Outcome of EC/EFSA questionnaire (2016) on use of Whole Genome Sequencing (WGS) for food‐ and waterborne pathogens isolated from animals, food, feed and related environmental samples in EU/EFTA countries

Whole Genome Sequencing (WGS) is becoming increasingly used in public health and food safety laboratories. To date, there is a wide variation in the level of implementation of WGS among laboratories from different sectors in different countries, the type of analysis employed and the data interpretation. To gather information on the WGS capacity of food safety/veterinary laboratories in the European Union (EU) and associated countries (EFTA), the European Commission (DG SANTE) and the European Food Safety Authority (EFSA), supported by the EU Reference laboratories (EURLs), prepared a survey among the EU/EFTA laboratory Networks for Salmonella, Listeria monocytogenes, Escherichia coli (VTEC), Campylobacter, Coagulase Positive Staphylococci, Antimicrobial Resistance and bacteriological and viral contaminants of bivalve molluscs. Questions on the general use of WGS, pathogens tackled, analysis purposes, pipelines and tools used, place of data storage and analysis, WGS research projects, needs for support, and future interest to implement WGS were addressed. By the end of 2016, WGS was already in use in reporting laboratories from 17 out of 30 EU/EFTA countries; in particular, WGS was reported to be used in all consulted EURLs, almost half of the National Reference Laboratories (44% affirmative respondents) and only few Official Laboratories (7% affirmative respondents). The main reason for not implementing WGS was the lack of capacity (budget and expertise). WGS was mainly used for outbreak investigations, followed by surveillance, and mostly for L. monocytogenes, E. coli and Salmonella analysis. Sequencing, sequence storage and analysis were mainly done ‘in house’. Several WGS pipelines/platforms/tools were in use for analysis of different microorganisms and purposes. The participating laboratories expressed a general willingness for collaboration with EURLs and European institutions. This report provides a first picture of the state of the art in relation to the use of WGS in European food safety laboratories at the end of 2016.