Metabarcoding Reveals a Potentially Undescribed Columnaris-Causing Bacterium in Peracute Skin Disease of Rainbow Trout (Oncorhynchus mykiss, Walbaum)

Columnaris-causing bacteria (CCB) represent a group of four Flavobacterium species, previously classified under Flavobacterium columnaris, causing a threatening condition in salmonid farming characterised by cutaneous and gill lesions, commonly referred to as 'saddleback disease'. A peracute skin disease outbreak with high mortality in rainbow trout (Oncorhynchus mykiss) farms in Northern Italy was investigated. The disease presented with skin discoloration and scale lifting without internal organ abnormalities, leading to a weekly cumulative mortality of up to 80%. The disease was successfully managed with Oxytetracycline treatment, with no relapses observed. Conventional investigation methods produced inconsistent results, prompting additional analyses. Metagenomic sequencing of the 16S rRNA identified Flavobacterium species differing from the classical CCB based on the alignment of the V3 and V4 regions, with best matches to Flavobacterium bernardetii, Flavobacterium aquicola, and Flavobacterium hiemivividum. Histopathology and SEM confirmed epidermal necrosis and bacterial infiltration in the dermis, with filamentous bacteria resembling Flavobacterium morphology yet differing from classical CCB lesions. These findings point to a previously undescribed Flavobacterium-related skin disease with significant economic implications, supporting the value of metagenomic in investigating microbial dynamics in aquaculture diseases, especially in sites exposed to external environments. Further research is required to clarify the pathogenic mechanisms and guide effective management strategies for future outbreaks.