By Francois Brenta


November 7, 2018.


Diseases in farm-raised species have proven to be the most significant threat to the aquaculture industry. With annual losses caused by diseases estimated at USD 6 billion, the global aquaculture industry faces a tremendous challenge. Continued growth in the sector will only be possible if sustainable production technologies and practices are more fully developed.
Diseases have negatively impacted all major species utilized in the commercial aquaculture industry.
In 2007, after three decades of sustained growth, the Chilean salmon farming industry was hit by a viral disease called infectious salmon anemia (ISA), resulting in the loss of approximately two-thirds of Chile's national production. As a direct consequence, approximetely 50% of all industry-related jobs were lost due. The overall financial impact of the ISA crisis was estimated at USD 2 billion (World Bank).
In Asia, the tilapia farming industry recently recorded year over year losses estimated at USD 480 million due to bacterial infections caused by Streptococcus. In other tilapia producing regions of the world, a viral disease known as the tilapia lake virus (TiLV), first discovered in Israel in 2009, was subsequently confirmed in Egypt, Colombia, Ecuador, Peru, Thailand, The Philippines. TiLV has continued to spread across other countries, threatening the USD 9.8 billion world tilapia industry. Egypt, which is the second largest tilapia producer in the world, has already lost more than USD 100 million to TiLV. Outbreaks have been reported in other affected countries with mortalities as high as 90%.

Mass mortality caused by the tilapia lake virus (TiLV)

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 USD 20 billion have been lost over the past decade due to several diseases. The vast majority 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, WSSV has caused losses of more than USD 8 billion. WSSV initially spread rapidly across South East Asia, causing losses estimated at USD 6 billion. By the end of 1999, the virus had literally destroyed the entire Ecuadorian shrimp farming industry, reducing its annual production to 30% of its pre-WSSV production levels and resulting in losses of more than USD 1 billion. By 2011, WSSV had been detected in Saudi Arabia, forcing the industry to insitute 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 WSSV


External symptoms caused by WSSV

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, EMS spread to Vietnam, Malaysia, Thailand, Mexico, Venezuela and other Latin American countries, causing annual losses of more than USD 1 billion.


EMS infected shrimp

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 reductions in growth. In Asia, the pathogen has already caused major economic losses. Typical impacts are reduction of harvestable size to 12g from the normal 18g harvest size, causing a 25% reduction of 25% in harvest volumes and economic losses of approximately 34% due to the premium prices paid for larger shrimp. On average, under typical Asian intensive shrimp farming conditions, a pond significantly infected with EHP will generate losses of USD 4,500 per hectare per cycle.

Given the numerous epizootic events over decades affecting various species and environments from the tropics to the subpolar oceanic range, it is clearly a matter of "when" and not "if" a disease will affect a species, region, country or aquaculture operation.

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

Governance and policies have been unable to keep up with aquaculture’s rapid expansion and the emergence of new disease epizootics. 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 ingrained and shoirt-sighted tendency for managers to attempt to produce beyond the carrying capacity and biological limits of a production system, causing disequilibrium and the unintended establishment of pathogen-friendly environment.

Under an ideal scenario, a holistic approach that combines proper biosecurity protocols, appropriate trade restrictions, targeted legislation that encourages and supports sustainable aquaculture practices, and transparency between stakeholders would all constitute key elements driving a sustainable aquaculture industry.

Biosecurity is frequently ignored by commercial aquaculture companies. This is unfortunate and short-sighted, as biosecurity is a powerful tool to mitigating risks within aquaculture facilities.

What's more, there is a lack of an inter-country regional biosecurity approach to aquaculture. 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. Australia, which was reportedly one of the most biosecure nations in the world, discovered that it had a major disease epizootic in its shrimp farming sector that most likely originated overseas. In its efforts to deal with the crisis, the Australian Prawn Farmers Association contracted an independent study to determine the level of WSSV prevalence in imported shrimp from Asia and it was discovered that 86% of all imports were WSSV+.

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, Australia's globally recognize research institutes, which had been aware of the spread of WSSV around the world and the damages it had caused to other nations shrimp farming sectors, could have pro-actively developed WSSV resistant lines under the assumption that WSSV would eventually land on Australia's shores.

Much like pandemics effecting humans, resources and efforts to develop diagnostic tools and accelerate the development of targeted treatments and technologies are genrally slow to develop and are frequently realized only after the majority of damages and losses occur.

Some governments and aquaculture industries have proven to have the right approach and can serve as a model for other countries and the own aquaculture sectors. 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, to not only recover from a major disease crisis but to even improve production results beyond pre-crisis production yields, proving that, biosecurity can indeed 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 sources is another 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 seedstock, which can and has resulted in the introduction of non-endemic diseases.

The first principle and objective of any animal production industry is to ensure a readily available supply of healthy and disease-free seedstock. Biosecurity lays out all the tools and methods to achieve that first objective.

Holistic approach to disease risk management

Under the holistic approach to disease risk management, 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.

The positive correlation between low temperatures combined with significant temperature fluctuations and WSSV outbreak

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.

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.

As has been widely reported, antibiotics have been used in unsustainable and indiscriminate ways in efforts to control bacterial diseases in farm-raised animlas, resulting in bacterial resistance and deterioration of the health of the farmed animals. A more 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

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.

Genetics is the most efficient tool to tackle diseases. It is the driver of animal performance and when combined with biosecurity, the overall efficiency of the system improves exponentially. Much like 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 selection criteria. Fast growth is a biosecurity strategy because it minimizes the time of exposure to pathogens, however in situations where pathogens are prevalent or anticipated, 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.

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.

Aquaculture risk pyramid

The risk pyramid rational can also be applied for establishing biosecurity plans by governments at regional and country level, or as just discussed, by aquaculture operators at the site and facility level. Regardless of the species, the farming technology or the scale, the ultimate goal 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 species being cultured.

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

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 in place is likely to have a far greater financial cost. 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 USD 0.05/kg of shrimp produced. Operating a family breeding program based on disease resistance and growth could cost USD 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 USD 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 also 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.