The World Health Organization (WHO) has published guidance on the use of whole genome sequencing (WGS) in food safety.
The manual consists of three parts. The first explains the minimum capacity requirements in a foodborne disease surveillance and response system before considering the implementation of WGS.
The second discusses how WGS can help support outbreak investigations, and the third describes the use of WGS in routine foodborne disease surveillance.
A related webinar was organized in June 2023, highlighting lessons learned, opportunities, challenges and national examples. The event features Dr. Eric Brown of the US Food and Drug Administration’s Center for Food Safety and Applied Nutrition (CFSAN).
WGS is useful for understanding foodborne diseases by improving routine surveillance, outbreak detection and response, and identifying the source, WHO said. Hopefully, the technology will help reduce the burden of foodborne illness.
The first guide covers the epidemiological capacity to detect outbreaks and conduct investigations, laboratory capacity to test clinical samples and capacity within the food safety system to respond to events and take control measures. It also provides options on how to integrate WGS into existing systems. The target audience is public health professionals such as epidemiologists and laboratory personnel who will use WGS as part of foodborne disease surveillance and response.
The paper highlights some issues, including the lack of an internationally agreed standardized approach for WGS analysis for microbial subtyping; staff using WGS have traditionally not been trained in genetic data analysis and interpretation and data sharing. WGS is not financially viable if only a few isolates are collected during outbreaks.
For WGS to be useful, the turnaround time must be fast to ensure that outbreaks are detected promptly and responded to as quickly as possible. Other factors to consider are human and financial resources and the objectives for using the technology.
The second guide covers how WGS can assist foodborne outbreak investigations. It is intended for countries in the initial stages of laboratory surveillance for selected pathogens and those with limited WGS experience who would like to begin building capacity.
The guidance outlines the advantages and disadvantages of building public health laboratory capacity versus outsourcing the wet lab component of WGS and sequence data analysis with bioinformatics. It also provides advice on building a business case for WGS and pilot studies.
Examples of the use of WGS are the US FDA investigation of a multistate outbreak of listeriosis linked to Blue Bell products and a multistate outbreak of listeria in Dole leafy greens produced at a facility in Springfield, Ohio.
WGS data alone do not confirm the source of an outbreak, but provide a stronger link and can help narrow the focus of investigation and improve epidemiological and follow-up findings, WHO said.
The third paper is for countries with experience in laboratory pathogen surveillance and covers surveillance trends over time as well as the use of WGS for AMR and virulence factor monitoring.
When using WGS for routine surveillance, WHO recommends that a country start with a single pathogen and scale up once there is laboratory and public health agency capacity.
One challenge facing laboratories and public health authorities is how to define clusters that require public health follow-up, as more are likely to be discovered with WGS. This is resource dependent and can be done by the number of isolates in a cluster or by a period of time.
Laboratory and public health personnel must decide how laboratory WGS results will be shared with public health agencies and about the frequency for reporting results to authorities.
The paper also shares how to assess the role of WGS in the monitoring system and set short-term and long-term goals.
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