Predominance of ancestral lineages of Mycobacterium tuberculosis in India

Abstract

Although India has the highest prevalence of tuberculosis (TB) worldwide, the genetic diversity of Mycobacterium tuberculosis in India is largely unknown. A collection of 91 isolates originating from 12 different regions spread across the country were analyzed by genotyping using 21 loci with variable-number tandem repeats (VNTRs), by spoligotyping, by principal genetic grouping (PGG), and by deletion analysis of M. tuberculosis-specific deletion region 1. The isolates showed highly diverse VNTR genotypes. Nevertheless, highly congruent groupings identified by using the 4 independent sets of markers permitted a clear definition of 3 prevalent PGG1 lineages, which corresponded to the "ancestral" East African-Indian, the Delhi, and the Beijing/W genogroups. A few isolates from PGG2 lineages and a single representative of the presumably most recent PGG3 were identified. These observations suggest a predominance of ancestral M. tuberculosis genotypes in the Indian subcontinent, which supports the hypothesis that India is an ancient endemic focus of TB.

Figure 1

Genetic relationships of Indian Mycobacterium tuberculosis isolates. The dendrogram based on mycobacterial interspersed repetitive units–variable-number tandem repeats (MIRU-VNTR) genotypes, generated by using the neighbor-joining algorithm, was rooted with M. canettii, the most divergent member of the M. tuberculosis complex. Corresponding spoligotypes of the TbD1+/EAI isolates, additional genogroups, principal genetic group (PGG), and M. tuberculosis–specific deletion region 1 (TbD1) status are indicated. Indian isolates included in the collection of Kremer et al. (16) were included as references. LAM, Latin American–Mediterranean; CAS, Central Asian; EAI, East Africa–Indian.

Figure 2

Geographic distribution of Mycobacterium. tuberculosis genotypes in northern, central, and southern India. PGG, principal genetic group; TbD1, M. tuberculosis–specific deletion region 1.