Surveillance of infectious diseases and antimicrobial resistance from sewage in Kibera (Nairobi, Kenya)

No single approach for adequately monitoring large populations and their environments for the emergence of novel pathogens exists. Recent developments in high-throughput sequencing offer the ability to rapidly identify nucleic acids from various organisms in clinical and environmental samples. Sewage systems are recognized as an important source of human pathogens, especially in crowed settings with poor infrastructure. Temporal metagenomic analysis are being applied to sewage samples from the Kibera informal settlement in Nairobi (Kenya) and compared to pathogens identified through an ongoing GDD-Kenya population-based infectious disease surveillance program. Comparison of disease trends and corresponding pathogens in sewage from this community will demonstrate the ability of this approach to detect potential outbreaks of disease and to develop corresponding intervention and prevention strategies.