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

Researchers analyzed wastewater from open drainage canals in Lagos, Nigeria during July and August 2024 using metagenomic sequencing. They detected a diverse virome dominated by enteroviruses, astroviruses, and caliciviruses, as well as partial and near-complete genomes of pathogens of public health concern, including noroviruses and enteroviruses. In addition to viruses, they identified bacterial pathogens including Vibrio cholerae and zoonotic pathogens such as Streptococcus suis. The analysis revealed the presence of antimicrobial resistance genes, including resistance to aminoglycosides, beta-lactams, and fluoroquinolones. The results demonstrated the utility of this method for pathogen monitoring in populations and established a baseline characterization of pathogen diversity in the region.