Use of Whole-Genome Sequencing for Food Safety and Public Health in the United States.

Eric Brown,Peter Gerner-Smidt,Uday Dessai,Sherri Mcgarry

doi:10.1089/fpd.2019.2662

Abstract

Whole-genome sequencing (WGS) is increasingly used by food regulatory and public health agencies in the United States to facilitate the detection, investigation, and control of foodborne bacterial outbreaks, and food regulatory and other activities in support of food safety. WGS has added a level of precision to the surveillance leading to faster and more efficient decision making in the preparedness and response to foodborne infections. In this review, we report the history of WGS technology at the Centers for Disease Control & Prevention (CDC), the Food and Drug Administration (FDA), and the United States Department of Agriculture's Food Safety and Inspection Service (USDA/FSIS) as it applies to food safety. The basic principle of the method, the analysis, and interpretation of the data are explained as is its major strengths and limitations. We also describe the benefits and possibilities of the WGS technology to the food industry throughout the farm-to-fork continuum and the prospects of metagenomic sequencing applied directly to the sample specimen with or without pre-enrichment culture.

Highlights

The United States has a diverse food supply with a significant amount of food that is imported from other countries
We report the history of Whole-genome sequencing (WGS) technology at the Centers for Disease Control & Prevention (CDC), the Food and Drug Administration (FDA), and the United States Department of Agriculture’s Food Safety and Inspection Service (USDA/FSIS) as it applies to food safety
WGS technology is extremely powerful and may provide most the information contained in an entire bacterial genome, in both an increasingly timely and cost-efficient manner

Summary

Introduction

The United States has a diverse food supply with a significant amount of food that is imported from other countries. Due to this successful application of the technology and a series of several successful retrospective WGS studies on outbreaks performed by FDA and others (Gilmour et al, 2010; Lewis et al, 2010; Lienau et al, 2011; Aarestrup et al, 2012; Allard et al, 2012), the regulatory and public health agencies decided to assess the utility of WGS as a tool to supplement or even replace PFGE as the preferred subtyping method for use in PulseNet. Initially, the technology was applied to retrospective characterization of historical isolates of different species to assess its potential for improving outbreak investigations. In collaboration with it public health partners, FSIS uses information from both WGS and PFGE in its regulatory decision-making process when applicable

Analytical Methods

Conclusion