Microbiomes

The skin is a complex ecosystem and is colonized by a wide variety of microorganisms, including bacteria, fungi, and viruses. The microbiome encompasses the full complement of microorganisms, their genes, and their metabolites. The normal skin microbiota is necessary for optimal skin fitness, modulating the innate immune response and preventing colonization of potentially pathogenic microorganisms.

Studies using sequencing of 16 S rRNA genes have revealed that the skin surfaces of humans and companion animals are inhabited by a highly diverse microbiota that was previously not appreciated by culture-based methods. Furthermore, there are topographic differences in the various skin surfaces, with the microbiota from similar skin locations of different people being more closely related than different skin locations from the same individual. Temperature, pH, moisture, environmental contact, and contact with mucous membranes are some of the factors that may influence the variability of bacterial abundance and distribution on the skin. In humans, Propionibacterium predominantly colonize the sebaceous areas, Staphylococcus and Corynebacterium are commonly found in moist areas, and gram-negative organisms are more likely to colonize dry skin areas such as the forearm or leg. The skin microbiota also changes with age, with infants having significantly different microbial populations than adults. Human skin also harbours a diverse fungal microbiome. The genus Malassezia is most abundant in all skin regions, with 11 of the 14 known Malassezia species being identified among skin sites.

The plantar heel is the most diverse site with higher representation of different fungal genera, including Malassezia, Aspergillus, Cryptococcus, Rhodotorula, and Epicoccum.

The Skin Microbiome in Healthy Dogs

The diversity of the skin microbiota in different cutaneous and mucocutaneous regions in healthy dogs has been demonstrated. Similar to humans, different skin sites from dogs are inhabited by a variable and unique microbiome, with significant individual variability between samples from different dogs and between different skin sites within the same dog. A large number of previously uncultured or rarely isolated microbes have been identified, demonstrating that the skin of dogs is inhabited by diverse microbial communities. Higher microbial diversity was observed in the haired skin (axilla, groin, periocular, pinna, dorsal nose, interdigital, lumbar) compared to mucosal surfaces or mucocutaneous junctions (lips, nose, ear, and conjunctiva). The nostril and conjunctiva showed the lowest, while the axilla and dorsal aspect of the nose showed highest microbial diversity. On average, around 300 different bacterial genera were identified on the canine dorsal nose. The most abundant phyla across all surfaces were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes (Rodrigues Hoffmann 2014).

The Skin Microbiome in Cutaneous Disease

The normal skin microbiota is necessary for optimal skin function, modulating the innate immune response and preventing colonization with potentially pathogenic microorganisms. In many skin conditions, it remains unclear if changes in the microbiome play a causal role in skin diseases or are rather the result of the disease. In humans with atopic dermatitis (AD) and psoriasis, the changes in the cutaneous microbiome have been proposed to be the result of an altered epidermal barrier function, Toll-like receptor 2 defects, decreases in antimicrobial peptides, and/or increased expression of extracellular matrix proteins (de Jongh 2005). These mechanisms are thought to be responsible for an increased abundance of Staphylococcus aureus and susceptibility to staphylococcal infections in AD patients.

Similar to humans, dogs develop AD with hypersensitivity to environmental allergens such as house dust mites and/or food allergens. Recurrent infections with Staphylococcus sp. are very common in AD dogs, and in some dogs bacterial products can also trigger lesions of AD, possibly due to an altered epidermal barrier function.

A marked reduction in microbial diversity is observed in children during AD flares, and it is proposed that these changes precede an increase in the severity of AD. The skin microbiome colonizing the haired skin of dogs with allergic skin disease also demonstrates a lower bacterial diversity when compared to the same skin sites (axilla, groin, and interdigital skin) of healthy dogs (Rodrigues Hoffmann 2014). Significant differences in bacterial taxa have been observed between allergic and healthy dogs, especially higher abundance of Betaproteobacteria in the skin of healthy dogs.

Using culture-based methods, the skin and nasal mucous membranes of atopic human patients and dogs are more often colonized with S. aureus and S. pseudintermedius, respectively, than healthy patients. Based on 16S rRNA pyrosequencing data, S. aureus markedly dominated affected skin regions, more commonly the antecubital and popliteal creases, in children with AD. Likewise, baseline and post flare samples from children with AD also had more abundance of S. aureus compared to the skin of healthy children. Allergen challenge in experimentally sensitized atopic dogs leads to bacterial dysbiosis with increased abundance of S. pseudintermedius at the site of lesion induction (Pierezan 2016).

The skin microbiota of atopic dogs has been longitudinally evaluated with parallel assessment of skin barrier function at disease flare, during antimicrobial therapy, and post-therapy. Sequencing of the bacterial 16S ribosomal RNA gene showed decreased bacterial diversity and increased proportions of Staphylococcus (S. pseudintermedius in particular) and Corynebacterium species compared with a cohort of healthy control dogs. Treatment restored bacterial diversity with decreased proportions of Staphylococcus species, concurrent with decreased canine atopic dermatitis severity. Skin barrier function, as measured by corneometry, pH, and transepidermal water loss also normalized with treatment. Bacterial diversity correlated with transepidermal water loss and pH level but not with corneometry results (Bradley 2016).

In cAD there is a predisposition to the development of coagulase-positive Staphylococcus species colonization and dermatitis as in AD. S. aureus is the primary coagulase-positive Staphylococcus species of human skin and mucosal sites. S. pseudintermedius is a skin and mucosal commensal in the dog and the most frequent pathogen isolated from dogs with skin or ear canal infections. Human S. pseudintermedius colonization is rare and primarily restricted to those with regular contact with dogs and cats. S. aureus is infrequently isolated from infection and carriage sites of dogs in clinical practice and in epidemiological surveys, and it is considered a comparatively infrequent canine pathogen. The dog may act as a potential vector of S. aureus, which raises zoonotic and anthropozoonotic concerns for potential transfer of pathogens, drug resistance, and genetic elements.

Microbiomes are often shared between dogs and humans, with pet owners having a more diverse microbiome than non-pet owners. Dogs that cohabit are also likely to have similar microbiomes. These concepts become very important in the context of antimicrobial resistance, where resistance genes can be spread from one bacteria to another and become established within the commensal population.

Biofilms

What is a Biofilm?

A bacterial biofilm is a complex, sessile community of bacteria embedded within a self-produced matrix of carbohydrates, proteins, and DNA (extracellular polymeric substance, EPS). Within a biofilm, bacteria have markedly altered metabolism, enhanced cell-to-cell communication, and are able to evade the host immune response and the effects of antimicrobials through their isolated metabolism along with physical and chemical protection of the biofilm matrix.

Biofilm formation is influenced by a number of factors including:

• Bacterial species:
• Environmental conditions: temperature, pH, oxygen concentration, iron availability
• Surface: rough versus smooth

The stages of biofilm formation progress from initial attachment to the surface, through a phase of maturation, to a final phase of dispersion. Once the biofilm has formed, it confers a number of survival advantages for the bacteria that can have significant effects on pathogenicity including:

• Creates a high density of bacteria
• Increased metabolic efficiency
• Evasion of host defenses such as phagocytosis
• Exchange of genes resulting in more virulent strains
• Increased production of toxins
• Protection against microbial agents
• Provides a nidus of infection that permits detachment allowing spread to other sites

How Are They Relevant?

Biofilms have a major impact on treatment and antimicrobial resistance, particularly in canine otitis externa. They are common and under-diagnosed, although they can be easily identified on otoscopy or cytology. Clinically, they form an adherent, thick, and slimy discharge that is often dark brown or black in both the external ear canal and middle ear cavity. On cytology they appear as variably thick veil-like material that may obscure bacteria and cells. Biofilms are clinically important as they inhibit cleaning, prevent penetration of antimicrobials and provide a protected reservoir of bacteria. Also, antimicrobials that require bacterial division will be less effective, as bacteria in biofilms are usually in a quiescent state. Biofilms may also enhance the development of antimicrobial resistance, especially in gram-negative bacteria that acquire stepwise resistance mutations to concentration-dependent antimicrobials.

Biofilm production by canine otitis isolates of P. aeruginosa is common and may play a role in the pathogenesis of disease. The MICs for biofilm-embedded bacteria differ from their planktonic counterparts, potentially leading to a lack of response to treatment. In one study, 40% of canine otic isolates of P. aeruginosa were classified as biofilm producers. Biofilm MICs for polymyxin B, neomycin, gentamicin, and enrofloxacin were significantly higher than for the planktonic form. If these medications are used for topical treatment of a Pseudomonas otitis, the concentration of the medication should be increased (Pye 2013).

N-acetyl cysteine (NAC) is a mucolytic with antibacterial and antioxidant properties. It is also otoprotective and can prevent chemotherapy induced hearing loss and contributes to detachment of biofilms associated with P. aeruginosa. Recently it has been demonstrated that NAC has an inhibitory effect in vivo against common pathogens isolated from canine otitis externa; S. pseudintermedius, Pseudomonas aeruginosa, Corynebacterium, and haemolytic Streptococcus. The product appears to be safe and well tolerated and has an inhibitory effect at a concentration of 1%; middle ear mucosal inflammation was reported at concentrations >2% and conductive hearing loss at 4% (May 2016). NAC could be incorporated as part of the ear cleaning routine if a biofilm is suspected.

References

1.  Bradley CW, Morris DO, Rankin SC, et al. Longitudinal evaluation of the skin microbiome and association with microenvironment and treatment in canine atopic dermatitis. J Invest Dermatol. 2016;136(6):1182–1190.

2.  de Jongh GJ, Zeeuwen PL, Kucharekova M, et al. High expression levels of keratinocyte antimicrobial proteins in psoriasis compared with atopic dermatitis. J Invest Dermatol. 2005;125(6):1163–1173.

3.  Hoffmann AR, Patterson AP, Diesel A, et al. The skin microbiome in healthy and allergic dogs. PloS One. 2014;9(1):e83197.

4.  May ER, Conklin KA, Bemis DA. Antibacterial effect of N-acetylcysteine on common canine otitis externa isolates. Vet Dermatol. 2016;27(3):188.

5.  Pierezan F, Olivry T, Paps JS, et al. The skin microbiome in allergen-induced canine atopic dermatitis. Vet Dermatol. 2016;27(5):332.

6.  Pye CC, Yu AA, Weese JS. Evaluation of biofilm production by Pseudomonas aeruginosa from canine ears and the impact of biofilm on antimicrobial susceptibility in vitro. Vet Dermatol. 2013;24(4):446.