Molecular characterization of rpoB gene encoding the RNA polymerase β subunit in rifampin-resistant Mycobacterium tuberculosis strains from south India

Polymerase chain reaction (PCR) mediated direct DNA sequencing was evaluated for rapid detection of Rifampicin resistance (RMP super(r)) of Mycobacterium tuberculosis. After amplification of the rpoB gene, the product was sequenced using ABI 310 Genetic Analyzer and the rifampicin resistance in M. tuberculosis were assessed using the sequence pattern. Among the 100 isolates, 83 isolates were rifampicin sensitive, exhibited a wild-type pattern on PCR mediated direct sequencing, and remaining 17 isolates were resistant. All the RMP super(r) isolates were multidrug resistant, that is, resistant to at least Rifampicin and isoniazid. The mutation rate at the most effected codon 526 in the 81 bp rifampin resistance-determining region (RRDR) of rpoB gene was determined to be 35.29% in isolates from South India. In addition, the mutation rate at the most affected codon 451 was in the out side of the 81 bp RRDR region of rpoB gene. A synonym mutation was detected (Thr arrow right Thr) at codon 526 in one isolate, which was inside the active site (codons 507-533) of RMP binding in the rpoB gene region. The sequencing analysis for genotypic evaluation of Rifampicin resistance in highly sensitive assay provides a practical alternative to in vitro testing in M. tuberculosis.