Pan-genomic analyses of Corynebacterium pseudotuberculosis andcharacterization of the biovars ovis and equi through comparative genomics

Abstract

Corynebacterium pseudotuberculosis is the causative agent of diverse communicable diseases in small ruminants (biovar ovis), horses, camels, buffalo and other animals (biovar equi), which mainly differ in symptoms and site of infection. Additionally, the diseases present a highly important economic problem worldwide and there is still a lack of efficient treatments against C. pseudotuberculosis. In this work, we describe the steps from the first genome sequencing of a strain of C. pseudotuberculosis to the pangenomic analyses of 15 strains isolated from different hosts and countries with diverse symptoms. Briefly, we introduce the genus Corynebacterium and the in silico analyses performed in pathogenic species of this genus to date. Then, we describe the implementation of a software for the prediction of pathogenicity islands (PAIs) in bacteria (PIPS), which outperformed the other available software, and identified 7 PAIs with important virulence factors in C. pseudotuberculosis biovar ovis. Moreover, we extend the analyses of PAIs to strains of C. pseudotuberculosis biovar equi and predict 49 putative vaccine targets, in silico, which are commonly shared by both biovars, ovis and equi. Finally, we present the phylogenomic, pan-genomic, core genomic, singletons and genomic plasticity analyses of the 15 strains of C. pseudotuberculosis, from both biovars. All the analyses performed here point for a clonal-like behavior of C. pseudotuberculosis, which could be the result of the facultative intracellular behavior of the species. Moreover, the biovar equi presents a higher variability in gene content when compared to biovar ovis, specially in PAI regions. Noteworthy, the strains from biovar ovis present a high degree of similarity in pili clusters of genes, whereas the biovar equi strains are very variable. The conservation of pili clusters of genes in biovar ovis could account for the ability of these strains to spread inside host tissues and penetrate live cells to live intracellularly, where they would have less contact to other organisms, thus, possibly explaining the clonal-like behavior of the biovar ovis.