The Genome of a Pathogenic Rhodococcus: Cooptive Virulence Underpinned by Key Gene Acquisitions

Michal Letek,Tom Buckley,Jolyon Holdstock,Wim G Meijer,Julian Parkhill,Alain Ocampo,John F Prescott,Ursula Fogarty,Alexia Hapeshi,Mandy Sanders,Michael A Quail,Iain Macarthur,Héctor Rodríguez,Jesús Navas,Mónica Blanco,Inna Cherevach,Ana Valero-Rello,Stephen D Bentley,Tom C Freeman,Patricia I Sosa González ,Mariela Scortti ,D P Leadon ,Ruth J Fahey ,José A Vázquez‐Boland

doi:10.1371/journal.pgen.1001145

Abstract

We report the genome of the facultative intracellular parasite Rhodococcus equi, the only animal pathogen within the biotechnologically important actinobacterial genus Rhodococcus. The 5.0-Mb R. equi 103S genome is significantly smaller than those of environmental rhodococci. This is due to genome expansion in nonpathogenic species, via a linear gain of paralogous genes and an accelerated genetic flux, rather than reductive evolution in R. equi. The 103S genome lacks the extensive catabolic and secondary metabolic complement of environmental rhodococci, and it displays unique adaptations for host colonization and competition in the short-chain fatty acid–rich intestine and manure of herbivores—two main R. equi reservoirs. Except for a few horizontally acquired (HGT) pathogenicity loci, including a cytoadhesive pilus determinant (rpl) and the virulence plasmid vap pathogenicity island (PAI) required for intramacrophage survival, most of the potential virulence-associated genes identified in R. equi are conserved in environmental rhodococci or have homologs in nonpathogenic Actinobacteria. This suggests a mechanism of virulence evolution based on the cooption of existing core actinobacterial traits, triggered by key host niche–adaptive HGT events. We tested this hypothesis by investigating R. equi virulence plasmid-chromosome crosstalk, by global transcription profiling and expression network analysis. Two chromosomal genes conserved in environmental rhodococci, encoding putative chorismate mutase and anthranilate synthase enzymes involved in aromatic amino acid biosynthesis, were strongly coregulated with vap PAI virulence genes and required for optimal proliferation in macrophages. The regulatory integration of chromosomal metabolic genes under the control of the HGT–acquired plasmid PAI is thus an important element in the cooptive virulence of R. equi.

Highlights

Rhodococcus bacteria belong to the mycolic acid-containing group of actinomycetes together with other major genera such as Corynebacterium, Mycobacterium and Nocardia [1]
We suggest that a few decisive niche-adaptive horizontal gene transfer (HGT) events in a direct ancestor of R. equi, such as acquisition of the plasmid vap ‘‘intramacrophage survival’’ pathogenicity island (PAI) [8] and the rpl ‘‘host colonization’’ HGT island (Figure 4), triggered the rapid conversion of a ‘‘preparasitic’’ commensal organism into a pathogen via the cooption of preexisting bacterial functions
Somewhat counterintuitively for an organism with a dual lifestyle as a soil saprotroph and intracellular parasite, the R. equi genome is significantly smaller than those of environmental rhodococci. This may reflect that the main R. equi habitats – herbivore intestine, manure and animal tissues– provide a richer and more stable environment than the chemically diverse and probably nutrient-scarce environments of the nonpathogenic species

Summary

Introduction

Rhodococcus bacteria belong to the mycolic acid-containing group of actinomycetes together with other major genera such as Corynebacterium, Mycobacterium and Nocardia [1]. The genus Rhodococcus comprises more than 40 species widely distributed in the environment, many with biotechnological applications as diverse as the biodegradation of hydrophobic compounds and xenobiotics, the production of acrylates and bioactive steroids, and fossil fuel desulfurization [2]. The rhodococci include an animal pathogen, Rhodococcus equi, the genome of which we report here. R. equi, a strictly aerobic coccobacillus, is a multihost pathogen that causes purulent infections in various animal species. In horses, it is the etiological agent of ‘‘rattles’’, a lung disease with a high mortality in foals [3]. R. equi causes chronic pyogranulomatous adenitis in pigs and cattle and severe opportunistic infections in humans, often in HIV-infected and immunosuppressed patients.

Author Summary

Conclusions

Findings

Materials and Methods