TABLE 4.
Summary of the MLPA probes designed and used in this studya
| Probe | Length (bp) | Target-specific sequence | Target or information provided (reference) |
|---|---|---|---|
| embB-306 | 142 | GTCGGACGACGGCTACATCCTGGGCATggcccgagtcgccgaccacgccggctac | EMB resistance marker (38) |
| katG-315 | 160 | caccggaaccggtaaggacgcgatcaccaCCGGCATCGAGGTCGTATGGACGAACACCCC | INH resistance marker (27) |
| inhA-15 | 178 | CGATTTCGGCCCGGCCGCGGCGAGATgataggttgtcggggtgactgccacagcc | INH resistance marker (27) |
| 16S rRNA | 202 | CACGGGATGCATGTCTTGTGGTGGAAAgcgctttagcggtgtgggatgagcccgcggc | 16S rRNA gene, M. tuberculosis complex specific |
| rpoB-176 | 229 | cacgttcatcatcaacgggaccgagcgtgtggtgTTCAGCCAGCTGGTGCGGTCGCCC | RIF resistance marker (1) |
| rpoB-531 | 256 | GTTGACCCACAAGCGCCGACTGTTggcgctggggcccggcggtctgtcacgt | RIF resistance marker (27) |
| rpoB-526G | 265 | caacccgctgtcggggttgaccGACAAGCGCCGACTGTCGGCGCTGGGGCC | RIF resistance marker (27) |
| rpoB-526T | 274 | caacccgctgtcggggttgaccTACAAGCGCCGACTGTCGGCGCTGGGGCC | RIF resistance marker (27) |
| rpoB-522 | 283 | agccaattcatggaccagaacaacccgctgtTGGGGTTGACCCACAAGCGCCGAC | RIF resistance marker (1) |
| IS6110 | 301 | GTCGAACTCGAGGCTGCCTACTACGCTcaacgccagagaccagccgccggctgaggtctcagat | Insertion element IS6110, M. tuberculosis complex specific |
| katG-463 | 319 | GATTGCCAGCCTTAAGAGCCAGATCCGggcatcgggattgactgtctcacagctagtttcgacc | Genotype marker, specific for PGG 2 and 3 (37) |
| gyrA-95 | 328 | GCACGGCGACGCGTCGATCTACGACACcctggtgcgcatggcccagccctgg | Genotype marker, specific for PGG 1 and 2 (37) |
| mutT2-58 | 355 | CCCGAGAGCTCGCCGAAGAACTGCgactcgaggtcgccgacctcgcggtggg | Genotype marker, specific for Beijing 2 (26) |
| mutT4-48 | 364 | CGACCCCGGCAACGGCGAAGGggtcccggtcccgctcacctcgtcgcgggt | Genotype marker, specific for Beijing 1, 2, and 3 (26) |
| ogt-12 | 373 | CGCACCATCGATAGCCCCATCGGAccattaaccctggccgggcatggctcggtgttga | Genotype marker, specific for Beijing 2 (26) |
| ogt-15 | 382 | taccgcaccatcgatagccccatcgggccattaaGCCTGGCCGGGCATGGCTCGGTGTTGA | Genotype marker, specific for Haarlem (26) |
| ogt-37 | 391 | cctgcggatgctcgagcagacgtatgagccaagccTCACACACTGGACACCCGACCCC | Genotype marker, specific for Beijing 3 and 4 (26) |
| TbD1 | 418 | GCGGTCGCGGGATTCAGCGTCTATcggttgcacggcatcttcggctcgcacgaca | Absent in modern M. tuberculosis strains |
a
Probes are named after the gene and specific codon or region that they target. Target-specific sequences of probes include sequences targeted by the M13-derived probe (lowercase letters) and the synthetic probe (capital letters), as well as the SNP/ligation site sequence (boldface). Sequences for the 16S rRNA gene, IS6110, and TbD1 were derived from the M. tuberculosis reference strain H37Rv.