Table 1.
Whole‐genome sequences of foodborne pathogens registered on NCBI platforms (up to 1 October 2019) and summary of the related genetic markers.
| Species | ID number | Number of sequenced strains | Representative strain | Size (Mb) | GC% | Genes | Proteins | Specific genetic markers |
|---|---|---|---|---|---|---|---|---|
| Escherichia | ||||||||
| E. coli | ID167 | 17 952 | K‐12 substr. MG1655 (Blattner et al., 1997) | 4.64 | 50.8 | 4498 | 4140 | fliC, Vt1, Vt2 (Gannon et al., 1997); uspA (Osek, 2001); lacZ (Foulds et al., 2002); rfbE, eae, stx1, stx2 (Ooka et al., 2009); ipaH (van den Beld and Reubsaet, 2012); lacY, uidA (Mendes Silva and Domingues, 2015); PhoA (Yang et al., 2016); cdtB (Hassan et al., 2018) |
| E. albertii | ID 1729 | 89 | KF1 | 4.70 | 49.7 | 4823 | 4380 | cdtB (Maheux et al., 2014); rpoB (Lindsey et al., 2015); EAKF1_ch4033 (Lindsey et al., 2017); 16S rDNA (Grillova et al., 2018) |
| E. fergusonii | ID 1877 | 18 | ATCC 35469T | 4.64 | 49.9 | 4618 | 4349 | yliE, EFER_1569, EFER_3126 (Simmons et al., 2014); EFER_0790 (Lindsey et al., 2017) |
| Salmonella | ||||||||
| S. enterica | ID 152 | 11 215 | CT18 | 5.13 | 51.9 | 4829 | 4473 | AceK, fliC, iagA, invA, oriC, sdf, sefA, ssaN, ssrA, STM2745, STM4492, 16S rRNA (Lee et al., 2009; Postollec et al., 2011); sseL, spvC (Peterson et al., 2010); hilA, fimA, hns (Jeyasekaran et al., 2011); avrA, stn, stm (Amin et al., 2016); spv, hut, fljB (Alzwghaibi et al., 2018) |
| S. bongori | ID1089 | 20 | NCTC 12419 | 4.46 | 51.3 | 4382 | 4068 | fljB, gatD, invA (Lee et al., 2009); fliC, gnd, mutS (Soler‐Garcia et al., 2014) |
| Staphylococcus | ||||||||
| S. aureus | ID 154 | 10 630 | NCTC 8325 | 2.82 | 32.9 | 2872 | 2767 | mecA, nuc, femA‐SA, femA‐SE, orfx‐SCCmec, spa, gyrB, 16S rRNA (Hirvonen, 2014); tuf, rpoB, gap, pyrH, ftsZ (Song et al., 2019); sea, seb, sec, sed, see (Omwenga et al., 2019) |
| S. epidermidis | ID 155 | 670 | ATCC 12228 | 2.56 | 32.1 | 2558 | 2482 | mecA, ermA, ermB, ermC, and msrA (Martineau et al., 2000); hld; ica, agrA, sarA (Frebourg et al., 2000); 16S rDNA and tuf (Kobayashi et al., 2009); femA‐SA, femA‐SE (Jukes et al., 2010); atlE, gap and mvaA (Kilic and Basustaoglu, 2011); recN (Iorio et al., 2011); adhesin fibrinogen binding protein (Sunagar et al., 2013); hla/yidD and hlb (Pinheiro et al., 2015); Gmk2, pta and SESB (Osmani Bojd et al., 2017); icaA, aap, bhp (Ribic et al., 2017) |
| S. lugdunensis | ID2548 | 26 | HKU09‐01 | 2.66 | 33.9 | 2567 | 2567 | Agr (Dufour et al., 2002); rpoB (Drancourt and Raoult, 2002); 16S rRNA (Skow et al., 2005); Fbl (Campos‐Pena et al., 2014) |
| S. saprophyticus | ID1350 | 108 | ATCC 15305 | 2.58 | 33.1 | 2523 | 2351 | 16S rRNA (Gaszewska‐Mastalarz et al., 1997); femA (Vannuffel et al., 1999); hrcA (Paiva‐Santos et al., 2016) |
| S. pseudintermedius | ID3429 | 223 | HKU10‐03 | 2.62 | 37.5 | 2517 | 2384 | SpsJ (Verstappen et al., 2017); sps (Phumthanakorn et al., 2017) |
| Listeria | ||||||||
| L. monocytogenes | ID 159 | 3063 | EGD‐e | 2.94 | 38.0 | 3055 | 2867 | hly, iap, mpl, prfA, inlA, inlB, actA (Gasanov et al., 2005); plcA, 16S RNA (Xu et al., 2008) |
| L. seeligeri | ID 1246 | 6 | SLCC3954 | 2.80 | 37.4 | 2790 | 2663 | 23S rRNA, iap (Paillard et al., 2003); lse24‐315 (Liu et al., 2004); 16S rRNA (Dalmasso et al., 2010); 5'‐exonuclease (Hage et al., 2014) |
| Shigella | ||||||||
| S. flexneri | ID 182 | 480 | 301 | 4.83 | 50.67 | 4788 | 4313 | ipaH, plasmid DNA, ial, 16S rRNA (Warren et al., 2006); she PAI (Farfan et al., 2010); invC, rfc (Ojha et al., 2013); genome marker (Sahl et al., 2015; Kim et al., 2017a) |
| S. boydii | ID 496 | 113 | 1221_SBOY | 4.84 | 50.7 | 5125 | 4745 | ipaH, 16S rRNA (Warren et al., 2006); invC (Ojha et al., 2013); wzy (Radhika et al., 2014); genome marker (Sahl et al., 2015; Kim et al., 2017a) |
| S. sonnei | ID 417 | 1338 | 4303 | 4.55 | 51.1 | 5275 | 4009 | ipaH, 16S rRNA (Warren et al., 2006); IS1 (Hsu et al., 2007); she PAI (Farfan et al., 2010); invC, wbgZ (Ojha et al., 2013); IpaBCD (Farshad et al., 2015); genome marker (Sahl et al., 2015; Kim et al., 2017a) |
| S. dysenteriae | ID 415 | 67 | Sd197 | 4.56 | 50.9 | 4834 | 4294 | ial, virA, 16S rRNA (Warren et al., 2006); invC, rfpB (Ojha et al., 2013); genome marker (Sahl et al., 2015; Kim et al., 2017a) |
| Campylobacter | ||||||||
| C. jejuni | ID149 | 1615 | NCTC 11168 | 1.64 | 30.5 | 1668 | 1572 | pDT1720 (Ng et al., 1997); CC2, CJ2 (Sails et al., 2001); ciaB, pldA, CDT (Ghorbanalizadgan et al., 2014); GTPase gene, hip, 16S rRNA, rrs, cdaF, porA, 16S‐23S ITS, Hyp, cjaA, ceuE, hipO, mapA, ceuA, askD, glyA, lpxA, ccoN, ORF‐C sequence, rpoB, oxidoreductase gene, cdtA, pepT (Frasao et al., 2017); flaA, cadF, racR, dnaJ, cdtB, and cdtC (Oh et al., 2017); gyrA (Sierra‐Arguello et al., 2018); ask, cdt (Kabir et al., 2019) |
| C. coli | ID1145 | 928 | Aerotolerant OR12 | 2.03 | 30.8 | 2185 | 2058 | arsP, arsR, arsC, acr3, arsB (Noormohamed and Fakhr, 2013); GTPase gene, hip, ceuA, CCCH, cdtB, porA, 16S‐23S ITS, ceuE, mapA, hipO, glyA, cadF, oxidoreductase gene, cdtA, pepT, 50S gene, VS1 (Frasao et al., 2017); ceuE (Rodgers et al., 2017); cadF, asp (Pavlova et al., 2016; Banowary et al., 2018) |