title: Comparative Genomics of Rhodococcus equi Virulence Plasmids Indicates Host-Driven Evolution of the vap Pathogenicity Island.
abstract: The conjugative virulence plasmid is a key component of the Rhodococcus equi accessory genome essential for pathogenesis. Three host-associated virulence plasmid types have been identified the equine pVAPA and porcine pVAPB circular variants, and the linear pVAPN found in bovine (ruminant) isolates. We recently characterized the R. equi pangenome (Anastasi E, et al. 2016. Pangenome and phylogenomic analysis of the pathogenic actinobacterium Rhodococcus equi. Genome Biol Evol. 8:3140-3148.) and we report here the comparative analysis of the virulence plasmid genomes. Plasmids within each host-associated type were highly similar despite their diverse origins. Variation was accounted for by scattered single nucleotide polymorphisms and short nucleotide indels, while larger indels-mostly in the plasticity region near the vap pathogencity island (PAI)-defined plasmid genomic subtypes. Only one of the plasmids analyzed, of pVAPN type, was exceptionally divergent due to accumulation of indels in the housekeeping backbone. Each host-associated plasmid type carried a unique PAI differing in vap gene complement, suggesting animal host-specific evolution of the vap multigene family. Complete conservation of the vap PAI was observed within each host-associated plasmid type. Both diversity of host-associated plasmid types and clonality of specific chromosomal-plasmid genomic type combinations were observed within the same R. equi phylogenomic subclade. Our data indicate that the overall strong conservation of the R. equi host-associated virulence plasmids is the combined result of host-driven selection, lateral transfer between strains, and geographical spread due to international livestock exchanges.
authors.affiliation: Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: Iain
authors.initials: I
authors.lastname: MacArthur
authors.affiliation: Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: Elisa
authors.initials: E
authors.lastname: Anastasi
authors.affiliation: Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: Sonsiray
authors.initials: S
authors.lastname: Alvarez
authors.affiliation: Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.|Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: Mariela
authors.initials: M
authors.lastname: Scortti
authors.affiliation: Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.|Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, United Kingdom.|Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: José A
authors.initials: JA
authors.lastname: Vázquez-Boland
mesh_terms: D000193:Actinomycetales Infections / Q000382:microbiology / Q000662:veterinary; D000818:Animals; D002417:Cattle; D019143:Evolution, Molecular; D044404:Genomic Islands; D054884:Host-Pathogen Interactions; D010802:Phylogeny; D010957:Plasmids; D016929:Rhodococcus equi / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity
keywords: Rhodococcus equi; comparative genomics; host tropism; host-associated virulence plasmids; pangenome analysis