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McMinn, Elizabeth J.; Alderson, Grace; Dodson, Hilary I.; Goodfellow, Michael; Ward, Alan C.

doi:10.1023/a:1010282616110

Cited by 39 publications

(8 citation statements)

References 33 publications

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“…Our whole-genome comparative analyses show that R. equi is largely monomorphic, not supporting the commonly held view that R. equi is heterogeneous (McMinn et al 2000; Jones and Goodfellow 2012; Jones et al 2013b) and its isolates phylogenetically very diverse (Gurtler et al 2004). The tendency of the core–genome sublineages to associate with a specific composition of the accessory genome and the lack of significant core–genome recombination indicate that R. equi evolution is primarily clonal.…”

Section: Discussioncontrasting

confidence: 93%

“…It is evident from our data that R. equi is not at the periphery or outwith the genus Rhodococcus , closer to the Nocardia , as previously claimed (Goodfellow et al 1998; McMinn et al 2000; Jones et al 2013b), but deeply embedded in the rhodococcal phylogeny. Indeed, the “ equi - defluvii-triatomae ” subclade (no.…”

Section: Discussionsupporting

confidence: 79%

“…Finally, our phylogenomic analyses resolve the lingering problem of R. equi taxonomy (Goodfellow et al 1998; McMinn et al 2000; Gurtler et al 2004; Jones and Goodfellow 2012; Ludwig et al 2012). It is evident from our data that R. equi is not at the periphery or outwith the genus Rhodococcus , closer to the Nocardia , as previously claimed (Goodfellow et al 1998; McMinn et al 2000; Jones et al 2013b), but deeply embedded in the rhodococcal phylogeny.…”

Section: Discussionmentioning

confidence: 76%

“…In comparison, the ANI values with members of the two other main Rhodococcus lines of descent as defined based on 16 rDNA phylogenies (McMinn, et al 2000; Jones and Goodfellow 2012), that is, the “ erythropolis ” clade ( R. erythropolis , R. jostii , R. opacus and R. fascians included in the analysis) and the “ rhodochrous ” clade” ( Rhodococcus rhodochrous , Rhodococcus rhodnii , Rhodococcus ruber , and Rhodococcus pyridinivorans included in the analysis), were 72.27–74.58% and 68.55–75.15%, respectively. The ANI with the recently described R. equi close relative, Rhodococcus defluvii (strain Ca11 T ) (Kampfer et al 2014), was 82.96%.…”

Section: Resultsmentioning

confidence: 99%

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Pangenome and Phylogenomic Analysis of the Pathogenic ActinobacteriumRhodococcus equi

et al. 2016

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We report a comparative study of 29 representative genomes of 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 PTS gene loss in the R. equi–R. defluvii sublineage. Thought to be asaccharolytic, rbsCB and glcP non-PTS sugar permease homologues were identified in the core genome and, albeit inefficiently, R. equi utilized their putative substrates, ribose and (irregularly) glucose. There was no correlation between R. equi whole-genome phylogeny 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 demonstrated that R. equi occupies a central position in the Rhodococcus phylogeny, not supporting the recently proposed transfer of the species to a new genus.

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Section: Discussioncontrasting

confidence: 93%

Section: Discussionsupporting

confidence: 79%

Section: Discussionmentioning

confidence: 76%

Section: Resultsmentioning

confidence: 99%

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Pangenome and Phylogenomic Analysis of the Pathogenic ActinobacteriumRhodococcus equi

et al. 2016

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“…Environmental source Soil [202] Pulmonary diseases/insect symbiont Insects [19,264,265] sources are phylogenetically very diverse [41][42][43][44]. It also appears that R. rhodnii is more closely related to the genus Tsukamurella than it is to other rhodococci.…”

Section: N Vinaceamentioning

confidence: 99%

Can whole genome analysis refine the taxonomy of the genusRhodococcus?

2004

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The current systematics of the genus Rhodococcus is unclear, partly because many members were originally included before the application of a polyphasic taxonomic approach, central to which is the acquisition of 16S rRNA sequence data. This has resulted in the reclassification and description of many new species. Hence, the literature is replete with new species names that have not been brought together in an organized and easily interpreted form. This taxonomic confusion has been compounded by assigning many xenobiotic degrading isolates with phylogenetic positions but without formal taxonomic descriptions. In order to provide a framework for a taxonomic approach based on multiple genetic loci, a survey was undertaken of the known genome characteristics of members of the genus Rhodococcus including: (i) genetics of cell envelope biosynthesis; (ii) virulence genes; (iii) gene clusters involved in metabolic degradation and industrially relevant pathways; (iv) genetic analysis tools; (v) rapid identification of bacteria including rhodococci with specific gene RFLPs; (vi) genomic organization of rrn operons. Genes encoding virulence factors have been characterized for Rhodococcus equi and Rhodococcus fascians. Based on peptide signature comparisons deduced from gene sequences for cytochrome P-450, mono- and dioxygenases, alkane degradation, nitrile metabolism, proteasomes and desulfurization, phylogenetic relationships can be deduced for Rhodococcus erythropolis, Rhodococcus globerulus, Rhodococcus ruber and a number of undesignated Rhodococcus spp. that may distinguish the genus Rhodococcus into two further genera. The linear genome topologies that exist in some Rhodococcus species may alter a previously proposed model for the analysis of genomic fingerprinting techniques used in bacterial systematics.

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Nocardiaand other Aerobic Actinomycetes

Conville

Witebsky

2010

Topley &Amp; Wilson's Microbiology and Microbial Infections

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Cited by 39 publications

References 33 publications

Pangenome and Phylogenomic Analysis of the Pathogenic ActinobacteriumRhodococcus equi

Pangenome and Phylogenomic Analysis of the Pathogenic ActinobacteriumRhodococcus equi

Can whole genome analysis refine the taxonomy of the genusRhodococcus?

Nocardiaand other Aerobic Actinomycetes

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