Evaluating surveillance strategies of the fish pathogens Flavobacterium columnare and Flavobacterium psychrophilum to provide epidemiological insights in fish farm outbreaks

The goal of this study was to establish the use of Illumina 16S V4 sequencing for accurately detecting two fish pathogens, Flavobacterium columnare and Flavobacterium psychrophilum. Using NGS methods to detect pathogens can provide similar accuracy to other pathogen detection methods (depending on the pathogen) while also providing a microbiome profile simultaneously. Lake water samples were inoculated with one or both of these pathogens and then processed and sequenced to validate this approach.