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Sensitive screening of eukaryotic communities in aquaculture for research and management is limited by the availability of technologies that can detect invading pathogens in an unbiased manner. Amplicon sequencing of 18S ribosomal DNA (rDNA) provides a potential pan-diagnostic test to overcome these biases; however, this technique is limited by a swamping effect of host DNA on low abundance parasite DNA. In this study, we have adapted a host 18S rDNA blocking assay to amplify eukaryotic DNA from salmonid tissue for amplicon sequencing. We demonstrate that effective salmonid 18S rDNA blocking enables sensitive detection of parasite genera in salmonid gill swabs. Furthermore, 18S rDNA amplicon sequencing with host blocking identified enriched pathogen communities in gill swabs from Atlantic salmon suffering from severe clinical gill infections compared to those exhibiting no clinical signs of gill infection. Application of host 18S rDNA blocking in salmonid samples led to improved detection of the amoebic parasite Neoparamoeba perurans, a parasite of significant threat to the Atlantic salmon aquaculture industry. These results reveal host 18S rDNA blocking as an effective strategy to improve the profiling and detection of parasitic communities in aquaculture species. This assay can be readily adapted to any animal species for improved eukaryotic profiling across agricultural and veterinary industries., (© 2024. The Author(s).)

Epitheliocystis, an intracellular bacterial infection in the gills and skin epithelium, has been frequently reported in Atlantic salmon (Salmo salar) during freshwater production in a number of countries. This study describes the prevalence and intensity of a natural epitheliocystis infection present in the gills of two strains of Atlantic salmon reared in either a flow-through (FT) or a recirculation aquaculture system (RAS) in Ireland. Repeated sampling of gills prior to and throughout seawater transfer, histology and quantitative real-time PCR were used to determine infection prevalence and intensity. Despite no clinical gill disease, and minor histopathological changes, epitheliocystis lesions were identified in histology at all time points. Specific PCR confirmed the presence of Candidatus Clavichlamydia salmonicola in both strains and its number of copies was correlated with intensity of epitheliocystis lesions. A significant interaction between hatchery system and fish strain on the prevalence and intensity of gill epitheliocystis was found both using histological and molecular methods. Specifically, fish from FT had higher prevalence and intensity than RAS reared fish and within FT, the Irish cohort were more affected than Icelandic., (© 2022 CSIRO. Journal of Fish Diseases published by John Wiley & Sons Ltd.)

The Tasmanian salmon industry had remained relatively free of major viral diseases until the emergence of pilchard orthomyxovirus (POMV). Originally isolated from wild pilchards, POMV is of concern to the industry as it can cause high mortality in farmed salmon (Salmo salar). Field observations suggest the virus can spread from pen to pen and between farms, but evidence of passive transmission in sea water was unclear. Our aim was to establish whether direct contact between infected and naïve fish was required for transmission, and to examine viral infection dynamics. Atlantic salmon post-smolts were challenged with POMV by either direct exposure via cohabitation or indirect exposure via virus-contaminated sea water. POMV was transmissible in sea water and direct contact between fish was not required for infection. Head kidney and heart presented the highest viral loads in early stages of infection. POMV survivors presented low viral loads in most tissues, but these remained relatively high in gills. A consistent feature was the infiltration of viral-infected melanomacrophages in different tissues, suggesting an important role of these in the immune response to POMV. Understanding POMV transmission and host-pathogen interactions is key for the development of improved surveillance tools, transmission models and ultimately for disease prevention., (© 2020 John Wiley & Sons Ltd.)

Hydrogen peroxide (H 2 O 2 ) is a commonly used treatment for a range of parasitic diseases of marine finfish, including amoebic gill disease (AGD). While this treatment is partially effective at reducing parasite load, H 2 O 2 can have detrimental effects on the host under certain conditions. Treatment temperature and dose concentration are two factors that are known to influence the toxicity of H 2 O 2 ; however, their impact on the outcome of AGD treatment remains unclear. Here, we investigated the effects of treatment temperature (8, 12 or 16°C) and dose concentration (750, 1,000, 1,250 mg/L) on the efficacy of H 2 O 2 to treat AGD. We demonstrated that a 20-min bath treatment of H 2 O 2 at all doses reduced both parasite load and gross gill score significantly. Parasite load and gross gill score were lowest in the 1,000 mg/L treatment performed at 12°C. At the high dose and temperature combinations, H 2 O 2 caused moderate gill damage and a significant increase in the plasma concentration of electrolytes (sodium, chloride and potassium). Taken together, our study demonstrates that higher H 2 O 2 treatment temperatures can adversely affect the host and do not improve the effectiveness of the treatment., (© 2019 John Wiley & Sons Ltd.)

Freshwater bathing for 2–3 h is the main treatment to control amoebic gill disease of marine-farmed Atlantic salmon. Recent in vitro studies have demonstrated that amoebae (Neoparamoeba perurans) detach when exposed to freshwater and that some eventually reattach to culture plates when returned to seawater. Here, we evaluated the potential for gill-detached N. perurans to survive a commercially relevant treatment and infect AGD-naïve fish and whether holding used bathwater for up to 6 h post treatment would lower infectivity. AGD-affected fish were bathed in freshwater for 2 h. Naïve salmon were exposed to aliquots of the used bathwater after 2, 4, 6 and 8 h. The inoculation was performed at 30 ppt for 2 h, followed by gradual dilution with seawater. Sampling at 20 days post inoculation (dpi) and 40 dpi confirmed rapid AGD development in fish inoculated in 2 h used bathwater, but a slower AGD development following exposure to 4 h bathwater. AGD signs were variable and reduced following longer bathwater holding times. These results suggest that viable amoebae are likely returned to seawater following commercial freshwater treatments, but that the risk of infection can be reduced by retention of bathwater before release. [ABSTRACT FROM AUTHOR]

The gill mucosal microbiome of Atlantic salmon has a significant impact on mucosal health and physiology under homeostatic conditions, but the microbial community may itself be influenced by host genetics, the culture system and seawater transfer. In this study, the impact of two commercial strains of Atlantic salmon, reared in two parallel hatchery systems (flow-through -FT and recirculation -RAS) on the gill microbiome was investigated. Samples of gill mucosal microbiome, tank biofilm and water were collected from the fish cohorts at the hatcheries and following seawater transfer. Though the gill microbiome of fish from the two commercially equivalent FT and RAS hatcheries had similar beta and alpha diversity, the alpha diversity indicators of bacterial communities of gills significantly increased after seawater input. Ultimately, no effect of the genetic strain on the gill microbiome was detected. Our results showed that under commercially equivalent FT or RAS hatchery systems with a common water source, two strains of Atlantic salmon had comparable gill microbiomes. • Gill microbiome of two commercial genetic fish strains was compared • Atlantic salmon reared in RAS and FT systems with common water source had comparable gill microbiome • Seawater transfer was a major factor influencing gill microbiome diversity [ABSTRACT FROM AUTHOR]