Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics

Abstract

Background.: India is home to 25% of all tuberculosis cases and the second highest number of multidrug resistant cases worldwide. However, little is known about the genetic diversity and resistance determinants of Indian Mycobacterium tuberculosis, particularly for the primary lineages found in India, lineages 1 and 3.

Methods.: We whole genome sequenced 223 randomly selected M. tuberculosis strains from 196 patients within the Tiruvallur and Madurai districts of Tamil Nadu in Southern India. Using comparative genomics, we examined genetic diversity, transmission patterns, and evolution of resistance.

Results.: Genomic analyses revealed (11) prevalence of strains from lineages 1 and 3, (11) recent transmission of strains among patients from the same treatment centers, (11) emergence of drug resistance within patients over time, (11) resistance gained in an order typical of strains from different lineages and geographies, (11) underperformance of known resistance-conferring mutations to explain phenotypic resistance in Indian strains relative to studies focused on other geographies, and (11) the possibility that resistance arose through mutations not previously implicated in resistance, or through infections with multiple strains that confound genotype-based prediction of resistance.

Conclusions.: In addition to substantially expanding the genomic perspectives of lineages 1 and 3, sequencing and analysis of M. tuberculosis whole genomes from Southern India highlight challenges of infection control and rapid diagnosis of resistant tuberculosis using current technologies. Further studies are needed to fully explore the complement of diversity and resistance determinants within endemic M. tuberculosis populations.

Keywords: CAS lineage; EAI lineage; India; Indo-Oceanic lineage; drug resistance..

Figure 1.

Phylogeny of all 223 newly sequenced strains, together with 243 previously published strains from Comas et al. Branches are colored according to lineage, and outer ticks are colored according to dataset of origin and geographic location. For each strain, we performed variant detection relative to the M. tuberculosis H37Rv reference genome (see Detailed Methods) and identified a total of 67722 variable SNP loci that were used to construct this phylogeny. .

Figure 2.

Clonal groups overlaid onto a phylogeny of all 223 newly sequenced strains from Southern India. Tree branches are colored by lineage, as in Figure 1. The central rings of dots indicate susceptibility phenotypes for isoniazid (11), rifampicin (11), ethambutol (11), and streptomycin (11) (from inside to outside, marked as “IRES”). A gray “Missing” mark indicates that no conclusive phenotype was available. Moving outward, the next ring is a numeric patient identifier, followed by clonal group ID (in red) and treatment center. Clonal groups are boxed in red. Treatment centers P01-P14 are in Tiruvallur, whereas all Madurai strains are from the Gov. Rajaji Hospital. Clonal groups D16 and D24 contained a strain that lacked patient information and were excluded from further analysis.