Whole-genome sequencing revealed concurrent outbreaks of shigellosis in the English Orthodox Jewish Community caused by multiple importations of Shigella sonnei from Israel

Abstract

In December 2013, Public Health England (PHE) observed an increase in the number of cases of Shigella sonnei linked to the Orthodox Jewish Community (OJC). Ultimately, 52 cases of S. sonnei phage type (PT) P and PT7 were notified between November 2013 and July 2014. Whole-genome sequencing (WGS) was performed on a HiSeq 2500 platform (Illumina) on isolates of S. sonnei submitted to PHE during the investigation. Quality trimmed sequence reads were mapped to a reference genome using BWA-MEM, and single-nucleotide polymorphisms (SNPs) were identified using GATK2. Analysis of the core genome SNP positions (>90 % consensus, minimum depth 10×, MQ≥30) revealed that isolates linked to the outbreak could be categorized as members of distinct monophyletic clusters (MPCs) representing concurrent regional outbreaks occurring in the OJCs across the United Kingdom. A dated phylogeny predicted the date of the most recent common ancestor of the MPCs to be approximately 3.1 years previously [95 % highest posterior density (HPD), 2.4-3.4]. Isolates of S. sonnei from cases from the OJCs in Israel included in the phylogeny, branched from nodes basal to the UK OJC outbreak clusters, indicating they were ancestral to the UK OJC isolates, and that the UK isolates represented multiple importations of S. sonnei into the UK population from Israel. The level of discrimination exhibited by WGS facilitated the identification of clusters of isolates within the closely related bacterial populations circulating in the OJC that may be linked to a unique point sources or transmission routes, thus enabling a more appropriate public health response and targeted interventions.

Keywords: Orthodox Jewish Community; Shigella sonnei; outbreak.

Fig. 1.

Epidemic curve showing confirmed cases of S. sonnei (phage types P and 7) in residents of the London boroughs of Barnet, Hackney and Haringey notified between 12 November 2013 and 10 July 2014 (n=52).

Fig. 2.

S. sonnei phage type P and 7 according to age band (years) and gender notified between 12/11/2013 and 10/07/2014 (n=52).

Fig. 3.

Maximum-likelihood tree of S. sonnei strains circulating in OJ communities in England between 2008 and 2014 split into MPCs. MPC1 (red) consisted of six cases from Oldham including three household contacts; MPC2 (green) consisted of 17 cases from the London borough of Barnet, and included four household clusters; and MPC3 (blue) consisted of 25 cases, 19 of whom resided in the London boroughs of Hackney and Harringey. The three household clusters are highlighted by superscript numbers (^{1, 2, 3}) The child-minder is highlighted with an asterisk (*).