Genomic epidemiology of the commercially important pathogen Renibacterium salmoninarum within the Chilean salmon industry.

Renibacterium salmoninarum is the causative agent of Bacterial Kidney Disease (BKD), which is a commercially important disease of salmonids. Typing by conventional methods provides little information on the evolution and spread of this pathogen as R. salmoninarum has a low mutation rate and limited standing variation within the population. Here we apply whole genome sequencing to 42 R. salmoninarum isolates from Chile, primarily from salmon farms, in order to understand the epidemiology of BKD in this country. All of the Chilean isolates were members of farm-associated Clade 1. The data are consistent with multiple introductions to Chile, followed by widespread geographical spread of the disease over a 30 year period. In multiple cases the estimated dates of introduction coincide with major events in the development of the Chilean aquaculture industry. We find evidence for a Coho salmon associated lineage, indicating that host switching may not be as frequent as previously thought or that other significant barriers to transmission exist in the Chilean salmon production chain. Understanding of the genomic epidemiology of BKD can inform disease intervention and improve sustainability of the commercially important aquaculture industry.