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

 

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.

From 14 June 2022 to 15 June 2022

APPLICATION CLOSED - PARTICIPANTS HAS BEEN SELECTED

agenda

Three foodborne pathogens in the joint EFSA-ECDC database. The first three editions focused on the analysis of Pulsed Field Gel Electrophoresis profiles, the molecular data accepted at that time in the database. However, a transition to WGS data for implementation in this database is foreseen for the near future, and it was agreed that, starting from the last edition held at EURL Listeria monocytogenes in 2019, the joint courses should be focused on the analysis of NGS data.
Unfortunately, due to the Covid-19 pandemic, no joint trainings could be organised in 2020 and 2021.
Following a discussion in the Inter EURLs WG on NGS, it was decided that the 2022 edition will be jointly organised by all the EURLs part of the WG, namely: EURL VTEC, EURL Listeria monocytogenes, EURL Salmonella, EURL Coagulase Positive Staphylococci, EURL Parasites, EURL Foodborne viruses, EURL AMR, EURL Campylobacter.

The training course will be held at the Istituto Superiore di Sanità (EURL E. coli) in Rome, Italy, on June 14th-15th 2022. The course will start on June 14th at 9h30 and will finish on June 15th at 14h30. The training course will focus on the main features and the use of bioinformatics for analysis of WGS data at a basic level:

❶  Introduction to Next Generation Sequencing (NGS) data formats,
❷ Analysis of NGS data: local and remote options, closed and custom platforms (Galaxy, Ridom Seqsphere+, etc.),
❸ Basic tools for analysis: quality check and trimming,
❹ Assembly, basic typing of the strains using different approaches.

 

An overview of the possibilities will be given to the participants through hands-on demonstrations and exercises on dry lab analysis. At the end of the course, the participants are expected to be able to use basic bioinformatics tools for analysis of NGS data.

Please note that the participants will be asked to bring their own laptops.

The EURLs will evaluate the applications and will select the participants based on the following criteria:

► Training needs of the NRL doing the request (may also be based on performance in PTs),
► Participation in previous training initiatives on the same topics,
► Role of the applicant in the NRL,
► Appropriate basic skills of the applicant for a fruitful course,
► If a given laboratory has several NRL mandates, only one applicant from the same laboratory can participate.

 

The EURLs will reimburse, according to the usual EU Regulations, the expenses related to travel and accommodation of the selected applicants.