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Ecology, global diversity and evolutionary mechanisms in the Mycobacterium tuberculosis complex

Nature Reviews Microbiology (2025)Cite this article

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Abstract

With the COVID-19 pandemic receding, tuberculosis (TB) is again the number one cause of human death to a single infectious agent. TB is caused by bacteria that belong to the Mycobacterium tuberculosis complex (MTBC). Recent advances in genome sequencing have provided new insights into the ecology and evolution of the MTBC. This includes the discovery of new phylogenetic lineages within the MTBC, a deeper understanding of the host tropism among the various animal-adapted lineages, enhanced knowledge on the evolutionary dynamics of antimicrobial resistance and transmission, as well as a better grasp of the within-host MTBC diversity. Moreover, advances in long-read sequencing are increasingly highlighting the relevance of structural genomic variation in the MTBC. These findings not only shed new light on the biology and epidemiology of TB, but also give rise to new questions and research avenues. The purpose of this Review is to summarize these new insights and discuss their implications for global TB control.

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Fig. 1: The global phylogeny of the MTBC.
Fig. 2: The global phylogeography of the human-adapted MTBC.
Fig. 3: The TB burden caused by each human-adapted MTBC lineage.
Fig. 4: Examples of dominant MDR MTBC genotypes.

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Acknowledgements

The authors thank all other members of their group for the stimulating discussions. Their work is supported by the Swiss National Science Foundation (grants 320030-227432, 320030L-231163 and CRSII5_213514) and the European Research Council (883582-ECOEVODRTB).

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Authors and Affiliations

  1. Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland

    Galo A. Goig, Etthel M. Windels, Chloé Loiseau, Christoph Stritt, Loza Biru, Sonia Borrell, Daniela Brites & Sebastien Gagneux

  2. University of Basel, Basel, Switzerland

    Galo A. Goig, Etthel M. Windels, Chloé Loiseau, Christoph Stritt, Loza Biru, Sonia Borrell, Daniela Brites & Sebastien Gagneux

  3. Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland

    Etthel M. Windels

  4. Swiss Institute for Bioinformatics, Lausanne, Switzerland

    Etthel M. Windels

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G.A.G., E.M.W., C.L., C.S., L.B., S.B., D.B. and S.G. researched data for the article. G.A.G., E.M.W., C.L., C.S., S.B., D.B. and S.G. contributed substantially to discussion of the content, wrote the article, and reviewed and/or edited the manuscript before submission.

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Goig, G.A., Windels, E.M., Loiseau, C. et al. Ecology, global diversity and evolutionary mechanisms in the Mycobacterium tuberculosis complex. Nat Rev Microbiol (2025). https://doi.org/10.1038/s41579-025-01159-w

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