Antibiotics in the Reef Tank

Reefkeeping brings the dynamic and fragile beauty of the coral reef into our living rooms, but with it comes the responsibility of maintaining healthy ecosystems for our aquatic companions. When fish fall ill, the temptation to reach for antibiotics as a quick solution is understandable. However, mounting scientific evidence reveals that the misuse of these powerful medications poses serious risks not only to our aquariums but potentially to human health as well.

The Aquarium as a Reservoir for Antibiotic Resistance

Recent research shows that the ornamental fish industry represents a significant but underrecognized contributor to the global antibiotic resistance crisis (Chan et al., 2025). Unlike food fish aquaculture, which faces stricter regulatory oversight, the aquarium fish trade operates with minimal oversight, employing a broader range of antibiotics including fluoroquinolones, tetracyclines, and nitrofurans.

Studies consistently find that most globally exported aquarium fish carry antibiotic residues, with concentrations in carriage water rivaling those found in treated sewage effluent (Wu et al., 2023; Li et al., 2022). Research has detected significant levels of antibiotics including oxytetracycline (up to 29.0 μg/L), doxycycline, enrofloxacin, and oxalinic acid in ornamental fish transport water across multiple countries.

The Problem with Prophylactic Treatment

Some aquarists make the understandable and well-meaning mistake of adding antibiotics to their tanks “just in case” or at the first sign of stress in their fish. This prophylactic approach creates far more problems than it solves and contradicts established best practices in aquaculture medicine. Importantly, this same concern applies to aquarium products that contain antibiotics but don’t disclose it – using these products preventatively would mean constantly dosing low levels of antibiotics to your tank.

When antibiotics are used without a specific bacterial infection present, they indiscriminately kill beneficial bacteria throughout the aquarium system. In marine tanks, beneficial bacteria are the foundation of biological filtration, converting toxic ammonia to nitrite, then to less harmful nitrate. Broad-spectrum antibiotics, applied at high doses prophylactically (preventatively) can crash this biological filter, leading to spikes in ammonia and nitrite that can be more dangerous than the original problem.

Additionally, many fish health issues stem from viral infections, parasites, or environmental stress—conditions that antibiotics cannot treat and may actually worsen by compromising the fish’s natural bacterial flora.

The Growing Threat of Antibiotic Resistance

The overuse and misuse of antibiotics in aquarium systems contributes significantly to antibiotic resistance. Research shows very high levels of resistance in ornamental fish bacteria, with studies reporting resistance rates of 92% to streptomycin, 88% to trimethoprim, and 62% to sulfamethoxazole in Aeromonas species from ornamental fish (Welch et al., 2017).

Antibiotic resistance genes can be spread from one species to another, and they don’t remain confined to our aquariums. They can be transferred to humans through direct contact with infected fish or contaminated water, potentially causing serious infections that are difficult to treat.

Human Pathogens in Marine Aquariums

Importantly, this discussion of antibiotic resistance is not confined to fish or coral pathogens. There are known human pathogens sometimes found in saltwater aquariums. It would be best to not have these pathogens in our tanks at all, but if they do show up, we sure don’t want to make them antibiotic resistant.

Vibrio species are among the most concerning pathogens in marine systems. Vibrio vulnificus alone causes severe hemorrhagic septicemia in fish and poses significant zoonotic risks to humans (Cheng et al., 2022). Molecular studies show high genetic diversity among V. vulnificus strains, with different types requiring specific treatment approaches.

Mycobacterium marinum causes chronic granulomatous disease in fish and represents a serious zoonotic threat. Research indicates that 41.7% of ornamental fish may carry M. marinum DNA, with 23.6% culture-positive (Aubry et al., 2017). This pathogen often shows resistance to multiple antibiotics and can cause persistent skin infections in humans.

Targeted Treatment: The Right Medicine for the Right Pathogen

Effective antibiotic therapy requires identifying the specific pathogen causing the problem. Just as a physician wouldn’t prescribe the same antibiotic for every infection, aquarists should match their treatment to the disease.

DNA Testing for Reefkeeping

Modern molecular diagnostic techniques have revolutionized our ability to conclusively identify fish pathogens. DNA testing services like AquaBiomics based on DNA sequencing provide genus, species, or in some cases even strain-level identification of pathogens.

Diagnosis: DNA testing is often useful after fish or corals have died, to answer the questions “what killed them?” It also provides key insights into the appropriate choice of treatments. No vet would prescribe a treatment without first diagnosing the disease – DNA testing allows us to do the same.

Treatment monitoring: DNA-based methods allow for real-time monitoring of treatment efficacy by quantifying pathogen loads during antibiotic therapy, ensuring complete pathogen elimination before fish are transferred to display systems.

Best Practices for Responsible Antibiotic Use

Never Use Antibiotics Prophylactically. Only use antibiotics when you have confirmed a bacterial infection, ideally through DNA testing.
Always Quarantine, Treat sick fish in a separate quarantine system, never in the display tank. Use molecular testing to verify successful treatment completion.
Complete the Full Course. Never stop antibiotic treatment early, even if fish appear to recover. Incomplete treatment courses are a primary driver of resistance development.
Choose the Right Antibiotic. Use DNA testing to identify the specific pathogen and select appropriate treatment. Different bacterial species require different antibiotics, and resistance patterns vary significantly.
Monitor Treatment Efficacy. Use follow-up DNA testing to confirm successful pathogen elimination. This may be particularly important for human pathogens like Mycobacterium marinum.

Conclusion

The responsible use of antibiotics in marine aquariums requires a fundamental shift from reactive to proactive management approaches. By integrating DNA testing with established quarantine protocols, aquarists can achieve superior health outcomes while minimizing resistance development.

The extra effort required for responsible antibiotic use—implementing quarantine systems with diagnostic capabilities, learning to identify specific diseases through molecular methods, and resisting the urge to “treat everything just in case”—ultimately leads to healthier fish, more stable aquarium systems, and the preservation of critical medications for treating disease.

References

Aubry, A., Mougari, F., Reibel, F., & Cambau, E. (2017). Mycobacterium marinum. Microbiology Spectrum, 5(2). https://doi.org/10.1128/microbiolspec.TNMI7-0038-2016

Chan, C. A.-Y., Tang, Y.-L., Cheng, M.-H., Cheng, K.-W., Wong, S.-N., Lam, Y.-K., Lam, C.-M., Lau, K.-L., & Mo, W.-Y. (2025). Antibiotic abuse in ornamental fish: An overlooked reservoir for antibiotic resistance. Microorganisms, 13(4), 937. https://doi.org/10.3390/microorganisms13400937

Cheng, Y., et al. (2022). Identification and whole-genome sequencing analysis of Vibrio vulnificus strains causing pearl gentian grouper disease in China. BMC Microbiology, 22, 195.

Hemamalini, V. V., et al. (2022). A critical review on the antimicrobial resistance, antibiotic residue and metagenomics-assisted antimicrobial resistance gene detection in freshwater aquaculture environment. Aquaculture Research, 53(1), 1-28.

Li, K., et al. (2022). Uses of antibiotics in ornamental fish in Hong Kong and the antibiotic resistance in the associated zoonotic pathogens. Microorganisms, 10(12), 2446.

Luo, M., et al. (2024). Isolation, identification, and characteristics of Aeromonas veronii from diseased crucian carp (Carassius auratus gibelio). Frontiers in Microbiology, 10, 2742.

Welch, T. J., et al. (2017). Antimicrobial drug resistance in fish pathogens. Microbiology Spectrum, 5(6), ARBA-0017-2017.

Wu, H., et al. (2023). Prevalence of antibiotic resistance genes in wastewater collected from ornamental fish market in northern China. Environmental Pollution, 273, 116504.