Wastewater metagenomic sequencing enables broad pathogen and resistome monitoring in Lagos, Nigeria.

Population-scale pathogen surveillance is limited worldwide, particularly in resource-constrained settings, where clinical systems only monitor select priority pathogens and reach only those who can access healthcare. Wastewater-based epidemiology addresses many of these gaps, offering cost-effective surveillance that is adaptable across diverse implementation contexts. In Lagos, Nigeria, a high enteric pathogen burden coincides with a complex sanitation landscape. However, circulating pathogen diversity in Lagos is largely uncharacterised outside of outbreak contexts. Here we characterize human-associated pathogen diversity in Lagos with virus-enriched metagenomic and metatranscriptomic sequencing of untreated wastewater sampled from open drainage canals from July-August 2024. We detected a diverse human-associated virome dominated by enteric adenoviruses, astroviruses and caliciviruses. We recovered numerous partial and near-complete genomes from pathogens of public health concern, including noroviruses, enteroviruses and sapoviruses. Although our enrichment targeted viruses, we detected diverse bacterial pathogens, including recurrent detection of Vibrio cholerae , other enteric bacteria, and zoonotic pathogens such as Streptococcus suis. We also detected antimicrobial resistance genes, including aminoglycoside, beta-lactam and fluoroquinolone resistance and clinically important genes such as mcr . Together, these results establish a regional baseline of pathogen diversity and demonstrate the utility of virus-enriched sequencing for integrated wastewater surveillance.