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dc.identifier.citationMeehan CJ, Goig GA, Kohl TA et al (2019) Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nature Reviews Microbiology. 17(9): 533-545.
dc.description.abstractWhole 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.
dc.description.sponsorshipEuropean Research Council grant (INTERRUPTB; no. 311725), European Research Council grant (TB-ACCELERATE; no. 638553), Foundation for Innovative New Diagnostics, German Center for Infection Research (DZIF), Deutsche Forschungsgemeinschaft (German Research Foundation) under Germany’s Excellence Strategy (EXC 22167–390884018), FWO Odysseus G0F8316N, US National Institutes of Health BD2K K01 (MRF ES026835), Agence Nationale de la Recherche (ANR-16-CD35-0009)
dc.subjectAntimicrobial resistance
dc.subjectBacterial genetics
dc.subjectClinical microbiology
dc.subjectCommunication and replication
dc.subjectClinical microbiology
dc.subjectInfectious-disease diagnostics
dc.subjectPolicy and public health in microbiology
dc.subjectWhole genome amplification
dc.titleWhole genome sequencing of Mycobacterium tuberculosis: current standards and open issues
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