Pangenome and phylogenomic analysis of the pathogenic actinobacterium Rhodococcus equi

Abstract

We report acomparative studyof 29 representative genomesof the animal pathogen Rhodococcus equi. The analyses showed that R. equi is genetically homogeneous and clonal, with a large core genome accounting for&80%of an isolates' gene content. An open pangenome, even distribution of accessory genes among the isolates, and absence of significant core-genome recombination, indicated that gene gain/loss is a main driver of R. equi genome evolution. Traits previously predicted to be important in R. equi physiology, virulence and niche adaptation were part of the core genome. This included the lack of a phosphoenolpyruvate:carbohydrate transport system (PTS), unique among the rhodococci except for the closely related Rhodococcus defluvii, reflecting selective PTSgeneloss in the R. equi-R. defluvii sublineage. Thought tobe asaccharolytic, rbsCBand glcPnon-PTS sugarpermeasehomologues were identified in the core genome and, albeit inefficiently, R. equi utilized their putative substrates, ribose and (irregularly) glucose. Therewas no correlation between R. equiwhole-genomephylogeny and host or geographical source, with evidence of global spread of genomovars. The distribution of host-Associated virulence plasmid types was consistent with the exchange of the plasmids (and corresponding host shifts) across the R. equi population, and human infection being zoonotically acquired. Phylogenomic analyses demonstratedthat R.equioccupies a central positionintheRhodococcus phylogeny,not supportingthe recentlyproposed transferof the species to a new genus.