Transmission of extended spectrum β-lactamase-producing Escherichia coli and antimicrobial resistance gene flow across One Health compartments in eastern Africa: a whole-genome sequence analysis from a prospective cohort study

This study used whole-genome sequencing of more than 2,300 ESBL-producing E. coli isolates from humans, animals, and environmental sources in Malawi and Uganda to understand how antimicrobial resistance spreads across interconnected One Health compartments. The researchers found exceptionally high genetic diversity, with many sequence types and numerous plasmids carrying key ESBL genes such as blaCTX-M-15 and blaCTX-M-27, enabling multiple routes of dissemination. Genomic and SNP analyses showed frequent mixing and transmission of resistant E. coli strains between humans, animals, and the environment, highlighting constant spillover in all directions. These findings demonstrate that AMR in eastern Africa is strongly shaped by cross-compartment circulation, underscoring the need for a genuine One Health approach—particularly improvements in water, sanitation, and hygiene—to reduce environmental reservoirs and interrupt transmission pathways.