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. 2017 Jan;145(2):289-298.
doi: 10.1017/S0950268816001941. Epub 2016 Oct 26.

Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis

T Inns  1   2   3 , P M Ashton  4 , S Herrera-Leon  5 , J Lighthill  6 , S Foulkes  1 , T Jombart  7 , Y Rehman  1 , A Fox  8 , T Dallman  3   4 , E DE Pinna  4 , L Browning  9 , J E Coia  10 , O Edeghere  1 , R Vivancos  1   2   3
Affiliations

Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis

T Inns et al. Epidemiol Infect. 2017 Jan.

Abstract

Since April 2015, whole genome sequencing (WGS) has been the routine test for Salmonella identification, surveillance and outbreak investigation at the national reference laboratory in England and Wales. In May 2015, an outbreak of Salmonella Enteritidis cases was detected using WGS data and investigated. UK cases were interviewed to obtain a food history and links between suppliers were mapped to produce a food chain network for chicken eggs. The association between the food chain network and the phylogeny was explored using a network comparison approach. Food and environmental samples were taken from premises linked to cases and tested for Salmonella. Within the outbreak single nucleotide polymorphism defined cluster, 136 cases were identified in the UK and 18 in Spain. One isolate from a food containing chicken eggs was within the outbreak cluster. There was a significant association between the chicken egg food chain of UK cases and phylogeny of outbreak isolates. This is the first published Salmonella outbreak to be prospectively detected using WGS. This outbreak in the UK was linked with contemporaneous cases in Spain by WGS. We conclude that UK and Spanish cases were exposed to a common source of Salmonella-contaminated chicken eggs.

Keywords: Epidemiology; outbreak; salmonellosis; traceback; whole genome sequencing.

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Conflict of interest statement

None.

Figures

Fig. 1.
Fig. 1.
Distribution of cases over time, by resident country of case. Specimen date used when onset date unavailable, 2015 (n = 40).
Fig. 2.
Fig. 2.
An unrooted phylogenetic tree of 742 diverse Salmonella Enteritidis (eBurst group 4), built with 28 117 variant positions. The 136 outbreak isolates are highlighted in red.
Fig. 3.
Fig. 3.
Maximum likelihood phylogenetic tree of the whole genome sequencing cluster containing the outbreak strains. Food isolate node label is highlighted in red.
Fig. 4.
Fig. 4.
Summary of egg food chain network, arrows show inferred direction of egg supply or exposure (total cases = 43).
Fig. 5.
Fig. 5.
Jitter plot showing the relationship between the phylogenetic distance and the distance between cases on the food chain network, with cubic spline.
See this image and copyright information in PMC

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