A Serological Assessment and Development of a Microbiome and Virome Analysis in Beef Calves
Advisorvan der Meer, Frank
Committee MemberSycuro, Laura
van Marle, Guido
Bovine Respiratory Disease Complex
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AbstractBovine Respiratory Disease Complex (BRDC) is a multifactorial disease and the leading cause of morbidity and mortality on feedlots. In many instances, metaphylactic administration of antimicrobials is used to both treat and prevent BRDC. However, this practice is becoming less sustainable due to increasing antimicrobial resistance. Therefore, methods such as preconditioning are being explored to reduce BRDC incidence and the associated antimicrobial use. Preconditioning includes aspects such as fence line weaning and a strategic vaccination schedule to prepare cattle for life on the feedlot. The serological component of this study aimed to demonstrate a higher proportion of preconditioned (PC) animals would arrive on the feedlot with antibodies present than their auction derived (AD) and ranch-sourced (RS) counterparts. The vaccination protocol was evaluated by collecting serum samples from PC, AD, and RS calves upon arrival at the feedlot. Enzyme-linked immunosorbent assays were used to detect antibodies against viral BRDC-associated pathogens: Bovine Viral Diarrhoea Virus, Infectious Bovine Rhinotracheitis, Bovine Parainfluenza Virus Type 3, Bovine Respiratory Syncytial Virus, and Bovine Coronavirus (BoCoV). Significant differences were only found between PC and AD calves as well as PC and RS calves for BoCoV. A metatranscriptomics pilot study was also included in this work to determine optimal downstream processing of deep nasal swabs (DNS). Four PC calves that showed signs of BRDC during preconditioning were utilized in the pilot study. A total RNA isolation was performed on DNS before samples were divided in two, creating an “A” and “B” for each sample. “A” samples underwent rRNA depletion and poly-A tailed mRNA depletion. While “B” samples only had rRNA depleted. Results were interpreted through two bioinformatic alignment tools MetPhlAn3 and Kaiju. MetPhlAn3 identified a total of 20 species, while Kaiju identified over 5000. However, Kaiju also had a significantly high rate of false-positive when reporting positive controls; therefore, results from Kaiju must be interpreted with a high degree of caution. Data from both ELISA’s and the pilot study can provide insight for future directions for this project and, in doing so, support preconditioning as a viable method for the prevention of BRDC.
CitationLouden, J. (2022). A serological assessment and development of a microbiome and virome analysis in beef calves (Unpublished master's thesis). University of Calgary, Calgary, AB.
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