Table 1.
Primer sequences and PCR conditions for quadruplex phylo-grouping of E. coli
| Target gene | Primer sequence | Size (bp) | PCR conditions | Reference |
|---|---|---|---|---|
| arpA (phylogenetic grouping) | F (5-AACGCTATTCGCCAGCTTGC-3) R (5-TCTCCCCATACCGTACGCTA-3) |
400 | PCR reactions were performed in a total volume of 25 µL by ready-to go PCR beads using 20 pmol of each primers for all targets except arpA (40 pmol) and trpA (12 pmol). The cycling conditions were as follow: denaturation 4 min at 94 °C, 30 cycles of 5 s at 94 °C and 20 s at 59 °C, 20 s at 72 °C and a final extension step of 5 min at 72 °C | [24] |
| chuA (phylogenetic grouping) | F (5-GACGAACCAACGGTCAGGAT-3) R (5-TGCCGCCAGTACCAAAGACA-3) |
288 | ||
| yjaA (phylogenetic grouping) | F (5-TGAAGTGTCAGGAGACGCTG-3) R (5-ATGGAGAATGCGTTCCTCAAC-3) |
211 | ||
| TspE4C2 (phylogenetic grouping) | F (5-GAGTAATGTCGGGGCATTCA-3) R (5-GCGCCAACAAAGTATTACG-3) |
152 | ||
| Internal control trpA | F (5-CGGCGATAAAGACATCTTCAC-3) R (5-GCAACGCGGCCTGGCGGAAG-3) |
489 |