Aquaculture Pathogens and Antimicrobial Resistance: A One Health Perspective
Abstract
1. Introduction
1.1. Major Pathogens in Aquaculture
| SL.No. | PATHOGEN | SOURCE | HOSTS | DESCRIPTION | REFERENCES |
|---|---|---|---|---|---|
| 1 | Streptococcus iniae | Marine and freshwater environments | Tilapia (Oreochromis niloticus), Yellowtail (Seriola quinqueradiata), Rainbow trout (Oncorhynchus mykiss), Coho salmon (Oncorhynchus kisutch) | Common resistance genes include tet(M), tet(O), erm(B), erm(A), mef(A), aadA, aph(3′)-III, conferring resistance to tetracyclines, macrolides, and aminoglycosides. MDR isolates are increasingly reported in aquaculture | [14,15] |
| 2 | Edwardsiella tarda | Freshwater and marine aquaculture | Japanese flounder (Paralichthys olivaceus), Eel (Anguilla japonica), Tilapia (Oreochromis niloticus), Catfish (Clarias spp.) | Frequently harbors tet(A), tet(B), sul1, sul2, floR, qnrS, blaTEM, catA, leading to resistance against tetracyclines, sulfonamides, quinolones, β-lactams, chloramphenicol, and florfenicol. Plasmid mediated MDR is commonly reported | [16,17] |
| 3 | Tenacibaculum dicentrarch | Marine Water | European seabass (Dicentrarchus labrax), Atlantic salmon (Salmo salar), Rainbow trout (Oncorhynchus mykiss), Turbot (Scophthalmus maximus), Sole (Solea solea) and Gilthead sea bream (Sparus aurata) | Resistance has been reported against oxytetracycline, florfenicol, and sulfonamides. Resistant isolates commonly harbor tet(M), tet(B), sul1, sul2, floR, and MDR strains are increasingly detected in marine aquaculture | [18,19] |
| 4 | Flavobacterium columnare | Freshwater | Channel catfish (Ictalurus punctatus), Tilapia (Oreochromis niloticus), Carp (Cyprinus carpio), Rainbow trout (Oncorhynchus mykiss | Resistance has been reported to oxytetracycline and florfenicol. Resistance determinants include tet(A), tet(M), floR, with efflux pumps and biofilm formation contributing to reduced antimicrobial susceptibility. MDR isolates have emerged in intensive aquaculture | [20,21] |
| 5 | Aeromonas spp. | freshwater fishes | Garra rufa, Catla catla, Labeo rohita, Cirrhinus mrigala | Common ARGs include blaTEM, blaCTX-M, cphA, tetA, tetE, sul1, sul2, qnrS, floR. High prevalence of MDR strains resistant to β-lactams, tetracyclines, quinolones, sulfonamides, and phenicols. | [22,23] |
| 6 | Mycobacterium spp. | freshwater, marine and brackish water | striped bass (Morone saxatilis), Sea bass (Dicentrarchus labrax), turbot (Scophthalmus maximus), Florida pompano (Trachinotus carolinus), sygnathids | Exhibits intrinsic resistance to multiple antibiotics including rifampicin rpoB, isoniazid katG, inhA, ethambutol embB, embC, embA, and streptomycin rpsL, rrs. Biofilm formation, lipid-rich cell wall, and efflux pumps contribute to reduced antimicrobial susceptibility | [24,25] |
| 7 | Vibrio spp. | predominantly marine and brackish water fish, some cases of freshwater | yellow croaker (Pseudosciaena crocea), European sea bass (Dicentrarchus labrax), seahorses (H. kuda), Orange-spotted grouper (Epinephelus coioides), Tiger puffer (T. rubripes) | Frequently harbor tetA, tetB, sul1, sul2, qnrA, qnrS, floR, blaTEM and exhibit resistance to tetracyclines, quinolones, β-lactams, sulfonamides, and florfenicol. MDR strains are increasingly reported in aquaculture. | [26,27] |
1.2. Antimicrobial Use (AMU) Patterns in Aquaculture
1.3. Antimicrobial Resistance in Aquaculture
1.4. Prevalence and Trends of AMR in Aquaculture Settings
1.5. Environmental Implications of AMR in Aquaculture
2. Human Health Implications
3. Animal Health and Welfare
3.1. Impact of AMR on Aquaculture Animal Health
3.2. Strategies for Improving Animal Welfare and Reducing AMR
3.3. Global Surveillance and Stewardship Initiatives
4. Public–Private Collaboration in Aquaculture Production
4.1. Integrated Surveillance Strategies for Addressing AMR in Aquaculture
4.2. Policy and Regulations on Antimicrobial Use in Aquaculture
5. Future Directions and Research Needs
5.1. Novel Therapeutic Approaches: Bacteriophages and SynComs
5.2. Integrating Genomic and AI Technologies
5.3. Research Priorities and Implementation Challenges
- Development of host-specific bacteriophages and standardized therapeutic protocols for regulatory adoption.
- Integration of multi-omics approaches genomics, transcriptomics, proteomics, and metabolomics into probiotic design and environmental risk assessment.
- Implementation of environmental DNA (eDNA) monitoring systems to evaluate the long-term ecological effects of antimicrobial interventions.
- Establishment of international phage therapy guidelines that harmonize efficacy, safety, and biocontainment strategies across aquaculture sectors.
5.4. Aligning with Global Sustainable Goals
6. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
| AMR | Antimicrobial Resistance |
| UV | Ultraviolet |
| Spp. | Species |
| HGT | Horizontal Gene Transfer |
| MDR | Multidrug Resistance |
| ARGs | Antibiotic Resistance Genes |
| A. hydrophila | Aeromonas hydrophila |
| VCIAs | Veterinary Critically Important Antimicrobials |
| POPs | Persistent Organic Pollutants |
| FAO | Food and Agriculture Organization |
| ADI | Acceptable Daily Intake |
| WOAH | World Organisation for Animal Health |
| AMC | Antimicrobial Consumption |
| UNEP | United Nations Environment Programme |
| FDA | Food and Drug Administration |
| ESBL | Extended-Spectrum β-lactamase |
| eDNA | environmental DNA |
| CRISPR | Clustered Regularly Interspaced Short Palindromic Repeats |
| WHO | The World Health Organization |
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Geetha, A.A.; Soorej, M.; Alex, E.; Rajesh, D.; Babu, N.S.; Ishani, F.; Renjith, S.; Sajeev, A.; Jacob, J.P.; Nair, B.G.; et al. Aquaculture Pathogens and Antimicrobial Resistance: A One Health Perspective. Int. J. Mol. Sci. 2026, 27, 8125. https://doi.org/10.3390/ijms27188125
Geetha AA, Soorej M, Alex E, Rajesh D, Babu NS, Ishani F, Renjith S, Sajeev A, Jacob JP, Nair BG, et al. Aquaculture Pathogens and Antimicrobial Resistance: A One Health Perspective. International Journal of Molecular Sciences. 2026; 27(18):8125. https://doi.org/10.3390/ijms27188125
Chicago/Turabian StyleGeetha, Avani Anu, Mydhily Soorej, Elishia Alex, Dhruva Rajesh, Nikhila S. Babu, Fathima Ishani, Sreelekshmi Renjith, Athul Sajeev, Jithu Paul Jacob, Bipin G. Nair, and et al. 2026. "Aquaculture Pathogens and Antimicrobial Resistance: A One Health Perspective" International Journal of Molecular Sciences 27, no. 18: 8125. https://doi.org/10.3390/ijms27188125
APA StyleGeetha, A. A., Soorej, M., Alex, E., Rajesh, D., Babu, N. S., Ishani, F., Renjith, S., Sajeev, A., Jacob, J. P., Nair, B. G., Kumar, G., Madhavan, A., & Babu, P. (2026). Aquaculture Pathogens and Antimicrobial Resistance: A One Health Perspective. International Journal of Molecular Sciences, 27(18), 8125. https://doi.org/10.3390/ijms27188125

