TABLE 2.
List of 70 C. difficile isolates and genomes (toxinotypes and cluster/outbreak isolates) for evaluation of the novel cgMLST scheme
| Isolate | Cladea | BAPS partition | MLST STa | PCR ribotypeb | Toxinotypec | % cgMLST targets | NCBI or ENA SRA accession no. (reference) |
|---|---|---|---|---|---|---|---|
| EX623 | 1 | Cd06 | 24 | 102 | I | 99.5 | ERS2039514 (this study) |
| IS 25 | 1 | Cd06 | 58 | 258 | XII | 99.6 | ERS2050180 (this study) |
| IS 58 | 5 | Cd03 | 11 | 033 | XIa | 97.7 | ERS2050181 (this study) |
| J9965 | 2 | Cd06 | 194 | SLO 032 | Xb | 98.7 | ERS2050182 (this study) |
| K095 | 1 | Cd06 | 2 | 014 | XVIII | 99.9 | ERS2039515 (this study) |
| KK2443/2006 | 1 | Cd06 | 19 | SLO 037 | XXVII | 98.9 | ERS2039516 (this study) |
| OCD 5/2 | 5 | Cd03 | 11 | 033 | XIc | 97.7 | ERS2039517 (this study) |
| R 10870 | 2 | None | 114 | 111 | XIVa | 99.1 | ERS2050183 (this study) |
| R 11402 | 5 | Cd03 | 11 | 288 (CE) | XIb | 97.6 | ERS2050184 (this study) |
| R 9385 | 2 | Cd06 | 116 | 122 | XIVb | 99.6 | ERS2050185 (this study) |
| R 9367 | 1 | Cd06 | 55 | 070 | XIII | 99.8 | ERS2039518 (this study) |
| SE 881 | 5 | Cd03 | 11 | 045 | V | 98.8 | ERS2050186 (this study) |
| SE 844 | 2 | None | 192 | 080 | IIIa | 99.6 | ERS2050187 (this study) |
| TFA/V14-10 | 2 | Cd06 | 231 | 153 (CE) | XId | 99.4 | ERS2039519 (this study) |
| TR13 | 1 | Cd06 | 17 | 018 | XIX | 99.4 | ERS2039541 (this study) |
| TR14 | 1 | Cd06 | 182 | SLO 005 | XX | 99.9 | ERS2039542 (this study) |
| 1732874 | 2 | Cd06 | 226 | SLO 228 | IXd | 99.6 | ERS2039496 (this study) |
| 3073 | 2 | Cd06 | 41 | SLO 042 | IIId | 99.6 | ERS2039506 (this study) |
| 51377 | 5 | Cd03 | 11 | 127 | VI | 98.8 | ERS2050169 (this study) |
| 51680 | 2 | Cd06 | 67 | 019 | IXa | 99.6 | ERS2050170 (this study) |
| 57267 | 5 | None | 193 | 063 | VII | 98.4 | ERS2050171 (this study) |
| 597B | None | 122 | 131 | 0/v | 99.3 | Reference 22 | |
| 55767 | 3 | None | 5 | 023 | IV | 98.7 | ERS2039507 (this study) |
| 7325 | 2 | Cd06 | 1 | 027 | XXV | 99.5 | ERS2050172 (this study) |
| 7459 | 1 | Cd06 | 16 | 050 (CE) | XXVI | 99.3 | ERS2039509 (this study) |
| 8864 | 2 | Cd06 | 62 | 591 (CE) | Xa | 99.7 | ERS2050174 (this study) |
| AC008 | 1 | Cd06 | 53 | 103 | II | 99.9 | ERS2039510 (this study) |
| AI 541 | 2 | Cd06 | 231 | 251 | IIIe | 99.6 | ERS2039511 (this study) |
| CD07-468 | 2 | Cd06 | 197 | 027 | XXII | 99.6 | ERS2050175 (this study) |
| CD07-140 | 1 | Cd06 | 3 | 001 | XXIX | 98.8 | ERS2039512 (this study) |
| CD08-070 | 5 | Cd03 | 11 | 126 | XXVIII | 99.1 | ERS2050176 (this study) |
| CD10-055 | Cd04 | 369 | SLO 201 | XXXIV | 96.2 | ERS2039513 (this study) | |
| CH6223 | 4 | None | 198 | SLO 035 | XXI | 98.5 | ERS2050177 (this study) |
| CH6230 | 2 | Cd06 | 123 | 251 | IIIc | 99.3 | ERS2050178 (this study) |
| ES 130 | 5 | Cd03 | 166 | SLO 101 | XXX | 98.7 | Reference 42 |
| WA 151 | 5 | Cd03 | 167 | SLO 098 | XXI | 98.4 | Reference 42 |
| VPI 10463 | 1 | Cd06 | 46 | 087 | 0 | 99.4 | ERS2039543 (this study) |
| TFA/V20-1 | 2 | Cd06 | 41 | 244 | IXb | 99.5 | ERS2039540 (this study) |
| C00006623 | 1 | Cd06 | 2 | 99.8 | ERX103559 (9) | ||
| C00006624 | 1 | Cd06 | 10 | 99.8 | ERX103560 (9) | ||
| C00006625 | 4 | Cd05 | 37 | 98.9 | ERX103561 (9) | ||
| C00006626 | 4 | Cd05 | 37 | 99.5 | ERX103562 (9) | ||
| C00006627 | 3 | None | 5 | 98.5 | ERX103563 (9) | ||
| C00006628 | 1 | Cd06 | 10 | 99.8 | ERX103564 (9) | ||
| C00006629 | 1 | Cd06 | 54 | 99.3 | ERX103565 (9) | ||
| C00006630 | 3 | None | 5 | 98.7 | ERX103566 (9) | ||
| M68 | 4 | Cd05 | 37 | 017 | VIII | 98.8 | NC_017175 (15, 40, 43) |
| R20291 | 2 | Cd06 | 1 | 027 | III | 99.6 | NC_013316 (15, 40, 43) |
| P1 | 2 | Cd06 | 1 | 99.6 | SRX821661 (15) | ||
| P2 | 2 | Cd06 | 1 | 99.7 | SRX821763 (15) | ||
| P3 | 2 | Cd06 | 1 | 99.7 | SRX821764 (15) | ||
| P4 | 2 | Cd06 | 1 | 99.7 | SRX821765 (15) | ||
| P5 | 2 | Cd06 | 1 | 99.7 | SRX821766 (15) | ||
| P6 | 2 | Cd06 | 1 | 99.7 | SRX821767 (15) | ||
| P7 | 2 | Cd06 | 1 | 99.7 | SRX821768 (15) | ||
| P8 | 1 | Cd06 | 2 | 99.8 | SRX821769 (15) | ||
| P9 | 4 | Cd05 | 37 | 99.6 | SRX821770 (15) | ||
| P10 | 4 | Cd05 | 37 | 99.6 | SRX821771 (15) | ||
| P11 | 1 | Cd06 | 2 | 99.9 | SRX821772 (15) | ||
| P12 | 4 | None | 81 | 99.5 | SRX821773 (15) | ||
| P13A | 2 | Cd06 | 1 | 99.7 | SRX821774 (15) | ||
| P13B | 2 | Cd06 | 1 | 99.7 | SRX821775 (15) | ||
| P13C | 2 | Cd06 | 1 | 99.7 | SRX821777 (15) | ||
| P14 | 1 | Cd06 | 8 | 99.7 | SRX821778 (15) | ||
| P15 | 1 | Cd06 | 8 | 99.7 | SRX821779 (15) | ||
| P16 | 2 | Cd06 | 1 | 99.7 | SRX821780 (15) | ||
| P17 | 2 | Cd06 | 1 | 99.7 | SRX821781 (15) | ||
| P18 | 2 | Cd06 | 1 | 99.7 | SRX821782 (15) | ||
| P19 | 4 | None | 81 | 99.5 | SRX821783 (15) | ||
| P20 | 4 | None | 81 | 99.5 | SRX821784 (15) |
a
MLST STs were in accordance to the C. difficile MLST database (https://pubmlst.org/cdifficile/), and clades were determined in this study (see Table S1).
c
Toxinotypes were given in accordance with the recent update on C. difficile toxinotyping (7).