TABLE 1.
Strains investigated with the FDA-ECID microarray and whole-genome sequencing
| Strain | Groupa | GenBank ID | Other designation(s) | Serotypeb |
stx1 |
stx2 |
eae |
ehxA |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| O |
H |
||||||||||||||||
| Reported | ECID | WGS | Reported | ECID | WGS | ECID | WGS | ECID | WGS | ECID | WGS | ECID | WGS | ||||
| K-12 | A | U00096 | MG1655 | Rough | 16 | 16 | 48 | 48 | 48 | − | − | − | − | − | − | − | − |
| EC1439 | A | AIFV | DEC 6A | 111 | 111 | 111 | 12 | 12 | 12 | − | − | − | − | − | − | − | − |
| EC1440 | A | AIFW | DEC 6B | 111 | 111 | 111 | 12 | 12 | 12 | − | − | − | − | − | − | − | − |
| EC1441 | A | AIFX | DEC 6C | 111 | 111 | 111 | 12 | 12 | 12 | − | − | − | − | − | − | − | − |
| EC1442 | A | AIFY | DEC 6D | 111 | 111 | 111 | 4 | 4 | 4 | − | − | − | − | − | − | − | − |
| EC1443 | A | AIFZ | DEC 6E | 111 | 111 | 111 | NM | 4 | 4 | − | − | − | − | − | − | − | − |
| EC1445 | A | AIGB | DEC 7B | 149 | 157 | 157 | NM | 42 | 42 | − | − | − | − | − | − | − | − |
| EC1444 | B1 | AIGA | DEC 7A | 157 | 157 | 157 | 43 | 43 | 43 | − | − | − | − | − | − | − | − |
| EC1446 | B1 | AIGC | DEC 7C | 157 | 157 | 157 | 43 | 43 | 43 | − | − | − | − | − | − | − | − |
| EC1447 | B1 | AIGD | DEC 7D | 157 | 157 | 157 | 43 | 43 | 43 | − | − | − | − | − | − | − | − |
| EC1448 | B1 | AIGE | DEC 7E | 157 | 157 | 157 | NM | 43 | 43 | − | − | − | − | − | − | − | − |
| EC1449 | B1 | AIGF | DEC 8A | 111 | 111 | 111 | NM | 8 | 8 | a | a | − | − | γ2 | γ2 | + | + |
| EC1450 | B1 | AIGG | DEC 8B | 111 | 111 | 111 | 8 | 8 | 8 | a | a | a/c/d | a | γ2 | γ2 | + | + |
| EC1451 | B1 | AIGH | DEC 8C | 111 | 111 | 111 | NM | 11 | 11 | a | a | − | − | β1 | β1 | + | + |
| EC1452 | B1 | AIGI | DEC 8D | 111 | 111 | 111 | 11 | 11 | 11 | − | − | − | − | β1 | β1 | + | + |
| EC1453 | B1 | AIGJ | DEC 8E | 111 | 111 | 111 | 8 | 8 | 8 | a | a | − | − | γ2 | γ2 | − | − |
| EC1454 | B1 | AIGK | DEC 9A | 26 | 26 | 26 | 11 | 11 | 11 | − | − | − | − | β1 | β1 | − | − |
| EC1455 | B1 | AIGL | DEC 9B | 26 | 26 | 26 | NM | 11 | 11 | − | − | − | − | β1 | β1 | − | − |
| EC1456 | B1 | AIGM | DEC 9C | 26 | 26 | 26 | NM | 11 | 11 | − | − | − | − | β1 | β1 | − | − |
| EC1457 | B1 | AIGN | DEC 9D | 26 | 26 | 26 | 11 | 11 | 11 | − | − | − | − | β1 | β1 | − | − |
| EC1458 | B1 | AIGO | DEC 9E | 26 | 26 | 26 | 11 | 11 | 11 | − | − | − | − | β1 | β1 | − | − |
| EC1459 | B1 | AIGP | DEC 10A | 26 | 26 | 26 | 11 | 11 | 11 | a | a | − | − | β1 | β1 | + | −/+d |
| EC1460 | B1 | AIGQ | DEC 10B | 26 | 26 | 26 | 11 | 11 | 11 | a | a | − | − | β1 | β1 | + | −/+ |
| EC1461 | B1 | AIGR | DEC 10C | 26 | 26 | 26 | 11 | 11 | 11 | a | a | − | − | β1 | β1 | − | − |
| EC1462 | B1 | AIGS | DEC 10D | 26 | 26 | 26 | 11 | 11 | 11 | − | − | − | − | β1 | β1 | + | + |
| EC1463 | B1 | AFAI | DEC 10E | 26 | 26 | 26 | 11 | 11 | 11 | a | a | − | − | β1 | β1 | + | − |
| EC1464 | B1 | AIGU | DEC 10F (RDEC-1) | 15 | 15 | 15 | NM | 11 | 11 | − | − | − | − | β1 | β1 | − | − |
| EC1465 | B1 | AIGV | DEC 11A | 128 | 128 | 128 | 2 | 2 | 2 | − | − | − | − | β1 | β1 | − | − |
| EC1466 | B1 | AIGW | DEC 11B | 128 | 128 | 128 | 2 | 2 | 2 | − | − | − | − | β1 | β1 | − | − |
| EC1467 | B1 | AIGX | DEC 11C | 45 | 45 | 45 | 2 | 2 | 2 | a | a | − | − | ε1 | ε1 | + | + |
| EC1468 | B1 | AIGY | DEC 11D | 128 | 128 | 128 | 2 | 2 | 2 | − | − | − | − | β1 | β1 | − | − |
| EC1469 | B1 | AIGZ | DEC 11E | 128 | 128 | 128 | 2 | 2 | 2 | − | − | − | − | β1 | β1 | − | − |
| EC1470 | B1 | AIHA | DEC 12A | 111 | 111 | 111 | 2 | 2 | 2 | − | − | − | − | β1 | β1 | − | − |
| EC1471 | B1 | AIHB | DEC 12B | 111 | 111 | 111 | 2 | 2 | 2 | − | − | − | − | β1 | β1 | − | − |
| EC1472 | B1 | AIHC | DEC 12C | 111 | 111 | 111 | NM | 2 | 2 | − | − | − | − | β1 | β1 | − | − |
| EC1473 | B1 | AIHD | DEC 12D | 111 | 111 | 111 | 2 | 2 | 2 | − | − | − | − | β1 | β1 | − | − |
| EC1474 | B1 | AIHE | DEC 12E | 111 | 111 | 111 | NM | 2 | 2 | − | − | − | − | β1 | β1 | − | − |
| EC1375 | B1 | AAJX | DEC 12F (B171) | 111 | 111 | 111 | NM | 2 | 2 | − | − | − | − | β1 | β1 | − | − |
| EC1475 | B1 | AIHF | DEC 13A | 128 | 128 | 128 | 7 | 7 | 7 | − | − | − | − | − | − | − | − |
| EC1476 | B1 | AIHG | DEC 13B | 128 | 128 | 128 | 7 | 7 | 7 | − | − | − | − | − | − | − | − |
| EC1477 | B1 | AIHH | DEC 13C | 128 | 128 | 128 | 7 | 7 | 7 | − | − | − | − | − | − | − | − |
| EC1478 | B1 | AIHI | DEC 13D | 128 | 128 | 128 | 7 | 7 | 7 | − | − | − | − | − | − | − | − |
| EC1479 | B1 | AIHJ | DEC 13E | 128 | 128 | 128 | 47 | 7 | 7 | − | − | − | − | − | − | − | − |
| EC1480 | B1 | AIHK | DEC 14A | 128 | 86 | 86 | 21 | 8 | 8 | − | − | − | − | − | − | − | − |
| EC1481 | B1 | AIHL | DEC 14B | 128 | 128 | 128 | 21 | 21 | 21 | − | − | − | − | − | − | − | − |
| EC1482 | B1 | AIHM | DEC 14C | 128 | 128 | 128 | 21 | 21 | 21 | − | − | − | − | − | − | − | − |
| EC1483 | B1 | AIHN | DEC 14D | 128 | 128 | 128 | NM | 21 | 21 | − | − | − | − | − | − | − | − |
| EC1484 | B1 | AIGT | DEC 14E | 128 | 128 | 128 | 21 | 21 | 21 | − | − | − | − | − | − | − | − |
| EC1485 | B1 | AIHO | DEC 15A | 111 | 111 | 111 | 21 | 21 | 21 | − | − | − | − | − | − | − | − |
| EC1486 | B1 | AIHP | DEC 15B | 111 | 111 | 111 | 21 | 21 | 21 | − | − | − | − | − | − | − | − |
| EC1487 | B1 | AIHQ | DEC 15C | 111 | 111 | 111 | 21 | 21 | 21 | − | − | − | − | − | − | − | − |
| EC1488 | B1 | AIHR | DEC 15D | 111 | 111 | 111 | 21 | 21 | 21 | − | − | − | − | − | − | − | − |
| EC1489 | B1 | AIHS | DEC 15E | 111 | 111 | 111 | 21 | 21 | 21 | − | − | − | − | − | − | − | − |
| EC1514 | B1 | CP000800 | E24377A | 139 | NT | 139vc | 28 | 28 | 28 | − | − | − | − | − | − | − | − |
| EC1517 | B1 | AAJW | E110019 | 111 | 111 | 111 | 9 | 9 | 9 | − | − | − | − | α4 | α4 | − | − |
| EC1518 | B1 | AAJV | E22 | 103 | 103 | 103 | 2 | 2 | 2 | − | − | − | − | β1 | β1 | − | − |
| EC1520 | B1 | CP005998 | B7A | 148 | 148 | 148 | 28 | 28 | 28 | − | − | − | − | − | − | − | − |
| EC1892 | B1 | CP003297 | 2009EL-2050 | 104 | 104 | 104 | 4 | 4 | 4 | − | − | a/c/d | a | − | − | − | − |
| EC1893 | B1 | CP003301 | 2009EL-2071 | 104 | 104 | 104 | 4 | 4 | 4 | − | − | a/c/d | a | − | − | − | − |
| EC1894 | B1 | CP003289 | 2011C-3493 | 104 | 104 | 104 | 4 | 4 | 4 | − | − | a/c/d | a | − | − | − | − |
| EC1908 | B1 | CU928145 | 55989 | 104 | 104 | 104 | 4 | 4 | 4 | − | − | − | − | − | − | − | − |
| EC1412 | B2 | AIEV | DEC 1A | 55 | 55 | 55 | 6 | 6 | 6 | − | − | − | − | α1 | α1 | − | − |
| EC1413 | B2 | AIEW | DEC 1B | 55 | 55 | 55 | 6 | 6 | 6 | − | − | − | − | α1 | α1 | − | − |
| EC1414 | B2 | AIEX | DEC 1C | 55 | 55 | 55 | 6 | 6 | 6 | − | − | − | − | α1 | α1 | − | − |
| EC1415 | B2 | AIEY | DEC 1D | 55 | 55 | 55 | 6 | 6 | 6 | − | − | − | − | α1 | α1 | − | − |
| EC1416 | B2 | AIEZ | DEC 1E | 55 | 55 | 55 | 6 | 6 | 6 | − | − | − | − | α1 | α1 | − | − |
| EC1417 | B2 | AIFA | DEC 2A | 55 | 55 | 55 | 6 | 6 | 6 | − | − | − | − | α1 | α1 | − | − |
| EC1418 | B2 | AFJB | DEC 2B | 55 | 55 | 55 | NM | 6 | 6 | − | − | − | − | α1 | α1 | − | − |
| EC1419 | B2 | AIFB | DEC 2C | 55 | 55 | 55 | 6 | 6 | 6 | − | − | − | − | α1 | α1 | − | − |
| EC1420 | B2 | AIFC | DEC 2D | 55 | 55 | 55 | 6 | 6 | 6 | − | − | − | − | α1 | α1 | − | − |
| EC1421 | B2 | AIFD | DEC 2E | 55 | 55 | 55 | 6 | 6 | 6 | − | − | − | − | α1 | α1 | − | − |
| EC1519 | B2 | AAJU | F11 | 6 | 6 | 6 | 31 | 31 | 31 | − | − | − | − | − | − | − | − |
| EC1521 | B2 | AE014075 | CFT073 | 6 | 6 | 6 | 1 | 1 | 1 | − | − | − | − | − | − | − | − |
| EC1274 | E | CP008957 | EDL933 | 157 | 157 | 157 | 7 | 7 | 7 | a | a | a/c/d | a | γ1 | γ1 | + | + |
| EC1276 | E | BA000007 | Sakai | 157 | 157 | 157 | 7 | 7 | 7 | a | a | a/c/d | a | γ1 | γ1 | + | + |
| EC1422 | E | AIFE | DEC 3A | 157 | 157 | 157 | 7 | 7 | 7 | a | a | a/c/d | a | γ1 | γ1 | + | + |
| EC1423 | E | AIFF | DEC 3B | 157 | 157 | 157 | 7 | 7 | 7 | a | a | a/c/d | a | γ1 | γ1 | + | + |
| EC1424 | E | AIFG | DEC 3C | 157 | 157 | 157 | 7 | 7 | 7 | a | a | a/c/d | a | γ1 | γ1 | + | + |
| EC1425 | E | AIFH | DEC 3D | 157 | 157 | 157 | 7 | 7 | 7 | a | a | a/c/d | a | γ1 | γ1 | + | + |
| EC1426 | E | AIFI | DEC 3E | 157 | 157 | 157 | 7 | 7 | 7 | − | − | a/c/d | c | γ1 | γ1 | + | + |
| EC1427 | E | AIFJ | DEC 3F (493/89) | 157 | 157 | 157 | NM | 7 | 7 | − | − | a/c/d | a | γ1 | γ1 | + | + |
| EC1428 | E | AIFK | DEC 4A | 157 | 157 | 157 | 7 | 7 | 7 | − | − | − | − | γ1 | γ1 | + | + |
| EC1429 | E | AIFL | DEC 4B | 157 | 157 | 157 | 7 | 7 | 7 | − | − | a/c/d | a, c | γ1 | γ1 | + | + |
| EC1430 | E | AIFM | DEC 4C | 157 | 157 | 157 | 7 | 7 | 7 | − | − | − | − | γ1 | γ1 | + | + |
| EC1431 | E | AIFN | DEC 4D | 157 | 157 | 157 | 7 | 7 | 7 | − | − | a/c/d | c | γ1 | γ1 | + | + |
| EC1432 | E | AIFO | DEC 4E | 157 | 157 | 157 | 7 | 7 | 7 | a | a | − | − | γ1 | γ1 | + | + |
| EC1433 | E | AIFP | DEC 4F (EDL933) | 157 | 157 | 157 | 7 | 7 | 7 | a | a | a/c/d | a | γ1 | γ1 | + | + |
| EC1434 | E | AIFQ | DEC 5A | 55 | 55 | 55 | 7 | 7 | 7 | − | − | − | − | γ1 | γ1 | − | − |
| EC1435 | E | AIFR | DEC 5B | 55 | 55 | 55 | 7 | 7 | 7 | − | − | − | − | γ1 | γ1 | − | − |
| EC1436 | E | AIFS | DEC 5C | 55 | 55 | 55 | 7 | 7 | 7 | − | − | − | − | γ1 | γ1 | − | − |
| EC1437 | E | AIFT | DEC 5D | 55 | 55 | 55 | 7 | 7 | 7 | − | − | − | − | γ1 | γ1 | − | − |
| EC1438 | E | AIFU | DEC 5E | 55 | 55 | 55 | 7 | 7 | 7 | − | − | − | − | γ1 | γ1 | − | − |
| EC1734 | E | AKMO | 09PF 532 | 157 | 157 | 157 | 7 | 7 | 7 | − | − | a/c/d | a | γ1 | γ1 | + | + |
| EC1738 | E | AKMN | 550659 | 157 | 157 | 157 | 7 | 7 | 7 | − | − | a/c/d | c | γ1 | γ1 | + | + |
| EC4045 | E | ABHL | FD 888 C1 | 157 | 157 | 157 | 7 | 7 | 7 | − | − | a/c/d | a, c | γ1 | γ1 | + | + |
| EC4076 | E | ABHQ | BAC0600006766 | 157 | 157 | 157 | 7 | 7 | 7 | − | − | a/c/d | a, c | γ1 | γ1 | + | + |
| EC4115 | E | CP001164 | 06MMIS0960 | 157 | 157 | 157 | 7 | 7 | 7 | − | − | a/c/d | a, c | γ1 | γ1 | + | + |
| EC4206 | E | ABHK | 06X04242 | 157 | 157 | 157 | 7 | 7 | 7 | − | − | a/c/d | a, c | γ1 | γ1 | + | + |
| EC4401 | E | ABHR | 06E02109 | 157 | 157 | 157 | 7 | 7 | 7 | − | − | a/c/d | a, c | γ1 | γ1 | + | + |
| EC2822 | CL1 | AEJX | TW15838 | NA | 2 | 2 | NA | 45 | 45 | a | a | a/c/d | a | − | − | + | + |
| EC2817 | CL3 | AEJW | TW09231 | NA | NT | 10-likec | NA | 52 | 52 | − | − | − | − | − | − | − | − |
| EC2819 | CL4 | AEMF | TW11588 | NA | NT | 36-likec | NA | NT | 5/56-likec | − | − | − | − | − | − | − | − |
| EC2818 | CL5 | AEME | TW09308 | NA | NT | 139v-likec | NA | 56 | 56 | − | − | − | − | − | − | − | − |
a
E. coli phylogroup or cryptic lineage (CL).
b
NA, not available; NM, nonmotile; NT, nontypeable.
c
Not represented on the array.
d
Negative in the WGS contigs but positive in the SRA reads.