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A Federated Bioinformatics Platform for Public Health Microbial Genomics

172PHM
  • Project Leaders: Fiona Brinkman, Gary van Domselaar, William Hsiao
  • Institutions: Simon Fraser University (SFU)
  • Budget: $1562534
  • Program/Competition: Bioinformatics and Computational Biology Competitions
  • Genome Centre(s): Genome Canada
  • Fiscal Year: 2013
  • Status: Closed

Despite advances in medical, sanitary, and public health practices, communicable diseases remain a serious threat to the health and economies of Canadians and people worldwide. Whole genome sequencing of disease-causing bacteria provides the highest resolution and most comprehensive data available to identify and track these organisms, but computational tools are needed to more rapidly analyse the data.

 

This project reported the creation of a secure, user-friendly, open source Integrated Rapid Infectious Disease Analysis (IRIDA) computational platform to enable more rapid, standards-compliant high quality genome-based analysis of infectious disease outbreaks linked with other epidemiological data. It is now in use in Federal and Provincial public health labs, and is being deployed to other Federal Departments and Agencies as part of PulseNet Canada’s national strategy to modernize foodborne surveillance by incorporating next-generation sequencing and high performance bioinformatics computing. Nationally, clinical microbiologists and epidemiologists have initiated using IRIDA to investigate and report on foodborne disease outbreaks in real time. The IRIDA platform is also being used for additional large-scale national and international collaborations. IRIDA has been installed now in other jurisdictions/countries on four continents. This resource is of particular interest since it is the only freely available, open source platform that can perform genomic epidemiology analyses in a secure environment locally (i.e. within a jurisdiction), yet provide user-friendly web-based access. It complements centralized resources such as those at NCBI, and commercial resources that some countries cannot afford.

 

A public IRIDA version is also set up on Compute Canada resources and is being made available in 2017 for wider researcher use. Additional public software developed as IRIDA modules are also publicly available as web servers and/or open source code for local installation. The research has been disseminated through the 55 software packages, over 30 publications, and over 150 presentations and workshops. The contextual information standards (ontologies GenEpiO and FoodOn) have been chosen for an upcoming draft ISO policy on the use of genomics in food microbiology for food safety. They have led the formation of a GenEpiO consortium of researchers for such ontology development, now involving 70 researchers from 15 countries. IRIDA project has directly translated into 4 new grants to continue the work, and the NML has secured 5 permanent staff positions to continue to support the IRIDA core platform.