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Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis

Philip Supply 1 Michael Marceau 1 Sophie Mangenot 2 David Roche 3, 2 Carine Rouanet 1 Varun Khanna 4 Laleh Majlessi 5 Alexis Criscuolo 6 Julien Tap 6 Alexandre Pawlik 4 Laurence Fiette 7, 8 Mickael Orgeur 4 Michel Fabre 9 Cécile Parmentier 4 Wafa Frigui 4 Roxane Simeone 4 Eva C. Boritsch 4 Anne-Sophie Debrie 10, 1 Eve Willery 1 Danielle Walker 11 Michael A. Quail 11 Laurence Ma 12 Christiane Bouchier 12 Grégory Salvignol 3, 2 Fadel Sayes 5 Alessandro Cascioferro 4 Torsten C Seemann 13 Valérie Barbe 14, 2 Camille Locht 15, 1 Maria-Cristina Gutierrez 1, 16 Claude Leclerc 5 Stephen D Bentley 11 Timothy Stinear 17 Sylvain Brisse 6 Claudine Médigue 3, 2 Julian Parkhill 11 Stéphane Cruveiller 3, 2 Roland Brosch 4, * 
Abstract : Global spread and limited genetic variation are hallmarks of M. tuberculosis, the agent of human tuberculosis. In contrast, Mycobacterium canettii and related tubercle bacilli that also cause human tuberculosis and exhibit unusual smooth colony morphology are restricted to East Africa. Here, we sequenced and analyzed the whole genomes of five representative strains of smooth tubercle bacilli (STB) using Sanger (4-5× coverage), 454/Roche (13-18× coverage) and/or Illumina DNA sequencing (45-105× coverage). We show that STB isolates are highly recombinogenic and evolutionarily early branching, with larger genome sizes, higher rates of genetic variation, fewer molecular scars and distinct CRISPR-Cas systems relative to M. tuberculosis. Despite the differences, all tuberculosis-causing mycobacteria share a highly conserved core genome. Mouse infection experiments showed that STB strains are less persistent and virulent than M. tuberculosis. We conclude that M. tuberculosis emerged from an ancestral STB-like pool of mycobacteria by gain of persistence and virulence mechanisms, and we provide insights into the molecular events involved.
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Submitted on : Friday, May 22, 2020 - 12:01:13 PM
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Philip Supply, Michael Marceau, Sophie Mangenot, David Roche, Carine Rouanet, et al.. Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis. Nature Genetics, 2013, 45 (2), pp.172-179. ⟨10.1038/ng.2517⟩. ⟨pasteur-02615220⟩



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