European Union Reference Laboratories support the National food, feed and veterinary Reference Laboratories with rolling out whole genome sequencing in Europe.

The Inter European Union Reference Laboratories (EURLs) Working Group on Next Generation Sequencing (NGS) involves eight EURLs for microbiological food and feed hazards and has been working since 2017 to promote the adoption of NGS by the National Reference Laboratories (NRLs) in the European Union. This work illustrates the results of the first 5 years of activity. By working together, the EURLs involved have released guidance documents for assisting NRLs in all the steps of NGS, helping the transition from classical molecular methods towards whole genome sequencing while ensuring harmonization, with the final aim of improving preparedness in the use of NGS to characterize microbial hazards and trace the sources of infection.

Salmonella enterica Newserovar Abeokuta Genome Sequence, Strain OG19FER4 Isolated from Poultry Feed in Nigeria.

This report announces the genome of a newly confirmed Salmonella serovar (Salmonella enterica serovar Abeokuta) that was isolated from a poultry feed sample collected on a farm in Abeokuta, capital of Ogun State in Nigeria. Salmonella Abeokuta has not been identified outside Nigeria, nor does it appear to be a cause for concern for animal and human health.

An international outbreak of Salmonella enterica serotype Enteritidis linked to eggs from Poland: a microbiological and epidemiological study.

BACKGROUND: Salmonella spp are a major cause of food-borne outbreaks in Europe. We investigated a large multi-country outbreak of Salmonella enterica serotype Enteritidis in the EU and European Economic Area (EEA). METHODS: A confirmed case was defined as a laboratory-confirmed infection with the outbreak strains of S Enteritidis based on whole-genome sequencing (WGS), occurring between May 1, 2015, and Oct 31, 2018. A probable case was defined as laboratory-confirmed infection with S Enteritidis with the multiple-locus variable-number tandem repeat analysis outbreak profile. Multi-country epidemiological, trace-back, trace-forward, and environmental investigations were done. We did a case-control study including confirmed and probable cases and controls randomly sampled from the population registry (frequency matched by age, sex, and postal code). Odds ratios (ORs) for exposure rates between cases and controls were calculated with unmatched univariable and multivariable logistic regression. FINDINGS: 18 EU and EEA countries reported 838 confirmed and 371 probable cases. 509 (42%) cases were reported in 2016, after which the number of cases steadily increased. The case-control study results showed that cases more often ate in food establishments than did controls (OR 3·4 [95% CI 1·6-7·3]), but no specific food item was identified. Recipe-based food trace-back investigations among cases who ate in food establishments identified eggs from Poland as the vehicle of infection in October, 2016. Phylogenetic analysis identified two strains of S Enteritidis in human cases that were subsequently identified in salmonella-positive eggs and primary production premises in Poland, confirming the source of the outbreak. After control measures were implemented, the number of cases decreased, but increased again in March, 2017, and the increase continued into 2018. INTERPRETATION: This outbreak highlights the public health value of multi-country sharing of epidemiological, trace-back, and microbiological data. The re-emergence of cases suggests that outbreak strains have continued to enter the food chain, although changes in strain population dynamics and fewer cases indicate that control measures had some effect. Routine use of WGS in salmonella surveillance and outbreak response promises to identify and stop outbreaks in the future. FUNDING: European Centre for Disease Prevention and Control; Directorate General for Health and Food Safety, European Commission; and National Public Health and Food Safety Institutes of the authors' countries (see Acknowledgments for full list).

Validation of EN ISO 6579-1 - Microbiology of the food chain - Horizontal method for the detection, enumeration and serotyping of Salmonella - Part 1 detection of Salmonella spp.

The European and International Standard method for the detection of Salmonella spp. in samples from the primary production stage, EN ISO 6579:2002/Amd.1:2007, was validated by an interlaboratory study in the frame of Mandate M/381, ordered by the European Commission and accepted by the European Standardisation Organisation (CEN). In addition to this study, results from two interlaboratory studies organised earlier by the European Union Reference Laboratory (EURL) for Salmonella were used for determination of the performance characteristics. Parallel to the performance evaluation for the Mandate, the revision of EN ISO 6579:2002 started. Part of this revision was the incorporation of the standardised method for detection of Salmonella in samples from the primary production stage (EN ISO 6579:2002/Amd.1:2007) and its performance characteristics in the new part 1 of EN ISO 6579. The 2002 version of EN ISO 6579 already contained performance characteristics for the detection of Salmonella in food samples, but LOD50 values (contamination level at which 50% of the samples are found positive) were not yet included. To be in line with the performance characteristics determined for detection of Salmonella spp. in samples from the primary production stage, LOD50 values for detection of Salmonella in food samples were calculated from the raw data of the validation studies performed in 2000. In this paper, the performance characteristics of EN ISO 6579-1:2017 are determined based not only on the results of the interlaboratory study carried out in 2013 under the Mandate, but also on several other interlaboratory studies. These performance characteristics consist of specificity, sensitivity and LOD50.

The new ISO 6579-1: A real horizontal standard for detection of Salmonella, at last!

Up to 2016, three international standard methods existed for the detection of Salmonella spp. in food, animal feed and samples from the primary production stage: ISO 6785:2001 for milk and milk products, ISO 6579:2002 for (other) food and animal feed and Annex D of ISO 6579:2007 for samples from the primary production stage. In 2009, an ISO/CEN working group started with the revision of ISO 6579:2002 with two main aims: combining the three aforementioned standards in one document and improving the information in ISO 6579:2002. Additionally it was decided to split ISO 6579 into three parts, where part 1 describes the detection, part 2 the enumeration by mini-MPN (published in 2012) and part 3 the serotyping of Salmonella (published in 2014). This paper describes the experiments and choices made for improving the part on detection of Salmonella (ISO 6579-1). The final voting stage on (draft) ISO 6579-1 was finished by the end of December 2016, with a positive outcome. Finally, a real horizontal standard became available for detection of Salmonella in food, animal feed, environmental samples in the area of food production and food handling and in samples from the primary production stage in 2017.

Detection of Salmonella in fresh cheese, poultry products, and dried egg products by the ISO 6579 Salmonella culture procedure and the AOAC official method: collaborative study.

Three food types were analyzed for the presence of Salmonella by the AOAC culture method and by the International Organization for Standardization (ISO 6579:2002) culture method. Paired test portions of each food type were simultaneously analyzed by both methods. A total of 21 laboratories representing federal government agencies and private industry, in the United States and Europe, participated in this interlaboratory study. Foods were artificially contaminated with Salmonella and competing microflora if naturally contaminated sources were not available. No statistical differences (p < 0.05) were observed between the AOAC and ISO culture methods for fresh cheese and dried egg products. A statistically significant difference was observed for one of the 2 lots of poultry from the first trial. The poultry meat used in this run was radiation sterilized, artificially contaminated with Salmonella and competitive flora, and then lyophilized. A second trial was conducted with 2 separate lots of raw ground chicken that were naturally contaminated. The results from the second trial showed no statistical difference between the 2 culture methods. A third trial involving 4 laboratories was conducted on 2 separate lots of naturally contaminated raw poultry. Again, no statistically significant differences occurred. It is recommended that ISO 6579:2002 culture method for Salmonella be adopted Official First Action for the analysis of fresh cheese, fresh chilled and frozen poultry, and dried egg products.

Optimisation of ISO 10705-1 on enumeration of F-specific bacteriophages.

During the European project 'Bacteriophages in bathing waters' (January 1996-June 1999), research was carried out to optimise the method for detection and enumeration of F-specific (RNA) phages in water. It was evaluated whether further optimisation would be possible/needed for the procedure as described in the standard method of the International Organisation for Standardisation (ISO) 10705-1. The research focused mainly on optimisation of the different steps for culturing the host strain WG49 Salmonella Typhimurium. It was concluded that all steps described in ISO 10705-1 are necessary and, if followed carefully, using a culture of host strain WG49 Salmonella Typhimurium of good quality, reliable results could be obtained for the enumeration of F-specific RNA phages.