Prospective Salmonella Enteritidis surveillance and outbreak detection using whole genome sequencing, Minnesota 2015-2017.

J M Rounds,A J Taylor,D J Boxrud,S E Wirth,D Eikmeier,M M Nichols,C Medus,K E Smith,V Lappi

doi:10.1017/s0950268820001272

J M Rounds, A J Taylor + Show 7 more

Open Access

https://doi.org/10.1017/s0950268820001272

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Journal: Epidemiology and Infection	Publication Date: Jan 1, 2020
Citations: 16	License type: CC BY 4.0

Affiliation: Minnesota Department of Health

Abstract

Clusters of Salmonella Enteritidis cases were identified by the Minnesota Department of Health using both pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) single nucleotide polymorphism analysis from 1 January 2015 through 31 December 2017. The median turnaround time for obtaining WGS results was 11 days longer than for PFGE (12 vs. 1 day). WGS analysis more than doubled the number of clusters compared to PFGE analysis, but reduced the total number of cases included in clusters by 34%. The median cluster size was two cases for WGS compared to four for PFGE, and the median duration of WGS clusters was 27 days shorter than PFGE clusters. While the percentage of PFGE clusters with a confirmed source (46%) was higher than WGS clusters (32%), a higher percentage of cases in clusters that were confirmed as outbreaks reported the vehicle or exposure of interest for WGS (78%) than PFGE (46%). WGS cluster size was a significant predictor of an outbreak source being confirmed. WGS data have enhanced S. Enteritidis cluster investigations in Minnesota by improving the specificity of cluster case definitions and has become an integral part of the S. Enteritidis surveillance process.

Highlights

At the Minnesota Department of Health (MDH) Public Health Laboratory (PHL), Whole genome sequencing (WGS) was routinely performed in parallel with pulsed-field gel electrophoresis (PFGE) subtyping and epidemiological investigation to detect and investigate S
The increased case definition specificity provided by WGS helped confirm the scope of the outbreaks. This prospective study demonstrated that WGS is a more discriminatory and useful subtyping method than PFGE for the detection and investigation of S
WGS reduced the total number of cases included in clusters by 34%, and clusters were smaller on average

Summary

Introduction

Prospective use of WGS single nucleotide polymorphism (SNP) analysis in combination with real-time epidemiological investigation for outbreak surveillance is in its infancy, but has shown promise [9, 16,17,18]. All clusters identified by PFGE subtyping and WGS SNP analysis were investigated epidemiologically as potential outbreaks. Enteritidis clusters identified using either PFGE and/or WGS SNP analysis during 2015–2017. We demonstrate the utility of an SNP-based analysis subtyping method as a valuable tool for identifying outbreaks and supporting the epidemiological investigation of S.

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