Antibiotic resistance is a growing global health emergency, with experts predicting it could cause 10 million deaths annually by 2050. A major contributor to this crisis is the overuse of antibiotics in aquaculture the farming of fish and seafood.
Antibiotics like oxytetracycline and amoxicillin are heavily used in crowded fish farms to prevent diseases, but these drugs often leak into waterways, creating environments where antibiotic-resistant bacteria (ARB) thrive.
These bacteria evolve to survive the drugs designed to kill them, making infections harder to treat in humans and animals.
In South Korea, where this study was conducted, aquaculture farms face significant challenges due to high antibiotic use and inadequate wastewater treatment.
Researchers focused on three sites in Tongyeong: a fish farm, a sea pineapple farm, and an oyster farm near a wastewater plant, to understand how resistance spreads in marine environments.
Limitations of Traditional Antibiotic Resistance Tests
For decades, scientists have relied on two methods to detect antibiotic-resistant bacteria antibiotic susceptibility testing (AST) and minimum inhibitory concentration (MIC) tests.
AST involves growing bacteria in labs and exposing them to antibiotic discs to check survival rates, while MIC tests measure the smallest antibiotic dose needed to stop bacterial growth.
However, both methods fail to detect viable but non-culturable (VBNC) bacteria dormant cells that remain alive but refuse to grow in lab conditions. These VBNC bacteria can reactivate later, spreading resistance genes through water or seafood.
Traditional tests also take 24–48 hours to deliver results, delaying critical decisions during disease outbreaks. This study highlights how these outdated methods underestimate risks, especially in aquaculture, where diverse bacterial communities interact.
PMA-qPCR A Breakthrough in Detecting Resistant Bacteria
To overcome these limitations, researchers tested a new method called PMA-qPCR (Propidium Monoazide-quantitative PCR), which combines two technologies to detect live bacteria accurately.
Propidium monoazide (PMA), a chemical dye, binds to DNA from dead bacteria and blocks its detection during analysis. Quantitative PCR (qPCR) then amplifies DNA from live cells, including VBNC bacteria, delivering results within hours.
In the study, PMA-qPCR identified 40% more live bacteria in aquaculture samples than traditional methods. For example, at a fish farm in Tongyeong, dormant Vibrio cells survived high antibiotic doses but were invisible to MIC tests.
PMA-qPCR detected these hidden threats, proving its potential to revolutionize how we monitor antibiotic resistance.
Key Findings on Antibiotic Resistance in Aquaculture
The study uncovered critical insights into how antibiotic resistance spreads in aquaculture. At the fish farm (Site 1), Vibrio species dominated and showed high resistance to sulfadiazine, a common antibiotic.
In contrast, the sea pineapple farm (Site 2) hosted mixed bacteria like Pseudoditeromonas and Halarcobacter, which were susceptible to nalidixic acid and rifampicin.
The oyster farm near a wastewater plant (Site 3) contained soil bacteria like Arthrobacter, likely introduced through treated wastewater.
Class 1 and 3 integrons genetic elements that help bacteria share resistance genes were widespread in Vibrio populations, accelerating resistance spread.
Rifampicin stood out as the most effective antibiotic, killing bacteria instead of forcing them into dormancy. These findings highlight how environmental factors and antibiotic overuse shape resistance patterns.
Reducing Public Health Risks in Aquaculture
The study’s results have urgent implications for aquaculture practices and public health. First, adopting PMA-qPCR for routine monitoring can help detect hidden threats like VBNC bacteria and track resistance trends.
Second, reducing antibiotic use is critical. At Site 1, excessive antibiotic use correlated with the highest resistance rates. Alternatives like probiotics (beneficial bacteria) and vaccines could prevent diseases without fueling resistance.
Third, wastewater treatment plants must be upgraded to filter out antibiotics and resistant bacteria before releasing water into ecosystems. Finally, global collaboration is essential.
Resistant bacteria from Korean fish farms could spread worldwide through seafood exports, requiring international efforts to regulate antibiotic use and share data.
Challenges in Adopting PMA-qPCR Technology
Despite its promise, PMA-qPCR faces hurdles. The technology requires expensive equipment like qPCR machines (15,000–30,000), making it inaccessible for small-scale farms in developing countries.
Skilled personnel are also needed to handle complex steps, such as optimizing dye concentrations. Standardizing protocols across labs is another challenge organizations like the Clinical and Laboratory Standards Institute (CLSI) must develop uniform guidelines for marine testing.
However, solutions like subsidized equipment, training programs, and simplified kits could make PMA-qPCR more accessible.
Sustainable Aquaculture Combating Antibiotic Resistance
The fight against antibiotic resistance demands immediate action. Governments must fund affordable PMA-qPCR solutions and enforce stricter regulations on antibiotic use, similar to the EU’s ban on growth-promoting drugs in livestock.
Aquaculture farms should invest in sustainable practices like probiotics and vaccines, which have succeeded in poultry and dairy industries.
Public awareness campaigns can educate consumers about antibiotic-resistant bacteria in seafood, driving demand for safer products.Researchers must also study how VBNC bacteria reactivate and spread resistance genes to develop targeted treatments.
Why PMA-qPCR Is Vital Against Antibiotic Resistance
Antibiotic resistance is often called a “silent pandemic” because, unlike viral outbreaks, its deadly consequences spread gradually and invisibly.
Resistant bacteria quietly evolve in environments like aquaculture farms, hospitals, and wastewater systems, making infections harder to treat over time.
This crisis threatens to undo decades of medical progress, as common antibiotics lose their effectiveness against increasingly resilient pathogens.
PMA-qPCRÂ (Propidium Monoazide-quantitative PCR) is a groundbreaking technology that addresses this challenge by overcoming a critical limitation of traditional testing methods.
Conventional techniques like antibiotic susceptibility testing (AST) or minimum inhibitory concentration (MIC) tests fail to detect viable but non-culturable (VBNC) bacteria—dormant cells that remain alive but refuse to grow in lab cultures.
These VBNC cells act as hidden reservoirs of resistance genes. Under favorable conditions (e.g., warmer temperatures or nutrient-rich environments), they can reactivate, multiply, and spread resistance traits to other bacteria through horizontal gene transfer. PMA-qPCR solves this by:
- Selectively Detecting Live Bacteria: Using a dye (propidium monoazide) that binds only to dead cells’ DNA, blocking its amplification during testing.
- Identifying Resistance Genes: Amplifying DNA from live bacteria, including VBNC cells, to pinpoint resistance genes like int1 (Class 1 integron) that drive resistance spread.
Faster, Accurate Monitoring: PMA-qPCR delivers results in hours (vs. days for traditional tests), allowing rapid responses to outbreaks. For example, in Korean fish farms, the study found VBNC Vibrio surviving high antibiotic doses—cells that MIC tests missed.
Public Health Protection: Resistant bacteria from aquaculture can enter the food chain via seafood or contaminate coastal waters, eventually reaching humans. PMA-qPCR helps track these risks early.
Sustainable Aquaculture: By revealing the true scale of resistance, this technology encourages farms to reduce antibiotic overuse and adopt alternatives like probiotics or vaccines.
Global Collaboration: Resistant bacteria ignore borders. For instance, resistant Vibrio from Korean farms could spread globally via seafood exports. International bodies like the WHO and FAO must standardize monitoring and data-sharing protocols.
Conclusion
The study on PMA-qPCR’s effectiveness marks a turning point in addressing antibiotic resistance, a crisis threatening global health. Traditional methods like AST and MIC tests, while useful, fail to detect dormant VBNC bacteria, allowing resistance to spread undetected. PMA-qPCR bridges this gap by identifying live bacteria, including hidden threats, with unmatched accuracy. The findings from Korean aquaculture sites reveal the urgent need to reduce antibiotic overuse, upgrade wastewater treatment, and adopt sustainable practices.
Rifampicin’s effectiveness in killing bacteria, rather than forcing dormancy, offers a rare advantage, but its use must be carefully managed. The path forward requires collaboration across governments, industries, and researchers. Affordable access to PMA-qPCR, stricter regulations, and public education are critical steps.
By embracing these solutions, we can protect aquaculture’s role in feeding the world while safeguarding human health. The fight against antibiotic resistance is not just about saving lives today—it’s about preserving the power of medicines for future generations. The tools exist; now, we need the collective will to use them.
Power Terms
Antibiotic Resistance: This is the ability of bacteria to survive antibiotics meant to kill them, making infections harder to treat. Overuse of antibiotics in humans, animals, or aquaculture accelerates this problem, risking millions of lives by 2050.
Aquaculture: This is refers to farming fish, shellfish, or aquatic plants for food. While it supplies over half of the world’s seafood, crowded fish farms often overuse antibiotics, spreading resistant bacteria into ecosystems.
Viable but Non-Culturable (VBNC) Bacteria: These are dormant bacteria that survive antibiotics but don’t grow in lab tests. They can reactivate later, spreading resistance undetected. For example, dormant Vibrio in fish farms evade traditional tests but remain dangerous.
Antibiotic Susceptibility Testing (AST): AST is a lab method to check if bacteria die when exposed to antibiotics. While widely used, it misses VBNC bacteria and takes 1–2 days for results, delaying critical decisions.
Minimum Inhibitory Concentration (MIC): MIC measures the smallest antibiotic dose needed to stop bacterial growth. Doctors use it to prescribe effective treatments, but it fails to detect dormant VBNC cells.
Propidium Monoazide (PMA): PMA is a dye that binds to DNA from dead bacteria, hiding them in tests. This ensures only live bacteria (including VBNC) are counted, improving accuracy in methods like PMA-qPCR.
Quantitative PCR (qPCR): qPCR is a fast DNA-amplification tool to detect live bacteria. It identifies resistance genes in hours, unlike traditional methods that take days.
PMA-qPCR: This advanced method combines PMA dye and qPCR to detect live antibiotic-resistant bacteria, including VBNC cells. It found 40% more threats in aquaculture than older tests.
Oxytetracycline: A common antibiotic used in fish farms to treat infections. Overuse leaks into water, allowing resistant bacteria like Vibrio to multiply.
Integrons: These genetic elements help bacteria share resistance genes. Class 1 and 3 integrons in Vibrio speed up resistance spread in aquaculture environments.
Rifampicin: An antibiotic that kills bacteria instead of forcing them into dormancy. It was effective in the study but must be used carefully to avoid new resistance.
Probiotics: Beneficial bacteria added to aquaculture systems to fight pathogens naturally. For example, Bacillus strains can replace antibiotics in shrimp farms.
Wastewater Treatment: Processes to clean water by removing antibiotics and resistant bacteria. Poor treatment at fish farms spreads resistance into oceans.
Vibrio: A bacteria genus causing infections in humans. In Korean fish farms, Vibrio showed high resistance to sulfadiazine, a common antibiotic.
Pseudoditeromonas: Marine bacteria found in sea pineapple farms. Some species were susceptible to antibiotics, showing resistance varies by environment.
Halarcobacter: Bacteria detected in aquaculture that resist antibiotics like nalidixic acid. Their presence near wastewater suggests pollution drives resistance.
Arthrobacter: Soil bacteria found in oyster farms near wastewater plants, indicating land-based pollution spreads resistance to marine ecosystems.
Sulfadiazine: An antibiotic to which Vibrio bacteria showed high resistance. Overuse in fish farms reduces its effectiveness for human treatments.
Nalidixic Acid: An antibiotic used for gut infections. Resistant Halarcobacter in sea pineapple farms highlight cross-environmental resistance risks.
Clinical and Laboratory Standards Institute (CLSI): An organization that sets lab testing guidelines. The study urges CLSI to create standards for PMA-qPCR in marine testing.
Silent Pandemic: A term for antibiotic resistance’s slow, global spread. Unlike fast outbreaks like COVID-19, it could kill 10 million annually by 2050.
Sustainable Aquaculture: Eco-friendly farming practices like reducing antibiotics. Probiotics, vaccines, and PMA-qPCR monitoring are key solutions.
Gene Transfer: The process where bacteria share resistance genes, often via integrons. Aquaculture accelerates this, spreading resistance to humans through water or food.
Public Health Risks: Resistant bacteria from seafood can infect humans, causing untreatable diseases. PMA-qPCR helps track these risks in water and food.
Global Collaboration: International efforts to regulate antibiotics, fund solutions like PMA-qPCR, and share data. Resistant bacteria spread through trade, requiring unified action.
Reference:
Son, H.-S., Yun, K.-W., Seong, M.-J., Lee, S.-M., & Kim, M.-C. (2025). Propidium monoazide-quantitative PCR for antibiotic sensitivity testing and minimum inhibitory concentration testing of antibiotic-resistant bacteria. Water Biology and Security, 100406. https://doi.org/10.1016/j.watbs.2025.100406