Mycobacterium tuberculosis becomes resistant to the first line of drug treatment i.e. Rifampin and Isoniazid. Isoniazid (INH) together with rifampicin (RFP) forms the cornerstone of a short chemotherapy course for tuberculosis (TB) treatment.   Resistance to Rifampin (RIF) and Isoniazid (INH) is caused by the mutations in the rpoB and katG gene which codes for the β-subunit of RNA polymerase and catalase‐peroxidase respectively. The amplification refractory mutation system (ARMS) PCR technique was used to detect mutations in the rpoB gene of Mycobacterium tuberculosis strains. Overall, DNA samples from 41 phenotypic MDR-TB were subjected to ARMS PCR using three different codon specific primers (516,526 and 531). These three codons occupy large portion of total mutation responsible for rifampin resistance. Out of the total DNA samples, 33 were bearing mutation in any of the three codons mentioned. In our study, the highest number of samples had mutation in codon 531 (96.97%) followed by codon 516(18.18%) and codon 526 (12.12%) respectively. Polymerase Chain Reaction Restriction Fragment Length Polymorphism (PCR-RFLP) technique was performed on the above mentioned samples to detect mutation in KatG gene. The katG Ser315Thr mutation was observed in 24(72.72%) out of 33 samples. Thus, ARMS PCR and PCR-RFLP techniques can be used as an alternative diagnostic tool for detection of rifampin and isoniazid resistance in Mycobacterium tuberculosis strains.

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