Table 1 The number and proportion of genomes within major C. jejuni clonal complexes and C. coli Clades from the collection used in this study that encode intact and inactive capC autotransporter genes. The number and proportion of genomes that do not encode capC or capD is also shown
Clonal | Total | capC1 | capC2 | capC3 | capC4 | capC/capD | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Complex | Genomes | Intact | Inactive | Intact | Inactive | Intact | Inactive | Intact | Inactive | absent | |||||||||
ST-21 | 1500 | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 45 | (3%) | 0 | – | 2 | (0.13%) | 1452 | (96.8%) |
ST-22 | 112 | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 112 | (100%) |
ST-42 | 105 | 1 | (0.95%) | 0 | – | 0 | – | 0 | – | 0 | – | 8 | (7.61%) | 0 | – | 0 | – | 96 | (91.4%) |
ST-45 | 543 | 309 | (56.9%) | 20 | (3.68%) | 0 | – | 0 | – | 203 | (37.3%) | 9 | (1.65%) | 0 | – | 0 | – | 2 | (0.36%) |
ST-48 | 375 | 2 | (0.53%) | 7 | (1.86%) | 0 | – | 0 | – | 3 | (0.8%) | 361 | (96.2%) | 0 | – | 0 | – | 2 | (0.53%) |
ST-52 | 82 | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 82 | (100%) | 0 | – | 0 | – | 0 | – |
ST-61 | 130 | 0 | – | 0 | – | 0 | – | 0 | – | 1 | (0.76%) | 4 | (3.07%) | 0 | – | 0 | – | 125 | (96.1%) |
ST-206 | 300 | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 297 | (99%) | 0 | – | 1 | (0.33%) | 2 | (0.66%) |
ST-257 | 394 | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 19 | (4.82%) | 0 | – | 375 | (95.1%) | 0 | – |
ST-283 | 99 | 98 | (98.9%) | 0 | – | 0 | – | 0 | – | 1 | (1.01%) | 0 | – | 0 | – | 0 | – | 0 | – |
ST-353 | 339 | 4 | (1.17%) | 0 | – | 0 | – | 0 | – | 3 | (0.88%) | 311 | (91.7%) | 18 | (5.30%) | 1 | (0.29%) | 2 | (0.58%) |
ST-354 | 214 | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 213 | (99.5%) | 1 | (0.46%) | 0 | – | 0 | – |
ST-403 | 56 | 0 | – | 55 | (98.2%) | 0 | – | 0 | – | 0 | – | 1 | (1.78%) | 0 | – | 0 | – | 0 | – |
ST-443 | 168 | 0 | – | 0 | – | 0 | – | 0 | – | 1 | (0.59%) | 0 | – | 3 | (1.78%) | 0 | – | 0 | – |
ST-464 | 379 | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 377 | (99.4%) | 0 | – | 0 | – | 2 | (0.52%) |
ST-573 | 61 | 1 | (1.63%) | 0 | – | 0 | – | 0 | – | 14 | (22.9%) | 3 | (4.91%) | 43 | (70.4%) | 0 | – | 0 | – |
ST-574 | 99 | 0 | – | 0 | – | 0 | – | 0 | – | 3 | (3.03%) | 96 | (96.9%) | 0 | – | 0 | – | 0 | – |
ST-658 | 110 | 1 | (0.90%) | 0 | – | 0 | – | 0 | – | 0 | – | 108 | (98.1%) | 0 | – | 1 | (0.90%) | 0 | – |
ST-677 | 78 | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 77 | (98.7%) | 0 | – | 1 | (1.28%) | 0 | – |
None | 434 | 26 | (5.99%) | 5 | (1.15%) | 10 | (2.30%) | 1 | (0.23%) | 65 | (14.9%) | 222 | (51.1%) | 32 | (7.37%) | 25 | (5.76%) | 46 | (10.5%) |
Clade1a (ST-828) | 1189 | 29 | (2.43%) | 0 | – | 60 | (5.04%) | 2 | (0.16%) | 204 | (17.1%) | 3 | (0.25%) | 787 | (66.1%) | 51 | (4.28%) | 54 | (4.54%) |
Clade1b (ST-1150) | 20 | 0 | – | 0 | – | 0 | – | 0 | – | 1 | (5%) | 0 | – | 1 | (5%) | 0 | – | 18 | (90%) |
Clade1c | 26 | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 26 | (100%) |
Clade 2 | 40 | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 40 | (100%) |
Clade 3 | 72 | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 0 | – | 3 | (4.16%) |