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

Valeria Michelacci; Adrien Asséré; Simone Cacciò; Marina Cavaiuolo; Kirsten Mooijman; Stefano Morabito; Susanne Karlsmose Pedersen; Maroua Sayeb; Bo Segerman; Magnus Simonsson; Hanna Skarin; Rosangela Tozzoli; Angela van Hoek; Rene Sjøgren Hendriksen

doi:10.1099/mgen.0.001074

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

Microb Genom. 2023 Jul;9(7):mgen001074. doi: 10.1099/mgen.0.001074.

Affiliations

¹ European Union Reference Laboratory for Escherichia coli including Shiga toxin-producing E. coli, Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy.
² European Union Reference Laboratory for Listeria monocytogenes, Laboratory for Food Safety, Anses, Maisons-Alfort, France.
³ European Union Reference Laboratory for Parasites, Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
⁴ European Union Reference Laboratory for Coagulase Positive Staphylococci, Laboratory for Food Safety, Anses, Maisons-Alfort, France.
⁵ European Union Reference Laboratory for Salmonella, National Institute for Public Health and the Environment, Bilthoven, Netherlands.
⁶ European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark.
⁷ European Union Reference Laboratory for Campylobacter, National Veterinary Institute, Uppsala, Sweden.
⁸ European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Uppsala, Sweden.

Abstract

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.

Keywords: EURL; Europe; NRL; bioinformatic analysis; capacity building; next generation sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Europe
European Union
High-Throughput Nucleotide Sequencing*
Laboratories*
Whole Genome Sequencing