<p class="MDPI12titleori1" style="mso-line-height-alt: 14.0pt;"><span style="mso-bidi-font-size: 18.0pt; mso-ligatures: standardcontextual;">Genomic Ecology of ESBL-Producing <em>Escherichia coli</em> Across Human, Animal and Environmental Interfaces in Oman: A One Health Analysis of Resistance, Virulence and Plasmid Dynamics

Background: Antimicrobial resistance is a One Health problem driven by the intricate interactions across human, animal, and environmental interfaces that enable microbial exchange and movement of mobile genetic elements encoding resistance and virulence. This study investigated the genomic epidemiology of ESBL and non-ESBL Escherichia coli across One Health interfaces in Oman. Methods: This prospective cross-sectional study analysed 245 non-duplicate Escherichia coli isolates from clinical, animal (diseased and healthy), sewage and water sources. Antimicrobial susceptibility testing was performed phenotypically, and a representative subset of ESBL and non-ESBL Escherichia coli from the three interfaces (n=50) underwent whole-genome sequencing to determine MLST, phylogroups, resistance genes, virulence determinants and plasmid replicons. Results: ESBL prevalence was highest in human isolates (73%), followed by sewage (28.6%) and animals (16.3% diseased; 8% healthy). blaCTX-M-15 predominated in humans, whereas blaCTX-M-55 dominated in animals and sewage, suggesting ecological partitioning with partial overlap. Quinolone resistance was least in the animal interface. Sewage isolates harboured the most complex resistome, including rmtB and plasmid-mediated quinolone resistance genes. MLST analysis revealed high diversity in human isolates, including globally recognised ExPEC lineages (ST10, ST38, ST73, ST127, ST131), while ST224 dominated in animals with evidence of possible spillover to humans. ST167 was confined to sewage, consistent with environmental maintenance of high-risk clones. Phylogroup structuring showed predominance of A, B2 and D among human isolates and A, B1, E among animal and sewage isolates. Virulence profiling demonstrated broader virulome diversity in humans, but shared core determinants (fimH, sitA, traT) across all domains. IncFIB(AP001918) was the dominant plasmid replicon, particularly among ESBL isolates, underscoring its role in horizontal gene dissemination. Alarmingly, mutation in pmrB (V161G) was identified in a healthy animal isolate pointing to a need for greater colistin restriction in animal husbandry. Conclusions: This study highlights plasmid-mediated resistance and shared virulence determinants linking reservoirs, although AMR profile was quite distinct across the three interfaces, with human isolates demonstrating greater resistance than animal isolates suggesting healthcare driven AMR in Oman. Continued integrated genomic surveillance is essential to monitor gene flow and inform coordinated antimicrobial stewardship strategies.