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Recent Submissions

  • PersonMetadata only
    Short, Ian
  • PersonMetadata only
    Jones, Grace
  • PublicationOpen Access
    Herd-level occurrence and risk factors associated with respiratory and enteric pathogens from dairy calves in Ontario: A cross-sectional study
    (American Dairy Science Association, 2025-01) Umaña Sedó, S.G.; Winder, C.B.; Perry, K.V.; Caswell, J.L.; Mee, J.F.; MacNicol, J.; Renaud, D.L.; Ontario Ministry of Agriculture, Food and Rural Affairs
    This cross-sectional herd-level study aimed to determine the occurrence of and risk factors for pathogens associated with neonatal calf diarrhea (NCD) and bovine respiratory disease (BRD) on Ontario dairy farms. From April to August 2022, a convenience sample of 100 dairy farms was visited once. A questionnaire covering farm biosecurity, calving and colostrum management, preweaning nutrition, and housing was administered on-farm. At each farm visit, approximately 5 calves between 2 and 35 d old were randomly selected for fecal sampling. Furthermore, approximately 5 calves between 21 to 122 d old were randomly selected for nasopharyngeal sampling. In total, 363 fecal samples (from 83 dairy farms) and 390 nasopharyngeal swab samples (from 80 dairy farms) were collected. Fecal samples were analyzed individually using a multiplex PCR to identify bacterial and parasitic enteric pathogens. Nasopharyngeal swabs were analyzed as one pooled sample per farm using bacterial culture and real-time PCR. The most common enteric pathogens detected at herd-level were Cryptosporidium parvum (67.4%) and Escherichia coli K99+ (13.2%). The most common respiratory pathogens detected at herd-level were Pasteurella multocida (62.5%), bovine coronavirus (42.5%), and Mycoplasma bovis (21.2%). Multivariable logistic models were built to explore associations between the most common pathogens and herd-level predictors selected from the questionnaire. Herd positivity for C. parvum was positively associated with having more than 61 preweaning calves per year and feeding mainly whole milk to calves. The presence of M. bovis was positively associated with herds that combined manual and automatic milk-feeding systems, and the presence of bovine coronavirus was positively associated with having more than 98 preweaning calves during the year. Univariable Poisson regression models were built to explore the association between the most common pathogens and preweaning calf mortality. Herds that were positive for C. parvum, M. bovis, or bovine coronavirus had a greater risk of preweaning calf mortality. These results provide insights for future research on pathogens associated with NCD and BRD and offer guidance for veterinarians and dairy farmers in implementing disease control measures in dairy calf herds
  • PublicationOpen Access
    Antimicrobial use in pig herds in Ireland: analysis of a national database (2019–2023)
    (2025-05-02) Bolton, Julie; O’Neill, Lorcan; Garvan, Caroline; Byrne, Andrew W.
    Abstract Background Antimicrobial resistance (AMR) in human and animal pathogens remains a global One-Health threat. The associations between antimicrobial use (AMU) and the evolution and dissemination of AMR bacteria, and their resistance genes, highlight the importance of monitoring and regulating AMU. Here, we present an analysis of national monitoring data of AMU in pig facilities in Ireland from 2019 to 2023 via the recently established National AMU Database. AMU was measured using two metrics (mg per corrected population units (mg/PCU) and defined daily dose (DDDvet/PCU)). Temporal trend models were fit using regression models with population average effects given there were multiple observations per herd, while controlling for herd type and size. Results Linear spline models revealed no significant change in overall usage from Q1-2019 until mid-2020, followed by a significant decrease in usage until mid-2022. There was evidence of increases in usage from mid-2022 until the end of the time series; the exact timing of the changes in trends varied by the AMU metric. A multinomial logit regression model suggested that there was a significantly decreased probability of premix use relative to oral administration from Q3-2021 through Q4-2023 (OR: 0.70 − 0.58; P < 0.03). The predicted probability that a high priority critically important antimicrobial (HPCIA) was used in a herd during a year-quarter declined by an average of 9% per quarter (OR: 0.91; 95% CI: 0.90–0.92; p < 0.001) over the study period. The mean decline in use of cephalosporin (3rd /4th generation), fluoroquinolone and macrolide (a former HPCIA) per quarter were estimated to be -12% (95% CI: -8– -15%), -9% (95% CI: -8– -10%) and − 4% (95% CI: -2– -4%), respectively. Conclusions This exploration of AMU in pigs in Ireland revealed significant changes in overall usage, with both decreases and increases. There were declines in usage of HPCIA agents. Additionally, there was evidence of a significant decline in the use of oral premixes, coinciding with policy change. Further monitoring of AMU is essential to understand how the pig farming sector is responding to policy changes (e.g., increasing AMU in response to zinc oxide bans).
  • PublicationOpen Access
    Understanding the barriers and enablers to agroforestry adoption in Ireland through an innovation systems approach
    (Elsevier, 2025-07) Irwin, Rachel; Short, Ian; Ní Dhubháin, Áine
    The innovation of agroforestry is relatively new in Ireland, with uptake lagging behind targets. This study aimed to identify the reasoning behind this and identify the main barriers to the uptake of agroforestry. The Innovation Systems Approach was used as the analytical framework to the study whereby a structural-functional analysis was used to identify the main barriers/blocking mechanisms. Thirty-three interviews across all four domains of the innovation system (research, intermediary, enterprise and influencing) were undertaken with actors from the wider agricultural and forestry sectors networks. The results demonstrate the following key failures of the current Irish Agroforestry Innovation system: a low level of knowledge of agroforestry; a lack of research undertaken and capacity; a lack of interaction between actors; policy issues; and a lack of goals within actor organisations in supporting and promoting agroforestry. The paper provides a number of recommendations aimed at reducing the identified failures laid out as a set of goals.

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