Strain diversity and relative transmission of <i>Mycobacterium tuberculosis</i> in south coastal Karnataka, India

Background There are no published reports on the strain diversity and relative transmission of Mycobacterium tuberculosis isolates circulating in Karnataka State, India. Objective To explore the strain diversity of M. tuberculosis isolates and their relative transmission in south coastal Karnataka using spoligotyping and mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) typing. Design A total of 108 clinical isolates of M. tuberculosis were processed for spoligotyping, and 12-locus MIRU-VNTR typing and cluster analysis was performed. Results Spoligotyping data of 108 isolates revealed 63 spoligotype patterns: 36 (80 isolates, 74.1%) patterns corresponded to spoligotype international types (SITs), whereas 27 (28 isolates, 25.9%) patterns were orphans. A further 57 (52.8%) isolates were clustered into 12 clusters; 51 (47.2%) isolates were unique. The largest spoligotype cluster comprised SIT 48 (L1.2.2), followed by SIT 1942 (L3) and SIT 11 (L1.1.2). Combined MIRU-VNTR typing and spoligotyping analysis further differentiated these 108 isolates into five clusters of two isolates each and 98 individual patterns. Conclusions Combined use of spoligotyping and MIRU-VNTR typing is best suited for genotyping studies in this region. Very high genetic diversity was observed among the clinical isolates. Further elaborate studies are required for a better understanding of the genetic diversity and transmission dynamics of the strains circulating in this region.