Differential Transcriptomic Profile of LF-89 and EM-90 During an Spatial Separation Co-Culture in Atlantic Salmon.

Salmonid rickettsial septicemia (SRS) is a critical sanitary problem in the Chilean aquaculture industry since it induces the highest mortality rate in salmonids among all infectious diseases. , a facultative intracellular bacterium, is the biological agent of SRS. In Chile, two genogroups of , designated as LF-89 and EM-90, have been identified. Previous studies suggested that their cohabitation triggers the expression of virulence effectors, which may be related to a higher pathogenicity in salmonids during co-infection with both genogroups. Therefore, we aimed to evaluate if the physical contact between two isolates from LF-89 and EM-90 is necessary to activate this effect. Through a spatially separated co-culture inside Atlantic salmon () post smolts and RNA-seq analysis, we compared the differentially expressed genes (DEGs) with previous results from an mixed co-culture. The results showed that although the LF-89-like isolate and the EM-90-like isolate had a similar DEG profile under both co-culture conditions, important virulence factors observed during the mixed co-cultures (i.e., flagellar-related genes, CydD, and NCS2) were absent in the spatially separated co-cultures. Hence, the synergistic effect linked to increased pathogenicity to the host may be driven by the physical co-localization and contact between the LF-89-like and EM-90-like isolates.