Table 2.
Polymerase chain reaction (PCR) primers, targets, and amplicon sizes used for genotyping
| Target gene | Primer | Sequence | Amplicon size (bp) | References |
|---|---|---|---|---|
| rfb O139 cluster | O139F | AGCCTCTTTATTACGGGTGG | [43, 44] | |
| rfb O139 cluster | O139R | GTCAAACCCGATCGTAAAGG | 449 | [43, 44] |
| rfb O1 cluster | O1F | GTTTCACTGAACAGATGGG | [43, 44] | |
| rfb O1 cluster | O1R | GGTCATCTGTAAGTACAAC | 192 | [43, 44] |
| ctx | ctxA1 | CTCAGACGGGATTTGTTAGGCACG | [2] | |
| ctx | ctxA2 | TCTATCTCTGTAGCCCCTATTACG | 301 | [2] |
| toxR | UtoxF | GASTTTGTTTGGCGYGARCAAGGTT | [19] | |
| toxR | VctoxR | GGTTAGCAACGATGCGTAAG | 640 | [19] |
| rpoB | CM32b-F | CGGAACGGCCTGACGTTGCAT | [20] | |
| rpoB | 1110F-R | GTAGAAATCTACCGCATGATG | 984 | [20] |
| rpoB | 1661F* | TTYATGGAYCARAACAACCC | – | [20] |
| rpoB | 1783b* | GGACCTTYAGGNGTTTCGAT | – | [20] |
| hlyA class/ET | hlyA-489F | GGCAAACAGCGAAACAAATACC | 727/738 | [5, 6] |
| hlyA ET | hlyA-744F | GAGCCGGCATTCATCTGAAT | 481 | [5, 6] |
| hlyA class/ET | hlyA-1184R | CTCAGCGGGCTAATACGGTTTA | [5, 6] | |
| tcpA | tcpA-F_Class-ET | CACGATAAGAAAACCGGTCAAGAG | [5, 6] | |
| tcpA class | tcpA-R_class | TTACCAAATGCAACGCCGAATG | 620 | [5, 6] |
| tcpA ET | tcpA-R_ET | AATCATGAGTTCAGCTTCCCGC | 453 | [5, 6] |
| TTSS vcsC2 | TTSS_vcsC2-A | CGTTACCGATGCTATGGGT | [2] | |
| TTSS vcsC2 | TTSS_vcsC2-B | AGAAGTCGGTTGTTTCGGTAA | 535 | [2] |
| TTSS vcsN2 | TTSS_vcsN2-A | CAGTTGAGCCAATTCCATT | [2] | |
| TTSS vcsN2 | TTSS_vcsN2-B | GACCAAACGAGATAATG | 484 | [2] |
| TTSS vspD | TTSS_vspD-A | AACTCGAAGAGCAGAAAAAAGC | [2, 31] | |
| TTSS vspD | TTSS_vspD-B | CTTCCCGCTTTTGATGAAATG | 422 | [2, 31] |
| TTSS vcsV2 | TTSS_vcsV2-A | TTTGGCTCACTTGATGGG | [2, 31] | |
| TTSS vcsV2 | TTSS_vcsV2-B | GCCACATCATTGCTTGCT | 742 | [2, 31] |
| mshA | VC0409-F | ATTCTCGGTATCTTGGCCGTC | [7] | |
| mshA | VC0409-R | ACAAGCAGTTCCAGCAACCC | 459 | [7] |
| rstR class | VC-rstR-class-F | CTCATCAGCAAAGCCTCCATC | [7] | |
| rstR class | VC-rstR-class-R | TAGCAAATGGTATCGGCGTTG | 241 | [7] |
| rstR ET | VC1455-F | AGCCAACCAAAGAAAGGCAAT | [7] | |
| rstR ET | VC1455-R | TCATCTGTGGCCCATCTTCC | 186 | [7] |
| rstR Calc | VC-rstR-calc-F | CCAGCATTTCTGTTTCTTTG | [7] | |
| rstR Calc | VC-rstR-calc-R | GGCAACAAAGCACATTAAAG | 104 | [7] |
| dth | VCA1111-F | CAACCATGCACTAAATTGCCC | This study | |
| dth | VCA1111-R | TGGAAGTCATTACACCCACGC | 526 | This study |
| chxA | VC-chxA-F | TGTGTGATGATGCTTCTGG | [33] | |
| chxA | VC-chxA-R | TTATTTCAGTTCATCTTTTCGC | 2000 | [33] |
| rtxA | VC1451-F | GATTCTTCCGTTCAAGCTCCG | This study | |
| rtxA | VC1451-R | TGGTTCAGGCTGTTGCACAC | 2571 | This study |
| rtxC | VC1450-F | TGCAAATCTCACATTAGCGCA | This study | |
| rtxC | VC1450-R | CCACTGCACCTTTCGGATACA | 430 | This study |
| ompU | ompU-F | ACGCTGACGGAATCAACCAAAG | [2] | |
| ompU | ompU-R | GCGGAAGTTTGGCTTGAAGTAG | 869 | [2] |
| zot | zot-F | TCGCTTAACGATGGCGCGTTTT | [2] | |
| zot | zot-R | AACCCCGTTTCACTTCTACCCA | 947 | [2] |
| ace | ace-F | TAAGGATGTGCTTATGATGGACACCC | [2] | |
| ace | ace-R | CGTGATGAATAAAGATACTCATAGG | 289 | [2] |
| VSP-1 | Vch-VspI-fo | GCTCTCGCCAGCAAGGAGCTG | [7] | |
| VSP-1 | Vch-VspI-re | CCGTCGAAGTGAACGGCGAAC | 1700 | [7] |
| VSP-2 | Vch-VspII-fo | TGCCCATTCCGCTAAGTGTTC | [7] | |
| VSP-2 | Vch-VspII-re | GCAAAAGCACTGCGTAAACTG | 800 | [7] |
*Sequencing primers