Phenotypic and Genotypic Antimicrobial Resistance Profiles of Flavobacterium psychrophilum and Flavobacterium branchiophilum Isolated From Rainbow Trout (Oncorhynchus mykiss) in Slovenia.
Katarina Pavlin, Bojan Papić, Irena Zdovc, Tanja Knific, Igor Gruntar, Rosvita Sitar, Diana Žele Vengušt, Marija Seničar, Matjaž Ocepek, Tanja Švara
Author Information
Katarina Pavlin: Institute of Pathology, Wild Animals, Fish and Bees, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia. ORCID
Bojan Papić: Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia.
Irena Zdovc: Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia.
Tanja Knific: Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia.
Igor Gruntar: Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia.
Rosvita Sitar: National Veterinary Institute, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia.
Diana Žele Vengušt: National Veterinary Institute, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia.
Marija Seničar: National Veterinary Institute, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia.
Matjaž Ocepek: Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia.
Tanja Švara: Institute of Pathology, Wild Animals, Fish and Bees, Veterinary Faculty, University of Ljubljana, Ljubljana, 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.
