TABLE 3.

USA300-0114 putative antimicrobial resistance and virulence factor genes

GeneCOL ORF no.aCOL descriptionResult forb:Comment
USA300-0114USA400USA500-0004USA100
Resistance genes
    arsBSA1823Arsenical pump membrane protein++++
    arsCSA1824Arsenate reductase++
    bacASA0743Bacitracin resistance protein++++
    blaZAF086644-cds1beta-Lactamase++++
    cadBAF134905-cds1Low-level cadmium resistance+++
    ddhSA25352-Hydroxyacid dehydrogenase (associated with vancomycin resistance)++++
    fosBSA2326Fosfomycin resistance protein+++
    HypotheticalSA2413Drug resistance transporter++++
    HypotheticalSA0772Aluminum resistance protein++++
    HypotheticalSA1327Aluminum resistance protein++++
    HypotheticalSA2348Drug transporter++++
    HypotheticalSA2437Drug resistance transporter++++
    mecASA0033Penicillin-binding protein 2++++
    msrASA1397Peptide methionine sulfoxide reductase++++
    msrASA2683Peptide methionine sulfoxide reductase++++
    msrASA1459Peptide methionine sulfoxide reductase++++
    msrSAAB016613-cds3Erythromycin resistance protein++
    norASA0754Drug transporter++++
    semBSA2347Drug resistance transporter++++
    vgaSA2036ABC transporter++++
Virulence genes
    Regulatory genes
        agrASA2026Accessory gene regulator protein A (type 1)++++
        agrBSA2023Accessory gene regulator protein B (type 1)++++
        agrBSA2023Accessory gene regulator protein B (type 1)++USA400 agr type III; USA100 agr type II
        agrDAccessory gene regulator protein D (type 1)++USA400 agr type III; USA100 agr type II
        icaRSA2688Intercellular adhesion regulator++++
        sarASA0672Staphylococcal accessory regulator A++++
        sarRSA2287Staphylococcal accessory regulator R++++
        sarS (sarH1)SA0096Staphylococcal accessory regulator S++++
        sarTSA2506Staphylococcal accessory regulator T+±++USA400 87.5% positive
        sarUSA2507Staphylococcal accessory regulator U++++
        sarVSA2258Staphylococcal accessory regulator V++++
        saeSSA0765Sensor histidine kinase++++
        saeRSA0766Response regulator++++
        mgrASA0746Transcriptional regulator++++
        arlSSA1450Sensor histidine kinase++++
        arlRSA1451Response regulator++++
        rotSA1812Transcriptional regulator++++
        svrASA0416Transcriptional regulator++++
        srrASA1535Response regulator++++
        TRAPSA1891RNAIII-activating protein++++
        yycGSA0020Sensory box histidine kinase++++
    Cell surface genes
        AmidaseSA2666N-Acetylmuramoyl-l-alanine amidase domain protein++++
        cap5ASA0136Capsular polysaccharide synthesis++++
        cap5BSA0137Capsular polysaccharide synthesis++++
        cap5CSA0138Capsular polysaccharide synthesis++++
        cap5DSA0139Capsular polysaccharide synthesis++++
        cap5ESA0140Capsular polysaccharide synthesis++++
        cap5FSA0141Capsular polysaccharide synthesis++++
        cap5GSA0142Capsular polysaccharide synthesis++++
        cap5HSA0143Capsular polysaccharide synthesis+++USA400 capsule type 8
        cap5ISA0144Capsular polysaccharide synthesis+++USA400 capsule type 8
        cap5JSA0145Capsular polysaccharide synthesis+++USA400 capsule type 8
        cap5KSA0146Capsular polysaccharide synthesis+++USA400 capsule type 8
        cap5LSA0147Capsular polysaccharide synthesis++++
        cap5MSA0148Capsular polysaccharide synthesis++++
        cap5NSA0149Capsular polysaccharide synthesis++++
        cap5OSA0150Capsular polysaccharide synthesis++++
        cap5PSA0151Capsular polysaccharide synthesis++++
        capASA2687CapA protein++++
        capBSA2686CapB protein++++
        capCSA2685CapC protein++++
        clfAClumping factor A++++
        clfBSA2652Clumping factor B++++
        ebhSA1472Pathogenicity protein++
        ebhSA1472Pathogenicity protein++
        ebhSA1472Pathogenicity protein++
        ebhSA1472Pathogenicity protein+++
        ebhSA1472Pathogenicity protein+±++USA400 87.5% positive
        ebhSA1472Pathogenicity protein++++
        Hypothetical(SA1267)Similar to streptococcal adhesin emb++++
        icaASA2689IcaA protein++++
        icaBSA2691IcaB protein++++
        icaCSA2692IcaC protein++++
        icaDSA2690IcaD protein++++
        isaASA2584Immunodominant antigen A++++
        isaBSA2660Immunodominant antigen B++++
        sdrCSA0608SdrC protein++++
        sdrESA0610SdrE protein+++
        sai-1SA113929-kDa cell surface protein++++
        fnbAFibronectin-binding protein A++
        fnbBFibronectin binding protein B++
        Hypothetical(SA2284)Similar to accumulation- associated protein+±++USA400 87.5% positive
        pls homologSA2505LPXTG motif cell wall anchor domain protein+++
        HypotheticalSA2676LPXTG motif cell wall anchor domain protein++++
        HypotheticalSA2676LPXTG motif cell wall anchor domain protein+++
        HypotheticalPredicted ORFLPXTG motif cell wall anchor domain protein+++
        HypotheticalPredicted ORFLPXTG motif cell wall anchor domain protein++++
        HypotheticalSA1781LPXTG motif cell wall anchor domain protein++++
        HypotheticalSA0119LPXTG motif cell wall anchor domain protein++++
        HypotheticalSA1141LPXTG motif cell wall anchor domain protein++++
        spaSA0095Immunoglobulin G binding protein++++
        isdBSA1138LPXTG motif cell wall anchor domain protein++++
        HypotheticalSA1806LPXTG motif cell wall anchor domain protein+++
        HypotheticalSA1806LPXTG motif cell wall anchor domain protein++++
        fmtB (mrp)SA2150Cell wall protein+++
        fmtB (mrp)SA2150Cell wall protein++
    Exoenzymes
        aurSA2659Aureolysin++++
        coaSA0209Coagulase++++
        splASA1869Serine protease++++
        splBSA1868Serine protease++++
        splCSA1867Serine protease++++
        splDSA1866Serine protease++++
        splESA1865Serine protease+±+USA400 62.5% positive
        splFSerine protease++++
        hysASA2194Hyaluronate lyase++USA400 and USA500 alleles present
        gehSA0317Lipase precursor++++
        sspASA1057V8 protease++++
        sspBSA1970Serine protease++++
        sspBSA1056Staphopain++++
        lipSA2694Lipase++++
        plcSA00781-Phosphatidylinositol phosphodiesterase precursor++++
    Exotoxins and enterotoxins
        set10(SA0386)Exotoxin 10++++
        set11(SA0387)Exotoxin 11++++
        set12(SA0388)Exotoxin 12++++
        set13SA0473Exotoxin 5; N315 exotoxin 13++++
        set14SA0474Exotoxin 4; N315 exotoxin 14++++
        set7SA0469Exotoxin 2; N315 exotoxin 7++++
        set8SA0470Exotoxin 2; N315 exotoxin 8++++
        set9(SA0385)Exotoxin 9+++
        HypotheticalBAB94252_1Similar to MW-2 exotoxin 21++
        Exotoxin 2SA0472Exotoxin 2++++
        Exotoxin 3SA0468Exotoxin 3++
        Exotoxin 3SA0478Exotoxin 3++
        entSA0886Staphylococcal enterotoxin+±+USA400 87.5% positive
        entBSA0172Isochorismatase++++
        EnterotoxinSA1657Similar to enterotoxin A++++
        seiSA0887Staphylococcal extracellular enterotoxin type I+±+USA400 87.5% positive
        hldSA2022delta-Hemolysin++++
        hlb(SA1811)Truncated beta-hemolysin++++
        hlgASA2419gamma-Hemolysin++++
        hlgBSA2422Leucocidin precursor++++
        hlgCSA2421Leucocidin precursor++++
        lukDSA1880Leucotoxin LukD++++
        lukFSA2004Leucocidin precursor++++
        lukF-PVAB006796PVL+±USA400 62.5% positive
        lukMSA2006Leucotoxin LukM++++
        lukSSA1881Synergohymenotropic toxin++++
        lukS-PVAB006796PVL+±USA400 62.5% positive
        HypotheticalSA2295Similar to secretory antigen precursor SsaA++++
        HypotheticalSA2557Similar to secretory antigen precursor SsaA++++
        HypotheticalSA0507Similar to autolysin++++
        ssaASA2291Secretory antigen precursor SsaA++++
  • a ORFs in parentheses refer to S. aureus strain N315.

  • b +, presence of gene; −, absence of gene; ±, gene was not present in any isolates of the PFT tested.