Sequence diversity of the intergenic spacer region of the rRNA gene of Malassezia globosa colonizing the skin of patients with atopic dermatitis and healthy individuals

Comparison of Nested PCR and RFLP for Identification and Classification of Malassezia Yeasts from Healthy Human Skin

BACKGROUND

Malassezia yeasts are normal flora of the skin found in 75~98% of healthy subjects. The accurate identification of the Malassezia species is important for determining the pathogenesis of the Malassezia yeasts with regard to various skin diseases such as Malassezia folliculitis, seborrheic dermatitis, and atopic dermatitis.

OBJECTIVE

This research was conducted to determine a more accurate and rapid molecular test for the identification and classification of Malassezia yeasts.

METHODS

We compared the accuracy and efficacy of restriction fragment length polymorphism (RFLP) and the nested polymerase chain reaction (PCR) for the identification of Malassezia yeasts.

RESULTS

Although both methods demonstrated rapid and reliable results with regard to identification, the nested PCR method was faster. However, 7 different Malassezia species (1.2%) were identified by the nested PCR compared to the RFLP method.

CONCLUSION

Our results show that RFLP method was relatively more accurate and reliable for the detection of various Malassezia species compared to the nested PCR. But, in the aspect of simplicity and time saving, the latter method has its own advantages. In addition, the 26S rDNA, which was targeted in this study, contains highly conserved base sequences and enough sequence variation for inter-species identification of Malassezia yeasts.

The range of molecular methods for typing Malassezia

PURPOSE OF REVIEW

The recent sequencing of the whole genome of Malassezia globosa and M. restricta forms the basis for molecular epidemiology studies and instigates investigations into their respective virulence factors. Thus, reviewing current knowledge on Malassezia molecular typing methods would reveal the pros and cons of each method and would highlight potential scarcity of epidemiological data regarding this ubiquitous fungal commensal and pathogen.

RECENT FINDINGS

Methods employed for Malassezia molecular typing can be categorized into those detecting sequence variations of strains and those that selectively amplify polymorphic DNA markers for discriminating Malassezia species subtypes. The former exploit rRNA gene sequence variations in order to trace M. globosa, M. restricta and M.pachydermatis subtypes associated with specific skin diseases, or detect M. furfur geographical variations. Polymorphic DNA amplification methods, such as amplified fragment length polymorphism analysis, demonstrated association of M. furfur subtypes with the origin of the strain (skin or systemic isolate), whereas PCR-fingerprinting of the mini-satellite DNA clustered M. furfur strains according to their geographic origin and disease origin. Moreover, much typing work has already been performed regarding the zoophilic species M. pachydermatis and the relevant methods can be adapted for studying the anthropophilic Malassezia species.

SUMMARY

In the near future, molecular typing will be a powerful tool in epidemiological studies that could be employed for the elucidation of the pathobiology of Malassezia species in associated skin diseases

Isolation of 19 strains of Malassezia dermatis from healthy human skin in Korea

This research was conducted on the cultured samples of 160 healthy men and women aged 0-80 years without any skin disease. Nineteen clinical isolates of Malassezia dermatis showed positive in a catalase test and all grew in 0.5% Tween-60 and 0.1% Tween-80 added to 2% glucose/1% peptone culture medium. Round and ellipsoidal yeast cells and budding of the yeast cells were observed by microscopy, resembling Malassezia sympodialis, Malassezia furfur and Malassezia nana. The 26S rDNA polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) pattern was the same as for M. dermatis (JCM 11348), the standard strain. 26S rDNA and ITS1 sequencing were performed for exact identification, showing 99% accordance with M. dermatis (AB070361), M. dermatis (AB070356), confirming the species to be new and first to be reported in Korea. Taking a molecular biological classification approach by analyzing the 26S rDNA PCR-RFLP patterns, we have successfully isolated 19 cases of M. dermatis- the first in Korea.

The Investigation on the Distribution of Malassezia Yeasts on the Normal Korean Skin by 26S rDNA PCR-RFLP

BACKGROUND

Malassezia yeasts are normal flora of the skin that are discovered in 75~98% of health subjects, but since its association with various skin disorders have been known, many studies have been conducted in the distribution of the yeasts.

OBJECTIVE

To isolate, identify, and classify Malassezia yeasts from the normal human skin of Koreans by using the rapid and accurate molecular biology method (26S rDNA PCR-RFLP) which overcome the limits of morphological and biochemical methods, and to gather a basic database that will show its relation to various skin diseases.

METHODS

Malassezia yeasts were cultured from clinically healthy human skin using scrub-wash technique at five sites (forehead, cheek, chest, upper arm, and thigh) and swabbing technique at scalp in 160 participants comprised of 80 males and 80 females aged from 0 to 80. Identification of obtained strains were placed into the one of the 11 species by 26S rDNA PCR-RFLP.

RESULTS

An overall positive culture rate was 62.4% (599/960). As shown in the experiment groups by their age, the positive culture rate was the highest (74.2%) in the age 21~30 and 31~40 (89/120). In the experiment groups by different body areas, the scalp showed the highest positive culture rate of 90% (144/160). On analysis of 26S rDNA PCR-RFLP, M. globosa was the most predominant species in the age 0~10 (32.8%), 11~20 (28.9%), 21~30 (32.3%). M. restricta was identified as predominant species in the age 41~50 (27.9%), 61~70 (31.5%) and 71~80 (24.0%). In the age 31~40 years, M. sympodialis was found to be the most common species (24.6%). According to body site, M. restricta was more frequently recovered in the scalp (56.8%), forehead (39.8%) and cheek (24.0%) and while M. globosa was more frequently recovered in the chest (36.8%). Higher positive culture rates of Malassezia yeasts were shown in male subjects than female counterparts in all body areas except scalp (p<0.05). Especially in this study, M. dermatis, newly isolated Malassezia species from atopic dermatitis patient in Japan, was isolated and identified in 19 cases (1.9%) in healthy subjects.

CONCLUSION

The key is to recognize the existence of a difference in the type of Malassezia species in different ages as well as body areas, which reflects differing skin lipid levels in various ages and different body areas. Moreover, 26S rDNA PCR-RFLP analysis which was opted in this study could provide a sensitive and rapid identification system for Malassezia species, which may be applied to epidemiological surveys and clinical practice.

The role of Malassezia in atopic dermatitis affecting the head and neck of adults

Atopic dermatitis is a common chronic skin condition. A subset of patients with head and neck dermatitis may have a reaction to Malassezia flora fueling their disease. Although there are no documented differences in Malassezia species colonization, patients with head and neck atopic dermatitis are more likely to have positive skin prick test results and Malassezia-specific IgE compared with healthy control subjects and patients with atopy without head and neck dermatitis. There is no clear relationship with atopy patch testing. The reaction to Malassezia is likely related to both humoral- and cell-mediated immunity. Clinically, Malassezia allergy may be suspected in patients with atopic dermatitis and: (1) head and neck lesions; (2) exacerbations during adolescence or young adulthood; (3) severe lesions recalcitrant to conventional therapy; and (4) other atopic diseases. There is literature to suggest that these patients will benefit from a 1- to 2-month course of daily itraconazole or ketoconazole followed by long-term weekly treatment.

Analysis of Malassezia microbiota in healthy superficial human skin and in psoriatic lesions by multiplex real-time PCR

Yeasts from the genus Malassezia are members of the normal biota of human skin, and may play a role in dermatopathology. Our previous study of the fungal microbiota from healthy subjects and from patients with psoriasis using clone library analysis revealed the presence of five Malassezia species and four uncharacterized phylotypes. We now compared the Malassezia microbiota from six healthy body locations and two psoriatic lesions, and evaluated its stability over time using multiplex real-time PCR. Samples from each body location were obtained monthly, for 4 months. Dual-labeled probes were designed to recognize four Malassezia sp. and two uncharacterized groups, and a genus-specific probe was also developed. A good correspondence was obtained between real-time PCR data and clone library analyses. Malassezia restricta was the most abundant species in the majority of samples, and high amounts of Malassezia globosa were also detected. The uncharacterized phylotype 1 was usually detected in lower proportions, nevertheless it was present in most samples. The microbiota was host-specific and relatively stable over time. In accordance with our previous observations, no significant dichotomy between samples from healthy skin and from psoriatic lesions was found; the samples clustered according to the subject, rather than health status.

Molecular Analysis of Malassezia Microflora in Seborrheic Dermatitis Patients: Comparison with Other Diseases and Healthy Subjects

Malassezia species colonize the skin of normal and various pathological conditions including pityriasis versicolor (PV), seborrhoeic dermatitis (SD) and atopic dermatitis (AD). To elucidate the pathogenic role of Malassezia species in SD, Malassezia microflora of 31 Japanese SD patients was analyzed using a PCR-based, culture-independent method. Nested PCR assay using the primers in the rRNA gene indicated that the major Malassezia species in SD were M. globosa and M. restricta, found in 93 and 74% of the patients, respectively. The detection rate and number of each species varied similarly in SD, PV and healthy subjects (HSs), whereas AD showed higher values. Real-time PCR assay showed that the lesional skin harbored approximately three times the population of genus Malassezia found in nonlesional skin (P<0.05), and that M. restricta is a significantly more common species than M. globosa in SD (P<0.005). Genotypic analysis of the rRNA gene showed that the M. globosa and M. restricta from SD patients fell into specific clusters, and could be distinguished from those collected from HSs, but not from those colleted from AD patients. Our results indicate that certain strains of M. restricta occur in the lesional skin of SD patients.

Multilocus mutation scanning for the analysis of genetic variation within Malassezia (Basidiomycota: Malasseziales)

Members of the genus Malassezia are budding yeasts, characterized by a thick cell wall. Recently, these yeasts have received attention as emerging pathogens. They are common commensals on the skin of animals and can become pathogenic under the influence of various predisposing factors. Central to studying their taxonomy, systematics, and ecology and to diagnosis is the accurate identification of species or operational taxonomic units. To overcome the limitations of current phenotypic and biochemical methods of identification, a PCR-coupled SSCP approach, utilizing sequence variation (0.4-33.5%) in short regions (approximately 250-270 bp) of the first internal transcribed spacer (ITS-1) of nuclear ribosomal DNA and the chitin synthase-2 gene (chs-2), was assessed for the identification and differentiation of different species/genotypes of Malassezia, characterized previously by DNA sequencing. Genomic DNA samples (n = 30) from Malassezia isolates cultured from canine skin scrapings were assessed by SSCP analysis of the two different genetic loci, and unequivocal delineation between genotypes and species was achieved. This SSCP approach is considered to provide a practical tool for the rapid and reliable genetic characterization of Malassezia genotypes/species from dogs and for investigating their population genetics and ecology. It will also provide a powerful tool for studies of Malassezia isolates from other animal species.

Molecular characterization of Malassezia isolates from dogs using three distinct genetic markers in nuclear DNA

Little precise information is available on the systematics, genetics, ecology and epidemiology of yeasts of the genus Malassezia from different animal species. In the present study, one hundred and four isolates of Malassezia (lipid dependent or non-lipid dependent) from dogs were characterized by their chitin synthase 2 gene (CHS2), and the large subunit (LSU) and the first internal transcribed spacer (ITS-1) of nuclear ribosomal DNA sequences, and compared genetically with well-defined reference strains of Malassezia pachydermatis and heterologous species, including Malassezia furfur and Candida albicans. For each locus examined, three main sequence types (i.e. A, B and C) represented all of the 104 isolates, which were designated as genotypes A, B and C, respectively. A fourth, minor sequence type was also defined for the ITS-1. The nucleotide differences among genotypes was consistent with the magnitudes of intraspecific variability reported in previous studies. The genetic analysis of the sequence data sets (for individual loci) showed that all Malassezia genotypes clustered (with moderate to strong support) with the reference sequences of M. pachydermatis to the exclusion of the outgroups M. furfur and C. albicans. The present study reveals that multiple genetic variants of M. pachydermatis occur on dogs. The multilocus approach employed herein provides a foundation for future investigations of M. pachydermatis from other animals and humans, and their ecology and epidemiology.

Molecular analysis of fungal microbiota in samples from healthy human skin and psoriatic lesions

Psoriasis, a common cutaneous disease of unknown etiology, may be triggered by infections, including those due to fungi. Since the fungal community of human skin is poorly characterized, we aimed to analyze the mycological microbiota in healthy skin and psoriatic lesions. Twenty-five skin samples from five healthy subjects (flexor forearm) and three patients with psoriasis were analyzed using broad-range 18S ribosomal DNA (rDNA) and 5.8S rDNA/internal transcribed spacer 2 (ITS2) Malassezia-specific PCR primers. Broad-range PCR analysis indicated that most organisms resembled Malassezia. Malassezia-specific 5.8S/ITS2 analysis of 1,374 clones identified five species and four unknown phylotypes, potentially representing new species. The species distribution appears largely host specific and conserved in different sites of healthy skin. In three subjects, the Malassezia microbiota composition appeared relatively stable over time. Samples of Malassezia microbiota from healthy skin and psoriatic lesions were similar in one patient but substantially different in two others. These data indicate the predominance of Malassezia organisms in healthy human skin, host-specific variation, stability over time, and as yet, no consistent patterns differentiating psoriatic skin from healthy skin.

Microcoding and flow cytometry as a high-throughput fungal identification system for Malassezia species

Yeasts of the genus Malassezia have been associated with a variety of dermatological disorders in humans and domestic animals. With the recent recognition of new members of the genus, new questions are emerging with regard to the pathogenesis and epidemiology of the new species. As new species are recognized, a precise and comprehensive identification system is needed. Herein is described a bead suspension culture-based array that combines the specificity and reliability of nucleic acid hybridization analysis with the speed and sensitivity of the Luminex analyser. The developed 16-plex array consisted of species- and group-specific capture probes that acted as 'microcodes' for species identification. The probes, which were designed from sequence analysis in the D1/D2 region of rRNA and internal transcribed spacer (ITS) regions, were covalently bound to unique sets of fluorescent beads. Upon hybridization, the biotinylated amplicon was detected by the addition of a fluorochrome coupled to a reporter molecule. The hybridized beads were subsequently analysed by flow cytometric techniques. The developed array, which allowed the detection of species in a multiplex and high-throughput format, was accurate and fast, since it allowed precise identification of species and required less than 1 h following PCR amplification. The described protocol, which can integrate uniplex or multiplex PCR reactions, permitted the simultaneous detection of target sequences in a single reaction, and allowed single mismatch discrimination between probe and non-target sequences. The assay has the capability to be expanded to include other medically important pathogenic species in a single or multiplex array format.

Identification of medically important yeast species by sequence analysis of the internal transcribed spacer regions

Infections caused by yeasts have increased in previous decades due primarily to the increasing population of immunocompromised patients. In addition, infections caused by less common species such as Pichia, Rhodotorula, Trichosporon, and Saccharomyces spp. have been widely reported. This study extensively evaluated the feasibility of sequence analysis of the rRNA gene internal transcribed spacer (ITS) regions for the identification of yeasts of clinical relevance. Both the ITS1 and ITS2 regions of 373 strains (86 species), including 299 reference strains and 74 clinical isolates, were amplified by PCR and sequenced. The sequences were compared to reference data available at the GenBank database by using BLAST (basic local alignment search tool) to determine if species identification was possible by ITS sequencing. Since the GenBank database currently lacks ITS sequence entries for some yeasts, the ITS sequences of type (or reference) strains of 15 species were submitted to GenBank to facilitate identification of these species. Strains producing discrepant identifications between the conventional methods and ITS sequence analysis were further analyzed by sequencing of the D1-D2 domain of the large-subunit rRNA gene for species clarification. The rates of correct identification by ITS1 and ITS2 sequence analysis were 96.8% (361/373) and 99.7% (372/373), respectively. Of the 373 strains tested, only 1 strain (Rhodotorula glutinis BCRC 20576) could not be identified by ITS2 sequence analysis. In conclusion, identification of medically important yeasts by ITS sequencing, especially using the ITS2 region, is reliable and can be used as an accurate alternative to conventional identification methods.

The role of sebaceous gland activity and scalp microfloral metabolism in the etiology of seborrheic dermatitis and dandruff

Most common scalp flaking disorders show a strong correlation with sebaceous gland (SG) activity. Early SG activity in the neonate results in microfloral colonization and cradle cap. After maternal hormonal control subsides, there is little SG activity until puberty, when the SG turns on under sex hormone control. When the SG activity increases, the present but low Malassezia population has a new food source and proliferates, resulting in the scalp itching and flaking common to greater than 50% of adults. Dry scalp flaking, dandruff, and seborrheic dermatitis are chronic scalp manifestations of similar etiology differing only in severity. The common etiology is a convergence of three factors: (1) SG secretions, (2) microfloral metabolism, and (3) individual susceptibility. Dandruff and seborrheic dermatitis (D/SD) are more than superficial stratum corneum disorders, including alteration of the epidermis with hyperproliferation, excess lipids, interdigitation of the corneal envelope, and parakeratosis. The pathogenic role of Malassezia in D/SD has recently been elucidated, and is focused on their lipid metabolism. Malassezia restricta and M. globosa require lipids. They degrade sebum, free fatty acids from triglycerides, consume specific saturated fatty acids, and leave behind the unsaturates. Penetration of the modified sebaceous secretions results in inflammation, irritation, and scalp flaking.

Distribution of Malassezia species in pityriasis versicolor and seborrhoeic dermatitis in Greece. Typing of the major pityriasis versicolor isolate M. globosa

BACKGROUND

The expansion of the genus Malassezia has generated interest in the epidemiological investigation of the distribution of new species in a range of dermatoses, on which variable results have been reported from different geographical regions. No data are thus far available from South-east Europe (Greece).

OBJECTIVES

To study the distribution of Malassezia species in pityriasis versicolor (PV) and seborrhoeic dermatitis (SD) and to investigate whether polymorphisms in the internal transcribed spacer (ITS) 1 region facilitate detection of M. globosa and M. sympodialis subtypes.

METHODS

In total, 109 patients with PV and SD and positive Malassezia cultures were included in the study. Age, gender, primary/recurrent episode, disease extent and clinical form of PV were recorded. ITS 1 polymorphisms of M. globosa and M. sympodialis type and clinical strains were investigated by polymerase chain reaction (PCR)-single-strand conformational polymorphism (SSCP) analysis.

RESULTS

Malassezia globosa was the prevalent species isolated from PV and SD either alone (77% and 39%, respectively) or in combination (13% and 18%, respectively) with other Malassezia species. The pigmented form of PV was strongly correlated with the female gender. PCR-SSCP differentiated five subgroups of M. globosa with one being associated with extensive clinical disease. All M. sympodialis isolates displayed a homogeneous ITS 1 PCR-SSCP profile.

CONCLUSIONS

Malassezia species isolation rates were in agreement with those reported from South-west Europe. PCR-SSCP of the ITS 1 is useful for highlighting prospective clinical implications of M. globosa subtypes.

Antifungal activities of tacrolimus and azole agents against the eleven currently accepted Malassezia species

The lipophilic yeast Malassezia is an exacerbating factor in atopic dermatitis (AD) and colonizes the skin surface of patients with AD. With the goal of reducing the number of Malassezia cells, we investigated the antifungal activities of a therapeutic agent for AD, tacrolimus, and the azole agents itraconazole and ketoconazole against Malassezia species in vitro. We examined 125 strains of the 11 currently accepted Malassezia species by using the agar dilution method. All strains of the 11 Malassezia species were very susceptible to both azole agents, with MICs ranging from 0.016 to 0.25 mug/ml. Tacrolimus had antifungal activities against half of the strains, with MICs ranging from 16 to 32 mug/ml. Two of the major cutaneous floras, Malassezia globosa and Malassezia restricta, have several genotypes in the intergenic spacer region of the rRNA gene; the azole agents had slightly higher MICs for specific genotype strains of both microorganisms. A combination of azole agents and tacrolimus had a synergistic effect against Malassezia isolates, based on a fractional inhibitory index of 0.245 to 0.378. Our results provide the basis for testing these agents in future clinical trials to reduce the number of Malassezia cells colonizing the skin surface in patients with AD.

Malassezia Baillon, emerging clinical yeasts

The human and animal pathogenic yeast genus Malassezia has received considerable attention in recent years from dermatologists, other clinicians, veterinarians and mycologists. Some points highlighted in this review include recent advances in the technological developments related to detection, identification, and classification of Malassezia species. The clinical association of Malassezia species with a number of mammalian dermatological diseases including dandruff, seborrhoeic dermatitis, pityriasis versicolor, psoriasis, folliculitis and otitis is also discussed.

Fluconazole-resistant pathogens Candida inconspicua and C. norvegensis: DNA sequence diversity of the rRNA intergenic spacer region, antifungal drug susceptibility, and extracellular enzyme production

The opportunistic fungal pathogens Candida inconspicua and C. norvegensis are very rarely isolated from patients and are resistant to fluconazole. We collected 38 strains of the two microorganisms isolated from Europe and Japan, and compared the polymorphism of the rRNA intergenic spacer (IGS) and internal transcribed spacer (ITS) regions, antifungal drug susceptibility, and extracellular enzyme production as a potential virulence factor. While the IGS sequences of C. norvegensis were not very divergent (more than 96.7% sequence similarity among the strains), those of C. inconspicua showed remarkable diversity, and were divided into four genotypes with three subtypes. In the ITS region, no variation was found in either species. Since the sequence similarity of the two species is approximately 70% at the ITS region, they are closely related phylogenetically. Fluconazole resistance was reconfirmed for the two microorganisms but they were susceptible to micafungin and amphotericin B. No strain of either species secreted aspartyl proteinase or phospholipase B. These results provide basal information for accurate identification, which is of benefit to global molecular epidemiological studies and facilitates our understanding of the medical mycological characteristics of C. inconspicua and C. norvegensis.

Identification and typing of Malassezia species by amplified fragment length polymorphism and sequence analyses of the internal transcribed spacer and large-subunit regions of ribosomal DNA

Malassezia yeasts are associated with several dermatological disorders. The conventional identification of Malassezia species by phenotypic methods is complicated and time-consuming, and the results based on culture methods are difficult to interpret. A comparative molecular approach based on the use of three molecular techniques, namely, amplified fragment length polymorphism (AFLP) analysis, sequencing of the internal transcribed spacer, and sequencing of the D1 and D2 domains of the large-subunit ribosomal DNA region, was applied for the identification of Malassezia species. All species could be correctly identified by means of these methods. The results of AFLP analysis and sequencing were in complete agreement with each other. However, some discrepancies were noted when the molecular methods were compared with the phenotypic method of identification. Specific genotypes were distinguished within a collection of Malassezia furfur isolates from Canadian sources. AFLP analysis revealed significant geographical differences between the North American and European M. furfur strains.

Malassezia yeasts in the pathogenesis of atopic dermatitis

Atopic dermatitis is a common skin condition, the aetiology of which is multifactorial, involving genetic, immunological and environmental factors. In recent years, it has been suggested that various microbial organisms may also be involved in the pathogenesis of the disease. Yeasts belonging to the Malassezia genus have received particular attention. These yeasts, known to be a part of the normal skin flora, have been shown to be capable of inducing immunoglobulin (Ig)E-mediated and T-cell mediated immune responses postulated to contribute to chronic inflammation in the skin, particularly in the head and neck region, where colonization with Malassezia is the greatest. Considerable evidence now exists to support this idea, raising the possibility that specific antifungal therapy may be a useful treatment measure in some atopic patients who have a head and neck pattern of dermatitis.

Activation pattern of Langerhans cells in the afferent and efferent phases of contact hypersensitivity

Langerhans cells are MHC class II (Ia) positive antigen-presenting cells that play a crucial role in the induction of contact hypersensitivity (CHS). The topical application of a hapten modifies the cell surface moieties of Langerhans cells, and activates Langerhans cells to increase their size and Ia intensity. The haptenated and activated Langerhans cells emigrate from the epidermis and thus the in situ density of Langerhans cells usually decreases during 24-48 h after the hapten application in CHS. To determine whether the early activation pattern of Langerhans cells is different between the afferent phase and the efferent phase of CHS, we compared the density and morphologic changes of Langerhans cells in CHS to trinitrochlorobenzene using nonsensitized and sensitized mice. We found that the application of a hapten induces more significant enlargement of Langerhans cell size in the afferent phase than in the efferent phase, whereas the reduction of Langerhans cell density is more marked in the efferent than in the afferent phase of CHS. Moreover, topical immunosuppressive drugs inhibit the in situ activation of Langerhans cells.