Table 2 Primer sequences, anticipated amplicon size, and amplification conditions
Name | Amplicon size (bp) | Cycle Number | Annealing Temperature (°C) and Time | Primer sequence | Purpose | Reference |
|---|---|---|---|---|---|---|
stx1 | 348 | 25 | 56 °C, 60s | F: 5′-CAGTTAATGTGGTGGCGAAGG-3′ R: 5′-CACCAGACAATGTAACCGCTG-3’ | Detect Shiga toxins and their subtypes [14] | [14] |
stx1c | 498 | 30 | 56 °C, 60s | F:TTTTCACATGTTACCTTTCCT R:CATAGAAGGAAACTCATTAGG | [34] | |
stx1d | 192 | 30 | 56 °C, 60s | F:CTTTTCAGTTAATGCGATTGCT R:AACCCCATGATATCGACTGC | ||
stx2 | 584 | 25 | 56 °C, 60s | F:ATCCTATTCCCGGGAGTTTACG R:GCGTCATCGTATACACAGGAGC | [14] | |
stx2a | 349 | 25 | 65 °C, 40s | F:GCGATACTGRGBACTGTGGCC R:CCGKCAACCTTCACTGTAAATGTG | [35] | |
stx2c | 124 | 30 | 65 °C, 40s | F:GCGGTTTTATTTGCATTAGT R:AGTACTCTTTTCCGGCCACT | [34] | |
stx2d | 175 | 30 | 65 °C, 40s | F:GGTAAAATTGAGTTCTCTAAGTAT R:CAGCAAATCCTGAACCTGACG | ||
stx2e | 267 | 30 | 65 °C, 40s | F:ATGAAGAAGATGTTTATAGCG R:TCAGTTAAACTTCACCTGGGC | ||
stx2f | 428 | 30 | 65 °C, 40s | F:AGATTGGGCGTCATTCACTGGTTG R:TACTTTAATGGCCGCCCTGTCTCC | ||
stx2g | 573 | 30 | 65 °C, 40s | F:GTTATATTTCTGTGGATATC R:GAATAACCGCTACAGTA | ||
eae | 682 | 35 | 58 °C, 20s | F:ATTACTGAGATTAAGGCTGAT R:ATTTATTTGCAGCCCCCCAT | Detect intimin [14] | [36] |
ehxA | 166 | 25 | 56 °C, 60s | F:GTTTATTCTGGGGCAGGCTC R:CTTCACGTCACCATACATAT | Detect enterohemo-lysin [14] | [14] |
tetA | 210 | 30 | 58 °C, 60s | F:GCTACATCCTGCTTGCCTTC R:CATAGATCGCCGTGAAGAG | Detect Tet (A, B, C, D, E, and G), control active efflux of tetracyclin [22] | [37] |
tetB | 659 | 30 | 56 °C, 60s | F:TTGGTTAGGGGCAAGTTTTG R:GTAATGGGCCAATAACACCG | ||
tetC | 418 | 30 | 58 °C, 60s | F:CTTGAGAGCCTTCAACCCAG R:ATGGTCGTCATCTACCTGCC | ||
tetD | 787 | 30 | 60 °C, 60s | F:AAACCATTACGGCATTCTGC R:GACCGGATACACCATCCATC | ||
tetE | 278 | 30 | 58 °C, 60s | F:AAACCACATCCTCCATACGC R:AAATAGGCCACAACCGTCAG | ||
tetG | 468 | 30 | 60 °C, 60s | F:GCTCGGTGGTATCTCTGCTC R:AGCAACAGAATCGGGAACAC | ||
intl1 | 280 | 33 | 64 °C, 30s | F: CCTCCCGCACGATGATC R: TCCACGCATCGTCAGGC | Detect class 1 and 2 integrons [38] | [21] |
intI2 | 300 | 33 | 64 °C, 30s | F: GCAAACGCAAGCATTCATTA R: ACGGATATGCGACAAAAAGG | ||
blaCTX-M | 500 | 35 | 55 °C, 1 min | F: TTTGCGATGTGCAGTACCAGTAA R: CTCCGCTGCCGGTTTTATC | Detect extended-spectrum β-lactamase (E. coli) [38] | |
blaCTX-M-1 | 415 | 35 | 55 °C, 1 min | F: AAAAATCACTGCGCCAGTTC R: AGCTTATTCATCGCCACGTT | ||
blaTEM | 800 | 30 | 55 °C, 1 min | T1: CCGTGTCGCCCTTATTCC T2: AGGCACCTATCTCAGCGA | Detect ampicillin-resistance gene [38] | |
VNTR-3 | (333–334) to (476–477) | 35 | 65 °C, 20s | F:GGCGGTAAGGACAACGGGGTGTTTGAATTG R:GAACAACCTAAAACCCGCCTCGCCATCG | Detect VNTRs in STEC [39] | [27] |
VNTR-34 | (170–172) to (313–314) | F:GACAAGGTTCTGGCGTGTTACCAACGG R:GTTACAACTCACCTGCGAATTTTTTAAGTCCC | ||||
VNTR-9 | (474–475) to (613–614) | GCGCTGGTTTAGCCATCGCCTTCTTCC GTGTCAGGTGAGCTACAGCCCGCTTACGCTC | ||||
VNTR-25 | (122–124) to (191–192) | GCCGGAGGAGGGTGATGAGCGGTTATATTTAGTG GCGCTG AAAAGACATTCTCTGTTTGGTTTACACGAC | ||||
VNTR-17 | (135–136) to (247–248) | GCAGTTGCTCGGTTTTAACATTGCAGTGATGA GGAAATGGTTTACATGAGTTTGACGATGGCGATC | ||||
VNTR-19 | (283–284) to (356–357) | GCAGTGATCATTATTAGCACCGCTTTCTGGATGTTC GGGGCAGGGAATAAGGCCACCTGTTAAGC | ||||
VNTR-36 | (123–124) to (240–242) | GGCGTCCTTCATCGGCCTGTCCGTTAAAC GCCGCTGAAAGCCCACACCATGC | ||||
VNTR-37 | (157–158) to (273–274) | GCCGCCCCTTACATTACGCG GACATTC GCAGGAGAACAACAAAACAGACAGTAATCAGAGCAGC |