Table 3.
Primers and PCR conditions for detecting mupirocin, fusidic acid and retapamulin resistance genes in this study
| Gene | Primer name | Primer sequence (5′-3′) | PCR amplification program | Size | Reference |
|---|---|---|---|---|---|
| Molecular mechanisms related to mupirocin resistance | |||||
| mupA | mupA-F | TATATTATGCGATGGAAGGTTGG | Initial pre-denaturation at 94 °C for 5 min; 30 cycles of denaturation (30 s at 94 °C), annealing (30 s; at 53 °C for mupA, and 55 °C for mupB, Smr, Mrm and Lmr), and extension (50 s at 72 °C), followed by a final extension step of 7 min at 72 °C | 457 bp | 5 |
| mupA-R | AATAAAATCAGCTGGAAAGTGTTG | ||||
| mupB | mupB-F | CTAGAAGTCGATTTTGGAGTAG | 674 bp | ||
| mupB-R | AGTGTCTAAAATGATAAGACGATC | ||||
| ileS (including the following 3 fragments) | |||||
| Smr | Smr-F | ATAAAGGTAAAAAGCCAGTTTATTGGT | 200 bp | 38 | |
| Smr-R | TAATCGCAACATTTGATGGAATTGTC | ||||
| Mrm | Mrm-F | TCCCAGCAGATATGTATTTAGAAGGT | 450 bp | ||
| Mrm-R | AACCACTTGGTCAGGTACAATCACA | ||||
| Lmr | Lmr-F | GTAAATCTTTAGGTAATGTGATTGTAC | 690 bp | ||
| Lmr-R | TCTTCTTTAACATGTGGTGTATGAGA | ||||
| Molecular mechanisms associated with fusidic acid resistance | |||||
| fusA | fusA-F | TTTACCCTGAGTGTGTTCT | Initial pre-denaturation at 94 °C for 5 min; 30 cycles of denaturation (30 s at 94 °C), annealing (30 s; at 53 °C for fusB-D and fusE, and 40 °C for fusA), and extension (2 min, at 72 °C for fusA; 50 s, at 72 °C for other genes), followed by a final extension step of 7 min at 72 °C | 2250 bp | 7 |
| fusA-R | TACATTTAAGCTCACCTTGT | ||||
| fusB | fusB-F | TCATATAGATGACGATATTG | 496 bp | 26 | |
| fusB-R | ACAATGAATGCTATCTCGAC | ||||
| fusC | fusC-F | GATATTGATATCTCGGACTT | 128 bp | ||
| fusC-R | AGTTGACTTGATGAAGGTAT | ||||
| fusD | fusD-F | TGCTTATAATTCGGTCAACG | 525 bp | ||
| fusD-R | TGGTTACATAATGTGCTATC | ||||
| fusE | fusE-F | CCTAGTGACGTAACAGTAAC | 505 bp | ||
| fusE-R | CGGCGWACRTATTCACCTTG | ||||
| Molecular mechanisms associated with retapamulin resistance | |||||
| rplC | rplC-F | AACCTGATTTAGTTCCGTCTA | Initial pre-denaturation at 94 °C for 5 min; 30 cycles of denaturation (30 s at 94 °C), annealing (30 s; at 50 °C for vgaA and vgaALC, 52 °C for vgaB, vagC, vgaE, lsaA-C and lsaE, and 55 °C for rplC, cfr, vgaAv, salA and 23S RNA V), and extension (2 min, at 72 °C for vgaC, vgaE and salA; 50 s, at 72 °C for other genes), followed by a final extension step of 7 min at 72 °C | 822 bp | 8 |
| rplC-R | GTTGACGCTTTAATGGGCTTA | ||||
| cfr | cfr-F | GAGATAACAGATCAAGTTTTA | 1050 bp | 39 | |
| cfr-R | CGAGTATATTCATTACCTCAT | ||||
| vgaA | vgaA-F | TCACATGATCGCGCTTTTTTAGAT | 770 bp | 29 | |
| vgaA-R | TCGCTCTCCACCACTTAAGACACT | ||||
| vgaAv | vgaAv-F | CTCTTTGTACGAGTATATGG | 770 bp | 40 | |
| vgaAv-R | GTTTCTTAGTAGCTCGTTGAGC | ||||
| vgaALC | vgaALC-F | CATTATCGCCATCTGTCA | 541 bp | 9 | |
| vgaALC-R | AATTCTTCCGAAGGTTCA | ||||
| vgaB | vgaB-F | TGACAATATGAGTGGTGGTG | 577 bp | ||
| vgaB-R | GCGACCATGAAATTGCTCTC | ||||
| vgaC | vgaC-F | CGTATGCCCAGAGTGAG | 1073 bp | ||
| vgaC-R | GAGTGCTTCCGTATCCA | ||||
| vgaE | vgaE-F | GAAATATGGGAAATAGAAGATGG | 995 bp | ||
| vgaE-R | TGATTCTCTAACCACTCTTC | ||||
| lsaA | lsaA-F | ACCGTGAAGGTGATAAGT | 500 bp | ||
| lsaA-R | TTGGGTGTAATCTAACTGAT | ||||
| lsaB | lsaB-F | TCCACTGCCGTTCTTTCC | 715 bp | ||
| lsaB-R | AGCCATGTACCGTCCTTT | ||||
| lsaC | lsaC-F | GGCTATGTAAAACCTGTATTTG | 429 bp | ||
| lsaC-R | ACTGACAATTTTTCTTCCGT | ||||
| lsaE | lsaE-F | TTGTACGGAATGTATGG | 675 bp | ||
| lsaE-R | TTCGCTTCTATTAAGCACTCTT | ||||
| salA | salA-F | CGATGAACCAACAAACCACA | 981 bp | 10 | |
| salA-R | AGGACCGAACCTTGAAATGA | ||||
| 23S RNA V | 23S RNA-F | TGGGCACTGTCTCAACGA | 634 bp | 41 | |
| 23S RNA-R | GGATAGGGACCGAACTGTCTC | ||||
| MLST typing | 43 | ||||
| arcC | arcC-F | TTGATTCACCAGCGCGTATTGTC | Initial pre-denaturation at 94 °C for 5 min; 30 cycles of denaturation (30 s at 94 °C), annealing (30 s; at 55 °C for 7 house-keeping genes), and extension (50 s, at 72 °C for other genes), followed by a final extension step of 7 min at 72 °C | 456 bp | |
| arcC-R | AGGTATCTGCTTCAATCAGCG | ||||
| aroE | aroE-F | ATCGGAAATCCTATTTCACATTC | 456 bp | ||
| aroE-R | GGTGTTGTATTAATAACGATATC | ||||
| glpF | glpF-F | CTAGGAACTGCAATCTTAATCC | 465 bp | ||
| glpF-R | TGGTAAAATCGCATGTCCAATTC | ||||
| gmk | gmk-F | ATCGTTTTATCGGGACCATC | 429 bp | ||
| gmk-R | TCATTAACTACAACGTAATCGTA | ||||
| pta | pta-F | GTTAAAATCGTATTACCTGAAGG | 474 bp | ||
| pta-R | GACCCTTTTGTTGAAAAGCTTAA | ||||
| tpi | tpi-F | TCGTTCATTCTGAACGTCGTGAA | 402 bp | ||
| tpi-R | TTTGCACCTTCTAACAATTGTAC | ||||
| yqiL | yqiL-F | CAGCATACAGGACACCTATTGGC | 516 bp | ||
| yqiL-R | CGTTGAGGAATCGATACTGGAAC | ||||