Differential transcriptomic profile of Piscirickettsia salmonis LF-89 and EM-90 during an in vivo spatial separation co-culture in Atlantic salmon

Salmonid Rickettsial Syndrome (SRS), caused by Piscirickettsia salmonis, is the most important disease in the Chilean aquaculture industry since it induces the highest mortality rates among infectious diseases. P. salmonis is a facultative intracellular bacterium comprising two genetically distinct groups (LF-89 and EM-90) in Chile. Previous data suggest that their cohabitation triggers the expression of virulence effectors, which could be related to a higher pathogenicity in salmon during a co-infection. Therefore, we evaluated whether the physical contact between two isolates from LF-89 and EM-90 was needed to activate this effect. Through a spatially separated in vivo co-culture inside Atlantic salmon followed by RNA-seq analysis, we compared the differential expressed genes (DEGs) with our previous results from an in vivo mixed co-culture. Data showed that LF-89 presented a similar virulence factor profile compared to the mixed co-culture. In contrast, EM-90 had more downregulated DEGs and the flagellar-related genes observed during mixed co-culture were absent. Hence, the synergistic effect related to increased pathogenicity to the host may be driven by the physical co-localization of both LF-89 and EM-90 P. salmonis isolates. Overall design: To investigate the transcriptomic changes of P. salmonis in spatially separated co-cultures compared to mixed co-cultures of P. salmonis EM-90 and LF-89, we inserted dialysis bags with the bacterial cultures inside Atlantic salmon for 6 days. Then extracted the total RNA to perform an RNA-seq analysis comparing the transcriptomics profiles of both types of co-cultures The GSM7508520-GSM7508522 (in GSE235725/PRJNA987513) raw data are being re-analyzed in the current study and the resulting processed data files are linked as Series supplementary files: Sample Accns SRA Experiment BioSample processed_data_files GSM7508520 SRX20775587 SAMN35982295 Sample_10_7-*.counts GSM7508521 SRX20775588 SAMN35982294 Sample_11_8-*.counts GSM7508522 SRX20775589 SAMN35982293 Sample_12_9-*.counts