Epidemiology of antimicrobial resistance in non-typhoidal salmonella, and diarrhoeagenic escherichia coli from children, food and livestock in Dagoretti, Nairobi, Kenya
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Date
2025-11
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Kenyatta University
Abstract
There is currently insufficient evidence regarding the risk of antimicrobial resistance (AMR) and its transmission in vulnerable weaning children, under complementary feeding. As part of the Urban Infant Foodscape project, pathogenic Escherichia coli and non-typhoidal Salmonella were isolated from children 6-24 months old, their foods, and household livestock within 585 enrolled households in the peri-urban area of Dagoretti Sub-County, Nairobi, Kenya. This study sought to elucidate the epidemiology of antimicrobial resistance carriage in these isolates. Analysis included phenotypic AMR screening and whole-genome sequencing of 82 multidrug resistant phenotypes. Household risk factors associated with AMR based on survey data were assessed. Fourteen non-typhoidal Salmonella (0.8% prevalence) and 274 (16.46% pooled prevalence) pathogenic E. coli were isolated from 540 children, 296 livestock, and 859 food samples along the value chain. The most common resistant phenotypes among children isolates were SXT, AMP and TET at 76.2% (95%CI: 68.1-82.5%), 70.8% (95%CI: 62.3-78.0%) and 45.4% (95%CI: 37.1-53.9%) respectively. The most frequently identified genotypes included mdf(A), blaTEM-1B, sul2, sul1, aph(6)-Id, aph(3’)-Ib, tet(A), tet(B), dfrA14, and dfrA8, conferring resistance to MLS (macrolide, lincosamides, streptogramin), β-lactams, sulphonamides, aminoglycosides, tetracyclines, and trimethoprim, respectively. While children isolates had a higher AMR gene carriage, there was no statistically significant difference from livestock hosts, suggesting a potential overlap and shared resistance elements between these host groups. These antimicrobial resistance patterns were significantly associated with specific dietary habits and food handling practices, on-site garbage and livestock waste disposal, as well as diarrhoeal illness within the past week. These results highlight the complex interplay between environmental, health, and antibiotic resistance factors in both children and livestock within the household. The findings of this study offer actionable insights for public health interventions and strategies (for instance water, sanitation, and hygiene-WASH, good food handling and preparation practices with respect to specific dietary habits), serving as a catalyst for further longitudinal studies essential to track changes in resistance patterns over time, accounting for variations in dietary habits, food safety practices, and health status
Description
A thesis submitted in fulfilment of the requirements for the award of the degree of doctor of philosophy (biotechnology) in the school of pure and applied sciences of Kenyatta University,
November 2024
Prof. Joseph J. N. Ngeranwa
Dr. Elizabeth A. J. Cook