Development and characterization of complex DNA fingerprinting probes for the infectious yeast Candida dubliniensis

Population structure and molecular genetic characterization of 5-flucytosine-susceptible and -resistant clinical Candida dubliniensis isolates from Kuwait

Candida dubliniensis and Candida albicans are two closely related species. Although C. dubliniensis is less pathogenic, it has a higher propensity to develop resistance to fluconazole and some strains exhibit intrinsic resistance to 5-flucytosine (5-FC). All 5-FC-resistant isolates from Kuwait were previously shown to belong to one of seven internal transcribed spacer (ITS) region of rDNA-based haplotypes. This study performed fingerprinting of C. dubliniensis isolates by multilocus sequence typing (MLST) to determine population structure of 5-FC-resistant and -susceptible strains and compared the results with data from a global collection of isolates. Fifty-two C. dubliniensis isolates previously analyzed and 58 additional isolates mostly collected during 2010–2013 and characterized by phenotypic and molecular methods were used. ITS-based haplotypes were identified by haplotype-specific PCR and/or by PCR-DNA sequencing of rDNA. Population structure was determined by 8-loci-based MLST. E-test was used to determine susceptibility to 5-FC, fluconazole, voriconazole and amphotericin B. Five ITS haplotypes (ITSH) were detected among 110 C. dubliniensis isolates. The ITSH1 was most common (n = 80 isolates) followed by ITSH4 (n = 25 isolates). Two isolates each belonged to ITSH5 and ITSH8 while one isolate belonged to ITSH7. MLST identified 16 diploid sequence types (DSTs) including six new DSTs. DST11 (n = 52) and DST14 (n = 25) were dominant genotypes and were confined (together with DST21) to Middle-Eastern countries. Other DSTs (excluding some new DSTs) had a wider global distribution as they were identified from various other countries. Only ITSH4 isolates (n = 25) belonged to DST14, were resistant to 5-FC and contained S29L mutation in CdFCA1. ITSH5, ITSH7 and ITSH8 isolates belonged to different DSTs. Thus, clinical C. dubliniensis isolates in Kuwait exhibited limited genotypic heterogeneity and most isolates belonged to region-specific DSTs. All 5-FC-resistant C. dubliniensis isolates belonged to ITSH4 and MLST-based DST14 genotype. Placement of some isolates into additional ITS haplotypes is also supported by MLST data.

Comparison of Switching and Biofilm Formation between MTL-Homozygous Strains of Candida albicans and Candida dubliniensis

Candida albicans and Candida dubliniensis are highly related species that share the same main developmental programs. In C. albicans, it has been demonstrated that the biofilms formed by strains heterozygous and homozygous at the mating type locus (MTL) differ functionally, but studies rarely identify the MTL configuration. This becomes a particular problem in studies of C. dubliniensis, given that one-third of natural strains are MTL homozygous. For that reason, we have analyzed MTL-homozygous strains of C. dubliniensis for their capacity to switch from white to opaque, the stability of the opaque phenotype, CO2 induction of switching, pheromone induction of adhesion, the effects of minority opaque cells on biofilm thickness and dry weight, and biofilm architecture in comparison with C. albicans. Our results reveal that C. dubliniensis strains switch to opaque at lower average frequencies, exhibit a far lower level of opaque phase stability, are not stimulated to switch by high CO2, exhibit more variability in biofilm architecture, and most notably, form mature biofilms composed predominately of pseudohyphae rather than true hyphae. Therefore, while several traits of MTL-homozygous strains of C. dubliniensis appear to be degenerating or have been lost, others, most notably several related to biofilm formation, have been conserved. Within this context, the possibility is considered that C. dubliniensis is transitioning from a hypha-dominated to a pseudohypha-dominated biofilm and that aspects of C. dubliniensis colonization may provide insights into the selective pressures that are involved.

Prevalence of Candida albicans-closely related yeasts, Candida africana and Candida dubliniensis, in vulvovaginal candidiasis

Isolates of Candida africana and C. dubliniensis were recovered from patients with vulvovaginal candidiasis (VVC). The isolates were initially identified as C. albicans through use of the API Candida System. We retrospectively reexamined 1014 vaginal isolates presumptively determined to be C. albicans at the Department of Obstetrics and Gynecology of Peking University Shenzhen Hospital from 1 January 2003 through 31 December 2012. Our objective was to determine, via detection of the HWP1 gene, if any of the isolates were C. africana or C. dubliniensis. One and a half percent of these isolates (15/1014) were found to be C. africana, whereas C. dubliniensis was not detected. The 15 C. africana isolates were susceptible to nystatin, fluconazole, itraconazole, miconazole, and clotrimazole. Candida africana could not be recovered from clinical vaginal specimens from the 15 patients at follow-up on days 7-14 and days 30-35 when treated with different antifungal agents. We conclude that C. africana, but not C. dubliniensis, was present in the vaginal samples of patients with VVC. The C. africana isolates were susceptible to the tested antifungal agents. VVC caused by C. africana appears to respond well to current therapies.

Molecular tools for cryptic Candida species identification with applications in a clinical laboratory

Candida spp. includes more than 160 species but only 20 species pose clinical problems. C. albicans and C. parapsilosis account for more than 75% of all the fungemias worldwide. In 1995 and 2005, one C. albicans and two C. parapsilosis-related species were described, respectively. Using phenotypic traits, the identification of these newly described species is inconclusive or impossible. Thus, molecular-based procedures are mandatory. In the proposed educational experiment we have adapted different basic molecular biology techniques designed to identify these species including PCR, multiplex PCR, PCR-based restriction endonuclease analysis and nuclear ribosomal RNA amplification. During the classes, students acquired the ability to search and align gene sequences, design primers, and use bioinformatics software. Also, in the performed experiments, fungal molecular taxonomy concepts were introduced and the obtained results demonstrated that classic identification (phenotypic) in some cases needs to be complemented with molecular-based techniques. As a conclusion we can state that we present an inexpensive and well accepted group of classes involving important concepts that can be recreated in any laboratory.

Genotypic heterogeneity and molecular basis of 5-flucytosine resistance among Candida dubliniensis isolates recovered from clinical specimens in Kuwait

There is a paucity of information about genotypic heterogeneity among Candida dubliniensis isolates recovered from different geographic regions. This study explored genotypic heterogeneity among 103 C. dubliniensis strains obtained over a six-year period from clinical specimens in Kuwait. Genotype assignment was based on amplification with genotype-specific primers and sequencing of rDNA. Susceptibility to 5-flucytosine was determined by means of the Etest. DNA sequencing of cytosine deaminase was performed to determine the molecular basis of resistance to 5-flucytosine. DNA sequencing of rDNA identified seven different genotypes, i.e., 68 (66%) isolates were found to belong to genotype 1, 25 to genotype 4, six to genotype 5 and one each to genotypes 6-9. Strains of genotype 2 or genotype 3 were not detected. All isolates of genotype 4 but none of other genotypes were resistant to 5-flucytosine and the resistant strains all contained S29L mutation. Isolates of all other genotypes contained wild-type codon 29 in cytosine deaminase. A simple, PCR-RFLP-based method has been developed to facilitate rapid detection of S29L mutation in cytosine deaminase. A noteworthy observation of our study is the identification of five new genotypes of C. dubliniensis isolates, recovered from oral/respiratory specimens from patients of Middle Eastern origin. Furthermore, all 5-flucytosine resistant C. dubliniensis isolates in Kuwait belonged to genotype 4 only.

Candida albicans or Candida dubliniensis?

Candida albicans is increasing as an opportunistic pathogen causing candidemia and candidiasis worldwide. In addition, other non-albicans Candida species are now also associated with pertinent infections. These include the closely related C. dubliniensis, which shares many phenotypic similarities with C. albicans. These similarities pose problems in the identification of isolates and have previously led to misidentification of these species. As a result, several identification techniques based on phenotypic and genotypic characteristics have been developed to differentiate between these Candida species. This review will focus on the similarities and differences between these two Candida species highlighting different identification methods and their advantages and disadvantages.

Comparison of phenotypic methods for the identification of Candida dubliniensis

BACKGROUND/PURPOSE

Mixed infections caused by different Candida species are the rule rather than the exception. The discrimination between the two closely related species Candida albicans and Candida dubliniensis is not trivial. Therefore, there is a need for fast, reliable, and inexpensive methods with high specificity for the identification and differentiation of these two Candida species, which are frequently detected in the oral cavities of patients with a human immunodeficiency virus infection.

METHODS

We applied several phenotypic identification methods (growth on Rice-agar, Bird-seed agar, CHROMagar Candida, API ID 32C; growth at 42 degrees C and 45 degrees C) and compared them with genotyping by arbitrarily primed-polymerase chain reaction.

RESULTS

A sensitivity of 44% for the identification of C. dubliniensis was achieved for growth on Rice-agar, 97% for discrimination on Bird-seed agar, 95% with the assimilation profile index API ID 32C, and 97% when grown at 45 degrees C. We found two API codes not described for C. dubliniensis so far. Additionally, 88% of our C. dubliniensis isolates assimilated palatinose, in contrast to the 1% described in the API reference manual.

CONCLUSION

According to our results, cultivation of Candida isolates on Bird-seed agar after screening on CHROMagar Candida is a very sensitive, simple, and cost-effective method for discriminating C. dubliniensis from C. albicans in routine practice.

Mechanisms of antifungal drug resistance in Candida dubliniensis

Candida dubliniensis was first described in 1995 and is the most closely related species to the predominant human fungal pathogen Candida albicans. C. dubliniensis is significantly less prevalent and less pathogenic than C. albicans and is primarily associated with infections in HIV-infected individuals and other immunocompromised cohorts. The population structure of C. dubliniensis consists of three well-defined major clades and is significantly less diverse than C. albicans. The majority of C. dubliniensis isolates are susceptible to antifungal drugs commonly used to treat Candida infections. To date only two major patterns of antifungal drug resistance have been identified and the molecular mechanisms of these are very similar to the resistance mechanisms that have been described previously in C. albicans. However, significant differences are evident in the predominant antifungal drug mechanisms employed by C. dubliniensis, differences that reflect its more clonal nature, its lower prevalence and characteristics of its genome, the complete sequence of which has only recently been determined.

Longitudinal genotyping of Candida dubliniensis isolates reveals strain maintenance, microevolution, and the emergence of itraconazole resistance

We investigated the population structure of 208 Candida dubliniensis isolates obtained from 29 patients (25 human immunodeficiency virus [HIV] positive and 4 HIV negative) as part of a longitudinal study. The isolates were identified as C. dubliniensis by arbitrarily primed PCR (AP-PCR) and then genotyped using the Cd25 probe specific for C. dubliniensis. The majority of the isolates (55 of 58) were unique to individual patients, and more than one genotype was recovered from 15 of 29 patients. A total of 21 HIV-positive patients were sampled on more than one occasion (2 to 36 times). Sequential isolates recovered from these patients were all closely related, as demonstrated by hybridization with Cd25 and genotyping by PCR. Six patients were colonized by the same genotype of C. dubliniensis on repeated sampling, while strains exhibiting altered genotypes were recovered from 15 of 21 patients. The majority of these isolates demonstrated minor genetic alterations, i.e., microevolution, while one patient acquired an unrelated strain. The C. dubliniensis strains could not be separated into genetically distinct groups based on patient viral load, CD4 cell count, or oropharyngeal candidosis. However, C. dubliniensis isolates obtained from HIV-positive patients were more closely related than those recovered from HIV-negative patients. Approximately 8% (16 of 194) of isolates exhibited itraconazole resistance. Cross-resistance to fluconazole was only observed in one of these patients. Two patients harboring itraconazole-resistant isolates had not received any previous azole therapy. In conclusion, longitudinal genotyping of C. dubliniensis isolates from HIV-infected patients reveals that isolates from the same patient are generally closely related and may undergo microevolution. In addition, isolates may acquire itraconazole resistance, even in the absence of prior azole therapy.

Erythematous oral candidiasis in patients with controlled type II diabetes mellitus and complete dentures

Diabetes mellitus (DM) is a systemic condition characterized by a deficient sugar metabolism, which affects the immune system and favors the development of yeasts. The aim of the present study was to perform biochemical, morphological, exoenzyme analyses of Candida species and the molecular identification (DNA) of C. albicans in patients with type II diabetes mellitus. The exoenzyme quantification was compared to non-diabetic patients as controls. Two hundred and seventy-four patients who make use of complete dentures were evaluated, 28 of whom had diabetes and erythematous oral candidiasis. Other thirty patients presented the same clinical feature but without diabetes. Samples were isolated for biochemical identification (auxonogram), morphological identification (production of germ tubes) and PCR molecular identification (DNA). The capability of the Candida samples in producing phospholipases and proteinases was also determined. The diabetic patients had a greater diversity of Candida species (Fischer's exact test, P = 0.04). The production of proteinases by C. albicans in patients with diabetes was greater than in the control group (unpaired "t" test P < 0.003). However, there was no difference between groups for phospholipase production (unpaired "t" test P > 0.05). It was concluded that patients with controlled DM exhibited systemic conditions predisposing C. albicans proteinase increased production.

A Ser29Leu substitution in the cytosine deaminase Fca1p is responsible for clade-specific flucytosine resistance in Candida dubliniensis

The population structure of the opportunistic yeast pathogen Candida dubliniensis is composed of three main multilocus sequence typing clades (clades C1 to C3), and clade C3 predominantly consists of isolates from the Middle East that exhibit high-level resistance (MIC(50) > or = 128 microg/ml) to the fungicidal agent flucytosine (5FC). The close relative of C. dubliniensis, C. albicans, also exhibits clade-specific resistance to 5FC, and resistance is most commonly mediated by an Arg101Cys substitution in the FUR1 gene encoding uracil phosphoribosyltransferase. Broth microdilution assays with fluorouracil (5FU), the toxic deaminated form of 5FC, showed that both 5FC-resistant and 5FC-susceptible C. dubliniensis isolates exhibited similar 5FU MICs, suggesting that the C. dubliniensis cytosine deaminase (Fca1p) encoded by C. dubliniensis FCA1 (CdFCA1) may play a role in mediating C. dubliniensis clade-specific 5FC resistance. Amino acid sequence analysis of the CdFCA1 open reading frame (ORF) identified a homozygous Ser29Leu substitution in all 12 5FC-resistant isolates investigated which was not present in any of the 9 5FC-susceptible isolates examined. The tetracycline-inducible expression of the CdFCA1 ORF from a 5FC-susceptible C. dubliniensis isolate in two separate 5FC-resistant clade C3 isolates restored susceptibility to 5FC, demonstrating that the Ser29Leu substitution was responsible for the clade-specific 5FC resistance and that the 5FC resistance encoded by FCA1 genes with the Ser29Leu transition is recessive. Quantitative real-time PCR analysis showed no significant difference in CdFCA1 expression between 5FC-susceptible and 5FC-resistant isolates in either the presence or the absence of subinhibitory concentrations of 5FC, suggesting that the Ser29Leu substitution in the CdFCA1 ORF is the sole cause of 5FC resistance in clade C3 C. dubliniensis isolates.

Molecular epidemiology of global Candida dubliniensis isolates utilizing genomic-wide, co-dominant, PCR-based markers for strain delineation

The molecular epidemiology of Candida dubliniensis has been studied using large complex DNA probes for Southern analysis and has revealed the existence of distinct genotypes within this species. The aim of the present study was to utilize a PCR-based analysis of molecular co-dominant markers to assess the relatedness of a global and temporally diverse collection of well characterized isolates of C. dubliniensis. Sixty-two C. dubliniensis strains were collected from the authors of previously published studies. Co-dominant PCR-based markers utilizing five separate PCR fingerprints were obtained in the present investigation. Phylogenetic and statistical analyses utilizing permutation tests were undertaken to assess correlations amongst the isolates. Three distinct PCR-groups were observed and there was evidence that strains isolated since 1990 were genotypically more similar to each other than they were to strains recovered prior to 1990.

The enigma of the major repeat sequence of Candida albicans

The major repeat sequence, discovered in the yeast Candida albicans, is a stretch of repeated DNA that occurs nine times in the haploid genome of this opportunistic fungal pathogen and probably a similar number of times in the genome of Candida dubliniensis. In C. albicans it constitutes 1-2% of the genome. Its occurrence is limited to those two species. Despite its major role as a genomic feature, its function, mode of expansion in size due to duplication of internal subunits, and its origin and mechanism of distribution throughout the genome are not understood, although it is associated with chromosome translocations, chromosome length polymorphisms and regulation of the yeast-hypha dimorphic transition. The polymorphism of the major repeat sequence has been exploited in epidemiology and taxonomic studies. This review describes its sequence, occurrence, use in epidemiology and examines the evidence for its role in chromosome dynamics.

DNA fingerprinting Candida species

It is sometimes necessary to assess the genetic relatedness of isolates to identify the origin of an infection. In addition, evidence is accumulating that drug resistance can be associated with strains from a particular clade and that strains can exhibit anatomical specificity. It may, therefore, be valuable in the near future to screen for strains with a propensity for drug resistance. While a number of methods exist for genetically fingerprinting the infectious fungi, only a few provide the necessary resolution not only for distinguishing whether strains are highly related or unrelated, but also for grouping a strain in a particular clade. Here, we provide the procedures for performing the two methods that have proven most effective in the past 5 years: Southern blot hybridization of restriction fragments with complex probes and multilocus sequence typing (MLST).

Multilocus sequence typing reveals that the population structure of Candida dubliniensis is significantly less divergent than that of Candida albicans

The pathogenic yeast Candida dubliniensis is phylogenetically very closely related to Candida albicans, and both species share many phenotypic and genetic characteristics. DNA fingerprinting using the species-specific probe Cd25 and sequence analysis of the internal transcribed spacer (ITS) region of the ribosomal gene cluster previously showed that C. dubliniensis is comprised of three major clades comprising four distinct ITS genotypes. Multilocus sequence typing (MLST) has been shown to be very useful for investigating the epidemiology and population biology of C. albicans and has identified many distinct major and minor clades. In the present study, we used MLST to investigate the population structure of C. dubliniensis for the first time. Combinations of 10 loci previously tested for MLST analysis of C. albicans were assessed for their discriminatory ability with 50 epidemiologically unrelated C. dubliniensis isolates from diverse geographic locations, including representative isolates from the previously identified three Cd25-defined major clades and the four ITS genotypes. Dendrograms created by using the unweighted pair group method with arithmetic averages that were generated using the data from all 10 loci revealed a population structure which supports that previously suggested by DNA fingerprinting and ITS genotyping. The MLST data revealed significantly less divergence within the C. dubliniensis population examined than within the C. albicans population. These findings show that MLST can be used as an informative alternative strategy for investigating the population structure of C. dubliniensis. On the basis of the highest number of genotypes per variable base, we recommend the following eight loci for MLST analysis of C. dubliniensis: CdAAT1b, CdACC1, CdADP1, CdMPIb, CdRPN2, CdSYA1, exCdVPS13, and exCdZWF1b, where "Cd" indicates C. dubliniensis and "ex" indicates extended sequence.

Heterozygosity of genes on the sex chromosome regulates Candida albicans virulence

In the mouse model for systemic infection, natural a/alpha strains of C. albicans are more virulent and more competitive than their spontaneous MTL-homozygous offspring, which arise primarily by loss of one chromosome 5 homologue followed by duplication of the retained homologue (uniparental disomy). Deletion of either the a or alpha copy of the MTL locus of natural a/alpha strains results in a small decrease in virulence, and a small decrease in competitiveness. Loss of the heterozygosity of non-MTL genes along chromosome 5, however, results in larger decreases in virulence and competitiveness. Natural MTL-homozygous strains are on average less virulent than natural MTL-heterozygous strains and arise by multiple mitotic cross-overs along chromosome 5 outside of the MTL region. These results are consistent with the hypothesis that a competitive advantage of natural a/alpha strains over MTL-homozygous offspring maintains the mating system of C. albicans.

Extensive chromosome rearrangements distinguish the karyotype of the hypovirulent species Candida dubliniensis from the virulent Candida albicans

Candida dubliniensis and Candida albicans, the most common human fungal pathogen, have most of the same genes and high sequence similarity, but C. dubliniensis is less virulent. C. albicans causes both mucosal and hematogenously disseminated disease, C. dubliniensis mostly mucosal infections. Pulse-field electrophoresis, genomic restriction enzyme digests, Southern blotting, and the emerging sequence from the Wellcome Trust Sanger Institute were used to determine the karyotype of C. dubliniensis type strain CD36. Three chromosomes have two intact homologues. A translocation in the rDNA repeat on chromosome R exchanges telomere-proximal regions of R and chromosome 5. Translocations involving the remaining chromosomes occur at the Major Repeat Sequence. CD36 lacks an MRS on chromosome R but has one on 3. Of six other C. dubliniensis strains, no two had the same electrophoretic karyotype. Despite extensive chromosome rearrangements, karyotypic differences between C. dubliniensis and C. albicans are unlikely to affect gene expression. Karyotypic instability may account for the diminished pathogenicity of C. dubliniensis.

Use of fluconazole as a surrogate marker to predict susceptibility and resistance to voriconazole among 13,338 clinical isolates of Candida spp. Tested by clinical and laboratory standards institute-recommended broth microdilution methods

Clinical laboratories frequently face the problem of delayed availability of commercially prepared approved reagents for performing susceptibility testing of new antimicrobials. Although this problem is encountered more often with antibacterial agents, it is also an issue with antifungal agents. A current example is voriconazole, a new triazole antifungal with an expanded spectrum and potency against Candida spp., Aspergillus spp., and other opportunistic fungal pathogens. The present study addresses the use of fluconazole as a surrogate marker to predict the susceptibility of Candida spp. to voriconazole. Reference broth microdilution MIC results for 13,338 strains of Candida spp. isolated from more than 200 medical centers worldwide were used. Voriconazole MICs and interpretive categories (susceptible, < or =1 microg/ml; susceptible dose dependent, 2 microg/ml; resistant, > or =4 microg/ml) were compared with those of fluconazole by regression statistics and error rate bounding analyses. For all 13,338 isolates, the absolute categorical agreement was 91.6% (false susceptible or very major error [VME], 0.0%). Since voriconazole is 16- to 32-fold more potent than fluconazole, the performance of fluconazole as a surrogate marker for voriconazole susceptibility was improved by designating those isolates with fluconazole MICs of < or =32 microg/ml as being susceptible to voriconazole, resulting in a categorical agreement of 97% with 0.1% VME. Clinical laboratories performing antifungal susceptibility testing of fluconazole against Candida spp. can reliably use these results as surrogate markers until commercial FDA-approved voriconazole susceptibility tests become available.

Development and evaluation of a rapid latex agglutination test using a monoclonal antibody to identify Candida dubliniensis colonies

Cell components of the dimorphic pathogenic fungus Candida dubliniensis were used to prepare monoclonal antibodies (MAbs). One MAb, designated 12F7-F2, was shown by indirect immunofluorescence to be specific for a surface antigen of Candida dubliniensis yeast cells. No reactivity was observed with other fungal genera or with other Candida species, including Candida albicans, that share many phenotypic features with C. dubliniensis. The use of different chemical and physical treatments for cell component extraction suggested that the specific epitope probably resides on a protein moiety absent from C. albicans. However, we failed to identify the target protein by Western blotting, owing to its sensitivity to heat and sodium dodecyl sulfate. MAb 12F7-F2 was further used to develop a commercial latex agglutination test to identify C. dubliniensis colonies (Bichro-dubli Fumouze test; Fumouze Diagnostics). The test was validated on yeast strains previously identified by PCR and on fresh clinical isolates; these included 46 C. dubliniensis isolates, 45 C. albicans isolates, and other yeast species. The test had 100% sensitivity and specificity for C. dubliniensis isolated on Sabouraud dextrose, CHROMagar Candida, and CandiSelect media and 97.8% sensitivity for C. dubliniensis grown on Candida ID medium. The test is rapid (5 min) and easy to use and may be recommended for routine use in clinical microbiology laboratories and for epidemiological investigations.

Molecular identification of Candida dubliniensis isolated from oral lesions of HIV-positive and HIV-negative patients in São Paulo, Brazil

Candida dubliniensis is a new, recently described species of yeast. This emerging oral pathogen shares many phenotypic and biochemical characteristics with C. albicans, making it hard to differentiate between them, although they are genotypically distinct. In this study, PCR (Polymerase Chain Reaction) was used to investigate the presence of C. dubliniensis in samples in a culture collection, which had been isolated from HIV-positive and HIV-negative patients with oral erythematous candidiasis. From a total of 37 samples previously identified as C. albicans by the classical method, two samples of C. dubliniensis (5.4%) were found through the use of PCR. This study underscores the presence of C. dubliniensis, whose geographical and epidemiological distribution should be more fully investigated.

Candida dubliniensis: ten years on

Candida dubliniensis was first described as a novel species in 1995. This organism is very closely related to the important human yeast pathogen, Candida albicans. However, despite the very close phylogenetic relationship between C. albicans and C. dubliniensis and the fact that they share a large number of phenotypic traits, epidemiological and virulence model data indicate that the former is a far more successful pathogen. In order to investigate the molecular basis of the lower virulence of C. dubliniensis recent comparative genomic hybridisation studies have revealed the absence and divergence of specific genes implicated in candidal virulence. Data from the C. dubliniensis genome sequencing project will allow a complete comparison between the genomes of the two species to be performed and thus enhance our understanding of candidal virulence and how virulence has evolved in Candida species.

Novel 5-flucytosine-resistant clade of Candida dubliniensis from Saudi Arabia and Egypt identified by Cd25 fingerprinting

DNA fingerprinting of Candida dubliniensis isolates using the species-specific probe Cd25 previously showed that this species consists of two distinct groups, termed Cd25 group I and Cd25 group II. The present study investigated the population structure of 30 C. dubliniensis oral isolates from Saudi Arabia and Egypt using Cd25 fingerprinting and rRNA gene internal transcribed spacer region-based genotyping. Cd25 fingerprinting analysis of these isolates revealed two distinct populations, the first of which consisted of 10 closely related genotype 1 isolates (average similarity coefficient [S(AB)] value, 0.86). The second population of 20 isolates was much more heterogeneous (average S(AB) value, 0.35) and consisted of two distinct subpopulations, one of which consisted of genotype 3 isolates (n = 13) and the other of genotype 4 isolates (n = 7). A mixed dendrogram generated from the fingerprint data from the 30 Saudi Arabian and Egyptian isolates, 5 Israeli isolates, and 51 previously characterized international isolates (32 of Cd25 group I and 19 of Cd25 group II) revealed the presence of three distinct main clades. The first corresponded to the previously described Cd25 group I and contained all the Saudi Arabian, Egyptian, and Israeli genotype 1 isolates mixed with international isolates. The second clade corresponded to the previously described Cd25 group II and contained three Israeli isolates, one genotype 2 isolate, one genotype 3 isolate, and a genotype 4 variant isolate, which were mixed with international isolates. The third clade has not been described before and consisted solely of the 20 Saudi Arabian and Egyptian genotype 3 and 4 isolates identified in this study and a previously described genotype 4 Israeli isolate. All 20 Cd25 group III isolates exhibited high-level resistance to 5-flucytosine (MIC > or = 128 microg/ml), whereas all Cd25 group I and Cd25 group II isolates tested (10 Saudi Arabian and Egyptian, 16 Israeli, and 24 international) were susceptible to 5-flucytosine (MIC < or = 0.125 microg/ml). The results of this study show for the first time the presence of a novel 5-flucytosine-resistant clade of C. dubliniensis (Cd25 group III) that is predominant among isolates from Saudi Arabia and Egypt and absent from a previously characterized international collection of 98 isolates from 15 countries.

The closely related species Candida albicans and Candida dubliniensis can mate

Because Candida dubliniensis is closely related to Candida albicans, we tested whether it underwent white-opaque switching and mating and whether white-opaque switching depended on MTL homozygosity and mating depended on switching, as they do in C. albicans. We also tested whether C. dubliniensis could mate with C. albicans. Sequencing revealed that the MTLalpha locus of C. dubliniensis was highly similar to that of C. albicans. Hybridization with the MTLa1, MTLa2, MTLalpha1, and MTLalpha2 open reading frames of C. albicans further revealed that, as in C. albicans, natural strains of C. dubliniensis exist as a/alpha, a/a, and alpha/alpha, but the proportion of MTL homozygotes is 33%, 10 times the frequency of natural C. albicans strains. C. dubliniensis underwent white-opaque switching, and, as in C. albicans, the switching was dependent on MTL homozygosis. C. dubliniensis a/a and alpha/alpha cells also mated, and, as in C. albicans, mating was dependent on a switch from white to opaque. However, white-opaque switching occurred at unusually high frequencies, opaque cell growth was frequently aberrant, and white-opaque switching in many strains was camouflaged by an additional switching system. Mating of C. dubliniensis was far less frequent in suspension cultures, due to the absence of mating-dependent clumping. Mating did occur, however, at higher frequencies on agar or on the skin of newborn mice. The increases in MTL homozygosity, the increase in switching frequencies, the decrease in the quality of switching, and the decrease in mating efficiency all reflected a general deterioration in the regulation of developmental processes, very probably due to the very high frequency of recombination and genomic reorganization characteristic of C. dubliniensis. Finally, interspecies mating readily occurred between opaque C. dubliniensis and C. albicans strains of opposite mating type in suspension, on agar, and on mouse skin. Remarkably, the efficiency of interspecies mating was higher than intraspecies C. dubliniensis mating, and interspecies karyogamy occurred readily with apparently the same sequence of nuclear migration, fusion, and division steps observed during intraspecies C. albicans and C. dubliniensis mating and Saccharomyces cerevisiae mating.

Automated genotyping of Saccharomyces cerevisiae using the RiboPrinter®

This research note addresses the development of an automated molecular typing system for yeast. Specifically, our objectives were to generate specific probes for genotyping yeast with an automated fingerprinting system. We have adapted the RiboPrinter microbial characterization system for use with Saccharomyces cerevisiae yeast using alternative probes based on specific multi-copy gene families. Manual construction and labeling of probes proved successful in initial experiments. Results indicate that this method could be applied to food or clinical environments if the appropriate probes are developed.

Reduced azole susceptibility in genotype 3 Candida dubliniensis isolates associated with increased CdCDR1 and CdCDR2 expression

Candida dubliniensis is a recently identified yeast species primarily associated with oral carriage and infection in individuals infected with the human immunodeficiency virus. The species can be divided into at least four genotypes on the basis of the nucleotide sequence of the internal transcribed spacer region of the rRNA operon. Previous studies have shown that a small number of clinical isolates belonging to genotype 1 are resistant to the commonly used antifungal drug fluconazole. The aim of the present study was to investigate the molecular mechanisms responsible for reduced susceptibility to azole drugs in C. dubliniensis genotype 3 isolates obtained from a patient with fluconazole-recalcitrant oral candidiasis. Four isolates from a single clinical sample, one susceptible, the other three exhibiting reduced susceptibilities to fluconazole, itraconazole, ketoconazole, voriconazole, and posaconazole, were examined. Results showed that reduced susceptibility to azole drugs was associated with an increase in the expression of the multidrug transporters CdCDR1 and CdCDR2 which correlated with reduced intracellular accumulation of radiolabeled fluconazole and an increase in the activity of energy-dependent efflux mechanisms. In contrast to observations made in previous studies, overexpression of the multidrug transporter CdMDR1 was not observed. Despite a thorough investigation of all commonly encountered mechanisms of azole resistance, no other mechanism could be associated with reduced susceptibility to azole drugs in the clinical isolates studied. This is the first report of CdCDR2 involvement in azole resistance in C. dubliniensis.

Bacterial contamination of dental chair units in a modern dental hospital caused by leakage from suction system hoses containing extensive biofilm

Within six months of opening of the new Dublin Dental Hospital in September 1998, areas of corrosion were observed on many of the baseplates of the hospital's 103 dental chair units (DCUs) at the site of attachment of the suction hoses. The corroded areas were heavily contaminated with Pseudomonas spp. and related genera posing a risk of cross-infection, particularly for immunocompromised patients. These species were used as marker organisms to investigate the source of the contamination. P. aeruginosa was the predominant species recovered from 41 selected DCU baseplates (61% prevalence), whereas P. putida (46% prevalence) and P. aeruginosa (43% prevalence) were predominant at the attachment ends of 37 selected high-volume suction hoses. Forty-one selected isolates of P. aeruginosa from 13 DCU baseplates, 16 high-volume suction hoses and 12 coarse filter housings (another suction system site) from 19 separate DCUs were serotyped to determine the similarity of isolates at each site. The majority of isolates (68.3%) belonged to serotype O:10, while the remainder belonged to serotypes O:6 (7.3%), O:11 (7.3%), O:14 (9.8%) and O:5/O:16 (7.3%). Of the isolates from DCU baseplates, additional isolates with the same serotype were recovered from other suction system sites in 10/13 (77%) cases. Isolates of only one serotype were recovered from each of the 19 DCUs investigated. Forty-one serotyped isolates were also subject to computer-assisted analysis of SpeI-generated DNA fingerprint profiles, and similarity coefficient (S(AB)s) values were calculated for each pairwise combination of isolate profiles. The data obtained showed that the isolates consisted of two distinct main populations, each containing separate clades corresponding to specific serotypes. Serotype O:6 (three isolates), O:11 (three isolates) and O:5/O:16 (three isolates) belonged to a single strain in each case. Serotypes O:14 (four isolates) and O:10 (28 isolates) belonged to two strains in each case. The two serotype O:10 strains, termed fingerprint groups I (four isolates from three DCUs) and II (24 isolates from 10 DCUs), were the most distantly related of all the strains identified. These findings demonstrated that the hospital DCUs had become colonized with a small number of P. aeruginosa strains, one of which (serotype O:10, fingerprint group II) predominated. These results also confirmed that DCU baseplate contamination was most likely to be due to leakage from suction system hoses at the baseplate attachment sites, probably due to loosening during use. Replacement hose connectors that firmly retained the suction hoses in the attachment sites so that they could not be loosened by movement of the suction hoses solved this problem, and eliminated further contamination of the DCU baseplates.

Evaluation of a rapid immunochromatographic assay for identification of Candida albicans and Candida dubliniensis

Candida dubliniensis was first established as a novel yeast species in 1995. It is particularly associated with recurrent episodes of oral candidosis in human immunodeficiency virus (HIV)-infected patients, but it has also been detected at other anatomical sites and at a low incidence level in non-HIV-infected patients. It shares so many phenotypic characteristics with C. albicans that it is easily misidentified as such. No rapid, simple, and commercial test that allows differentiation between C. dubliniensis and C. albicans has been developed, until now. Accurate species identification requires the use of genotype-based techniques that are not routinely available in most clinical microbiology diagnostic laboratories. The present study was designed to evaluate the efficiency of a new test (the immunochromatographic membrane [ICM] albi-dubli test; SR2B, Avrille, France) to differentiate between C. albicans and C. dubliniensis. The organisms evaluated were strains whose identities had previously been confirmed by PCR tests and freshly isolated clinical strains and included 58 C. albicans isolates, 60 C. dubliniensis isolates, and 82 isolates belonging to other species of yeast. The ICM albi-dubli test is based on the principle of immunochromatographic analysis and involves the use of two distinct monoclonal antibodies that recognize two unrelated epitopes expressed by both species or specific to only one species. The assay requires no complex instrumentation for analysis and can be recommended for routine use in clinical microbiology laboratories. Results are obtained within 2 h and 30 min and are easy to interpret. This evaluation demonstrated the good performance of this immunochromatographic test for C. albicans and C. dubliniensis isolated on Sabouraud dextrose agar, CHOROMagar Candida, and CandidaSelect, with sensitivities and specificities ranging from 93.1 to 100%. These parameters decreased, however, to 91.4% when the test was performed with yeast isolated with Candida ID.

High prevalence of oral colonization byCandida dubliniensisin HIV-positive patients in Argentina

Candida dubliniensis is a recently described yeast species, closely related to Candida albicans. This work represents the first general survey of the carriage of C. dubliniensis in the oral cavities of HIV-positive patients in Argentina. We studied 133 strains isolated from 162 HIV-positive patients, using the following identification tests: chlamydospore production on corn meal agar with Tween 80; colony color on CHROMagar Candida media; differential growth at 45 degrees C on potato dextrose agar; D-xylose assimilation; chlamydospore formation on sunflower seed agar (SSA); carbohydrate assimilation profiles using the API 20 C Aux commercial kit and PCR using primers that hybridize to the class IV intron of the ACT1 gene. Out of the 133 strains, 21 were identified as C. dubliniensis, representing approximately 13% of the 162 patients in this study. From these data, we conclude that although the PCR assay is the most reliable method, clamydospore formation on SSA is an easier and less expensive test for the screening of C. dubliniensis in the routine laboratory. Our results show that C. dubliniensis has a high prevalence among HIV-positive patients in Argentina.

Cross-resistance between fluconazole and ravuconazole and the use of fluconazole as a surrogate marker to predict susceptibility and resistance to ravuconazole among 12,796 clinical isolates of Candida spp

Cross-resistance within a class of antimicrobial agents is a problem that is often encountered with antibacterial agents, and it is also an issue with antifungal agents. A current example is ravuconazole, a new triazole antifungal with an expanded spectrum and potency against Candida spp., Aspergillus spp., and other opportunistic fungal pathogens. The present study addresses the issue of cross-resistance between fluconazole and ravuconazole and the use of fluconazole as a surrogate marker to predict the susceptibility of Candida spp. to ravuconazole. Reference broth microdilution MIC results for 12,796 strains of Candida spp. isolated from more than 200 medical centers worldwide were used. Ravuconazole MICs and tentative interpretive categories (susceptible, </=1 microg/ml; resistant, >/=2 microg/ml) were compared with those of fluconazole by using regression statistics and error rate bounding analyses. For all 12,796 isolates, the absolute categorical agreement rate was 92.5% (rate of false-susceptible results, or very major errors [VME], 0.1%). Ravuconazole was active (MIC, </=1 microg/ml) against 99.9% of the fluconazole-susceptible isolates, 96% of the fluconazole-susceptible dose-dependent isolates, and 49% of the fluconazole-resistant isolates, including 99% of the Candida krusei isolates. Since ravuconazole is 16- to 32-fold more potent than fluconazole, the performance of fluconazole as a surrogate marker for ravuconazole susceptibility was improved by designating those isolates with fluconazole MICs of </=32 microg/ml susceptible to ravuconazole, resulting in a categorical agreement rate of 98.3%, with a VME rate of 0.3% (99 and 0.4%, respectively, when C. krusei was omitted). Cross-resistance between fluconazole and ravuconazole applies most directly to fluconazole-resistant Candida glabrata and is variable among other species of Candida. Fluconazole may serve as a surrogate marker to predict the susceptibility of Candida spp. to ravuconazole.

In vitro susceptibilities of rare Candida bloodstream isolates to ravuconazole and three comparative antifungal agents

We determined the in vitro susceptibilities of 643 strains of Candida spp., representing 13 species rarely isolated from blood, to ravuconazole as well as three licensed systemic antifungal agents (amphotericin B, fluconazole, and flucytosine). The organisms included 234 isolates of C. krusei, 102 isolates of C. guilliermondii, 103 isolates of C. lusitaniae, 18 isolates of C. famata, 29 isolates of C. kefyr, 20 isolates of C. pelliculosa, 13 isolates of C. rugosa, 101 isolates of C. dubliniensis, 4 isolates of C. inconspicua, 11 isolates of C. lipolytica, 1 isolate of C. sake, and 2 isolates of C. lambica and 5 isolates of C. zeylanoides. MIC determinations were made by the National Committee for Clinical Laboratory Standards reference broth microdilution method and Etest (amphotericin B). Ravuconazole demonstrated excellent activity (98% susceptible at MIC < or = 1 microg/mL) against all species with the exception of C. inconspicua (75% [3 of 4]). By comparison, decreased susceptibility to fluconazole and/or amphotericin B was observed among isolates of C. krusei, C. guilliermondii, C. famata, C. rugosa, C. inconspicua, and C. lambica. These findings illustrate the fact that many of the less common species of Candida exhibit decreased susceptibility to one or more of the established systemically active antifungal agents. Ravuconazole is clearly an "extended-spectrum" triazole with potent in vitro activity against these rare and potentially "emerging" opportunistic pathogens.

Release of a potent polymorphonuclear leukocyte chemoattractant is regulated by white-opaque switching in Candida albicans

Previous studies employing transmembrane assays suggested that Candida albicans and related species, as well as Saccharomyces cerevisiae, release chemoattractants for human polymorphonuclear leukocytes (PMNs). Because transmembrane assays do not definitively distinguish between chemokinesis and chemotaxis, single-cell chemotaxis assays were used to confirm these findings and test whether mating-type or white-opaque switching affects the release of attractant. Our results demonstrate that C. albicans, C. dubliniensis, C. tropicalis, C. parapsilosis, and C. glabrata release bona fide chemoattractants for PMNs. S. cerevisiae, however, releases a chemokinetic factor but not a chemoattractant. Characterization of the C. albicans chemoattractant revealed that it is a peptide of approximately 1 kDa. Whereas the mating type of C. albicans did not affect the release of chemoattractant, switching did. White-phase cells released chemoattractant, but opaque-phase cells did not. Since the opaque phase of C. albicans represents the mating-competent phenotype, it may be that opaque-phase cells selectively suppress the release of chemoattractant to facilitate mating.

Comparison of the epidemiology, drug resistance mechanisms, and virulence of and

Candida dubliniensis is a pathogenic yeast species that was first identified as a distinct taxon in 1995. Epidemiological studies have shown that C. dubliniensis is prevalent throughout the world and that it is primarily associated with oral carriage and oropharyngeal infections in human immunodeficiency virus (HIV)-infected and acquired immune deficiency syndrome (AIDS) patients. However, unlike Candida albicans, C. dubliniensis is rarely found in the oral microflora of normal healthy individuals and is responsible for as few as 2% of cases of candidemia (compared to approximately 65% for C. albicans). The vast majority of C. dubliniensis isolates identified to date are susceptible to all of the commonly used antifungal agents, however, reduced susceptibility to azole drugs has been observed in clinical isolates and can be readily induced in vitro. The primary mechanism of fluconazole resistance in C. dubliniensis has been shown to be overexpression of the major facilitator efflux pump Mdr1p. It has also been observed that a large number of C. dubliniensis strains express a non-functional truncated form of Cdr1p, and it has been demonstrated that this protein does not play a significant role in fluconazole resistance in the majority of strains examined to date. Data from a limited number of infection models reflect findings from epidemiological studies and suggest that C. dubliniensis is less pathogenic than C. albicans. The reasons for the reduced virulence of C. dubliniensis are not clear as it has been shown that the two species express a similar range of virulence factors. However, although C. dubliniensis produces hyphae, it appears that the conditions and dynamics of induction may differ from those in C. albicans. In addition, C. dubliniensis is less tolerant of environmental stresses such as elevated temperature and NaCl and H(2)O(2) concentration, suggesting that C. albicans may have a competitive advantage when colonising and causing infection in the human body. It is our hypothesis that a genomic comparison between these two closely-related species will help to identify virulence factors responsible for the far greater virulence of C. albicans and possibly identify factors that are specifically implicated in either superficial or systemic candidal infections.

Candida albicansclades

DNA fingerprinting with the complex probe Ca3 has revealed the following five Candida albicans clades: group I, group II, group III, group SA and group E. These groups exhibit geographical specificity. Group SA is relatively specific (i.e., highly enriched) to South Africa, group E is relatively specific to Europe, and group II is absent in the Southwest USA and South America. The maintenance of deep-rooted clades side by side in the same geographical locale and the apparent absence of subclade structure suggest little recombination between clades, but higher rates of recombination within clades. Exclusive 5-fluorocytosine resistance in the majority of group I isolates reinforces the above conclusions on recombination, and demonstrates that clades differ phenotypically. The ramifications of these findings with regard to pathogenesis are discussed. In particular, these findings lay to rest the idea that one strain represents all strains of C. albicans, support the need for a worldwide analysis of population structure and clade-specific phenotypic characteristics, and demonstrate that in the future, pathogenic characteristics must be analyzed in representatives from all five clades.

Molecular mechanisms of itraconazole resistance in Candida dubliniensis

It has previously been shown that overexpression of the CdMDR1 gene is a major contributor to resistance in fluconazole-resistant isolates of Candida dubliniensis. However, since CdMdr1p does not mediate transport of other azole drugs such as itraconazole, we investigated the molecular mechanisms of stable resistance to itraconazole obtained in three strains of C. dubliniensis (two with nonfunctional CdCDR1 genes and one with functional CdCDR1 genes) by serial exposure to this antifungal agent in vitro. Seven derivatives that were able to grow on agar medium containing 64 micro g of itraconazole per ml were selected for detailed analysis. These derivatives were resistant to itraconazole, fluconazole, and ketoconazole but were not cross resistant to inhibitors. CdMDR1 expression was unchanged in the seven resistant derivatives and their parental isolates; however, all seven derivatives exhibited increased levels of CdERG11 expression, and six of the seven derivatives exhibited increased levels of CdCDR1 expression compared to the levels of expression by their respective parental isolates. Except for one derivative, the level of rhodamine 6G efflux was decreased in the itraconazole-resistant derivatives compared to the level of efflux in their parental isolates, suggesting altered membrane properties in these derivatives. Analysis of their membrane sterol contents was consistent with a defective sterol C5,6-desaturase enzyme (CdErg3p), which was confirmed by the identification of mutations in the alleles (CdERG3) encoding this enzyme and their lack of functional complementation in a Saccharomyces cerevisiae erg3 mutant. The results of this study show that the loss of function of CdErg3p was the primary mechanism of in vitro-generated itraconazole resistance in six of the seven the C. dubliniensis derivatives. However, the mechanism(s) of itraconazole resistance in the remaining seventh derivative has yet to be determined.

Racial distribution of Candida dubliniensis colonization among South Africans

Candida dubliniensis is a yeast species that has only recently been differentiated from Candida albicans. C. dubliniensis colonization was initially associated with human immunodeficiency virus (HIV)-positive individuals. Because of the large proportion of AIDS patients in South Africa, we tested the generality of this association by assessing the prevalence of C. dubliniensis colonization among 253 black HIV-positive individuals, 66 healthy black individuals, 22 white HIV-positive individuals, and 55 healthy white individuals in South Africa carrying germ tube-positive yeasts in their oral cavities. Molecular fingerprinting with Ca3, a complex DNA fingerprinting probe specific for C. albicans, and Cd25, a complex DNA fingerprinting probe specific for C. dubliniensis, provides the first conclusive evidence of the existence of C. dubliniensis among South African clinical yeast isolates and reveals a higher relative prevalence of this species among white healthy individuals (16%) than among HIV-positive white individuals (9%), black healthy individuals (0%), and black HIV-positive individuals (1.5%). A cluster analysis separated South African C. dubliniensis isolates into two previously described groups, groups I and II, with the majority of isolates clustering in group I. Isolates from white healthy individuals exhibited a higher level of relatedness. A comparison of the C. dubliniensis isolates from South Africa with a general collection of C. dubliniensis isolates collected worldwide revealed no South Africa-specific clade, as has been demonstrated for C. albicans. These results suggest that in South Africa, C. dubliniensis carriage is influenced more by race than by HIV infection status.

The use of Niger seed agar to screen for Candida dubliniensis in the clinical microbiology laboratory

Candida dubliniensis is a recently described pathogenic yeast that is closely related to C. albicans. The germ tube test is used routinely in diagnostic laboratories for the identification of C. albicans, and C. dubliniensis may also produce germ tubes under the same conditions. We evaluated a previously described method for differentiating between the two species using Niger seed agar (Staib agar). The aim was to find a useful, user-friendly and cost-effective method for use in diagnostic work. C. albicans produces only yeast cells on this medium after 24 h at 37 degrees C, while C. dubliniensis produces extensive hyphal and pseudohyphal growth that is easily observed. Of 495 yeasts isolated in, or sent for identification to, a diagnostic mycology laboratory 9 isolates (1.8%) were found to be C. dubliniensis. The method was found to be valuable for screening yeasts before proceeding to further identification if positive for hyphal/pseudohyphal growth on Niger seed agar. This method is therefore suitable for the screening of selected yeast isolates in order to identity C. dubliniensis and will further our understanding of the clinical importance of this species.

Molecular typing for fungi--a critical review of the possibilities and limitations of currently and future methods

Invasive fungal infections represent an increasing problem in patients with inherited and acquired immunodeficiencies. Molecular biotyping techniques, such as DNA fingerprinting, are useful tools to increase our knowledge of the pathogenic organisms that cause them, and thus to improve their treatment and develop prevention strategies. In the present review, we evaluate and discuss the possibilities and limitations of the methods currently used for biotyping strains of fungal species. These include techniques based on restriction fragment length polymorphism (RFLP) with or without hybridization to probes (Southern), PCR-based techniques, electrophoretic karyotyping (EK), and multilocus enzyme electrophoresis (MLEE). Additionally, we discuss newer techniques that are being developed for the fingerprinting of fungal strains. Among them, we review conformation-based polymorphism scanning methods, such as single-strand conformation polymorphism analysis (SSCP) and heteroduplex mobility assays, sequencing strategies such as multilocus sequence typing (MLST) and DNA microarrays.

Microevolutionary changes and chromosomal translocations are more frequent at RPS loci in Candida dubliniensis than in Candida albicans

The Cd1 fingerprinting probe of Candida dubliniensis, which is extremely effective in identifying microevolutionary changes in infecting populations, generates hybridization patterns that are similar to those generated by the Candida albicans fingerprinting probe Ca3. Since Ca3 recognizes microevolutionary changes through the repeat sequence RPS, it was suggested that Cd1 also contains a RPS-like element. To test this possibility, the C. albicans RPS unit was used as a probe, and an RPS-like element, RPSd1, was cloned from C. dubliniensis. The sequence of RPSd1 was 76% homologous to that of the C. albicans RPS unit RPS620 and the organization, including the non-RPS 3' and 5' bordering sequences, was highly similar. This analysis revealed additional copies of the repeat extraalt element and short additional repeat (SAR) sequences in both RPSd1 and RPS620 not previously identified in the latter. This analysis has allowed us to develop a model of RPSd1 organization and to revise the model for RPS620 organization. An estimate of the average frequency of reorganization (duplication and deletion) per RPS unit in C. dubliniensis was similar to that for C. albicans, but the estimate of frequency of reorganization per C. dubliniensis genome was higher, most probably as a result of the higher estimated average number of RPS clusters in C. dubliniensis. These results demonstrate that the microevolutionary changes identified by the Cd1 fingerprinting probe are based on the reorganization of RPS-like elements and are, therefore, similar to the microevolutionary changes identified by the Ca3 probe of C. albicans. Linkage analysis of pairs of markers situated on either side of an RPS cluster on chromosome 7 further revealed frequent recombination between non-homologous chromosomes at the RPS cluster in C. dubliniensis strains, but not in C. albicans strains, suggesting that RPS clusters may function as recombination hot spots in C. dubliniensis.

Replacement of Candida albicans with C. dubliniensis in human immunodeficiency virus-infected patients with oropharyngeal candidiasis treated with fluconazole

Candida dubliniensis is an opportunistic yeast that has been increasingly implicated in oropharyngeal candidiasis (OPC) in human immunodeficiency virus (HIV)-infected patients but may be underreported due to its similarity with Candida albicans. Although most C. dubliniensis isolates are susceptible to fluconazole, the inducibility of azole resistance in vitro has been reported. Thus, the use of fluconazole prophylaxis in the treatment of these patients may have contributed to the increasing rates of isolation of C. dubliniensis. In this study, yeast strains were collected from the oral cavities of HIV-infected patients enrolled in a longitudinal study of OPC. Patients received fluconazole for the suppression or treatment of OPC, and isolates collected at both study entry and end of study were chosen for analysis. Samples were plated on CHROMagar Candida medium for initial isolation and further identified by Southern blot analysis with the species-specific probes Ca3 (for C. albicans) and Cd25 (for C. dubliniensis). Fluconazole MICs were determined by using NCCLS methods. At study entry, susceptible C. albicans isolates were recovered from oral samples in 42 patients who were followed longitudinally (1 to 36 months). C. albicans strains from 12 of these patients developed fluconazole resistance (fluconazole MIC, >/=64 micro g/ml). C. dubliniensis was not detected at end of study in any of these patients. Of the remaining 30 patients, eight (27%) demonstrated a replacement of C. albicans by C. dubliniensis when a comparison of isolates obtained at baseline and those from the last culture was done. For the 22 of these 30 patients in whom no switch in species was detected, the fluconazole MICs for initial and end-of-study C. albicans isolates ranged from 0.125 to 2.0 micro g/ml. For the eight patients in whom a switch to C. dubliniensis was detected, the fluconazole MICs for C. dubliniensis isolates at end of study ranged from 0.25 to 64 micro g/ml: the fluconazole MICs for isolates from six patients were 0.25 to 2.0 micro g/ml and those for the other two were 32 and 64 micro g/ml, respectively. In conclusion, a considerable number of patients initially infected with C. albicans strains that failed to develop fluconazole resistance demonstrated a switch to C. dubliniensis. C. dubliniensis in this setting may be underestimated due to lack of identification and may occur due to the impact of fluconazole on the ecology of oral yeast species.

Adherence of different Candida dubliniensis isolates in the presence of fluconazole

BACKGROUND

The recently described yeast species Candida dubliniensis is closely related to C. albicans and has been recovered predominantly from the oral cavities of HIV-infected individuals and AIDS patients who are often receiving fluconazole as prophylactic or therapeutic treatment for oropharyngeal candidiasis. Like C. albicans, C. dubliniensis secretes aspartic proteinases which in C. albicans have been shown to be involved in adherence.

OBJECTIVE

To explain the increasing prevalence of C. dubliniensis in AIDS patients and to investigate the virulence factors of this yeast.

METHODS

An in vitro assay was developed to compare the adherence to epithelial cells of C. dubliniensis from HIV-patients with that of C. albicans.

RESULTS

All C. albicans isolates adhered better than the 22 C. dubliniensis isolates. In the presence of fluconazole, the C. dubliniensis isolates tested showed increased adherence as compared with controls without fluconazole. In contrast, all C. albicans isolates decreased in adherence to epithelial cells in the presence of fluconazole independently of their in vitro susceptibility to this drug. Proteinase antigens are present on the surface of C. dubliniensis cells adherent to epithelial target cells. In the presence of fluconazole this proteinase antigen was more strongly expressed.

CONCLUSION

Increased adherence of C. dubliniensis strains in the presence of fluconazole could explain its high recovery rate from HIV-positive patients in recent years. The induction of proteinase secretion in the presence of fluconazole found for most of the C. dubliniensis isolates could be one of the factors involved in adherence.

Molecular mechanisms of fluconazole resistance in Candida dubliniensis isolates from human immunodeficiency virus-infected patients with oropharyngeal candidiasis

Candida dubliniensis is a newly identified species of Candida that is phenotypically similar to but genetically distinct from C. albicans. This organism has been recovered with increasing frequency from the oral cavities of human immunodeficiency virus (HIV)-infected and AIDS patients and has been implicated as a causative agent of oral candidiasis and systemic disease. In the present study we characterized the molecular mechanisms of resistance to fluconazole (FLC) in C. dubliniensis clinical isolates from two different HIV-infected patients with oropharyngeal candidiasis. Isolates were identified to the species level by phenotypic and genotypic tests. DNA-typing techniques were used to assess strain identity. Antifungal susceptibility testing was performed by NCCLS techniques. Northern blotting analysis was used to monitor the expression of genes encoding lanosterol demethylase (ERG11) and efflux transporters (CDR and MDR1) in matched sets of C. dubliniensis-susceptible and -resistant isolates by using probes generated from their homologous C. albicans sequences. In addition, ERG11 genes were amplified by PCR, and their nucleotide sequences were determined in order to detect point mutations with a possible effect in the affinity for azoles. Decreasing susceptibilities to FLC were detected in C. dubliniensis isolates recovered from both patients during the course of treatment. FLC-resistant C. dubliniensis isolates from one patient demonstrated combined upregulation of the MDR1, CDR1, and ERG11 genes. Among the isolates from the second patient, all isolates showing decreased susceptibility to FLC demonstrated upregulation of MDR1, whereas the levels of mRNA for the ERG11 genes remained constant and the expression of CDR genes was negligible. Fourteen point mutations were found in the ERG11 genes of the isolates with decreased susceptibility to FLC. These data demonstrate that the development of azole resistance in C. dublinensis clinical isolates from HIV-infected patients treated with FLC is mediated by multiple molecular mechanisms of resistance, similar to the observations found in the case of C. albicans.

Utility of a pre-optimized kit for random amplified polymorphic DNA in typing Candida albicans

The utility of a pre-optimized kit for random amplified polymorphic DNA (RAPD) was assessed in typing diverse strains of Candida albicans from epidemiologically unrelated inpatients (interpatient analysis) and in detecting clonal variations that maybe present within individual patient isolates (intrapatient analysis). Stool samples from inpatients were cultured on Inhibitory Mold agar. Nine individual colonies from all patients with > or =9 colonies of C. albicans (n = 18) were selected, frozen, and karyotyped using CHEF genomic DNA plug kits and CHEF-DRIII. Each of the selected colonies was then analyzed by RAPD, utilizing the selected kit, with 6 primers. Interpatient analysis revealed 9 karyotypes and 17 RAPD composites. RAPD discrimination was significantly better (p < 0.001). Intrapatient analysis revealed 34 (21%) and 33 (20.4%) variants among 162 colonies tested by RAPD and karyotyping, respectively. The results were discordant in 25 variants, all with differences of 1-3 bands. These results illustrate that this pre-optimized kit for RAPD provides excellent discrimination of genetically unrelated strains. Its performance in delineating subtle clonal differences was comparable with karyotyping; both methods failed to detect all minor genetic variations. The ease of use and quick turnaround time of this kit offer a practical and reliable method for typing diverse strains of C. albicans, but may be inadequate for assessing microevolution.

Identification of four distinct genotypes of Candida dubliniensis and detection of microevolution in vitro and in vivo

The present study investigates further the population structure of Candida dubliniensis and its ability to exhibit microevolution. Using 98 isolates (including 80 oral isolates) from 94 patients in 15 countries, we confirmed the existence of two distinct populations within the species C. dubliniensis, designated Cd25 group I and Cd25 group II, respectively, on the basis of DNA fingerprints generated with the C. dubliniensis-specific probe Cd25. The majority of Cd25 group I isolates (48 of 71, 67.6%) were from human immunodeficiency virus (HIV)-infected individuals, whereas the majority of Cd25 group II isolates (19 of 27, 70.4%) were from HIV-negative individuals (P < or = 0.001). Nucleotide sequence analysis of the internal transcribed spacer (ITS) regions of the rRNA genes from 19 representative isolates revealed the presence of four separate genotypes. All of the Cd25 group I isolates tested belonged to genotype 1, while the Cd25 group II population was comprised of three distinct genotypes (genotypes 2 to 4), which corresponded to distinct clades within the Cd25 group II population. These findings were confirmed using genotype-specific PCR primers with 70 isolates. We also showed that C. dubliniensis can exhibit microevolution in vivo and in vitro as occurs in other yeast species. DNA fingerprinting using the C. dubliniensis probes Cd25, Cd24, and Cd1 and karyotype analysis of multiple oral isolates recovered from the same specimen from each of eight separate patients revealed microevolution in six of eight of the clonal populations. Similarly, sequential clonal isolates from various anatomical sites in two separate patients exhibited microevolution. Microevolution was also shown to occur when two clinical isolates susceptible to fluconazole were exposed to the drug in vitro. The epidemiological significance of the four C. dubliniensis genotypes and the ability of C. dubliniensis to undergo microevolution has yet to be established.

Carriage frequency, intensity of carriage, and strains of oral yeast species vary in the progression to oral candidiasis in human immunodeficiency virus-positive individuals

Candida samples were taken over a period of 2 years from 54 human immunodeficiency virus (HIV)-positive asymptomatic subjects to evaluate changes in yeast carriage, intensity of carriage, and genotype over time. Overall, we found that HIV-positive patients with CD4(+)-cell counts of between 200 and 400/microl had significantly more yeast colonization than healthy control subjects. Of the 54 patients, 11 developed thrush. We found that intensity of carriage in these 11 patients increased significantly in the progression from asymptomatic yeast carrier to an episode of oral thrush. Also, the most common yeast species isolated was Candida albicans; however, we did see a number of patients harboring multiple species at the same time. Using the C. albicans-specific probe Ca3, we found that 54% (n = 6) of the 11 patients who developed thrush maintained genetically similar strains throughout the study period, with minor genetic variations in all patients except one. Forty-six percent of these patients had either multiple strains throughout the study period (n = 2), strain replacement (n = 1), or species replacement (n = 2). Of the patients who had multiple strains, one (I4) was infected by two different strains of Candida dubliniensis distinguished by a recently developed species-specific probe. These results suggest that commensal strains colonizing HIV-positive individuals can undergo alterations prior to producing an episode of thrush.

MDR1-mediated drug resistance in Candida dubliniensis

Candida dubliniensis is a recently described opportunistic fungal pathogen that is closely related to Candida albicans. Candida dubliniensis readily develops resistance to the azole antifungal agent fluconazole, both in vitro and in infected patients, and this resistance is usually associated with upregulation of the CdMDR1 gene, encoding a multidrug efflux pump of the major facilitator superfamily. To determine the role of CdMDR1 in drug resistance in C. dubliniensis, we constructed an mdr1 null mutant from the fluconazole-resistant clinical isolate CM2, which overexpressed the CdMDR1 gene. Sequential deletion of both CdMDR1 alleles was performed by the MPA(R)-flipping method, which is based on the repeated use of a dominant mycophenolic acid resistance marker for selection of integrative transformants and its subsequent deletion from the genome by FLP-mediated, site-specific recombination. In comparison with its parental strain, the mdr1 mutant showed decreased resistance to fluconazole but not to the related drug ketoconazole. In addition, we found that CdMDR1 confers resistance to the structurally unrelated drugs 4-nitroquinoline-N-oxide, cerulenin, and brefeldin A, since the enhanced resistance to these compounds of the parent strain CM2 compared with the matched susceptible isolate CM1 was abolished in the mdr1 mutant. In contrast, CdMDR1 inactivation did not cause increased susceptibility to amorolfine, terbinafine, fluphenazine, and benomyl, although overexpression of CdMDR1 in a hypersusceptible Saccharomyces cerevisiae strain had previously been shown to confer resistance to these compounds. The effect of CdMDR1 inactivation was identical to that seen in two similarly constructed C. albicans mdr1 mutants. Therefore, despite species-specific differences in the amino acid sequences of the Mdr1 proteins, overexpression of CaMDR1 and CdMDR1 in clinical C. albicans and C. dubliniensis strains seems to confer the same drug resistance profile in both species.

Differentiation of Candida albicans and Candida dubliniensis by fluorescent in situ hybridization with peptide nucleic acid probes

The recent discovery of Candida dubliniensis as a separate species that traditionally has been identified as Candida albicans has led to the development of a variety of biochemical and molecular methods for the differentiation of these two pathogenic yeasts. rRNA sequences are well-established phylogenetic markers, and probes targeting species-specific rRNA sequences have been used in diagnostic assays for the detection and identification of microorganisms. Peptide nucleic acid (PNA) is a DNA mimic with improved hybridization characteristics, and the neutral backbone of PNA probes offers significant advantages in whole-cell in situ hybridization assays. In this study, we developed PNA probes targeting the rRNAs of C. albicans and C. dubliniensis and applied them to a fluorescence in situ hybridization method (PNA FISH) for differentiation between C. albicans and C. dubliniensis. Liquid cultures were smeared onto microscope slides, heat fixed, and then hybridized for 30 min. Unhybridized PNA probe was removed by washing, and smears were examined by fluorescence microscopy. Evaluation of the PNA FISH method using smears of 79 C. dubliniensis and 70 C. albicans strains showed 100% sensitivity and 100% specificity for both PNA probes. We concluded that PNA FISH is a powerful tool for the differentiation of C. albicans and C. dubliniensis.

Candida dubliniensis at a cancer center

Candida dubliniensis, a germ tube-positive yeast first described and identified as a cause of oral candidiasis in patients with acquired immunodeficiency syndrome in Europe in 1995, has an expanding clinical and geographic distribution that appears to be similar to that of the other germ tube-positive yeast, Candida albicans. This study determined the frequency, clinical spectrum, drug susceptibility profile, and suitable methods for identification of this emerging pathogen at a cancer center in 1998 and 1999. Twenty-two isolates were recovered from 16 patients with solid-organ or hematologic malignancies or acquired immunodeficiency syndrome. Two patients with cancer had invasive infection, and 14 were colonized with fungus or had superficial fungal infection. All isolates produced germ tubes and chlamydospores at 37 degrees C, did not grow at 45 degrees C, and gave negative reactions with d-xylose and alpha-methyl-d-glucoside in the API 20 C AUX and ID 32 C yeast identification systems. Phenotypic identification was confirmed by molecular beacon probe technology. All isolates were susceptible to the antifungal drugs amphotericin B, 5-fluorocytosine, fluconazole, itraconazole, and ketoconazole.

PCR fingerprinting: a convenient molecular tool to distinguish between Candida dubliniensis and Candida albicans

Candida dubliniensis was recently identified as a germ-tube- and chlamydospore-positive yeast, phenotypically and morphologically indistinguishable from the phylogenetically closely related yeast species C. albicans and its synonymized variant C. stellatoidea. The high similarity between these yeast species causes significant problems in the correct identification of C. dubliniensis in a standard clinical mycology laboratory. Polymerase chain reaction (PCR) fingerprinting was successfully applied here to distinguish between clinical isolates of the two closely related species. Microsatellite ([GACA]4) and minisatellite ([5'-GAGGGTGGCGGTTCT-3'], derived from the core-sequence of the wild-type phage M13) specific oligonucleotides were used as single primers in PCR to amplify hypervariable inter-repeat DNA sequences from 16 C. dubliniensis strains and 11 C. albicans strains. Each species, represented by its ex-type strain, could be identified by a distinct species-specific multilocus pattern, allowing identification to species level for all clinical isolates. In addition, the PCR fingerprinting generated strain-specific profiles, making this method applicable to epidemiological investigations. PCR fingerprinting using the primer M13 is proposed here as a simple, reliable and highly reproducible molecular tool to differentiate between strains of C. albicans and C. dubliniensis.

Cloning and characterization of a complex DNA fingerprinting probe for Candida parapsilosis

Candida parapsilosis accounts for a significant number of nosocomial fungemias, but in fact, no effective and verified genetic fingerprinting method has emerged for assessing the relatedness of independent isolates for epidemiological studies. A complex 15-kb DNA fingerprinting probe, Cp3-13, was therefore isolated from a library of C. parapsilosis genomic DNA fragments. The efficacy of Cp3-13 for DNA fingerprinting was verified by a comparison of its clustering capacity with those of randomly amplified polymorphic DNA analysis and internally transcribed spacer region sequencing, by testing species specificity, and by assessing its capacity to identify microevolutionary changes both in vitro and in vivo. Southern blot hybridization of EcoRI/SalI-digested DNA with Cp3-13 provides a fingerprinting system that (i) identifies the same strain in independent isolates, (ii) discriminates between unrelated isolates, (iii) separates independent isolates into valid groups in a dendrogram, (iv) identifies microevolution in infecting populations, and (v) is amenable to automatic computer-assisted DNA fingerprint analysis. This probe is now available for epidemiological studies.