Isolation and Identification of Pathogenic Bacteria from Dead Fish in Rainbow Trout (Oncorhynchus mykiss) Farms in Türkiye

Abstract

Aquaculture has emerged as an important component of global food security, and rainbow trout (Oncorhynchus mykiss) is among the most commercially valuable freshwater species. However, the intensification of trout farming has made fish populations increasingly vulnerable to bacterial infections, posing serious threats to both animal welfare and economic sustainability. This study was conducted to systematically isolate and identify the dominant bacterial pathogens involved in trout mortality cases observed in aquaculture farms in two geographically and climatically distinct regions of Türkiye (Gaziantep and Antalya). A total of 60 lethal fish samples were subjected to integrated microbiological diagnosis combining traditional culture-based methods (including Gram staining and a series of biochemical tests) with high-resolution proteomic identification methods via Matrix-Assisted Laser Desorption/Ionization–Time of Flight Mass Spectrometry (MALDI-TOF MS). Most of the isolates were taxonomically classified as Aeromonas hydrophila, Yersinia ruckeri, Pseudomonas fluorescens, and Flavobacterium psychrophilum, pathogens known to play a role in systemic and opportunistic infections in cold-water fish species. The spatial distribution of these bacterial agents revealed significant ecological variability, indicating a strong correlation between pathogen prevalence and environmental parameters such as water temperature, rearing conditions, and geographical location. In particular, MALDI-TOF MS provided high-accuracy species-level identification and showed over 90% agreement with traditional biochemical classification, thereby highlighting its utility as a rapid and reliable diagnostic tool for surveying aquatic diseases. In addition to its etiological importance, the study also provides region-specific epidemiological information on the spatial distribution of bacterial pathogens under changing environmental conditions. By offering this dual perspective, the research provides critical information for the development of targeted disease management frameworks and advocates for the integration of molecular diagnostics and sustainable biological control applications in the aquaculture industry.