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

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...

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Bibliographic Details
Published in:	Nature reviews. Microbiology Vol. 17; no. 9; pp. 533 - 545
Main Authors:	Meehan, Conor J, Goig, Galo A, Kohl, Thomas A, Verboven, Lennert, Dippenaar, Anzaan, Ezewudo, Matthew, Farhat, Maha R, Guthrie, Jennifer L, Laukens, Kris, Miotto, Paolo, Ofori-Anyinam, Boatema, Dreyer, Viola, Supply, Philip, Suresh, Anita, Utpatel, Christian, van Soolingen, Dick, Zhou, Yang, Ashton, Philip M, Brites, Daniela, Cabibbe, Andrea M, de Jong, Bouke C, de Vos, Margaretha, Menardo, Fabrizio, Gagneux, Sebastien, Gao, Qian, Heupink, Tim H, Liu, Qingyun, Loiseau, Chloé, Rigouts, Leen, Rodwell, Timothy C, Tagliani, Elisa, Walker, Timothy M, Warren, Robin M, Zhao, Yanlin, Zignol, Matteo, Schito, Marco, Gardy, Jennifer, Cirillo, Daniela M, Niemann, Stefan, Comas, Inaki, Van Rie, Annelies
Format:	Journal Article
Language:	English
Published:	England Nature Publishing Group 01.09.2019
Subjects:	Bioinformatics Computational Biology - methods Computational Biology - standards Drug Resistance, Bacterial Gene sequencing Genomes Health surveillance Humans International standards Molecular Diagnostic Techniques - methods Molecular Diagnostic Techniques - standards Molecular Epidemiology - methods Molecular Epidemiology - standards Mycobacterium tuberculosis Mycobacterium tuberculosis - classification Mycobacterium tuberculosis - genetics Mycobacterium tuberculosis - isolation & purification Phylogeny Pipelines Practice Guidelines as Topic Public health Quality control Tuberculosis Tuberculosis - epidemiology Tuberculosis - microbiology Whole genome sequencing Whole Genome Sequencing - methods Whole Genome Sequencing - standards
ISSN:	1740-1526, 1740-1534, 1740-1534
Online Access:	Get full text
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Summary:	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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 ObjectType-Literature Review-3 ObjectType-Review-3 content type line 23
ISSN:	1740-1526 1740-1534 1740-1534
DOI:	10.1038/s41579-019-0214-5