Transcriptome Analysis of Atlantic Salmon (Salmo salar) Skin in Response to Sea Lice and Infectious Salmon Anemia Virus Co-Infection Under Different Experimental Functional Diets

Abstract

Sea lice (Lepeophtheirus salmonis) are ectoparasitic copepods that cause significant economic loss in marine salmoniculture. In commercial salmon farms, infestation with sea lice can enhance susceptibility to other significant pathogens, such as the highly contagious infectious salmon anemia virus (ISAv). In this study, transcriptomic analysis was used to evaluate the impact of four experimental functional feeds (i.e. 0.3% EPA/DHA+high-ω6, 0.3% EPA/DHA+high-ω6+immunostimulant (IS), 1% EPA/DHA+high-ω6, and 1% EPA/DHA+high-ω3) on Atlantic salmon (Salmo salar) during a single infection with sea lice (L. salmonis) and a co-infection with sea lice and ISAv. The overall objectives were to compare the transcriptomic profiles of skin between lice infection alone with co-infection groups and assess differences in gene expression response among animals with different experimental diets. Atlantic salmon smolts were challenged with L. salmonis following a 28-day feeding trial. Fish were then challenged with ISAv at 18 days post-sea lice infection (dpi), and maintained on individual diets, to establish a co-infection model. Skin tissues sampled at 33 dpi were subjected to RNA-seq analysis. The co-infection’s overall survival rates were between 37%-50%, while no mortality was observed in the single infection with lice. With regard to the infection status, 756 and 1303 consensus differentially expressed genes (DEGs) among the four diets were identified in “lice infection vs. pre-infection” and “co-infection vs. pre-infection” groups, respectively, that were shared between the four experimental diets. The co-infection groups (co-infection vs. pre-infection) included up-regulated genes associated with glycolysis, the interferon pathway, complement cascade activity, and heat shock protein family, while the down-regulated genes were related to antigen presentation and processing, T-cell activation, collagen formation, and extracellular matrix. Pathway enrichment analysis conducted between infected groups (lice infection vs. co-infection) resulted in several immune-related significant GO terms and pathways unique to this group, such as “autophagosome”, “cytosolic DNA-sensing pathway” and “response to type I interferons”. Understanding how experimental functional feeds can impact the host response and the trajectory of co-infections will be an essential step in identifying efficacious intervention strategies that account for the complexities of disease in open cage culture.

Keratinocytes Drive the Epithelial Hyperplasia Key to Sea Lice Resistance in Coho Salmon

“…However, our results do not provide clear support for the importance of the complement immune response to sea lice resistance. This is consistent with previous observations of both the upregulation [139,147] and downregulation [104] of complement proteins in Atlantic salmon in response to sea lice. Our results therefore support earlier suggestions that activation of the complement pathway may not be sufficient to grant sea lice immunity in Atlantic salmon [139].…”

“…Both species were reared in a Recirculating Aquaculture System at the Center for Aquaculture Technologies (PEI, Canada) in freshwater until post-smolt stage (approximately 15 g), after which fish were gradually transferred to saltwater and reared to a target weight of approximately 25 g. During the experiment, fish were kept in 135 L tanks at approximately 12 °C. Triplicate tanks of each species were treated with locally-sourced (n = 49 / fish, [147]) Lepeophtheirus salmonis Page: 24 copepodids and maintained for 60 hours and sampled every 12 hours. Untreated control fish were maintained in parallel tanks and sampled at 36 hours into the experiment.…”

Differentially expressed proteins and microbial communities of the skin regulate disease resistance to Chinese tongue sole (Cynoglossus semilaevis)

“…conducted a transcriptomic analysis of sea lice ( Lepeophtheirus salmonis ) and infectious salmon anemia virus (ISAv) co-infection of the Atlantic salmon ( Salmo salar ) skin. The study found that the up-regulated genes were associated with glycolysis, the interferon pathway, complement cascade activity, and heat shock protein family, while the down-regulated genes were related to antigen presentation and processing, T-cell activation, collagen formation, and extracellular matrix ( 15 ). Co-infection of sea lice ( Lepeophtheirus salmonis ) with formalin-killed Aeromonas salmonicida activated the pathways involved in the innate (e.g., neutrophil degranulation) and adaptive immunity (e.g., antibody formation), and endothelial cell migration ( 20 ).…”

Effects of Low-Lipid Diets on Growth, Haematology, Histology and Immune Responses of Parr-Stage Atlantic Salmon (Salmo salar)

“…Kim, Park, Kwon and Park [ 75 ] showed that the expression of chemokines and chemokine-related genes ( ccl19a.1 , cxl10 and ccl19 ) increased in the kidneys of flounder infected with VHSV. In addition, the expression levels of several pro-inflammatory chemokine genes ( ccl19 and ccl20 ) in Atlantic salmon were increased via immunostimulants (often pathogen-associated molecular patterns), and the chemokine genes ( ackr3 , ackr4 and ccr9 ) were upregulated after infectious salmon’s anaemia virus infection [ 78 ]. In the present study, the expression levels of ccl19a.1 , cxl10 , ccl19 , cxcl12a , ccl25b , ccl20a.3 , cxcl9 , ackr3b , ackr4b and ccr9 did not differ between the RTF1 and ASF groups.…”