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

Stability of allelic frequencies and distributions of Candida albicans microsatellite loci from U.S. population-based surveillance isolates

Allelic distributions and frequencies of five Candida albicans microsatellite loci have been determined for strains isolated from the bloodstream and obtained through active population-based surveillance in two U.S. metropolitan areas between 1998 and 2000. These data were compared to data for isolates obtained from two other U.S. regions in 1992 to 1993. In a majority of pairwise combinations between sites, no evidence was seen for shifts in microsatellite allelic frequencies. One to three alleles were highly predominant and correlated with major genotypes. These data both support the concepts of allelic stability and genetic equilibria and suggest that, in the United States, strains of C. albicans isolated from the bloodstream may form a defined, genetically homogeneous population across geographical distance and time.

Clonal reproduction and limited dispersal in an environmental population of Cryptococcus neoformans var gattii isolates from Australia

Cryptococcus neoformans var. gattii is a causative agent of cryptococcosis and is thought to have a specific ecological association with a number of Eucalyptus species in Australia. However, the role that the tree plays in the life cycle of the fungus and the nature of the infectious propagule are not well understood. This study set out to examine whether sexual recombination is occurring in a natural population of C. neoformans var. gattii and whether the fungus disseminates between colonized trees. Thirty C. neoformans var. gattii isolates, consisting of both the alpha and a mating types, were collected from 13 Eucalyptus camaldulensis trees growing along a riverbank in Renmark, South Australia. The genetic diversity within the population was studied by using amplified fragment length polymorphism fingerprinting, and each isolate was assigned a unique multilocus genotype. Population genetic analyses of the multilocus data found no evidence of genetic exchange between members of the population, indicating a clonal population structure. Canonical variate analysis was then used to study the relationship between isolates from different colonized trees. Isolates from individual trees were strongly correlated, and it appeared that dispersal between trees was not occurring to any appreciable extent. These results suggest that the eucalypt may not be the primary niche for C. neoformans var. gattii but that the decaying wood present in hollows on these trees may provide a favorable substrate for extensive clonal propagation of the yeast cells.

Multilocus sequence typing suggests the chytrid pathogen of amphibians is a recently emerged clone

Chytridiomycosis is a recently identified fungal disease associated with global population declines of frogs. Although the fungus, Batrachochytrium dendrobatidis, is considered an emerging pathogen, little is known about its population genetics, including the origin of the current epidemic and how this relates to the dispersal ability of the fungus. In this study, we use multilocus sequence typing to examine genetic diversity and relationships among 35 fungal strains from North America, Africa and Australia. Only five variable nucleotide positions were detected among 10 loci (5918 bp). This low level of genetic variation is consistent with the description of B. dendrobatidis as a recently emerged disease agent. Fixed (i.e. 100%) or nearly fixed frequencies of heterozygous genotypes at two loci suggested that B. dendrobatidis is diploid and primarily reproduces clonally. In contrast to the lack of nucleotide polymorphism, electrophoretic karyotyping of multiple strains demonstrated a number of chromosome length polymorphisms.

Evolution of drug resistance in Candida albicans

The widespread deployment of antimicrobial agents in medicine and agriculture is nearly always followed by the evolution of resistance to these agents in the pathogen. With the limited availability of antifungal drugs and the increasing incidence of opportunistic fungal infections, the emergence of drug resistance in fungal pathogens poses a serious public health concern. Antifungal drug resistance has been studied most extensively with the yeast Candida albicans owing to its importance as an opportunistic pathogen and its experimental tractability relative to other medically important fungal pathogens. The emergence of antifungal drug resistance is an evolutionary process that proceeds on temporal, spatial, and genomic scales. This process can be observed through epidemiological studies of patients and through population-genetic studies of pathogen populations. Population-genetic studies rely on sampling of the pathogen in patient populations, serial isolations of the pathogen from individual patients, or experimental evolution of the pathogen in nutrient media or in animal models. Predicting the evolution of drug resistance is fundamental to prolonging the efficacy of existing drugs and to strategically developing and deploying novel drugs.

Oral fungal and bacterial infections in HIV-infected individuals: an overview in Africa

Oral opportunistic infections developing secondary to human immunodeficiency virus (HIV) infection have been reported from the early days of the epidemic and have been classified by both the EC-Clearinghouse and the World Health Organisation (WHO). Among the fungal infections, oral candidiasis, presenting in African HIV-infected patients has been sporadically documented. We review the literature with respect to candidal carriage, oral candidiasis prevalence and the predictive value of oral candidiasis for a diagnosis of underlying HIV disease in African HIV-infected patients. The use of oral candidiasis as a marker of disease progression, the species of yeasts isolated from the oral cavity in Africa and the resistance of the yeasts to antifungal agents and treatment regimens are discussed. Orofacial lesions as manifestations of the systemic mycoses are rarely seen in isolation and few cases are reported in the literature from Africa. In spite of the high incidence of noma, tuberculosis, chronic osteomyelitis and syphilis in Africa, surprisingly there have been very few reported cases of the oral manifestations of these diseases in HIV-positive individuals. Orofacial disease in HIV-infected patients is associated with marked morbidity, which is compounded by malnutrition. The authors indicate specific research areas, initially directed at the most effective management strategies, which would complete data in this important area.

Recovery and studies on chlamydospore-negative Candida albicans isolated from clinical specimens

During a period of 31 months, we isolated 3525 strains of Candida albicans from different patient specimens. Twenty-five of these (0.71%), obtained from female patients, displayed morphological and biochemical characteristics different from those seen in typical C. albicans. The failure to produce chlamydospores in cornmeal agar was the common denominator in this group. The strains were categorized into three groups: Group I contained 13 isolates that produced germ tubes but were unable to assimilate trehalose (TRE), glucosamine (GLN) and N-acetylglucosamine (NAG); Group II contained four isolates that were germ-tube positive and able to assimilate TRE, GLN and NAG; and Group III contained eight isolates that were germ-tube negative and able to assimilate TRE, GLN and NAG. These isolates were further studied to determine their biotypes, serotypes, extracellular proteinase production and antifungal susceptibility. Group I isolates were of serotype B, whereas Groups II and III were serotype A. All isolates produced high to moderate amounts of extracellular proteinase. Six group I isolates were resistant to 5-fluorocytosine, whereas all groups II and III isolates were susceptible to this drug. Five of the 12 isolates of group II and III were resistant to fluconazole, itraconazole and ketoconazole.

Diversity of commensal yeasts within and among healthy hosts

We sampled commensal yeasts from three body sites of 24 healthy individuals to examine the patterns of commensal yeast species distribution and strain relatedness within and among individuals. To examine the short-term dynamics, each individual was sampled three times every 35-40 days at each of three body sites: mouth, fingernail, and toenail. The hosts included six genealogically unrelated individuals and 18 that belonged to four families. A total of 63 morphologically distinct colonies were isolated, identified, and genotyped. Nine yeast species were recovered, including 28 isolates of Candida albicans; 26 of C. parapsilosis; 2 each of C. krusei and C. tropicalis; and 1 each of C. famata, C. glabrata, C. guilliermondii, C. lusitaniae and Trichosporon beigelii. A significant difference in total yeast recovery rate between families was observed. However, body sites did not differ in the rates of yeast recovery. The three body sites showed different species distributions with the fingernail sample containing the highest species diversity, followed by the toenail sample. The oral sample contained the lowest species diversity with all 23 oral isolates being C. albicans. Among the 63 strains, forty-six unique genotypes were identified by PCR fingerprinting. Eleven shared-genotypes were identified, seven of which were from the same body site of the same host. The other four were from different members of the same family. Several family-specific genotypes and genotype clusters were found but the results were inconsistent with strict familial transmission of human commensal yeasts. A single host can have multiple species or multiple genotypes of the same species at the same or different body sites. Changes of species and genotypes over the sampling period for the same body site of individual hosts were also observed, including one direct observation of familial yeast transmission between two members of the same family during our sampling period. Our results indicate dynamic processes of yeast colonization, maintenance and evolution in healthy human hosts.

Usefulness of multilocus sequence typing for characterization of clinical isolates of Candida albicans

Molecular characterization of Candida albicans isolates is essential for understanding the epidemiology of nosocomial infections caused by this yeast. Here, we investigated the potential value of multilocus sequence typing (MLST) for characterizing epidemiologically related or unrelated C. albicans strains of various clinical origins. Accordingly, we sequenced the internal regions (loci) of six selected housekeeping genes of 40 C. albicans clinical isolates and 2 reference strains. In all, 68 polymorphic nucleotide sites were identified, of which 65 were found to be heterozygous in at least one isolate. Ten to 24 different genotypes were observed at the different loci, resulting, when combined, in 39 unique genotype combinations or diploid sequence types (DSTs). When MLST was applied to 26 epidemiologically unrelated isolates and the 2 reference strains, it allowed the identification of 27 independent DSTs, thus demonstrating a discriminatory power of 99.7. Using multidimensional scaling together with the minimum spanning tree method to analyze interstrain relationships, we identified six groups of genetically related isolates on the basis of bootstrap values of greater than 900. Application of MLST to 14 epidemiologically related isolates showed that those recovered from patients in the same hospital ward during the same 3 months had specific DSTs, although 73% of these isolates were genetically very close. This suggests that MLST can trace minute variations in the sequences of related isolates. Overall, MLST proved to be a highly discriminatory and stable method for unambiguous characterization of C. albicans.

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.

PCR fingerprinting of Candida albicans associated with chronic hyperplastic candidosis and other oral conditions

The purpose of this study was to genotype strains of Candida albicans to determine whether specific types were associated with chronic hyperplastic candidosis (CHC). A total of 67 candidal isolates from CHC patients (n = 17) and from patients with other oral conditions (n = 21) were genotyped by PCR fingerprinting employing two interrepeat primer combinations (1245 and 1246 primers or 1251 primer) and a single minisatellite-specific M13 primer. The most suitable primer for fingerprint analysis was found to be primer 1251, yielding well-resolved banding patterns. For the 67 isolates tested, PCR fingerprinting delineated 25 (1245 and 1246 primers), 27 (1251 primer), and 25 (M13 primer) profiles. The majority of C. albicans isolates from multiple sites within the mouth produced identical profiles (six out of nine subjects examined). For patients for whom a series of longitudinal isolates was available, strain persistence for up to 7 years was evident for five out of eight individuals, despite episodes of antifungal therapy. Computer-assisted comparison of the interrepeat PCR fingerprints identified seven distinct profiles that were shared among isolates from different individuals. However, no association was evident among isolates of C. albicans from specific clinical conditions. Eight isolates that were initially identified as C. albicans but having atypical PCR profiles were later confirmed as Candida dubliniensis. In conclusion, the genotypic data do not indicate clonal restriction of C. albicans with respect to CHC. Furthermore, these results have demonstrated that in the majority of individuals, colonizing populations of C. albicans are clonal in nature and exhibit strain persistence.

Evidence for a more recently evolved clade within a Candida albicans North American population

Candida albicans is diploid and displays a primarily clonal mode of reproduction. There is, however, evidence for meiosis and the degree to which this occurs in nature is unknown. Although random mating would act to obscure clonal lineages, previous studies have demonstrated that collections of North American isolates display three major partitions with no evidence of geographic clustering. To better understand the extent of sexuality and its role in the phylogeny of the species, a reference subset of 50 isolates representing this tripartite division was analysed using 1 minisatellite, 5 microsatellites (MSs) and 15 nuclear polymorphisms (NP). A total of 87 alleles were observed for 21 loci and 12/16 informative loci exhibited a departure from Hardy-Weinberg expectations (G(2)</=0.05). We did not observe an absolute correlation between MSs and NP, although isolates with identical NP genotypes were correlated with a previously defined, predominant class (putative group I). The use of additional markers did not give increased support for the tripartite structure of the population. However, (9/19) group I isolates were found to be highly related, differing by only one or a few alleles. Designated subgroup A, the interpretation is that these isolates are related by descent and that they are of a more recent evolutionary origin, diverging from an ancestral group I clone. The reason for their relative abundance in the population is unknown; one possibility is that they may be under positive selection.

Differentiation between Candida dubliniensis and Candida albicans by fatty acid methyl ester analysis using gas-liquid chromatography

Candida dubliniensis is often found in mixed culture with C. albicans, but its recognition is hampered as the color of its colonies in primary culture on CHROMagar Candida varies. Furthermore, definite identification of C. dubliniensis is difficult to achieve, time-consuming, and expensive. Therefore, a method to discriminate between these two closely related yeast species by fatty acid methyl ester (FAME) analysis using gas-liquid chromatography (Sherlock Microbial Identification System [MIS]; MIDI, Inc., Newark, Del.) was developed. Although the chromatograms of these two species revealed no obvious differences when applying FAME analysis, a new library (CADLIB) was successfully created using Sherlock Library Generation Software (MIDI). The amount and frequency of FAME was analyzed using library training files (n = 10 for each species), preferentially those comprising reference strains. For testing the performance of the CADLIB, clinical isolates genetically assigned to the respective species (C. albicans, n = 32; C. dubliniensis, n = 28) were chromatographically analyzed. For each isolate tested, MIS computed a similarity index (SI) indicating a hierarchy of possible strain fits. When using the newly created library CADLIB, the SIs for C. albicans and C. dubliniensis ranged from 0.11 to 0.96 and 0.53 to 0. 93 (for all but one), respectively. Only three isolates of C. albicans (9.4%) were misidentified as C. dubliniensis, whereas all isolates of C. dubliniensis were correctly identified. Resulting differentiation accuracy was 90.6% for C. albicans and 100% for C. dubliniensis. Cluster analysis and principal component analysis of the resulting FAME profiles showed two clearly distinguishable clusters matching up with two assigned species for the strains tested. Thus, the created library proved to be well suited to discriminate between these two species.

Induction of mating in Candida albicans by construction of MTLa and MTLalpha strains

Although the diploid fungus Candida albicans, a human pathogen, has been thought to have no sexual cycle, it normally possesses mating-type-like orthologs (MTL) of both of the Saccharomyces cerevisiae mating-type genes (MAT) a and alpha. When strains containing only MTLa or MTLalpha were constructed by the loss of one homolog of chromosome 5, the site of the MTL loci, MTLa and MTLalpha strains mated, but like mating types did not. Evidence for mating included formation of stable prototrophs from strains with complementing auxotrophic markers; these contained both MTL alleles and molecular markers from both parents and were tetraploid in DNA content and mononucleate.

Assessment of genetic relatedness of vaginal isolates of Candida albicans from different geographical origins

PCR fingerprinting with single non-specific primers was used to type vaginal isolates of C. albicans from Portugal, Angola, Madagascar, and two regions of Germany (Berlin and Munich). In addition to analysing isolates that exhibited the normal biotype of C. albicans, the study included atypical strains that failed to assimilate glucosamine and N-acetylglucosamine, which were isolated from women in Angola and Madagascar. A total of 212 strains of C. albicans were studied, representing 87 different multi-locus genotypes. The genotypes of strains from each geographical population were highly similar but not identical. There was one exception: a strain from Portugal grouped with the typical strains from Angola. The typical and especially the atypical populations from Africa displayed less genotype variation than the populations from Europe. The Portuguese samples exhibited the greatest genotypic heterogeneity. Distance analysis (UPGMA) revealed a statistically weak correlation between genotype and geographical origin of the C. albicans isolates.