Genomic investigation of ESBL-producing Escherichia coli reveals likely transmission within and between One Health sectors in Jakarta, Indonesia

Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E. coli) threaten public health and economic development. Transmission dynamics within One Health sectors in endemic settings remain poorly defined. We employ a One Health genomic epidemiology approach to investigate ESBL-E. coli transmission in Jakarta. We sequenced 266 ESBL-E. coli isolates from human, chicken and environmental samples revealing a diverse population with 96 sequence types (STs), highlighting ST131 in human samples and ST410 in environmental niches. Clonal strains of ST410 and ST10 in upstream and downstream waterways indicate environmental dissemination. Average Nucleotide Identity (ANI) and single nucleotide polymorphism (SNP) analyses identified likely transmission events, including potential nosocomial spread of ST131 and waterborne transmission routes connecting hospital effluent, rivers, and community sources. These findings demonstrate AMR transmission across human, animal, and environmental sectors. Integrating One Health genomic surveillance is critical to monitor and mitigate ESBL-E. coli spread. Improved sanitation, responsible antibiotic use, and ongoing monitoring is needed.