Table 1.
Oligonucleotide primers used and VNTRs analyzed in this study
| VNTR | Primer | Sequence (5′–3′) | Repeat unit size (bp) | Expected size (bp) (no. of repeats) for strain Philadelphia-1 |
|---|---|---|---|---|
| Lpms01 | Lpms01R | GCATATGACAAAGCCTTGGC | 45 | 494 (8) |
| Lpms01F | TGAATTTCTCCCTCTTGCTTG | |||
| Lpms01F-NED | NED-TGAATTTCTCCCTCTTGCTTG | |||
| Lpms03 | Lpms03R | TGATGGTCTCAATGGTTCCG | 96 | 942 (8) |
| Lpms03F | GGACAAACAACCAATGAAGC | |||
| Lpms03F-VIC | VIC-GGACAAACAACCAATGAAGC | |||
| Lpms13 | Lpms13R | GCATCGGACTGAGCAAAGTA | 24 | 793 (11) |
| Lpms13F | CTCACCAGGATGCTTTGTCG | |||
| Lpms13F-NED | NED-CTCACCAGGATGCTTTGTCG | |||
| Lpms19 | Lpms19R | TCCAGAGGCTCTGGATTATC | 21 | 128 (4) |
| Lpms19F | GAACTATCAGAAGGAGGCGA | |||
| Lpms19F-VIC | VIC-GAACTATCAGAAGGAGGCGA | |||
| Lpms31 | Lpms31R | ATCGCCTAATTGCCGCCTA | 45 | 1,043 (17) |
| Lpms31F | CCTCGCAAGCCTATGTGG | |||
| Lpms31F-FAM | FAM-CCTCGCAAGCCTATGTGG | |||
| Lpms33 | Lpms33R | CGAGGAAATCTTCTTCAGCC | 125 | 317 (1) |
| Lpms33F | GACACCACAGCAGTTTGAAC | |||
| Lpms33F-VIC | VIC-GACACCACAGCAGTTTGAAC | |||
| Lpms34 | Lpms34R | ATGCAGGATGTTTGCGCATG | 125 | 265 (1) |
| Lpms34F | AAGGAATAAGGCGCAGCAC | |||
| Lpms34F-FAM | FAM-AAGGAATAAGGCGCAGCAC | |||
| Lpms35 | Lpms35R | TATCAACCTCATCATCCCTG | 18 | 205 (3) |
| Lpms35F | GAATCTGAAACAGTTGAGGATG | |||
| Lpms35F-PET | PET-GAATCTGAAACAGTTGAGGATG | |||
| Lpms38 | Lpms38R | GGATTGCCTTGGGCATTAAT | 8 | 264 (3) |
| Lpms38F | CCTATCAACAGATGACGCTT | |||
| Lpms38F-NED | NED-CCTATCAACAGATGACGCTT | |||
| Lpms39 | Lpms39R | CCAACTCCTCAACGCAACAA | 6 | 79 (6) |
| Lpms39F | CTTGACGAAGTAGGTGTGGG | |||
| Lpms39F-PET | PET-CTTGACGAAGTAGGTGTGGG | |||
| Lpms40 | Lpms40R | TTACCCAAGCCCTTATTGCG | 6 | 198 (4) |
| Lpms40F | TAGATCTCTTGCCGAGCTTC | |||
| Lpms40F-FAM | FAM-TAGATCTCTTGCCGAGCTTC | |||
| Lpms44 | Lpms44R | TTATGCGAGAGTTTCATGA | 6 | 173 (9) |
| Lpms44F | GCTACTGCAGCAACATCC | |||
| Lpms44F-NED | NED-GCTACTGCAGCAACATCC |