Genotypic and phenotypic diversity of the multidrug-resistant Mycobacterium tuberculosis strains from eastern India

Abstract Background The genomic diversity of M. tuberculosis has been explored in the northern and southern states of India using whole genome sequencing, but insight into the eastern region remains limited. The study aims to understand the diversity and drug resistance phenotypes in eastern region using sequencing based approach. Methods A total of 118 M. tuberculosis isolates from Sikkim (n = 53), Meghalaya (n = 1), and Odisha (n = 48) were sequenced. After filtering out low quality isolates based on taxonomic classification and depth of coverage, variant calling was performed. Results We observed a high prevalence of multi-drug resistant (MDR) TB lineage 2 (n = 52) isolates in northeast whereas there was a mixed representation of lineage 1 (n = 30) & lineage 3 (n = 11) in Odisha. The MDR TB isolates from Sikkim posed a high rate of fluoroquinolone resistance and pairwise SNV distances(≤10) showed evidence of local transmission in the region. We observed occurrence of genetic variations in genes associated with bedaquiline and delamanid resistance. Conclusion Our findings show the diversity of M. tuberculosis vary across the eastern regions, in north eastern states lineage 2 has a dominant presence were as lineage 1 and 3 has mixed representation in Odisha. The high prevalence of fluoroquinolone resistance in north eastern region associated with variations in gyrA gene and local transmission.