Temporal sampling of rainbow trout fry for characterizing Flavobacterium psychrophilum dynamics in a Recirculating Aquaculture System

Introduction: Infections caused by the Gram-negative bacterium Flavobacterium psychrophilum have a negative impact on fish production. These infections are classically treated with antibiotics worldwide and there is an increased focus on developing alternative strategies such as e.g. phage therapy. To support the development of these strategies, a better understanding of the pathogen dynamics in fish facilities is however needed.

Methodology: In this study, we set up a sampling scheme at an aquaculture facility in Denmark over a one-year period (July 2023 – July 2024) for the isolation of F. psychrophilum from external and internal rainbow trout organs. The same batches of fish in two specific RAS systems at the facility were sampled at regular intervals during the period the fish were kept in the facility. For each sampling point, 8-9 fish were sampled from each system, weight and length recorded and samples of organs streaked on TYES-A. Water samples were also collected. The identity of the newly collected bacteria was confirmed by MALDI-TOF. Further, serotypes were characterized and DNA extracted, sequenced (WGS, Oxford Nanopore R10.4.1 pore chemistry) and analysed (e.g. MLST, pangenome).

Results: The sampling effort resulted in the isolation of 85 Flavobacterium psychrophilum isolates from the internal and external organs of 93 fish and one water sample. A mixed population of F. psychrophilum in the RAS systems were observed: different serotypes in fish from the same RAS system and sometimes in the same fish/organ were observed. As expected, prevalence of one serotype during a RTFS outbreak was observed. The analysis of the genomic data will be presented.

Conclusions: The study of pathogen dynamics in a RAS system is of great importance when developing alternative strategies focused on prophylaxis and control like phage therapy.