EURL Working Group on NGS
Rene S. Hendriksen, PhDResearch group of Genomic EpidemiologyNational Food Institute, Technical University of Denmark
Annual EURL AR workshop 5-6 April 2018
DTU, Kgs. Lyngby, Denmark
DTU Food, Technical University of Denmark
Objectives of the WG
• To promote the use of NGS across the EURLs' networks
• Build WGS capacity within the EU and among NRLs
• Ensure liaison with the work of the EURLs and the work of EFSA and ECDC on the WGS mandate sent by the Commission,
– ensure no overlap of activities between the WG and EFSA-ECDC work
2
DTU Food, Technical University of Denmark
• EURL E. coli (WG coordinator)
• EURL Listeria monocytogenes
• EURL CPS (Coagulase Positive Staphylococci)
• EURL Salmonella
• EURL Campylobacter
• EURL Parasites
• EURL AR
• EURL Food borne viruses
• Observers: SANTE G4, EFSA, ECDC
WG participants
DTU Food, Technical University of Denmark
Proficiency Testing (EURL AR lead)
• Development of guidance documents or SOPs defining the architecture of WGS-based PT schemes in terms
– Methodology of PT organization– What data to be extracted from WGS and returned to the PT provider– How to analyse PT results by the EURLs
• Reports containing the main conclusions from the analyses performed in the framework of PT programs on WGS carried out by one (or more) EURL(s)
– Submitted to the WG for discussion and harmonization before being sent to the Commission and to the agencies EFSA and ECDC
DTU Food, Technical University of DenmarkDTU Food, Technical University of Denmark
Proficiency testing – GMI PTreplacing conventional microbiology
DTU Food, Technical University of DenmarkDTU Food, Technical University of Denmark
Proficiency testing – GMI PTreplacing conventional microbiology
DTU Food, Technical University of Denmark
WGS laboratory procedures (EURL P lead)
• Evaluation of available DNA Nucleic acid Extraction SOPs developed by existing projects (EU Compare, EFSA projects, ENGAGE and INNUENDO, others) to validate the performances and suitability for the NRLs network
• To potential work on reducing the time from culture to sequencing testing different library preparation and sequencing kits
DTU Food, Technical University of Denmark8
Building Global Capacity Guidelines and resource hubs
Protocols and SOPs will be shared soon on the COMPARE site
A WHO landscape paper and surveillance guideline about to be issued
DTU Food, Technical University of Denmark
Bioinformatics tools (EURL VTEC lead)
• Development of guidance documents or reports on different bioinformatics tools for NGS data mining (with the exclusion of the cluster analyses including quality parameters of sequence data
• Defining criteria of selection of tools to support NRLs
• Develop, set up and (if possible) validate, and produce tutorials for bioinformatics tools and pipelines for those NRLs that do not have/use proprietary software or other resources
DTU Food, Technical University of Denmarkhttp://cge.cbs.dtu.dk/services/all.php
Building Global Capacity Center for Genomic Epidemiology
DTU Food, Technical University of Denmark
WGS Cluster Analysis: (EURL Campy lead)
• Development of tutorials, guidance documents defining criteria of selection of software (open source and commercial)
– including requirement of quality parameters for WGS data, to support NRLs in cluster analysis of WGS data
DTU Food, Technical University of Denmark
Bench marking (EURL Listeria lead)
• Development of guidance document defining how to bench marking analytical methods and pipelines
DTU Food, Technical University of Denmark
Trainings on WGS (EURL CPS lead)
• Definition of a common structure for training events (courses, e-Learning, ad hoc training stages, organized jointly or by the single EURLs) in view to harmonize the trainings delivered to the NRLs.
• Practical training on WGS data production: DNA extraction, library prep, operation of sequencing equipment
• WGS data analysis
12,800 learners356 Completers4.6/5.0 Ratings
DTU Food, Technical University of Denmark
WGS Cluster Analysis: (EURL Campy lead)
• Development of tutorials, guidance documents defining criteria of selection of software (open source and commercial)
– including requirement of quality parameters for WGS data, to support NRLs in cluster analysis of WGS data
DTU Food, Technical University of Denmark
Reference and confirmatory testing using WGS (EURL Salmonella Lead)
• Giving suggestions for control strains for testing pipelines
• Development of guidance document for the use of and/or validation of the use of NWGS for confirmatory testing and typing (e.g. use of WGS for Salmonella serotyping, testing for virulence genes of E. coli)
DTU Food, Technical University of Denmark16 4 April 2018
Building Global Capacity Guidelines and resource hubs
EU to adopt WGS in the legislation replacing conventional microbiology for monitoring
Continuing benchmarking in COMPARE
DTU Food, Technical University of Denmark
Follow-up of ISO activities on WGS
• Some members of the WG should participate in the WG 25 “WGS for typing and genomic characterization” of ISO/TC 34/SC 9 “Food products-Microbiology” and/or follow the activities of this group closely, so that is known what harmonised documents for NWGS are developed internationally
• Activities on pipelines and data analysis – The WG could work towards aligning activities in view to establish the
future EU database on WGS. The WG may define single positions, when consulted by the EFSA-ECDC steering committee dealing with the WGS mandate.
DTU Food, Technical University of Denmark
WG 25 “WGS for typing and genomic characterization” of ISO/TC 34/SC 9
ISO WG 25 Face to Face Meeting Lausanne Switzerland May 14-15 2018 -Nestle Research Center
DTU Food, Technical University of Denmark
New initiatives –COMPARE ECDC pilot Salm Surv
Courtesy to Guy Cochrane, ENA for sharing slides
DTU Food, Technical University of Denmark
New initiatives –COMPARE ECDC pilot Salm Surv
Courtesy to Guy Cochrane, ENA for sharing slides
DTU Food, Technical University of Denmark
Thank you for your attention
Rene S. Hendriksen, PhD
Research group of Bacterial Genomics and Antimicrobial Resistance
WHO Collaborating Centre for Antimicrobial Resistance in Food borne Pathogens
European Union Reference Laboratory for Antimicrobial Resistance
National Food Institute, Technical University of Denmark
