Sewage surveillance of antibiotic resistance genes and pathogens from settlements in Kenya

The goal of the project is to identify antibiotic resistance genes, mobile genetic elements and bacterial pathogens present in sewage in settlements in Nairobi, Kenya.

During the COVID-19 pandemic, many organizations showed that surveillance of sewage can be a sensitive tool to monitor the circulation of pathogens, especially the SARS-CoV-2 virus responsible for COVID-19. This method relies on the premise that the virus will be shed, especially in faecal matter. Monitoring of sewage systems therefore allows for rapid detection of the presence and spread of pathogens in a given catchment area.


To determine the prevalence of various antibiotic resistance genes and mobile genetic elements in sewage in Nairobi using high-throughput quantitative polymerase chain reaction arrays.

Expected outcome

Identification and mapping of the presence of antibiotic-resistant genes, pathogens and mobile genetic elements across catchment areas in Nairobi.


  • Kenya Water Institute
  • Nairobi City Water and Sewerage Company
  • Nairobi Metropolitan Services
  • Resistomap Inc.
  • Waternet