Protocol for the PATHOME study: a cohort study on urban societal development and the ecology of enteric disease transmission among infants, domestic animals and the environment.
Kelly K Baker, Sheillah Simiyu, Phylis Busienei, Fanta D Gutema, Bonphace Okoth, John Agira, Christine S Amondi, Abdhalah Ziraba, Alexis G Kapanka, Abisola Osinuga, Collins Ouma, Daniel K Sewell, Sabin Gaire, Innocent K Tumwebaze, Blessing Mberu
Author Information
Kelly K Baker: Department of Occupational and Environmental Health, The University of Iowa College of Public Health, Iowa City, Iowa, USA kelly-k-baker@uiowa.edu. ORCID
Sheillah Simiyu: Division of Population Dynamics and Urbanization, African Population and Health Research Center, Nairobi, Kenya.
Phylis Busienei: Division of Population Dynamics and Urbanization, African Population and Health Research Center, Nairobi, Kenya.
Fanta D Gutema: Department of Occupational and Environmental Health, The University of Iowa College of Public Health, Iowa City, Iowa, USA.
Bonphace Okoth: Division of Population Dynamics and Urbanization, African Population and Health Research Center, Nairobi, Kenya.
John Agira: Division of Population Dynamics and Urbanization, African Population and Health Research Center, Nairobi, Kenya.
Christine S Amondi: Division of Population Dynamics and Urbanization, African Population and Health Research Center, Nairobi, Kenya.
Abdhalah Ziraba: Division of Health and Wellbeing, African Population and Health Research Center, Nairobi, Kenya.
Alexis G Kapanka: Department of Occupational and Environmental Health, The University of Iowa College of Public Health, Iowa City, Iowa, USA.
Abisola Osinuga: Department of Occupational and Environmental Health, The University of Iowa College of Public Health, Iowa City, Iowa, USA.
Collins Ouma: Maseno University, Maseno, Nyanza, Kenya.
Daniel K Sewell: Department of Biostatistics, The University of Iowa College of Public Health, Iowa City, Iowa, USA.
Sabin Gaire: Department of Biostatistics, The University of Iowa College of Public Health, Iowa City, Iowa, USA.
Innocent K Tumwebaze: Division of Population Dynamics and Urbanization, African Population and Health Research Center, Nairobi, Kenya. ORCID
Blessing Mberu: Division of Population Dynamics and Urbanization, African Population and Health Research Center, Nairobi, Kenya.
INTRODUCTION: Global morbidity from enteric infections and diarrhoea remains high in children in low-income and middle-income countries, despite significant investment over recent decades in health systems and water and sanitation infrastructure. Other types of societal development may be required to reduce disease burden. Ecological research on the influence of household and neighbourhood societal development on pathogen transmission dynamics between humans, animals and the environment could identify more effective strategies for preventing enteric infections. METHODS AND ANALYSIS: The 'enteric pathome'-that is, the communities of viral, bacterial and parasitic pathogens transmitted from human and animal faeces through the environment is taxonomically complex in high burden settings. This integrated cohort-exposure assessment study leverages natural socioeconomic spectrums of development to study how pathome complexity is influenced by household and neighbourhood infrastructure and hygiene conditions. We are enrolling under 12-month-old children in low-income and middle-income neighbourhoods of two Kenyan cities (Nairobi and Kisumu) into a 'short-cohort' study involving repeat testing of child faeces for enteric pathogens. A mid-study exposure assessment documenting infrastructural, behavioural, spatial, climate, environmental and zoonotic factors characterises pathogen exposure pathways in household and neighbourhood settings. These data will be used to inform and validate statistical and agent-based models (ABM) that identify individual or combined intervention strategies for reducing multipathogen transmission between humans, animals and environment in urban Kenya. ETHICS AND DISSEMINATION: The protocols for human subjects' research were approved by Institutional Review Boards at the University of Iowa (ID-202004606) and AMREF Health Africa (ID-ESRC P887/2020), and a national permit was obtained from the Kenya National Commission for Science Technology and Innovation (ID# P/21/8441). The study was registered on Clinicaltrials.gov (Identifier: NCT05322655) and is in pre-results stage. Protocols for research on animals were approved by the University of Iowa Animal Care and Use Committee (ID 0042302).
