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Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak

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Pearce, Madison E., Alikhan, Nabil-Fareed, Dallman, Timothy J., Zhou, Zhemin, Grant, Kathie and Maiden, Martin C. J. (2018) Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak. International Journal of Food Microbiology, 274 . pp. 1-11. doi:10.1016/j.ijfoodmicro.2018.02.023

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Official URL: https://doi.org/10.1016/j.ijfoodmicro.2018.02.023

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Abstract

Multi-country outbreaks of foodborne bacterial disease present challenges in their detection, tracking, and notification. As food is increasingly distributed across borders, such outbreaks are becoming more common. This increases the need for high-resolution, accessible, and replicable isolate typing schemes. Here we evaluate a core genome multilocus typing (cgMLST) scheme for the high-resolution reproducible typing of Salmonella enterica (S. enterica) isolates, by its application to a large European outbreak of S. enterica serovar Enteritidis. This outbreak had been extensively characterised using single nucleotide polymorphism (SNP)-based approaches. The cgMLST analysis was congruent with the original SNP-based analysis, the epidemiological data, and whole genome MLST (wgMLST) analysis. Combination of the cgMLST and epidemiological data confirmed that the genetic diversity among the isolates predated the outbreak, and was likely present at the infection source. There was consequently no link between country of isolation and genetic diversity, but the cgMLST clusters were congruent with date of isolation. Furthermore, comparison with publicly available Enteritidis isolate data demonstrated that the cgMLST scheme presented is highly scalable, enabling outbreaks to be contextualised within the Salmonella genus. The cgMLST scheme is therefore shown to be a standardised and scalable typing method, which allows Salmonella outbreaks to be analysed and compared across laboratories and jurisdictions. [Abstract copyright: Copyright © 2018. Published by Elsevier B.V.]

Item Type: Journal Article
Divisions: Faculty of Medicine > Warwick Medical School > Biomedical Sciences
Faculty of Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection
Faculty of Medicine > Warwick Medical School
SWORD Depositor: Library Publications Router
Journal or Publication Title: International Journal of Food Microbiology
Publisher: Elsevier
ISSN: 1879-3460
Official Date: 2 June 2018
Dates:
DateEvent
2 June 2018Published
28 February 2018Available
27 February 2018Accepted
Date of first compliant deposit: 21 February 2019
Volume: 274
Page Range: pp. 1-11
DOI: 10.1016/j.ijfoodmicro.2018.02.023
Status: Peer Reviewed
Publication Status: Published
Publisher Statement: ** From PubMed via Jisc Publications Router. ** History: received 27-10-2017; revised 23-02-2018; accepted 27-02-2018.
Access rights to Published version: Open Access

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