Lack of consistent short sequence repeat polymorphisms in genetically homologous colonizing and invasive Candida albicans strains

DNA microsatellite genotyping of potentially pathogenic Candida albicans and C. dubliniensis isolated from the oral cavity and dental prostheses

This study investigated the incidence, genetic diversity, antifungal sensitivity, and virulence of Candida albicans and C. dubliniensis isolated from subjects using dental prostheses and subjects clinically indicated for the first prosthetic rehabilitation. Subjects were divided into four groups and samples were collected twice: at first rehabilitation by removable partial (A) and total (C) dental prostheses, and replacement of the removable partial (B) and total (D) prostheses. Yeasts were genotyped using DNA microsatellite markers. Microbiological methods were used to screen for azole antifungal resistance and exoenzyme production. In the initial sampling, oral colonization by Candida was observed in 31 (53.4%) subjects in groups A (33.3%), B (68.2%), and D (65%); 20 (47.6%) subjects displayed colonization of prostheses: groups B (50%) and D (45%). The second sampling (±30 days) revealed Candida in 2 (3.4%: oral cavity) and 4 (6.9%: prosthetic) subjects from group B. C. albicans and C. dubliniensis displayed both polyclonal and monoclonal patterns of infection. Azole-resistant C. albicans and SAPs⁺ strains were prevalent. Related strains were found in one or several oral sites (mucosa and prosthesis), as well as intra- and inter-subject, -gender, -group, and -time of sampling. However, the patterns of clonality can be altered under dental care.

Comparison of MALDI-TOF mass spectra with microsatellite length polymorphisms in Candida albicans

Candida albicans is the most frequent yeast involved in human infections. Its population structure can be divided into several genetic clades, some of which have been associated with antifungal susceptibility. Therefore, detecting and monitoring fungal clones in a routine laboratory setting would be a major epidemiological advance. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectra results are now widely used as bar codes to identify microorganisms in clinical microbiology laboratories. This study aimed at testing MALDI-TOF mass spectra bar codes to identify clades among a set of C. albicans isolates. Accordingly, 102 clinical strains were genotyped using 10 microsatellite markers and analyzed via MALDI-TOF mass spectrometry. The mass spectra were compared with a reference spectral library including 33 well-characterized collection strains, using a Microflex(TM) system and Biotyper(TM) software, to test the capacity of the spectrum of a given isolate to match with the reference mass spectrum of an isolate from the same genetic clade. Despite high confidence species identification, the spectra failed to significantly match with the corresponding clade (p = 0.74). This was confirmed with the MALDI-TOF spectra similarity dendrogram, in which the strains were dispersed irrespective of their genetic clade. Various attempts to improve intra-clade spectra recognition were unsuccessful. In conclusion, MALDI-TOF mass spectra bar code analysis failed to reliably recognize genetically related C. albicans isolates. Further studies are warranted to develop alternative MALDI-TOF mass spectra analytical approaches to identify and monitor C. albicans clades in the routine clinical laboratory.

Candida identification: a journey from conventional to molecular methods in medical mycology

The incidence of Candida infections have increased substantially in recent years due to aggressive use of immunosuppressants among patients. Use of broad-spectrum antibiotics and intravascular catheters in the intensive care unit have also attributed with high risks of candidiasis among immunocompromised patients. Among Candida species, C. albicans accounts for the majority of superficial and systemic infections, usually associated with high morbidity and mortality often caused due to increase in antimicrobial resistance and restricted number of antifungal drugs. Therefore, early detection of candidemia and correct identification of Candida species are indispensable pre-requisites for appropriate therapeutic intervention. Since blood culture based methods lack sensitivity, and species-specific identification by conventional method is time-consuming and often leads to misdiagnosis within closely related species, hence, molecular methods may provide alternative for accurate and rapid identification of Candida species. Although, several molecular approaches have been developed for accurate identification of Candida species but the internal transcribed spacer 1 and 2 (ITS1 and ITS2) regions of the rRNA gene are being used extensively in a variety of formats. Of note, ITS sequencing and PCR-RFLP analysis of ITS region seems to be promising as a rapid, easy, and cost-effective method for identification of Candida species. Here, we review a number of existing techniques ranging from conventional to molecular approaches currently in use for the identification of Candida species. Further, advantages and limitations of these methods are also discussed with respect to their discriminatory power, reproducibility, and ease of performance.

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.

National surveillance of fungemia in Denmark (2004 to 2009)

A 6-year nationwide study of fungemia in Denmark was performed using data from an active fungemia surveillance program and from laboratory information systems in nonparticipating regions. A total of 2,820 episodes of fungemia were recorded. The incidence increased from 2004 to 2007 (7.7 to 9.6/100,000) and decreased slightly from 2008 to 2009 (8.7 to 8.6/100,000). The highest incidences were seen at the extremes of age (i.e., 11.3 and 37.1/100,000 for those <1 and 70 to 79 years old, respectively). The rate was higher for males than for females (10.1 versus 7.6/100,000, P = 0.003), with the largest difference observed for patients >50 years of age. The species distribution varied significantly by both age and gender. Candida species accounted for 98% of the pathogens, and C. albicans was predominant, although the proportion decreased (64.4% to 53.2%, P < 0.0001). C. glabrata ranked second, and the proportion increased (16.5% to 25.9%, P = 0.003). C. glabrata was more common in adults and females than in children and males, whereas C. tropicalis was more common in males (P = 0.020). C. krusei was a rare isolate (4.1%) except at one university hospital. Acquired resistance to amphotericin and echinocandins was rare. However, resistance to fluconazole (MIC of >4 μg/ml) occurred in C. albicans (7/1,183 [0.6%]), C. dubliniensis (2/65 [3.1%]), C. parapsilosis (5/83 [6.0%]), and C. tropicalis (7/104 [6.7%]). Overall, 70.8% of fungemia isolates were fully fluconazole susceptible, but the proportion decreased (79.7% to 68.9%, P = 0.02). The study confirmed an incidence rate of fungemia in Denmark three times higher than those in other Nordic countries and identified marked differences related to age and gender. Decreased susceptibility to fluconazole was frequent and increasing.

Molecular phylogenetics and epidemiology of Candida albicans

Candida albicans, a diploid yeast commensal and opportunist pathogen, has evolved unusual mechanisms for maintenance of genetic diversity in the absence of a complete sexual cycle. These include chromosomal polymorphisms, mitotic recombination events, and gains and losses of heterozygosity, superimposed on a fundamentally clonal mode of reproduction. Molecular typing of C. albicans strains shows geographical evolutionary associations but these have become partially blurred, probably as a result of extensive human travel. Individual patients usually carry a single C. albicans strain type, but this may undergo microvariation leading to detection of mixtures of closely related types. Associations have been found between clade 1, the most common multilocus sequence typing cluster of related C. albicans strains, and resistance to flucytosine and terbinafine. There are also clade-related associations with lengths of tandem repeats in some cell-surface proteins, but not with virulence or type of infection.

Molecular analysis of Candida albicans isolates from clinical specimens

The aim of this study was to genotype Candida albicans strains isolated from various clinical specimens by using CA-INT-R and CA-INT-L primer pairs designed to span the region that includes the site of the transposable group-1 intron in the 25S rRNA gene. A total of 194 C. albicans isolates (28 invasive and 166 noninvasive) were genotyped. The frequencies of genotypes A, B, C and D were found as 51.0, 29.4, 19.1 and 0.5%, respectively. Statistically significant difference was determined between frequency of genotype distribution between invasive and noninvasive isolates (P < 0.001). Genotype C was more prevalent among invasive isolates while genotype A was in noninvasive ones. Furthermore, six different subtypes were determined among genotype A C. albicans isolates by restriction endonuclease analysis using a previously constructed differentiation scheme consisting of HaeIII and MspI digestions. This study demonstrated the genetic diversity of clinical isolates of C. albicans in our hospital.

Comparative genomics and molecular dynamics of DNA repeats in eukaryotes

Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, "tandem repeats" and "dispersed repeats." Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences.

Molecular typing of Aspergillus species

Aspergillus species are widely distributed fungi that release large amounts of airborne conidia, which are dispersed in the environment. Several Aspergillus species have been described as human pathogens. Molecular techniques have been developed to investigate the epidemiological relation between environmental and clinical isolates. Several typing methods have been described for Aspergillus species, most of them with reference to Aspergillus fumigatus. Here, we summarise all the different available molecular typing techniques for Aspergillus. The performance of these techniques is evaluated with respect to their practical feasibility, and their interpretation and discriminatory power assessed. For A. fumigatus isolates, a large extent of genetic variability is demonstrated and therefore fingerprinting techniques with high discriminatory power and high reproducibility are required for this species. Afut1-restriction fragment length polymorphism and microsatellite typing showed the highest discriminatory power. In addition, the microsatellites show excellent reproducibility. Other typing techniques are still useful for smaller epidemiological problems and for less well-equipped laboratories.

Variable number tandem repeat typing of bacteria

Analysis of bacterial genomes revealed a high percentage of DNA consisting of repeats, in which DNA motifs existed in multiple copies. Study of these DNA motifs has resulted in the development of variable number tandem repeat (VNTR) or multilocus variant-repeat analysis (MLVA) assays, which have shown to be valuable bacterial typing methods, especially in relation to disease outbreaks. The VNTR-based assay is based on direct PCR amplification of a specific locus, which is well defined. The range and polymorphism index of each locus can be calculated. This chapter describes the VNTR analysis of Neisseria meningitides-based on separation in low resolution media agarose, and VNTR analysis of Salmonella enterica subsp. enterica serovars Typhimurium-based on high resolution capillary electrophoresis.

Assessment of Candida glabrata strain relatedness by pulsed-field gel electrophoresis and multilocus sequence typing

In this study, 80 Candida glabrata isolates from intensive care unit and human immunodeficiency virus (HIV)-infected patients were typed by multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and mating type class determination. Among the 25 patients with multiple isolates, 19 patients (76%) contained multiple isolates exhibiting identical or highly related PFGE and MLST genotypes, which may indicate the maintenance or microvariation of one C. glabrata strain in each patient. However, isolates from six patients (24%) displayed different sequence types, PFGE genotypes, or mating type classes, which may indicate colonization with more than one clone over time or strain replacement. High correlations among PFGE genotypes, sequence types, and mating types were found (P < 0.01). MLST exhibited less discriminatory power than PFGE with BssHII. The genotypes, sequence types, and mating type classes were independent of anatomic sources, drug susceptibility, and HIV infection status.

Microevolution in genomic short sequence repeats of Candida albicans in non-neutropenic patients

The genome of the yeast Candida albicans harbours many genomic short sequence repeats (SSRs). These are stable upon transition of colonization to infection in immune-compromised patients. We show here that in non-neutropenic patients this transition may coincide with variation in several of the SSRs. This may have implications for stage-specific expression of C. albicans pathogenicity factors.

Microsatellite based typing of Aspergillus fumigatus: Strengths, pitfalls and solutions

Microsatellites, or short tandem repeats (STR's), are popular tools to discriminate between microbial isolates. Here, we report on the robustness of a microsatellite panel for discrimination of Aspergillus fumigatus isolates. Two major PCR artefacts (stutter peaks and minus-A peaks) can complicate correct interpretation of STR data. We investigated the effect of alterations to the various components of the PCR amplification mixtures on these PCR artefacts and on the reproducibility of this assay. Some extreme conditions led to a loss of signal, but, under all conditions where a signal was obtained, identical typing results were produced. Furthermore, pitfalls with the exchange of results between labs are discussed. These pitfalls are primarily associated with sizing of the obtained PCR fragments.

Molecular tools for differentiating probiotic and clinical strains of Saccharomyces cerevisiae

The subtype of the Saccharomyces cerevisiae yeast species known as S. cerevisiae Hansen CBS 5926 was formerly believed to be a separate species, Saccharomyces boulardii. It is widely considered non-pathogenic and is used as a probiotic agent for treatment and prevention of diarrhea. The biological properties of Saccharomyces spp. show considerable intraspecies variability and the beneficial properties of probiotic yeasts are considered strain-specific. Septicemia and fungemia caused by S. boulardii have recently been described in both immunocompromised and immunocompetent patients receiving biotherapy with this yeast. It cannot be distinguished from other S. cerevisiae strains by phenotypic criteria, so identification of these infections requires molecular typing. To identify the most effective approach for distinguishing S. boulardii, we typed 35 isolates of S. cerevisiae, of which 27 were from various clinical specimens and 8 were isolates of S. boulardii (6 obtained from probiotic preparations and 2 from clinical specimens) using four different molecular methods, two based on PCR-restriction enzyme analysis or sequencing of rDNA spacer regions, the third based on microsatellite polymorphism analysis of the S. cerevisiae genes YKL139w and YLR177w, and the last based on hybridization analysis with retrotransposon Ty917. Several clinical isolates appeared to be identical to one or more other isolates with the first three methods used, whereas with the Ty917 hybridization method all of the isolates tested appeared to be very heterogeneous. The eight S. boulardii isolates were clearly distinguishable from the clinical S. cerevisiae isolates only with Ty917 hybridization and microsatellite DNA analyses. In the latter method, the eight S. boulardii isolates exhibited an allelic variant at one of loci tested that was not shared with any other strain. Our results suggest that microsatellite polymorphism analysis of the YKL139w and YLR177w genes, as well as the analysis by Ty917 hybridization, are the most useful tools for a correct identification of S. boulardii strains.

Use of a novel panel of nine short tandem repeats for exact and high-resolution fingerprinting of Aspergillus fumigatus isolates

Here we describe a new panel of short tandem repeats (STRs) for a novel exact typing assay that can be used to discriminate between Aspergillus fumigatus isolates. A total of nine STR markers were selected from available genomic A. fumigatus sequences and were divided into three multicolor multiplex PCRs. Each multiplex reaction amplified three di-, tri-, or tetranucleotide repeats, respectively. All nine STR markers were used to analyze 100 presumably unrelated A. fumigatus isolates. For each marker, between 11 and 37 alleles were found in this population. One isolate proved to be a mixture of at least two different isolates. With the remaining 99 isolates, 96 different fingerprinting profiles were obtained. The Simpson's diversity index for the individual markers ranged from 0.77 to 0.97. The diversity index for the multiplex combination of di-, tri-, and tetranucleotide repeats ranged from 0.9784 to 0.9968. The combination of all nine markers yielded a Simpson's diversity index of 0.9994, indicative of the high discriminatory power of these new loci. In theory, this panel of markers is able to discriminate between no less than 27 x 10(9) different genotypes. The multicolor multiplex approach allows large numbers of markers to be tested in a short period of time. The exact nature of the assay combines high reproducibility with the easy exchange of results and makes it a very suitable tool for large-scale epidemiological studies.

New microsatellite multiplex PCR for Candida albicans strain typing reveals microevolutionary changes

Five new microsatellite loci were described and characterized for use as molecular markers for the identification and genetic differentiation of Candida albicans strains. Following the typing of 72 unrelated clinical isolates, the analysis revealed that they were all polymorphic, presenting from 5 to 30 alleles and 8 to 46 different genotypes. The discriminatory power obtained by combining the information generated by three microsatellites used in a multiplex PCR amplification strategy was 0.99, the highest ever reported. The multiplex PCR was later used to test a total of 114 C. albicans strains, including multiple isolates from the same patient collected from different body locations and along episodes of vulvovaginal infections. Three different scenarios for strain relatedness were identified: (i) different isolates that were revealed to be the same strain, (ii) isolates that were the same strain but that apparently underwent a process of microevolution, and (iii) isolates that corresponded to different strains. Analysis of the microevolutionary changes between isolates from recurrent infections indicated that the genotype alterations observed could be the result of events that lead to the loss of heterozygosity (LOH). In one case of recurrent infection, LOH was observed at the CAI locus, and this could have been related to exposure to fluconazole, since such strains were exposed to this antifungal during treatment. The analysis of microsatellites by a multiplex PCR strategy was found to be a highly efficient tool for the rapid and accurate differentiation of C. albicans strains and adequate for the identification of fine microevolutionary events that could be related to strain microevolution in response to environmental stress conditions.

Genotype distribution of Candida albicans isolates by 25S intron analysis with regard to invasiveness

The aim of this study was to genotype Candida albicans strains isolated from patients with invasive and non-invasive deep-seated infections. For this purpose, 301 C. albicans isolates (81 invasive and 220 non-invasive) were genotyped by using specific PCR primers designed to span the transposable group I intron of the 25S rDNA gene. Fifty-three of the 81 invasive isolates were genotype A (65.4%), eight were genotype B (9.9%) and 20 were genotype C (24.7%), while 98 of the 220 non-invasive isolates were genotype A (44.6%), 46 were genotype B (20.9%) and 76 were genotype C (34.5%). Genotype A was more prevalent among invasive isolates and genotypes B and C were more prevalent among non-invasive isolates (P = 0.0046). Genotypes D and E which represent C. dubliniensis were not found. These results indicate that there may be a relationship between C. albicans genotypes and invasiveness; genotype A being more invasive than others. The presence or absence of the transposable group I intron in the 25S rDNA gene may be important in determining the invasiveness of C. albicans.

Use of variable-number tandem repeats to examine genetic diversity of Neisseria meningitidis

Repetitive DNA motifs with potential variable-number tandem repeats (VNTR) were identified in the genome of Neisseria meningitidis and used to develop a typing method. A total of 146 meningococcal isolates recovered from carriers and patients were studied. These included 82 of the 107 N. meningitidis isolates previously used in the development of multilocus sequence typing (MLST), 45 isolates recovered from different counties in Norway in connection with local outbreaks, and 19 serogroup W135 isolates of sequence type 11 (ST-11), which were recovered in several parts of the world. The latter group comprised isolates related to the Hajj outbreak of 2000 and isolates recovered from outbreaks in Burkina Faso in 2001 and 2002. All isolates had been characterized previously by MLST or multilocus enzyme electrophoresis (MLEE). VNTR analysis showed that meningococcal isolates with similar MLST or MLEE types recovered from epidemiologically linked cases in a defined geographical area often presented similar VNTR patterns while isolates of the same MLST or MLEE types without an obvious epidemiological link showed variable VNTR patterns. Thus, VNTR analysis may be used for fine typing of meningococcal isolates after MLST or MLEE typing. The method might be especially valuable for differentiating among ST-11 strains, as shown by the VNTR analyses of serogroup W135 ST-11 meningococcal isolates recovered since the mid-1990s.

Detection and selection of microsatellites in the genome of Paracoccidioides brasiliensis as molecular markers for clinical and epidemiological studies

Paracoccidioides brasiliensis, a thermodimorphic fungus, is the causative agent of the prevalent systemic mycosis in Latin America, paracoccidioidomycosis (PCM). Here, we describe the microsatellite patterns observed in a collection of P. brasiliensis random sequence tags. We identified 1,117 microsatellite patterns in about 3.8 Mb of unique sequences (0.47% of the total DNA used in the analysis). The majority of these microsatellites (87.5%) are found in noncoding sequences. We used two polymorphic microsatellites located on noncoding and coding sequences, as well as two microsatellites located on introns, as molecular markers to discriminate P. brasiliensis isolates, to look for relationships between the genetic background of the strains and the types of human disease they cause. We did not observe any correlation between the clinical form of human PCM and four simple sequence repeat patterns analyzed.

Characterization of cDNA encoding immunoglobulin light chain of the mandarin fish (Siniperca chuatsi)

Immunoglobulin light chain cDNA sequences of a perciform fish, the mandarin fish Siniperca chuatsi were amplified from head kidney mRNA by reverse transcription (RT)-PCR and RACE methods using degenerated primer and gene specific ones. In cDNA sequences of the VL region, nucleotide exchanges were present mainly within CDRs, although a lesser degree of variability was also found in FRs. Moreover, the length of CDR1 and CDR3 in the mandarin fish is shorter than in most other fish species. In the middle of S. chuatsi CL region, a microsatellite sequence (AGC)(6-8) was found, which is also present in another perciform species, the spotted wolffish (Anarhichas minor). The comparison of amino acid sequence of the mandarin fish CL domain with those of other vertebrates showed the highest degree of similarity of 94.5% to the spotted wolffish, while the similarity with rainbow trout (Oncorhynchus mykiss) Ig L1 (62.7%) and channel catfish (Ictalurus punctatus) Ig LG (55.9%) isotypes is also higher. However, there is only 50% identity in the VL regions between the mandarin fish and the wolffish. The sequence similarity of the mandarin fish CL domain with those of higher vertebrate did not readily allow it to be classified as kappa or lambda isotype. The phylogenetic analyses also demonstrated that the CL genes of the mandarin fish and most other teleost fish cluster as a separate branch out of the mammal kappa and lambda branches.

Analysis of microsatellites in 13 hemiascomycetous yeast species: mechanisms involved in genome dynamics

We have analyzed all di-, tri-, and tetranucleotide repeats in the partially sequenced genomes of 13 hemiascomycetous yeast species, and compared their sequences, lengths, and distributions to those observed in the genome of Saccharomyces cerevisiae. We found that most of the 13 species exhibit a unique distribution of microsatellites, not correlated to the base composition of their genome. Species close to S. cerevisiae exhibit a similar distribution, while species more distantly related show a more divergent distribution. We propose that de novo formation and continuous loss of microsatellites are active processes generating new DNA sequences. We also show that hemiascomycete-specific genes encoding transcription factors contain trinucleotide repeats more frequently than expected from their average frequency distribution. These transcription factors might play an important role in the speciation process, by regulating gene expression through DNA-protein or protein-protein interactions mediated by stretches of charged amino acids encoded by trinucleotide repeats.

Highly polymorphic microsatellite for identification of Candida albicans strains

The polymorphism of a new microsatellite locus (CAI) was investigated in a total of 114 Candida albicans strains, including 73 independent clinical isolates, multiple isolates from the same patient, isolates from several episodes of recurrent vulvovaginal infections, and two reference strains. PCR genotyping was performed automatically, using a fluorescence-labeled primer, and in the 73 independent isolates, 26 alleles and 44 different genotypes were identified, resulting in a discriminatory power of 0.97. CAI was revealed to be species specific and showed a low mutation rate, since no amplification product was obtained when testing other pathogenic Candida species and no genotype differences were observed when testing over 300 generations. When applying this microsatellite to the identification of strains isolated from recurrent vulvovaginal infections in eight patients, it was found that 13 out of 15 episodes were due to the same strain. When multiple isolates, obtained from the same patient and plated simultaneously, were typed for CAI, the same genotype was found in each case, confirming that the infecting population was clonal. Moreover, the same genotype appeared in isolates from the rectum and the vagina, revealing that the former could be a reservoir of potentially pathogenic strains. This new microsatellite proves to be a valuable tool to differentiate C. albicans strains. Furthermore, when compared to other molecular genotyping techniques, CAI proved to be very simple, highly efficient, and reproducible, being suitable for low-quantity and very-degraded samples and for application in large-scale epidemiological studies.

Genotypic subgrouping of clinical isolates of Candida albicans and Candida dubliniensis by 25S intron analysis

AIMS

To determine the frequency, distribution and association of genotypes of Candida albicans and C. dubliniensis in invasive and noninvasive clinical isolates.

METHODS

Twenty-one invasive and 18 noninvasive isolates were examined by PCR amplification of a transposable intron region in the 25S rRNA gene. Isolates were genotyped following analysis of the size of resulting DNA amplicons. The isolates could be subdivided into four genotypes (A-D).

RESULTS

There was no significant difference between the frequency and genotype distribution of the invasive and noninvasive Candida isolates.

IMPACT OF THE STUDY

Therapeutic prophylaxis against candidal infections remains an area of controversy. Any diagnostic markers that reflect the potential of isolates to become invasive should be fully explored, so that more focused antifungal intervention should be targeted at these patients with these potential invasive markers. This study demonstrated that analysis of the transposable intron region in the 25S rRNA gene may be useful in helping to differentiate C. albicans from C. dubliniensis isolates, without the need for sequence analysis, which may not be readily available at primary diagnostic laboratories. However, employment of this genotypic assay is not a suitable locus to determine invasiveness and other more reliable markers of invasiveness should be sought.

Analysis of microsatellite markers of Candida albicans used for rapid typing

To obtain a rapid genotyping method of Candida albicans, three polymorphic microsatellite markers were investigated by multiplex PCR. The three loci, called CDC3, EF3, and HIS3, were chosen because they are on different chromosomes so as to improve the chances of finding polymorphisms. One set of primers was designed for each locus, and one primer of each set was dye-labeled to read PCR signals by using an automatic sequencer. Amplifications were performed directly from the colonies harvested on the agar plate without a sophisticated DNA extraction step. At total of 27 reference strains and 73 clinical independent isolates were tested. The numbers of allelic associations were 10, 22, and 25 for the loci CDC3, EF3, and HIS3, respectively. The combined discriminatory power of the three microsatellites markers was 0.97. The markers were stable after 25 subcultures, and the amplifications were specific for C. albicans. An initial study of 17 clinical isolate pairs, including blood culture and peripheral sites, showed a similar genotype for 15 of them, confirming that candidemia usually originates from the colonizing isolate. Therefore, microsatellite marker analysis with multiplex PCR and automated procedures has a high throughput and should be suitable for large epidemiologic studies of C. albicans.

Differentiation of strains of Xylella fastidiosa by a variable number of tandem repeat analysis

Short sequence repeats (SSRs) with a potential variable number of tandem repeat (VNTR) loci were identified in the genome of the citrus pathogen Xylella fastidiosa and used for typing studies. Although mono- and dinucleotide repeats were absent, we found several intermediate-length 7-, 8-, and 9-nucleotide repeats, which we examined for allelic polymorphisms using PCR. Five genuine VNTR loci were highly polymorphic within a set of 27 X. fastidiosa strains from different hosts. The highest average Nei's measure of genetic diversity (H) estimated for VNTR loci was 0.51, compared to 0.17 derived from randomly amplified polymorphic DNA (RAPD) analysis. For citrus X. fastidiosa strains, some specific VNTR loci had a H value of 0.83, while the maximum value given by specific RAPD loci was 0.12. Our approach using VNTR markers provides a high-resolution tool for epidemiological, genetic, and ecological analysis of citrus-specific X. fastidiosa strains.

A highly polymorphic degenerate microsatellite for molecular strain typing of Candida krusei

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.

Microsatellite typing as a new tool for identification of Saccharomyces cerevisiae strains

Since Saccharomyces cerevisiae appears to be an emerging pathogen, there is a need for a valuable molecular marker able to distinguish among strains. In this work, we investigated the potential value of microsatellite length polymorphism with a panel of 91 isolates, including 41 clinical isolates, 14 laboratory strains, and 28 strains with industrial relevance. Testing seven polymorphic regions (five trinucleotide repeats and two dinucleotide repeats) in a subgroup of 58 unrelated strains identified a total of 69 alleles (6 to 13 per locus) giving 52 different patterns with a discriminatory power of 99.03%. We found a cluster of clinical isolates sharing their genotype with a bakery strain, suggesting a digestive colonization following ingestion of this strain with diet. With the exception of this cluster of isolates and isolates collected from the same patient or from patients treated with Saccharomyces boulardii, all clinical isolates gave different and unique patterns. The genotypes are stable, and the method is reproducible. The possibility to make the method portable is of great interest for further studies using this technique. This work shows the possibility to readily identify S. boulardii (a strain increasingly isolated from invasive infections) using a unique and specific microsatellite allele.

Comparative genotyping of Candida albicans bloodstream and nonbloodstream isolates at a polymorphic microsatellite locus

Molecular typing studies have shown that the predominant form of reproduction of Candida albicans is clonal and that, in a majority of situations, persistent or recurrent infections are due to a unique strain. Characterization of distinct subpopulations and correlation with clinical features may thus be important to understanding the pathogenesis of candidiasis. In a clonal model, a unique polymorphic marker may identify populations with different biological properties. We therefore compared 48 bloodstream isolates and 48 nonbloodstream matched strains of C. albicans at the elongation factor 3-encoding gene (CEF3) polymorphic microsatellite locus of C. albicans. Sizing of the alleles was performed by automated capillary electrophoresis. A new, 137-bp allele was characterized, and seven nondescribed combinations were observed, resulting in 15 and 11 distinct CEF3 profiles in bloodstream and control strains, respectively. Genotypes 126-135, 130-136, and 131-131 accounted for 60.4% of both bloodstream and control strains. Four bloodstream isolates but no control strains displayed the 135-135 combination. None of the other genotypes was present at an increased frequency in bloodstream isolates. Bloodstream and nonbloodstream strains of C. albicans thus have a heterogeneous structure at the CEF3 locus, with three major and multiple minor allelic combinations.

Trinucleotide repeats and other microsatellites in yeasts

Microsatellites are direct tandem DNA repeats found in all genomes. A particular class of microsatellites, called trinucleotide repeats, is responsible for a number of neurological disorders in humans. We review here our current state of knowledge on trinucleotide repeat instability, and discuss the molecular mechanisms that may be involved in trinucleotide repeat expansions leading to fatal diseases in humans. We also present original data on microsatellite distribution in several microbial genomes, and on the use of microsatellites as physical markers to accurately and easily genotype yeast strains.

The role of short sequence repeats in epidemiologic typing

Short sequence repeats (SSRs), also known as variable number of tandem repeats or micro-satellites, are inherently unstable entities that undergo frequent variation in the number of repeated units through slipped strand mispairing during DNA synthesis. In humans, unit number variability in SSRs has been associated with the occurrence of specific genetic diseases, whereas in micro-organisms SSRs have been elegantly linked to modulation of gene expression. Knowledge of the functional constraints imposed upon the SSRs sheds light on their potential use as molecular clocks for monitoring microbial genome evolution. Although microbial SSR genotypes have been used with increasing frequency for studying the epidemiology and evolution of microbial strains and isolates, such approaches should be used with caution.