Table 1.
Oligonucleotide primer pairs used
| Procedure and gene/amplicon | Primer designation | Sequence (5′–3′) | Reference or source | Product size (bp) |
|---|---|---|---|---|
| Detection of TET resistance genes | ||||
| tet(M) | TETM3 | ATGGAAGCCCAGAAAGGAT | 11 | 740 |
| TETM2 | GAACTCGAACAAGAGGAAAGC | 11 | ||
| tet(O) | TETO1 | AACTTAGGCATTCTGGCTCAC | 11 | 519 |
| TETO2 | TCCCACTGTTCCATATCGTCA | 11 | ||
| PCR evidence of Tn916 | ||||
| int916 | int-for | GCGTGATTGTATCTCACT | 12 | 1,046 |
| int-rev | GACGCTCCTGTTGCTTCT | 12 | ||
| xis916 | xis-for | AAGCAGACTGAGATTCCTA | 13 | 194 |
| xis-rev | GCGTCCAATGTATCTATAA | 13 | ||
| orf7-orf8a | O15 | GTACGTCCACCAATGTGG | 14 | 902 |
| O16 | GCACGCTTCCACGAAAGGAG | 14 | ||
| orf20-IR18–19a | J12 | CCCATTGAAGACGCAGAAGT | 15 | 801 |
| J11 | AAAAATCCCTACCGCACT | 15 | ||
| orf24-orf20a | TN6-rev | CCATCAAACATTCATTCAGC | 15 | 3,358 |
| J13 | GGTTTTGTGGTTAGTTTT | 15 | ||
| PCR mapping of Tn5801.Sagb | ||||
| int5801 | 1812 | GTCCATACGTTCCTAAAGTCGTC | 8 | 726 |
| 1811 | CCGATATTGAGCCTATTGATGTG | 8 | ||
| sav400 | 400R | TCGTATTTCAAGGCTTCGTC | This study | 369 |
| 400F | TACCGAAGAGTCCATCAAAC | This study | ||
| sav408 | 408R | AATGTAGGGGCGACTTGATG | This study | 1,005 |
| 408F | ACTGGCTTATGGCGTTTCTC | This study | ||
| sav409 | 409R | GCAGACAAACCAAGATAAGC | This study | 940 |
| 409F | GAGAGCGAATCAAAGCCAAC | This study | ||
| sav413 | 413R | AACACCGTTGTCGTCTCCAC | This study | 743 |
| 413F | TTGCTAGTAATATAAGGGCGA | This study | ||
| sav414 | 414R | ATTAGATACACAACATCCTCATC | This study | 579 |
| 414F | ACAGGCAATCCCATCAGAAC | This study | ||
| sav415 | 415R | TAGATGAGGCTTGATACACC | This study | 677 |
| 415F | TTCTCGTAACGGCTCCTATG | This study | ||
| int5801-tet(M) | 1812 | GTCCATACGTTCCTAAAGTCGTC | 8 | 4,971 |
| TETM2 | GAACTCGAACAAGAGGAAAGC | 11 | ||
| tet(M)-sav400 | TETM3 | ATGGAAGCCCAGAAAGGAT | 11 | 3,362 |
| 400F | TACCGAAGAGTCCATCAAAC | This study | ||
| sav400-sav408 | 400R | TCGTATTTCAAGGCTTCGTC | This study | 9,331 |
| 408F | ACTGGCTTATGGCGTTTCTC | This study | ||
| sav408-sav409 | 408R | AATGTAGGGGCGACTTGATG | This study | 2,612 |
| 409F | GAGAGCGAATCAAAGCCAAC | This study | ||
| sav409-sav411 | 409R | GCAGACAAACCAAGATAAGC | This study | 2,142 |
| 411F | GAGATTAGCAGAAGGTATTGTG | This study | ||
| sav409-sav413 | 409R | GCAGACAAACCAAGATAAGC | This study | 3,874 |
| 413F | TTGCTAGTAATATAAGGGCGA | This study | ||
| sav413-sav414 | 413R | AACACCGTTGTCGTCTCCAC | This study | 1,968 |
| 414F | ACAGGCAATCCCATCAGAAC | This study | ||
| sav414-sav415 | 414R | ATTAGATACACAACATCCTCATC | This study | 3,295 |
| 415F | TTCTCGTAACGGCTCCTATG | This study | ||
| Tn5801.Sag chromosomal integration sitec | ||||
| SAG967 (guaA) | LJ967 | CGTGAAGAAATCGCTAAAG | This study | 1,228 |
| int5801 | 1811 | CCGATATTGAGCCTATTGATGTG | 8 | |
| sav411 | CF1 | TTCAAAGGAACAGAAGCGGG | This study | 1,414 |
| SAG964 | RJ964 | GAAGTAGAAGAGAGCCATAG | This study | |
| Search for circular form | ||||
| int5801 | 1811 | CCGATATTGAGCCTATTGATGTG | 8 | |
| sav411 | CF1 | TTCAAAGGAACAGAAGCGGG | This study |
a
ORFs numbered according to the reported organization of Tn916 (GenBank accession no. U09422).
b
Tn5801 from the genome of S. aureus Mu50 (DDBJ accession no. BA000017; sav genes) was used as the reference sequence. In PCR assays, S. aureus Mu50 (ATCC 700699) was used as a positive control and S. pneumoniae BM4200 (Pasteur Institute Collection), harboring the Tn916-like transposon Tn1545 (1), was used as a negative control.
c
The genome of S. agalactiae strain 2603V/R (GenBank accession no. AE009948; SAG genes) was used as the reference sequence.