Application of DNA Typing Methods to the Study of the Epidemiology of Malassezia pachydermatis

A Novel Mycovirus Evokes Transcriptional Rewiring in the Fungus Malassezia and Stimulates Beta Interferon Production in Macrophages

Malassezia species represent the most common fungal inhabitant of the mammalian skin microbiome and are natural skin commensal flora. However, these fungi are also associated with a variety of clinical skin disorders. Recent studies have reported associations of Malassezia with Crohn’s disease and pancreatic cancer, further implicating this fungal genus in inflammatory and neoplastic disease states. Because M. sympodialis has lost genes involved in RNA interference (RNAi), we hypothesized Malassezia could harbor dsRNA mycoviruses. Indeed, we identified a novel mycovirus of the totivirus family in several Malassezia species and characterized the MsMV1 mycovirus of M. sympodialis. We found conditions that lead to curing of the virus and analyzed isogenic virus-infected/virus-cured strains to determine MsMV1 genetic and pathogenic impacts. MsMV1 induces a strong overexpression of transcription factors and ribosomal genes, while downregulating cellular metabolism. Moreover, MsMV1 induced a significantly higher level of beta interferon expression in cultured macrophages. This study sheds light on the mechanisms of pathogenicity of Malassezia, focusing on a previously unidentified novel mycovirus.

Mycoviruses infect fungi, and while most persist asymptomatically, there are examples of mycoviruses having both beneficial and detrimental effects on their host. Virus-infected Saccharomyces and Ustilago strains exhibit a killer phenotype conferring a growth advantage over uninfected strains and other competing yeast species, whereas hypovirus-infected Cryphonectria parasitica displays defects in growth, sporulation, and virulence. In this study, we identify a double-stranded RNA (dsRNA) mycovirus in five Malassezia species. Sequence analysis reveals it to be a totivirus with two dsRNA segments: a larger 4.5-kb segment with genes encoding components for viral replication and maintenance, and a smaller 1.4-kb segment encoding a novel protein. Furthermore, transcriptome sequencing (RNA-seq) of virus-infected versus virus-cured Malassezia sympodialis revealed an upregulation of dozens of ribosomal components in the cell, suggesting the virus modifies the transcriptional and translational landscapes of the cell. Given that Malassezia is the most abundant fungus on human skin, we assessed the impact of the mycovirus in a murine epicutaneous infection model. Although infection with virus-infected strains was not associated with an increased inflammatory response, we did observe enhanced skin colonization in one of two virus-infected M. sympodialis strains. Noteworthy, beta interferon expression was significantly upregulated in bone marrow-derived macrophages when challenged with virus-infected, compared to virus-cured, M. sympodialis, suggesting that the presence of the virus can induce an immunological response. Although many recent studies have illuminated how widespread mycoviruses are, there are relatively few in-depth studies about their impact on disease caused by the host fungus. We describe here a novel mycovirus in Malassezia and its possible implications in pathogenicity.

Biology, diagnosis and treatment of Malassezia dermatitis in dogs and cats Clinical Consensus Guidelines of the World Association for Veterinary Dermatology

BACKGROUND

The genus Malassezia is comprised of a group of lipophilic yeasts that have evolved as skin commensals and opportunistic cutaneous pathogens of a variety of mammals and birds.

OBJECTIVES

The objective of this document is to provide the veterinary community and other interested parties with current information on the ecology, pathophysiology, diagnosis, treatment and prevention of skin diseases associated with Malassezia yeasts in dogs and cats.

METHODS AND MATERIAL

The authors served as a Guideline Panel (GP) and reviewed the literature available prior to October 2018. The GP prepared a detailed literature review and made recommendations on selected topics. The World Association of Veterinary Dermatology (WAVD) Clinical Consensus Guideline committee provided guidance and oversight for this process. The document was presented at two international meetings of veterinary dermatology societies and one international mycology workshop; it was made available for comment on the WAVD website for a period of six months. Comments were shared with the GP electronically and responses incorporated into the final document.

CONCLUSIONS AND CLINICAL IMPORTANCE

There has been a remarkable expansion of knowledge on Malassezia yeasts and their role in animal disease, particularly since the early 1990's. Malassezia dermatitis in dogs and cats has evolved from a disease of obscurity and controversy on its existence, to now being a routine diagnosis in general veterinary practice. Clinical signs are well recognised and diagnostic approaches are well developed. A range of topical and systemic therapies is known to be effective, especially when predisposing factors are identified and corrected.

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.

Genetic typing of Malassezia pachydermatis from different domestic animals

In the present study, random amplification of polymorphic DNA, which detects DNA polymorphism in fungal genomic DNA, was applied for genetic typing of Malassezia pachydermatis isolates. Fifty-five isolates from different domestic animals and body sites and the neotype strain CBS 1879 were characterized. Primers M13 and OPT-20 were used to analyse their genetic relatedness and similarity. This technique allowed us to distinguish four different genetic types. The predominant genetic type was observed in isolates recovered from different anatomical locations in all animals. It was the only genetic type found in cats, horse, goat and pig. The other three genetic types were observed only in isolates from external ear canals of dogs. Types II and IV were only recovered from external otitic ears and type III from healthy ears. An animal was colonised by more than one type of M. pachydermatis and different genetic types were detected in the same body site. Some genetic types were only isolated from diseased skin.

Apparent cross-infection with a single strain of Malassezia pachydermatis on a pig farm

Twenty-nine isolates of Malassezia pachydermatis were recovered from a single farm of 100 pigs in Croatia. In contrast, 290 farm pigs from other locations (northern parts of Croatia and Slovenia) yielded only two non-lipid dependent isolates of M. pachydermatis using the same swabbing procedure. Ten of the 29 isolates from a single farm had their identity confirmed by karyotyping, and were typed by restriction fragment length polymorphism (RFLP) analysis. All but one of these isolates sub-typed were indistinguishable, one isolate produced a slightly different RFLP profile. Control isolates recovered from dog skin gave RFLP profiles that were easily distinguished from those produced by the pig isolates. These results suggest that a single strain of M. pachydermatis had colonised this pig herd.

The genetic diversity of clinical isolates of Malassezia pachydermatis from dogs and cats

Molecular investigation of 110 clinical isolates of non-lipid-dependent Malassezia pachydermatis from dogs and cats was carried out by random amplification of polymorphic DNA (RAPD) and chitin synthase 2 (CHS2) gene sequence analyses. The RAPD analysis indicated that the clinical isolates of M. pachydermatis constituted four distinct genetic types (A, B, C and D). Moreover, the results from CHS2 gene analysis completely agreed with those from the RAPD analyses. The clinical isolates of M. pachydermatis were obtained from normal external ears, lesions of atopic dermatitis, flea allergic dermatitis, otitis externa, pyoderma and seborrheic dermatitidis in dogs and cats. Type A consisted of 93 clinical isolates as well as the ex-neotype strain of M. pachydermatis. The isolates of type A M. pachydermatis originated from lesions of all kinds of diseases. They were predominant on dog and cat skin. The other types, B, C, and D were isolated mainly from otitis externa.

Identification and typing of Malassezia yeasts using amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD) and denaturing gradient gel electrophoresis (DGGE)

Three molecular tools, amplified fragment length polymorphism (AFLP), denaturing gradient gel electrophoresis (DGGE) and random amplified polymorphic DNA (RAPD) analysis, were explored for their usefulness to identify isolates of Malassezia yeasts. All seven species could be separated by AFLP and DGGE. Using AFLP, four genotypes could be distinguished within M. furfur. AFLP genotype 4 contained only isolates from deep human sources, and ca. 80% of these isolates were from patients with systemic disease. Most of the systemic isolates belonged to a single RAPD genotype. This suggests that systemic conditions strongly select for a particular genotype. Although the clinical use of DGGE may be limited due to technical demands, it remains a powerful tool for the analysis of complex clinical samples.

Characterization of Malassezia species by means of phenotypic characteristics and detection of electrophoretic karyotypes by pulsed-field gel electrophoresis (PFGE)

A total of 220 isolates of the genus Malassezia obtained from affected skin of animals and humans were included in this study. The isolates were examined for their belonging to the known species Malassezia pachydermatis, Malassezia sympodialis, Malassezia furfur, Malassezia obtusa, Malassezia restricta, Malassezia globosa and Malassezia slooffiae by means of phenotypic and biochemical characteristics as well as their ability to assimilate polyethylen(20)-sorbitan-esters (Tween 20, 40, 60, 80). The electrophoretic karyotypes of all isolates were studied by pulsed-field gel electrophoresis. Of the 220 Malassezia isolates examined, 217 were identified as M. pachydermatis and three were classified as M. sympodialis. Moreover, the proof of limited lipid-dependence of M. pachydermatis indicated that the commonly used criterion 'lipid-independence' is not sufficient to differentiate this species from the other known Malassezia species.

Malassezia pachydermatis: a review

Malassezia pachydermatis is of importance in both veterinary and human medicine. Its taxonomic status and physiological characteristics are now better understood. Skin disease associated with this lipophilic yeast is now commonly recognized, especially in dogs. However, further studies are required to elucidate the mechanisms which allow this yeast to proliferate and induce disease. Skin colonization is common in pet carnivores which consequently constitute a source of M. pachydermatis for susceptible humans. In the future, the development of efficient typing systems should allow better understanding of the transmission mechanisms.

Molecular heterogeneity in clinical isolates of Malassezia pachydermatis from dogs

Molecular investigation of 16 strains, conventionally identified to be Malassezia pachydermatis, isolated from dogs in Japan was carried out by random amplification of polymorphic DNA (RAPD) and chitin synthase 2 (CHS2) gene sequence analyses. The RAPD band patterns of 13 clinical isolates were identical to that of standard strain of M. pachydermatis (CBS-1879). The other three clinical isolates were different from the standard strain of M. pachydermatis in RAPD patterns, and two of the three isolates were identical. About 620 bp genomic DNA fragments of the CHS2 gene were amplified from the same 16 clinical isolates of M. pachydermatis by polymerase chain reaction (PCR) and sequenced. The phylogenetic analysis of the nucleotide sequences of CHS2 gene fragments of the 16 clinical isolates revealed that the 13 strains were genetically very close to the standard strain of M. pachydermatis and the other two isolates were genetically close to the standard strain of M. furfur rather than M. pachydermatis. The remaining one isolate was phylogenetically distinct from all the seven Malassezia species reported so far.

Molecular typing of Malassezia species with PFGE and RAPD

The currently recognized seven species of Malassezia all have different karyotypes which do not vary intraspecifically, except in M. furfur which displayed two different karyotypes. In contrast, random amplified polymorphic DNA (RAPD) typing showed the presence of genetic variation in all species. It is concluded that karyotype analysis is useful for species identification, and RAPD typing can be used in epidemiological investigations.

Epidemiological analysis of Malassezia pachydermatis isolates by partial sequencing of the large subunit ribosomal RNA

The opportunistic yeast Malassezia pachydermatis is commonly recovered from both normal and diseased skin of warm-blooded animals. The diversity of M pachydermatis isolates obtained from a wide range of hosts was investigated by the partial sequencing of the large subunit (LSU) ribosomal RNA. Among 100 isolates examined, seven types (Ia-Ig) were discriminated on the basis of nucleotide sequence diversity. The seven types differed by one to five mutations, all of them corresponding to transitions. The predominant sequence, type Ia, appeared to be ubiquitous since it was observed in isolates recovered from domestic and wild carnivora, from a monkey and from man. In contrast the sequence types Ic, Id and Ig seemed to be more host-specific; they included isolates recovered exclusively from rhinoceros, dogs and ferrets, respectively. None of the seven sequence types correlated with isolation from healthy skin or a particular lesion (otitis externa or other dermatitis). The study indicated that the skin of an animal may be colonised by more than one type of M pachydermatis.

The genus Malassezia with description of four new species

The genus Malassezia has been revised using morphology, ultrastructure, physiology and molecular biology. As a result the genus has been enlarged to include seven species comprising the three former taxa M. furfur, M. pachydermatis and M. sympodialis, and four new taxa M. globosa, M. obtusa, M. restricta and M. slooffiae. The descriptions of all the species include morphology of the colonies and of the cells, together with ultrastructural details. The physiological properties studied were the presence of catalase, the tolerance of 37 degrees C and the ability to utilize certain concentrations of Tween 20, 40, 60 and 80 as a source of lipid in a simple medium. Information is given for each of the taxa on mole% GC and also the rRNA sequence from the comparison previously described for the genus.

Characterization of markedly lipid-dependent Malassezia pachydermatis isolates from healthy dogs

When 244 Malassezia colonies which had been isolated from a colony of Beagle dogs using modified Dixon's agar were sub-cultured on Sabouraud's dextrose agar to determine their lipid dependence, 30 showed poor growth resembling M. furfur, whereas the remainder were typical of M. pachydermatis. Eight of the 10 poor growing isolates selected for further study formed colonies typical of M. pachydermatis after five passages on Sabouraud's dextrose agar at 4 d intervals and two continued to show poor growth. Nine isolates had enzyme profiles identical to those of typical M. pachydermatis isolates, and one resembled M. furfur. However, seven of the poor growing isolates which were karyotyped had patterns typical of M. pachydermatis. Poor growing isolates and their non-lipid-dependent 'revertants' had identical restriction fragment length polymorphism patterns and poly(GT) hybridization profiles. These observations show that some M. pachydermatis isolates grow poorly when sub-cultured onto Sabouraud's dextrose agar and may be incorrectly identified as M. furfur if further studies are not performed.