TABLE 1.
Primers sequences and PCR conditions used in this study
| Primer | Oligonucleotide sequence (5′ to 3′) | GenBank accession no. or reference (gene) | Position of amplicon | PCR conditions | Reference(s) |
|---|---|---|---|---|---|
| TEM-F | ATA AAA TTC TTG AAG AC | 36 (blaTEM-1) | 208-228 | 1 cycle of 12 min at 94°C; 35 cycles of 1 min at 94°C, 1 min at 58°C, 1 min at 72°C; 1 cycle of 10 min at 72°C | 30 |
| TEM-R | TTA CCA ATG CTT AAT CA | 1075-1055 | |||
| SHV-F | GGG TTA TTC TTA TTT GTC GC | M59181 (blaSHV-1) | 58-77 | 1 cycle of 12 min at 94°C; 35 cycles of 1 min at 94°C, 1 min at 56°C, 1 min at 72°C; 1 cycle of 10 min at 72°C | 30 |
| SHV-R | TTA GCG TTG CCA GTG CTC | 988-971 | |||
| CTX-M-9-F | GTG ACA AAG AGA GTG CAA CGG | AF174129 (blaCTXM-9 in In60) | 6339-6359 | 1 cycle of 12 min at 94°C; 35 cycles of 1 min at 94°C, 1 min at 62°C, 1 min at 72°C; 1 cycle of 10 min at 72°C | 9, 33 |
| CTX-M-9-R | ATG ATT CTC GCC GCT GAA GCC | 7195-7175 | |||
| CTX-M-10-F | CCG CGC TAC ACT TTG TGG C | AY598759 (blaCTXM-10 in pRYC21) | 4924-4942 | 1 cycle of 12 min at 94°C; 35 cycles of 1 min at 94°C, 1 min at 58°C, 1 min at 72°C; 1 cycle of 10 min at 72°C | 9, 25 |
| CTX-M-10-R | TTA CAA ACC GTT GGT GAC G | 5885-5867 | |||
| ChuA.1 | GAC GAA CCA ACG GTC AGG AT | 1 cycle of 12 min at 94°C; 35 cycles of 30 s at 94°C, 30 s at 59°C, 30 s at 72°C; 1 cycle of 7 min at 72°C | 8 | ||
| ChuA.2 | TGC CGC CAG TAC CAA AGA CA | ||||
| YjaA.1 | TGA AGT GTC AGG AGA CGC TG | 8 | |||
| YjaA.2 | ATG GAG AAT GCG TTC CTC AAC | ||||
| TspE4C2.1 | GAG TAA TGT CGG GGC ATT CA | AF222188 | 8-28 | 8 | |
| TspE4C2.2 | CGC GCC AAC AAA GTA TTA CG | 160-141 | |||
| IntI1-F | GGT CAA GGA TCT GGA TTT CG | U49101 (int1) | 786-766 | 1 cycle of 12 min at 94°C; 30 cycles of 30 s at 94°C, 30s at 62°C, 1 min at 72°C; 1 cycle of 8 min at 72°C | 23 |
| IntI1-R | ACA TGC GTG TAA ATC ATC GTC | 303-324 | |||
| 5′CS | GGC ATC CAA GCA GCA AG | M73819 (class 1 integron) | 1190-1206 | 1 cycle of 12 min at 94°C; 35 cycles of 1 min at 94°C, 1 min at 60°C, 2 min at 72°C; 1 cycle of 10 min at 72°C | 21 |
| 3′CS | AAG CAG ACT TGA CCT GA | 1342-1326 | |||
| IntI2-F | CAC GGA TAT GCG ACA AAA AGG T | L10818 (int2) | 219-240 | Same as for int1 | 23 |
| IntI2-R | GTA GCA AAC GAG TGA CGA AAT G | 1007-986 | |||
| attI2-F | GAC GGC ATG CAC GAT TTG TA | AY183453 (class 2 integron) | 1943-1962 | 1 cycle of 12 min at 94°C; 35 cycles of 1 min at 94°C, 1 min at 58°C, 3.5 min at 72°C; 1 cycle of 10 min at 72°C | This work |
| orfX-R | GAT GCC ATC GCA AGT ACG AG | 4848-4928 | 42 | ||
| IntI3-F | AGT GGG TGG CGA ATG AGT G | D50438 (int3) | 178-196 | 1 cycle of 12 min at 94°C; 30 cycles of 30 s at 94°C, 30 s at 60°C, 1 min at 72°C; 1 cycle of 8 min at 72°C | 12 |
| IntI3-R | TGT TCT TGT ATC GGC AGG TG | 777-758 |