Whole-Genome Characterisation of Multidrug-Resistant Escherichia coli from the Livestock-Human-Environment Interface in South West Nigeria: An Original One Health Resistome Analysis

This dissertation provides an original whole-genome-based One Health resistome analysis of multidrug-resistant Escherichia coli from livestock, human, and environmental reservoirs at the livestock-human interface in South West Nigeria, encompassing Lagos, Ogun, Oyo, Osun, Ekiti, and Ondo States. Escherichia coli is the principal carrier of transferable antimicrobial resistance genes across the One Health interface and its genomic characterisation in Nigerian settings is foundational for understanding AMR transmission dynamics yet has not been comprehensively undertaken. The dissertation employs a longitudinal cross-sectional design, collecting E. coli isolates from poultry, cattle, pigs, farm workers, abattoir workers, domestic contacts, wastewater, and agricultural soil at 25 interface sites over 24 months. Whole genome sequencing using Illumina short-read and Oxford Nanopore long-read platforms is performed on 600 isolates. Pan-genome analysis, ARG cataloguing, plasmid replicon typing, and insertion sequence analysis are conducted. Phylogenomic clustering using core genome MLST identifies shared lineages across One Health compartments. The dissertation proposes the Nigerian E. coli One Health AMR Transmission Network (NEOATN) as an original analytical and theoretical contribution. Primary findings document 14 ESBL and carbapenem-resistant E. coli sequence types shared across livestock-human-environment compartments at the same sites, with IncF and IncI1 plasmids as the predominant ARG mobilisation vehicles. The dissertation provides the largest Nigerian E. coli WGS dataset published and original empirical evidence for local One Health AMR transmission at agricultural interfaces. Keywords: E. coli, whole genome sequencing, antimicrobial resistance, One Health, South West Nigeria.