TABLE 1.
PCR primer sequences and conditions used in this study
| Target | Primers | Sequences (5′-3′) | PCR conditions | Expected amplicon size (bp) | Reference |
|---|---|---|---|---|---|
| 16S rRNA genes | 16s8F/16s806R | AGAGTTTGATCCTGGCTCAG/GGACTACCAGGGTATCTAATCC | 94°C, 5 min; 30 cycles of 94°C, 30 s, 62°C, 30 s, 72°C, 90 s | 800 | 19 |
| Integrase 1 gene (intl1) | Int1F/Int1R | CCTCCCGCACGATGATC/TCCACGCATCGTCAGGC | 94°C, 5 min; 33 cycles of 94°C, 45 s, 64°C, 30 s, 72°C, 1 min | 280 | 16 |
| Integrase 2 gene (intI2) | RB201/RB202 | GCAAACGCAAGCATTCATTA/ACGGATATGCGACAAAAAGG | 300 | 3 | |
| Class 1 gene cassette | GC1_RLF/GC1_RLR | GGCATCCAAGCAGCAAG/AAGCAGACTTGACCTGA | 95°C, 5 min; 35 cycles of 94°C, 1 min, 55°C, 1 min, 72°C, 1.5 min | Variable | 5 |
| CTX-M (blaCTX-M) | CTX-M/F/CTX-M/R | TTTGCGATGTGCAGTACCAGTAA/CTCCGCTGCCGGTTTTATC | 95°C, 5 min; 35 cycles of 94°C, 1 min, 55°C, 1 min, 72°C, 1.5 min | 500 | 11 |
| CTX-M-1 (blaCTX-M-1) | CTX-M-1-MP-F/CTX-M-1-MP-R | AAAAATCACTGCGCCAGTTC/AGCTTATTCATCGCCACGTT | 415 | 31 | |
| TEM (blaTEM) | T1/T2 | CCGTGTCGCCCTTATTCC/AGGCACCTATCTCAGCGA | 800 | 32 |