The World Health Organization (WHO) recently published a three-part guide describing how whole genome sequencing (WGS) can be used as tool to strengthen foodborne illness surveillance and response. The first part covers WGS for foodborne disease surveillance and response, the second part relates to WGS for outbreak investigations, and the third part discusses WGS for routine surveillance.

First, the guide explains the minimum capacity requirements of a foodborne illness surveillance and response system prior to considering the implementation of WGS. The requirements include epidemiological capacity for detecting outbreaks and conducting outbreak investigations, laboratory capacities to test clinical specimens, and capacity within the food safety system in order to respond to events and carry out control measures.

For epidemiological capacity, there must exist a functional event-based surveillance system, rapid risk assessment, and the ability to conduct epidemiological investigations during outbreaks. For a country’s laboratory capacity, it is important that specimens from the field can be tested and foodborne pathogens can be identified. There also needs to be a designated laboratory with the required experience and resources to routinely culture and identify priority foodborne pathogens such as Salmonella, Listeria monocytogenes, and Shiga-toxin producing Escherichia coli (STEC).

A laboratory quality management system also needs to be in place before a country considers using WGS. Capabilities in the food safety sector depend on whether appropriate food and environmental samples can be collected during foodborne illness outbreaks, samples can be tested at a laboratory, there are food safety laws and regulations to support control measures, and food safety personnel can control the distribution of implicated food items. WHO provides an assessment tool to audit existing capacities, which can then be used to determine which of two options should be chosen for the implementation of WGS: for outbreak investigations or for the enhanced surveillance of foodborne pathogens.

The WHO guide defines how WGS can be used for outbreak and surveillance. Often, the initial application of WGS related to foodborne illness is in the context of an outbreak investigation. WHO stressed the importance of identifying the goals and objectives of WGS use within an existing surveillance or outbreak response system. Articulating such goals and objectives makes it possible to review the options for sequencing, which include outsourcing all or parts of WGS, or using a public health laboratory.

The availability of human and financial resources is key to using WGS for surveillance and outbreak response. Both the outbreak and surveillance sections contain step-by-step guidance on implementing WGS. The approach is the same, even though the context is different, and is listed as follows:

1. The first step is to form a working group of relevant stakeholders
2. The second step involves describing what already exists in the surveillance or outbreak response system
3. The third step contains advice on building a business case for WGS, and how to communicate effectively to engage decision-makers to see the value in WGS.

Once there is a commitment to using WGS, WHO provides guidance on how to run and evaluate a pilot study. Pilot studies are useful in determining how WGS will work for future surveillance and outbreak investigations of foodborne illnesses.