Genetic typing of Malassezia pachydermatis from different domestic animals

Survey of Malassezia sp and dermatophytes in the cutaneous microbiome of free-ranging golden-headed lion tamarins (Leontopithecus chrysomelas - Kuhl, 1820)

BACKGROUND

Data about the presence of fungi on the cutaneous surface of wild animals are scarce. The aim of this study was to survey dermatophytes and Malassezia sp in the external ear canal and haircoat of Leontopithecus chrysomelas.

METHODS

A total of 928 clinical samples were collected from 232 animals: For Malassezia screening 696 samples were studied, 464 of cerumen and 232 of haircoat; another 232 haircoat samples were studied for dermatophyte analysis.

RESULTS

A geophilic dermatophyte, Microsporum cookie, was isolated from one young female. Lipodependent Malassezia was isolated from 76 animals and 87 clinical samples, 26 from the cerumen and 61 from the haircoat (statistically significant); there were no differences related to gender and age.

CONCLUSIONS

Results suggested that lipodependent Malassezia is part of the skin microbiome of these animals. The prevalence of dermatophytes was too low and probably not relevant for the health of the studied population.

Is Malassezia nana the main species in horses' ear canal microbiome?

The objective of this study was to characterize genotypically Malassezia spp. isolated from the external ear canal of healthy horses. Fifty-five horses, 39 (70.9%) males and 16 (29.1%) females, from different breeds and adults were studied. External ear canals were cleaned and a sterile cotton swab was introduced to collect cerumen. A total of 110 samples were cultured into Dixon medium and were incubated at 32 °C for up to 15 days. Macro- and micromorphology and phenotypic identification were performed. DNA was extracted, strains were submitted to polymerase chain reaction technique, and the products obtained were submitted to Restriction Fragment Length Polymorphism using the restriction enzymes BstCI and HhaI. Strains were sent off to genetic sequencing of the regions 26S rDNA D1/D2 and ITS1-5.8S-ITS2 rDNA. Malassezia spp. were isolated from 33/55 (60%) animals and 52/110 (47%) ear canals. No growth on Sabouraud dextrose agar was observed, confirming the lipid dependence of all strains. Polymerase chain reaction-Restriction fragment length polymorphism permitted the molecular identification of Malassezia nana – 42/52 (81%) and Malassezia slooffiae – 10/52 (19%). Sequencing confirmed RFLP identification. It was surprising that M. nana represented over 80% of the strains and no Malassezia equina was isolated in this study, differing from what was expected.

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin

Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina, (Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens. Malassezia are typically isolated from warm-blooded animals, are dominant members of the human skin mycobiome and are associated with common skin disorders. To characterize the genetic basis of the unique phenotypes of Malassezia spp., we sequenced the genomes of all 14 accepted species and used comparative genomics against a broad panel of fungal genomes to comprehensively identify distinct features that define the Malassezia gene repertoire: gene gain and loss; selection signatures; and lineage-specific gene family expansions. Our analysis revealed key gene gain events (64) with a single gene conserved across all Malassezia but absent in all other sequenced Basidiomycota. These likely horizontally transferred genes provide intriguing gain-of-function events and prime candidates to explain the emergence of Malassezia. A larger set of genes (741) were lost, with enrichment for glycosyl hydrolases and carbohydrate metabolism, concordant with adaptation to skin’s carbohydrate-deficient environment. Gene family analysis revealed extensive turnover and underlined the importance of secretory lipases, phospholipases, aspartyl proteases, and other peptidases. Combining genomic analysis with a re-evaluation of culture characteristics, we establish the likely lipid-dependence of all Malassezia. Our phylogenetic analysis sheds new light on the relationship between Malassezia and other members of Ustilaginomycotina, as well as phylogenetic lineages within the genus. Overall, our study provides a unique genomic resource for understanding Malassezia niche-specificity and potential virulence, as well as their abundance and distribution in the environment and on human skin.

Malassezia are the dominant eukaryotic residents of human skin and are associated with the most common skin disorders, including dandruff, atopic dermatitis, eczema, and others. Despite significant effort, the role of Malassezia in skin disease and homeostasis remains unclear. Malassezia are also unique among fungi by requiring lipids for growth, but the breadth and genetic basis of their lipophilic lifestyle has not been comprehensively studied. Here we report the complete genomes of all 14 Malassezia species (including multiple strains of the most common species found on humans) and systematically identify features that define the genus and its sub-lineages, including horizontally transferred genes likely to represent key gain-of-function events and which may have enabled evolution of the genus from plant to animal inhabitants. Genus wide expansion of lipid hydrolases and loss of carbohydrate metabolism genes underscore the entire genus’ gradual evolution to lipid-dependency, which was confirmed even in the previously thought to be lipophilic M. pachydermatis, via genomics with experimental confirmation. Finally, these reference genomes will serve as a valuable resource for future metagenomic investigations into the role of Malassezia species in normal healthy skin and diseases.

Genotyping and antifungal susceptibility testing of multiple Malassezia pachydermatis isolates from otitis and dermatitis cases in pets: is it really worth the effort?

A total of 216 colonies of Malassezia pachydermatis from 28 cases of fungal otitis or dermatitis in pets were genotyped by M13 fingerprinting and tested for antifungal susceptibility. A huge genetic diversity was found (157 M13 types in total), with all animals having a polyclonal pattern of infection (5.4 ± 1.5 genotypes/sample). Furthermore, analysis of molecular variance (AMOVA) revealed that most genetic diversity (44%) was found at the within sample level. In contrast, variability in antifungal susceptibility among isolates from the same sample was less important, with different M13 types displaying in most cases identical or very similar MIC results. Most isolates displayed high in vitro susceptibility to amphotericin B, terbinafine and all azoles tested except fluconazole, for which MIC values were always ≥4 μg/ml and a 26.9% of isolates displayed values ≥32 μg/ml. We conclude that although characterization of multiple yeast isolates results in a considerable increase in laboratory workload and expenses, it may help to get a better understanding of the epidemiology of M. pachydermatis in a given patient population.

Molecular analysis of Malassezia pachydermatis isolated from canine skin and ear in Korea

We investigated Malassezia species and genotypes colonizing dogs, comparing those recovered from the ear canal with those from other anatomical body sites, as well as from diseased and healthy skin. The Malassezia isolates were obtained from four types of skin samples, i.e., diseased ear, diseased skin, healthy ear, and healthy skin. Sequences of the 26S ribosomal DNA region, the intergenic spacer 1 (IGS-1) and the internal transcribed spacer 1 (ITS-1) DNA region were analyzed. These confirmed the presence of Malassezia pachydermatis, which could be separated into three main sequence genotype groups (A, B, C). Genotype A was the most common, only two genotype B isolates were recovered from diseased skin lesion and genotype C was more likely to be isolated from ear samples than from other healthy or diseased-skin sites. The present findings provide the basis for further studies of genotypic diversity in M. pachydermatis, as well as their pathogenic potential.

The Malassezia genus in skin and systemic diseases

In the last 15 years, the genus Malassezia has been a topic of intense basic research on taxonomy, physiology, biochemistry, ecology, immunology, and metabolomics. Currently, the genus encompasses 14 species. The 1996 revision of the genus resulted in seven accepted taxa: M. furfur, M. pachydermatis, M. sympodialis, M. globosa, M. obtusa, M. restricta, and M. slooffiae. In the last decade, seven new taxa isolated from healthy and lesional human and animal skin have been accepted: M. dermatis, M. japonica, M. yamatoensis, M. nana, M. caprae, M. equina, and M. cuniculi. However, forthcoming multidisciplinary research is expected to show the etiopathological relationships between these new species and skin diseases. Hitherto, basic and clinical research has established etiological links between Malassezia yeasts, pityriasis versicolor, and sepsis of neonates and immunocompromised individuals. Their role in aggravating seborrheic dermatitis, dandruff, folliculitis, and onychomycosis, though often supported by histopathological evidence and favorable antifungal therapeutic outcomes, remains under investigation. A close association between skin and Malassezia IgE binding allergens in atopic eczema has been shown, while laboratory data support a role in psoriasis exacerbations. Finally, metabolomic research resulted in the proposal of a hypothesis on the contribution of Malassezia-synthesized aryl hydrocarbon receptor (AhR) ligands to basal cell carcinoma through UV radiation-induced carcinogenesis.

Advances in the identification of Malassezia

Members of the genus Malassezia are lypophilic and/or lipid-dependent, unipolar budding yeasts that can become pathogenic under the influence of particular predisposing factors (e.g., changes in the cutaneous microenvironment and/or alterations in host defences). This genus comprises at least 14 species, which have been identified traditionally based on their morphology and biochemical features. However, phenetic characteristics often do not allow the identification or delineation of closely related Malassezia spp., such that molecular tools need to be used to assist in fundamental studies of the epidemiology and ecology of Malassezia as well as aspects of the pathogenesis and disease caused by members of this genus. This article briefly reviews the morphological and biochemical methods commonly used for the identification of Malassezia as well as DNA technological methods that have been established for the specific identification of members of this genus and the diagnosis of their infections. New avenues for the development of improved molecular-diagnostic methods to overcome diagnostic limitations and to underpin fundamental investigations of this interesting group of yeasts are proposed.

CHARACTERIZATION OF TYPICAL AND ATYPICAL MALASSEZIA SPP. FROM CATTLE AND DOG BY RANDOM AMPLIFIED POLYMORPHIC DNA ANALYSIS

ABSTRACT There are few numbers of biochemical tests for specie classification in the genus Malassezia and these can to fail in the identification of the atypical isolates. In this study, typical and atypical isolates were analysed by random amplification of polymorphic DNA (RAPD) to compare with biochemical-physiological characteristics of the Malassezia species from bovine and canine ears. RAPD band patterns using OPA4 primer clustered all isolates according its biochemicalphysiological characteristics in the species from cattle and dog. Malassezia nana and M. sympodialis isolates were sub-clustered in separated sub-branches and both were from a different branch of the other species. The DNA pattern of the two atypical lipid-dependent M. pachydermatis strains was similar with of other typical strains but it did not show the one specific band of 200bp. Future studies in the specific RAPD bands of genetic profiles can be important to corroborate the identification of typical and atypical isolates of the genus Malassezia.

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

RAPD differentiation of Malassezia spp. from cattle, dogs and humans

The molecular characterization of Malassezia spp. isolates from animals and humans has not been thoroughly studied. We have analysed the DNA profile by random amplified polymorphic DNA (RAPD)-PCR to compare the genetic diversity between isolates from the external ears of cattle, dogs and humans. The analysis of electrophoretic profiles on 8% polyacrylamide gel and their phenograms showed genetic heterogeneity between RAPD profiles of Malassezia furfur and Malassezia slooffiae isolates from humans and cattle and between Malassezia pachydermatis isolates from dogs and cattle. Intra-species variations in DNA pattern of Malassezia isolates and the presence of specific genetic types in cattle, dogs or humans were observed. A review of genetic heterogeneity of these yeast in veterinary and human medicine studies is given considering a possible transmission animal to human or human to animal. Additional studies must clarify the differences between the RAPD band patterns observed in this and other studies, which would facilitate monitoring of Malassezia spp. carriage in domestic animals and in humans.

Malassezia spp. overgrowth in allergic cats

A series of 18 allergic cats with multifocal Malassezia spp. overgrowth is reported: atopic dermatitis was diagnosed in 16, an adverse food reaction in another and one was euthanized 2 months after diagnosis of Malassezia overgrowth. All the cats were otherwise healthy and those tested (16 out of 18) for feline leukaemia or feline immunodeficiency virus infections were all negative. At dermatological examination, multifocal alopecia, erythema, crusting and greasy adherent brownish scales were variably distributed on all cats. Cytological examination revealed Malassezia spp. overgrowth with/without bacterial infection in facial skin (n = 11), ventral neck (n = 6), abdomen (n = 6), ear canal (n = 4), chin (n = 2), ear pinnae (n = 2), interdigital (n = 1) and claw folds skin (n = 1). Moreover, in two cats Malassezia pachydermatis was isolated in fungal cultures from lesional skin. Azoles therapy alone was prescribed in seven, azoles and antibacterial therapy in eight and azoles with both antibacterial and anti-inflammatory therapy in three of the cats. After 3-4 weeks of treatment, substantial reduction of pruritus and skin lesions was observed in all 11 cats treated with a combined therapy and in five of seven treated solely with azoles. Malassezia spp. overgrowth may represent a secondary cutaneous problem in allergic cats particularly in those presented for dermatological examination displaying greasy adherent brownish scales. The favourable response to treatment with antifungal treatments alone suggests that, as in dogs, Malassezia spp. may be partly responsible for both pruritus and cutaneous lesions in allergic cats.

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.

Genotyping by RAPD-PCR analyses of Malassezia furfur strains from pityriasis versicolor and seborrhoeic dermatitis patients

Malassezia furfur is lypophilic yeast commonly associate with dermatological disorders. In the present work, we described the isolation of 47 M. furfur strains from three groups of patients: pityriasis versicolor (21 isolates), seborrhoeic dermatitis (15 isolates) and seborrhoeic dermatitis of the HIV positive patients (11 isolates). To investigate the identity of the strains at molecular level, DNA genomic of M. furfur strains were prepared and used to RAPD-PCR analyses. RAPD assay were carried out using two decamer primers and bands pattern generated were analyzed by an Unweighted Pair-Group Method (UPGMA). Dendrogram established a distinct differentiation between M. furfur isolates from pityriasis versicolor and seborrhoeic dermatitis patients with or without AIDS. We concluded that RAPD typing presented a high discriminatory power between strains studied in this work and can be applied in epidemiological investigation of skin disease causing by M. furfur.

Genetic and biochemical characterization ofMalassezia pachydermatiswith particular attention to pigment-producing subgroups

The aim of the study was the characterization of Malassezia pachydermatis and its pigment-producing subgroup using biochemical tests and RAPD. It was of interest to determine whether particular RAPD patterns could be used to indicate pigment production, as well as a close genetic relatedness to Malassezia furfur. Therefore, 210 strains of M. pachydermatis were examined for morphology, catalase and ss-glucosidase activity, lipid and carbohydrate assimilation and the tryptophan-dependent synthesis of pigments. Of these, 114 strains were subjected to RAPD analyses. A multivariate logistic regression model was applied to classify M. pachydermatis isolates regarding their pigment production by using genetic and biological parameters. Biological and RAPD findings showed a high biological and genetic diversity within the species M. pachydermatis and within pigment producers. RAPD analysis revealed 28 genotypes within 114 strains tested. Pigment producing strains could not be assigned to a common RAPD profile, but a genetic relatedness of pigment-producing M. pachydermatis with M. furfur can be assumed. A particular RAPD pattern allowed statistically significant probability of pigment production (P<0.001) and might be used as a tool to rapidly detect pigment producing M. pachydermatis, e.g. in Malassezia-associated pityriasis versicolor. The reported method is useful for identification of pigment producing M. pachydermatis isolates and has advantages over established tests.

Biofilm development by clinical isolates ofMalassezia pachydermatis

Malassezia pachydermatis fungemia has been reported in patients receiving parenteral nutrition. Biofilm formation on catheters may be related to the pathogenesis of this mycosis. We investigated the biofilm-forming ability of 12 M. pachydermatis strains using a metabolic activity plate-based model and electronic microscopic evaluation of catheter surfaces. All M. pachydermatis strains developed biofilms but biofilm formation showed variability among the different strains unrelated to their clinical origin. This study demonstrates the ability of M. pachydermatis to adhere to and form biofilms on the surfaces of different materials, such as polystyrene and polyurethane.

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.