Table 2.
List of primers used in the virulence genotyping.
| Virulence marker | Locus description | Primers | Frag. (bp) | Tm (°C) | References |
|---|---|---|---|---|---|
| EAEC VIRULENCE GENES | |||||
| aatA | Dispersin transporter (earlier pCVD432) | CTGGCGAAAGACTGTATCAT | 630 | 60 | Pereira et al., 2007 |
| CCATGTATAGAAATCCGCTGTT | |||||
| aggR | Transcription activator | CTAATTGTACAATCGATGTA | 324 | 50 | Pereira et al., 2010 |
| CTGAAGTAATTCTTGAAT | |||||
| aapA | Dispersin | CTTTTCTGGCATCTTGGGT | 328 | 56 | This study |
| TTATTTAACCCATTCGGTTAGAGC | |||||
| aggA | Aggregative adherence fimbria (AAF-I) | GCTAACGCTGCGTTAGAAAGACC | 421 | 60 | Pereira et al., 2007 |
| GGAGTATCATTCTATATTCGCC | |||||
| aafA | AAF-II | GACAACCGCAACGCTGCGCTG | 233 | 50 | Pereira et al., 2007 |
| GATAGCCGGTGTAATTGAGCC | |||||
| agg-3A | AAF-III | GTATCATTGCGAGTCTGGTATTCAG | 462 | 56 | Bernier et al., 2002 |
| GGGCTGTTATAGAGTAACTTCCAG | 58 | ||||
| hdaB-A | AAF-IV | CTGTAGGACGTAGGTAATGAAACTG | 993 | This study | |
| AAACTCCAGGCGTTAACGTCTG | |||||
| agg-5A | AAF-V | AGCAGCAACAGCAAATCC | 342 | 56 | This study |
| CCGTAACCACTTCCTCGT | |||||
| pet | Plasmid-encoded toxin | CCGCAAATGGAGCTGCAAC | 1133 | 60 | Pereira et al., 2007 |
| CGAGTTTTCCGCCGTTTTC | |||||
| pic | Mucinase | TTCAGCGGAAAGACGAA | 500 | 60 | Pereira et al., 2007 |
| TCTGCGCATTCATACCA | |||||
| UPEC VIRULENCE GENES | |||||
| fyuA | Yersiniabactin siderophore receptor | TGAGTGGGAAATACACCACC | 715 | 54 | This study |
| TTACCCGCATTGCTTAATGTC | |||||
| yfcV | YfC fimbria | ATCCGTGTTGGCTGGC | 280 | 54 | This study |
| GGTCATGGGCGCAGTT | |||||
| chuA | Heme receptor | TAACTGTCATAGCGGGTTCC | 439 | 55 | This study |
| AGTCTCTGAGCGGTTTAGTG | |||||
| vat | Vacuolating autotransporter toxin | CAGAACATTTGCTCCCTTGT | 1102 | 53 | This study |
| ACACGTTCAGGATTCAGT | |||||
| papC | Pyelonephritis-associated pilus | GACGGCTGTACTGCAGGGTGTGGCG | 328 | 60 | Daigle et al., 1994 |
| ATATCCTTTCTGCAGGGATGCAATA | |||||
| focA | Fimbria F1C (focA-sfaD) | GAAAGTAGATGGAGCTAAAAGCAAT | 496 | 54 | This study |
| CATGACATGCCAGTGGTTTC | |||||
| sfa | Fimbria S | CTCCGGAGAACTGGGTGCATCTTAC | 407 | 60 | Daigle et al., 1994 |
| CGGAGGAGTAATTACAAACCTGGCA | |||||
| cnf | Cytotoxic necrotizing factor | GTGAAGCTCAACGAGACTAT | 826 | 53 | This study |
| TCAGTAGCTCCTCTCATCAA | |||||
| GENERAL E. COLI ADHESINS | |||||
| csgA | Curli fimbria | CTCTGACTTGACTATTACC | 199 | 50 | This study |
| AGATGCAGTCTGGTCAAC | |||||
| ag43 | Self-recognizing protein (adhesin) | CGATCGATAAGCTAATAATAACC | 552 | 55 | This study |
| GAAGACCACCACTGGTGACA | |||||
| pilS | Plasmid-encoded type IV pili | ATGAGCGTCATAACCTGTTC | 532 | 58 | Dudley et al., 2006 |