TABLE 1.
PCR primers used in this study
| Primer | Target gene | Sequence (5′-3′) | GenBank accession number (nucleotide position) |
|---|---|---|---|
| O7 right probe fwd | Z0262 | TCATGGCACAGACCCGTATTCAGC | AE005199 (1391-1368) |
| O7 right probe rev | TTCATGTCAGGCGCGGTATTTTTG | AE005199 (941-964) | |
| O7 internal probe fwd | Z0260 | CCCAGCCGCCATTACCCACAACAT | AE005198 (10861-10838) |
| O7 internal probe rev | GCTTCAGCGCGTCCGTATCCAGTA | AE005198 (10339-10362) | |
| O7 left probe fwd | Z0245 | AAAAGGTCTGGCATTTGACATTT | AE005197 (2185-2163) |
| O7 left probe rev | GCTGGATATCTCATCTGGATTTTG | AE005197 (1785-1809) | |
| O43/48 right probe fwd | Z1214 | CGGTGGGCGCTTATCAGG | AE005276 (12918-12935) |
| O43/48 right probe rev | GGGCCATCGCGTTTCTCA | AE005276 (13931-13914) | |
| O43/48 internal probe fwd | terA | AACCGGCTGAAACCTGATGTC | AE005273 (8830-8850) |
| O43/48 internal probe rev | AATTGCGCCGTTTTCGTTTAC | AE005273 (9675-9655) | |
| O43/48 left probe fwd | Z1128 | TTGCCTACAGGAAAGACACG | AE005270 (7869-7888) |
| O43/48 left probe rev | TGCTACGCCTCAGAATAATACC | AE005270 (8273-8252) | |
| O43 left junction fwd | clpA | CGCCATACCGTCAGCCGTCTTA | AE005269 (9750-9771) |
| O43 left junction rev | Z1120 | CATTTCCCCCGCCCCTTTACT | AE005270 (409-389) |
| O43 right junction fwd | Z1226 | GGGACCGGTGGGGATTTCAT | AE005277 (5971-5990) |
| O43 right junction rev | serW | CCCCCTCACCGCCAGATTAT | AE005277 (6429-6410) |
| O48 left junction fwd | ycdU | GGGGGACCGCCTGAAATAAATCT | AE005306 (1826-1848) |
| O48 left junction rev | Z1559 | ACTCGCCCCGGAATGTCACTG | AE005306 (2988-2968) |
| O48 right junction fwd | Z1664 | CTGCGGCTGCTGGCTGATG | AE005314 (3417-3435) |
| O48 right junction rev | serX | GTGAGGTGTCCGAGTGGCTGAAG | AE005314 (4286-4264) |
| O122 right probe fwd | Z4334 | AGACCCGCCACCCCACGATGTAT | AE005528 (6644-6666) |
| O122 right probe rev | Z4336 | CTGCGGCCCCGGAAAATGAAA | AE005528 (7801-7781) |
| O122 internal probe fwd | Z4326 | TTCAGGAAAACAAGGGGACAAATA | AE005527 (9726-9749) |
| O122 internal probe rev | TGCCAAGTACGCCACAATA | AE005527 (10640-10622) | |
| O122 left probe fwd | ATACGCCAGAGCCGACCAGACCA | AE005527 (3094-3116) | |
| O122 left probe rev | AACCCAGCGCCCCATCGTATTG | AE005527 (4328-4307) | |
| Efa1 fwd | efa1 5′ region | TGGGCAGAACATTTTCACCAGTTG | AJ277443 (46852-46830) |
| Efa1 rev | CTTTCAGGTGGGGAACCATATGGC | AJ277443 (46111-46127) | |
| Efa1 3′ fwd | efa1 3′ region | TGCGCACAATTGACTACAGAGGAA | AJ277443 (38050-38027) |
| Efa1 3′ rev | ATACGACCATCAGGGGAATCAC | AJ277443 (37337-37358) | |
| EspF fwd | espF | CTTCATTTACTCCCTCTCGTCCGGC | AJ277443 (36069-36093) |