Search Results (372)

The objective of this study was to evaluate relationships between antimicrobial use (AMU) and antimicrobial resistance (AMR) in isolates from farmed Atlantic salmon that could represent finfish pathogens in the British Columbia (BC) aquaculture industry using historical surveillance data. Antimicrobial susceptibility data were obtained for 1040 bacterial isolates from farmed Atlantic salmon submissions to the BC Animal Health Centre for 2007–2018. Antimicrobial use data were provided by the BC Ministry of Agriculture and Food from feed mill prescriptions for BC farmed Atlantic salmon for 2007–2018. Multivariable logistic regression models for all bacterial isolates with a random intercept for species were developed to determine associations with outcomes of resistance to trimethoprim-sulfadiazine (SXT), oxytetracycline (OXY), and florfenicol (FLOR). Resistance to SXT, FLOR, and/or OXY were all significantly associated with each resistance outcome in their respective models. Only the SXT resistance model was significantly associated with AMU, specifically potentiated sulfonamide use, but use was not significantly associated with AMR for any other resistance outcome. The results of this study contribute to the rapidly growing and increasingly pertinent body of literature on AMU and AMR in the unique marine aquaculture environment. Future research at the farm level linking pen-specific AMU to AMR outcomes will provide more understanding of selection pressure for AMR at the local level and provide more guidance for antimicrobial stewardship in finfish aquaculture. Full article

Marine fish are a good dietary source of important macro- and micronutrients. In addition to fresh fish, fish with varying degrees of industrial processing—frozen, marinated, smoked, canned, etc.—is used extensively in the food market. This study comprehensively characterizes the protein content, fat content, and fatty acid composition of various commercially available canned marine fish species. All canned fish muscle and cod liver were in salted brine, to eliminate the influence of other ingredients. All samples obtained from muscle had a relatively high protein content, mostly between 15 and 21 g/100 g. The fat content was highly variable, ranging from a few tenths to 15 g/100 g. Of the fatty acids, PUFAs predominated in almost all samples. The fatty acid composition of canned fish was very similar to the fatty acid composition of fresh fish. The fact that the content of highly oxylabile PUFAs practically did not differ compared to fresh fish indicates that the preservation process does not lead to significant oxidative damage to this type of product. A significant benefit of eating marine fish is the intake of highly unsaturated fatty acids EPA and DHA of the omega-3 fatty acid series. Mainly mackerel and sardines are an excellent source of these two acids. Atlantic salmon and sockeye salmon are also very good sources. As a result, consuming an average of 3 g of cod liver, 10 g of mackerel, 15 g of sardines, or 30 g of Atlantic and sockeye salmon is sufficient to ensure the recommended daily intake of EPA and DHA. Full article

Atlantic salmon populations have declined in many regions and are affected by several natural and anthropogenic factors throughout their lives. We investigated the role of environmental drivers and the effect of dam construction on the trend in catches of spawning adults of a migratory population currently at risk. For this purpose, we examined the salmon catches from 1914 to 2020 in the Minho River (NW Portugal, SW Europe), located at the southern limit of this species’ distribution. There was a decline in catches over time with an inverse and significant relationship between the trend in catches and lagged temperature. Delayed effects of this type may indicate temperature influences on survival during early life history stages. Similarly, the trend in catches decreased with the increasing number of dams. A forecast model built for the period before the construction of the first major dam in this river (before 1955), including lagged temperature, resulted in a decreasing trend in the number of catches. This demonstrates that catches would have declined due to temperature effects even without dam construction. This does not diminish the role of dams in the observed decline; rather, it reveals that temperature-driven declines would have occurred independently. Nonetheless, efficient management and conservation of this imperiled population require further detailed biological information on the number of returning spawning adults and salmons’ survival throughout their life cycle. Full article

Monitoring the freshness of Salmo salar within cold chain logistics is paramount for ensuring food safety. However, conventional physicochemical and microbiological assays are impeded by inherent limitations, including destructiveness and significant time latency, rendering them inadequate for the real-time, non-invasive inspection demands of modern industry. Here, we present a novel detection framework synergizing hyperspectral imaging (400–1000 nm) with the Transformer deep learning architecture. Through a rigorous comparative analysis of twelve preprocessing protocols and four feature wavelength selection algorithms (Lasso, Genetic Algorithm, Successive Projections Algorithm, and Random Frog), prediction models for Total Volatile Basic Nitrogen (TVB-N) and Total Viable Count (TVC) were established. Furthermore, the capacity of the Transformer to capture long-range spectral dependencies was systematically investigated. Experimental results demonstrate that the model integrating Savitzky-Golay (SG) smoothing with the Transformer yielded optimal performance across the full spectrum, achieving determination coefficients (R²) of 0.9716 and 0.9721 for the Prediction Sets of TVB-N and TVC, respectively. Following the extraction of 30 characteristic wavelengths via the Successive Projections Algorithm (SPA), the streamlined model retained exceptional predictive precision (R² ≥ 0.95) while enhancing computational efficiency by a factor of approximately six. This study validates the superiority of attention-mechanism-based deep learning algorithms in hyperspectral data analysis. These findings provide a theoretical foundation and technical underpinning for the development of cost-effective, high-efficiency portable multispectral sensors, thereby facilitating the intelligent transformation of the aquatic product supply chain. Full article

Genomic prediction has been increasingly applied in aquaculture selective breeding; however, systematic evaluations of prediction accuracy across multiple aquaculture species and analytical methods under a unified and comparable framework remain limited. In this study, we conducted a comprehensive comparative assessment of genomic prediction performance across four representative aquaculture species, including Atlantic salmon (Salmo salar), gilthead sea bream (Sparus aurata), common carp (Cyprinus carpio), and rainbow trout (Oncorhynchus mykiss), using ten genomic prediction models including GBLUP, Bayesian and machine learning methods. Prediction accuracy varied widely among species and models, ranging from 0.49 to 0.85, and was strongly associated with trait heritability. High-heritability traits consistently achieved higher prediction accuracies, with rainbow trout and common carp exhibiting the best overall performance (0.75–0.83 and 0.73–0.85, respectively), whereas Atlantic salmon and gilthead sea bream showed lower and more variable accuracies (0.49–0.61 and 0.49–0.66). No single model performed optimally across all species. Machine learning-based approaches achieved the highest prediction accuracy in specific cases but exhibited pronounced species-dependent variability, while GBLUP provided stable and well-calibrated predictions with consistently low bias. Incremental SNP feature selection further improved prediction accuracy by 2.8–4.2% in three species using only 0.54–9.64% of the available markers, whereas no improvement was observed for a low-heritability trait. These results show that genomic prediction performance is highly context-dependent and underscores the importance of jointly considering trait genetic architecture, population characteristics, model choice, and marker selection when optimizing genomic selection strategies in aquaculture breeding programs. Full article

Early detection and effective monitoring of aquatic environments are essential for detecting and mitigating potential ecological threats to aquatic organisms and for ensuring the sustainable management of freshwater ecosystems. Passive sampling is an emerging approach for environmental DNA (eDNA) collection in aquatic systems while active sampling involves controlled collection and filtration of water. This study evaluates active and passive sampling methods in a riverine system for detecting eDNA from Atlantic salmon (Salmo salar) and its lethal ectoparasite Gyrodactylus salaris. Sampling was conducted in the Sande River, Vestfold County, Norway. The loop-mediated isothermal amplification (LAMP) method was employed due to its high efficiency and specificity for amplifying target genes. The selected genetic markers were mitochondrial cytochrome B (Cyt B) DNA for S. salar and cytochrome c oxidase 1 (COX1) for G. salaris. The results indicate that host eDNA was readily detected using both sampling methods, whereas detection of G. salaris was more effective using active sampling. These findings provide valuable insight into optimizing eDNA detection protocols for both host and parasite, demonstrating specificity and sensitivity of LAMP in detecting the target organisms. This case study contributes to the development of conservation strategies aimed at preserving Atlantic salmon populations and freshwater biodiversity. Full article

The induction of triploidy, a strategy to mitigate unwanted pre-harvest sexual maturation and a genetic containment measure for escaped farmed Atlantic salmon (Salmo salar), may give rise to challenges because of the distinct environmental and dietary requirements of sterile triploid fish. Smoltification is a critical phase in the life cycle of Atlantic salmon, so knowledge about parr–smolt transformation in triploids is important for the salmon farming industry. This study covered an investigation of hepatic expression of growth hormone receptor (GHrec) and insulin-like growth factor-I (IGF-I) genes, both of which are intimately involved in the regulation of osmoregulation and growth. Additionally, hepatic presence and location of IGF-I mRNA were examined using RNAscope^®, an advanced in situ hybridization technique. Triplicate groups of juvenile diploid and triploid salmon were reared at low temperature (10 °C) and fed either a standard diet or one enriched with hydrolyzed fish proteins from the start of feeding onwards. Liver samples were collected from three fish per tank each month from October to December (2454–3044 degree-days post-start feeding), the period encompassing smoltification, and hepatic expression of IGF-I and GHrec genes was quantified by real-time PCR. The results indicated that neither ploidy nor diet significantly influenced IGF-I or GHrec gene expression, suggesting that, under our conditions, triploidy and diet did not adversely affect this molecular pathway linked to growth and osmoregulation. IGF-I gene expression exhibited significant temporal variation, correlating with the progression of smoltification, while GHrec gene expression showed a similar, albeit non-significant, trend. Triploids exhibited IGF-I and GHrec gene expression patterns comparable to diploids, and both the temporal changes and lack of difference between triploids and diploids were mirrored in the quantification of IGF-I mRNA within the liver cells. The potential applicability to a commercial aquaculture setting requires further investigation. Full article

Antimicrobial use (AMU) in finfish aquaculture production raises concerns about the link between AMU and the development of antimicrobial resistance (AMR) in bacteria found in aquatic organisms and potential transmission to humans and the environment. The objective of this study was to describe the antimicrobial susceptibilities of a historical collection of bacterial isolates from diagnostic submissions from farmed finfish in British Columbia (BC), Canada. Antimicrobial susceptibility data were obtained from the BC Ministry of Agriculture via submissions to the Animal Health Centre for 2007 to 2018 for florfenicol (FLOR), oxytetracycline (OXY), trimethoprim-sulfadiazine (SXT), and triple-sulfa compound (TRI). There were 1237 unique isolates from all finfish species (68 unique bacterial species), of which 1042 were from Atlantic salmon. For all fish species, the most common bacterial species isolated were Aeromonas salmonicida (n = 174), Aliivibrio wodanis (n = 84), and Yersinia ruckeri (n = 79). Resistance was detected to most antimicrobials tested, but levels were generally low. Resistance to FLOR was only detected in A. salmonicida. Low annual isolate numbers precluded genera-specific annual comparisons for all pathogens. Multi-drug resistance was detected, but at low levels. These results provide an important baseline for antimicrobial susceptibility data from bacterial isolates that may cause disease in finfish aquaculture in BC, Canada that will support future Canadian AMR surveillance in farmed aquaculture. Full article

Fine sediment infiltration is widely discussed as a stressor to wild salmonids’ spawning success, but its mechanisms and severity in wild salmonid redds are difficult to measure. This study examined wild Atlantic salmon (Salmo salar) redd survival using emergence traps in two small coastal streams with differing agricultural land-use intensities on Prince Edward Island, Canada. Measured environmental parameters included stream and hyporheic dissolved oxygen, water velocity, water level, redd temperature, redd substrate composition, and stream suspended solids. Wild Atlantic salmon redds were equipped with emergence traps during May to June in two study years to evaluate survival. No single environmental factor was strongly associated with the success of individual redd emergence. However, the West River exhibited approximately two-fold-higher portions of silt and clay in redd substrates. Despite this, only modest reductions in hyporheic dissolved oxygen were observed and appeared to be related to high discharge events rather than sediment accumulation. Mortality rates were highly variable across all study sites on both rivers, which may be attributed to fertilization success rather than environmental conditions, as natural mortality was at least 50%. Entombment of alevin from accumulated fine sediments was noted in several redds on the West River, suggesting this mechanism may contribute to mortality even when oxygen levels are adequate. Overall, the study highlights the resilience of salmon embryos with moderate hypoxic episodes and the challenges of linking sediment metrics to mortality in wild Atlantic salmon redds. Full article

Visible-Near-Infrared (Vis-NIR) spectroscopy, spanning approximately 400 to 2500 nm, is an innovative technology with growing relevance for diagnostics performed at the point of care (POC). This review explores the potential of Vis-NIR in veterinary medicine, highlighting its advantages over complex techniques like Raman and Fourier transform infrared spectroscopy (FTIR) by being rapid, non-invasive, reagent-free, and compatible with miniaturized, portable devices. The methodology involves directing a broadband light source, often using LEDs, toward the sample (e.g., blood, urine, faeces), collecting spectral information related to molecular vibrations, which is then analyzed using chemometric methods. Successful veterinary applications include hemogram analysis in dogs, cats, and Atlantic salmon, and quantifying blood in ovine faeces for parasite detection. Key limitations include spectral interference from strong absorbers like water and hemoglobin, and the limited penetration depth of light. However, combining Vis-NIR with Self-Learning Artificial Intelligence (SLAI) is shown to isolate and mitigate these multi-scale interferences. Vis-NIR spectroscopy serves as an important complement to centralized laboratory testing, holding significant potential to accelerate clinical decisions, minimize stress on animals during assessment, and improve diagnostic capabilities for both human and animal health, aligning with the One Health concept. Full article

This study evaluated the optimal dietary lipid level for Atlantic salmon (Salmo salar) reared in freshwater, aiming to provide foundational knowledge for the development of cost-effective and nutritionally balanced aquafeeds. Four experimental diets were formulated to contain comparable crude protein levels (47%) but graded lipid levels of 14% (L14), 16% (L16), 18% (L18), and 20% (L20), and were fed to salmon with an initial mean body weight of 241.5 ± 9.7 g during a 12-week feeding trial. Fish in the L16 group exhibited the highest weight gain (WG) and feed efficiency (FE), whereas those in the L14 group showed significantly reduced growth performance. Antioxidant analysis revealed that glutathione peroxidase (GPx) activity was lowest in the L14 group (p < 0.05), while plasma glucose concentration was minimized in the L16 group (p < 0.05). Transcriptomic profiling of liver tissue from the L14 and L16 groups identified 2117 differentially expressed genes (DEGs). Genes associated with lipid metabolism were more highly expressed in the L16 group, whereas immune- and inflammation-related genes were upregulated in the L14 group. These findings suggest that a dietary lipid level of approximately 16% is most favorable for promoting growth, metabolic stability, and overall health in freshwater-reared Atlantic salmon, thereby providing practical guidance for optimizing feed formulation and improving the economic efficiency of freshwater salmon aquaculture. Full article

Atlantic salmon (Salmo salar) populations in the Arctic River Teno (Tana) and other North Atlantic rivers have declined at the same time as pink salmon (Oncorhynchus gorbuscha) have begun to spawn extensively in these rivers in odd-numbered years. In the River Teno, especially, the number of one-sea-year Atlantic salmon ascendants has decreased. In this short review, we assess, based on current information, how the abundance of pink salmon may weaken the survival of Atlantic salmon. Our hypothesis is based on recent evidence from Atlantic salmon in the Baltic Sea showing that the high marine lipid content in the diet of Atlantic salmon post-smolts impairs their growth and survival and is manifested in low numbers of ascendants and in poor thiamine (vitamin B1) status in both juvenile and spawning Baltic salmon. The high energy density of lipids increases the need for thiamine in the metabolism, and the high content of highly unsaturated fatty acids (n–3 HUFAs), like docosahexaenoic acid (DHA, 22:6n–3), in marine fish lipids increases the rate of lipid peroxidation, which consumes thiamine as it acts as an antioxidant against lipid peroxidation. The review presents information that could be used in planning possible future research on the topic. Full article

Aeromonas salmonicida is a major pathogen in aquaculture, and its ability to form biofilms contributes significantly to antibiotic resistance and chronic infections. This study investigated the effects of four antibiotics—ampicillin, amoxicillin, oxytetracycline, and doxycycline—at various concentrations on bacterial growth, biofilm formation, and gene expression related to antibiotic resistance and quorum sensing (QS) in two subspecies: A. salmonicida subsp. masoucida (ASM) and A. salmonicida subsp. salmonicida (ASS). Bacterial isolates from Atlantic salmon were identified using 16S rRNA and vapA gene sequencing. Growth inhibition was more pronounced in ASS than ASM under high antibiotic concentrations. Conversely, sub-inhibitory concentrations (sub-MICs) enhanced biofilm formation in both subspecies, particularly in ASM. PCR results showed that tetA and tetE resistance genes were present only in ASM. qRT-PCR analysis revealed that expression of QS-related genes (ahyI and ahyR) was generally downregulated under tetracycline treatment, while litR expression varied across antibiotic conditions and strains. Some isolates showed increased litR expression alongside elevated biofilm formation, suggesting involvement of additional regulatory mechanisms. These results highlight the potential for sub-MIC antibiotic exposure to promote biofilm development and modulate gene expression, emphasizing the need for careful antibiotic use in aquaculture and providing insight into alternative pathogen control strategies. Full article

Background/Objectives: This study aimed to characterize Vibrio anguillarum strain 23FBVib0271 (VA) isolated from rainbow trout and Aeromonas salmonicida salmonicida strain 17FBASa0016 (ASS) and A. salmonicida masoucida strain 23FBAer0174 (ASM) isolated from Atlantic salmon in the Republic of Korea. Their physiological traits, pathogenicity, and antigenicity were examined, and formalin-inactivated vaccines were developed to evaluate safety and immunogenicity in Atlantic salmon (Salmo salar). Methods: Formalin-inactivated VA, ASS and ASM were administered intraperitoneally, and protective efficacy was determined after six weeks. Serum biochemical parameters (AST, ALT, ALP, glucose) and histopathology were analyzed for safety. ELISA and real-time PCR targeting IL-1β, BCL6, membrane-bound IgM, and secretory IgM were performed to assess immune responses. Results: Vaccination provided relative percent survivals of 100%, 75%, and 95% for VA, ASS and ASM, respectively, without adverse physiological or histological effects. Immunological analyses revealed strong antibody production and upregulation of immune-related genes. Conclusions: Formalin-inactivated vaccines from VA, ASS and ASM are safe and effectively induce protective humoral immunity in Atlantic salmon by promoting antigen-specific antibody responses and immune gene activation. Full article

The infectious pancreatic necrosis virus (IPNV) used to be one of the largest loss factors in Atlantic salmon farming. Since 2009, marker-assisted selection for resistance to IPN, targeting a single major quantitative trait locus (QTL), has led to a ten-fold decrease in the number of IPN outbreaks in Norway. However, some IPN-related problems remain, due to isolates of the virus which seem to bypass the resistance mechanism of the QTL. We comparatively characterized a classical isolate affected by the IPN-QTL (cIPNV) and an isolate that circumvents the QTL-based protection (rIPNV). Using both in vivo and in vitro challenges, the viral infection dynamics and host responses were evaluated by RT-qPCR and by gene ontology (GO) enrichment analysis from the RNA sequencing data of infected hepatocytes and the whole liver. Overall, cIPNV showed rapid replication with pronounced lytic cytopathology and enrichment for DNA damage, apoptosis and cell cycle disruption GO terms, while rIPNV exhibited slower accumulation of viral RNA and a transcriptional footprint consistent with pro-survival states in hepatocytes. While further research is needed to resolve the causality of QTL evasion, this work provides a first characterization of the pathogenicity of emerging QTL-insensitive IPNV isolates. Full article