TABLE 1.
Primer pairs used for detection of marker genes indicative of a particular pathotype
| Pathovar and target gene | Primer | Sequence (5′ to 3′) | Product size (bp) | Concn (μM) | Annealing temp (°C) |
|---|---|---|---|---|---|
| LEE-positive strains (EPEC, ATEC, STEC) | |||||
| escV | MP3-escV-F | ATTCTGGCTCTCTTCTTCTTTATGGCTG | 544 | 0.4 | 63 |
| MP3-escV-R | CGTCCCCTTTTACAAACTTCATCGC | 0.4 | |||
| Typical EPEC | |||||
| bfpB | MP3-bfpB-F | GACACCTCATTGCTGAAGTCG | 910 | 0.1 | 63 |
| MP3-bfpB-R | CCAGAACACCTCCGTTATGC | 0.1 | |||
| STEC | |||||
| stx1 | MP4-stx1A-F | CGATGTTACGGTTTGTTACTGTGACAGC | 244 | 0.2 | 63 |
| MP4-stx1A-R | AATGCCACGCTTCCCAGAATTG | 0.2 | |||
| stx2 | MP3-stx2A-F | GTTTTGACCATCTTCGTCTGATTATTGAG | 324 | 0.4 | 63 |
| MP3-stx2A-R | AGCGTAAGGCTTCTGCTGTGAC | 0.4 | |||
| ETEC | |||||
| elt | MP2-LT-F | GAACAGGAGGTTTCTGCGTTAGGTG | 655 | 0.1 | 63 |
| MP2-LT-R | CTTTCAATGGCTTTTTTTTGGGAGTC | 0.1 | |||
| estIa | MP4-STIa-F | CCTCTTTTAGYCAGACARCTGAATCASTTG | 157 | 0.4 | 63 |
| MP4-STIa-R | CAGGCAGGATTACAACAAAGTTCACAG | 0.4 | |||
| estIb | MP2-STI-F | TGTCTTTTTCACCTTTCGCTC | 171 | 0.2 | 63 |
| MP2-STI-R | CGGTACAAGCAGGATTACAACAC | ||||
| EIEC | |||||
| invE | MP2-invE-F | CGATAGATGGCGAGAAATTATATCCCG | 766 | 0.2 | 63 |
| MP2-invE-R | CGATCAAGAATCCCTAACAGAAGAATCAC | 0.2 | |||
| EAEC | |||||
| astA | MP-astA-F | TGCCATCAACACAGTATATCCG | 102 | 0.4 | 63 |
| MP2-astA-R | ACGGCTTTGTAGTCCTTCCAT | 0.4 | |||
| aggR | MP2-aggR-F | ACGCAGAGTTGCCTGATAAAG | 400 | 0.2 | 63 |
| MP2-aggR-R | AATACAGAATCGTCAGCATCAGC | 0.2 | |||
| pic | MP2-pic-F | AGCCGTTTCCGCAGAAGCC | 1,111 | 0.2 | 63 |
| MP2-pic-R | AAATGTCAGTGAACCGACGATTGG | 0.2 | |||
| E. coli | |||||
| uidA | MP2-uidA-F | ATGCCAGTCCAGCGTTTTTGC | 1,487 | 0.2 | 63 |
| MP2-uidA-R | AAAGTGTGGGTCAATAATCAGGAAGTG | 0.2 | |||
| ShET2 homologue | |||||
| ent | ent-F | TGGGCTAAAAGAAGACACACTG | 629 | 0.4 | 58 |
| ent-R | CAAGCATCCTGATTATCTCACC | 0.4 |