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    The Comparative Risk of Antimicrobial Resistance Transfer from Pig, Poultry and Bovine Manure to Grassland

    Tyrrell, Ciara (2022) The Comparative Risk of Antimicrobial Resistance Transfer from Pig, Poultry and Bovine Manure to Grassland. PhD thesis, National University of Ireland Maynooth.

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    Antimicrobial resistance (AMR) is a multifactorial issue involving an intertwining relationship between animals, humans and the environment. Therefore, it is critical to fully understand all potential routes of AMR transmission. Manure landspreading introduces bacteria, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) into the environment as well as altering the indigenous resistome and microbiome. Grassland consists of ~70% of global agricultural land and is a vital source of food for livestock. The phyllosphere of plants is an under-researched area regarding the impact of agricultural management practices. Therefore, the grass phyllosphere is a possible source of AMR transmission to livestock, which may enter the food chain. Despite the important role grassland plays in food security, the temporal impact of manure application on its resistome and microbiome is unknown. Additionally, the comparative risk associated with different manure sources is unclear. This thesis aimed to compare the temporal and contrasting impact pig, cow and chicken manure had on grassland microbiomes and resistomes using 16S rRNA amplicon sequencing and high-throughput qPCR (HT-qPCR). Additionally, through culture- dependent approaches the antimicrobial resistance profiles of the WHO priority pathogens Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa isolated from the manures and grassland were assessed and the molecular mechanisms of their resistance were investigated using PCR and whole genome sequencing (WGS). The manures, soil and the grass phyllosphere, both pre and post manuring, contained a diverse range of ARGs, MGEs and opportunistic pathogens, including the priority pathogens E. coli, K. pneumoniae and A. baumanii. Additionally, manure application resulted in an increased diversity of ARGs and MGEs being detected in grass and soil. In Ireland, current agricultural practices involve returning animals to land six weeks after splash-plate manure spreading. In this study, manure spreading altered the microbiome and resistome of grassland, however temporal analysis aligned with this current Irish agricultural practice, indicating that current guidelines are sufficient to reduce the spread of AMR to livestock. Pig manure was associated with the greatest change in the microbiome and resistome however overall, temporal patterns of manure types were similar, indicating that time had a greater impact than manure type. Overall, these results demonstrate the role of the grass phyllosphere as a novel reservoir of AMR and that current agricultural practices are sufficient to mitigate AMR dissemination.

    Item Type: Thesis (PhD)
    Keywords: Comparative Risk; Antimicrobial Resistance Transfer; Pig; Poultry; Bovine Manure; Grassland;
    Academic Unit: Faculty of Science and Engineering > Biology
    Item ID: 16511
    Depositing User: IR eTheses
    Date Deposited: 13 Sep 2022 15:27
      Use Licence: This item is available under a Creative Commons Attribution Non Commercial Share Alike Licence (CC BY-NC-SA). Details of this licence are available here

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