No abstract

In spring 2016, Greece reported an outbreak caused by a previously undescribed Salmonella enterica subsp. enterica serotype (antigenic formula 11:z41:e,n,z15) via the Epidemic Intelligence Information System for Food- and Waterborne Diseases and Zoonoses (EPIS-FWD), with epidemiological evidence for sesame products as presumptive vehicle. Subsequently, Germany, Czech Republic, Luxembourg and the United Kingdom (UK) reported infections with this novel serotype via EPIS-FWD. Concerned countries in collaboration with the European Centre for Disease Prevention and Control (ECDC) and European Food Safety Authority (EFSA) adopted a common outbreak case definition. An outbreak case was defined as a laboratory-confirmed notification of the novel Salmonella serotype. Between March 2016 and April 2017, 47 outbreak cases were notified (Greece: n = 22; Germany: n = 13; Czech Republic: n = 5; Luxembourg: n = 4; UK: n = 3). Whole genome sequencing revealed the very close genetic relatedness of isolates from all affected countries. Interviews focusing on sesame product consumption, suspicious food item testing and trace-back analysis following Salmonella spp. detection in food products identified a company in Greece where sesame seeds from different countries were processed. Through European collaboration, it was possible to identify and recall sesame spread as one contaminated food item serving as vehicle of infection and trace it back to its origin.

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.