Table 1.
Target Genes, Sequences of PCR Oligonucleotide Primers and Expected PCR Product Size
| Target Gene | Sequence (5’ – 3’) | Amplicon Size (bp) | Ta/Extension Time | Source |
|---|---|---|---|---|
| Resistance to beta-lactam antibiotics (β-lactamases encoding genes) | ||||
| blaTEM | F: ATAAAATTCTTGAAGAC R: TTACCAATGCTTAATCA |
1075 | 42°C/1 min | [66] |
| blaCTX-M1-like genes | F: TTAATTCGTCTCTTCCAGA R: CAGCGCTTTTGCCGTCTAAG |
1042 | 45°C/1 min | |
| blaCMY-like genes | F: ATGATGAAAAAATCGATATG R: TTATTGCAGTTTTTCAAGAATG |
1146 | 45°C/1 min | |
| Resistance to aminoglycoside antibiotics | ||||
| aac(3)-II | F: TGAAACGCTGACGGAGCCTC R: GTCGAACAGGTAGCACTGAG |
369 | 55°C/30 s | [66] |
| aac(6′)-Ib-cr | F: TTGCGATGCTCTATGAGTGGCTA R: CTCGAATGCCTGGCGTGTTT |
482 | 55°C/30 s | [67] |
| Resistance to quinolones | ||||
| qnrA | F: ATTTCTCACGCCAGGATTTG R: GATCGGCAAAGGTTAGGTCA |
516 | 52°C/40 s | [67] |
| qnrB | F: GATCGTGAAAGCCAGAAAGG R: ATGAGCAACGATGCCTGGTA |
476 | ||
| qnrS | F: GCAAGTTCATTGAACAGGGT R: TCTAAACCGTCGAGTTCGGCG |
428 | ||
| Resistance to tetracyclines | ||||
| tetA | F: GCTACATCCTGCTTGCCT R: CATAGATCGCCGTGAAGA |
210 | 52°C/30 s | [68] |
| tetB | F: TTGGTTAGGGGCAAGTTTTG R: GTAATGGGCCAATAACACCG |
600 | 52°C/40 s | |
| Resistance to sulfonamides | ||||
| sulI | F: TGGTGACGGTGTTCGGCATTC R: GCGAAGGTTTCCGAGAAGGTG |
790 | 56°C/50 s | [66] |
| sulII | F: CGGCATCGTCAACATAACCT R: TGTGCGGATGAAGTCAGCTC |
721 | 56°C/50 s | |
| Type of E. coli pathotype (virulence-associated genes in E. coli) | ||||
| EPEC: eaeA | F: AAACAGGTGAAACTGTTGCC R: CTCTGCAGATTAACCCTCTGC |
454 | 52°C/30 s | [7] |
| EAEC: aggR | F: CTAATTGTACAATCGATGTA R: ATGAAGTAATTCTTGAAT |
308 | 42°C/30 s | |
| EAEC: pCVD432 | F: CTGGCGAAAGACTGTATCAT R: CAATGTATAGAAATCCGCTGTT |
630 | 55°C/40 s | |
| STEC/EHEC: stx | F: GAGCGAAATAATTTATATGTG R: TGATGATGGCAATTCAGTAT |
518 | 42°C/30 s | [69] |
| ETEC: est | F: TTAATAGCACCCGGTACAAGCAGG R: CCTGACTCTTCAAAAGAGAAAATTAC |
147 | 52°C/30 s | |
| ETEC: elt | F: TCTCTATGTGCATACGGAGC R: CCATACTGATTGCCGCAAT |
322 | 52°C/30 s | |
| EIEC: ipaH | F: GTTCCTTGACCGCCTTTCCGATACCGTC R: GCCGGTCAGCCACCCTCTGAGAGTAC |
619 | 58°C/40 s | |
Abbreviations: PCR, polymerase chain reaction; E. coli; Escherichia coli; EPEC, enteropathogenic E. coli; EAEC, enteroaggregative E. coli; STEC, Shiga toxin-producing E. coli; ETEC, enterotoxigenic E. coli; EIEC, enteroinvasive E. coli; EHEC, enterohemorrhagic E. coli; Ta, annealing temperature; bp, base pair.