Salmonid Rickettsial Septicemia Research Articles

Salmon-IgM Functionalized-PLGA Nanosystem for Florfenicol Delivery as an Antimicrobial Strategy against Piscirickettsia salmonis.

Salmonid rickettsial septicemia (SRS), caused by Piscirickettsia salmonis, has been the most severe health concern for the Chilean salmon industry. The efforts to control P. salmonis infections have focused on using antibiotics and vaccines. However, infected salmonids exhibit limited responses to the treatments. Here, we developed a poly (D, L-lactide-glycolic acid) (PLGA)-nanosystem functionalized with Atlantic salmon IgM (PLGA-IgM) to specifically deliver florfenicol into infected cells. Polymeric nanoparticles (NPs) were prepared via the double emulsion solvent-evaporation method in the presence of florfenicol. Later, the PLGA-NPs were functionalized with Atlantic salmon IgM through carbodiimide chemistry. The nanosystem showed an average size of ~380-410 nm and a negative surface charge. Further, florfenicol encapsulation efficiency was close to 10%. We evaluated the internalization of the nanosystem and its impact on bacterial load in SHK-1 cells by using confocal microscopy and qPCR. The results suggest that stimulation with the nanosystem elicits a decrease in the bacterial load of P. salmonis when it infects Atlantic salmon macrophages. Overall, the IgM-functionalized PLGA-based nanosystem represents an alternative to the administration of antibiotics in salmon farming, complementing the delivery of antibiotics with the stimulation of the immune response of infected macrophages.

Utilization of publicly available data to summarize spatio-temporal patterns of fish health events of Atlantic salmon (Salmo salar) reported by marine finfish industries in British Columbia (BC), Canada.

Atlantic salmon aquaculture companies in British Columbia (BC) must report fish health events to Fisheries and Oceans Canada (DFO) as part of their licensing conditions. Our study aimed to summarize these fish health events reported by Atlantic salmon sites in BC to identify spatial and spatio-temporal clusters. We conducted descriptive, retrospective global, and local cluster analyses using Moran's I and scan statistics. Between 2016 and 2022, 265 fish health events were reported. The annual incidence ranged from 5.60 (95% CI: 3.90-7.80) to 6.86 (95% CI: 4.70-9.60) health events per 100 active site-months. The most common events were yellow mouth (60.75%; 161/265) and salmonid rickettsial septicaemia (SRS) (15.47%; 41/265). The Moran's I index was positive and significant for yellow mouth, SRS, and overall fish health events at different distance bands. Most of the spatial and spatio-temporal clusters were identified in the west-central and southwestern parts of Vancouver Island. Our study hypothesizes that management practices, environmental conditions, and water quality parameters may have influenced the increased reporting of fish health events in these regions. Overall, the study highlights the potential of publicly available data for practical risk mapping in understanding the patterns of farmed Atlantic salmon diseases in BC.

Salmonid Rickettsial Septicemia (SRS) disease dynamics and Atlantic salmon immune response to Piscirickettsia salmonis LF-89 and EM-90 co-infection

In Chile, Piscirickettsia salmonis contains two genetically isolated genogroups, LF-89 and EM-90. However, the impact of a potential co-infection with these two variants on Salmonid Rickettsial Septicemia (SRS) in Atlantic salmon (Salmo salar) remains largely unexplored. In our study, we evaluated the effect of P. salmonis LF-89-like and EM-90-like co-infection on post-smolt Atlantic salmon after an intraperitoneal challenge to compare changes in disease dynamics and host immune response. Co-infected fish had a significantly lower survival rate (24.1%) at 21 days post-challenge (dpc), compared with EM-90-like single-infected fish (40.3%). In contrast, all the LF-89-like single-infected fish survived. In addition, co-infected fish presented a higher presence of clinical lesions than any of the single-infected fish. The gene expression of salmon immune-related biomarkers evaluated in the head kidney, spleen, and liver showed that the EM-90-like isolate and the co-infection induced the up-regulation of cytokines (e.g., il-1β, ifnγ, il8, il10), antimicrobial peptides (hepdicin) and pattern recognition receptors (PRRs), such as TLR5s. Furthermore, in serum samples from EM-90-like and co-infected fish, an increase in the total IgM level was observed. Interestingly, specific IgM against P. salmonis showed greater detection of EM-90-like antigens in LF-89-like infected fish serum (cross-reaction). These data provide evidence that P. salmonis LF-89-like and EM-90-like interactions can modulate SRS disease dynamics in Atlantic salmon, causing a synergistic effect that increases the severity of the disease and the mortality rate of the fish. Overall, this study contributes to achieving a better understanding of P. salmonis population dynamics.

The Effect of an Attenuated Live Vaccine against Salmonid Rickettsial Septicemia in Atlantic Salmon (Salmo salar) Is Highly Dependent on Water Temperature during Immunization.

Salmonid Rickettsial Septicemia (SRS), caused by the bacterium Piscirickettsia salmonis, is the main reason for antibiotic usage in the Chilean aquaculture industry. In 2016, a live attenuated vaccine (ALPHA JECT LiVac® SRS, PHARMAQ AS) was licensed in Chile and has been widely used in farmed salmonids since then. In experimental injection and cohabitation laboratory challenge models, we found that the vaccine is effective in protecting Atlantic salmon (Salmo salar) for at least 15 months against P. salmonis-induced mortality. However, the protection offered by the vaccine is sensitive to temperature during immunization. Fish vaccinated and immunized at 10 °C and above were well protected, but those immunized at 7 °C and 8 °C (the lower end of the temperature range commonly found in Chile) experienced a significant loss of protection. This temperature-dependent loss of effect correlated with the amount of vaccine-strain RNA detected in the liver the first week after vaccination and with in vitro growth curves, which failed to detect any growth at 8 °C. We found that good vaccine efficacy can be restored by exposing fish to 15 °C for the first five days after vaccination before lowering the temperature to 7 °C for the remaining immunization period. This suggests that maintaining the correct temperature during the first few days after vaccination is crucial for achieving a protective immune response with ALPHA JECT LiVac® SRS. Our results emphasize the importance of temperature control when vaccinating poikilothermic animals with live vaccines.

Cohabitation of Piscirickettsia salmonis genogroups (LF-89 and EM-90): synergistic effect on growth dynamics

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 co-cultures, 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.

Bacterial networks in Atlantic salmon with Piscirickettsiosis

An unbalanced composition of gut microbiota in fish is hypothesized to play a role in promoting bacterial infections, but the synergistic or antagonistic interactions between bacterial groups in relation to fish health are not well understood. We report that pathogenic species in the Piscirickettsia, Aeromonas, Renibacterium and Tenacibaculum genera were all detected in the digesta and gut mucosa of healthy Atlantic salmon without clinical signs of disease. Although Piscirickettsia salmonis (and other pathogens) occurred in greater frequencies of fish with clinical Salmonid Rickettsial Septicemia (SRS), the relative abundance was about the same as that observed in healthy fish. Remarkably, the SRS-positive fish presented with a generalized mid-gut dysbiosis and positive growth associations between Piscirickettsiaceae and members of other taxonomic families containing known pathogens. The reconstruction of metabolic phenotypes based on the bacterial networks detected in the gut and mucosa indicated the synthesis of Gram-negative virulence factors such as colanic acid and O-antigen were over-represented in SRS positive fish. This evidence indicates that cooperative interactions between organisms of different taxonomic families within localized bacterial networks might promote an opportunity for P. salmonis to cause clinical SRS in the farm environment.

High‐throughput genotyping in estimating genetic resources and detecting pathogens in aquaculture

High‐throughput genotyping in estimating genetic resources and detecting pathogens in aquaculture

Nutrient Scarcity in a New Defined Medium Reveals Metabolic Resistance to Antibiotics in the Fish Pathogen Piscirickettsia salmonis.

Extensive use of antibiotics has been the primary treatment for the Salmonid Rickettsial Septicemia, a salmonid disease caused by the bacterium Piscirickettsia salmonis. Occurrence of antibiotic resistance has been explored in various P. salmonis isolates using different assays; however, P. salmonis is a nutritionally demanding intracellular facultative pathogen; thus, assessing its antibiotic susceptibility with standardized and validated protocols is essential. In this work, we studied the pathogen response to antibiotics using a genomic, a transcriptomic, and a phenotypic approach. A new defined medium (CMMAB) was developed based on a metabolic model of P. salmonis. CMMAB was formulated to increase bacterial growth in nutrient-limited conditions and to be suitable for performing antibiotic susceptibility tests. Antibiotic resistance was evaluated based on a comprehensive search of antibiotic resistance genes (ARGs) from P. salmonis genomes. Minimum inhibitory concentration assays were conducted to test the pathogen susceptibility to antibiotics from drug categories with predicted ARGs. In all tested P. salmonis strains, resistance to erythromycin, ampicillin, penicillin G, streptomycin, spectinomycin, polymyxin B, ceftazidime, and trimethoprim was medium-dependent, showing resistance to higher antibiotic concentrations in the CMMAB medium. The mechanism for antibiotic resistance to ampicillin in the defined medium was further explored and was proven to be associated to a decrease in the bacterial central metabolism, including the TCA cycle, the pentose-phosphate pathway, energy production, and nucleotide metabolism, and it was not associated with decreased growth rate of the bacterium or with the expression of any predicted ARG. Our results suggest that nutrient scarcity plays a role in the bacterial antibiotic resistance, protecting against the detrimental effects of antibiotics, and thus, we propose that P. salmonis exhibits a metabolic resistance to ampicillin when growing in a nutrient-limited medium.

Effectiveness of a proteoliposome-based vaccine against salmonid rickettsial septicaemia in Oncorhynchus mykiss

Salmonid rickettsial septicaemia (SRS) is a contagious disease caused by Piscirickettsia salmonis, an intracellular bacterium. SRS causes an estimated economic loss of $700 million USD to the Chilean industry annually. Vaccination and antibiotic therapy are the primary prophylactic and control measures used against SRS. Unfortunately, commercially available SRS vaccines have not been shown to have a significant effect on reducing mortality. Most vaccines contain whole inactivated bacteria which results in decreased efficacy due to the limited ability of the vaccine to evoke a cellular mediated immune response that can eliminate the pathogen or infected cells. In addition, SRS vaccine efficacy has been evaluated primarily with Salmo salar (Atlantic salmon). Vaccine studies using Oncorhynchus mykiss (rainbow trout) are scarce, despite SRS being the leading cause of infectious death for this species. In this study, we evaluate an injectable vaccine based on P. salmonis proteoliposome; describing the vaccine security profile, capacity to induce specific anti-P. salmonis IgM and gene expression of immune markers related to T CD8 cell-mediated immunity. Efficacy was determined by experimental challenge with P. salmonis intraperitoneally. Our findings indicate that a P. salmonis proteoliposome-based vaccine is able to protect O. mykiss against challenge with a P. salmonis Chilean isolate and causes a specific antibody response. The transcriptional profile suggests that the vaccine is capable of inducing cellular immunity. This study provides new insights into O. mykiss protection and the immune response induced by a P. salmonis proteoliposome-based vaccine.

RNA-Seq-Based Analysis of Cortisol-Induced Differential Gene Expression Associated with Piscirickettsia salmonis Infection in Rainbow Trout (Oncorhynchus mykiss) Myotubes.

Simple SummarySkeletal muscle is the most abundant tissue in fish and the main product of the Chilean salmonid aquaculture industry. Intensive farming conditions generate stress and increased susceptibility to infectious diseases, such as salmonid rickettsial septicemia (SRS), that directly affect this tissue. However, the immunocompetence of skeletal muscle during infection is poorly understood. To further explore the interplay between pathogen infection and stress on this tissue, we analyze the transcriptional profile of isolated rainbow trout (Oncorhynchus mykiss) muscle cells pretreated with 3 h of the stress hormone cortisol, and then infected with the SRS etiologic agent Piscirickettsia salmonis for 8 h, using RNA sequencing technology. For the first time, the obtained data reveals the biological processes related to programmed cell death, negative regulation of cell proliferation, and innate immune response. These results are validated by real-time qPCR. Furthermore, cortisol pretreatment significantly stimulated bacterial gene expression compared to infected cells. These data demonstrated that fish skeletal muscle can activate an intrinsic immune-like response against P. salmonis that is differentially regulated by cortisol. The information provided here will help us to understand the molecular mechanisms of fish muscle cells respond to infection, which could prevent P. salmonis outbreaks in skeletal muscle under stress conditions.Salmonid rickettsial septicemia (SRS) is the major infectious disease of the Chilean salmonid aquaculture industry caused by Piscirickettsia salmonis. Intensive farming conditions generate stress and increased susceptibility to diseases, being skeletal muscle mainly affected. However, the interplay between pathogen infection and stress in muscle is poorly understood. In this study, we perform an RNA-seq analysis on rainbow trout myotubes that are pretreated for 3 h with cortisol (100 ng/mL) and then infected with P. salmonis strain LF-89 for 8 h (MOI 50). Twelve libraries are constructed from RNA samples (n = 3 per group) and sequenced on Illumina HiSeq 4000. A total of 704,979,454 high-quality reads are obtained, with 70.25% mapped against the reference genome. In silico DETs include 175 total genes—124 are upregulated and 51 are downregulated. GO enrichment analysis reveals highly impacted biological processes related to apoptosis, negative regulation of cell proliferation, and innate immune response. These results are validated by RT-qPCR of nine candidate transcripts. Furthermore, cortisol pretreatment significantly stimulated bacterial gene expression of ahpC and 23s compared to infection. In conclusion, for the first time, we describe a transcriptomic response of trout myotubes infected with P. salmonis by inducing apoptosis, downregulating cell proliferation, and intrinsic immune-like response that is differentially regulated by cortisol.

Increased dietary availability of selenium in rainbow trout (Oncorhynchus mykiss) improves its plasma antioxidant capacity and resistance to infection with Piscirickettsia salmonis

Salmonid Rickettsial Septicaemia (SRS), caused by Piscirickettsia salmonis, is the most important infectious disease in the Chilean salmon farming industry. An opportunity to control this disease is to use functional micronutrients to modulate host mechanisms of response to the infection. Since P. salmonis may affect the host antioxidant system in salmonids, particularly that dependent on selenium (Se), we hypothesized that fish’s dietary selenium supplementation could improve the response to the bacterial infection. To address this, we defined a non-antibiotic, non-cytotoxic concentration of selenium to evaluate its effect on the response to in vitro infections of SHK-1 cells with P. salmonis. The results indicated that selenium supplementation reduced the cytopathic effect, intracellular bacterial load, and cellular mortality of SHK-1 by increasing the abundance and activity of host glutathione peroxidase. We then prepared diets supplemented with selenium up to 1, 5, and 10 mg/kg to feed juvenile trout for 8 weeks. At the end of this feeding period, we obtained their blood plasma and evaluated its ability to protect SHK-1 cells from infection with P. salmonis in ex vivo assays. These results recapitulated the observed ability of selenium to protect against infection with P. salmonis by increasing the concentration of selenium and the antioxidant capacity in fish’s plasma. To the best of our knowledge, this is the first report of the protective capacity of selenium against P. salmonis infection in salmonids, becoming a potential effective host-directed dietary therapy for SRS and other infectious diseases in animals at a non-antibiotic concentration.

Non-Specific Antibodies Induce Lysosomal Activation in Atlantic Salmon Macrophages Infected by Piscirickettsia salmonis.

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.

Pharmacological iron-chelation as an assisted nutritional immunity strategy against Piscirickettsia salmonis infection

Salmonid Rickettsial Septicaemia (SRS), caused by Piscirickettsia salmonis, is a severe bacterial disease in the Chilean salmon farming industry. Vaccines and antibiotics are the current strategies to fight SRS; however, the high frequency of new epizootic events confirms the need to develop new strategies to combat this disease. An innovative opportunity is perturbing the host pathways used by the microorganisms to replicate inside host cells through host-directed antimicrobial drugs (HDAD). Iron is a critical nutrient for P. salmonis infection; hence, the use of iron-chelators becomes an excellent alternative to be used as HDAD. The aim of this work was to use the iron chelator Deferiprone (DFP) as HDAD to treat SRS. Here, we describe the protective effect of the iron chelator DFP over P. salmonis infections at non-antibiotic concentrations, in bacterial challenges both in vitro and in vivo. At the cellular level, our results indicate that DFP reduced the intracellular iron content by 33.1% and P. salmonis relative load during bacterial infections by 78%. These findings were recapitulated in fish, where DFP reduced the mortality of rainbow trout challenged with P. salmonis in 34.9% compared to the non-treated group. This is the first report of the protective capacity of an iron chelator against infection in fish, becoming a potential effective host-directed therapy for SRS and other animals against ferrophilic pathogens.

Development of a Piscirickettsia salmonis immersion challenge model to investigate the comparative susceptibility of three salmon species.

Piscirickettsia salmonis, the aetiological agent of salmonid rickettsial septicaemia (SRS), is a global pathogen of wild and cultured marine salmonids. Here, we describe the development and application of a reproducible, standardized immersion challenge model to induce clinical SRS in juvenile pink (Oncorhynchus gorbuscha), Atlantic (Salmo salar) and sockeye salmon (O. nerka). Following a 1‐hr immersion in 105 colony‐forming units/ml, cumulative mortality in Atlantic salmon was 63.2% while mortality in sockeye salmon was 10%. Prevalence and levels of the bacterium in kidney prior to onset of mortality were lower in sockeye compared with Atlantic or pink salmon. The timing and magnitude of bacterial shedding were estimated from water samples collected during the exposure trials. Shedding was estimated to be 82‐fold higher in Atlantic salmon as compared to sockeye salmon and peaked in the Atlantic salmon trial at 36 d post‐immersion. These data suggest sockeye salmon are less susceptible to P. salmonis than Atlantic or pink salmon. Finally, skin lesions were observed on infected fish during all trials, often in the absence of detectable infection in kidney. As a result, we hypothesize that skin is the primary point of entry for P. salmonis during the immersion challenge.

Development of simulation models for transmission of Salmonid Rickettsial Septicaemia between salt water fish farms in Chile.

This study aimed at estimating parameters representing between-farm transmission of Salmonid Rickettsial Septicaemia (SRS) in Chile, and developing and validating simulation models to predict weekly spread of SRS between farms in Los Lagos (Region 10), using InterSpread Plus. The model parameters were estimated by analyses of the historical SRS outbreak data. The models incorporated time and distance-dependent transmission kernels, representing the probabilities of waterborne spread of SRS between farms. Seven candidate transmission kernels were estimated, with varying maximum distance of between-farm SRS spread (15-60km). Farms were categorized by size (small; medium; large) and species (Coho salmon; Atlantic salmon; rainbow trout). The time that it took a farm to recover from infection was parameterized to be shortest for small Coho farms (median: 7weeks), followed by medium and large Coho farms (median: 25weeks), Atlantic salmon farms (median: 42weeks, any size) and rainbow trout farms (median: 43weeks, any size). The relative infectiousness parameters of rainbow trout farms were 1.5-6.3 times that of Coho or Atlantic salmon, or those of large farms was 1.3-4.2 times that of small or medium farms. The models predicted SRS prevalence in Region 10 between 2013 and 2015 (79weeks) with 76.5%-93.0% overall accuracy. The model with a transmission kernel of <20km (P20) achieved a maximum overall accuracy (93.0%). Within each neighbourhood, the accuracy of P20 varied between 32.4% and 88.1%; 13/20 neighbourhoods had a reasonable temporal agreement between the simulated and actual dynamics of SRS (within 5th-95th percentiles), but 5/20 neighbourhoods underestimated and 2/20 overestimated the SRS spread. The model could be used for evaluation of semi-global control policies in Region 10, while addition of other factors such as seasonality, ocean currents, and movement of infected fish may improve the model performance at a finer scale.

Is between-farm water-borne pathogen dissemination an important driver in the epidemiology of salmonid rickettsial septicaemia in Chile?

Although the bacterium Piscirickettsia salmonis has been detected in many salmon-producing countries around the world, losses caused by salmonid rickettsial septicaemia (SRS) are mostly occurring in the Chilean aquaculture industry. Horizontal transmission of SRS between salmonid farms was suggested, based on the existence of spatiotemporal correlation in the level of disease between neighbouring sea farms. However, it remains unclear to which extent between-farm water-borne pathogen dissemination is important in the epidemiology of SRS in Chile. Such information is critical to assess the level of risk of transmission of SRS from one farm to another at different mortality incidence levels and to apply appropriate and cost-effective mitigation measures. In this study, we used weekly SRS mortality data from all salmonid farms in the Los Lagos region between January 2012 and September 2018 to model the spatiotemporal autocorrelation in the SRS-attributed mortality in the study area. A generalized additive regression modelling framework was adopted, using a linear functional component to model the influence of other farms on the target farm. Several nested statistical models were built to compare the significance of different covariates. Predicted values of SRS mortality on the target farm, conditional on different distance, time lag and mortality values from the source farms were estimated from the best model. The results showed that there was a statistically significant association between the weekly mortality incidence at source farms and the mortality incidence at target farms during the same week and during the previous weeks. This study did not provide evidence that the spatiotemporal correlation observed in SRS mortality may be due to water-borne pathogen dissemination between farms and alternative explanatory mechanisms should be investigated. It remains possible that the patterns of lagged correlation observed between source and target farm mortality may be due to a model artefact. In addition, there was no evidence of a threshold effect above which farms pose a substantially larger health risk to their neighbours. Stronger evidence for or against between-farm transmission of P. salmonis may be obtained by different methods.

Use of regulatory data to describe and identify risk factors for salmonid rickettsial septicaemia in Chile, 2011–2017

The bacterial disease salmonid rickettsial septicaemia (SRS) has caused substantial economic losses in the salmonid aquaculture industry, particularly in Chile. Increasing understanding of the epidemiology of this disease is important for improving the productivity and sustainability of the industry: by identifying important influences on disease occurrence, interventions can be identified and optimised to minimise disease occurrence and its effect on the industry. This study aimed to describe SRS-attributed mortality across production species, time and space in the Chilean salmonid industry; identify risk factors for mortality attributed to SRS; and generate additional hypotheses for future investigations of SRS epidemiology in the Chilean salmonid industry. Regulatory data held in the Sistema de Fiscalización de la Acuicultura and Informe Ambiental para la Acuicultura databases of Servicio Nacional de Pesca y Acuicultura (‘Sernapesca’, the Chilean National Fisheries and Aquaculture Service) were analysed using the information-theoretic approach for risk factor analysis. Post hoc modelling generated hypotheses for future investigations. Analyses determined associations between the outcomes of SRS-attributed mortality incidence risk and rate across salmonid production cycles with a range of putative risk factors. Results indicate that salmonid production species is a key driver of the risk of a Chilean salmonid production cycle experiencing SRS-attributed mortality, and the SRS-attributed mortality rate amongst affected cycles. Compared to Atlantic salmon, rainbow trout and coho salmon production cycles were less likely to report SRS-attributed mortality (rainbow trout: incidence risk ratio = 0.17, 95% CI 0.07–0.40, p < .001; coho salmon: incidence risk ratio 0.05, 95% CI 0.02–0.11, p < .001). Amongst affected production cycles, coho salmon had a relatively reduced incidence rate of SRS-attributed mortality (incidence rate ratio = 0.32, 95% CI 0.20–0.49, p < .001) whilst rainbow trout had a relatively increased rate (incidence rate ratio = 3.60, 95% CI 2.51–5.17, p < .001). The incidence rate of SRS-attributed mortality was considerably lower in one region (Region XII: incidence rate ratio = 0.000003, 95% CI 0.0000003–0.00002; p < .001) compared to other regions (Regions X and XI). Further hypotheses for investigation generated in this study include associations between aspects of vaccination strategy and improved SRS-attributed mortality outcomes. This study highlights specific considerations for further epidemiological investigations using routinely collected Chilean aquaculture regulatory data.

Effectiveness of antimicrobial treatment of salmonid rickettsial septicaemia in commercial salmon and trout farms in Chile

Salmonid rickettsial septicaemia (SRS) is the most important disease of farmed salmonid fish in Chile and the main driver of a high rate of antimicrobial use. This study evaluated the effectiveness of antimicrobial treatment of SRS outbreaks, using industry-generated data from 8318 cage-level production cycles stocked between 2003 and 2018. We defined SRS outbreaks by a specified level of SRS-attributed mortality over a 3-week period and calculated the mortality rate attributed to SRS and unknown causes during a follow-up period from the start of treatment until resolution of the outbreak. The post-treatment mortality rate was used as a proxy for assessing the effectiveness of the antimicrobial treatment on the magnitude of the SRS outbreak. After developing a causal diagram, we analyzed the data with generalized, mixed-effects regression models within an information-theoretic framework. For producers of Atlantic salmon, our results suggest that treatment should be provided to all infected cages on the farm, without interruption, as soon as possible after the start of the SRS outbreak. For producers of rainbow trout, our results suggest that treatment should be initiated as early as possible after the start of the SRS outbreak and with longer treatment durations if using in-feed florfenicol treatments. In the rainbow trout model, the large proportion of unexplained variance at the company and farm level indicates that lessons can be learned from the experience of other companies and farms. This study demonstrates the value of integrating aquaculture industry-generated health and management data to support applied epidemiological research.

Effectiveness of vaccination for the control of salmonid rickettsial septicaemia in commercial salmon and trout farms in Chile

Salmon rickettsial septicaemia (SRS, or piscirickettsiosis) is a major disease of the Chilean salmonid aquaculture industry. Although numerous vaccines for SRS are currently registered for use in Chile, there is little evidence of their effectiveness under field conditions. In this study, we aimed to quantify the effectiveness of different vaccination strategies in delaying the time from stocking to the first SRS outbreak and reducing SRS-attributable mortality over the full production cycle for Atlantic salmon, rainbow trout and coho salmon. We analysed data from 5446 cage-level production cycles across 248 farms using linear mixed-effects models and Cox regression within an information-theoretic framework. In Atlantic salmon and rainbow trout (but not in coho salmon), we found some freshwater vaccination regimens to be significantly better than others. In contrast to some previous studies, we did not observe a beneficial effect of booster vaccinations in the seawater phase of production. Our study highlights that the occurrence of SRS is influenced by multiple factors, and illustrates opportunities and challenges in using routine industry-generated data for epidemiological research.

Chilean aquaculture and the new challenges: Pathogens, immune response, vaccination and fish diversification

In Chile, the salmon and trout farmed fishing industries have rapidly grown during the last years, becoming one of the most important economic sources for the country. However, infectious diseases caused by bacteria, virus, mycoses and parasites, result in losses of up to 700 million dollars per year for the Chilean aquaculture production with the consequent increase of antibiotic and antiparasitic usage. After 30 years of its first appearance, the main salmon health problem is still the salmonid rickettsial septicaemia (SRS), which together with other disease outbreaks, reveal that vaccines do not provide acceptable levels of long-lasting immune protection in the field. On the other hand, due to the large dependence of the industry on salmonids production, the Chilean government promoted the Aquaculture diversification program by 2009, which includes new species such as Merluccius australis, Cilus gilberti and Genypterus chilensis, however, specific research regarding the immune system and vaccine development are issues that still need to be addressed and must be considered as important as the farm production technologies for new fish species. Based on the experience acquired from the salmonid fish farming, should be mandatory an effort to study the immune system of the new species to develop knowledge for vaccination approaches, aiming to protect these aquaculture species before diseases outbreaks may occur.This review focuses on the current status of the Chilean aquaculture industry, the challenges related to emerging and re-emerging microbial pathogens on salmonid fish farming, and the resulting needs in the development of immune protection by rational designed vaccines. We also discussed about what we have learn from 25 years of salmonid researches and what can be applied to the new Chilean farmed species on immunology and vaccinology.