Pangenome and Phylogenomic Analysis of the Pathogenic Actinobacterium<i>Rhodococcus equi</i>

Anastasi, Elisa; MacArthur, Iain; Scortti, Mariela; Alvarez, Sonsiray; Giguère, Steeve; Vázquez‐Boland, José A.

doi:10.1093/gbe/evw222

Cited by 50 publications

(97 citation statements)

References 37 publications

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“…Despite no evidence of phylogeographic associations, a wide global circulation of genotypes was observed, probably related to international livestock trade. In addition, the virulence plasmid type is strongly associated with specific adapted animal-hosts and humans, supporting the notion that R. equi infection in humans possesses zoonotic nature (Anastasi et al, 2016).…”

Section: Rhodococcus Equi Isolates Recovered From Human Cases Havesupporting

confidence: 56%

Novel bovine-associated pVAPN plasmid type in Rhodococcus equi identified from lymph nodes of slaughtered cattle and lungs of people living with HIV/AIDS

Ribeiro

Lara

Silva

et al. 2017

Transbound Emerg Dis

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Rhodococcus equi is a well-recognized Gram-positive intracellular facultative bacterium that is opportunistic in nature, which causes pyogranulomatous infections in humans and multiple host animals. The pathogenicity of the microorganism has been attributed to the presence of plasmid-encoded virulence-associated proteins (Vap). To date, three host-associated virulence plasmid types of R. equi have been identified as follows: the circular pVAPA and pVAPB, related, respectively, to equine and porcine isolates, and a recently described linear pVAPN plasmid associated with bovine strains, although these three types are found in human isolates. Recent phylogenomic studies support the evidence that human R. equi infection is zoonotically acquired. Nevertheless, data regarding distribution and prevalence of the host-adapted virulence plasmid types of R. equi isolated from meat animals are scarce or unnoticed. Here, the three host-associated virulence plasmid types (pVAPA, pVAPB, and pVAPN) were investigated in 154 R. equi isolates recovered from lymph nodes of cattle with lymphadenitis (n = 31), faeces of cattle without enteric signs (n = 49), as well as different clinical specimens from human patients (n = 74). The analysis of virulence profile of 74 R. equi from humans revealed six (8.1%) isolates pVAPB (type 8), two (2.7%) pVAPN, and one (1.3%) pVAPB (type 11), all of which were from lung samples from people living with HIV/AIDS. From the lymph node samples of cattle, 41.9% (13 of 31) isolates revealed pVAPN type, whereas all isolates from faecal samples were negative for three host-associated types. Here, recently described bovine-associated pVAPN type was detected in R. equi isolates recovered from the lungs of people living with HIV/AIDS and lymph nodes from slaughtered cattle intended for human consumption; a finding that represents a public health concern, mainly in countries where undercooked or raw meat are traditionally consumed.

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Section: Rhodococcus Equi Isolates Recovered From Human Cases Havesupporting

confidence: 56%

Novel bovine-associated pVAPN plasmid type in Rhodococcus equi identified from lymph nodes of slaughtered cattle and lungs of people living with HIV/AIDS

Ribeiro

Lara

Silva

et al. 2017

Transbound Emerg Dis

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“…Despite multiple calls to revisit complex rhodococcal taxonomy202122252729, a recent study based on the analyses of fewer rhodococcal genome sequences presented an alternative phylogenomic view even though similar species-groups were recovered49. In contrast, the present study is based on more extensive and comprehensive phylogenomic and taxogenomic analyses of a larger genomic dataset, including more type strains.…”

Section: Discussionmentioning

confidence: 89%

Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

Sangal

Goodfellow

Jones

et al. 2016

Sci Rep

108

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Prokaryotic systematics provides the fundamental framework for microbiological research but remains a discipline that relies on a labour- and time-intensive polyphasic taxonomic approach, including DNA-DNA hybridization, variation in 16S rRNA gene sequence and phenotypic characteristics. These techniques suffer from poor resolution in distinguishing between closely related species and often result in misclassification and misidentification of strains. Moreover, guidelines are unclear for the delineation of bacterial genera. Here, we have applied an innovative phylogenetic and taxogenomic approach to a heterogeneous actinobacterial taxon, Rhodococcus, to identify boundaries for intrageneric and supraspecific classification. Seven species-groups were identified within the genus Rhodococcus that are as distantly related to one another as they are to representatives of other mycolic acid containing actinobacteria and can thus be equated with the rank of genus. It was also evident that strains assigned to rhodococcal species-groups are underspeciated with many misclassified using conventional taxonomic criteria. The phylogenetic and taxogenomic methods used in this study provide data of theoretical value for the circumscription of generic and species boundaries and are also of practical significance as they provide a robust basis for the classification and identification of rhodococci of agricultural, industrial and medical/veterinary significance.

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“…2008; Anastasi et al. 2016; our unpublished observations) and the genomic analysis of the plasmids confirms this.…”

Section: Discussionmentioning

confidence: 99%

Comparative Genomics of Rhodococcus equi Virulence Plasmids Indicates Host-Driven Evolution of the vap Pathogenicity Island

MacArthur

Anastasi

Alvarez

et al. 2017

Genome Biology and Evolution

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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.

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Pangenome and Phylogenomic Analysis of the Pathogenic ActinobacteriumRhodococcus equi

Cited by 50 publications

References 37 publications

Novel bovine-associated pVAPN plasmid type in Rhodococcus equi identified from lymph nodes of slaughtered cattle and lungs of people living with HIV/AIDS

Novel bovine-associated pVAPN plasmid type in Rhodococcus equi identified from lymph nodes of slaughtered cattle and lungs of people living with HIV/AIDS

Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

Comparative Genomics of Rhodococcus equi Virulence Plasmids Indicates Host-Driven Evolution of the vap Pathogenicity Island

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