Strain diversity and relative transmission of Mycobacterium tuberculosis 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.