Experiences from an NRL of the implementation of WGS

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Ashlyn Sanders
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1 GEMAN FEDEAL INSTITUTE FO ISK ASSESSMENT Experiences from an NL of the implementation of WGS Burkhard Malorny,23,32 13a 23,6,1b,26,13 1,,6,12 1b,21,6a, 19,21,a 1,1b,,a,6 7,12,21,3, DNC 1 a,5a 19 1,,6,3 1 b b 29 1b 13 21C b b 1b 9b 26 7a

2 Microbiological National eference Laboratories at Bf Nominated according regulation (EU) 2/200 Approx. typing of isolates per year Accredited according to ISO Animal Food Others Feed NL for Salmonella Source of isolates NL for Campylobacter NL for E. coli incl. VTEC NL for coagulase-positive Staphylococci incl. S. aureus NL for Listeria monocytogenes NL for Antibiotic esistance NL for Monitoring Bacteriological and Viral Contamination of Bivalve Molluscs NL Trichinella Seite 2

3 Timeline introducing NGS at Bf 2007 : Asking to buy a oche 5 GS FLX 20: Asking to buy an IonTorrent PGM Sequencer 2012: Prompt invitation to do investments in NGS instruments 2015: Concept for application of NGS at Bf 2017: Bioinformatician, strengthening of IT infrastructure Time 2012: Visit of CGE at DTU End of 201: MiSeq and Ion Torrent in the lab available 2016: Fragment Analyzer Feb. 2016: Start ENGAGE Mid of 2017: NextSeq available + new staff positions. End of 2017: Nanopore 201: PacBio Sequel planned 2019/2020: More staff? Seite 3

Phases of implementation NGS for NLs Development of a concept to implement NGS Starting position

(instruments, staff, IT) Convincing of decision makers: Think like them!

starting pilot studies (e.g. phylogentic study, comparative studies traditional methods vs.

4 Phases of implementation NGS for NLs Development of a concept to implement NGS Starting position (infrastructure, staff, IT) SWOT analysis Estimated sequencing demand Development strategy and goals Costs (instruments, staff, IT) Convincing of decision makers: Think like them! Equipment procurement, staff hiring, bioinformatic set up Training of motivated staff Designing and starting pilot studies (e.g. phylogentic study, comparative studies traditional methods vs. NGS) Implementation of NGS for outbreak studies Establishing of quality control management system outine screening of isolates (increasing isolate numbers) Optimization Seite

Issues that need to be adressed when implementing NGS in NLs Infrastructure Instruments, IT, lab staff members Validation and quality control (QC)

Participation/establishing of working groups Strengthen interpretation and harmonization of NGS Data management, sharing, interpretation Balanced system,

5 Issues that need to be adressed when implementing NGS in NLs Infrastructure Instruments, IT, lab staff members Validation and quality control (QC) procedures Accreditation according ISO Forming of interdisciplinary teams and education Training of internal and external staff members Participation/establishing of working groups Strengthen interpretation and harmonization of NGS Data management, sharing, interpretation Balanced system, clear rules (code of conducts), privacy Uploading of assembled data (small datasets) eporting system Setting up secure databases In-house, national, international Seite 5

6 Many challenges and solutions lessons learned Convincing decision makers to invest in new expensive technology Find colleagues to support you (internal/external) Write a concept as basis for discussions As governmental institute we have highly restricted data secure rules and slow internet speed Use this situation to convince decision makers in setting up an extended internal IT infrastructure if not possible: start using commercial programs and open-source platforms (e.g. CGE, Patric), a powerful 5000 PC might be enough Not enough staff capacity Try to get funding and hire young highly motivated employees (students, Ph.D students, assistences) No sequence infrastructure available Cooperate with universities and institutes in your neighborhood having facility available Seite 6

system Attend GMI ring-trials Set up an in-house validation study Teaching of Technical

7 Many challenges and solutions lessons learned Exgange of data Create trust in your community and an open mind for new technologies and data exchange possibilities No QC system Attend GMI ring-trials Set up an in-house validation study Teaching of Technical Assistance motivate by including them in analysis of sequence data (show them the results) Seite 7

php/colloquium-reports/item/62-applications-of-clinicalmicrobial-next-generation-sequencing.

8 ecommended compendium Applications of Clinical Microbial Next-Generation Sequencing, 2016, American Academy of Microbiology, Washington, academy.asm.org. Download from: Genomics Into Practice PHG Foundation (2015), ISBN Download from: Seite

9 GEMAN FEDEAL INSTITUTE FO ISK ASSESSMENT Thank you for your attention Burkhard Malorny German Federal Institute for isk Assessment Max-Dohrn-Str Berlin, GEMANY Phone Fax bfr@bfr.bund.de

EURL WORKING GROUP ON WHOLE GENOME SEQUENCING AND PULSENET INTERNATIONAL

EURL WORKING GROUP ON WHOLE GENOME SEQUENCING AND PULSENET INTERNATIONAL EURL-Campylobacter workshop, 9/10-2018 Joakim Skarin, SVA Objectives of the WG-NGS To promote the use of NGS across the EURL networks