TABLE 2.

Primers used to detect MDR tuberculosis

Target geneaPrimer set (direction)Nucleotide sequencePositionsbProduct size (bp)
PCR primers
    rpoBPR1 (forward)5′-CCGCGATCAAGGAGTTCTTC-3′1256-1275315
PR2 (reverse)5′-ACACGATCTCGTCGCTAACC-3′1570-1551
    katGPR3 (forward)5′-GTGCCCGAGCAACACCCACCCATTACAGAAAC-3′1-322,223
PR4 (reverse)5′-TCAGCGCACGTCGAACCTGTCGAG-3′2223-2200
    mabA promoterPR5 (forward)5′-ACATACCTGCTGCGCAATTC-3′−217 to −1981,362
PR6 (reverse)5′-GCATACGAATACGCCGAGAT-3′1145-1126
    embBPR7 (forward)5′-CCGACCACGCTGAAACTGCTGGCGAT-3′640-6652,748
PR8 (reverse)5′-GCCTGGTGCATACCGAGCAGCATAG-3′3387-3303
    pncAPR9 (forward)5′-GGCGTCATGGACCCTATATC-3′−80 to −61670
PR10 (reverse)5′-CAACAGTTCATCCCGGTTC-3′590-572
    rpsLPR11 (forward)5′-CCAACCATCCAGCAGCTGGT-3′4-23572
PR12 (reverse)5′-GTCGAGAGCCCGCTTGAGGG-3′575-556
    rrs (16S RNA)PR13 (forward)5′-AAACCTCTTTCACCATCGAC-3′428-4471,329
PR14 (reverse)5′-GTATCCATTGATGCTCGCAA-3′1756-1737
    gyrAPR15 (forward)5′-GATGACAGACACGACGTTGC-3′−1-19398
PR16 (reverse)5′-GGGCTTCGGTGTACCTCAT-3′397-379
Sequencing primers
    rpoBPR175′-TACGGCGTTTCGATGAAC-3′ (complementary strand)1529-1512
    katGPR185′-ACGTAGATCAGCCCCATCTG-3′ (complementary strand)689-670
PR195′-GAGCCCGATGAGGTCTATTG-3′574-593
PR205′-CCGATCTATGAGCGGATCAC-3′1162-1181
PR215′-GAACAAACCGACGTGGAATC-3′1729-1748
    mabA promoterPR225′-ACATACCTGCTGCGCAATTC-3′−217 to −198
    embBPR235′-ACGCTGAAACTGCTGGCGAT-3′646-665
PR245′-GTCATCCTGACCGTGGTGTT-3′1462-1481
PR255′-GGTGGGCAGGATGAGGTAGT-3′ (complementary strand)1596-1577
PR265′-CACAATCTTTTTCGCCCTGT-3′2007-2026
PR275′-GCGTGGTATCTCCTGCCTAAG-3′2581-2601
    pncAPR285′-GGCGTCATGGACCCTATATC-3′−80 to −61
    rpsLPR295′-CCAACCATCCAGCAGCTGGT-3′4-23
    rrs (16S RNA)PR305′-CAGGTAAGGTTCTTCGCGTTG-3′ (complementary strand)979-959
PR315′-GTTCGGATCGGGGTCTGCAA-3′1291-1310
    gyrAPR325′-GATGACAGACACGACGTTGC-3′−1-19
  • a The complete sequences of target genes in M. tuberculosis H37Rv are in the GenBank database under accession no. NC_000962.

  • b Numbering based on nucleotide position relative to the initiation codon of each gene.