The World Health Organization (WHO) has released a guide for use of whole genome sequencing (WGS) in food safety.

The guidance comes in three parts. The first explains the minimum capacity requirements in the foodborne disease surveillance and response system prior to considering implementation of WGS.

The second discusses how WGS can help to support outbreak investigations and the third describes the usage of WGS in routine surveillance of foodborne diseases.

A related webinar was organized in June 2023 wher lessons learned, opportunities, challenges and national examples were highlighted. The event featured Dr. Eric Brown, from the Center for Food Safety and Applied Nutrition (CFSAN), at the U.S. Food and Drug Administration.

WGS is useful for understanding foodborne diseases through enhancing routine surveillance, outbreak detection and response and for source identification, said WHO. It is hoped the technology will help reduce the burden of foodborne illness.

Part one
The first guide covers the epidemiological capacity for detecting outbreaks and conducting investigations, laboratory capabilities to test clinical specimens, and capacity within the food safety system to respond to events and take control measures. It also provides options on how to integrate WGS within existing systems. The target audience is public health professionals, such as epidemiologists and lab staff who will use WGS as part of foodborne diseases surveillance and response.

The document highlights some issues including a lack of an internationally agreed standardized approach for the analysis of WGS for microbial subtyping; staff using WGS have not traditionally been trained in the analysis and interpretation of genetic data and data sharing. WGS is not financially viable if only a few isolates are collected during outbreaks.

For WGS to be useful, turnaround time needs to be quick to ensure outbreaks are detected in a timely fashion and responded to as quickly as possible. Other factors to consider are human and financial resources and the objectives for using the technology.

Part two
The second guide covers how WGS can support foodborne outbreak investigations. It is meant for countries in the initial stages of lab-based surveillance for seleced pathogens and those with limited WGS experience that would like to begin building capacity.

The guide sets out the pros and cons of building capacity in the public health lab compared to outsourcing the wet lab component of WGS and analysis of the sequence data with bioinformatics. It also provides advice on putting together a business case for WGS and pilot studies.

Examples of WGS use are the U.S. FDA investigating a multistate outbreak of listeriosis linked to Blue Bell creameries products and a multistate outbreak of Listeria in Dole leafy greens products produced at a facility in Springfield, Ohio.

WGS data alone does not confirm the source of an outbreak, but it provides a stronger link and can assist in narrowing the focus of the investigation and improve epidemiological and traceback findings, said WHO.

Part three
The third document is for countries experienced in lab-based surveillance of pathogens and covers monitoring trends over time as well as using WGS for AMR and virulence factor monitoring.

When using WGS for routine surveillance, WHO recommends that a country starts with a single pathogen, and scales up once capacities are in place in the lab and the public health agency.

One challenge that labs and public health authorities face is how to define clusters that require public health follow-up, as with WGS it is likely more will be detected. This depends on resources and could be done by the number of isolates in a cluster or by date range.

Lab and public health staff need to decide how WGS results from the lab will be shared with public health agencies and on the frequency for reporting results to authorities.

The document also shared how to evaluate the role of WGS in the surveillance system and setting short and long-term goals.