Equine Veterinary Journal ISSN 0425-1644 DOI: 10.1111/evj.12399

Charting stormy waters: A commentary on the nomenclature of the equine pathogen variously named Prescottella equi, Rhodococcus equi and Rhodococcus hoagii To those not working in the field, the discipline of microbial systematics (which encompasses classification, nomenclature and identification) can appear arcane and its practitioners pedantic. However, systematics is a fundamental scientific discipline, not least as it provides the bedrock for diagnostic microbiology and allows scientists to communicate unambiguously. Nevertheless, challenging problems occasionally arise that test both taxonomists (seeking to provide clarity and order) and the patience of the wider scientific community. The nomenclatural history of Rhodococcus equi is one such problem and so here we hope to clarify recent developments with regard to the nomenclature of this taxon. First it is necessary to briefly explain some concepts regarding the nomenclature of prokaryotes, which is governed by the principles and rules of the International Code of Nomenclature of Prokaryotes (‘the Code’; [1]). Principle 6 of the Code states that ‘the correct name of a taxon is based upon valid publication, legitimacy, and priority of publication’ (see Box 1). In turn, Principle 5 of the Code states that ‘the application of the names of taxa is determined by means of nomenclatural types’. The type strains of bacterial species are permanent living embodiments of validly named species that have to be deposited in two service culture collections in different countries, so that they are readily available for study. Implementation of the Code is overseen by the International Committee for Systematics of Prokaryotes (ICSP). Legitimate names (Box 1) conform to the Code, while valid names are those included in the Approved Lists of Bacterial Names [2] or its subsequent updates, including the Notification and Validation Lists that are regularly published on behalf of the ICSP in the International Journal of Systematic and Evolutionary Microbiology (IJSEM). Names omitted from the Approved Lists of Bacterial Names [2] lost their standing in nomenclature, a development that at a stroke swept away thousands of meaningless names and brought order to the nomenclature of prokaryotes.

Another fine mess . . . The original classification and naming of the equine pathogen that veterinarians and researchers now most commonly refer to as Rhodococcus equi was made by Magnusson, with the description of Corynebacterium equi Magnusson 1923. After several decades of taxonomic confusion, during which time multiple alternative names circulated (e.g. Nocardia restricta), stability was achieved with the

reclassification of the bacterium in the genus Rhodococcus as R. equi [3]. Importantly, the name R. equi was included in the Approved Lists of Bacterial Names [2]. However, subsequent to the work of Goodfellow and Alderson [3], it became apparent that the type strain of R. equi should be classified in the same species as the type strain of Corynebacterium hoagii (Morse 1912; Eberson 1918: reviewed in [4]). That R. equi and C. hoagii are indeed the same species was confirmed by Kämpfer et al. [5] and is also supported by our analyses of the genomes of the type strains of each (unpublished data). The type strain of C. hoagii was isolated and classified by Morse in 1912 and the name was also included in the Approved Lists of Bacterial Names. Thus, according to the rules of the Code, both C. hoagii and R. equi are valid names but the species epithet hoagii (1912) has priority over equi (1923). In recognition of this, a formal proposal for the reclassification of R. equi as Rhodococcus hoagii was made [5] and this name has been validated by inclusion in a Notification List [6].

You couldn’t make it up . . . Aside from the issue of the correct species epithet, additional complications have arisen regarding the genus name. Firstly, we have proposed the reclassification of R. equi into a novel genus, Prescottella, as Prescottella equi comb. nov [7,8]. Although some in the ‘R. equi community’ are reluctant to accept this proposal, the reclassification is well supported by molecular, phylogenetic and numerical taxonomic data [7] and so stands as a well justified ‘taxonomic opinion’. However, in 2013 we agreed, following correspondence with the then Chair of the ICSP and the Editor of IJSEM, not to request the validation of the names Prescottella and Prescottella equi until the issue of the correct species epithet (equi vs. hoagii) was resolved (see below). Secondly, Tindall [9] has recently established that the genus name Rhodococcus Zopf 1891 is itself illegitimate because it is a later synonym of the algal genus name Rhodococcus Hansgirg 1884 (which therefore has priority). Although there are confounding taxonomic arguments about the status of the algal genus name Rhodococcus Hansgirg 1884, these remain secondary until the classification of this algal taxon is formally resolved by algal taxonomists. Thus currently, and for the foreseeable future, neither R. equi nor R. hoagii can be considered legitimate bacterial names as the bacterial name Rhodococcus is illegitimate and so, according to the Code, should not be used.

BOX 1: Definitions of relevance to bacterial nomenclature

Is there light at the end of the tunnel?

Correct name: the valid, legitimate name for a taxon. Effectively published name: a name that has been proposed in a generally available publication format but which has not been validated (see Valid name). Illegitimate name: a name that contravenes the rules of the International Code of Nomenclature of Prokaryotes. Legitimate name: a name that conforms to the rules of the International Code of Nomenclature of Prokaryotes. Nomenclatural Type: For prokaryotic species, a type strain (which need not be the most typical or representative strain) deposited in recognised culture collections and to which the species name is permanently associated. Priority: if two names compete for priority and if both names date from 1 January 1980 on an Approved List, the priority shall be determined by the date of the effective publication of the name before 1 January, 1980 (Rule 24b of the Code). Valid name: a name that has been included in the Approved Lists of Bacterial Names [2] or a subsequent Notification or Validation List.

The problematic matter of the priority of the species epithet hoagii over equi has been addressed by Garrity [10]. Taxonomic practice allows that ‘When strict adherence to the Rules of bacteriological nomenclature would only produce chaos or would not result in nomenclatural stability, exceptions to the Rules may be requested of the Judicial Commission of the ICSP’ (IJSEM, http://ijs.sgmjournals.org/site/misc/ifora.xhtml). Garrity [10] presented just such a ‘Request for an Opinion’ (RfaO) i.e. to conserve the well-established species epithet equi. The Code indicates that the Judicial Commission should rule on a RfaO, considering any appeals or comments submitted in response to the RfaO, after (i.e. not less than) 12 months following the date of publication (January 2014 in this case [10]). Regrettably it seems likely to be some time before the Judicial Commission will rule – the most recent Opinion (No. 96) was published in October 2014 following an RfaO published in 2007 and nine RfaO predating that of Garrity [10] are currently awaiting Opinions. If the Judicial Commission rules in favour of the species epithet equi (as we hope), then this will allow us to request the formal validation of the name Prescottella equi. As we can see no obvious reason why this request would not be approved, we would therefore expect that the name would

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Update on the nomenclature of Rhodococcus equi

M. Goodfellow et al.

then be added to the Approved Lists of Bacterial Names by inclusion in a Validation List. If this happens, Prescottella equi will become the only valid and legitimate name for the taxon i.e. the correct name. This should, at last, allow nomenclatural stability and consequently we hope that, in this circumstance, clinicians and scientists working on this taxon will adopt the name P. equi. As the scientific community readily adapted to the reclassification of C. equi as R. equi, we would hope for a similar response in future with respect to the reclassification of R. equi as P. equi. If the Judicial Commission rules in favour of the species epithet hoagii, then we will have to formally propose the new combination Prescottella hoagii comb. nov. This name would then be submitted for validation and, assuming it is approved, it would become the correct (i.e. valid and legitimate) name for the taxon. Although this would also provide a stable nomenclature, we hope that this is not the outcome as we recognise and support the understandable desire of the veterinary community to retain the direct link between the name of the bacterial species and its most important attribute i.e. as an equine pathogen. As noted above, resolution of this vexing nomenclatural problem is thus dependent on the ruling from the Judicial Commission on the Garrity RfaO [10]. We hope that this will be sooner rather than later. In the meantime, the taxon is regrettably left without a valid, legitimate name (Box 2) and so we would recommend the veterinary community describe this bacterium

BOX 2: The current formal status of names relevant to this commentary Corynebacterium equi Magnusson 1923: a validly published name considered to be a synonym of Rhodococcus equi. Prescottella equi (Magnusson 1923) Jones et al. 2013: an effectively published but currently illegitimate name, as the species epithet hoagii has priority over equi; if eventually validated, will become the only validly published and legitimate name for the taxon. Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977: a validly published name rendered illegitimate as the species epithet hoagii has priority over equi. Also problematic as the bacterial genus name Rhodococccus Zopf 1891 is illegitimate. Rhodococcus hoagii (Morse 1912) Kämpfer et al. 2014: a validly published name, currently the correct name of the taxon but rendered problematic as the bacterial genus name Rhodococccus Zopf 1891 is illegitimate.

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as Rhodococcus equi (Rhodococcus hoagii/Prescottella equi) at first usage in any publications. All three names could also be added as keywords. For full details of the taxonomic and nomenclatural arguments reviewed here, interested readers are referred to the scholarly taxonomic notes written by Tindall [4,9]. M. Goodfellow, V. Sangal†, A. L. Jones† and I. C. Sutcliffe† School of Biology, University of Newcastle, Newcastle upon Tyne, UK † Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK.

References 1. Lapage, S.P., Sneath, P.H.A., Lessel, E.F., Skerman, V.B.D., Seeliger, H.P.R. and Clark, W.A. (1992) International Code of Nomenclature of Bacteria (1990 Revision). American Society for Microbiology, Washington, DC. 2. Skerman, V.B.D., McGowan, V. and Sneath, P.H.A. (1980) Approved lists of bacterial names. Int. J. Syst. Bacteriol. 30, 225-420. 3. Goodfellow, M. and Alderson, G. (1977) The actinomycete-genus Rhodococcus: a home for the ‘rhodochrous’ complex. J. Gen. Microbiol. 100, 99-122. 4. Tindall, B.J. (2014) The correct name of the taxon that contains the type strain of Rhodococcus equi. Int. J. Syst. Evol. Microbiol. 64, 302-308. 5. Kämpfer, P., Dott, W., Martin, K. and Glaeser, S.P. (2014) 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. 64, 755-761. 6. Oren, A. and Garrity, G. (2014) Notification that new names of prokaryotes, new combinations and new taxonomic opinions have appeared in volume 64, part 3, of the IJSEM. Int. J. Syst. Evol. Microbiol. 64, 1827-1829. 7. Jones, A.L., Sutcliffe, I.C. and Goodfellow, M. (2013) Prescottia equi gen. nov., comb. nov.: a new home for an old pathogen. Antonie Van Leeuwenhoek 103, 655-671. 8. Jones, A.L., Sutcliffe, I.C. and Goodfellow, M. (2013) Proposal to replace the illegitimate genus name Prescottia Jones et al. 2013 with the genus name Prescottella gen. nov. and to replace the illegitimate combination Prescottia equi Jones et al. 2013 with Prescottella equi comb. nov. Antonie Van Leeuwenhoek 103, 1405-1407. 9. Tindall, B.J. (2014) A note on the genus name Rhodococcus Zopf 1891 and its homonyms. Int. J. Syst. Evol. Microbiol. 64, 1062-1064. 10. Garrity, G.M. (2014) Conservation of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 and rejection of Corynebacterium hoagii (Morse 1912) Eberson 1918. Int. J. Syst. Evol. Microbiol. 64, 311-312.

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Charting stormy waters: A commentary on the nomenclature of the equine pathogen variously named Prescottella equi, Rhodococcus equi and Rhodococcus hoagii.

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