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The sustainability of the salmon farming industry is being challenged by increased mortality rates. Scotland's open-source salmon production data provides the possibility of developing an industry-wide mortality monitoring model, valuable for identifying and addressing unexpected increases in mortality without needing data sharing agreements across different companies. This study aimed to utilize these data to develop a hierarchical dynamic linear model (DLM) for monitoring monthly mortality of maricultured Atlantic salmon in Scotland. We evaluated whether considering the hierarchical structure present in the data (country, region, and site) would improve mortality predictions when compared to the production cycle level DLMs developed in a previous study. Our findings demonstrated that the hierarchical DLM outperformed the production cycle level DLMs, confirming the value of this more complex modelling approach. Nevertheless, the hierarchical model, like the production cycle level DLMs, exhibited some uncertainty in the mortality predictions. When mortality is higher than expected, site level warnings are generated, which can encourage producers and inspectors to further investigate the cause. Between 2015 and 2020, approximately 25% of the production cycles and 50% of the sites encountered at least one warning, with most warnings happening in the summer and autumn months. Additionally, the hierarchical model enabled monitoring mortality at multiple levels. This information is useful for various stakeholders as part of a monitoring system, offering insights into mortality trends at national, regional, and sites levels that may benefit from strategic resource management. Recommendations for model improvements include utilizing shorter data aggregation periods, such as weekly, which are not currently available as open-source data. [ABSTRACT FROM AUTHOR]

Introduction: Piscirickettsia salmonis, the causative agent of Piscirickettsiosis, poses a significant threat to the Chilean aquaculture industry, resulting in substantial economic losses annually. The pathogen, first identified as specie in 1992, this pathogen was divided into two genogroups: LF-89 and EM-90, associated with different phenotypic mortality and pathogenicity. Traditional genotyping methods, such as multiplex PCR, are effective but limited by their cost, equipment requirements, and the need for specialized expertise. Methods: This study validates Loop-mediated Isothermal Amplification (LAMP) as a rapid and specific alternative for diagnosing P. salmonis infections. We developed the first qPCR and LAMP assay targeting the species-conserved tonB receptor gene (tonB-r, WP_016210144.1) for the specific species-level identification of P. salmonis. Additionally, we designed two genotyping LAMP assays to differentiate between the LF-89 and EM-90 genogroups, utilizing the unique coding sequences Nitronate monooxygenase (WP_144420689.1) for LF-89 and Acid phosphatase (WP_016210154.1) for EM-90. Results: The LAMP assays demonstrated sensitivity and specificity comparable to real-time PCR, with additional benefits including rapid results, lower costs, and simplified operation, making them particularly suitable for field use. Specificity was confirmed by testing against other salmonid pathogens, such as Renibacterium salmoninarum, Vibrio ordalii, Flavobacterium psychrophilum, Tenacibaculum maritimum, and Aeromonas salmonicida, with no cross-reactivity observed. Discussion: The visual detection method and precise differentiation between genogroups underscore LAMP's potential as a robust diagnostic tool for aquaculture. This advancement in the specie detection (qPCR and LAMP) and genotyping of P. salmonis represents a significant step forward in disease management within the aquaculture industry. The implementation of LAMP promises enhanced disease surveillance, early detection, and improved management strategies, ultimately benefiting the salmonid aquaculture sector. [ABSTRACT FROM AUTHOR]

Introduction: With the continuous growth of Atlantic salmon (Salmo salar L.) aquaculture, appropriate management of nutrient-rich waste streams from both land- and sea-based production has become increasingly important. Following a circular approach, nutrients contained in aquaculture sludge can be utilized for biomass production of the polychaete Hediste diversicolor. While the potential for upcycling nutrients has been established previously, this study aimed to assess nutrient flows in H. diversicolor fed aquaculture sludge as understanding these will be crucial for optimizing future large-scale production of this species. Materials and methods: We investigated the effect of low and high feed supply of smolt sludge on the nutrient flows of carbon (C), nitrogen (N), and phosphorus (P) in H. diversicolor on an individual level. Hereby we assessed ingestion, defecation, excretion, respiration, and uptake for growth. Results and discussion: Nutrient flows differed between the nutrients C, N, and P in the high feed supply group where C uptake for growth was significantly higher than N and P uptake, and N uptake was significantly higher than P uptake. In contrast, no significant differences were observed in the low feed supply group. In the high feed supply group, most of the ingested C, N, and P by H. diversicolor was allocated to uptake for growth (76% C, 83% N, 85% P) with smaller proportions allocated to defecation (7% C, 7% N, 11% P) and respiration/ excretion (18% C, 9% N, 5% P). The results from the low feed supply group suggest insufficient nutrient supply as most ingested C was allocated to respiration (84%), while most N was expended on uptake for growth (45%), and ingested P was either taken up for growth (58%) or spent on defecation (34%). Overall, nutrient uptake reflected the smolt sludge composition rather than nutrient requirements for H. diversicolor, which may be a short-term effect and needs to be investigated further. The flow of nutrients was strongly affected by feed supply, as ingestion, defecation, excretion, and uptake for growth were significantly higher in the high feed supply group than in the low feed supply group. [ABSTRACT FROM AUTHOR]

Brewer's spent yeast (BSY), derived from Saccharomyces cerevisiae used in beer production, is a valuable protein source for aquafeeds. Estimations of apparent digestibility coefficients (ADC) for nutrients in BSY are crucial for its inclusion in aquafeeds. ADC estimations for Saccharomyces cerevisiae protein in rainbow are hardly comparable from a methodological point of view, whereas the ADC estimations for BSY protein in Atlantic salmon are only based on stripped feces, which are known to produce underestimations. Therefore, new determinations of ADC of BSY nutrients are necessary for the inclusion of this ingredient in practical diets for salmonids. This study is focused on determining unbiased ADC values for protein and energy from BSY in juvenile Salmo salar. To reduce systematic biases, fecal samples were collected using stripping and decantation methods, which are known to produce under-and overestimations, respectively. 780 fish (25.16± 4.88g) were stocked in six tanks. A reference diet (50% protein, 20% lipid, 1% Cr2O3) was provided to three tanks, and a test diet (70,30 reference diet to BSY) to the other three. ADC for BSY protein was 84.70± 1.04% (decantation) and 70.50± 4.03% (stripping). For gross energy, stripped feces yielded an ADC of 52.04± 5.30%, while decantation resulted in 63.80± 1.17%. Thus, ADC estimates were taken as the average of the stripping-value and the decantation-value, resulting in 77.6% for BSY crude protein, which is appreciably higher than previously measured values in S. salar fed undisrupted S. cerevisiae, and in 57.9% for gross energy. [ABSTRACT FROM AUTHOR]

In this study, we explored the effects of chronic stress on lumpfish (Cyclopterus lumpus) physiological, immune response, health, and plasma free amino acids. 3 groups of lumpfish were exposed to 1-minute air exposure. 1 group was exposed to stress once per week, a second group exposed 2 times per week, and a third group exposed 4 times per week. The present study revealed significant alterations in immunity and increased nutritional demands, particularly the branched chain amino acids and lysine. Cortisol levels fluctuated, with significantly higher levels halfway through the experiment on the groups that were stressed more often. Though, by the end of the experiment, there were no significant differences in cortisol levels between groups. Regardless of stress exposure, cataract developed in virtually all sampled fish, pointing toward a potential dietary imbalance. A transient immunomodulation of stress was visible. While in early stages stress had an immune enhancing effect, as seen by the increase in plasma nitric oxide and peroxidase in the group most frequently exposed to stress, these differences were not apparent by the end of the experiment. Additionally, the worst health condition was found in this group. Our results underscore the complex interplay between stress, immunity and nutrition, highlighting the need for tailored dietary strategies and improved rearing practices. [ABSTRACT FROM AUTHOR]

In recent years, the salmon farming industry has grown significantly worldwide, and in the Faroe Islands, it has become a major industry with an annual production of over 94,000 tonnes, yielding 24% of the GDP. According to environmental regulations, the ocean floor is monitored during every production cycle at all farming sites, involving macrofaunal, sensory, and chemical analyses. However, the impact of farming activity on microorganisms in the Faroe Islands remains unknown. This study aimed to assess the impact of Atlantic salmon farming on benthic microbial communities, giving a better understanding of the effects on the foundation of the benthic food web and to assess if these are more prone to environmental impact than traditional macrofaunal biomonitoring. Sediment cores were sampled along a transect from directly below the salmon cages to a background reference site. The sampling occurred prior to the release of salmon into the cages ('before stocking') and immediately before the salmon were harvested ('peak biomass'). The 16S rRNA (V4-V5) gene was sequenced on an Illumina MiSeq from our sediment samples at the surface, 3 cm, and 10 cm depth. Significant shifts in microbial community composition were observed between 'before stocking' and 'peak biomass', as well as between different depth layers. Microbial diversity increased with increasing distance from the cages and was at its highest 'before stocking', indicating a significant impact of the salmon farming on the microbial community structure. In contrast to the regularly executed environmental monitoring, the results from this study showed an impact on the sediments by the salmon farming, underlining the powerful alternative of DNA-metabarcoding when biomonitoring an aquaculture area. [ABSTRACT FROM AUTHOR]

Particulate calcium oxide (CaO) has been successfully used for the control of sea urchin and starfish populations. Recent studies have proven its efficacy in killing planktonic copepods, making it a promising and cheap option for salmon louse control in the Atlantic salmon (Salmo salar) farming industry. Additionally, preliminary laboratory tests demonstrated that exposure to 0.2 g/L-0.6 g/L of fine CaO particles induced significant mortality of salmon louse (Lepeophtheirus salmonis) in the planktonic stages. The present study investigated the effects of water treatment with fine CaO particles [0.2 g/L or 127.4 g/m²; 0.1mm-0.3 mm], conducted twice a week for three consecutive weeks at 5℃ and 12℃ on Atlantic salmon post-smolt in a flow-through system. The study compared mortality rates and histopathology of skin, eyes, gills, and intestines between treated and untreated control salmon. The results indicated that CaO exposure did not induce fish mortality or histopathological damages in the skin, eyes, or intestines. Although there were no significant effects of CaO exposure on gill inflammation or hyperplasia, the exposure did increase the occurrence of gill vascular injuries and necrosis in small portions of the tissue (< 10% of the respiratory gill tissue in most of the samples) by 60% and 35%, respectively. The effect was not modulated by temperature or time. The results indicate that the CaO treatment protocol used in this study is not lethal to Atlantic salmon and is safe for most analyzed tissues. Nonetheless, the induction of vascular damage and necrosis in the gill, albeit in small tissue portions, emphasizes the need for further research. It is crucial to develop a protocol that avoids such lesions, ensuring the secure application of CaO as an antiparasitic treatment in salmon aquaculture. [ABSTRACT FROM AUTHOR]

Introduction: Hypoxia is defined as a critically low-oxygen condition of water, which, if prolonged, can be harmful to fish and many other aquatic species. In the context of ocean salmon fish farming, early detection of hypoxia events is critical for farm managers to mitigate these events to reduce fish stress, however in complex natural systems accurate forecasting tools are limited. The goal of this research is to use a machine learning approach to forecast oxygen concentration and predict hypoxia events in marine net-pen salmon farms. Methods: The developed model is based on gradient boosting and works in two stages. First, we apply auto-regression to build a forecasting model that predicts oxygen concentration levels within a cage. We take a global forecasting approach by building a model using the historical data provided by sensors at several marine fish farms located in eastern Canada. Then, the forecasts are transformed into binary probabilities that indicate the likelihood of a low-oxygen event. We leverage the cumulative distribution function to compute these probabilities. Results and discussion: We tested our model in a case study that included several cages across 14 fish farms. The experiments suggest that the model can detect future hypoxic events with a commercially acceptable false alarm rate. The resulting probabilistic predictions and oxygen concentration forecasts can help salmon farmers to prioritize resources, and reduce harm to crops. [ABSTRACT FROM AUTHOR]

Infectious salmon anemia (ISA) is an infectious disease primarily affecting farmed Atlantic salmon, Salmo salar, which is caused by the ISA virus (ISAV). ISAV belongs to the Orthomyxoviridae family. The disease is a serious condition resulting in reduced fish welfare and high mortality. In this study, we designed an amplicon-based sequencing protocol for whole genome sequencing of ISAV. The method consists of 80 ISAV-specific primers that cover 92% of the virus genome and was designed to be used on an Illumina MiSeq platform. The sequencing accuracy was investigated by comparing sequences with previously published Sanger sequences. The sequences obtained were nearly identical to those obtained by Sanger sequencing, thus demonstrating that sequences produced by this amplicon sequencing protocol had an acceptable accuracy. The amplicon-based sequencingmethod was used to obtain the whole genome sequence of 12 different ISAV isolates froma small local epidemic in the northern part of Norway. Analysis of the whole genome sequences revealed that segment reassortment took place between some of the isolates and could identify which segments that had been reassorted. [ABSTRACT FROM AUTHOR]

This research article describes Chile's climate change adaptation policies and plans for marine aquaculture in Chile, with a focus on the nationally important salmon farming industry, and assesses whether they have adequately addressed legal barriers to adaptation and the need for legal transformation. The article first outlines Chile's climate change law, policies, and institutional framework, as reflected in the 2022 Framework Act on Climate Change, the 2020 updated Nationally Determined Contribution, the 2022 Strengthening of the Nationally Determined Contribution, and the 2022 Long-Term Climate Strategy. The article highlights the special attention given to the ocean-climate nexus in both international and national policy agendas. It then summarizes and assesses the adaptation policies and plans for the aquaculture sector. Three main shortcomings are identified: the lack of implementation of committed activities, the lack of a strategic vision for the role of aquaculture in a changing climate and oceans, and the lack of attention to the limits of adaptation resulting from existing regulatory frameworks. The article then strengthens this assessment with a legal analysis of the adaptive capacity of aquaculture planning and leasing frameworks. This assessment concludes that mainstreaming climate change into existing planning instruments is an ineffective adaptation measure due to the fragmented, rigid, and inefficient legal framework for the planning of aquaculture and other uses of the coastal zone. In turn, the leasing system is too rigid to allow for effective adaptation. Various mechanisms to introduce flexibility are suggested. The article concludes by highlighting an unprecedented window of opportunity to advance strategic, coherent, long-term, and transformative adaptation, resulting from concurrent initiatives to reform or update aquaculture law, policy, and adaptation planning and the principled approach to climate action embedded in the Framework Act on Climate Change. [ABSTRACT FROM AUTHOR]

Nano compounds, especially metal-organic frameworks (MOFs), have significant properties. Among the most important properties of these compounds, which depend on their specific surface area and porosity, are biological properties, such as anticancer and antibacterial properties. In this study, a new titanium/BTB metal-organic framework (Ti/BTB-MOF) was synthesized by using titanium nitrate and 1,3,5-Tris(4-carboxyphenyl)benzene (BTB) under microwave radiation. The structure of the synthesized Ti/BTB-MOF was characterized and confirmed using X-ray diffraction (XRD) patterns, X-ray photoelectron spectroscopy (XPS) analysis, Fourier transform infrared (FT-IR) spectra, energy- dispersive X-ray (EDAX) analysis mapping, scanning electron microscope (SEM) images, thermogravimetric analysis (TGA) curves, and Brunauer-Emmett-Teller (BET) analysis. The in vitro anticancer properties of Ti/BTB-MOF were evaluated using the MTT method against MG-63/bone cancer cells and A-431/skin cancer cells. The in vitro antibacterial activity was tested using the Clinical and Laboratory Standards Institute (CLSI) guidelines. In the anticancer activity, IC50 (half-maximal inhibitory concentration) values of 152 μg/mL and 201 μg/mL for MG-63/bone cancer cells and A-431/skin cancer cells, respectively, were observed. In the antibacterial activity, minimum inhibitory concentrations (MICs) of 2-64 μg/mL were observed against studied pathogenic strains. The antimicrobial activity of Ti/ BTB-MOF was higher than that of penicillin and gentamicin. Therefore, the synthesized Ti/BTB-MOF could be introduced as a suitable bioactive candidate. [ABSTRACT FROM AUTHOR]

Introduction: Little is known about the proteomic changes at the portals of entry in rainbow trout after infection with the myxozoan parasites, Myxobolus cerebralis, and Tetracapsuloides bryosalmonae. Whirling disease (WD) is a severe disease of salmonids, caused by the myxosporean M. cerebralis, while, proliferative kidney disease (PKD) is caused by T. bryosalmonae, which instead belongs to the class Malacosporea. Climate change is providing more suitable conditions for myxozoan parasites lifecycle, posing a high risk to salmonid aquaculture and contributing to the decline of wild trout populations in North America and Europe. Therefore, the aim of this study was to provide the first proteomic profiles of the host in the search for evasion strategies during single and coinfection with M. cerebralis and T. bryosalmonae. Methods: One group of fish was initially infected with M. cerebralis and another group with T. bryosalmonae. After 30 days, half of the fish in each group were co-infected with the other parasite. Using a quantitative proteomic approach, we investigated proteomic changes in the caudal fins and gills of rainbow trout before and after co-infection. Results: In the caudal fins, 16 proteins were differentially regulated post exposure to M. cerebralis, whereas 27 proteins were differentially modulated in the gills of the infected rainbow trout post exposure to T. bryosalmonae. After co-infection, 4 proteins involved in parasite recognition and the regulation of host immune responses were differentially modulated between the groups in the caudal fin. In the gills, 11 proteins involved in parasite recognition and host immunity, including 4 myxozoan proteins predicted to be virulence factors, were differentially modulated. Discussion: The results of this study increase our knowledge on rainbow trout co-infections by myxozoan parasites and rainbow trout immune responses against myxozoans at the portals of entry, supporting a better understanding of these host-parasite interactions. [ABSTRACT FROM AUTHOR]

This article provides an overview of the Norwegian feed system for farmed Atlantic salmon, focusing on its sustainability and robustness. The authors use the Food Systems Approach and gather stakeholder inputs to assess the system. The text discusses the perspectives of feed and animal producers in the aquaculture sector, relevant regulations, and environmental and socio-economic drivers. It also highlights the importance of reducing phosphorus and nitrogen emissions from aquaculture and the vulnerability of the feed system to global conflicts and events. The document concludes by emphasizing the need for a thorough understanding of the feed system and its potential impact on the sustainability of the aquaculture industry. [Extracted from the article]

Introduction: Ocean equity is a key aim of blue economy frameworks globally and is a pillar of the international High Level Panel for A Sustainable Ocean Economy. However, the Panel offers only a general definition of ocean equity, with limited guidance for countries. Canada, as a party to the High Level Panel's blue economy agenda, is developing its own blue economy strategy, seeking to reshape its ocean-based industries and advocate for new ones. How equity will be incorporated across scales is not yet known but has implications for how countries like Canada will develop their ocean-based industries. This raises important questions, including what are Canada's equity commitments in relation to its blue economy and how will they be met? Currently, the industries identified in Canada's emerging blue economy narratives are governed through both federal and provincial legislation and policies. These will shape how equity is implemented at different scales. Methods: In this paper, we examine how the term equity is defined in relevant federal and provincial legislation and look to how understandings of equity found in critical feminist, environmental justice, and climate justice scholarship could inform policy and its implementation within Canada's blue economy. We focus on two industries that are important for Canada's blue economy: offshore oil and marine salmon aquaculture in the Canadian province of Newfoundland and Labrador. We investigate how existing legislation and policy shapes the characterization, incorporation, and implementation of equity in these industries. Results and discussion: Our analysis highlights how a cohesive approach to ocean equity across the scales of legislation and policy is needed to ensure more robust engagement with social and environmental equity issues in blue economy discourse and implementation. [ABSTRACT FROM AUTHOR]

In this study, we explored the effects of chronic stress on lumpfish (Cyclopterus lumpus) physiological, immune response, health, and plasma free amino acids. 3 groups of lumpfish were exposed to 1-minute air exposure. 1 group was exposed to stress once per week, a second group exposed 2 times per week, and a third group exposed 4 times per week. The present study revealed significant alterations in immunity and increased nutritional demands, particularly the branched chain amino acids and lysine. Cortisol levels fluctuated, with significantly higher levels halfway through the experiment on the groups that were stressed more often. Though, by the end of the experiment, there were no significant differences in cortisol levels between groups. Regardless of stress exposure, cataract developed in virtually all sampled fish, pointing toward a potential dietary imbalance. A transient immunomodulation of stress was visible. While in early stages stress had an immune enhancing effect, as seen by the increase in plasma nitric oxide and peroxidase in the group most frequently exposed to stress, these differences were not apparent by the end of the experiment. Additionally, the worst health condition was found in this group. Our results underscore the complex interplay between stress, immunity and nutrition, highlighting the need for tailored dietary strategies and improved rearing practices.

In recent years, the salmon farming industry has grown significantly worldwide, and in the Faroe Islands, it has become a major industry with an annual production of over 94,000 tonnes, yielding 24% of the GDP. According to environmental regulations, the ocean floor is monitored during every production cycle at all farming sites, involving macrofaunal, sensory, and chemical analyses. However, the impact of farming activity on microorganisms in the Faroe Islands remains unknown. This study aimed to assess the impact of Atlantic salmon farming on benthic microbial communities, giving a better understanding of the effects on the foundation of the benthic food web and to assess if these are more prone to environmental impact than traditional macrofaunal biomonitoring. Sediment cores were sampled along a transect from directly below the salmon cages to a background reference site. The sampling occurred prior to the release of salmon into the cages (‘before stocking’) and immediately before the salmon were harvested (‘peak biomass’). The 16S rRNA (V4-V5) gene was sequenced on an Illumina MiSeq from our sediment samples at the surface, 3 cm, and 10 cm depth. Significant shifts in microbial community composition were observed between ‘before stocking’ and ‘peak biomass’, as well as between different depth layers. Microbial diversity increased with increasing distance from the cages and was at its highest ‘before stocking’, indicating a significant impact of the salmon farming on the microbial community structure. In contrast to the regularly executed environmental monitoring, the results from this study showed an impact on the sediments by the salmon farming, underlining the powerful alternative of DNA-metabarcoding when biomonitoring an aquaculture area.

Ballan wrasse (Labrus bergylta) are commonly used as cleaner fish in salmon farms as a biological treatment to mitigate sea lice infestation. Improved welfare for cleaner fish both during production of these fish and when in sea-cages with salmon is crucial for the industry's development. A common operational procedure in ballan wrasse production is transporting juveniles from one landbased farm to another for further on-growing. Episodes of increased mortality have been reported after such transportations. In this study, the relationship between transport stress and post-transport mortality at the on-growing facility was examined. It was also investigated if light sedation with AQUI-S® can mitigate stress during transport. Stress was quantified by measuring cortisol release rate to the tank water during transport. This was investigated in 10 commercial live carrier truck transports (6 without AQUI-S® sedation and 4 with sedation during loading and transport). The total time of transport varied between 12 and 21h. In general, mortality was significantly higher (1.0± 0.6% day-1) the first five days posttransport compared to 15-20days post transport (0.5% day-1). There was also a strong relationship between fish weight at transport and post-transport mortality, where higher mean weight at transport reduced mortality. In contrast to what was expected, AQUI-S® treatment during transport procedures increased cortisol excretion rate, suggesting a stimulating effect of AQUI-S® on the stress axis in ballan wrasse. Considering these results, the value of using AQUI-S® to reduce stress during transport of juvenile ballan wrasse might be questioned. However, there was no relationship between cortisol release rate during transport and post-transport mortality. Furthermore, this study emphasizes that water cortisol measurements can be used as a none-invasive tool for monitoring stress and can be integrated into the welfare evaluation during commercial fish transports. [ABSTRACT FROM AUTHOR]

Salmonid alphavirus (SAV) causes pancreas disease (PD), which negatively impacts farmed Atlantic salmon. In this study, fish were vaccinated with a DNA-PD vaccine (DNA-PD) and an oil-adjuvanted, inactivated whole virus PD vaccine (Oil-PD). Controls were two non-PD vaccinated groups. Fish were kept in one tank and challenged by cohabitation with SAV genotype 2 in seawater. Protection against infection and mortality was assessed for 84 days (Efficacy study). Nineteen days post challenge (dpc), subgroups of fish from all treatment groups were transferred to separate tanks and cohabited with naïve fish (Transmission study 1) or fish vaccinated with a homologous vaccine (Transmission study 2), to evaluate virus transmission for 26 days (47 dpc). Viremia, heart RT-qPCR and histopathological scoring of key organs affected by PD were used to measure infection levels. RT-droplet digital PCR quantified shedding of SAV into water for transmission studies. The Efficacy study showed that PD associated growth-loss was significantly lower and clearance of SAV2 RNA significantly higher in the PD-DNA group compared to the other groups. The PD-DNA group had milder lesions in the heart and muscle. Cumulative mortality post challenge was low and not different between groups, but the DNA-PD group had delayed time-to-death. In Transmission study 1, the lowest water levels of SAV RNA were measured in the tanks containing the DNA-PD group at 21 and 34 dpc. Despite this, and irrespective of the treatment group, SAV2 was effectively transmitted to the naïve fish during 26-day cohabitation. At 47 dpc, the SAV RNA concentrations in the water were lower in all tanks compared to 34 dpc. In Transmission study 2, none of the DNA-PD immunized cohabitants residing with DNA-PD-vaccinated, pre-challenged fish got infected. In contrast, Oil-PD immunized cohabitants residing with Oil-PDvaccinated, pre-challenged fish, showed infection levels similar to the naïve cohabitants in Transmission study 1. The results demonstrate that the DNA-PD vaccine may curb the spread of SAV infection as the DNA-PD vaccinated, SAV2 exposed fish, did not spread the infection to cohabiting DNA-PD vaccinated fish. This signifies that herd immunity may be achieved by the DNA-PD vaccine, a valuable tool to control the PD epizootic in farmed Atlantic salmon. [ABSTRACT FROM AUTHOR]

Dissolved oxygen (DO), an important water-quality parameter required to support aquatic life, is a critical factor for determining the general biological health of the aquatic ecosystem, and the concentration of DO is a critical factor in determining salmon growth and welfare. This study used longitudinal DO concentration, recorded hourly from 21 aquaculture sites, each with loggers in three separate cages, in four areas in British Columbia, Canada, between 2015 and 2017. The measurements were evaluated based on the recommended DO concentrations for protection of salmonids from hypoxia. Using a two-stage time-series analysis, we described variations in DO concentrations measured over the study period and their associations with environmental factors. Based on the water quality criteria for DO concentration, 42.3, 56.5, and 1.2% of the hourly DO data from the overall 21 aquaculture sites were classified as ‘optimal’, ‘suboptimal’, and ‘stressed’, respectively. The frequency of hypoxic episodes differed substantially among seasons, aquaculture sites and even among cages within sites. The effects of environmental variables on DO concentration had markedly different patterns depending on the season. Significant associations with DO concentrations were observed for temperatures in the summer and winter months, and both wind direction and remotely-sensed estimated absorption from phytoplankton [aph(443)] in the winter months. The time-series regression model results showed overall (year-round) associations of temperature, wind speed, and aph(443) with DO concentrations. Describing DO measurements at these aquaculture sites provided an understanding of how much they deviated from the recommended DO concentrations, as well as provide baseline information for future water resource planning, including continued and improved water quality monitoring in aquaculture areas. [ABSTRACT FROM AUTHOR]

Introduction: The food-energy-water (FEW) nexus highlights the interdependencies between the systems that people rely on for these essential resources. For example, globally, over two thirds of freshwater withdrawals are used to produce food, and another 10% is used during energy generation. In addition, the food system uses one eighth of global net energy. Seafood is a nutritionally important food, and it is critical to use freshwater and energy resources efficiently throughout seafood supply chains to safeguard future supplies and to reduce environmental impacts. Diverse seafood production methods result in highly variable resource use across supply chains, which may contribute to siloed efforts within supply chains to improve efficiency, instead of larger efforts that involve multiple seafood supply chains. Additionally, efforts to develop and implement efficiency strategies must be informed by fishers, aquaculturists, processors, and other seafood supply chain actors to avoid investing time and resources into strategies that will have low uptake. A significant proportion of seafood is imported into the U.S., so engaging with industry and stakeholders in the U.S. and abroad is critical for understanding and improving the FEW nexus associated with seafood consumed by Americans. Methods: To understand how resources are being used, current and potential strategies to improve resource use, and relevant motivations and barriers, we conducted 47 semi-structured interviews from 2019 to 2021 with seafood supply chain actors, including producers and processors. Seafood supply chains included were farmed catfish produced in the U.S., farmed pangasius and shrimp produced in Vietnam, farmed Atlantic salmon produced in Norway, and wild-caught sockeye and pink salmon caught in the U.S. Results: We provide detailed descriptions of stages within each supply chain regarding resource use and efficiency strategies, and report higher-level findings that apply across supply chains. There was variation across settings regarding how resources are used and opportunities and barriers for improving efficiencies, but we also found commonalities in settings, indicating that resource-saving strategies or innovations could lead to increased efficiency across multiple supply chains. Interviewees shared that cost savings drove past adoption of, and high interest in, energy conservation practices. Generally, direct costs did not motivate reduced use of freshwater, but associated costs like energy to run pumps and supplies to treat contaminated surface water drove interest in reducing water use. Discussion: Efforts to improve resource use in the U.S. seafood supply should focus on identifying and scaling-up strategies that (i) involve improved efficiency of more than one resource and/or (ii) apply across multiple settings. This work should involve partnerships between industry, government agencies, and academic researchers, and should be informed by supply chain actors' experiences and insights. The qualitative insights from this study encompass rich descriptions of FEW-relevant factors at the level of specific supply chain stages as well as findings across six major seafood supply chains in three countries. The study provides an essential complement to existing quantitative characterizations of resource use, and enables nuanced and informed responses to challenges. [ABSTRACT FROM AUTHOR]

Introduction: Focusing on circular bioeconomy and finding solutions for managing finite and scarce resources such as phosphorus are issues that need to be addressed across sectors to attain food security. Land-based aquaculture of Atlantic salmon (Salmo salar L.) smolt and post-smolt results in a large output of aquaculture sludge. These nutrient-rich side streams from aquaculture production constitute a valuable resource for cultivation of polychaetes Hediste diversicolor. The aim of this study was to evaluate the capacity of H. diversicolor to upcycle carbon (C), nitrogen (N), and phosphorus (P) contained in aquaculture sludge from Norwegian salmon production. Material and methods: We investigated the effect of two diets, smolt sludge and post-smolt sludge, which were supplied at four different feed levels, on the gain of C, N, and P in H. diversicolor and established uptake rates for the upcycling of these nutrients. Additionally, we examined how different feed composition (type of diet) and supply (feel level) influenced C, N, and P content as well as the elemental ratios of H. diversicolor. Results and discussion: Polychaetes fed with both types of sludge were shown to incorporate C, N, and P from their diets into biomass. Incorporation of C, N, and P in polychaete biomass was highest at the highest feed levels, following specific growth rates. Uptake of diet C, N, and P into polychaete biomass was similar for both diets and across feed levels. On average, C and N uptake rates amounted to 2-10% and 2-15%, respectively, while values for P uptake were lower at 0.5-1.5%. C, N, and P content of polychaetes was not affected by different diets or feed levels while the C:N ratio increased with increasing feed supply. Overall, we found that H. diversicolor can successfully take up nutrients contained in aquaculture sludge and thus can be beneficial for upcycling of side streams from Atlantic salmon production. [ABSTRACT FROM AUTHOR]

Piscirickettsia salmonis, the biological agent of Salmonid Rickettsial Septicemia (SRS), is a facultative intracellular bacterium that can be divided into two genogroups (LF-89 and EM-90) with different virulence levels and patterns. Studies have found co-infection of these genogroups in salmonid farms in Chile, but it is essential to assess whether this interaction within the host is related to virulence and changes in pathogen dynamics. In this study, we studied four isolates from EM-90 and one LF-89 isolate chosen based on their genomic differences. The aim was to evaluate how co-cultivation affects bacterial growth performance and virulence factor expression in Atlantic salmon (Salmo salar) in vitro and in vivo. In vitro results using FN2 medium, showed a similar growth curve between co-cultures of LF-89 and EM-90 compared to EM-90 monocultures. This was explained by the higher ratio of EM-90 to LF-89 in all co-cultures. When evaluating the expression of virulence factors, it was discovered that the luxR gene was expressed only in EM-90-like isolates and that there were significant differences between mono- and co-cultures for flaA and cheA, suggesting a response to cohabitation. Moreover, during in vivo cocultures, transcriptomic analysis revealed an upregulation of transposases, flagellum-related genes (fliI and flgK), transporters, and permeases that could unveil novel virulence effectors used in the early infection process of P. salmonis. Thus, our work has shown that cohabitation of P. salmonis genogroups can modulate their behavior and virulence effector expression. These data can contribute to new strategies and approaches to improve the current health treatments against this salmonid pathogen. [ABSTRACT FROM AUTHOR]

The present study was undertaken to address the recent spate of pasteurellosis outbreaks among sea-farmed Atlantic salmon (Salmo salar) in Norway and Scotland, coinciding with sporadic disease episodes in lumpfish (Cyclopterus lumpus) used for delousing purposes in salmon farms. Genome assemblies from 86 bacterial isolates cultured from diseased salmon or lumpfish confirmed them all as bona fide members of the Pasteurellaceae family, with phylogenetic reconstruction dividing them into two distinct branches sharing <88% average nucleotide identity. These branches therefore constitute two separate species, namely Pasteurella skyensis and the as-yet invalidly named "Pasteurella atlantica". Both species further stratify into multiple discrete genomovars (gv.) and/or lineages, each being nearly or fully exclusive to a particular host, geographic region, and/or time period. Pasteurellosis in lumpfish is, irrespective of spatiotemporal origin, linked almost exclusively to the highly conserved "P. atlantica gv. cyclopteri" (Pac). In contrast, pasteurellosis in Norwegian sea-farmed salmon, dominated since the late-1980s by "P. atlantica gv. salmonicida" (Pas), first saw three specific lineages (Pas-1, -2, and -3) causing separate, geographically restricted, and short-lived outbreaks, before a fourth (Pas-4) emerged recently and became more widely disseminated. A similar situation involving P. skyensis (Ps) has apparently been unfolding in Scottish salmon farming since the mid-1990s, where two historic (Ps-1 and -2) and one contemporary (Ps-3) lineages have been recorded. While the epidemiology underlying all these outbreaks/epizootics remains unclear, repeated detection of 16S rRNA gene amplicons very closely related to P. skyensis and "P. atlantica" from at least five cetacean species worldwide raises the question as to whether marine mammals may play a part, possibly as reservoirs. In fact, the close relationship between the studied isolates and Phocoenobacter uteri associated with harbor porpoise (Phocoena phocoena), and their relatively distant relationship with other members of the genus Pasteurella, suggests that both P. skyensis and "P. atlantica" should bemoved to the genus Phocoenobacter. [ABSTRACT FROM AUTHOR]

Tenacibaculosis occurs due to the marine bacterial pathogen Tenacibaculum maritimum. This ulcerative disease causes high mortalities for various marine fish species worldwide. Several external clinical signs can arise, including mouth erosion, epidermal ulcers, fin necrosis, and tail rot. Research in the last 15 years has advanced knowledge on the traits and pathogenesis mechanisms of T. maritimum. Consequently, significant progress has been made in defining the complex host-pathogen relationship. Nevertheless, tenacibaculosis pathogenesis is not yet fully understood. Continued research is urgently needed, as demonstrated by recent reports on the re-emerging nature of tenacibaculosis in salmon farms globally. Current sanitary conditions compromise the development of effective alternatives to antibiotics, in addition to hindering potential preventive measures against tenacibaculosis. The present review compiles knowledge of T. maritimum reported after the 2006 review by Avendaño-Herrera and colleagues. Essential aspects are emphasized, including antigenic and genomic characterizations and molecular diagnostic procedures. Further summarized are the epidemiological foundations of the T. maritimum population structure and elucidations as to the virulence mechanisms of pathogenic isolates, as found using biological, microbiological, and genomic techniques. This comprehensive source of reference will undoubtable serve in tenacibaculosis prevention and control within the marine fish farming industry. Lastly, knowledge gaps and valuable research areas are indicated as potential guidance for future studies. [ABSTRACT FROM AUTHOR]

Ophryotrocha craigsmithi (Wiklund, Glover & Dahlgren, 2009) has repeatedly been observed in high densities at salmonid fish farms in Norway and has been shown to feed on the organic waste released during fish production. This species has therefore been pointed out as a candidate for the benthic component of integrated multitrophic aquaculture (IMTA). Little is known about the life history traits of Ophryotrocha species found at greater depths in temperate waters. Insight into life traits is of key importance in evaluating the bio-mitigation and harvest potential of (benthic) species within IMTA systems. In this study, we aimed to describe key life history traits for O. craigsmithi, such as growth, reproductive pattern, and offset of reproduction. The main findings are as follows: (I) O. craigsmithi exhibits early sexual maturation and rapid growth, going from 5 to 16 mm in length in 8 weeks; (II) their estimated lifetime is approximately 15 weeks with a generation time of 4 weeks; (III) there are strong indications that they are gonochoric semicontinuous spawners; (IV) the majority of mature eggs ranged from 120 to 150 µm; and (V) the larvae developed into a free-swimming stage after approximately 1 week. To this end, we present a framework for assessing the suitability of deposit-feeding polychaetes as candidate species in IMTA, considering environmental adaptiveness, production potential, as well as carbon and nitrogen mitigation capacity. On the basis of this, O. craigsmithi shows a high suitability as an extractive farmed species in benthic IMTA.

Piscirickettsiosis is a fish disease caused by the Gram-negative bacterium Piscirickettsia salmonis. This disease has a high socio-economic impact on the Chilean salmonid aquaculture industry. The bacterium has a cryptic character in the environment and their main reservoirs are yet unknown. Bacterial biofilms represent a ubiquitous mechanism of cell persistence in diverse natural environments and a risk factor for the pathogenesis of several infectious diseases, but their microbiological significance for waterborne veterinary diseases, including piscirickettsiosis, have seldom been evaluated. This study analyzed the in vitro biofilm behavior of P. salmonis LF-89T (genogroup LF-89) and CA5 (genogroup EM-90) using a multi-method approach and elucidated the potential arsenal of virulence of the P. salmonis LF-89T type strain in its biofilm state. P. salmonis exhibited a quick kinetics of biofilm formation that followed a multi-step and highly strain-dependent process. There were no major differences in enzymatic profiles or significant differences in cytotoxicity (as tested on the Chinook salmon embryo cell line) between biofilm-derived bacteria and planktonic equivalents. The potential arsenal of virulence of P. salmonis LF-89T in biofilms, as determined by wholetranscriptome sequencing and differential gene expression analysis, consisted of genes involved in cell adhesion, polysaccharide biosynthesis, transcriptional regulation, and gene mobility, among others. Importantly, the global gene expression profiles of P. salmonis LF-89T were not enriched with virulencerelated genes upregulated in biofilm development stages at 24 and 48 h. An enrichment in virulence-related genes exclusively expressed in biofilms was also undetected. These results indicate that early and mature biofilm development stages of P. salmonis LF-89T were transcriptionally no more virulent than their planktonic counterparts, which was supported by cytotoxic trials, which, in turn, revealed that both modes of growth induced important and very similar levels of cytotoxicity on the salmon cell line. Our results suggest that the aforementioned biofilm development stages do not represent hot spots of virulence compared with planktonic counterparts. This study provides the first transcriptomic catalogue to select specific genes that could be useful to prevent or control the (in vitro and/or in vivo) adherence and/or biofilm formation by P. salmonis and gain further insights into piscirickettsiosis pathogenesis. [ABSTRACT FROM AUTHOR]

This article analyzes the role of agency in reducing environmental risk in the Norwegian salmon farming industry. The theoretical starting point is recent literature on change agency which focuses on the different ways in which actors purposely act to renew existing and create new regional industry growth paths, and reproductive agency which focuses on how actors, explicitly and implicitly, maintain existing structures to uphold status quo. Departing from a current risk society ambiguity in the industry and an explorative multi-scalar study of industrial innovation processes, we analysis how change agency combined with reproductive agency play out. The analysis shows that change agency affecting transformative agency capacity reducing environmental risk is connected to institutional entrepreneurship in terms of a Development Licenses Program on the national level and to Schumpeterian innovative entrepreneurship in terms of Development Licenses Projects on firm level. Moreover, the study shows how reproductive agency also affects the capacity to cope with environmental risks in terms of risk reducing place-based leadership illustrated by cooperation and bottom-up, self-organized area cooperation on the regional level, and in terms of risk creation illustrated by a global growth logic across geographical levels. On this ground, it is argued that the theoretical contribution of the study is that the transformative capacity to reduce environmental risks of an industry rests on multi-scalar change- and reproductive agency and how these are combined.

Plant-based protein sources, such as soybean, are widely used in fish nutrition due to their market availability, wide distribution and acceptable nutritional quality. However, in some fish species, soybean meal-based diets cause gut inflammation, decreasing both nutrient absorption and growth rates. A suitable alternative to avoid these problems could be the application of additives with anti-inflammatory activity to the diet. In this study, an Aloe vera (Aloe barbadensis Miller, AV) extract was analyzed as a dietary additive to reduce the gut inflammation in Atlantic salmon (Salmo salar) fed with soybean meal (SBM) diet. Fish were distributed in four duplicated groups and fed 28 days with fish meal control diet (FM), AV inclusion diet (AV), FM diet supplemented with AV (FM+AV), SBM diet to induce enteritis and SBM+AV. The fish gut response to these treatments was analyzed in distal intestine by histopathological scores, tissue morphometric measurements and immune gene expression parameters. The score results in fish fed with SBM-based diet clearly showed enteritis, meanwhile fish fed with AV supplemented diet significantly reduced the intestinal SBM signs of damage. These findings were associated to reduction of goblet cells number, lamina propria thickness and sub-epithelial mucosa size, with a significant decrease on pro-inflammatory cytokine il-1β to basal levels, similar to those present in fish fed FM diets. In conclusion, the administration of AV in salmon diet showed a protective intestinal activity against the detrimental effects of SBM, opening the possibility to improve its use as a feed additive in aquafeeds.

Aquaculture impacts on marine benthic ecosystems are widely recognized and monitored. However, little is known about the community changes occurring in the water masses surrounding aquaculture sites. In the present study, we studied the eukaryotic communities inside and outside salmonid aquaculture cages through time to assess the community changes in the neighbouring waters of the farm. Water samples were taken biweekly over five months during the production phase from inside the cages and from nearby points located North and South of the salmon farm. Eukaryotic communities were analyzed by eDNA metabarcoding of the partial COI Leray-XT fragment. The results showed that eukaryotic communities inside the cages were significantly different from those in the outside environment, with communities inside the cages having higher diversity values and more indicator species associated with them. This is likely explained by the appearance of fouling species that colonize the artificial structures, but also by other species that are attracted to the cages by other means. Moreover, these effects were highly localized inside the cages, as the communities identified outside the cages, both North and South, had very similar eukaryotic composition at each point in time. Overall, the eukaryotic communities, both inside and outside the cages, showed similar temporal fluctuations through the summer months, with diversity peaks occurring at the end of July, beginning of September, and in the beginning of November, with the latter showing the highest Shannon diversity and richness values. Hence, our study suggests that seasonality, together with salmonid aquaculture, are the main drivers of eukaryotic community structure in surface waters surrounding the farm. [ABSTRACT FROM AUTHOR]

Flavobacterium psychrophilum, the etiological agent of bacterial coldwater disease and rainbow trout fry syndrome, causes considerable losses in salmonid aquaculture globally. Systemic F. psychrophilum infections in rainbow trout (Oncorhynchus mykiss) lead to a range of clinical signs, including ulcerative lesions in the skin and muscle and splenitis. Previous studies offered an integrative analysis of the skeletal muscle response to F. psychrophilum infection in rainbow trout. However, little is known about the molecular mechanism of immune response in the spleen, which is an important immune organ of rainbow trout. Here, we investigated the timecourse splenic transcriptome profiles in uninfected rainbow trout (CK) and F. psychrophilum-infected rainbow trout at day 3 and day 7 (D3, D7) by RNA-seq analyses. Among the 7,170 differentially expressed genes (DEGs) in the three comparisons (D3 vs. CK, D7 vs. CK, D3 vs. D7), 1,286 DEGs showed consistent upregulation or downregulation at D3 and D7 and were associated with pattern recognition, acute-phase response, complement cascade, chemokine and cytokine signaling, and apoptosis. The Real time quantitative PCR (RT-qPCR) analysis of eight DEGs confirmed the accuracy of the RNA-Sequencing (RNAseq) data. Our results reflected a general process from pathogen recognition to inflammatory cytokine generation and delineated a putative Toll-like receptor signaling pathway in rainbow trout spleen, following F. psychrophilum infection. Taken together, these results provide new insights into the molecular mechanism of the immune response to F. psychrophilum infection and are a valuable resource for future research on the prevention and control of bacterial coldwater disease during salmon culture. [ABSTRACT FROM AUTHOR]

Fish disease surveillance methods can be complicated and time consuming, which limits their value for timely intervention strategies on aquaculture farms. Novel molecular-based assays using droplet digital Polymerase Chain Reaction (ddPCR) can produce immediate results and enable high sample throughput with the ability to multiplex several targets using different fluorescent dyes. A ddPCR tetraplex assay was developed for priority salmon diseases for farmers in New Zealand including New Zealand Rickettsia -like organism 1 (NZ-RLO1), NZ-RLO2, Tenacibaculum maritimum , and Yersinia ruckeri. The limit of detection in singleplex and tetraplex assays was reached for most targets at 10−9 ng/μl with, respectively, NZ-RLO1 = 0.931 and 0.14 copies/μl, NZ-RLO2 = 0.162 and 0.21 copies/μl, T. maritimum = 0.345 and 0.93 copies/μl, while the limit of detection for Y. ruckeri was 10−8 with 1.0 copies/μl and 0.7 copies/μl. While specificity of primers was demonstrated in previous studies, we detected cross-reactivity of T. maritimum with some strains of Tenacibaculum dicentrarchi and Y. ruckeri with Serratia liquefaciens , respectively. The tetraplex assay was applied as part of a commercial fish disease surveillance program in New Zealand for 1 year to demonstrate the applicability of tetraplex tools for the salmonid aquaculture industry. [ABSTRACT FROM AUTHOR]

Piscine orthoreovirus (PRV) is a virus in the genus Orthoreovirus of the Reoviridae family, first described in 2010 associated with Heart and Skeletal Muscle Inflammation (HSMI) in Atlantic salmon (Salmo salar). Three phases of PRV infection have been described, the early entry and dissemination, the acute dissemination phase, and the persistence phase. Depending on the PRV genotype and the host, infection can last for life. Mechanisms of immune response to PRV infection have been just beginning to be studied and the knowledge in this matter is here revised. PRV induces a classical antiviral immune response in experimental infection of salmonid erythrocytes, including transcriptional upregulation of ifn-α , rig-i , mx , and pkr. In addition, transcript upregulation of tcra, tcrb, cd2, il-2, cd4-1, ifn-γ, il-12, and il-18 has been observed in Atlantic salmon infected with PRV, indicating that PRV elicited a Th1 type response probably as a host defense strategy. The high expression levels of cd8a , cd8b , and granzyme-A in PRV-infected fish suggest a positive modulatory effect on the CTL-mediated immune response. This is consistent with PRV-dependent upregulation of the genes involved in antigen presentation, including MHC class I, transporters, and proteasome components. We also review the potential immune mechanisms associated with the persistence phenotype of PRV-infected fish and its consequence for the development of a secondary infection. In this scenario, the application of a vaccination strategy is an urgent and challenging task due to the emergence of this viral infection that threatens salmon farming. [ABSTRACT FROM AUTHOR]

Stress related to salmon aquaculture practices (handling, sub-optimal nutrition, diseases, and environmental problems) may compromise fish welfare. This study describes the effects of two hydrolyzed Debaryomyces hansenii yeast-based products (LAN4 and LAN6) on physiological and immune responses of Atlantic salmon (Salmo salar) parr exposed to short hypoxia stress. A commercial-like diet (control diet: CD) and two experimental diets (CD supplemented with 0.1% of either component LAN4 or LAN6) were fed to fish for 8 weeks. At the end of the feeding experiment, fish were exposed to 1-min hypoxia and samples were collected at 0, 1, 3, 6, 12, and 24 h post-stress. Results showed that plasma cortisol reached a peak at 1 h post-stress in CD and LAN6 groups, whereas no significant increase in cortisol levels was detected in the LAN4 group. Moreover, the LAN6 group enhanced IL-10 responses to hypoxia, when compared to the control and LAN4 group. This suggests a regulation of immunosuppressive profiles in fish fed LAN4. Hypoxia stress increased TNFα in all groups, which indicates that fish may compensate for the short-term stress response, by modulating innate immune molecules. The apparent suppression of hypoxia responses in the LAN4 group coincided with the detection of differences in goblet cells size and Muc-like proteins production in DI; and upregulation (1 h post-stress) of pathways related to oxygen transport, hemoglobin complex, and glutathione transferase activity and the downregulation of fatty acid metabolism (6 h post-stress) in gills. To conclude, a 1-min hypoxia stress exposure affects the response to stress and immunity; and D. hansenii -based yeast products are promising components in functional aquafeeds for salmon due to their ability to counteract possible consequences of hypoxic stress. [ABSTRACT FROM AUTHOR]

Piscirickettsiosis (SRS) has been the most important infectious disease in Chilean salmon farming since the 1980s. It was one of the first to be described, and to date, it continues to be the main infectious cause of mortality. How can we better understand the epidemiological situation of SRS? The catch-all answer is that the Chilean salmon farming industry must fight year after year against a multifactorial disease, and apparently only the environment in Chile seems to favor the presence and persistence of Piscirickettsia salmonis. This is a fastidious, facultative intracellular bacterium that replicates in the host's own immune cells and antigen-presenting cells and evades the adaptive cell-mediated immune response, which is why the existing vaccines are not effective in controlling it. Therefore, the Chilean salmon farming industry uses a lot of antibiotics—to control SRS—because otherwise, fish health and welfare would be significantly impaired, and a significantly higher volume of biomass would be lost per year. How can the ever-present risk of negative consequences of antibiotic use in salmon farming be balanced with the productive and economic viability of an animal production industry, as well as with the care of the aquatic environment and public health and with the sustainability of the industry? The answer that is easy, but no less true, is that we must know the enemy and how it interacts with its host. Much knowledge has been generated using this line of inquiry, however it remains insufficient. Considering the state-of-the-art summarized in this review, it can be stated that, from the point of view of fish immunology and vaccinology, we are quite far from reaching an effective and long-term solution for the control of SRS. For this reason, the aim of this critical review is to comprehensively discuss the current knowledge on the interaction between the bacteria and the host to promote the generation of more and better measures for the prevention and control of SRS. [ABSTRACT FROM AUTHOR]

Bacterial cell envelopes play a critical role in host-pathogen interactions. Macromolecular components of these structures have been closely linked to the virulence of pathogens. Piscirickettsia salmonis is a relevant salmonid pathogen with a worldwide distribution. This bacterium is the etiological agent of piscirickettsiosis, a septicemic disease that causes a high economic burden, especially for the Chilean salmon farming industry. Although P. salmonis has been discovered long ago, its pathogenicity and virulence mechanisms are not completely understood. In this work, we present a genetic approach for producing in-frame deletion mutants on genes related to the biosynthesis of membrane-associated polysaccharides. We provide a detailed in vitro phenotype description of knock-out mutants on wzx and wcaJ genes, which encode predicted lipopolysaccharide (LPS) flippase and undecaprenyl-phosphate glucose phosphotransferase enzymes, respectively. We exhibit evidence that the wzx mutant strain carries a defect in the probably most external LPS moiety, while the wcaJ mutant proved to be highly susceptible to the bactericidal action of serum but retained the ability of biofilm production. Beyond that, we demonstrate that the deletion of wzx , but not wcaJ , impairs the virulence of P. salmonis in an intraperitoneally infected Atlantic salmon, Salmo salar , model of piscirickettsiosis. Our findings support a role for LPS in the virulence of P. salmonis during the onset of piscirickettsiosis. [ABSTRACT FROM AUTHOR]

Lumpfish are utilized to combat ectoparasitic epidemics in salmon farming. Research gaps on both cleaning behavior and client preferences in a natural environment, emphasizes the need to investigate the physiological impacts on lumpfish during cohabitation with piscivorous Atlantic salmon. Lumpfish (39.9 g, S.D ± 8.98) were arranged in duplicate tanks (n = 40 per treatment) and exposed to Live Atlantic salmon (245.7 g, S.D ± 25.05), salmon Olfaction or lifelike salmon Models for 6 weeks. Growth and health scores were measured every second week. In addition, the final sampling included measurements of neuromodulators, body color, and plasma cortisol. A stimulation and suppression test of the hypothalamic-pituitary-interrenal (HPI) axis was used for chronic stress assessment. Results showed that growth, health scores, and body color remained unaffected by treatments. Significant reductions in levels of brain dopamine and norepinephrine were observed in Live compared to Control. Plasma cortisol was low in all treatments, while the stimulation and suppression test of the HPI axis revealed no indications of chronic stress. This study presents novel findings on the impact on neuromodulators from Atlantic salmon interaction in the lumpfish brain. We argue that the downregulation of dopamine and norepinephrine indicate plastic adjustments to cohabitation with no negative effect on the species. This is in accordance with no observed deviations in welfare measurements, including growth, health scores, body color, and stress. We conclude that exposure to salmon or salmon cues did not impact the welfare of the species in our laboratory setup, and that neuromodulators are affected by heterospecific interaction. [ABSTRACT FROM AUTHOR]

Advances in tag technology now make it possible to monitor the behavior of small groups of individual fish as bioindicators of population wellbeing in commercial aquaculture settings. For example, tags may detect unusual patterns in fish heart rate, which could serve as an early indicator of whether fish health or welfare is becoming compromised. Here, we investigated the use of commercially available heart rate biologgers implanted into 24 Atlantic salmon weighing 3.6 ± 0.8 kg (mean ± SD) to monitor fish over 5 months in a standard 12 m × 12 m square sea cage containing ∼6,000 conspecifics. Post tagging, fish established a diurnal heart rate rhythm within 24 h, which stabilized after 4 days. Whilst the registered tagged fish mortality over the trial period was 0%, only 75% of tagged fish were recaptured at harvest, resulting in an unexplained tag loss rate of 25%. After 5 months, tagged fish were approximately 20% lighter and 8% shorter, but of the similar condition when compared to untagged fish. Distinct diurnal heart rate patterns were observed and changed with seasonal day length of natural illumination. Fish exhibited lower heart rates at night [winter 39 ± 0.2 beats per min (bpm), spring 37 ± 0.2 bpm, summer 43 ± 0.3 bpm, mean ± SE] than during the day (winter 50 ± 0.3 bpm, spring 48 ± 0.2 bpm, summer 49 ± 0.2 bpm) with the difference between night and day heart rates near half during the summer (6 bpm) compared to winter and spring (both 11 bpm). When fish experienced moderate and severe crowding events in early summer, the highest hourly heart rates reached 60 ± 2.5 bpm and 72 ± 2.4 bpm, respectively, on the day of crowding. Here, if the negative sublethal effects on fish that carry tags (e.g., growth rate) can be substantially reduced, the ability to monitor diurnal heart rate patterns across seasons and detect changes during crowding events, and using heart rate biologgers could be a useful warning mechanism for detecting sudden changes in fish behavior in sea cages. [ABSTRACT FROM AUTHOR]

Sea lice (Caligus rogercresseyi) are external parasites that affect farmed salmonids in Chile, and the scale of their sanitary and economic impact cannot be overstated. Even though space–time patterns suppose parasite aggregation, specific locations related to different infestation levels, as well as their associated factors across the geographic range involved, had not been investigated as of the writing of the present article. The understanding of the effects and factors entailed by the presence of C. rogercresseyi may be deemed a key element of Integrated Pest Management (IPM). In the present study, the multivariate spatial scan statistic was used to identify geographic areas and times of C. rogercresseyi infestation and to estimate the factors associated with such patterns. We used official C. rogercresseyi monitoring data at the farm level, with a set of 13 covariates, to provide adjustment within the analyses. The analyses were carried out for a period of 5 years (2012–2016), and they included three fish species (Salmo salar, Oncorhynchus mykiss, and Oncorhynchus kisutch) in order to assess the consistency of the identified clusters. A retrospective multinomial, spatial, and temporal scan test was implemented to identify farm clusters of either of the different categories of C. rogercresseyi infested farms: baseline, medium, and high, based on the control chemical threshold established by the health authority. The baseline represents adequate farm performance against C. rogercresseyi infestation. Then, production and environmental factors of the medium and high infestation farms were compared with the baseline using regression techniques. The results revealed a total of 26 clusters (p < 0.001), of which 12 correspond to baseline, 1 to medium, and the remaining 13 to high infestation clusters. In general, baseline clusters are detected in a latitudinal gradient on estuarine areas, with increasing relative risks to complex island water systems. There is a spatial structure in specific sites, north of Los Lagos Region and central Aysén Region, with high infestation clusters and epidemic peaks during 2013. In addition, average weight, salmon species, chemotherapeutants, latitude, temperature, salinity, and year category are factors associated with these C. rogercresseyi patterns. Recommendations for an IPM plan are provided, along with a discussion that considers the involvement of stock density thresholds by salmon species and the spatial structure of the efficacy of chemical control, both intended to avoid the advance of resistance and to minimize environmental residues.

In salmon farming, viruses are responsible for outbreaks that produce significant economic losses for which there is a lack of control tools other than vaccines. Type I interferon has been successfully used for treating some chronic viral infections in humans. However, its application in salmonids depends on the proper design of a vehicle that allows its massive administration, ideally orally. In mammals, administration of recombinant probiotics capable of expressing cytokines has shown local and systemic therapeutic effects. In this work, we evaluate the use of Lactococcus lactis as a type I Interferon expression system in Atlantic salmon, and we analyze its ability to stimulate the antiviral immune response against IPNV, in vivo and in vitro. The interferon expressed in L. lactis , even though it was located mainly in the bacterial cytoplasm, was functional, stimulating Mx and PKR expression in CHSE-214 cells, and reducing the IPNV viral load in SHK-1 cells. In vivo , the oral administration of this L. lactis producer of Interferon I increases Mx and PKR expression, mainly in the spleen, and to a lesser extent, in the head kidney. The oral administration of this strain also reduces the IPNV viral load in Atlantic salmon specimens challenged with this pathogen. Our results show that oral administration of L. lactis producing Interferon I induces systemic effects in Atlantic salmon, allowing to stimulate the antiviral immune response. This probiotic could have effects against a wide variety of viruses that infect Atlantic salmon and also be effective in other salmonids due to the high identity among their type I interferons. [ABSTRACT FROM AUTHOR]

Piscirickettsia salmonis is a bacterial pathogen that severely impact the aquaculture in several countries as Canada, Scotland, Ireland, Norway, and Chile. It provokes Piscirickettsiosis outbreaks in the marine phase of salmonid farming, resulting in economic losses. The monophyletic genogroup LF-89 and a divergent genogroup EM-90 are responsible for the most severe Piscirickettsiosis outbreaks in Chile. Therefore, the development of methods for quick genotyping of P. salmonis genogroups in field samples is vital for veterinary diagnoses and understanding the population structure of this pathogen. The present study reports the development of a multiplex PCR for genotyping LF-89 and EM-90 genogroups based on comparative genomics of 73 fully sequenced P. salmonis genomes. The results revealed 2,322 sequences shared between 35 LF-89 genomes, 2,280 sequences in the core-genome of 38 EM-90 genomes, and 331 and 534 accessory coding sequences each genogroup, respectively. A total of 1,801 clusters of coding sequences were shared among all tested genomes of P. salmonis (LF-89 and EM-90), with 253 and 291 unique sequences for LF-89 and EM-90 genogroups, respectively. The Multiplex-1 prototype was chosen for reliable genotyping because of differences in annealing temperatures and respective reaction efficiencies. This method also identified the pathogen in field samples infected with LF-89 or EM-90 strains, which is not possible with other methods currently available. Finally, the genome-based multiplex PCR protocol presented in this study is a rapid and affordable alternative to classical sequencing of PCR products and analyzing the length of restriction fragment polymorphisms. [ABSTRACT FROM AUTHOR]

The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3–V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach. [ABSTRACT FROM AUTHOR]

Chile is the second largest global producer of farmed salmon. The growth of salmon production has not been free of environmental challenges, such as the increasing use of pesticides to control the parasitic load of the sea lice Caligus rogercresseyi. The lack of the specificity of pesticides can potentially affect non-target organisms, as well as the structure and functioning of aquatic ecosystems. The aim of this study, was to understand the effect of pesticides on natural microbial communities to the addition of the anti-lice pesticide azamethiphos, deltamethrin and emamectin benzoate, and their potential impact in ammonium uptake rates in the coast off central-southern Chile and Northern Patagonia. The addition of pesticides on natural microbial communities resulted in a rapid response in ammonium uptake, which was significant for the single use of pesticide, azamethiphos and emamectin benzoate, as well as the combination, azamethiphos, deltamethrin and emamectin benzoate. In northern Patagonia, azamethiphos addition produced a 53% decrease in photoautotrophic uptake. However, an increase, although variable, was observed in chemoautotrophic uptake. Emamectin benzoate produced a 36 to 77% decrease in chemo and photoautotrophic ammonium uptake, respectively. The combined use of pesticides, also produced up to 42% decrease in both photo and chemoautotrophic assimilation. We conclude that the use of pesticides in salmon farming produces diverse responses at the microbial level, stimulating and/or inhibiting microbial communities with subsequent impact on nitrogen budgets. Further studies are necessary to understand the impact of pesticides in the ecology of central-southern and northern Patagonia, Chile.

An effective and economical vaccine against the Piscirickettsia salmonis pathogen is needed for sustainable salmon farming and to reduce disease-related economic losses. Consequently, the aquaculture industry urgently needs to investigate efficient prophylactic measures. Three protein-based vaccine prototypes against Piscirickettsia salmonis were prepared from a highly pathogenic Chilean isolate. Only one vaccine effectively protected Atlantic salmon (Salmo salar), in correlation with the induction of Piscirickettsia-specific IgM antibodies and a high induction of transcripts encoding pro-inflammatory cytokines (i.e., Il-1β and TNF-α). In addition, we studied the proteome fraction protein of P. salmonis strain Austral-005 using multidimensional protein identification technology. The analyzes identified 87 proteins of different subcellular origins, such as the cytoplasmic and membrane compartment, where many of them have virulence functions. The other two prototypes activated only the innate immune responses, but did not protect Salmo salar against P. salmonis. These results suggest that the knowledge of the formulation of vaccines based on P. salmonis proteins is useful as an effective therapy, this demonstrates the importance of the different research tools to improve the study of the different immune responses, resistance to diseases in the Atlantic salmon. We suggest that this vaccine can help prevent widespread infection by P. salmonis , in addition to being able to be used as a booster after a primary vaccine to maintain high levels of circulating protective antibodies, greatly helping to reduce the economic losses caused by the pathogen. [ABSTRACT FROM AUTHOR]

Piscirickettsia salmonis , an aggressive intracellular pathogen, is the etiological agent of salmonid rickettsial septicemia (SRS). This is a chronic multisystemic disease that generates high mortalities and large losses in Chilean salmon farming, threatening the sustainability of the salmon industry. Previous reports suggest that P. salmonis is able to survive and replicate in salmonid macrophages, inducing an anti-inflammatory environment and a limited lysosomal response that may be associated with host immune evasion mechanisms favoring bacterial survival. Current control and prophylaxis strategies against P. salmonis (based on the use of antibiotics and vaccines) have not had the expected success against infection. This makes it urgent to unravel the host-pathogen interaction to develop more effective therapeutic strategies. In this study, we evaluated the effect of treatment with IgM-beads on lysosomal activity in Atlantic salmon macrophage-enriched cell cultures infected with P. salmonis by analyzing the lysosomal pH and proteolytic ability through confocal microscopy. The impact of IgM-beads on cytotoxicity induced by P. salmonis in infected cells was evaluated by quantification of cell lysis through release of Lactate Dehydrogenase (LDH) activity. Bacterial load was determined by quantification of 16S rDNA copy number by qPCR, and counting of colony-forming units (CFU) present in the extracellular and intracellular environment. Our results suggest that stimulation with antibodies promotes lysosomal activity by lowering lysosomal pH and increasing the proteolytic activity within this organelle. Additionally, incubation with IgM-beads elicits a decrease in bacterial-induced cytotoxicity in infected Atlantic salmon macrophages and reduces the bacterial load. Overall, our results suggest that stimulation of cells infected by P. salmonis with IgM-beads reverses the modulation of the lysosomal activity induced by bacterial infection, promoting macrophage survival and bacterial elimination. This work represents a new important evidence to understand the bacterial evasion mechanisms established by P. salmonis and contribute to the development of new effective therapeutic strategies against SRS. [ABSTRACT FROM AUTHOR]

Cell-derived extracellular vesicles (EVs) participate in cell-cell communication via transfer of molecular cargo including genetic material like miRNAs. In mammals, it has previously been established that EV-mediated transfer of miRNAs can alter the development or function of immune cells, such as macrophages. Our previous research revealed that Atlantic salmon head kidney leukocytes (HKLs) change their morphology, phagocytic ability and miRNA profile from primarily "monocyte-like" at Day 1 to primarily "macrophage-like" at Day 5 of culture. Therefore, we aimed to characterize the miRNA cargo packaged in EVs released from these two cell populations. We successfully isolated EVs from Atlantic salmon HKL culture supernatants using the established Vn96 peptide-based pull-down. Isolation was validated using transmission electron microscopy, nanoparticle tracking analysis, and Western blotting. RNA-sequencing identified 19 differentially enriched (DE) miRNAs packaged in Day 1 versus Day 5 EVs. Several of the highly abundant miRNAs, including those that were DE (e.g. ssa-miR-146a, ssa-miR-155 and ssa-miR-731), were previously identified as DE in HKLs and are associated with macrophage differentiation and immune response in other species. Interestingly, the abundance relative of the miRNAs in EVs, including the most abundant miRNA (ssa-miR-125b), was different than the miRNA abundance in HKLs, indicating selective packaging of miRNAs in EVs. Further study of the miRNA cargo in EVs derived from fish immune cells will be an important next step in identifying EV biomarkers useful for evaluating immune cell function, fish health, or response to disease. [ABSTRACT FROM AUTHOR]

Infectious pancreatic necrosis virus (IPNV) infection has been a major problem in salmonid aquaculture. Marker-assisted selection of individuals with resistant genotype at the major IPN quantitative trait locus (IPN-QTL) has significantly reduced mortality in recent years. We have identified host miRNAs that respond to IPNV challenge in salmon fry that were either homozygous resistant (RR) or homozygous susceptible (SS) for the IPN-QTL. Small RNA-sequenced control samples were compared to samples collected at 1, 7, and 20 days post challenge (dpc). This revealed 72 differentially expressed miRNAs (DE miRNAs). Viral load (VL) was lower in RR vs. SS individuals at 7 and 20 dpc. However, analysis of miRNA expression changes revealed no differences between RR vs. SS individuals in controls, at 1 or 7 dpc, while 38 "high viral load responding" miRNAs (HVL-DE miRNAs) were identified at 20 dpc. Most of the HVL-DE miRNAs showed changes that were more pronounced in the high VL SS group than in the low VL RR group when compared to the controls. The absence of differences between QTL groups in controls, 1 and 7 dpc indicates that the QTL genotype does not affect miRNA expression in healthy fish or their first response to viral infections. The miRNA differences at 20 dpc were associated with the QTL genotype and could, possibly, contribute to differences in resistance/susceptibility at the later stage of infection. In silico target gene predictions revealed that 180 immune genes were putative targets, and enrichment analysis indicated that the miRNAs may regulate several major immune system pathways. Among the targets of HVL-DE miRNAs were IRF3, STAT4, NFKB2, MYD88, and IKKA. Interestingly, TNF-alpha paralogs were targeted by different DE miRNAs. Most DE miRNAs were from conserved miRNA families that respond to viral infections in teleost (e.g., miR-21, miR-146, miR-181, miR-192, miR-221, miR-462, miR-731, and miR-8159), while eight were species specific. The miRNAs showed dynamic temporal changes implying they would affect their target genes differently throughout disease progression. This shows that miRNAs are sensitive to VL and disease progression, and may act as fine-tuners of both immediate immune response activation and the later inflammatory processes. [ABSTRACT FROM AUTHOR]

The salmon gill poxvirus (SGPV) is a large DNA virus that infects gill epithelial cells in Atlantic salmon and is associated with acute high mortality disease outbreaks in aquaculture. The pathological effects of SGPV infection include gill epithelial apoptosis in the acute phase of the disease and hyperplasia of gill epithelial cells in surviving fish, causing damage to the gill respiratory surface. In this study, we sampled gills from Atlantic salmon presmolts during a natural outbreak of SGPV disease (SGPVD). Samples covered the early phase of infection, the acute mortality phase, the resolving phase of the disease and control fish from the same group and facility. Mortality, the presence and level of SGPV and gill epithelial apoptosis were clearly associated. The gene expression pattern in the acute phase of SGPVD was in tune with the pathological findings and revealed novel transcript-based disease biomarkers, including pro-apoptotic and proliferative genes, along with changes in expression of ion channels and mucins. The innate antiviral response was strongly upregulated in infected gills and chemokine expression was altered. The regenerating phase did not reveal adaptive immune activity within the study period, but several immune effector genes involved in mucosal protection were downregulated into the late phase, indicating that SGPV infection could compromise mucosal defense. These data provide novel insight into the infection mechanisms and host interaction of SGPV. [ABSTRACT FROM AUTHOR]

The gill of teleost fish is a multifunctional organ involved in many physiological processes such as gas exchange, osmotic and ionic regulation, acid-base balance and excretion of nitrogenous waste. Due to its extensive interface with the environment, the gill plays a key role as a primary mucosal defense tissue against pathogens, as manifested by the presence of the gill-associated lymphoid tissue (GIALT). In recent years, the prevalence of multifactorial gill pathologies has increased significantly, causing substantial losses in Atlantic salmon aquaculture. The transition from healthy to unhealthy gill phenotypes and the progression of multifactorial gill pathologies, such as proliferative gill disease (PGD), proliferative gill inflammation (PGI) and complex gill disorder (CGD), are commonly characterized by epithelial hyperplasia, lamellar fusion and inflammation. Routine monitoring for PGD relies on visual inspection and non-invasive scoring of the gill tissue (gross morphology), coupled with histopathological examination of gill sections. To explore the underlying molecular events that are associated with the progression of PGD, we sampled Atlantic salmon from three different marine production sites in Scotland and examined the gill tissue at three different levels of organization: gross morphology with the use of PGD scores (macroscopic examination), whole transcriptome (gene expression by RNA-seq) and histopathology (microscopic examination). Our results strongly suggested that the changes in PGD scores of the gill tissue were not associated with the changes in gene expression or histopathology. In contrast, integration of the gill RNA-seq data with the gill histopathology enabled us to identify common gene expression patterns associated with multifactorial gill disease, independently from the origin of samples. We demonstrated that the gene expression patterns associated with multifactorial gill disease were dominated by two processes: a range of immune responses driven by pro-inflammatory cytokines and the events associated with tissue damage and repair, driven by caspases and angiogenin. [ABSTRACT FROM AUTHOR]

Salmon gill poxvirus (SGPV) can cause serious gill disease in Atlantic salmon (Salmo salar L.) and represents a significant problem to aquaculture industries in Northern Europe. Here, a single-tube multi-locus variable-number tandem-repeat (VNTR) analysis (MLVA) genotyping assay, targeting eight VNTR loci, was developed for studying the epizootiology of SGPV. Through MLVA typing of SGPV positive samples from 180 farmed and wild Atlantic salmon in Northern Europe, the first molecular population study of this virus was undertaken. Comparison of resulting MLVA profiles by cluster analysis revealed considerable micro-diversity, while only a limited degree of specific clustering by country of origin could be observed, and no clustering relating to the severity of disease outbreaks. Phylogenetic analysis, based on genomic data from six SGPV specimens (three Norwegian, one Scottish, one Faroese and one Canadian), complemented and corroborated MLVA by pointing to a marked transatlantic divide in the species, with one main, relatively conserved, SGPV lineage as predominant in Europe. Within certain fjord systems and individual freshwater salmon smolt farms in Norway, however, discrete MLVA clustering patterns that prevailed over time were observed, likely reflecting local predominance of specific SGPV sub-lineages. MLVA typing was also used to refute two suspected instances of vertical SGPV transmission from salmon broodstock to offspring, and to confirm a failed disinfection attempt in one farm. These novel insights into the previously undocumented population structure of SGPV provide important clues, e.g., regarding the mechanisms underlying spread and recurrence of the virus amongst wild and farmed salmon populations, but so far no indications of more or less virulent SGPV sub-lineages have been found. The MLVA scheme represents a highly sensitive genotyping tool particularly well suited for illuminating SGPV infection routes, and adds to the relatively low number of MLVA protocols that have so far been published for viral species. Typing is reasonably inexpensive, with a moderate technological requirement, and may be completed within a single working day. Resulting MLVA profiles can be readily shared and compared across laboratories, facilitating rapid placement of samples in an international ezpizootiological context. [ABSTRACT FROM AUTHOR]

Salmon farming industry in Chile currently uses a significant quantity of antimicrobials to control bacterial pathologies. The main aims of this study were to investigate the presence of transferable sulfonamide- and trimethoprim-resistance genes, sul and dfr, and their association with integrons among bacteria associated to Chilean salmon farming. For this purpose, 91 Gram-negative strains resistant to sulfisoxazole and/or trimethoprim recovered from various sources of seven Chilean salmonid farms and mainly identified as belonging to the Pseudomonas genus (81.0%) were studied. Patterns of antimicrobial resistance of strains showed a high incidence of resistance to florfenicol (98.9%), erythromycin (95.6%), furazolidone (90.1%) and amoxicillin (98.0%), whereas strains exhibited minimum inhibitory concentrations (MIC90) values of sulfisoxazole and trimethoprim of >4,096 and >2,048 μg mL−1, respectively. Strains were studied for their carriage of these genes by polymerase chain reaction, using specific primers, and 28 strains (30.8%) were found to carry at least one type of sul gene, mainly associated to a class 1 integron (17 strains), and identified by 16S rRNA gene sequencing as mainly belonging to the Pseudomonas genus (21 strains). Of these, 22 strains carried the sul1 gene, 3 strains carried the sul2 gene, and 3 strains carried both the sul1 and sul2 genes. Among these, 19 strains also carried the class 1 integron-integrase gene intI1, whereas the dfrA1, dfrA12 and dfrA14 genes were detected, mostly not inserted in the class 1 integron. Otherwise, the sul3 and intI2 genes were not found. In addition, the capability to transfer by conjugation these resistance determinants was evaluated in 22 selected strains, and sul and dfr genes were successfully transferred by 10 assayed strains, mainly mediated by a 10 kb plasmid, with a frequency of transfer of 1.4 × 10−5 to 8.4 × 10−3 transconjugant per recipient cell, and exhibiting a co-transference of resistance to florfenicol and oxytetracycline, currently the most used in Chilean salmon industry, suggesting an antibacterial co-selection phenomenon. This is the first report of the characterization and transferability of integrons as well as sul and dfr genes among bacteria associated to Chilean salmon farms, evidencing a relevant role of this environment as a reservoir of these genes.