Reply to Weinberg, to Hughes, and to Limper

TO THE EDITOR—The opinion of Weinberg [1] that “It is disadvantageous ... to change the name ... ” (p. 1209), which was echoed by Limper [2], is a debatable point. On the basis of the available evidence and history of discovery [3–7], we disagree. The assertion by Hughes [8] that there has been inconsistency in the spelling of the new name is based on an incomplete understanding of the history of this issue. The species name “jiroveci” is the original spelling under the International Code of Zoological Nomenclature, which governed Pneumocystis nomenclature in 1976, when it was (incorrectly) considered to be a protozoon. The species name “jirovecii” is correct under the International Code of Botanical Nomenclature (ICBN) [9], under which we operate today [7]. Under either code, objecting to a name on the basis of pronunciation and spelling is irregular and ad hoc at best, and it seems frivolous when weighed against the scientific and historical issues that traditionally guide nomenclature decisions. Both Hughes [8] and Weinberg [1] refer to the ICBN, but neither appears to fully appreciate either the options or limitations offered by the ICBN or its role in the current controversy. Weinberg [1] clouds the issue by implying that the researcher Jírovec is not deserving of having the human pathogen, Pneumocystis jirovecii, named after him, an opinion earlier expressed by Hughes [10]. ICBN article 51.1 specifically rules out such arguments [9]. The statement by Hughes that “... there is no authoritative body to proclaim official approval of nomenclature for this fungus” [8, p. 1211] is not correct. Conservation of a name is a formal process involving publication in Taxon, votes by the Committee for Fungi, and finally, votes by the International Botanical Congress. If approved, the conserved name becomes part of the ICBN. Although they both advocate conservation, neither Hughes nor Weinberg (nor anyone else) has submitted a formal proposal. The debate came to the attention of the Committee for Fungi, and an informal preliminary research inquiry [7] revealed that P. carinii Delanoë and Delanoë 1912 [11], P. jirovecii Frenkel 1976 [12], and P. jirovecii Frenkel 1999 [13] were all invalid. Therefore, one of us (S.A.R.) asked the Committee for Fungi and International Botanical Congress at Vienna in 2005 to change ICBN article 45 to make an exception for fungi [14]. This change was made, thereby rendering valid the names P. carinii (from 1912), and P. jirovecii (from 1976, but not from 1999) [7]. In addition, we and Frenkel have selected (for both species) types reflecting their protologues and historical application and have discussed orthography and formae speciales names [7]. In addition to the validity and typifications of the names having been established, the Pneumocystis Working Group, convened to address such issues, has supported the recognition of multiple species and the application of the name P. jirovecii to the human pathogen [4–6]. Therefore, it is no surprise that ∼50 of the 80 or so articles that were published in the last 6 months of 2005 that used a species name to refer to human Pneumocystis referred to it as P. jirovecii (according to a PubMed search using “Pneumocystis” as the search term). This trend contradicts the statements of Hughes [2] and Limper [8], who both claim that the name P. jirovecii is unpopular. It is disappointing that Limper [2] and Weinberg [1] seem to think that no progress in taxonomy of Pneumocystis can be made because an in vitro system that sustains proliferation of these organisms is lacking. Contrary to this point of view, phylogenetics, which is an established mainstay of taxonomy that is particularly well suited to addressing questions pertaining to uncultivated microbes (such as those in the genus Pneumocystis), has made possible nearly all of the progress that has been made in understanding the complexity of this genus [3]. Limper [2] creates the false impression that Pneumocystis populations are all undefined and ill understood. In fact, we have demonstrated that one can understand the reasons for variation among these populations through DNA sequence analysis. For example, studies by us and our colleagues [15, 16] have identified 2 species that infect laboratory rats. Some rats carry P. carinii only, whereas others carry both P. carinii and Pneumocystis wakefieldiae. This being the case, investigators who define the microbes that they obtain from rats simply by virtue of the fact that they came from rats run the risk of ascribing characteristics to P. carinii that are actually attributable to P. wakefieldiae (and vice versa). To find an illustration of a probable erroneous attribution of a P. wakefieldiae gene to P. carinii, we need look no farther than the study [17] cited by Limper [2] in support of his point about variation among populations of rat-derived Pneumocystis. Our analysis of the data in that article [17] suggests that the cdc2 cDNA described was from P. carinii, but the cdc2 gene described was from P. wakefieldiae. Thus, the “considerable genetic sequence diversity” [2, pg. 1210) that Limper observed in the cdc2 sequences reported by Thomas et al. [17] is not necessarily indicative of variation within P. carinii, and it likely reflects the diversity between P. carinii and P. wakefieldiae. The origin of the cdc2 gene described by Thomas et al. [17] awaits clarification, which can be easily accomplished by direct analysis of the P. wakefieldiae genome. However, these data focus attention on the possibility of a mistaken attribution of a gene from one species to another, a hazard that stems from performing studies involing organisms that are solely defined by their source. Limper [2] questions whether human-derived Pneumocystis truly represents a single unique species. The citation he provides in support of this query does not raise this question [18] but instead describes patient samples that exhibit far less genetic divergence than that between P. carinii and P. wakefieldiae; this is a result that has been reported hundreds of times. It is encouraging to see him acknowledge the possibility of multiple species of human Pneumocystis. This acknowledgement raises another question, however. What will these species be called? Obviously, they could not all be called P. carinii. Potential conflicts of interest. All authors: no conflicts.

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