Candidemia surveillance in Brazil: evidence for a geographical boundary defining an area exhibiting an abatement of infections by Candida albicans group 2 strains. J Clin Microbiol. 2010;48:3062-3067. [PMID: 20592158 DOI: 10.1128/JCM.00262-10]

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 diversity and molecular epidemiology of Candida albicans from vulvovaginal candidiasis patients

Candida albicans (C. albicans) is a common cause of vulvovaginal candidiasis (VVC). In this paper, the genetic diversity and molecular epidemiology of 173C. albicans strains were investigated by multilocus sequence typing (MLST). A total of 52 diploid sequence types (DSTs) were recognized, and 27 (51.9%) of which have not been reported in the MLST database. Genotyping was performed on the multiple isolates collected from patients with recurrent VVC (RVVC, referring to VVC which attacks more than 4 times in one year) in different acute infectious phases. The results showed that 59.1% (26/44) of the patients suffered a relapse, with DST 79 (65.4%) as the dominant genotype. The etiology of the remaining 40.9% (18/44) of patients was reinfection, and the main genotypes included DST 79 (33.3%), DST 124 (8.6%) and DST 1895 (8.6%). DST 79 (45%) and DST 1395 (7.5%) were the main isolates of VVC patients, while DST 79 (24.1%), DST 727 (6.9%), DST 732 (6.9%) and DST 1867 (6.9%) were the main types of healthy volunteers. The results of the genotypes between RVVC patients and other groups were statistically different. Furthermore, cluster analysis was carried out on 1468 isolates, among which 1337 were downloaded from the MLST database, 130 were divided into 8 Clades in the present study and the remaining one was taken as a singleton. 92.3% isolates from relapse patients, 58.3% isolates from re-infected patients, 77.5% isolates from VVC patients and 51.7% isolates from volunteers were distributed in Clade 1. The analysis of the genotypes of multiple isolates from RVVC patients further demonstrated that point mutation and loss of heterozygosity contributed to the microevolution of C. albicans.

Genotyping of clinical isolates of Candida glabrata from Iran by multilocus sequence typing and determination of population structure and drug resistance profile

Candida glabrata is often the second most common causative agent for candidiasis following Candida albicans. Despite the importance of C. glabrata infections, few epidemiological studies have been conducted on this issue. The goal of this study was genotyping of clinical isolates of C. glabrata by multilocus sequence typing (MLST) technique for determination of the endemic prevalent genotypes and any association between isolation source and drug resistance. A total of 50 C. glabrata clinical isolates from Iran were analyzed by MLST and tested for in-vitro susceptibilities to amphotericin-B, caspofungin, fluconazole, and voriconazole according to the Clinical Laboratory Standards Institute (CLSI) M27-A4 document guidelines. Among these isolates, 16 distinct STs were identified, indicating a discriminatory power index of 0.9029. The three major sequence types (STs) were ST-59, ST-74, and ST-7 with 10, 8, and 7 isolates, respectively. Furthermore, a total of 11 new sequences were found, to which no allele numbers were assigned in the MLST database. All the isolates were susceptible to amphotericin B and caspofungin. Fluconazole resistance was shown in four isolates. Also, a sole isolate was voriconazole resistant. This study shows that the population structure of C. glabrata in Iran consists of groups closely related to the global database as well as to some new clonal clusters and STs. Regarding the high prevalence of 11 new sequences found in this study, it can be concluded that, these new alleles are among the endemic genotypes of Iran. The genotypes or STs were independent of drug susceptibility and anatomic sources.

Multilocus sequence typing of Candida albicans isolates from the oral cavities of patients undergoing haemodialysis

This study evaluates the prevalence, diversity, and genetic profiles of Candida albicans isolates recovered from the oral cavities of haemodialysis patients. Oral swab samples were obtained from haemodialysis patients (n = 126) and healthy control subjects (n = 233) and Candida species were characterised. There was no significant difference between the haemodialysis and control groups in the prevalence of yeast carriers (23.6% vs. 31.0%, respectively) or C. albicans carriers (19.8% vs. 21.0%, respectively). C. albicans was the most populous species in both cohorts, followed by C. parapsilosis. C. parapsilosis and C. glabrata were more prevalent in the haemodialysis group than in the control group (C. parapsilosis 5.6% vs. 0.9% and C. glabrata 3.2% vs. 0.4%, respectively; P < 0.05). C. albicans isolates were analysed by multilocus sequence typing and the results were used to construct a phylogenetic tree. Most haemodialysis isolates were placed into Clade 4 (20.0%) and Clade 19 (16.0%) and most control isolates into Clade 8 (17%) and Clade 4 (14.9%). Differences in the strain abundance in each clade were not statistically significant between the two groups. Moreover, there was no significant association between the health status or diagnosis and either the sequence types or clades.

Clonal Strain Persistence of Candida albicans Isolates from Chronic Mucocutaneous Candidiasis Patients

Chronic mucocutaneous candidiasis (CMC) is a primary immunodeficiency disorder characterised by susceptibility to chronic Candida and fungal dermatophyte infections of the skin, nails and mucous membranes. Molecular epidemiology studies of CMC infection are limited in number and scope and it is not clear whether single or multiple strains inducing CMC persist stably or are exchanged and replaced. We subjected 42 C. albicans individual single colony isolates from 6 unrelated CMC patients to multilocus sequence typing (MLST). Multiple colonies were typed from swabs taken from multiple body sites across multiple time points over a 17-month period. Among isolates from each individual patient, our data show clonal and persistent diploid sequence types (DSTs) that were stable over time, identical between multiple infection sites and exhibit azole resistant phenotypes. No shared origin or common source of infection was identified among isolates from these patients. Additionally, we performed C. albicans MLST SNP genotype frequency analysis to identify signatures of past loss of heterozygosity (LOH) events among persistent and azole resistant isolates retrieved from patients with autoimmune disorders including CMC.

Multilocus sequence typing of Candida albicans isolates from oral and gastric mucosa of dyspeptic patients

AIM: To detect the genetic profiles of Candida albicans (C. albicans) strains in the digestive tract of dyspeptic patients by multilocus sequence typing (MLST), and to explore whether lesion of the gastric mucosa is closely related to the genotype of C. albicans.

METHODS: A total of 111 oral swab samples and 102 gastric mucosa samples were collected from patients with gastritis or gastric ulcer. In addition, 162 oral swab samples collected from healthy volunteers were used as a control group. Candida species isolates from separate samples were identified by amplifying the ITS1-5.8S-ITS2 region sequence. C. albicans isolates were characterized and analyzed by multilocus sequence typing, and submitted to the C. albicans MLST database. The phylogenetic tree was constructed by the method of unweighted-pair group method using average linkages (UPGMA) to analyze the relationship between the evolutionary clades and gastric mucosal inflammation lesion.

RESULTS: In the oral mucosa swab samples of the control group and patient group, the positive rates of Candida spp. were 29.6% vs 36.0%, and the constitute ratios of C. albicans were 64.6% vs 95%, respectively. In the gastric samples of the patient group, the positive rate of Candida spp. was 41.4%, and the constituent ratio of C. albicans was 97.8%. Both the positive rate and constituent ratio of C. albicans in the patient group were significantly higher than those in the control group (χ² = 4.071, P < 0.01; χ² = 7.650, P = 0.006). In C. albicans MLST detection, the positive rate of genotype ST1593 was significantly higher in the patient group than in the control group (60% vs 14.8%; χ² = 12.815, P < 0.001). The different evolutionary clades of C. albicans strains were closely related to the inflammatory lesion of the gastric mucosa (Kendall's tau-b r = 0.591, P < 0.001).

CONCLUSION: C. albicans could be detected in the gastric mucosa of patients with dyspepsia, and its special genotype is closely related to the inflammatory lesion of the gastric mucosa.

Multilocus Sequence Typing of Pathogenic Candida albicans Isolates Collected from a Teaching Hospital in Shanghai, China: A Molecular Epidemiology Study

Molecular typing of Candida albicans is important for studying the population structure and epidemiology of this opportunistic yeast, such as population dynamics, nosocomial infections, multiple infections and microevolution. The genetic diversity of C. albicans has been rarely studied in China. In the present study, multilocus sequence typing (MLST) was used to characterize the genetic diversity and population structure of 62 C. albicans isolates collected from 40 patients from Huashan Hospital in Shanghai, China. A total of 50 diploid sequence types (DSTs) were identified in the 62 C. albicans isolates, with 41 newly identified DSTs. Based on cluster analysis, the 62 isolates were classified into nine existing clades and two new clades (namely clades New 1 and New 2). The majority of the isolates were clustered into three clades, clade 6 (37.5%), clade 1 (15.0%) and clade 17 (15.0%). Isolates of clade New 2 were specifically identified in East Asia. We identified three cases of potential nosocomial transmission based on association analysis between patients' clinical data and the genotypes of corresponding isolates. Finally, by analyzing the genotypes of serial isolates we further demonstrated that the microevolution of C. albicans was due to loss of heterozygosity. Our study represents the first molecular typing of C. albicans in eastern China, and we confirmed that MLST is a useful tool for studying the epidemiology and evolution of C. albicans.

Genetic diversity of medically important and emerging Candida species causing invasive infection

BACKGROUND

Genetic variation in the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region has been studied among fungi. However, the numbers of ITS sequence polymorphisms in the various Candida species and their associations with sources of invasive fungal infections remain poorly investigated. Here, we characterized the intraspecific and interspecific ITS diversity of Candida spp. strains collected from patients with bloodstream or oroesophageal candidiasis.

METHODS

We selected cultures of representative medically important species of Candida as well as some rare and emerging pathogens. Identification was performed by micromorphology and by biochemical testing using an ID32C system, as well as by the sequencing of rDNA ITS. The presence of intraspecific ITS polymorphisms was characterized based on haplotype networks, and interspecific diversity was characterized based on Bayesian phylogenetic analysis.

RESULTS

Among 300 Candida strains, we identified 76 C. albicans, 14 C. dubliniensis, 40 C. tropicalis, 47 C. glabrata, 34 C. parapsilosis (sensu stricto), 31 C. orthopsilosis, 3 C. metapsilosis, 21 Meyerozyma guilliermondii (C. guilliermondii), 12 Pichia kudriavzevii (C. krusei), 6 Clavispora lusitaniae (C. lusitaniae), 3 C. intermedia, 6 Wickerhamomyces anomalus (C. pelliculosa), and 2 C. haemulonii strains, and 1 C. duobushaemulonii, 1 Kluyveromyces marxianus (C. kefyr), 1 Meyerozyma caribbica (C. fermentati), 1 Pichia norvegensis (C. norvegensis), and 1 Lodderomyces elongisporus strain. Out of a total of seven isolates with inconsistent ID32C profiles, ITS sequencing identified one C. lusitaniae strain, three C. intermedia strains, two C. haemulonii strains and one C. duobushaemulonii strain. Analysis of ITS variability revealed a greater number of haplotypes among C. albicans, C. tropicalis, C. glabrata and C. lusitaniae, which are predominantly related to endogenous sources of acquisition. Bayesian analysis confirmed the major phylogenetic relationships among the isolates and the molecular identification of the different Candida spp.

CONCLUSIONS

Molecular studies based on ITS sequencing are necessary to identify closely related and emerging species. Polymorphism analysis of the ITS rDNA region demonstrated its utility as a genetic marker for species identification and phylogenetic relationships as well as for drawing inferences concerning the natural history of hematogenous infections caused by medically important and emerging Candida species.

Molecular fingerprints to identify Candida species

A wide range of molecular techniques have been developed for genotyping Candida species. Among them, multilocus sequence typing (MLST) and microsatellite length polymorphisms (MLP) analysis have recently emerged. MLST relies on DNA sequences of internal regions of various independent housekeeping genes, while MLP identifies microsatellite instability. Both methods generate unambiguous and highly reproducible data. Here, we review the results achieved by using these two techniques and also provide a brief overview of a new method based on high-resolution DNA melting (HRM). This method identifies sequence differences by subtle deviations in sample melting profiles in the presence of saturating fluorescent DNA binding dyes.

Particular Candida albicans strains in the digestive tract of dyspeptic patients, identified by multilocus sequence typing

Background

Candida albicans is a human commensal that is also responsible for chronic gastritis and peptic ulcerous disease. Little is known about the genetic profiles of the C. albicans strains in the digestive tract of dyspeptic patients. The aim of this study was to evaluate the prevalence, diversity, and genetic profiles among C. albicans isolates recovered from natural colonization of the digestive tract in the dyspeptic patients.

Methods and Findings

Oral swab samples (n = 111) and gastric mucosa samples (n = 102) were obtained from a group of patients who presented dyspeptic symptoms or ulcer complaints. Oral swab samples (n = 162) were also obtained from healthy volunteers. C. albicans isolates were characterized and analyzed by multilocus sequence typing. The prevalence of Candida spp. in the oral samples was not significantly different between the dyspeptic group and the healthy group (36.0%, 40/111 vs. 29.6%, 48/162; P > 0.05). However, there were significant differences between the groups in the distribution of species isolated and the genotypes of the C. albicans isolates. C. albicans was isolated from 97.8% of the Candida-positive subjects in the dyspeptic group, but from only 56.3% in the healthy group (P < 0.001). DST1593 was the dominant C. albicans genotype from the digestive tract of the dyspeptic group (60%, 27/45), but not the healthy group (14.8%, 4/27) (P < 0.001).

Conclusions

Our data suggest a possible link between particular C. albicans strain genotypes and the host microenvironment. Positivity for particular C. albicans genotypes could signify susceptibility to dyspepsia.