Multilocus Sequence Typing Is a Reliable Alternative Method to DNA Fingerprinting for Discriminating among Strains of
            <i>Candida albicans</i>

Robles, Juan Carlos; Koreen, Larry; Park, Steven; Perlin, David S.

doi:10.1128/jcm.42.6.2480-2488.2004

Cited by 72 publications

(62 citation statements)

References 32 publications

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“…The percent concordance between any two typing techniques for a particular set of isolates was calculated as previously described with cross-classification analysis of all possible pairs of those isolates (22,38,39). Simpson's index of diversity, which indicates the probability that among a group of isolates any two randomly selected isolates will have different genotypes (19), was used to measure discriminatory power.…”

Section: Methodsmentioning

confidence: 99%

Comparative Sequencing of the Serine-Aspartate Repeat-Encoding Region of the Clumping Factor B Gene ( clfB ) for Resolution within Clonal Groups of Staphylococcus aureus

Koreen

Ramaswamy

Naidich³

et al. 2005

J Clin Microbiol

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Molecular techniques such as spa typing and multilocus sequence typing use DNA sequence data for differentiating Staphylococcus aureus isolates. Although spa typing is capable of detecting both genetic microand macrovariation, it has less discriminatory power than the more labor-intensive pulsed-field gel electrophoresis (PFGE) and costly genomic DNA microarray analyses. This limitation hinders strain interrogation for newly emerging clones and outbreak investigations in hospital or community settings where robust clones are endemic. To overcome this constraint, we developed a typing system using DNA sequence analysis of the serine-aspartate (SD) repeat-encoding region within the gene encoding the keratin-and fibrinogen-binding clumping factor B (clfB typing) and tested whether it is capable of discriminating within clonal groups. We analyzed 116 S. aureus strains, and the repeat region was present in all isolates, varying in sequence and in length from 420 to 804 bp. In a sample of 36 well-characterized genetically diverse isolates, clfB typing subdivided identical spa and PFGE clusters which had been discriminated by whole-genome DNA microarray mapping. The combination of spa typing and clfB typing resulted in a discriminatory power (99.5%) substantially higher than that of spa typing alone and closely approached that of the whole-genome microarray (100.0%). clfB typing also successfully resolved genetic differences among isolates differentiated by PFGE that had been collected over short periods of time from single hospitals and that belonged to the most prevalent S. aureus clone in the United States. clfB typing demonstrated in vivo, in vitro, and interpatient transmission stability yet revealed that this locus may be recombinogenic in a primarily clonal population structure. Taken together, these data show that the SD repeat-encoding region of clfB is a highly stable marker of microvariation, that in conjunction with spa typing it may serve as a DNA sequence-based alternative to PFGE for investigating genetically similar strains, and that it is useful for analyzing collections of isolates in both long-term population-based and local epidemiologic studies.Strain typing techniques for Staphylococcus aureus, the leading cause of nosocomial infections (28), have become widely used. These techniques aid in both local/short-term epidemiologic outbreak investigations and global/long-term population-based studies of methicillin-resistant and -susceptible S. aureus (MRSA and MSSA, respectively). Macrorestriction digests using pulsed-field gel electrophoresis (PFGE) have been shown to be highly effective in outbreak settings (48). Multilocus enzyme electrophoresis (MLEE), multilocus sequence typing (MLST), and sequence analysis of the repeat region within the coagulase gene, i.e., coa typing, are effective techniques for analyzing S. aureus strains in long-term study settings (10,42), and the sequence analysis of the repeat region within the protein A gene, spa typing, can effectively be used in both settings (22,41)....

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Section: Methodsmentioning

confidence: 99%

Comparative Sequencing of the Serine-Aspartate Repeat-Encoding Region of the Clumping Factor B Gene ( clfB ) for Resolution within Clonal Groups of Staphylococcus aureus

Koreen

Ramaswamy

Naidich³

et al. 2005

J Clin Microbiol

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“…Moreover, the portability of MLST data allows results from different laboratories to be compared (33,34). MLST was first utilized to genetically characterize pathogenic bacteria but has now been expanded for use in genetic and population studies of fungi and protozoa (48,67).…”

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Genetic Characterization of Trichomonas vaginalis Isolates by Use of Multilocus Sequence Typing

et al. 2012

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dIn this study, we introduce a multilocus sequence typing (MLST) scheme, comprised of seven single-copy housekeeping genes, to genetically characterize Trichomonas vaginalis. Sixty-eight historical and recent isolates of T. vaginalis were sampled from the American Type Culture Collection and female patients at area health care facilities, respectively, to assess the usefulness of this typing method. Forty-three polymorphic nucleotide sites, 51 different alleles, and 60 sequence types were distinguished among the 68 isolates, revealing a diverse T. vaginalis population. Moreover, this discriminatory MLST scheme retains the ability to identify epidemiologically linked isolates such as those collected from sexual partners. Population genetic and phylogenetic analyses determined that T. vaginalis population structure is strongly influenced by recombination and is composed of two separate populations that may be nonclonal. MLST is useful for investigating the epidemiology, genetic diversity, and population structure of T. vaginalis.

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“…An agreed consensus scheme between the different laboratories examined seven loci, AAT1a, ACC1, ADP1, MPIb, SYA1, VPS13, and ZWF1b, and allowed the application of MLST to the analysis of C. albicans epidemiology and population structure (7-9, 16, 36, 52). MLST analysis has since been demonstrated to be as sensitive as DNA fingerprinting (43), and due to the nature of the data (i.e., DNA sequences of specific loci), these can be used to create a large database generated by multiple laboratories (7). In the case of C. albicans, it has also been shown that the strain groupings identified by MLST correlate with clades of C. albicans organisms identified using the species-specific DNA fingerprinting probe Ca3 (52).…”

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Multilocus Sequence Typing Reveals that the Population Structure of Candida dubliniensis Is Significantly Less Divergent than That of Candida albicans

et al. 2008

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The pathogenic yeast Candida dubliniensis is phylogenetically very closely related to Candida albicans, and both species share many phenotypic and genetic characteristics. DNA fingerprinting using the species-specific probe Cd25 and sequence analysis of the internal transcribed spacer (ITS) region of the ribosomal gene cluster previously showed that C. dubliniensis is comprised of three major clades comprising four distinct ITS genotypes. Multilocus sequence typing (MLST) has been shown to be very useful for investigating the epidemiology and population biology of C. albicans and has identified many distinct major and minor clades. In the present study, we used MLST to investigate the population structure of C. dubliniensis for the first time. Combinations of 10 loci previously tested for MLST analysis of C. albicans were assessed for their discriminatory ability with 50 epidemiologically unrelated C. dubliniensis isolates from diverse geographic locations, including representative isolates from the previously identified three Cd25-defined major clades and the four ITS genotypes. Dendrograms created by using the unweighted pair group method with arithmetic averages that were generated using the data from all 10 loci revealed a population structure which supports that previously suggested by DNA fingerprinting and ITS genotyping. The MLST data revealed significantly less divergence within the C. dubliniensis population examined than within the C. albicans population. These findings show that MLST can be used as an informative alternative strategy for investigating the population structure of C. dubliniensis. On the basis of the highest number of genotypes per variable base, we recommend the following eight loci for MLST analysis of C. dubliniensis: CdAAT1b, CdACC1, CdADP1, CdMPIb, CdRPN2, CdSYA1, exCdVPS13, and exCdZWF1b, where "Cd" indicates C. dubliniensis and "ex" indicates extended sequence.Candida dubliniensis is a pathogenic yeast species that is phenotypically, genetically, and phylogenetically very closely related to Candida albicans, the yeast species most commonly associated with infection in humans (49, 51). Despite their close relationship, C. albicans is significantly more pathogenic (49, 50). C. dubliniensis is most commonly associated with oral carriage and infection in human immunodeficiency virus (HIV)-infected and diabetic patients, although it has been identified as a minor constituent of the commensal floras in the oral cavities of healthy individuals (40,49,50). Although C. dubliniensis has also been recovered from patients with systemic infections, its incidence is far lower than that of C. albicans. While the latter is responsible for 40 to 60% of cases of candidemia, C. dubliniensis has been identified in only 1 to 2% of blood culture yeast samples (11,15,27,(29)(30)(31). These epidemiological data are reflected in the results of animal infection model studies that demonstrated that C. albicans is significantly more pathogenic than C. dubliniensis (22,47,56). The reasons for the lower viru...

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Multilocus Sequence Typing Is a Reliable Alternative Method to DNA Fingerprinting for Discriminating among Strains of Candida albicans

Cited by 72 publications

References 32 publications

Comparative Sequencing of the Serine-Aspartate Repeat-Encoding Region of the Clumping Factor B Gene ( clfB ) for Resolution within Clonal Groups of Staphylococcus aureus

Comparative Sequencing of the Serine-Aspartate Repeat-Encoding Region of the Clumping Factor B Gene ( clfB ) for Resolution within Clonal Groups of Staphylococcus aureus

Genetic Characterization of Trichomonas vaginalis Isolates by Use of Multilocus Sequence Typing

Multilocus Sequence Typing Reveals that the Population Structure of Candida dubliniensis Is Significantly Less Divergent than That of Candida albicans

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