Table 1.
Oligonucleotide name | Target gene | Oligonucleotide 5′ ➔ 3′ | Amplification product (bp) | References |
---|---|---|---|---|
E. coli marker | ||||
uidA-forward | uidA | ATGTGCTGTGCCTGAACC | 450 | [60] |
uidA-reverse | ATTGTTTGCCTCCCTGCTG | |||
Virulence genes for extra-intestinal pathogenic E. coli | ||||
papC-forward | papC | GACGGCTGTACTGCAGGGTGTGGCG | 350 | [61] |
papC-reverse | ATATCCTTTCTGCAGGGATGCAATA | |||
SfaSf | sfaS | GTGGATACGACGATTACTGTG | 240 | [62] |
SfaSr | CCGCCAGCATTCCCTGTATTC | |||
Afaf | afa/dra | GGCAGAGGGCCGGCAACAGGC | 592 | [62] |
Afar | CCCGTAACGCGCCAGCATCTC | |||
FyuAf | fyuA | TGATTAACCCCGCGACGGGAA | 880 | [62] |
FyuAr | CGCAGTAGGCACGATGTTGTA | |||
yfcV-forward | yfcV | ACATGGAGACCACGTTCACC | 292 | [63] |
yfcV-reverse | GTAATCTGGAATGTGGTCAGG | |||
Vat-forward | vat | TCAGGACACGTTCAGGCATTCAGT | 1100 | [63] |
Vat-reverse | GGCCAGAACATTTGCTCCCTTGTT | |||
KpsMIIf | kpsMT II | GCGCATTTGCTGATACTGTTG | 272 | [62] |
KpsMIIr | CATCCAGACGATAAGCATGAGCA | |||
Quinolone resistance genes | ||||
gyrA11753 | gyrA | GTATAACGCATTGCCGC | 251 | [64] |
gyrA12004 | TGCCAGATGTCCGAGAT | |||
EC-PAR-A | parC | CTGAATGCCAGCGCCAAATT | 189 | [65] |
EC-PAR-B | GCGAACGATTTCGGATCGTC | |||
qnrA-forward | qnrA | TCAGCAAGAGGATTTCTCA | 605 | [66] |
qnrA-reverse | GGCAGCACTATTACTCCCA | |||
qnrB-forward | qnrB | GATCGTGAAAGCCAGAAAGG | 469 | [12] |
qnrB-reverse | ACGATGCCTGGTAGTTGTCC | |||
qnrS-forward | qnrS | ACGACATTCGTCAACTGCAA | 417 | [12] |
qnrS-reverse | TAAATTGGCACCCTGTAGGC | |||
qnrC-forward | qnrC | GGGTTGTACATTTATTGAATC | 447 | [64] |
qnrC-reverse | TCCACTTTACGAGGTTCT | |||
qnrD-forward | qnrD | CGAGATCAATTTACGGGGAATA | 582 | [27] |
qnrD-reverse | AACAAGCTGAAGCGCCTG | |||
qepA-forward | qepA | CTGCAGGTACTGCGTCATG | 403 | [67] |
qepA-reverse | CGTGTTGCTGGAGTTCTTC | |||
aac-forward | acc-(6′)-lb | TTGCGATGCTCTATGAGTGGCTA | 482 | [26] |
aac-reverse | CTCGAATGCCTGGCGTGTTT | |||
Beta-lactamase resistant genes | ||||
blaTEM-forward | bla TEM | GAGTATTCAACATTTTCGT | 857 | [30] |
blaTEM-reverse | ACCAATGCTTAATCAGTGA | |||
blaSHV-forward | bla SHV | TCGCCTGTGTATTATCTCCC | 768 | [30] |
blaSHV-reverse | CGCAGATAAATCACCACAATG | |||
blaOXA-1-forward | bla OXA-1 | GCAGCGCCAGTGCATCAAC | 198 | [30] |
blaOXA-1-reverse | CCGCATCAAATGCCATAAGTG | |||
blaOXA-7-forward | bla OXA-7, -9 | AGTTCTCTGCCGAAGCC | 591 | [30] |
blaOXA-7-reverse | TCTCAACCCAACCAACCC | |||
blaPSE-4-forward | bla PSE-4 | CTGCTCGTATAGGTGTTTCC | 705 | [30] |
blaPSE-4-reverse | TCGCATCATTTCGCTCTTC | |||
blaCTX-M-3-f | bla CTX-M-3 | AATCACTGCGTCAGTTCAC | 701 | [30] |
blaCTX-M-3-r | TTTATCCCCCACAACCCAG | |||
blaCTX-M-forward | bla CTX-M | AAGGCGTTTTGACAGACTATT | 920 | This study |
blaCTX-M-reverse | GGTGACGATTTTAGCCGC |