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Visceral mycoses in Atlantic salmon (Salmo salar): The role of opportunistic fungal pathogens in fish health and mortality in salmon aquaculture systems



In 2017, there were several cases in British Columbia (BC) in which farmed Atlantic salmon exhibited elevated mortality after being transferred from freshwater to seawater net pens. Many of the affected fish were shown to have fungal infections in several organs, including the spleen, liver and kidney. Cultures of these fungal pathogens allowed them to be identified as species from the genera Exophiala spp. and Ochroconis spp., which are types of darkly pigmented ascomycete fungi. In one company, 4% of all summer mortalities within the affected farms were attributed to this complication, with estimated losses of approximately $60,000. To make matters worse, in January 2018, similar fungal infections were identified in a new cohort (i.e., year class) of salmon transferred to a new site in September 2017.

The general objective of this project was to improve our understanding of opportunistic fungal pathogens in the genera Exophiala and Ochroconis that are known to cause infections and disease in Atlantic salmon.
Specifically, the proposed research aimed to:

  1. survey the temporal and spatial distribution of these pathogens in selected farm facilities;
  2. establish the prevalence of these infections among different age classes of fish and within host tissues;
  3. study the infection process in controlled trials to confirm the infectivity of pathogenic isolates and evaluate their impact upon fish health; and
  4. identify measures to reduce the impact of these fungi upon fish health in production systems.


Ochroconis spp. were the most commonly detected fungal agents and kidney was the primary site of infection. The infections were detected at a higher rate in freshwater-reared juvenile salmon compared with those detected in salmon in seawater net pens. Similarly, the fungi Exophiala salmonis, Ochroconis globalis and Ochroconis anomala were identified in fish from both fresh water and seawater sites. In contrast, Exophiala psychrophila was only detected at one ocean site.

In the laboratory trial, a low prevalence of pre-existing fungus infection was detected in the experimental fish. Treated fish were injected with a fungal inoculum, controls were injected with culture medium. At 4 weeks post-injection, infection was detected in 1 of 36 treated fish and in 0 of 36 controls. At 8 weeks post-injection, infection was detected in 2 of 39 treated fish and in 4 of 39 controls. All detected infections were similar to the pre-existing infection.

The project provided baseline information on the incidence of these infections, the fungal species implicated, and provided molecular tools for their detection in British Columbia. This information will inform disease management strategies that will improve fish health and thereby increase productivity and reduce financial losses due to poor growth and mortality associated with fungal mycoses in salmon aquaculture.


de la Bastide, P.Y., T. Finston, J. Dechka, J. Scantlebury, W.A. Untereiner, S.R.M. Jones and W.E. Hintz. Dematiaceous fungal infections of Atlantic salmon (Salmo salar): species identification, tissue detection and incidence among age classes of commercial populations. (In preparation).

Program name

Aquaculture Collaborative Research and Development Program (ACRDP)



Principal investigator

Simon Jones, research scientist, Fisheries and Oceans Canada, Pacific Biological Station, Pacific Region

Team members

Terrie Finston, research associate, University of Victoria
Paul de la Bastide, research associate, University of Victoria
Will Hintz, professor of biology, University of Victoria


Barry Milligan, Fish Health Director and veterinarian, Cermaq Canada Ltd.

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