Whole Genome Sequencing of Mycobacterium tuberculosis Clinical Isolates From India Reveals Genetic Heterogeneity and Region-Specific Variations That Might Affect Drug Susceptibility.

Jayshree Advani,Mrutyunjay Suar,Shashidhar Buggi,Praveen Kumar Pachouri,Prashant Upadhyay,Farah Naaz,Akhilesh Pandey,Rajesh Singh,Harsha Gowda,Jitendra Yadav,Oishi Chatterjee,Renu Verma,Umesh D Gupta,Devendra S Chauhan,Srikanth Prasad Tripathy,T S Keshava Prasad,Raju Ravikumar

doi:10.3389/fmicb.2019.00309

Abstract

Whole genome sequencing (WGS) of Mycobacterium tuberculosis has been constructive in understanding its evolution, genetic diversity and the mechanisms involved in drug resistance. A large number of sequencing efforts from across the globe have revealed genetic diversity among clinical isolates and the genetic determinants for their resistance to anti-tubercular drugs. Considering the high TB burden in India, the availability of WGS studies is limited. Here we present, WGS results of 200 clinical isolates of M. tuberculosis from North India which are categorized as sensitive to first-line drugs, mono-resistant, multi-drug resistant and pre-extensively drug resistant isolates. WGS revealed that 20% of the isolates were co-infected with M. tuberculosis and non-tuberculous mycobacteria species. We identified 12,802 novel genetic variations in M. tuberculosis isolates including 343 novel SNVs in 38 genes which are known to be associated with drug resistance and are not currently used in the diagnostic kits for detection of drug resistant TB. We also identified M. tuberculosis lineage 3 to be predominant in the northern region of India. Additionally, several novel SNVs, which may potentially confer drug resistance were found to be enriched in the drug resistant isolates sampled. This study highlights the significance of employing WGS in diagnosis and for monitoring further development of MDR-TB strains.

Highlights

Tuberculosis is one of the leading causes of death worldwide
We carried out Whole genome sequencing (WGS) of 200 culture confirmed M. tuberculosis clinical isolates from North India spanning a broad range of drug resistance profiles (50 sensitive to four first line drugs, 12 rifampicin mono-resistant, 31 isoniazid mono-resistant, 6 streptomycin mono-resistant, 91 multi-drug resistant (MDR) and 10 Pre-extensively-drug resistant (XDR)) (Supplementary Table S1)
The isolates were collected over a period of 4 years (2010–2014) at the National JALMA Institute of Leprosy and other Mycobacterial Diseases, Agra, India

Summary

Introduction

Tuberculosis is one of the leading causes of death worldwide. According to the recent WHO report, there were an estimated 10.0 million cases of TB and 1.3 million deaths during the year 2017. Whole genome sequencing (WGS) studies from across the globe have revealed genetic diversity of Mycobacterium tuberculosis and have provided significant insights into its evolution and transmission (Casali et al, 2014; Walker et al, 2015; Nikolayevskyy et al, 2016). They have revealed specific genotypes associated with drug resistance

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