Modern lineages of Mycobacterium tuberculosis were recently introduced in western India and demonstrate increased transmissibility

Background Mycobacterium tuberculosis (Mtb) transmissibility may vary between lineages (or variants) and this may contribute to the slow decline of tuberculosis (TB) incidence. The objective of our study was to compare transmissibility across four major lineages (L1-4) of Mtb among participants from two cohort studies in Pune, India.

Methods We performed whole-genome sequencing (WGS) of Mtb sputum culture-positive isolates from participants in two prospective cohort studies of adults with pulmonary TB seeking care at public treatment centers in Pune, Maharashtra. We performed genotypic susceptibility prediction for both first- and second-line drugs using a previously validated random forest model. We used single nucleotide substitutions (SNS) and maximum likelihood estimation to build isolate phylogenies by lineage. We used Bayesian molecular dating to estimate ancestral node ages and compared tree characteristics using a two-sample Kolmogorov-Smirnov (KS) test.

Results Of the 642 isolates from distinct study participants that underwent WGS, 612 met sequence quality criteria. The median age of the 612 participants was 31 years (IQR 24.4-44.2), the majority were male (64.7%) and sputum smear-positive (83.3%), and 6.7% had co-infection with HIV. Most isolates belonged to L3 (44.6%). The majority (61.1%) of multidrug-resistant isolates (MDR, resistant to isoniazid and rifampin) belonged to L2 (P < 0.001 [Fisher’s Exact]). There was no significant difference in host characteristics between participants infected with the four major lineages. In phylogenetic analysis, we measured shorter terminal branch lengths in the L2 tree compared to L1 and L3 trees indicating less time elapsing between transmission and sampling and higher transmissibility (median branch lengths: L2 - 3.3, L3 - 7.8, p <0.001). Branching times for L2 and L4 were more recent than L1 and L3 indicating recent introduction into the region (p < 0.01 [KS test]).

Conclusion Modern Mtb lineages (L2 and L4) were more recently introduced in western India, compared to older lineages (L1 and L3). L2 shows a higher frequency of drug-resistance and higher transmissibility. Our findings highlight the need for contact tracing around cases of TB due to L2, and heightened surveillance of TB antibiotic resistance in India.

Competing Interest Statement
The authors have declared no competing interest.

Funding Statement
This study was funded by: The Impact of Diabetes on TB Treatment Outcomes (R01A1097494 to JG); RePORT India consortium (C-TRIUMPh: Cohort for TB Research by the Indo-US Medical Partnership USB1-31147-XX-13 to VM, AG, AK, RK, RL, NG, NP, JAT and U.S. Civilian Research and Development Foundation, NIH, Indian Department of Biotechnology), the US CRDF [OISE-17-63221 to VM] and BWI CTU (NIAID UM1AI069465). AD was supported through the Boston Children's Hospital OFD/BTREC/CTREC Faculty Career Development Fellowship and the Bushrod H. Campbell and Adah F. Hall Charity Fund/Charles A. King Trust Postdoctoral Fellowship. MRF is funded by the NIH (R01 AI55765). MIG was supported by the German Research Foundation (GR5643/1-1). DME, MS and the sequencing work was supported by the ReSeqTB sequencing platform, with direct funding from the Bill & Melinda Gates Foundation (OPP1115887). JAT was supported by NIAID (K23AI135102 and R21AI122922).