Molecular Identification, Phylogenetic Placement and Antimicrobial Resistance Profiles of Flavobacteriaceae Isolates Recovered From Rainbow Trout Farms in Türkiye

Members of the family Flavobacteriaceae are frequently associated with disease episodes in freshwater aquaculture and may complicate fish‐health management. This study characterized yellow‐orange‐pigmented bacterial isolates recovered from rainbow trout ( Oncorhynchus mykiss ) farms in Türkiye. Sampling was conducted from April 2024 to September 2025 at net‐cage farms in the Kayseri Yamula Dam and hatcheries in Pınarbaşı and along Fethiye Eşen Creek. Seventy moribund or recently dead fish displaying clinical signs were examined together with four water and four sediment samples. Twenty‐two bacterial isolates were obtained exclusively from fish tissues; no target colonies were recovered from the water or sediment samples under the culture conditions used. The isolates were initially characterized using biochemical tests and a published Flavobacterium ‐targeting PCR assay, followed by taxonomic assignment based on 16S rRNA gene sequencing and BLAST searches. Eighteen isolates showed their closest BLAST matches to sequences assigned to Chryseobacterium spp., including C. piscicola and C. piscium , whereas four showed their closest matches to Flavobacterium spp., including F. psychrophilum and F. columnare . Phylogenetic analysis was used to assess the placement of the isolates relative to their respective reference sequences; species‐level identity was not inferred from tree topology alone. Disk‐diffusion assays assessed phenotypic susceptibility to erythromycin, sulphadiazine, oxytetracycline and florfenicol, whereas targeted PCR assays separately screened all 22 isolates for floR , tetA , tetB , tetC , tetM , ermA and sul1 . Resistance to erythromycin, florfenicol, sulphadiazine and oxytetracycline was observed in 19, 13, 11 and nine isolates, respectively, and floR and ermA were the most frequently detected target genes. These findings document the frequent recovery of Chryseobacterium ‐associated isolates in the sampled fish and the occurrence of antimicrobial resistance determinants. Experimental infection studies are required to establish causation and pathogenicity.