Pathogenic bacteria are a persistent threat to aquaculture sustainability, with Flavobacterium, Aeromonas, and Vibrio species being of particular concern due to their capacity to cause disease outbreaks and their potential for antimicrobial resistance (AMR). Among them, Flavobacterium columnare and Flavobacterium psychrophilum are well-recognized agents of columnaris disease and cold-water disease, respectively, both associated with high mortality in farmed fish populations. Opportunistic pathogens such as Aeromonas and Vibrio further exacerbate fish health challenges, particularly under suboptimal environmental conditions.
As part of the European Partnership on Animal Health and Welfare (EUPAHW), sampling campaigns were conducted during winter and summer-2025 across ten aquaculture farms in Belgium, including five trout farms in Wallonia and four farms in Flanders producing sturgeon, mussel, oyster, trout, burbot, bullhead, and pikeperch. Skin and gill mucus from finfish, whole organisms from shellfish, as well as water and sediment samples were collected to recover and characterize pathogenic bacteria. From the winter campaign, 86 presumptive isolates of F. psychrophilum were recovered on tryptone yeast extract salts agar (TYESA) supplemented with tobramycin and neomycin, while 39 presumptive F. columnare isolates were obtained on modified Shieh agar with tobramycin. Species confirmation is currently being carried out using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and species-specific quantitative PCR. So far, four F. psychrophilum isolates have been identified, while no F. columnare isolates have been identified from the winter campaign; the remaining analyses are ongoing. In parallel, the recovery and identification of Aeromonas and Vibrio spp. from the same aquaculture environments are in progress. Minimum inhibitory concentration (MIC) testing will be performed upon completion of species confirmation to assess antimicrobial resistance profiles. This ongoing study aims to provide a comprehensive overview of the occurrence and resistance potential of Flavobacterium, Aeromonas, and Vibrio spp. in Belgian aquaculture.
Keywords: Antimicrobial resistance, Flavobacterium, Aeromonas, Vibrio, MALDI-TOF, qPCR