Table 1 16S rRNA, virulence and antibiotic resistance genes primer sequences, expected amplicons sizes and PCR cycling conditions
Target microorganism | Target gene | Primer sequence (5′ → 3′) | Amplicon size (bp) | PCR cycling condition | Reference |
|---|---|---|---|---|---|
Salmonella spp./ E. coli | 16S rRNA | F: GAG TTT GAT CCT GGC TCA R: TAC GGC TAC CTT GTT ACG ACT T | 1500 | 5 min initial denaturation at 94 °C followed by 35 cycles of 94 °C for 40 s, 58 °C for 40 s, 72 °C for 40 s and final extension at 72 °C for 7 min | [41] |
Salmonella spp. | InvA (Virulence gene) | F: ACA GTG CTC GTT TAC GAC CTG AAT R: AGA CGA CTG GTA CTG ATC GAT AAT | 244 | 5 min initial denaturation at 94 °C followed by 35 cycles of 94 °C for 1 min, 58 °C for 1 min, 72 °C for 1 min and final extension at 72 °C for 10 min | [42] |
Salmonella spp. | hilA (Virulence gene) | F:CGTGAAGGGATTATCGCAGT R: TCCGGGAATACATCTGAGC | 600 | 5 min initial denaturation at 94 °C followed by 35 cycles of 94 °C for 1 min, 65 °C for 1 min, 72 °C for 1 min and final extension at 72 °C for 10 min | [43] |
E. coli | uidA (Virulence gene) | F: AAA ACG GCA AGAAAA AGC AG R: ACG CGT GGT TAACAG TCT TGC G | 147 | 5 min initial denaturation at 94 °C followed by 35 cycles of 94 °C for 40 s, 58 °C for 40 s, 72 °C for 40 s and final extension at 72 °C for 7 min | [44] |
Antibiotic resistance genes | blaTEM-1 |  F: TTG GGT GCA CGA GTGGGT R: TAA TTG TTG CCG GGA AGC | 500 | 5 min initial denaturation at 94 °C followed by 35 cycles of 94 °C for 1 min, 57 °C for 1 min, 72 °C for 1 min and final extension at 72 °C for 10 min | [45] |
|  | blaCMY-2 |  F: ATA ACC ACC CAG TCA CGC R: CAG TAG CGA GAC TGC GCA | 600 | 5 min initial denaturation at 94 °C followed by 35 cycles of 94 °C for 1 min, 58 °C for 1 min, 72 °C for 1 min and final extension at 72 °C for 10 min | [45] |
|  | blaCTX-M | F: CGC TTT GCG ATG TGC AG R: ACC GCG ATA TCG TTG GT | 590 | 5 min initial denaturation at 94 °C followed by 35 cycles of 94 °C for 1 min, 52 °C for 1 min, 72 °C for 1 min and final extension at 72 °C for 10 min | [46] |
|  | blaZ | F: ACT TCA ACA CCT GCT GCT TTC R: TGA CCA CTT TTA TCA GCA ACC | 490 | 94 °C for 5 min followed by 30 cycles of denaturation 94 °C for 30 s, annealing 60 °C for 30 s, extension 72 °C for 90 s and final incubation at 72 °C for 5 min | [47] |
|  | catI | F: AGTTGCTCAATGTACCTATAACC R: TTGTAATTCATTAAGCATTCTGCC | 280 | 5 min at 94 °C, followed by 30 cycles of 94 °C for 30 s, 50 °C for 30 s and 72 °C for 1.5 min and final incubation at 72 °C for 5 min. | [48] |
|  | sul2 | F: CGG CAT CGT CAA CAT AAC C R: GTG TGC GGA TGA AGT CAG | 720 | 5 min initial denaturation at 94 °C followed by 35 cycles of 94 °C for 1 min, 58 °C for 1 min, 72 °C for 1 min and final extension at 72 °C for 10 min | [49] |
|  | tetA | F: GCT ACA TCC TGC TTG CCT TC R: CAT AGA TCG CCG TGA AGA GG | 210 | 5 min initial denaturation at 94 °C followed by 35 cycles of 94 °C for 1 min, 60 °C for 1 min, 72 °C for 1 min and final extension at 72 °C for 10 min | [50] |
|  | tetC | F: CTT GAG AGC CTT CAA CCC AG R: ATG GTC GTC ATC TAC CTG CC | 418 | 5 min initial denaturation at 94 °C followed by 35 cycles of 94 °C for 1 min, 62 °C for 1 min, 72 °C for 1 min and final extension at 72 °C for 10 min | [50] |
|  | dfrA7 | F: GGT AAT GGC CCT GAT ATC CC R: TGT AGA TTT GAC CGC CAC C | 280 | 5 min initial denaturation at 94 °C followed by 35 cycles of 94 °C for 1 min, 58 °C for 1 min, 72 °C for 1 min and final extension at 72 °C for 10 min | [51] |
|  | strA | F: CTT GGT GAT AAC GGC AAT TC R: CCA ATC GCA GAT AGA AGG C | 548 | 5 min initial denaturation at 94 °C followed by 35 cycles of 94 °C for 1 min, 56 °C for 1 min, 72 °C for 1 min and final extension at 72 °C for 10 min | [52] |
|  | aadA | F: GTG GAT GGC GGC CTG AAG CC R: AAT GCC CAG TCG GCA GCG | 525 | 5 min initial denaturation at 94 °C followed by 35 cycles of 94 °C for 40 s, 60 °C for 40 s, 72 °C for 40 s and final extension at 72 °C for 7 min | [52] |