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Benning S, Pritsch K, Radl V, Siani R, Wang Z, Schloter M. (Pan)genomic analysis of two Rhodococcus isolates and their role in phenolic compound degradation. Microbiol Spectr 2024; 12:e0378323. [PMID: 38376357 PMCID: PMC10986565 DOI: 10.1128/spectrum.03783-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/25/2024] [Indexed: 02/21/2024] Open
Abstract
The genus Rhodococcus is recognized for its potential to degrade a large range of aromatic substances, including plant-derived phenolic compounds. We used comparative genomics in the context of the broader Rhodococcus pan-genome to study genomic traits of two newly described Rhodococcus strains (type-strain Rhodococcus pseudokoreensis R79T and Rhodococcus koreensis R85) isolated from apple rhizosphere. Of particular interest was their ability to degrade phenolic compounds as part of an integrated approach to treat apple replant disease (ARD) syndrome. The pan-genome of the genus Rhodococcus based on 109 high-quality genomes was open with a small core (1.3%) consisting of genes assigned to basic cell functioning. The range of genome sizes in Rhodococcus was high, from 3.7 to 10.9 Mbp. Genomes from host-associated strains were generally smaller compared to environmental isolates which were characterized by exceptionally large genome sizes. Due to large genomic differences, we propose the reclassification of distinct groups of rhodococci like the Rhodococcus equi cluster to new genera. Taxonomic species affiliation was the most important factor in predicting genetic content and clustering of the genomes. Additionally, we found genes that discriminated between the strains based on habitat. All members of the genus Rhodococcus had at least one gene involved in the pathway for the degradation of benzoate, while biphenyl degradation was mainly restricted to strains in close phylogenetic relationships with our isolates. The ~40% of genes still unclassified in larger Rhodococcus genomes, particularly those of environmental isolates, need more research to explore the metabolic potential of this genus.IMPORTANCERhodococcus is a diverse, metabolically powerful genus, with high potential to adapt to different habitats due to the linear plasmids and large genome sizes. The analysis of its pan-genome allowed us to separate host-associated from environmental strains, supporting taxonomic reclassification. It was shown which genes contribute to the differentiation of the genomes based on habitat, which can possibly be used for targeted isolation and screening for desired traits. With respect to apple replant disease (ARD), our isolates showed genome traits that suggest potential for application in reducing plant-derived phenolic substances in soil, which makes them good candidates for further testing against ARD.
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Affiliation(s)
- Sarah Benning
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Karin Pritsch
- Research Unit for Environmental Simulations, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Viviane Radl
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Roberto Siani
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Zhongjie Wang
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Chair for Environmental Microbiology, TUM School of Life Sciences, Technical University Munich, Munich, Germany
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2
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Ranganath N, Mendoza MA, Stevens R, Kind D, Wengenack N, Shah A. Rhodococcus infection: a 10-year retrospective analysis of clinical experience and antimicrobial susceptibility profile. J Clin Microbiol 2024; 62:e0153723. [PMID: 38349145 PMCID: PMC10935630 DOI: 10.1128/jcm.01537-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/07/2024] [Indexed: 02/24/2024] Open
Abstract
Rhodococcus equi is an opportunistic pathogen known to cause pulmonary and extrapulmonary disease among immunocompromised patients. Treatment is frequently challenging due to intrinsic resistance to multiple antibiotic classes. While non-equi Rhodococcus spp. are prevalent, their clinical significance is poorly defined. There is also limited data on antibiotic susceptibility testing (AST) of Rhodococcus infection in humans. We conducted a single-center, retrospective cohort study evaluating clinical characteristics, microbiologic profile, and AST of Rhodococcus infections between June 2012 and 2022 at our tertiary academic medical center. Identification of Rhodococcus spp. was performed by Sanger 16S rRNA gene sequencing and/or matrix-assisted laser desorption ionization-time of flight mass spectrometry, and AST was performed by agar dilution. Three hundred twenty-two isolates of Rhodococcus spp. were identified from blood (50%), pulmonary (26%), and bone/joint (12%) sources. R. equi/hoagii, R. corynebacterioides, and R. erythropolis were the most frequently isolated species, with 19% of isolates identified only to genus level. One hundred ninety-nine isolates evaluated for AST demonstrated high-level resistance to amoxicillin/clavulanate, cephalosporins, and aminoglycosides. More than 95% susceptibility to imipenem, vancomycin, linezolid, rifampin, and clarithromycin was observed. Non-equi species showed a significantly more favorable AST profile relative to R. equi. Clinically significant Rhodococcus infection was rare with 10 cases diagnosed (majority due to R. equi) and managed. The majority of patients received 2- or 3-drug combination therapy for 2-6 months, with favorable clinical response. Significant differences in AST were observed between R. equi and non-equi species. Despite high antimicrobial resistance to several antibiotic classes, imipenem and vancomycin remain appropriate empiric treatment options for R. equi. Future research evaluating mechanisms underlying antimicrobial resistance is warranted.
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Affiliation(s)
- Nischal Ranganath
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Maria Alejandra Mendoza
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Ryan Stevens
- Department of Pharmacy, Mayo Clinic, Rochester, Minnesota, USA
| | - Dalton Kind
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Nancy Wengenack
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Aditya Shah
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
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3
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Sangal V, Goodfellow M, Jones AL, Sutcliffe IC. A stable home for an equine pathogen: valid publication of the binomial Prescottella equi gen. nov., comb. nov., and reclassification of four rhodococcal species into the genus Prescottella. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Opinion 106 of the Judicial Commission has clarified the nomenclature of the taxon variously named
Rhodococcus equi
, ‘Prescottella equi’ and
Rhodococcus hoagii
. As a consequence, we present here the genus name
Prescottella
and that of its nomenclatural type species,
Prescottella equi
comb. nov., for valid publication and propose the reclassification of four rhodococcal species as novel combinations in the genus, namely Prescottella agglutinans Guo et al. 2015 comb. nov., Prescottella defluvii Kämpfer et al. 2014 comb. nov., Prescottella soli Li et al. 2015 comb. nov. and Prescottella subtropica Lee et al. 2019 comb. nov. In addition, we note that a clinical isolate, strain 86–07 (=W8901), likely represents an additional species within the genus
Prescottella
. Nearly a century after the original description of the type strain of the type species as
Corynebacterium equi
, we provide a stable home for
Prescottella equi
and its relatives.
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Affiliation(s)
- Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Amanda L. Jones
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Iain C. Sutcliffe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
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4
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Garrido-Sanz D, Redondo-Nieto M, Martín M, Rivilla R. Comparative Genomics of the Rhodococcus Genus Shows Wide Distribution of Biodegradation Traits. Microorganisms 2020; 8:microorganisms8050774. [PMID: 32455698 PMCID: PMC7285261 DOI: 10.3390/microorganisms8050774] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/17/2020] [Accepted: 05/20/2020] [Indexed: 11/24/2022] Open
Abstract
The genus Rhodococcus exhibits great potential for bioremediation applications due to its huge metabolic diversity, including biotransformation of aromatic and aliphatic compounds. Comparative genomic studies of this genus are limited to a small number of genomes, while the high number of sequenced strains to date could provide more information about the Rhodococcus diversity. Phylogenomic analysis of 327 Rhodococcus genomes and clustering of intergenomic distances identified 42 phylogenomic groups and 83 species-level clusters. Rarefaction models show that these numbers are likely to increase as new Rhodococcus strains are sequenced. The Rhodococcus genus possesses a small “hard” core genome consisting of 381 orthologous groups (OGs), while a “soft” core genome of 1253 OGs is reached with 99.16% of the genomes. Models of sequentially randomly added genomes show that a small number of genomes are enough to explain most of the shared diversity of the Rhodococcus strains, while the “open” pangenome and strain-specific genome evidence that the diversity of the genus will increase, as new genomes still add more OGs to the whole genomic set. Most rhodococci possess genes involved in the degradation of aliphatic and aromatic compounds, while short-chain alkane degradation is restricted to a certain number of groups, among which a specific particulate methane monooxygenase (pMMO) is only found in Rhodococcus sp. WAY2. The analysis of Rieske 2Fe-2S dioxygenases among rhodococci genomes revealed that most of these enzymes remain uncharacterized.
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5
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Vázquez-Boland JA, Scortti M, Meijer WG. Conservation of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 and rejection of Rhodococcus hoagii (Morse 1912) Kämpfer et al. 2014. Int J Syst Evol Microbiol 2020; 70:3572-3576. [PMID: 32375930 PMCID: PMC7395624 DOI: 10.1099/ijsem.0.004090] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 01/07/2020] [Accepted: 02/18/2020] [Indexed: 01/07/2023] Open
Abstract
A recent taxonomic study confirmed the synonymy of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 and Corynebacterium hoagii (Morse 1912) Eberson 1918. As a result, both R. equi and C. hoagii were reclassified as Rhodococcus hoagii comb. nov. in application of the principle of priority of the Prokaryotic Code. Because R. equi is a well-known animal and zoonotic human pathogen, and a bacterial name solidly established in the veterinary and medical literature, we and others argued that the nomenclatural change may cause error and confusion and be potentially perilous. We have now additionally found that the nomenclatural type of the basonym C. hoagii, ATCC 7005T, does not correspond with the original description of the species C. hoagii in the early literature. Its inclusion as the C. hoagii type on the Approved Lists 1980 results in a change in the characters of the taxon and in C. hoagii designating two different bacteria. Moreover, ATCC 7005, the only strain in circulation under the name C. hoagii, does not have a well documented history; it is unclear why it was deposited as C. hoagii and a possible mix-up with a Corynebacterium (Rhodococcus) equi isolate is a reasonable assumption. We therefore request the rejection of Rhodococcus hoagii as a nomen ambiguum, nomen dubium and nomen perplexum in addition to nomen periculosum, and conservation of the name Rhodococcus equi, according to Rules 56ab of the Code.
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Affiliation(s)
- José A. Vázquez-Boland
- Microbial Pathogenesis Group, Edinburgh Medical School (Biomedical Sciences - Infection Medicine), University of Edinburgh, Chancellor’s Building, Little France campus, Edinburgh EH16 4SB, UK
| | - Mariela Scortti
- Microbial Pathogenesis Group, Edinburgh Medical School (Biomedical Sciences - Infection Medicine), University of Edinburgh, Chancellor’s Building, Little France campus, Edinburgh EH16 4SB, UK
| | - Wim G. Meijer
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
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6
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Vázquez‐Boland JA, Meijer WG. The pathogenic actinobacterium Rhodococcus equi: what's in a name? Mol Microbiol 2019; 112:1-15. [PMID: 31099908 PMCID: PMC6852188 DOI: 10.1111/mmi.14267] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2019] [Indexed: 12/17/2022]
Abstract
Rhodococcus equi is the only recognized animal pathogenic species within an extended genus of metabolically versatile Actinobacteria of considerable biotechnological interest. Best known as a horse pathogen, R. equi is commonly isolated from other animal species, particularly pigs and ruminants, and causes severe opportunistic infections in people. As typical in the rhodococci, R. equi niche specialization is extrachromosomally determined, via a conjugative virulence plasmid that promotes intramacrophage survival. Progress in the molecular understanding of R. equi and its recent rise as a novel paradigm of multihost adaptation has been accompanied by an unusual nomenclatural instability, with a confusing succession of names: "Prescottia equi", "Prescotella equi", Corynebacterium hoagii and Rhodococcus hoagii. This article reviews current advances in the genomics, biology and virulence of this pathogenic actinobacterium with a unique mechanism of plasmid-transferable animal host tropism. It also discusses the taxonomic and nomenclatural issues around R. equi in the light of recent phylogenomic evidence that confirms its membership as a bona fide Rhodococcus.
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Affiliation(s)
- José A. Vázquez‐Boland
- Microbial Pathogenesis Group, Edinburgh Medical School (Biomedical Sciences – Infection Medicine)University of EdinburghChancellor's Building, Little France campusEdinburghEH16 4SBUK
| | - Wim G. Meijer
- UCD School of Biomolecular and Biomedical ScienceUniversity College DublinDublin 4Ireland
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8
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Current taxonomy of Rhodococcus species and their role in infections. Eur J Clin Microbiol Infect Dis 2018; 37:2045-2062. [PMID: 30159693 DOI: 10.1007/s10096-018-3364-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
Abstract
Rhodococcus is a genus of obligate aerobic, Gram-positive, partially acid-fast, catalase-positive, non-motile, and none-endospore bacteria. The genus Rhodococcus was first introduced by Zopf. This bacterium can be isolated from various sources of the environment and can grow well in non-selective medium. A large number of phenotypic characterizations are used to compare different species of the genus Rhodococcus, and these tests are not suitable for accurate identification at the genus and species level. Among nucleic acid-based methods, the most powerful target gene for revealing reliable phylogenetic relationships is 16S ribosomal RNA gene (16S rRNA gene) sequence analysis, but this gene is unable to differentiation some of Rhodococcus species. To date, whole genome sequencing analysis has solved taxonomic complexities in this genus. Rhodococcus equi is the major cause of foal pneumonia, and its implication in human health is related to cases in immunocompromised patients. Macrolide family together with rifampicin is one of the most effective antibiotic agents for treatment rhodococcal infections.
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9
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10
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Silva LJ, Souza DT, Genuario DB, Hoyos HAV, Santos SN, Rosa LH, Zucchi TD, Melo IS. Rhodococcus psychrotolerans sp. nov., isolated from rhizosphere of Deschampsia antarctica. Antonie Van Leeuwenhoek 2017; 111:629-636. [PMID: 29143212 DOI: 10.1007/s10482-017-0983-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 11/10/2017] [Indexed: 12/01/2022]
Abstract
A novel actinobacterium, designated strain CMAA 1533T, was isolated from the rhizosphere of Deschampsia antarctica collected at King George Island, Antarctic Peninsula. Strain CMAA 1533T was found to grow over a wide range of temperatures (4-28 °C) and pH (4-10). Macroscopically, the colonies were observed to be circular shaped, smooth, brittle and opaque-cream on most of the culture media tested. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CMAA 1533T belongs to the family Nocardiaceae and forms a distinct phyletic line within the genus Rhodococcus. Sequence similarity calculations indicated that the novel strain is closely related to Rhodococcus degradans CCM 4446T, Rhodococcus erythropolis NBRC 15567T and Rhodococcus triatomae DSM 44892T (≤ 96.9%). The organism was found to contain meso-diaminopimelic acid, galactose and arabinose in whole cell hydrolysates. Its predominant isoprenologue was identified as MK-8(H2) and the polar lipids as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The major fatty acids were identified as Summed feature (C16:1 ω6c and/or C16:1 ω7c), C16:0, C18:1 ω9c and 10-methyl C18:0. The G+C content of genomic DNA was determined to be 65.5 mol%. Unlike the closely related type strains, CMAA 1533T can grow at 4 °C but not at 37 °C and was able to utilise adonitol and galactose as sole carbon sources. Based on phylogenetic, chemotaxonomic and physiological data, it is concluded that strain CMAA 1533T (= NRRL B-65465T = DSM 104532T) represents a new species of the genus Rhodococcus, for which the name Rhodococcus psychrotolerans sp. nov. is proposed.
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Affiliation(s)
- Leonardo Jose Silva
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Pádua Dias Avenue, 11, Piracicaba, São Paulo, 13418-900, Brazil.,Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340 Highway, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil
| | - Danilo Tosta Souza
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340 Highway, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil
| | - Diego Bonaldo Genuario
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340 Highway, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil
| | - Harold Alexander Vargas Hoyos
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Pádua Dias Avenue, 11, Piracicaba, São Paulo, 13418-900, Brazil.,Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340 Highway, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil
| | - Suikinai Nobre Santos
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340 Highway, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil
| | - Luiz Henrique Rosa
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Presidente Antônio Carlos Avenue, 6627, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Tiago Domingues Zucchi
- Agrivalle, Agricultural Biotechnology, Tranquillo Giannini Avenue, 1090, Salto, São Paulo, 13329-600, Brazil
| | - Itamar Soares Melo
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340 Highway, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil.
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11
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Sangal V, Goodfellow M, Jones AL, Schwalbe EC, Blom J, Hoskisson PA, Sutcliffe IC. Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa. Sci Rep 2016; 6:38392. [PMID: 27924912 PMCID: PMC5141411 DOI: 10.1038/srep38392] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/08/2016] [Indexed: 01/14/2023] Open
Abstract
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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Affiliation(s)
- Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Michael Goodfellow
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Amanda L Jones
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Edward C Schwalbe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Jochen Blom
- Heinrich-Buff-Ring 58, Justus-Liebig-Universität, 35392 Gießen, Germany
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Iain C Sutcliffe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
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12
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Tindall BJ. Rule 27 of the International Code of Nomenclature of prokaryotes: the basonym is not enough. Int J Syst Evol Microbiol 2016; 66:4897-4899. [DOI: 10.1099/ijsem.0.001369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- B. J. Tindall
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B 38124, Braunschweig, Germany
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13
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Anastasi E, MacArthur I, Scortti M, Alvarez S, Giguère S, Vázquez-Boland JA. Pangenome and Phylogenomic Analysis of the Pathogenic Actinobacterium Rhodococcus equi. Genome Biol Evol 2016; 8:3140-3148. [PMID: 27638249 PMCID: PMC5174736 DOI: 10.1093/gbe/evw222] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
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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Affiliation(s)
- Elisa Anastasi
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Iain MacArthur
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Mariela Scortti
- 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
| | - Sonsiray Alvarez
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Steeve Giguère
- Department of Large Animal Medicine, University of Georgia, Georgia, USA
| | - José A Vázquez-Boland
- 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.,Grupo de Patogenómica Bacteriana, Universidad de Léon, León, Spain
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14
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Giles C, Ndi O, Barton MD, Vanniasinkam T. An Adenoviral Vector Based Vaccine for Rhodococcus equi. PLoS One 2016; 11:e0152149. [PMID: 27008624 PMCID: PMC4805240 DOI: 10.1371/journal.pone.0152149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 03/09/2016] [Indexed: 11/26/2022] Open
Abstract
Rhodococcus equi is a respiratory pathogen which primarily infects foals and is endemic on farms around the world with 50% mortality and 80% morbidity in affected foals. Unless detected early and treated appropriately the disease can be fatal. Currently, there is no vaccine available to prevent this disease. For decades researchers have endeavoured to develop an effective vaccine to no avail. In this study a novel human adenoviral vector vaccine for R. equi was developed and tested in the mouse model. This vaccine generated a strong antibody and cytokine response and clearance of R. equi was demonstrated following challenge. These results show that this vaccine could potentially be developed further for use as a vaccine to prevent R. equi disease in foals.
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Affiliation(s)
- Carla Giles
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Olasumbo Ndi
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Mary D. Barton
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Thiru Vanniasinkam
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
- * E-mail:
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15
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Taxonomic update on proposed nomenclature and classification changes for bacteria of medical importance, 2013-2014. Diagn Microbiol Infect Dis 2015; 83:82-8. [PMID: 26014276 DOI: 10.1016/j.diagmicrobio.2015.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 04/28/2015] [Indexed: 12/21/2022]
Abstract
A key aspect of medical, public health, and diagnostic microbiology laboratories is the accurate and rapid reporting and communications regarding infectious agents of clinical significance. Microbial taxonomy in the age of molecular diagnostics and phylogenetics causes changes in this taxonomy at a rapid rate further complicating this process. This review focuses on the description of new species and classification changes proposed over the past 2 years.
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16
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Goodfellow M, Sangal V, Jones AL, Sutcliffe IC. Charting stormy waters: A commentary on the nomenclature of the equine pathogen variously namedPrescottella equi,Rhodococcus equiandRhodococcus hoagii. Equine Vet J 2015; 47:508-9. [DOI: 10.1111/evj.12399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Goodfellow
- School of Biology; University of Newcastle; Newcastle upon Tyne UK
| | - V. Sangal
- Faculty of Health and Life Sciences; Northumbria University; Newcastle upon Tyne UK
| | - A. L. Jones
- Faculty of Health and Life Sciences; Northumbria University; Newcastle upon Tyne UK
| | - I. C. Sutcliffe
- Faculty of Health and Life Sciences; Northumbria University; Newcastle upon Tyne UK
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17
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Rhodococcus agglutinans sp. nov., an actinobacterium isolated from a soil sample. Antonie van Leeuwenhoek 2015; 107:1271-80. [DOI: 10.1007/s10482-015-0421-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 02/27/2015] [Indexed: 11/26/2022]
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18
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Li SH, Yu XY, Park DJ, Hozzein WN, Kim CJ, Shu WS, Wadaan MAM, Ding LX, Li WJ. Rhodococcus soli sp. nov., an actinobacterium isolated from soil using a resuscitative technique. Antonie van Leeuwenhoek 2014; 107:357-66. [PMID: 25417053 DOI: 10.1007/s10482-014-0334-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 11/14/2014] [Indexed: 10/24/2022]
Abstract
A Gram-positive, aerobic, non-motile, non-spore forming strain, designated DSD51W(T), was isolated using a resuscitative technique from a soil sample collected from Kyoto park, Japan, and characterized by using a polyphasic approach. The morphological and chemotaxonomic properties of the isolate were typical of those of members of the genus Rhodococcus. Strain DSD51W(T) was found to form a coherent cluster with Rhodococcus hoagii ATCC 7005(T), Rhodococcus equi NBRC 101255(T), Rhodococcus defluvii Call(T) and Rhodococcus kunmingensis YIM 45607(T) as its closest phylogenetic neighbours in 16S rRNA gene sequence analysis. However, the DNA-DNA hybridization values with the above strains were 58.2 ± 2.2, 58.4 ± 1.9, 45.1 ± 1.4 and 40.3 ± 4.7 %, respectively. In combination with differences in physiological and biochemical properties, strain DSD51W(T) can be concluded to represent a novel species of the genus Rhodococcus, for which the name Rhodococcus soli sp. nov. is proposed, with the type strain DSD51W(T) (=KCTC 29259(T) = JCM 19627(T) = DSM 46662(T) = KACC 17838(T)).
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Affiliation(s)
- Shan-Hui Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
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19
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Genomic analyses confirm close relatedness between Rhodococcus defluvii and Rhodococcus equi (Rhodococcus hoagii). Arch Microbiol 2014; 197:113-6. [PMID: 25410549 DOI: 10.1007/s00203-014-1060-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/03/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022]
Abstract
Rhodococcus defluvii strain Ca11(T) was isolated from a bioreactor involved in extensive phosphorus removal. We have sequenced the whole genome of this strain, and our comparative genomic and phylogenetic analyses confirm its close relatedness with Rhodococcus equi (Rhodococcus hoagii) strains, which share >80 % of the gene content. The R. equi virulence plasmid is absent though most of the chromosomal R. equi virulence-associated genes are present in R. defluvii Ca11(T). These data suggest that although R. defluvii is an environmental organism, it has the potential to colonize animal hosts.
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20
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Su X, Liu Y, Hashmi MZ, Hu J, Ding L, Wu M, Shen C. Rhodococcus biphenylivorans sp. nov., a polychlorinated biphenyl-degrading bacterium. Antonie van Leeuwenhoek 2014; 107:55-63. [DOI: 10.1007/s10482-014-0303-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/07/2014] [Indexed: 11/30/2022]
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21
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Giles C, Vanniasinkam T, Ndi S, Barton MD. Rhodococcus equi (Prescottella equi)vaccines; the future of vaccine development. Equine Vet J 2014; 47:510-8. [DOI: 10.1111/evj.12310] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 06/12/2014] [Indexed: 12/29/2022]
Affiliation(s)
- C. Giles
- School of Pharmacy and Medical Sciences; University of South Australia; Adelaide Australia
| | - T. Vanniasinkam
- School of Biomedical Sciences; Charles Sturt University; Wagga Wagga New South Wales Australia
| | - S. Ndi
- School of Pharmacy and Medical Sciences; University of South Australia; Adelaide Australia
| | - M. D. Barton
- School of Pharmacy and Medical Sciences; University of South Australia; Adelaide Australia
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22
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Kämpfer P, Dott W, Martin K, Glaeser SP. Rhodococcus defluvii sp. nov., isolated from wastewater of a bioreactor and formal proposal to reclassify [Corynebacterium
hoagii] and Rhodococcus equi as Rhodococcus hoagii comb. nov. Int J Syst Evol Microbiol 2014; 64:755-761. [DOI: 10.1099/ijs.0.053322-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, non-endospore-forming rod-shaped bacterium, strain Ca11T, was isolated from a bioreactor with extensive phosphorus removal and was studied in detail for its taxonomic allocation. 16S rRNA gene sequence analysis revealed closest sequence similarity of the strain to type strains of [
Corynebacterium hoagii
] and
Rhodococcus equi
(98.9 %),
Rhodococcus koreensis
and
Rhodococcus wratislaviensis
(both 98.4 %),
Rhodococcus opacus
and
Rhodococcus canchipurensis
(both 98.0 %) followed by
Rhodococcus kunmingensis
and
Rhodococcus imtechensis
(97.7 %). Phylogenetic trees showed a distinct clustering of strain Ca11T with the type strains of [
C. hoagii
],
R. equi
, and
R. kunmingensis
separate to all other species of the genus
Rhodococcus
. The quinone system of strain Ca11T was composed of dihydrogenated menaquinones with 8 (major amount) as well as 7 and 6 isoprenoid units [MK-8(H2), MK-7(H2), MK-6(H2)]. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, one unknown phospholipid and an unidentified glycolipid. The fatty acid profile was similar to that reported for
R. equi
and contained major amounts of C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0, supporting the allocation of the strain to the genus
Rhodococcus
. Physiological and biochemical characterization and DNA–DNA hybridization with type strains of the most closely related species allowed clear phenotypic and genotypic differentiation of the isolate. On the basis of these results, strain Ca11T ( = DSM 45893T = LMG 27563T) represents a novel species of the genus
Rhodococcus
, with the proposed name Rhodococcus defluvii sp. nov. In addition, a polyphasic taxonomic analysis of [
Corynebacterium hoagii
] DSM 20295T and
Rhodococcus equi
DSM 20307T indicated that the two strains belong to the same species, for which the name Rhodococcus hoagii comb. nov. takes priority, according to the Rules of the Bacteriological Code.
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Affiliation(s)
- P. Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - W. Dott
- Institut für Hygiene und Umweltmedizin, RWTH Aachen, Germany
| | - K. Martin
- Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V., Hans-Knöll-Institut, D-07745 Jena, Germany
| | - S. P. Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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23
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Sangal V, Jones AL, Goodfellow M, Sutcliffe IC, Hoskisson PA. Comparative genomic analyses reveal a lack of a substantial signature of host adaptation in Rhodococcus equi ('Prescottella equi'). Pathog Dis 2014; 71:352-6. [PMID: 24376240 DOI: 10.1111/2049-632x.12126] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/04/2013] [Accepted: 12/18/2013] [Indexed: 01/09/2023] Open
Abstract
Rhodococcus equi ('Prescottella equi') is a pathogenic actinomycete primarily infecting horses but has emerged as an opportunistic human pathogen. We have sequenced the genome of the type strain of this species, R. equi strain C7(T) , and compared the genome with that of another foal isolate 103S and of a human isolate ATCC 33707. The R. equi strains are closely related to each other and yet distantly related to other rhodococci and Nocardia brasiliensis. The comparison of gene contents among R. equi strains revealed minor differences that could be associated with host adaptation from foals to humans, including the presence of a paa operon in the human isolate, which is potentially involved in pathogenesis.
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Affiliation(s)
- Vartul Sangal
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK; Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
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24
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25
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Garrity GM. Conservation of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 and rejection of Corynebacterium hoagii (Morse 1912) Eberson 1918. Int J Syst Evol Microbiol 2014; 64:311-312. [DOI: 10.1099/ijs.0.059741-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A recent review of the nomenclatural history of
Rhodococcus equi
and its heterotypic synonyms reveals a situation in which the strict application of the Rules of the International Code of Nomenclature of Prokaryotes have resulted in the renaming of this known zoonotic pathogen, which may be reasonably viewed as a perilous name. This situation can be remedied only by the Judicial Commission rendering an opinion to conserve the name
Rhodococcus equi
and to reject its earlier heterotypic synonym,
Corynebacterium hoagii
.
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Affiliation(s)
- George M. Garrity
- Department of Microbiology and Molecular Genetics, Michigan State University, Biomedical and Physical Sciences Building, 567 Wilson Road, East Lansing, MI 48824, USA
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26
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Tindall BJ. The correct name of the taxon that contains the type strain of Rhodococcus equi. Int J Syst Evol Microbiol 2014; 64:302-308. [DOI: 10.1099/ijs.0.059584-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Based on a nomenclatural point of view, the name
Rhodococcus equi
is associated, as required by the Bacteriological Code, with a defined position, rank and circumscription. A search of the literature indicates that the name
Rhodococcus equi
(Magnusson 1923) Goodfellow and Alderson 1977 has also been shown to be a synonym of
Corynebacterium equi
Magnusson 1923,
Corynebacterium hoagii
(Morse 1912) Eberson 1918 and
Nocardia restricta
(Turfitt 1944) McClung 1974. Application of the rules of the Bacteriological Code together with the currently inferred taxonomic concept associated with the species bearing the name
Rhodococcus equi
indicates that this is not the correct name of this taxon and the use of that name in the context of a circumscription that includes the type strain of the species
Corynebacterium hoagii
is contrary to the Rules of the Code.
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Affiliation(s)
- B. J. Tindall
- Leibniz-Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7b, D-38124 Braunschweig, Germany
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