Aquaculture’s role in the growing threat of antimicrobial resistance

Antimicrobial resistance (AMR) is often described as a “silent pandemic”. Unlike a fast-moving viral outbreak, AMR spreads gradually with bacteria evolving and adapting until the medicines we rely on no longer work. The consequences are profound. AMR contributed to an estimated 4.95 million deaths in 2019. These numbers are expected to increase to 8-10 million deaths by 2050. AMR now threatens routine surgery, cancer treatment, and infection control.  

Human activities, including the widespread use and misuse of antibiotics in human medicine, livestock production, and aquaculture, have dramatically accelerated AMR. In response, the World Health Organisation (WHO) has established the One Health initiative — linking human health, animal production and environmental systems. Aquaculture sits squarely within that nexus. 

Aquaculture, antibiotic use, and how AMR enters our food supply 

As with any intensive animal production system, disease outbreaks can and do occur. Antimicrobials have therefore been used in aquaculture for treatment and, in some cases, for prevention. 

What makes aquaculture distinct is its environmental interface. Aquaculture operations are often open or semi-open systems. When medicated feed is used, some antibiotics pass into surrounding waters and sediments. This creates ecological conditions where resistant bacteria and antimicrobial resistance genes can emerge and persist. 

Research has shown that aquaculture environments can act as reservoirs and amplification points for resistance genes. But how does this connect to human health? 

There are three main pathways by which AMR linked to aquaculture may reach seafood consumers: 

1. Direct exposure to resistant bacteria: Farmed seafood can carry bacteria naturally present in aquatic environments, including species such as Vibrio, Aeromonas, and occasionally E. coli. If these bacteria are resistant to antibiotics, and if seafood is eaten raw or undercooked, humans may be directly exposed. Even when cooking kills bacteria, improper handling — such as cross-contamination in kitchens — can transfer resistant microbes to other foods.  

2. Transfer of resistance genes in the gut: Resistance genes do not need to arrive in a fully pathogenic bacterium to pose a risk. Many bacteria exchange genetic material through horizontal gene transfer. If resistant bacteria from seafood enter the human gut, they may pass resistance genes to other bacteria, including opportunistic pathogens. 

3. Antibiotic residues and selective pressure: Antibiotic residues in seafood products can contribute to low-level exposure in humans.  

Together, these pathways illustrate why AMR in aquaculture is not confined to farm boundaries. It can move along supply chains and into human microbial ecosystems. 

The most found farmed seafood in Canadian grocers are farmed salmon, both domestic and imported (e.g., Chile), and imported shrimp from various countries.   

In Canada, salmon farming primarily uses the antibiotics oxytetracycline and florfenicol. These are considered ‘highly important’ antibiotics by the WHO. Highly important antibiotics are considered medically essential for treating serious human infections, with few or no other alternatives. On average, a B.C. salmon farm will use 1.3 antibiotics per year. Resistance genes associated with these antibiotic classes have been detected in sediments near B.C. and Atlantic farms.  

Imported salmon from Chile has the highest antibiotics use of all salmon farming regions globally with approximately 351 tons used in 2024. This is mostly driven by the ‘highly important’ antibiotics, oxytetracycline, and florfenicol. Like Canada, resistant bacteria and resistance genes have been detected in farm environments and surrounding sediments. 

Canada imports farmed shrimp from countries such as China, India, Vietnam, Thailand and Ecuador. Because shrimp are not widely vaccinated, bacterial disease has historically driven antibiotic use in some regions – particularly the recurrent use of oxytetracycline and florfenicol. Prohibited or off label use of fluoroquinolones has also been documented Similarly to salmon, studies show that antibiotics used in shrimp ponds can accumulate in sediments and that resistance genes are detectable in surrounding ecosystems. 

Antimicrobial resistance is not solely a hospital problem. It is shaped by how we produce food — including seafood. AMR requires a commitment to antimicrobial stewardship across seafood supply chains – from producers to major retailers. That’s why Living Oceans has teamed up with McGill University’s Antimicrobial Resistance Centre and World Animal Protection on a study to find out the prevalence of AMR within farmed salmon and shrimp sold in Canadian retailers. Stay tuned!