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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Abstract
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) |
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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 |
URI: | https://mural.maynoothuniversity.ie/id/eprint/16511 |
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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