Reply to Kidd et al., “New Names for Fungi of Medical Importance: Can We Have Our Cake and Eat It Too?”

Abstract

We are grateful to Dr Kidd and her colleagues for the sensible and supportive stance adopted in their letter (1) in reply to our recent manuscript summarising proposed name changes for fungi of medical importance (2), and for offering voices of reason in the heated Twitter exchanges that ensued following the publication of said taxonomy update.…

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Reply to Kidd et al., “New Names for Fungi of Medical
Importance: Can We Have Our Cake and Eat It Too?”
Andrew M. Borman,
a,b
Elizabeth M. Johnson
a,b
a
UK National Mycology Reference Laboratory, Public Health England South-West, Bristol, United Kingdom
b
Medical Research Council Centre for Medical Mycology (MRC CMM), University of Exeter, Exeter, United Kingdom
We are grateful to Dr. Kidd and her colleagues for the sensible and supportive
stance adopted in their letter (1) in reply to our recent manuscript summarizing
proposed name changes for fungi of medical importance (2), and for offering voices of
reason in the heated Twitter exchanges that ensued following the publication of said
taxonomy update. Since neither author of the original manuscript is particularly active
on social media, we only became aware of the resultant Twitter maelstrom after alerts
from colleagues overseas. Like Kidd et al., we were surprised by some predictions
warning of impending patient harm if such names were adopted, and the implicit sug-
gestion in several Tweets that clinicians might ignore reports of isolation of an orga-
nism if it was one that they had not previously encountered.
As Kidd et al. pointed out in their reply to our original nomenclatural update,
nomenclatural changes are not new to mycology, and thousands have been intro-
duced, and accepted by the medical community over recent decades. To the example
of Cryptococcus neoformans (formerly Torula histolytica) cited by Kidd et al., one could
also question who now would refer to Candida albicans as “Monilia albicans,”which
was still in use by some of the old school when we started our careers, as was the dis-
ease name “moniliasis”in place of candidiasis (or more correctly candidosis)? Who
would refer to Candida glabrata (now Nakaseomyces glabrata)as“Torulopsis glabrata”
which many were fighting to retain late into the 1990s? As we explained in the original
update, and as echoed by Kidd et al., the potential for taxonomic and clinical confusion
engendered by such changes has always been successfully managed in the past by re-
petitive iteration of the new name together with the most recent previous incarnation,
and this is the approach that we have suggested that laboratories continue to adopt
with future taxonomic revisions.
While it is reassuring that a number of highly respected mycology reference labora-
tories worldwide have also chosen to implement these long-overdue changes and
drip-feed them to their users, we share the disappointment of Kidd et al. that the
recent reference document updates from both the Clinical and Laboratory Standards
Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing
(EUCAST) continue to refer to all “Candida”species by their previous (now often obso-
lete) names (3, 4). As pointed out in the update, and restated by Kidd et al., medical
mycologists have accepted for decades that the genus “Candida”is an artificial and
highly heterogeneous construct, containing species from dozens of extremely unre-
lated teleomorph genera. What was largely ignored in the social media outcry that fol-
lowed the recent taxonomic update (presumably because a significant proportion of
those offended by the suggestions had not read the full update and references) is that
many of the proposed changes are neither recent nor novel. For example, the genus
Clavispora was erected in 1979 with Clavispora lusitaniae (ex-Candida lusitaniae) as the
type strain on the basis of sexual compatibility studies (5). Similarly, Candida krusei was
reassigned to the genus Pichia in 2008 based on comprehensive phylogenetic analyses
Citation Borman AM, Johnson EM. 2021. Reply
to Kidd et al., “New names for fungi of medical
importance: can we have our cake and eat it
too?”J Clin Microbiol 59:e02896-20. https://doi
.org/10.1128/JCM.02896-20.
Editor Alexander J. McAdam, Boston Children’s
Hospital
©Crown copyright 2021. The government of
Australia, Canada, or the UK (“the Crown”)
owns the copyright interests of authors who
are government employees. The Crown
Copyright is not transferable.
Address correspondence to Andrew M.
Borman, Andy.Borman@nbt.nhs.uk.
This is a response to a letter by Kidd et al.
https://doi.org/10.1128/JCM.02730-20.
Accepted manuscript posted online 2
December 2020
Published 18 February 2021
March 2021 Volume 59 Issue 3 e02896-20 Journal of Clinical Microbiology jcm.asm.org 1
AUTHOR REPLY

(6) and formally shown to be indistinguishable from P. kudriavzevii by whole-genome
sequence analyses in 2018 (7). Although some commercial identification platforms and
databases are slow in update implementation, genetic databases are much more up-
to-date. As an example of such, a BLASTN nucleotide alignment of GenBank sequence
KC601852 (which corresponds to the rDNA genes of the type strain of Candida krusei
ATCC 6258) against the public synchronized databases retrieves .1,000 highly scoring
hits, all matching isolates named as Pichia kudriavzevii. Thus, the recent taxonomic
update attempted to summarize all such proposals/taxonomic reaffiliations in a single
place, as sooner or later the wider medical mycology community and the clinicians
that this community serves will be confronted by them.
The fact that Candida krusei has now been properly reclassified as a Pichia species
makes perfect sense when you realize that many Pichia species are fluconazole resist-
ant, unlike most true Candida species. Equal clarity should also come from the reclassi-
fication of Candida glabrata as Nakaseomyces glabrata and many of the other sug-
gested changes as the underlying taxonomic relationships become more apparent.
These changes may seem unnecessarily complicated and unfamiliar now but are well
supported by genomic analyses and will help to predict expected antifungal suscepti-
bility profiles and many other phenotypic characteristics. We should of course for
many years continue to refer to the old name in parentheses, until the next generation
of physicians, infectious disease specialists, microbiologists, and mycologists become
familiar with the new taxonomy. Change is often challenging but when it leads ulti-
mately to greater clarity and understanding of the genotypic and phenotypic interre-
latedness of the mycological world and its patient interface, it should be embraced as
a helpful development and not dismissed as an irrelevant nuisance dreamt up by taxo-
nomists to enable mycologists to maintain their professional mystique.
REFERENCES
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Microbiol 59:e02730-20. https://doi.org/10.1128/JCM.02730-20.
2. Borman AM, Johnson EM. 2020. Name changes for fungi of medical impor-
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JCM.01811-20.
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Author Reply Journal of Clinical Microbiology
March 2021 Volume 59 Issue 3 e02896-20 jcm.asm.org 2