Antimicrobial Resistance Gene Mobilisation Between Livestock, Humans, and the Environment in Nigerian Agricultural Communities: A Metagenomic One Health Analysis

This dissertation provides an original metagenomic One Health analysis of antimicrobial resistance gene (ARG) mobilisation between livestock, human, and environmental reservoirs in agricultural communities across Nigeria's North West and South South geopolitical zones. The transmission of ARGs across the One Health interface represents one of the most serious and poorly characterised aspects of the global antimicrobial resistance crisis, and Nigerian agricultural systems where antibiotics are widely misused in livestock production represent high-priority settings for this research. The dissertation employs a longitudinal metagenomic design, collecting samples from livestock faeces, human rectal swabs, and soil and water from shared agricultural environments at 20 sites over 18 months, encompassing pre-monsoon, monsoon, and post-monsoon periods. Shotgun metagenomics using Illumina NovaSeq is applied to total DNA extracts. ARG cataloguing using CARD and ResFinder databases identifies the resistome composition at each compartment. Mobile genetic element (MGE) analysis identifies plasmids, integrons, and transposons as ARG vectors. Network analysis maps ARG sharing patterns across the One Health interface. The dissertation proposes an original ARG Mobilisation Network Model (AMNM) as a theoretical contribution explaining the conditions that facilitate ARG transmission across compartments. Original contributions include the first Nigerian One Health resistome dataset, the AMNM theoretical framework, and an evidence-based antibiotic stewardship intervention matrix. Keywords: antimicrobial resistance genes, metagenomics, One Health, Nigeria, resistome.