Human wastewater contamination drives the emergence of multidrug-resistant bacteria in the Galápagos marine ecosystem

Antimicrobial resistance poses a global threat to public health. Mobile microbiological laboratories can enable environmental monitoring of antimicrobial resistance, particularly in geographically remote and resource-limited locations, such as the Galápagos archipelago. Here, we report the development of a mobile laboratory for antimicrobial resistance surveillance of marine sites surrounding San Cristóbal, the archipelago’s second most populated island, which has experienced rapid urbanization and intense international tourism pressure. On-site metagenomic sequencing of wastewater-contaminated marine sites reveals a stark shift in microbial genera and a higher count of antimicrobial resistance genes compared to uncontaminated marine sites, mirroring metagenomic results of local untreated sewage. Over 40% of lactose-fermenting Enterobacteriaceae isolates collected directly from sewage or marine environments near sites of wastewater outfall exhibit multidrug resistance. Long-read sequencing and de novo assembly of bacterial genomes and plasmids from multidrug-resistant Escherichia coli reveal frequent and rapid reassortment of antimicrobial resistance genes on plasmids, generating a diverse and functional resistome on the island. This study not only provides a framework for conducting antimicrobial resistance research in low-resource settings but also underscores the impact of wastewater contamination on the environmental antimicrobial resistance landscape and highlights potential threats to human and animal health. The Galápagos archipelago is a remote region known for its unique biodiversity. Here, the authors use a mobile laboratory to identify untreated wastewater as a source of multidrug-resistant bacteria in marine coastal waters emphasizing the need to manage the impact of increased urbanization on public health and biodiversity.