Next Generation Sequencing

This page provides information and documents generated by the Inter-European Union Reference Laboratories Working Group on Next Generation Sequencing.

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. The WG includes all the EURLs operating in the field of the microbiological contamination of food and feed and is coordinated by the EURL for E. coli.  

Membership of the Inter EURL WG on NGS: 

EURL-E. coli (coordinator)
EURL-Listeria monocytogenes 
EURL-Coagulase Positive Staphylococci 
EURL-Salmonella 
EURL-Campylobacter 
EURL-Parasites 
EURL-Antimicrobial Resistance 
EURL-Food borne viruses 
Observers: SANTE G4, EFSA, ECDC 

The documents are meant to provide guidance to the laboratories in the area of application of NGS and have been produced by the WG with the aim of being diffused to all the networks of NRLs. These documents are aggregated in the Zenodo community Inter Biorisks-EURLs WG on NGS.

Deliverable Document Curated by
1 Overview of conducted and planned PTs EURL-Antimicrobial Resistance
2 Reference WGS collection EURL-Salmonella
3 Guidance document for WGS-laboratory procedures EURL-Parasites
4 Bioinformatics tools for basic analysis of Next Generation Sequencing data EURL-E. coli
5 Guidance document for cluster analysis of whole genome sequence data EURL-Campylobacter
6 Guidance document for NGS-Benchmarking EURL-Listeria monocytogenes
7 Inventory of training supports EURL-Coagulase Positive Staphylococci
8 Survey on the use of NGS across the NRLs networks EURL-E. coli
9 Supporting document for preparing high quality DNA for Whole Genome Sequencing EURL-E. coli
10 Guidelines for Dry-Lab Quality Control Metrics and Acceptance Thresholds in Short-Read WGS of zoonotic and indicator bacteria EURL-Listeria monocytogenes
11 Guidelines for amplicon sequencing of the capsid region of noroviruses EURL-Food borne virues

 

Last reviewed 16/12/2025