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Domrazek K, Jurka P. Application of Next-Generation Sequencing (NGS) Techniques for Selected Companion Animals. Animals (Basel) 2024; 14:1578. [PMID: 38891625 PMCID: PMC11171117 DOI: 10.3390/ani14111578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Next-Generation Sequencing (NGS) techniques have revolutionized veterinary medicine for cats and dogs, offering insights across various domains. In veterinary parasitology, NGS enables comprehensive profiling of parasite populations, aiding in understanding transmission dynamics and drug resistance mechanisms. In infectious diseases, NGS facilitates rapid pathogen identification, characterization of virulence factors, and tracking of outbreaks. Moreover, NGS sheds light on metabolic processes by elucidating gene expression patterns and metabolic pathways, essential for diagnosing metabolic disorders and designing tailored treatments. In autoimmune diseases, NGS helps identify genetic predispositions and molecular mechanisms underlying immune dysregulation. Veterinary oncology benefits from NGS through personalized tumor profiling, mutation analysis, and identification of therapeutic targets, fostering precision medicine approaches. Additionally, NGS plays a pivotal role in veterinary genetics, unraveling the genetic basis of inherited diseases and facilitating breeding programs for healthier animals. Physiological investigations leverage NGS to explore complex biological systems, unraveling gene-environment interactions and molecular pathways governing health and disease. Application of NGS in treatment planning enhances precision and efficacy by enabling personalized therapeutic strategies tailored to individual animals and their diseases, ultimately advancing veterinary care for companion animals.
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Affiliation(s)
- Kinga Domrazek
- Institute of Veterinary Medicine, Warsaw University of Life Sciences—SGGW, Nowoursynowska 159c, 02-776 Warsaw, Poland;
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Cain CL, White E, Citron LE, Zheng Q, Morris DO, Grice EA, Bradley CW. Longitudinal evaluation of the cutaneous and rectal microbiota of German shepherd dogs with perianal fistulas undergoing therapy with ciclosporin and ketoconazole. Vet Dermatol 2024. [PMID: 38616572 DOI: 10.1111/vde.13249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/18/2024] [Accepted: 03/27/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND Perianal fistulas are painful ulcers or sinus tracts that disproportionately affect German shepherd dogs and are proposed as a spontaneous animal model of fistulising Crohn's disease. OBJECTIVES To characterise the rectal and cutaneous microbiota in German shepherd dogs with perianal fistulas and to investigate longitudinal shifts with lesion resolution during immunomodulatory therapy. ANIMALS Eleven German shepherd dogs with perianal fistulas and 15 healthy German shepherd dogs. MATERIALS AND METHODS Affected dogs were evaluated and swabbed at three visits, 30 days apart, while undergoing treatment with ciclosporin and ketoconazole. Healthy German shepherd dogs were contemporaneously sampled. Sites included the rectum, perianal skin and axilla. The microbiome was evaluated following sequencing of the V4 hypervariable region of the 16S ribosomal RNA (rRNA) gene. RESULTS Alpha diversity was not significantly different between healthy and affected dogs at each of the three body sites (p > 0.5), yet rectal and perianal beta diversities from affected dogs differed significantly from those of healthy dogs at Day 0 (p = 0.004). Rectal and perianal relative abundance of Prevotella spp. increased and perianal Staphylococcus spp. relative abundance decreased in affected dogs over time, coincident with lesion resolution. CONCLUSIONS AND CLINICAL RELEVANCE Changes in lesional cutaneous and rectal microbiota occur in German shepherd dogs with perianal fistulas and shift over time with lesion resolution during immunomodulatory therapy. Further investigations of the role of cutaneous and enteric microbiota in the pathogenesis of perianal fistulas, and whether manipulation of microbial populations may ameliorate disease, are needed.
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Affiliation(s)
- Christine L Cain
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ellen White
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lindsey E Citron
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Qi Zheng
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Daniel O Morris
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elizabeth A Grice
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Charles W Bradley
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Wells JR, Hillier A, Holland R, Mwacalimba K, Noli C, Panter C, Tatlock S, Wright A. Development and validation of a questionnaire to assess owner and canine quality-of-life and treatment satisfaction in canine allergic dermatitis. Vet Dermatol 2024. [PMID: 38361109 DOI: 10.1111/vde.13242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 12/06/2023] [Accepted: 01/28/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND Animal and owner quality-of-life (QoL) is pivotal in treatment decisions. Accurate measurement of owner-reported QoL and treatment satisfaction (TS) supports disease burden and treatment benefit evaluation. OBJECTIVES Develop and evaluate an owner-completed canine dermatitis QoL and TS questionnaire (CDQoL-TSQ) in allergic dogs. MATERIALS AND METHODS The CDQoL-TSQ was drafted following review of existing measures and expert input. Content validity was assessed through interviews with owners of allergic dogs. Psychometric properties of the QoL domains (Canine QoL, Owner QoL) were evaluated. Score interpretation was derived. RESULTS Twenty dog owners were interviewed. Item wording was amended following the first 10 interviews. Data from 211 owners were used in the psychometric evaluation. The Canine QoL domain demonstrated strong internal consistency (α = 0.89), test-retest reliability (ICC2,1 = 0.844), moderate convergent validity (r = 0.41) and moderate-high known-groups validity (effect size 0.37-0.64). The Owner QoL domain demonstrated strong internal consistency (α = 0.73), high convergent validity (r = 0.63) and moderate-high known-groups validity (0.43-0.63). Test-retest reliability approached moderate strength (ICC2,1 = 0.490). Group-level interpretation analysis showed minimal important difference of 7.0-13.6 points for dogs and 13.0-13.6 for owners. For individual dogs a change of 6.3 or 12.5 points for dogs, and 12.5 or 18.8 for owners indicates a response. CONCLUSIONS AND CLINICAL RELEVANCE The CDQOL-TSQ is a two-part assessment to evaluate QoL and TS in canine allergic dermatitis. The QoL questionnaire demonstrated validity and reliability, and interpretation of scores was derived, making it suitable for use in research and practice. The TS module is suitable for clinical setting use to improve owner-veterinarian communication.
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Affiliation(s)
- J R Wells
- Patient-Centered Outcomes, Adelphi Values Ltd, Bollington, UK
- Clinical Outcomes Assessment Department, Sanofi, UK
| | | | | | | | - C Noli
- Servizi Dermatologici Veterinari, Peveragno, Italy
| | - C Panter
- Patient-Centered Outcomes, Adelphi Values Ltd, Bollington, UK
| | - S Tatlock
- Patient-Centered Outcomes, Adelphi Values Ltd, Bollington, UK
| | - A Wright
- Zoetis, Parsippany, New Jersey, USA
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Santoro D, Saridomichelakis M, Eisenschenk M, Tamamoto-Mochizuki C, Hensel P, Pucheu-Haston C. Update on the skin barrier, cutaneous microbiome and host defence peptides in canine atopic dermatitis. Vet Dermatol 2024; 35:5-14. [PMID: 37990608 DOI: 10.1111/vde.13215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023]
Abstract
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.
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Affiliation(s)
- Domenico Santoro
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | | | | | - Chie Tamamoto-Mochizuki
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | | | - Cherie Pucheu-Haston
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
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Rodrigues Hoffmann A, Ramos MG, Walker RT, Stranahan LW. 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. Vet Pathol 2023; 60:812-828. [PMID: 37222139 DOI: 10.1177/03009858231173715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
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.
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Secker B, Shaw S, Atterbury RJ. Pseudomonas spp. in Canine Otitis Externa. Microorganisms 2023; 11:2650. [PMID: 38004662 PMCID: PMC10673570 DOI: 10.3390/microorganisms11112650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/22/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Canine otitis externa (OE) is a commonly diagnosed condition seen in veterinary practice worldwide. In this review, we discuss the mechanisms of the disease, with a particular focus on the biological characteristics of Pseudomonas aeruginosa and the impact that antibiotic resistance has on successful recovery from OE. We also consider potential alternatives to antimicrobial chemotherapy for the treatment of recalcitrant infections. P. aeruginosa is not a typical constituent of the canine ear microbiota, but is frequently isolated from cases of chronic OE, and the nature of this pathogen often makes treatment difficult. Biofilm formation is identified in 40-95% of P. aeruginosa from cases of OE and intrinsic and acquired antibiotic resistance, especially resistance to clinically important antibiotics, highlights the need for alternative treatments. The role of other virulence factors in OE remains relatively unexplored and further work is needed. The studies described in this work highlight several potential alternative treatments, including the use of bacteriophages. This review provides a summary of the aetiology of OE with particular reference to the dysbiosis that leads to colonisation by P. aeruginosa and highlights the need for novel treatments for the future management of P. aeruginosa otitis.
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Affiliation(s)
- Bailey Secker
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire LE12 5RD, UK; (B.S.); (S.S.)
- School of Biosciences, University of Nottingham, College Road, Sutton Bonington, Leicestershire LE12 5RD, UK
| | - Stephen Shaw
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire LE12 5RD, UK; (B.S.); (S.S.)
| | - Robert J. Atterbury
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire LE12 5RD, UK; (B.S.); (S.S.)
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Discepolo D, Kelley R, Watson A, Perry E. Impacts to canine dermal microbiota associated with repeated bathing. Front Vet Sci 2023; 10:1204159. [PMID: 37621867 PMCID: PMC10446845 DOI: 10.3389/fvets.2023.1204159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/18/2023] [Indexed: 08/26/2023] Open
Abstract
Introduction Working dogs routinely operate in environmental conditions which may necessitate daily bathing to remove contaminants or soilage. The impacts of frequent or repeated bathing on the canine dermal microbiota are unknown. The objective of this study was to characterize changes in canine dermal microbial populations following repeated daily bathing. Methods Labrador retrievers (n = 16) were bathed daily using a dilute dish detergent solution (1.6% detergent solution) over the course of 14 days. Dermal microbial DNA was collected via sterile swabs (n = 142) taken at days 0, 7, 14, 16, 21, 28, 35, 42, and 49 and analyzed for alpha diversity, beta diversity and relative abundance to assess changes in the dermal microbiota via 16 s sequencing. Results Results indicate that daily bathing significantly increased Shannon diversity, Chao1, and several rare amplicon sequence variants. Although typically reported in highest abundance, relative abundance was decreased in the phyla Actinobacteria, Firmicutes, and Proteobacteria (p < 0.05). Conclusion Repeated daily bathing with dilute dish detergent significantly reduced normal healthy dermal microbial taxa and created significant changes in the dermal microbiota of canines. Disruption to the canine dermal microbiota may cause negative impacts to canine dermal health and require further investigation.
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Affiliation(s)
- Dakota Discepolo
- Department of Animal Science, Food and Nutrition, Southern Illinois University, Carbondale, IL, United States
| | - Russell Kelley
- Royal Canin USA, Pet Heath Nutrition Center, Lewisburg, OH, United States
| | - Adrian Watson
- Royal Canin USA, Pet Heath Nutrition Center, Lewisburg, OH, United States
| | - Erin Perry
- Department of Animal Science, Food and Nutrition, Southern Illinois University, Carbondale, IL, United States
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Horsman S, Meler E, Mikkelsen D, Mallyon J, Yao H, Magalhães RJS, Gibson JS. Nasal microbiota profiles in shelter dogs with dermatological conditions carrying methicillin-resistant and methicillin-sensitive Staphylococcus species. Sci Rep 2023; 13:4844. [PMID: 36964169 PMCID: PMC10039040 DOI: 10.1038/s41598-023-31385-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/10/2023] [Indexed: 03/26/2023] Open
Abstract
Dermatological conditions may be complicated by Staphylococcus spp. infections influencing skin and nasal microbiota. We investigated the associations between the resident nasal microbiota of shelter dogs with and without dermatological conditions carrying methicillin-resistant and -sensitive Staphylococcus spp. Nasal sampling of 16 dogs with and 52 without dermatological conditions were performed upon shelter admission (baseline), and then bi-weekly until discharge (follow-up). All samples were cultured for Staphylococcus spp., while 52 samples underwent microbiota analysis. Two elastic net logistic regression (ENR) models (Model 1-baseline samples; Model 2-follow-up samples) were developed to identify predictive associations between dermatological conditions and the variables: signalment, antimicrobial treatment, and nasal microbial genera. Follow-up nasal samples of dogs with dermatological conditions had decreased microbiota diversity and abundance compared to dogs without dermatological conditions. Our ENR models identified predictive differences in signalment and nasal microbial genera between baseline and follow-up samples. Co-occurrence networks showed nasal microbial genera were more dissimilar when comparing dogs with and without dermatological conditions at follow-up. Overall, this study is the first to investigate Staphylococcus spp. carriage effects on nasal microbial genera in a canine animal shelter population, and ultimately reveals the importance of investigating decolonisation and probiotic therapies for restoring nasal microbiota.
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Affiliation(s)
- Sara Horsman
- School of Veterinary Science, The University of Queensland, Gatton, QLD, 4343, Australia.
| | - Erika Meler
- School of Veterinary Science, The University of Queensland, Gatton, QLD, 4343, Australia
| | - Deirdre Mikkelsen
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - John Mallyon
- School of Veterinary Science, The University of Queensland, Gatton, QLD, 4343, Australia
| | - Hong Yao
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Ricardo J Soares Magalhães
- School of Veterinary Science, The University of Queensland, Gatton, QLD, 4343, Australia
- Children Health and Environment Program, Child Health Research Centre, The University of Queensland, South Brisbane, QLD, 4101, Australia
| | - Justine S Gibson
- School of Veterinary Science, The University of Queensland, Gatton, QLD, 4343, Australia
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Rojas-Gätjens D, Valverde-Madrigal KS, Rojas-Jimenez K, Pereira R, Avey-Arroyo J, Chavarría M. Antibiotic-producing Micrococcales govern the microbiome that inhabits the fur of two- and three-toed sloths. Environ Microbiol 2022; 24:3148-3163. [PMID: 35621042 DOI: 10.1111/1462-2920.16082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/20/2022] [Accepted: 05/20/2022] [Indexed: 11/30/2022]
Abstract
Sloths have a dense coat on which insects, algae, and fungi coexist in a symbiotic relationship. This complex ecosystem requires different levels of control, however, most of these mechanisms remain unknown. We investigated the bacterial communities inhabiting the hair of two- (Choloepus Hoffmani) and three-toed (Bradypus variegatus) sloths and evaluated their potential for producing antibiotic molecules capable of exerting control over the hair microbiota. The analysis of 16S rRNA amplicon sequence variants (ASVs) revealed that the communities in both host species are dominated by Actinobacteriota and Firmicutes. The most abundant genera were Brevibacterium, Kocuria/Rothia, Staphylococcus, Rubrobacter, Nesterenkonia, and Janibacter. Furthermore, we isolated nine strains of Brevibacterium and Rothia capable of producing substances that inhibited the growth of common mammalian pathogens. The analysis of the biosynthetic gene clusters (BCGs) of these nine isolates suggests that the pathogen-inhibitory activity could be mediated by the presence of siderophores, terpenes, beta-lactones, Type III polyketide synthases (T3PKS), ribosomally synthesized, and post-translationally modified peptides (RiPPs), non-alpha poly-amino acids (NAPAA) like e-Polylysin, ectoine or nonribosomal peptides (NRPs). Our data suggest that Micrococcales that inhabit sloth hair could have a role in controlling microbial populations in that habitat, improving our understanding of this highly complex ecosystem. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica
| | | | - Keilor Rojas-Jimenez
- Escuela de Biología, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Reinaldo Pereira
- Laboratorio Nacional de Nanotecnología (LANOTEC), CeNAT-CONARE, 1174-1200, San José, Costa Rica
| | | | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica
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