SRS Background

THIS IS A WORKING SYNTHESIS PREPARED BY ACUAIM SPA FOR THE PGSA CONSULTIVE COMMITTEE, IN ORDER TO INFORM ABOUT THE CONTEXT OF THE PROJECT BASED ON THE FOLLOWING ORIGINAL REPORTS: "Establishment of multidisciplinary and integrated research lines and their impact on levels of health intervention against P. salmonis in farmed salmon "by EpiVet EIRL (2017); "SRS: A review of the disease, risk factors and control strategies" by Ausvet (2017); "Scoping Report for Sanitary Management in Aquaculture" by SERNAPESCA (2017); and Estimated Economic Costs for SRS and Caligus Associated with PGSA Impact Indicators "by SERNAPESCA (2017).


Piscirickettsiosis or Salmon Rickettisal Syndrome (SRS) is a severe disease of members of the genera Salmo and Oncorhynchus caused by the bacterium Piscirickettsia salmonis. Since its appearance in 1989, it has caused major economic losses in the aquaculture industry in Chile and around the world. The first reported outbreaks of P. salmonis in Chile occurred at the end of 1989 although some suggest that the disease may have been present as early as 1983. In the first reports of SRS, Coho salmon (Oncorhynchus kisutch, Walbaum, 1792) were effected with up to 90% mortality on some farms. Later, piscirickettsiosis was also detected in Atlantic salmon (Salmo salar, Linnaeus, 1758) and rainbow trout (Oncorhynchus mykiss).

Economic analysis completed in 1989 estimated losses of approximately US $10 million resulting from mortality of 1.5 million fish. In 2006, the Technological Institution of Salmon (INTESAL), Chile estimated that the direct losses caused by piscirickettsiosis were approximately US $100 million in the outgrowing phase in sea water (Cabezas 2006). In addition, the institute estimated a further US $400 million was lost due to piscirickettsiosis in potential harvest. This represents close to 25% of the total revenue from salmon exports in the same year. Piscirickettsiosis is evolving and becoming progressively resistant to treatment, increasing in its virulence and hence causing greater clinical severity under the same management conditions with every outbreak. For this reason, it is considered one of the most significant threats to the sustainability of the salmon industry.

Risk factors identified for mass mortality from piscirickettsiosis include failure to vaccinate or ineffective vaccination, close proximity to other infected farms, increases in water temperature, water salinity, improper nutrition and stress. Strategies to prevent the disease and minimize mortality include reducing stress, reducing density, restricting movements of boats, fish and people, screening of brood stock, treating with antibiotics and vaccination.

Antibiotics have been used to control the disease however resistance to penicillin, streptomycin, oxolinic acid and oxytetracycline has been reported and in general, salmonids respond poorly to treatment. Effective, long-term protection against lethal challenges of P. salmonis with vaccination has also proven difficult to achieve in field conditions. Current vaccination protocols include whole cells, inactivated or adjuvant injectable vaccines followed by an oral booster vaccine. The main challenge in preventing the disease through vaccination is the decline of antibodies that begins approximately 800 degrees days after the primary vaccine is administered and the subsequent increase in susceptibility to disease. Hence, at least one booster is required to maintain immunity. A plasmid or DNA vaccine was trialed in 2003 but was ultimately ineffective. On the other hand, immunization of salmon with live and replicating Arthrobacter davidanieli has shown promising results in protection against Piscirickettsiosis.

Overview of Rickettsial Salmon Septicemia

The pathogenic agent

Basic biology

P.salmonis is a gram-negative bacteria that is mostly non-motile, aerobic, un-encapsulated, pleomorphic, fastidious, usually coccoid and found in pairs or ringed structures. It replicates by binary fission within cytoplasmic vacuoles in the cells of susceptible fish hosts and cell lines. In laboratory conditions, replication is optimal at 15–18 °C, hindered above 20°C and below 10°C, and completely ceases above 25°C. Previously, P.salmonis was considered to be cultivable only in eukaryotic cell lines. However, recent reports show that the bacterium may be cultured on cysteine-enriched agar media, confirming facultative intracellular properties. Whilst it’s route of entry is not completely understood, it is known to primarily infect and multiply within macrophages.


Analysis of the genetic content of P.salmonis may help to improve our understanding of the pathogen, it’s infective processes and the fluidity with which genes seem to be exchanged. The genomes of relatively few strains of the pathogen have been sequenced however one recent study describes two genetic groups of P.salmonis in Chile, whilst another identified a specific gene whose expression is directly proportional to in vitro cytopathogenicity.


Virulence factors of P.salmonis are poorly understood. It is known to secrete extracellular products (ECPs) and at least some of their components produce cytotoxic effects in vitro and may mediate some of the tissue damage seen in vivo in salmonid fish. The near to complete inhibition of the in vitro effect of these ECPs by proteinase K treatment indicates they are peptides and therefore, they can be categorized as exotoxins. It has also been suggested that outer membrane vesicles play a role in delivering virulence factors to host cells. One study found isolates from Chile were more virulent than those from Norway and Canada.

The host and disease

Susceptible hosts

The principle hosts for P.salmonis are salmonid fish. Following the first recorded outbreaks in coho salmon, disease has been reported in rainbow trout, cherry salmon, Atlantic salmon and Oncorhynchus masou (Walbaum) in Chile, as well as salmonid fish in Canada, Ireland, Scotland and Norway. The only confirmed non-salmonid hosts of P.salmonis are captive white sea bass.

Modes of transmission

The mode of transmission for the pathogen and consequent disease spread is poorly understood, however horizontal transmission via water is assumed to play the key role. No vector or reservoir has been identified; however, the bacteria has been shown to replicate in insect and frog-derived cell lines, raising suspicion that an invertebrate vector may exist. Marine finfish species and mollusks have also been suspected of being reservoir hosts but testing has failed to demonstrate infection. Some have suggested the pathogen usually enters via the skin, either by penetration or through skin injuries or through the gills. Oral exposure is unlikely to be important because low pH and digestive enzymes are capable of inactivating the pathogen. Transmission can occur in both fresh and salt water but the low survival of the bacterium in fresh water minimizes the probability of disease onset.

Clinical signs and mortality

The incubation period for piscirickettsiosis depends on the isolate, the dose, the route of infection, and environmental and host factors such as immune status and age. In various studies, death has been reported between 8–29 days post infection.

The greatest losses from piscirickettsiosis occur in Chile where the reported mortality rate ranges from 30% to 90%. In the Northern Hemisphere, mortality rates are reported to be substantially lower (0.6 to 18%).

Vaccination can reduce mortality when fish are first transferred to salt water, but these vaccinated fish usually become increasingly susceptible and are prone to more aggressive outbreaks later in the production cycle.

Risk factors

The epidemiology of the pathogen is relatively unknown and hence determining risk factors is problematic. Despite this, some risk factors have been identified and are described in the following sections.

Water temperature

A correlation between water temperature and incidence rate of disease has been established in Atlantic salmon, rainbow trout and Coho salmon, with higher temperatures appearing to hasten disease. In one study, fish were injected with a lethal dose of P.salmonis to test the efficacy of a vaccine and there was no death amongst fish kept in ambient seawater at 7.5 to 8.5 °C, compared to mortalities of up to 47.6% in the fish kept at 16°C. Another anecdotal report described an outbreak in Scotland being resolved by naturally falling temperatures. In addition, databases of outbreaks between January 2009 and December 2012 in Chile show clear correlation in the incidence of SRS and the average water temperature. Some suggest that fluctuations in temperature can also predispose fish to the disease.

Time in salt water

P.salmonis can survive for long periods in sea water but is rapidly inactivated in fresh water, hence most outbreaks occur in the sea or estuarine waters. Despite this, the disease has occasionally been reported in rainbow trout only ever maintained in fresh water. Given its affinity for sea water, not surprisingly the probability of SRS outbreaks on a farm has been shown to be positively correlated to the amount of time spent in salt water. An analysis of Chilean aquaculture industry data collected between 2009 and 2012 found that the odds of reporting SRS in Atlantic salmon as 2.38 times greater for fish in their fourth month at sea compared to their second month at sea. The odds of reporting SRS in Coho salmon and rainbow trout became significantly greater after four and five months at sea, respectively. Time at sea is likely to be correlated with other variables such as mean body weight, waning of vaccine-derived immunity, infection pressure from neighboring farms, prevalence of other infections/infestations and possibly stressors associated with biomass density and competition.

Infection pressure from SRS-infected neighbours

A strong and consistent correlation between the number of neighboring farms with SRS and the risk of developing disease has been demonstrated, when neighboring farms are within a seaway distance of 7.5km for Atlantic salmon and rainbow trout and 10km for Coho salmon. The risk posed by neighboring farms with a seaway distance up to 10km away is also probably part of the reason why SRS continues to plague the industry in Chile, despite the obligatory biosecurity measures that have been adopted since 2009 (including prohibited movement and mandatory fallowing). Given that effective transmission distances in aquatic environments are influenced by ocean currents, hydrographic modeling may be useful in better understanding the risks posed by neighboring farms. In addition to transmission via water, there may be other modes of transmission from infected neighbours; for example, through the movement of boats, machinery or people.

Farm size

Rees and colleagues found a significant positive association between farm size and the chance of SRS outbreaks in Atlantic salmon, but this association was not statistically significant rainbow trout and coho salmon. In addition, the authors noted that the apparent association was difficult to interpret because it was potentially confounded by year effect (because farms changed in size over time) and the fact that the number of fish on a farm increase in the initial three months of the grow-out cycle. Their model did not separate these effects.

Stocking density

Researchers inoculated rainbow trout with P.salmonis and evaluated their mortality at different temperatures and stocking rates. The group kept at 20kg/m and 14°C when looking at density alone, had significantly higher mortality than fish kept at 5kg/ m3 and 14°C. This is not surprising given the complex interactions known to exist between stress, stocking density and disease.

Concurrent disease and nutrition

It has been found that infection with Caligus rogercresseyi significantly increased mortality in fish infected with Piscirickettsia salmonis. They also found that resistance to coinfection with two pathogens is a heritable trait in Atlantic salmon but that different genes control these processes, It have been recently found that arachidonic acid and vitamin E had effects on immune markers and significantly reduced cumulative mortality in fish exposed to the SRS pathogen.

Disease control

The efficient control of SRS in Chile has been difficult to achieve, partly because antibiotics have limited effect and commercially available vaccines are only partially effective. Whilst prophylactic control of infections through good management practices—such as periods of fallowing—have been proposed as an alternative to medical treatments, the disease persists despite the introduction of industry wide biosecurity measures in Chile in 2009. Evidence relating to current disease control measures is summarised below.


As of 2016, there were 33 vaccines against SRS commercially available in Chile. Most of these vaccines are killed P.salmonis bacterin and are administered by intraperitoneal (IP) injection. Two oral vaccines are available and one that is delivered via immersion. Generally, IP administration offers the highest levels of protection but is also associated with stress from handling and adverse effects at the site of vaccination. Sometimes, small fish are vaccinated orally or by immersion initially and then boosted with an IP preparation. The potency and safety of the vaccines is generally evaluated using in vivo techniques but few studies have assessed efficacy against different pathogenic strains (most use the same strains) and via different routes of exposure to the pathogen. Hence, there is a high level of concern regarding the efficacy of bacterin vaccines under field conditions and the general consensus is that longer term effectiveness of the vaccines is variable. In addition, Jakob and colleagues suggested that in rainbow trout at least, commercial vaccines delay the time to first outbreak but do not significantly reduce overall mortality from the disease (Jakob et al. 2014). However, they also suggested that booster vaccines have the potential to lower mortality associated with the disease in Atlantic salmon.

In Chile, most farmers administer injectable vaccine in pre-smolts prior to transfer to seawater. In general, it appears that vaccinations can provide protection against the initial outbreaks of SRS that tend to occur when fish are transferred to sea water, but the fish then become susceptible to new and more aggressive strains of P.salmonis resulting in outbreaks at 10–12 months after transfer, causing greater economic losses. This has led to suggestions that large fish should be revaccinated at 10–12 months and oral immunisation has been nominated as the most practical way of delivering this booster. In a recent trial, different vaccines were administered and the IgM levels of fish, as well as mortality, were observed in field. Results suggest that high levels of specific IgM antibodies developed from both oral and IP vaccines, reaching a maximum at 600–800 degree days after inoculation and this level of antibodies was protective. However, when specific anti-SRS IgM antibodies decreased below 2000ng/mL, a window of susceptibility of infection was observed, confirming previous suggestions that one round of vaccination only delays the first outbreak. The authors concluded that several oral immunisations may be essential to uphold high enough levels of antibodies to maintain protection for the whole production cycle. A study of oral booster vaccination of fish (species not reported) in 222 cages from 12 sea sites in Chile found that mortality following two oral boosters was significantly lower than no booster (OR = 1.32, 95% CI 1.05–1.67), and the use of at least one booster delayed the time to first SRS outbreak by 41–92 days compared to no booster.

Despite some progress, a deeper understanding of the biology of the pathogen, the nature of host innate and adaptive immune responses to vaccination/infection, and the application of new technologies is needed to improve the efficacy and effectiveness of vaccination.

Antimicrobial usage and resistance

In 2014, 563200 kilograms of antibiotics (mostly florfenicol and oxytetracycline) were administered to control SRS. However, producers have reported only partial success with antibiotic treatment and in general antimicrobial use has had limited effect on control SRS.

Despite P.salmonis being sensitive to many commonly used fish antibiotics in vitro, in field conditions infected salmonids respond poorly to treatment, possibly because concentrations are insufficient to reach the intracellular area where the pathogen resides. Clarithromycin, chloramphenicol, erythromycin, gentamicin, oxytetracycline, sarafloxacin, oxolinic acid, florfenicol and flumequine have all been shown to inhibit bacterial growth in vitro, but oxytetracycline and florfenicol are the only antibiotics routinely used by the industry.
Resistance to penicillin, streptomycin, oxolinic acid and oxytetracycline has been reported. However, a study in 2016 analysed the susceptibility of 292 P.salmonis isolates and found that only 1.7% and 3.1% of the isolates were resistant to oxytetracycline and florfenicol, respectively.

These results suggest that resistance only partially explains treatment failure. It is difficult to identify other causes of treatment failure because no clinical field trials have been reported for this disease; however, Price and colleagues recently assessed the correlation between additional factors and treatment failure. Their results suggested that mortality level before treatment and fish weight at the start of treatment, in addition to the type of antibiotic used, all had a significant effect on the treatment outcome. Farms with lower mortality when therapy was initiated were less likely to experience treatment failure, and in fish treated with florfenicol, treatment failure was more likely when the average fish weight was less. Lastly, treatment failure was more likely when florfenicol was used. Price proposed explanations for these results including higher pathogen loads in pens affected by disease, the failure of fish to feed (and therefore ingest medication) once they are already infected with the disease, difficulty penetrating the blood-brain barrier in the later stages of disease and failure of little fish to access adequate feed on farms where there is a larger spread of weights due to hierarchical behaviour. They suggested that the differences in elimination half-life between florfenicol (12 hours at 11°C) and oxytetracycline (50 hours at 8°C) may at least partially explain the difference in treatment failure between the two products. At least one genomic sequence of a resistant isolate has been described.

In addition to the ineffectiveness of antimicrobial treatment, there is concern relating to the importance of normal microbiota in fish species, how antimicrobial use effects microbiota and how microbiota contribute to the overall health of fish. Furthermore, disease impact probably does not only result from mortality but also from the environmental impact of large amount of antibiotics been used and the effect this has only the selection of resistant types. Lastly, international markets are now increasingly aware of the potential health risks associated with indiscriminate use of antimicrobials, leading to maximal residue limits being set for the flesh and skin of fish.

Biosecurity measures

It is assumed that farmed fish become infected with P.salmonis after they come into contact with infected water. Infection seems to depend on the presence of large cultured fish populations and if diseased fish are removed, bacteria remain viable in sea water but with diminishing concentration over time. The number of bacterial units in farm water that is empty decreases to zero around 50 days after the last fish are removed. Therefore, good management practices such as fallowing and limiting the movement of fish and equipment between farms should assist in controlling SRS. This logic motivated the introduction of industry wide biosecurity measures in Chile in 2009 including mandatory fallowing at farm and neighbourhood levels, restrictions on the movement of fish between farms and compulsory disinfection of equipment. Despite these changes, SRS continues to occur, raising concerns about just how far the disease can spread and whether the pathogen may actually be endemic in fish farming areas. Rees and colleagues investigated the distance effect and found that the probability of a farm reporting SRS was positively associated with the number of infected neighbours, with the best fit models including sea-distances between 7.5 and 10km: this indicates that reducing disease on one farm can help to protect neighbouring farms.

Selection for resistance

Selective breeding for resistance in aquaculture represents a realistic and sustainable approach for controlling disease. Traditional aquaculture selection programs involve sib-testing where phenotype information is generated by experimental infection of full-sib family groups. But the reliability of this method in standard selection schemes is limited because breeding candidates are chosen based on parent estimated breeding values (EBV), resulting in only 50% of the genetic variation being exploited. Despite this, studies suggest there is moderate to medium heritability (.11 to .41) for resistance to P.salmonis in Atlantic salmon, indicating potential for selective breeding. In addition, novel methods of selection, such as genomic selection (as opposed to traditional pedigree based methods) show promise for accelerating genetic progress against SRS in Chile.


There has been much progress in the knowledge of P.salmonis in recent years. However, adequate control and treatment of SRS has been difficult, largely because of the absence of effective commercial vaccines and the limited impact of antibiotics. Whilst biosecurity measures are being implemented, evidence of their effectiveness is yet to be documented. Temperature, time in salt water, stocking density, farm size and proximity to infected neighbours have all been identified as risk factors. However, it is likely that further risk factors exist. Future work should focus on identifying risk factors that can be mitigated through interventions.


What factors (risk or protective factors) regulate the time of the infection, the clinical presentation and the magnitude of an SRS outbreak? If these exist, how do they act or interact?

Retrospective studies have determined that water temperature, sea water time and a distance of less than 10 km from a farming center handling an SRS outbreak are possible risk factors for the appearance of an outbreak of this disease. Furthermore, the efficacy of antibiotic treatments have been evaluated against SRS outbreaks, demonstrating that a high pre-treatment mortality level is related to a lower probability of success for florfenicol or oxytetracycline treatments. Additionally, a weight increase in the specimens treated with florfenicol is directly related to an increase in pre-treatment mortality rates, as well as to a higher number of treatment failures.

What role do vector density and non-salmonid reservoirs play in the P. salmonis dynamic?

Samplings of native fish from zones with aquaculture activities showed various species susceptible to P. salmonis, primarily sea bass (Eleginops maclovinus) and silverside (Odontesthes regia), which presented a clear phylogenetic relationship with P. salmonis isolates linked to outbreaks in farming centers. Exposure of sea bass to P. salmonis extracts showed this species’ low susceptibility for developing SRS.

How do P. salmonis strains differ in terms of pathogenicity and virulence, and how does the host respond to these differences?

P. salmonis isolates of different origins were used to evaluate the effect of the external membrane vesicles in virulence. A difference in the protein expressions of the distinct P. salmonis strains was shown, possibly related to the different virulence that each isolate presented. Moreover, a study evaluating the pathogenicity of the SLGO-95 strain in rainbow trout showed that this species is highly susceptible to this strain. This allowed for an evaluation of the progression of the infection, starting from the attachment of the bacteria to the epithelium and the gills, to the spreading by means of blood vessels into deeper tissues, up until distribution in the whole organism.

What are the processes related to the emergence of resistance to drugs and what is the timeframe for the development of this resistance in P. salmonis?

The determinants that generate resistance to antimicrobials in P. salmonis have not been entirely explained; however, it has been shown that certain strains of P. salmonis present a mutation in the gyrA gene, associated with an alteration in quinolone functioning against these isolates, in addition to presenting various genes that express proteins, intensifying the resistance to florfenicol and tetracyclines by exporting these compounds. It was demonstrated that the use of florfenicol generates an overexpression of acrAB genes related with efflux systems in gram-negative bacteria.

What are the conditions that determine whether P. salmonis establishes an infection or whether it is removed by the immune system?

Various factors have been associated with the adaptation or persistence of P. salmonis in the host’s cells, mainly the overexpression of virulence factors. Recent studies have noted an increase in the expression of clpB and bipA genes, as well as of Toll-like receptors (TLR’s) and interleukin 1β (IL-1β) during P. salmonis infections in in vitro models of Atlantic salmon. Similarly, an increase in the expression of TLR’s, IL-1β, IL-10, GBP1 and in the proteins associated with the Icm/Dot secretion system has been noted during P. salmonis infections in experimental models derived from rainbow trout. When comparing the susceptibility to P. salmonis for Atlantic salmon specimens both resistant and susceptible to SRS, it has been shown that a pro-inflammatory immune response prevails in the susceptible specimens, whereas the mononuclear phagocyte system acts to a greater extent in resistant fish. Interestingly, hepcidin expression is higher following infection from inactivated P. salmonis isolates rather than with infective isolates. Another study demonstrated a difference in susceptibility between two Atlantic salmon populations having distinct gene expressions for iron homeostasis at a cellular level, showing that the quantity of intracellular iron diminishes in resistant strains, serving as a defense mechanism against P. salmonis infections; likewise, gene expression related to iron absorption, usage, storage and regulation was showed in P. salmonis, as well as various other genes related to the survival of bacteria inside the host. Using sequencing methods, it was possible to determine the differences in the presentation of genes linked to virulence factors between strains with different degrees of pathogenicity; however, it remains impossible to comprehensively determine what exactly causes the difference in virulence between different P. salmonis strains. The identification of molecules present in external membrane vesicles generated by P. salmonis helped determine the fact that these molecules contain virulence factors that help with the pathogenicity of the bacteria, although the mechanism is not yet completely understood. Concerning the P. salmonis entry and intracellular invasion, it was possible to determine that clathrin is the protein necessary for internalization, and that actin is a fundamental protein during a bacterial invasion in cytosol, as well as during an immune evasion.

What is the correlation between bacterial dynamics, damage and inflammation and the host? What is the correlation between the bacterial load (the abundance of P. salmonis) and the magnitude of the antibacterial immune response?

The evaluation of the P. salmonis load in different tissues coming from resistant specimens and from those susceptible to infection revealed that the bacterial load was significantly higher in susceptible specimens, and that regardless of the degree of resistance to P. salmonis, the muscle was a tissue that presented a high bacterial load in terms of kidney deterioration.

What is the mechanism involved in the immune response against multiple pathogens? What role do stress and the threshold for immunity play?

A study of the effect of a P. salmonis and C. rogercresseyi co-infection showed that there are significant differences in mortality for P. salmonis infections and for P. salmonis and C. rogercresseyi double infections, demonstrating the importance of the Caligidosis in the SRS dynamic. In addition, it was shown that the resistance mechanisms for P. salmonis infections and for co-infections with both pathogens were genetically different. Another study demonstrated that an increase in ovigerous females could be indirectly related to stress generated by diseases caused by P. salmonis or Neoparamoeba perurans.

What is the most effective antibiotic currently available? What is its sensitivity like?

The extended use of antimicrobials in aquaculture has caused the appearance of various strains resistant to different types of antibiotics. A study evaluated the susceptibility of different P. salmonis isolates to quinolone treatments, and enrofloxacin was the treatment that showed the best results in isolates both susceptible and resistant to flumequin and oxolinic acid deterioration. A comparison of strains with different years of origin showed that younger strains present higher levels of resistance to florfenicol, the most used antibiotic in the national industry, and that in the majority of the cases the resistance to florfenicol is higher than the resistance to oxytetracicline. However, another study researching 20 different P. salmonis strains showed that oxytetracicline and florfenicol are the most effective antibiotics, florfenicol being more effective than oxytetracicline.

How should alternative treatments (prebiotics, additives, immunostimulants, etc.) be developed and used? How can their optimal functioning be assured?

Different compounds have been evaluated as potential immune system stimulators. Prolactin has been evaluated for its immunostimulant function, demonstrating that it permits an overexpression of TLR’s and of other molecules associated with the immune response. Regarding plant or seaweed derived compounds, in vitro tests showed that molecules derived from Heliotropium spp. have an antimicrobial effect on in vitro P. salmonis. Another approach helped demonstrate that a fucoidan and diterpene-based phytopharmaceutical administered as a food additive against a P. salmonis pathogenic strain helped increase the inflammatory cytokine expression and diminish the cytotoxic effect in vitro, as well as diminish the mortality in in vivo tests. Similarly, the use of antibodies obtained from buds immunized against P. salmonis substantially improved the protection against P. salmonis in in vitro and in vivo tests, showing its potential as a possible therapeutic agent. However, when using arachidonic acid and vitamin E, no significant changes or improvements in the immune system were noted.

What are the areas of the genome (the genetic markers) that codify the resistance mechanisms against C. rogercresseyi and P. salmonis?

Recently, various studies regarding the Atlantic salmon genome have related certain genetic markers with resistance to P. salmonis, mainly genes involved in the immune response.

How can genetic selection for resistance to diseases interfere with ideal productive and sanitary characteristics?

When evaluating the correlation between the characteristics that determine resistance to P. salmonis and the harvest weight for Coho salmon, it was shown that the selection of characteristics that foment resistance for this pathogen are negatively related to the characteristics that promote a higher crop weight. Similarly, it was demonstrated that the selection of characteristics in Atlantic salmon that favor a higher weight for a given specimen are related slightly negatively to the characteristics that confer resistance to P. salmonis, and they are positively related with characteristics that determine resistance to C. rogercresseyi.

What are the areas of the genome (the genetic markers) for the pathogens that codify resistance mechanisms against drugs?

It has been shown that the expression of genes associated with aquaporins is different during an infection in Atlantic salmon and in Coho salmon. An evaluation of genes associated with resistance to C. rogercresseyi was carried out and showed that a gene associated with the alpha-1 collagen, linked to cytokine signaling, is expressed in resistant families.The overexpression of genes associated with iron homeostasis was shown in Atlantic salmon infected with C. rogercresseyi, however there is no clear evidence as to whether the parasite depends on the use of heme groups during its life cycle. It was estimated that the maximum amount of parasites tolerated by Atlantic salmon before generating a physiological imbalance is 6.

How can antigen absorption, processing and presentation for the fish’s immune system be improved at the mucosa level as a booster vaccine strategy?

An oral vaccine against P. salmonis was recently developed which allows the generation of adequate IgM levels in the specimens for a duration of approximately 2800 and 3200 ATU (Accumulated thermal units) , allowing for the maintenance of optimal antibody levels during the fattening stage, following the decline of IgM levels caused by the intraperitoneal vaccine. The scientific information published between 2014 and 2016 is for the most part based on experimental research. However, there are still many questions to be answered through applied research, preferably by means of observational studies that evaluate the most relevant aspects of previous experimental studies.

Proposed Research lines

Proposed Research lines for addressing the 61 Baseline Research Questions (BRQ) related to SRS.

Early detection of P. salmonis infections


  1. To establish an early detection system for P. salmonis through the joint evaluation of diagnostic tests and mortality patterns under field conditions.


  1. To evaluate the characteristics of the diagnostic tests for P. salmonis (sensitivity, specificity, predictive value, etc.) in laboratories and in the field.
  2. To determine the repeatability of the results from different sampling models and sampling procedures.
  3. To evaluate the relationship between laboratory diagnostics and mortality patterns under field conditions.
  4. To propose recommendations that aim towards a P. salmonis control program, taking into consideration the results of this research line.

Epidemiological studies for P. salmonis infections in farmed salmon


  1. To identify risk factors and protective factors for P. salmonis infections in farmed salmon.


  1. To determine the mortality patterns for SRS and their relationship with other mortalities during the fattening stage for farmed salmon.
  2. To identify risk factors and protective factors that modulates the presentation of SRS at cage-level, farming center-level and CMF-Level (Cluster of Marine Facilities Level)
  3. To establish a risk score system at cage-level and farming center-level based on identified factors.
  4. To propose recommendations that aim towards a P. salmonis control program taking into consideration the results of this research line.

P. salmonis transmission between cages, farming centers and CMF


  1. To identify the transmission mechanisms for P. salmonis, within and between farming centers, including CMF.


  1. To identify and quantify the direct and indirect transmission mechanisms for P. salmonis, within and between farming centers.
  2. To establish the relationship between transmission rates for P. salmonis within and between farming centers.
  3. To design an intra and inter-center dispersion model prototype for P. salmonis.
  4. To propose recommendations that aim towards a P. salmonis control program taking into consideration the results of this research line.

Epidemiological modeling for P. salmonis


  1. To implement an epidemiological model for quantifying SRS, its impact and the evaluation of control strategies.


  1. To design, program and implement an epidemiological model for SRS.
  2. To incorporate risk factors and protective factors at farming center level and CMF level.
  3. To incorporate the spatial dimension and to determine its role in SRS dispersion between farming centers and CMF.
  4. To evaluate control strategies that minimizes the impact of SRS at farming center level and ACS level.
  5. To propose recommendations that aim towards a P. salmonis control program taking into consideration the results of this research line.

SRS spatial characterization


  1. To spatially characterize SRS risk areas based on oceanographic influences.


  1. To identify the influence of climatic, oceanographic, bathymetric and other variables on SRS’s presentation.
  2. To characterize spatial areas with a high or low SRS potential (the definition of high and low sanitary risk areas).
  3. To define a spatial zoning model for SRS sanitary management.
  4. To propose recommendations that aim towards a P. salmonis control program, taking into consideration the results of this research line.

The ecosystem’s role in the dispersion of P. salmonis


  1. To establish the influences of the ecosystem on the abundance of P. salmonis and the impact of P. salmonis on the ecosystem.


  1. To quantify the surrounding ichthyofauna’s role in the abundance and reservoir capacity of P. salmonis.
  2. To identify biological interaction at a phytoplanktonic level (predation, competition) and its influence on the abundance of P. salmonis.
  3. To quantify the consequences of the superabundance of nutrients in the bacteria’s population dynamics.
  4. To propose recommendations that aim towards a control program for P. salmonis, taking into consideration the results of this research line.

Establishing a research-based regulatory framework for the control and prevention of SRS


  1. To propose a set of regulations and procedures derived from research results with proven impacts regarding public, animal and environmental health.


  1. To integrate and coordinate the results of the WP into consolidated regulations based on research.
  2. To integrate the public Q&A feedback into the technical feedback.
  3. To define a research-based SRS control program.
  4. To propose recommendations that aim towards a control program for P. salmonis, taking into consideration the results of this research line.

The economy of SRS control, control strategies and surveillance


  1. To define SRS control and surveillance strategies based on an economic and animal health framework.


  1. To estimate the costs associated with SRS prevention, control and surveillance at farming center level and ACS level.
  2. To define sanitary-productive performance indicators and SRS’s impact on these indicators.
  3. To identify the best SRS control and surveillance strategies based on an economic analysis.
  4. To propose recommendations that aim towards a control program for P. salmonis, taking into consideration the results of this research line.

P. salmonis transmission and virulence


  1. To establish the transmission and virulence mechanisms for P. salmonis.


  1. To identify vertical and horizontal transmission mechanisms for P. salmonis between farmed salmon.
  2. To determine the role of freshwater and saltwater in the viability and virulence of P. salmonis.
  3. To identify the different P. salmonis strains and their relationship to virulence, pathogenicity and host response.
  4. To propose recommendations that aim towards a control program for P. salmonis, taking into consideration the results of this research line.

The susceptibility of P. salmonis in the environment


  1. To determine the characteristics of P. salmonis in environmental conditions related to its survival, interaction with inert surfaces and its population structure.


  1. To evaluate P. salmonis’ survival outside of the host for different strains in field conditions.
  2. To determine the interaction between bacteria and inert materials associated with salmon farming.
  3. To define the spatial population structure of P. salmonis based on genetic markers.
  4. To propose recommendations that aim towards a control program for P. salmonis, taking into consideration the results of this research line.

Host immune response to P. salmonis


  1. To establish criteria for the immune response, smolt quality and farmed salmon well-being and their association with P. salmonis.


  1. To define immune mechanisms related to the establishment of P. salmonis infections in field conditions.
  2. To evaluate the role that smolt quality and farmed salmon well-being play in the bacterial infection and magnitude of SRS.
  3. To identify patterns for the time sequence between SRS and other sanitary conditions.
  4. To propose recommendations that aim towards a control program for P. salmonis, taking into consideration the results of this research line.

“Omics” approaches for determining P. salmonis resistance


  1. To identify sanitary strategies that minimize anti-parasitic resistance.


  1. To identify the antimicrobial resistance for P. salmonis.
  2. To define the time interval for the appearance of resistance and to determine the frequency of resistant bacteria in farming centers.
  3. To define drugs, treatment models and strategies that minimize the risk of antimicrobial resistance for P. salmonis.
  4. To propose recommendations that aim towards a control program for P. salmonis, taking into consideration the results of this research line.

Studies regarding antimicrobial efficacy and effectiveness against P. salmonis


  1. To quantify the efficacy (laboratory) and effectiveness (clinical trial) for available antibacterial products used against P. salmonis.


  1. To determine the pharmacokinetic and pharmacodynamic characteristics, as well as the efficacy of antimicrobials used against P. salmonis.
  2. To determine the effectiveness of antimicrobial products against P. salmonis infections in farmed salmon in field conditions.
  3. To identify the factors that influences the efficacy, effectiveness and other characteristics that affect therapeutic success.
  4. To propose recommendations that aim towards a control program for P. salmonis, taking into consideration the results of this research line.

Therapeutic models against P. salmonis


  1. To identify the optimal therapeutic models against P. salmonis at various levels.


  1. To determine antimicrobial administration in field conditions and its relationship with clinical signs, laboratory diagnostics and mortalities associated with the case of SRS.
  2. To identify environmental and sanitary-productive variations that alters the therapeutic model and the prescribed dosage in field conditions.
  3. To evaluate therapeutic rotation, spatial scale and other characteristics of treatments that optimize antibiotic use against P. salmonis.
  4. To propose recommendations that aim towards a control program for P. salmonis, taking into consideration the results of this research line.

“Omics” approaches for determining resistance to P. salmonis


  1. To define genetic markers that codifies resistance mechanisms against P. salmonis in farmed salmon.


  1. To identify techniques, protocols and methods that favor the host’s resistance to P. salmonis, based on “Omics” technologies.
  2. To compare the response of resistance mechanisms in experimental conditions versus field conditions.
  3. To evaluate the potential interference of resistance mechanisms against the bacteria and other sanitary-productive characteristics.
  4. To propose recommendations that aim towards a control program for P. salmonis, taking into consideration the results of this research line.