Whole genome sequencing as a tool to strengthen foodborne disease surveillance and response: module 2: whole genome sequencing in foodborne disease outbreak investigations

Overview

Whole genome sequencing (WGS) is a laboratory technique that has the potential to change how we detect and monitor microbial hazards in the food chain, as well as how we assess, investigate and manage food safety risks. It is anticipated that this technology will help reduce the burden of foodborne diseases, given its advantages over previous low-resolution typing and detection methods. 

The purpose of this publication is to provide guidance on the capacities that need to be in place before WGS can be successfully used for the surveillance of and response to foodborne diseases, options for implementing WGS and how to integrate WGS within existing systems.

Module 2: Whole genome sequencing in foodborne disease outbreak investigations 

The outbreak module and web annex discusses how WGS can be used to support foodborne disease outbreak investigations. It is meant for countries in the initial stages of laboratory-based surveillance for selected foodborne pathogens. The module describes how WGS can be used in the investigation of outbreaks detected by existing surveillance systems.