TABLE 1.
Phylogenetic characteristics of tested STEC isolatesa
| Farm or reference strain | Sample no. | Animal | % of STEC in the total no. of E. coli strains | DNA-based serotypeb | Virulence marker(s)c | No. of isolates |
|---|---|---|---|---|---|---|
| Farm | ||||||
| 1 | 1 | Goat 1 | 19.1 | O113:H4 | stx1c, stx2b, hlyA, espI, astA, iha, ireA | All |
| 2 | Goat 2 | 100.0 | O91:H14 | stx1a, hlyA, espP, espI, saa, iha, ireA, lpfA | All | |
| 3 | Goat 3 | 100.0 | O113:H4 | stx1c, stx2b, hlyA, espI, astA, iha, ireA, (lpfA) | All | |
| 4 | Goat 4 | 100.0 | O113:H4 | stx1c, stx2b, hlyA, espI, astA, iha, ireA | All | |
| 5 | Goat 5 | 100.0 | O113:H4 | stx1c, stx2b, hlyA, espI, astA, (iha), ireA | All | |
| 2 | 6 | Goat 1 | 36.1 | NT:H19 | stx1c, hlyA, ireA, lpfA, pic | All |
| 7 | Goat 2 | 6.6 | O157:H8 | stx1c, stx2b, hlyA, katP, espI, iha, ireA, lpfA | 1 | |
| NT:H8 | stx1c, stx2b, hlyA, espI, iha, (ireA), lpfA | 4 | ||||
| 8 | Sheep 3 | 24.8 | NT:H21 | stx1c, stx2b, hlyA, (astA), (efa1), lpfA, (hlyE), (bfpA) | All | |
| 9 | Sheep 4 | 31.1 | O55:H21 | stx1c, stx2b, hlyA, lpfA | 1 | |
| NT:H21 | stx1c, stx2b, hlyA, lpfA | 4 | ||||
| 10 | Sheep 5 | 0.9 | O104:H16 | stx1c, stx2b, hlyA, espI, iha, lpfA | 1 | |
| 3 | 11 | Sheep 1 | 100.0 | O113:H4 | stx1c, stx2b, hlyA, espI, astA, iha, ireA | All |
| 12 | Sheep 2 | 8.9 | O128:H2 | stx1c, stx2b, hlyA, espI, iha, ireA, lpfA | 4 | |
| NT:H19 | stx1c, hlyA, espI, iha, ireA, lpfA | 1 | ||||
| 13 | Sheep 3 | 100.0 | O113:H4 | stx1c, stx2b, hlyA, espI, astA, iha, ireA | All | |
| 14 | Sheep 4 | 100.0 | O113:H4 | stx1c, stx2b, hlyA, espI, astA, iha, ireA | All | |
| 15 | Sheep 5 | 100.0 | O91:H14 | stx1a, stx2b, espI, iha, ireA, lpfA | 3 | |
| O113:H4 | stx1c, stx2b, hlyA, espI, (astA), iha, (ireA), (lpfA) | 2 | ||||
| 16 | Sheep 6 | 3.9 | O103:H21 | stx1a, stx2b, (espI), (iha), (ireA), lpfA | 3 | |
| O103:H21 | stx1c, stx2b, (hlyA), (espI), astA, (ireA), lpfA | 2 | ||||
| 17 | Goat 7 | 2.7 | O145:H6 | stx1c, stx2b, (hlyA), (espI), astA, (iha) | All | |
| 18 | Goat 8 | 100.0 | O103:H34 | stx1c, stx2b, eae, tir, hlyA, espA, espC, espF, espI, nleB, nleC, astA, iha, toxB, hlyE | 1 | |
| O113:H4 | stx1c, stx2b, hlyA, espI, astA, iha, ireA, (toxB), (lpfA) | 3 | ||||
| O9:H4 | stx1c, stx2b, hlyA, espI, astA, iha, ireA | 1 | ||||
| 4 | 19 | Goat 1 | 10.8 | NT:H19 | stx1c, hlyA, astA, ireA, lpfA, pic | All |
| 20 | Goat 2 | 2.1 | O145:NT | (astA), iha, ireA | All | |
| 21 | Sheep 3 | 49.6 | NT:H19 | stx1c, hlyA, (astA), (ireA), lpfA, pic | 4 | |
| O157:H56 | astA | 1 | ||||
| 5 | 22 | Goat 1 | 4.5 | O157:H4 | stx1c, hlyA, espI, (iha) | 2 |
| NT:H38 | astA, lpfA | 2 | ||||
| 23 | Goat 2 | 52.5 | O157:H4 | stx1c, hlyA, espI, iha, ireA, toxB | All | |
| 24 | Goat 3 | 33.3 | O157:H4 | stx1c, (stx2b), hlyA, espI, iha, ireA, (toxB), (K88) | All | |
| 25 | Goat 4 | 32.3 | O157:H4 | (stx1c), hlyA, espI, iha, ireA, (toxB), K88 | All | |
| 26 | Goat 5 | 39.7 | O157:H4 | stx1c, (stx2b), hlyA, espI, iha, ireA, K88 | All | |
| 27 | Goat 6 | 100.0 | NT:H19 | stx1c, stx2b, ireA, lpfA, pic | All | |
| 28 | Sheep 7 | 47.3 | O157:H4 | stx1c, hlyA, espI, iha, ireA, K88 | All | |
| 29 | Sheep 8 | 1.8 | NT:H7 | (stx2b), lpfA | All | |
| 6 | 30 | Goat 1 | 0.0 | |||
| 31 | Goat 2 | 0.0 | ||||
| 32 | Goat 3 | 0.7 | O157:H10 | (stx1c), (hlyA), (espI), (iha), (ireA), lpfA | 2 | |
| NT:H21 | hlyA, espI, iha, ireA, lpfA | 1 | ||||
| 33 | Goat 4 | 1.7 | O7:H37 | stx2b, espI, iha, ireA | 1 | |
| NT:H8 | stx2b, hlyA, espI, iha, lpfA | 1 | ||||
| 34 | Sheep 5 | 0.9 | O26:H21 | stx2b, lpfA | 1 | |
| NT:H21 | lpfA | 3 | ||||
| 35 | Sheep 6 | 0.4 | O157:H49 | lpfA | 1 | |
| NT:H28 | lpfA | 2 | ||||
| NT:H49 | lpfA | 1 | ||||
| 36 | Sheep 7 | 100.0 | O157:H8 | stx1c, stx2b, espI, iha, lpfA | 1 | |
| NT:H8 | stx1c, stx2b, espI, iha, lpfA | 3 | ||||
| 37 | Sheep 8 | 100.0 | NT:H8 | stx1c, stx2b, espI, iha, (ireA), lpfA, (K88) | All | |
| 38 | Sheep 9 | 0.1 | O79:H8 | (stx1c), (stx2b), (lpfA) | All | |
| 7 | 39 | Goat 1 | 24.0 | NT:H4 | stx1c, stx2b, hlyA, espI, (espP), astA, iha | All |
| 40 | Goat 2 | 11.3 | NT:H19 | stx1c, stx2b, hlyA, (espI), (iha), lpfA, (pic) | All | |
| 41 | Goat 3 | 2.7 | NT:H4 | stx1c, (stx2b), hlyA, (espI), (espP), (iha), lpfA, (pic) | All | |
| 42 | Goat 4 | 12.3 | O26:H19 | stx1c, hlyA, lpfA, pic | 2 | |
| NT:H19 | stx1c, hlyA, lpfA, pic | 2 | ||||
| 8 | 43 | Sheep 1 | 1.0 | NT:H21 | stx1c, hlyA, espI, iha, lpfA | 3 |
| NT:H8 | stx1c, lpfA | 1 | ||||
| 44 | Sheep 2 | 4.6 | NT:H21 | stx1c, hlyA, espI, iha, lpfA | 2 | |
| NT:H8 | stx1c, hlyA, espI, iha, lpfA | 2 | ||||
| 45 | Sheep 3 | 3.9 | NT:H21 | stx1c, hlyA, espI, iha, lpfA | 3 | |
| NT:H8 | stx1c, hlyA, espI, iha, lpfA | 1 | ||||
| 46 | Goat 4 | 0.0 | ||||
| 47 | Goat 5 | 12.3 | NT:H21 | β-eae, hlyA, espB, espF, espI, espJ, nleA, iha, (lpfA) | All | |
| 48 | Goat 6 | 25.9 | NT:H19 | stx1c, stx2b, hlyA, espI, iha, lpfA, pic | All | |
| Reference strainsd | ||||||
| EHEC EDL 933 | O157:H7 | stx1a, stx2a, γ-eae, tir, hlyA, espA, espF, espJ, espP, katP, nleA, nleB, nleC, tccP, etpD, astA, iha, toxB | ||||
| EPEC E2348/69 | NT:H6 | α-eae, tir, espA, espC, espF, espJ, nleA, nleB, nleC, efa1, cif, astA, toxB, bfpA | ||||
| EHEC DD-23137 (outbreak strain) | O104:H4 | stx2a, iha, pic, ctxM1, tem1 |
a
A table with data presented isolate by isolate is available in Table SA2 in the supplemental material.
b
NT, not detectable by microarray.
c
Virulence markers in parentheses were not found in all isolates of the corresponding serotype.
d
Virulence markers of selected reference strains. The complete lists of the results for all reference strains are available in Table SA1 in the supplemental material.