The Inter-European Union Reference Laboratories (EURLs) Working Group (WG) has been established by the European Commission with the aim to promote the use of Next Generation Sequencing (NGS) across the EURLs' networks, build NGS capacity within the EU and ensure liaison with the work of the EURLs and the work of EFSA and ECDC on the NGS mandate sent by the Commission. Membership of the Inter EURL WG on NGS include: 

EURL E. coli (coordinator)

EURL Listeria monocytogenes 

EURL CPS 

EURL Salmonella 

EURL Campylobacter 

EURL Parasites 

EURL AR 

EURL Food borne viruses 

Observers: SANTE G4, EFSA, ECDC 

 

The EURLs WG on NGS prepared general documents to provide guidance to the NRLs laboratories in the area of application of NGS and have been produced by the working group with the aim of being diffused to all the networks of NRLs: 

• ►Overview of conducted and planned PTs – curated by EURL-Antimicrobial Resistance
• ►Reference Whole Genome Sequencing collection  – curated by EURL-Salmonella
• ►NGS laboratory procedures – curated by EURL-Parasites
• ►Bioinformatics tools for basic analysis of Next Generation Sequencing data  – curated by EURL-E. coli
• ►Guidance document for cluster analysis of whole genome sequence data  – curated by EURL-Campylobacter
• ►Guidance document for NGS-Benchmarking  – curated by EURL-Listeria monocytogenes
• ►Inventory of training supports – curated by EURL-Coagulase-Positive Staphylococci
• ►Survey on the use of NGS across the NRLs networks – curated by EURL-E. coli
• ►Preparing high quality DNA for Whole Genome Sequencing – curated by EURL-E. coli

 

A short communication illustrate the results of the first five years of activity - > European Union Reference Laboratories support the National food, feed and veterinary Reference Laboratories with rolling out whole genome sequencing in Europe | Microbial Genomics

 

A Zenodo community of the WG is available here

 

The inter-EURL WG on NGS organised joined training sessions on WGS:

-14^th - 15^th June 2022 at the Istituto Superiore di Sanità (ISS) in Rome (IT) EURL E.coli

-20^th – 21^st June 2023 at the National Institute for Public Health and the Environment (RIVM) in Bilthoven (NL) - EURL Salmonella. Training supports are available for the first and second day

Proficiency Tests on Next Generation Sequencing: approaches in use at the European Union Reference Laboratories (Webinar, 29 September, 2023): According to Regulation (EU) 2017/625 (Article 101), the National Reference Laboratories shall, where appropriate, organize inter-laboratory comparative testing or Proficiency Tests between official laboratories. This event, organized by the Inter EURLs WG on NGS, aimed at presenting the approaches used by EURLs AMR, Campylobacter, Listeria monocytogenes, Salmonella and VTEC for Proficiency Tests on NGS, to share experiences learnt and serve as guidelines for the organization of Proficiency Tests on NGS at the Member State level. 

The inter-EURLs WG on NGS co-organised with EFSA the "Science meets Policy" conferences:

• 2023: EFSA with the inter-EURL working group on Next Generation Sequencing (NGS) organised the “Science Meets Policy” conference on “EU initiatives towards the large-scale use of Next Generation Sequencing (NGS) to tackle foodborne threats” (online and in Parma), held on 5-6 September 2023.  Presentations now available  
• 2020: The inter-EURLs WG on NGS organised a "Science meets Policy" conference entitled "Modern technologies to enable response to crises. Next Generation Sequencing to tackle food-borne diseases", held on 25 September 2020. -> Presentations available on EURL for E. coli website.