGCaAAAAA




TAGGTGATCTATTTTATaAAATTGATAAATATATCAGTTTTAATAAATGTA




AAATTGAGATACTTAAAAGTCTCAAACAAGGATTACTTCAAAAAATTTTTA




TATAA


 


41
CC5 hsdS1 ED98
atgagtaatacacaaaagaaaaatgtgccagagttgagattcccagggtttgaaggcgaatgggaaga



forward
gaagcagttgggggatcttacagatagagtaattaggaaaaataaaaacttagaatcgaaaaagccttta




acaatatccggacagttaggtttaattgatcaaacagaatattttagtaaatcagtttcgtcgaaaaatctag




aaaattatacactaataaagaatggagaattcgcgtataacaaaagttattctaatggatacccattaggg




gctattaaaagattaactagatatgatagtggtgtattgtcctotttgtatatttgtttttctattaaaagtgaaatgt




ctaaagacttcatggaagcatattttgattcgacacactggtatagagaagtttctggaattgcagttgaggg




tgcaagaaatcacggattattaaatgtttctgtgaatgatttttttactattctaattaaatatccaagtttagaag




aacagcaaaaaataggcaagttcttcagcaaactcgaccgacaaattgaattagaagaacaaaagctt




gaattacttcaacaacagaaaaaaggctatatgcagaaaattttctcacaggaactgcgattcaaagatg




agaatggtgaagattatccagattgggaaaatagcaaaatagaaaaatatttaaaagagagaaacgaa




cgttctgacaaagggcaaatgctttcagtaactataaatagtggcattataaaatttagtgaattggatagaa




aagataattcaagtaaagataaaagtaattataaagtagttaggaaaaatgatattgcatataattctatga




gaatgtggcaaggggctagtggtaaatcaaattataatgggattgttagccctgcatatactgtgctttatcc




aacacaaaatactagctcattatttattggatataagtttaaaacacatagaatgattcataaatttaaaatta




attcacaaggattaacatcagatacatggaacttaaaatataaacaattaaaaaatataaatatagatata




cctgtattggaggaacaagaaaagataggtgatttctttaaaaaaatggatatattgataagtaaacagaa




aatgaaaattgaaatattagaaaaagagaaacaatcctttttacaaaaaatgttcttataa


 


42
CC5 hsdS1
ATGAGTAATACACAAAAGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT




TTGAAGGCGAATGGGAAGAGAAGCAGTTGGGGGATCTTACAGATAGAG




TAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCC




GGACAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAAATCAGTTTC




GTCGAAAAATCTAGAAAATTATACACTAATAAAGAATGGAGAATTCGCGT




ATAACAAAAGTTATTCTAATGGATACCCATTAGGGGCTATTAAAAGATTA




ACTAGATATGATAGTGGTGTATTGTCCTCTTTGTATATTTGTTTTTCTATT




AAAAGTGAAATGTCTAAAGACTTCATGGAAGCATATTTTGATTCGACACA




CTGGTATAGAGAAGTTTCTGGAATTGCAGTTGAGGGTGCAAGAAATCAC




GGATTATTAAATGTTTCTGTGAATGATTTTTTTACTATTCTAATTAAATAT




CCAAGTTTAGAAGAACAGCAAAAAATAGGCAAGTTCTTCAGCAAACTCG




ACCGACAAATTGAATTAGAAGAACAAAAGCTTGAATTACTTCAACAACAG




AAAAAAGGCTATATGCAGAAAATTTTCTCACAGGAACTGCGATTCAAAG




ATGAGAATGGTGAAGATTATCCAGATTGGGAAAATAGCAAAATAGAAAA




ATATTTAAAAGAGAGAAACGAACGTTCTGACAAAGGGCAAATGCTTTCA




GTAACTATAAATAGTGGCATTATAAAATTTAGTGAATTGGATAGAAAAGA




TAATTCAAGTAAAGATAAAAGTAATTATAAAGTAGTTAGGAAAAATGATA




TTGCATATAATTCTATGAGAATGTGGCAAGGGGCTAGTGGTAAATCAAA




TTATAATGGGATTGTTAGCCCTGCATATACTGTGCTTTATCCAACACAAA




ATACTAGCTCATTATTTATTGGATATAAGTTTAAAACACATAGAATGATTC




ATAAATTTAAAATTAATTCACAAGGATTAACATCAGATACATGGAACTTAA




AATATAAACAATTAAAAAATATAAATATAGATATACCTGTATTGGAGGAA




CAAGAAAAGATAGGTGATTTCTTTAAAAAAATGGATATATTGATAAGTAA




ACAGAAAATGAAAATTGAAATATTAGAAAAAGAGAAACAATCCTTTTTAC




AAAAAATGTTCTTATAA


 


43
CC5 hsdS2
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGAT




TTGAGGGCGAATGGGAAGAGAAGAAGTTAGGGAATCTTACTACCAAAAT




AGGTAGTGGAAAGACTCCCAAAGGTGGAAGTGAAAACTATACAAACAAA




GGCATACCATTTTTAAGGAGTCAAAATATTAGAAATGGTAAATTAAATCT




TAATGACTTAGTTTATATTAGTAAAGATATAGATGATGAGATGAAAAATA




GTAGAACGTACTATGGTGATGTTCTTTTAAATATTACAGGAGCATCAATA




GGTAGAACAGCCATTAATTCGATAGTTGAAACGCATGCTAATTTAAATCA




ACATGTATGTATTATTAGATTAAAAAAAGAGTATTATTATAATTTTTTTGG




ACAGTATCTATTATCAAGAAAAGGTAAAAGAAAAATTTTCCTTGCACAAA




GTGGAGGTAGTCGAGAAGGACTAAACTTCAAAGAAATTGCTAATTTAAA




AATCTTCACCCCAACTATATTTGAAGAACAACAAAAAATAGGACAATTCT




TCAGCAAACTTGACCAACAAATTGAATTAGAAGAACAAAAACTTGAATTA




CTTCAACAACAGAAAAAATGCTATATACAGAAAATCTTCTCACAAGAATT




ACGATTCAAAGATGAAGAAGGTAATTACTATAAAGGATGGAACAAAAAG




CAATTAAAAGATGTATTAGAATTTAGTAATAAAAGAACTATTAATGAAAAT




GAATATCCTGTTTTAACATCGTCAAGACAAGGTTTAATACTTCAGTCAGA




CTACTATAAAGATAGGAAAACTTTTGCAGAGAGTAATATTGGGTATTTCA




TACTCCCTAAAAATCATATAACATACCGTTCAAGAAGCGACGATGGAATT




TTTAAGTTTAATTTAAATCTAATGATTGATGTAGGTATTATTAGTAAATAT




TACCCTGTCTTTAAAGGGATAGATGCAAATCAATATTATTTAACATTACA




CTTAAACTATCAACTGAAAAAAGAATATATTAAATATGCAACTGGTACAT




CACAATTGGTACTCTCACAAAAAGACTTGCAAAACATAAAGACTAAATTG




CCATCTTATGAAGAACAACAAAAAATCGGTGATTTTTTCAGTGAAATAGA




TAGATTGGTTGAAAAACAATCTTCAAAAGTCGGACGATTAAAAGTACGTA




AAAAAGAACTATTACAAAAAATGTTTGTTTAA


 


44
CC5 hsdS2 ED98
atgagtaatacacaaacgaaaaatgtgccagagttgagattcccaggatttgagggcgaatgggaaga




gaagaagttagggaatcttactaccaaaataggtagtggaaagactcccaaaggtggaagtgaaaact




atacaaacaaaggcataccatttttaaggagtcaaaatattagaaatggtaaattaaatcttaatgacttagt




ttatattagtaaagatatagatgatgagatgaaaaatagtagaacgtactatggtgatgttcttttaaatattac




aggagcatcaataggtagaacagccattaattcgatagttgaaacgcatgctaatttaaatcaacatgtat




gtattattagattaaaaaaagagtattattataatttttttggacagtatctattatcaagaaaaggtaaaagaa




aaattttccttgcacaaagtggaggtagtcgagaaggactaaacttcaaagaaattgctaatttaaaaatct




tcaccccaactatatttgaagaacaacaaaaaataggacaattcttcagcaaacttgaccaacaaattga




attagaagaacaaaaacttgaattacttcaacaacagaaaaaatgctatatacagaaaatcttctcacaa




gaattacgattcaaagatgaagaaggtaattactataaaggatggaacaaaaagcaattaaaagatgta




ttagaatttagtaataaaagaactattaatgaaaatgaatatcctgttttaacatcgtcaagacaaggtttaat




acttcagtcagactactataaagataggaaaacttttgcagagagtaatattgggtatttcatactccctaaa




aatcatataacataccgttcaagaagcgacgatggaatttttaagtttaatttaaatctaatgattgatgtaggt




attattagtaaatattaccctgtctttaaagggatagatgcaaatcaatattatttaacattacacttaaactatc




aactgaaaaaagaatatattaaatatgcaactggtacatcacaattggtactctcacaaaaagacttgcaa




aacataaagactaaattgccatcttatgaagaacaacaaaaaatcggtgattttttcagtgaaatagatag




attggttgaaaaacaatcttcaaaagtcggacgattaaaagtacgtaaaaaagaactattacaaaaaatg




tttgtttaa


 


45
CC8 hsd1
ATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGT



USA300
TTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAG




TAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCC




GGACAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAAATCAGTTTC




GTCGAAAAATCTAGAAAATTATACACTAATAAAGAATGGAGAATTCGCGT




ATAACAAAAGTTATTCTAATGGATACCCATTAGGGGCTATTAAAAGATTA




ACTAGATATGATAGTGGTGTATTGTCCTCTTTGTATATTTGTTTTTCTATT




AAAAGTGAAATGTCTAAAGACTTCATGGAAGCATATTTTGATTCGACACA




CTGGTATAGAGAAGTTTCTGGAATTGCAGTTGAGGGTGCAAGAAATCAC




GGATTATTAAATGTTTCTGTGAATGATTTTTTTACTATTCTAATTAAATAT




CCAAGTTTAGAAGAACAGCAAAAAATAGGCAAGTTCTTCAGCAAACTCG




ACCGACAAATTGAATTAGAAGAACAAAAGCTTGAATTACTTCAACAACAG




AAAAAAGGCTATATGCAGAAAATTTTCTCACAGGAACTGCGATTCAAAG




ATGAGAATGGTGAAGATTATCCAGATTGGGAAAATAGCAAAATAGAAAA




ATATTTAAAAGAGAGAAACGAACGTTCTGACAAAGGGCAAATGCTTTCA




GTAACTATAAATAGTGGCATTATAAAATTTAGTGAATTGGATAGAAAAGA




TAATTCAAGTAAAGATAAAAGTAATTATAAAGTAGTTAGGAAAAATGATA




TTGCATATAATTCTATGAGAATGTGGCAAGGGGCTAGTGGTAAATCAAA




TTATAATGGGATTGTTAGCCCTGCATATACTGTGCTTTATCCAACACAAA




ATACTAGCTCATTATTTATTGGATATAAGTTTAAAACACATAGAATGATTC




ATAAATTTAAAATTAATTCACAAGGATTAACATCAGATACATGGAACTTAA




AATATAAACAATTAAAAAATATAAATATAGATATACCTGTATTGGAGGAA




CAAGAAAAGATAGGTGATTTCTTTAAAAAAATGGATATATTGATAAGTAA




ACAGAAAATGAAAATTGAAATATTAGAAAAAGAGAAACAATCCTTTTTAC




AAAAAATGTTCTTATAA


 


46
CC8 hsdS2
ATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGATTCCCAGGAT



USA300
TTGAAGGCGAATGGGAAGAGAAGAAGTTAGGGAATCTTACTACCAAAAT




AGGTAGTGGAAAGACTCCCAAAGGTGGAAGTGAAAACTATACAAACAAA




GGCATACCATTTTTAAGGAGTCAAAATATTAGAAATGGTAAATTAAATCT




TAATGACTTAGTTTATATTAGTAAAGATATAGATGATGAGATGAAAAATA




GTAGAACGTACTATGGTGATGTTCTTTTAAATATTACAGGAGCATCAATA




GGTAGAACAGCCATTAATTCGATAGTTGAAACGCATGCTAATTTAAATCA




ACATGTATGTATTATTAGATTGAAAAAAGAGTATTATTATAATTTTTTTGG




ACAGTATCTATTATCAAGAAAAGGTAAAAGGAAAATTTTCCTTGCACAAA




GTGGAGGTAGTCGAGAAGGTCTAAACTTCAAAGAAATTGCTAATTTAAA




AATCTTCACCCCAACTATATTTGAAGAACAGCAAAAAATAGGCAAGTTCT




TCAGCAAACTCGACCGACAAATTGAATTAGAAGAACAAAAACTTGAATT




GCTTCAACAACAGAAAAAAGGCTATATGCAGAAAATCTTCACACAAGAA




TTGCGATTCAAAGATGAGAATGGTGAAGAATATCCAGAGTGGGAAAACA




AATTCATAAAAGACATCTTTATCTTTGAAAATAATAGAAGAAAACCAATTA




CTTCTTCATTAAGAGAAAAGGGGTTATACCCTTACTATGGTGCAACTGG




AATTATTGATTACGTAAAAGATTATTTATTCAATAATGAAGAACGATTACT




AATAGGAGAAGATGGTGCAAAATGGGGGCAGTTTGAGACGAGTAGCTT




TATTGCTAATGGGCAATACTGGGTAAATAATCATGCGCATGTAGTTAAAA




GTAATGATCATAATTTGTTTTTTATGAATTATTATTTAAATTTTAAAGAACT




ACGAGCATTTGTCACAGGTAATGCACCAGCTAAATTAACTCATGCGAAC




TTATGCAATATAAATCTTAAAATACCTTGTCTCACTGAACAAGATAAAGT




AAGTGCATTGTTAAAATCTATAGACAATAAAATGAATAATCAAATGAATA




GAATTGAGTTATTAAAAGAACGTAAAAAAGGACTATTACAAAAAATGTTT




ATTTAA


 


47
CC12 hsdS1
ATGAGTAATACACAAAAGAAAAATGTGCCAGAGTTGAGATTCCCAGAGT




TTGAAGGCGAATGGGAAGAGAAGCAGTTAGGGGATCTTACAGATAGAG




TAATTAGGAAAAATAAAAACTTAGAATCGAAAAAAGCCTTTAACAATATC




CGGACAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAAATCAGTTT




CGTCGAAAAATCTAGAAAATTATACACTAATAAAGAATGGAGAATTCGC




GTATAACAAAAGTTATTCTAATGGATACCCATTAGGGGCTATTAAAAGAT




TAACTAGATATGATAGTGGTGTATTGTCCTCTTTGTATATTTGTTTTTCTA




TTAAAAGTGAAATGTCTAAAGACTTCATGGAAGCATATTTTGATTCGACA




CACTGGTATAGAGAAGTTTCTGGAATTGCAGTTGAGGGTGCAAGAAATC




ACGGATTATTAAATGTTTCTGTGAATGATTTTTTTACTATTCTAATTAAAT




ATCCAAGTTTAGAAGAACAGCAAAAAATAGGCAAGTTCTTCAGCAAACT




CGACCGACAAATTGAATTAGAAGAACAAAAGCTTGAATTACTTCAACAA




CAGAAAAAAGGCTATATGCAGAAAATTTTCTCACAGGAACTGCGATTCA




AAGATGAGAATGGTGAAGATTATCCAGATTGGGAAAATAGCAAAATAGA




AAAATATTTAAAAGAGAGAAACGAACGTTCTGACAAAGGGCAAATGCTT




TCAGTAACTATAAATAGTGGCATTATAAAATTTAGTGAATTGGATAGAAA




AGATAATTCAAGTAAAGATAAAAGTAATTATAAAGTAGTTAGGAAAAATG




ATATTGCATATAATTCTATGAGAATGTGGCAAGGGGCTAGTGGTAAATC




AAATTATAATGGGATTGTTAGCCCTGCATATACTGTGCTTTATCCAACAC




AAAATACTAGCTCATTATTTATTGGATATAAGTTTAAAACACATAGAATGA




TTCATAAATTTAAAATTAATTCACAAGGATTAACATCAGATACATGGAACT




TAAAATATAAACAATTAAAAAATATAAATATAGATATACCTGTATTGGAGG




AACAAGAAAAGATAGGTGATTTCTTTAAAAAAATGGATATATTGATAAGT




AAACAGAAAATGAAAATTGAAATATTAGAAAAAGAGAAACAATCCTTTTT




ACAAAAAATGTTCTTATAA


 


48
CC1 hsdS1
ATGAGTAATACACAAAAGAAAAATGTGCCAGAGTTGAGGTTCCCAGGGT



MSSA476
TTGAAGGCGAATGGGAAGAGAAGAAGTTAGGGGACCTTACTACCAAAA




TAGGTAGTGGAAAGACTCCCAAAGGTGGAAGTGAAAACTATACAAACAA




AGGCATACCATTTTTAAGGAGTCAAAATATTAGAAATGGTAAATTAAATC




TTAATGACTTAGTTTATATTAGTAAAGATATAGATGATGAGATGAAAAATA




GTAGAACGTACTATGGTGATGTTCTTTTAAATATTACAGGAGCATCAATA




GGTAGAACAGCCATTAATTCGATAGTTGAAATACATGCTAATTTAAATCA




ACATGTATGTATTATTAGATTGAAAAAAGAGTATTATTATAATTTTTTTGG




ACAGTATCTATTATCAAGAAAAGGTAAAAGGAAAATTTTCCTTGCACAAA




GTGGAGGTAGTCGAGAAGGACTAAACTTCAAAGAAATTGCTAATTTAAA




AATCTTCACCCCAACTATATTTGAAGAGCAGCAAAAAATAGGCGAATTC




ATCAGCAAACTTGACCGACAAATTGAATTAGAAGAACAAAAACTTGAATT




ACTTCAGCAACAGAAAAAAGGCTATATGCAGAAAATCTTCTCGCAAGAA




TTGCGATTCAAAGATGAGGAAGGTAAAGATTATCCAGATTGGAAATCAA




AATCAATTCAAGAAATATTTGAGAATAAGGGTGGCACTGCTCTAGAAAC




AGAATTTAATTTTGACGGTAATTATAAAGTTATAAGTATAGGAAGTTATTC




TATAAATAGCACTTATAATGATCAAAATATAAGAGTCAATAAAAATAAAAA




AACTGAAAAATATATTTTATCAAAAGGCGACTTAGCAATGGTATTAAATG




ATAAAACAAAAGATGGGAAAATTATAGGTAGAAGTATATTTATAGATAAA




GATAATCAATATATTTATAATCAAAGAACTGAAAGATTAATACCATTTGCT




GAAAATGATAATAAATTTTTATGGTTCTTAATGAATACAGATTTAATTAGA




AATAAAATAAAAGGTATGATGCAAGGAGCAACCCAAGTTTATATAAATTA




TTCATCTATTAAATTGATATCTATACAATTGCCACTTCTTGAAGAACAACA




GAAAATAAGAGGGTTTCTAGAAGTTTTATCTGGAATAACTACTAAACAAT




TGCACAAGATAGACCAATTAAAAGAGAGGAAAAAGGCGTTTTTACAGAA




AATGTTTATTTGA


 


49
t337 hsds1
atgagtaatacacaaaagaaaaatgtgcctgagttgagattcccagggtttgaaggcgaatgggaagag




aagcaatttgctgattttactaaaataaatcaaggattgcagattgctattaatgaacgtaaaactgaatattc




tccagagttgtatttttatataacaaatgaatttttaagaccaaatagtcaaactaaatattttatcgaaaatcc




ccctcaatcagtaattgcaaataaagaagatattttaatgactagaacaggtaatactggaaaagtagtaa




ctaatgtatttggagcgtttcataataatttttttaaaattaaatttgataaaaatctgtatgatagattgtttttagta




gaggttttaaattcatctaagatacaaaataaaatactatctttagcaggatcttcgacgataccagatttaa




accatagtgatttttatagtattagttcttcttatccgctgcttagagaacagcaaaaaataggtaaattcttcag




caaacttgaccgacaaattgaactagaagaacaaaaacttgaattactaaaacaacagaaaaaaggct




atatgcagaaaatcttctcgcaagaattgcgattcaaagatgagaatggaaatgattatccagagtggga




atcaaaatcaattcaagaaatatttgagaataagggtggcactgctctagaaacagaatttaattttgacgg




taattataaagttataagtataggaagttattctataaatagcacttataatgatcaaaatataagagtcaata




aaaataaaaaaactgaaaaatatattttatcaaaaggcgacttagcaatggtattaaatgataaaacaaa




agatgggaaaattataggtagaagtatatttatagataaagataatcaatatatttataatcaaagaactga




aagattaataccatttgctgaaaatgataataaatttttatggttcttaatgaatacagatttaattagaaataa




aataaaaggtatgatgcaaggagcaacccaagtttatataaattattcatctattaaattgatatctatacaat




tgccacttcttgaagaacaacagaaaataagaggttttctagaagtcttgtctggaataactactgaacaatt




gcacaagatagaccaattaaaagagaggaaaaaggcgtttttacagaaaatgtttatttga


 


50
CC1 hsdS2
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGAT



MSSA476
TTGAGGGCGAATGGGAAGAGAAGAAGTTAGGGAATCTTACTACCAAAAT




AGGTAGTGGAAAGACTCCCAAAGGTGGAAGTGAAAACTATACAAACAAA




GGCATACCATTTTTAAGGAGTCAAAATATTAGAAATGGTAAATTAAATCT




TAATGACTTAGTTTATATTAGTAAAGATATAGATGATGAGATGAAAAATA




GTAGAACGTACTATGGTGATGTTCTTTTAAATATTACAGGAGCATCAATA




GGTAGAACAGCCATTAATTCGATAGTTGAAACGCATGCTAATTTAAATCA




ACATGTATGTATTATTAGATTGAAAAAAGAGTATTATTATAATTTTTTTGG




ACAGTATCTATTATCAAGAAAAGGTAAAAGGAAAATTTTCCTTGCACAAA




GTGGAGGTAGTCGAGAAGGTCTAAACTTCAAAGAAATTGCTAATTTAAA




AATCTTCACCCCAACTATATTTGAAGAACAGCAAAAAATAGGCAAGTTCT




TCAGCAAACTCGACCGACAAATTGAATTAGAAGAACAAAAACTTGAATT




GCTTCAACAACAGAAAAAAGGCTATATGCAGAAAATCTTCACACAAGAA




TTGCGATTCAAAGATGAGAATGGTGAAGAATATCCAGAGTGGGAAAACA




AATTCATAAAAGACATCTTTATCTTTGAAAATAATAGAAGAAAACCAATTA




CTTCTTCATTAAGAGAAAAGGGGTTATACCCTTACTATGGTGCAACTGG




AATTATTGATTACGTAAAAGATTATTTATTCAATAATGAAGAACGATTACT




AATAGGAGAAGATGGTGCAAAATGGGGGCAGTTTGAGACGAGTAGCTT




TATTGCTAATGGGCAATACTGGGTAAATAATCATGCGCATGTAGTTAAAA




GTAATGATCATAATTTGTTTTTTATGAATTATTATTTAAATTTTAAAGAACT




ACGAGCATTTGTCACAGGTAATGCACCAGCTAAATTAACTCATGCGAAC




TTATGCAATATAAATCTTAAAATACCTTGTCTCACTGAACAAGATAAAGT




AAGTGCATTGTTAAAATCTATAGACAATAAAATGAATAATCAAATGAATA




GAATTGAGTTATTAAAAGAACGTAAAAAAGAACTATTACAAAAAATGTTT




ATTTAA


 


51
CC22 hsdS1
ATGAGTAATACACAAAAGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT



EMRSA15
TTGAAGGCGAATGGGAAGAGAAGAAGTTAGGGGATCTTACAGATAGAG




TAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCC




GGACAGTTAGGTTTAATTGATCAAACAGAATACTTTAGTAAATCAGTTTC




GTCGAAAAATCTAGAAAATTATACACTAATAAAGAATGGAGAATTCGCGT




ATAACAAAAGTTATTCTAATGGATACCCATTAGGGGCTATTAAAAGATTA




ACTAGATATGATAGTGGTGTATTGTCCTCTTTGTATATTTGTTTTTCTATT




AAAAGTGAAATGTCTAAAGACTTCATGGAAGCATATTTTGATTCGACACA




CTGGTATAGAGAAGTTTCTGGAATTGCAGTTGAGGGTGCAAGAAATCAC




GGATTATTAAATGTTTCTGTGAATGATTTTTTTACTATTCTAATTAAATAT




CCAAGTTTAGAAGAACAGCAAAAAATAGGCAAGTTCTTCAGCAAACTCG




ACCGACAAATTGAATTAGAAGAACAAAAGCTTGAATTACTTCAACAACAG




AAAAAAGGCTATATGCAGAAAATCTTCTCACAGGAATTGCGATTTAAGAA




TGAGAATGGTAATGATTATCCTGATTGGGAAAGAATTAAATTTTTTGATG




TAATTGATAAAGTAATAGATTTTAGAGGGAGAACACCAAAAAAATTAAAT




ATGGAATGGTCTGACGAAGGGTATTTAGCATTATCAGCAGTCAATGTAA




AAAAAGGCTATATTGATTTTAATGTAGAGGCGAAATATGGAAATCTAGAT




TTATATACTAGATGGATGAGAGGAAATGAATTATATAAGGGGCAAGTATT




ATTTACAACTGAAGCGCCAATGGGCAATGTAGCACAGGTTCCGGATAAT




AAAGGATATATATTAAGTCAAAGAACTATCGCGTTTAATTCAAATGAAAA




AATCACTGATAACTTTTTAGCATCATTGTTGAGCTCTGAAAATGTTTATAA




TGATTTATTAAAATTGTGTAGTGGTGCTACAGCAAAAGGTGTGAGTCAA




AAAAATTTAAATCGACTATACGTTACTATTCCACATTCCATATCAGAGCA




AGAAGAGATTGCTGAATTCTTTAGAAAAATTAATCAATTGGTTGAGTTGC




AAAAATATAAAATTGAACATACTAAAAGTCAAAAACAAGTGTTTTTACAAA




AGATGTTTATTTAA


 


52
NOH4
ATGAGTAATACACAAAAGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT




TTGAAGGCGaATGGGAAGAGAAGAAGTTAGGGGATCTTACAGATAGAG




TAATTAGGaAAAATaAAAACTTAGAATCGaAAAAGCCTTTAACAATATCCG




GACAGTTAGGTTTAATTGATCAAACAGAATACTTTAGTAAATCAGTTTCG




TCGAAAAATCTAGAAAATTATACACTAATAAAGAATGGAGAATTCGCGTA




TAACAAAAGTTATTCTAATGGATACCCATTAGGGGCTATTAAAAGATTAA




CTAGATATGATAGTGGTGTATTGTCCTCTTTGTATATTTGTTTTTCTATTA




AAAGTGAAATGTCTAAAGACTTCATGGAAGCATATTTTGATTCGACACAC




TGGTATAGAGAAGTTTCTGGAATTGCAGTTGAGGGTGCAAGAAATCACG




GATTATTAAATGTTTCTGTGAATGATTTTTTTACTATTCTaATTAAATATCC




aAGTTTAGAAGAACAGCAAAAAATAGGCAAGTTCTTCAGCAAACTCGAC




CGACAAATTGAATTAGAAGAACAAAAGCTTGaATTACTTCAACAACAGAA




AAAAGGCTATATGCAGAAAATCTTCTCACAGGAATTGCGATTTAAGAAT




GAGAATGGTAATGATTATCCTGATTGGGaAAGAATTAAATTTTTTGATGT




AATTGATAAAGTAATAGATTTTAGAGGGAGAACACCAAAAAAtTAAATAT




GGAATGGTCTGACGAAGGGTATTTAGCATTATCAGCAGTCAATGTAAAA




AAAGGCTATATTGATTTTAATGTAGAGGCGAAATATGGAAATCTAGATTT




ATATACTAGATGGATGAGAGGAAATGAATTATATAAGGGGCAAGTATTA




TTTACAACTGAAGCGCCAATGGGCAATGTAGCACAGGTTCCGGATAATA




AAGGATATATATTAAGTCAAAGAACTATCGCGTTTAATTCAAATGAAAAA




ATCACTGATAACTTTTTAGCATCATTGTTGAGCTCTGAAAATGTTTATAAT




GATTTATTAAAATTGTGTAGTGGTGCTACAGCAAAAGGTGTGAGTCAAA




AAAATTTAAATCGACTATACGTTACTATTCCACATTCCATATCAGAGCAA




GAAGAGATTGCTGAATTCTTTAGAAAAATTAATCAATTGGTTGAGTTGCA




AAAATATAAAATTGAACATACTAAAAGTCAAAAACAAGTGTTTTTACAAAA




GATGTTTATTTAA


 


53
CC239 hsdS1
ATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGATTCCCAGGAT



TW20
TTGAAGGCGAATGGGAAGAGAAGAAGTTAGGGAATCTTACTACCAAAAT




AGGTAGTGGAAAGACTCCCAAAGGTGGAAGTGAAAACTATACAAACAAA




GGCATACCATTTTTAAGGAGTCAAAATATTAGAAATGGTAAATTAAATCT




TAATGACTTAGTTTATATTAGTAAAGATATAGATGATGAGATGAAAAATA




GTAGAACGTACTATGGTGATGTTCTTTTAAATATTACAGGAGCATCAATA




GGTAGAACAGCCATTAATTCGATAGTTGAAACGCATGCTAATTTAAATCA




ACATGTATGTATTATTAGATTGAAAAAAGAGTATTATTATAATTTTTTTGG




ACAGTATCTATTATCAAGAAAAGGTAAAAGGAAAATTTTCCTTGCACAAA




GTGGAGGTAGTCGAGAAGGTCTAAACTTCAAAGAAATTGCTAATTTAAA




AATCTTCACCCCAACTATATTTGAAGAACAGCAAAAAATAGGCAAGTTCT




TCAGCAAACTCGACCGACAAATTGAATTAGAAGAACAAAAACTTGAATT




GCTTCAACAACAGAAAAAAGGCTATATGCAGAAAATCTTCACACAAGAA




TTGCGATTCAAAGATGAGAATGGTGAAGAATATCCAGAGTGGGAAAACA




AATTCATAAAAGACATCTTTATCTTTGAAAATAATAGAAGAAAACCAATTA




CTTCTTCATTAAGAGAAAAGGGGTTATACCCTTACTATGGTGCAACTGG




AATTATTGATTACGTAAAAGATTATTTATTCAATAATGAAGAACGATTACT




AATAGGAGAAGATGGTGCAAAATGGGGGCAGTTTGAGACGAGTAGCTT




TATTGCTAATGGGCAATACTGGGTAAATAATCATGCGCATGTAGTTAAAA




GTAATGATCATAATTTGTTTTTTATGAATTATTATTTAAATTTTAAAGAACT




ACGAGCATTTGTCACAGGTAATGCACCAGCTAAATTAACTCATGCGAAC




TTATGCAATATAAATCTTAAAATACCTTGTCTCACTGAACAAGATAAAGT




AAGTGCATTGTTAAAATCTATAGACAATAAAATGAATAATCAAATGAATA




GAATTGAGTTATTAAAAGAACGTAAAAAAGGACTATTACAAAAAATGTTT




ATTTAA


 


54
CC239 hsdS2
ATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGATTCCCAGGAT



TW20
TTGAAGGCGAATGGGAAGAGAAGAAGTTAGGGAATCTTACTACCAAAAT




AGGTAGTGGAAAGACTCCCAAAGGTGGAAGTGAAAACTATACAAACAAA




GGCATACCATTTTTAAGGAGTCAAAATATTAGAAATGGTAAATTAAATCT




TAATGACTTAGTTTATATTAGTAAAGATATAGATGATGAGATGAAAAATA




GTAGAACGTACTATGGTGATGTTCTTTTAAATATTACAGGAGCATCAATA




GGTAGAACAGCCATTAATTCGATAGTTGAAACGCATGCTAATTTAAATCA




ACATGTATGTATTATTAGATTGAAAAAAGAGTATTATTATAATTTTTTTGG




ACAGTATCTATTATCAAGAAAAGGTAAAAGGAAAATTTTCCTTGCACAAA




GTGGAGGTAGTCGAGAAGGTCTAAACTTCAAAGAAATTGCTAATTTAAA




AATCTTCACCCCAACTATATTTGAAGAACAGCAAAAAATAGGCAAGTTCT




TCAGCAAACTCGACCGACAAATTGAATTAGAAGAACAAAAACTTGAATT




GCTTCAACAACAGAAAAAAGGCTATATGCAGAAAATCTTCACACAAGAA




TTGCGATTCAAAGATGAGAATGGTGAAGAATATCCAGAGTGGGAAAACA




AATTCATAAAAGACATCTTTATCTTTGAAAATAATAGAAGAAAACCAATTA




CTTCTTCATTAAGAGAAAAGGGGTTATACCCTTACTATGGTGCAACTGG




AATTATTGATTACGTAAAAGATTATTTATTCAATAATGAAGAACGATTACT




AATAGGAGAAGATGGTGCAAAATGGGGGCAGTTTGAGACGAGTAGCTT




TATTGCTAATGGGCAATACTGGGTAAATAATCATGCGCATGTAGTTAAAA




GTAATGATCATAATTTGTTTTTTATGAATTATTATTTAAATTTTAAAGAACT




ACGAGCATTTGTCACAGGTAATGCACCAGCTAAATTAACTCATGCGAAC




TTATGCAATATAAATCTTAAAATACCTTGTCTCACTGAACAAGATAAAGT




AAGTGCATTGTTAAAATCTATAGACAATAAAATGAATAATCAAATGAATA




GAATTGAGTTATTAAAAGAACGTAAAAAAGGACTATTACAAAAAATGTTT




ATTTAA


 


55
CC151 hsdS2
ATGAGTAATACACAAAGGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT



RF122
TTGAAGGCGAATGGGAAGAGAAGAAGTTAGGGGATCTTACTACCAAAAT




AGGTAGTGGAAAGACTCCCAAAGGTGGAAGTGAAAACTATACAAACAAT




GGCATACCATTTTTAAGGAGTCAAAATATTAGAAATGGTAAATTAAATCT




TAATGACTTAGTTTATATTAGTAAAGATATAGATGATGAGATGAAAAATA




GTAGAACGTACTATGGTGATGTTCTTTTAAATATTACAGGAGCATCAATA




GGTAAAACAGCCATTAATTCGATAGTTGAAACGCATGCTAATTTAAATCA




ACATGTATGTATTATTAGATTGAAAAAAGAGTATTATTATAATTTTTTTGG




ACAGTAACTATTATCAAGAAAAGGAAAAAGGAAAATTTTCCTTGCACAAA




GTGGAGGTAGTCGAGAAGGACTAAACTTCAAAGAAATTGCTAATTTAAA




AATCTTCACCCCAACTATATTTGAAGAACAGCAAAAAATAGGCAAGTTCT




TCAGCAAACTTGACCGACAAATTGAATTAGAAGAACAAAAACTTGAATTA




CTTCAACAACAGAAAAAAGGCTATATGCAGAAAATCTTCTCACAGGAATT




ACGATTCAAAGACGAGAATGGTGAAGAATATCCAAATTGGGAAAACAAA




TTCATAAAAGACATCTTTATATTTGAAAATAATAGAAGAAAACCAATTACT




TCTTCATTAAGAGAAAAGGGGCTATACCCTTACTATGGCGCAACTGGAA




TTATTGATTACGTGAAAGAATATTTATTCAATAATGAGGAACGATTACTA




ATAGGAGAAGATGGTGCAAAATGGGGGCAGTTTGAGACGAGTAGCTTT




ATTGCTAATGGGCAATACTGGGTAAATAATCATGCGCATGTAGTTAAAA




GTAATGATCATAATTTGTTTTTTATGAATTATTATTTAAATTTTAAAGAACT




ACGAGCATTTGTGATAGGTAATGCACCAGCTAAATTAACTCATGCGAAC




TTATGCAATATAAATCTTAAAATACCTTGTCTCACTGAACAAGATAAAGT




AAGTGCATTGTTAAAATCTATAGACAATAAAATGAATAATCAAATGAATA




GAATTGAGTTATTAAAAGAACGTAAAAAAGGACTATTACAAAAAATGTTT




ATTTAA


 


56
CC771 hsdS
atgagtaatacacaaacgaaaaatgtgccagagttgagattcccagggtttgaaggcgaatgggaaga




gaagaagttaggggatcttggcctgtttcaaaaaagttattctttttcgagagctaaagaaggaaacggtaa




aactaaacatattcattatggtgatattcattcaaaatttaaaacagtcttagatagtgatggtaatatccctaa




tataattgagaaagctgtatttgagttgattcaaaaaggagacattgtttttgcggatgcatcagaagattata




gtgacctaggaaaagcagttatgatagatttcaaaccgaattcattgatttctggcttacatacacacctattt




agaccgcttaacaatgcaatttctaattttttgattttttacacaaaaactctgagttataaaaaattcattagac




agcaaggtacaggaatatcagtacttggtatatcaaaaaaaagtttattaaatttgaatgtattaataccacg




aagtgaattagaacaacaaaaagtaggcaagttcttcagcaaactcgaccgacaaattgaattagaag




aacaaaaaatcgaattacttcaacaacagaaaaaaggctatatacagaaaatcttctcacaagaattgc




gatttaaggatgagaatggagatgattatccggagtgggaagaaactactataaaagaaattgctcaaat




taacacaggaaagaaagatacaaaagatgccattactaatgggagttatgatttttacgttagatctccgat




agtttataaaattaatacttttagttatgaaggagaggctattttaactgtaggagatggagttggcgtaggta




aagttttccactatgtaaatgggaaatttgattatcatcaaagagtatacaaaatatctgactttaagaattatt




atggattattgttattttattatttttcacaaaactttitaaaagaaacaaagaaatatagtgcgaagacatcagt




tgattcagttagaaaagacatggttgctaatatgaaagtaccacgtcctatttatatagaacaggaaaaaat




cggtcaattcattaaaaaagtagacaacaaaataaaaattcagaaacaagtgattgaattacttaaacaa




cgcaaaaaggcattacttcaaaagatgtttatttaa


 


57
CC133 hsdS1
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT




TTGAAGGCGAATGGGAAGAGAAGAAGTTAGGGGATCTTGGCCTGTTTC




AAAAAAGTTATTCTTTTTCGAGAGCTAAAGAAGGAAACGGTAAAACTAAA




CATATTCATTATGGTGATATTCATTCAAAATTTAAAACAGTCTTAGATAGT




GATGGTAATATCCCTAATATAATTGAGAAAGCTGTATTTGAGTTGATTCA




AAAAGGAGACATTGTTTTTGCGGATGCATCAGAAGATTATAGTGACCTA




GGAAAAGCAGTTATGATAGATTTCAAACCGAATTCATTGATTTCTGGCTT




ACATACACACCTATTTAGACCGCTTAACAATGCAATTTCTAATTTTTTGAT




TTTTTACACAAAAACTCTGAGTTATAAAAAATTCATTAGACAGCAAGGTA




CAGGAATATCAGTACTTGGTATATCAAAAAAAAGTTTATTAAATTTGAAT




GTATTAATACCACGAAGTGAATTAGAACAACAAAAAGTAGGCAAGTTCTT




CAGCAAACTCGACCGACAAATTGAATTAGAAGAACAAAAAATCGAATTA




CTTCAACAACAGAAAAAAGGCTATATACAGAAAATCTTCTCACAAGAATT




GCGATTTAAGGATGAGAATGGAGATGATTATCCGGAGTGGGAAGAAAC




TACTATAAAAGAAATTGCTCAAATTAACACAGGAAAGAAAGATACAAAAG




ATGCCATTACTAATGGGAGTTATGATTTTTACGTTAGATCTCCGATAGTT




TATAAAATTAATACTTTTAGTTATGAAGGAGAGGCTATTTTAACTGTAGG




AGATGGAGTTGGCGTAGGTAAAGTTTTCCACTATGTAAATGGGAAATTT




GATTATCATCAAAGAGTATACAAAATATCTGACTTTAAGAATTATTATGG




ATTATTGTTATTTTATTATTTTTCACAAAACTTTTTAAAAGAAACAAAGAAA




TATAGTGCGAAGACATCAGTTGATTCAGTTAGAAAAGACATGGTTGCTA




ATATGAAAGTACCACGTCCTATTTATATAGAACAGGAAAAAATCGGTCAA




TTCATTAAAAAAGTAGACAACAAAATAAAAATTCAGAAACAAGTGATTGA




ATTACTTAAACAACGCAAAAAGGCATTACTTCAAAAGATGTTTATTTAA


 


58
CC151 hsdS1
ATGAGTAATACACAAAAGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT



RF122
TTGAAGGCGAATGGGAAGAGAAGAAGTTAGGGGAAATTTTTCAAATAAT




TTCTGGTTCAACACCACTAAAATCAAATAAAAAGTTTTATGAAAATGGTA




ATATTAATTGGGTCAAAACGACAGATTTAAATAATTCTAAAGTTACGCAT




AGTAAAGAAAAAATAACTGAATATGCTATGAATAGTTTGAAATTAAAATTA




GTGCCTAAAAATTCAGTACTTATAGCTATGTATGGTGGTTTTAATCAAAT




TGGTCGAACAGGTTTGTTAAAAATAGATGCCACAATAAATCAAGCAATTT




CAGCCTTATTAATGAATCATGAAACGAATCCAGAATTTATACAAGCATAT




CTAAATTATCAAGTTAAGGGGTGGAAGAGATATGCAGCAAGTAGCAGAA




AAGACCCGAATATAACTAAAAAAGACATAGAACAATTTAAAGTTCCTTAT




GTTAGTATTAATGAACAGCAAAAAATAGGCGAATTCTTCAGCAAGCTTG




ACCGACAAATTGAGTTAGAAGAACAAAAACTAGAATTACTTCAACAACAA




AAAAAGGCTATATGCAGAAAATCTTCTCACAAGAATTGCGATTCAAAGAT




GAGAATGGTGAAGATTACCCGGAGTGGGAAGAGACAAAACTCCAACAA




ATTATAGGAGGTTAAAGACGGTACTCATGAAAGTCCTAAGCCCACTGAC




AATGGTTATTTATTAGTAACTTCAAAAAATTTAAAAAATAATAAATTAGAT




TTGAGTGAATCTTATAGTATTTCTAAAGAAGATTATGAAAGTATAAATAAA




AGATCTAAAGTTGAAAAAGGCGACATTTTATTTGGAATGATAGGGACAA




TAGGAAATCCTATTCTATTAGAAGACGAAGGATTCGCTATAAAAAATGTT




GCTTTGCTAAAAACGAGTTGTTTACAAGAAAAGTATTACATATTGAACTT




CCTCAAATCTATAGCTATTGCTAAACAATTTTATAAAACGAATGCTGGAG




GAACTCAAAAATTTATTTCTTTAGGAGTTATAAGAGATTTAAAAATTGATT




TTCCATCTTTAGAGGAATCGACTAAAATAGGAATTTTATTTAACAAATTA




GATGAATTGATTAAAAATCAATCAATAAAAATTGTTTTATTAAGACGGCG




AAAAAAAGCCTTACTTAAATCGATGTTTATTTAA


 


59
CC75 hsdS2
ATGAGTAATACAGGAAAAATGAACGTGCCAGAGTTGAGATTCCCAGGAT




TTGAAGGCGAATGGGAAGAGAAGGAATTAAGAGAGTTAAGAAACCCTA




AGGATAAATATAGTTATACAGGTGGGCCTTTTGGCTCTGATTTAAAAAAA




TCTGACTATACAACTGATGGGATACAAATTATTCAACTTCAAAACATTGG




AGATGGATATTTCTATAATAGTAATAAGGTCTTTACATCTAATGAGAAAG




CAGAAGTACTTAAAAGTTGTAATGTATTTCCAGGAGATATAGTTATTGCT




AAAATGGCAGATCCTATAGCAAGAGCAGCGATTGTACCGGATAATAATA




TAGGGAAATATCTAATGGCCTCAGATGGGATAAGATTAAGTGTTGACAC




AGTACATTTCAATACAAAGTTTGTACTTGAGTGTATAAATAGAAAAAGTT




TTAGAAAAAAAGTTGAGGATAATAGTTCGGGGTCAACTCGAATGAGAAT




AGGACTAAGTACATTAGGTAGTCTAACTTTAAAAACCACAACACTAAAAG




AACAACAAAAAATAGGACAATTCTTCAGCAAACTTGACCGACAAATTGTA




CTAGAAGAACAAAAACTTGAATTACTTCAACAACAGAAAAAAGGCTATAT




GCAGAAAATCTTTTCACAAGAATTGCGATTCAAAGATGAGAATGGTAAT




GATTATCCAGATTGGGAAGAGAAGCAATTAGGGGAATTATCACAAATTG




TACGAGGGGCTTCTCCTAGACCTATTAAAGATCCTAAATGGTTTAATAAA




GAATCAGATATAGGATGGCTAAGAATTTCTGATGTTACAAATCAAAACG




GGAAAATTTATCATTTGGAACAAAAATTATCAATTGAAGGTCAAGAAAAA




ACAAGGGTTTTAGTAACAACACATTTATTATTAAGTATTGCGGCAAGTAT




TGGAAAACCTGTAATGAATTTTGTGAAAACGGGAGTTCATGATGGATTTT




TAATATTTTTAAAGCCTAAGTTTAATTTATTCTTTATGTACTATTGGCTTG




AATATTTCAAGGATAAATGGAGTAAATACGGTCAACCAGGTAGTCAGGT




TAATTTAAATTCAGAAATTGTCAAATCTCAGACACTGAATATGCCAAGCA




ATCACGAACAAGAAAAAGTGGGACAGTTTTTTAATAGAAATGAAAAACTA




ATTGAATTGCAGCAAGAAAAAATAATGTATATCAAGCGATGTAAGCAGG




TTTTACTTCAAAAAATGTTTATATAA


 


60
CC152 hsdS1
ATGAGTAATACACAAAAGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT




TTGAAGGCGAATGGGAAGAGAAGAAGCTAGGGGATATTACAGATAGAT




TAATTAGGAAAAATAAAAACTTAGAATCGAAAAAGCCTTTAACAATATCC




GGACAGTTAGGTTTAATTGATCAAACAGAATATTTTAGTAAATCAGTTTC




GTCGAAAAATCTAGAAAATTATACACTAATAAAGAATGGAGAATTCGCGT




ATAACAAAAGTTATTCTAATGGATACCCATTAGGGGCTATTAAAAGATTA




ACTAGATATGATAGTGGTGTATTGTCCTCTTTGTATATTTGCTTTTCTATT




AAAAGTGAAATGTCTAAAGACTTCATGGAAGCATATTTTGATTCGACACA




CTGGTATAGAGAAGTTTCAGGAATTGCAGTTGAGGGTGCAAGAAATCAC




GGATTATTAAATATTTCTGTGAATGATTTTTTTTACTATTCTAATTAAATATC




CAAGTTTAGAAGAACAGAGAAAAATAGGTGACTTCTTCATCAAACTTGA




CCGGCAAATTGAATTAGAAGAACAAAAACTTGAATTACTTCAACAACAGA




AAAAAGGCTATATGCAGAAAATCTTCTCACAGGAACTGCGATTTAAGGA




TGAGAATGGTAATGATTATCCAGAGTGGGAAGAGAAAAAGTTAGGGGA




ACTTGGCCTATTTCAAAAAAGTTATTCTTTTTCGAGAGCTAAAGAAGGAA




ACGGTAAAACTAAGCATATTCATTATGGTGATATTCATTCAAAATTTAAAA




CAGTATTAGATAGTGACGGCAATATCCCTAATATAATTGAGGAAGCTGT




ATTTGAATTGGTTCAAAAAGGTGACATTATTTTTGCGGATGCATCAGAAG




ATTATAGTGACCTAGGAAAAGCAGTTATGATAGATTTCGAACCGAATTCA




TTGATTTCTGGATTACATACACACCTATTTAGACCGTTTAACAATGTAATT




TCTAATTTTTTGATCTTTTACACAAAAACTCTTAGTTATAAAAAATTCATTA




GACAGCAAGGTACAGGAATATCAGTACTTGGTATATCAAAAAAAAGTTT




ATTAAATTTGGATGTATTAATACCACAAAATGAATTAGAACAACAAAAAAT




CGGTCAGTTCTTTAGCAAAATCGACCGACAAATTGAATTGGAACAACAA




AAGTTAGAATTACTTCAACAACAGAAAAAATCCTTACTTCAATCGATGTT




TATTTAA


 


61
CC75 hsds2
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT




TTGAAGGCGAATGGGAAGAGAAGGAATTAGGGGAAATTTTTCAAATAAT




TTCTGGTTCAACACCACTAAAATCAAATAAAGAGTTTTATGAAAATGGTA




ATATTAATTGGGTCAAAACGACAGATTTAAATAATTCTAAAGTTACGCAT




AGTAAAGAAAAAATAACTGAATATGCTATGAAAAGTTTGAAATTAAAATT




AGTGCCTAAAAATTCAGTACTTATAGCTATGTATGGTGGTTTTAATCAAA




TTGGTAGAACAGGTTTGTTAAAAATAGATGCCACAATAAATCAAGCAATT




TCAGCCTTATTAATGAATCATGAAACGAATCCAGAATTTATACAAGCATT




TCTAAATTATCAAGTTAAGGGTTGGAAGCGATATGCAGCAAGTAGCAGA




AAAGACCCGAATATAACTAAAAAAGACATAGAACAATTTAAAGTTCCTTA




TGTTAGTATTAATGAACAGCAAAAAATAGGCGAATTCTTCAGTAAAATTG




ACCACCAAATCGAGTTAGAAGAACAAAAACTTGAATTACTTCAACAACA




GAAGAAAGGCTATATGCAGAAAATCTTCTCGCAGGAATTGCGATTCAAA




GATGAGAATGGTGAAGATTATCCGGATTGGGAAGTTACTACTATACAAA




ATATTACAAAATATACCAGTTCGAAGAAGTCTTCTAATCAATATGCTGAC




AAGGATAATTCTAAAGGTTATCCAGTTTATGATGCCGTTCAAGAGATTG




GTAAAGATTCAAATTATGATATAGAAGAATCGTATATTTCTATTTTGAAG




GATGGAGCAGGAGTTGGTCGATTAAATTTAAGGCCAGGAAAATCATCC




GTAATTGGAACTATGGGCTACATACAGTCAAATAATGTAGATATTGAATT




CCTTTATTATCGAATGAAAGTAGTAGATTTTAAAAAGTATATAATTGGAA




GTACTATACCGCATTTGTACTTCAAAGACTATTCTAAAGAAACTTTATATA




TACCTTCAAGCATTCAAGAACAAGCAAAGATTGGTATGTTTATTTCAAAT




TTGGATAAGTTGATTGAAAATAAAAACCTTAAATTAAACTGTTTAAAACAA




TTAAAACAAGGATTGCTACAATCTATGTTTATTTAA


 


62
CC7 hsdS1
ATGAGTAATACACAAAAGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT



TCH959
TTGAAGGCGAATGGGAAGAGAAGCAGTTGGGGGAAGTAGGTACATTTA



(USA300)
CTTCAGGTGGGACACCCCTGAAATCAAAATCAGAGTATTGGAATGGAGA




TATTCCATGGATTACAACAGGTGATATTCATAACATAAAAAGAGAAAATA




TAACTAATTTTATAACAGAGAAGGGTTTAAATGAATCATCGGCAAAATTA




ATAACTAATGAGGCGATTTTAATAGCTATGTATGGTCAAGGTAAAACTAG




AGGAATGTCAGCAATATTGAATTTTGAGGCAACAACTAACCAAGCATGT




GCTATATATCAAACTAATCAAAATATTAATTTTGTTTTTCAATACTTTCAG




AAATTATATAAATTTTTACGCTCATTATCTAATGAGGGAAGTCAAAAGAA




TTTAAGTTTAAGTTTGTTGAAAGAAATTACTTTAAATTATCCTAATGAACA




AGAACAGAAAAAAATAGGTGTCTTCTTCAGCAAACTTGACCGACAAATT




GAATTAGAAGAACAAAAACTCGAATTACTTCAACAACAGAAAAAAGGCT




ATATGCAGAAAATTTTCTCACAGGAACTGCGATTCAAAGATGAGAATGG




TGAAGATTATCCAGATTGGAAAGAGAAGAAGTTAGGGGATATTACAGAA




CAATCTATGTATGGTATAGGTGCATCTGCAACAAGGTTTGATTCGAAAA




ATATATATATAAGAATTACTGATATTGATGAAAAATCAAGGAAATTAAATT




ATCAAAACTTAACTACACCTGATGAAGTTAATAATAAGTACAAGCTGAAA




AGAAATGATATTCTTTTTGCACGAACTGGTGCTAGCACGGGCAAAAGTT




ATATTCACAAAGAAGAAAAGGATATTTATAATTACTATTTCGCTGGATTTT




TAATAAAATTTGAAATAAACGAACAAAATAGTCCTTTGTTCATTTACCAAT




TTACACTAACATCAAAATTTAACAAATGGGTGAAGGTCATGTCTGTAAGA




TCTGGTCAACCGGGTATTAATAGTGAAGAATATGCAAAATTACCTTTAGT




TTTGCCCAATAAGTTAGAACAGCAAAAAATAGCAGAATTCTTAGATAGAT




TTGACCAACAAATTGAATTAGAAAAACAAAAAATAGAAATACTTCAACAA




CAGAAAAAAGGCTTACTTCAATCGATGTTTATTTAA


 


63
CC42 hsdS1
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT



C427
TTGAAGGCGAATGGGAAGAGAAGAAGGTTGGCGAGTTATTAGAATTTAA




AAATGG1TTAAATAAAGGAAAAGAATATTTTGGCTCAGGATCGTCGATTG




TTAACTTCAAAGATGTATTTAATAACAGGAGCTTAAATACAAATAATCTG




ACTGGAAAAGTTAATGTGAATAGCAAAGAACTAAAAAATTATTCTGTTGA




AAAGGGTGATGTTTTTTTTACAAGGACTAGTGAGGTAATTGGTGAAATA




GGTTATCCGTCTGTAATTTTAAATGACCCTGAAAATACTGTGTTTAGTGG




ATTTGTATTAAGAGGGCGGCCTAAATCAGGAATTGATTTAATAAATAATA




ATTTTAAAAGATATGTCTTTTTTACTAATTCATTTAGAAAAGAAATGATTA




CAAAAAGTTCTATGACAACTAGAGCTTTAACATCAGGTAGCGCAATTAAT




AAAATGAAGGTCATATACCCTGTTTCGGCTAAAGAACAGAGAAAAATAG




GTGACTTCTTCAGCAAACTCGACCGACAAATTGAATTAGAAGAACAAAA




GCTTGAATTACTTCAACAACAAAAAAAAGGCTATATGCAGAAAATCTTCT




CACAGGAACTGCGATTCAAAGATGAGAATAGTGAAGATTATCCACATTG




GGAAAATAGCAAAATAGAAAAATATTTAAAAGAGAGAAACGAACGTTCT




GACAAAGGTCAAATGCTTTCAGTAACTATAAATAGTGGCATTATAAAATT




TAGTGAATTGGATAGAAAAGATAATTCAAGTAAAGATAAAAGTAATTATA




AAGTAGTTAGGAAAAATGATATTGCATATAATTCTATGAGAATGTGGCAA




GGGGCTAGTGGTAGATCAAATTATAATGGGATTGTTAGCCCTGCATATA




CTGTGCTTTATCCAACACAAAATACTAGCTCATTATTTATTGGATATAAG




TTTAAAACACATAGAATGATTCATAAATTTAAAATTAATTCACAAGGATTA




ACATCAGATACATGGAACTTAAAATATAAACAATTAAAAAATATAAATATA




GATATACCTGTATTGGAGGAACAAGAAAAGATAGGTGATTTCTTTAAAAA




AATGGATATATTGATTAGTAAACAGAAAATAAAAATTGAAATATTAGAAAA




AGAGAAACAATCCTTTTTACAAAAGATGTTCTTATAA


 


64
CC42 hsdS2
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT



C427
TTGAAGGCGAATGGGAAGAGAAAAAGTTAGGGGATCTTATAAAAGTTAA




TTCTGGAAAAGATTATAAACATTTGGAAAAAGGTGATATACCAGTCTATG




GTACTGGCGGTTATATGACAAGTGTTTCAGAACCACTAAGTGAAATTGA




TGCTGTTGGTATTGGGAGAAAAGGGACTATAAACAAACCATATTTGCTT




GAGGCGCCGTTTTGGACGGTGGATACATTATTTTATTGTACACCTAAAA




AAGAAACAGACATACTATTTATATTAAGTTTATTTAGAAAAATAAATTGGA




AAGTATACGATGAATCAACAGGTGTGCCAAGCTTAAGTAAACAAACCAT




TAATAAAATAAATAGATTTGTCCCTTCAAATAAAGAGCAGCAAAAAATAG




GCGAATTCTTCATCAAACTCGACCGACAAATTGAATTAGAAGAACAAAA




ACTTGAATTACTTCAACAACAGAAAAAAGGCTATATGCAGAAAATCTTCT




CACAGGAATTGCGATTCAAGGATGAGAATGGAAACGATTATCCGAATTG




GGAAGAGAAGAAAATAGAAGATATAGCAAGCCAAGTATATGGAGGCGG




AACACCAAATACAAAGATTAAAGAATTTTGGAATGGAGATATTCCATGGA




TTCAAAGCTCTGACGTAAAAGTAAATGATTTGATTCTACGACAATGTAAT




AAATTTATTTCCAAGAATTCAATTGAGCTTTCTTCTGCAAAACTTATTCCT




GCCAATTCAATTGCAATAGTTACAAGAGTCGGGGTTGGAAAACTGTGTT




TGGTAGAATTTGATTATGCTACAAGTCAAGATTTTTTATCATTAAGTAGT




CTTAAATATGACAAATTATACTCATTATATTCATTGCTATATACAATGAAA




AAAATTAGCGCTAATCTACAAGGAACTTCAATTAAAGGTATAACAAAAAA




AGAGTTGTTAGATAGTATAATAAAGATACCCCATAATCTAGAAGAACAGC




AAAAAATAGGTGATCTATTTTATAAAATTGATAAATATATCAGTTTTAATA




AATGTAAAATTGAGATACTTAAAAGTCTCAAACAAGGATTACTTCAAAAA




ATTTTTATATAA


 


65
CC133 hsdS2
ATGAGTAATACACAAAAGAAAAATGTGCCAGAATTGAGGTTCCCAGGGT




TTGAAGGCGAATGGGAAGAAAAGAAGCTAGAAAGTATTATAAAAGTTAA




TTCTGGAAAAGATTATAAACATTTGGATAAAGGCGATATACCAGTCTATG




GTACTGGCGGTTATATGACAAGTGTTTCAGAACCACTAAGTGAAATTGA




TGCTGTTGGTATTGGGAGAAAAGGGACTATAAACAAACCATATTTGCTT




GAGGCGCCGTTTTGGACGGTGGATACATTATTTTATTGTACACCTAAAA




AAGAAACAGACATACTATTTATATTAAGTTTATTTAGAAAAATAAATTGGA




AAGTATACGATGAATCAACAGGTGTGCCAAGCTTAAGTAAACAAACCAT




TAATAAAATAAATAGATTTGTCCCTACAAATAAAGAGCAGCAAAAAATAG




GCAAGTTCTTCAGCAAACTTGACCGACAAATTGAACTACAAGAACAAAA




ACTTGAATTACTTCAACAACAGAAAAAAGGCTATATGCAGAAAATTTTCT




CACAGGAATTGCGATTCAAGGATGAGAATGGTAATGATTATCCGGAGTG




GGAAAATGTAATGCTTCAAAAAGTTTTGAAAGACAAAACTGAAGGTATAA




AGAGAGGACCTTTTGGAGGAGCATTAAAGAAAGATATATTTGTAGAAAG




CGGTTATGCAGTTTATGAACAAAGGAATGCAATTTATGATATAAGTAACT




TTAGATATTATATAAACGAAAATAAATATAAAGAAATGCAATCATTTTCGG




TTCAACCAAATGATATAATAATGAGTTGCTCAGGTACTATTGGAAGATTA




GCACTCATTCCTCATAATTATACAAAGGGAATTATAAACCAAGCGCTTAT




TAGATTTAGAACTAACCATAAAATTAGAAGTGAATTCTTTTTGATATTTAT




GAGGAGCAATCAAATGCAAAGAAAAATCCTAGAGGCAAATCCTGGGTC




GGCAATAACCAATTTAGTGCCTGTAAAAGAATTGAAATTAATCCCATTTC




CATTACCTGTAAAGTTTGAACAGGATAAAATTAGTCAATTTATACATATTA




TAAATCGACGTATTGAACAATCTGAAAAAAAGATTGAAAGTCTAAAAAAT




CGTAAACAAGGATTTCTTCAAAAGTTATTTGTTTAA


 


66
CC10 hsdS1
ATGAGTAATACACAAAAGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT




TTGAAGGCGAATGGGAAGAAAAGAAGCTAGAAAGTATTATAAAAGTTAA




TTCTGGAAAAGATTATAAACATTTGGATAAAGGCGATATACCAGTCTATG




GTACTGGCGGTTATATGACAAGTGTTTCAGAACCACTAAGTGAAATTGA




TGCTGTTGGTATTGGGAGAAAAGGGACTATAAACAAACCATATTTGCTT




GAGGCGCCGTTTTGGACGGTGGATACATTATTTTATTGTACACCTAAAA




AAGAAACAGACATACTATTTATATTAAGTTTATTTAGAAAAATAAATTGGA




AAGTATACGATGAATCAACAGGTGTGCCAAGCTTAAGTAAACAAACCAT




TAATAAAATAAATAGATTTGTCCCTACAAATAAAGAGCAGCAAAAAATAG




GCAAGTTCTTCAGCAAACTTGACCGACAAATTGAATTAGAAGAACAAAA




ACTTGAATTACTTCAACAACAGAAAAAAGGCTATATGCAGAAAATCTTCT




CGCAAGAATTGCGATTCAAAGATGAGAATGGTAATGATTATCCAGAGTG




GGAAAATGTAATGCTTCAAAAAGTTTTGAAAGACAAAACTGAAGGTATAA




AGAGAGGACCTTTTGGAGGAGCATTAAAGAAAGATATATTTGTAGAAAG




CGGTTATGCAGTTTATGAACAAAGGAATGCAATTTATGATATAAGTAACT




TTAGATATTATATAAACGAAAATAAATATAAAGAAATGCAATCATTTTCGG




TTCAACCAAATGATATAATAATGAGTTGCTCAGGTACTATTGGAAGATTA




GCACTCATTCCTCAGAATTATACAAAGGGAATTATAAACCAAGCGCTTAT




TAGATTTAGAACTAACCATAAAATTAGAAGTGAATTCTTTTTGATATTTAT




GAGGAGCAATCAAATGCAAAGAAAAATTCTAGAGGCAAATCCTGGGTC




GGCAATAACCAATTTAGTGCCTGTAAAAGAATTGAAATTAATCCCATTTC




CATTACCTGTAAAGTTTGAACAGGATAAAATTAGTCAATTTATACTTATTA




TAAATCGACGTATTGAATAA


 


67
CC10hsdS2 D139
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGAT




TTGAAGGCGAATATTCTTTAGACATTTTTGGAAATCTAGCAACGAATAAG




AGTGATAAATTTAACCCTCAAAATGAGGATGCAAGTATTGATATAGAATT




GGATTGTATTGAACAAAATACGGGTCGATTAATTAAAATTTATAATTCAA




AAGAATTTTCAAGTCAAAAAAATAAATTCAATCCACAAAATGTTTTGTATG




GGAAGCTCAGACCATATTTGAATAAGTATTATTTTACAAAAAAAAGTGGA




GTGTGTTCATCAGAAATATGGGTTTTGAAATCAACGAAAGAAGATAAATT




ATTGAATTTATTTCTATATTATTTTATACAAACAAAACGATATTCTGATGTT




GCTAGTAAATCGGCTGGTTCTAAGATGCCAAGGGCTGATTGGGGTTTA




GTAGAAAATATAAGAGTATATTTTCCAGAATTATGTGAACAGCAAAAAAT




AGGCGAATTCTTCAGCAAACTCGACCGACAAATTGAACTAGAAGAACAA




AAACTTGAGTTACTTCAACAACAGAAAAAAGGCTATATGCAGAAAATCTT




CTCACAGGAATTGCGATTTAAGGATGAGAATGGTAATGATTATCCTGAG




TGGGAGAAAAAGAAACTAAAAGAAATAGCTTATGTTTATACAGGAAACA




CGCCAAGTAAAAAAGAAAATATATATTGGATTAAAGGTGAATACGTTTGG




GTTACACCTACTGATATTAATAATAGTAAAAATATTTATGAAAGTGAACAT




AAATTAACCCAAGAAGGTTATAAAAAAGCAAGACAATTACCAGAAAATAC




ACTATTGGTTACGTGTATAGCTAGTATAGGAAAAAACGCAATATTGAGAA




AACAGGGCTCGTGTAATCAACAAATAAATGCAGTAGTCCCATTTGAAAA




TATAAATATAGATTATCTTTATTATATTTCTGATTCATTATCAACGTTCATG




AAGTCTATTGCAGGAAAAACGGCTACACAAATAGTTAATAAAAACACTTT




CGAAAATTTGGAACTTTATTTAGCTTCTTTTGAAGAACAGAATAAAATAG




CAGATTTAATTAGCTCACTAGAAGAATTAATTGAAAAGCAAGCATCGAAG




TTAATTAAAATGAAGAGTCGTAAACAAGGATTGCTTCAAAAAATGTTTAT




TTAA>H19_hsdS1ATGAGTAATACACAAAAGAAAAATGTGCCAGAGTTGA




GATTCCCAGGGTTTGAAGGCGAATGGGAAGAAAAGAAGCTAGAAAGTA




TTATAAAAGTTAATTCTGGAAAAGATTATAAACATTTGGATAAAGGCGAT




ATACCAGTCTATGGTACTGGCGGTTATATGACAAGTGTTTCAGAACCAC




TAAGTGAAATTGATGCTGTTGGTATTGGGAGAAAAGGGACTATAAACAA




ACCATATTTGCTTGAGGAGCCGTTTTGGACGGTGGATACATTATTTTATT




GTACACCTAAAAAAGAAACAGACATACTATTTATATTAAGTTTATTTAGAA




AAATAAATTGGAAAGTATACGATGAATCAACAGGTGTGCCAAGCTTAAG




TAAACAAACCATTAATAAAATAAATAGATTTGTCCCTACAAATAAAGAGC




AGCAAAAAATAGGCAAGTTCTTCAGCAAACTTGACCGACAAATTGAATT




AGAAGAACAAAAACTTGAATTACTTCAACAACAGAAAAAAGGCTATATGC




AGAAAATCTTCTCGCAAGAATTGCGATTCAAAGATGAGAATGGTAATGA




TTATCCAGAGTGGGAAAATGTAATGCTTCAAAAAGTTTTGAAAGACAAAA




CTGAAGGTATAAAGAGAGGACCTTTTGGAGGAGCATTAAAGAAAGATAT




ATTTGTAGAAAGCGGTTATGCAGTTTATGAACAAAGGAATGCAATTTATG




ATATAAGTAACTTTAGATATTATATAAACGAAAATAAATATAAAGAAATGC




AATCATTTTCGGTTCAACCAAATGATATAATAATGAGTTGCTCAGGTACT




ATTGGAAGATTAGCACTCATTCCTCAGAATTATACAAAGGGAATTATAAA




CCAAGCGCTTATTAGATTTAGAACTAACCATAAAATTAGAAGTGAATTCT




TTTTGATATTTATGAGGAGCAATCAAATGCAAAGAAAAATTCTAGAGGCA




AATCCTGGGTCGGCAATAACCAATTTAGTGCCTGTAAAAGAATTGAAAT




TAATCCCATTTCCATTACCTGTAAAGTTTGAACAGGATAAAATTAGTCAA




TTTATACTTATTATAAATCGACGTATTGAACAATCTGAAAAAAAGATTGAA




AGTCTAAAAAATCGTAAACAAGGATTTCTTCAAAAGTTATTTGTTTAA


 


68
H19 hsdS2
ATGAGTAATACACAAACGAAAAATGTGCCAGAGTTGAGATTCCCAGGAT




TTGAAGGCGAATATTCTTTAGACATTTTTGGAAATCTAGCAACGAATAAG




AGTGATAAATTTAACCCTCAAAATGAGGATGCAAGTATTGATATAGAATT




GGATTGTATTGAACAAAATACGGGTCGATTAATTAAAATTTATAATTCAA




AAGAATTTTCAAGTCAAAAAAATAAATTCAATCCACAAAATGTTTTGTATG




GGAAGCTCAGACCATATTTGAATAAGTATTATTTTACAAAAAAAAGTGGA




GTGTGTTCATCAGAAATATGGGTTTTGAAATCAACGAAAGAAGATAAATT




ATTGAATTTATTTCTATATTATTTTATACAAACAAAACGATATTCTGATGTT




GCTAGTAAATCGGCTGGTTCTAAGATGCCAAGGGCTGATTGGGGTTTA




GTAGAAAATATAAGAGTATATTTTCCAGAATTATGTGAACAGCAAAAAAT




AGGCGAATTCTTCAGCAAACTCGACCGACAAATTGAACTAGAAGAACAA




AAACTTGAGTTACTTCAACAACAGAAAAAAGGCTATATGCAGAAAATCTT




CTCACAGGAATTGCGATTTAAGGATGAGAATGGTAATGATTATCCTGAG




TGGGAGAAAAAGAAACTAAAAGAAATAGCTTATGTTTATACAGGAAACA




CGCCAAGTAAAAAAGAAAATATATATTGGATTAAAGGTGAATACGTTTGG




GTTACACCTACTGATATTAATAATAGTAAAAATATTTATGAAAGTGAACAT




AAATTAACCCAAGAAGGTTATAAAAAAGCAAGACAATTACCAGAAAATAC




ACTATTGGTTACGTGTATAGCTAGTATAGGAAAAAACGCAATATTGAGAA




AACAGGGCTCGTGTAATCAACAAATAAATGCAGTAGTCCCATTTGAAAA




TATAAATATAGATTATCTTTATTATATTTCTGATTCATTATCAACGTTCATG




AAGTCTATTGCAGGAAAAACGGCTACACAAATAGTTAATAAAAACACTTT




CGAAAATTTGGAACTTTATTTAGCTTCTTTTGAAGAACAGAATAAAATAG




CAGATTTAATTAGCTCACTAGAAGAATTAATTGAAAAGCAAGCATCGAAG




TTAATTAAAATGAAGAGTCGTAAACAAGGATTGCTTCAAAAAATGTTTAT




TTAA


 


69
IS256
ATGAGTAATACACATATGAAAAATGTGCCAGAGTTGAGATTCCCAGAAT




TTGAAGGCGAGTGGGAAGAGAAGCAATTTGCTGATTTTACTAAAATAAA




TCAAGGATTACAGATTGCTATTAATGAACGTAAAACTGAATATTCTCCAG




AGTTGTATTTTTATATAACAAATGAATTTTTAAGACCAAATAGTCAAACTA




AATATTTTATCGAAAATCCCCCTCAATCAGTAATTGCAAATAAAGAAGAT




ATTTTAATGACTAGAACAGGTAATACTGGAAAAGTAGTAACTAATGTATT




TGGAGCGTTTCATAATAATTTTTTTAAAATTAAATTTGATAAAAATCTGTA




TGATAGATTGTTTTTAGTAGAGGTTTTAAATTCATCTAAGATACAAAATAA




AATATTATCTTTAGCAGGATCTTCGACGATACCAGATTTAAACCATAGTG




ATTTTTATAGTATTAGTTCTTCTTATCCGCTGCTTAGAGAACAGCAAAAA




ATAGGTGATTTTTTCAGCAAAATCGATCGACAAATTGAACTACAAGAACA




AAAACTTGAATTACTTCAACAACAGAAAAAAGGCTATATGCAGAAAATTT




TCTCACAGGAACTGCGATTCAAAGATGAGAATGGTGAAGATTATCCAGA




TTGGAAAGAGAAGAAGTTAGGGGATATTACAGAACAATCTATGTATGGT




ATAGGTGCATCTGCAACAAGGTTTGATTCGAAAAATATATATATAAGAAT




TACTGATATTGATGAAAAATCAAGGAAATTAAATTATCAAAACTTAACTAC




ACCTGATGAACTTAATAATAAGTACAAGCTGAAAAGAAATGATATTCTTT




TTGCACGAACTGGTGCTAGCACGGGAAAAAGTTATATTCACAAAGAAGA




AAAGGATATTTATAATTACTATTTCGCTGGATTTTTAATAAAATTTGAAAT




AGACGAACAAAATAATCCTTTGTTCATTTACCAATTTACACTAACATCAA




AATTTAACAAATGGGTGAAGGTCATGTCTGTAAGATCTGGTCAACCGGG




CATTAATAGTGAAGAATATGCAAAATTACCTTTAGTTTTGCCCAATAAATT




AGAACAGCAAAAAATAGCAAAATTCTTAGATAGATTTGACCGACAAATTG




AATTAGAAAAACAAAAAATAGAAATACTTCAACAACAGAAAAAAGGCTTA




CTTCAATCGATGTTTATTTAA


 


70
CC80 hsdS
ATGAGTAATACACAAANGAAAAATGTGCCAGAGTTGAGATTCCCAGGGT



HT2005-175
TTGAAGGCGAATGGGAAGAGAAGCAATTTGCTGATTTTACTAAAATAAA




TCAAGGATTACAGATTGCTATTAATGAACGTAAAACTGAATATTCTCCAG




AGTTGTATTTTTATATAACAAACGAATTTTTAAGACCAAATAGTCAAACTA




AATATTTTATCGAAAATCCCCCTCAATCAGTAATTGCAAATAAAGAAGAT




ATTTTAATGACTAGAACAGGTAATACTGGAAAAGTAGTAACTAATGTATT




TGGAGCGTTTCATAATAATTTTTTTAAAATTAAATTTGATAAAAATCTGTA




TGATAGATTGTTTTTAGTAGAGGTTTTAAATTCATCTAAGATACAAAATAA




AATACTATCTTTAGCAGGATCTTCGACGATACCAGATTTAAACCATAGTG




ATTTTTATAGTATTAGTTCTTCTTATCCGCTGCTTAGAGAACAGCAAAAA




ATAGGTAAATTCTTCAGCAAACTCGACCGACAAATTGAATTAGAAGAAC




AAAAGCTTGAATTACTTCAACAACAGAAAAAAGGCTATATGCAGAAAATC




TTCTCACAGGAATTGCGATTTAAGGACGAGAATGGAAATGATTATCCGG




ATTGGGAGAAAAAGAAACTAAAAGAAATAGCTTGTGTTTATACAGGAAA




CACGCCAAGTAAAAAAGAAAATATATATTGGAATAAGGGTGAATACGTTT




GGGTTACACCTACTGACATTAATAATAGTAAAAATATTTATGAAAGTGAA




AACAAATTAACCCAAGAAGGCTATAAAAAAGCAAGACAATTACCAGAAA




ATACACTATTGGTTACGTGTATAGCTAGTATAGGAAAAAACGCAATATTG




AGAAAACAGGGCTCGTGTAATCAACAAATAAATGCAGTAGTTCCATTTG




AAAATATAAATATAGATTATCTTTATTATATTTCTGATTCATTATCAACGTT




CATGAAATCTATTGCAGGAAAAACGGCTACACAAATAGTTAATAAAAACA




CTTTCGAAAATTTGGAAATTTATTTAGCTCCTTTTGAAGAACAGAATAAA




ATAGCAGATTTAATTAGCTCACTAGAAGAATTAATTGAAAAGCAAGCATC




GAAGTTAATTAAAATGAAGAGTCGTAAACAAGGAATGCTTCAAATAATGT




TTATTTAA


 


71
CC59 hsdS
ATGAGTAATACACAAAAGAAAAATGTGCCAGAGTTGAGGTTCCCAGAGT



HT2001-751
TTGAAGGCGAGTGGGAAGAAAGGAAGTTAGGGGATCTTATAAAAGTTAA




TTCTGGAAAAGATTATAAACATTTGGATAAAGGCGATATACCAGTCTATG




GTACTGGCGGTTATATGACAAGTGTTTCAGAACCACTAAGTGAAATTGA




TGCTGTTGGTATTGGGAGAAAAGGGACTATAAACAAACCATATTTGCTT




GAGGCGCCGTTTTGGACGGTGGATACATTGTTTTATTGTACACCTGAAA




AAGAAGCAGACATACTATTTATATTAAGTTTATTTAGAAAAATAAATTGGA




AATTATACGATGAATCAACAGGTGTGCCAAGCTTAAGCAAGCAAACCAT




TAATAAAATAAATAGACTTGTCCCTACAAATAAAGAACAACAAAAAATAG




GCGAGTTCTTCAGCAAACTCGACCGACAAATTGAATTAGAAGAACAAAA




ACTTGAATTACTTCAACAACAGAAAAAAGGCTATATGCAGAAAATTTTCT




CACAGGAACTGCGATTCAAAGATGAGAATGGTGAAGATTATTCGGAGTG




GGAAGAGAGAAGATTTGCTGATATATTTAAATTTCATAATAAACTAAGAA




AGCCAATTAAAGAAAATTTAAGAGTAAAGGGTTCTTATCCATATTATGGT




GCTACAGGTATTATTGATTACGTTGACGACTTTATATTTGACGGGAATTA




TTTACTTATTGGAGAAGATGGTGCAAATATTATTACTAGAAGTGCACCCC




TAGTGTACTTAGTAAATGGAAAGTTTTGGGTAAATAATCATGCTCATATA




TTATCTCCTTTAAATGGAAATATACAGTACTTGTATCAAGTTGCAGAATT




AGTTAATTATGAAAAATACAATACTGGAACTGCTCAGCCTAAATTAAACA




TTCAAAATTTAAAAATTATTAATGTTGTAATTTCAACGAATTTAGAAGAAC




AACAAAAAATCGGAAGCTTTTTAAGTAAACTTGATCGTCAAATCGATTTA




GAAGAACAAAAACTCGAATTACTTCAACAACGAAAAAAAGCCTTACTTAA




ATCGATGTTTGTTTAA









Antibiotic Resistance

As mentioned herein above particular embodiments of the invention relates to the any of the methods described herein further comprising amplification primers and/or probes which are specific and sensitive for determining the presence of nucleic acid(s) from a bacterial antibiotic resistance gene selected from the group consisting of mecA and vanA in any sample suspected of containing said S. aureus nucleic acid(s) thereby determining MRSA, wherein each of said nucleic acid(s) or variant(s) or part(s) thereof comprises a selected target region hybridizable with said primers or probes; said method comprising the following steps: contacting said sample with said probes or primers and detecting the presence of amplified products or hybridized probes as an indication of the presence said specific S. aureus antibiotic resistance genes and thus MRSA.
In a particular embodiment the method above is a multiplex PCR as described herein above.
Thus, another embodiment of the invention relates to the any of the methods described herein further comprising the evaluation of MRSA mediated by a bacterial antibiotic resistance gene selected from the group consisting of mecA and vanA directly from a test sample or a S. aureus, which comprises the following steps: a) treating said sample with an aqueous solution containing at least one pair of, one of said primers being capable of hybridizing selectively with one of the two complementary strands of said bacterial antibiotic resistance gene that contains a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template, said at least one pair of primers being chosen from a nucleotide sequence within the group consisting of SEQ ID NOS: 7 and 8, respectively with regard to said bacterial antibiotic resistance gene, a sequence complementary thereof, and a variant thereof; b) synthesizing an extension product of each of said primers, said extension product containing the target sequence, and amplifying said target sequence, if any, to a detectable level; and c) detecting the presence and/or amount of said amplified target sequence as an indication of a bacterial resistance mediated by one of said bacterial antibiotic resistance genes.
In a particular embodiment the method of the invention is a microarray method as described herein above.
Thus one embodiment of the invention relates to the any of the methods described herein further comprising the evaluation of MRSA mediated by a bacterial antibiotic resistance gene selected from the group consisting of mecA and vanA, directly from a test sample or a bacterial culture, which comprises the following steps: a) depositing and fixing on an solid support or leaving in solution the S. aureus nucleic acid(s) of the sample or of a substantially homogeneous population of S. aureus isolated from this sample, or inoculating said sample or said substantially homogeneous population of S. aureus isolated from this sample on an solid support, and lysing in situ said inoculated sample or isolated bacteria to release the S. aureus nucleic acid(s), said S. aureus nucleic acid(s) being made in a substantially single-stranded form; b) contacting said single-stranded nucleic acid(s) with a probe, said probe comprising at least one single-stranded nucleotide sequence complementary to sau1hsdS1 of CC398 or sau1hsdS2 of CC398 and a variant thereof, more specifically at least one single-stranded nucleotide sequence complementary to the nucleotide sequence defined in: SEQ ID NO: 1, which specifically hybridizes with said bacterial antibiotic resistance gene, respectively; and c) detecting the presence of a hybridization complex as an indication of a bacterial resistance mediated by said one of said bacterial antibiotic resistance genes.
In specific embodiment the antibiotic resistance gene is mecA.
Preferably the methods may be used for the distinction between MRSA and MSSA strains of S. aureus. 
Thus methods may be used for the simultaneous detection of a bacterial antibiotic resistance gene and nucleic acid(s) of a clone-specific hsdS gene, preferably CC398.
In one embodiment where the methods further comprises the detection of a bacterial antibiotic resistance gene and/or evaluation of MRSA there is provided that the clonal complex is complex is not CC1, CC5, CC8, CC22, CC30 or CC45. In some embodiments it is further provided that said clonal complex may not be any one or more of: CC12, CC15, CC25, CC51, CC151, CC97, CC771, CC130, CC188, and/or CC873
Device
A further aspect of the present invention relates to a device for the detection of the presence of S. aureus nucleic acid(s), preferably for the detection, identification and/or typing of any S. aureus clonal complex, wherein the device comprises means for measuring the presence of clone-specific hsdS nucleic acid(s). and optionally for the presence of antibiotic resistance nucleic acid(s), preferably mecA nucleic acid(s), wherein the device comprises means for measuring the presence of S. aureus clone-specific hsdS nucleic acid(s). nucleic acid(s). The means for measuring the presence of S. aureus nucleic acid(s) in a sample may for example be a test system that applies any of the above mentioned systems, such as a PCR based assay or a microarray.
A device according to the present invention may for example comprise a rapid, qualitative and/or quantitative test system mounted on a solid support for the determination of S. aureus nucleic acid(s), preferably clone-specific nucleic acid(s) from the hsdS gene and optionally for the presence of antibiotic resistance nucleic acid(s), preferably mecA nucleic acid(s), in biological samples.
A solid support according to the present invention may comprise a material having a rigid or semi-rigid surface. Such materials will preferably take the form of plates or slides, small beads, pellets, disks, capillary tubes or other convenient forms, although other forms may be used. In some embodiments, at least one surface of the solid support will be substantially flat. In other embodiments, a roughly spherical shape is preferred. The solid support may be biological, non-biological, organic, inorganic, or a combination of any of these, existing as particles, strands, precipitates, gels, sheets, tubing, spheres, containers, capillaries, pads, slices, films, plates, slides, etc. The solid support is preferably flat but may take on alternative surface configurations. For example, the solid support may contain raised or depressed regions on which reactions including, but not limited to, hybridization, ligation, and cleavage takes place. In some embodiments, the solid support will be chosen to provide appropriate light-absorbing characteristics. For example, the support may be a polymerized Langmuir Blodgett film, functionalized glass, Si, Ge, GaAs, GaP, SiO2, SiN4, modified silicon, or any one of a variety of gels or polymers such as (poly)tetrafluoroethylene, (poly)vinyliden-difluoride, polystyrene, polycarbonate, or combinations thereof. Other suitable solid support materials will be readily apparent to those of skill in the art. Preferably, the surface of the solid support will contain reactive groups, which could be carboxyl, amino, hydroxyl, thiol, or the like. More preferably, the surface will be optically transparent and will have surface Si—H functionalities, such as are found on silica surfaces. The solid support is preferably contacted by an array of ordered sets of molecules comprising or essentially consisting of dsDNA and/or ssDNA fragments that are preferably covalently attached to the solid support. In this way the DNA fragments are identified by their two dimensional position in the array.
The solid support can be used in any phase in performing any of the above assays, including dipsticks, membranes, absorptive pads, beads, microtiter wells, test tubes, and the like. Preferred are test devices which may be conveniently used by the testing personnel or the patient for self-testing, having minimal or no previous training. Such preferred test devices include dipsticks and membrane assay systems. The preparation and use of such conventional test systems is well described in the patent, medical, and scientific literature.
A particular aspect of the invention regards a solid support coated with a set of probes for identification, detection and/or typing of any S. aureus clonal complex from an extract of its genomic DNA, each probe being able to specifically hybridize with a relevant gene or with a representative fragment thereof susceptible to be present in said genomic DNA to be tested, characterized in that said relevant genes whose presence or absence is to be determined using the set of probes comprise the following genes: a) a clone-specific hsdS gene, for identification, detection and/or typing said S. aureus clonal complex, and b) at least one gene considered as a negative control, said gene being absent in the genome of said S. aureus species, and optionally c) a gene for antibiotic resistance.
Thus, in a particular embodiment the device comprises a solid support coated with a set of separated or compartmentalised probes for identification or typing of any S. aureus clonal complex from an extract of its genomic DNA, each probe being able to specifically hybridize with a relevant gene or with a representative fragment thereof susceptible to be present in said genomic DNA to be tested, characterized in that said relevant genes whose presence or absence is to be determined using the set of probes comprise the following genes: a) a clone-specific hsdS gene, for typing said S. aureus clonal complex, and b) at least one gene considered as a negative control, said gene being absent in the genome of said S. aureus species, and optionally c) a gene for antibiotic resistance.
Thus a very specific embodiment of the invention relates to DNA micro-array for identification, detection and/or typing of a S. aureus bacterial strain comprising the solid support described herein.
Another very specific embodiment of the invention relates to a device comprising a DNA micro-array for identification, detection and/or typing of a S. aureus bacterial strain comprising the solid support described herein
In other embodiments of the invention the device may be a dipstick. Dipsticks may allow visual detection and confirmation of PCR-amplified S. aureus-specific transcripts by hybridization within minutes.
Dipsticks that can detect PCR products have for example recently been described by Deborggraeve et al. (2006) and Kalogianni et al. (2007). The PCR products may for example be biotinylated at the one end by using an upstream primer labelled with biotin at the 5′ end.
Deborggraeve et al. (2006) describes a dry-reagent strip (4 mm×70 mm) consisting of an immersion pad, a conjugation pad, a laminated membrane and an absorbent pad assembled on a plastic adhesive backing that provides rigidity. The four parts are positioned in such a way that their ends overlapped in order to ensure continuous flow (by capillary action) of the developing solution from the wicking pad up to the absorbent pad. Gold nanoparticles (40 nm diameter) functionalized with poly(dT) strands, are placed on the conjugate pad and allowed to dry at room temperature. Streptavidin (27 pmol) is immobilized by physical adsorption on the test zone of the strip. Similarly, poly(dA) strands (1.2 pmol) are immobilized on the control zone of the strip.
The assay entails rapid hybridization of the amplified fragments (target DNA), in solution, with a dATP-tailed oligonucleotide probe, application to the sample loading area on the conjugate pad of the strip and immersion of the strip (via the immersion pad) in the developing solution. The developing solution migrates to the opposite end of the strip, by capillary forces, and causes rehydration of the poly(dT)-functionalized gold nanoparticles (Au NP), which are then connected to the probe via hybridization of the poly(dT) strands with the poly(dA) tail of the probe. As the solution passes through the test zone of the strip, the hybrids are captured by immobilized streptavidin, thus resulting in accumulation of Au NP which is detected visually as a characteristic red line. The red color of the Au NP is due to the plasmon resonance peak at 520 nm. The excess of poly(dT)-Au NP are captured by immobilized poly(dA) strands at the control zone of the strip, giving a second red line. In the absence of the translocation, no red line is observed at the test zone. A red line, however, is always formed at the control zone to confirm the proper functioning of the strip. Consequently, a sample is positive for a certain translocation when a red line is observed both in the test and the control zone.
Thus, biotinylated PCR products can then be mixed with a tailed oligonucleotide probe and allowed to hybridize. An aliquot of the solution may then be applied to the conjugate pad of the strip and the latter may be immersed into an appropriate developing solution (for example glycerol and SDS in phosphate-buffered saline). The formation of a red line in the test zone of the strip signifies the presence of a translocation-specific amplified sequence in the sample. A red line is always formed at the control zone of the strip to confirm the proper functioning of the test. Thus, a result is positive when a red line is observed both in the test zone and control zone, whereas in the absence of the translocation, a red line is formed only in the control zone.
Thus, some aspects of the invention regards, device for the detection of the presence of a specific S. aureus clonal complex, strain or lineage, wherein the device comprises means for measuring the presence of clonal complex, strain or lineage specific nucleic acid(s).
In specific embodiments the device is for the detection, identification and/or typing of any S. aureus clonal complex, wherein the device comprises means for measuring the presence of clone-specific hsdS nucleic acid(s). In one embodiment there is provided that the clonal complex is complex is not CC1, CC5, CC8, CC22, CC30 or CC45. In some embodiments it is further provided that said clonal complex may not be any one or more of: CC12, CC15, CC25, CC51, CC151, CC97, CC771, CC130, CC188, and/or CC873
In a particular embodiment the clonal complex, strain or lineage specific hsdS nucleic acid(s) are CC398 specific. In particular embodiments the primer of SEQ ID NO: 2 (CAGTATTAAAGAGGTGACATGACCCCT) may be used as a means for detecting clonal complex, strain or lineage specific hsdS nucleic acid(s).
In a further embodiment of the device is a dipstick. The dipstick may be any dipstick including but not limited to the dipstick described herein above.
Another embodiment regards a device for the detection of the presence of a specific S. aureus strain or lineage and a bacterial resistance gene selected from the group consisting of mecA and vanA, preferably mecA for the detection of MRSA, wherein the device comprises means for measuring the presence of strain or lineage specific nucleic acid(s). In one embodiment there is provided that the clonal complex is complex is not CC1, CC5, CC8, CC22, CC30 or CC45. In some embodiments it is further provided that said clonal complex may not be any one or more of: CC12, CC15, CC25, CC51, CC151, CC97, CC771, CC130, CC188, and/or CC873
In a preferred embodiment the strain or lineage specific nucleic acid(s) are CC398 specific and in an even more preferred embodiment the device is a dipstick.
Alternatively a dipstick may be used in the present aspect of the invention on any biological sample that is or may be converted to a fluid is preferred. Particularly biological samples that are obtainable from a body as a fluid are preferred; examples hereof include, and are not limited to: blood, serum, plasma, urine, cerebrospinal fluid, synovial fluid, ascites, semen, and saliva. Most preferable are serum and plasma samples.
Kit of Parts
All the materials and reagents required the detection of S. aureus clone-specific nucleic acid(s) according to the present invention can be assembled together in a kit, such kit includes at least elements in aid of assessing the presence of S. aureus clone-specific nucleic acid(s) in a biological sample obtained from an individual, and the instruction on how to do so. In specific embodiments the kit is for identification, detection and/or typing of any S. aureus clonal complex, comprising any suitable combination of clone-specific primers or probes. In an even more specific embodiment the kit is for identification, detection and/or typing CC398 S. aureus clonal complex, comprising any suitable combination of clone-specific primers or probes selected from the group consisting of SEQ ID NOS: 2, 3, 4, 5 and 6, sequences complementary thereof, and variants thereof. Preferably, the primers are the primers specified in SEQ ID NO: 2 and SEQ ID NO: 6.
The kit of parts may further comprise equipment for obtaining one or more biological samples, such equipment may for example be tools for taking swab samples such as sterile cotton buds, as well as syringes, vials or other. The kit of parts may be packed for single use or for repeated usage, and the elements therein may be disposable such as to be disposed of after a single use or may be of a quality that allows repeated usage.
Thus in one embodiment the invention relates to a kit for identification, detection and/or typing a S. aureus bacterial strain comprising the solid support described herein or the DNA micro-array described herein.
The kit may in some embodiment further comprise any suitable combination of primers selected from the group consisting of SEQ ID NOS: 7 and 8 sequences complementary thereof, and variants thereof for the simultaneous detection and/or quantification of the nucleic acid(s) of any combination of the bacterial resistance genes selected from the group consisting of mecA and vanA, preferably mecA for the detection of MRSA.
Preferably, the primers are the primers specified in SEQ ID NO: 2 and SEQ ID NO: 6 for the identification, detection and/or typing of CC398 S. aureus and the primers specified in SEQ ID NO: 7 and SEQ ID NO: 8 for the detection of the mecA gene.
In some embodiments the kit for identification, detection and/or typing a bacterial strain, comprises

    
    
        a. means for taking a sample from a subject
        b. means for mailing said sample to institution for the determining the presence of a specific S. aureus clonal complex, strain or lineage and optionally MRSA in a sample.
    
    


In other embodiments the kit for identification, detection and/or typing a bacterial strain, comprises

    
    
        a. means for taking a sample from a subject
        b. means for at the place where the sample is being taken, determining the presence of a specific S. aureus clonal complex, strain or lineage and optionally MRSA in a sample.
    
    


In one embodiment there is provided that the clonal complex is not CC1, CC5, CC8, CC22, CC30 or CC45. In some embodiments it is further provided that said clonal complex may not be any one or more of: CC12, CC15, CC25, CC51, CC151, CC97, CC771, CC130, CC188, and/or CC873
In a particular embodiment the specific S. aureus clonal complex, strain or lineage is CC398.
In the above test kit, the reagents may be supplied from storage bottles or one or more of the test tubes may be prefilled with the reagents or controls.
The components of the kit may also be provided in dried or lyophilized forms. When reagents or components are provided as a dried form, reconstitution generally is by the addition of a suitable solvent. It is envisioned that the solvent also may be provided in another container means.
The kits of the present invention also will typically include a means for containing the reagents such as vials or tubes in close confinement for commercial sale such as, e.g. injection or blow-molded plastic containers into which the desired vials are retained. The kits will also comprise a set of instructions on how to perform the assay.
The kit according to the present invention may furthermore comprise a device according to the invention as described above here in the section termed “device”.
In a preferred embodiment there is provided a kit for identification, detection and/or typing of a S. aureus CC398 bacterial strain, comprising any suitable combination of primers selected from the group consisting of SEQ ID NOS: 2, 3, 4, 5 and 6, sequences complementary thereof, and variants thereof. Preferably, the primers are the primers specified in SEQ ID NO: 2 and SEQ ID NO: 6 for the identification, detection and/or typing of CC398 S. aureus. 
In another preferred embodiment the kit further comprises any suitable combination of primers selected from the group consisting of SEQ ID NOS: 7 and 8, sequences complementary thereof, and variants thereof for the simultaneous detection and/or quantification of the nucleic acid(s) of the bacterial resistance gene MecA for the detection of MRSA. Preferably, the primers are the primers specified in SEQ ID NO: 2 and SEQ ID NO: 6 for the identification, detection and/or typing of CC398 S. aureus and the primers specified in SEQ ID NO: 7 and SEQ ID NO: 8 for the detection of the mecA gene.
Items
One embodiment of the invention relates to a method using amplification primers and/or probes which are specific and sensitive for determining the presence of nucleic acid(s) from a S. aureus strain or lineage in any sample suspected of containing said S. aureus nucleic acid(s) thereby identifying, detecting and/or typing said S. aureus strain or lineage, wherein each of said nucleic acid(s) or variant(s) or part(s) thereof comprises a selected target region hybridizable with said probes or primers; said method comprising the following steps: contacting said sample with said primers, or probes and detecting the presence of amplified products or hybridized probes as an indication of the presence of said specific S. aureus strain or lineage thereby identifying, detecting and/or typing said S. aureus strain or lineage.
In one embodiment there is provided that the clonal complex is complex is not CC1, CC5, CC8, CC22, CC30 or CC45. In some embodiments it is further provided that said clonal complex may not be any one or more of: CC12, CC15, CC25, CC51, CC151, CC97, CC771, CC130, CC188, and/or CC873 In a preferred embodiment the clonal complex is CC398.
In another embodiment the nucleic acid(s) from a S. aureus strain or lineage is a species specific restriction-modification (RM) gene.
In another embodiment the nucleic acid(s) from a S. aureus strain or lineage is an hsdS gene.
In another embodiment the nucleic acid(s) from a S. aureus strain or lineage is sau1hsdS1 or sau1hsdS2.
In another embodiment the S. aureus strain or lineage is CC398.
Another embodiment of the invention relates to a method using amplification primers and/or probes which are specific and sensitive for determining the presence of nucleic acid(s) from S. aureus strain or lineage CC398 in any sample suspected of containing said S. aureus CC398 nucleic acid(s) thereby identifying, detecting and/or typing said S. aureus strain or lineage, wherein each of said nucleic acid(s) or variant(s) or part(s) thereof comprises a selected target region hybridizable with said probes or primers; said method comprising the following steps: contacting said sample with said primers or probes and detecting the presence of amplified products or hybridized probes as an indication of the presence of said specific S. aureus strain or lineage thereby identifying, detecting and/or typing said S. aureus strain or lineage.
In another embodiment said nucleic acid(s) are amplified d by a method selected from the group consisting of: polymerase chain reaction (PCR), ligase chain reaction (LCR), nucleic acid sequence-based amplification (NASBA), self-sustained sequence replication (3SR), strand displacement amplification (SDA), branched DNA signal amplification (bDNA), transcription-mediated amplification (TMA), cycling probe technology (CPT), real-time PCR, quantitative PCR, nested PCR, and multiplex PCR.
In a specific embodiment said nucleic acid(s) are amplified by PCR.
In another embodiment said amplification primers are capable of hybridizing with any hsdS sequence or a sequence complementary thereof, for the identification, detection and/or typing of a S. aureus clonal complex, strain or lineage.
In another embodiment said primers comprise a forward primer and one or more reverse primers.
In another embodiment said amplification primers or probes are capable of hybridizing with sau1hsdS1 of CC398 or sau1hsdS2 of CC398 or a sequence complementary thereto. Thus is one very preferred embodiment the amplification primers are capable of hybridizing the nucleotide sequence defined in: SEQ ID NO: 1 or a sequence complementary thereto.
In another embodiment said one or more primers or probes are selected from the group consisting of CAGTATTAAAGAGGTGACATGACCCCT (SEQ ID NO: 2), CACCTGAATCACCGTTTAATGCC (SEQ ID NO: 3), CGAGCACCTGAATCACCGTTT (SEQ ID NO: 4) and TGGGATATGAAGTGGCATTTCC (SEQ ID NO: 5).
In another embodiment said forward primer targets the upstream conserved region of the hsdS gene as defined by SEQ ID NO: 1 or SEQ ID NOS: 13-71.
In another embodiment said forward primer is AGGGTTTGAAGGCGAATGGG (SEQ ID NO: 6).
In another embodiment said one or more reverse primers are S. aureus strain or lineage specific primers.
In another embodiment said one or more reverse primers are selected from the group consisting of CAGTATTAAAGAGGTGACATGACCCCT (SEQ ID NO: 2), CACCTGAATCACCGTTTAATGCC (SEQ ID NO: 3), CGAGCACCTGAATCACCGTTT (SEQ ID NO: 4) and TGGGATATGAAGTGGCATTTCC (SEQ ID NO: 5).
In another embodiment said at least one of the one or more reverse primers is the CC398 specific primer CAGTATTAAAGAGGTGACATGACCCCT (SEQ ID NO: 2).
In another embodiment the final concentration of the each primer is in a concentration range of 0.01 μM to 10 μM, for example 0.05 μM to 5 μM, such as 0.1 to 1 μM, for example 0.2 μM.
In another embodiment the final concentration of each primer is 0.2 μM.
In another embodiment the method further comprises labelling the S. aureus nucleic acid(s) in a sample or of a substantially homogeneous population of said S. aureus isolated from this sample and putting said labelled S. aureus nucleic acid(s) into contact with a solid support coated with an array of probes in suitable conditions for hybridization, each probe being able to specifically hybridize with a relevant gene or with a representative fragment thereof, susceptible to be present in said sample to be tested, wherein said relevant genes whose presence or absence is to be determined using the set of probes comprise the following genes: a) at least one gene considered as a positive control whose presence in a genome is characteristic for the S. aureus strain or lineage, and b) at least one gene considered as a negative control, said gene being absent in the genome of the S. aureus strain or lineage, and optionally c) a gene for antibiotic resistance.
In another embodiment the method further comprises a) depositing and fixing on an solid support or leaving in solution the said S. aureus nucleic acid(s) of the sample or of a substantially homogeneous population of said S. aureus isolated from this sample, or inoculating said sample or said substantially homogeneous population of S. aureus isolated from this sample on an solid support, and lysing in situ said inoculated sample or said isolated S. aureus to release the said S. aureus DNA, said S. aureus DNA being made in a substantially single-stranded form.
In another embodiment the method further comprises labelling the S. aureus nucleic acid(s) in a sample and putting said labelled S. aureus nucleic acid(s) into contact with a solid support coated with an array of probes in suitable conditions for hybridization, each probe being able to specifically hybridize with a relevant gene or with a representative fragment thereof, susceptible to be present in said sample to be tested, wherein said relevant genes whose presence or absence is to be determined using the set of probe comprise the following genes: a) at least one gene considered as a positive control whose presence in a genome is characteristic for the S. aureus CC398 strain or lineage, and b) at least one gene considered as a negative control, said gene being absent in the genome of the S. aureus CC398 strain or lineage, and optionally c) a gene for antibiotic resistance.
In another embodiment the method is performed directly on a test sample.
In another embodiment the nucleic acid(s) are extracted from a test sample using a bacterial genomic DNA purification kit.
In another embodiment the test sample is derived from an animal.
In another embodiment the test sample is derived from poultry.
In another embodiment the test sample is derived from a mammal. In another embodiment the mammal is selected from the group consisting of humans, pigs, horses and cows.
In another embodiment the method is performed directly from a test sample consisting of a nasal swabs, throat swabs, mouth swabs, hand swabs and blood.
In another embodiment the method is performed directly from a test sample consisting of a bacterial culture or suspension.
In another embodiment the sample of nucleic acid(s) is is derived from strains and/or lineages of persons staying in a health care facility for an extended period of time, health care workers, farm workers, veterinarian staff, persons involved in sales to farms and any person involved in the handling of livestock and/or butchery.
In another embodiment the sample of nucleic acid(s) is derived from strains and/or lineages of one individual patient or hospital.
In another embodiment several lineages and/or hospital isolates are analysed.
In another embodiment the method further comprising a culturing of the strains and/or lineages of S. aureus before the analysis.
Yet another embodiment of the invention relates to a method for the detection, identification and/or typing of a S. aureus strain or lineage, in a test sample which comprises the following steps: a) treating said sample with an aqueous solution containing at least one pair of oligonucleotide primers, one of said primers being capable of hybridizing selectively with one of the two complementary strands of said S. aureus clone-specific hsdS gene that contains a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template, said at least one pair of primers being chosen from a nucleotide sequence within the clone-specific hsdS gene respectively with regard to said S. aureus clonal complex, a sequence complementary thereof, and a variant thereof; b) synthesizing an extension product of each of said primers, said extension product containing the target sequence, and amplifying said target sequence, if any, to a detectable level; and c) detecting the presence and/or amount of said amplified target sequence as an indication of the presence and/or amount of said S. aureus clonal complex, in said test sample.
Yet another embodiment of the invention relates to a method for the detection, identification and/or typing of a S. aureus strain or lineage, directly from a test sample or from bacterial cultures, which comprises the following steps a) depositing and fixing on an solid support or leaving in solution the said S. aureus nucleic acid(s) of the sample or of a substantially homogeneous population of said S. aureus isolated from this sample, or inoculating said sample or said substantially homogeneous population of S. aureus isolated from this sample on an solid support, and lysing in situ said inoculated sample or said isolated S. aureus to release the said S. aureus DNA, said S. aureus DNA being made in a substantially single-stranded form; b) contacting said single-stranded DNA with a probe, said probe comprising at least one single-stranded nucleic acid which nucleotide sequence is sequence complementary to a sequence of SEQ ID NO: 1, and a variant thereof, which specifically and ubiquitously anneals with strains or lineages of S. aureus, under conditions such that the nucleic acid(s) of said probe can selectively hybridize with said S. aureus DNA, whereby a hybridization complex is formed; and c) detecting the presence of said hybridization complex on said solid support or in said solution as an indication of the presence and/or amount of said S. aureus, in said test sample.
Still another embodiment of the invention relates to a method for obtaining hsdS sequences from any S. aureus strain or lineage directly from a test sample or a bacterial culture, which comprises the following steps: a) treating said sample with an aqueous solution containing at least one pair of primers having a sequence selected within the nucleotide sequences defined in SEQ ID NOS: 9, 10, 11 and 12 and a variant thereof, one of said primers being capable of hybridizing selectively with one of the two complementary strands of said S. aureus hsdS gene that contains a target sequence, and the other of said primers being capable of hybridizing with the other of said strands so as to form an extension product which contains the target sequence as a template; b) synthesizing an extension product of each of said primers, said extension product containing the target sequence, and amplifying said target sequence, if any, to a detectable level; and c) detecting the presence and/or amount of said amplified target sequence; and d) determining the nucleotide sequence of the said amplified target sequence by using any DNA sequencing method.
In another embodiment the method further comprises amplification primers and/or probes which are specific and sensitive for determining the presence of nucleic acid(s) from a bacterial antibiotic resistance gene selected from the group consisting of MecA in any sample suspected of containing said antibiotic resistance gene, thereby determining MRSA, wherein each of said nucleic acid(s) or variant(s) or part(s) thereof comprises a selected target region hybridizable with said primers or probes; said method comprising the following steps: contacting said sample with said probes or primers and detecting the presence of amplified products or hybridized probes as an indication of the presence of said mecA.
Yet another embodiment of the invention relates to an improved method of treatment for an infection by MRSA, comprising a method described herein and performing a treatment of MRSA based, at least in part, on said identification, detection and/or typing of S. aureus. 
Yet another embodiment of the invention relates to a method of improving the hygiene in hospital, comprising a method described herein and performing hygiene measures in said hospital based, at least in part, on said identification, detection and/or typing of S. aureus. 
Yet another embodiment of the invention relates to a solid support coated with a set of probes for identification, detection and/or typing of a S. aureus bacterial strain from an extract of its genomic DNA, each probe being able to specifically hybridize with a relevant gene or with a representative fragment thereof susceptible to be present in said genomic DNA to be tested, characterized in that said relevant genes whose presence or absence is to be determined using the set of probes comprise the following genes: a) at least one gene considered as a positive control whose presence in a genome is characteristic for the S. aureus species, and b) at least one gene considered as a negative control, said gene being absent in the genome of said S. aureus species, and optionally d) a gene for antibiotic resistance.
Another embodiment relates to a solid support coated with a set of probes for identification, detection and/or typing of CC398 S. aureus bacterial strain from an extract of its genomic DNA, each probe being able to specifically hybridize with a relevant gene or with a representative fragment thereof susceptible to be present in said genomic DNA to be tested, characterized in that said relevant genes whose presence or absence is to be determined using the set of probes comprise the following genes: a) the sau1hsdS1 gene of SEQ ID NO: 1, which is considered as a positive control whose presence in a genome is characteristic for CC398 S. aureus, and b) at least one gene considered as a negative control, said gene being absent in the genome of said S. aureus species, and c) a restriction-modification (RM) gene and optionally d) a gene for antibiotic resistance.
Yet another embodiment of the invention relates to a DNA micro-array for identification, detection and/or typing of a S. aureus bacterial strain comprising the solid support of described herein. Still another embodiment relates to a micro-array for identification and typing of a S. aureus CC398 bacterial strain comprising the solid support described herein.
Yet another embodiment of the invention relates to a kit for identification, detection and/or typing of a S. aureus bacterial strain comprising the solid support described herein or the DNA micro-array described herein.
Yet another embodiment of the invention relates to a kit for identification, detection and/or typing of a S. aureus clonal complex, comprising any suitable combination of clone-specific primers. Still another embodiment relates to a kit for identification, detection and/or typing of a S. aureus CC398 clonal complex, comprising any suitable combination of primers selected from the group consisting of SEQ ID NOS: 2, 3, 4, 5 and 6, sequences complementary thereof, and variants thereof, more specifically the specific primers are selected from the group consisting of SEQ ID NOS: 2 and 6, sequences complementary thereof, and variants thereof.
In another embodiment of the invention the kit further comprises any suitable combination of primers selected from the group consisting of SEQ ID NOS: 7 and 8 sequences complementary thereof, and variants thereof for the simultaneous detection and/or quantification of the nucleic acid(s) of any combination of the bacterial resistance genes selected from the group consisting of mecA for the detection of MRSA.
Yet another embodiment of the invention relates to a kit for identification, detection and/or typing of a bacterial strain, comprising

    
    
        a. means for taking a sample from a subject
        b. means for mailing said sample to institution for identification, detection and/or typing of any S. aureus clonal complex and optionally for detection of MRSA in a sample.
    
    


Yet another embodiment of the invention relates to a kit for identification, detection and/or typing of a bacterial strain, comprising

    
    
        a. means for taking a sample from a subject
        b. means for at the place where the sample is being taken, identification, detection and/or typing of any S. aureus clonal complex and optionally for detection of MRSA in a sample.
    
    


Yet another embodiment of the invention relates to a device for the detection of the presence of a specific S. aureus strain or lineage, wherein the device comprises means for measuring the presence of strain or lineage specific nucleic acid(s).
Yet another embodiment of the invention relates to a device for the detection of the presence of a specific S. aureus strain or lineage and a bacterial resistance gene selected from the group consisting of MecA, for the detection of MRSA, wherein the device comprises means for measuring the presence of strain or lineage specific nucleic acid(s).
In another embodiment the strain or lineage specific nucleic acid(s) are CC398 specific
In another embodiment the device is a dipstick.
EXAMPLES
Example 1
Design of Primers Specific for the sau1hsdS1 Gene in S. aureus CC398
A 489-bp region within the sau1hsdS1 gene was tentatively amplified in 8 S. aureus strains belonging to CC398-related spa types using the non-specific primers AF (SEQ ID NO: 6) and BF (SEQ ID NO: 22) published by Cockfield et al. (2008). However, this experiment yielded negative results. The experiment was repeated using the forward primer AF (SEQ ID NO: 6) and 4 novel reverse primers (SEQ ID NOS: 2-5) targeting two conserved regions in the 5′-end of the gene. By this approach PCR products of approximately 475-bp were obtained from all strains. Alignment of the sequences from the 8 strains revealed that they were 100% identical (see FIG. 3), indicating that this region is highly conserved within CC398 (SEQ ID NO: 1). interestingly, the sau1hsdS1 sequence in CC398 was distantly related (37% amino acid identity) to the sequence of the same gene in other S. aureus lineages. Four putative CC398-reverse primers (ST398 r1 to ST398 r4 (SEQ ID NOS: 2-5)) were designed and tested on the same 8 strains used in the previous experiment. The primer ST398 r1 (SEQ ID NO: 2) yielded an amplification product of approximately 320-bp in all strains. This primer was selected for further validation of the test on a large collection of S. aureus of animal and human origin. All PCR reactions were performed using Applied Biosystems AmpliTaq Gold and associated buffers according to the manufacturer's directions. Primers were used at a concentration of 0.2 μM each. The PCR conditions were as follows: 12 min at 94° C., then 35 cycles of 30 sec at 95° C., 30 sec at 61° C. and 1 min at 72° C. The products were separated on 1.5% agarose gels.
Example 2
Validation of the PCR Test for Identification of S. aureus CC398
The primers AF (SEQ ID NO: 6) and ST398 r1 (SEQ ID NO: 2) were tested on a large strain collection composed by 65 CC398 strains previously identified by MLST and/or spa typing and representative of 8 spa types, and by 211 non-CC398 strains of human and animal origin, including CC5, CC8, CC15, CC20, CC22, CC30, CC45, CC80 and CC152 (Table 1). All CC398 strains were positive (100% sensitivity) whereas all non-CC398 strains were negative (100% specificity).







TABLE 2







List of strains used to validate the PCR test













Strain code
Host
spa repeat succession
spa type
MLST/CC
mecA
CC398 PCR





DTU-70-95-9
Swine
08-16-02-25-02-25-24-25
t2876
CC398
Negative
Positive


A-7
Swine
08-16-02-25-02-25-34-24-24-25
t1793
CC398
Negative
Positive


A-6
Swine
08-16-02-25-02-25-34-24-24-25
t1793
CC398
Negative
Positive


A-17
Swine
08-16-02-25-02-25-34-24-24-25
t1793
CC398
Negative
Positive


A-3
Swine
08-16-02-25-02-25-34-24-24-25
t1793
CC398
Negative
Positive


A-2
Swine
08-16-02-25-02-25-34-24-24-25
t1793
CC398
Negative
Positive


A-4
Swine
08-16-02-25-02-25-34-24-24-25
t1793
CC398
Negative
Positive


A-12
Swine
08-16-02-25-02-25-34-24-24-25
t1793
CC398
Negative
Positive


A-16
Swine
08-16-02-25-02-25-34-24-24-25
t1793
CC398
Negative
Positive


83 (P4)
Swine
08-16-02-25-02-25-34-24-24-25
t1793
CC398
Negative
Positive


P-99
Swine
08-16-02-25-02-25-34-24-25
t034
CC398
Negative
Positive


P-77
Swine
08-16-02-25-02-25-34-24-25
t034
CC398
Negative
Positive


P-60
Swine
08-16-02-25-02-25-34-24-25
t034
CC398
Negative
Positive


P-88
Swine
08-16-02-25-02-25-34-24-25
t034
CC398
Negative
Positive


B-11
Swine
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


B-7
Swine
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


B-6
Swine
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


B-10
Swine
08-16-02-25-02-25-34-24-25
t034
CC398
Negative
Positive


40315
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


40555
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


40850
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


42541
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


43511
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


43943
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


44184
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


44697
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


44738
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


45009
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


45145
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


45228
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


46428
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


47258
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


47432
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


47695
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


47769
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


47771
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


47772
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


47773
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


50148
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


51726
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


52290
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


52518
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


52944
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


53169
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


55488
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


55600
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


55729
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


55730
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


56755
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


56922
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


A213 (H1)
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


K90 (H2)
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


A165 (H3)
Human
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


53 (P1)
Swine
08-16-02-25-02-25-34-24-25
t034
CC398
Positive
Positive


62 (P2)
Swine
08-16-02-25-02-25-34-24-25
t034
CC398
Negative
Positive


78 (P3)
Swine
08-16-02-25-02-25-34-24-25
t034
CC398
Negative
Positive


P-79
Swine
08-16-02-25-02-25-34-24-25
t034
CC398
Negative
Positive


288
Human
08-16-02-25-02-25-34-25
t571
CC398
Positive
Positive


DTU-7
Swine
08-16-02-25-02-25-34-25
t571
CC398
Negative
Positive


51225
Human
08-16-02-25-24-25
t108
CC398
Positive
Positive


DTU-34
Swine
08-16-02-25-24-25
t108
CC398
positive
Positive


K101 (H4)
Human
08-16-02-25-34-24-25
t011
CC398
Positive
Positive


7515
Human
08-16-02-25-34-24-25
t011
CC398
Positive
Positive


P-100
Swine
08-16-20-25-02-25-39-24-25
t034
CC398
Negative
Positive


P-93 sub hvid
Swine
08-16-34-24-25
t1255
CC398
Negative
Positive


D93
Dog
08-16-02-43-34-16-02-17-16
t1651
ND
Negative
Negative


S57 F8
Cattle
04-17
t524
ND
Negative
Negative


S57 F9
Cattle
04-17
t524
ND
Negative
Negative


DTU-A11
Cattle
04-17
t524
ND
Negative
Negative


C22496-2
Sheep
03-16-12-21-17-23-13-17-17-17-23-24
t2678
ND
Negative
Negative


C22511-1
Sheep
03-16-12-21-17-23-13-17-17-17-23-24
t2678
ND
Negative
Negative


C21336-1
Cattle
03-16-12-21-17-23-13-17-17-17-23-25
t3046
ND
Negative
Negative


CC2247
Sheep
03-16-12-21-17-23-13-17-23-24
t3042
ND
Negative
Negative


C22071
Sheep
03-16-12-21-17-23-24
t3045
ND
Negative
Negative


C22492
Goat
03-16-21-17-23-13-17-17-17-23-24
t1166
ND
Negative
Negative


L62
Horse
03-16-21-17-23-13-17-17-17-23-24
t1166
ND
Negative
Negative


C22559
Sheep
03-21-17-23-13-17-17-23-24
t3047
ND
Negative
Negative


C22528-3
Cattle
04-17
t524
ND
Negative
Negative


D91
Dog
04-12-12-17
t227
CC25
Negative
Negative


L44
Horse
04-20-17-111-16-109-24-17
t1294
ND
Negative
Negative


L8-2
Horse
04-20-17-111-16-109-24-17
t1294
ND
Negative
Negative


C21875
Horse
04-20-17-111-16-109-24-17
t1294
ND
Negative
Negative


L174
Horse
04-20-17-111-16-109-24-17
t1294
ND
Negative
Negative


C22365
Horse
04-20-17-25-16-16-109-24-50
t3044
ND
Negative
Negative


C22748-3
Cattle
04-20-17-31-24
t2873
ND
Negative
Negative


L134-1-2
Horse
04-20-69-31-70-13-17-16-16
t2484
ND
Negative
Negative


L147 sub 1
Horse
04-20-69-31-70-13-17-16-16-16-16
t3043
ND
Negative
Negative


L43
Horse
04-20-69-31-70-13-17-16-16-16-16
t3043
ND
Negative
Negative


L155 sub 1
Horse
04-20-69-31-70-13-17-16-16-16-16
t3043
ND
Negative
Negative


DTU-28
Poultry
04-44-33-31-12-16-34-17-25-22-34
t2038
ND
Negative
Negative


DTU-1B1
Swine
07-16-23-02-34
t899
CC9
Negative
Negative


P-71
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


P-84
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


P-70
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


P-81
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


P-66 Yellow
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


P-80
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


P-91
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


P-65
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


P-75
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


P-63
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


P-61
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


P-74
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


P-73
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


P-90
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


P-87
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


P-89
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


P-72
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


P93
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


C22928-2
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


P-98
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


DTU-12
Swine
07-16-23-23-02-12-23-02-34
t337
CC9
Negative
Negative


S57 F3
Cattle
07-16-23-23-23-02-34
t2839
CC9
Negative
Negative


DTU-9
Swine
07-16-23-23-23-02-34
t2839
CC9
Negative
Negative


DTU-27
Poultry
07-23-12-12-34-34-33-34
t203
CC80
Negative
Negative


DTU-A44
Cattle
07-23-12-21-17-34-34-34-34-34-33-34
t527
CC80
Negative
Negative


D57
Dog
07-23-12-34-34-12-12-12-23-02-12-23
t774
CC15
Negative
Negative


D56
Dog
07-23-12-34-34-12-12-23-02-12-23
t084
CC15
Negative
Negative


C22917 sub
Horse
07-23-12-34-34-12-12-23-02-12-23
t084
CC15
Negative
Negative


42394
Human
07-23-12-34-34-33-34
t044
CC80
Positive
Negative


42492
Human
07-23-12-34-34-33-34
t044
CC80
Positive
Negative


2710-2001
Human
07-23-12-34-34-33-34
t044
CC80
Positive
Negative


4003-2001
Human
07-23-12-34-34-33-34
t044
CC80
Positive
Negative


41722
Human
07-23-12-34-34-34-33-34
t376
CC80
Positive
Negative


D35
Dog
07-23-21-17-34-12-23-02-12-23
t091
CC20
Negative
Negative


44886
Human
07-56-12-17-16-16-33-31-57-12
t355
ST152/377
Positive
Negative


53153
Human
07-56-12-17-16-16-33-31-57-12
t355
ST152/377
Positive
Negative


289
Human
08-02-25-24-25
t567
CC398
Positive
Positive


42481
Human
08-16-02-16-02-25-17-24
t019
CC30
Positive
Negative


42655
Human
08-16-02-16-02-25-17-24
t019
CC30
Positive
Negative


2294-2001
Human
08-16-02-16-02-25-17-24
t019
CC30
Positive
Negative


40323
Human
08-16-02-16-34
t230
CC45
Positive
Negative


45954
Human
08-16-02-16-34
t230
CC45
Positive
Negative


45955
Human
08-16-02-16-34
t230
CC45
Positive
Negative


41602
Human
08-16-02-16-34-13-17-34-16-34
t015
CC45
Positive
Negative


41623
Human
08-16-02-16-34-13-17-34-16-34
t015
CC45
Positive
Negative


52759
Human
08-16-02-16-34-13-17-34-16-34
t015
CC45
Positive
Negative


1781-2001
Human
09-02-16-34-13-17-34-16-34
t065
CC45
Positive
Negative


C22823
Poultry
11-10-21-17-34-24-34-22-25
t304
CC8
Negative
Negative


40326
Human
11-12-21-17-34-24-34-22-25
t024
CC8
Positive
Negative


41047
Human
11-12-21-17-34-24-34-22-25
t024
CC8
Positive
Negative


41103
Human
11-12-21-17-34-24-34-22-25
t024
CC8
Positive
Negative


42474
Human
11-12-21-17-34-24-34-22-25
t024
CC8
Positive
Negative


42738
Human
11-12-21-17-34-24-34-22-25
t024
CC8
Positive
Negative


44611
Human
11-12-21-17-34-24-34-22-25
t024
CC8
Positive
Negative


47894
Human
11-12-21-17-34-24-34-22-25
t024
CC8
Positive
Negative


53148
Human
11-12-21-17-34-24-34-22-25
t024
CC8
Positive
Negative


51414
Human
11-19-12-05-17-34-24-34-22-25
t064
CC8
Positive
Negative


43484
Human
11-19-12-21-17-34-24-34-22-25
t008
CC8
Positive
Negative


43596
Human
11-19-12-21-17-34-24-34-22-25
t008
CC8
Positive
Negative


44065
Human
11-19-12-21-17-34-24-34-22-25
t008
CC8
Positive
Negative


44329
Human
11-19-12-21-17-34-24-34-22-25
t008
CC8
Positive
Negative


44628
Human
11-19-12-21-17-34-24-34-22-25
t008
CC8
Positive
Negative


45544
Human
11-19-12-21-17-34-24-34-22-25
t008
CC8
Positive
Negative


46744
Human
11-19-12-21-17-34-24-34-22-25
t008
CC8
Positive
Negative


46763
Human
11-19-12-21-17-34-24-34-22-25
t008
CC8
Positive
Negative


43332
Human
15-12-16-02-16-02-25-17-24-24
t012
CC30
Positive
Negative


53463
Human
15-12-16-02-16-02-25-17-24-24
t012
CC30
Positive
Negative


D42
Dog
15-12-16-02-24-24
t030
CC8
Negative
Negative


50587
Human
15-12-16-02-25-17-24
t037
CC8
Positive
Negative


51772
Human
15-12-16-02-25-17-24
t037
CC8
Positive
Negative


52294
Human
15-12-16-02-25-17-24
t037
CC8
Positive
Negative


2769-2001
Human
15-12-16-02-25-17-24
t037
CC8
Positive
Negative


45141
Human
15-12-16-16-02-16-02-25-17-24
t318
CC30
Positive
Negative


47500
Human
15-12-16-16-02-16-02-25-17-24
t318
CC30
Positive
Negative


50293
Human
15-12-16-16-02-16-02-25-17-24
t318
CC30
Positive
Negative


53318
Human
15-12-16-16-02-16-02-25-17-24
t318
CC30
Positive
Negative


D90
Dog
15-12-16-17-25-17-24
t3055
CC30
Negative
Negative


C21209-6
Swine
15-12-16-34-02-25-17-24
t1333
CC30
Negative
Negative


C21209-5
Swine
15-12-16-34-02-25-17-24
t1333
CC30
Negative
Negative


C22348
Swine
15-12-16-34-02-25-17-24
t1333
CC30
Negative
Negative


C22356-2
Swine
15-12-16-34-02-25-17-24
t1333
CC30
Negative
Negative


C21209-1
Swine
15-12-16-34-02-25-17-24
t1333
CC30
Negative
Negative


C212094
Swine
15-12-16-34-02-25-17-24
t1333
CC30
Negative
Negative


DTU-13
Swine
15-12-16-34-02-25-17-24
t1333
CC30
Negative
Negative


DTU-15
Swine
15-12-16-34-02-25-17-24-17-24
t2840
CC30
Negative
Negative


3715-2001
Human
26-17-20-17-12-17-16
t045
CC5
Positive
Negative


51302
Human
26-17-20-17-12-17-16?
t045
CC5
Positive
Negative


3081-03
Human
26-17-20-17-12-17-17-16
t003
CC5
Positive
Negative


40012
Human
26-17-20-17-12-17-17-16
t003
CC5
Positive
Negative


41348
Human
26-17-20-17-12-17-17-16
t003
CC5
Positive
Negative


41389
Human
26-17-20-17-12-17-17-16
t003
CC5
Positive
Negative


43102
Human
26-17-20-17-12-17-17-16
t003
CC5
Positive
Negative


43209
Human
26-17-20-17-12-17-17-16
t003
CC5
Positive
Negative


43519
Human
26-17-20-17-12-17-17-16
t003
CC5
Positive
Negative


44607
Human
26-17-20-17-12-17-17-16
t003
CC5
Positive
Negative


4563-2001
Human
26-17-20-17-12-17-17-16
t003
CC5
Positive
Negative


43052
Human
26-17-25-17-25-16-28
t541
CC22
Positive
Negative


D66
Dog
26-17-34-17-12-17-17-16
t1335
ND
Negative
Negative


L31-3-2
Horse
26-23-12-21-17-34-34-34-34-33-34
t2112
ND.
Negative
Negative


L31-1
Horse
26-23-12-21-17-34-34-34-34-33-34
t2112
ND.
Negative
Negative


42295
Human
26-23-13-23-05-17-25-17-25-16-28
t223
CC22
Positive
Negative


2244-2001
Human
26-23-13-23-31-05-17-25-16-16-28
t016
CC30
Positive
Negative


40322
Human
26-23-13-23-31-05-17-25-17-25-16-28
t005
CC22
Positive
Negative


43514
Human
26-23-13-23-31-05-17-25-17-25-16-28
t005
CC22
Positive
Negative


40135
Human
26-23-13-23-31-29-17-31-29-17-25-17-25-16-28
t022
CC22
Positive
Negative


42223
Human
26-23-13-23-31-29-17-31-29-17-25-17-25-16-28
t022
CC22
Positive
Negative


45193
Human
26-23-13-23-31-29-17-31-29-17-25-17-25-16-28
t022
CC22
Positive
Negative


DTU-72
Poultry
26-23-17-17-16
t2049
CC5
Negative
Negative


D16
Dog
26-23-17-34-17-20-17-12-16
t548
CC5
Negative
Negative


C13167
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13060
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13197
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13197
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13167
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13167
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13167
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13156
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13156
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


22352
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


22352
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


22352
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13212
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13212
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


22352
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


22352
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13060
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13351
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13212
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13115
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13262
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13167
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13033
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13033
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13033
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13262
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13131
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13041
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13041
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13041
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13212
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


22352
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13167
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13167
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13262
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


22352
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13156
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13212
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


22352
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


22352
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13060
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13131
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


22352
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13131
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13197
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13197
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


22352
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


22352
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


22352-Poul
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C21898
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C21898
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C21898
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C21899
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C21899
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C22352
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C22428
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C22438
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C22505
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C13262
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


C21899
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


DTU-21
Poultry
26-23-17-34-17-20-17-12-17-16
t002
CC5
Negative
Negative


42584
Human
26-23-17-34-17-20-17-12-17-16
t002
CC5
Positive
Negative


42965
Human
26-23-17-34-17-20-17-12-17-16
t002
CC5
Positive
Negative


44634
Human
26-23-17-34-17-20-17-12-17-16
t002
CC5
Positive
Negative


45542
Human
26-23-17-34-17-20-17-12-17-16
t002
CC5
Positive
Negative


47901
Human
26-23-17-34-17-20-17-12-17-16
t002
CC5
Positive
Negative


51412
Human
26-23-17-34-17-20-17-12-17-16
t002
CC5
Positive
Negative


C13292
Poultry
26-23-17-34-17-20-17-12-17-17
t002
CC5
Negative
Negative


C13292
Poultry
26-23-17-34-17-20-17-12-17-17
t002
CC5
Negative
Negative


DTU-71
Poultry
26-23-17-34-17-20-17-12-17-17-16
t306
CC5
Negative
Negative


47143
Human
26-23-23-13-23-31-29-17-31-29-17-25-17-25-16-28
t032
CC22
Positive
Negative


47908
Human
26-23-23-13-23-31-29-17-31-29-17-25-17-25-16-28
t032
CC22
Positive
Negative


53349
Human
26-23-23-13-23-31-29-17-31-29-17-25-17-25-16-28
t032
CC22
Positive
Negative


1983-2000
Human
26-30-17-34-17-20-17-12-17-16
t001
CC5
Positive
Negative


23757-1999
Human
26-30-17-34-17-20-17-12-17-16
t001
CC5
Positive
Negative


40638
Human
26-30-17-34-17-20-17-34-17-20-17-12-17-16
t041
CC5
Positive
Negative





ND, not determined.






Example 3
Development of the Multiplex PCR for Discrimination Between MRSA and MSSA CC398 Strains
In order to allow differentiation between MRSA and MSSA variants of CC398, the CC398-specific primer set AF (SEQ ID NO: 6) ST398 r1 (SEQ ID NO: 2) was combined with primers mecup1 (SEQ ID NO: 7)-mecup2 (SEQ ID NO: 8) targeting the methicillin resistance mecA gene. Such primers have been designed in a previous study to develop a diagnostic kit (EVIGENE MRSA) produced by Statens Serum Institut for rapid MRSA identification (Poulsen et al. 2003). The multiplex PCR was tested on 4 S. aureus strains representing MSSA non-CC398 (strain ATCC 6538), MRSA non-CC398 (strain ATCC 33591), MSSA CC398 (SSI 52615) and MRSA (KVL 288). The results of this experiment are shown in FIG. 1.
REFERENCES


    Bannerman T L. 2003. Staphylococcus, Micrococcus and other catalase-positive cocci that grow aerobically. In Manual of Clinical Microbiology, 8th edition. Eds. Murray P R, Baron E J, Jorgensen J H, Pfaller M A, Yolken R H. Pp. 384-404. American Society for Microbiology, Washington, D.C.
    Chambers 1997. Methicillin resistance in staphylococci: molecular and biochemical basis and clinical implications. Clin. Microbiol. Rev. 10: 781-791.
    Cockfield J D, Pathak S, Edgeworth J D, and Lindsay J A. 2008. Rapid determination of hospital-acquired meticillin-resistant S. aureus lineages. J. Med. Microbiol. 56: 614-619.
    Deborggraeve S, Claes F, Laurent T, Mertens P, Leclipteux T, Dujardin J C, Herdewijn P, and Buscher P. 2006 Molecular dipstick test for diagnosis of sleeping sickness, J. Clin. Microbiol. 44: 2884-2889.
    Enright, M C, Day N P J, Davies C E, Peacock S J, and Spratt B G. 2000. Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of S. aureus. J. Clin. Microbiol. 38: 1008-1015.
    European Commission 2007. Commission decision of 20 Dec. 2007 concerning a financial contribution from the Community towards a survey on the prevalence of Salmonella spp. and Methicillin-resistant S. aureus in herds of breeding pigs to be carried out in the Member States (2008/55/EC). Official Journal of The European Union 17 Jan. 2008.
    Kalogianni D P, Bravous V, Christopoulos T K, Ioannou P C, and Zoumbos N C. 2007. Dry-reagent disposable dipstick test for visual screening of seven leukemia-related chromosomal translocations. Nucleic Acids Res. 35: e23.
    Koreen L, Ramaswamy S V, Graviss E A, Naidich S, Musser J M, and Kreiswirth B N. 2004. spa typing method for discriminating among S. aureus isolates: implications for use of a single marker to detect genetic micro- and macrovariation. J. Clin. Microbiol. 42: 792-799.
    Lewis H C, Molbak K, Reese C, Aarestrup F M, Selchau M, Sarum M, et al. Pigs as source of methicillin-resistant S. aureus CC398 in humans, Denmark. Emerg. Inf. Dis. 2008; 14: 1383-1389
    Moodley, A., Nightingale, E. C., Stegger, M., Nielsen, S. S, Skov, R., Guardabassi, L. 2008. High risk of nasal carriage of methicillin resistant S. aureus among Danish veterinary practitioners. Scand. J. Work Environ. Health 34: 151-157.
    Murchan S, Kaufmann M E, Deplano A, de Ryck R, Struelens M, Zinn C E, Fussing V, Salmenlinna S, Vuopio-Varkila J, El Solh N, Cuny C, Witte W, Tassios P T, Legakis N, van Leeuwen W, van Belkum A, Vindel A, Laconcha I, Garaizar J, Haeggman S, Olsson-Liljequist B, Ransjo U, Coombes G, Cookson B. 2003. Harmonization of pulsed-field gel electrophoresis protocols for epidemiological typing of strains of methicillin-resistant S. aureus: a single approach developed by consensus in 10 European laboratories and its application for tracing the spread of related strains. J Clin Microbiol. 41:1574-85
    Poulsen A B, Skov R, and Pallesen L V. 2003. Detection of methicillin resistance in coagulase-negative staphylococci and in staphylococci directly from simulated blood cultures using the EVIGENE MRSA Detection Kit, J. Antimicrob. Chemother. 51: 419-421.
    Vannuffel P, Gigi J, Ezzedine H, Vandercam B, Delmee M, Wauters G, Gala J L. 1996. Specific detection of methicillin-resistant Staphylococcus species by multiplex PCR. J. Clin. Microbiol. 34:1599.
    van Loo I, Huijsdens X, Tiemersma E, de Neeling A, van de Sande-Bruinsma N, Beaujean D, Voss A, Kluytmans J. Emergence of methicillin-resistant S. aureus of animal origin in humans. Emerg Infect Dis. 2007; 13:1834-1839
    Voss A, Loeffen F, Bakker J, Klaassen C, and Wulf M. 2005. Methicillin-resistant Staphylcoccus aureus in pig farming. Emerg. Infect. Dis. 11:1965-6.
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All patent and non-patent references cited in the application, or in the present application, are also hereby incorporated by reference in their entirety.

## Claims

1. A method for differentiating between Methicillin-resistant S. aureus (MRSA) and Methicillin-susceptible S. aureus (MSSA) variants of S. aureus clonal complex 398 (CC398) in a sample from an animal subject, comprising:
contacting the S. aureus nucleic acid in said sample or in a substantially homogeneous population of said S. aureus nucleic acid isolated from said sample with first forward primer SEQ ID NO: 6 and first reverse primer sequence selected from the group consisting of SEQ ID NO: 2 through 5, synthesizing a first extension product of said first forward primer and said first reverse primer, amplifying said first extension product, and detecting the presence of said first extension product; and
contacting said S. aureus nucleic acid in said sample with primers SEQ ID NO: 7 and SEQ ID NO: 8, synthesizing a second extension product of primers SEQ ID NO: 7 and SEQ ID NO: 8, amplifying said second extension product, and detecting the presence of said second extension product;
wherein the presence of said first extension product in combination with the absence of said second extension product indicates the presence of MSSA in said sample, and wherein the presence of said first extension product in combination with the presence of said second extension product indicates the presence of MRSA in said sample.

2. The method according to claim 1, wherein said first reverse primer is SEQ ID NO: 2.

3. The method according to claim 1, wherein if the presence of MRSA in said sample is indicated, the method further comprises treatment of said subject for MRSA.

4. The method according to claim 1, wherein said subject is a mammal.

5. A method for differentiating between Methicillin-resistant S. aureus (MRSA) and Methicillin-susceptible S. aureus (MSSA) variants of S. aureus clonal complex 398 (CC398) in a sample from an animal subject, comprising:
labelling the S. aureus nucleic acid in said sample or in a substantially homogeneous population of said S. aureus isolated from said sample;
hybridizing the labelled nucleic acid with at least one first probe selected from the group consisting of SEQ ID NOS: 2-6 coated on a solid support and at least one second probe selected from SEQ ID NO: 7 and 8 coated on a solid support; and
detecting the presence of said labelled nucleic acid in association with said at least one first probe and/or said at least one second probe;
wherein the presence of said labelled nucleic acid in association with said at least one first probe in combination with the absence of said labelled nucleic acid in association with at least one second probe indicates the presence of MSSA in said sample, and
wherein the presence of said labelled nucleic acid in association with said at least one first probe in combination with the presence of said labelled nucleic acid in association with at least one second probe indicates the presence of MRSA in said sample.

6. The method according to claim 5, wherein said at least one first probe is SEQ ID NO: 2 or SEQ ID NO: 6.

7. The method according to claim 5, wherein if the presence of MRSA in said sample is indicated, the method further comprises treatment of said subject for MRSA.

8. The method according to claim 7, wherein said subject is a mammal.

9. A method for differentiating between Methicillin-resistant S. aureus (MRSA) and Methicillin-susceptible S. aureus (MSSA) variants of S. aureus clonal complex 398 (CC398) in a sample from an animal subject, comprising:
labelling at least one first probe selected from the group consisting of SEQ ID NOS: 2-6 and labelling at least one second probe selected from SEQ ID NO: 7 and 8;
hybridizing said at least one first probe and said at least one second probe with said sample coated on a solid support or with a substantially homogeneous population of said S. aureus isolated from said sample coated on a solid support; and
detecting the presence of said at least one first probe and/or said at least one second probe;
wherein the presence of said at least one first probe in combination with the absence of said at least one second probe indicates the presence of MSSA in said sample, and
wherein the presence of said at least one first probe in combination with the presence of said at least one second probe indicates the presence of MRSA in said sample.

10. The method according to claim 9, wherein said at least one first probe is SEQ ID NO: 2 or SEQ ID NO: 6.

11. The method according to claim 9, wherein if the presence of MRSA in said sample is indicated, the method further comprises treatment of said subject for MRSA.

12. The method according to claim 11, wherein said subject is a mammal.