EURL Working Group on NGS

Transcription

1 EURL Working Group on NGS Rene S. Hendriksen, PhD Research group of Genomic Epidemiology National Food Institute, Technical University of Denmark Annual EURL AR workshop 5-6 April 2018 DTU, Kgs. Lyngby, Denmark

2 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

3 WG participants 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

4 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

5 Proficiency testing GMI PT replacing conventional microbiology

6 Proficiency testing GMI PT replacing conventional microbiology

7 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

8 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 8

9 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

10 Building Global Capacity Center for Genomic Epidemiology

11 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

12 Bench marking (EURL Listeria lead) Development of guidance document defining how to bench marking analytical methods and pipelines

13 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 learners 356 Completers 4.6/5.0 Ratings

14 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

15 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)

16 Building Global Capacity Guidelines and resource hubs EU to adopt WGS in the legislation replacing conventional microbiology for monitoring Continuing benchmarking in COMPARE 16 4 April 2018

17 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.

18 WG 25 WGS for typing and genomic characterization of ISO/TC 34/SC 9 ISO WG 25 Face to Face Meeting Lausanne Switzerland May Nestle Research Center

19 New initiatives COMPARE ECDC pilot Salm Surv Courtesy to Guy Cochrane, ENA for sharing slides

20 New initiatives COMPARE ECDC pilot Salm Surv Courtesy to Guy Cochrane, ENA for sharing slides

21 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