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

Conor J Meehan, Galo A Goig, Thomas A Kohl, Lennert Verboven, Anzaan Dippenaar, Matthew Ezewudo, Maha R 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 M Ashton, Daniela Brites, Andrea M CabibbeBouke C de Jong, Margaretha de Vos, Fabrizio Menardo, Sebastien Gagneux, Qian Gao, Tim H Heupink, Qingyun Liu, Chloé Loiseau, Leen Rigouts, Timothy C Rodwell, Elisa Tagliani, Timothy M Walker, Robin M Warren, Yanlin Zhao, Matteo Zignol, Marco Schito, Jennifer Gardy, Daniela M Cirillo, Stefan Niemann, Inaki Comas, Annelies Van Rie

Research output: Contribution to journalA1: Web of Science-articlepeer-review


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.

Original languageEnglish
JournalNature Reviews Microbiology
Issue number9
Pages (from-to)533-545
Number of pages13
Publication statusPublished - 2019


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