Occurrence of salmonid alphavirus and piscine orthoreovirus-1 infections in migrating salmon (Salmo salar L.) post-smolt in western Norway.

Viral diseases are a serious problem in Atlantic salmon (Salmo salar L.) farming in Norway, often leading to reduced fish welfare and increased mortality. Disease outbreaks in salmon farms may lead to spread of viruses to the surrounding environment. There is a public concern that viral diseases may negatively affect the wild salmon populations. Pancreas disease (PD) caused by salmonid alphavirus (SAV) and heart and skeletal muscle inflammation (HSMI) caused by piscine orthoreovirus-1 (PRV-1) are common viral diseases in salmon farms in western Norway. In the current study, we investigated the occurrence of SAV and PRV-1 infections in 651 migrating salmon post-smolt collected from three fjord systems (Sognefjorden, Osterfjorden and Hardangerfjorden) located in western Norway in 2013 and 2014 by real-time RT-PCR. Of the collected post-smolts, 303 were of wild origin and 348 were hatchery-released. SAV was not detected in any of the tested post-smolt, but PRV-1 was detected in 4.6% of them. The Ct values of PRV-1 positive fish were usually high (mean 32.0; range: 20.1-36.8). PRV-1 prevalence in post-smolts from the three fjords was 6.1% in Sognefjorden followed by 4.8% in Osterfjorden and 2.3% in Hardangerfjorden. The prevalence PRV-1 was significantly higher in wild (6.9%) compared to hatchery-released post-smolt (2.6%). The occurrence of PRV-1 infection in the fish was lowest in the Hardangerfjorden which has the highest fish farming intensity. Our results suggest that SAV infection are uncommon in migrating smolt while PRV-1 infection can be detected at low level. These findings suggest that migrating smolts were at low risk from SAV or PRV-1 released from salmon farms located in their migration routes in 2013 and 2014.

Analysing mortality patterns in salmon farming using daily cage registrations.

This study describes the patterns of mortality and investigates the sources of variation in mortality during the marine phase of commercial salmon farming. The study included daily mortality records from stocking to harvest of 21 million salmon from ten hatcheries in 136 fish-groups (fish in the same cage from the same hatchery). The fish was stocked in 2017-2018 at 21 marine farms within two Norwegian companies. The sources of variation in mortality were investigated using multilevel linear regression models with 'fish-group' nested within 'farm' as a random effect, cross-classified with 'hatchery'. In the final model, 'fish-group' was the source of most variation (70%). Furthermore, the mortality categories 'smolt-related mortality', 'infectious diseases' and 'handling and treatment' were responsible for 10%, 17% and 29% of the total number of dead fish respectively. Overall, the study shows that smolt-related mortality is one of the major causes of death in the first part of the production, while handling and treatment was the dominating cause of mortality in total. Mortality varied by fish-group to a large extent. This means that targeted preventive strategies to decrease mortality for individual fish-groups might be more effective than overall measures at farm or hatchery level.

Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes.

Increasing anthropogenic impact and global change effects on natural ecosystems has prompted the development of less expensive and more efficient bioassessments methodologies. One promising approach is the integration of DNA metabarcoding in environmental monitoring. A critical step in this process is the inference of ecological quality (EQ) status from identified molecular bioindicator signatures that mirror environmental classification based on standard macroinvertebrate surveys. The most promising approaches to infer EQ from biotic indices (BI) are supervised machine learning (SML) and the calculation of indicator values (IndVal). In this study we compared the performance of both approaches using DNA metabarcodes of bacteria and ciliates as bioindicators obtained from 152 samples collected from seven Norwegian salmon farms. Results from standard macroinvertebrate-monitoring of the same samples were used as reference to compare the accuracy of both approaches. First, SML outperformed the IndVal approach to infer EQ from eDNA metabarcodes. The Random Forest (RF) algorithm appeared to be less sensitive to noisy data (a typical feature of massive environmental sequence data sets) and uneven data coverage across EQ classes (a typical feature of environmental compliance monitoring scheme) compared to a widely used method to infer IndVals for the calculation of a BI. Second, bacteria allowed for a more accurate EQ assessment than ciliate eDNA metabarcodes. For the implementation of DNA metabarcoding into routine monitoring programmes to assess EQ around salmon aquaculture cages, we therefore recommend bacterial DNA metabarcodes in combination with SML to classify EQ categories based on molecular signatures.

Chilean salmon farming vulnerability to external stressors: The COVID 19 as a case to test and build resilience.

This study addresses the risk and vulnerability of Chilean salmon production to hazards resulting from the COVID-19 pandemic threat, including limited access to farms, limited processing capacity and reduced market demand. The role of different management approaches in reducing risk and vulnerability is also explored. Results suggest that concession areas having the largest accumulated and current biomass have the highest risk, which is also transferred to the municipal level. The scenarios modelled with better management practices that reduce diseases were able to reduce risks by 30-40%. The largest risk reduction is achieved when production biomass is divided in a more equitable manner among concession areas, suggesting the need for strategic improvements in spatial planning of the activity in the marine environment according to ecosystem carrying capacity and better practices. Improving adaptation capacity can reduce vulnerability between 20% and 30% for municipalities; for example, providing local employment can be a win-win management measure under the COVID-19 threat because it reduces movement of people and facilitates handling and responses to emergencies. A larger footprint in local economies and employment can also improve social perception and acceptance of the sector, thus contributing to improve adaptation changes and governance to face the threats. The framework used here to perform a risk and vulnerability assessment of salmon farming to the pandemic-associated threats can also be useful for other aquaculture systems elsewhere, provided that relevant information is available.

Sea trout adapt their migratory behaviour in response to high salmon lice concentrations.

Sea trout face growth-mortality trade-offs when entering the sea to feed. Salmon lice epizootics resulting from aquaculture have shifted these trade-offs, as salmon lice might both increase mortality and reduce growth of sea trout. We studied mortality and behavioural adaptations of wild sea trout in a large-scale experiment with acoustic telemetry in an aquaculture intensive area that was fallowed (emptied of fish) synchronically biannually, creating large variations in salmon lice concentrations. We tagged 310 wild sea trout during 3 years, and gave half of the individuals a prophylaxis against further salmon lice infestation. There was no difference in survival among years or between treatments. In years of high infestation pressure, however, sea trout remained closer to the river outlet, used freshwater (FW) habitats for longer periods and returned earlier to the river than in the low infestation year. This indicates that sea trout adapt their migratory behaviour by actively choosing FW refuges from salmon lice to escape from immediate mortality risk. Nevertheless, simulations show that these adaptations can lead to lost growth opportunities. Reduced growth can increase long-term mortality of sea trout due to prolonged exposure to size-dependent predation risk, lead to lower fecundity and, ultimately, reduce the likelihood of sea migration.

Exposure to teflubenzuron negatively impacts exploratory behavior, learning and activity of juvenile European lobster (Homarus gammarus).

Infestations with salmon lice, a parasitic copepod, is a major problem in the salmon farming industry. Teflubenzuron is an in-feed pharmaceutical applied to control lice outbreaks; the standard medication is 10 mg per kg fish per day for seven days. Surveys reveal that teflubenzuron accumulates and persists in the sediment around fish farms and causes deformities and mortality in juvenile European lobster (Homarus gammarus), a species commonly found in the vicinity of salmon farms in Norway. To date, there is no information on sub-lethal effects of teflubenzuron on, for example, behavior. We conducted an experiment to assess possible difference in the shelter seeking behavior of teflubenzuron-exposed (N = 19) vs. not exposed (N = 19) H. gammarus juveniles. The teflubenzuron-exposed juveniles had been given very low concentrations, 1.7 µg per pellet twice per week for 113 days prior to this experiment. The concentration of teflubenzuron was estimated to be less than 1 ng/g lobster when they were tested in the behavior experiment. Animals were placed in a lane with a shelter at one end. Once a lobster had found and entered the shelter, they were repeatedly displaced back to the opposite end of the lane, for a total of 3 repeated runs per animal. Three of the exposed juveniles failed to settle in the shelter, and the remaining teflubenzuron-exposed animals took significantly more time to explore the environment and to find and recognize shelter. Furthermore, exposed lobsters also exhibited slower walking speed compared to the controls. These results demonstrate that teflubenzuron significantly reduces exploratory behavior, learning and activity of juvenile H. gammarus. Thus, exposure to teflubenzuron could increase predation mortality of juvenile lobsters in the wild.

Occurrence and Distribution of Deltamethrin and Diflubenzuron in Surface Sediments from the Reloncaví Fjord and the Chiloé Inner-Sea (~ 39.5ºS -43ºS), Chilean Patagonia.

Surface sediments from Reloncaví Fjord and the Chiloé inner sea in Chilean Patagonia were extracted and analyzed to estimate deltamethrin and diflubenzuron levels. These antiparasitary pesticides have been used for decades in the salmon industry. Relationships were determined between pesticide concentrations and organic carbon percent in sediments. Deltamethrin (0.39-1.05 µg g-1 dw) was found at all sampling sites but diflubenzuron (0.06-0.09 µg g-1 dw) at only five. Diflubenzuron levels were similar for sediments from other fjord areas. However, deltamethrin concentration was 2-3 fold higher than other studies on this area. The organic carbon percent was correlated positively and significantly with diflubenzuron, but not with deltamethrin. Our results suggest that the high deltamethrin concentrations in sediments are due to the increased use of pyrethroids around salmon farming areas. But, the diflubenzuron levels can be explained by degradation processes.

Tenacibaculum finnmarkense sp. nov., a fish pathogenic bacterium of the family Flavobacteriaceae isolated from Atlantic salmon.

A novel Gram-stain negative, aerobic, non-flagellated, rod-shaped gliding bacterial strain, designated HFJ(T), was isolated from a skin lesion of a diseased Atlantic salmon (Salmo salar L.) in Finnmark, Norway. Colonies were observed to be yellow pigmented with entire and/or undulating margins and did not adhere to the agar. The 16S rRNA gene sequence showed that the strain belongs to the genus Tenacibaculum (family Flavobacteriaceae, phylum 'Bacteroidetes'). Strain HFJ(T) exhibits high 16S rRNA gene sequence similarity values to Tenacibaculum dicentrarchi NCIMB 14598(T) (97.2 %). The strain was found to grow at 2-20 °C and only in the presence of sea salts. The respiratory quinone was identified as menaquinone 6 and the major fatty acids were identified as summed feature 3 (comprising C16:1 ω7c and/or iso-C15:0 2-OH), iso-C15:0, anteiso-C15:0, iso-C15:1 and iso-C15:0 3-OH. The DNA G+C content was determined to be 34.1 mol%. DNA-DNA hybridization and comparative phenotypic and genetic tests were performed with the phylogenetically closely related type strains, T. dicentrarchi NCIMB 14598(T) and Tenacibaculum ovolyticum NCIMB 13127(T). These data, as well as phylogenetic analyses, suggest that strain HFJ(T) should be classified as a representative of a novel species in the genus Tenacibaculum, for which the name Tenacibaculum finnmarkense sp. nov. is proposed; the type strain is HFJ (T) = (DSM 28541(T) = NCIMB 42386(T)).

Amplified recruitment pressure of biofouling organisms in commercial salmon farms: potential causes and implications for farm management.

The development of biofouling on finfish aquaculture farms presents challenges for the industry, but the factors underlying nuisance growths are still not well understood. Artificial settlement surfaces were used to examine two possible explanations for high rates of biofouling in Norwegian salmon farms: (1) increased propagule release during net cleaning operations, resulting in elevated recruitment rates; and (2) potential reservoir effects of farm surfaces. The presence of salmon farms was associated with consistently and substantially (up to 49-fold) elevated recruitment rates. Temporal patterns of recruitment were not driven by net cleaning. Resident populations of biofouling organisms were encountered on all submerged farm surfaces. Calculations indicate that a resident population of the hydroid Ectopleura larynx, a major biofouling species, could release between 0.3 × 10(9) and 4.7 × 10(9) larvae per farm annually. Such resident populations could form propagule reservoirs and be one explanation for the elevated recruitment pressure at salmon farms.

Quantifying antimicrobial consumption in the Chilean salmon industry using standardized metrics and indicators: The case of florfenicol and oxytetracycline.

The adoption of standardized metrics and indicators of antimicrobial use (AMU) in the food animal industry is essential for the success of programs aimed at promoting the responsible and judicious use of antimicrobials in this activity. The objective of this study was to introduce the use of standardized AMU metrics and indicators to quantify the use of florfenicol and oxytetracycline in the Chilean salmon industry, and in this way evaluate the feasibility of their use given the type of health and production information currently managed by the National Fisheries and Aquaculture Service (SERNAPESCA), the Chilean agency responsible for regulating aquaculture in Chile. The data available from SERNAPESCA allowed the construction and evaluation of the most data-demanding AMU metrics and indicators. Consequently, the use of florfenicol and oxytetracycline administered by oral and parenteral routes was quantified using the treatment incidence based on both animal defined daily dose (TIDDDvet) and animal used daily dose (TIUDDA). To that end, the study included information from 1320 closed production cycles from farms rearing Atlantic salmon, coho salmon and rainbow trout that were active between January 2017 and December 2021. By applying standardized AMU metrics and indicators, we were able to determine that the median of TIDDDvet for florfenicol was 75.1 (80 % range, 20.0-158.0) DDDvet per ton-year at risk for oral procedures and 0.36 (80 % range, 0.07-1.19) DDDvet per ton-year at risk for parenteral procedures. For oxytetracycline, the median TIDDDvet was 3.09 (80 % range, 0.74-42.8) and 0.47 (80 % range, 0.09-1.68) DDDvet per ton-year at risk for oral and parenteral procedures, respectively. The median TIUDDA for treatments with florfenicol was 45.6 (80 % range, 10.9-96.5) UDDA per ton-year at risk for oral treatments and 0.28 (80 % range, 0.05-0.80) UDDA per ton-year at risk for parenteral treatments. For oxytetracycline, the median TIUDDA was 2.63 (80 % range, 0.61-28.2) UDDA per ton-year at risk for oral treatments and 0.41 (80 % range, 0.08-1.29) UDDA per ton-year at risk for parenteral treatments. This study demonstrates that it is feasible to move from traditional AMU metrics and indicators to standardized ones in the Chilean salmon industry. This is possible because the competent authority requires salmon farms to report detailed health and production information at a high frequency. The use of standardized AMU metrics and indicators can help the authority to have a more comprehensive view of the antimicrobial use in the Chilean salmon industry.

The combined impact of land use change and aquaculture on sediment and water quality in oligotrophic Lake Rupanco (North Patagonia, Chile, 40.8°S).

Water and sediment quality in North Patagonia's large, oligotrophic lakes are expected to suffer as native forest continues to be fragmented and degraded by its conversion to cropping and pasture land uses. These changes in land use are expected to increase diffuse nutrient loads to the region's lakes. In addition, these lakes are home to the world's second largest salmon aquaculture industry which provides additional point sources of nutrients within the lakes. We studied the combined influences of land use change and salmon farming on the nutrient concentrations in a North Patagonian lake (Lake Rupanco, 233 km(2) water surface, 163 m average depth) in four sub-watersheds ranging in disturbance from near-pristine forest to 53% converted to cropping and pasture. Nitrogen exports from the tributary sub-watersheds increased from 33 kg TN/km(2)/y to 621 kg TN/km(2)/y as the proportion of crop and pasture land increased. The combined nutrient load from land use change and salmon farming has led to significant differences in the nitrogen concentrations of the lake's water column and sediments in the near-shore zones across the lake. Total nitrogen concentrations in the sediments varied from 37 ± 18 mg/kg in near-pristine sub-watersheds without salmon farming to 6400 ± 698 mg/kg where the sub-watershed was dominated by crop and pasture lands combined with the presence of salmon farming. These results demonstrate the importance of considering the impacts of both salmon farming and land use on water and sediment quality for future environmental planning, management and decision making.

Exploring the Effects of Acute Stress Exposure on Lumpfish Plasma and Liver Biomarkers.

This study aimed to expand knowledge on lumpfish stress physiology by investigating the effects of acute stress on primary (i.e., cortisol) and secondary (e.g., metabolites) stress responses, as well as oxidative stress biomarkers, from stress exposure to a recovery phase. The results showed that the lumpfish physiological response to 1 min air exposure is mild, in line with recent studies, and comparable to that described for white sturgeons. Cortisol seems to be the most reliable acute stress biomarker in lumpfish, with a significant increase in plasma 30 min after stress exposure, returning to resting levels 2 h after exposure. In contrast, glucose and lactate were not significantly altered by short-term air exposure. Effects on hepatic energy mobilisation were also detected following the acute stress. This study showed that acute 1 min air exposure seems tolerable, allowing a swift recovery. However, more studies on the impacts of air exposure and repeated acute stressors on lumpfish stress and immune responses are required to develop industry standards for lumpfish health and welfare monitoring.

The relationship between salmon (Salmo salar) farming and cell abundance of harmful algal taxa.

The effects of nutrient effluents from fish cage aquaculture are an important eutrophication concern. It has been proposed that marine fish farm derived nutrients have the potential to increase phytoplankton abundance and lead to intensification of Harmful Algal Blooms (HABs), and that these blooms may negatively impact both the finfish and the shellfish industry. This study addressed this hypothesis using farmed salmon biomass in Scottish marine waters (as a proxy for nutrient load added to the water column as a consequence of fish farming) cell abundance of HAB taxa that most frequently impact shellfish farms and human health in the region (Dinophysis spp., Alexandrium spp. and Pseudo-nitzschia spp.), and cell abundance of one phytoplankton species of particular concern to the salmon farming industry (Karenia mikimotoi). Data from a 15-year weekly HAB monitoring programme and parallel national monitoring data relating to salmon farm stocking biomass were summarised in 5 km per 5 km aggregation boxes. Linear regression models were used to assess (i) inter-annual variation in cell abundance and total annual farmed salmon biomass; (ii) intra-annual (monthly) variation in harmful phytoplankton cell abundance and salmon biomass; (iii) a further analysis included seasonal effects within the intra-annual analysis. Farmed salmon biomass alone had a non-significant effect on cell abundance of any of the studied phytoplankton taxa. In contrast, a significant effect on cell abundance was found when using location, month or season as the predictive variable. Despite the non-significant impact of fish biomass on phytoplankton counts, the relationship varied seasonally, with a different response of Dinophysis spp. indicating a taxa specific interaction. A possible explanation for the lack of a significant relationship between farmed salmon and harmful phytoplankton cell abundance is that aquaculture farms are generally located in hydrodynamically energetic locations where recurrent flushing likely allows efficient dilution of nutrients. Overall, the analyses suggest that current levels of salmon farming activities do not markedly impact the abundance of routinely monitored biotoxin producing or fish killing phytoplankton taxa in Scottish waters.

The economic impact of decreased mortality and increased growth associated with preventing, replacing or improving current methods for delousing farmed Atlantic salmon in Norway.

Impacts of salmon lice is a major concern for a sustainable production of farmed Atlantic salmon in Norway. Most treatment methods for removal of salmon lice have associated increased mortality and decreased growth in a period after delousing, which affects the profitability of the farmer, and causes poor welfare and sustainability. In addition, the variance in mortality and growth, especially after non-medicinal treatment methods, is high, which makes it hard for a farmer to decide which control measure to apply to keep lice levels below the legal limit. In this study, we have applied a stochastic partial budget approach to assess the economic impact of reducing mortality and increasing growth of farmed Atlantic salmon by preventing, replacing and improving current delousing methods in Norway. We have simulated a production cycle of two different smolt-groups to find the outcome (harvested biomass, average end weight of the salmon, number of dead fish and feed consumption) of production cycles without or with two, three or four delousing treatments in the on-growing phase at sea. The results suggest that accounting for the biological losses associated with lice treatments is important when making choices of delousing strategies. The biological costs of increased mortality and decreased growth associated with especially non-medicinal treatments are expected to be high, but varies substantially. Therefore, the economic benefit of preventing or improving can also be high. The calculations imply that salmon producers could invest a considerable amount in measures for prevention or improvement of thermal treatments before break-even. For example could a farmer use on average 535,313 €/cage/ 1-yearling production in measure to prevent four thermal treatments before it is no longer economical beneficial. Depending on the performance of the four thermal treatments a farmer could use from 319,196-737,934 €/cage/ 1-yearling production on measures of improvement. Replacing one thermal treatment with another immediate treatment method has a minor economic benefit. The results further shows that sales value and feed consumption constitutes the largest share of the change in profit between different treatment regimes. The results from this study also show that not taking into account the risk of mortality and reduced growth associated with the different treatment methods of delousing, could lead to underestimating the benefit of improving, preventing and replacing treatments.

Qualitative Risk Assessment for Antimicrobial Resistance among Humans from Salmon Fillet Consumption Due to the High Use of Antibiotics against Bacterial Infections in Farmed Salmon.

Background: Worldwide, aquaculture is considered as a hotspot environment for antimicrobial resistance (AMR) due to the intense use of antibiotics in its productive systems. Chile is the second largest producer of farmed salmon worldwide, and tons of antibiotics are used to control bacterial diseases, such as Salmon Rickettsial Syndrome (SRS) and Bacterial Kidney Disease (BKD). However, studies determining the risk of consuming salmon fillets that have been treated with antibiotics during the salmon production are limited. Consulting leading experts in the field could provide a knowledge base to identify and address this question and research gaps. Methods: Multisectoral risk perception of AMR through salmon fillet consumption was evaluated by eliciting expert data obtained through discussions during a workshop and from questionnaires given to experts from academia (n = 15, 63%), the public sector (n = 5, 21%), and the salmon industry (n = 4, 17%). Results: The qualitative risk analysis suggested an overall 'low' probability of AMR acquisition by consumption of salmon fillet that had been treated during the production cycle. The risk perception varied slightly between production stages in freshwater and seawater. In consensus with all sectors, this overall 'low', but existing, risk was probably associated with bacterial infections and the use of antibiotics. Conclusions: As it is essential to reduce the use of antibiotics in the Chilean salmon industry, this intersectoral approach and consensual results could favor effective implementation of targeted initiatives for the control and prevention of major bacterial diseases.

Distinct polymer-dependent sorption of persistent pollutants associated with Atlantic salmon farming to microplastics.

Interactions of microplastics and persistent organic pollutants (POPs) associated with Atlantic salmon farming were studied to assess the potential role of microplastics in relation to the environmental impact of aquaculture. HDPE, PP, PET and PVC microplastics placed for 3 months near fish farms sorbed POPs from aquafeeds. PET and PVC sorbed significantly higher levels of dioxins and PCBs compared to HDPE, while the levels sorbed to PP were intermediate and did not differ statistically from PET, PVC or HDPE. In addition, the composition of dioxins accumulated in caged blue mussels did not reflect the patterns observed on the microplastics, probably due to polymer-specific affinity of POPs. In conclusion, the results of this study show that microplastics occurring near fish farms can sorb aquafeed-associated POPs and, therefore, microplastics could potentially be vectors of such chemicals in the marine environment and increase the environmental impact of fish farming.

Heterosigma akashiwo in Patagonian Fjords: Genetics, Growth, Pigment Signature and Role of PUFA and ROS in Ichthyotoxicity.

Heterosigma akashiwo is the only raphidophyte described for Chilean waters. A recent 2021 fish-killing bloom event of this raphidophyte ignited scientific research, but the ichthyotoxic mechanism and environmental conditions that promote its growth are still unclear. This is the first study confirming the occurrence of H. akashiwo in Chilean waters on the basis of the region D1/D2 of the 28S ribosomal gene. The pigment signature of the CREAN_HA03 strain revealed chlorophyll-a, fucoxanthin, and violaxanthin as the most abundant pigments, but profiles were variable depending on culture and field conditions. A factorial temperature−salinity growth experiment showed a maximal growth rate of 0.48 d−1 at 17 °C and 35 in salinity, but reached a maximal cell abundance of ~50,000 cells mL−1 at 12 °C and 25 in salinity. The fatty acid profile included high levels of saturated (16:0) and polyunsaturated (18:4 ω3; 20:5 ω3) fatty acids, but superoxide production in this strain was low (~0.3 pmol O2− cell−1 h−1). The RTgill-W1 bioassay showed that the H. akashiwo strain was cytotoxic only at high cell concentrations (>47,000 cells mL−1) and after cell rupture. In conclusion, salmon mortality during H. akashiwo bloom events in Patagonian fjords is likely explained by the high production of long-chain PUFAs at high cell densities, but only in the presence of high ROS production.

Characterization of a Novel Variant of the Quinolone-Resistance Gene qnrB (qnrB89) Carried by a Multi-Drug Resistant Citrobacter gillenii Strain Isolated from Farmed Salmon in Chile.

The main objective of this study was to characterize using whole-genome sequencing analysis, a new variant of the qnrB gene (qnrB89) carried by a fluoroquinolone-susceptible bacterium isolated from mucus of farmed Salmo salar fingerling in Chile. Citrobacter gillenii FP75 was identified by using biochemical tests and 16S ribosomal gene analysis. Nucleotide and amino acid sequences of the qnrB89 gene exhibited an identity to qnrB of 81.24% and 91.59%, respectively. The genetic environment of qnrB89 was characterized by the upstream location of a sequence encoding for a protein containing a heavy metal-binding domain and a gene encoding for a N-acetylmuramoyl-L-alanine amidase protein, whereas downstream to qnrB89 gene were detected the csp and cspG genes, encoding cold-shock proteins. The qnrB89 gene was located on a large chromosomal contig of the FP75 genome and was not associated with the 10-kb plasmid and class 1 integron harbored by the FP75 strain. This study reports for the first time the carriage of a qnrB gene by the C. gillenii species, and its detection in a bacterial strain isolated from farmed salmon in Chile.

Genetic Characterization of the Tetracycline-Resistance Gene tet(X) Carried by Two Epilithonimonas Strains Isolated from Farmed Diseased Rainbow Trout, Oncorhynchus mykiss in Chile.

The main objective of this study was to characterize the tet(X) genes, which encode a monooxygenase that catalyzes the degradation of tetracycline antibiotics, carried by the resistant strains FP105 and FP233-J200, using whole-genome sequencing analysis. The isolates were recovered from fin lesion and kidney samples of diseased rainbow trout Oncorhynchus mykiss, during two Flavobacteriosis outbreaks occurring in freshwater farms located in Southern Chile. The strains were identified as Epilithonimonas spp. by using biochemical tests and by genome comparison analysis using the PATRIC bioinformatics platform and exhibited a minimum inhibitory concentration (MIC) of oxytetracycline of 128 µg/mL. The tet(X) genes were located on small contigs of the FP105 and FP233-J200 genomes. The sequences obtained for the tet(X) genes and their genetic environment were compared with the genomes available in the GenBank database of strains of the Chryseobacterium clade belonging to the Flavobacterium family, isolated from fish and carrying the tet(X) gene. The Tet(X) proteins synthesized by the Chilean Epilithonimonas strains showed a high amino acid similarity (range from 84% to 100%), with the available sequences found in strains belonging to the genus Chryseobacterium and Flavobacterium isolated from fish. An identical neighborhood of tet(X) genes from both Chilean strains was observed. The genetic environment of tet(X) observed in the two strains of Epilithonimonas studied was characterized by the upstream location of a sequence encoding a hypothetical protein and a downstream located alpha/beta hydrolase-encoding gene, similar to the observed in some of the tet(X) genes carried by Chryseobacterium and Flavobacterium strains isolated from fish, but the produced proteins exhibited a low amino acid identity (25-27%) when compared to these synthesized by the Chilean strains. This study reports for the first time the carriage of the tet(X) gene by the Epilithonimonas genus and their detection in fish pathogenic bacteria isolated from farmed salmonids in Chile, thus limiting the use of therapies based on oxytetracycline, the antimicrobial most widely used in Chilean freshwater salmonid farming. This results suggest that pathogenic strains of the Chryseobacterium clade occurring in Chilean salmonid farms may serve as important reservoirs of tet(X) genes.

Different antibiotic profiles in wild and farmed Chilean salmonids. Which is the main source for antibiotic in fish?

Fish from both aquaculture and wild capture are exposed to veterinary and medicinal antibiotics (ABs). This study explored the occurrence and probable source of 46 antibiotic residues in muscle of farmed salmon and wild trout from Chile. Results showed that at least one AB was detected in all studied samples. Diverse patterns were observed between farmed and wild specimens, with higher ABs concentrations in wild fish. Considering antimicrobial resistance, detected ABs corresponded to the categories B (Restrict), C (Caution) and D (Prudence) established by Antimicrobial Advice Ad Hoc Expert Group (European Medicines Agency). Multivariate statistic was used to verify differences between farmed and wild populations, looking for the probable source of ABs as well. Principal components analysis (PCA) revealed that ciprofloxacin, moxifloxacin, enrofloxacin, amoxicillin, penicillin G, oxolinic acid, sulfamethoxazole, trimethoprim and clarithromycin were associated with wild samples, collected during the cold season. Conversely, norfloxacin, sulfaquinoxaline, sulfadimethoxine, nitrofurantoin, nalidixic acid, penicillin V, doxycycline, flumequine, oxacillin, pipemidic acid and sulfamethizole were associated with wild samples collected during the warm season. All farmed salmon samples were associated with ofloxacin, tetracycline, cephalexin, erythromycin, azithromycin, roxithromycin, sulfabenzamide, sulfamethazine, sulfapyridine, sulfisomidin, and sulfaguanidine. In addition, linear discriminant analysis showed that the AB profile in wild fish differ from farmed ones. Most samples showed ABs levels below the EU regulatory limit for edible fish, except for sulfaquinoxaline in one sample. Additionally, nitrofurantoin (banned in EU) was detected in one aquaculture sample. The differences observed between farmed and wild fish raise questions on the probable source of ABs, either aquaculture or urban anthropic activities. Further research is necessary for linking the ABs profile in wild fish with the anthropic source. However, to our knowledge, this is the first report showing differences in the ABs profile between wild and aquaculture salmonids, which could have both environmental and health consequences.