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  • Writer's pictureJuliette Alemany

When pathogens become invincible: the antimicrobial resistance issue in aquaculture

Antimicrobial resistance (AMR) in aquaculture is one of those topics that has always existed but has only recently attracted a great deal of attention, becoming the main topic of discussion among the scientific community today. AMR is now considered a global public health problem (Mesalhy Aly and Albutti 2014). Aquaculture encompasses various sizes of farms as well as a wide range of growing methods. It is therefore difficult to collect enough data on antimicrobial use at the international level to establish clear conclusions on the causes and consequences of AMR. However research is growing on this topic, and this article aims at introducing the topic of AMR to non-specialists.

What is antimicrobial resistance (AMR)?

First thing first, what does AMR mean? Antimicrobial is a generic word that describes the chemical components used to fight diseases that originate from microbial activities. When we talk about AMR, we designate the bacteria that became resistant to the chemicals meant to kill them. So yes, today’s article is about these tiny little organisms that all of a sudden decided to revolt. Instead of quietly accepting their death, they upgraded their genetic material, and they got equipped with new weapons to fight the antimicrobial components.

Why do some bacteria become resistant?

When a fish tank gets infected and all individuals are at risk of being killed, it is common practice to use antibiotics to cure the disease. The problem is when antibiotics are used in big quantities or at a high frequency, without working on prevention measures as plan A, and without properly assessing the most adequate treatment. Another bad practice is to treat an entire population when only a few individuals are infected. Let’s imagine that our little bacteria is constantly under attack, even for no good reason. Over time, she will not let the aggressor beat her up constantly. She will be smart about it, will observe the enemy and learn from him, until one day she can teach her family how to fight back!

A selective pressure occurs, with resistant bacteria surviving and multiplying, and passing to the next generation the weapons (gene mutation) that allow them to resist the antibiotics. This phenomenon is called vertical gene transfer. Another possibility for bacteria to become resistant is to receive weapons from their neighbors. A resistant bacteria can ‘teach’ a non-resistant bacteria how to fight. The following figure taken from Lundborg and Tamhankar (2017) illustrates this phenomenon that we call horizontal gene transfer.

Figure 1: How a plasmid, which might contain antibiotic genes, gets copied from one bacterium to another


What are the potential consequences of AMR?

Once pathogens develop resistance to antimicrobials, it becomes increasingly difficult to treat the associated diseases. This is the most direct consequence of the development of resistant bacteria: it takes longer to cure diseases, and in some cases, it might not even be possible to find an effective treatment. This means production loss, which leads to bad economic consequences.

When human activities encourage the development of resistant bacteria, not only do we face the risk of running out of solutions against some bacteria, but we also bring a threat at a larger scale: the resistant bacteria won’t usually stay contained in the environment where they were raised. They want to travel and see the world! At the first opportunity, they will run into a natural watercourse.

Resistant bacteria are much more likely to emerge near aquaculture facilities because the selective pressure is artificially increased by human activities. There are now growing concerns around the globalization of AMR, and it becomes clear that some human pathogens have probably originated in aquatic bacteria (Cabello et al. 2013). The development of resistant bacteria is nothing new in our knowledge of evolution. It is however worrying how fast new resistant strains are developing (Santos and Ramos 2018).


What are the possible solutions to AMR?

The main role of antibiotics is to control the multiplication of bad bacteria in a fish long enough for the individual’s immune system to fight back the bacteria. Instead of automatically considering using antibiotics, it is essential to identify and remove any source of stress. Another important step is to choose the right antibiotic. Ideally, a fish health specialist should run sensitivity tests that consist in applying antibiotics to a sample of infected fish (Mesalhy Aly and Albutti 2014). Probiotics as an alternative to antibiotics are being investigated but have to be used with caution as these are still bacteria that can therefore also become resistant (Watts et al. 2017).

There is a clear link between animal welfare and antimicrobial resistance. Stress is an important factor in immunity decrease. Therefore usual factors that decrease animal welfare such as bad control of water parameters, poor feed quality, or bad enclosure hygiene lead to increased risks of infection that ultimately result in antibiotics overuse. Priority should be given to good aquaculture practices such as effective biosecurity and high water and feed quality that will prevent the occurrence of diseases (Preena et al. 2020).

Figure 2: Prophylaxis may help a shrimp farm to reduce issues linked to AMR

Around the world, the use of antibiotics differs greatly from one country to another. A major variable influencing antibiotic misuse is how strictly governmental organizations regulate the practices. Europe, North America, and Japan have the strictest regulations on antibiotic use (Watts et al. 2017). However, most countries still have a long way to go before reaching this level of regulation, and similarly to fisheries management, this pressing issue can’t be solved without a clear commitment from governmental entities.

In parallel, the work of certification bodies can help to translate a global consumers’ demand into an actionable list of requirements. Strong partnerships between certification bodies, governmental organizations, and technology companies are the way forward to breach the gap of extensive data collection, effective data analysis, best practices advocacy, better regulation, and stronger verification.

The notion of One Health is now getting widely acknowledged by the scientific community. It relies on the idea that the overuse of antibiotics is a worldwide topic that can’t be considered from the sole perspective of agriculture or aquaculture (Cabello et al. 2016). We must take a step back to see the global picture: our world is interconnected, and anything we put in the water can end up on our plates. To solve a global issue such as AMR, we must foster cooperation and coordinated planning.



Cabello, Felipe C, Henry P Godfrey, Alejandro H Buschmann, and Humberto J Dölz. 2016. “Aquaculture as yet Another Environmental Gateway to the Development and Globalisation of Antimicrobial Resistance.” The Lancet Infectious Diseases 16 (7): e127–33.

Cabello, Felipe C., Henry P. Godfrey, Alexandra Tomova, Larisa Ivanova, Humberto Dölz, Ana Millanao, and

Alejandro H. Buschmann. 2013. “Antimicrobial Use in Aquaculture Re-Examined: Its Relevance to Antimicrobial Resistance and to Animal and Human Health.” Environmental Microbiology 15 (7): 1917–42.

Lundborg, Cecilia Stålsby, and Ashok J. Tamhankar. 2017. “Antibiotic Residues in the Environment of South East Asia.” BMJ 358 (September): j2440.

Mesalhy Aly, Salah, and Aqel Albutti. 2014. “Antimicrobials Use in Aquaculture and Their Public Health Impact.” Journal of Aquaculture Research & Development 5 (4).

Preena, Prasannan Geetha, Thangaraj Raja Swaminathan, Vattiringal Jayadradhan Rejish Kumar, and Isaac Sarojini Bright Singh. 2020. “Antimicrobial Resistance in Aquaculture: A Crisis for Concern.” Biologia 75 (9): 1497–1517.

Santos, Lúcia, and Fernando Ramos. 2018. “Antimicrobial Resistance in Aquaculture: Current Knowledge and Alternatives to Tackle the Problem.” International Journal of Antimicrobial Agents 52 (2): 135–43.

Watts, Joy E. M., Harold J. Schreier, Lauma Lanska, and Michelle S. Hale. 2017. “The Rising Tide of Antimicrobial Resistance in Aquaculture: Sources, Sinks and Solutions.” Marine Drugs 15 (6): 158.


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