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Int J Food Microbiol. 2018 Jun 2;274:1-11. doi: 10.1016/j.ijfoodmicro.2018.02.023. Epub 2018 Feb 28.

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

Author information

1
Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, United Kingdom; National Institute for Health Research, Health Protection Research Unit, Gastrointestinal Infections, University of Oxford, United Kingdom. Electronic address: Madison.pearce@zoo.ox.ac.uk.
2
Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom. Electronic address: N-F.Alikhan@warwick.ac.uk.
3
Public Health England, Gastrointestinal Bacteria Reference Unit, 61 Colindale Avenue, London NW9 5EQ, United Kingdom. Electronic address: tim.dallman@phe.gov.uk.
4
Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom. Electronic address: Zhemin.Zhou@warwick.ac.uk.
5
Public Health England, Gastrointestinal Bacteria Reference Unit, 61 Colindale Avenue, London NW9 5EQ, United Kingdom. Electronic address: Kathie.Grant@phe.gov.uk.
6
Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, United Kingdom; National Institute for Health Research, Health Protection Research Unit, Gastrointestinal Infections, University of Oxford, United Kingdom. Electronic address: Martin.Maiden@zoo.ox.ac.uk.

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.

KEYWORDS:

Core genome multilocus sequence typing (cgMLST); Outbreak; Phylogeny; Salmonella; Single nucleotide polymorphisms (SNPs); Whole-genome sequencing (wgs)

PMID:
29574242
PMCID:
PMC5899760
DOI:
10.1016/j.ijfoodmicro.2018.02.023
[Indexed for MEDLINE]
Free PMC Article

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