Microsatellite-based genotyping of Candida albicans isolated from patients with superficial candidiasis

Analysis of Microsatellite Length Polymorphism for Clinical Isolates of Candida albicans from Animals

Background: Candida albicans has been shown as the most common species of Candida collected from different animals. Objectives: This study aimed to evaluate the genetic diversity and genetic relationships among C. albicans isolates collected from clinical specimens of animals suffering from candidiasis using microsatellite length polymorphism (MLP). Methods: We used MLP for a group of 60 C. albicans strains isolated from various animal species (dog: 16, cat: 10, horse: 10, cow: 14, chicken: 10), previously defined as animal clinical isolates. Three loci, including EF3, CDC3, and HIS3, were amplified, and the products ran onto an ABI XL 370 genetic analyzer, and fragment sizes were determined. Results: Of the 60 clinical strains illustrated, 49 different genotypes were identified with a discriminatory power index of 0.991. A total of 17 alleles and 26 different combinations were identified for EF3 locus, six alleles and 13 combinations for CDC3 locus, and 17 alleles and 27 combinations for HIS3 locus. The most common genotypes were GP9 (four strains) and GP1 and GP33 (three strains). Wright’s fixation index (FST) values were calculated to assess inter-group genetic diversity for all pairwise combinations of the five sub-populations of C. albicans isolated from the different animal hosts. The highest FST values related to C. albicans isolated from chicken to three sub-populations of cats (FST: 0.1397), cows (FST: 0.0639), and horses (FST: 0.0585). Conclusions: The results indicated a moderate genetic differentiation (0.05 < FST < 0.15) between C. albicans strains isolated from cats, cows, and horses as a mammal vs. chickens.

Genotypic diversity and antifungal susceptibility pattern of Candida albicans species isolated from hospitalized paediatric patients with urinary tract infection in Iran

AIMS

The present study aimed to determine the microsatellite length polymorphism (MLP) genotypic patterns and antifungal susceptibility profiles of Candida albicans isolated from patients with candiduria.

METHODS AND RESULTS

DNA of 50 C. albicans isolates was used for molecular identification based on the ITS₁ -5.8s-ITS₂ region. MLP assays were performed to amplify three loci (EF3, CDC3 and HIS3), and PCR products were used for fragment analysis. Antifungal susceptibility tests were performed according to CLSI M27 4th ed guidelines. In all, 38 different genotypes were detected with the three polymorphic loci among C. albicans isolates, and only one genotype was homozygous. In comparison to other countries, our genotypes were divided into three clusters, two of which were linked to France and a third of which was linked to Austria. The genetic structures of the 50 C. albicans isolates revealed varied heterozygosity and significant Hardy-Weinberg equilibrium at the EF3 locus. Only one (2%) and four (8%) of isolates showed resistance to fluconazole and itraconazole, respectively. In C. albicans genotype G25, one (2%) of the isolates showed cross-resistance and non-wild-type resistance to posaconazole, itraconazole and fluconazole.

CONCLUSION

MLP typing is a useful tool to analyse the genetic structure of C. albicans isolates. High genetic diversity (38 genotypes) was detected in the isolates tested here. Compared to isolates in other countries, the ones from our patients had a clear relationship with French and Austrian isolates.

SIGNIFICANCE AND IMPACT OF THE STUDY

Iranian isolates of C. albicans have a distinct genotype and show similarities only with French and Austrian isolates.

Association between CAI microsatellite, multilocus sequence typing, and clinical significance within Candida albicans isolates

Candida albicans bloodstream infection (BSI) is epidemiologically important because of its increasing frequency and serious outcome. Strain typing and delineation of the species are essential for understanding the phylogenetic relationship and clinical significance. Microsatellite CAI genotyping and multilocus sequence typing (MLST) were performed on 285 C. albicans bloodstream isolates from patients in Chang Gung Memorial Hospital at Linkou (CGMHL), Taiwan from 2003 to 2011. Data regarding demographics, comorbidities, risk factors, and clinical outcomes were recorded within adult patients with C. albicans BSI. Both CAI genotyping and MLST yielded comparable discriminatory power for C. albicans characterization. Besides, the distribution of CAI repetition showed a satisfactory phylogenetic association, which could be a good alternative method in the molecular phylogenetics of C. albicans and epidemiological studies. As for the clinical scenario, clade 17 isolates with CAI alleles either possessing 29 or more repetitions were related to higher 14-day and 30-day mortality, and shorter median survival days.

Oral Candida albicans colonization in healthy individuals: prevalence, genotypic diversity, stability along time and transmissibility

In this study, 181 healthy individuals, including 29 couples, were analysed regarding oral yeast colonization using a culture-based approach. Results showed that 39% of the individuals were yeast carriers, 89% being colonized with Candida albicans, 5% with C. guilliermondi, 3% with C. lusitaniae and 3% with C. parapsilosis. Sixty-two percent of the couples had at least one member colonized. Colonization and CFU counts were higher in the couples´ group. Eighty percent of the volunteers were colonized with C. albicans strains with only one CAI genotype, while two but similar CAI genotypes inhabited the oral cavity of the remaining 20% individuals. The same CAI genotypes were found in 66.6% of the couples when both were colonized. Our results indicate that the intimacy among couples increases the probability of heavy cross-colonization, which is potentiated when one member of the couple is a smoker.

Genetic diversity and antifungal susceptibility of Candida albicans isolated from Iranian patients

A total of 105 independent Candida albicans strains isolated from patients in Iran were investigated. According to CLSI documents M27-A3 and M27-S4, the 24 h geometric mean MICs of caspofungin, itraconazole, and fluconazole were 0.27, 3.19, and 11.91 μg/ml, respectively. Microsatellites analysis of CEF3, CAIII, LOC4 Loci identified 93 different allelic genotypes clustered apart into six different clades. Antifungal susceptibility was not linked with the source of isolation and the corresponding genotype of C. albicans strains.

Microsatellite analysis of genotype distribution patterns of Candida albicans vulvovaginal candidiasis in Nanjing, China and its association with pregnancy, age and clinical presentation

PURPOSE

To characterize the genotype distribution pattern of Candida albicans associated with vulvovaginal candidiasis (VVC) in Nanjing, China by microsatellite genotyping.

METHODS

A questionnaire was completed by each patient diagnosed with VVC. A total of 208 independent C. albicans was isolated from 208 patients. Microsatellite genotyping characterized the genotype distribution by analysis of the CAI locus marker.

RESULTS

PCR of CAI fragments showed the three major genotypes contained 30:45, 21:21 and 32:46 alleles among the 51 genotypes detected, accounting for 29.3, 13.0 and 12.0 % of 208 clinical isolates. Genotype distributions had a similar pattern among different clinical presentations (P = 0.219). In both groups of the (21-30) and (31-40) years, 30:45 was the most frequent genotype allele detected. In the (21-30) year females, 16.5 % of the isolated strains had the genotype 21:21, while the same genotype in the group of (31-40) years was 6.9 %. Genotype distributions were significant difference between the pregnant and non-pregnant women (P < 0.001). 30:45 was detected only one in the 23 pregnant women.

CONCLUSIONS

The results indicated a unique genotype distribution of C. albicans associated with VVC in Nanjing, eastern China and a different distribution pattern was also detected in pregnant women compared to non-pregnant women.

Phenotypic diversity and correlation between white-opaque switching and the CAI microsatellite locus in Candida albicans

Candida albicans is a commensal fungal pathogen that is often found as part of the human microbial flora. The aim of the present study was to establish a relationship between diverse genotypes and phenotypes of clinical isolates of C. albicans. Totally 231 clinical isolates were collected and used for genotyping and phenotypic switching analysis. Based on the microsatellite locus (CAI) genotyping assay, 65 different genotypes were identified, and some dominant types were found in certain human niches. For example, the genotypes of 30-44 and 30-45 were enriched in vaginal infection samples. C. albicans has a number of morphological forms including the single-celled yeasts, multicellular filaments, white, and opaque cell types. The relationship between the CAI genotype and the ability to undergo phenotypic switching was examined in the clinical isolates. We found that the strains with longer CAA/G repeats in both alleles of the CAI locus were more opaque competent. We also discovered that some MTL heterozygous (a/alpha) isolates could undergo white-opaque switching when grown on regular culture medium (containing glucose as the sole carbon source). Our study establishes a link between phenotypic switching and genotypes of the CAI microsatellite locus in clinical isolates of C. albicans.

Multilocus microsatellite markers for molecular typing of Candida tropicalis isolates

Background

Candida tropicalis is considered to be the leading pathogen causing nosocomial fungemia and hepatosplenic fungal infections in patients with cancer, particularly those with leukemia. Microsatellite-based typing methods using sets of genetic markers have been developed and reported for population structure analysis of C. albicans, C. glabrata, and C. parapsilosis, but no studies have been published for genetic analysis of C. tropicalis. The objective of this study was to develop new microsatellite loci that have the ability to distinguish among C. tropicalis isolates.

Results

DNA sequences containing over 10 bi- or tri-nucleotide repeats were selected from the C. tropicalis genome database. Thirty PCR primers sets specific for the microsatellite loci were designed and tested using eight clinically independent isolates. According to the amplification efficiency, specificity, and observed polymorphisms, eight markers were selected for further population structure analysis and molecular typing. Sixty-five independent C. tropicalis isolates were genotyped using these 8 markers. Based on these analyses, six microsatellite loci were confirmed, although two loci were found to be with unstable flanking areas. The six polymorphic loci displayed 4–22 alleles and 7–27 genotypes. The discriminatory power of the six loci ranged from 0.70 to 0.95. Genotyping results obtained by microsatellite analysis were compared to PCR-fingerprinting and multi-locus sequence typing (MLST). The comparisons showed that microsatellite analysis and MLST had the similar discriminatory power for C. tropicalis, which were more powerful than PCR-fingerprinting.

Conclusions

This is the first attempt to develop new microsatellite loci for C. tropicalis. These newly developed markers will be a valuable resource for the differentiation of C. tropicalis isolates. More C. tropicalis isolates will need to be sequenced and analyzed in order to fully show the potential of these newly developed microsatellite markers.

Analysis of the clonality of Candida tropicalis strains from a general hospital in Beijing using multilocus sequence typing

Multilocus sequence typing (MLST) based on six loci was used to analyze the relationship of 58 Candida tropicalis isolates from individual patients in a general hospital in Beijing, China. A total of 52 diploid sequence types (DSTs) were generated by the MLST, all of which were new to the central database. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrograms were constructed, which showed that the 58 isolates were distributed robustly and 6 main groups were clustered regardless of the specimen source and medical department. The minimum spanning tree (MST) of the 58 isolates (52 DSTs) and all 401 isolates (268 DSTs) in the C. tropicalis central database (http://pubmlst.org/ctropicalis/) indicated that the isolates in this study clustered in three relative pure clonal complexes, and 2 clustered with isolates from Taiwan, Belgium, Brazil, and the US. This study presents the first MLST analysis of C. tropicalis isolates from Mainland China, which may be useful for further studies on the similarity, genetic relationship, and molecular epidemiology of C. tropicalis strains worldwide.

Genotypes of Candida albicans involved in development of candidiasis and their distribution in oral cavity of non-candidiasis individuals

Genotype characteristics and distribution of commensal Candida albicans should be studied to predict the development of candidiasis, however, extensive genotype analysis of commensal C. albicans has not been made. In this study, 508 C. albicans isolates were collected from patients with/without candidiasis and divided into 4 isolate groups (SG-1, oral cavity of non-candidiasis patients; SG-2, patients with cutaneous candidiasis; SG-3, patients with vaginal candidiasis; SG-4, patients with candidemia). These isolates were characterized to study the relationship between genotypes and pathogenicity using microsatellite analysis. Using CDC3 and CAI, 5 genotypes (I, 111: 115/33: 41; II, 115: 119/23: 23; III, 115: 123/18: 27; IV, 115: 123/33: 40; and V, 123: 127/32: 41) were found in 4.2%, 8.9%, 7.1%, 2.2% and 3.1% of the isolates, respectively. Genotypes II and III were commonly found in all isolate groups. These genotypes were further divided into 28 types by additional HIS3 and CAIII microsatellite markers. In this analysis, C. albicans with type 6 and type 23 was widely distributed as a commensal species in the oral cavity of non-candidiasis patients and found to be related with candidiasis development. Additionally, genotypes I and IV were found in SG-2 and/or SG-4, suggesting that the fungus with those genotypes is also involved in this development. In contrast, genotype V was not identified in any infective isolates.