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Updated: Dec 18, 2025
Quasi-metagenomic Analysis of Salmonella from Food and Environmental Samples
Published on: October 25, 2018
Prospective Salmonella Enteritidis surveillance and outbreak detection using whole genome sequencing, Minnesota
J M Rounds1, A J Taylor1, D Eikmeier1
1Minnesota Department of Health, Saint Paul, Minnesota, USA.
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.
Insights
Whole genome sequencing (WGS) identified more Salmonella Enteritidis clusters than pulsed-field gel electrophoresis (PFGE), though WGS clusters were smaller and shorter. WGS improved outbreak source identification specificity.
Area of Science:
- Microbiology
- Epidemiology
- Genomics
Background:
- Salmonella Enteritidis (S. Enteritidis) outbreaks pose a significant public health challenge.
- Traditional methods like pulsed-field gel electrophoresis (PFGE) have limitations in outbreak investigations.
- Whole genome sequencing (WGS) offers a higher resolution approach to pathogen typing.
Purpose of the Study:
- To compare the effectiveness of whole genome sequencing (WGS) and pulsed-field gel electrophoresis (PFGE) for identifying Salmonella Enteritidis clusters.
- To evaluate the impact of WGS on outbreak investigations, including cluster definition, size, duration, and source identification.
Main Methods:
- Retrospective analysis of S. Enteritidis cases in Minnesota from 2015-2017.
- Comparison of cluster identification using PFGE and WGS single nucleotide polymorphism (SNP) analysis.
- Assessment of turnaround times, cluster characteristics, and outbreak source confirmation rates for both methods.
Main Results:
- WGS identified more clusters than PFGE but with smaller median size and shorter duration.
- WGS had a longer median turnaround time (12 days) compared to PFGE (1 day).
- Despite fewer confirmed sources overall, WGS clusters showed higher specificity and a greater percentage of reported outbreak vehicles/exposures.
Conclusions:
- WGS enhances S. Enteritidis cluster investigations by improving the specificity of case definitions.
- WGS has become an integral part of S. Enteritidis surveillance in Minnesota.
- WGS data, particularly cluster size, are significant predictors of confirmed outbreak sources.
