The Long Read

Disease management in aquaculture: ‘It is about tipping the balance in favor of the animal’

By Jane Byrne

- Last updated on GMT

Aerial shot above a circular fish farm in a loch, Scottish Highlands, United Kingdom © GettyImages/Abstract Aerial Art
Aerial shot above a circular fish farm in a loch, Scottish Highlands, United Kingdom © GettyImages/Abstract Aerial Art

Related tags Skretting BioMar Salmon Aquaculture shrimp IoT disease RAS

The prevalence of infectious diseases in the aquaculture industry requires a multi-pronged approach to control; the experts agree there is no one silver bullet in terms of managing health and welfare in fish and shrimp farming.

Elisabeth Aasum, global RD manager health at BioMar, told us: “It requires a holistic approach, looking at the entire production cycle, considering the feed alongside making decisions about the right smolt to use, ensuring the vaccine strategy is optimal, knowing when to move fish, when to harvest, and how to treat them, given ongoing disease challenges.”

Charles McGurk, R&D director at fish feed manufacturer, Skretting, echoed that. An integrated health management model, he said, ensures there is good genetic stock to start with, and top level biosecurity, it consists of reducing stress levels as much as possible, and applying all the good husbandry practices.

“Of course, vaccination has changed the industry. We wouldn't be in the situation we are in now, particularly in relation to salmon farming, without the fantastic vaccines that have been developed and that is the case across the other species as well, apart from shrimp.”

And functional feeds also play a role, said McGurk. Indeed, a critical focus for Skretting is looking at how, through supporting an integrated health approach, there can be less industry reliance on chemotherapeutants such as antibiotics and parasiticides whatever the challenge is, whether it is environmental or pathogenic. “In that way, we hope we can tip the balance in favor of the animal.”

It is critical to have conversations with customers about their long-term production approach and feed is part of that discussion, said Aasum. “It is all about facilitating a sustainable industry, adapting nutrition to support fish and shrimp when needed.”

Join me and 350+ leaders from across the aquaculture value chain at the Blue Food Innovation Summit​ in London. I will moderate the panel, ‘Fortifying Aquatic Health: Proactive Disease Management via Monitoring, Vaccination and Novel Feed Additives’ on Wednesday, May 24. 

Fortifying Aquatic Health

Gorjan Nikolik, aquaculture and seafood analyst, Rabobank, agrees with the BioMar and Skretting leads about what makes up the fundamentals of an integrated health management strategy for this space. How all the elements correlate is equally important, he said.

“Scotland’s salmon industry will be the fastest growing European region after Iceland in the next few years and that has a lot to do with Bakkafrost bringing in a post-smolt technology, high-quality feed, and a different way of thinking about farm management,” said the analyst.


Breeding, of course, is fundamental when it comes to supporting animal health.

With different genetic based strategies in shrimp farming, it is possible to either breed for resistance or to generate pure breeds, commented Nikolik.

“One of the big developments in the past few years has been the new breeds of black tiger prawn (Penaeus monodon).

“Genetics has an interplay with environment. The more environmental control – like with a Recirculating Aquaculture System (RAS) - the greater the genetics focus is on breeding for fast growth, and purity, not resistance.

“In Ecuadorian shrimp farming, the trend has been to breed for resistance, or for tolerance. The goal is not focused on purifying the breed,” said Nikolik.

The breeding programs there start with specially selected, disease-free shrimp from the farms.

“The Ecuadorian farmers acknowledge that they cannot win the war anyway, that they have big ponds, no cover, no liners, and that they can’t control all the pathogens either. So instead, they select for shrimp, at the individual pond level, with the best resistance to local disease,” added the Rabobank representative.

Those programs, along with the Ecuadorian shrimp business model, are paying off. The country has increased shrimp production by 100% in a decade, reaching over 1m tons in 2021, and valued by Ecuador's Central Bank at US$5.3bn (Ekos, 2022).

White shrimps or Litopenaeus vannamei © GettyImages/chayakorn lotongkum


Vaccines will continue to be a huge driver in terms of disease management in aquaculture, said Nikolik, who cited progress in Chile in relation to vaccines for controlling SRS.

“We have also seen a lot of development work in the area of oral vaccines,” said the Rabobank expert.

Oral vaccines can be administered either via formulated feed, through encapsulation in a diverse range of polymers, or by the process of bio-encapsulation in live feeds such as rotifers, daphnia, and artemia.

BioMar has been supporting certain suppliers or pharmaceutical companies in the development of oral vaccines for salmonids, bringing knowledge on how to apply them within feed.

However, the lack of immune response seen with oral vaccines in fish compared to injectable ones, most likely down to the degradation of the antigen as the vaccine passes through the stomach of the fish, remains a development bottleneck, said Aasum.

Indeed, she maintains that the injection method delivers the most direct delivery of antigen to the immune system.

Skretting has also been supporting development work in that space.

When used for boosting, an oral delivery system may be capable of enhancing or extending protection, improving the duration of the immune response, said McGurk.

There are other advantages in leveraging the oral route, in not having to inject the fish. But he agrees that it can be quite challenging to ensure the efficacy of oral vaccines.

While there are numerous vaccines that are effective, that have made a massive difference to the industry, making it possible for the salmonid farming industry to reduce its overall use of antibiotics, there are defined biological limits in relation to vaccine programs in aquaculture, acknowledged McGurk.

Fish need to be of a certain size and maturity to be able to respond to vaccines.

Shrimp, he said, cannot be vaccinated against specific pathogens, although they can benefit from compounds that stimulate their innate immune responses. Shrimp do not have adaptive immune systems. They lack the appropriate cells, pathways to respond to specific pathogens and the long-term 'memory' to deal with recurring infections, he explained.

Also, for some pathogens, it is challenging to develop vaccines, noted the expert. “We can't vaccinate against everything, essentially.”

Salmon Rickettsial Syndrome (SRS) is a difficult bacterial disease to deal with, he said. “It is an intra-cellular bacterium, so it actually goes into the cells of the fish, into the immune cells, and then it becomes quite difficult to treat.”

That is the reason existing vaccines are not effective in controlling it.

“There is lot of work going on to try and find methods other than antibiotics to either prevent SRS or to help the fish to better cope with the challenge. We have been evaluating the effectiveness of functional feeds to address this, and we see that there's some distinct potential in that respect.”

Modifying the microbiome

The Skretting team, he continued, is collaborating with colleagues in Nutreco Exploration (NutEx) on those kinds of nutritional strategies, but technologies that are applicable across all aquaculture species and geographies.

“It is using established approaches, if you like, but doing so in a more refined way. So, we are looking at phytogenics, plant products that confer specific physiological effects, and we also have a microtechnology program, in the context of biome-actives, substances that we can use that have modifying effects on the microbiome, again to help to tip the balance in the favor of the fish or shrimp.”


Skretting’s parent company, Nutreco, has also been investing in next-generation technologies like bacteriophages to provide solutions to the critical health challenges of aquaculture. 

“On the fundamental level of whether they work there is no question, bacteriophages kill bacteria, that is how they propagate, that is their modus operandi. But then, of course, when you are looking to make a product containing a cocktail of bacteriophages that will give the desired effect, that's when it gets much, much more complex. And that is where you need to be really sophisticated in the approaches you take, to select the correct bacteriophages and to find a way of delivering those that can give an efficacious response.

“But there are a lot of biotech companies using very innovative solutions and technologies now, and we see that there's really scope for a breakthrough on this horizon,” said McGurk.

Salmon farm in Kvænangen Fjord, Norway © GettyImages/alxpin

Stress busters

BioMar looks to optimize resources by identifying what are the most stressful stages in the production cycle, then it uses the tools it has at hand, or via industry collaboration, to support the fish or shrimp during those challenging periods, with the goal of improving both production performance and efficiency.

Salmon undergo significant changes when they transition from fresh water to sea water, for example. They are entering a completely different environment, explained Aasum.

In addition to being exposed to a higher infection risk in the sea, the fish’s immune defense and barriers are stressed as a result of the smoltification process. Consequently, the fish are exposed to a risk of disease and increased mortality during this phase. “We have extensive documentation showing how we support the fish during this transfer through the use of probiotics, live lactic acid bacteria, to stabilize the microbiota and further ensuring a better base for growth and robustness,” continued Aasum.

Marine fish larvae will also benefit from probiotic supplementation, she said. Again, BioMar has robust data showing that feed containing P. acidilactici MA18/5M, known under the commercial name of Bactocell, has a beneficial impact in terms of reduction of deformities in larvae; the presence of the probiotic improves uptake of bone building minerals, such as phosphorus, in the early life stages.

Boosting diseases defenses 

Probiotics are effective in shrimp production as well, she said.

When shrimp feed is supplemented with such inputs, the cellular and humoral components of the innate immune system of farmed shrimp become more efficient.

“As shrimp do not have that adaptive immunity, we look to stabilize and support their innate immune system. And probiotics are part of that, improving resistance against Vibrio sp. Infections,” outlined Aasum.

Yeast products contain compounds that boost disease defense in shrimp and other fish, according to the BioMar expert. Mannooligosaccharides (MOS), which are derived from yeast cell wall mannan, can protect the external surfaces of the fish, by improving both quantity and quality of the mucus layers.

External pathogens can encounter and colonize the first defense barriers of the fish: skin, gill, and mucus, causing significant health issues in both marine and freshwater species.

The mucus layer is a vital component of the innate immune mechanism in fish, providing a physical and chemical barrier against pathogens, making them less susceptible to disease, and so protecting it is critical in terms of fish health, she said.

Prebiotics – which are mostly nondigestible carbohydrates - are more powerful when used in combination with probiotics, she continued. The sugars and carbohydrates serve as food for the beneficial lactic acid bacteria. Both are working together to confer a health benefit in fish and shrimp. “We continue to evaluate various combinations.”

Cermaq's iFarm concept hopes to use artificial intelligence and machine learning to recognise individual fish in a cage and develop health records. If successful, it will let the aquaculture industry achieve better health and welfare outcomes for their fish and could represent a huge leap forward for the sector, according to a report on The Fish Site. © GettyImages/Shutthiphong Chandaeng

Data crunching

AI tools, diagnostic platforms, cameras, sensors, software, and big data are also increasingly employed to streamline production and offer potential in terms of health management, pointed out Nikolik.

“The salmon companies are the leaders in this space. There is a lot of knowledge and science coming into the salmon sector, the players are big, and they have the capacity to learn, to apply new insights to their production systems.”

Decision-making is increasingly driven now by data, knowledge, and accurate mathematical models, he maintains.

Ecto, a US company backed by Rabobank’s venture fund, has a platform that uses multi-generational data to automatically build models for the early detection of patterns associated with biological risks.

Another company, Bluegrove, has hydroacoustic technology that listens to and perceives the behavior of a farm’s salmon population 24/7 regardless of underwater visibility and light.

Armed with this data and reaching past the limitations of a camera, the idea is that farmers can make informed decisions to improve their feeding system and potentially gain insights into the welfare of their salmon.

While the salmon industry is using this kind of technology in a big way, players in Mediterranean-based sea bream and sea bass production are also beginning now to take advantage of such monitoring aids. And the technology is becoming much more affordable, commented Kristoffer Tveit, digital innovation director at Skretting.

“Ten years ago, a farmer would have had a few sensors that they moved about from cage to cage to conduct spot measurements. Now the main producers are investing in at least one sensor or camera per unit, and they leave them there permanently, monitoring production day in and day out.”

Tveit, of course, looks at the IoT space from the perspective of a feed supplier.

Skretting is actively involved in digitalization of the sector, with tools dedicated to facilitating precision farming. The focus is on using rich data to calculate the expected farm performance, and to provide tailored feeding protocol recommendations to enable production enhancements.

The tools, though, can also serve as an early warning system for health problems in the production environment, said Tveit.

“Regular monitor of feeding should be in line with expectations day by day or hour by hour – if we detect loss of appetite or irregular feed intake, usually that indicates that something is off in this population of animals, whether that is fish or shrimp. That sounds an alarm that the production unit needs more attention, a closer look.

“That is, predominantly, where we are today.”

But there are multiple projects and initiatives in play to exploit the technology even further, to read animal behavior, including AI-supported camera imaging technology to aid health related monitoring, noted Tveit.

The biggest challenge is that monitoring of the animals directly, particularly in the murky waters typical of shrimp farming, where a visible-light camera is not going to detect anything. “But underwater microphones can now record the sound of shrimp activity, of their behavior. So far, they have been used in monitoring appetite; the focus has been on precision feeding.”

The industry is not there yet in terms of analyzing these sound patterns of feeding behavior to answer questions about the health status of a population of shrimp. But Tveit is confident that will materialize in the not-too-distant future.

However, it also follows that, with widespread camera and sensor installations, comes a lot of data, a constant video stream. “It takes quite a back-end system to receive and monitor and calculate that data, so there is a whole infrastructure around that needs to be in place. You cannot have humans sitting there eyeballing every camera. It needs to be artificial intelligence that reads and sets alarms when applicable.”

Cleaner fish

The salmon industry is also deploying laser technology to kill sea lice in pens, Nikolik said.

And not to be forgotten, he continued, are cleaner fish like lumpfish. Their use is quite widespread today, helping producers deal with the scourge of sea lice infestations in Atlantic salmon. “There is a really significant lumpfish breeding industry now that has grown up around that.”

Sea lice on surface of salmon © GettyImages/naturediver

Staying ahead of the curve

McGurk maintains that for Skretting, and the industry as a whole, to be successful and sustainable, it is critical to be ahead of the curve, to be proactive and to try, as much as possible, to deal with problems before they exist.

“That is easier said than done but we need to, at least, maximize the opportunity for success, to safeguard and use innovative solutions.

“The way I see it, nature is always looking [to reach a state of] equilibrium. So, let's try and do the same, to get the balance right, to ensure animal welfare, productivity, and profitability, while supporting livelihoods and providing a good, healthy protein source for a growing population, which really underpins everything.” 

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