Antibiotics have revolutionized medicine and animal production, yet their extensive use has accelerated the emergence and spread of antimicrobial resistance (AMR). Beyond clinical contexts, livestock and aquaculture are now recognized as major contributors to the global resistome. This review synthesizes evidence across cattle, poultry, swine, sheep and goats, and aquaculture, highlighting how antimicrobial usage shapes resistance at the human–animal–environment interface. A substantial proportion of administered drugs is excreted unmetabolized, leading to the accumulation of unmetabolized antimicrobial residues, antibiotic-resistant bacteria (ARB), and antibiotic resistance genes (ARGs) in soils, manures, waters, sediments, and air. These reservoirs function as long-term sources and dissemination pathways through runoff, leaching, bioaerosols, effluents, and biological vectors. Despite different production systems, similar ARG families dominate, particularly those conferring resistance to tetracyclines, sulfonamides, and β-lactams. Mobile genetic elements and co-selectors such as heavy metals, disinfectants, and microplastics reinforce their persistence. Aquaculture, where water serves both as habitat and vector, emerges as a critical hotspot, while small ruminant systems remain under-researched despite their importance in many low- and middle-income countries. This synthesis highlights convergent patterns across sectors: antimicrobial use drives ARG enrichment; manures, litters, sediments, and effluents act as persistent reservoirs; and dissemination routes connect farms, ecosystems, and human populations. Within a One Health framework, mitigation requires preventive strategies—vaccination, biosecurity, and optimized waste management—supported by harmonized stewardship policies and integrated environmental surveillance.

The growth of aquaculture production in recent years has revealed multiple challenges, including the rise of antimicrobial resistance (AMR) in aquatic animal production, which is currently attracting significant attention from multiple one-health stakeholders. While antibiotics have played a major role in the treatment of bacterial infections for almost a century, a major consequence of their use is the increase in AMR, including the emergence of AMR in aquaculture. The AMR phenomenon creates a situation where antibiotic use in one system (e.g., aquaculture) may impact another system (e.g., terrestrial–human). Non-prudent use of antibiotics in aquaculture and animal farming increases the risk of AMR emergence, since bacteria harboring antibiotic resistance genes can cross between compartments such as wastewater or other effluents to aquatic environments, including intensive aquaculture. Transferable antimicrobial resistance gene (AMG) elements (plasmids, transposons, integrons, etc.) have already been detected in varying degrees from pathogenic bacteria that are often causing infections in farmed fish (Aeromonas, Vibrio, Streptococcus, Pseudomonas, Edwardsiella, etc.). This review of current veterinary approaches for the prevention and control of AMR emergence in aquaculture focuses on the feasibility of alternatives to antimicrobials and supplemental treatment applications during on-farm bacterial disease control and prevention. The use of vaccines, bacteriophages, biosurfactants, probiotics, bacteriocins, and antimicrobial peptides is discussed.

Autogenous vaccines are a critical tool in aquaculture for managing bacterial diseases when commercial vaccines are unavailable or ineffective. To improve vaccine efficacy, this study explored how different cultivation conditions influence virulence gene expression in two major fish pathogens, Aeromonas salmonicida subsp. salmonicida and Aeromonas hydrophila . Isolates were cultured in nutrient-rich (tryptic soy broth [TSB]) and nutrient-limited (Mueller–Hinton broth [MH]) media, with and without supplementation of 1% fetal bovine serum (tryptic soy broth supplemented with 1% FBS [TSB1] and Müller–Hinton supplemented with 1% FBS [MH1]), to mimic environmental and host-like conditions. Total RNA was sequenced using the Oxford Nanopore MinION platform, and gene expression was quantified using featureCounts and Salmon, followed by differential expression analysis with DESeq2. Results revealed that culture conditions significantly shaped transcriptomic profiles. TSB1 promoted the highest and most consistent expression of classical virulence genes such as aerA , exeC , and fliP , due to serum-derived host signals. In contrast, MH induced higher expression of genes linked to motility and early host interaction, including flpI and exeB , despite overall lower transcriptional activity. These findings highlight the complementary expression of virulence factors under distinct nutritional conditions. Heatmaps and principal component analysis (PCA) confirmed clustering of expression profiles across media types. In relation to our findings, TSB1 is therefore recommended as the primary medium for bacterin production in autogenous vaccine development. However, combining cultures grown in both TSB1 and MH may capture a broader antigen repertoire, enhancing immune recognition and protection. This transcriptomics-based strategy presents as a rational framework for designing next-generation autogenous vaccines in aquatic veterinary medicine.

Rapid and accurate diagnosis of infectious diseases in aquaculture is essential for preventing major economic and ecological losses. Traditional culture-based methods focus on isolation of individual pathogens, and often are burdened with extended processing times, particularly during investigations of polymicrobial infections. Application of Oxford Nanopore Technologies (ONT) sequencing offers a rapid, culture-independent workflow for the identification of bacterial and fungal pathogens directly from fish tissues. Swab and organ samples from four cases (1: Salmo spp.; 2: Cyprinus carpio; 3: Salvelinus fontinalis; 4: Heniochus acuminatus) were analyzed using ONT long-read sequencing for metagenomic screening and bioinformatic classification. The results revealed case-, species-, and tissue-specific microbial profiles, with external tissues showing higher microbial diversity and internal organs enriched in pathogenic taxa. Dominant pathogens included Streptococcus iniae, Aeromonas hydrophila, Pseudomonas spp., and Saprolegnia parasitica, alongside opportunistic zoonotic bacteria such as Escherichia coli and Acinetobacter baumannii. We demonstrate the potential for diagnostic application of ONT sequencing in investigations and detection of multi-pathogen infections, including assessments of microbial community structure changes during disease outbreaks in aquatic species. The presented workflow enables rapid, cost-effective, and comprehensive pathogen profiling, supporting early disease surveillance and improved management in aquatic veterinary practice.

European aquaculture is increasingly shaped by regulatory efforts to reduce unnecessary antimicrobial use and limit antimicrobial resistance risks across the human–animal–environment interface. These efforts are necessary, especially where antimicrobials are used routinely or as a substitute for husbandry or a remedy for biosecurity failures. However, stewardship in aquaculture cannot be reduced to legal restriction or lower antimicrobial input alone. Fish diseases occur in heterogeneous systems, including recirculating systems, flow-through farms, ponds, hatcheries and marine cages, with different patterns of pathogen entry, treatment delivery and environmental exposure. This review examines antimicrobial use in European aquaculture through the conditions required to make reduction clinically and environmentally workable. Its central argument is that regulatory transformation depends on implementation capacity. Aquatic veterinarians are expected to justify and reduce antimicrobial use while responding to bacterial disease events that may progress rapidly, affect populations and threaten welfare. This decision space becomes difficult where diagnostic access, authorised medicinal products, vaccines, records, surveillance systems or aquatic veterinary expertise are limited. Prevention, biosecurity, diagnostics and surveillance are discussed as decision-enabling infrastructure rather than generic sustainability measures. They reduce preventable disease pressure, help distinguish bacterial from non-bacterial morbidity, support justified treatment and provide feedback on health and environmental outcomes. The aquatic environment is treated not only as a recipient of residues, resistant bacteria and resistance genes but also as a source of risk, exposure and governance information. Responsible antimicrobial reduction is, therefore, not simple minimisation. Sustainable disease management depends on connecting regulatory ambition with veterinary decision-making, therapeutic feasibility, diagnostic support and environmental feedback.