Epidemiological investigation of emerging infectious diseases of farmed fish in Canada

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The increase in demand for seafood has led to rapid growth of aquaculture industry, including netpen based salmon production. Canada's Blue Economy Strategy 2040 envisions Canada to be top three best sustainable producer of seafood. However, the industry is challenged by an increase in the emergence, severity, and prevalence of infectious diseases in the marine ecosystem. Many aquatic animal diseases are associated with pronounced shifts in microbial community structures or genetic and functional changes in reservoir non-virulent progenitor variants. Mouthrot (MR; tenacibaculosis), and infectious salmon anemia (ISA) are emerging diseases in Atlantic salmon aquaculture in Canada, the most important bacterial and viral diseases threatening the sustainability of salmon aquaculture. Tenacibaculum maritimum is the principal causative agent of MR; however, other Tenacibaculum spp are also likely involved. The non-virulent strains of the ISA virus are likely the reservoir present in the farm environment, from which the virulent strains emerge. However, the epidemiology and factors associated with outbreaks and severity of disease are mostly unknown for Canadian aquaculture. We surmise that infectious agents involved in these diseases are present on the farms as opportunistic agents and that a multifactorial etiology is involved in their outbreaks. We also hypothesize that outbreaks result from changes in the genetic make-up of the agent and, or microbial community structure in the affected fish due to stressors, such as increased water temperature, management, etc. The short-term goal of my on-farm observational research is to elucidate the interactions between host, pathogen(s), and environment to understand the occurrence, transmission, and risk factors associated with these emerging infectious diseases in salmon aquaculture in Canada using MR and ISA as example cases. The long-term goal of my research program is to understand the effects of changing ecosystems, and farm and wild interactions to enhance the aquatic epidemiology research program for sustainable aquaculture and fishery. Some of the questions this research will answer are: how abundant are non-virulent strains of infectious agents, and how likely are they to convert to virulent strains and result in clinical outbreaks? To what extent do the environmental and other factors interact with these microbial and genetic shifts? Key results on the genomic characteristics of the infectious agents and the identification of factors involved in the emergence of disease will help in efficient management of the disease by formulating mitigation strategies in the short term and reducing antibiotic use, providing informed guidance for outbreak prevention and help achieve Canada's Blue Economy Strategy 2040 sustainable sea food production target in the long term. Knowledge gained on the epidemiology of these diseases in farmed fish can potentially be applied to mitigate their impact on wild salmon.