A practical tool for disease risk management

by Francois Brenta


With a projected global seafood consumption estimated at 151 million tons by 2030, aquaculture is expected to exceed captured fisheries by reaching 61% of global seafood supply, equivalent to a total of 93 million tons.


Source: Fish to 2030 – World Bank


With annual losses caused by diseases estimated at US$6 billion (FAO), the world aquaculture industry is facing a tremendous challenge to keep expanding. Growth will only be possible if it can rely on sustainable production technologies.


Diseases have proven to be the most significant threat to the aquaculture industry well known for its long history of disease related crisis with catastrophic economic and social consequences affecting globally 18.7 million people working directly in aquaculture and approximately 60 million people working in secondary and post-harvest activities (FAO).


In 2007, after 3 decades of sustained growth, the Chilean salmon farming industry was hit by a viral disease called the infectious salmon anemia (ISA) losing two thirds of their national production due to mortalities and termination of infected batches. As a direct consequence, 50% of direct and indirect jobs were lost due to affected operations not being restocked. The overall financial impact of the ISA crisis is estimated at US$2 billion (World Bank).

Mass mortality cause by the infectious salmon anemia (ISA)

Damages to internal organs caused by the infectious salmon anemia (ISA)



In Asia, the tilapia farming industry is recording yearly losses estimated at US$480 million due to bacterial infections caused by streptococcus and US$18 million due to parasitic infections (Fish Vet Group). A viral disease known as the tilapia lake virus (TiLV), first discovered in Israel in 2009, has been confirmed in Egypt, Colombia, Ecuador, Peru, Thailand and Philippines (FAO) threatening the US$9.8 billion world tilapia industry (CGIAR). Egypt (ranked second world tilapia producer) has already lost more than US$100 million (WorldFish). TiLV outbreaks have been reported in other affected countries with mortalities as high as 90%.


Mass mortality caused by the tilapia lake virus (TiLV)


External symptoms caused by:


Streptococcusbacterial infection

Tilapia lake virus (TiLV)


Gill parasite infestation




Crustaceans are particularly sensitive to diseases because of the nature of their primitive immune system. Unlike fish, they cannot be vaccinated and antibiotics are inefficient in treating most cases of bacterial infection. More than US$20 billion have been lost over the past decade due to several diseases, however, most of the damage has been caused by the white spot syndrome virus (WSSV), the early mortality syndrome (EMS) and Enterocytozoon hepatopenaei (EHP).


Since its appearance in Taiwan in 1992, the white spot syndrome virus (WSSV) has caused losses for more than US$8 billion to the world shrimp farming industry (World Bank). The virus spread rapidly across South East Asia causing losses of US$6 billion and by mid-1999 the virus literally destroyed the Ecuadorian shrimp farming industry by reducing production down to 30% of its pre-WSSV production levels, generating losses of more than US$ 1 billion. In 2011, the WSSV was detected in Saudi Arabia, forcing the industry to a complete shut-down by late 2012. The most recent case of WSSV outbreak was reported in late 2016 in Australia where 16% of the industry was forced to harvest, terminate and proceed with a complete dry-out.


Mass mortality caused by the white spot syndrome virus (WSSV)



External symptoms caused by the white spot syndrome virus


The Early Mortality Syndrome (EMS) also known as Acute Hepatopanceatic Necrosis syndrome (AHPNS) is a bacterial disease caused by Vibrio parahaemolyticus with a toxin gene bearing plasmid; first detected in China in 2009 it has spread to Vietnam, Malaysia, Thailand, Mexico, Venezuela and other Latin American countries causing annual losses for more than US$1 billion (GAA).


External symptoms caused by EMS                             EMS infected shrimp (left), healthy shrimp (right)



Atrophied and pale hepotopancreas and empty gut caused by EMS                         Normal hepatopancreas and full gut          

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Enterocytozoon hepatopenaei (EHP) was first detected in Thailand in 2009. The microsporidian which is the causative agent of Hepatopanceatic microsporidiosis (HPM) is not known to cause mortalities however it is associated with severe growth retardation. In Asia, the pathogen has already caused major economic losses. Typical impacts are reduction of harvestable size to 12g from the usual 18g harvest size, causing a reduction of 25% in Kg/ha and a loss of 34% in price target because of the difference in size category. Attempts to grow beyond 12g results in very significant FCR increment which is economically unsustainable. On average, under typical Asian intensive shrimp farming conditions, a pond significantly infected with EHP will generate losses of US$ 4500 per hectare per cycle.


External symptoms caused by EHP                                                                                    Microsporidian causing EHP




Given the numerous epizootic events over decades affecting various species and environments from the tropics to Patagonia, it is clearly a matter of “when” and not “if “a disease will affect a region, country o aquaculture operation.


From a global perspective, the occurrence of diseases is driven by governance, trade, health management and climate change. Most disease outbreaks have happened in developing countries where 90% of aquaculture takes place, reducing revenues, eliminating jobs, threatening food security and undermining development goals.


Governance has been unable to keep up with aquaculture’s rapid expansion. There are major deficiencies in terms of legislation, environmental management, disease surveillance, access to diagnostic services, and establishing dialogue with the industry.


There are also many examples of unsustainable production practices even among industrial large scale aquaculture operations. There is an overall trend to produce beyond carrying capacities, hence causing disequilibrium and favoring pathogen-friendly environments.


Under an ideal scenario, a holistic approach combining elements of biosecurity, adequate trade restrictions, a comprehensive legislation supporting sustainable aquaculture production technologies and transparency between stakeholders would constitute the key elements for the success of a long term sustainable world aquaculture industry.


Biosecurity is often ignored. It is however a powerful tool to manage the economic impact of diseases on aquaculture businesses, by protecting from external risks, mitigating risks within aquaculture facilities, and proactively dealing with disease crisis situations based on rational scientific knowledge and economic realities driving businesses towards recovery. A disease should always be considered as a business risk.


There is a lack of inter-country regional biosecurity approach among aquaculture producing nations. Most of aquaculture production comes from outdoor exposed systems, therefore it is to be expected that diseases will be easily transmitted. At the regional level, biosecurity needs to be managed by creating risk zones based on the criteria that pathogens evolve in a specific environment with available hosts and favorable conditions where the pathogen can replicate. Governance, research and industry initiatives should be common to countries operating under the same biosecurity risk zone.


Trade is one of the most significant causes of disease transmission. In Australia, supposedly one of the most biosecure nations in the world, after the 2016 white spot syndrome virus outbreak the Australian Prawn Farmers Association requested an independent study to determine the level of WSSV prevalence in shrimp shipments imported from Asia. It was discovered that 86% were WSSV positive (FFVS report 2017).


Given the international regulations of the World Trade Organization and the interests of other industries competing to generate a larger percentage of the GDP, it is unrealistic to expect a country to shut down its borders. There are however mechanisms for a country to protect its domestic aquaculture industry by guiding or investing in sustainable technological solutions; for example, in Australia, government-research institutions which were aware of the spread of WSSV around the world could have pro-actively developed domestication and WSSV resistant lines under the assumption that the risk of having WSSV in Australia was becoming higher.

Once a disease is established in an outdoor production system and its surrounding environment, it is unrealistic to assume that it can be eradicated, and especially in the case of the WSSV given the unusual large number of WSSV hosts.


The World Organization for Animal Health (OIE) has established that if a country does not detect a specific pathogen in its environment for a period of two years, it can claim to be declared free of that pathogen (even after a disease outbreak). Although adopting such a strategy can be beneficial to remove trade barriers it does not mean that the pathogen is not present in the environment. Depending on environmental conditions and if the intensity of post-outbreak farming activities is significantly reduced after removal of the infected batches, the pathogen may be present at very low prevalence and remain undetected within standard sampling protocols.


In Australia, the WSSV is still considered as non-endemic and the government has allocated AU$9 million on a two-year national WSSV testing program to obtain proof of WSSV freedom as per OIE standards.


From a governance perspective, until the pathogen is not officially declared as endemic, efforts to promote in-country practical diagnostic tools, approve regulations for the use of adequate therapeutants or technologies or allocate resources to focus research on dealing with that pathogen will not happen or at least not entirely and not efficiently.


From an industry risk management perspective, pretending that a pathogen has been eradicated from an open environment is the wrong approach.


Some governments and aquaculture industries have proven to have the right focus to solve disease crisis. The case of the Chilean salmon farming industry is probably one of the greatest success stories where government institutions and industry stakeholders were able, through proper dialogue and rigorous implementation of biosecurity systems, not only to recover from a major disease crisis but to even improve production results beyond pre-crisis production yields, proving that, biosecurity systems contribute significantly to the improvement of aquaculture production because it lays down with clarity the entire production process and obliges to critically analyze the process.


Productivity in terms of Kg harvested per smolt stocked (a) and average harvest weight (b) of Atlantic Salmon, pre-and post-ISA crisis (Alvial 2011).


The use of seedstock from non-certified disease free sources is another very significant cause of disease transmission, often driven by a lack of knowledge regarding diseases, lack of government control and lack of in-country efficient broodstock breeding programs and good quality seed suppliers. Aquaculture operators are often tempted to import non-certified seedstock which adds the risk of introducing non-endemic diseases.


The first principle of any animal production industry is to ensure supply of healthy and performant seedstock. Biosecurity lays out all the tools and methods to achieve that.


Holistic approach to disease risk management (Francois Brenta)


Disease prevention is based on good health status, good water quality, good feeds, good husbandry and good genetics.


The first step to disease risk management is understanding that cultured animals and pathogens evolve in a common ecosystem and that at any given time environmental conditions can become favorable for the pathogen to develop a disease situation.


The comfort of the animal must be the primary focus of the operator; therefore, the culture environment must be kept within the lowest possible stress conditions. Water quality fluctuations are an important stress factor that can trigger diseases. Water parameters must be kept at optimum levels for the target specie and as stable as possible to minimize stress.


Air supply failure causing massive drop in dissolved oxygen concentration and a tremendous stress situation

Graph showing positive correlation between low temperatures combined with significant temperature fluctuations and WSSV outbreak (Francois Brenta)

Animal health monitoring should be done at two levels: by visual observations as frequently as possible to detect symptomatic cases that may harbor an infection; by a routine surveillance program acting as a series of check points along the process to detect pathogens even in asymptomatic animals. Organs, tissues and diagnostic methods vary among species, target pathogens, and whether the sample is destructive (lethal) or non-destructive.

Visual observations



Symptomatic (sick) animals




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Organs removal for wet mount



Digestive tube




Wet mount for microscopic examination




Tissue removal for PCR










Polymerase Chain Reaction (PCR)



Fixation for Histopathology


In cases of very low pathogen prevalence, infections can be expected to be just below PCR detection level and not equally present in all target tissues, therefore making it difficult to detect, especially if only one organ is sampled. Though destructive sampling may significantly increase the chances of detection of pathogens on asymptomatic animals, it is often seen as an obstacle depending on the value of the animal, such as in cases of broodstock. The decision whether to destructively test animals or the choices of organs or tissues is case specific. If applicable, the chances of detection are significantly improved by sampling multiple tissues from the same animal.


Shrimp experimentally infected with WSSV showing differences of infection levels in different organs / tissues within the same animal: P1-P10 pleopods; Gills; HL hemolymph; LO lymphoid organ (Francois Brenta)

For decades, antibiotics have been used in unsustainable indiscriminate ways to control bacterial diseases, resulting in bacterial resistance and deterioration of the health of farmed animals. A novel sustainable approach is to promote stable environments using microbial communities such as bioflocs, biofilms and probiotics. Microbial communities are very efficient in promoting in situ water bioremediation by breaking down ammonia into nitrate; improving animal nutrition by providing an important source of microbial protein; and improving animal health by providing a rich source in bioactive compounds that can enhance growth, survival, gonadal development, reproductive performance and stimulate innate immune system of aquatic animals.


Bioflocs and biofilms are formed by a diverse ecosystem of microorganisms such as bacteria, zooplankton, protozoa, ciliates, flagellates, nematodes, phytoplankton and particulate organic matter. Bioflocs are found as clusters suspended in the water column by the action of significant mechanical aeration; biofilms are a complex benthic structure covered by a matrix of polysaccharide material. Probiotic bacteria, associated mostly with Bacillus sp. can be found in bioflocs, biofilms, as part of the animal’s microbial flora or brought into the system through an external source; the principle of probiotics is to outcompete pathogenic organisms by competitive exclusion. Quorum sensing plays in important role in microbial dominance.


Benefits of using microbial communities in aquaculture (Francois Brenta)


Adequate nutrition is key to ensure that animals have the right level of energy to sustain growth and to compensate for the inevitable stress even under optimum culture conditions.  Although feed specifications can vary among suppliers, there are well established international quality standards. Feeding methods however are extremely variable among operators and differences in performance can vary significantly depending on feed management practices. For a given batch, a superior performance reflects a higher level of health and therefore a lower biosecurity risk.

Production results of P. vannamei cultured over 16-week period comparing standard feeding protocol (SFP), standard feeding protocol + 15% feed input (SFP+15%), automatic feeder with timer (Timer) and automatic feeder with acoustic feedback (AQ1) showing additional 19% gain in final weight from Timer method and 49% from AQ1 method vs. standard method (Carter E. Ullman-Auburn University)


Genetics is the most efficient tool to tackle diseases; it is the driver of animal performance; when combined with biosecurity, the overall efficiency of the system improves exponentially. Alike biosecurity, breeding programs are a very powerful risk management tool. The most popular selection criteria are typically growth and disease resistance.  Although there is a known antagonism between the inheritance of fast growth and disease resistance traits, well balanced breeding programs should combine both. Growing fast in outdoor systems is also a biosecurity strategy because it minimizes the time of exposure to pathogens, however in situations where pathogens are highly prevalent and disease is inevitable, having disease resistant lines is also very important. Aquaculture business models should clearly define what proportion of growth vs. survival provides the best cost effectiveness.


Effect of breeding programs and biosecurity in Asian shrimp production: two periods of growth defined by technological innovation and two eras of crisis defined by diseases (CPF)

Effect of breeding programs: Special Pathogen Free (SPF) dominate Asia; Pond reared broodstock dominate Latin America (CPF)


Effect of breeding programs on the development of early mortality syndrome (EMS/AHPNS) resistant lines (CPF)


Aquaculture production process is a series of inter-independent activities that share common risks of pathogen transmission. From a long-term business risk management perspective, seedstock is the first area of focus, followed by nursery and grow-out. Without predictable seedstock supply, grow-out production cannot be sustained.


The risk pyramid defines how actions and investments in managing the risks should be prioritized by order of significance. The first step is always to ensure animals are healthy, followed by water and mechanical vectors.


The risk pyramid rational can be applied for establishing biosecurity plans by governments at regional and country level, or by aquaculture operators at site and facility level. Regardless of the specie, farming technology or scale, the objective is always risk mitigation.


Pathogen transmission can be vertical or horizontal. Both pathways play an important role in infection mechanisms and therefore in determining risk mitigation protocols and pathogen surveillance programs. Vertical transmission involves transfer of pathogens from parent material (broodstock, eggs, spermatophore and feces) to offspring (descendants). Pathogens can be transmitted inside the egg (intra ovum) or externally (per ovum). This infection mechanism is pathogen specific and therefore it significantly influences risk mitigation protocols for quarantine, breeding programs and hatcheries. Horizontal transmission involves transfer of pathogens between animals, water and mechanical vectors. This infection mechanism is common to all pathogens; however, some mechanical carriers may be more critical if they are also part of the food chain of the cultured specie.


Pathogen risk mitigation can be done by exclusion or control mechanisms. In indoor production systems, pathogen exclusion can be maintained, however in outdoor production systems, exclusion may no longer be achievable cost effectively, therefore a combination of disease resistance and practical biosecurity risk mitigation measures is the best approach.


When monitoring animal health, asymptomatic animals may be sampled under the scope of a routine surveillance program and the presence of pathogens may be undetected or detected in which case a management decision must be made. If symptomatic animals are observed, they must be sampled for diagnostic; the observation will most likely correlate with some sort of infection, not necessarily caused by a specific pathogen, however, the clinical condition of the batch should trigger a management decision because the disease situation will certainly evolve into a disease outbreak.


Management decision matrix in cases of infection (Francois Brenta)


Contingency protocols should clearly define control measures for disposal of mortalities and organic wastes related to the farming environment, effluent treatment if applicable, and for the risks of pathogen horizontal transmission related to harvest and post-harvest activities.


In cases of disease outbreak, recovery timeframes are significantly faster if pre-established emergency protocols and resources are available. Biosecurity plans should incorporate this aspect of risk management.


Just like any other management tool, biosecurity has a cost, but the risk from not having a biosecurity system may have much greater financial consequences. It is difficult to segregate the cost of biosecurity from improvement and innovation costs because of the holistic nature of biosecurity and its impact on overall efficiency. For an industrial shrimp farming operation, the cost of diagnostic and animal health monitoring is approximately US$0.05 per Kg of shrimp produced. Operating a family breeding program based on disease resistance and growth could cost US$500,000 per year, however the expected gain in performance may be 15 to 50 times the value of the cost. Capital costs involved in the implementation of biosecurity will vary according to the farming technology and the level of biosecurity intended. As a rule of thumb, the higher the investment, the lower the risk of diseases and the more predictable the outcome. For intensive production systems, cost effective water treatment can be done with ozone. This technology has the advantage of producing very high oxidation levels in a short period of time followed by fast breakdown of free radicals. For an industrial scale operation, to treat 1m3 per day the capital cost is approximately US$60, including 100% redundancy. Other chemicals may be used to disinfect water, however, a higher cost in reservoir capacity may be required due to the significant additional time required for the breakdown of toxic products generated by the breakdown of chemicals.


The focus of biosecurity actions and investments must be primarily on seedstock production followed by early juvenile stages in preparation of the final grow-out stage. The more extensive the production systems, the less feasible it becomes to justify investments including in biosecurity and the less predictable the outcome. Intensive systems are more capital demanding but at the same time may justify additional investment in biosecurity to reduce the risk of failure.  Risk management should be part of any region, country or private aquaculture company’s working culture as it will impact the economy and social structure around it.

There is evidence that effects of climate change are transforming ecosystems. Changes in pathogen transmission mode, virulence and disease susceptibility are to be expected. Climate change may widen the geographical distribution of infectious diseases. Environmental deterioration is more likely to affect the tropics where most of aquaculture takes place. Pathogenic microorganisms are likely to adapt to environmental changes faster than their hosts creating more frequent and devastating disease outbreaks. With more disease challenges to come, biosecurity risk management and genetics will become unavoidable to sustain the aquaculture industry around the world.