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Abi Younes JN, Campbell JR, Otto SJG, Gow SP, Woolums AR, Jelinski M, Lacoste S, Waldner CL. Variation in Pen-Level Prevalence of BRD Bacterial Pathogens and Antimicrobial Resistance Following Feedlot Arrival in Beef Calves. Antibiotics (Basel) 2024; 13:322. [PMID: 38666998 PMCID: PMC11047553 DOI: 10.3390/antibiotics13040322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/29/2024] Open
Abstract
Antimicrobials are crucial for treating bovine respiratory disease (BRD) in beef feedlots. Evidence is needed to support antimicrobial use (AMU) decisions, particularly in the early part of the feeding period when BRD risk is highest. The study objective was to describe changes in prevalence and antimicrobial susceptibility of BRD bacterial pathogens at feedlot processing (1 day on feed (1DOF)), 12 days later (13DOF), and for a subset at 36DOF following metaphylactic antimicrobial treatment. Mixed-origin steer calves (n = 1599) from Western Canada were managed as 16 pens of 100 calves, receiving either tulathromycin (n = 1199) or oxytetracycline (n = 400) at arrival. Deep nasopharyngeal swabs collected at all time points underwent culture and antimicrobial susceptibility testing (AST). Variability in the pen-level prevalence of bacteria and antimicrobial susceptibility profiles were observed over time, between years, and metaphylaxis options. Susceptibility to most antimicrobials was high, but resistance increased from 1DOF to 13DOF, especially for tetracyclines and macrolides. Simulation results suggested that sampling 20 to 30 calves per pen of 200 reflected the relative pen-level prevalence of the culture and AST outcomes of interest. Pen-level assessment of antimicrobial resistance early in the feeding period can inform the evaluation of AMU protocols and surveillance efforts and support antimicrobial stewardship in animal agriculture.
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Affiliation(s)
- Jennifer N. Abi Younes
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada; (J.N.A.Y.)
| | - John R. Campbell
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada; (J.N.A.Y.)
| | - Simon J. G. Otto
- School of Public Health, University of Alberta, Edmonton, AB T6G 1C9, Canada;
| | - Sheryl P. Gow
- Canadian Integrated Program for Antimicrobial Resistance Surveillance, Public Health Agency of Canada, Saskatoon, SK S7L 0Z2, Canada
| | - Amelia R. Woolums
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
| | - Murray Jelinski
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada; (J.N.A.Y.)
| | - Stacey Lacoste
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada; (J.N.A.Y.)
| | - Cheryl L. Waldner
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada; (J.N.A.Y.)
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Manzulli V, Schiavone A, Castellana S, Albenzio M, Cafiero MA, Camarda A, Capozzi L, D'Angelo F, Parisi A, Vasco I, Sciancalepore D, Marino L, Serrecchia L, Rondinone V, Campaniello M, Crescenzo G, Galante D, Pugliese N. Psychrobacter raelei sp. nov., isolated from a dog with peritonitis. Int J Syst Evol Microbiol 2024; 74. [PMID: 38683659 DOI: 10.1099/ijsem.0.006353] [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: 05/01/2024] Open
Abstract
A strain belonging to the genus Psychrobacter, named PraFG1T, was isolated from the peritoneal effusion of a stray dog during necropsy procedures. The strain was characterized by the phylogenetic analyses based on the nucleotide sequences of 16S and 23S rRNA genes and of gyrB, which placed the strain in the genus Psychrobacter. The nucleotide sequence of the chromosome confirmed the placement, showing an average nucleotide identity of 72.1, 77.7, and 77.5 % with the closest related species, namely Psychrobacter sanguinis, Psychrobacter piechaudii, and Psychrobacter phenylpyruvicus, respectively, thus indicating a novel species. The polyphasic characterization by biochemical and fatty acid profiling as well as MALDI-TOF supported those findings. The strain was halotolerant, capable of growing within a temperature range between 4 and 37 °C, it was positive for catalase and oxidase, indole producing, nitrate reducing, and not able to use 5-keto-d-gluconic acid as a carbon source. Taken together, the data suggest that strain PraFG1T could be considered as representing a novel species, with the name Psychrobacter raelei sp. nov. (type strain PraFG1T=CIP 111873T=LMG 32233T).
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Affiliation(s)
- Viviana Manzulli
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Antonella Schiavone
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Italy
- Moredun Research Institute, Edinburgh, UK
| | - Stefano Castellana
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Putignano, Italy
| | - Marzia Albenzio
- Dipartimento di Scienze Agrarie, Alimenti, Risorse naturali e Ingegneria, Università di Foggia, Foggia, Italy
| | - Maria Assunta Cafiero
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Antonio Camarda
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Italy
| | - Loredana Capozzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Putignano, Italy
| | - Francesca D'Angelo
- Dipartimento di Scienze Agrarie, Alimenti, Risorse naturali e Ingegneria, Università di Foggia, Foggia, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Putignano, Italy
| | - Ilaria Vasco
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Dario Sciancalepore
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Italy
| | - Leonardo Marino
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Luigina Serrecchia
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Valeria Rondinone
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Maria Campaniello
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Giuseppe Crescenzo
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Italy
| | - Domenico Galante
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Nicola Pugliese
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari, Valenzano, Italy
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Frucchi APS, Dall Agnol AM, Caldart ET, Bronkhorst DE, Alfieri AF, Alfieri AA, Headley SA. The Role of Mycoplasma bovirhinis in the Development of Singular and Concomitant Respiratory Infections in Dairy Calves from Southern Brazil. Pathogens 2024; 13:114. [PMID: 38392852 PMCID: PMC10892079 DOI: 10.3390/pathogens13020114] [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: 12/30/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The role of Mycoplasma bovirhinis in the development of pulmonary disease in cattle is controversial and was never evaluated in cattle from Latin America. This study investigated the respiratory infection dynamics associated with M. bovirhinis in suckling calves from 15 dairy cattle herds in Southern Brazil. Nasal swabs were obtained from asymptomatic (n = 102) and calves with clinical manifestations (n = 103) of bovine respiratory disease (BRD) and used in molecular assays to identify the specific genes of viral and bacterial disease pathogens of BRD. Only M. bovirhinis, bovine coronavirus (BCoV), ovine gammaherpesvirus 2 (OvGHV2), Histophilus somni, Pasteurella multocida, and Mannheimia haemolytica were detected. M. bovirhinis was the most frequently diagnosed pathogen in diseased (57.8%; 59/102) and asymptomatic (55.3%; 57/103) calves at all farms. BCoV-related infections were diagnosed in diseased (52%; 53/102) and asymptomatic (51.4%; 53/103) calves and occurred in 93.3% (14/15) of all farms. Similarly, infectious due to OvGHV2 occurred in diseased (37.2%; 38/102) and asymptomatic (27.2%; /28/103) calves and were diagnosed in 80% (12/15) of all farms investigated. Significant statistical differences were not identified when the two groups of calves were compared at most farms, except for infections due to OvGHV2 that affected five calves at one farm. These results demonstrated that the respiratory infection dynamics of M. bovirhinis identified in Southern Brazil are similar to those observed worldwide, suggesting that there is not enough sufficient collected data to consider M. bovirhinis as a pathogen of respiratory infections in cattle. Additionally, the possible roles of BCoV and OvGHV2 in the development of BRD are discussed.
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Affiliation(s)
- Ana Paula Souza Frucchi
- Laboratory of Animal Virology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Londrina 86057-970, Brazil; (A.P.S.F.); (A.M.D.A.); (D.E.B.); (A.F.A.); (A.A.A.)
| | - Alais Maria Dall Agnol
- Laboratory of Animal Virology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Londrina 86057-970, Brazil; (A.P.S.F.); (A.M.D.A.); (D.E.B.); (A.F.A.); (A.A.A.)
| | - Eloiza Teles Caldart
- Laboratory of Protozoology and Parasitic Diseases, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Londrina 86057-970, Brazil;
| | - Dalton Everton Bronkhorst
- Laboratory of Animal Virology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Londrina 86057-970, Brazil; (A.P.S.F.); (A.M.D.A.); (D.E.B.); (A.F.A.); (A.A.A.)
| | - Alice Fernandes Alfieri
- Laboratory of Animal Virology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Londrina 86057-970, Brazil; (A.P.S.F.); (A.M.D.A.); (D.E.B.); (A.F.A.); (A.A.A.)
- Multi-User Animal Health Laboratory (LAMSA), Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Londrina 86057-970, Brazil
- National Institute of Science and Technology for Dairy Production Chain (INCT–LEITE), Universidade Estadual de Londrina, Londrina 86057-970, Brazil
| | - Amauri Alcindo Alfieri
- Laboratory of Animal Virology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Londrina 86057-970, Brazil; (A.P.S.F.); (A.M.D.A.); (D.E.B.); (A.F.A.); (A.A.A.)
- Multi-User Animal Health Laboratory (LAMSA), Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Londrina 86057-970, Brazil
- National Institute of Science and Technology for Dairy Production Chain (INCT–LEITE), Universidade Estadual de Londrina, Londrina 86057-970, Brazil
| | - Selwyn Arlington Headley
- Multi-User Animal Health Laboratory (LAMSA), Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Londrina 86057-970, Brazil
- National Institute of Science and Technology for Dairy Production Chain (INCT–LEITE), Universidade Estadual de Londrina, Londrina 86057-970, Brazil
- Laboratory of Animal Pathology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Londrina 86057-970, Brazil
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Zhang Z, Zhang C, Zhong Y, Yang S, Deng F, Li Y, Chai J. The spatial dissimilarities and connections of the microbiota in the upper and lower respiratory tract of beef cattle. Front Cell Infect Microbiol 2023; 13:1269726. [PMID: 38029262 PMCID: PMC10660669 DOI: 10.3389/fcimb.2023.1269726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
Bovine respiratory disease (BRD) causes morbidity and mortality in cattle. The critical roles of the respiratory microbiota in BRD have been widely studied. The nasopharynx was the most popular sampling niche for BRD pathogen studies. The oral cavity and other niches within the respiratory tract, such as nostrils and lung, are less assessed. In this study, oropharyngeal swabs (OS), nasal swabs (NS), nasopharyngeal swabs (NP), and bronchoalveolar lavage (BAL) were collected from calves located in four countries and analyzed for investigation of the dissimilarities and connections of the respiratory microbiota. The results showed that the microbial diversity, structure, and composition in the upper and lower respiratory tract in beef cattle from China, the USA, Canada, and Italy were significantly different. The microbial taxa for each sampling niche were specific and associated with their local physiology and geography. The signature microbiota for OS, NS, NP, and BAL were identified using the LEfSe algorithm. Although the spatial dissimilarities among the respiratory niches existed, the microbial connections were observed in beef cattle regardless of geography. Notably, the nostril and nasopharynx had more similar microbiomes compared to lung communities. The major bacterial immigration patterns in the bovine respiratory tract were estimated and some of them were associated with geography. In addition, the contribution of oral microbiota to the nasal and lung ecosystems was confirmed. Lastly, microbial interactions were characterized to reveal the correlation between the commercial microbiota and BRD-associated pathogens. In conclusion, shared airway microbiota among niches and geography provides the possibility to investigate the common knowledge for bovine respiratory health and diseases. In spite of the dissimilarities of the respiratory microbiota in cattle, the spatial connections among these sampling niches not only allow us to deeply understand the airway ecosystem but also benefit the research and development of probiotics for BRD.
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Affiliation(s)
- Zhihao Zhang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Chengqian Zhang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Yikai Zhong
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Shuli Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Feilong Deng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Ying Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Jianmin Chai
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
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Howe S, Kegley B, Powell J, Chen S, Zhao J. Effect of bovine respiratory disease on the respiratory microbiome: a meta-analysis. Front Cell Infect Microbiol 2023; 13:1223090. [PMID: 37743862 PMCID: PMC10516580 DOI: 10.3389/fcimb.2023.1223090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
Background Bovine respiratory disease (BRD) is the most devastating disease affecting beef and dairy cattle producers in North America. An emerging area of interest is the respiratory microbiome's relationship with BRD. However, results regarding the effect of BRD on respiratory microbiome diversity are conflicting. Results To examine the effect of BRD on the alpha diversity of the respiratory microbiome, a meta-analysis analyzing the relationship between the standardized mean difference (SMD) of three alpha diversity metrics (Shannon's Diversity Index (Shannon), Chao1, and Observed features (OTUs, ASVs, species, and reads) and BRD was conducted. Our multi-level model found no difference in Chao1 and Observed features SMDs between calves with BRD and controls. The Shannon SMD was significantly greater in controls compared to that in calves with BRD. Furthermore, we re-analyzed 16S amplicon sequencing data from four previously published datasets to investigate BRD's effect on individual taxa abundances. Additionally, based on Bray Curtis and Jaccard distances, health status, sampling location, and dataset were all significant sources of variation. Using a consensus approach based on RandomForest, DESeq2, and ANCOM-BC2, we identified three differentially abundant amplicon sequence variants (ASVs) within the nasal cavity, ASV5_Mycoplasma, ASV19_Corynebacterium, and ASV37_Ruminococcaceae. However, no ASVs were differentially abundant in the other sampling locations. Moreover, based on SECOM analysis, ASV37_Ruminococcaceae had a negative relationship with ASV1_Mycoplasma_hyorhinis, ASV5_Mycoplasma, and ASV4_Mannheimia. ASV19_Corynebacterium had negative relationships with ASV1_Mycoplasma_hyorhinis, ASV4_Mannheimia, ASV54_Mycoplasma, ASV7_Mycoplasma, and ASV8_Pasteurella. Conclusions Our results confirm a relationship between bovine respiratory disease and respiratory microbiome diversity and composition, which provide additional insight into microbial community dynamics during BRD development. Furthermore, as sampling location and sample processing (dataset) can also affect results, consideration should be taken when comparing results across studies.
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Affiliation(s)
- Samantha Howe
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, United States
| | - Beth Kegley
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, United States
| | - Jeremy Powell
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, United States
| | - Shicheng Chen
- Medical Laboratory Sciences Program, College of Health and Human Sciences, Northern Illinois University, DeKalb, IL, United States
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, United States
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Centeno-Martinez RE, Mohan S, Davidson JL, Schoonmaker JP, Ault A, Verma MS, Johnson TA. The bovine nasal fungal community and associations with bovine respiratory disease. Front Vet Sci 2023; 10:1165994. [PMID: 37441557 PMCID: PMC10335396 DOI: 10.3389/fvets.2023.1165994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/07/2023] [Indexed: 07/15/2023] Open
Abstract
Introduction Effective identification and treatment of bovine respiratory disease (BRD) is an ongoing health and economic issue for the dairy and beef cattle industries. Bacteria pathogens Pasteurellamultocida, Mycoplasmabovis, Mannheimia haemolytica, and Histophilus somni and the virus Bovine herpesvirus-1 (BHV-1), Bovine parainfluenza-3 virus (BPIV-3), Bovine respiratory syncytial virus (BRSV), Bovine adenovirus 3 (BAdV3), bovine coronavirus (BoCV) and Bovine viral diarrhea virus (BVDV) have commonly been identified in BRD cattle; however, no studies have investigated the fungal community and how it may also relate to BRD. Methods The objective of this study was to understand if the nasal mycobiome differs between a BRD-affected (n = 56) and visually healthy (n = 73) Holstein steers. Fungal nasal community was determined by using Internal Transcribed Spacer (ITS) sequencing. Results The phyla, Ascomycota and Basidiomycota, and the genera, Trichosporon and Issatchenkia, were the most abundant among all animals, regardless of health status. We identified differences between healthy and BRD animals in abundance of Trichosporon and Issatchenkia orientalis at a sub-species level that could be a potential indicator of BRD. No differences were observed in the nasal fungal alpha and beta diversity between BRD and healthy animals. However, the fungal community structure was affected based on season, specifically when comparing samples collected in the summer to the winter season. We then performed a random forest model, based on the fungal community and abundance of the BRD-pathobionts (qPCR data generated from a previous study using the same animals), to classify healthy and BRD animals and determine the agreement with visual diagnosis. Classification of BRD or healthy animals using ITS sequencing was low and agreed with the visual diagnosis with an accuracy of 51.9%. A portion of the ITS-predicted BRD animals were not predicted based on the abundance of BRD pathobionts. Lastly, fungal and bacterial co-occurrence were more common in BRD animals than healthy animals. Discussion The results from this novel study provide a baseline understanding of the fungal diversity and composition in the nasal cavity of BRD and healthy animals, upon which future interaction studies, including other nasal microbiome members to further understand and accurately diagnose BRD, can be designed.
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Affiliation(s)
| | - Suraj Mohan
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, United States
| | - Josiah Levi Davidson
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, United States
| | - Jon P. Schoonmaker
- Department of Animal Science, Purdue University, West Lafayette, IN, United States
| | - Aaron Ault
- Department of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, United States
| | - Mohit S. Verma
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, United States
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, United States
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, United States
| | - Timothy A. Johnson
- Department of Animal Science, Purdue University, West Lafayette, IN, United States
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Goto Y, Fukunari K, Suzuki T. Multiplex RT-qPCR Application in Early Detection of Bovine Respiratory Disease in Healthy Calves. Viruses 2023; 15:v15030669. [PMID: 36992378 PMCID: PMC10057971 DOI: 10.3390/v15030669] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Bovine respiratory diseases (BRD) are associated with various predisposing factors, such as physical and physiological stress factors, and bacterial and viral pathogens. These stressors and viruses suppress immune defenses, leading to bacterial growth in the upper respiratory tract and invasion of pathogens into the lower respiratory tract. Therefore, continuous monitoring of the causative pathogens would contribute to the early detection of BRD. Nasal swabs and sera from 63 clinically healthy calves were continuously collected from seven farms in Iwate prefecture from 2019 to 2021. We attempted to monitor dynamics of BRD-associated pathogens by multiplex real-time RT-PCR (RT-qPCR) using their nasal swab samples. In addition, we attempted to monitor fluctuation of antibody titers against each BRD-associated pathogen by virus neutralization test (VNT) using their sera. In contrast, nasal swabs from 89 calves infected with BRD were collected from 28 farms in Iwate prefecture from 2019 to 2021. We attempted to analyze their nasal swab samples by multiplex RT-qPCR aim to detect BRD-associated pathogens that are dominant in this region. As a result, our analyses using samples from clinically healthy calves showed that positive results by multiplex RT-qPCR were closely related to a significant increase of antibody titers by VNT in bovine coronavirus (BCoV), bovine torovirus (BToV), and bovine respiratory syncytial virus (BRSV). In addition, our data exhibited that BCoV, BToV, BRSV, bovine parainfluenza virus 3, and Mycoplasma bovis have been more frequently detected in calves infected with BRD compared to those detected in clinically healthy calves. Moreover, the data presented herein revealed co-infections by combination multiple viral pathogens with bacterial pathogens are closely involved in the onset of BRD. Taken together, our study demonstrates multiplex RT-qPCR which can simultaneously analyze multiple pathogens, including viruses and bacteria, and is useful for the early detection of BRD.
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Affiliation(s)
- Yusuke Goto
- Central Iwate Prefectural Livestock Health and Hygiene Center, Takizawa 020-0605, Iwate, Japan
| | - Kazuhiro Fukunari
- Central Iwate Prefectural Livestock Health and Hygiene Center, Takizawa 020-0605, Iwate, Japan
| | - Tohru Suzuki
- Division of Zoonosis Research and Division of Hygiene Management, Sapporo Research Station, National Institute of Animal Health, NARO, Sapporo 062-0045, Hokkaido, Japan
- Correspondence: ; Tel.: +81-11-851-2132; Fax: +81-11-853-0767
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Characterisation of the Upper Respiratory Tract Virome of Feedlot Cattle and Its Association with Bovine Respiratory Disease. Viruses 2023; 15:v15020455. [PMID: 36851669 PMCID: PMC9961997 DOI: 10.3390/v15020455] [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: 12/20/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 02/10/2023] Open
Abstract
Bovine respiratory disease (BRD) is a major health problem within the global cattle industry. This disease has a complex aetiology, with viruses playing an integral role. In this study, metagenomics was used to sequence viral nucleic acids in the nasal swabs of BRD-affected cattle. The viruses detected included those that are well known for their association with BRD in Australia (bovine viral diarrhoea virus 1), as well as viruses known to be present but not fully characterised (bovine coronavirus) and viruses that have not been reported in BRD-affected cattle in Australia (bovine rhinitis, bovine influenza D, and bovine nidovirus). The nasal swabs from a case-control study were subsequently tested for 10 viruses, and the presence of at least one virus was found to be significantly associated with BRD. Some of the more recently detected viruses had inconsistent associations with BRD. Full genome sequences for bovine coronavirus, a virus increasingly associated with BRD, and bovine nidovirus were completed. Both viruses belong to the Coronaviridae family, which are frequently associated with disease in mammals. This study has provided greater insights into the viral pathogens associated with BRD and highlighted the need for further studies to more precisely elucidate the roles viruses play in BRD.
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Chappell DE, Barnett DC, James K, Craig B, Bain F, Gaughan E, Schneider C, Vaala W, Barnum SM, Pusterla N. Voluntary Surveillance Program for Equine Influenza Virus in the United States during 2008-2021. Pathogens 2023; 12:pathogens12020192. [PMID: 36839464 PMCID: PMC9961984 DOI: 10.3390/pathogens12020192] [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: 12/07/2022] [Revised: 01/06/2023] [Accepted: 01/21/2023] [Indexed: 01/31/2023] Open
Abstract
A voluntary upper respiratory biosurveillance program in the USA received 9740 nasal swab submissions during the years 2008-2021 from 333 veterinarians and veterinary clinics. The nasal swabs were submitted for qPCR testing for six common upper respiratory pathogens:equine influenza virus (EIV), equine herpesvirus-1 (EHV-1), equine herpesvirus-4 (EHV-4), Streptococcus equi subspecies equi (S. equi), equine rhinitis A virus (ERAV), and equine rhinitis B virus (ERBV). Additional testing was performed for equine gamma herpesvirus-2 (EHV-2) and equine gamma herpesvirus-5 (EHV-5) and the results are reported. Basic frequency statistics and multivariate logistic regression models were utilized to determine the associations between risk factors and EIV positivity. The EIV qPCR-positivity rate was 9.9%. Equids less than 9 years of age with a recent history of travel and seasonal occurrence in winter and spring were the most common population that were qPCR positive for EIV. This ongoing biosurveillance program emphasizes the need for molecular testing for pathogen identification, which is critical for decisions associated with therapeutics and biosecurity intervention for health management and vaccine evaluations and development.
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Affiliation(s)
- Duane E. Chappell
- Merck Animal Health, Madison, NJ 07940, USA
- Correspondence: ; Tel.: +1-866-349-3497
| | | | | | | | | | | | | | | | - Samantha M. Barnum
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Nicola Pusterla
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
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10
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Crosby WB, Pinnell LJ, Richeson JT, Wolfe C, Castle J, Loy JD, Gow SP, Seo KS, Capik SF, Woolums AR, Morley PS. Does swab type matter? Comparing methods for Mannheimia haemolytica recovery and upper respiratory microbiome characterization in feedlot cattle. Anim Microbiome 2022; 4:49. [PMID: 35964128 PMCID: PMC9375289 DOI: 10.1186/s42523-022-00197-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Background Bovine respiratory disease (BRD) is caused by interactions among host, environment, and pathogens. One standard method for antemortem pathogen identification in cattle with BRD is deep-guarded nasopharyngeal swabbing, which is challenging, costly, and waste generating. The objective was to compare the ability to recover Mannheimia haemolytica and compare microbial community structure using 29.5 inch (74.9 cm) deep-guarded nasopharyngeal swabs, 16 inch (40.6 cm) unguarded proctology swabs, or 6 inch (15.2 cm) unguarded nasal swabs when characterized using culture, real time-qPCR, and 16S rRNA gene sequencing. Samples for aerobic culture, qPCR, and 16S rRNA gene sequencing were collected from the upper respiratory tract of cattle 2 weeks after feedlot arrival.
Results There was high concordance of culture and qPCR results for all swab types (results for 77% and 81% of sampled animals completely across all 3 swab types for culture and qPCR respectively). Microbial communities were highly similar among samples collected with different swab types, and differences identified relative to treatment for BRD were also similar. Positive qPCR results for M. haemolytica were highly concordant (81% agreed completely), but samples collected by deep-guarded swabbing had lower amounts of Mh DNA identified (Kruskal–Wallis analysis of variance on ranks, P < 0.05; Dunn-test for pairwise comparison with Benjamini–Hochberg correction, P < 0.05) and lower frequency of positive compared to nasal and proctology swabs (McNemar’s Chi-square test, P < 0.05). Conclusions Though differences existed among different types of swabs collected from individual cattle, nasal swabs and proctology swabs offer comparable results to deep-guarded nasopharyngeal swabs when identifying and characterizing M. haemolytica by culture, 16S rRNA gene sequencing, and qPCR. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00197-6.
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11
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Freeman CN, Herman EK, Abi Younes J, Ramsay DE, Erikson N, Stothard P, Links MG, Otto SJG, Waldner C. Evaluating the potential of third generation metagenomic sequencing for the detection of BRD pathogens and genetic determinants of antimicrobial resistance in chronically ill feedlot cattle. BMC Vet Res 2022; 18:211. [PMID: 35655189 PMCID: PMC9161498 DOI: 10.1186/s12917-022-03269-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/26/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Bovine respiratory disease (BRD) is an important cause of morbidity and mortality and is responsible for most of the injectable antimicrobial use in the feedlot industry. Traditional bacterial culture can be used to diagnose BRD by confirming the presence of causative pathogens and to support antimicrobial selection. However, given that bacterial culture takes up to a week and early intervention is critical for treatment success, culture has limited utility for informing rapid therapeutic decision-making. In contrast, metagenomic sequencing has the potential to quickly resolve all nucleic acid in a sample, including pathogen biomarkers and antimicrobial resistance genes. In particular, third-generation Oxford Nanopore Technology sequencing platforms provide long reads and access to raw sequencing data in real-time as it is produced, thereby reducing the time from sample collection to diagnostic answer. The purpose of this study was to compare the performance of nanopore metagenomic sequencing to traditional culture and sensitivity methods as applied to nasopharyngeal samples from segregated groups of chronically ill feedlot cattle, previously treated with antimicrobials for nonresponsive pneumonia or lameness.
Results
BRD pathogens were isolated from most samples and a variety of different resistance profiles were observed across isolates. The sequencing data indicated the samples were dominated by Moraxella bovoculi, Mannheimia haemolytica, Mycoplasma dispar, and Pasteurella multocida, and included a wide range of antimicrobial resistance genes (ARGs), encoding resistance for up to seven classes of antimicrobials. Genes conferring resistance to beta-lactams were the most commonly detected, while the tetH gene was detected in the most samples overall. Metagenomic sequencing detected the BRD pathogens of interest more often than did culture, but there was limited concordance between phenotypic resistance to antimicrobials and the presence of relevant ARGs.
Conclusions
Metagenomic sequencing can reduce the time from sampling to results, detect pathogens missed by bacterial culture, and identify genetically encoded determinants of resistance. Increasing sequencing coverage of target organisms will be an essential component of improving the reliability of this technology, such that it can be better used for the surveillance of pathogens of interest, genetic determinants of resistance, and to inform diagnostic decisions.
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12
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Centeno-Martinez RE, Glidden N, Mohan S, Davidson JL, Fernández-Juricic E, Boerman JP, Schoonmaker J, Pillai D, Koziol J, Ault A, Verma MS, Johnson TA. Identification of bovine respiratory disease through the nasal microbiome. Anim Microbiome 2022; 4:15. [PMID: 35193707 PMCID: PMC8862248 DOI: 10.1186/s42523-022-00167-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 02/04/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Bovine respiratory disease (BRD) is an ongoing health and economic challenge in the dairy and beef cattle industries. Multiple risk factors make an animal susceptible to BRD. The presence of Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis in lung tissues have been associated with BRD mortalities, but they are also commonly present in the upper respiratory tract of healthy animals. This study aims to compare the cattle nasal microbiome (diversity, composition and community interaction) and the abundance of BRD pathogens (by qPCR) in the nasal microbiome of Holstein steers that are apparently healthy (Healthy group, n = 75) or with BRD clinical signs (BRD group, n = 58). We then used random forest models based on nasal microbial community and qPCR results to classify healthy and BRD-affected animals and determined the agreement with the visual clinical signs. Additionally, co-occurring species pairs were identified in visually BRD or healthy animal groups. RESULTS Cattle in the BRD group had lower alpha diversity than pen-mates in the healthy group. Amplicon sequence variants (ASVs) from Trueperella pyogenes, Bibersteinia and Mycoplasma spp. were increased in relative abundance in the BRD group, while ASVs from Mycoplasma bovirhinis and Clostridium sensu stricto were increased in the healthy group. Prevalence of H. somni (98%) and P. multocida (97%) was high regardless of BRD clinical signs whereas M. haemolytica (81 and 61%, respectively) and M. bovis (74 and 51%, respectively) were more prevalent in the BRD group than the healthy group. In the BRD group, the abundance of M. haemolytica and M. bovis was increased, while H. somni abundance was decreased. Visual observation of clinical signs agreed with classification by the nasal microbial community (misclassification rate of 32%) and qPCR results (misclassification rate 34%). Co-occurrence analysis demonstrated that the nasal microbiome of BRD-affected cattle presented fewer bacterial associations than healthy cattle. CONCLUSIONS This study offers insight into the prevalence and abundance of BRD pathogens and the differences in the nasal microbiome between healthy and BRD animals. This suggests that nasal bacterial communities provide a potential platform for future studies and potential pen-side diagnostic testing.
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Affiliation(s)
| | - Natalie Glidden
- Department of Animal Science, Purdue University, West Lafayette, IN, USA
| | - Suraj Mohan
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, USA
| | - Josiah Levi Davidson
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, USA
| | | | | | - Jon Schoonmaker
- Department of Animal Science, Purdue University, West Lafayette, IN, USA
| | - Deepti Pillai
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, USA
| | - Jennifer Koziol
- Department of Veterinary Clinical Science, Purdue University, West Lafayette, IN, USA
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, USA
| | - Aaron Ault
- Department of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, USA
| | - Mohit S Verma
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, USA
| | - Timothy A Johnson
- Department of Animal Science, Purdue University, West Lafayette, IN, USA.
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13
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Chai J, Capik SF, Kegley B, Richeson JT, Powell JG, Zhao J. Bovine respiratory microbiota of feedlot cattle and its association with disease. Vet Res 2022; 53:4. [PMID: 35022062 PMCID: PMC8756723 DOI: 10.1186/s13567-021-01020-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/06/2021] [Indexed: 12/15/2022] Open
Abstract
Bovine respiratory disease (BRD), as one of the most common and costly diseases in the beef cattle industry, has significant adverse impacts on global food security and the economic stability of the industry. The bovine respiratory microbiome is strongly associated with health and disease and may provide insights for alternative therapy when treating BRD. The niche-specific microbiome communities that colonize the inter-surface of the upper and the lower respiratory tract consist of a dynamic and complex ecological system. The correlation between the disequilibrium in the respiratory ecosystem and BRD has become a hot research topic. Hence, we summarize the pathogenesis and clinical signs of BRD and the alteration of the respiratory microbiota. Current research techniques and the biogeography of the microbiome in the healthy respiratory tract are also reviewed. We discuss the process of resident microbiota and pathogen colonization as well as the host immune response. Although associations between the microbiota and BRD have been revealed to some extent, interpreting the development of BRD in relation to respiratory microbial dysbiosis will likely be the direction for upcoming studies, which will allow us to better understand the importance of the airway microbiome and its contributions to animal health and performance.
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Affiliation(s)
- Jianmin Chai
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Sarah F Capik
- Texas A&M AgriLife Research and Department of Veterinary Pathobiology, Texas A&M College of Veterinary Medicine and Biomedical Sciences, Canyon, TX, 79015, USA
| | - Beth Kegley
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - John T Richeson
- Department of Agricultural Sciences, West Texas A&M University, Canyon, TX, 79016, USA
| | - Jeremy G Powell
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Jiangchao Zhao
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, 72701, USA.
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14
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Hall JA, Isaiah A, Bobe G, Estill CT, Bishop-Stewart JK, Davis TZ, Suchodolski JS, Pirelli GJ. Feeding selenium-biofortified alfalfa hay during the preconditioning period improves growth, carcass weight, and nasal microbial diversity of beef calves. PLoS One 2020; 15:e0242771. [PMID: 33259499 PMCID: PMC7707589 DOI: 10.1371/journal.pone.0242771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/09/2020] [Indexed: 01/04/2023] Open
Abstract
We previously reported that feeding Se-biofortified alfalfa hay to weaned beef calves in a preconditioning program decreases morbidity and mortality during the feedlot period. To understand the mode of action by which supranutritional Se supplementation supports calf health, we examined the effect of agronomic Se-biofortification on nasal microbiome and fecal parasites. Recently weaned Angus-cross beef calves (n = 30) were randomly assigned to two groups and fed an alfalfa hay-based diet for 9 weeks in a preconditioning program. Alfalfa hay was harvested from fields fertilized with sodium selenate at a rate of 0 or 90 g Se/ha. Calculated Se intake from dietary sources was 1.09 and 27.45 mg Se/calf per day for calves consuming alfalfa hay with Se concentrations of 0.06 and 3.47 mg Se/kg dry matter, respectively. Feeding Se-biofortified alfalfa hay for 9 weeks was effective at increasing whole-blood Se concentrations (556 ± 11 vs 140 ± 11 ng/mL; P < 0.001) and increasing body weight (PTreatment, = 0.03) in weaned beef calves. Slaughter yield grades were higher for calves that had been fed Se-enriched alfalfa hay during the preconditioning period (PTreatment = 0.008). No significant differences were observed in fecal parasite load, which remained low. The nasal microbiome and microbiota diversity within calves and across calves expanded from weaning (week 0) to the feedlot period (week 12), which was promoted by feeding Se-biofortified alfalfa hay. Especially concerning was the expansion of nasal Mycoplasmataceae in the feedlot, which reached over 50% of the total microbiota in some calves. In conclusion, we identified dietary Se-biofortified alfalfa hay as a potential promoter of nasal microbiome genome and microbiota diversity, which may explain in part high-Se benefits for prevention of bovine respiratory disease complex in beef calves.
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Affiliation(s)
- Jean A. Hall
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States of America
- * E-mail:
| | - Anitha Isaiah
- Gastrointestinal Laboratory, College of Veterinary Medicine, Department of Small Animal Clinical Sciences, Texas A&M University, TX, United States of America
| | - Gerd Bobe
- Department of Animal and Rangeland Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR, United States of America
- Linus Pauling Institute, Oregon State University, Corvallis, OR, United States of America
| | - Charles T. Estill
- Department of Animal and Rangeland Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR, United States of America
- Department of Clinical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States of America
| | - Janell K. Bishop-Stewart
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States of America
| | - T. Zane Davis
- USDA-ARS-Poisonous Plant Research Lab, Logan, UT, United States of America
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, College of Veterinary Medicine, Department of Small Animal Clinical Sciences, Texas A&M University, TX, United States of America
| | - Gene J. Pirelli
- Department of Animal and Rangeland Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR, United States of America
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15
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Su A, Tong J, Fu Y, Müller S, Weldearegay YB, Becher P, Valentin-Weigand P, Meens J, Herrler G. Infection of bovine well-differentiated airway epithelial cells by Pasteurella multocida: actions and counteractions in the bacteria-host interactions. Vet Res 2020; 51:140. [PMID: 33225994 PMCID: PMC7681981 DOI: 10.1186/s13567-020-00861-2] [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: 07/08/2020] [Accepted: 10/22/2020] [Indexed: 12/31/2022] Open
Abstract
Pasteurella (P.) multocida is a zoonotic pathogen, which is able to cause respiratory disorder in different hosts. In cattle, P. multocida is an important microorganism involved in the bovine respiratory disease complex (BRDC) with a huge economic impact. We applied air–liquid interface (ALI) cultures of well-differentiated bovine airway epithelial cells to analyze the interaction of P. multocida with its host target cells. The bacterial pathogen grew readily on the ALI cultures. Infection resulted in a substantial loss of ciliated cells. Nevertheless, the epithelial cell layer maintained its barrier function as indicated by the transepithelial electrical resistance and the inability of dextran to get from the apical to the basolateral compartment via the paracellular route. Analysis by confocal immunofluorescence microscopy confirmed the intactness of the epithelial cell layer though it was not as thick as the uninfected control cells. Finally, we chose the bacterial neuraminidase to show that our infection model is a sustainable tool to analyze virulence factors of P. multocida. Furthermore, we provide an explanation, why this microorganism usually is a commensal and becomes pathogenic only in combination with other factors such as co-infecting microorganisms.
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Affiliation(s)
- Ang Su
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, 30559, Hannover, Germany
| | - Jie Tong
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Yuguang Fu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Sandy Müller
- Institute of Microbiology, University of Veterinary Medicine Hannover, Foundation, 30559, Hannover, Germany
| | | | - Paul Becher
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, 30559, Hannover, Germany
| | - Peter Valentin-Weigand
- Institute of Microbiology, University of Veterinary Medicine Hannover, Foundation, 30559, Hannover, Germany
| | - Jochen Meens
- Institute of Microbiology, University of Veterinary Medicine Hannover, Foundation, 30559, Hannover, Germany.
| | - Georg Herrler
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, 30559, Hannover, Germany.
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16
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Guo T, Zhang J, Chen X, Wei X, Wu C, Cui Q, Hao Y. Investigation of viral pathogens in cattle with bovine respiratory disease complex in Inner Mongolia, China. Microb Pathog 2020; 153:104594. [PMID: 33157218 DOI: 10.1016/j.micpath.2020.104594] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/30/2020] [Accepted: 10/26/2020] [Indexed: 11/25/2022]
Abstract
As a multifactor disease, the bovine respiratory disease complex (BRDC) causes high morbidity and mortality that is devastating to the cattle industry. To assess viral infections in beef cattle suffering from respiratory diseases in Inner Mongolia, 302 nasal swabs and serum samples were randomly collected from cattle with mild respiratory symptoms between March 2018 and May 2019. Our results showed that the rate of RT-PCR results positive for nucleic acids of viral pathogens in 6 cities was between 54 and 80%.The rates of bovine viral diarrhea virus (BVDV), bovine herpesvirus 1 (BHV-1), bovine parainfluenza virus type 3(BPIV3), and bovine respiratory syncytial virus(BRSV)infections were 44.70% (135/302), 24.83% (75/302), 5.63% (17/302), and 6.95% (21/302),respectively. There are also 8.94% (27/302) of samples were positive for BVDV and BHV-1, and 3.97% (12/302) of samples were positive for BPIV3 and BRSV. In addition, the RT-PCR products were sequenced, and phylogenetic analysis based on these sequences was performed. The results indicated that: a) all of the BVDV isolates were BVDV-1 and were classified as BVDV-1a (66.67%) and BVDV-1b (33.33%); b) all of the BHV-1 isolates were classified as subtype 1.1; 44.44% of the isolates were closely related to modified live viral vaccine strains, and 55.56% of the isolates were closer to epidemic strains; c) all of the BPIV3 isolates belonged to BPIV3c; d) all of the BRSV isolates were classified into subgroup III. It is suggested that an important cause of respiratory diseases for beef cattle is viral infection, and phylogenetic analysis can help us choose the proper strain to develop a vaccine.
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Affiliation(s)
- Ting Guo
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, 010018, China; Key Laboratory of Clinical Diagnosis and Treatment Techniques for Animal Disease, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China.
| | - Jianhua Zhang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, 010018, China; Key Laboratory of Clinical Diagnosis and Treatment Techniques for Animal Disease, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
| | - Xindi Chen
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, 010018, China; Key Laboratory of Clinical Diagnosis and Treatment Techniques for Animal Disease, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
| | - Xin Wei
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, 010018, China; Key Laboratory of Clinical Diagnosis and Treatment Techniques for Animal Disease, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
| | - Chunxia Wu
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, 010018, China; Key Laboratory of Clinical Diagnosis and Treatment Techniques for Animal Disease, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
| | - Qi Cui
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, 010018, China; Key Laboratory of Clinical Diagnosis and Treatment Techniques for Animal Disease, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
| | - Yongqing Hao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, 010018, China; Key Laboratory of Clinical Diagnosis and Treatment Techniques for Animal Disease, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China.
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17
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McMullen C, Alexander TW, Orsel K, Timsit E. Progression of nasopharyngeal and tracheal bacterial microbiotas of feedlot cattle during development of bovine respiratory disease. Vet Microbiol 2020; 248:108826. [PMID: 32891954 DOI: 10.1016/j.vetmic.2020.108826] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/13/2020] [Indexed: 01/04/2023]
Abstract
It is generally accepted that as bovine respiratory disease (BRD) develops, bacterial pathogens first proliferate in the nasopharynx and then colonize the lungs, leading to bronchopneumonia. However, such temporal changes have never been definitively demonstrated. Therefore, the objective was to describe the progression of the nasopharyngeal and tracheal bacterial microbiotas of feedlot cattle during development of BRD. Nasopharyngeal swabs and tracheal wash samples were collected from 24 heifers over 20 d after arrival at a feedlot. Heifers were assessed daily and sampled based on reticulo-rumen/rectal temperatures and development of clinical signs of BRD. The study end point for each heifer was either at BRD treatment (BRD group; n = 15) or day 20 if the heifer remained healthy or did not meet BRD treatment criteria (TOL group; n = 9). Total DNA was extracted from each sample and the 16S rRNA gene (V3-V4) sequenced. Alpha and beta diversity were compared between BRD-TOL groups and sampling locations over time. There were no common patterns of change over time in composition or diversity of either the nasopharyngeal or tracheal bacterial microbiotas of cattle that developed BRD. Health status affected bacterial composition (R2 = 0.043; < 0.001), though this effect was low compared to variation among individual animals (R2 = 0.335; < 0.001) and effects of days on feed (R2 = 0.082; < 0.001). Specific bacterial taxa (Moraxella and Mycoplasma dispar) nevertheless appeared to have a potential role in respiratory health.
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Affiliation(s)
| | - Trevor W Alexander
- Lethbridge Research and Development Center, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Karin Orsel
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Edouard Timsit
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada; Simpson Ranch Chair in Beef Cattle Health and Wellness, University of Calgary, Calgary, AB, Canada; Ceva Santé Animale, Libourne, France.
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18
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Myer PR, McDaneld TG, Kuehn LA, Dedonder KD, Apley MD, Capik SF, Lubbers BV, Harhay GP, Harhay DM, Keele JW, Henniger MT, Clemmons BA, Smith TPL. Classification of 16S rRNA reads is improved using a niche-specific database constructed by near-full length sequencing. PLoS One 2020; 15:e0235498. [PMID: 32658916 PMCID: PMC7357769 DOI: 10.1371/journal.pone.0235498] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 06/17/2020] [Indexed: 12/21/2022] Open
Abstract
Surveys of microbial populations in environmental niches of interest often utilize sequence variation in the gene encoding the ribosomal small subunit (the 16S rRNA gene). Generally, these surveys target the 16S genes using semi-degenerate primers to amplify portions of a subset of bacterial species, sequence the amplicons in bulk, and assign to putative taxonomic categories by comparison to databases purporting to connect specific sequences in the main variable regions of the gene to specific organisms. Due to sequence length constraints of the most popular bulk sequencing platforms, the primers selected amplify one to three of the nine variable regions, and taxonomic assignment is based on relatively short stretches of sequence (150-500 bases). We demonstrate that taxonomic assignment is improved through reduced unassigned reads by including a survey of near-full-length sequences specific to the target environment, using a niche of interest represented by the upper respiratory tract (URT) of cattle. We created a custom Bovine URT database from these longer sequences for assignment of shorter, less expensive reads in comparisons of the upper respiratory tract among individual animals. This process improves the ability to detect changes in the microbial populations of a given environment, and the accuracy of defining the content of that environment at increasingly higher taxonomic resolution.
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Affiliation(s)
- Phillip R. Myer
- Department of Animal Science, University of Tennessee Institute of Agriculture, University of Tennessee, Knoxville, TN, United States of America
| | - Tara G. McDaneld
- USDA-ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States of America
| | - Larry A. Kuehn
- USDA-ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States of America
| | - Keith D. Dedonder
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States of America
| | - Michael D. Apley
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States of America
| | - Sarah F. Capik
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States of America
| | - Brian V. Lubbers
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States of America
| | - Gregory P. Harhay
- USDA-ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States of America
| | - Dayna M. Harhay
- USDA-ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States of America
| | - John W. Keele
- USDA-ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States of America
| | - Madison T. Henniger
- Department of Animal Science, University of Tennessee Institute of Agriculture, University of Tennessee, Knoxville, TN, United States of America
| | - Brooke A. Clemmons
- Department of Animal Science, University of Tennessee Institute of Agriculture, University of Tennessee, Knoxville, TN, United States of America
| | - Timothy P. L. Smith
- USDA-ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States of America
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19
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Timsit E, McMullen C, Amat S, Alexander TW. Respiratory Bacterial Microbiota in Cattle: From Development to Modulation to Enhance Respiratory Health. Vet Clin North Am Food Anim Pract 2020; 36:297-320. [PMID: 32451027 DOI: 10.1016/j.cvfa.2020.03.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The respiratory tract of cattle is colonized by complex bacterial ecosystems also known as bacterial microbiotas. These microbiotas evolve over time and are shaped by numerous factors, including maternal vaginal microbiota, environment, age, diet, parenteral antimicrobials, and stressful events. The resulting microbiota can be diverse and enriched with known beneficial bacteria that can provide colonization resistance against bacterial pathogens or, on the contrary, with opportunistic pathogens that can predispose cattle to respiratory disease. The respiratory microbiota can be modulated by nonantimicrobial approaches to promote health, creating new potential strategies for prevention and treatment of bovine respiratory disease.
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Affiliation(s)
- Edouard Timsit
- Ceva Santé Animale, 10 Avenue de la Ballastière, Libourne 33500, France.
| | - Chris McMullen
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Samat Amat
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada; Lethbridge Research and Development Center, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada; Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Trevor W Alexander
- Lethbridge Research and Development Center, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
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Wynn EL, Schuller G, Loy JD, Workman AM, McDaneld TG, Clawson ML. Differentiation of Mannheimia haemolytica genotype 1 and 2 strains by visible phenotypic characteristics on solid media. J Microbiol Methods 2020; 171:105877. [PMID: 32088258 DOI: 10.1016/j.mimet.2020.105877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 02/11/2020] [Accepted: 02/19/2020] [Indexed: 10/25/2022]
Abstract
Genotype 2 Mannheimia haemolytica associate with the lungs of cattle with bovine respiratory disease more frequently than genotype 1 strains. Different colony colors and morphologies were identified between genotype 1 and 2 solid media cultures. Genotype of strains, and frequency differences between them in mixed cultures are discernable by visual inspection.
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Affiliation(s)
- Emily L Wynn
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Gennie Schuller
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - John D Loy
- University of Nebraska-Lincoln, Institute of Agriculture and Natural Resources, School of Veterinary Medicine and Biomedical Sciences, Lincoln, NE, USA
| | - Aspen M Workman
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Tara G McDaneld
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Michael L Clawson
- United States Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA.
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21
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Lindholm-Perry AK, Kuehn LA, McDaneld TG, Miles JR, Workman AM, Chitko-McKown CG, Keele JW. Complete blood count data and leukocyte expression of cytokine genes and cytokine receptor genes associated with bovine respiratory disease in calves. BMC Res Notes 2018; 11:786. [PMID: 30390697 PMCID: PMC6215650 DOI: 10.1186/s13104-018-3900-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 10/30/2018] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE The purpose of this study was to evaluate potential relationships between cytokine gene expression, complete blood counts (CBC) and animals that were sick or would become sick. The CBC and the transcript abundance of cytokines and their receptors expressed in leukocytes were measured from calves at two early timepoints, and again after diagnosis with bovine respiratory disease (BRD). RESULTS Blood was collected from calves at pre-conditioning (n = 796) and weaning (n = 791) for CBC. Blood counts were also measured for the calves with BRD (n = 13), and asymptomatic calves (n = 75) after weaning. The CBC were compared for these animals at 3 time points. At diagnosis, neutrophils were higher and basophils lower in sick animals (P < 0.05). To further characterize BRD responses, transcript abundance of 84 cytokine genes were evaluated in 5 calves with BRD and 9 asymptomatic animals at all time points. There was more data for CBC than transcript abundance; hence, animal and temporary environmental correlations between CBC and transcript abundance were exploited to improve the power of the transcript abundance data. Expression of CCL16, CXCR1, CCR1 was increased in BRD positive animals compared to controls (P-corrected < 0.1). Cytokine expression data may help to provide insight into an animal's health.
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Affiliation(s)
| | - Larry A. Kuehn
- USDA, ARS, U.S. Meat Animal Research Center, P.O. Box 166, Clay Center, NE 68933 USA
| | - Tara G. McDaneld
- USDA, ARS, U.S. Meat Animal Research Center, P.O. Box 166, Clay Center, NE 68933 USA
| | - Jeremy R. Miles
- USDA, ARS, U.S. Meat Animal Research Center, P.O. Box 166, Clay Center, NE 68933 USA
| | - Aspen M. Workman
- USDA, ARS, U.S. Meat Animal Research Center, P.O. Box 166, Clay Center, NE 68933 USA
| | | | - John W. Keele
- USDA, ARS, U.S. Meat Animal Research Center, P.O. Box 166, Clay Center, NE 68933 USA
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