Integration of Genomics Technologies in the Management of Food Safety and Outbreaks in Europe

Molecular typing has developed rapidly in recent years; becoming part of routine strain characterisation in many laboratories in the EU. Two years after the 2011 STEC O104:H4 outbreak, the European Commission asked EFSA and ECDC to provide technical support for the collection of molecular typing data for foodborne pathogens from human and non-human samples and to perform regular joint analyses of these molecular typing data. The molecular typing project is part of the actions envisaged by the Commission to enhance crisis preparedness and management in the food and feed area, in order to ultimately ensure a more effective and rapid containment of future food and feed-related emergencies and crises.

The purpose of the joint ECDC-EFSA molecular typing project is to share comparable typing data in a common repository, so that microbiological data from humans can be linked to similar data from the food chain. This will enable and support early detection and investigation of cross-border foodborne outbreaks. At present, the molecular typing data collection covers PFGE for Salmonella spp., Listeria monocytogenes, and STEC, together with MLVA for Salmonella Typhimurium and Salmonella Enteritidis.

Given the important role of whole genome sequencing (WGS) analysis in recent, multinational, foodborne outbreak investigations, such as the extended 2016 S. Enteritidis outbreak, and the gradually increasing capacity of public health and food laboratories, discussions are ongoing at the European level regarding the possible integration of WGS into food safety management and on the collection of WGS data at the European level. The molecular typing project represents a foundation that will, in the future, enable the collection of other typing data, similar to WGS, at European level.