A DNA polymorphism specific to Candida albicans strains exceptionally successful as human pathogens

Prevalence of specific and phylogenetically closely related genotypes in the population of Candida albicans associated with genital candidiasis in China

Genitourinary candidiasis, which is most frequently caused by Candida albicans, is a common problem worldwide. The pathogenesis of the infection, especially recurrence of the infection, remains to be elucidated. This study analyzed 199 independent Chinese C. albicans isolates using multilocus sequence typing (MLST) and microsatellite typing, with the focus on the isolates associated with vulvovaginal candidiasis (VVC) of Chinese women. MLST data of 221 vaginal isolates from other countries available from the consensus MLST database of C. albicans were retrieved for comparison. A total of 124 diploid sequence types (DSTs) were recognized from the Chinese C. albicans isolates, among which, 98 (79.0%) have not been reported in the MLST database of the species. The majority of the VVC (71.6%) and balanitis (92.3%) isolates from China were located in clade 1 of C. albicans; while only 40.6% of the vaginal isolates and 7.8% of the oral isolates from healthy volunteers were found in the same clade. Furthermore, 69.1% of the VVC and 84.5% of the balanitis isolates concentrated in a cluster of clade 1 with DST 79 as the primary founder. The isolates in this cluster possessed microsatellite genotypes CAI 30-45, CAI 32-46 and their close derivatives. Interestingly, a remarkable difference in genotype distribution patterns between Chinese and non-Chinese vaginal isolates of C. albicans was observed. Only 11.3% of the non-Chinese vaginal isolates compared were located in the cluster concentrated with Chinese VVC isolates. The results suggest significant association of specific and genetically similar genotypes with genital infections in China.

Increased mortality in young candidemia patients associated with presence of a Candida albicans general-purpose genotype

The yeast Candida albicans causes life-threatening candidemia. A general-purpose genotype (GPG; corresponds to clade 1) causes more infections than other C. albicans genotypes. To investigate if GPG strains also cause higher mortality, we developed a duplex PCR assay which was 98% accurate in identifying GPG strains in an international collection of strains typed with probe Ca3. We applied the assay to 635 European C. albicans candidemia isolates. Of these, 18% conformed to the GPG genotype, 4% were of a borderline genotype, and 78% were of a non-GPG genotype, broadly consistent with genotype distributions in earlier studies. The prevalence of GPG strains was increased in females and in younger patients, exceeding 40% in infants aged ≤1 year. Logistic regression confirmed sex and age as significant determinants of GPG prevalence. Across the entire patient cohort, there was no difference in mortality for patients infected with GPG strains or other strains (36% versus 37%). However, mortality in patients aged ≤48 years was 33% for infection with GPG strains but only 15% for infection with other strains (z test; P < 0.01). Mortality rates associated with GPG and non-GPG strains were comparable in older patients (39% versus 46%). A logistic regression analysis confirmed the age-dependent impact of genotype on mortality. Thus, GPG strains may be more virulent than other strains in younger patients. Because candidemia is usually caused by endogenous strains, our PCR assay could potentially be used as a risk assessment tool for identifying younger patients most at risk of death from candidemia.

Candidemia surveillance in Brazil: evidence for a geographical boundary defining an area exhibiting an abatement of infections by Candida albicans group 2 strains

Prospective population surveillance has been conducted for candidemia in Brazil (A. L. Colombo, M. Nucci, B. J. Park, et al., J. Clin. Microbiol. 44:2816-2823, 2006). In the present study, a total of 63 isolates from 61 patients, representing 11 medical centers from nine geographic regions, were characterized by multilocus sequence typing (MLST). A total of 48 unique profiles or diploid sequence types (DSTs) were observed, with nine new sequence types (STs) and 32 new DSTs. There were no apparent correlations between center/region and DST patterns. Subtypes were compared to those in a known characterized reference set, including a large database of strains obtained worldwide. Significantly, only one C. albicans group 2 isolate was found in our collection, although isolates from this particular group are commonly found worldwide. These data, combined with information from other previously reported studies, establish a statistically significant diminishment of group 2 strains in Central and South America, including Mexico and portions of the Southwestern United States.

Impact of genetic background on allele selection in a highly mutable Candida albicans gene, PNG2

In many microbes rapid mutation of highly mutable contingency genes continually replenishes a pool of variant alleles from which the most suitable are selected, assisting in rapid adaptation and evasion of the immune response. In some contingency genes mutability is achieved through DNA repeats within the coding region. The fungal human pathogen Candida albicans has 2600 repeat-containing ORFs. For those investigated (ALS genes, HYR1, HYR2, CEK1, RLM1) many protein variants with differing amino acid repeat regions exist, as expected for contingency genes. However, specific alleles dominate in different clades, which is unexpected if allele variation is used for short-term adaptation. Generation of new alleles of repeat-containing C. albicans ORFs has never been observed directly. Here we present evidence for restrictions on the emergence of new alleles in a highly mutable C. albicans repeat-containing ORF, PNG2, encoding a putative secreted or cell surface glycoamidase. In laboratory cultures new PNG2 alleles arose at a rate of 2.8×10⁻⁵ (confidence interval 3.3×10⁻⁶−9. 9×10⁻⁵) per cell per division, comparable to rates measured for contingency genes. Among 80 clinical isolates 17 alleles of different length and 23 allele combinations were distinguishable; sequence differences between repeat regions of identical size suggest the existence of 36 protein variants. Specific allele combinations predominated in different genetic backgrounds, as defined by DNA fingerprinting and multilocus sequence typing. Given the PNG2 mutation rate, this is unexpected, unless in different genetic backgrounds selection favors different alleles. Specific alleles or allele combinations were not preferentially associated with C. albicans isolates from particular body sites or geographical regions. Our results suggest that the mutability of PNG2 is not used for short-term adaptation or evasion of the immune system. Nevertheless the large number of alleles observed indicates that mutability of PNG2 may assist C. albicans strains from different genetic backgrounds optimize their interaction with the host in the long term.

Molecular phylogenetics and epidemiology of Candida albicans

Candida albicans, a diploid yeast commensal and opportunist pathogen, has evolved unusual mechanisms for maintenance of genetic diversity in the absence of a complete sexual cycle. These include chromosomal polymorphisms, mitotic recombination events, and gains and losses of heterozygosity, superimposed on a fundamentally clonal mode of reproduction. Molecular typing of C. albicans strains shows geographical evolutionary associations but these have become partially blurred, probably as a result of extensive human travel. Individual patients usually carry a single C. albicans strain type, but this may undergo microvariation leading to detection of mixtures of closely related types. Associations have been found between clade 1, the most common multilocus sequence typing cluster of related C. albicans strains, and resistance to flucytosine and terbinafine. There are also clade-related associations with lengths of tandem repeats in some cell-surface proteins, but not with virulence or type of infection.

Property differences among the four major Candida albicans strain clades

A selection of 43 Candida albicans isolates, chosen to represent the four major strain clades of the species and also intraclade diversity, was screened for their virulence in the murine intravenous challenge model of C. albicans infection, for a range of properties measurable in vitro that might relate to virulence, and for the numbers of midrepeat sequences in genes of the ALS and HYR families. Heterozygosity at the mating type locus and low whole-cell acid phosphatase activity and growth rate at 40 degrees C were found to be significantly positively associated with the most virulent isolates. Acid phosphatase activity and growth in 2 M NaCl were statistically significant variables between clades by univariate analysis. Isolates in different clades also differed significantly in midrepeat sequence alleles of ALS2, ALS4, ALS6, ALS7, ALS9, HYR1, and HYR2. There was no association between the midrepeat alleles of any ALS or HYR gene and the virulence of isolates to mice. Genome-wide transcript profiles of 20 isolates (5 per clade) grown under two conditions showed considerable variation between individual isolates, but only a small number of genes showed statistically significant differential gene expression between clades. Analysis of the expression profiles by overall strain virulence revealed 18 open reading frames differing significantly between isolates of high, intermediate, and low virulence. Four of these genes encoded functions related to phosphate uptake and metabolism. This finding and the significant association between whole-cell acid phosphatase activity and virulence led us to disrupt PHO100, which encodes a predicted periplasmic acid phosphatase. The pho100Delta mutant was mildly but significantly attenuated in terms of survival curves in the mouse model. The study has extended the range of properties known to differ between C. albicans clades and suggests a possible but minor role of phosphate metabolism in the virulence of the species.

Loss of heterozygosity in commensal isolates of the asexual diploid yeast Candida albicans

Candida albicans is a commensal and the most frequent fungal pathogen of humans. One mechanism of genetic variation in this diploid asexual yeast involves loss of heterozygosity (LOH). LOH events occur upon infection and contribute to the acquisition of antifungal resistance in patients. In contrast, little is known about the nature and extent of LOH events during commensalism. Using a combination of single nucleotide polymorphism typing, positional transcript profiling and karyotyping, we have characterized related C. albicans commensal isolates that differ by LOH events. Most of these LOH events encompassed the entirety of the chromosome or a large region extending to the telomere, suggesting chromosome loss or mitotic recombination/break-induced replication events, respectively. They were frequently accompanied by karyotype alterations such as chromosome length polymorphism and copy number variations at other chromosomes. These results demonstrate the high plasticity of the C. albicans genome during commensalism.

Microevolution in genomic short sequence repeats of Candida albicans in non-neutropenic patients

The genome of the yeast Candida albicans harbours many genomic short sequence repeats (SSRs). These are stable upon transition of colonization to infection in immune-compromised patients. We show here that in non-neutropenic patients this transition may coincide with variation in several of the SSRs. This may have implications for stage-specific expression of C. albicans pathogenicity factors.

The human commensal yeast, Candida albicans, has an ancient origin

Candida albicans, the primary causative agent of candidiasis, is a ubiquitous member of the human flora and is capable of causing severe invasive disease. Despite its importance as a human pathogen, little is known concerning those factors creating and maintaining genetic diversity within the species and how extant strains reflect their evolutionary history. Based on nucleotide polymorphism frequencies, we estimated the time to a most recent common ancestor for the species to be about 3-16 million years, with variation due to molecular clock calibration. As C. albicans genotypes have broad geographic associations, this suggests that the origins of DNA sequence variation in extant populations coincided with early hominid evolution. This is consistent with an emerging view of a genetically complex organism that is able to survive under host immunity as an obligate commensal species.

Sixty alleles of the ALS7 open reading frame in Candida albicans: ALS7 is a hypermutable contingency locus

The ALS (agglutinin-like sequence) gene family encodes proteins that play a role in adherence of the yeast Candida albicans to endothelial and epithelial cells. The proteins are proposed as virulence factors for this important fungal pathogen of humans. We analyzed 66 C. albicans strains, representing a worldwide collection of 266 infection-causing isolates, and discovered 60 alleles of the ALS7 open reading frame (ORF). Differences between alleles were largely caused by rearrangements of repeat elements in the so-called tandem repeat domain (21 different types occurred) and the VASES region (19 different types). C. albicans is diploid, and combinations of ALS7 alleles generated 49 different genotypes. ALS7 expression was detected in samples isolated directly from five oral candidosis patients. ORFs in the opposite direction contained within the ALS7 ORF were also transcribed in all strains tested. Isolates representing a more pathogenic general-purpose genotype (GPG) cluster of strains tended to have more tandem repeats than other strains. Two types of VASES regions were largely exclusive to GPG strains; the remaining types were largely exclusive to noncluster strains. Our results provide evidence that ALS7 is a hypermutable contingency locus and important for the success of C. albicans as an opportunistic pathogen of humans.