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

2019; Nature Portfolio; Volume: 17; Issue: 9 Linguagem: Inglês

10.1038/s41579-019-0214-5

1740-1534

Conor J. Meehan, Galo A. Goig, Thomas A. Kohl, Lennert Verboven, Anzaan Dippenaar, Matthew Ezewudo, Maha Farhat, Jennifer L. Guthrie, Kris Laukens, Paolo Miotto, Boatema Ofori-Anyinam, Viola Dreyer, Philip Supply, Anita Suresh, Christian Utpatel, Dick van Soolingen, Yang Zhou, Philip Ashton, Daniela Brites, Andrea Maurizio Cabibbe, Bouke C. de Jong, Margaretha de Vos, Fabrizio Menardo, Sébastien Gagneux, Qian Gao, Tim H. Heupink, Qingyun Liu, Chloé Loiseau, Leen Rigouts, Timothy C. Rodwell, Elisa Tagliani, A Sarah Walker, Robin M. Warren, Yanlin Zhao, Matteo Zignol, Marco Schito, Jennifer L. Gardy, Daniela María Cirillo, Stefan Niemann, Iñaki Comas, Annelies Van Rie,

Genomics and Phylogenetic Studies

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. Whole genome sequencing (WGS) offers new opportunities in the clinical management and surveillance of Mycobacterium tuberculosis. In this Review, Meehan and colleagues explore 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.