Genome British Columbia - Genome Genomics

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Strategic Salmon Health Initiative

Project Leaders:
Brian Riddell and Kristi Miller

Lead Institutions:
Pacific Salmon Foundation and Department of Fisheries and Oceans Canada

Members of the Public Interest Panel:
Vincent Erenst, Susan Farlinger, Gerry Kristianson, Peter Ladner, Deana Machin, Patrick Marshall, Gary Marty, Don McLeod, John Nightingale, Jay Ritchlin, Les Rombough


The Strategic Salmon Health Initiative has been initiated for a variety of reasons, the primary one being the high mortality rate of juvenile salmon during their early ocean migration. There is a strong belief within the scientific community that infectious disease may be a significant factor in this mortality, but not enough is known about what disease agents might affect Pacific salmon in their natural habitats. What is known comes almost exclusively from observations of cultured fish (both in hatcheries and aquaculture).

The project intends to clarify the presence and/or absence of microbes in Pacific salmon. To address this issue the initiative will involve a four-phased program to discover the microbes present in Pacific salmon that may reduce the productivity of our Pacific salmon. In the initial phase of the work the primary goal is to obtain collections of wild, hatchery and aquaculture salmonids from southern BC. This phase will provide a tissue inventory for assessment of microbes carried both by wild and cultured salmon in BC. The first steps also include the development of a stakeholder consultation process that will provide input to the information needs, public engagement and communications and ways to integrate research on microbes and disease on BC salmon.

The phases of the Strategic Salmon Health Initiative are as follows:

  • Phase 1 (completed) established a large-scale sampling program, run over 12 months, for wild, hatchery and aquaculture salmon that was conducted in 2012 and early 2013. These samples were combined with similar samples collected from 2008 through 2012 to facilitate the broad scale microbe surveillance plan to be implemented in Phase 2. This Phase did not conduct analysis on samples.
  • Phase 2 of the Strategic Salmon Health Initiative involves rigorous analysis of the tissue samples collected in Phase 1 and in previous research. This phase of the research project has been divided into two sub-phases (2a and 2b).  Phase 2a is focused on evaluating the new technology platform and Phase 2b focuses on the application of the platform to identify microbes in the large sample collection.
    • Phase 2a (underway) focuses on the development and evaluation of the innovative research platform that will be used to analyze the samples gathered in Phase 1. This technology, the Fluidigm BioMarkTM HD System, offers an ability to analyze samples on an unprecedented scale. The platform is able to analyze up to 96 unique assays  simultaneously. With appropriate controls and running duplicate samples across 2-3 sample arrays, the load of 45 microbes in more than 200 salmon samples can be analyzed in a day. In total the analysis will be looking at over 90% of infectious agents known to cause disease in salmon- no other known study is doing quantitative analysis at this level.**
    • Phase 2b (~18-24 months) will consist of the microbe monitoring study and epidemiology aspects. In addition to novel research using the Fluidigm technology, a portion of the samples collected for molecular monitoring will also undergo histopathological analysis and gene expression profiling to identify microbes most likely to associate with disease. DFO Audit samples from dying farmed fish will also shed light on microbes associated with mortality of salmon in BC. Epidemiology analyses will be performed to identify distributional patterns of microbes in wild, hatchery and aquaculture salmon. In its entirety, Phase 2 (a & b) is the discovery phase wherein points of focus and hypotheses are identified for testing in Phase 3.
  • Phase 3 (~24 months) will focus in on the microbes identified in Phase 2, with an emphasis on microbes that have not been extensively researched previously and that are thought to be of pathological significance in Pacific salmon. The team will conduct laboratory challenge studies of pathogenicity to provide further understanding of disease processes and dynamics in wild fish. This Phase is intended to begin towards the end of Phase 2 to expedite information needs on microbes that are newly discovered in BC salmon.
  • Phase 4 (~12-18 months) will include reporting of research and presentations to management agencies on the potential utility of methods developed and the application of outcomes to future monitoring. The culmination of the project will likely be in 2017/2018 when data has been compiled and research outcomes are clear.

** Results generated in this research project use novel technology and new molecular assays that will have been evaluated for this research project but may not that been accepted for diagnostic applications.  Research findings produced through this project will be made publicly available as summarized results until scientific publication after which each dataset can then be released for broad use within the scientific community.  Results may be released in support of building research collaborations but the intellectual property of these results will be protected until publication.

Click here to see a glossary of terms.

APPENDIX D- Guidelines for DFO Release of Information

 Communication flow associated with reporting of scientific information 

  • Throughout the Phases of the project the SSHI team will be engaging with Collaborating Scientific Advisors, the Executive Scientific Committee and the Context Advisory Committee. The SSHI team will also be in an ongoing reporting and engagement cycle with the CFIA regarding reportable microbes.
  • Twice annually a report will be provided to the Department of Fisheries and Ocean (DFO) one month before the Public Interest Panel (PIP) meeting so that managers, regulators and policy makers in the National Aquatic Animal Health Program (NAAHP), the Aquaculture Management Division (AMD), the Salmon Enhancement Program (SEP), and Fisheries management (Fisheries) can be briefed. 
  • This bi-annual report will only include results from reportable microbes that have been validated (or accepted) by the CFIA.
  • The Pacific Salmon Foundation (PSF) and Genome BC will be provided with the full report two weeks prior to the PIP meeting, and at the same time, the Aquaculture industry will be provided with a report on all results pertaining to aquaculture samples.  One week before the meeting the bi-annual report will be provided to the PIP for discussion at the subsequent meeting.  
  • The SSHI team will report to the PIP through presentations and written reports provided by the Project Leaders.
  • PSF and DFO will consult with each other on news media outreach and response to enquiries, but PSF will be principally responsible for coordination of public statements and media relations on behalf of the SSHI investigators.
  • Brian Riddell is the principal spokesperson, in consultation with SSHI co-lead Dr. Kristi Miller-Saunders (DFO), and with communications support from Michael Meneer (PSF) and Sally Greenwood (Genome BC). Enquiries will initially be directed to Meneer and Greenwood who will manage responses in consultation with DFO, Genome BC and other relevant parties.
  • In the case of news media engagement regarding reportable pathogens under the Canadian Animal Health Act, news media strategy and response will be determined by the Canadian Food Inspection Agency, though the SSHI team will make every effort to participate with CFIA in a coordinated response.
  • In conjunction with the scientific reporting PSF and Genome BC may decide to release key messages outlining the progress of the project at various times throughout the project, providing clear messaging on what can and cannot be concluded from the scientific information, and will provide these messages to communications officers at DFO and PSF ahead of time.
  • PSF and Genome BC will undertake quarterly briefings with the DFO Minister and senior B.C. provincial Ministers.

*Noted that this chart does not reflect final confirmation from CFIA re: release of information. 

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