Table 1.
DNA oligonucleotides used in the analysis of STEC by PCR.
| Gene Location | Target Gene | Sequence (5′ to 3′) | Amplicon Size (bp) |
References |
|---|---|---|---|---|
| Bacteriophage-encoded genes | stx1 |
F: ATAAATCGCCATTCGTTGACTAC R: AGAACGCCCACTGAGATCATC |
180 | (Paton and Paton42) |
| stx2 |
F: GGCACTGTCTGAAACTGCTCC R: TCGCCAGTTATCTGACATTCTG |
255 | (Paton and Paton42) | |
| stx1c |
F1: CCTTTCCTGGTACAACTGCGGTT R1: CAAGTGTTGTACGAAATCCCCTCTGA |
252 | (Scheutz et al.5) | |
| stx1d |
F1: CAGTTAATGCGATTGCTAAGGAGTTTACC R2: CTCTTCCTCTGGTTCTAACCCCATGATA |
203 | (Scheutz et al.5) | |
| stx2a |
F2: GCGATACTGRGBACTGTGGCC R3: CCGKCAACCTTCACTGTAAATGTG |
349 | (Scheutz et al.5) | |
| stx2c |
F1: GAAAGTCACAGTTTTTATATACAACGGGTA R2: CCGGCCACYTTTACTGTGAATGTA |
177 | (Scheutz et al.5) | |
| stx2d |
F1: AAARTCACAGTCTTTATATACAACGGGTG R1: TTYCCGGCCACTTTTACTGTG O55-R: TCAACCGAGCACTTTGCAGTAG |
179 235 |
(Scheutz et al.5) | |
| stx2e |
F1: CGGAGTATCGGGGAGAGGC R2: CTTCCTGACACCTTCACAGTAAAGGT |
411 | (Scheutz et al.5) | |
| stx2f |
F1: TGGGCGTCATTCACTGGTTG R1: TAATGGCCGCCCTGTCTCC |
424 | (Scheutz et al.5) | |
| stx2g |
F1: CACCGGGTAGTTATATTTCTGTGGATATC R1: GATGGCAATTCAGAATAACCGCT |
573 | (Scheutz et al.5) | |
| eaeA |
F: GACCCGGCACAAGCATAAGC R: CCACCTGCAGCAACAAGAGG |
384 | (Paton and Paton42) | |
| Plasmid-encoded genes | ehxA |
F: GCATCATCAAGCGTACGTTCC R: AATGAGCCAAGCTGGTTAAGCT |
584 | (Paton and Paton42) |
| katP |
wkat-F: AACTTATTTCTCGCATCATCC wkat-B: CTTCCTGTTCTGATTCTTCTGG |
2125 | (Brunder et al.10) | |
| espP |
F: AAACAGCAGGCACTTGAACG R: GGAGTCGTCAGTCAGTAGAT |
1830 | (Brunder et al.12) | |
| etpD |
D1- CGTCAGGAGGATGTTCAG D13R- CGACTGCACCTGTTCCTGATTA |
1062 | (Schmidt et al.14) | |
| saa |
F: CGTGATGAACAGGCTATTGC R: ATGGACATGCCTGTGGCAAC |
119 | (Paton and Paton, 2002) | |
| subA |
SubHCDF: TATGGCTTCCCTCATTGC C SubSCDR: TATAGCTGTTGCTTCTGACG |
556 | (Paton and Paton, 2005) | |
| Pathogenicity Island-encoded genes | ||||
| OI-71 | nleA (Z6024) |
F: ATGAACATTCAACCGACCATAC R: GACTCTTGTTTCTTGGATTATATCAAA |
1296 | (Coombes et al.19) |
| OI-122 | nleB (Z4328) |
F: GGAAGTTTGTTTACAGAGACG R: AAAATGCCGCTTGATACC |
297 | (Coombes et al.19) |
| OI-36 | nleB2 (Z0985) |
F: GTTAATACTAAGCAGCATCC R: CCATATCAAGATAGATACACC |
475 | (Coombes et al.19) |
| OI-36 | nleC (Z0986) |
F: ACAGTCCAACTTCAACTTTTCC R: ATCGTACCCAGCCTTTCG |
777 | (Coombes et al.19) |
| OI-36 | nleD (Z0990) |
F: GGTATTACATCAGTCATCAAGG R: TTGTGGAAAACATGGAGC 426 |
426 | (Coombes et al.19) |
| OI-122 | nleE (Z4329) |
F: GTATAACCAGAGGAGTAGC R: GATCTTACAACAAATGTCC |
260 | (Coombes et al.19) |
| OI-71 | nleF (Z6020) |
F: ATGTTACCAACAAGTGGTTCTTC R: ATCCACATTGTAAAGATCCTTTGTT |
567 | (Coombes et al.19) |
| OI-71 | nleG (Z6010) |
F: ATGTTATCGCCCTCTTCTATAAAT R: ACTTAATACTACACTAATAAGATCCA |
902 | (Coombes et al.19) |
| OI-71 | nleG2-1 (Z6025) |
F: ACCAGAAACCTGACTTCG R: CAGCATCTTCATATACTACAGC |
406 | (Coombes et al.19) |
| OI-57 | nleG2-3 |
F: GGATGGAACCATACCTGG R: CGCAATCAATTGCTAATGC |
551 | (Coombes et al.19) |
| OI-57 | nleG5-2 |
F: TGGAGGCTTTACGTCATGTCG R: CCGGAACAAAGGGTTCACG |
504 | (Coombes et al.19) |
| OI-57 | nleG6-2 |
F: CGGGTCAGTGGATGATATGAGC R: AAGTAGCATCTAGCGGTCGAGG |
424 | (Coombes et al.19) |
| OI-71 | nleG9 (Z2560) |
F: GTTCGTGCCCGAATTGTAGC R: CACCAACCAAACGAGAAAATG |
409 | (Coombes et al.19) |
| OI-71 | nleH1-2 (Z6021) |
F: AACGCCTTATATTTTACC R: AGCACAATTATCTCTTCC |
589 | (Coombes et al.19) |
| OI-36 | nleH1-1 (Z0989) |
F: GTTACCACCTTAAGTATCC R: GTTTCTCATGAACACTCC |
456 | (Coombes et al.19) |
| OI-122 | ent/espL2 |
F: GAATAACAATCACTCCTCACC R: TTACAGTGCCCGATTACG |
433 | (Coombes et al.19) |
| OI-122 | Efa1 (Z4332) |
Z4321-a: ATGAGTGGTTCAAGACTGG Z4321-b: CCAACTCCAACAGTAAATCC |
521 | (Karmali et al.18) |
| OI-122 | Efa1 (Z4332) |
Z4326-a: GGATGGAACCATACCTGG Z4326-b: CGCAATCAATTGCTAATGC |
551 | (Karmali et al.18) |
| OI-122 | sen (Z4326) |
Z4332-a: CTCCCAGAGATAATTTTGAGG Z4332-b: CAACTGTATGCGAATAGTACTC |
504 | (Karmali et al.18) |
| OI-122 | pagC |
Z4333-a: CTGTCAGACGATGACATTGG Z4333-b: GAAGGATGGGCATTGTGTC |
547 | (Karmali et al.18) |
| OI-43/48 | ureC |
F: TCT AAC GCC ACA ACC TGT AC R: GAG GAA GGC AGA ATA TTG GG |
397 | (Nakano et al.27) |
| OI-43/48 | Ter-island |
F: GAC AAA CTC TCC GGG ATA ACT CA R: TGC GGG TGC TGG TGT GGG ATA A |
356 | (Taylor et al.26) |
| OI-43/48 | iha |
Iha-I: CAG TTC AGT TTC GCA TTC ACC Iha-II: GTA TGG CTC TGA TGC GAT G |
1305 | (Janka et al.44) |