TABLE 1.
Genomic islands in six sequenced staphylococcal genomes
| Inland | Genes found on islandb | Type, location of island (predicted integration sequencea) for:
|
Allele family member(s) | |||||
|---|---|---|---|---|---|---|---|---|
|
S. aureus
|
S. epidermidis
|
|||||||
| COL | Mu50 | N315 | MW2 | RP62A | ATCC 12228 | |||
| vSa1 | Enterotoxin genes (seb, tsst, ear) | 903332-919283 (A) | NP | NP | NP | NP | NP | SaPI1, SaPI3 |
| vSa2 | sec, tsst | NP | NP | NP | NP | NP | NP | SaPIbov |
| vSa3 | Type I, fhuD; type II, sel2, sec4, ear | NP | I, 868373-882872 (B) | NP | II, 839358-853808 (B) | NP | NP | SaPI3 |
| vSa4 | Type I, sel, sec3, tsst; type II, four unknown ORFs | II, 2072899-2076041 (C) | I, 2148912-2133235 (D) | I, 2056679-2072358 (D) | II, 2097809-2100950 (C) | NP | NP | SaPI2 |
| vSaα | Type I, set6-15, lpl1-9; type II, set16-26, lpl10-14, type III, set1-5, lpl2,7,8,11,13 | III, 465424-489723 | I, 461919-491326 | I, 436162-466813 | II, 416307-452099 | NP | NP | |
| vSaβ | Type I, splA-F, lukDE, ear, epidermin gene cluster; type II, splA-F, lukDE, ear, seg, sen, sei, sem, seo, epidermin gene cluster | I, 1902466-1938731 | II, 1932523-1961464 | I, 1854608-1881615 | I, 1890800-1922552 | NP | NP | |
| vSaγ | set, eta, psmβ | 1173206-1193358 | 1208629-1230219 | 1132235-1153775 | 1133469-1153549 | NP | NP | |
| vSeγ | psmβ | 734975-737635 | 840908-843572 | |||||
| SCCmec | mecA, ermA, bleO, addD | I, 68085-34173 (E) | II, 87085-34158 (E) | II, 87119-34153 (E) | IV, 58278-34150 (E) | II, 2536574-2584194 (F) | NP | Types I, II, III, IVa, IVb |
| SSCpbp4 | pbp4, merT, merB, merA, tagF | NP | NP | NP | NP | NP | 32031-99960 (G) | |
| φSa1 | 72 ORFs | NP | 917453-962005 (H) | NP | NP | NP | NP | φ11, φETA |
| φSa2 | lukS-PV, lukF-PV | NP | NP | NP | 1575042-1529123 (I) | NP | NP | φSLT |
| φSa3 | sak, sea, sep, seg2, sek2 | NP | 2126304-2083238 (J) | 2049591-2005321 (J) | 2088820-2046205 (J) | NP | NP | φ42 |
| φCOL | Integrated in geh | 354674-398267 (K) | NP | NP | NP | NP | NP | φL-54 |
| φSPβ | Integrated in yeeE, LPXTG surface protein gene | NP | NP | NP | NP | 1567637-1694334 (L) | NP | |
| Tn5801 | tetM, two unknown ORFs | NP | I, 436002-461791 (M) | NP | II, 415784-417798 (M) | NP | NP | |
| vSe1 | Type I, cadCD; type II, one unknown ORF | NP | NP | NP | NP | I, 2250348-2267496 (N) | II, 2255537-2259992 (N) | |
| vSe2 | srtA, two LPXTG surface protein genes | NP | NP | NP | NP | NP | 1558081-1519667 (O) | |
A, TTATTCCTGCTAAATAA; B, TCCCGCCGTCTCCAT; C, GTTTTACATCATTCC[CT]GGCAT; D, GTTTTACATCATTCCCGGCAT; E, TTATGATA[CA]GC[CT]TCT; F, TTATGATA[TA]GCTTCT; G, TCATTTATGATATGCTTCT; H, TCGAAATGGAAGGTAGTATTGGATAGCTTTAAAC[CA][CG]CGTTGTTAAGCCATTCTTGACTTCCGGAAATGG[CG]TAT; I, AAATAAACATATC[GA]TCATAATGTGATGGT; J, TGTATCCAAACTGG; K, ATCATACAAGGATGGGAT; L, CAATGCATAAAA; M, GAGTGGGAATA; N, CTAAATATTTTC; O, CGGAGAGTGAGGGAT. NP, not present.
Gene symbols: sortase, srtA; cadmium efflux, cadCD; lipase, geh; staphylococcal kinase, sak; β-lactamase, ear; ferric hydroxamate uptake, fhuD; leukotoxin, lukDE; tandem lipoprotein, lpl; PSM beta subunit, psm β; staphylococcal entertoxins, sec3, sec4, seg, seg2, sea, sek2, sel, sel2, sem, sen, seo, sep; serine protease, splA-F; toxic shock syndrome toxin, tsst; panton-valentine leukocidin components S and F, lukS-PV, lukF-PV; methicillin resistance, mecA; penicillin binding protein 4, pbp4; ermA, bleO, addD, tetM, yeeE; alkytmercury lyase, merB; mercury transport protein, merT; mercuric reductase, merA; teichoic acid biosynthesis protein F, tagF.