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McPherson A, Tranter B, Phipps A, Laven R, House J, Zadoks RN, Rowe S. Etiology and epidemiology of digital dermatitis in Australian dairy herds. J Dairy Sci 2024; 107:5924-5941. [PMID: 38331178 DOI: 10.3168/jds.2023-24258] [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: 09/29/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
Bovine digital dermatitis (BDD) is an important cause of lameness in dairy cows worldwide. However, very little is known about this disease in Australian herds, which are predominantly managed on pasture. The primary objectives of this cross-sectional study were to describe the presence and prevalence of BDD in Australian dairy herds and to characterize the microbiota of healthy skin and M4 lesions of BDD-affected, pasture-managed cows. Cows from 71 dairy herds were examined at milking time to identify the presence of BDD lesions. True prevalence was estimated using Bayesian methods with informative priors for sensitivity and specificity. Biopsy samples (n = 60) were collected from cows with and without BDD lesions in 7 pasture-based herds. The microbiota in the superficial and deep strata of each tissue biopsy were characterized via sequencing of the V3-V4 region of the bacterial ribosomal RNA gene. Lesions were detected in 1,817 (11.5%) of 15,813 cows and in 68 of 71 (95.8%) herds. The median herd-level apparent and true prevalences of BDD were 8.5% and 18.1%, respectively, but prevalences varied considerably between farms. On farms with BDD, M4 lesions accounted for 70% to 100% of all lesions (interquartile range = 95.1%-100%, median = 100%); M2 lesions (i.e., large ulcerative lesions) were observed at low prevalence (<2.2%) in the few herds (7/71, 9.9%) where they were found. There was a significant difference in the composition of the microbiota between healthy skin and M4 lesions but not between superficial and deep tissue layers. Several gut- and effluent-associated bacterial taxa, including Lentimicrobium and Porphyromonas, which have previously been associated with BDD, were abundant in BDD lesions but not in control biopsies. Our study supports the idea that such taxa are involved in, although possibly not essential to, lesion development and persistence in pasture-managed cows in Australia. Our results also suggest that Dichelobacter may contribute to the disease process. We conclude that BDD is likely to occur in most Australian dairy farms, but that further studies are needed to identify its effect on cow welfare and productivity. Further investigation of the etiology of BDD in Australian dairy herds is also necessary to inform prevention and control strategies.
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Affiliation(s)
- Andrew McPherson
- Sydney School of Veterinary Science, University of Sydney, Camden, New South Wales, 2570, Australia
| | - Bill Tranter
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, 4810, Australia; Tableland Veterinary Service, Malanda, Queensland, 4885, Australia
| | - Ash Phipps
- Rochester Veterinary Practice, Rochester, Victoria, 3561, Australia
| | - Richard Laven
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North 4474, New Zealand
| | - John House
- Sydney School of Veterinary Science, University of Sydney, Camden, New South Wales, 2570, Australia
| | - Ruth N Zadoks
- Sydney School of Veterinary Science, University of Sydney, Camden, New South Wales, 2570, Australia
| | - Sam Rowe
- Sydney School of Veterinary Science, University of Sydney, Camden, New South Wales, 2570, Australia.
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Wong NST, Malmuthuge N, Gellatly D, Nordi WM, Alexander TW, Ortega-Polo R, Janzen E, Jelinski M, Schwartzkopf-Genswein K. Characterization of the Hoof Bacterial Communities of Active Digital Dermatitis Lesions in Feedlot Cattle. Microorganisms 2024; 12:1470. [PMID: 39065237 PMCID: PMC11278616 DOI: 10.3390/microorganisms12071470] [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: 05/25/2024] [Revised: 07/03/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Digital dermatitis (DD) is a costly hoof infection, causing lameness and pain in feedlot cattle. DD lesions can develop nonlinearly through a series of clinical stages, which can be classified by Dopfer's M-stage scoring system. This widely adopted lesion scoring system recognizes five DD stages, where M1 (early lesion), M2 (acute ulcerative lesion), and M4.1 (chronic proliferative lesion with new developing lesion) are considered active but separate stages of the disease. This study assessed the skin surface microbiota of the active DD lesions of feedlot cattle. The DD lesions from three commercial feedlots were swabbed and then scored according to Dopfer's M-stage scoring system. Swab samples were collected from 12 M2- and 15 M4.1-stage lesions. A total of 21 control swab samples from healthy contralateral feet (DD control) were classified as stage M0. An additional six skin swabs (M0) were collected from completely healthy (CH control) cattle with no lesions. The bacterial communities of active DD lesions (M2 and M4.1) and healthy skin (M0) were profiled using 16S amplicon sequencing. Diversity analyses showed that the hoof bacterial communities of M2 and M4.1 lesions were each distinct from those of M0 skin. However, the bacterial communities between the two active lesion stages were not different from each other. A significant increase in the relative abundance of Spirochaetota and Fusobacteriota and an overall decrease in bacterial diversity contributed to the altered bacterial communities in M2 and M4.1 lesions compared to those of healthy skin (M0). Although stages M2 and M4.1 are considered clinically different stages, the lesion-associated bacterial community is similar between the two active stages.
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Affiliation(s)
- Nicholas S. T. Wong
- Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5C9, Canada; (N.S.T.W.); (K.S.-G.)
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (N.M.); (T.W.A.); (R.O.-P.)
| | - Nilusha Malmuthuge
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (N.M.); (T.W.A.); (R.O.-P.)
| | - Désirée Gellatly
- Technology Access Centre for Livestock, Olds College of Agriculture & Technology, Olds, AB T4H 1R6, Canada
| | - Wiolene M. Nordi
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (N.M.); (T.W.A.); (R.O.-P.)
| | - Trevor W. Alexander
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (N.M.); (T.W.A.); (R.O.-P.)
| | - Rodrigo Ortega-Polo
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (N.M.); (T.W.A.); (R.O.-P.)
| | - Eugene Janzen
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
| | - Murray Jelinski
- Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5C9, Canada; (N.S.T.W.); (K.S.-G.)
| | - Karen Schwartzkopf-Genswein
- Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5C9, Canada; (N.S.T.W.); (K.S.-G.)
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (N.M.); (T.W.A.); (R.O.-P.)
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Wong NST, Malmuthge N, Gellatly D, Nordi WM, Alexander TW, Ortega Polo R, Janzen E, Schwartzkopf-Genswein K, Jelinski M. Characterization of the hoof bacterial communities in feedlot cattle affected with digital dermatitis, foot rot or both using a surface swab technique. Anim Microbiome 2024; 6:2. [PMID: 38254160 PMCID: PMC10804539 DOI: 10.1186/s42523-023-00277-1] [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: 05/17/2023] [Accepted: 10/20/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Lameness is defined as altered or abnormal gait due to dysfunction of the locomotor system, and is a health issue of feedlot cattle, having major economic, labour, and welfare implications. Digital dermatitis (DD-a lesion of the plantar surface of the foot) and foot rot (FR-affects the interdigital cleft) are common infectious causes of lameness in feedlots. These hoof lesions can occur alone or in combination (DD + FR) in the same hoof. A total of 208 hoof swabs were collected from three commercial feedlots located in southern Alberta. Every lesion sample was matched with a corresponding control skin sample taken from a healthy contralateral foot. Control skin samples were also collected from cattle with no lesion on any feet. Bacterial communities of three types of hoof lesions (DD, DD + FR, FR) and healthy skin were profiled using 16S amplicon sequencing. RESULTS Alpha diversity analysis revealed a lower bacterial diversity on DD and FR lesions compared to control skin. Beta diversity analysis showed that bacterial communities of DD, FR, and DD + FR lesions were distinct from those of the control skin. While the impact of feedlot was minimal, lesion type contributed to 22% of the variation observed among bacterial communities (PERMANOVA-R = 0.22, P < 0.01). Compared to the corresponding control skin, there were 11, 12, and 3 differentially abundant (DA) bacterial genera in DD, DD + FR, and FR lesions, respectively. CONCLUSIONS The bacterial community description of a DD + FR lesion is a novel finding. Not only did lesions lead to altered bacterial communities when compared to healthy skin, but the composition of those communities also differed depending on the hoof lesion. The 16S amplicon sequencing of surface swabs has significant value as a research tool in separating different hoof lesions and can provide additional insights to the polybacterial etiology of DD and FR in feedlot cattle.
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Affiliation(s)
- Nicholas S T Wong
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Nilusha Malmuthge
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Désirée Gellatly
- Technology Access Centre for Livestock, Olds College of Agriculture and Technology, Olds, Canada
| | - Wiolene M Nordi
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Trevor W Alexander
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Rodrigo Ortega Polo
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Eugene Janzen
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Karen Schwartzkopf-Genswein
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada.
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada.
| | - Murray Jelinski
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
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Bay V, Gillespie A, Ganda E, Evans NJ, Carter SD, Lenzi L, Lucaci A, Haldenby S, Barden M, Griffiths BE, Sánchez-Molano E, Bicalho R, Banos G, Darby A, Oikonomou G. The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions. MICROBIOME 2023; 11:4. [PMID: 36624507 PMCID: PMC9830885 DOI: 10.1186/s40168-022-01440-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Bovine Digital Dermatitis (BDD) is a prevalent infectious disease, causing painful foot skin lesions and lameness in cattle. We describe herein the bovine foot skin microbiota and its associations with BDD using 16S rRNA gene amplicon and shotgun metagenomic sequencing on samples from 259 dairy cows from three UK dairy farms. RESULTS We show evidence of dysbiosis, and differences in taxonomy and functional profiles in the bovine foot skin microbiome of clinically healthy animals that subsequently develop BDD lesions, compared to those that do not. Our results suggest that taxonomical and functional differences together with alterations in ecological interactions between bacteria in the normal foot skin microbiome may predispose an animal to develop BDD lesions. Using genome-wide association and regional heritability mapping approaches, we provide first evidence for interactions between host genotype and certain members of the foot skin microbiota. We show the existence of significant genetic variation in the relative abundance of Treponema spp. and Peptoclostridium spp. and identify regions in the bovine genome that explain a significant proportion of this variation. CONCLUSIONS Collectively this work shows early changes in taxonomic and functional profiles of the bovine foot-skin microbiota in clinically healthy animals which are associated with subsequent development of BDD and could be relevant to prevention of disease. The description of host genetic control of members of the foot skin microbiota, combined with the association of the latter with BDD development offer new insights into a complex relationship that can be exploited in selective breeding programmes. Video Abstract.
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Affiliation(s)
- V Bay
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Faculty of Agriculture, Ege University, İzmir, Turkey
| | - A Gillespie
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - E Ganda
- Department of Animal Science, Penn State University, State College, PA, USA
| | - N J Evans
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - S D Carter
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - L Lenzi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - A Lucaci
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - S Haldenby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - M Barden
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - B E Griffiths
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | | | - R Bicalho
- FERA Diagnostics and Biologicals, College Station, TX, USA
| | - G Banos
- Scotland's Rural College (SRUC), Easter Bush, Midlothian, UK
| | - A Darby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - G Oikonomou
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
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YİĞİTARSLAN K, KIRBAŞ İ. Classification of digital dermatitis with image processing and machine learning methods. MEHMET AKIF ERSOY ÜNIVERSITESI VETERINER FAKÜLTESI DERGISI 2022. [DOI: 10.24880/maeuvfd.1133145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
In this study, it was aimed to perform the detection and grading of Digital Dermatitis (DD) disease, which is common in dairy cattle and causes serious economic losses, using artificial intelligence techniques in a computer environment with high accuracy without the need for any expert intervention.
Within the scope of the study, because of the examinations performed on 168 cows of Holstein breed, aged 4-7 years, whose lameness was detected in dairy farms located in the center and districts of Burdur region, pictures of lesions due to DD were taken, and 4 groups were formed according to the degree of size. The photographs obtained were first labelled according to the degree of disease by a faculty member specialized in podiatry. Afterwards, the tagged photographs were reproduced using artificial intelligence image augmentation techniques, and a sample of 1,000 datasets was carried out for each disease degree. The photographs that make up the dataset were processed using the inception v3 deep learning algorithm and more than 2,000 numerical features were extracted. Then, machine learning models were developed using 6 different machine learning algorithms to classify these features. The results obtained were examined in detail with the help of tables and graphics, and it showed that the developed artificial intelligence models could be used in the classification of DD case photos with a cumulative accuracy value above 0.87.
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Thomas AD, Pajor EA, Caddey B, Goldhawk C, Martins L, Orsel K. An experimental model to induce digital dermatitis in beef calves. BMC Vet Res 2022; 18:238. [PMID: 35739561 PMCID: PMC9219410 DOI: 10.1186/s12917-022-03345-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/14/2022] [Indexed: 11/10/2022] Open
Abstract
Background Digital dermatitis (DD) is a multifactorial infectious disease affecting the skin on feet of cattle causing erosion and inflammation above the heel bulbs. Some cases of DD cause lameness and significantly impact animal welfare and productivity. While DD has emerged as a concern for the beef industry, key information regarding early detection and its impact on cattle behaviour is lacking. The primary objective of this study was to determine if an established DD experimental model for dairy calves could be used to induce DD lesions in beef calves. A secondary objective was to describe changes in behaviour and pain associated with induction of DD lesions. Eight beef calves acquired from a single cow-calf operator were enrolled in the study. Upon enrolment, calves were evaluated and determined to be free of foot lesions. Within the experimental environment, calves were housed in individual pens and assigned to two groups (mock-inoculated and inoculated). Both hind feet of each calf were enrolled. Within calf, inoculation protocol was consistent, and a 28-day experimental protocol was employed. Two days prior to inoculation, both hind feet of each calf were abraded (area above the heel bulbs and below the dewclaws), moistened, and wrapped to facilitate an anaerobic condition. Feet were inoculated with macerated DD lesion material or mock inoculum and remained wrapped until clinical signs of DD or protocol endpoint. Results After a period of 14 to 18 days post inoculation, three of five inoculated calves developed clinical signs (lameness), and upon close inspection, DD lesions were present on at least one hind foot. Two of five inoculated calves did not develop lesions within 28 days. Zero of three mock-inoculated calves developed DD. Treponema spp. were detected by quantitative polymerase chain reaction from biopsies of induced lesions. Measurements of behaviour prior to disease induction were numerically different between DD affected and mock-inoculated calves. Conclusions An experimental infection model established for dairy cattle was used to successfully induce acute DD lesions in three of five inoculated beef calves. This model can provide a framework to study intervention protocols and to evaluate the impact of DD on behaviour and pain.
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Affiliation(s)
- Anice D Thomas
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Edmond A Pajor
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Benjamin Caddey
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Christy Goldhawk
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Larissa Martins
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Karin Orsel
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada.
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Wilson-Welder JH, Mansfield K, Han S, Bayles DO, Alt DP, Olsen SC. Lesion Material From Treponema-Associated Hoof Disease of Wild Elk Induces Disease Pathology in the Sheep Digital Dermatitis Model. Front Vet Sci 2022; 8:782149. [PMID: 35097043 PMCID: PMC8790030 DOI: 10.3389/fvets.2021.782149] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/29/2021] [Indexed: 12/26/2022] Open
Abstract
A hoof disease among wild elk (Cervus elaphus) in the western United States has been reported since 2008. Now present in Washington, Oregon, Idaho, and California, this hoof disease continues to spread among elk herds suggesting an infectious etiology. Causing severe lesions at the hoof-skin junction, lesions can penetrate the hoof-horn structure causing severe lameness, misshapen hooves, and in some cases, sloughed hooves leaving the elk prone to infection, malnutrition, and premature death. Isolated to the feet, this disease has been termed treponeme-associated hoof disease due to the numerous Treponema spp. found within lesions. In addition to the Treponema spp., treponeme-associated hoof disease shares many similarities with digital dermatitis of cattle and livestock including association with several groups of anaerobic bacteria such as Bacteroides, Clostridia, and Fusobacterium, neutrophilic inflammatory infiltrate, and restriction of the disease to the foot and hoof tissues. To determine if there was a transmissible infectious component to this disease syndrome, elk lesion homogenate was used in a sheep model of digital dermatitis. Ten animals were inoculated with lesion material and lesion development was followed over 7 weeks. Most inoculated feet developed moderate to severe lesions at 2- or 4-weeks post-inoculation timepoints, with 16 of 18 feet at 4 weeks also had spirochetes associated within the lesions. Histopathology demonstrated spirochetes at the invading edge of the lesions along with other hallmarks of elk hoof disease, neutrophilic inflammatory infiltrates, and keratinocyte erosion. Treponema-specific PCR demonstrated three phylotypes associated with elk hoof disease and digital dermatitis were present. Serum of infected sheep had increased anti-Treponema IgG when compared to negative control sheep and pre-exposure samples. Analysis of the bacterial microbiome by sequencing of the bacterial 16S rRNA gene showed a community structure in sheep lesions that was highly similar to the elk lesion homogenate used as inoculum. Bacteroidies, Fusobacterium, and Clostridia were among the bacterial taxa overrepresented in infected samples as compared to negative control samples. In conclusion, there is a highly transmissible, infectious bacterial component to elk treponeme-associated hoof disease which includes several species of Treponema as well as other bacteria previously associated with digital dermatitis.
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Affiliation(s)
- Jennifer H. Wilson-Welder
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture (USDA), Ames, IA, United States
- *Correspondence: Jennifer H. Wilson-Welder
| | - Kristin Mansfield
- Washington Department of Fish and Wildlife, Spokane Valley, WA, United States
| | - Sushan Han
- Colorado State University Diagnostic Medicine Center, Fort Collins, CO, United States
| | - Darrell O. Bayles
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture (USDA), Ames, IA, United States
| | - David P. Alt
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture (USDA), Ames, IA, United States
| | - Steven C. Olsen
- Infectious Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture (USDA), Ames, IA, United States
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Thomas AD, Orsel K, Cortés JA, Pajor EA. Impact of digital dermatitis on feedlot cattle behaviour. Appl Anim Behav Sci 2021. [DOI: 10.1016/j.applanim.2021.105468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Caddey B, De Buck J. Meta-Analysis of Bovine Digital Dermatitis Microbiota Reveals Distinct Microbial Community Structures Associated With Lesions. Front Cell Infect Microbiol 2021; 11:685861. [PMID: 34336713 PMCID: PMC8322762 DOI: 10.3389/fcimb.2021.685861] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/16/2021] [Indexed: 01/04/2023] Open
Abstract
Bovine digital dermatitis (DD) is a significant cause of infectious lameness and economic losses in cattle production across the world. There is a lack of a consensus across different 16S metagenomic studies on DD-associated bacteria that may be potential pathogens of the disease. The goal of this meta-analysis was to identify a consistent group of DD-associated bacteria in individual DD lesions across studies, regardless of experimental design choices including sample collection and preparation, hypervariable region sequenced, and sequencing platform. A total of 6 studies were included in this meta-analysis. Raw sequences and metadata were identified on the NCBI sequence read archive and European nucleotide archive. Bacterial community structures were investigated between normal skin and DD skin samples. Random forest models were generated to classify DD status based on microbial composition, and to identify taxa that best differentiate DD status. Among all samples, members of Treponema, Mycoplasma, Porphyromonas, and Fusobacterium were consistently identified in the majority of DD lesions, and were the best genera at differentiating DD lesions from normal skin. Individual study and 16S hypervariable region sequenced had significant influence on final DD lesion microbial composition (P < 0.05). These findings indicate that members of Treponema, Mycoplasma, Porphyromonas, and/or Fusobacterium may have significant roles in DD pathogenesis, and should be studied further in respect to elucidating DD etiopathogenic mechanisms and developing more effective treatment and mitigation strategies.
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Affiliation(s)
- Ben Caddey
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Jeroen De Buck
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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Tracking Reservoirs of Antimicrobial Resistance Genes in a Complex Microbial Community Using Metagenomic Hi-C: The Case of Bovine Digital Dermatitis. Antibiotics (Basel) 2021; 10:antibiotics10020221. [PMID: 33672258 PMCID: PMC7926801 DOI: 10.3390/antibiotics10020221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 02/08/2023] Open
Abstract
Bovine digital dermatitis (DD) is a contagious infectious cause of lameness in cattle with unknown definitive etiologies. Many of the bacterial species detected in metagenomic analyses of DD lesions are difficult to culture, and their antimicrobial resistance status is largely unknown. Recently, a novel proximity ligation-guided metagenomic approach (Hi-C ProxiMeta) has been used to identify bacterial reservoirs of antimicrobial resistance genes (ARGs) directly from microbial communities, without the need to culture individual bacteria. The objective of this study was to track tetracycline resistance determinants in bacteria involved in DD pathogenesis using Hi-C. A pooled sample of macerated tissues from clinical DD lesions was used for this purpose. Metagenome deconvolution using ProxiMeta resulted in the creation of 40 metagenome-assembled genomes with ≥80% complete genomes, classified into five phyla. Further, 1959 tetracycline resistance genes and ARGs conferring resistance to aminoglycoside, beta-lactams, sulfonamide, phenicol, lincosamide, and erythromycin were identified along with their bacterial hosts. In conclusion, the widespread distribution of genes conferring resistance against tetracycline and other antimicrobials in bacteria of DD lesions is reported for the first time. Use of proximity ligation to identify microorganisms hosting specific ARGs holds promise for tracking ARGs transmission in complex microbial communities.
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Espiritu HM, Mamuad LL, Kim SH, Jin SJ, Lee SS, Kwon SW, Cho YI. Microbiome Shift, Diversity, and Overabundance of Opportunistic Pathogens in Bovine Digital Dermatitis Revealed by 16S rRNA Amplicon Sequencing. Animals (Basel) 2020; 10:ani10101798. [PMID: 33022998 PMCID: PMC7599724 DOI: 10.3390/ani10101798] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/22/2020] [Accepted: 09/30/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Bovine digital dermatitis (BDD) is a foot infection known as the primary cause of lameness in cattle due to painful lesions, posing serious impacts on the productivity and welfare of affected animals. Members of the bacterial group Treponema have long been considered as the main causative agents because previous investigations by bacterial isolation, tissue analyses, and high molecular sequencing have persistently identified this group in BDD. However, other studies indicated that the presence of several bacteria on the lesion due to the slurry environment the cattle foot are exposed to, suggests an interdependent polybacterial nature which could also play a role in disease development and progression. Therefore, we analyzed the diversity and relationship of the diverse microbiome in BDD lesions compared to normal skin from cattle foot by using next-generation high throughput sequencing. Based on the results obtained, we concluded that the shift in microbial composition which leads to richer diversity in BDD, and the overabundance of opportunistic bacterial pathogens could be associated with BDD pathogenesis. Abstract This study analyzed the diversity and phylogenetic relationship of the microbiome of bovine digital dermatitis (BDD) lesions and normal skin from cattle foot by using 16S rRNA amplicon sequencing. Three BDD samples and a normal skin sample were pre-assessed for analysis. The Illumina Miseq platform was used for sequencing and sequences were assembled and were categorized to operational taxonomic units (OTUs) based on similarity, then the core microbiome was visualized. The phylogeny was inferred using MEGA7 (Molecular evolutionary genetics analysis version 7.0). A total of 129 and 185 OTUs were uniquely observed in normal and in BDD samples, respectively. Of the 47 shared OTUs, 15 species presented increased abundance in BDD. In BDD and normal samples, Spirochetes and Proteobacteria showed the most abundant phyla, respectively, suggesting the close association of observed species in each sample group. The phylogeny revealed the evolutionary relationship of OTUs and the Euclidean distance suggested a high sequence divergence between OTUs. We concluded that a shift in the microbiome leads to richer diversity in BDD lesions, and the overabundance of opportunistic pathogens and its synergistic relationship with commensal bacteria could serve as factors in disease development. The influence of these factors should be thoroughly investigated in future studies to provide deeper insights on the pathogenesis of BDD.
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Affiliation(s)
- Hector M. Espiritu
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922, Korea; (H.M.E.); (L.L.M.); (S.-h.K.); (S.-j.J.); (S.-s.L.)
| | - Lovelia L. Mamuad
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922, Korea; (H.M.E.); (L.L.M.); (S.-h.K.); (S.-j.J.); (S.-s.L.)
| | - Seon-ho Kim
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922, Korea; (H.M.E.); (L.L.M.); (S.-h.K.); (S.-j.J.); (S.-s.L.)
| | - Su-jeong Jin
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922, Korea; (H.M.E.); (L.L.M.); (S.-h.K.); (S.-j.J.); (S.-s.L.)
| | - Sang-suk Lee
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922, Korea; (H.M.E.); (L.L.M.); (S.-h.K.); (S.-j.J.); (S.-s.L.)
| | - Seok-won Kwon
- Woosarang Animal Hospital, Yongin, Gyeonggi 17026, Korea;
| | - Yong-il Cho
- Department of Animal Science and Technology, Sunchon National University, Suncheon, Jeonnam 57922, Korea; (H.M.E.); (L.L.M.); (S.-h.K.); (S.-j.J.); (S.-s.L.)
- Correspondence: ; Tel.: +82-61-750-3234
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