Analysis of the otic mycobiota in dogs with otitis externa compared to healthy individuals

Microbiological Survey and Evaluation of Antimicrobial Susceptibility Patterns of Microorganisms Obtained from Suspect Cases of Canine Otitis Externa in Gran Canaria, Spain

A retrospective study of microbiological laboratory results from 2020 to 2022, obtained from a veterinary diagnostic laboratory of the island of Gran Canaria, Spain, focused on canine otitis cases, was performed. The objective of this study was to analyze the pathogen distribution, antimicrobial susceptibility, prevalence of multidrug resistant phenotypes and the role of coinfections in otitis cases in order to provide up-to-date evidence that could support effective control strategies for this prevalent pathology. A total of 604 submissions were processed for the diagnosis of canine external otitis. Of the samples analyzed, 472 were positive for bacterial or fungal growth (78.1%; 95% CI: 74.8-81.4%). A total of 558 microbiological diagnoses were obtained, divided in 421 bacterial (75.4%; 95% CI: 71.8-79.0%) and 137 fungal (24.6%; 95% CI: 20.9-28.1%) identifications. Staphylococcus pseudintermedius, Malassezia pachydermatis and Pseudomonas aeruginosa were the most prevalent microorganisms detected in clinical cases of otitis. High level antimicrobial resistance was found for Pseudomonas aeruginosa (30.7%), Proteus mirabilis (29.4%), Staphylococcus pseudintermedius (25.1%) and Escherichia coli (19%). Multidrug-resistant phenotypes were observed in 47% of the bacteria isolated. In addition, a 26.4% prevalence of methicillin-resistant Staphylococcus pseudintermedius was detected. The high prevalence of antimicrobial resistant phenotypes in these bacteria highlights the current necessity for constant up-to-date prevalence and antimicrobial susceptibility data that can support evidence-based strategies to effectively tackle this animal and public health concern.

Early life programming by diet can play a role in risk reduction of otitis in dogs

Introduction

Otitis in dogs is often chronic while local treatment primarily consists of flushing, antibiotics, and/or antifungals. We were interested in finding early life variables that associate with otitis later in life, preferably some that could be modified.

Methods

A cross-sectional hypothesis-driven study with longitudinal data was performed to search for associations between pre- and postnatal exposures, and the incidence of owner-reported otitis in dogs at over 1 year of age. The multivariate logistic regression analysis study included data from 3,064 dogs and explored 26 different early life variables at four early life stages: prenatal, neonatal, postnatal, and puppyhood. We compared two feeding patterns, a non-processed meat-based diet (NPMD, raw) and an ultra-processed carbohydrate-based diet (UPCD, dry).

Results

We report that eating a NPMD diet significantly decreased the risk of otitis later in life, while eating a UPCD diet significantly increased the risk. This was seen in different life stages of mother or puppy: The maternal diet during pregnancy (p=0.011) and the puppies' diet from 2 to 6 months of age (p=0.019) were both significantly associated with otitis incidence later in life, whereas the puppies' first solid diet, was associated in the same way, but did not reach significance (p=0.072). Also, analyzing food ratios showed that when puppies were consuming >25% of their food as NPMD it significantly decreased their incidence of otitis later in life, while a ratio of >75% UPCD in their diet significantly increased their risk of otitis. Also, if the dog was born in the current family, was exposed to sunlight for more than 1 hour daily, and was raised on a dirt floor during puppyhood, there was a lower risk of otitis development later in life.

Discussion

The findings only suggest causality, and further studies are required. However, we propose that veterinarians, breeders, and owners can impact otitis risk by modifying factors such as diet and environment.

Physicochemical properties of otic products for Canine Otitis Externa: comparative analysis of marketed products

BACKGROUND

Otitis externa is a commonly diagnosed dermatological disorder in canines. The pathogens primarily involved in canine otitis externa (COE) include Staphylococcus pseudintermedius, Pseudomonas aeruginosa, Proteus mirabilis, and Malassezia pachydermatis. As COE tends to be superficial, medications delivered topically are often effective and practical in managing the condition. As such, there is a wide variety of approved topical products currently available in the market. The efficacy of topical dosage forms can be dependent on various factors such as the pharmacology of active constituents and the physicochemical properties of the formulation, including pH, viscosity, spreadability, and bio-adhesion. Currently, there is a lack of published literature available on the optimal properties of topical COE products. In this study, we compared the physicochemical properties of nine commercially available otic veterinarian products in Australia used clinically to manage COE.

RESULTS

Based on our comparative analysis, the pH (6.26 ± 0.04) of an aqueous-based product was similar to a healthy dog's external auditory canal. Products containing polymers exhibited higher viscosity and bio-adhesion. Spreadability was inversely related to viscosity and Osurnia ® a product with high viscosity demonstrated the lowest spreadability. Aqueous-based otic products showed better syringebility whereas oil-based systems required higher force to expel the products. Variability in droplet size was noted. Derm Otic, Baytril Otic, and Aurizon Ear Drops had the lower standard deviation which indicates they would give a more consistent dose.

CONCLUSIONS

Findings from this work provide considerations for industry researchers or formulation scientists working in the area of otic dosage formulations.

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.

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.

The Characterization of a Novel Phage, pPa_SNUABM_DT01, Infecting Pseudomonas aeruginosa

The bacterial genus Pseudomonas is a common causative agent of infections in veterinary medicine. In this study, we focused on Pseudomonas aeruginosa canine otitis externa isolates. Due to prolonged antibiotic treatment of otitis externa, antibiotic resistance is common and has become a major complication. Many alternatives to antibiotics have been studied, with bacteriophages emerging as the most promising alternatives. Here, we isolated and characterized a novel phage, pPa_SNUABM_DT01, by investigating its morphology, growth, lysis kinetics, and genomic characteristics. Phages have a vigorous capacity to eliminate bacterial cells through bacterial lysis. This capacity is dependent on the multiplicity of infection (MOI), but even at low MOIs, the phage successfully inhibited bacterial regrowth. The phage genome was 265,520 bp in size and comprised 312 putative open reading frames (ORFs). Comparative genome analysis demonstrated that the phage is a novel species in Myoviridae. The nucleotide similarity was moderately high compared with the Pseudomonas virus, Noxifer. However, a phylogenetic analysis and a dot plot indicated that pPa_SNUABM_DT01 is not closely related to the Phikzvirus or Noxifervirus genus but, instead, belongs to a novel one. The genome comparisons also indicate that the phage, pPa_SNUABM_DT01, could be a novel genus.

Frequency and predisposing factors for canine otitis externa in the UK - a primary veterinary care epidemiological view

BACKGROUND

Otitis externa is a commonly diagnosed disorder in dogs and can carry a high welfare impact on affected animals. This study aimed to report the prevalence and explore the role of breed and aural conformation as predisposing factors for canine otitis externa in the UK. The study used a cohort design of dogs under UK primary veterinary care at clinics participating in the VetCompass Programme during 2016. Risk factor analysis used multivariable logistic regression modelling.

RESULTS

The study included a random sample of 22,333 dogs from an overall population of 905,554 dogs under veterinary care in 2016. The one-year period prevalence of otitis externa was 7.30% (95% confidence interval [CI]: 6.97 to 7.65). Breed and ear carriage were the highest ranked risk factors. Compared with crossbred dogs, sixteen breed types showed increased odds, including: Basset Hound (odds ratio [OR] 5.87), Chinese Shar Pei (OR 3.44), Labradoodle (OR 2.95), Beagle (OR 2.54) and Golden Retriever (OR 2.23). Four breeds showed protection (i.e. reduced odds) of otitis externa: Chihuahua (OR 0.20), Border Collie (OR 0.34), Yorkshire Terrier (OR 0.49) and Jack Russell Terrier (OR 0.52). Designer breed types overall had 1.63 times the odds (95% CI 1.31 to 2.03) compared with crossbred dogs. Compared with breeds with erect ear carriage, breeds with pendulous ear carriage had 1.76 times the odds (95% CI 1.48 to 2.10) and breeds with V-shaped drop ear carriage had 1.84 times the odds (95% CI 1.53 to 2.21) of otitis externa.

CONCLUSIONS

Breed itself and breed-associated ear carriage conformation are important predisposing factors for canine otitis externa. Greater awareness of these associations for both predisposed and protected breeds could support veterinary practitioners to promote cautious and low-harm approaches in their clinical advice on preventive care for otitis externa, especially in predisposed breeds.

Evaluation of the ocular surface mycobiota in clinically normal horses

The eye is host to myriad bacterial, fungal, and viral organisms that likely influence ocular surface physiology in normal and diseased states. The ocular surface mycobiota of horses has not yet been described using NGS techniques. This study aimed to characterize the ocular surface fungal microbiota (mycobiota) in healthy horses in 2 environmental conditions (stalled versus pasture). Conjunctival swabs of both eyes were obtained from 7 adult stallions stabled in an open-air pavilion and 5 adult mares living on pasture. Genomic DNA was extracted from ocular surface swabs and sequenced using primers that target the Internal Transcribed Spacer 1 (ITS1) region of the fungal genome on an Illumina platform. Sequences were processed using Quantitative Insights Into Molecular Ecology (QIIME 2.0) and taxonomy assigned with the Findley et al. 2013 ITS1 database. The most abundant genera identified were Leptosphaerulina (22.7%), unclassified Pleosporaceae (17.3%), Cladosporium (16.2%), Alternaria (9.8%), unclassified Pleosporales (4.4%), unclassified Montagnulaceae (2.9%), Fusarium (2.5%), and Pestalotiopsis (1.4%). Fungal community composition (Jaccard, R = 0.460, p = 0.001) and structure (Bray-Curtis, R = 0.811, p = 0.001) were significantly different between pastured mares and stabled stallions. The ocular surface of pastured mares had significantly increased fungal species richness and diversity compared to stabled stallions (Shannon p = 0.0224, Chao1 p = 0.0118, Observed OTUs p = 0.0241). Relative abundances of Aspergillus (p = 0.005) and Alternaria spp. (p = 0.002) were significantly increased in the mycobiota of pastured mares. This is the first report to describe the mycobiota of the equine ocular surface. Environmental factors such as housing influence the composition, structure, and richness of the equine ocular surface mycobiota.

Rapid and real-time identification of fungi up to species level with long amplicon nanopore sequencing from clinical samples

The availability of long-read technologies, like Oxford Nanopore Technologies, provides the opportunity to sequence longer fragments of the fungal ribosomal operon, up to 6 Kb (18S-ITS1-5.8S-ITS2-28S) and to improve the taxonomy assignment of the communities up to species level and in real-time. We assess the applicability for taxonomic assignment of amplicons targeting a 3.5 Kb region (V3 18S-ITS1-5.8S-ITS2-28S D2) and a 6 Kb region (V1 18S-ITS1-5.8S-ITS2-28S D12) with the What's in my pot (WIMP) classifier. We used the ZymoBIOMICSTM mock community and different microbiological fungal cultures as positive controls. Long amplicon sequencing correctly identified Saccharomyces cerevisiae and Cryptococcus neoformans from the mock community and Malassezia pachydermatis, Microsporum canis and Aspergillus fumigatus from the microbiological cultures. Besides, we identified Rhodotorula graminis in a culture mislabelled as Candida spp. We applied the same approach to external otitis in dogs. Malassezia was the dominant fungal genus in dogs' ear skin, whereas Ma. pachydermatis was the main species in the healthy sample. Conversely, we identified a higher representation of Ma. globosa and Ma. sympodialis in otitis affected samples. We demonstrate the suitability of long ribosomal amplicons to characterize the fungal community of complex samples, either healthy or with clinical signs of infection.

Effect of an anti-inflammatory pomegranate otic treatment on the clinical evolution and microbiota profile of dogs with otitis externa

BACKGROUND

Canine otitis externa (OE) is a common disease characterised by inflammation of the epithelial tissue of the external ear canal. Secondary infections are frequent, and Malassezia pachydermatis and Staphylococcus pseudintermedius are routinely isolated and treated with antifungal and antibiotic compounds.

HYPOTHESIS/OBJECTIVES

To analyse the otitis ear microbiome before and after a treatment with prednisolone plus pomegranate or antimicrobial drugs ANIMALS: 15 dogs with nonpurulent OE.

METHODS AND MATERIALS

A 30 day, double-blinded, multicentre, randomized and controlled parallel-group (1:1) trial was conducted in 15 dogs with nonpurulent OE, following two different topical treatments (prednisolone plus pomegranate versus prednisolone plus antibiotic and antifungal drugs). On days (D)0, D15 and D30, serum and skin otic samples were collected, and clinical examination and microbiome analysis (bacteria and fungi) were performed. Results were compared with validated otitis clinical scores to assess the effectiveness of both treatments.

RESULTS

Nine bacterial and four fungal families were detected during the three time-points tested. An increase in fungal diversity (Shannon index) and composition was the most significant change observed after both treatments. At treatment D15 and D30, the reduction in clinical signs was statistically significant in both treatment groups (P ≤ 0.05). Prednisolone plus pomegranate cleanser treatment was able to control the clinical signs of otitis as well as the bacterial and fungal overgrowth.

CONCLUSIONS AND CLINICAL IMPORTANCE

Mild otitis cases associated with microbial overgrowth may be managed with topical antiseptic and anti-inflammatory agents without the need for antibiotic and/or antifungal compounds.

External ear canal mycobiome of some rabbit breeds

The genus Malassezia is part of the normal skin mycobiota of a wide range of warm-blooded animals. In this genus, M. cuniculi is the only species described from rabbits. However, Malassezia species are rarely studied in lagomorphs. In the present study, the presence of Malassezia was assessed in samples from the external ear canal of healthy rabbits of different breeds. Cytological and culture techniques, Sanger sequencing, and Next-generation sequencing (NGS) were used to describe the ear mycobiota in the samples. Although no growth was observed in the cultured plates, cytological examination revealed the presence of round cells similar to those of Malassezia yeasts. For metagenomics analysis, the D1/D2 domain of the large subunit of the ribosomal DNA (LSU rDNA) was PCR amplified and the resulting reads were mapped against a custom-made cured database of 26S fungal sequences. NGS analysis revealed that Basidiomycota was the most abundant phylum in all the samples followed by Ascomycota. Malassezia was the most common genus presenting the highest abundance in the external ear canal. Malassezia phylotype 131 and M. cuniculi were the main sequences detected in the external auditory canal of rabbits. The study included both lop-eared and erect-eared rabbits and no differences were observed in the results when comparing both groups. This is the first attempt to study the external ear canal mycobiome of rabbits of different breeds using NGS.

LAY SUMMARY

In the present study, the presence of Malassezia was assessed in samples from the external ear canal of healthy rabbits of different breeds. Cytological and culture techniques, Sanger sequencing, and Next-generation sequencing (NGS) were used to describe the ear mycobiota in the samples.

The use of multicomponent ear drops in the treatment of otitis of various etiologies in animals

OBJECTIVE

The objective of this study was to investigate the efficacy of newly developed multicomponent ear drops for the treatment of otitis caused by parasites, bacteria, and fungi in dogs, cats, ferrets, fancy rabbits, and foxes.

MATERIALS AND METHODS

A new drug for veterinary use was developed that contained levofloxacin hemihydrate (0.3%), clotrimazole (0.1%), dexamethasone sodium phosphate (0.1%), and moxidectin (0.01%). In the initial stage of otoacariasis (or the ear form of psoroptic scab), the drug was used twice with an interval of 5-7 days. When otoacariasis (psoroptic scab) was complicated by otitis of bacterial and/or fungal etiology, the drug was used as follows: instilled once a day, within 10-14 days in the ear canal for 2-5 drops of the drug. The study of therapeutic efficacy was performed on cats, dogs, ferrets, foxes, and fancy rabbits with ear pathology.

RESULTS

The recovery of cats, ferrets, dogs, and foxes after the double use of ear drops during otoacariasis was established. In the ear form of psoroptic scab in fancy rabbits after treatment, Psoroptes cuniculi mites were not detected. The specific (antimicrobial and antifungal) activity of the drug was confirmed in vivo using the following scheme of drug use: the drug was instilled once a day, within 10-14 days in the ear canal, 2-5 drops of the drug in animals with external otitis and otitis media.

CONCLUSION

The rational combination of active components developed in this study is effective and safe for use in animals with microbial diseases of the ears.

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.

The otic microbiota and mycobiota in a referral population of dogs in eastern USA with otitis externa

BACKGROUND

Canine otitis externa (OE) is a common inflammatory disease that is frequently complicated by secondary bacterial and/or yeast infections. The otic microbial population is more complex than appreciated by cytological methods and aerobic culture alone.

HYPOTHESIS/OBJECTIVES

Differences in bacterial and fungal populations of the external ear canal will correlate with specific cytological and culture-based definitions of bacterial and Malassezia otitis.

ANIMALS

Forty client-owned dogs; 30 with OE and 10 with healthy ears.

METHODS AND MATERIALS

Prospective study comparing cytological samples, aerobic bacterial cultures and culture-independent sequencing-based analyses of the external ear canal. Subjects with OE included 10 dogs with only cocci [≥25/high power field (HPF)] on cytological evaluation and culture of Staphylococcus spp.; 10 dogs with rods (≥25/HPF) and exclusive culture of Pseudomonas aeruginosa; 10 dogs with only yeast on cytological results morphologically compatible with Malassezia spp. (≥5/HPF).

RESULTS

Staphylococcus was the most abundant taxa across all groups. Ears cytologically positive for cocci had decreased diversity, and all types of OE were associated with decreased fungal diversity compared to controls.

CONCLUSIONS AND CLINICAL IMPORTANCE

Cytological and culture-based assessment of the ear canal is not predictive of the diverse microbiota of the ear canal in cases of Pseudomonas or Malassezia otitis. Less abundant bacterial taxa in cases of staphylococcal OE are worth scrutiny for future biological therapy.