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.

Le domaine du microbiome s'est considérablement développé au cours de la dernière décennie, et les études publiées fournisse une vue d'ensemble des micro­organismes présents sur la peau des animaux de compagnie. Avec la croissance continue et l'intérêt concernant ce domaine, des interrogations ont été soulevées concernant les méthodes de collecte des échantillons, la contamination des réactifs, le traitement des données et les facteurs environnementaux qui peuvent nuire à l'interprétation des données (en particulier en ce qui concerne les échantillons de peau à faible biomasse). Dans un souci de transparence, il est important de rendre compte de toutes les étapes, de la collecte des échantillons à l'analyse des données, y compris l'utilisation de contrôles appropriés, et de rendre les données séquentielles et les métadonnées des échantillons accessibles au public. Même s'il y existe toujours des variations entre les études, les efforts de normalisation des méthodes réduiront les variables confusionnelles et permettront la reproductibilité et la comparabilité des résultats entre les études. Les études sur le microbiome des animaux de compagnie incluent souvent des cas cliniques, et la petite taille des échantillons peut entraîner un manque de signification statistique dans les petits ensembles de données. La possibilité de combiner les résultats d'études standardisées par le biais de méta­analyses atténuerait les limites de ces petites études et permettrait une interprétation plus solide des résultats, qui pourrait alors éclairer les décisions cliniques. Dans cette revue narrative, nous visons à présenter les considérations relatives à la conception d'une étude destinée à évaluer le microbiome cutané des animaux de compagnie, depuis la conception jusqu'à l'analyse des données.

A área dos estudos do microbioma cresceu significativamente na última década e trabalhos publicados forneceram uma visão geral dos microrganismos que habitam a pele de animais de companhia. Com crescimento do interesse neste campo, surgiram preocupações em relação aos métodos de coleta de amostras, contaminação de reagentes, processamento de dados e fatores ambientais que podem prejudicar a interpretação dos dados (especialmente no que diz respeito a amostras de pele com baixa biomassa). Para garantir a transparência, é importante relatar todas as etapas desde a coleta da amostra até a análise dos dados, incluindo o uso de controles adequados, e disponibilizar publicamente os dados da sequência e os metadados da amostra. Embora a variação entre estudos continue a existir, os esforços para padronizar os métodos reduzirão as variáveis de confusão e permitirão a reprodutibilidade e a comparabilidade dos resultados entre os estudos. Os estudos de microbioma de animais de companhia geralmente incluem casos clínicos, e amostras pequenas podem resultar na ausência de significância estatística em bases de dados pequenas. A capacidade de combinar resultados de estudos padronizados através de meta­análises reduziria as limitações destes estudos menores, proporcionando uma interpretação mais robusta dos resultados que poderiam então influenciar as condutas clínicas. Nesta revisão narrativa, pretendemos apresentar considerações para o delineamento de estudos de microbioma cutâneo de animais de companhia, desde a concepção até a análise dos dados.

El campo del microbioma ha crecido significativamente en la última década y los estudios publicados han proporcionado una visión general de los microorganismos que habitan en la piel de los animales de compañía. Con el continuo crecimiento e interés en este campo, han surgido preocupaciones con respecto a los métodos de recolección de muestras, la contaminación de los reactivos, el procesamiento de datos y los factores ambientales que pueden afectar la interpretación de los datos (especialmente en relación con las muestras de piel de baja biomasa). Para garantizar la transparencia, es importante informar todos los pasos desde la recolección de muestras hasta el análisis de datos, incluido el uso de controles adecuados, y hacer que los datos de secuencia y los metadatos de muestras estén disponibles públicamente. Si bien seguirá existiendo variación entre estudios, los esfuerzos para estandarizar los métodos reducirán las variables de confusión y permitirán la reproducibilidad y comparabilidad de los resultados entre los estudios. Los estudios del microbioma de animales de compañía a menudo incluyen casos clínicos, y los tamaños de muestra pequeños pueden resultar en una falta de significancia estadística dentro de conjuntos de datos pequeños. La capacidad de combinar resultados de estudios estandarizados a través de metanálisis mitigaría las limitaciones de estos estudios más pequeños, proporcionando una interpretación más sólida de los resultados que luego podría informar las decisiones clínicas. En esta revisión narrativa, nuestro objetivo es presentar consideraciones para diseñar un estudio para evaluar el microbioma de la piel de animales de compañía, desde la concepción hasta el análisis de los datos.

Facial and systemic mucormycosis caused by Lichtheimia corymbifera in a goat: case report and literature review of fungal infections in goats.

An 8-y-old Pygora doe was presented to the University of California-Davis, Veterinary Medical Teaching Hospital because of non-healing facial swelling of 2-wk duration. The lesion grew despite medical treatment, causing discomfort masticating, little-to-no airflow from the right nasal passage, and led to euthanasia. On gross examination, a large facial mass with a draining tract through the skin and hard palate was identified. On section, the mass was brown-pink, homogeneous, and friable. Abscess-like masses were identified in the lungs and kidney. Histopathology of the face, including oral and nasal cavities, salivary glands, and lymph nodes, as well as the lung and kidney lesions, revealed large areas of necrosis with numerous wide ribbon-like, mostly aseptate, fungal hyphae consistent with zygomycetes. PCR for fungal organisms performed on formalin-fixed, paraffin-embedded tissue from the face identified Lichtheimia corymbifera (formerly Absidia corymbifera) of the order Mucorales and an Aspergillus sp. The lesion was suspected to have started either as a fungal rhinitis or dental feed impaction, subsequently spreading to the face and systemically to the lungs and kidney. We describe here the lesions associated with facial mucormycosis in a goat and present a literature review of L. corymbifera infection in veterinary species and fungal infections in goats.

Gastrointestinal tract pathology of the owl monkey (Aotus spp.).

Owl monkeys are small nocturnal new world primates in the genus Aotus that are most used in biomedical research for malaria. Cardiomyopathy and nephropathy are well-described common diseases contributing to their morbidity and mortality; less is known about lesions affecting the gastrointestinal tract. Records from a 14-year period (2008-2022) at the Keeling Center for Comparative Medicine and Research were queried to identify instances of spontaneous gastrointestinal disease that directly contributed to the cause of death from the 235 adult owl monkeys submitted for necropsy. Of the 235, 10.6% (25/235) had gastrointestinal disease listed as a significant factor that contributed to morbidity and mortality. Diagnoses included candidiasis (3/25), gastric bloat (4/25), and intestinal incarceration and ischemia secondary (11/25), which included intussusception (4/25), mesenteric rent (3/25), strangulating lipoma (2/25), intestinal torsion (1/25), and an inguinal hernia (1/25). Intestinal adenocarcinomas affecting the jejunum (4/25) were the most common neoplasia diagnosis. Oral squamous cell carcinoma (1/25) and intestinal lymphoma (2/25) were also diagnosed. This report provides evidence of spontaneous lesions in the species that contribute to morbidity and mortality.

Common superficial and deep cutaneous bacterial infections in domestic animals: A review.

The skin covers the external surface of animals, and it is constantly exposed to and inhabited by different microorganisms, including bacteria. Alterations in the skin barrier allow commensal and/or pathogenic bacteria to proliferate and penetrate deep into the lower layers of the skin. Being the first barrier to the external environment, the skin is prone to injuries, allowing the penetration of microorganisms that may lead to severe deep infections. Companion animals, especially dogs, are prone to bacterial infections, often secondary to allergic dermatitis. When environmental conditions are unfavorable, horses, cattle, sheep, and goats can develop superficial infections, such as those caused by Dermatophilus congolensis. Deep inflammation is commonly caused by Mycobacterium spp., which results in granulomatous to pyogranulomatous dermatitis and panniculitis. Likewise, bacteria such as Nocardia spp. and Actinomyces spp. can cause deep pyogranulomatous inflammation. Bacteria that lead to deep necrotizing lesions (eg, necrotizing fasciitis/flesh-eating bacteria) can be severe and even result in death. This review includes an overview of the most common cutaneous bacterial infections of domestic animals, highlighting the main features and histologic morphology of the bacteria, cutaneous structures involved, and the type of inflammatory infiltrates.

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.

Skin biopsy guidelines: tips and advice from veterinary pathologists to practitioners.

Skin diseases are one of the most common problems seen in veterinary practices around the world. Many patients are presented with severe and/or chronic lesions, often refractory to treatment, and collection of skin biopsies is often beneficial to obtain or confirm a diagnosis and to help guide a management plan for patients. To obtain valuable information from skin biopsies, practitioners should follow recommended guidelines based on drug withdrawal and washout period, identification, and proper collection of skin lesions, which should be at different stages of progression, as well as include a thorough clinical history and differential list. These different steps taken prior to the submission of samples will often increase the chances of a more accurate diagnosis. Practitioners should also understand it may not always be possible for pathologists to provide a definitive diagnosis, but the information provided with skin biopsies can often be used to guide an appropriate treatment plan. This review will present general guidelines and suggestions to help obtain the most diagnostic skin samples for histopathological evaluation.

Paraconiothyrium cyclothyrioides, a novel cutaneous fungal pathogen in a dog and a cat.

A dog and a cat presented with pyogranulomatous mycotic pododermatitis. Panfungal PCR and next-generation sequencing identified Paraconiothyrium cyclothyrioides with 100% identity. Paraconiothyrium cyclothyrioides can rarely cause cutaneous infection and systemic disease in immunocompromised humans. This is the first report of infections in domestic animal species.

Un chien et un chat sont présentés avec une pododermatite pyogranulomateuse d'origine fongique. La PCR panfongique et le séquençage de nouvelle génération ont identifié Paraconiothyrium cyclothyrioides avec un pourcentage d'identité de 100 %. Rarement, Paraconiothyrium cyclothyrioides peut provoquer une infection cutanée et une maladie systémique chez des humains immunodéprimés. Il s'agit du premier signalement d'infection dans des espèces animales domestiques.

Un perro y un gato presentaron pododermatitis micótica piogranulomatosa. La PCR panfúngica y la secuenciación de última generación identificaron Paraconiothyrium cyclothyrioides con un 100 % de identidad. Paraconiothyrium cyclothyrioides rara vez puede causar infección cutánea y enfermedad sistémica en humanos inmunocomprometidos. Este es el primer reporte de infecciones en especies de animales domésticos.

Um cão e um gato foram apresentados com pododermatite micótica piogranulomatosa. PCR panfúngico e sequenciamento de última geração identificaram Paraconiothyrium cyclothyrioides com 100% de identidade. Paraconiothyrium cyclothyrioides pode raramente causar infecções cutâneas e doença sistêmica em humanos imunocomprometidos. Este á o primeiro relato de infecções em animais domésticos.

An ancient haplotype containing antimicrobial peptide gene variants is associated with severe fungal skin disease in Persian cats.

Dermatophytosis, also known as ringworm, is a contagious fungal skin disease affecting humans and animals worldwide. Persian cats exhibit severe forms of the disease more commonly than other breeds of cat, including other long-haired breeds. Certain types of severe dermatophytosis in humans are reportedly caused by monogenic inborn errors of immunity. The goal of this study was to identify genetic variants in Persian cats contributing to the phenotype of severe dermatophytosis. Whole-genome sequencing of case and control Persian cats followed by a genome-wide association study identified a highly divergent, disease-associated haplotype on chromosome F1 containing the S100 family of genes. S100 calcium binding protein A9 (S100A9), which encodes a subunit of the antimicrobial heterodimer known as calprotectin, contained 13 nonsynonymous variants between cases and controls. Evolutionary analysis of S100A9 haplotypes comparing cases, controls, and wild felids suggested the divergent disease-associated haplotype was likely introgressed into the domestic cat lineage and maintained via balancing selection. We demonstrated marked upregulation of calprotectin expression in the feline epidermis during dermatophytosis, suggesting involvement in disease pathogenesis. Given this divergent allele has been maintained in domestic cat and wildcat populations, this haplotype may have beneficial effects against other pathogens. The pathogen specificity of this altered protein should be investigated before attempting to reduce the allele frequency in the Persian cat breed. Further work is needed to clarify if severe Persian dermatophytosis is a monogenic disease or if hidden disease-susceptibility loci remain to be discovered. Consideration should be given to engineering antimicrobial peptides such as calprotectin for topical treatment of dermatophytosis in humans and animals.

Immunophenotype of the inflammatory response in the central and enteric nervous systems of cockatiels (Nymphicus hollandicus) experimentally infected with parrot bornavirus 2.

Proventricular dilatation disease is a lethal disease of psittacine birds. In this study, we characterized the local cellular immune response in the brain, proventriculus, and small intestine of 27 cockatiels (Nymphicus hollandicus) experimentally infected with parrot bornavirus 2 (PaBV-2). Perivascular cuffs in the brain were composed of CD3+ T-lymphocytes and Iba1+ macrophages/microglia in most cockatiels (n = 26). In the ganglia of the proventriculus, CD3+ T-lymphocytes (n = 17) and Iba1+ macrophages (n = 13) prevailed. The ganglia of the small intestine had a more homogeneous distribution of these leukocytes, including PAX5+ B-lymphocytes (n = 9), CD3+ T-lymphocytes (n = 8), and Iba1+ macrophages (n = 8). Our results indicate that perivascular cuffs in the brain and the inflammatory infiltrate in the proventriculus of PaBV-2-infected cockatiels is predominately composed of T-lymphocytes, while the inflammatory infiltrates in the ganglia of the small intestine are characterized by a mixed infiltrate composed of T-lymphocytes, B-lymphocytes, and macrophages.

Cytokine expression in feline allergic dermatitis and feline asthma.

BACKGROUND: The pathogenesis of feline allergic dermatitis (FAD) is unclear, with several differences from allergic dermatitis in dogs and humans. HYPOTHESIS/OBJECTIVES: To survey cytokine expression levels in healthy cats and cats affected with allergic dermatitis or asthma. ANIMALS: Formalin-fixed, paraffin-embedded skin biopsies from 22 cats with allergic dermatitis and 21 cats without allergic dermatitis were used for cutaneous assays. Serum was obtained from 17 healthy cats, 18 cats with allergic dermatitis, and 18 cats with a presumptive diagnosis of asthma. METHODS AND MATERIALS: Cutaneous mRNA expression was evaluated with quantitative PCR [interleukin (IL)-31 and IL-31 Receptor A] and RNA in situ hybridisation (ISH) [IL-5, IL-31, IL-31RA, IL-33 and Oncostatin M receptor (OSMR)-ß]. IL-31 protein concentrations were evaluated in serum with an enzyme-linked immunosorbent assay. Serum levels of 19 additional cytokines were evaluated using a Luminex panel. RESULTS: IL-31, IL-31RA, IL-5 and IL-33 mRNA expression were either expressed in low quantities or undetectable in most samples. By contrast, OSMR-ß expression was significantly higher in the skin of allergic versus healthy cats (P < 0.0001). Although serum IL-31 was detected in a larger number of cats with allergic dermatitis than healthy cats, and concentrations appeared to be higher in cats with allergies, this difference was not statistically significant. Cats affected by asthma also exhibited insignificantly higher concentrations of IL-31 in the serum. CONCLUSIONS AND CLINICAL RELEVANCE: Our results suggest that feline allergic diseases may exhibit different pathomechanisms from allergic diseases affecting other species. These findings are useful in guiding further therapeutic development toward targets that may have a role in the pathogenesis of feline allergic skin disease.

Characterization of the cutaneous mycobiota in Persian cats with severe dermatophytosis.

BACKGROUND: Persian cats are predisposed to chronic and severe dermatophytosis. Alterations to the cutaneous microbiota are one potential contributor to this predisposition. OBJECTIVES: To characterise the cutaneous and environmental fungal microbiota of Persian cats with chronic, severe dermatophytosis, and to compare the fungal microbiota of cats with and without dermatophytosis. ANIMALS: Thirty-six client-owned cats, including 26 Persian cats and 10 domestic long hair (DLH) cats. METHODS AND MATERIALS: Skin and home environment swabs were collected from Persian cats with severe, chronic dermatophytosis as well as groups of healthy control cats (Persian and DLH). Sequencing of the internal transcribed spacer 1 (ITS1) region was performed in addition to ITS1 quantitative PCR and fungal culture. RESULTS: Next-generation sequencing (NGS) targeting the fungal ITS region detected Microsporum sp. DNA from all Persian cats diagnosed with dermatophytosis and from environmental samples of their homes. A significant difference in community structure was identified between cases and controls, largely resulting from the Microsporum spp. DNA in samples from affected cats. Persian cats with dermatophytosis do not exhibit decreased fungal diversity. NGS failed to identify dermatophyte DNA on two culture-positive asymptomatic Persian controls and identified Trichophyton rubrum DNA from a culture-negative asymptomatic Persian control. CONCLUSIONS: Aside from M. canis, our results indicate that an underlying fungal dysbiosis is not likely to play a role in development of dermatophytosis in Persian cats. Other explanations for predisposition to this disease, such as a primary immunodeficiency, ineffective grooming or unique features of Persian cat hair should be investigated.

Nasopharyngeal nephroblastoma in a 3-month-old Boer goat.

A 3-mo-old, female Boer goat was presented because of respiratory difficulties. Tachypnea and inspiratory dyspnea were noted during physical examination. Thoracic radiographs were unremarkable; however, upper airway and nasal passage radiographs revealed a soft tissue mass within the nasal passages. The patient underwent cardiorespiratory arrest and did not respond to resuscitation efforts during endoscopy. A large, pedunculated, semi-firm mass originated from the soft palate and obstructed 90% of the nasopharynx on autopsy. Histologically, the mass was composed of primitive cells that multifocally formed tubules and glomeruloid structures intermingled with areas of fusiform and blastemal cells. The neoplastic cells were positive for cytokeratin (tubular and glomeruloid cells), vimentin (fusiform population and blastemal cells), and Wilms tumor 1 protein (glomeruloid structures) on immunohistochemistry, consistent with a triphasic nephroblastoma. To our knowledge, nasopharyngeal nephroblastoma has not been reported previously in any species.

Pyogranulomatous panniculitis in a domestic cat associated with Pseudomonas luteola infection.

Pseudomonas luteola, a pathogen causing disease in humans, has in animals been reported only in rainbow trout and ferrets. This case report describes pyogranulomatous panniculitis in a cat associated with P. luteola infection. Organisms were seen histologically and identified with PCR and sequencing. Lesions resolved after treatment with marbofloxacin.

Pseudomonas luteola, un pathogène de l'homme, a été décrit chez l'animal seulement chez le furet et la truite arc en ciel. Ce cas clinique décrit une panniculite pyogranulomateuse chez un chat associée à une infection à P. luteola. Les organismes ont été vus à l'examen histopathologique et identifiés par PCR et séquençage. Les lésions se sont résolues après un traitement à la marbofloxacine.

Pseudomonas luteola, un patógeno que causa una enfermedad en los seres humanos, se ha reportado en animales solo en truchas arco iris y hurones. Este caso clínico describe una paniculitis piogranulomatosa en un gato asociada con una infección por P. luteola. Los organismos se observaron histológicamente y se identificaron mediante PCR y secuenciación. Las lesiones se resolvieron después del tratamiento con marbofloxacina.

Pseudomonas luteola é um patógeno causador de doença em humanos e, em animais, há relatos de sua ocorrência apenas em furões e trutas arco-íris. Este relato descreve um caso de paniculite piogranulomatosa em um gato associada à infecção por P. luteola. Os microrganismos foram observados histologicamente e identificados por PCR e sequenciamento. As lesões foram resolvidas após tratamento com marbofloxacino.

Characterization of staphylococcal communities on healthy and allergic feline skin.

BACKGROUND: Various Staphylococcus species have been demonstrated to play important roles on the skin, including causing disease and protecting the host from pathogens. Although culture-based studies have isolated various Staphylococcus spp. from feline skin, very little is known regarding the species-level communities on the host. HYPOTHESIS/OBJECTIVES: To describe the species-level staphylococcal communities inhabiting the skin of healthy cats and cats with allergic dermatitis. ANIMALS: Skin swabs from the ear canal and groin of 11 healthy and 10 allergic (nonlesional) cats were obtained. METHODS AND MATERIALS: DNA was extracted from the skin swabs and used for next-generation sequencing targeting the V1-3 region of the 16S rRNA gene. Following a standard microbiota analysis of the sequencing data, species-level assignment for the staphylococcal sequences were obtained using a staphylococci-specific database. RESULTS: Staphylococcus spp. had similar relative abundance in healthy and allergic samples. The most abundant staphylococcal species were S. epidermidis in healthy samples, and S. felis and S. capitis in allergic samples. The composition of staphylococcal communities, as well as relative abundance of Staphylococcus spp., was variable between body sites and individual cats sampled. CONCLUSIONS AND CLINICAL RELEVANCE: These results demonstrate that diverse staphylococcal communities inhabit the skin of healthy and allergic cats, and provide a starting point for further research into the importance of Staphylococcus spp. in feline allergic skin disease.

Outbreak of Paranannizziopsis australasiensis Infection in Captive African Bush Vipers (Atheris squamigera).

We report the epidemiological, clinical and pathological features of an outbreak of Paranannizziopsis australasiensis (order Onygenales) in captive African bush vipers (Atheris squamigera) (ABVs) that died suddenly. The snakes had multifocal, raised, white-grey to dark brown discoloured cutaneous patches. Microscopically, all had integumentary lesions characterized by multifocal to coalescent necroheterophilic epidermitis with superficial and intraepidermal fungal elements and bacteria. Concurrent epidermal hyperplasia, hyperkeratosis and intracellular and intercellular oedema, often leading to vesiculation, and fasciitis/superficial myositis, were consistent findings in all snakes, while ulceration (9/11) and dysecdysis (5/11) varied. A panfungal polymerase chain reaction targeting the internal transcribed spacer-2 region, and gene sequencing, confirmed P. australasiensis infection in three cases. This is the first report of P. australasiensis in the USA and the first record of paranannizziopsis infection in African bush vipers. P. australasiensis should be considered in the differential diagnosis of dermatomycosis in snakes and represents a potential threat to reptile conservation programmes.

Characterization of Cutaneous Bacterial Microbiota from Superficial Pyoderma Forms in Atopic Dogs.

Although Staphylococcus pseudintermedius is considered the major pathogen associated with superficial canine pyoderma, no study has investigated the entire bacterial community in these lesions with molecular techniques. The objectives of this study were to characterize the bacterial microbiota in two forms of superficial canine pyoderma lesions, superficial bacterial folliculitis (SBF) and epidermal collarette (EC), especially in terms of the staphylococcal community. Swabs from 12 SBF and 9 EC lesions were obtained from eight and six atopic dogs, respectively. Eight samples from the axilla and groin of four healthy dogs served as controls. DNA was extracted for 16S rRNA gene sequencing and quantitative polymerase chain reaction of Staphylococcus spp. and S. pseudintermedius. Healthy skin samples harbored significantly more diverse bacterial communities than pyoderma samples. Healthy samples had communities that were more similar to each other, and were distinct from pyoderma samples. Staphylococcus spp. abundance was increased in pyoderma samples, especially those from EC samples. Although determining species-level identities of staphylococcal sequences revealed many species, S. pseudintermedius was the primary staphylococcal species found in all sample types. As expected, there are many differences in the microbiota when comparing healthy and canine pyoderma lesions samples. These lesions do not seem to be associated with a change in the relative abundance of specific Staphylococcus species, but simply an overall increase in Staphylococcus spp. abundance. The results of this study provide a starting point for future studies investigating how antimicrobial treatments may further change the microbiota associated with these lesions.

The canine skin and ear microbiome: A comprehensive survey of pathogens implicated in canine skin and ear infections using a novel next-generation-sequencing-based assay.

This study analyzed the complex bacterial and fungal microbiota of healthy and clinically affected canine ear and skin samples. A total of 589 canine samples were included: 257 ear swab samples (128 healthy vs. 129 clinically affected) and 332 skin swab samples (172 healthy vs. 160 clinically affected) were analyzed using next-generation sequencing (NGS) to determine both relative and absolute abundances of bacteria and fungi present in the samples. This study highlighted the canine microbiota of clinically affected cases was characterized by an overall loss of microbial diversity, high microbial biomass, with overgrowth of certain members of the microbiota. The observed phenotype of these samples was best described by the combination of both relative and absolute microbial abundances. Compared to healthy samples, 78.3% of the clinically affected ear samples had microbial overgrowth; 69.8% bacterial overgrowth, 16.3% fungal overgrowth, and 7.0% had both bacterial and fungal overgrowth. The most important microbial taxa enriched in clinically affected ears were Malassezia pachydermatis, Staphylococcus pseudintermedius, Staphylococcus schleiferi, and a few anaerobic bacteria such as Finegoldia magna, Peptostreptococcus canis, and Porphyromonas cangingivalis. The anaerobic microbes identified here were previously not commonly recognized as pathogens in canine ear infections. Similar observations were found for skin samples, but yeasts and anaerobes were less abundant when compared to clinically affected cases. Results highlighted herein, signify the potential of NGS-based methods for the accurate quantification and identification of bacterial and fungal populations in diagnosing canine skin and ear infections, and highlight the limitations of traditional culture-based testing.

Colorectal basidiobolomycosis in a dog.

A 7-year-old castrated male French Bulldog was examined for chronic large intestinal enteropathy. A colonic mass and thickened rectal mucosa were identified, and histopathologic examination of endoscopic biopsy specimens disclosed eosinophilic proctitis with large (5-20 µm), irregularly shaped, pauciseptate hyphae that were Gomori methenamine silver and periodic acid-Schiff positive. Amplification and sequencing of ribosomal DNA extracted from paraffin-embedded tissues yielded a sequence with 97% identity to GenBank sequences for Basidiobolus ranarum. After itraconazole, terbinafine, and prednisone administration, clinical signs resolved rapidly, and sonographic lesions were largely absent after 6 weeks. Treatment was discontinued by the owner 15 weeks after diagnosis. Three weeks later, the dog collapsed acutely and was euthanized. Necropsy identified metastatic islet cell carcinoma and grossly unremarkable colorectal tissues. However, histopathology of the rectum disclosed multifocal submucosal granulomas with intralesional hyphae morphologically similar to those previously observed. This report is the first to describe medical treatment of gastrointestinal basidiobolomycosis in a dog.

Histoplasmosis and multicentric lymphoma in a Nubian goat.

Following treatment for pneumonia, a 1-y-old female Nubian goat was presented because of a persistent fever for 3 mo and peripheral lymphadenopathy for 1 mo. Cytology and histology of the superficial cervical and prefemoral lymph nodes demonstrated a moderate-to-marked "left-shifted" lymphoid population, suggestive of lymphoma, and extremely rare extracellular, 2-4 µm, oval, basophilic yeast, consistent with Histoplasma capsulatum. On immunohistochemistry, >95% of the lymphocytes demonstrated positive cytoplasmic and membranous immunoreactivity for CD3. Histoplasma spp. urine antigen and serum antibody testing were positive and negative, respectively. Panfungal PCR and sequencing of DNA extracted from scrolls of formalin-fixed, paraffin-embedded tissue yielded matches to H. capsulatum with 99-100% identity. Given the poor prognosis and persistent pyrexia, the animal was euthanized. Postmortem examination confirmed concurrent multicentric, intermediate-size, T-cell, lymphoblastic lymphoma and histoplasmosis; lesions consistent with intestinal coccidiosis and suspected pulmonary Rhodococcus equi were also noted. Although dimorphic fungi have been described previously in goats, lesions of Histoplasma spp. had not been documented in this species, to our knowledge. Given the low disease burden, it is suspected that the lymphoma was primary, leading to an immunocompromised state and development of secondary, opportunistic infections.