Identification of Missing Probes in rpoB gene in Rifampicin Resistant PTB and EPTB Cases Using Xpert MTB/RIF Assay in Sirmaur, Himachal Pradesh

Introduction India has the highest number of TB (27%) and MDR/RR-TB (24%) cases among the notified TB patients. Xpert MTB/ RIF assay is a fully automated cartridge-based real-time PCR to detect MTB and resistance to rifampicin within two hours using three specific primers and five unique molecular probes to target the rpoB gene. This study was done to detect RR-TB cases and frequency of missing probes, which target mutations in rpoB gene, in the different groups of study population in Sirmaur district of Himachal Pradesh. Methods All, pulmonary and extrapulmonary specimens, were processed for AFB microscopy and Xpert MTB/RIF assay to diagnose TB and RR-TB. Results Xpert detected MTBC in 721 patients. Using AFB microscopy, only 284 samples were positive. Of these MTB positive patients, 671 had pulmonary TB and 50 were EPTB cases. Resistance to RIF was detected in 31 (4.29%) cases of which resistance in presumptive tuberculosis group and presumptive drug resistant tuberculosis was 1.51% and 9.30% respectively. Twentyeight (4.17%) PTB cases and three (6%) EP-TB cases were resistant to RIF. The frequency of probe E was highest (77.41%) and mutation combination of probes C and D and E and D was 3.22%. Conclusion Drug resistance in the MTBC is mainly conferred through point mutations in specific gene targets in the bacterial genome. Molecular assays like Genexpert gives rapid diagnosis and Rifampicin resistance. This study helps to provide baseline data of mutations with in the 81 bp of rpoB gene and stresses the need to further evaluate the mutation patterns in this part of the country.