Pearls
`
`Emerging and Emerged Pathogenic Candida Species:
`Beyond the Candidaalbicans Paradigm
`
`Nicolas Papon1*, Vincent Courdavault1, Marc Clastre1, Richard J. Bennett2
`
`1 Universite´ Franc¸ois-Rabelais de Tours, EA2106, Biomole´cules et Biotechnologies Ve´ ge´ tales, Tours, France, 2 Department of Microbiology and Immunology, Brown
`University, Providence, Rhode Island, United States of America
`
`Candidaalbicans and Non-albicansCandida (NAC)
`Species Infections: General Information in
`Predisposing Conditions and Clinical Incidence
`
`Many ascomycete yeast species from the Candida genus are
`widely distributed in nature and act as common saprophytic
`constituents of the normal human microflora. However, some of
`these fungal species can also become opportunistic pathogens
`following a transition from a commensal to a pathogenic phase,
`induced by alterations in the host environment. Candida species
`thereby rarely trigger infection in healthy people, but
`take
`advantage of a locally or systematically impaired immune system
`to proliferate in the host and cause diseases termed ‘‘candidiasis.’’
`Such fungal infections can be subdivided into three major groups:
`cutaneous (skin and its appendages), mucosal
`(oropharyngeal,
`esophageal, and vulvovaginal) and systemic (bloodstream infec-
`tions,
`i.e., candidemia and other forms of invasive candidiasis
`[IC]). While superficial candidiasis (cutaneous and mucosal)
`is
`often observed in AIDS patients, oropharyngeal
`thrush and
`vaginitis are more frequently seen in immunocompetent infants
`and adult women, respectively. Candidemia and IC are common
`in cancer patients or in transplant individuals following immuno-
`suppression. Candidiasis currently represents the fourth leading
`cause of nosocomial infections, at 8% to 10%, and mortality due to
`systemic candidiasis remains high, ranging from 15% to 35%
`depending on the infecting Candida species [1].
`Although Candida albicans remains the most frequently isolated
`agent of candidiasis, non-albicans Candida (NAC) species now
`account
`for a substantial part of clinical
`isolates collected
`worldwide in hospitals. NAC species of particular clinical
`importance include Candida glabrata, Candida tropicalis, Candida
`parapsilosis, and Candida krusei
`(synonym: Issatchenkia orientalis), as
`well as the less-prominent species Candida guilliermondii, Candida
`lusitaniae, Candida kefyr, Candida famata (synonym: Debaryomyces
`hansenii), Candida inconspicua, Candida rugosa, Candida dubliniensis,
`and Candida norvegensis (Table 1). A complementary set of about 20
`opportunistic NAC species is also known, but exhibits lower
`isolation rates [2].
`
`Trends in Species Distribution and Antifungal
`Susceptibility of NAC Species
`
`Global surveillance programs (e.g. SENTRY and ARTEMIS)
`provide a tremendous amount of data regarding global trends in
`various aspects of NAC candidiasis
`including geographical
`variation in the frequency of species, distribution by specimen
`type and patient age, as well as changes in the antifungal
`susceptibility of collected NAC isolates [2].
`four decades
`An overview of
`the literature from the last
`highlights an important fact: Due to the growing size of the
`population at special risk (due to neutropenia, immunosuppres-
`sion, metabolic dysfunction, and anticancer chemotherapy),
`candidiasis remains a persistent public health problem, and the
`
`proportion of NAC species among Candida isolates recovered from
`patients is increasing. Whereas NAC species accounted for 10%–
`40% of all systemic candidiasis from 1970 to 1990, this proportion
`reached 35%–65% in the last two decades [3]. A recent ten-year
`analysis of the worldwide distribution of NAC species indicated
`that C. glabrata remains the most common NAC species and that C.
`parapsilosis, C. tropicalis, and C. krusei are also frequently isolated
`(Table 1). C. guilliermondii and C.
`lusitaniae have shown gradual
`emergence as a cause of invasive candidiasis, while C. kefyr, C.
`famata, C.
`inconspicua, C. rugosa, C. dubliniensis, and C. norvegensis,
`although rarely isolated, are now considered emerging NAC
`species, as their isolation rate has increased between 2- and 10-fold
`over the last 15 years [2].
`Interestingly, significant geographic variation in the frequency
`of NAC species occurs. Among marked trends, C. glabrata is more
`prominent in North America than in Latin America. In addition,
`C.
`tropicalis is frequently isolated in Asia-Pacific and less often
`encountered in the rest of the world, whilst C. parapsilosis remains
`3-fold more commonly recovered in North America than in
`Europe. Finally, C. guilliermondii and C. rugosa are more prominent
`in Latin America, and C. inconspicua and C. norvegensis in Europe [2]
`than in the rest of the world.
`Antifungal compounds currently used to treat systemic candi-
`diasis belong to three families: polyenes, azoles, and echinocan-
`dins. Most of the NAC species exhibit particular patterns of
`primary resistance or reduced susceptibility toward these antifun-
`gals (Table 1). For example, a high level of resistance toward azoles
`is well known for C. krusei, C. inconspicua, C. rugosa, and C. norvegensis,
`whereas C. parapsilosis and C. guilliermondii stand out due to their
`decreased susceptibility to echinocandins [4].
`
`A Particular Codon Usage in Most NAC Species
`Delays Development of Genetic Tools
`
`Since the end of the last century, the clinical importance of NAC
`species has promoted research aimed at identifying molecular
`events underlying pathogenicity and antifungal resistance in these
`emerging yeasts. However, the development of genetic approaches
`
`Citation: Papon N, Courdavault V, Clastre M, Bennett RJ (2013) Emerging and
`Emerged Pathogenic
`Candida
`Species:
`Beyond the Candida
`albicans
`Paradigm. PLoS Pathog 9(9): e1003550. doi:10.1371/journal.ppat.1003550
`
`Editor: Joseph Heitman, Duke University Medical Center, United States of
`America
`
`Published September 26, 2013
`Copyright: ß 2013 Papon et al. This is an open-access article distributed under
`the terms of
`the Creative Commons Attribution License, which permits
`unrestricted use, distribution, and reproduction in any medium, provided the
`original author and source are credited.
`
`Funding: The authors received no specific funding for this study.
`
`Competing Interests: The authors have declared that no competing interests
`exist.
`
`* E-mail: nicolas.papon@univ-tours.fr
`
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`Selectablemarkers,Reportergenes,Regulatablesystems
`
`Available
`
`Diploid
`
`ND
`
`Selectablemarkers
`
`Selectablemarkers,Reportergenes
`
`Selectablemarkers
`
`Selectablemarkers
`
`Selectablemarkers,Reportergenes
`
`Selectablemarkers,Reportergenes,Regulatablesystems
`
`Selectablemarkers,Reportergenes
`
`Selectablemarkers,Reportergenes,Regulatablesystems
`
`Selectablemarkers,Reportergenes,Regulatablesystems
`
`Haploid
`
`ND
`
`Available
`
`Haploid
`
`Available
`
`ND
`
`Available
`
`Haploid
`
`Available
`
`Haploid
`
`Available
`
`Diploid
`
`Available
`
`Diploid
`
`Available
`
`Diploid
`
`Available
`
`Haploid
`
`Available
`
`Diploid
`
`+
`
`2
`
`+
`
`2
`
`+
`
`+
`
`+
`
`+
`
`+
`
`+
`
`2
`
`+
`
`+
`
`Yeast,Pseudohyphae
`
`Moleculartoolsavailableg
`
`PloidyeGenomesequencef
`
`Sex.d
`
`Morphologyc
`
`doi:10.1371/journal.ppat.1003550.t001
`gfromreferences[5,10].
`ffromreferences[19,21–24].
`efromreference[21].
`dfromreference[6],Sex.:sexualorparasexualreproduction;ND:unknown.
`cfromreference[14].
`bfromreference[1],(+++):strongprimaryresistance;(+):moderateprimaryresistance;(R+++):strongsecondaryresistance(acquired).
`afromreference[2],Freq.:frequencyofisolation(range).
`
`Yeast,Pseudohyphae
`
`Yeast,Pseudohyphae,Hyphae
`
`Yeast,Pseudohyphae
`
`Yeast,Pseudohyphae
`
`Yeast,Pseudohyphae
`
`Yeast,Pseudohyphae
`
`Yeast,Pseudohyphae
`
`Yeast,Pseudohyphae
`
`Yeast,Pseudohyphae
`
`Yeast,Pseudohyphae
`
`Yeast,Pseudohyphae,Hyphae
`
`Yeast,Pseudohyphae,Hyphae
`
`Polyenes(+++),Azoles(+++)
`Azoles(+++)
`Azoles(+)
`
`Polyenes(R+++)
`Echinocandins(+),Azoles(+)
`Polyenes(+),Azoles(+++)
`Echinocandins(+)
`
`Polyenes(+),Azoles(+)
`
`Azoles(+++)
`
`0.1%(0.02–0.1)
`
`0.1%(0.1–0.2)
`
`0.2%(0.1–1)
`
`0.2%(0.1–0.5)
`
`6.0%(4–14)
`
`7.2%(5–13)
`
`11.3%(7–21)
`
`63.8%(49–68)
`
`Resistanceb
`
`Freq.a
`
`0.3%(0.1–0.5)
`
`C.famata(D.hansenii)
`
`0.5%(0.3–0.6)
`
`C.kefyr(K.marxianus)
`
`0.6%(0.5–0.6)
`
`0.7%(0.1–2)
`
`C.lusitaniae
`
`C.guilliermondii
`
`2.4%(1–4)
`
`C.krusei(I.orientalis)
`
`C.norvegensis
`
`C.dubliniensis
`
`C.rugosa
`
`C.inconspicua
`
`C.parapsilosis
`
`C.tropicalis
`
`C.glabrata
`
`C.albicans
`
`Species
`
`Table1.IntroducingcharacteristicsofCandidaspecies.
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`in NAC species has been hindered by three main factors: (i) most
`pioneering studies during the early stages of the ‘‘pathogenic yeast
`genetics’’ field were carried out in C. albicans; (ii) the particular codon
`usage of most of Candida species has precluded the direct use of S.
`cerevisiae or bacterial molecular tools in these NAC species [5]; (iii)
`most pathogenic Candida species have limited modes of sexual
`reproduction unlike S. cerevisiae [6].
`Originally, the genus name Candida was attributed to yeast
`species able to form hyphae or pseudohyphae (Table 1) and for
`which no sexual
`spores were observed. Nevertheless, recent
`phylogenetic analysis has clarified that Candida species actually
`represent a polyphyletic group within the Saccharomycotina [7]
`(Figure 1). More precisely, C.
`tropicalis, C.
`parapsilosis, C.
`guilliermondii, C.
`lusitaniae, C. famata, C. rugosa, and C. dubliniensis
`form part of the Candida CTG clade and translate CTG codons as
`serine instead of leucine. In contrast, C. glabrata and C. kefyr belong
`to the Saccharomycetaceae, with C. glabrata and S. cerevisiae falling
`within the whole genome duplication (WGD) clade. The
`remaining species C. krusei, C.
`inconspicua, and C. norvegensis are
`probably closely related in the Saccharomycetaceae clade, which
`could give insights into their common resistance toward azole
`antifungals.
`During the late 1990s, C. glabrata genetics was by far the most
`advanced of the NAC species due to its haploid status, its classical
`codon usage (allowing the direct use of S. cerevisiae tools), and its
`high frequency of isolation in hospitals [8]. Genetic studies of
`CTG clade species expanded in the 2000s and focused on the
`development of molecular
`tools, as well as
`transformation
`procedures, due to the biotechnological potential of
`several
`Candida yeasts (C. guilliermondii, C. famata, C. tropicalis, and C. rugosa)
`as well as clinical incidence (C. dubliniensis and C. parapsilosis) [5,9].
`Specifically, drug-resistant markers and reporter genes (encoding
`fluorescent protein variants, luciferase, or beta-galactosidase) were
`adapted by changing CTG codons to allow their functionality in
`this particular clade [5] (Table 1).
`
`Figure 1. Schematic representation illustrating the phylogeny
`of NAC species. C. tropicalis, C. parapsilosis, C. guilliermondii, C.
`lusitaniae, C. famata (D. hansenii), C. rugosa, and C. dubliniensis form part
`of the Candida CTG clade and translate CTG codons as serine instead of
`leucine. In contrast, C. glabrata and C. kefyr (K. marxianus) belong to the
`Saccharomycetaceae, with C. glabrata and S. cerevisiae falling within the
`‘‘whole genome duplication’’ (WGD) clade. The remaining species C.
`krusei (I. orientalis), C.
`inconspicua, and C. norvegensis are probably
`closely related in the Saccharomycetaceae clade. The branch lengths
`are arbitrary.
`doi:10.1371/journal.ppat.1003550.g001
`
`Mechanisms Underlying Antifungal Resistance,
`Virulence, and Morphological Transitions in NAC
`Species: Is Candidaalbicans the Rule or the
`Exception?
`
`C. albicans genetics, with the construction and phenotypical
`analysis of targeted mutant strains since 1994, has provided a
`foundation for understanding fundamental processes in pathogenic
`yeasts [10]. Intense research in C. albicans from the end of the 20th
`century shed light on the molecular mechanisms involved in drug
`resistance [11], biofilm formation [12], adherence [13], yeast-
`hyphal switching and its role in virulence [14], and sexual mating
`[15,16]. C. albicans has therefore become the model yeast for
`investigating the multiple factors controlling the host–pathogen
`interaction. As a result, C. albicans biology is now the paradigm for
`Candida research in the medical mycology community.
`In response to the clinical emergence of NAC species, research
`programs were initiated to further understand these opportunistic
`yeasts. The first studies highlighted marked differences in behavior
`between different Candida species. This included stress adaptation
`[17], which may come from the fact
`that each species has
`independently evolved to promote survival
`in their respective
`natural niches and their specific host. It must also be kept in mind
`that each Candida species displays specific traits such as ploidy,
`sexual behavior (if any) [6], and morphology [14] (Table 1). These
`could directly impact their ability to adapt to the host’s response,
`to disseminate in the organism, and to develop resistance
`mechanisms to antifungals during treatments.
`Due to the lack of genetic and molecular resources, researchers
`have often assumed that if a yeast species is related to another
`yeast species, the underlying molecular and cellular mechanisms
`must also be closely related. However, even within a clade, the
`genetic distance between any two NAC species is often larger than
`the genetic distance between humans and some fishes [18].
`Therefore, in no way should it be argued that C. albicans makes the
`rules for all NAC species. As a corollary, in future investigations,
`the biology of each Candida species should continue to be addressed
`on a case-by-case basis.
`
`Perspectives: Genome Resources and
`Postgenomic Technologies Dedicated to NAC
`
`A large range of rapidly evolving genomic and postgenomic
`approaches,
`including genome sequences and gene expression
`data, have recently enhanced the understanding of Candida yeasts
`pathogenicity.
`The first published genomes of Candida species were C. glabrata
`in 2003 (alongside the C. famata genome sequence) [19], followed
`by C. albicans [20] in 2004, which has further strengthened the
`prominent role of C. albicans and C. glabrata in the field. In January
`2005, the Broad Institute Fungal Genome Initiative, in collabo-
`ration with the Wellcome Trust Sanger Institute, made available
`the sequences of five CTG clade genomes, including C. tropicalis, C.
`parapsilosis, C. dubliniensis, C. guilliermondii, and C. lusitaniae [21,22].
`Finally, genome sequences of C. kefyr (teleomorph Kluyveromyces
`marxianus) [23] and C. krusei [24] were recently published. These
`genome resources have provided new insights into gene family
`evolution within Candida species and identified gene families
`enriched in the most common pathogenic NAC species [21]. This
`area of research is further supported by the creation of databases
`dedicated to genome annotation,
`including gene ontology
`browsers
`specializing in metabolic pathways, virulence, and
`morphogenesis
`[25]. These bioinformatics
`tools provide an
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`accurate annotation of NAC genome sequences and give precious
`help to future Candida gene evolutionary analyses.
`Postgenomic technologies have also emerged to support the
`Candida research field. Quantitative transcriptional profiling
`strategies (e.g. RNA-Seq, microarray) currently allow the active
`screening of genes commonly or
`specifically required for
`pathogenicity, morphogenesis, and antifungal resistance in multi-
`ple Candida species [26–28].
`Thanks to the growing number of yeast genome sequences
`available, as well as the utilization of postgenomic approaches,
`the palette of newly identified pathogenicity-related genes in
`NAC species is now predicted to increase rapidly. However,
`efforts need to continue toward the development of classical
`
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