Next generation microbiological risk assessment: opportunities of whole genome sequencing (WGS) for foodborne pathogen surveillance, source tracking and risk assessment

Kalliopi Rantsiou,Sophia Kathariou,Annet Winkler,Panos Skandamis,Manuel Jimmy Saint-Cyr,Katia Rouzeau-Szynalski,Alejandro Amézquita

doi:10.1016/j.ijfoodmicro.2017.11.007

Abstract

Whole genome sequencing (WGS) of important foodborne pathogens is a technology under development, but is already employed in routine surveillance by public health agencies and is being increasingly exploited in tracing transmission routes and identifying contamination events (source tracking) that take place in the farm-to-fork continuum. Furthermore, data generated from WGS, complemented by other –omics data, have the potential to be integrated into and strengthen microbiological risk assessment. In this paper, we discuss the contribution of WGS in diverse areas important to food safety and public health. Additionally, an outlook of future WGS applications, which should contribute to our understanding of the ecology and physiology of foodborne microorganisms, is presented.

Highlights

In the past few years, the intensive use of high-throughput Generation Sequencing (NGS) technologies has led to an unprecedented increase in speed and cost-effectiveness of the acquisition of very high volumes of nucleic acid sequence data (Deng et al, 2016)
The aim of this paper is to present the current status and the opportunities of Whole genome sequencing (WGS) applications in foodborne pathogen surveillance, in understanding reservoirs, delineating transmission routes and integrating genomic data into risk assessment
The results showed that WGS was able, under a routine surveillance set-up, to provide information of the pathogenic potential of each isolate, enabling the prediction of clinical outcomes and the monitoring of emergence of hypervirulent isolates

Summary

Introduction

In the past few years, the intensive use of high-throughput Generation Sequencing (NGS) technologies has led to an unprecedented increase in speed and cost-effectiveness of the acquisition of very high volumes of nucleic acid sequence data (Deng et al, 2016). In the United States the CDC is performing WGS on all isolates from human listeriosis cases and retrospectively on stored isolates from earlier cases of disease (Jackson et al, 2016) This would ensure that isolates can be compared after different time periods. As WGS evolves from a research tool to a routine surveillance instrument, different pipelines, software and platforms are used to perform sequencing data analysis. In the context of food safety management systems (FSMS) and the implementation of measures to prevent foodborne pathogen contamination, food business operators (FBO) routinely monitor the production environment Such monitoring programs rely on classical microbiological methods but may be complemented by molecularbased methods to obtain a more precise view of the hygienic state of the environment and a much more extended view of the ecological richness. The aim of this paper is to present the current status and the opportunities of WGS applications in foodborne pathogen surveillance, in understanding reservoirs, delineating transmission routes and integrating genomic data into risk assessment

Foodborne pathogen surveillance

Understanding reservoirs and delineating transmission routes

Contribution to risk assessment: “upgrading” hazard identification

Other applications of WGS in food safety

Conclusions and future perspectives