Expert Opinion on the introduction of next-generation typing methods for food- and waterborne diseases in the EU and EEA
Setting up whole genome sequencing as a new typing method for food- and waterborne pathogens is far from trivial, in particular when it is intended for routine use for public health. This report describes many of the aspects that should be taken into account. It systematically covers the entire process from sample provision and sequencing to data analysis and collaboration with other organisations. As such, it is meant as a guide for countries that are planning to introduce whole genome sequencing for routine public health purposes.
Executive summary
Molecular typing, and typing in general, has a long history of application to surveillance of food- and waterborne diseases for public health purposes. The advent of new microbial typing and detection techniques, in particular whole genome sequencing (WGS) and culture-independent diagnostic methods, brings about a fundamental change in the way diagnostics and typing are performed for foodborne infections.
To respond to the needs related to the introduction of WGS into public health microbiology, and to facilitate the further development of EU/EEA-wide molecular-typing-enhanced surveillance for Food- and waterborne diseases, an expert group (FWD-NEXT Expert Group) was formed. This group, with members from ten countries, and composed of microbiologists, epidemiologists and bioinformaticians, worked on the introduction of next-generation typing methods for surveillance of food- and waterborne diseases.
This report, produced by the group, focuses on four pathogens: Salmonella, Listeria monocytogenes, verocytotoxin–producing Escherichia coli (VTEC) and Campylobacter. It is written from the country perspective and covers the entire process from sample provision and sequencing to data analysis, and finally data sharing and collaboration between different organisations. The main audiences of the report are therefore national public health reference laboratories, national level epidemiologists and their immediate stakeholders. In addition, IT departments of organisations that will be performing WGS on a routine basis may also find parts of the report relevant for their planning, especially on data storage and computing capacity requirements.