Retrospective analysis of whole genome sequencing compared to prospective typing data in further informing the epidemiological investigation of an outbreak of Shigella sonnei in the UK

Abstract

The aim of this study was to retrospectively assess the value of whole genome sequencing (WGS) compared to conventional typing methods in the investigation and control of an outbreak of Shigella sonnei in the Orthodox Jewish (OJ) community in the UK. The genome sequence analysis showed that the strains implicated in the outbreak formed three phylogenetically distinct clusters. One cluster represented cases associated with recent exposure to a single strain, whereas the other two clusters represented related but distinct strains of S. sonnei circulating in the OJ community across the UK. The WGS data challenged the conclusions drawn during the initial outbreak investigation and allowed cases of dysentery to be implicated or ruled out of the outbreak that were previously misclassified. This study showed that the resolution achieved using WGS would have clearly defined the outbreak, thus facilitating the promotion of infection control measures within local schools and the dissemination of a stronger public health message to the community.

Fig. 1.

Epidemic curve showing onset week of all cases of S. Sonnei meeting the case definitions as described previously (see Materials and methods section). OJ, Orthodox Jewish.

Fig. 2.

(a) Minimum spanning tree illustrating the population structure of domestically acquired S. sonnei in the UK in 2011 based on multi-locus variable number tandem repeat analysis (MLVA) profiles with the cluster of strains associated with the Orthodox Jewish (OJ) community highlighted. The numbers of strains in each cluster are represented by the size of the circles. Clusters highlighted grey differ by single locus variants. MLVA cluster key: red (18 cases) = main cluster (MC); blue (two cases) = sporadic cluster 3, (SC3); green (one case) = sporadic cluster 1 (SC1); yellow (one case) = sporadic cluster 2 (SC2) (see Table 1). (b) Maximum-likelihood tree of OJ community split into three phylogentic clusters (PCs). Cases that were included in the outbreak investigation are labelled A–W, strains OJ1 and OJ2 represent OJ cases not included in the outbreak investigation.