TABLE 2.
Concordance between STEC identification by PCR and WGSb
| Strain | ST | SG | PCR | WGS | In silico PCR | BLAST (%Cov; %ID) | Sub-typification |
|---|---|---|---|---|---|---|---|
| PY1-3 | 58 | O65:H8 | – | – | – | ||
| PY2-3 | 394 | O17:H18 | stx1, stx2 | stx1, stx2 | stx1, stx2 | stx1a, stx2d | |
| PY2-4 | 11729 | O74:H42 | stx1, stx2 | stx1, stx2 | stx1, stx2 | stx1a, stx2c | |
| PY3-1 | 196 | O8:H7 | stx2 | stx2 | stx2 | stx2a | |
| PY3-2 | 162 | O8:H19 | stx2 | stx2 | – | stx2a | |
| PY4-1 | 1423 | O48:H7 | stx1, stx2 | stx2 | stx2 | stx1 (47%; 66%) | stx2a |
| PY4-3 | 442 | O156:H21 | stx1, stx2 | stx1, stx2 | stx1, stx2 | stx2c | |
| PY5-3 | 6353 | O132:H18 | stx2 | – | – | stx2 (8%; 95%) | |
| PY5-4 | 906 | O150:H8 | stx2 | – | – | stx2 (8%; 95%) | |
| PY6-3 | 3576 | O8:H7 | stx1, stx2 | stx1 | stx1 | stx2 (39%; 67%) | stx1a |
| PY6-4 | 3234 | O21:H8 | stx2 | stx2 | stx2 | stx2a | |
| PY7-2 | ND | O159:H21 | stx1, stx2 | – | – | stx1 (0%), stx2 (8%; 95%) | |
| PY7-3 | 10079 | O129:H23 | stx1, stx2 | – | – | stx1 (0%), stx2 (4%; 95%) | |
| PY8-1 | 3692 | O2:H45 | stx1, stx2 | stx1 | stx1 | stx2 (39%; 67%) | stx1a |
| PY8-2 | ND | OgN12:H31 | stx2 | – | – | stx2 (5%; 77%) | |
| PY9-1 | 164 | O27:H8 | stx1, stx2 | – | – | stx1 (0%), stx2 (5%; 77%) | |
| PY9-2 | 1248 | O5:H21 | stx1, stx2 | stx2 | stx2 | stx1 (47%; 66%) | stx2b, stx2c |
| PY10-2 | 200 | O128:H28 | – | – | – | ||
| PY10-4 | 1611 | O125:H19 | stx1, stx2 | – | – | stx1 (0%), stx2 (5%; 77%) | |
| PY11-1 | 58 | O49:H30 | stx1, stx2 | – | – | stx1 (0%), stx2 (5%; 77%) | |
| PY14-1 | 1423 | O48:H7 | stx1, stx2 | stx1a, stx2 | stx2 | stx2a | |
| PY25-1 | 297 | O179:H8 | stx2 | stx2 | stx2 | stx2d | |
| PY29-1 | 99 | O96:H19 | stx2 | stx2 | stx2 | stx2a | |
| PY34-1 | 1727 | O20:H7 | stx2 | stx2 | stx2 | stx2c | |
| PY42-1 | 11729 | O74:H42 | stx1, stx2 | stx1, stx2 | stx1, stx2 | stx1a, stx2c | |
| PY46-1 | 362 | O7:H10 | stx1, stx2 | stx1 | stx1 | stx2 (39%; 67%) | stx1a |
| PY50-1 | 4145 | O22:H16 | stx2 | stx2 a | – | stx2b, stx2d | |
| PY53-1 | 297 | O93:H46 | stx2 | stx2 | stx2 | stx2d | |
| PY58-1 | 658 | O185:H28 | stx1, stx2 | stx1, stx2 | stx1, stx2 | stx1a, stx2a | |
| PY101-1 | 2520 | OgN31:H49 | stx1, stx2 | stx2 | stx2 | stx1 (47%; 65%) | stx2a |
| PY110-1 | 348 | O110:H28 | stx1, stx2 | stx1 | stx1 | stx2 (50%; 66%) | stx1d |
| PY119-1 | 162 | O8:H19 | stx1, stx2 | – | – | stx1 (11%; 71%), stx2 (37%; 95%) | |
| PY175-1 | 388 | O153:H41 | stx1, stx2 | stx2 | stx2 | stx1 (58%; 65%) | stx2a, stx2b |
| PY194-1 | 3576 | O8:H7 | stx1, stx2 | stx2 | stx2 | stx1 (47%; 66%) | stx2a |
| PY222-3 | 2387 | O185:H7 | stx1 | stx1 | stx1 | stx1a | |
| PY233-4 | 58 | O155:H21 | stx1, stx2 | – | – | stx1 (0%), stx2 (8%; 77%) | |
| PY233-5 | 8135 | O116:H21 | stx1, stx2 | stx1, stx2 | stx1, stx2 | stx1a, stx2a | |
| PY233-8 | 446 | O22:H8 | stx2 | stx2 | stx2 | stx2a | |
| PY233-9 | 446 | O22:H8 | stx2 | stx2 | stx2 | stx2a | |
| PY240-1 | 11729 | O74:H42 | stx1, stx2 | stx1, stx2 | stx1, stx2 | stx1a, stx2c |
a
Only subunit B was detected.
b
“–” indicates that the gene was not detected.