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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 publication

DOI

10.1038/s41579-019-0214-5

Type

Journal article

Journal

Nature reviews. Microbiology

Publication Date

09/2019

Volume

17

Pages

533 - 545

Addresses

Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.

Keywords

Humans, Mycobacterium tuberculosis, Tuberculosis, Molecular Diagnostic Techniques, Computational Biology, Phylogeny, Drug Resistance, Bacterial, Practice Guidelines as Topic, Molecular Epidemiology, Whole Genome Sequencing