Monitoring the Microbial Prevalence in Farmed Trout Species from an Aquaculture Facility in Kosovo

Abstract The primary objective of this research was to evaluate and quantify the presence of mesophilic bacteria on the skin and within the muscle tissue of farmed rainbow trout. Fish specimens were obtained during the summer from a cold-water fish breeding facility in the Istog region of the Republic of Kosovo. A limited number of fish samples were collected under sterile conditions, reflecting the exploratory scope of this study and constraints in sample availability. Most samples were identified as Oncorhynchus mykiss (rainbow trout), while a smaller proportion corresponded to Oncorhynchus mykiss (golden rainbow trout). The microbiological analysis of the samples was conducted utilizing ISO standard methods for analysing mesophilic bacteria, Escherichia coli , Enterobacteriaceae , coliforms, and Enterococcus faecalis . Results revealed higher contamination on the skin surface compared to muscle tissue, with consistent levels across both trout species. Although differences between tissues were observed, they did not reach statistical significance ( p > 0.05), likely due to the limited sample size. Variations among samples indicated the influence of handling practices and environmental factors on microbial presence. The analysis showed that coliforms accounted for 37.13% of microbial presence, followed by other mesophilic bacteria at 35.14% and E. faecalis at 26.92%, with minimal presence of E. coli and Enterobacteriaceae . These findings underscore the importance of further research into external factors affecting microbial growth in aquaculture environments and suggest the need for systematic monitoring and control measures to enhance hygiene standards in fish farming operations.