Statistical and Agent-Based Modelling of Complex Microbial Systems: A Means for Understanding Enteric Disease Transmission among Children in Urban Neighbourhoods of Nairobi and Kisumu in Kenya – PATHOME Study

Project Period

January 2020 - December 2024

Project Partners

  • University of Iowa

Diarrheal disease, caused by enteric infections, is the second leading cause of diarrheal morbidity and mortality in low-income countries. In Kenya alone, the burden of diarrhea is higher among the low-middle income areas in various counties and regions, including the Western, Nairobi, and Coastal regions.

The PATHOME study is a multi-disciplinary collaboration between APHRC and the University of Iowa. The study aims study aims to develop and validate agent-based models (ABMs) for predicting which social and environmental urban developmental interventions (e.g., animal penning, building latrines or drains, concrete floors) best prevent multi-pathogen transmission to infants in low to middle-income communities in Nairobi and Kisumu. Environmental, behavioral, spatial, economic, and microbial data collected from the study will be used to characterize pathways for diarrhoeal disease transmission (including the role of humans and animals) and predict the best possible interventions for preventing these transmissions.

The study hypothesizes that joint modeling of enteric pathome agents across households and neighborhoods representing contrasts in urban societal development will show that development leads to pathome evolution from complex to simple community structures, thus lowering detection frequencies for individual pathogen taxa. Longitudinal data from cohorts of children between 0 and 12 months of age and their caregivers in urban neighborhoods of Kisumu and Nairobi will be collected through a 14- day period. The resultant models will integrate all sources of information to identify which exposure conditions are most strongly linked to pathogen detection in infants.

Project Funders

  • Project Funder



Chief of Staff

Abdhalah Ziraba

Ziraba is an Epidemiologist and a Medical Doctor. His research…

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Theme Leader, Population Dynamics and Urbanization In Africa

Blessing Mberu

Blessing is a Senior Research Scientist and Head of Urbanization…

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Research Scientist

Sheillah Simiyu

Sheillah works on Water, Sanitation and Hygiene (WASH) within the…

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Research Officer

Phylis Jepkorir Busienei

Phylis is an early-career, public health scientist with an interest…

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Senior Program Accountant

Fidelis Mutiso Katumo

Fidelis is involved in the financial management of Urbanization and…

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