Progress 07/15/22 to 07/14/23
Outputs
Target Audience:The target audience for the reporting period includes national and international researchers studying a wide range of respiratory pathogens infecting not only cattle but also other ruminant species. This was accomplished through an oral presentation at the 2023Conference of Respiratory Workers in Animal Disease conference, Chicago, IL. Results of the grant to date were presented. Changes/Problems:To date, we have completed sample collection for year one and two of the grant on approximately 700 calves at the US Meat Animal Research Center. For the two years of sample collection, we did not have a significant outbreak of bovine respiratory disease (BRD) at the feedlot after weaning (<5% of calves diagnosed with BRD). With this low incidence of BRD in the feedlot, we were unable to collect any samples from calves with severe BRD as outline in our project plan. As previously reported, we did have a BRD outbreak for approximately 90 calves two months prior to weaning in year one. Data from this outbreak was published in 2022 and previous outbreaks at the US Meat Animal Research Center will be utilized to evaluate bacterial and viral profiles of calves with severe incidence of BRD. With restrictions being lifted after the pandemic, our collaborator Dr. Louise Cosby was able to bring in livestock but staffing limitations have not allow for animal work to be initiated until recently. Dr. Louise Cosby has been able to hire and install an individual into the animal handling facility, and this will allow us to begin the animal work for Objective 3; however, completion of the sampling and lab work will not be completed until after the current end date of the grant (July 2023).We were granted a non-funded year extension to complete this objective. What opportunities for training and professional development has the project provided?Undergraduate students have been trained in the sample collection (nasal swab and blood) and processing (DNA extraction). These trainings have been provided by scientists and other trained personnel overseeing these activities. How have the results been disseminated to communities of interest?An oral presentation was presented at the Conference of Research Workers in Animal Disease (CRWAD) meeting in 2023. This presentation summarized the sample collection and data analysis completed to date. What do you plan to do during the next reporting period to accomplish the goals?For this study, calves will be brought into the AFBI facility by Dr. Louise Cosby in two groups (BRSV and BHV-1 group). The first group (BRSV group) will be brought into the facility for acclimation in April 2023 along with a control group. After acclimation of the calves, infection and sample collection will occur in May and June of 2023 for the BRSV and their control group. The second group (BHV-1 group) will be brought into the facility for acclimation in July 2023 along with a control group. After acclimation of the calves, infection and sample collection would occur in August and September of 2023 for the BHV-1 and their control group. Processing of the samples and analysis of the data will occur from September to December 2023.
Impacts
What was accomplished under these goals?
Objective 1:Investigate the prevalence and distribution of species in the respiratory microbiome and virome associated with BRDC in beef herds at the US Meat Animal Research Center (USMARC) and in beef and dairy herds in Ireland.Completed. 1. Completion of sample (nasal swabs and blood) collection in 2019 and 2020. Approximately 800 calves at the US Meat Animal Research Center were collected each year. These samples were collected at selected timepoints prior to weaning and when calves are diagnosed with BRDC after weaning at the feedlot. 2. Completion of collection of samples (nasal swabs and blood) in 2019 for approximately 50 calves of the 800 total when an outbreak of BRDC occurred two months prior to weaning at the feedlot. 3. Completion of collection of samples (nasal swabs and blood) from beef and dairy herds in Ireland in 2019 and 2020. Objective 2:Employ next-generation sequencing (NGS), third-generation sequencing (TGS), bioinformatic technologies, and high throughput sensitive and rapid diagnostics to identify respiratory viral and bacterialagents associated with BRDC.Completed. 1. Completion of sample processing for DNA and RNA extraction (USMARC and Ireland). 2. Completion of sequencing for bacterial and viral agents (USMARC and Ireland). 3. Identification of changes in the bacterial and viral agents (USMARC and Ireland). Objective 3:Elucidate the dynamics of secondary viral and bacterial infection by monitoring experimentally virus infected animals in longitudinal studies.Not completed. 1. Facilities at the Agri Food and Biosciences Institute have been approved for animal use. 2. Permit for importation of samples (RNA and cDNA) from Ireland has been submitted. 3. Staff has been put into place, and we will be able to begin animal studies for the objective in April 2023.
Publications
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2023
Citation:
T. G. McDaneld, B. Earley, S. L. Cosby, K. Duffy, M. McGee, L. A. Kuehn, A. M. Workman, G. Conant, P. Cormican, M. McCabe, C. Duffy, H. Turkington, K. Lemon, M. McMenamy, V. Smyth, T. P. L. Smith. Characterization of the respiratory microbiome and virome associated with Bovine Respiratory Disease Complex. CRWAD 2023, Chicago, IL.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2022
Citation:
McDaneld, T. G., Workman, A. M., Chitko-McKown, C. G., Kuehn, L. A., Dickey, A., and Bennett, G. L. 2022. Detection of Mycoplasma bovirhinis and bovine coronavirus in an outbreak of bovine respiratory disease in nursing beef calves. Frontiers in Microbiomes. Volume 1. https://doi.org/10.3389/frmbi.2022.1051241.
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Progress 07/15/21 to 07/14/22
Outputs
Target Audience:The target audience for the reporting period includes national and international researchers studying a wide range of respiratory pathogens infecting not only cattle but also other ruminant species. This was accomplished through a posterpresentation at the 2021Conference of Research Workers in Animal Disease conference, Chicago, IL. Results of the grant to date were presented. Changes/Problems:To date, we have completed sample collection for year one and two of the grant on approximately 700 calves at the US Meat Animal Research Center. For the two years of sample collection, we did not have a significant outbreak of bovine respiratory disease (BRD) at the feedlot after weaning (<5% of calves diagnosed with BRD). WIth this low incidence of BRD in the feedlot, we were unable to collect any samples from calves with severe BRD as outline in our project plan. As previously reported, we did have a BRD outbreak for approximately 90 calves two months prior to weaning in year one. Data from this outbreak and previous outbreaks at the US Meat Animal Research Center will be utilized to evaluate bacterial and viral profiles of calves with severe incidence of BRD. The COVID-19 pandemic has continued to provided a challenge for the research being completed, as researchers and technicians at the US Meat Animal Research Center, Teagasc, and AFBI were asked to telework 100% beginning in March of 2020. At the US Meat Animal Research Center, we have begun to phase back to work. Collaborators at Teagasc and AFBI have also begun to phase back to work. Dispite these challenges, we have been able to complete collection of samples (Objective 1) and complete evlauation of those samples (Objective 2). However, our collaborator at AFBI has also been unable to initiate studies for Objective 3 due to issues with facilities. We were granted a non-funded year extension to complete this objective and plan to initiate this the end of 2022. What opportunities for training and professional development has the project provided?Undergraduate students have been trained in the sample collection (nasal swab and blood) and processing (DNA extraction). These trainings have been provided by scientists and other trained personnel overseeing these activities. How have the results been disseminated to communities of interest?Poster and oral presentationswere presented and the Conference of Research Workers in Animal Disease (CRWAD) meeting in 2021. These presentations summarized the sample collection and data analysiscompleted to date. What do you plan to do during the next reporting period to accomplish the goals?Specific plans for next reporting period are listed by objective/goal and bolded: 1) Identify the prevalence and distribution of species in the respiratory microbiome and virome associated with BRD in beef herds at the US Meat Animal Research Center (USMARC) and in beef and dairy herds in Ireland. Collection has been completed in previous progress report. 2) Use sequencing technologies to identify respiratory viral and bacterial agents associated with BRD. Complete processing (DNA and RNA extraction) of nasal samples collected in US Meat Animal Research Center and Ireland herds and begin sequencing of samples for identification of bacterial and viral pathogens. Complete computation analysis of the sequence data. 3) Elucidate the dynamics of secondary viral and bacterial infection by monitoring experimentally virus infected animals inPerform experimental infection of calves with known viral pathogens associated with BRD (completed by AFBI PD (Northern Ireland)). Collect samples (nasal swabs and blood samples) from infected calves that will be processed and evaluated in non-funded extension year 4of the grant.
Impacts
What was accomplished under these goals?
Objective 1: Investigate the prevelance and distribution of species in the respiratory microbiome and virome associated with BRD in beef herds at the US Meat Animal Research Center (USMARC) and in beef and dairy herds in Ireland. Collection of samples for this objective was completed in 2021. Objective 2: Employ next-generation sequencing (NGS), third-generation sequencing (TGS), bioinfomatic technologies, and high throughput sensitive and rapid diagnostics to identify respiratory viral and bacterial agents associated with BRD. Efforts that we have conducted in reporting period include: 1. Samples (nasal swabs) from USMARC have been processed for DNA and RNA extraction. 2. Sequencing is concluding for the bacterial and viral pathogens. 3. Analysis is continuing for the sequence data of the bacterial and viral pathogens. Objective 3: Elucidate the dynamics of secondary viral and bacterial infection by monitoring experimentally virus infected animals in longitudinal studies. Efforts that we have conducted in reporting period include: 1. Infection challenge studies by our AFBI (Northern Ireland) PD have been delayed due to COVID-19 challenges. These challenges will the discussed later.
Publications
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2021
Citation:
T. G. McDaneld, B. Earley, S. L. Cosby, M. McGee, I. Cuevas-Gomez, L. A. Kuehn, A. M. Workman, G. Conant, P. Cormican, M. McCabe, C. Duffy, K. Lemon, M. McMenamy, V. Smyth, and T. P. L. Smith. TRI-PARTITE
COLLABORATIVE: Characterization of the respiratory microbiome and virome associated with Bovine Respiratory Disease Complex. CRWAD 2021, Chicago, IL
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2021
Citation:
K. Ni? Dhufaigh, M. McCabe, P. Cormican, I. Cuevas-Gomez, M. McGee, T. McDaneld, B. Earley. Characterization of the respiratory virome of Irish beef weanlings associated with bovine respiratory disease. CRWAD 2021, Chicago, IL.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2021
Citation:
K. Ni? Dhufaigh, M. McCabe, P. Cormican, I. Cuevas-Gomez, M. McGee, T. McDaneld, B. Earley. Characterization of the beef nasopharyngeal microbiome associated with bovine respiratory disease. CRWAD 2021, Chicago, IL.
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Progress 07/15/20 to 07/14/21
Outputs
Target Audience:The target audience for the reporting period includes national and international researchers studying a wide range of respiratory pathogens infecting not only cattle but also other ruminant species. This was accomplished through an oral presentation at the 2020 Conference of Research Workers in Animal Disease conference, Chicago, IL. Results of the grant to date were presented. Changes/Problems:To date, we have completed sample collection for year one and two of the grant on approximately 700 calves at the US Meat Animal Research Center. SImilar to what we reported in year one, we did not have a significant outbreak of bovine respiratory disease (BRD) at the feedlot after weaning (<5% of calves diagnosed with BRD). WIth this low incidence of BRD in the feedlot, we were unable to collect any samples from calves with severe BRD as outline in our project plan. As previously reported, we did have a BRD outbreak for approximately 90 calves two months prior to weaning in year one. Data from this outbreak and previous outbreaks at the US Meat Animal Research Center will be utilized to evaluate bacterial and viral profiles of calves with severe incidence of BRD. The COVID-19 pandemic has continued to provided a challenge for the research being completed, as researchers and technicians at the US Meat Animal Research Center, Teagasc, and AFBI were asked to telework 100% beginning in March of 2020. At the US Meat Animal Research Center, we have continued to suggest employees telework and employees will begin to phase back to work beginning October 1st. Collaborators at Teagasc and AFBI have also begun to phase back to work. Dispite these challenges, we have been able to complete collection of samples (Objective 1) and begin evlauation of those samples (Objective 2). Our collaborator at AFBI has also been able to bring animals into their facility for initiation of studies for Objective 3. What opportunities for training and professional development has the project provided?Undergraduate students have been trained in the sample collection (nasal swab and blood) and processing (DNA extraction). These trainings have been provided by scientists and other trained personnel overseeing these activities. How have the results been disseminated to communities of interest?An oral presentation was completed at the Conference of Research Workers in Animal Disease (CRWAD) meeting in 2020. This talk presented to results completed in year one of the grant. Our collaborators at Teagasc and AFBI also published two manuscripts from their work evaluating thoracic ultrasonography as a technique to identify calves with bovine respiratory disease. What do you plan to do during the next reporting period to accomplish the goals?Specific plans for next reporting period are listed by objective/goal and bolded: 1) Identify the prevalence and distribution of species in the respiratory microbiome and virome associated with BRD in beef herds at the US Meat Animal Research Center (USMARC) and in beef and dairy herds in Ireland. Collection of samples (nasal swabs and blood) was completed in year one and two of the project period. Therefore, this objective is completed and we will focus on Objective 2 and 3 for year 3 of the project period. 2) Use sequencing technologies to identify respiratory viral and bacterial agents associated with BRD. Complete processing (DNA and RNA extraction) of nasal samples collected for year two in the US Meat Animal Research Center and Ireland herds and begin sequencing of samples for identification of bacterial and viral pathogens and determine taxonomic assignment of 16S sequence. From this taxonomic assignment, we will be able to identify novel bacterial and viral species that are associated with BRD in US and Irish cattle herds. Begin gene-centric analyses of bacterial taxonomic data provide insights about the function of these bacteria. 3) Elucidate the dynamics of secondary viral and bacterial infection by monitoring experimentally virus infected animals in longitudinal studies. Complete experimental infection of calves with known viral pathogens associated with BRD (completed by AFBI PD (Northern Ireland)). Collect samples (nasal swabs and blood samples) from infected calves that will evaluated for bacterial and viral profiles. Additionally, these samples will be evaluated for T- and B-cell repertoires of the immune system.
Impacts
What was accomplished under these goals?
Specific accompllishments for the reporting period are listed by objective/goal and bolded: Objective 1: Investigate the prevelance and distribution of species in the respiratory microbiome and virome associated with bovine respiratory disease (BRD) in beef herds at the US Meat Animal Research Center (USMARC) and in beef and dairy herds in Ireland. Efforts that we have conducted in reporting period include: 1. Collected samples (nasal swabs and blood) for year two from approximately 700 calves at the US Meat Animal Research Center. These samples were collected at selected timepoints prior to weaning and when calves are diagnosed with BRD after weaning in the feedlot. 2. Herds for sampling of year two in Ireland were selected for monitoring and sampling. Nasal samples were collected from these calves. Objective 2: Employ next-generation sequencing (NGS), third-generation sequencing (TGS), bioinfomatic technologies, and high throughput sensitive and rapid diagnostics to identify respiratory viral and bacterial agents associated with BRD. Efforts that we have conducted in reporting period include: 1. Samples (nasal swabs) from USMARC collected in year one and year two have been processed for DNA and RNA extraction to evaluate the bacterial and viral profiles. 2. Evaluation of samples (nasal swabs) from USMARC collected in year one and year two, determined that calves diagnosed with BRD in the feedlot have increased abundance of bacterial pathogens including Mycoplasma sp., Sneathia sp., Bergeyella sp., and Corynebacterium sp. compared to control cohorts. Bovine corova virus and bovine respiratory syncytial virus were also detected in feedlot calves diagnosed with BRD. Objective 3: Elucidate the dynamics of secondary viral and bacterial infection by monitoring experimentally virus infected animals in longitudinal studies. Efforts that we have conducted in reporting period include: 1. Infection challenge studies by our AFBI (Northern Ireland) PD have been delayed due to COVID-19 challenges. Our AFBI partner was able to initiate infection challenges earlier this year. These challenges will the discussed later.
Publications
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
T. G. McDaneld, B. Earley, S. L. Cosby, M. McGee, I. Cuevas-Gomez, L. A. Kuehn, A. M. Workman, G. Conant, P. Cormican, M. McCabe, C. Duffy, K. Lemon, M. McMenamy, V. Smyth, and T. P. L. Smith. TRI-PARTITE COLLABORATIVE: Characterization of the respiratory microbiome and virome associated with Bovine Respiratory Disease Complex. CRWAD 2020, Chicago, IL
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Cuevas-G�mez I., McGee M., McCabe M., Cormican P., O'Riordan E., McDaneld T., Earley B. Growth performance and hematological changes of weaned beef calves diagnosed with respiratory disease using respiratory scoring and thoracic ultrasonography. J Anim Sci. 2020 Nov 1;98(11):skaa345. doi: 10.1093/jas/skaa345. PMID: 33095858; PMCID: PMC7694598.
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Cuevas-G�mez I., McGee M., S�nchez J.M., O'Riordan E., Byrne N., McDaneld T., Earley B. Association between clinical respiratory signs, lung lesions detected by thoracic ultrasonography and growth performance in pre-weaned dairy calves. Ir Vet J. 2021 Mar 25;74(1):7. doi: 10.1186/s13620-021-00187-1. PMID: 33766106; PMCID: PMC7992334.
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Progress 07/15/19 to 07/14/20
Outputs
Target Audience:For this reporting period, we have focused on sample collection and therefore have not reported results to targeted audiences. An initial presentation to informresearch scientists and educators of the overall goals of the grant was made through a poster at the 2019 Conference of Research Workers in Animal Disease conference, Chicago, IL. Changes/Problems:To date, we have completed sample collection for year one of the grant on approximately 700 calves at the US Meat Animal Research Center. While we did not have a significant outbreak of BRD at the feedlot after weaning (<5% of calves diagnosed with BRD), we did have a BRD outbreak for approximately 90 calves two months prior to weaning. While the treatment rate for BRD at the feedlot was lower than expected, we will continue sample collection in year two and continue to collect samples on outbreaks that occur prior to weaning. The COVID-19 pandemic also provided a challenge for the research being completed asresearchers and technicians at the US Meat Animal Research Center, Teagasc, and AFBI have been asked to telework 100% from March-July. At the US Meat Animal Research Center, we have just begun to phase back into work. Challenge studies at AFBI have also been delayed as animals have not been able to be brought into facilities due to COVID-19 regulations. What opportunities for training and professional development has the project provided?Undergraduate students have been trained in the sample collection (nasal swab and blood) and processing (DNA extraction). These trainings have been provided by scientists and other trained personnel overseeing these activities. How have the results been disseminated to communities of interest?A poster was presented and the Conference of Research Workers in Animal Disease (CRWAD) meeting in November of 2019. This poster presented to goals and methods of the grant and the sample collection completed to date. What do you plan to do during the next reporting period to accomplish the goals?Specific plans for next reporting period are listed by objective/goal and bolded: 1)Identify the prevalence and distribution of species in the respiratory microbiome and virome associated with BRD in beef herds at the US Meat Animal Research Center (USMARC) and in beef and dairy herds in Ireland. Collect samples (nasal swabs and blood) on a group of approximately 700 calves at the US Meat Animal Research Center and selected beef and dairy herds in Irelandto complete 2nd year of sampling. 2)Use sequencing technologies to identify respiratory viral and bacterialagents associated with BRD. Complete processing (DNA and RNA extraction) of nasal samples collected in US Meat Animal Research Centerand Ireland herds and begin sequencing of samples for identification of bacterial and viral pathogens. Begin computation analysis of the sequence data. 3)Elucidate the dynamics of secondary viral and bacterial infection by monitoring experimentally virus infected animals in longitudinal studies. Perform experimental infection of calves with known viral pathogens associated with BRD (completed by AFBI PD (Northern Ireland)). Collect samples (nasal swabs and blood samples) from infected calves that will be processed and evaluated in year 3 of the grant.
Impacts
What was accomplished under these goals?
Objective 1: Investigate the prevelance and distribution of species in the respiratory microbiome and virome associated with BRD in beef herds at the US Meat Animal Research Center (USMARC) and in beef and dairy herds in Ireland. Efforts that we have conducted in reporting period include: Collected samples (nasal swabs and blood) for year one from approximately 700 calves at the US Meat Animal Research Center. These samples were collected at selected timepoints prior to weaning and when calves are diagnosed with BRD after weaning at the feedlot. Approximately 90 calves of the 700 total were sampled (nasal swabs and blood) when an outbreak of BRD occurred two months prior to weaning. Herds for sampling in Ireland were selected for monitoring and sampling. Nasal samples were collected from these calves. Objective 2: Employ next-generation sequencing (NGS), third-generation sequencing (TGS), bioinfomatic technologies, and high throughput sensitive and rapid diagnostics to identify respiratory viral and bacterial agents associated with BRD. Efforts that we have conducted in reporting period include: Samples (nasal swabs) from USMARC have been processed for DNA and RNA extraction. Evaluation of thesamples collected from the BRD outbreak prior to weaning revealed all calves were nasally shedding bovine corona virus and a large percentage had a coinfection with Mycoplasma sp. Objective 3: Elucidate the dynamics of secondary viral and bacterial infection by monitoring experimentally virus infected animals in longitudinal studies. Efforts that we have conducted in reporting period include: Infection challenge studies by our AFBI (Northern Ireland)PDhave been delayed due to COVID-19 challenges. These challenges will the discussed later.
Publications
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2019
Citation:
T. G. McDaneld, B. Earley, S. L. Cosby, M. McGee, I. Cuevas-Gomez, L. A. Kuehn, A. M. Workman, G. Conant, P. Cormican, M. McCabe, C. Duffy, K. Lemon, M. McMenamy, V. Smyth T. P. L. Smith. TRI-PARTITE COLLABORATIVE: Characterization of the respiratory microbiome and virome associated with Bovine Respiratory Disease Complex. Poster presentation. CRWAD 2019, Chicago, IL.
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