The European Food Safety Authority (EFSA) has published guidelines for reporting whole genome sequencing (WGS)-based typing data through the EFSA One Health WGS System. The guidelines include information about the EFSA One Health WGS System, such as its design, its users and their relative data visibility, and its rules on data ownership and intellectual property. The guidelines also describe the types and formats of data that can be submitted to the EFSA One Health WGS System, as well as the required steps of the reporting procedure.

The EFSA One Health WGS System was developed in response to a 2019 European Commission (EC) mandate that directed EFSA and the European Center for Disease Prevention and Control (ECDC) to implement and manage two interoperable systems for WGS data collection and analysis. The EC mandate specifically cited the need for WGS data for human and nonhuman isolates of Salmonella enterica, Listeria monocytogenes, and Escherichia coli, including Shiga toxin-producing E. coli (STEC).

The EFSA One Health WGS System is intended to serve as a tool for the rapid detection of multi-country foodborne illness outbreaks by allowing for the collection and storage of WGS-based typing data for isolates from human food, animal feed, animals, farms, and food processing environments in a single, dedicated database. The system will be used as a repository of data that can be referenced in the case of a foodborne illness outbreak. Data submission can be performed programmatically or through an intuitive interface that also allows for data access and visualization.

The EFSA system is designed to be interoperable with the ECDC system to enable the detection of joint clusters of human and nonhuman isolates through an automatic exchange of data. EFSA’s system will serve as the collection point for data related to foodborne pathogens of nonhuman origin, while the ECDC system will contain data related to foodborne pathogens of human origin. 

EU Member States and European Economic Area (EEA) countries are welcome to voluntarily submit WGS-based typing data and epidemiological data for isolates of nonhuman origin to the EFSA One Health WGS System for the purpose of molecular surveillance and monitoring of S. enterica, L. monocytogenes, E. coli, and STEC, whether or not the data is directly related to a foodborne illness event. In the case of ongoing, multi-country foodborne illness outbreak investigations, EU Member States and EEA countries must provide relevant data to support the outbreak investigation. 

EFSA will use the data submitted to its One Health WGS System to make inter-sectoral analyses of pathogens, conduct joint risk assessments, and support outbreak investigations. EFSA may also use the submitted data to create aggregated reports.