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Domselaar GMI8 Beijing Canadian WGS Surveillance Experience

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The use of WGS data for surveillance systems: the Canadian experience.

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Domselaar GMI8 Beijing Canadian WGS Surveillance Experience

  1. 1. The use of WGS data for surveillance systems: the Canadian experience Gary Van Domselaar Chief, Bioinformatics National Microbiology Lab Public Health Agency of Canada 11 May 2016
  2. 2. The NML’s Current Enteric Disease Surveillance Program 2 NATIONAL MICROBIOLOGY LABORATORY PROVINCIAL PUBLIC HEALTH LABORATORIES CLINICAL ISOLATES SENTINEL SURVEILLANCE (FoodNet Canada) CLINICAL, FOOD, ENVIRONMENTAL CANADIAN FOOD INSPECTION AGENCY (Regulatory) FOOD ISOLATES LISTERIA - E. COLI O157:H7 - SALMONELLA - SHIGELLA PFGE/MLVA PUBLIC HEALTH ACTION
  3. 3. Early Work in WGS for Outbreak Investigation: Listeria 2008 3
  4. 4. Early Work in WGS for Outbreak Investigation: Haiti Cholera Outbreak 2010 - 4
  5. 5. GRDI Shared Priority Project on Food and Water Safety 2012 5
  6. 6. 6 PulseNet Genomic Epidemiology Roadmap PulseNet Canada Genomic Epidemiology Roadmap Aleisha Reimer with contributions from Drs Celine Nadon, Morag Graham, and PulseNet Canada members October 16, 2013 Based on existing PulseNet model De-centralized sequencing and analysis Parallel, centralized storage & analysis of national data sets Continued NML support in reference testing, training, certification & proficiency Continued method development, refinement, and KT
  7. 7. Implementation Plan 7
  8. 8. Implementation Retrospective Study Prospective Study Surveillance Outbreak Response Baseline Data 8 Pilot Projects: Retrospective and Prospective Studies
  9. 9. 9 Overview of Retro1000 Project DELIVERABLES 1. Expanded and accessible national database of draft genomes 2. Standardized/harmonized procedures for sample prep, sequencing, bioinformatics analysis, and quality control – including interlaboratory validation 3. Interpretation criteria and/or elements for proper use of WGS data for public health 4. Quarterly and final reports Select isolates for sequencing (n=1000 each) NGS (Illumina MiSeq) Analysis (SNVPhyl and wgMLST) Conclusions and Reporting APPROACH Inter-laboratory comparisons Procedures, criteria, recommendations
  10. 10. Organisms selected by PNC Steering Committee # isolates already Sequenced Listeria monocytogenes 400 E. coli O157 530 S. Enteritidis 21 S. Typhimurium 0 S. Heidelberg 66 S. Thompson 429 Overview of Retro1000 Project
  11. 11. Real-time Investigations Supported by WGS, PulseNet Canada 2014 11 Organism Case or Outbreak Details (putative/confirmed vehicle) L. monocytogenes Collaboration with USA (lettuce product) L. monocytogenes Collaboration with USA (RTE meat product) Salmonella Thompson National laboratory investigation to support outbreak response in a single province – see sidebar (potential chicken products) E. coli O157:H7 Large outbreak in a single province (pork products) L. monocytogenes Ongoing cluster of common PFGE pattern L. monocytogenes Collaboration with USA (caramel apples) S. Enteritidis Collaboration with USA (bean sprouts)
  12. 12. National Public Health Agency Provincial Public Health Agency Academic/Public Partnership among provincial public health agencies, national public health agencies and academic institutes to bridge the gaps between advancements in genomic epidemiology and real-life and real-time use cases in public health agencies - Project Team has direct access to state of the art researches in academia - Project Team is directly embedded in user organization
  13. 13. IRIDA Design • Carefully designed and engineered software platform is just the starting point… User Interface Security File system Metadata Storage Application logic REST API Workflow Execution Manager Continuous Integration Documentation
  14. 14. Canada’s Byzantine Public Health System Source: M. Taylor, BCCDC Provincial public health dept. National laboratory Local public health dept. Provincial laboratory Cases Physicians Frontline lab Information BioinformaticsandAnalyticalCapacities
  15. 15. Local Storage Remote APIs IRIDA’s Federated Design List Samples 15
  16. 16. Application Ontology Controls Metadata Build On, Work With: OBI TypON NGSOnto NIAID-GSC-BRC core metadata MIxS Ontology NCBI Biosample etc TRANS – Pathogen Transmission EPO Exposure Ontology Infectious Disease Ontology CARD, ARO for AMR USDA Nutrient DB EFSA Comp. Food Consump. DB Example gaps to be filled: Expand food ontology; expand CARD AMR data with others.
  17. 17. Analytical Tool Quality Control Module Quality Metrics Quality Control IRIDA’S QA/QC Model
  18. 18. IRIDA Workflows: Portable and Transparent Pipelines • Use Galaxy as workflow engine – large community support • Retools to address usability, security, and other limitations • Version Controlled Pipeline Templates • Input files, parameters, and workflow are sent to IRIDA-specific Galaxy for execution • Results and provenance information are copied from Galaxy 1. Input files sent to Galaxy 3. Results downloaded from Galaxy IRIDA UI/DB Galaxy Assembly Tools Variant Calling Tools … REST API Shared File System Worker Worker 2. Tools executed on Galaxy workers
  19. 19. 19 IRIDA Pipelines: SNVPhyl
  20. 20. Genomic Surveillance of Antimircrobial Resistance 20 IRIDA Pipelines: Genomic Surveillance of AMR
  21. 21. SISTR: THE SALMONELLA IN SILICO TYPING RESOURCE │ https://lfz.corefacility.ca/sistr-app/ 21 In silico analysis of WGS data  assembly statistics  serovar prediction  in silico typing (MLST, cgMLST)  AMR prediction Comparative genomic analyses  cgMLST  accessory gene content  core SNPs Epidemiologic analysis  geospatial distribution  temporal distribution  source association
  22. 22. External Access via REST API 24 http://pathogenomics.sfu.ca/islandviewer IslandViewer Dhillon and Laird et al. 2015, Nucleic Acids Research http://kiwi.cs.dal.ca/GenGIS Parks et al. 2013, PLoS One
  23. 23. When will it be available? • Jun 1 2015: IRIDA 1.0 beta internal release – Release to collaborators for installation and full test • Jul 1 2015: IRIDA 1.0 beta1 – Announce Beta release, download, documentation available on website – www.irida.ca • Aug 1 2015: IRIDA 1.0 beta2 – Cloud installer, with documentation – Additional pipelines as available – Visualization as available
  24. 24. Outbreak investigationRoutine surveillance Canada’s long- term vision
  25. 25. Acknowledgements Project Leaders Fiona Brinkman – SFU Will Hsiao – PHMRL Gary Van Domselaar – NML University of Lisbon Joᾶo Carriҫo National Microbiology Laboratory (NML) Franklin Bristow Aaron Petkau Thomas Matthews Josh Adam Adam Olsen Tara Lynch Shaun Tyler Philip Mabon Philip Au Celine Nadon Matthew Stuart-Edwards Morag Graham Chrystal Berry Lorelee Tschetter Laboratory for Foodborne Zoonoses (LFZ) Eduardo Toboada Peter Kruczkiewicz Chad Laing Vic Gannon Matthew Whiteside Ross Duncan Steven Mutschall Simon Fraser University (SFU) Melanie Courtot Emma Griffiths Geoff Winsor Julie Shay Matthew Laird Bhav Dhillon Raymond Lo BC Public Health Microbiology & Reference Laboratory (PHMRL) and BC Centre for Disease Control (BCCDC) Judy Isaac-Renton Patrick Tang Natalie Prystajecky Jennifer Gardy Damion Dooley Linda Hoang Kim MacDonald Yin Chang Eleni Galanis Marsha Taylor Cletus D’Souza Ana Paccagnella University of Maryland Lynn Schriml Canadian Food Inspection Agency (CFIA) Burton Blais Catherine Carrillo Dominic Lambert Dalhousie University Rob Beiko Alex Keddy 27 McMaster University Andrew McArthur Daim Sardar European Nucleotide Archive Guy Cochrane Petra ten Hoopen Clara Amid European Food Safety Agency Leibana Criado Ernesto Vernazza Francesco Rizzi Valentina

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