Genotype analysis of Candida albicans isolates obtained from different body locations of patients with superficial candidiasis using PCRs targeting 25S rDNA and ALT repeat sequences of the RPS

Molecular genotyping of Candida albicans isolated from different sites may trace the etiological infection routes: Observation in China

BACKGROUND

Invasive candidiasis is a growing concern worldwide, especially in immunocompromised patients, including ICU patients.

OBJECTIVES

As Candida albicans is the leading cause of candidaemia, it is important to investigate the evolution of C. albicans in patients with candidaemia.

METHODS

We analysed 238 strains of C. albicans isolated from different body sites. Antifungal susceptibility testing, CAI loci genotyping and multilocus sequence typing (MLST) of all isolates were performed. The relationships among the total isolates that differed in sequence at only one of the seven housekeeping gene loci were analysed using eBURST.

RESULTS

Multilocus sequence typing analysis in 238 isolates by combining seven housekeeping alleles revealed 175 diploid sequence types, in which 84 were newly identified. eBURST analysis for these data recognised 19 clonal complexes (CCs) and 79 singletons. Besides, seventy-three CAI genotypes were identified. Blood isolates showed maximum genotypes (49), and the dominant genotypes were CAI 17-21 and CAI 21-21. Oral isolates possessed 25 CAI genotypes, and the dominant genotypes were CAI 17-21 and CAI 21-21 as well. Since isolates with CAI allele numbers <30 showed easier transmission, CAI 17-21 and CAI 21-21 were the most frequently transmitted. Finally, the CAI genotypes were classified into six groups.

CONCLUSIONS

This work revealed the oral and blood strains isolated from the patients with candidaemia in ICU shared the identical dominant CAI genotypes. Our data expanded the C. albicans MLST database and helped with understanding the evolution and spread of invasive candidiasis.

Genotyping of Candida albicans Strains Obtained from Oropharyngeal Candidiasis Patients Based on ABC and RPS Typing Systems

Background: Candida albicanss has been introduced as one of the most common causes of nosocomial infections. Molecular typing methods are powerful tools in epidemiology to investigate the infection source of candidiasis, identify the transmission routes, and control the measures. Objectives: This study aimed for genotyping C. albicans species isolated from oral cavities of the non-HIV patients who suffer from oropharyngeal candidiasis via combined ABC and repeat sequences (RPS) typing systems. Methods: In this study, 31 DNA samples of clinical isolates of C. albicans were evaluated in terms of 25s ribosomal DNA region sequence or ABC typing, and ALT repeats numbers within RPS. DNA was amplified in two separate reactions, and the PCR products were electrophoresed to identify the genotypes of the isolates. Based on the band's pattern, phylogenetic analysis was conducted by UPGMA, and the discriminatory power of ABC and RPS typing was measured by Simpson’s index of diversity. Results: Genotype A with (14 isolates, 45.2%) were the most frequent and followed by genotype B (10 isolates, 32.3%) and Genotype C (7 isolates, 22.6%), respectively. In addition, genotype 3 with 25 isolates (80.6%) were the most prevalent, followed by genotype 2/3 (4 isolates, 12.9%) and genotype 3/4 (2 isolates, 6.5%) respectively. No significant relationship was found between the obtained genotypes and drug-resistant isolates (P < 0.05). Conclusions: This study showed that 25s rDNA and RPS typing is a quick, simple, and cost-effective method with average discriminatory power and good reproducibility for C. albicans genotyping. It can be used for the epidemiology of C. albicans infections.

Genotype Analysis of Clinical Candida albicans Isolates Using PCRs Targeting 25S rDNA and ALT Repeat Sequences of the RPS and Antifungal Susceptibility in Ouagadougou (Burkina Faso)

Objective

Candida albicans is a yeast with multiple genotypes. It’s a commensal fungus colonizing various sites. However, when the host’s immune system weakens, it becomes pathogenic and is responsible for various lesions. In Burkina Faso, antifungal drugs are frequently used, particularly fluconazole, the most used systemic antifungal. This antifungal drug and other antifungal drugs are often used for self-medication or prescribed outside of antifungal susceptibility test results. These situations led to the emergence of Candida albicans strains resistant to antifungal drugs commonly used in Burkina Faso. The aim of this study was to determine the types of Candida albicans using PCRs targeting 25S rDNA and ALT repeat sequences of the RPS and to establish their azoles and polyenes susceptibility profile.

Material and methods

Antifungal susceptibility testing by disk diffusion method was performed in accordance with CLSI document M44-A for yeasts and the manufacturer’s instructions. Candida albicans isolates were genotyped using specific PCR primers of the rDNA and RPS genes.

Results

Ten (10) RPS types of Candida albicans were found in our study: The most common RPS types are A3 (40.6%), A2 (24.0%) and A2/3 (14.6%) for genotype A, B2/3 (5.2%) for genotype B and C2 (3.2%) for genotype C. The Azole resistance, especially fluconazole (74.4%), was the most common with genotype A, including A3 (36.6%), A2 (18. 3%). Polyene resistance was rare with nystatin, only A3 (1.2%) resistant isolate to nystatin was observed. For amphotericin B, the highest observed resistance rates were A3 (11.0%) and A2/3 (8.5%) for the genotype A and B2 (10.0%), B3 (10.0%) and B2/3 (10.0%) for genotype B.

Conclusion

Our study showed that Candida albicans resistance to azoles, especially to fluconazole, is an important phenomenon in Ouagadougou, and several genotypes RPS types are involved. Thus, fluconazole would not be an antifungal agent for first-line prescribing for treatment of candidiasis in Ouagadougou. This study will be continued to determine the molecular mechanisms involved in these antifungal resistances, for further research of new molecules with different action targets.

Genotyping of Candida albicans isolated from animals using 25S ribosomal DNA and ALT repeats polymorphism in repetitive sequence

Background and Purpose:

Candida albicans is the most prevalent Candida species isolated from animals. Candidiasis can be systemic in animals or may affect a single organ, such as the mouth, urinary tract, and skin. The aim of the present study was to determine the genetic diversity of C. albicans isolated from different animals and investigate the presence of a relationship between host specificity and genetic typing of C. albicans.

Materials and Methods:

For the purpose of the study, DNA extraction was performed on 27 clinical isolates of C. albicans obtained from animals. Subsequently, they were subjected to 25S ribosomal DNA amplification and ALT repeats in repetitive sequences (RPSs). The minimum inhibitory concentrations of fluconazole, ketoconazole, clotrimazole, nystatin, amphotericin B, and caspofungin were determined using the microdilution method based on the Clinical and Laboratory Standards Institute M27-S4 standard.

Results:

Out of 27 C. albicans strains, 11, 6, 5, and 5 cases were recognized as genotypes A (40.8%), E (22.2%), B (18.5%), and C (18.5%), respectively, through amplification using AS-I, which revealed 17 different types of C. albicans. By combining the two typing methods, 27 C. albicans strains were finally divided into 22 genotypes.

Conclusion:

Different genotypes showed genetic diversity among the C. albicans strains isolated from animal sources. The results revealed no special genotype relationship according to the host, anatomical source of isolation, and antifungal susceptibility.

Posttreatment Antifungal Resistance among Colonizing Candida Isolates in Candidemia Patients: Results from a Systematic Multicenter Study

The prevalence of intrinsic and acquired resistance among colonizing Candida isolates from patients after candidemia was investigated systematically in a 1-year nationwide study. Patients were treated at the discretion of the treating physician. Oral swabs were obtained after treatment. Species distributions and MIC data were investigated for blood and posttreatment oral isolates from patients exposed to either azoles or echinocandins for <7 or ≥ 7 days. Species identification was confirmed using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and internal transcribed spacer (ITS) sequencing, susceptibility was examined by EUCAST EDef 7.2 methodology, echinocandin resistance was examined by FKS sequencing, and genetic relatedness was examined by multilocus sequence typing (MLST). One hundred ninety-three episodes provided 205 blood and 220 oral isolates. MLST analysis demonstrated a genetic relationship for 90% of all paired blood and oral isolates. Patients exposed to azoles for ≥ 7 days (n = 93) had a significantly larger proportion of species intrinsically less susceptible to azoles (particularly Candida glabrata) among oral isolates than among initial blood isolates (36.6% versus 12.9%; P < 0.001). A similar shift toward species less susceptible to echinocandins among 85 patients exposed to echinocandins for ≥ 7 days was not observed (4.8% of oral isolates versus 3.2% of blood isolates; P > 0.5). Acquired resistance in Candida albicans was rare (<5%). However, acquired resistance to fluconazole (29.4%; P < 0.05) and anidulafungin (21.6%; P < 0.05) was common in C. glabrata isolates from patients exposed to either azoles or echinocandins. Our findings suggest that the colonizing mucosal microbiota may be an unrecognized reservoir of resistant Candida species, especially C. glabrata, following treatment for candidemia. The resistance rates were high, raising concern in general for patients exposed to antifungal drugs.

Influence of Culture Media on Microbial Fingerprints Using Raman Spectroscopy

Raman spectroscopy has a broad range of applications across numerous scientific fields, including microbiology. Our work here monitors the influence of culture media on the Raman spectra of clinically important microorganisms (Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis and Candida albicans). Choosing an adequate medium may enhance the reproducibility of the method as well as simplifying the data processing and the evaluation. We tested four different media per organism depending on the nutritional requirements and clinical usage directly on a Petri dish. Some of the media have a significant influence on the microbial fingerprint (Roosvelt-Park Institute Medium, CHROMagar) and should not be used for the acquisition of Raman spectra. It was found that the most suitable medium for microbiological experiments regarding these organisms was Mueller-Hinton agar.

Surveillance of the prevalence, antibiotic susceptibility, and genotypic characterization of invasive candidiasis in a teaching hospital in China between 2006 to 2011

Background

Invasive candidiasis is an important nosocomial infection associated with high mortality among immunosuppressive or critically ill patients. We described the incidence of invasive candidiasis in our hospital over 6 years and showed the antifungal susceptibility and genotypes of the isolated yeast.

Method

The yeast species were isolated on CHROMagar Candida medium and identified using an yeast identification card, followed by analysis of the D1/D2 domain of 26S rDNA. The susceptibilities of the isolates to flucytosine, amphotericin B, fluconazole, itraconazole, and voriconazole were tested using the ATB FUNGUS 3 system, and that to caspofungin was tested using E-test strips. C. albicans was genotyped using single-strand conformation polymorphism of CAI (Candida albicans I) microsatellite DNA combined with GeneScan data.

Results

From January 2006 to December 2011, a total of 259 isolates of invasive Candida spp. were obtained from 253 patients, among them 6 patients had multiple positive samples. Ninety-one stains were from blood and 168 from sterile fluids, accounting for 6.07% of all pathogens isolated in our hospital. Most of these strains were C. albicans (41.29% in blood/59.06% in sterile body fluids), followed by C. tropicalis (18.06%/25.72%), C. parapsilosis (17.42%/5.43%), C. glabrata (11.61%/3.99%) and other Candida spp. (11.61%/5.80%). Most Candida spp. were isolated from the ICU. The new species-specific CLSI candida MIC breakpoints were applied to these date. Resistance to fluconazole occurred in 6.6% of C. albicans isolates, 10.6% of C. tropicalis isolates and 15.0% of C. glabrata isolates. For the 136 C. albicans isolates, 54 CAI patterns were recognized. The C. albicans strains from blood or sterile body fluids showed no predominant CAI genotypes. C. albicans isolates from different samples from the same patient had the same genotype.

Conclusions

Invasive candidiasis has been commonly encountered in our hospital in the past 6 years, with increasing frequency of non-C. albicans. Resistance to fluconazole was highly predictive of resistance to voriconazole. CAI SSCP genotyping showed that all C. albicans strains were polymorphic. Invasive candidiasis were commonly endogenous infection.

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.

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

This study aimed to examine the genotype distribution of Candida albicans and the major genotypes involved in superficial candidiasis. The genotypes of C. albicans isolated from the infection sites of patients with superficial candidiasis (referred to as infection isolates) were analyzed by fragment analysis using 4 microsatellite markers (HIS3, CDC3, CAI and CAIII). Genotypes of the infection isolates were compared with those of C. albicans isolated from oral mucosa of non-candidiasis patients (referred to as oral isolates). Isolates of C. albicans showed 4 major genotypes for HIS3/CAI (" a " for 148 : 148 / 23 : 23," b " for 148 : 160 / 33 : 41," c " for 148 : 164 / 32 : 41 and " d " for 152 : 152 / 18 : 27). The genotypes " a "," b " and " d " were commonly found in oral (4.7, 8.8 and 7.6%, respectively) and infection (6.6, 9.2 and 15.4%, respectively) isolates. No isolates of genotype " c " were isolated from infection sites. The genotype " a " was found in the isolates from patients with genitalia candidiasis. Genotyping of multiple isolates from an individual patient showed that C. albicans from infection sites was genetically homogenous as compared with that of oral isolates, even in the same patient with candidiasis.

Genotyping of Candida albicans by fragment analysis of microsatellites combined with 25S rDNA and RPS-based strategies

Because of its high discriminatory potential, fragment analysis of microsatellites has been frequently used for genotyping of Candida albicans at the strain level. In order to evaluate a genotyping system based on the fragment analysis of microsatellites combined with PCRs targeting 25S rDNA and RPS, 456 independent strains of C. albicans were subjected to genotype analysis using 4 microsatellite markers (CDC3, HIS3, CA I and CA III), followed by 25S rDNA and RPS-based genotyping. The fragment analysis using CA I showed the highest discriminatory potential (DP=0.9782), followed by HIS3 (DP=0.8780). Using combined microsatellite markers, 456 C. albicans strains were divided into 384 genotypes (DP=0.9984). PCRs targeting 25S rDNA and RPS were performed to differentiate the strains that showed identical genotypes in the fragment analysis, resulting in 434 genotypes (DP=0.9996). The combined genotyping system showed high discriminatory power at the strain level, and therefore is useful for rapid genotyping in molecular epidemiological studies of candidiasis.

Molecular typing of clinical Candida strains using random amplified polymorphic DNA and contour-clamped homogenous electric fields electrophoresis

AIMS

This report describes an investigation into the genetic profiles of 38 Candida albicans and 19 Candida glabrata strains collected from a dental hospital of Monastir (Tunisia) and the Laboratory of Parasitology, Farhat Hached Hospital of Sousse (Tunisia), using two typing methods: random amplified polymorphic DNA (RAPD) and contour-clamped homogenous electric fields (CHEF).

METHODS AND RESULTS

The two methods (RAPD and CHEF electrophoresis) were able to identify clonal-related isolates from different patients. RAPD method using two primers (CA1 and CA2) exhibited the highest discriminatory power by discriminating 22 genotypes for C. albicans with CA1 oligonucleotides and 19 genotypes with CA2 primer. For C. glabrata, 17 genotypes were obtained when both primers CA1 and CA2 were combined. The CHEF karyotyping of C. albicans has discriminated only 17 different karyotypes.

CONCLUSION

The genotype of each isolate and genotypic difference among C. albicans and C. glabrata isolates were patient specific and not associated with the site of infection, geographic origin or date of isolation.

SIGNIFICANCE AND IMPACT OF THE STUDY

Identification of relatedness between Candida species using molecular approaches with high discriminatory power is important in determining adequate measures for interruption of transmission of this yeast.

[Structural and functional analyses of MRS (major repeated sequnece) in Candida albicans. Application for genotyping and the eternal way to the complete genome sequence]

There are several different types of repeated sequences in the genome of Candida albicans, including the MRS (Major repeated sequence). In 2004, the whole genome sequence of C. albicans was published. Assembly of the sequences to chromosomal length contigs was not achieved, mainly due to interruption of the sequences by MRS. However, MRS including Ca3, 27A and RPS have been playing important roles in a number of epidemiological studies and basic biological investigations into C. albicans chromosome loss events and associated phenotypic changes. Here we summarize structural analyses from subrepeat sequences to the chromosome level, and functional analyses of MRS.