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Vlasblom AA, Duim B, Patel S, Luiken REC, Crespo-Piazuelo D, Eckenberger J, Huseyin CE, Lawlor PG, Elend C, Wagenaar JA, Claesson MJ, Zomer AL. The developing pig respiratory microbiome harbors strains antagonistic to common respiratory pathogens. mSystems 2024:e0062624. [PMID: 39287382 DOI: 10.1128/msystems.00626-24] [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: 05/02/2024] [Accepted: 08/20/2024] [Indexed: 09/19/2024] Open
Abstract
In the global efforts to combat antimicrobial resistance and reduce antimicrobial use in pig production, there is a continuous search for methods to prevent and/or treat infections. Within this scope, we explored the relationship between the developing piglet nasal microbiome and (zoonotic) bacterial pathogens from birth until 10 weeks of life. The nasal microbiome of 54 pigs was longitudinally studied over 16 timepoints on 9 farms in 3 European countries (Germany, Ireland, and the Netherlands) using amplicon sequencing targeting the V3-V4 16S rRNA region as well as the tuf gene for its staphylococcal discrimination power. The piglets' age, the farm, and the litter affected the nasal microbiome, with piglets' age explaining 19% of the variation in microbial composition between samples. Stabilization of the microbiome occurred around 2 weeks post-weaning. Notably, while opportunistic pathogens were ubiquitously present, they did not cause disease. The piglet nasal microbiome often carried species associated with gut, skin, or vagina, which suggests that contact with the vaginal and fecal microbiomes shapes the piglet nasal microbiome. We identified bacterial co-abundance groups of species that were present in the nasal microbiomes in all three countries over time. Anti-correlation between these species and known bacterial pathogens identified species that might be exploited for pathogen reduction. Further experimental evidence is required to confirm these findings. Overall, this study advances our understanding of the piglet nasal microbiome, the factors influencing it, and its longitudinal development, providing insights into its role in health and disease. IMPORTANCE Our study on the nasal microbiota development in piglets across farms in three European countries found that the microbiomes developed similarly in all locations. Additionally, we observed that the colonization of porcine pathogens was either positively or negatively associated with the presence of other bacterial species. These findings enhance our knowledge of co-colonizing species in the nasal cavity and the identified microbial interactions that can be explored for the development of interventions to control pathogens in porcine husbandry.
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Affiliation(s)
- Abel A Vlasblom
- Faculty of Veterinary Medicine, Division of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Birgitta Duim
- Faculty of Veterinary Medicine, Division of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Shriram Patel
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
- SeqBiome Ltd., Cork, Ireland
| | - Roosmarijn E C Luiken
- Faculty of Veterinary Medicine, Division of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Daniel Crespo-Piazuelo
- Pig Development Department,Teagasc Animal & Grassland Research & Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Julia Eckenberger
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Chloe E Huseyin
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Peadar G Lawlor
- Pig Development Department,Teagasc Animal & Grassland Research & Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | | | - Jaap A Wagenaar
- Faculty of Veterinary Medicine, Division of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Marcus J Claesson
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Aldert L Zomer
- Faculty of Veterinary Medicine, Division of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
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Rigueira LL, Perecmanis S. Concerns about the use of antimicrobials in swine herds and alternative trends. Transl Anim Sci 2024; 8:txae039. [PMID: 38685989 PMCID: PMC11056889 DOI: 10.1093/tas/txae039] [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: 01/31/2024] [Accepted: 03/15/2024] [Indexed: 05/02/2024] Open
Abstract
Pig productivity in Brazil has advanced a lot in recent decades. Specialized breeds are more vulnerable to pathogens, which has boosted the use of antimicrobials by farmers. The selective pressure generated favors the emergence of resistant bacteria, which compromises the effectiveness of this treatment and limits therapeutic options. In addition to increasing costs and mortality rates in the production system, public awareness of this issue has increased. The authorities have imposed restrictive measures to control the use of antimicrobials and have banned their use as growth promoters. This literature review highlights biosecurity and animal welfare to prevent pig diseases. Hence, we describe alternatives to the use of antimicrobials in pig production for the selection of effective non-antibiotic feed additives that help maintain good health and help the pig resist disease when infection occurs.
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Affiliation(s)
- Luciana L Rigueira
- Department of Animal Health, Brasília University, 70910-900, Brasília, Brazil
- Secretary of Agriculture of Federal District, 70770-914, Brasília, Brazil
| | - Simone Perecmanis
- Department of Animal Health, Brasília University, 70910-900, Brasília, Brazil
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Martino L, Serrano B, Alomar J, Pérez L, Aragon V, Cobos A, Abarca ML, Yazdi Z, Soto E, Domingo M. Erysipelas with preferential brain and skin involvement in a Mediterranean bottlenose dolphin Tursiops truncatus. DISEASES OF AQUATIC ORGANISMS 2024; 157:31-43. [PMID: 38299848 DOI: 10.3354/dao03770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Infections by Erysipelothrix rhusiopathiae occur in domestic animals and cause the disease known as 'erysipelas'. The ubiquity of Erysipelothrix spp. makes infection possible in a wide range of vertebrates and invertebrates. Cetaceans are highly susceptible to erysipelas, especially those under human care. The number of cases documented in wild cetaceans is low, the pathogenesis is incompletely understood, and the full spectrum of lesions is not well defined. The possible serotypes and species of the genus that can cause disease are unknown. In October 2022, a common bottlenose dolphin Tursiops truncatus stranded in Vilassar de Mar (Catalonia) showing skin lesions consistent with 'diamond skin disease', a characteristic lesion of erysipelas shared by swine and cetaceans. Necropsy was performed following standardized procedures, and multiple samples were taken for histopathology and bacteriology. Erysipelothrix sp. grew in pure culture in many tissue samples. Genetic characterization by multi-locus sequence analysis identified the species as E. rhusiopathiae. Histologically, the main lesions were an intense suppurative vasculitis of leptomeningeal arteries and veins with abundant intramural Gram-positive bacilli and meningeal hemorrhages. Meningeal lesions were considered the cause of death. The affected skin showed moderate suppurative dermatitis. Herein we document a case of erysipelas in a Mediterranean common bottlenose dolphin with unusual lesions in the leptomeningeal vessels and marked skin tropism. To our knowledge, this is the first case of severe brain involvement in erysipelas in a cetacean. We also provide a review of available cases in wild cetaceans, to highlight the characteristics of the disease and improve future diagnosis.
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Affiliation(s)
- Laura Martino
- Servei de Diagnòstic de Patologia Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Bárbara Serrano
- Servei de Diagnòstic de Patologia Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Jaume Alomar
- Servei de Diagnòstic de Patologia Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Lola Pérez
- Facultat de Veterinària de Barcelona, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Virginia Aragon
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- IRTA Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
| | - Alex Cobos
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- IRTA Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
| | - Maria Lourdes Abarca
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Veterinary Mycology Group, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Zeinab Yazdi
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, California 95616, USA
| | - Esteban Soto
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, California 95616, USA
| | - Mariano Domingo
- Servei de Diagnòstic de Patologia Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- IRTA Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
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Li K, Pang S, Li Z, Ding X, Gan Y, Gan Q, Fang S. House ammonia exposure causes alterations in microbiota, transcriptome, and metabolome of rabbits. Front Microbiol 2023; 14:1125195. [PMID: 37250049 PMCID: PMC10213413 DOI: 10.3389/fmicb.2023.1125195] [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: 12/16/2022] [Accepted: 04/11/2023] [Indexed: 05/31/2023] Open
Abstract
Introduction Pollutant gas emissions in the current production system of the livestock industry have negative influences on environment as well as the health of farm staffs and animals. Although ammonia (NH3) is considered as the primary and harmful gas pollutant in the rabbit farm, less investigation has performed to determine the toxic effects of house ammonia exposure on rabbit in the commercial confined barn. Methods In this study, we performed multi-omics analysis on rabbits exposed to high and low concentration of house ammonia under similar environmental conditions to unravel the alterations in nasal and colonic microbiota, pulmonary and colonic gene expression, and muscular metabolic profile. Results and discussion The results showed that house ammonia exposure notably affected microbial structure, composition, and functional capacity in both nasal and colon, which may impact on local immune responses and inflammatory processes. Transcriptome analysis indicated that genes related to cell death (MCL1, TMBIM6, HSPB1, and CD74) and immune response (CDC42, LAMTOR5, VAMP8, and CTSB) were differentially expressed in the lung, and colonic genes associated with redox state (CAT, SELENBP1, GLUD1, and ALDH1A1) were significantly up-regulated. Several key differentially abundant metabolites such as L-glutamic acid, L-glutamine, L-ornithine, oxoglutaric acid, and isocitric acid were identified in muscle metabolome, which could denote house ammonia exposure perturbed amino acids, nucleotides, and energy metabolism. In addition, the widespread and strong inter-system interplay were uncovered in the integrative correlation network, and central features were confirmed by in vitro experiments. Our findings disclose the comprehensive evidence for the deleterious effects of house ammonia exposure on rabbit and provide valuable information for understanding the underlying impairment mechanisms.
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Arnold HK, Hanselmann R, Duke SM, Sharpton TJ, Beechler BR. Chronic clinical signs of upper respiratory tract disease associate with gut and respiratory microbiomes in a cohort of domestic felines. PLoS One 2022; 17:e0268730. [PMID: 36454958 PMCID: PMC9714858 DOI: 10.1371/journal.pone.0268730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022] Open
Abstract
Feline upper respiratory tract disease (FURTD), often caused by infections etiologies, is a multifactorial syndrome affecting feline populations worldwide. Because of its highly transmissible nature, infectious FURTD is most prevalent anywhere cats are housed in groups such as animal shelters, and is associated with negative consequences such as decreasing adoption rates, intensifying care costs, and increasing euthanasia rates. Understanding the etiology and pathophysiology of FURTD is thus essential to best mitigate the negative consequences of this disease. Clinical signs of FURTD include acute respiratory disease, with a small fraction of cats developing chronic sequelae. It is thought that nasal mucosal microbiome changes play an active role in the development of acute clinical signs, but it remains unknown if the microbiome may play a role in the development and progression of chronic clinical disease. To address the knowledge gap surrounding how microbiomes link to chronic FURTD, we asked if microbial community structure of upper respiratory and gut microbiomes differed between cats with chronic FURTD signs and clinically normal cats. We selected 8 households with at least one cat exhibiting chronic clinical FURTD, and simultaneously collected samples from cohabitating clinically normal cats. Microbial community structure was assessed via 16S rDNA sequencing of both gut and nasal microbiome communities. Using a previously described ecophylogenetic method, we identified 136 and 89 microbial features within gut and nasal microbiomes respectively that significantly associated with presence of active FURTD clinical signs in cats with a history of chronic signs. Overall, we find that nasal and gut microbial community members associate with the presence of chronic clinical course, but more research is needed to confirm our observations.
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Affiliation(s)
- Holly Kristin Arnold
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
| | - Rhea Hanselmann
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, United States of America
| | - Sarah M. Duke
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
| | - Thomas J. Sharpton
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
| | - Brianna R. Beechler
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
- Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon, United States of America
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Blanco-Fuertes M, Correa-Fiz F, López-Serrano S, Sibila M, Aragon V. Sow vaccination against virulent Glaesserella parasuis shapes the nasal microbiota of their offspring. Sci Rep 2022; 12:3357. [PMID: 35233006 PMCID: PMC8888576 DOI: 10.1038/s41598-022-07382-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/14/2022] [Indexed: 01/08/2023] Open
Abstract
Glaesserella parasuis is the etiological agent of Glässer's disease, a common pathology in the pork industry with higher prevalence in the postweaning period. Vaccination is one of the strategies to control this disease. Here, we investigated the effect that sow vaccination against virulent strains of G. parasuis had in the nasal microbiota of their offspring. Nasal swabs from fifteen days-old piglets from vaccinated (vs-P, n = 11) and unvaccinated sows (cs-P, n = 11) were obtained and DNA was extracted for 16S amplicon sequencing. Microbiota composition was different, with lower diversity in vs-P, and a strong clustering of the groups in beta diversity analysis. Among the 1509 sequences associated to either study group, all the sequences classified as G. parasuis (10 ASVs) had lower relative abundance in the vs-P group. A list of 32 inferred metabolic pathways were statistically different between groups. A distinctive structure of the two microbial networks was detected, with modules in the cs-P not conserved in the vs-P network. In conclusion, vaccination of the sows had a large effect in the microbiota composition of their offspring that went beyond the effect on the targeted pathogen. The mechanisms underneath these changes may include alteration of the microbiota network due to the elimination of the targeted pathogen and/or immunological changes.
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Affiliation(s)
- Miguel Blanco-Fuertes
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Barcelona, Spain
| | - Florencia Correa-Fiz
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Barcelona, Spain.
| | - Sergi López-Serrano
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Barcelona, Spain
| | - Marina Sibila
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Barcelona, Spain
| | - Virginia Aragon
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Barcelona, Spain.
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