Table 1.
Principal oligonucleotide primer pairs used
| Category and genea | Primer designation | Sequence (5′–3′) | Source or reference | Product size (bp) |
|---|---|---|---|---|
| Resistance genes | ||||
| erm(B) | ERMB1 | GAAAAGGTACTCAACCAAATA | 28 | 639 |
| ERMB2 | AGTAACGGTACTTAAATTGTTTAC | 28 | ||
| tet(M) | TETM2 | GAACTCGAACAAGAGGAAAGC | 19 | 740 |
| TETM3 | ATGGAAGCCCAGAAAGGAT | 19 | ||
| ICESp1116 mapping | ||||
| orf2 | ORF2-for | TTTTCCGAGTGCCGAAGGTGC | This study | 11,230 |
| orf11 | ORF11-rev | GCGTTACCCCTTTTTCTTTTCG | This study | |
| orf12 | ORF12-for | GACGGTTCCACCATCATTTATC | This study | 11,490 |
| orf23 | ORF23-rev | CTTTTTCTTCACTCGTAACCGT | This study | |
| orf24 | ORF24-for | AGACAATCAAGTTACTAATCAT | This study | 9,372 |
| orf31 | ORF31-rev | GTTTCCCATTTAGCCGTCA | This study | |
| orf31 | ORF31-for | GAAAAGAAACCCTGGTAAAAG | This study | 12,394 |
| Downstream of orf45 | 1116end-rev | GAGAATAATCATCAAGCCTAT | This study | |
| ICESp1116 junctions | ||||
| SPYALAB49_000242b | JUG-for | GCGTCTTGGAATCTGGTCA | This study | 621 |
| orf1 | ORF1-rev | CCTCTCTCAGCAAGAACTCGCCG | This study | |
| orf45 | ORF45-for | GTATGACAGGTATGAGATTTG | This study | 2,448 |
| SPYALAB49_000245b | EPI-rev | AGGCTCTTGCGGCGGGTAA | This study | |
| ICESp1116 circular form | ||||
| orf1 | ORF1-rev | CCTCTCTCAGCAAGAACTCGCCG | This study | 1,937 |
| orf45 | ORF45-for | GTATGACAGGTATGAGATTTG | This study | |
| Chromosomal empty target site | ||||
| SPYALAB49_000242b | JUG-for | GCGTCTTGGAATCTGGTCA | This study | 1,134 |
| SPYALAB49_000245b | EPI-rev | AGGCTCTTGCGGCGGGTAA | This study | |
| Inverse PCR assays | ||||
| orf2 | REPA-inv | GCACCTTCGGCACTCGGAAAA | This study | |
| REPA-for | CTAATGATACTGATATTAGT | This study | ||
| orf30 | BETA-inv | AGAAACGCCCTGTAACGCTT | This study | |
| BETA-for | GGAATCAGAACGCAAACG | This study | ||
| orf36 [erm(B)] | ERMB-inv | GTAAACAATTTAAGTACCGTTACT | This study | |
| ERMB-for | TATTTGGTTGAGTACTTTTTC | This study | ||
| orf44 (tndX) | TNDX-inv | CTTTGCTCGATAGGCTCTA | This study | |
| TNDX-for | CGGATTGATGAAATAGACAGT | This study |
a
Except for resistance genes and unless otherwise specified, designations are according to the ORF numbering of ICESp1116.
b
From the S. pyogenes Alab49 genome.