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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.

Original publication

DOI

10.1016/j.ijfoodmicro.2018.02.023

Type

Journal article

Journal

Int J Food Microbiol

Publication Date

02/06/2018

Volume

274

Pages

1 - 11

Keywords

Core genome multilocus sequence typing (cgMLST), Outbreak, Phylogeny, Salmonella, Single nucleotide polymorphisms (SNPs), Whole-genome sequencing (wgs), Animals, Foodborne Diseases, Genetic Variation, Genome, Bacterial, Multilocus Sequence Typing, Polymorphism, Single Nucleotide, Salmonella Infections, Animal, Salmonella enteritidis