Whole genome sequencing as a tool to strengthen foodborne disease surveillance and response: module 3: whole genome sequencing in foodborne disease routine surveillance

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 3: Whole genome sequencing in foodborne disease routine surveillance 

The surveillance module and web annex is about using WGS in routine surveillance of foodborne diseases. It is meant for countries experienced in laboratory-based surveillance of foodborne pathogens. WGS can be implemented where subtyping foodborne pathogens or replacing traditional typing methods is being considered. Routine surveillance includes outbreak detection, monitoring trends over time, and using WGS for AMR and virulence factor monitoring.