Atypical strains ofCandida albicansrecovered from AIDS patients

Extreme diversification driven by parallel events of massive loss of heterozygosity in the hybrid lineage of Candida albicans

Candida albicans is the most commonly reported species causing candidiasis. The taxonomic classification of C. albicans and related lineages is controversial, with Candida africana (syn. C. albicans var. africana) and Candida stellatoidea (syn. C. albicans var. stellatoidea) being considered different species or C. albicans varieties depending on the authors. Moreover, recent genomic analyses have suggested a shared hybrid origin of C. albicans and C. africana, but the potential parental lineages remain unidentified. Although the genomes of C. albicans and C. africana have been extensively studied, the genome of C. stellatoidea has not been sequenced so far. In order to get a better understanding of the evolution of the C. albicans clade, and to assess whether C. stellatoidea could represent one of the unknown C. albicans parental lineages, we sequenced C. stellatoidea type strain (CBS 1905). This genome was compared to that of C. albicans and of the closely related lineage C. africana. Our results show that, similarly to C. africana, C. stellatoidea descends from the same hybrid ancestor as other C. albicans strains and that it has undergone a parallel massive loss of heterozygosity.

Candida africana and its closest relatives

Candida africana is a recently described opportunistic yeast pathogen that has been linked to vaginal candidiasis. This yeast was first described, in 1995, as atypical chlamydospore-negative Candida albicans strain, and subsequently proposed as a new Candida species on the basis of morphological, biochemical and physiological characteristics clearly different from those of typical C. albicans isolates. Phylogenetic studies based on the comparison of ribosomal DNA sequences demonstrated that C. africana and C. albicans isolates are too closely related to draw any conclusions regarding the status of a new species. Therefore, on the basis of these studies, some authors considered C. africana as a biovar of C. albicans even if genetic differences may be found if additional regions of genomic DNA are sequenced. The taxonomic situation of C. africana and its phylogenetic relationship with other Candida species is still controversial and remains, at present, a matter of debate. Our goal is to review the current knowledge about C. africana and highlight the development of rapid and accurate tests for its discrimination from C. albicans, Candida dubliniensis and Candida stellatoidea. Furthermore, through the analysis of literature data, we have found that C. africana has a worldwide distribution and a considerable number of features making its study particularly interesting.

Molecular fingerprinting methods for the discrimination between C. albicans and C. dubliniensis

Opportunistic fungal pathogens are becoming increasingly important causes of both community-acquired and nosocomial infections. The most important fungal pathogens are yeast species belonging to the genus Candida. These species show differences in levels of resistance to antifungal agents and mortality. Consequently, it is important to correctly identify the causative organism to the species level. Identification of Candida dubliniensis in particular remains problematic because of the high degree of phenotypic similarity between this species and Candida albicans. However, as the differences between both are most pronounced at the genetic level, several studies have been conducted in order to provide a specific and rapid identification fingerprinting molecular test. In most candidal infectious, no single DNA fingerprinting technique has evolved as a dominant method, and each method has its advantages, disadvantages and limitations. Moreover, the current challenge of these techniques is to compile standardized patterns in a database for interlaboratory use and future reference. This review provides an overview of most common molecular fingerprinting techniques currently available for discrimination of C. albicans and C. dubliniensis.

Genetic relatedness of oral yeasts within and between patients with marginal periodontitis and subjects with oral health

BACKGROUND

Yeasts are found in periodontal pockets at a frequency of 15-21%. However, the genetic relatedness of oral yeasts within and between patients with marginal periodontitis is not clear.

OBJECTIVES

Assay genetic relatedness of oral yeasts from marginal periodontitis patients and oral health subjects, as well as genetic relatedness of yeasts from different oral sites in these two groups of participants.

MATERIAL AND METHODS

Yeast isolates were collected from 23 marginal periodontitis patients and 19 oral health subjects. Random amplified polymorphic DNA (RAPD) fingerprinting and the Dendron computer-assisted program for gel analyses were applied for estimation of genetic relatedness of yeasts.

RESULTS

The similarity coefficient (S(AB)) of the marginal periodontitis group ranged from 0.49 to 1.00 with an average of 0.64 +/- 0.11, whereas the S(AB) of the oral health group ranged from 0.62 to 1.00 with an average of 0.72 +/- 0.07. Three genetic clusters and 73 genotypes were obtained from the marginal periodontitis group, whereas three genetic clusters and 55 genotypes were found in the oral health group. In the pooled dendrogram, 57% of the yeast isolates and the type strain of Candida albicans fell in a major cluster V. There were no significant differences between the frequencies of clusters from the different oral sites within the two participant groups.

CONCLUSIONS

Genetically heterogeneous yeasts were found in the oral cavities of marginal periodontitis patients and oral health subjects. Similar genetic clustering patterns were obtained from the yeasts of the two groups, with cluster V being most predominant. Yeasts of the marginal periodontitis group were more genetically diverse than yeasts of the oral health group, and some yeasts of the marginal periodontitis group exhibited unique genetic patterns. There was no clear association between yeast genetic clusters and oral sites in the two participant groups.

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.

Rapid and unequivocal differentiation of Candida dubliniensis from other Candida species using species-specific DNA probes: comparison with phenotypic identification methods

Candida dubliniensis is a recently described opportunistic pathogen which shares many phenotypic characteristics with Candida albicans but which has been reported to rapidly acquire resistance to azole antifungal drugs. Therefore, differentiation of C. dubliniensis from C. albicans becomes important to better understand the clinical significance and epidemiologic role of C. dubliniensis in candidiasis. We compared phenotypic methods for the differentiation of C. dubliniensis from C. albicans (i.e. the ability to grow at elevated temperatures, colony color on CHROMagar Candida medium, and carbohydrate assimilation patterns) to amplify the results of a polymerase chain reaction (PCR) assay using universal fungal primers to the internal transcribed spacer 2 (ITS2) region of rDNA and species-specific DNA probes in an enzyme immunoassay format (PCR-EIA). DNA sequencing of the ITS1 rDNA region was also conducted. The C. dubliniensis ITS2 probe correctly identified all C. dubliniensis isolates without cross-reaction with any other Candida species tested (mean A(650 nm) +/- SE, C. dubliniensis probe with C. dubliniensis DNA, 0.372 +/- 0.01, n = 22; C. dubliniensis probe with other Candida species DNA, 0.001 +/- 0.02 n = 16, P < 0.001). All other Candida species tested (C. albicans, Candida glabrata, Candida krusei, Candida parapsilosis, and Candida tropicalis) were also correctly identified by the PCR-EIA without any detectable cross-reactions among species. Phenotypically, C. dubliniensis isolates demonstrated an increased sensitivity to heat compared to C. albicans isolates. At 42 degrees C, only 50% of C. dubliniensis isolates grew compared to 73% of C. albicans isolates and, at 45 degrees C, 91% of C. dubliniensis isolates failed to grow compared to 64% of C. albicans isolates. C. albicans was more likely to demonstrate a dark green or blue green colony color on CHROMagar Candida medium obtained from Becton Dickinson (i.e. 100% of C. albicans isolates were dark green or blue green versus 64% of C. dubliniensis isolates) whereas no difference in the percentage of C. albicans or C. dubliniensis isolates producing dark green or blue green colony color was detected using CHROMagar Candida medium from Hardy Diagnostics (82% for both species). The API 20C AUX carbohydrate assimilation system incorrectly identified C. dubliniensis as C. albicans in all but three cases: remaining isolates were misidentified as C. albicans/C. tropicalis, C. tropicalis/C. albicans, and Candida lusitaniae/C. albicans. In all, 82% of C. albicans isolates and 100% of C. dubliniensis isolates assimilated trehalose; the latter finding was opposite to that reported for C. dubliniensis in the API 20C AUX profile index. Xylose and alpha-methyl-D-glucoside assimilation, respectively, were negative for 100 and 95% of C. dubliniensis isolates and positive for 100 and 91% of C. albicans isolates, confirming earlier reports that assimilation results for xylose and alpha-methyl-D-glucoside may be helpful in the discrimination of these two species. However, conventional phenotypic species identification tests required days for completion, whereas the PCR-EIA could be completed in a matter of hours. In addition, identification of Candida species by ITS1 rDNA sequencing gave 100% correspondence to the results obtained by the PCR-EIA, confirming the specificity of the PCR-EIA method. These data indicate that although a combination of phenotypic methods may help differentiate C. dubliniensis from C. albicans to some extent, the PCR-EIA can provide a simple, rapid, and unequivocal identification of the most medically important Candida species in a single test.

Electrophoretic protein patterns and numerical analysis of Candida albicans from the oral cavities of healthy children

The aim of this research was to evaluate the protein polymorphism degree among seventy-five C. albicans strains from healthy children oral cavities of five socioeconomic categories from eight schools (private and public) in Piracicaba city, São Paulo State, in order to identify C. albicans subspecies and their similarities in infantile population groups and to establish their possible dissemination route. Cell cultures were grown in YEPD medium, collected by centrifugation, and washed with cold saline solution. The whole-cell proteins were extracted by cell disruption, using glass beads and submitted to SDS-PAGE technique. After electrophoresis, the protein bands were stained with Coomassie-blue and analyzed by statistics package NTSYS-pc version 1.70 software. Similarity matrix and dendrogram were generated by using the Dice similarity coefficient and UPGMA algorithm, respectively, which made it possible to evaluate the similarity or intra-specific polymorphism degrees, based on whole-cell protein fingerprinting of C. albicans oral isolates. A total of 13 major phenons (clusters) were analyzed, according to their homogeneous (socioeconomic category and/or same school) and heterogeneous (distinct socioeconomic categories and/or schools) characteristics. Regarding to the social epidemiological aspect, the cluster composition showed higher similarities (0.788 < S D < 1.0) among C. albicans strains isolated from healthy children independent of their socioeconomic bases (high, medium, or low). Isolates of high similarity were not found in oral cavities from healthy children of social stratum A and D, B and D, or C and E. This may be explained by an absence of a dissemination route among these children. Geographically, some healthy children among identical and different schools (private and public) also are carriers of similar strains but such similarity was not found among other isolates from children from certain schools. These data may reflect a restricted dissemination route of these microorganisms in some groups of healthy scholars, which may be dependent of either socioeconomic categories or geographic site of each child. In contrast to the higher similarity, the lower similarity or higher polymorphism degree (0.499 < S D < 0.788) of protein profiles was shown in 23 (30.6%) C. albicans oral isolates. Considering the social epidemiological aspect, 42.1%, 41.7%, 26.6%, 23.5%, and 16.7% were isolates from children concerning to socioeconomic categories A, D, C, B, and E, respectively, and geographically, 63.6%, 50%, 33.3%, 33.3%, 30%, 25%, and 14.3% were isolates from children from schools LAE (Liceu Colégio Albert Einstein), MA (E.E.P.S.G. "Prof. Elias de Melo Ayres"), CS (E.E.P.G. "Prof. Carlos Sodero"), AV (Alphaville), HF (E.E.P.S.G. "Honorato Faustino), FMC (E.E.P.G. "Prof. Francisco Mariano da Costa"), and MEP (E.E.P.S.G. "Prof. Manasses Ephraim Pereira), respectively. Such results suggest a higher protein polymorphism degree among some strains isolated from healthy children independent of their socioeconomic strata or geographic sites. Complementary studies, involving healthy students and their families, teachers, servants, hygiene and nutritional habits must be done in order to establish the sources of such colonization patterns in population groups of healthy children. The whole-cell protein profile obtained by SDS-PAGE associated with computer-assisted numerical analysis may provide additional criteria for the taxonomic and epidemiological studies of C. albicans.

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.

First characterization of Candida albicans by random amplified polymorphic DNA method in Nicaragua and comparison of the diagnosis methods for vaginal candidiasis in Nicaraguan women

A total of 106 women with vaginitis in Nicaragua were studied. The positive rate for the identification of Candida species was 41% (44 positive cultures out of 106 women with vaginitis). The sensitivity of microscopic examination of wet mount with the potassium hydroxide (KOH) was 61% and 70% with Gram's stain when using the culture of vaginal fluid as gold standard for diagnosis of candidiasis. Among the 44 positives cultures, isolated species of yeast from vaginal swabs were C. albicans (59%), C. tropicalis (23%), C. glabrata (14%) and C. krusei (4%). This study reports the first characterization of 26 C. albicans stocks from Nicaragua by the random amplified polymorphic DNA method. The genetic analysis in this small C. albicans population showed the existence of linkage disequilibrium, which is consistent with the hypothesis that C. albicans undergoes a clonal propagation.

Clonality structure in Candida dubliniensis

Multilocus enzyme electrophoresis was performed on 76 European strains of Candida dubliniensis. Ten of the 20 enzyme-encoding loci were polymorphic, giving rise to 10 electrophoretic types within the sample studied. Investigation of the population genetics of a subset of 36 strains from HIV-infected patients in London showed the existence of strong heterozygote deficits and excesses associated with significant linkage disequilibria between pairs of loci. These findings, together with the predominance of multilocus genotypes, strongly suggest that C. dubliniensis is mainly (if not totally) clonal. Analysis of genotypes of a larger number of strains should confirm this conclusion and improve our understanding of the epidemiology of this pathogen.

Ca3 fingerprinting of Candida albicans isolates from human immunodeficiency virus-positive and healthy individuals reveals a new clade in South Africa

To examine the question of strain specificity in oropharyngeal candidiasis associated with human immunodeficiency virus (HIV) infection, oral samples were collected from 1,196 HIV-positive black South Africans visiting three clinics and 249 Candida albicans isolates were selected for DNA fingerprinting with the complex DNA fingerprinting probe Ca3. A total of 66 C. albicans isolates from healthy black South Africans and 46 from healthy white South Africans were also DNA fingerprinted as controls. Using DENDRON software, a cluster analysis was performed and the identified groups were compared to a test set of isolates from the United States in which three genetic groups (I, II, and III) were previously identified by a variety of genetic fingerprinting methods. All of the characterized South African collections (three from HIV-positive black persons, two from healthy black persons, and one from healthy white persons) included group I, II, and III isolates. In addition, all South African collections included a fourth group (group SA) completely absent in the U.S. collection. The proportion of group SA isolates in HIV-positive and healthy black South Africans was 53% in both cases. The proportion in healthy white South Africans was 33%. In a comparison of HIV-positive patients with and without oropharyngeal symptoms of infection, the same proportions of group I, II, III, and SA isolates were obtained, indicating no shift to a particular group on infection. However, by virtue of its predominance as a commensal and in infections, group SA must be considered the most successful in South Africa. Why group SA isolates represent 53 and 33% of colonizing strains in black and white South Africans and are absent in the U.S. collection represents an interesting epidemiological question.

Molecular characterization of Candida spp. isolated from the oral cavities of patients from diverse clinical settings

Infections by Candida spp. have increased in medical importance over the past few decades. Our understanding of species identification, commensalisms, pathogenicity, person-to-person spread, and the development of antifungal resistance within specific strains has been greatly enhanced by the utilization of molecular epidemiological methodology. The aim of the current research was to assess the quantity, species and molecular characterization of oral yeast isolates from well-defined cohorts of immunocompetent patients from a diverse range of clinical settings. Oral rinse samples were assessed for the growth of yeast and degree of colonization. Isolates were defined to the species level by both phenotypic and molecular methods and strains were further genotypically subtyped. Significant variation was shown to exist in the number, species and genotypic subgroups of yeast isolated from the oral cavity in different patient groups. This variation could be attributed to the local oral conditions unique to these patient groups.

Subgingival strains of Candida albicans in relation to geographical origin and occurrence of periodontal pathogenic bacteria

Clonal diversity of subgingival yeast strains was determined in relation to geographical location and coexistence of selected periodontal pathogenic bacteria. A total of 60 dental patients from Finland, the United States and Turkey each contributed five Candida albicans isolates. C. albicans isolates were serotyped using slide agglutination and genotyped using polymerase chain reaction (PCR) amplification and a random sequence primer. In general, each study subject yielded C. albicans isolates belonging to the same serotype and genotype. C. albicans serotype A occurred more frequently in subjects from Finland and Turkey than in subjects from the United States. A total of 27 PCR-based C. albicans genotypes were identified. One C. albicans genotype occurred with particularly high frequency in subjects from Turkey and another genotype in subjects from the United States. Relationships were identified between C. albicans serotypes and genotypes. Further studies are needed to determine environmental factors of importance for subgingival colonization and persistence of C. albicans.

Typing of Candida albicans isolates by sequence analysis of the cytochrome b gene and differentiation from Candida stellatoidea

Including type strains, mitochondrial cytochrome b genes of 32 strains of Candida albicans and 6 strains of Candida stellatoidea, presently treated as a synonym for C. albicans, were partially sequenced. Analysis of 396-bp nucleotide sequences of the strains under investigation divided C. albicans isolates into three types: type I, type II, and type III; however, strains of C. stellatoidea represented distinct type IV isolates. Deduced amino acid sequences of type I, type II, and type III were identical and differed from that of type IV by one amino acid. Genotypes (rDNA type) of the test strains were also checked. Cytochrome b typing did not correlate with genotyping, and different genotypes occurred for one cytochrome b type. This study shows that cytochrome b gene sequences are useful for analyzing the genetic relatedness of C. albicans isolates and effective for differentiating C. stellatoidea from C. albicans.

Genotypic identification of Candida dubliniensis isolated from HIV patients by MLEE

Candida dubliniensis is a novel species only recently described. This emerging pathogen shares some of the phenotypic characteristics specific to C. albicans but is genetically different. In this study we typed four strains of atypical C. albicans isolated in our laboratory and compared them to 41 strains of C. albicans and 11 strains of C. dubliniensis by several phenotypic methods and by multilocus enzyme electrophoresis. Using factorial correspondence analysis, we distinguished C. dubliniensis and the atypical C. albicans strains from all strains of C. albicans. Atypical C. albicans strains were identified as C. dubliniensis.

Analysis of parity between protein-based electrophoretic methods for the characterization of oral Candida species

Electrophoretic studies of multilocus-enzymes (MLEE) and whole-cell protein (SDS-PAGE) were carried out in order to evaluate the parity between different methods for the characterization of five Candida species commonly isolated from oral cavity of humans by numerical taxonomy methods. The obtained data revealed that sodium dodecyl sulfate polyacrylamide gel electrophoresis is more efficient in grouping strains in their respective species while MLEE has much limited resolution in organizing all strains in their respective species-specific clusters. MLEE technique must be regarded for surveys in which just one species of Candida is involved.

Comparison of virulence factors of oral Candida dubliniensis and Candida albicans isolates in healthy people and patients with chronic candidosis

We determined differences in the expression of certain virulence factors between oral Candida dubliniensis and Candida albicans species. In addition, clonal differences were sought among C. albicans isolates recovered from patients with and without compromised immune system. The material comprised 93 clinical yeast isolates originated in 40 subjects (1-5 isolates per subject). All 26 C. dubliniensis isolates and 46 C. albicans isolates originated from healthy routine dental clinic patients. Additionally, 21 C. albicans isolates were collected from patients with autoimmune polyendocrinopathy-candidosis-ectodermal dystrophy (APECED), who have chronic candidosis as one manifestation of their immunocompromising disease. Polymerase chain reaction amplification using the random sequence primer OPE-03 enabled grouping of the C. dubliniensis isolates in 2 genotypes (I and II) and C. albicans isolates in 15 genotypes (I-XV). No significant difference was found in the distribution of genotypes between the patients with APECED and the healthy subjects. C. dubliniensis isolates exhibited high-frequency phenotypic switching significantly more frequently than did C. albicans isolates, and vice versa regarding phospholipase and proteinase production. Proteinase production was significantly more frequent among C. albicans genotype V than genotype IX isolates. No significant difference was found in expression of virulence factors of C. albicans isolates between the patients with APECED and the healthy subjects.

The ins and outs of DNA fingerprinting the infectious fungi

DNA fingerprinting methods have evolved as major tools in fungal epidemiology. However, no single method has emerged as the method of choice, and some methods perform better than others at different levels of resolution. In this review, requirements for an effective DNA fingerprinting method are proposed and procedures are described for testing the efficacy of a method. In light of the proposed requirements, the most common methods now being used to DNA fingerprint the infectious fungi are described and assessed. These methods include restriction fragment length polymorphisms (RFLP), RFLP with hybridization probes, randomly amplified polymorphic DNA and other PCR-based methods, electrophoretic karyotyping, and sequencing-based methods. Procedures for computing similarity coefficients, generating phylogenetic trees, and testing the stability of clusters are then described. To facilitate the analysis of DNA fingerprinting data, computer-assisted methods are described. Finally, the problems inherent in the collection of test and control isolates are considered, and DNA fingerprinting studies of strain maintenance during persistent or recurrent infections, microevolution in infecting strains, and the origin of nosocomial infections are assessed in light of the preceding discussion of the ins and outs of DNA fingerprinting. The intent of this review is to generate an awareness of the need to verify the efficacy of each DNA fingerprinting method for the level of genetic relatedness necessary to answer the epidemiological question posed, to use quantitative methods to analyze DNA fingerprint data, to use computer-assisted DNA fingerprint analysis systems to analyze data, and to file data in a form that can be used in the future for retrospective and comparative studies.

Genetic structure of typical and atypical populations of Candida albicans from Africa

Atypical isolates of the pathogenic yeast Candida albicans have been reported with increasing frequency. To investigate the origin of a set of atypical isolates and their relationship to typical isolates, we employed a combination of molecular phylogenetic and population genetic analyses using rDNA sequencing, PCR fingerprinting, and analysis of co-dominant DNA nucleotide polymorphisms to characterize the population structure of one typical and two atypical populations of C. albicans from Angola and Madagascar. The extent of clonality and recombination was assessed in each population. The analyses revealed that the structure of all three populations of C. albicans was predominantly clonal but, as in previous studies, there was also evidence for recombination. Allele frequencies differed significantly between the typical and the atypical populations, suggesting very low levels of gene flow between them. However, allele frequencies were quite similar in the two atypical C. albicans populations, suggesting that they are closely related. Phylogenetic analysis of partial sequences encoding the nuclear 26S rDNA demonstrated that all three populations belong to a single monophyletic group, which includes the type strain of C. albicans.

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

Using a strategy to clone large genomic sequences containing repetitive elements from the infectious yeast Candida dubliniensis, the three unrelated sequences Cd1, Cd24, and Cd25, with respective molecular sizes of 15,500, 10,000, and 16,000 bp, were cloned and analyzed for their efficacy as DNA fingerprinting probes. Each generated a complex Southern blot hybridization pattern with endonuclease-digested genomic DNA. Cd1 generated an extremely variable pattern that contained all of the bands of the pattern generated by the repeat element RPS of Candida albicans. We demonstrated that Cd1 does not contain RPS but does contain a repeat element associated with RPS throughout the C. dubliniensis genome. The Cd1 pattern was the least stable over time both in vitro and in vivo and for that reason proved most effective in assessing microevolution. Cd24, which did not exhibit microevolution in vitro, was highly variable in vivo, suggesting in vivo-dependent microevolution. Cd25 was deemed the best probe for broad epidemiological studies, since it was the most stable over time, was the only truly C. dubliniensis-specific probe of the three, generated the most complex pattern, was distributed throughout all C. dubliniensis chromosomes, and separated a worldwide collection of 57 C. dubliniensis isolates into two distinct groups. The presence of a species-specific repetitive element in Cd25 adds weight to the already substantial evidence that C. dubliniensis represents a bona fide species.

Molecular and phenotypic characterization of genotypic Candida albicans subgroups and comparison with Candida dubliniensis and Candida stellatoidea

There have been increased reports of the isolation of unusual genotypic groups of Candida albicans (groups C and D) based on a well-defined genotypic method; this method uses cellular DNA digested with the EcoRI enzyme and the restriction fragment length polymorphisms (RFLPs) generated by agarose gel electrophoresis. The aim of the present study was to use additional molecular tools to characterize these unusual strains and to compare them with authentic strains of C. dubliniensis, a recently delineated species, and type I C. stellatoidea. The RFLPs of PCR products generated from the intergenic transcribed spacer (ITS) region did not differentiate among C. albicans genotypes A, B, and C and type I C. stellatoidea. However, this method did differentiate the C. albicans genotype D strains, which were identical to C. dubliniensis. The RFLPs generated by HaeIII digestion of the PCR products of the V3 region of the 25S rRNA gene (rDNA) could differentiate the same groups as RFLP analysis of the PCR amplicon of the ITS region. C. albicans genotype B isolates have been shown to have a transposable intron in the 25S rDNA, whereas genotype A isolates do not; C. dubliniensis strains also have an intron that is larger than that in genotype B C. albicans strains but that is in the same location. PCR designed to span this region resulted in a single product for C. albicans genotype A (450 bp), B (840 bp), type 1 C. stellatoidea (840 bp), and C. dubliniensis (1,080 bp), whereas the C. albicans genotype C isolates had two major products (450 and 840 bp). All C. albicans genotype D isolates gave a PCR product identical to that given by C. dubliniensis. These results indicate that those strains previously designated C. albicans genotype D are in fact C. dubliniensis, that no differences were found between type 1 C. stellatoidea and C. albicans genotype B strains, and that the C. albicans genotype C strains appear to have the transposable intron incompletely inserted throughout the ribosomal repeats in their genomes. The results of the antifungal susceptibility testing of 105 of these strains showed that, for fluconazole, strains of C. dubliniensis were significantly more susceptible than strains of each of the C. albicans genotypes (genotypes A, B, and C). The flucytosine susceptibility results indicated that strains of C. albicans genotype A were significantly less susceptible than either C. albicans genotype B or C. albicans genotype C strains. These results indicate that there is a correlation between the Candida groups and antifungal susceptibility.