Table 2.
Quantitative PCR primer and probes used to target specific genes and organisms in tubewell water samples.
| Target organism (Relevance) |
Assay Gene Target (Assay type and annealing temperature) |
Oligonucleotide Sequencesa | Reference |
|---|---|---|---|
| EC23S (E. coli) | 23S rRNA (Fluorogenic Probe, 55°C) | EC23Sf, 5’ GAG CCT GAA TCA GTG TGT GTG 3’ EC23Sr, 5’ ATT TTT GTG TAC GGG GCT GT 3’ EC23Srv1Taq, 5’ CGC CTT TCC AGA CGC TTC CAC |
Knappett et al. 2011b |
| AllBac (all Bacteroides) | 16S rRNA (Fluorogenic Probe, 60°C) | AllBac296f, 5’-GAGAGGAAGGTCCCCCAC-3’ AllBac412r, 5’-CGCTACTTGGCTGGTTCAG-3’ AllBac375Taq, 5’CCATTGACCAATATTCCTCACTGCTGCCT(BHQ-1)-3’ |
Layton et al. 2006 |
| Shigella and EIEC E. coli (Dysentery type E. coli and Shigella) | ipaH (Fluorogenic Probe, 60°C) |
IpaH U1f- 5’ CCTTTTCCGCGTTCCTTG A-3’ IpaH L1r- 5’- CGGAATCCGGAGGTATTG C-3’ IpaH Taq- 5’-CGCCTTTCCGATACCGTCTCTGCA-3’ |
von Seidlein et al. 2006 |
| ETEC E. coli (Enterotoxigenic E. coli strains) | eltA (Heat labile toxin LT) (Fluorogenic Probe, 60°C) |
Elt311f- 5’ TCTGAATATAGCTCCGGCAGA-3’ Elt414r-5’ CAACCTTGTGGTGCATGATGA-3’ Elt383Taqr -5’ TTCTCTCCAAGCTTGGTGATCCGGT-3’ |
Modified from Persson et al. 2007 |
| Adeno (adenovirus 40/41 hexon gene) | Hexon (Fluorogenic Probe, 60°C) | AV40/41-117f, 5’- CAGCCTGGGGAACAAGTTCAG 3’ AV40/41-258r, 5’ -CAGCGTAAAGCGCACTTTGTAA 3’ AV40/41-157Taq, 5’ ACCCACGATGTAACCACAGACAGGTC 3’ |
Rajal et al. 2007 |
a
all probes synthesized with FAM (fluorescein) and black hole quencher 1 (BHQ1) from Biosearch Technologies.