Protecting aquatic species: strategies for pathogen management

In Brief

  • Diseases pose a significant threat to the modern aquaculture industry, impacting productivity and animal welfare.
  • Best practices and animal welfare in aquaculture prioritize protecting animals from infections and subsequent diseases.
  • The presence of opportunistic pathogens in aquaculture creates a constant risk of disease outbreaks.
  • Bacterial pathogens are a leading cause of disease in aquaculture, driving antibiotic use. However, viral and parasitic infections also raise significant concerns.
Figure 1: Key challenges faced by the aquaculture industry. Source: GOAL Survey 2022, Rabobank 2022

The hidden costs of disease in aquaculture: beyond mortality

Weakened productivity is linked to reduced profitability. Although the exact cost of disease is unknown, it is widely accepted to be in the tens of billions of dollars every year. Mortality is the most obvious loss in profit, but there are also many hidden costs associated with disease, for example:

  • Diagnostics & veterinary expertise
  • Medicines and chemical treatments
  • Time & labor
  • Lost growth performance
  • Feed losses & increased FCR
  • Market access & consumer reputation

Aquaculture practices drive pathogen proliferation

Intensive aquaculture practices such as antibiotic usage, disinfection and even feeding can favor the proliferation of pathogenic bacteria (Figure 2). This is because many pathogens are r-strategists, which means they have high growth rates, especially in non-competitive environments and can dominate in unstable conditions. The opposite, K-strategists, including many probiotics, grow slower but dominate in stable conditions. This means that a disease management plan is required throughout the production cycle. This should include continuous pathogen surveillance and prioritizing proactive strategies to avoid pathogenic outbreaks, or reactive measures such as antibiotics.

Figure 2: Examples of how current aquaculture practices promote r-selection, increase the probability of opportunistic bacteria (A) Disinfection of intake water. (B) Addition of feed to the system.

Source: Vadstein et al. 2018

Antibiotic reduction in aquaculture 

In line with other protein sectors, antibiotics have traditionally been used to treat bacterial infections in aquaculture. However, their overuse leads to antimicrobial resistance and consequently the industry has many initiatives to reduce its reliance, in favor of preventative healthcare. For example, in addition to meeting Aquaculture Stewardship Council (ASC) criterion, the Sustainable Shrimp Partnership (SSP) in Ecuador also expects its members to use zero antibiotics. Similarly, Norway have grown their salmon production volumes, whilst reducing their consumption of antibiotics by 99%. The Chilean salmon industry has also managed to reduce its antibiotic usage by 50% since 2017, although to a lesser extent. In 2022, Chilean salmon reported to use 458.6 g of antibiotics for every ton of Atlantic salmon produced (CSARP, 2022).

Feed additives as valuable health management tools

Functional feeds are an important part in a robust health management program, but there is no silver bullet. Consequently, multiple active components with complementary modes of action must be explored. Thes include, but are not limited to:

  • Direct inhibition: Many probiotic bacteria, organic acids and essential oils impact pathogen growth and survival.
  • Competitive exclusion: utilizing beneficial bacteria (probiotics) to compete with pathogens for much needed resources e.g., nutrients, adhesion sites.
  • Membrane damage: Gram-negative pathogens have an outermost layer of lipopolysaccharide. This gives them greater mitigation against antimicrobials and can pump out unwanted substances, like antibiotic metabolites. Breaking this membrane causes stress to the pathogen, disrupting the membrane functionality and reducing overall virulence.`
  • Quorum quenching: quorum sensing is a means of bacterial communication and is linked to pathogen virulence. Quorum quenching breaks these channels, disrupting virulence and biofilm formation.
  • Toxin degradation: endotoxins can be produced by several pathogens, which cause great damage to the animal. This is the case in Acute Hepatopancreatic Necrosis AHPND (Acute Hepatopancreatic Necrosis Disease), where a number of Vibrio spp. produce pirAB toxins which attack the hepatopancreas.

Salmon vs salmon rickettsial septicemia 

Salmon rickettsial septicemia (SRS), caused by the etiological agent Piscirickettsia salmonsis, has been the most important infectious disease in the Chilean salmon industry since the 1980’s, costing >300 million USD per annum. It is estimated, >95% of all antibiotics used in Chile are used to treat SRS. 

In a recent study, Biotronic® Top3, an enhanced acidifier was able to significantly reduce the mortality of Atlantic salmon after a 65-day Piscirickettsia salmonsis cohabitation challenge (55.0 ± 7.9% vs 72.2 ± 13.9%, respectively; P = 0.0064). In the same trial, it was calculated that the enhanced acidifier was able to reduce the probability of a mortality event by nearly 40%.

Figure 3: Survival of fish fed a control diet (D1), or supplemented with Biotronic® Top3 at 2 kg/ t, following a 65-day SRS challenge.

Interestingly, through in vitro investigations, it was demonstrated that the enhanced acidifier was also able to reduce the efflux pump activity in pathogens, which is an important mechanism for antimicrobial resistance. This suggests Biotronic® is also a useful tool in medicated feeds, as well as mitigation.

Tilapia vs hemorrhagic septicemia

A recent study investigated the effects of Biotronic® on tilapia health and performance when challenged with Aeromonas hydrophila. Tilapia young fish were divided into 12 tanks and fed one of four diets. The group that received Biotronic® showed improved survival rates and better growth, particularly in terms of feed conversion rate, compared to those given other organic acid products. Overall, the study suggests that Biotronic® may contribute to enhanced tilapia health and production efficiency.



Final weight (g)

Biomass (g)





84.7 ± 1.2

3 322 ± 49

3.30 ± 0.02

1.04 ± 0.02ab



87.0 ±  2.2

3 390 ± 61

3.34 ± 0.04

1.02 ± 0.02a


Comp 1

85.7 ±  1.4

3 342 ± 63

3.32 ±  0.03

1.03 ± 0.02ab


Comp 2

83.0 ± 0.4

3 256 ± 33

3.27 ±  0.01

1.06 ± 0.01b

Figure 4: Survival of fish fed different diets, following a 20-day A. hydrophila challenge. The table underneath presents the performance data during the eight-week growth phase of the trial.

Shrimp vs AHPND

Picture 1: tank with high organic matter, which is a strong contributor of shrimp disease.

Disease outbreaks can disrupt the balance of gut microbiota in shrimp, leading to a loss of microbial diversity. Research suggests a connection between these disruptions and disease severity. This highlights the importance of a healthy gut microbiome for shrimp resilience. This is partly why probiotics are gaining traction in aquaculture. In shrimp farming, probiotics can be used in feed to support gut health and potentially improve the animal's ability to cope with stressful situations, and they can also be used in water treatment for bioremediation.

However, disease may still occur and since its identification in China in 2009, Acute Hepatopancreatic Necrosis Disease (AHPND) has become a global problem in the shrimp industry, with an estimated loss of >40 billion USD. In a recent trial AquaStar® GH demonstrated in a dose dependent manner, after shrimp were challenged with Vibrio parahaemolyticus (immersion, 1 hour at 1.25 x 106 CFU/ ml). In the highest dosage, 1.7 g/ kg, a 60% improvement was observed relative to the control (Figure 5).

Figure 5: Survival of shrimp fed a control diet, or supplemented with AquaStar® GH in a dose dependent manner, following a V. parahaemolyticus challenge.



Pathogens are a constant threat for the aquaculture sector and a key bottleneck for future growth. The industry must collaborate and innovate together, building partnerships across the value chain to develop a more proactive approach to disease management, including the use of functional feed. This has double benefits, improving the health, welfare and survival of our fish and shrimp, but also a key strategy to reduce our reliance on antibiotics – for the good of people, the planet and profit. 

Published on

12 April 2024


  • Aquaculture
  • pathogen management

About the Authors

Benedict Standen,  Head of Aqua Marketing Global, Animal Nutrition & Health at dsm-firmenich

Benedict Standen is the Head of Aqua Marketing Global at dsm-firmenich Animal Nutrition & Health. He received his PhD from Plymouth University, where his research focus was feed additives in aquaculture.

Thiago Soligo,  Aqua Marketing Manager Latin America, Animal Nutrition & Health at dsm-firmenich

Thiago Soligo is the leader of Aquaculture for Latin American countries at dsm-firmenich Animal Nutrition & Health. He has a Master's degree in Aquaculture from the University of Santa Catarina and specializes in fish and shrimp production.


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