Wastewater metagenomic sequencing enables broad pathogen and resistome monitoring in Lagos, Nigeria
- 1Institute of Genomics and Global Health, Redeemers University
Abstract
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.
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BibTeX
@misc{parker2026wastewater,
title = {{Wastewater metagenomic sequencing enables broad pathogen and resistome monitoring in Lagos, Nigeria}},
author = {E. Parker and F. Oladipo and J. I. Levy and O. O. Ope-Ewe and H. Soumare and K. Andersen and A. N. Happi and C. T. Happi},
howpublished = {medRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.22.26363641},
url = {https://www.medrxiv.org/content/10.64898/2026.09.22.26363641v1},
note = {CC BY-ND},
}
RIS
TY - UNPB
TI - Wastewater metagenomic sequencing enables broad pathogen and resistome monitoring in Lagos, Nigeria
AU - E. Parker
AU - F. Oladipo
AU - J. I. Levy
AU - O. O. Ope-Ewe
AU - H. Soumare
AU - K. Andersen
AU - A. N. Happi
AU - C. T. Happi
PY - 2026
DA - 2026/09/22
PB - medRxiv
DO - 10.64898/2026.09.22.26363641
UR - https://www.medrxiv.org/content/10.64898/2026.09.22.26363641v1
AB - 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.
ER -