Decentralized Investigation of Bacterial Outbreaks Based on Hashed cgMLST.
Salmonella
WGS typing
cgMLST
comparative microbial genomics
molecular surveillance
Journal
Frontiers in microbiology
ISSN: 1664-302X
Titre abrégé: Front Microbiol
Pays: Switzerland
ID NLM: 101548977
Informations de publication
Date de publication:
2021
2021
Historique:
received:
19
01
2021
accepted:
25
03
2021
entrez:
5
7
2021
pubmed:
6
7
2021
medline:
6
7
2021
Statut:
epublish
Résumé
Whole-genome sequencing (WGS)-based outbreak investigation has proven to be a valuable method for the surveillance of bacterial pathogens. Its utility has been successfully demonstrated using both gene-by-gene (cgMLST or wgMLST) and single-nucleotide polymorphism (SNP)-based approaches. Among the obstacles of implementing a WGS-based routine surveillance is the need for an exchange of large volumes of sequencing data, as well as a widespread reluctance to share sequence and metadata in public repositories, together with a lacking standardization of suitable bioinformatic tools and workflows. To address these issues, we present
Identifiants
pubmed: 34220740
doi: 10.3389/fmicb.2021.649517
pmc: PMC8244591
doi:
Types de publication
Journal Article
Langues
eng
Pagination
649517Informations de copyright
Copyright © 2021 Deneke, Uelze, Brendebach, Tausch and Malorny.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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