First detection of florfenicol resistance in clinical isolates of Flavobacterium psychrophilum in a Danish rainbow trout farm

The EU One Health Action plan against AMR emphasizes the need to strengthen surveillance and research to support evidence-based decisions in the food production system. In Denmark, antimicrobial resistance in fish bacterial pathogens is evaluated in relation to commercial diagnostics cases and research projects focused on this topic.

Here, we focused on the bacterium Flavobacterium psychrophilum [etiological agent of Rainbow Trout Fry Syndrome (RTFS) and Bacterial Coldwater Disease (BCWD)] and assessed the antibiotic resistance patterns of eight recent isolates (2019-2023) from Danish rainbow trout freshwater farms (classical microbiology AST (Antimicrobial Susceptibility Testing) methods and whole genome sequencing (Oxford Nanopore R10.4.1 pore chemistry)).

The analyses showed changes in the resistance patterns towards antibiotics used in aquaculture facilities (e.g. oxolinic acid (OA)) and the emergence of florfenicol (FFC) resistance, drug of choice for the treatment of F. psychrophilum infections in Denmark since 1996. The emergence of FFC resistance was observed in three isolates collected in 2021, 2022 and 2023 in a rainbow trout RAS (Recirculating Aquaculture System) farm. The phenotypic resistance patterns were confirmed by the analysis of the genomes from 2021 and 2022 that identified acquired resistance (MFS transporter) towards florfenicol. OA resistance was also detected in this farm as well as in the other isolates included in the study. The sequenced isolates presenting OA resistance on phenotypic testing harboured missense mutations (nucleic acid mutations causing amino acid substitutions) in the Quinolone Resistance Determining Region (QRDR) of the DNA gyrase subunit A (gyrA).

Despite the small sample size of this study, we would like to bring attention to the topic of antimicrobial resistance in aquaculture pathogens and to underline the importance of efficient AST to support effective control measures. The isolates presenting the newly observed AMR patterns belong to a clonal complex (CC-01) that has not been detected previously in Denmark and other Nordic countries thus suggesting the possibility of linking the emergence of these new patterns of antibiotic resistance to the import of eyed eggs, underlining the need for a surveillance program.