ArticlePloS one2019
Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 2 of them syntheses that pooled it.
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Who cites it
20 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Antimicrobial resistance in community-acquired enteric pathogens among children aged ≤ 10-years in low-and middle-income countries: a systematic review and meta-analysis.Frontiers in microbiology · 2025Pooled it
- Systematic review of wastewater surveillance of antimicrobial resistance in human populations.Environment international · 2022Pooled it
- Protocols for genomic epidemiology and source attribution of enteric bacteria causing diarrhoeal disease across Africa.BMJ open · 2026Article
- Article
- Cholera in Kenya: A scoping review of current research, evidence gaps and future directions.PLOS global public health · 2026Article
- Astrovirus in the Brazilian Amazon: First detection of non-classical astroviruses (MLB-3) in the Americas.PloS one · 2026Article
- Detection of parasites in food and water matrices by shotgun metagenomics: A narrative review.Food and waterborne parasitology · 2025Review
- Advance Warning and Response Systems in Kenya: A Scoping Review.medRxiv : the preprint server for health sciences · 2025Article
- Can Wastewater Surveillance Enhance Genomic Tracking of Climate-Driven Pathogens?Microorganisms · 2025Review
- Article
- Metagenomic analysis of sewage for surveillance of bacterial pathogens: A release experiment to determine sensitivity.PloS one · 2024Article
- Metagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa.PloS one · 2024Article
- Study of the correlation between Covid-19 cases and deaths and basic sanitation in Brazil: Is this a possible secondary route of virus transmission?Journal of hazardous materials advances · 2022Article
- Study of domestic wastewater treatment using Moringa oleifera coagulant coupled with vertical flow constructed wetland in Kibera Slum, Kenya.Environmental science and pollution research international · 2022Article
- Wastewater surveillance of antibiotic-resistant bacterial pathogens: A systematic review.Frontiers in microbiology · 2022Review
- Global public health implications of human exposure to viral contaminated water.Frontiers in microbiology · 2022Review
- An implementation science approach to evaluating pathogen whole genome sequencing in public health.Genome medicine · 2021Article
- Occurrence of Human Enteric Viruses in Water Sources and Shellfish: A Focus on Africa.Food and environmental virology · 2021Review
- Zika Virus RNA Persistence in Sewage.Environmental science & technology letters · 2020Article
- Could Water and Sanitation Shortfalls Exacerbate SARS-CoV-2 Transmission Risks?The American journal of tropical medicine and hygiene · 2020Article
Corrections and comments
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Authors and funding
19 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWorldwide, the number of emerging and re-emerging infectious diseases is increasing, highlighting the importance of global disease pathogen surveillance. Traditional population-based methods may fail to capture important events, particularly in settings with limited access to health care, such as urban informal settlements. In such environments, a mixture of surface water runoff and human feces containing pathogenic microorganisms could be used as a surveillance surrogate.
methodWe conducted a temporal metagenomic analysis of urban sewage from Kibera, an urban informal settlement in Nairobi, Kenya, to detect and quantify bacterial and associated antimicrobial resistance (AMR) determinants, viral and parasitic pathogens. Data were examined in conjunction with data from ongoing clinical infectious disease surveillance.
resultsA large variation of read abundances related to bacteria, viruses, and parasites of medical importance, as well as bacterial associated antimicrobial resistance genes over time were detected. Significant increased abundances were observed for a number of bacterial pathogens coinciding with higher abundances of AMR genes. Vibrio cholerae as well as rotavirus A, among other virus peaked in several weeks during the study period whereas Cryptosporidium spp. and Giardia spp, varied more over time.
conclusionThe metagenomic surveillance approach for monitoring circulating pathogens in sewage was able to detect putative pathogen and resistance loads in an urban informal settlement. Thus, valuable if generated in real time to serve as a comprehensive infectious disease agent surveillance system with the potential to guide disease prevention and treatment. The approach may lead to a paradigm shift in conducting real-time global genomics-based surveillance in settings with limited access to health care.
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