Multilocus microsatellite analysis of European and African Candida glabrata isolates

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.

Enzymatic and antifungal susceptibility profiles of Candida glabrata isolates from pediatric patients and their genetic diversity based on microsatellite length polymorphism

This study aimed to detect different genotypes of Candida glabrata isolates in pediatric patients with and without neutropenia utilizing microsatellite length polymorphism (MLP) and its correlation with drug resistance and enzymatic activity were assessed. Samples from neutropenic and non-neutropenic patients were collected from November 2020 to November 2021. Thirty-six C. glabrata strains were isolated and identified using classical and molecular methods. Then, C. glabrata isolates were genotyped by the MLP technique, and their antifungal susceptibility was performed based on the CLSI M27 guideline. Eighteen different multi-loci genotypes (G1 - G18) were detected based on MLP analysis. Analysis of molecular variance revealed high genetic variation within populations (94%) and low genetic differentiation among populations (6%). Also, 40% (n=4) of isolates from neutropenic patients were non-wild-type for posaconazole, and 30% (n=3) were resistant to caspofungin. Very strong hemolytic and proteinase activity were seen in 97.2 and 86.1% of isolates. Candida glabrata strains from neutropenic patients were genetically divergent from other populations. The minimum spanning tree shows that observed genotypes were mainly related to previously reported genotypes from Iran, Spain, and China.

Genetic diversity assessed using PFGE, MLP and MLST in Candida spp. candidemia isolates obtained from a Brazilian hospital

Candida spp. are the main causative agents of invasive fungal infections in immunocompromised patients. Candidemia has attributable mortality rates of 15 to 35% and increases hospitalisation time and costs, thus making this disease a public health concern. This study aimed to use pulsed-field gel electrophoresis (PFGE), microsatellite length polymorphism (MLP) and multilocus sequence typing (MLST) to analyse the genetic relationships among 65 Candida spp. bloodstream isolates, including 35 Candida albicans, 15 Candida glabrata and 15 Candida tropicalis isolates, all of which were obtained from patients in a Brazilian hospital. Moreover, patient clinical data were assessed. All techniques resulted in high discriminatory indexes. C. albicans and C. tropicalis isolates showed high genetic variability, while C. glabrata isolates had relatively low genetic variability. Moreover, a cluster of C. glabrata isolates was identified in a hospital unit. New MLST sequence types, diploid sequence types and alleles are described. Relationships were not observed between the molecular typing results and clinical characteristics. The molecular typing of clinical strains increases our understanding of candidemia epidemiology and promotes the development of strategies that can reduce the incidence of this disease. Moreover, this study is the first to combine these techniques to genotype these three species in Brazil.

Genetic Analysis of Candida glabrata from Candiduric Patients Using Microsatellite Length Polymorphism, Antifungal Susceptibility, and Enzymatic Profiles

Background: Candida glabrata is the second agent of candiduria with increased resistance to antifungals. Microsatellite length polymorphism (MLP) is one of the genotyping techniques used in the epidemiological investigation to improve clinical management. Objectives: We aimed to detect different genotypes of C. glabrata isolates using six microsatellite markers and the MLP technique. Moreover, our genotypes' association with other countries' genotypes was illustrated using a minimum spanning tree. We investigated in vitro antifungal susceptibility and enzymatic activity profiles of the isolates. Methods: Six microsatellite markers were amplified using multiplex-PCR for 22 C. glabrata strains isolated from urine in pediatric patients admitted to the Abuzar Children's Hospital in Ahvaz, Iran. The PCR products were presented for fragment analysis, and the size of the alleles was determined. Antifungal susceptibility tests and extracellular enzyme activities were also performed. Results: Nineteen multilocus genotypes were detected so that 22.7% of the strains had identical genotypes. The isolates were wild-type for amphotericin B (0.0625 - 2 µg/mL), itraconazole (0.125 - 2 µg/mL), and voriconazole (0.0078 - 0.00625 µg/mL). All the isolates were sensitive to fluconazole at the minimum inhibitory concentration (MIC) range (0.0312 - 16 μg/mL), and three of them were resistant to caspofungin (MIC ≥ 0.5 μg/mL). Moreover, 72.7 and 68.2% of the isolates had no phospholipase and esterase activities. The highest potency of enzymatic activity was obtained in hemolysin and proteinase enzymes. A high genetic diversity (19 genotypes of the 22 isolates) existed among the urinary C. glabrata isolates. Based on the minimum spanning tree, two clusters of our genotypes were related to C. glabrata genotypes in a previous study in Iran, and the third cluster was entirely connected with Chinese genotypes. Conclusions: Most of the isolates were the non-wild type for posaconazole but were rarely resistant to other antifungals. Hemolysin and proteinase secreted as the main virulence factors among the urinary C. glabrata isolates.

Looking for New Antifungal Drugs from Flavonoids: Impact of the Genetic Diversity of Candida albicans on the in-vitro Response

BACKGROUND

In an era in which antimicrobial resistance is increasing at an alarming pace, it is very important to find new antimicrobial agents effective against pathogenic microrganisms resistant to traditional treatments. Among the notable breakthroughs in the past years of research in natural-drug discovery, there is the identification and testing of flavonoids, a group of plant-derived substances capable of promoting many beneficial effects on humans. These compounds show different biological activities such as inhibition of neuroinflammation and tumor growth as well as antimicrobial activity against many microbial pathogens.

METHODS

We undertook a review of protocols and standard strains used in studies reporting the inhibitory effects of flavonoids against Candida albicans by focusing our attention on genetic characterization of the strains examined. Moreover, using the C. albicans MLST-database, we performed a phylogenetic analysis showing the genetic variation occurring in this species.

RESULTS

Today, we have enough information to estimate genetic diversity within microbial species and recent data revealed that most of fungal pathogens show complex population structures in which not a single isolate can be designated as representative of the entire taxon. This is especially true for the highly divergent fungal pathogen C. albicans, in which the assumption that one or few "standard strains" can represent the whole species is overly unrealistic and should be laid to rest.

CONCLUSION

The goal of this article is to shed light on the extent of genetic variation in C. albicans and how this phenomenon can largely influence the activity of flavonoids against this species.

Molecular Typing of Candida glabrata

The yeast Candida glabrata has emerged, second only to Candida albicans, to be one of the most frequently isolated fungi in clinical specimen from human. Its frequent resistance towards azole antifungal drugs and the high capacity to form biofilms on indwelling catheters of individual isolates render it an often difficult to treat pathogen. Hence, there is a notably increasing scientific and clinical interest in this species. This has led to the development of a variety of molecular tools for genetic modification, strain collections, and last but not least different approaches to analyse the population structure among isolates of different geographical and clinical contexts. Often, these are used to study correlations (or the absence thereof) with different pathogenicity, virulence, or drug resistance traits. Three molecular methods have been used to type within the C. glabrata population on a genetic level by multiple studies: multi-locus sequence typing, microsatellite length polymorphisms, and clustering of whole-genome sequencing data, and these are subject of this review.

Microsatellite Typing and Antifungal Susceptibility of Candida glabrata Strains Isolated From Patients With Candida Vaginitis

Vulvovaginal candidiasis (VVC) is a yeast infection with a global reach and millions of dollars are spent annually for its diagnosis and treatment. Recently, Candida glabrata with different degrees of antifungal resistance has been considered as the second most common cause of vaginal infections. The aim of the present study is to determine the antifungal susceptibility and molecular epidemiology profiles of C. glabrata isolates from patients with VVC. Sixty-one C. glabrata isolates were examined for antifungal susceptibility using the EUCAST broth microdilution method. Moreover, microsatellite length polymorphism (MLP) was used for typing the C. glabrata isolates using six microsatellite markers. Overall, 13, 3.3, and 0% of the isolates were non-wild types to itraconazole, posaconazole, and voriconazole, respectively. Sixty (98.4%) isolates were an intermediate phenotype to fluconazole and only one isolate was fluconazole resistant. Microsatellite length polymorphism with a discriminatory power of 0.964 identified 35 distinct types and 24 singleton genotypes. The assessment of the population genetic structure revealed that the non-wild-type population had a moderate genetic differentiation compared to the wild type population (F_ST = 0.1457). It was also found that the most common genotypes were G27 (eight strains), G12 (six strains), and G4 (five strains). We found that eight strains were resistant/a non-wild phenotype to itraconazole. Five out of eight (62.5%) resistant/non-wild phenotype strains correlated to a predominant genotype (GT27) and the rest belonged to GT11 (12.5%), GT29 (12.5%), and GT28 (12.5%). The current study is the first molecular epidemiology study in the southwest of Iran and demonstrates the antifungal susceptibility profiles of C. glabrata in it. This study shows a wide range of the genetic diversity of C. glabrata (35 different genotypes) from VVC in the southwest of Iran. The majority of the non-wild isolates had a dominant genotype or genotypes related to this dominant genotype (clonal cluster one).

Fungal Genomes and Genotyping

The availability of complete fungal genomes is expanding rapidly and is offering an extensive and accurate view of this "kingdom." The scientific milestone of free access to more than 1000 fungal genomes of different species was reached, and new and stimulating projects have meanwhile been released. The "1000 Fungal Genomes Project" represents one of the largest sequencing initiative regarding fungal organisms trying to fill some gaps on fungal genomics. Presently, there are 329 fungal families with at least one representative genome sequenced, but there is still a large number of fungal families without a single sequenced genome. In addition, additional sequencing projects helped to understand the genetic diversity within some fungal species. The availability of multiple genomes per species allows to support taxonomic organization, brings new insights for fungal evolution in short-time scales, clarifies geographical and dispersion patterns, elucidates outbreaks and transmission routes, among other objectives. Genotyping methodologies analyze only a small fraction of an individual's genome but facilitate the comparison of hundreds or thousands of isolates in a small fraction of the time and at low cost. The integration of whole genome strategies and improved genotyping panels targeting specific and relevant SNPs and/or repeated regions can represent fast and practical strategies for studying local, regional, and global epidemiology of fungi.