Whole-genome sequencing for rapid, reliable and routine investigation of Mycobacterium tuberculosis transmission in local communities.

Details

Serval ID
serval:BIB_604EC4A7CD3F
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Whole-genome sequencing for rapid, reliable and routine investigation of Mycobacterium tuberculosis transmission in local communities.
Journal
New microbes and new infections
Author(s)
Zakham F., Laurent S., Esteves Carreira A.L., Corbaz A., Bertelli C., Masserey E., Nicod L., Greub G., Jaton K., Mazza-Stalder J., Opota O.
ISSN
2052-2975 (Print)
ISSN-L
2052-2975
Publication state
Published
Issued date
09/2019
Peer-reviewed
Oui
Volume
31
Pages
100582
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
Abstract
Contact investigations following the diagnosis of active tuberculosis (TB) are paramount for the control of the disease. Epidemiological data are very powerful for contact tracing but might be delayed and/or difficult to integrate, especially in the setting of multiple contact-tracing investigations. The aim of this study was to address the added-value of whole-genome sequencing (WGS) to routine local TB surveillance systems. From November 2016 to July 2017, the local TB surveillance system identified three clusters that could constitute a unique larger outbreak. Epidemiological and clinical information were integrated with WGS genotyping data of Mycobacterium tuberculosis strains obtained using a simple DNA extraction method coupled with sequencing using an Illumina MiSeq platform and an in-house bioinformatics pipeline for single nucleotide polymorphism (SNP) analysis. Epidemiological investigations identified three putative TB clusters potentially interrelated including eight patients with active TB. Seven M. tuberculosis isolates were available and analysed by WGS. Using a 5-SNP threshold to define recent transmission, WGS-based genotyping supported the occurrence of the three clusters as well as a link between clusters 1 and 2 (SNP ≤1), constituting a larger outbreak. This outbreak was clearly delineated by refuting a potential link with the third cluster (SNP >500). Genotyping data did not support the belonging of patient 7 to any studied cluster. This study illustrates the usefulness of WGS genotyping for routine TB surveillance systems in local communities to rapidly confirm or disprove epidemiological hypotheses and delineate TB clusters, especially in the context of multiple contact-tracing investigations.
Keywords
Contact investigation, Mycobacterium tuberculosis, genotyping outbreak, molecular epidemiology, whole-genome sequencing
Pubmed
Open Access
Yes
Create date
02/10/2019 16:39
Last modification date
29/01/2021 6:25
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