Genotypic characterisation, detection and prevalance of antimicrobial resistance genes on flavobacterium species cause of disease in rainbow trout (oncorhynchus mykiss walbaum 1792) hatcheries

Outbreaks in fish species due to the Flavobacterium genus cause significant economic losses. The best known of these species are Flavobacterium psychrophilum, F. columnare and F. branchiophilum, but in recent years, it has been reported that many new Flavobacterium species have also been isolated from fishes. The present study focused on three main goals: 1) to identify the isolate by sequence analysis, 2) to detect genotypes by their PCR-RFLP profiles and 3) to determine the antimicrobial resistance status of 109 Flavobacterium spp. that were isolated from rainbow trout (Oncorhynchus mykiss), Anatolian/mountain trout (Salmo trutta macrostigma), çoruh trout (Salmo coruhensis), brook trout (Salvelinus fontinalis) and black sea trout (Salmo trutta labrax). Each Flavobacterium species was identified by sequence analysis of the 16S rRNA region and by PCR-RFLP analysis using the 16S rRNA, gyrA and gyrB gene regions. Resistance of the Flavobacterium species to amoxicillin, oxytetracycline, oxalinic acid, sulfamethoxazole/trimethoprim, enrofloxacin, erythromycin and florfenicol antimicrobials was determined phenotypically (disk diffusion, minimum inhibitor concentrations) and genotypically (floR, tetA, tetB, tetC, sul1, sul2 sul3, qnrA, qnrB and qnrS). As a result of the sequence analysis, 27 different Flavobacterium species were identified. Twenty-six of these species were isolated for the first time in Turkey. F. antarcticum, F. terrigena, F. granuli, F. frigoris, F. saccharophilum, F. xueshanense and F. cutihirudinis species were the first Flavobacterium species detected in fish. F. psychrophilum isolates showed a genotypically homogeneous structure, and it was determined that the isolates were susceptible to amoxicillin and florfenicol, while enrofloxacin and oxalinic acid susceptibility was decreased in this species. Also in this study, the floR antimicrobial resistance gene in the F. branchiarum, F. branchiicola, F. collinsii, F. frigoris and F. psychrophilum species as well as the sul2 resistance gene in the F. branchiarum, F. branchiicola, F. collinsii, F. oncorhynchi, F. plurextorum, F. psychrophilum, F. spartansii F. terrigena and F. tiangeerense species were detected for the first time. Keywords; Flavobacterium spp., Antimicrobial Resistance, RFLP