Band pattern analysis of mutations in rifampicin resistance strain of Mycobacterium tuberculosis by Line Probe assay in patients from Delhi, India

Abstract Background The GenoType MTBDR plus , a commercial Line Probe Assay (LPA) kit from Hain Lifescience, Germany, is endorsed by India's RNTCP Program for diagnosis of DRTB cases among smear-positive sputum samples. Although the LPA has been studied in several laboratories, there is a wide variation in existing M. tuberculosis strains across the globe, and false results can occur due to the presence of unique genetic mutations in different settings. Aim and objective An attempt was made to carry out band pattern analysis using LPA and also to observe uncommon mutations in MDR strains. Materials and methods Sputum samples were collected from MDR suspects and transported to intermediate reference laboratory (IRL) at New Delhi Tuberculosis Centre in Delhi. Sputum decontamination, DNA extraction, amplification, hybridization, and band pattern analysis of Line Probe assay strips was performed as per manufacturer's instructions. Results Among the 3000 samples with interpretable LPA strips, rifampicin drug resistance with or without isoniazid was observed in 600 samples. The most common mutation detected by LPA in the rpoB gene was Ser516Leu (29.0%). Novel mutations reported in this study include mutation from CA G (Gin) to CA T (His) at codon 517, AG C (Ser)-AG G (Arg) at codon 512, A CA (Thr) to G CA (Ala) at codon 526, TTG (Leu)-CTG (Leu) s at codon 524. Conclusion High frequencies of uncommon mutations in rpoB gene by LPA were observed, highlighting possibility of those in-silico detected mutations that may not impart phenotypic resistance further.