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. 2019 Jul;16(7):504-512.
doi: 10.1089/fpd.2019.2650. Epub 2019 Jun 27.

Interpretation of Whole-Genome Sequencing for Enteric Disease Surveillance and Outbreak Investigation

John M Besser  1 , Heather A Carleton  1 , Eija Trees  1 , Steven G Stroika  1 , Kelley Hise  1 , Matthew Wise  1 , Peter Gerner-Smidt  1
Affiliations

Interpretation of Whole-Genome Sequencing for Enteric Disease Surveillance and Outbreak Investigation

John M Besser et al. Foodborne Pathog Dis. 2019 Jul.

Abstract

The routine use of whole-genome sequencing (WGS) as part of enteric disease surveillance is substantially enhancing our ability to detect and investigate outbreaks and to monitor disease trends. At the same time, it is revealing as never before the vast complexity of microbial and human interactions that contribute to outbreak ecology. Since WGS analysis is primarily used to characterize and compare microbial genomes with the goal of addressing epidemiological questions, it must be interpreted in an epidemiological context. In this article, we identify common challenges and pitfalls encountered when interpreting sequence data in an enteric disease surveillance and investigation context, and explain how to address them.

Keywords: foodborne disease epidemiology; foodborne outbreaks; molecular epidemiology.

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Conflict of interest statement

No competing financial interests exist.

Figures

<b>FIG. 1.</b>
FIG. 1.
Transmission networks (left) include both sampled (dark gray circle) and unsampled (clear circle) events leading to a phylogenetic tree (right) based on only samples (light gray circle). (Courtesy of Trevor Bedford).
<b>FIG. 2.</b>
FIG. 2.
Anatomy of a phylogenetic tree: horizontal lines and numbers represent relative genetic distance.
<b>FIG. 3.</b>
FIG. 3.
An allele matrix, pairwise comparison of isolates. Shading is based on a cutoff of <7 allele differences.
See this image and copyright information in PMC

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