Molecular epidemiology of global Candida dubliniensis isolates utilizing genomic-wide, co-dominant, PCR-based markers for strain delineation
School of Dental Science, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Victoria, Australia.Medical mycology: official publication of the International Society for Human and Animal Mycology (Impact Factor: 2.34). 05/2009; 47(8):789-95. DOI: 10.3109/13693780802641912
The molecular epidemiology of Candida dubliniensis has been studied using large complex DNA probes for Southern analysis and has revealed the existence of distinct genotypes within this species. The aim of the present study was to utilize a PCR-based analysis of molecular co-dominant markers to assess the relatedness of a global and temporally diverse collection of well characterized isolates of C. dubliniensis. Sixty-two C. dubliniensis strains were collected from the authors of previously published studies. Co-dominant PCR-based markers utilizing five separate PCR fingerprints were obtained in the present investigation. Phylogenetic and statistical analyses utilizing permutation tests were undertaken to assess correlations amongst the isolates. Three distinct PCR-groups were observed and there was evidence that strains isolated since 1990 were genotypically more similar to each other than they were to strains recovered prior to 1990.
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ABSTRACT: Candida dubliniensis is an emerging pathogen first described in 1995, which shares many phenotypic features with Candida albicans and therefore may be misidentified in microbial laboratories. Despite various phenotypic techniques described in the literature to differentiate the two species, the correct identification of C. dubliniensis remains problematic due to phenotypic similarities between these species. Thus, as the differences between both are best characterized at genetic levels, several molecular methods have been proposed to provide a specific and rapid identification of this species. Epidemiological studies have shown that C. dubliniensis is prevalent throughout the world and it is primarily associated with oral carriage and oropharyngeal infections in patients infected with human immunodeficiency virus (HIV). However, data acquired from its isolation from other healthy and immunocompromised patients are variable, and there is still no real consensus on the epidemiological relevance of this species. In this article, we review the various phenotypic methods used in the identification of C. dubliniensis and the epidemiological impact of this new species.Mycopathologia 06/2010; 169(6):431-43. DOI:10.1007/s11046-010-9286-5 · 1.53 Impact Factor
Article: Assessing similarity of DNA profiles[Show abstract] [Hide abstract]
ABSTRACT: The genetic similarity of strains of a pathogen can be assessed by using a matrix of dissimilarities that is derived from bands in their DNA profile which are present or absent. The dependence between elements of the dissimilarity matrix, if not accounted for, results in underestimation of the variance in comparisons between groups of strains which are differentiated according to the possession of an attribute. We examine a previously proposed statistic for determining whether a group of strains is more similar than expected. We show the limitations of this statistic and propose a new statistic which better addresses the hypotheses that are usually considered in this field of study. The statistic proposed is based on similarity between strains within the group of interest and with those outside. This statistic also needs to account for the dependence in the raw data, and we use the correlation between elements of the dissimilarity matrix to investigate how this dependence affects the underestimation of the variance. Using examples involving the pathogenic yeast Candida, we show how permutation tests can be applied to the differentiation of groups of strains.Applied Statistics 01/2011; 60(1):125-133. DOI:10.2307/41057555 · 1.49 Impact Factor
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ABSTRACT: There is a paucity of information about genotypic heterogeneity among Candida dubliniensis isolates recovered from different geographic regions. This study explored genotypic heterogeneity among 103 C. dubliniensis strains obtained over a six-year period from clinical specimens in Kuwait. Genotype assignment was based on amplification with genotype-specific primers and sequencing of rDNA. Susceptibility to 5-flucytosine was determined by means of the Etest. DNA sequencing of cytosine deaminase was performed to determine the molecular basis of resistance to 5-flucytosine. DNA sequencing of rDNA identified seven different genotypes, i.e., 68 (66%) isolates were found to belong to genotype 1, 25 to genotype 4, six to genotype 5 and one each to genotypes 6-9. Strains of genotype 2 or genotype 3 were not detected. All isolates of genotype 4 but none of other genotypes were resistant to 5-flucytosine and the resistant strains all contained S29L mutation. Isolates of all other genotypes contained wild-type codon 29 in cytosine deaminase. A simple, PCR-RFLP-based method has been developed to facilitate rapid detection of S29L mutation in cytosine deaminase. A noteworthy observation of our study is the identification of five new genotypes of C. dubliniensis isolates, recovered from oral/respiratory specimens from patients of Middle Eastern origin. Furthermore, all 5-flucytosine resistant C. dubliniensis isolates in Kuwait belonged to genotype 4 only.Medical mycology: official publication of the International Society for Human and Animal Mycology 09/2011; 50(3):244-51. DOI:10.3109/13693786.2011.597446 · 2.34 Impact Factor
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