JMIR Publications

ABSTRACT

Background:

Background:

Antimicrobial resistance (AMR) is a global health threat that increases the burden of infectious diseases and disproportionately affects communities of low socioeconomic status. Despite the call for community-level AMR data, prospective studies from rural sub-Saharan African communities to inform appropriate targeted interventions remain scarce. Given the role of enteric bacteria in AMR transmission, there is a need to understand the timing, risk factors, and ecological drivers of gut resistome acquisition and development during infancy. This protocol describes a community-based, prospective, observational birth cohort study in a rural South African community aimed at characterising the temporal dynamics of enteric bacteria resistomes during the first 24 months of life, and to identify drivers of antimicrobial resistance acquisition and development.

Objective:

This protocol describes a community-based, prospective, observational birth cohort study in a rural South African community aimed at characterising the temporal dynamics of enteric bacteria resistomes during the first 24 months of life, and to identify drivers of antimicrobial resistance acquisition and development.

Methods:

The study targets the enrollment of 200 newborns and their mothers within 17 days postpartum. Data on key exposures and variables include socio-demographics; perinatal and anthropometrics; feeding practices and dietary exposures; illness, medication, and vaccination history; breast milk metabolomic profiles; household socioeconomic status; maternal psychosocial and behavioral factors; hygiene and sanitation practices; environmental exposures including hydro-meteorological variables, in-house livestock and pets, and drinking water quality. Biological samples include stools from monthly collections and diarrhoea episodes for metagenomic analysis and breast milk for metabolomics. Planned analyses include assessment of the infant microbiome and resistome structure (diversity, abundance, and composition) across time points and modelling associations between risk factors and AMR outcomes. Additionally, a cross-sectional community survey on knowledge, attitude, and practice (KAP) on antimicrobial use is conducted to inform knowledge translation through Responsive Dialogues for the development of ethnographically relevant packages for community-level AMR stewardship.

Results:

Participant identification and enrollment began in August 2023. To date, 167 newborns have been enrolled, and data collection and follow-up is ongoing, with 20 participants already completed 24 months. The characteristics of the enrolled participants and presented in this protocol

Conclusions:

This study will offer a unique opportunity to generate longitudinal resistome data from a rural sub-African setting. The study is expected to contribute knowledge on the microbiome and resistome structure dynamics and trajectories associated with key risk factors of acquisition and development. In addition, co-produced, ethnographically tailored educational packages, informed by KAP and bacterial resistome data, will drive sustainable community-centered antimicrobial resistance awareness interventions.