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

Meehan, Conor J. and Goig, Galo A. and Kohl, Thomas A. and Verboven, Lennert and Dippenaar, Anzaan and Ezewudo, Matthew and Farhat, Maha R. and Guthrie, Jennifer L. and Laukens, Kris and Miotto, Paolo and Ofori-Anyinam, Boatema and Dreyer, Viola and Supply, Philip and Suresh, Anita and Utpatel, Christian and van Soolingen, Dick and Zhou, Yang and Ashton, Philip M. and Brites, Daniela and Cabibbe, Andrea M. and de Jong, Bouke C. and de Vos, Margaretha and Menardo, Fabrizio and Gagneux, Sebastien and Gao, Qian and Heupink, Tim H. and Liu, Qingyun and Loiseau, Chloé and Rigouts, Leen and Rodwell, Timothy C. and Tagliani, Elisa and Walker, Timothy M. and Warren, Robin M. and Zhao, Yanlin and Zignol, Matteo and Schito, Marco and Gardy, Jennifer and Cirillo, Daniela M. and Niemann, Stefan and Comas, Inaki and Van Rie, Annelies. (2019) Whole genome sequencing of Mycobacterium tuberculosis : current standards and open issues. Nature Reviews Microbiology, 17 (9). pp. 533-545.

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Official URL: https://edoc.unibas.ch/71962/

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Abstract

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.

Faculties and Departments:	09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH) 09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH) > Department of Medical Parasitology and Infection Biology (MPI) > Tuberculosis Ecology and Evolution Unit (Gagneux)
UniBasel Contributors:	Menardo, Fabrizio and Gagneux, Sebastien and Brites, Daniela
Item Type:	Article, refereed
Article Subtype:	Research Article
Publisher:	Nature Publishing Group
ISSN:	1740-1526
e-ISSN:	1740-1534
Note:	Publication type according to Uni Basel Research Database: Journal article
Identification Number:	doi: 10.1038/s41579-019-0214-5 pmid: 31209399
Last Modified:	18 Sep 2019 07:14
Deposited On:	18 Sep 2019 07:14

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