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

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.

Comparative genome analysis of VSP-II and SNPs reveals heterogenic variation in contemporary strains of Vibrio cholerae O1 isolated from cholera patients in Kolkata, India

“…In addition, WGS has been utilized in several studies to understand global transmission and phylogeny of pathogenic bacteria including V . cholerae , Shigella dysenteriae and Salmonella Enteritidis [18, 41, 42]. Our work characterized the transition of predominant strains during several continuous years at the epicenter of cholera.…”

Salmonella Thompson outbreak associated with consumption of chicken shawarma and the usefulness of genome sequencing in the investigation

“…The other strains of S. Thompson analyzed had three or more nucleotide variations and the epidemiological information available regarding the cases with these exposures was different. Genome sequencing has proven to be effective in several outbreaks (19)(20)(21)(22)(23). The use of the whole genome sequencing technique provides additional powers of discrimination, beyond serotyping and PFGE, to delimit and investigate an outbreak (20)(21)(22)(23)(24)(25).…”

Multi‐country outbreak of Salmonella Enteritidis infections linked to Polish eggs

“…Using Public Health England's (PHE) in-house pipeline and nomenclature for WGS analysis, the threshold for inclusion in one of the two WGS clusters was set to ≤5 SNP difference (t5 level) to at least one other case in the cluster [7][8][9]. The SNP addresses at t5 level for the two WGS clusters initially part of the outbreak confirmed case definition were 1.2.3.175.175.175.% (WGS cluster_175, accession number SRR3285443) and 1.2.3.18.359.360.% (WGS cluster_360; accession number: SRR4063700).…”