TABLE 3.
Primers and probes used in this study
| Targeta | Primer IDb | Sequence (5′–3′) | Amplicon (bp)/special fragment(s) in Fig. 3 (kb) |
Purpose(s)c | Reference or source |
|---|---|---|---|---|---|
| ctxA | ctxA-F | ACAGAGTGAGTACTTTGACC | 307 bp | PCR/CBH/Seq | 57 |
| ctxA-R | ATACCATCCATATATTTGGGAG | 307 bp/6.8 kb | PCR/CBH/Seq | 57 | |
| ctxB | ctxB-F | GATACACATAATAGAATTAAGGAT | 399 bp/3.8 kb, 7.0 kb | PCR/Seq | 58 |
| ctxB-R | TTGCCATACTAATTGCGG | PCR/Seq | This study | ||
| ctxB-com5-F (common) | ACTATCTTCAGCATATGCACATGG | MAMA PCR | This study | ||
| ctxB-cla3-R (classical) | CCTGGTACTTCTACTTGAAACG | 366 bp | MAMA PCR | 47 | |
| ctxB-e13-R (El Tor) | CCTGGTACTTCTACTTGAAACA | 366 bp | MAMA PCR | 47 | |
| orfU | orfU-F | CGTCACACCAGTTACTTTTCG | 1,072 bp | PCR/Seq | 43 |
| orfU-R | AGAATGTACGCCATCGC | PCR/Seq | 43 | ||
| orfU-R1 | CGAAAAGTAACTGGTGTGACG | 7.0 kb, 3.0 kb | PCR/Seq | This study | |
| zot | zot-1 | GGCTTAAACCTTGAACGC | 1,036 bp | PCR | This study |
| zot-2 | AACCCCGTTTCACTTCTAC | PCR | This study | ||
| zot-F1 | ATGAGTTTGAAACCATACACTTT | 2.1 kb, 0.75 kb, 3.0 kb | PCR/Seq | This study | |
| rstC | rstC-F | ATGAGTTTGAAACCATACACTTT | 225 bp/0.9 kb, 6.8 kb | PCR/CBH/Seq | 17 |
| rstC-R | TTACAGTGATGGATCAGTCAAT | 225 bp | PCR/CBH/Seq | 17 | |
| rstR | rstR-R (common) | TCGAGTTGTAATTCATCAAGAGTG | PCR/CBH/Seq | 20 | |
| rstR (classical)-F | CTTCTCATCAGCAAAGCCTCCATC | 474 bp | PCR | 20 | |
| rstR (El Tor)-F | GCACCATGATTTAAGATGCTC | 501 bp | PCR/CBH/Seq | 20 | |
| rstR (Calcutta)-F | CTGTAAATCTCTTCAATCCTAGG | 313 bp | PCR | 20 | |
| rstR (Environment)-F | GTTAACGCTTCAAGCCTG | 372 bp | PCR/CBH/Seq | This study | |
| rstR (El Tor)-R1 | GAGCATCTTAAATCATGGTGC | 0.9 kb, 2.1 kb | PCR/Seq | This study | |
| rstR (Environment)-R1 | CAGGCTTGAAGCGTTAAC | 0.9 kb, 3.8 kb, 0.75 kb | PCR/Seq | This study | |
| tcpA | tcpH1-F | AGCCGCCTAGATAGTCTGTG | 1,324 bp | PCR/Seq | 45 |
| tcpA4-R | TCGCCTCCAATAATCCGAC | PCR/Seq | 45 | ||
| tcpA-F | CACGATAAGAAAACCGGTCAAGAG | 2,108 bp | PCR/Seq | 25 | |
| tcpQ-R | GAGGACTGTTCTGCAAATCTGCTCAT | PCR | 34 | ||
| tcpA (classical)-R | TTACCAAATGCAACGCCGAATG | Seq | This study | ||
| tcpA (El Tor)-R | CGAAAGCACCTTCTTTCACACGTTG | Seq | This study | ||
| toxT | toxT-R | CCATGAATGTAGCACCAAG | PCR/Seq | This study | |
| toxT-F | CTTGTCTATTGTTCGTAAAGTG | 834 bp | PCR/Seq | This study | |
| toxT-F2 | CTGATGATCTTGATGCTATG | 298 bp | PCR/Seq | This study | |
| TLC | tlc-F | GGGAATGTTGAGTTCTCAGTG | 1,548 bp | PCR | 6 |
| tlc-R | GTTGCGAAGTGGATTTTGTG | PCR | 6 | ||
| RTX | rtx-F | CACTCATTCCGATAACCAC | 1,366 bp | PCR | 6 |
| rtx-R | GCGATTCTCAAAGAGATGC | PCR | 6 | ||
| T3SS-2 | vcsN2-F | CAACACCTTCAAAGCCTTG | 848 bp | PCR/CBH | This study |
| vcsN2-R | GCGAGCTCCAATTGAAAC | PCR/CBH | This study | ||
| NAG-ST | stn-F | GAGAAACCTATTCATTGC | 216 bp | PCR/CBH | 59 |
| stn-R | GCAAGCTGGATTGCAAC | PCR/CBH | 59 | ||
| VSP-I | VC0175F2 | TGAGGGCTGCTGAATAAG | 689 bp | PCR/CBH | This study |
| VC0175R2 | TTGGCTCTGGTGTAAAGG | PCR/CBH | This study | ||
| VC0183F2 | AATACCACAAAGGACGCAC | 687 bp | PCR/CBH | This study | |
| VC0183R2 | TGGCCTAACCATAAGCAG | PCR/CBH | This study | ||
| VSP-II | VSPII LA F2 | CGCACATACTCTTTGGTGGCATCAG | 10,091 bp | PCR/CBH | This study |
| VSP LA R2 | ACTCTCTCTGATGGTGATGGCCTTC | PCR/CBH | This study | ||
| chxA | chxAF1 | GTCGAAGATGAGTTAAACAT | 1,904 bp | PCR/CBH | 13 |
| chxAR1 | TTATTTCAGTTCATCTTTTCGC | PCR/CBH | 13 | ||
| VSP-I | VC0175F2 | TGAGGGCTGCTGAATAAG | 689 bp | PCR/CBH | This study |
| VC0175R2 | TTGGCTCTGGTGTAAAGG | PCR/CBH | This study | ||
| VC0183F2 | AATACCACAAAGGACGCAC | 687 bp | PCR/CBH | This study | |
| VC0183R2 | TGGCCTAACCATAAGCAG | PCR/CBH | This study | ||
| VSP-II | VSPII LA F2 | CGCACATACTCTTTGGTGGCATCAG | 10,091 bp | PCR/CBH | This study |
| VSP LA R2 | ACTCTCTCTGATGGTGATGGCCTTC | PCR/CBH | This study | ||
| chxA | chxAF1 | GTCGAAGATGAGTTAAACAT | 1,904 bp | PCR/CBH | 13 |
| chxAR1 | TTATTTCAGTTCATCTTTTCGC | PCR/CBH | 13 | ||
| recA | Vm-recA-F | CTGGGTGTTAATATCGATGAG | 73 bp | RT-PCR | This study |
| Vm-recA-R | TCACAAATTTCTAGTGCTTG | RT-PCR | This study | ||
| Vm-recA-P | CTACTGGTTTCTCAGCCAGATACCGGTGA | RT-PCR | This study | ||
| toxR | Vm-toxR-F | TCCGATTAGGCAGTAACGAAA | 83 bp | RT-PCR | This study |
| Vm-toxR-R | ATGCAAATCGTTGCGAGAAAC | RT-PCR | This study | ||
| Vm-toxR-P | TCGAATTCTTTGGCTGCTTGCTCAGC | RT-PCR | This study | ||
| toxS | Vm-ToxS-F | TGGCAATCGAAGATGGTTTCA | 76 bp | RT-PCR | This study |
| Vm-ToxS-R | ACATCAACACGGCTCAATGG | RT-PCR | This study | ||
| Vm-ToxS-P | TGATCAAAACCAAGAGTAACAGTCCAGCA | RT-PCR | This study | ||
| hns | Vm-hns-F | GCTTATTTCTGCACTTTCAGG | 85 bp | RT-PCR | This study |
| Vm-hns-R | GTCGATGTACTTGTATTTCGC | RT-PCR | This study | ||
| Vm-hns-P | ACTAAAGCAAAAGGCAAACGTGCTCCTCG | RT-PCR | This study | ||
| tcpA | Vm-tcpA-F | GCTCAGCGTGCGATTGACT | 76 bp | RT-PCR | This study |
| Vm-tcpA-R | GAGTAAGCGACACTTGGATTG | RT-PCR | This study | ||
| Vm-tcpA-P | ATGACCAAGGCTGCGCAAAATCTCA | RT-PCR | This study | ||
| toxT | Vm-toxT-F | CGAGATTCTAGTTCTTTTTTCAAAACC | 123 bp | RT-PCR | This study |
| Vm-toxT-R | TGATGCTATGGAGAAAATATCATGTT | RT-PCR | This study | ||
| Vm-toxT-P | TAATTCATCACAAACATCAGACCAACGCCA | RT-PCR | This study | ||
| ctxA | ctxA-F | GGAGGGAAGAGCCGTGGAT | 66 bp | RT-PCR | 49 |
| ctxA-R | CATCGATGATCTTGGAGCATTC | RT-PCR | 49 | ||
| ctxA-P | CATCATGCACCGCCGGGTTG | RT-PCR | 49 | ||
| tcpP | tcpP-F | TGGTACACCAAGCATAATACAGACTAAG | 100 bp | RT-PCR | 49 |
| tcpP-R | AGGCCAAAGTGCTTTAATTATTTGA | RT-PCR | 49 | ||
| tcpP-P | TACTCTGTGAATATCATCCTGCCCCCTGTC | RT-PCR | 49 | ||
| tcpH | tcpH-F | GCCGTGATTACAATGTGTTGAGTAT | 82 bp | RT-PCR | 49 |
| tcpH-R | TCAGCCGTTAGCAGCTTGTAAG | RT-PCR | 49 | ||
| tcpH-P | TCAACTCGGCAAAGGTTGTTTTCTCGC | RT-PCR | 49 | ||
a
“T3SS-2” and “NAG-ST” indicate type III secretion system 2 and heat-stable enterotoxin of V. cholerae, respectively.
b
“F,” “R,” and “P” indicate forward primer, reverse primer and probe, respectively. Gene names are indicated in the primer designations.
c
“CBH” and “Seq” indicate colony blot hybridization and sequencing analysis, respectively.