Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Nov 24;13(11):e076067.
doi: 10.1136/bmjopen-2023-076067.

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  1 , Sheillah Simiyu  2 , Phylis Busienei  2 , Fanta D Gutema  3 , Bonphace Okoth  2 , John Agira  2 , Christine S Amondi  2 , Abdhalah Ziraba  4 , Alexis G Kapanka  3 , Abisola Osinuga  3   5 , Collins Ouma  6 , Daniel K Sewell  7 , Sabin Gaire  7 , Innocent K Tumwebaze  2 , Blessing Mberu  2
Affiliations

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 et al. BMJ Open. .

Abstract

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).

Keywords: Epidemiology; Gastrointestinal infections; Infection control; MICROBIOLOGY; Neglected Diseases; Public health.

PubMed Disclaimer

Conflict of interest statement

Competing interests: None declared.

Figures

Figure 1
Figure 1
Conceptual model of the enteric Pathogen Transmission and Health Outcome Models of Enteric Disease (PATHOME) Study. Societal development of household water, latrines, flooring, animal health and hygiene conditions and neighbourhood infrastructure (drainage) and hygiene (animal penning, waste regulations) conditions triggers an evolutionary change in the enteric PATHOME from taxonomically complex to simple microbial community detection patterns in humans, animals and the environment.
Figure 2
Figure 2
Low-income and middle-income study neighbourhoods in Nairobi and Kisumu, Kenya, where households with 0-to-12 month of age children are enrolled into the Pathogen Transmission and Health Outcome Models of Enteric Disease (PATHOME) study. Yellow bars represent 100-m distance. Map image generated using Google Earth 2022. Intant image licensed to KKB on 22 November 2022 through Vectorstock Standard License.
Figure 3
Figure 3
Study design and timeline for Pathogen Transmission and Health Outcome Models of Enteric Disease household data and biological specimen collection. Symbols matching data collection activity placed under days when activities are implemented. Survey=self-reported data on household conditions. Diaper=provision of diapers for faeces collection. Infant=days of diaper/faeces collection. Chicken=animal faeces collected. Binoculars=structured observation days. Geotracker=24-hour time window where spatial movement is monitored. Toy ball=days of environmental sample collection. Mid-upper Arm Circumference tape=anthropometric data. Calendar=window of time for prospective self-reporting of infant diarrhoea symptoms. Attribution for tape measure image: Simon A. Eugster, Wikimedia Commons Creative Commons Attribution ShareAlike 3.0 CC BY-SA 3.0 (https://commons.wikimedia.org/wiki/File:Tape_measure_colored.jpeg). Image of child licensed through Vectorstock Standard License. The image of a chicken is a Public Domain CCO. The open-source image of ‘binoculars’ is licensed under the open-source Unlicense license. Diaper, survey, tracker and calendar images taken by or created by authors.
Figure 4
Figure 4
Flow diagram of the strategy for recovery, detection, quantification and confirmation of enteric pathogens in human and animal faeces and environmental fomites. Buffered Peptone water (BPW); Rappaport Vassiliadis Soya Peptone Broth (RVS); Half Fraser Broth (HFB); Bolton Broth (BB); modified Xylose Lysine Deoxycholate (mXLD); quantitative reverse transcription polymerase chain reaction (qRT-PCR); multiplex PCR (mPCR). Image of child licensed through Vectorstock Standard License. The image of a chicken is a Public Domain CCO. Soil, water, and house images created by authors.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. GBD Diarrhoeal Disease Collaborators . Estimates of the global, regional, and national morbidity, mortality, and aetiologies of diarrhoea in 195 countries: a systematic analysis for the global burden of disease study 2016. Lancet Infect Dis 2018;18:1211–28. - PMC - PubMed
    1. GBD Typhoid and Paratyphoid Collaborators . The global burden of typhoid and Paratyphoid fevers: a systematic analysis for the global burden of disease study 2017. Lancet Infect Dis 2019;19:369–81. 10.1016/S1473-3099(18)30685-6 - DOI - PMC - PubMed
    1. Platts-Mills JA, Babji S, Bodhidatta L, et al. . Pathogen-specific burdens of community diarrhoea in developing countries: a multisite birth cohort study (MAL-ED). Lancet Glob Health 2015;3:e564–75. 10.1016/S2214-109X(15)00151-5 - DOI - PMC - PubMed
    1. Fischer Walker CL, Perin J, Aryee MJ, et al. . Diarrhea incidence in Low- and middle-income countries in 1990 and 2010: a systematic review. BMC Public Health 2012;12:220. 10.1186/1471-2458-12-220 - DOI - PMC - PubMed
    1. Petri WA, Miller M, Binder HJ, et al. . Enteric infections, diarrhea, and their impact on function and development. J Clin Invest 2008;118:1277–90.:1277. 10.1172/JCI34005 - DOI - PMC - PubMed

Publication types

Associated data

-