INFORMATION ABOUT THE DEPARTMENT
Established by the Council of Higher Education of Türkiye (YÖK) through its directive dated July 16, 2010 (No. 16789), the Department of Aquatic Animal Diseases is a specialized academic unit dedicated to the health of cultured fish, ornamental fish, and other aquatic animals. Since its establishment, the department has actively engaged in education, research, and sectoral collaboration. Its primary mission is to train veterinarians who have a strong understanding of fish anatomy and physiology, environmental conditions and welfare principles in aquaculture systems, and who are competent in fish clinical examination, necropsy, sampling, and the diagnosis, treatment, and prevention of diseases. Additionally, the training emphasizes the responsible use of pharmaceuticals and biological products in aquatic animal production.
Within this scope, viral, bacterial, fungal, and parasitic diseases, as well as metabolic disorders and tumoral lesions in aquatic animals, are addressed both theoretically and practically in terms of etiology, epizootiology, diagnosis, and prevention strategies. At the undergraduate level, the department offers courses such as “Ichthyology,” “Aquatic Animal Diseases,” and “Aquatic Animal Production and Biotechnology,” which provide students with a solid foundation in core concepts and terminology. These theoretical gains are reinforced through laboratory work, field training, and applied teaching conducted in fish farms with which the department has cooperation agreements. Furthermore, within the 10th-semester Food Internship Program, special emphasis is placed on the public health implications of zoonotic pathogens, hygiene and food safety practices in seafood processing plants, and the role of veterinarians in official control and inspection processes. The educational approach of the department is rooted in a multidisciplinary and data-driven model. Alongside diagnostic methods for clinical and field pathogens, students receive hands-on training in techniques used in pharmacology, pathology, animal nutrition, microbiology, immunology, epidemiology, molecular genetics, and bioinformatics. In this way, they develop practical skills in pathogen isolation and purification, antimicrobial susceptibility testing, molecular diagnosis and serotyping, rapid identification using MALDI-TOF MS, vaccine development, and disease management under field conditions. Population-level assessment of current infections, determination of epidemiological cutoff values (ECOFF), monitoring resistance mechanisms, and integrating the One Health concept into the aquaculture sector are key sustainability-oriented components of this model. This educational framework is further strengthened and advanced at the institutional level through the interdisciplinary PhD Program in Aquatic Animal Diseases conducted within the Institute of Health Sciences. The departments jointly deliver the program in Aquatic Animal Diseases, Pathology, Pharmacology and Toxicology, Parasitology, Animal Nutrition and Nutritional Diseases, and Internal Medicine, providing specialized postgraduate training focused on cultured fish and other aquatic vertebrate and invertebrate species. The department undertakes a wide range of research projects supported by TÜBİTAK (1001, 1002, 1005, 2209-A, 3501), TAGEM, the European Union (EU Horizon), and institutional research funds (BAP). Its main research themes include field epidemiology, identification of new pathogenic species, investigation of antimicrobial resistance mechanisms, determination of ECOFF values, genomic and proteomic characterization, and vaccine development from local isolates. Examples include studies on the effects of mucilage in the Sea of Marmara on aquatic animal health, pathogenic bacteria and their resistance profiles in mussels, bacterial diseases causing high mortality in ornamental fish, and prototype vaccines developed from indigenous strains. Undergraduate and postgraduate students are actively involved in all stages of the research process, with their participation in fieldwork and laboratory activities supported through BAP, TÜBİTAK, and EU-funded projects. As a result, the Department of Aquatic Animal Diseases functions as a key national center for strengthening aquatic animal health, fostering international scientific collaboration, and supporting the sustainable production of aquatic animals.
RESEARCH AREAS
• Aquatic animal diseases (cultured fish, ornamental/aquarium fish, and other aquatic vertebrate and invertebrate species)
• Bacterial, viral, parasitic, and fungal diseases of cultured and ornamental fish
• Aquatic microbiology; systematic and taxonomic characterization of novel bacterial species (particularly Pseudomonas, Flavobacterium, Aeromonas, etc.)
• Fish vaccines, immunoprophylaxis, and selection of vaccine strains (such as Vagococcus salmoninarum, Flavobacterium psychrophilum)
• Molecular diagnostic methods (PCR, real-time PCR, multiplex qPCR, MLST/MLSA, and other genome-based typing approaches)
• Genomic, pangenomic, and phylogenomic analyses; elucidation of virulence and adaptation mechanisms of aquatic pathogens
• Investigation of virulence mechanisms of aquatic Aeromonas strains using transcriptomic approaches
• Antimicrobial resistance; determination of epidemiological cut-off (ECOFF) values; molecular characterization of resistance genes
• Food safety and public health in aquatic products within the framework of the One Health concept (such as E. coli, Vibrio species, STEC serotypes, microplastic and mould contamination in mussels)
• Fish welfare, husbandry conditions, metabolic disorders, and nutrition-related diseases such as fatty liver
• Experimental infection models; assessment of pathogenesis and pathological lesions
• Aquatic toxicology and the effects of chemicals used in aquaculture on fish health and the aquatic environment
LABORATORY INFRASTRUCTURE
• Aquatic Animal Necropsy and Sampling Unit: A fully equipped facility for necropsy of fish and other aquatic animals, tissue sampling, assessment of fish welfare, and macroscopic evaluation of pathological lesions.
• Microbiology Laboratory: Laminar flow cabinets, incubation systems, cold storage units, and collections of reference and clinical strains for isolating and identifying bacterial pathogens.
• Bacterial Incubation and Antimicrobial Susceptibility Unit: Determination of antimicrobial susceptibility and epidemiological cut-off values using MIC measurements, disk diffusion tests, and automated systems like Vitek II.
• Sterilization and Culture Media Preparation Unit: Autoclaves, drying ovens, and other sterilization equipment for preparing selective and differential media suitable for various bacterial groups.
• Molecular Genetics and Diagnostics Unit: DNA extraction systems, conventional PCR devices, real-time PCR platforms, infrastructure for multiplex qPCR analyses, and gel electrophoresis systems.
• Protein Analysis Laboratory: Equipment for SDS-PAGE and Western blotting, enabling protein and profile analyses of bacterial isolates and fish tissues.
• MALDI-TOF MS Microbial Diagnostics Laboratory: A MALDI-TOF MS (Bruker) system for rapid and reliable identification of bacterial agents in aquaculture facilities, supported by a local spectral library specific to rainbow trout farms.
• Bioinformatics and Genomic Analysis Unit: High-performance computing infrastructure and related software for analyzing whole genomes, pangenomes, phylogenomics, and transcriptomes, with opportunities for collaboration with national and international sequencing centers.
• DNA and Culture Bank: A culture collection and DNA archive for long-term preservation of reference and type strains, along with field and clinical isolates obtained in BAP-supported projects.
• Portable Infrastructure for Field Research: Portable sampling kits, instruments for measuring basic water quality parameters, and cold-chain equipment enabling sampling in fish farms, natural water bodies, and seafood processing facilities.
http://www.tarim.gov.tr/TAGEM
