River Tributaries as Conduits of Antimicrobial Resistance: Genomics of Escherichia coli Draining into Laguna de Bay, The Philippines

Laguna de Bay, the largest lake in the Philippines, is a critical multi-use water resource supporting fisheries, agriculture, recreation, and surrounding communities. It receives inflow from 21 river tributaries, draining densely populated areas where backyard farming, untreated wastewater inflow, and agricultural runoff are widespread. Unregulated antibiotic use in livestock and community settings may contribute to the emergence and spread of antimicrobial-resistant (AMR) bacteria across interconnected human, animal, and environmental compartments. Despite growing recognition of AMR as a One Health issue, data on environmental reservoirs of antimicrobial-resistance genes (ARGs) in Philippine freshwater systems remain limited.

In this study, Escherichia coli isolates were collected from river tributaries draining into Laguna de Bay and screened for ARGs using PCR. Isolates positive for extended-spectrum beta-lactamase genes, including blaSHV, bla TEM, and blaCTX-M-1, were selected for whole-genome sequencing using Oxford Nanopore long-read technology. Genome assembly and annotation were performed to characterize resistance gene profiles and their genomic context.

Whole-genome analysis revealed a diverse repertoire of ARGs, including clinically significant carbapenemase and oxacillinase genes not detected through PCR. The detection of blaNDM and blaOXA in environmental E. coli highlights the circulation of high-risk resistance determinants at the human–animal–environment interface. These findings indicate that river tributaries serve as important conduits for AMR dissemination into Laguna de Bay and underscore the value of genomics for One Health-oriented AMR surveillance in the Philippines.