Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues

Conor J. Meehan (1) , Galo A. Goig (2) , Thomas A. Kohl (3, 4) , Lennert Verboven (5) , Anzaan Dippenaar (6) , Matthew Ezewudo (7) , Maha R. Farhat (8, 9) , Jennifer L. Guthrie (10) , Kris Laukens (5) , Paolo Miotto (11) , Boatema Ofori-Anyinam (12, 13) , Viola Dreyer (3, 4) , Philip Supply (14) , Anita Suresh (15) , Christian Utpatel (3, 4) , Dick van Soolingen (16) , Yang Zhou (17) , Philip M. Ashton (18) , Daniela Brites (19, 20) , Andrea M. Cabibbe (11) , Bouke C. de Jong (1) , Margaretha de Vos (5) , Fabrizio Menardo (19, 20) , Sebastien Gagneux (19, 20) , Qian Gao (21) , Tim H. Heupink (5) , Qingyun Liu (21) , Chloé Loiseau (19, 20) , Leen Rigouts (1) , Timothy C. Rodwell (15) , Elisa Tagliani (11) , Timothy M. Walker (18, 22) , Robin M. Warren (6) , Yanlin Zhao (17) , Matteo Zignol (23) , Marco Schito (7) , Jennifer Gardy (10) , Daniela M. Cirillo (11) , Stefan Niemann (3, 4) , Inaki Comas (2) , Annelies van Rie (5)

1 ITM - Institute of Tropical Medicine [Antwerp]
2 IBV - Instituto de biomedicina [Valencia]
3 Forschungszentrum Borstel - Research Center Borstel
4 German Center for Infection Research - Partner Site Hamburg-Lübeck-Borstel-Riems
5 Universiteit Antwerpen = University of Antwerpen [Antwerpen]
6 Stellenbosch University
7 Critical Path Institute [Tucson, AZ]
8 HMS - Harvard Medical School [Boston]
9 Massachusetts General Hospital [Boston]
10 UBC - University of British Columbia
11 IRCCS San Raffaele Scientific Institute [Milan, Italie]
12 CGHSD - Center for Global Health Security and Diplomacy [Ottawa]
13 FDA Ghana - Food and Drugs Authority [Accra, Ghana]
14 CIIL - Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204
15 FIND - Foundation for Innovative New Diagnostics
16 RIVM - National Institute for Public Health and the Environment [Bilthoven]
17 Chinese Center for Disease Control and Prevention
18 University of Oxford
19 Swiss Tropical and Public Health Institute [Basel]
20 Unibas - Université de Bâle = University of Basel = Basel Universität
21 Fudan University [Shanghai]
22 John Radcliffe Hospital [Oxford University Hospital]
23 OMS / WHO - Organisation Mondiale de la Santé / World Health Organization Office

Whole genome sequencing (WGS) of Mycobacterium tuberculosis has rapidly progressed from a research tool to a clinical application for the diagnosis and management of tuberculosis and in public health surveillance. This development has been facilitated by drastic drops in cost, advances in technology and concerted efforts to translate sequencing data into actionable information. There is, however, a risk that, in the absence of a consensus and international standards, the widespread use of WGS technology may result in data and processes that lack harmonization, comparability and validation. In this Review, we outline the current landscape of WGS pipelines and applications, and set out best practices for M. tuberculosis WGS, including standards for bioinformatics pipelines, curated repositories of resistance-causing variants, phylogenetic analyses, quality control and standardized reporting.

Domaines: Microbiologie et Parasitologie; Génomique, Transcriptomique et Protéomique [q-bio.GN]

Conor J. Meehan, Galo A. Goig, Thomas A. Kohl, Lennert Verboven, Anzaan Dippenaar, et al.. Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nature Reviews Microbiology, 2019, 17 (9), pp.533-545. ⟨10.1038/s41579-019-0214-5⟩. ⟨hal-02347018⟩