Phenotypic and genotypic antimicrobial resistance profiles of Flavobacterium psychrophilum and Flavobacterium branchiophilum isolated from rainbow trout (Oncorhynchus mykiss) in Slovenia

Flavobacterium psychrophilum and Flavobacterium branchiophilum are important fish pathogens that cause considerable economic losses in freshwater aquaculture worldwide. Their antimicrobial resistance (AMR) profiles were evaluated using the latest Clinical and Laboratory Standards Institute broth microdilution method, which was adjusted for F. branchiophilum to achieve growth, and whole-genome sequencing (WGS). A total of 51 F. psychrophilum isolates and eight F. branchiophilum isolates from Slovenian farmed rainbow trout underwent phenotypic antimicrobial susceptibility testing. Overall, 86.3% of F. psychrophilum isolates were classified as non-wild-type (NWT) for oxytetracycline and enrofloxacin, and 90.2% of isolates were NWT for oxolinic acid. In contrast, all isolates tested were classified as wild-type (WT) for florfenicol and erythromycin. It was not possible to classify F. branchiophilum isolates as WT or NWT for the antimicrobials tested. A subset of F. psychrophilum (n = 7) and F. branchiophilum (n = 2) isolates was further characterised using WGS to investigate the mechanisms mediating antimicrobial resistance. In F. psychrophilum, the T83A or T83V substitution in GyrA was associated with reduced susceptibility to oxolinic acid. No other AMR genes or AMR-associated mutations were detected.