Seafood is a growing part of the economy, but its economic value is diminished by marine diseases. Infectious diseases are common in the ocean, and here we tabulate 67 examples that can reduce commercial species' growth and survivorship or decrease seafood quality. These impacts seem most problematic in the stressful and crowded conditions of aquaculture, which increasingly dominates seafood production as wild fishery production plateaus. For instance, marine diseases of farmed oysters, shrimp, abalone, and various fishes, particularly Atlantic salmon, cost billions of dollars each year. In comparison, it is often difficult to accurately estimate disease impacts on wild populations, especially those of pelagic and subtidal species. Farmed species often receive infectious diseases from wild species and can, in turn, export infectious agents to wild species. However, the impact of disease export on wild fisheries is controversial because there are few quantitative data demonstrating that wild species near farms suffer more from infectious diseases than those in other areas. The movement of exotic infectious agents to new areas continues to be the greatest concern.

Increased farm salmon production has heightened concerns about the association between disease on farm and wild fish. The controversy is particularly evident in the Broughton Archipelago of Western Canada, where a high prevalence of sea lice (ectoparasitic copepods) was first reported on juvenile wild pink salmon (Oncorhynchus gorbuscha) in 2001. Exposure to sea lice from farmed Atlantic salmon (Salmo salar) was thought to be the cause of the 97% population decline before these fish returned to spawn in 2002, although no diagnostic investigation was done to rule out other causes of mortality. To address the concern that sea lice from fish farms would cause population extinction of wild salmon, we analyzed 10-20 y of fish farm data and 60 y of pink salmon data. We show that the number of pink salmon returning to spawn in the fall predicts the number of female sea lice on farm fish the next spring, which, in turn, accounts for 98% of the annual variability in the prevalence of sea lice on outmigrating wild juvenile salmon. However, productivity of wild salmon is not negatively associated with either farm lice numbers or farm fish production, and all published field and laboratory data support the conclusion that something other than sea lice caused the population decline in 2002. We conclude that separating farm salmon from wild salmon-proposed through coordinated fallowing or closed containment-will not increase wild salmon productivity and that medical analysis can improve our understanding of complex issues related to aquaculture sustainability.B ecause salmon aquaculture production has rapidly increased over the past three decades, the potential for environmental impacts of salmon farms has generated heightened scientific and public interest (1, 2). One concern about salmon farms is that they are the source of ectoparasitic sea lice infestations that might reduce the marine survival of wild salmon (3, 4). In the Broughton Archipelago region of Western Canada (Fig. S1), farming of Atlantic salmon (Salmo salar) began in the late 1980s, and annual farm salmon production increased steadily to 17 Gg by 1999 (Fig. S2). Pink salmon (Oncorhynchus gorbuscha) is the most abundant wild salmon species in the Broughton Archipelago; they enter the marine environment at a very small size (0.2 g), and they return to natal streams to spawn 2 y after their parents (5). Because age at maturity never varies, they have distinct evenand odd-year populations ( Fig. S2 and SI Text). Record high numbers of pink salmon returned to spawn in rivers of the Broughton Archipelago in 2000 and 2001 (Dataset S1), but these returns were followed by population decline of 97% in 2002 and 88% in 2003 (Figs. S2 and S3 and SI Text). When juvenile pink salmon in the Broughton Archipelago were first examined for sea lice in June 2001, more than 90% were infested-leading to the hypothesis that sea lice from fish farms were the cause of population collapse in 2002 (4).Adult pink salmon are a natural host for the sea louse species Lepeophtheirus salmoni...

Global seafood provides almost 20% of all animal protein in diets, and aquaculture is, despite weakening trends, the fastest growing food sector worldwide. Recent increases in production have largely been achieved through intensification of existing farming systems, resulting in higher risks of disease outbreaks. This has led to increased use of antimicrobials (AMs) and consequent antimicrobial resistance (AMR) in many farming sectors, which may compromise the treatment of bacterial infections in the aquaculture species itself and increase the risks of AMR in humans through zoonotic diseases or through the transfer of AMR genes to human bacteria. Multiple stakeholders have, as a result, criticized the aquaculture industry, resulting in consequent regulations in some countries. AM use in aquaculture differs from that in livestock farming due to aquaculture’s greater diversity of species and farming systems, alternative means of AM application, and less consolidated farming practices in many regions. This, together with less research on AM use in aquaculture in general, suggests that large data gaps persist with regards to its overall use, breakdowns by species and system, and how AMs become distributed in, and impact on, the overall social-ecological systems in which they are embedded. This paper identifies the main factors (and challenges) behind application rates, which enables discussion of mitigation pathways. From a set of identified key mechanisms for AM usage, six proximate factors are identified: vulnerability to bacterial disease, AM access, disease diagnostic capacity, AMR, target markets and food safety regulations, and certification. Building upon these can enable local governments to reduce AM use through farmer training, spatial planning, assistance with disease identification, and stricter regulations. National governments and international organizations could, in turn, assist with disease-free juveniles and vaccines, enforce rigid monitoring of the quantity and quality of AMs used by farmers and the AM residues in the farmed species and in the environment, and promote measures to reduce potential human health risks associated with AMR.Electronic supplementary materialThe online version of this article (10.1007/s11625-017-0511-8) contains supplementary material, which is available to authorized users.

Piscine reovirus (PRV) is a double stranded non-enveloped RNA virus detected in farmed and wild salmonids. This study examined the phylogenetic relationships among different PRV sequence types present in samples from salmonids in Western Canada and the US, including Alaska (US), British Columbia (Canada) and Washington State (US). Tissues testing positive for PRV were partially sequenced for segment S1, producing 71 sequences that grouped into 10 unique sequence types. Sequence analysis revealed no identifiable geographical or temporal variation among the sequence types. Identical sequence types were found in fish sampled in 2001, 2005 and 2014. In addition, PRV positive samples from fish derived from Alaska, British Columbia and Washington State share identical sequence types. Comparative analysis of the phylogenetic tree indicated that Canada/US Pacific Northwest sequences formed a subgroup with some Norwegian sequence types (group II), distinct from other Norwegian and Chilean sequences (groups I, III and IV). Representative PRV positive samples from farmed and wild fish in British Columbia and Washington State were subjected to genome sequencing using next generation sequencing methods. Individual analysis of each of the 10 partial segments indicated that the Canadian and US PRV sequence types clustered separately from available whole genome sequences of some Norwegian and Chilean sequences for all segments except the segment S4. In summary, PRV was genetically homogenous over a large geographic distance (Alaska to Washington State), and the sequence types were relatively stable over a 13 year period.