Table 2 Primer sequences and PCR condition for detection of antimicrobial resistance and phylo-group genes
Target (subject) | Sequence (5’–3’) | PCR condition | Product size (bp) | Reference |
|---|---|---|---|---|
blaTEM (Resistance to β-lactam) | Fa-GCGGAACCCCTATTTG | 35 cycles: 95°C (30 s), 52°C (30 s), 72°C (60 s) | 963 | [11] |
Rb-ACCAATGCTTAATCAGTGAG | ||||
blaSHV (Resistance to β-lactam) | F-TTATCTCCCTGTTAGCCACC | 35 cycles: 95°C (30 s), 54°C (30 s), 72°C (30 s) | 795 | [12] |
R-GATTTGCTGATTTCGCTCGG | ||||
blaCTX-M (Resistance to β-lactam) | F-CGATGTGCAGTACCAGTAA | 35 cycles: 95°C (30 s), 60°C (30 s), 72°C (60 s) | 585 | [13] |
R-TTAGTGACCAGAATCAGCGG | ||||
sulI (Resistance to sulfonamide) | F-TTCGGCATTCTGAATCTCAC | 30 cycles: 94°C (30 s), 58°C (30 s), 72°C (60 s) | 822 | [14] |
R-ATGATCTAACCCTCGGTCTC | ||||
sulII (Resistance to sulfonamide) | F-GCGCTCAAGGCAGATGGCATT | 30 cycles: 94°C (30 s), 69°C (30 s), 72°C (60 s) | 293 | [15] |
R-GCGTTTGATACCGGCACCCGT | ||||
dhfrI (Resistance to trimethoprim) | F-AAGAATGGAGTTATCGGGAATG | 30 cycles: 94°C (30 s), 55°C (30 s), 72°C (60 s) | 391 | [14] |
R-GGGTAAAAACTGGCCTAAAATTG | ||||
dhfrV (Resistance to trimethoprim) | F-CTGCAAAAGCGAAAAACGG | 35 cycles: 94°C (30 s), 58°C (30 s), 72°C (60 s) | 432 | [14] |
R-AGCAATAGTTAATGTTTGAGCTAAAG | ||||
aadA (Resistance to aminoglycoside) | F-TGATTTGCTGGTTACGGTGAC | 30 cycles: 94°C (30 s), 58°C (30 s), 72°C (60 s) | 284 | [14] |
R-CGCTATGTTCTCTTGCTTTTG | ||||
stx1 (STEC) | F-CAGTTAATGTGGTGGCGAAGG | 35 cycles: 94°C (90 s), 60°C (90 s), 72°C (90 s) | 348 | [16] |
R-CACCAGACAATGTAACCGCTG | ||||
stx2 (STEC) | F-ATCCTATTCCCGGGAGTTTACG | 35 cycles: 94°C (90 s), 60°C (90 s), 72°C (90 s) | 584 | [16] |
R-GCGTCATCGTATACACAGGAGC | ||||
eae (EPEC) | F-TCAATGCAGTTCCGTTATCAGTT | 35 cycles: 94°C (90 s), 60°C (90 s), 72°C (90 s) | 482 | [16] |
R-GTAAAGTCCGTTACCCCAACCTG | ||||
stII (ETEC) | F-AAAGGAGAGCTTCGTCACATTTT | 35 cycles: 94°C (90 s), 60°C (90 s), 72°C (90 s) | 129 | [16] |
R-AATGTCCGTCTTGCGTTAGGAC | ||||
lt (ETEC) | F-GCACACGGAGCTCCTCAGTC | 35 cycles: 94°C (90 s), 60°C (90 s), 72°C (90 s) | 218 | [16] |
R-TCCTTCATCCTTTCAATGGCTTT | ||||
ipaH (EIEC) | F-CTCGGCACGTTTTAATAGTCTGG | 35 cycles: 94°C (90 s), 60°C (90 s), 72°C (90 s) | 933 | [16] |
R-GTGGAGAGCTGAAGTTTCTCTGC | ||||
aafII (EAEC) | F-CACAGGCAACTGAAATAAGTCTGG | 35 cycles: 94°C (90 s), 60°C (90 s), 72°C (90 s) | 378 | [16] |
R-ATTCCCATGATGTCAAGCACTTC | ||||
daaE (DAEC) | F-GAACGTTGGTTAATGTGGGGTAA | 35 cycles: 94°C (90 s), 60°C (90 s), 72°C (90 s) | 542 | [16] |
R-TATTCACCGGTCGGTTATCAGT | ||||
arpA (phylo-grouping) | F-AACGCTATTCGCCAGCTTGC | 30 cycles: 94°C (5 s), 59°C (20 s) and 1 cycle 72°C (5 min) | 400 | [5] |
R-TCTCCCCATACCGTACGCTA | ||||
chuA (phylo-grouping) | F-ATGGTACCGGACGAACCAAC | 30 cycles: 94°C (5 s), 59°C (20 s) and 1 cycle 72°C (5 min) | 288 | [5] |
R-TGCCGCCAGTACCAAAGACA | ||||
yjaA (phylo-grouping) | F-CAAACGTGAAGTGTCAGGAG | 30 cycles: 94°C (5 s), 59°C (20 s) and 1 cycle 72°C (5 min) | 211 | [5] |
R-AATGCGTTCCTCAACCTGTG | ||||
TspE4.C2 (phylo-grouping) | F-CACTATTCGTAAGGTCATCC | 30 cycles: 94°C (5 s), 59°C (20 s) and 1 cycle 72°C (5 min) | 152 | [5] |
R-AGTTTATCGCTGCGGGTCGC | ||||
arpA-group E (phylo-grouping) | F-GATTCCATCTTGTCAAAATATGCC | 30 cycles: 94°C (5 s), 57°C (20 s) and 1 cycle 72°C (5 min) | 301 | [5] |
R-GAAAAGAAAAAGAATTCCCAAGAG | ||||
trpA-group C (phylo-grouping) | F-AGTTTTATGCCCAGTGCGAG | 30 cycles: 94°C (5 s), 59°C (20 s) and 1 cycle 72°C (5 min) | 219 | [5] |
R-TCTGCGCCGGTCACGCCC |