Malassezia species dysbiosis in natural and allergen-induced atopic dermatitis in dogs

Considerations for performing companion animal skin microbiome studies

The microbiome field has grown significantly in the past decade, and published studies have provided an overview of the microorganisms inhabiting the skin of companion animals. With the continued growth and interest in this field, concerns have been raised regarding sample collection methods, reagent contamination, data processing and environmental factors that may impair data interpretation (especially as related to low-biomass skin samples). In order to assure transparency, it is important to report all steps from sample collection to data analysis, including use of proper controls, and to make sequence data and sample metadata publicly available. Whilst interstudy variation will continue to exist, efforts to standardise methods will reduce confounding variables, and allow for reproducibility and comparability of results between studies. Companion animal microbiome studies often include clinical cases, and small sample sizes may result in lack of statistical significance within small datasets. The ability to combine results from standardised studies through meta-analyses would mitigate the limitations of these smaller studies, providing for more robust interpretation of results which could then inform clinical decisions. In this narrative review, we aim to present considerations for designing a study to evaluate the skin microbiome of companion animals, from conception to data analysis.

Epidermal barrier impairment predisposes for excessive growth of the allergy-associated yeast Malassezia on murine skin

BACKGROUND

The skin barrier is vital for protection against environmental threats including insults caused by skin-resident microbes. Dysregulation of this barrier is a hallmark of atopic dermatitis (AD) and ichthyosis, with variable consequences for host immune control of colonizing commensals and opportunistic pathogens. While Malassezia is the most abundant commensal fungus of the skin, little is known about the host control of this fungus in inflammatory skin diseases.

METHODS

In this experimental study, MC903-treated mice were colonized with Malassezia spp. to assess the host-fungal interactions in atopic dermatitis. Additional murine models of AD and ichthyosis, including tape stripping, K5-Nrf2 overexpression and flaky tail mice, were employed to confirm and expand the findings. Skin fungal counts were enumerated. High parameter flow cytometry was used to characterize the antifungal response in the AD-like skin. Structural and functional alterations in the skin barrier were determined by histology and transcriptomics of bulk skin. Finally, differential expression of metabolic genes in Malassezia in atopic and control skin was quantified.

RESULTS

Malassezia grows excessively in AD-like skin. Fungal overgrowth could, however, not be explained by the altered immune status of the atopic skin. Instead, we found that by upregulating key metabolic genes in the altered cutaneous niche, Malassezia acquired enhanced fitness to efficiently colonise the impaired skin barrier.

CONCLUSIONS

This study provides evidence that structural and metabolic changes in the dysfunctional epidermal barrier environment provide increased accessibility and an altered lipid profile, to which the lipid-dependent yeast adapts for enhanced nutrient assimilation. Our findings reveal fundamental insights into the implication of the mycobiota in the pathogenesis of common skin barrier disorders.

Unveiling the mycobiota: The fungal frontier of human health

The microbiota and its effect on health has been extensively studied over the past decade. In many studies, the term microbiota has become synonymous with the bacterial component of the microbiota. Other microbes in the microbiota, such as viruses and fungi, have been neglected until recently. This special issue provides some background on the mycobiota and explores the role of gut fungi in human diseases such as cancer, metabolic diseases, and infection by Clostridiodes difficile, and describes the incidence of fungal infections in transplant patients. The mycobiota, once overlooked, now garners increasing attention.

Malassezia dermatitis in dogs and cats

Malassezia are members of the mycobiome of dogs and cats. In the presence of an underlying disease, these yeasts can proliferate, attach to the skin or mucosa to induce a secondary Malassezia dermatitis, otitis externa or paronychia. Since allergic dermatitis is one of the most common underlying causes, diagnostic investigation for allergy is often indicated. Cats may suffer from various other underlying problems, especially where Malassezia dermatitis is generalised. Malassezia dermatitis in dogs and cats is chronic, relapsing and pruritic. Direct cytology from dermatological lesions and the ear canal, showing "peanut-shaped" budding yeasts, facilitates a rapid and reliable diagnosis. Topical treatment includes antiseptic and antifungal azole-based products. Systemic treatment with oral antifungals is indicated only in severe or refractory disease. Identification and treatment of the underlying cause is essential for an optimal response. In this evidence-based narrative review, we discuss the clinical presentation of Malassezia dermatitis in dogs and cats, underlying comorbidities, and diagnostic considerations. Treatment is discussed in light of emerging evidence of antifungal resistance and the authors' clinical experience.

Update on the skin barrier, cutaneous microbiome and host defence peptides in canine atopic dermatitis

BACKGROUND

Canine atopic dermatitis (AD) is a complex inflammatory skin disease associated with cutaneous microbiome, immunological and skin barrier alterations. This review summarises the current evidence on skin barrier defects and on cutaneous microbiome dysfunction in canine AD.

OBJECTIVE

To this aim, online citation databases, abstracts and proceedings from international meetings on skin barrier and cutaneous microbiome published between 2015 and 2023 were reviewed.

RESULTS

Since the last update on the pathogenesis of canine AD, published by the International Committee on Allergic Diseases of Animals in 2015, 49 articles have been published on skin barrier function, cutaneous/aural innate immunity and the cutaneous/aural microbiome in atopic dogs. Skin barrier dysfunction and cutaneous microbial dysbiosis are essential players in the pathogenesis of canine AD. It is still unclear if such alterations are primary or secondary to cutaneous inflammation, although some evidence supports their primary involvement in the pathogenesis of canine AD.

CONCLUSION AND CLINICAL RELEVANCE

Although many studies have been published since 2015, the understanding of the cutaneous host-microbe interaction is still unclear, as is the role that cutaneous dysbiosis plays in the development and/or worsening of canine AD. More studies are needed aiming to design new therapeutic approaches to restore the skin barrier, to increase and optimise the cutaneous natural defences, and to rebalance the cutaneous microbiome.

Hyphae, pseudohyphae, yeasts, spherules, spores, and more: A review on the morphology and pathology of fungal and oomycete infections in the skin of domestic animals

Fungi are among the most common infectious agents affecting the skin of animals. The skin can serve as a port of entry for fungal infections, which can eventually become disseminated. In some regions of the world, oomycetes, such as Pythium and Lagenidium, are also responsible for a significant number of severe cutaneous infections. Histologic evaluation of fungal morphology, including size, shape, septation, branching, and budding characteristics, combined with the distribution of inflammatory infiltrates within different skin layers can potentially identify etiologic agents, guiding selection of antifungals and additional diagnostics. Fungal infections of the skin surface are typically caused by Malassezia and rarely Candida, with opportunistic fungi also capable of colonizing the skin surface, especially when the barrier is broken. Folliculocentric infections, caused by dermatophytes, result in mild to severe inflammation and can occasionally penetrate deep into the skin. A wide range of fungi, including agents of hyalohyphomycosis, phaeohyphomycosis, and dimorphic fungal infections, as well as oomycetes, result in nodular cutaneous and subcutaneous lesions. With the occasional exception of dimorphic fungi, fungal speciation often requires cultures performed on fresh tissues. However, molecular techniques such as pan-fungal polymerase chain reaction on paraffin blocks is becoming an increasingly useful tool to distinguish between cutaneous fungal pathogens. This review focuses on describing the clinical and histologic features of the most common fungal and oomycete infections affecting the skin of animals, divided according to distribution patterns of lesions and fungal or oomycete morphology.

A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs

BACKGROUND

Like its human counterpart, canine atopic dermatitis (cAD) is a chronic relapsing condition; thus, most cAD-affected dogs will require lifelong treatment to maintain an acceptable quality of life. A potential intervention is modulation of the composition of gut microbiota, and in fact, probiotic treatment has been proposed and tried in human atopic dermatitis (AD) patients. Since dogs are currently receiving intensive medical care, this will be the same option for dogs, while evidence of gut dysbiosis in cAD is still missing, although skin microbial profiling in cAD has been conducted in several studies. Therefore, we conducted a comprehensive analysis of both gut and skin microbiota in cAD in one specific cAD-predisposed breed, Shiba Inu. Additionally, we evaluated the impact of commonly used medical management on cAD (Janus kinase; JAK inhibitor, oclacitinib) on the gut and skin microbiota. Furthermore, we genotyped the Shiba Inu dogs according to the mitochondrial DNA haplogroup and assessed its association with the composition of the gut microbiota.

RESULTS

Staphylococcus was the most predominant bacterial genus observed in the skin; Escherichia/Shigella and Clostridium sensu stricto were highly abundant in the gut of cAD-affected dogs. In the gut microbiota, Fusobacteria and Megamonas were highly abundant in healthy dogs but significantly reduced in cAD-affected dogs. The abundance of these bacterial taxa was positively correlated with the effect of the treatment and state of the disease. Oclacitinib treatment on cAD-affected dogs shifted the composition of microbiota towards that in healthy dogs, and the latter brought it much closer to healthy microbiota, particularly in the gut. Additionally, even within the same dog breed, the mtDNA haplogroup varied, and there was an association between the mtDNA haplogroup and microbial composition in the gut and skin.

CONCLUSIONS

Dysbiosis of both the skin and the gut was observed in cAD in Shiba Inu dogs. Our findings provide a basis for the potential treatment of cAD by manipulating the gut microbiota as well as the skin microbiota. Video Abstract.

Part 1: Understanding the role of Malassezia spp. in skin disorders: Malassezia yeasts as commensal or pathogenic organisms of human and animal skin

INTRODUCTION

Malassezia spp. are a group of lipid-dependent basidiomycetes yeasts acting as commensal organisms of the human and animal skin. However, under some not well-defined circumstances, these yeasts may switch to opportunistic pathogens triggering a number of skin disorders with different clinical presentations. The genus comprises of 18 lipid-dependent species with a variable distribution in the hosts and pathologies thus suggesting a host- and microbe-specific interactions.

AREA COVERED

This review highlighted and discussed the most recent literature regarding the genus Malassezia as a commensal or pathogenic organisms highlighting Malassezia-associated skin disorders in humans and animals and their antifungal susceptibility profile. A literature search of Malassezia associated skin disorders was performed via PubMed and Google scholar (up to May 2023), using the different keywords mainly associated with Malassezia skin disorders and Malassezia antifungal resistance.

EXPERT OPINION

Malassezia yeasts are part of the skin mycobiota and their life cycle is strictly associated with the environment in which they live. The biochemical, physiological, or immunological condition of the host skin selects Malassezia spp. or genotypes able to survive in a specific environment by changing their metabolisms, thus producing virulence factors or metabolites which can cause skin disorders with different clinical presentations.

Part 2: Understanding the role of Malassezia spp. in skin disorders: pathogenesis of Malassezia associated skin infections

INTRODUCTION

Malassezia is a major component of the skin microbiome, a lipophilic symbiotic organism of the mammalian skin, which can switch to opportunistic pathogens triggering multiple dermatological disorders in humans and animals. This phenomenon is favored by endogenous and exogenous host predisposing factors, which may switch Malassezia from a commensal to a pathogenic phenotype.

AREA COVERED

This review summarizes and discusses the most recent literature on the pathogenesis of Malassezia yeasts, which ultimately results in skin disorders with different clinical presentation. A literature search of Malassezia pathogenesis was performed via PubMed and Google scholar (up to May 2023), using the following keywords: Pathogenesis and Malassezia;host risk factors and Malassezia, Malassezia and skin disorders; Malassezia and virulence factors: Malassezia and metabolite production; Immunology and Malassezia.

EXPERT OPINION

Malassezia yeasts can maintain skin homeostasis being part of the cutaneous mycobiota; however, when the environmental or host conditions change, these yeasts are endowed with a remarkable plasticity and adaptation by modifying their metabolism and thus contributing to the appearance or aggravation of human and animal skin disorders.

Efficacy of Antimicrobial Treatment in Dogs with Atopic Dermatitis: An Observational Study

There is a shortage of studies reporting the efficacy of antimicrobial treatment of dogs with atopic dermatitis (AD) and skin infections (SIs). The aim of this study was to evaluate the change in the severity of skin lesions and pruritus, and the overall efficacy of antimicrobial treatment, in dogs with AD and bacterial overgrowth/infection and/or Malassezia dermatitis. A total of 20 dogs with AD and SIs were prospectively enrolled (group A) and they were examined before and after the administration of systemic antimicrobials that resulted in the resolution of SIs. In addition, 19 dogs fulfilling the same inclusion criteria and treated with systemic, with or without topical antimicrobials, were included retrospectively (group B). Since there were no major differences between the groups, their results were combined. The severity of skin lesions decreased significantly, by 30% based on Canine Atopic Dermatitis Extent and Severity Index-4 (CADESI-4), by 28.1% based on the erythema domain of CADESI-4 and based on owner’s global assessment of the severity of skin lesions. Pruritus decreased significantly, by 34.7% based on the Pruritus Visual Analogue Scale (PVAS). The efficacy of antimicrobial treatment was assessed as good to excellent by the investigator and the owner in 55% and 60% of the dogs, respectively. Despite the significant improvement, there was high variability in the response to treatment among dogs. Further studies are needed to find factors that determine the response to antimicrobial treatment in dogs with AD and SIs.

Malassezia: Zoonotic Implications, Parallels and Differences in Colonization and Disease in Humans and Animals

Malassezia spp. are commensals of the skin, oral/sinonasal cavity, lower respiratory and gastrointestinal tract. Eighteen species have been recovered from humans, other mammals and birds. They can also be isolated from diverse environments, suggesting an evolutionary trajectory of adaption from an ecological niche in plants and soil to the mucocutaneous ecosystem of warm-blooded vertebrates. In humans, dogs and cats, Malassezia-associated dermatological conditions share some commonalities. Otomycosis is common in companion animals but is rare in humans. Systemic infections, which are increasingly reported in humans, have yet to be recognized in animals. Malassezia species have also been identified as pathogenetic contributors to some chronic human diseases. While Malassezia species are host-adapted, some species are zoophilic and can cause fungemia, with outbreaks in neonatal intensive care wards associated with temporary colonization of healthcare worker’s hands from contact with their pets. Although standardization is lacking, susceptibility testing is usually performed using a modified broth microdilution method. Antifungal susceptibility can vary depending on Malassezia species, body location, infection type, disease duration, presence of co-morbidities and immunosuppression. Antifungal resistance mechanisms include biofilm formation, mutations or overexpression of ERG11, overexpression of efflux pumps and gene rearrangements or overexpression in chromosome 4.

Study of the variation of the Malassezia load in the interdigital fold of dogs with pododermatitis

The yeast Malassezia pachydermatis is a common inhabitant of the skin and mucosae of dogs. However, under certain circumstances this yeast can overgrow and act as an opportunistic pathogen causing otitis and dermatitis in dogs. Canine pododermatitis is a common disorder in dogs in which M. pachydermatis acts as an opportunistic pathogen. In the present study, the presence of Malassezia yeasts was assessed and quantified in samples collected from the interdigital space of dogs with pododermatitis before and after treatment, and from healthy dogs. The samples were subjected to two different cytological examinations, culture on Sabouraud glucose agar and modified Dixon's agar and a quantitative PCR targeting the internal transcribed spacer (ITS) genomic region. A selection of samples was analyzed by next generation sequencing (NGS) using the D1D2 domain of the large subunit of the ribosomal DNA as target. The pododermatitis samples before treatment showed higher cell counts, colony-forming units and ITS copies than the rest of samples. The NGS analysis revealed that Ascomycota was the main phylum in the healthy and post-treatment samples. However, Basidiomycota and M. pachydermatis was more abundant in the pododermatitis samples before treatment. These results support M. pachydermatis as an opportunistic agent in canine pododermatitis by a variety of methods, and demonstrate the correlation between cytologic and molecular methods for quantification.

Dysbiosis of skin mycobiome in atopic dermatitis

Atopic dermatitis (AD) is a chronic and relapsing inflammatory skin disease with an increasing prevalence worldwide. The aetiology and pathogenesis of AD have not been fully elucidated. Previous studies have suggested the role of fungi as a triggering factor in the development AD. Here we conducted a systematic review to investigate the skin mycobiome profiles in AD and to address whether there is an association between fungal dysbiosis and AD. We searched Medline/PubMed, Embase and Web of Science for research studies published in English between January 1st, 2010 and April 21st, 2021. A total of 11 human studies and 3 animal studies were included in this analysis. Fungal dysbiosis was observed in AD lesions with a depleted amount of Malassezia and a higher abundance of filamentous fungi. A positive correlation between Candida and Staphylococcus was also demonstrated in AD. We supposed that specific species of Malassezia spp. and Candida spp. may play a role in the pathogenesis of AD by interacting with the pathogenic bacteria. Topical application of emollients could improve the skin barrier function and restore the skin fungal flora by increasing the amount of Malassezia. Further studies focusing on the complex interplay between specific skin fungi and the host can provide better insight into the role of microorganisms in the pathogenesis of AD.

Effect of topical medication on the nasomaxillary skin-fold microbiome in French bulldogs

BACKGROUND

Host-microbe interactions may influence dermatitis pathogenesis in the nasomaxillary folds of French bulldogs, which is often complicated by secondary bacterial and fungal infections.

OBJECTIVE

To assess the skin-fold microbiome in systemically healthy French bulldogs and to determine the influence of topical medications on this microbiome.

ANIMALS

Nineteen healthy French bulldogs.

METHODS AND MATERIALS

Next-generation DNA sequencing was applied to characterise the microbiome composition in the nasomaxillary folds of systemically healthy French bulldogs. Subsequently, the effect of two topical products on the fold microbiome was assessed. Seven dogs were treated with a protease product (Kalzyme; enzyme) that inhibits biofilm formation without biocidal activity, six dogs were treated with a 2% chlorhexidine diacetate solution (Nolvasan; CHX) with biocidal activity, and six dogs were untreated. Dogs were randomly assigned to each group, and the investigator was blinded.

RESULTS

The primary skin bacterial phyla inhabiting the folds at inclusion were Firmicutes, Actinobacteria and Proteobacteria. The primary skin fungal phyla were Ascomycota and Basidiomycota. Topical treatment increased the diversity of bacterial and fungal compositions over time (increase in microbial diversity score: enzyme 38%, chlorhexidine 11%, control <5%) and the relative abundance of pathogens reduced significantly (enzyme, P = 0.028; CHX, P = 0.048). A clear correlation (r²  = 0.83) was observed between the abundance of clinically relevant pathogens and microbial diversity.

CONCLUSIONS

The nasomaxillary skin-fold microbiome of healthy French bulldogs contained a high abundance of clinically relevant pathogens (mean 36.4%). Topical therapy with enzyme increased microbial diversity of skin folds and reduced the relative abundance of pathogens.

Malassezia Yeasts in Veterinary Dermatology: An Updated Overview

Lipophilic yeasts of the genus Malassezia are important skin commensals and opportunistic skin pathogens in a variety of animals. The species M. pachydermatis was first isolated from the skin of a captive Indian rhinoceros with an exfoliative dermatitis in 1925, recognized as an important otic pathogen of dogs in the 1950's, and finally accepted, after several years of controversy, as a common cause of canine dermatitis in the 1990's. Since then, there has been considerable research into the biology of Malassezia yeasts and their interaction with their animal hosts. In dogs and cats, M. pachydermatis is associated with ceruminous otitis externa and a "seborrhoeic" dermatitis, wherein pruritic, erythematous skin lesions, often with brown/black greasy, malodourous material matting hairs, preferentially develop in intertriginous areas. Skin disease is favored by folds, underlying hypersensitivity disorders, endocrinopathies, defects of cornification, and in cats, various visceral paraneoplastic syndromes. Diagnosis is based on detecting the yeast in compatible skin lesions, usually by cytology, and observing a clinical and mycological response to therapy. Treatment normally comprises topical or systemic azole therapy, often with miconazole-chlorhexidine shampoos or oral itraconazole or ketoconazole. Management of concurrent diseases is important to minimize relapses. Historically, wild-type Malassezia isolates from dogs and cats were typically susceptible to azoles, with the exception of fluconazole, but emerging azole resistance in field strains has recently been associated with either mutations or quadruplication of the ERG11 gene. These observations have prompted increased interest in alternative topical antifungal drugs, such as chlorhexidine, and various essential oils. Further clinical trials are awaited with interest.