Long-term serial culture of Piscirickettsia salmonis leads to a genomic and transcriptomic reorganization affecting bacterial in vitro virulence

The propagation of intracellular bacteria in culture mediums implies physiological adaptation to an artificial environment. If these conditions are persistent enough time, a permanent adaptation to the new environment can be expected. This study aimed to explore the genomic and transcriptomic rearrangements that the intracellular bacterium Piscirickettsia salmonis undergo during a long-term serial culture experiment and the potential impact on virulence. Here, PacBio and Illumina sequencing were conducted after 200 passages (~2 years) of P. salmonis in a cell-free culture medium. The results evidenced genomic rearrangements of the P. salmonis genome during the continuous culture period, where a chromosome segment of 35 Kb was translocated from the P0 bacterial chromosome to a P200 plasmid. Notably, the genomic structure of this segment revealed the presence of the Dot/Icm secretion system, which has been previously associated with P. salmonis pathogenesis. On the other hand, a reduced transcriptomic response was evidenced in P. salmonis after 200 passages affecting the expression of different pathways including iron acquisition and metabolism. Furthermore, in vitro infections revealed that after 200 passages P. salmonis is less capable of generating cytopathic effects than the original P0 form. Overall, our results evidence that the continuous propagation of P. salmonis leads to genomic and transcriptomic rearrangement that impact on bacterial virulence. These results open new perspectives about the adaptation of intracellular bacteria to artificial culture conditions, providing useful information to develop live attenuated vaccines against P. salmonis in salmon aquaculture.