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Vitamin D is a crucial micronutrient for vertebrate health that affects musculoskeletal function and likely modulates immune responses in tissues such as the skin. Infectious diseases are a critical concern in Atlantic salmon aquaculture due to the potential economic impact of stock losses, risks to fish welfare, and environmental sustainability. Since the skin is the first line of immunological defence, its ability to mediate host-pathogen interactions may be influenced by dietary vitamin D. This study examined the transcriptomic response of salmon skin after six months of dietary vitamin D supplementation, with an emphasis on immune-related gene expression. A total of 151 differentially expressed genes were identified, 27 of which are linked to inflammation, antigen presentation, and both innate and adaptive immunity. These results indicate that vitamin D could modulate cutaneous immune responses by reducing inflammation and enhancing innate defences, potentially improving resistance to many skin-associated salmon pathogens.

The salmon louse ( Lepeophtheirus salmonis ) poses a major challenge for Atlantic salmon ( Salmo salar ) aquaculture in the northern hemisphere. These ectoparasites feed on the blood, tissue, and mucus of their fish host, causing skin damage, increasing susceptibility to secondary infections, and, in severe cases, leading to fish mortality. The economic impact on aquaculture is substantial due to treatment and management costs. Effective management strategies rely on a comprehensive understanding of infection dynamics. To investigate these dynamics, we analysed a 30-year dataset on sea lice abundance from Atlantic salmon farms in Ireland, collected by the Marine Institute through the National Sea Lice Monitoring Programme. Using generalised linear mixed-effects models, we detected temporal fluctuations, with an overall decline in lice abundance. Seasonal variation was evident, with the lowest abundance in spring and the highest in autumn. Sea lice abundance was influenced by farm exposure, represented by bay mouth width, bay length, number of active farms per bay and dissolved oxygen levels. By identifying key factors driving infection patterns, this study provides valuable insights for predicting high-risk periods and optimising management strategies. These findings will inform strategies for salmon lice control, contributing to improved fish health and sustainability in aquaculture.

Over recent decades jellyfish have caused fish kill events and recurrent gill problems in marine-farmed salmonids. Common jellyfish (Aurelia spp.) are among the most cosmopolitan jellyfish species in the oceans, with populations increasing in many coastal areas. The negative interaction between jellyfish and fish in aquaculture remains a poorly studied area of science. Thus, a recent fish mortality event in Ireland, involving Aurelia aurita, spurred an investigation into the effects of this jellyfish on marine-farmed salmon. To address the in vivo impact of the common jellyfish (A. aurita) on salmonids, we exposed Atlantic salmon (Salmo salar) smolts to macerated A. aurita for 10 hrs under experimental challenge. Gill tissues of control and experimental treatment groups were scored with a system that rated the damage between 0 and 21 using a range of primary and secondary parameters. Our results revealed that A. aurita rapidly and extensively damaged the gills of S. salar, with the pathogenesis of the disorder progressing even after the jellyfish were removed. After only 2 hrs of exposure, significant multi-focal damage to gill tissues was apparent. The nature and extent of the damage increased up to 48 hrs from the start of the challenge. Although the gills remained extensively damaged at 3 wks from the start of the challenge trial, shortening of the gill lamellae and organisation of the cells indicated an attempt to repair the damage suffered. Our findings clearly demonstrate that A. aurita can cause severe gill problems in marine-farmed fish. With aquaculture predicted to expand worldwide and evidence suggesting that jellyfish populations are increasing in some areas, this threat to aquaculture is of rising concern as significant losses due to jellyfish could be expected to increase in the future.

Bacteria in the Shigella genus remain a major cause of dysentery in sub-Saharan Africa, and annually cause an estimated 600,000 deaths worldwide. Being spread by contaminated food and water, this study highlights how wild caught food, in the form of freshwater catfish, can act as vectors for Shigella flexneri in Southern Kenya. A metatranscriptomic approach was used to identify the presence of Shigella flexneri in the catfish which had been caught for consumption from the Galana river. The use of nanopore sequencing was shown to be a simple and effective method to highlight the presence of Shigella flexneri and could represent a potential new tool in the detection and prevention of this deadly pathogen. Rather than the presence/absence results of more traditional testing methods, the use of metatranscriptomics highlighted how primarily one SOS response gene was being transcribed, suggesting the bacteria may be dormant in the catfish. Additionally, COI sequencing of the vector catfish revealed they likely represent a cryptic species. Morphological assignment suggested the fish were widehead catfish Clarotes laticeps , which range across Africa, but the COI sequences from the Kenyan fish are distinctly different from C. laticeps sequenced in West Africa.

Water quality and the management of nitrogenous compounds are of key importance within aquaculture. In this paper, automated and portable analysers for in situ analysis of nitrite and nitrate in water were deployed in freshwater and saline recirculating aquaculture systems (RAS). The analysers were based upon ion chromatography (IC) and employed a NaCl eluent with an anion exchange guard column for low backpressure anion separation, in combination with selective 235 nm ultra-violet light-emitting diode (UV-LED) based absorbance detection. The analysers were monitored and delivered real-time concentration data using a cellular internet of things (IoT) module and cloud-based dashboard. Overall performance and chromatographic repeatability were tested across various temperature profiles and 500 sequential runs within the laboratory. Deployments in freshwater and saline RAS, with concentrations ranging between 0.1–3.6 mg L −1 nitrite and 0.6–392 mg L −1 nitrate, were successful and the analytical performance was comparable to that of accredited lab-based instrumentation.

Analysis of pathogen genome variation is essential for informing disease management and control measures in farmed animals. For farmed fish, the standard approach is to use PCR and Sanger sequencing to study partial regions of pathogen genomes, with second and third-generation sequencing tools yet to be widely applied. Here we demonstrate rapid and accurate sequencing of two disease-causing viruses affecting global salmonid aquaculture, salmonid alphavirus (SAV) and infectious salmon anaemia virus (ISAV), using third-generation nanopore sequencing on the MinION platform (Oxford Nanopore Technologies). Our approach complements PCR from infected material with MinION sequencing to recover genomic information that matches near perfectly to Sanger-verified references. We use this method to present the first SAV subtype-6 genome, which branches as the sister to all other SAV lineages in a genome-wide phylogenetic reconstruction. MinION sequencing offers an effective strategy for fast, genome-wide analysis of fish viruses, with major potential applications for diagnostics and robust investigations into the origins and spread of disease outbreaks.

Cardiomyopathy syndrome (CMS) is a severe cardiac disease of Atlantic salmon caused by the piscine myocarditis virus (PMCV), which was first reported in Ireland in 2012. In this paper, we describe the use of data-driven network modeling as a framework to evaluate the transmission of PMCV in the Irish farmed Atlantic salmon population and the impact of different mitigation measures. Input data included live fish movement data from 2009 to 2017, population dynamics events and the spatial location of the farms. With these inputs, we fitted a network-based stochastic infection spread model. After assumed initial introduction of the agent in 2009, our results indicate that it took 5 years to reach a between-farm prevalence of 100% in late 2014, with older fish being most affected. Local spread accounted for only a small proportion of new infections, being more important for sustained infection in a given area. Spread via movement of subclinically infected fish was most important for explaining the observed countrywide spread of the agent. Of the targeted intervention strategies evaluated, the most effective were those that target those fish farms in Ireland that can be considered the most connected, based on the number of farm-to-farm linkages in a specific time period through outward fish movements. The application of these interventions in a proactive way (before the first reported outbreak of the disease in 2012), assuming an active testing of fish consignments to and from the top 8 ranked farms in terms of outward fish movement, would have yielded the most protection for the Irish salmon farming industry. Using this approach, the between-farm PMCV prevalence never exceeded 20% throughout the simulation time (as opposed to the simulated 100% when no interventions are applied). We argue that the Irish salmon farming industry would benefit from this approach in the future, as it would help in early detection and prevention of the spread of viral agents currently exotic to the country.

Amoebic gill disease (AGD) caused by Neoparamoeba perurans, has emerged in Europe as a significant problem for the Atlantic salmon farming industry. Gross gill score is the most widely used and practical method for determining AGD severity on farms and informing management decisions on disease mitigation strategies. As molecular diagnosis of AGD remains a high priority for much of the international salmon farming industry, there is a need to evaluate the suitability of currently available molecular assays in conjunction with the most appropriate non-destructive sampling methodology. The aims of this study were to assess a non-destructive sampling methodology (gill swabs) and to compare a range of currently available real-time PCR assays for the detection of N. perurans. Furthermore a comparison of the non-destructive molecular diagnostics with traditional screening methods of gill scoring and histopathology was also undertaken. The study found that all molecular protocols assessed performed well in cases of clinical AGD with high gill scores. A TaqMan based assay (protocol 1) was the optimal assay based on a range of parameters including % positive samples from a field trial performed on fish with gill scores ranging from 0 to 5. A higher proportion of gill swab samples tested positive by all protocols than gill filament biopsies and there was a strong correlation between gill swabs tested by protocol 1 and gross gill score and histology scores. Screening for N. perurans using protocol 1 in conjunction with non-destructive gill swab samples was shown to give the best results.

Amoebic gill disease (AGD) is the primary health concern for Atlantic salmon Salmo salar farmed in Tasmania, Australia. Neoparamoeba perurans is the aetiological agent of AGD; however, a diversity of other amoebae colonise the gills, and their role in AGD is unknown. Previous studies which document these accompanying amoebae on AGD-affected farmed Atlantic salmon relied on culture-based techniques which do not accurately determine the prevalence and abundance of these species nor whether they correlate with AGD pathology. Drawing on our previous culture-based study, here we develop and apply 5 new Taqman quantitative PCR (qPCR) assays to profile the prevalence of multiple amoeba species on the gills of AGD-affected Atlantic salmon held at 2 Tasmanian farm sites over a 1 yr period. The prevalence and abundance of N. perurans was also assessed using a previously established qPCR method. N. perurans was the dominant species, and its abundance positively correlated with the progression of gross gill pathology. Only a small number of sporadic detections of Pseudoparamoeba and Vannellida species were observed. Nolandella spp. was the notable exception, as it was the most prevalent amoeba (92%) at 1 site at 1 sample time, during which no N. perurans were detected on gills but low levels of gross gill pathology were observed. N. perurans is the predominant species and primary pathogen of AGD; however, there were instances when they were not detected on diseased gills and Nolandella spp. were highly prevalent. The significance of Nolandella spp. in relation to AGD is not yet understood.

Sparc (osteonectin) is a multifunctional matricellular glycoprotein expressed by many differentiated cells. Members of this family mediate cell-matrix interactions rather than acting as structural components of the extracellular matrix (ECM); therefore, they can influence many remodelling events, including haematopoiesis. We have investigated the role of sparc in embryonic haematopoiesis using a morpholino antisense oligonucleotide-based knockdown approach. Knockdown of sparc function resulted in specific erythroid progenitor cell differentiation defects that were highlighted by changes in gene expression and morphology, which could be rescued by injection of sparc mRNA. Furthermore, a comparison of blood phenotypes of sparc and fgfs knockdowns with similar defects and the sparc rescue of the fgf21 blood phenotype places sparc downstream of fgf21 in the genetic network regulating haematopoiesis in zebrafish. These results establish a role for an ECM protein (Sparc) as an important regulator of embryonic haematopoiesis during early development in zebrafish.