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. 2022 Jun 29;10(3):e0159421.
doi: 10.1128/spectrum.01594-21. Epub 2022 Apr 20.

Mycobacterium tuberculosis Lineages Associated with Mutations and Drug Resistance in Isolates from India

Siva Kumar Shanmugam #  1 , Narender Kumar #  2 , Tamilzhalagan Sembulingam  1 , Suresh Babu Ramalingam  1 , Ashok Selvaraj  1 , Udhayakumar Rajendhiran  1 , Sudha Solaiyappan  1 , Srikanth P Tripathy  1 , Mohan Natrajan  1 , Padmapriyadarsini Chandrasekaran  1 , Soumya Swaminathan  3 , Julian Parkhill  4 , Sharon J Peacock  2 , Uma Devi K Ranganathan  1
Affiliations

Mycobacterium tuberculosis Lineages Associated with Mutations and Drug Resistance in Isolates from India

Siva Kumar Shanmugam et al. Microbiol Spectr. .

Abstract

Current knowledge on resistance-conferring determinants in Mycobacterium tuberculosis is biased toward globally dominant lineages 2 and 4. In contrast, lineages 1 and 3 are predominant in India. In this study, we performed whole-genome sequencing of 498 MDR M. tuberculosis isolates from India to determine the prevalence of drug resistance mutations and to understand the genomic diversity. A retrospective collection of 498 M. tuberculosis isolates submitted to the National Institute for Research in Tuberculosis for phenotypic susceptibility testing between 2014 to 2016 were sequenced. Genotypic resistance prediction was performed using known resistance-conferring determinants. Genotypic and phenotypic results for 12 antituberculosis drugs were compared, and sequence data were explored to characterize lineages and their association with drug resistance. Four lineages were identified although lineage 1 predominated (43%). The sensitivity of prediction for isoniazid and rifampicin was 92% and 98%, respectively. We observed lineage-specific variations in the proportion of isolates with resistance-conferring mutations, with drug resistance more common in lineages 2 and 3. Disputed mutations (codons 430, 435, 445, and 452) in the rpoB gene were more common in isolates other than lineage 2. Phylogenetic analysis and pairwise SNP difference revealed high genetic relatedness of lineage 2 isolates. WGS based resistance prediction has huge potential, but knowledge of regional and national diversity is essential to achieve high accuracy for resistance prediction. IMPORTANCE Current knowledge on resistance-conferring determinants in Mycobacterium tuberculosis is biased toward globally dominant lineages 2 and 4. In contrast, lineages 1 and 3 are predominant in India. We performed whole-genome sequencing of 498 MDR M. tuberculosis isolates from India to determine the prevalence of drug resistance mutations and to understand genomic diversity. Four lineages were identified although lineage 1 predominated (43%). The sensitivity of prediction for isoniazid and rifampicin was 92% and 98%, respectively. We observed lineage-specific variations in the proportion of isolates with resistance-conferring mutations, with drug resistance more common in lineages 2 and 3. Disputed mutations (codons 430, 435, 445, and 452) in the rpoB gene were more common in isolates other than lineage 2. Phylogenetic analysis and pairwise SNP difference revealed high genetic relatedness of lineage 2 isolates. WGS based resistance prediction has huge potential, but knowledge of regional and national diversity is essential to achieve high accuracy for resistance prediction.

Keywords: Mycobacterium tuberculosis; drug resistance; lineage; whole-genome sequencing.

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Conflict of interest statement

The authors declare a conflict of interest. J.P. reports personal fees from Next Gen Diagnostics, outside the submitted work. S.J.P. reports receiving funds from Next Gen Diagnostics, outside the submitted work.

Figures

FIG 1
FIG 1
(a) Phylogenetic tree of 486 isolates and phenotypic drug susceptibility results. (b) Pairwise SNP differences for the four lineages.
FIG 2
FIG 2
Genetic determinants of resistance. (a) Genetic determinants in isolates that were phenotypically resistant and susceptible to ethambutol. (b) Frequency of p.D94X and p.A90V mutations for isolates that were phenotypically resistant and susceptible to three fluoroquinolone drugs. (c) Distribution of genetic determinants of resistance to rifampicin in the four lineages.
FIG 3
FIG 3
Lineage, digital spoligotype, and IS6110 count for 486 study isolates.
See this image and copyright information in PMC

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