Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis

Matthias Merker, Jean-Philippe Rasigade, Maxime Barbier, Helen Cox, Silke Feuerriegel, Thomas A. Kohl, Egor Shitikov, Kadri Klaos, Cyril Gaudin, Rudy Antoine, Roland Diel, Sonia Borrell, Sebastien Gagneux, Vladyslav Nikolayevskyy, Sönke Andres, Valeriu Crudu, Philip Supply (), Stefan Niemann () and Thierry Wirth ()
Additional contact information
Matthias Merker: Research Center Borstel
Jean-Philippe Rasigade: EPHE, PSL University
Maxime Barbier: EPHE, PSL University
Helen Cox: University of Cape Town
Silke Feuerriegel: Research Center Borstel
Thomas A. Kohl: Research Center Borstel
Egor Shitikov: Federal Research and Clinical Centre of Physical-Chemical Medicine
Kadri Klaos: SA TUH United Laboratories, Mycobacteriology
Cyril Gaudin: Genoscreen
Rudy Antoine: Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Centre d’Infection et d’Immunité de Lille
Roland Diel: Schleswig-Holstein University Hospital
Sonia Borrell: Swiss Tropical and Public Health Institute
Sebastien Gagneux: Swiss Tropical and Public Health Institute
Vladyslav Nikolayevskyy: Imperial College London
Sönke Andres: Research Center Borstel
Valeriu Crudu: National TB Reference Laboratory, Institute of Phthisiopneumology
Philip Supply: Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Centre d’Infection et d’Immunité de Lille
Stefan Niemann: Research Center Borstel
Thierry Wirth: EPHE, PSL University

Nature Communications, 2022, vol. 13, issue 1, 1-11

Abstract: Abstract Transmission-driven multi-/extensively drug resistant (M/XDR) tuberculosis (TB) is the largest single contributor to human mortality due to antimicrobial resistance. A few major clades of the Mycobacterium tuberculosis complex belonging to lineage 2, responsible for high prevalence of MDR-TB in Eurasia, show outstanding transnational distributions. Here, we determined factors underlying the emergence and epidemic spread of the W148 clade by genome sequencing and Bayesian demogenetic analyses of 720 isolates from 23 countries. We dated a common ancestor around 1963 and identified two successive epidemic expansions in the late 1980s and late 1990s, coinciding with major socio-economic changes in the post-Soviet Era. These population expansions favored accumulation of resistance mutations to up to 11 anti-TB drugs, with MDR evolving toward additional resistances to fluoroquinolones and second-line injectable drugs within 20 years on average. Timescaled haplotypic density analysis revealed that widespread acquisition of compensatory mutations was associated with transmission success of XDR strains. Virtually all W148 strains harbored a hypervirulence-associated ppe38 gene locus, and incipient recurrent emergence of prpR mutation-mediated drug tolerance was detected. The outstanding genetic arsenal of this geographically widespread M/XDR strain clade represents a “perfect storm” that jeopardizes the successful introduction of new anti-M/XDR-TB antibiotic regimens.

Date: 2022
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DOI: 10.1038/s41467-022-32455-1

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