Table 2.
Oligonucleotides used in this study.
| Oligonucleotide name | Target gene | Oligonucleotide 5′ → 3′ | Amplification product (bp) | Reference |
|---|---|---|---|---|
| E. coli MARKER | ||||
| uidA-forward | uidA | ATGTGCTGTGCCTGAACC | 450 | This study. |
| uidA-reverse | ATTGTTTGCCTCCCTGCTG | |||
| VIRULENCE GENES FOR INTESTINAL PATHOGENIC E. coli | ||||
| VTcom-forward | stx1/stx2 | GAGCGAAATAATTTATATGTG | 518 | Toma et al., 2003 |
| VTcom-reverse | TGATGATGGCAATTCAGTAT | |||
| East-forward | eastI | ATGCCATCAACACAGTATAT | 110 | Vila et al., 2000 |
| East-reverse | GCGAGTGACGGCTTTGTAGT | |||
| AafAf | aafA | AAATTAATTCCGGCATGG | 518 | Huang et al., 2007 |
| AafAr | ATGTATTTTTAGAGGTTGAC | |||
| aggRks1 | aggR | GTATACACAAAAGAAGGAAGC | 254 | Aranda et al., 2007 |
| aggRksa2 | ACAGAATCGTCAGCATCAGC | |||
| AL65 | est | TTAATAGCACCCGGTACAAGCAGG | 147 | Toma et al., 2003 |
| Al125 | CCTGACTCTTCAAAAGAGAAAATTAC | |||
| LTL | elt | TCTCTATGTGCATACGGAGC | 322 | Toma et al., 2003 |
| LTR | CCATACTGATTGCCGCAAT | |||
| IpaIII | ipaH | GTTCCTTGACCGCCTTTCCGATACCGTC | 619 | Toma et al., 2003 |
| IpaIV | GCCGGTCAGCCACCCTCTGAGAGTAC | |||
| BFP1 | bfpA | AATGGTGCTTGCGCTTGCTGC | 326 | Aranda et al., 2007 |
| BFP2 | GCCGCTTTATCCAACCTGGTA | |||
| eae1 | eae | CTGAACGGCGATTACGCGAA | 880 | Aranda et al., 2007 |
| eae3 | CGAGACGATACGATCCAG | |||
| VIRULENCE GENES FOR EXTRA-INTESTINAL PATHOGENIC E. coli | ||||
| papC-forward | papC | GACGGCTGTACTGCAGGGTGTGGCG | 350 | Blanco et al., 1997 |
| papC-reverse | ATATCCTTTCTGCAGGGATGCAATA | |||
| SfaSf | sfaS | GTGGATACGACGATTACTGTG | 240 | Johnson and Stell, 2000 |
| SfaSr | CCGCCAGCATTCCCTGTATTC | |||
| Afaf | afa/dra | GGCAGAGGGCCGGCAACAGGC | 592 | Johnson and Stell, 2000 |
| Afar | CCCGTAACGCGCCAGCATCTC | |||
| FyuAf | fyuA | TGATTAACCCCGCGACGGGAA | 880 | Johnson and Stell, 2000 |
| FyuAr | CGCAGTAGGCACGATGTTGTA | |||
| KpsMIIf | kpsMT II | GCGCATTTGCTGATACTGTTG | 272 | Johnson and Stell, 2000 |
| KpsMIIr | CATCCAGACGATAAGCATGAGCA | |||
| QUINOLONE RESISTANCE GENES | ||||
| gyrA11753 | gyrA | GTATAACGCATTGCCGC | 251 | Wang et al., 2001 |
| gyrA12004 | TGCCAGATGTCCGAGAT | |||
| EC-PAR-A | parC | CTGAATGCCAGCGCCAAATT | 189 | Deguchi et al., 1997 |
| EC-PAR-B | GCGAACGATTTCGGATCGTC | |||
| qnrA-forward | qnrA | TCAGCAAGAGGATTTCTCA | 605 | Maynard et al., 2004 |
| qnrA-reverse | GGCAGCACTATTACTCCCA | |||
| qnrB-forward | qnrB | GATCGTGAAAGCCAGAAAGG | 469 | Robicsek et al., 2006b |
| qnrB-reverse | ACGATGCCTGGTAGTTGTCC | |||
| qnrS-forward | qnrS | ACGACATTCGTCAACTGCAA | 417 | Robicsek et al., 2006b |
| qnrS-reverse | TAAATTGGCACCCTGTAGGC | |||
| aac-forward | acc-(6′)-lb | TTGCGATGCTCTATGAGTGGCTA | 482 | Park et al., 2006 |
| aac-reverse | CTCGAATGCCTGGCGTGTTT | |||