Molecular genotyping of Candida species with special respect to Candida (Torulopsis) glabrata strains by arbitrarily primed PCR

Becker, Karsten; Badehorn, Dörte; Deiwick, Susanne; Peters, Georg; Fegeler, W.

doi:10.1099/0022-1317-49-6-575

Cited by 19 publications

(28 citation statements)

References 15 publications

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“…This method is technically simple, and if enough primers are used alone or in combinations, the large number of bands obtained ensures that some of the genomic polymorphisms between unrelated strains will be detected with a reasonable probability. However, AP-PCR suffers from a high sensitivity to reaction conditions (CaetanoAnolles, 1993 ;Meunier & Grimont, 1993), resulting in high centre-to-centre, and even experiment-to-experiment, variability (Becker et al, 2000 ;Taylor et al, 1999 ;Tyler et al, 1997). An alternative approach is to use locus-specific primers for known highly polymorphic loci.…”

Section: Abbreviations : Ap-pcr Arbitrarily Primed Pcr ; Vntr Variamentioning

confidence: 99%

A highly polymorphic degenerate microsatellite for molecular strain typing of Candida krusei The GenBank accession numbers for the sequences determined in this work are AF326279–AF326292.

Shemer¹,

Weissman²,

Hashman³

et al. 2001

Microbiology

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Simple sequence repeats, due to their high variability, are widely used for molecular epidemiology of pathogenic micro-organisms. However, their usefulness is restricted by their high instability and low information content. Here, a locus, CKTNR, in the fungal pathogen Candida krusei is described which displays considerable sequence, as well as length, heterogeneity. Alleles of this locus, which contains a degenerate trinucleotide repeat, appear to be stable. The CKTNR polymorphism could serve as the basis for a molecular typing system of C. krusei. Furthermore, analysis of the CKTNR allele distribution suggested that C. krusei reproduces mainly clonally.

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Section: Abbreviations : Ap-pcr Arbitrarily Primed Pcr ; Vntr Variamentioning

confidence: 99%

A highly polymorphic degenerate microsatellite for molecular strain typing of Candida krusei The GenBank accession numbers for the sequences determined in this work are AF326279–AF326292.

Shemer¹,

Weissman²,

Hashman³

et al. 2001

Microbiology

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“…The most widely applied include (i) multilocus sequence typing (MLST), which analyzes 6 relatively conserved housekeeping loci for single nucleotide polymorphisms (SNPs) (29,30), (ii) pulsed-field gel electrophoresis (PFGE), which compares total DNA banding patterns with or without restriction enzyme digestion (14,23,31), (iii) multilocus variable-number tandem-repeat analysis (MLVA, also known as microsatellite analysis), which examines length variation in 6 to 9 PCR-amplified loci that contain polymorphic tandem repeats (32)(33)(34)(35), and (iv) random amplification of polymorphic DNA (RAPD), which compares banding patterns following PCR with a nonspecific primer (26,36). In general, these methods are comparable in their strain resolution, achieving diversity indexes of ca.…”

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confidence: 99%

Evaluation of Polymorphic Locus Sequence Typing for Candida glabrata Epidemiology

et al. 2016

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The opportunistic yeast Candida glabrata is increasingly refractory to antifungal treatment or prophylaxis and relatedly is increasingly implicated in health care-associated infections. To elucidate the epidemiology of these infections, strain typing is required. Sequence-based typing provides multiple advantages over length-based methods, such as pulsed-field gel electrophoresis (PFGE); however, conventional multilocus sequence typing (targeting 6 conserved loci) and whole-genome sequencing are impractical for routine use. A commercial sequence-based typing service for C. glabrata that targets polymorphic tandem repeatcontaining loci has recently been developed. These CgMT-J and CgMT-M services were evaluated with 56 epidemiologically unrelated isolates, 4 to 7 fluconazole-susceptible or fluconazole-resistant isolates from each of 5 center A patients, 5 matched pairs of fluconazole-susceptible/resistant isolates from center B patients, and 7 isolates from a center C patient who responded to then failed caspofungin therapy. CgMT-J and CgMT-M generated congruent results, resolving isolates into 24 and 20 alleles, respectively. Isolates from all but one of the center A patients shared the same otherwise rare alleles, suggesting nosocomial transmission. Unexpectedly, Pdr1 sequencing showed that resistance arose independently in each patient. Similarly, most isolates from center B also clustered together; however, this may reflect a dominant clone since their alleles were shared by multiple unrelated isolates. Although distinguishable by their echinocandin susceptibilities, all isolates from the center C patient shared alleles, in agreement with the previously reported relatedness of these isolates based on PFGE. Finally, we show how phylogenetic clusters can be used to provide surrogate parents to analyze the mutational basis for antifungal resistance.

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“…Several studies of molecular typing to relate epidemiological information with molecular fingerprints have been made with C. glabrata (2,8,40). For C. glabrata only two papers exist that report quantitative measurements of intraspecific genetic diversity, genetic distance between strains, and mode of reproduction in nature (6,19).…”

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confidence: 99%

Genetic Diversity among Clinical Isolates of Candida glabrata Analyzed by Randomly Amplified Polymorphic DNA and Multilocus Enzyme Electrophoresis Analyses

Boldo-León¹,

Villa‐Tanaca²,

Zúñiga

et al. 2003

J Clin Microbiol

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The genetic diversity of 47 clinical and reference strains of Candida glabrata from several geographical origins and diverse clinical disorders, with different antifungal susceptibilities, as well as their genetic relationships were studied through multilocus enzyme electrophoresis (MLEE) and randomly amplified polymorphic DNA (RAPD) techniques. The genetic diversity estimated for 11 MLEE loci measured as average heterozygosity (h) was 0.055. A high level of genetic relatedness among isolates was established by cluster analysis. Forty-nine RAPD markers were analyzed, and the average genetic diversity among isolates, estimated by Shannon's index (H o ), was 0.372. The ⌽ ST values estimated through an analysis of molecular variance to assess genetic differentiation among isolates revealed no genetic differentiation among them. Our results revealed very low genetic diversity among isolates, a lack of differentiation, and no association with their geographic origin and the clinical characteristics.

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Molecular genotyping of Candida species with special respect to Candida (Torulopsis) glabrata strains by arbitrarily primed PCR

Cited by 19 publications

References 15 publications

A highly polymorphic degenerate microsatellite for molecular strain typing of Candida krusei The GenBank accession numbers for the sequences determined in this work are AF326279–AF326292.

A highly polymorphic degenerate microsatellite for molecular strain typing of Candida krusei The GenBank accession numbers for the sequences determined in this work are AF326279–AF326292.

Evaluation of Polymorphic Locus Sequence Typing for Candida glabrata Epidemiology

Genetic Diversity among Clinical Isolates of Candida glabrata Analyzed by Randomly Amplified Polymorphic DNA and Multilocus Enzyme Electrophoresis Analyses

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