Molecular Identification, Phylogenetic Placement andAntimicrobial Resistance Profiles of FlavobacteriaceaeIsolates Recovered From Rainbow Trout Farms in Türkiye

Creative Commons License

Kuzucu O., Bayrak H.

AQUACULTURE, FISH AND FISHERIES, cilt.10, sa.1002, ss.1-12, 2026 (ESCI)

Özet

Members of the family Flavobacteriaceae are frequently associated with disease episodes in freshwater aquaculture and maycomplicate fish-health management. This study characterized yellow-orange-pigmented bacterial isolates recovered from rainbowtrout (Oncorhynchus mykiss) farms in Türkiye. Sampling was conducted from April 2024 to September 2025 at net-cage farms inthe Kayseri Yamula Dam and hatcheries in Pınarbaşı and along Fethiye Eşen Creek. Seventy moribund or recently dead fishdisplaying clinical signs were examined together with four water and four sediment samples. Twenty-two bacterial isolates wereobtained exclusively from fish tissues; no target colonies were recovered from the water or sediment samples under the cultureconditions used. The isolates were initially characterized using biochemical tests and a published Flavobacterium-targeting PCRassay, followed by taxonomic assignment based on 16S rRNA gene sequencing and BLAST searches. Eighteen isolates showedtheir closest BLAST matches to sequences assigned to Chryseobacterium spp., including C. piscicola and C. piscium, whereas fourshowed their closest matches to Flavobacterium spp., including F. psychrophilum and F. columnare. Phylogenetic analysis was usedto assess the placement of the isolates relative to their respective reference sequences; species-level identity was not inferred fromtree topology alone. Disk-diffusion assays assessed phenotypic susceptibility to erythromycin, sulphadiazine, oxytetracycline andflorfenicol, whereas targeted PCR assays separately screened all 22 isolates for floR, tetA, tetB, tetC, tetM, ermA and sul1. Resistanceto erythromycin, florfenicol, sulphadiazine and oxytetracycline was observed in 19, 13, 11 and nine isolates, respectively, and floRand 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 studiesare required to establish causation and pathogenicity.