Epidemiology of antimicrobial resistant diarrheagenic Escherichia coli pathotypes from children, livestock and food in Dagoretti South, Nairobi Kenya

Peri-urban environments, characterized by dense human populations, cohabiting livestock, and complex food systems, serve as hotspots for food contamination and infectious diseases.

Children aged 6–24 months are particularly vulnerable as they often encounter contaminated food and water, increasing their risk of food-borne disease, with diarrhoea being a common symptom.

This study investigated the prevalence of antimicrobial resistance in pathogenic Escherichia coli from 6–24 months-old children, their food and cohabiting livestock in Dagoretti South subcounty in Nairobi, Kenya.

Out of 540 stool, 296 livestock faeces and 859 food samples collected from 585 randomly enrolled households, 16% harboured diarrhoeagenic E. coli pathotypes.

The predominant antimicrobial resistance phenotypes observed were trimethoprim-sulfamethoxazole (53%), ampicillin (48%) and tetracycline (41%).

Diarrhoeagenic E. coli from children showed significantly higher resistance to all antibiotics compared to those from livestock and food.

Overall, 30% of the 274 diarrhoeagenic E. coli isolates from all three sources exhibited multidrug resistance.

Network analysis of antimicrobial resistance co-occurrence revealed two clusters:

• ampicillin, trimethoprim-sulfamethoxazole, tetracycline, amoxicillin/clavulanic acid and chloramphenicol; and
• nalidixic acid, ciprofloxacin, gentamicin and ceftriaxone.

These findings emphasize the need for One Health interventions to curb emergence and spread of antimicrobial resistance in these close contact populations.

Citation
Okumu, N.O., Muloi, D.M., Moodley, A., Ochieng, L., Watson, J., Kiarie, A., Ngeranwa, J.J.N., Cumming, O. and Cook, E.A.J. 2025. Epidemiology of antimicrobial resistant diarrheagenic Escherichia coli pathotypes from children, livestock and food in Dagoretti South, Nairobi Kenya. International Journal of Antimicrobial Agents 107419.

Photo: Pouring boiled milk in Waithaka, Nairobi, Kenya (ILRI/Shadrack Isingoma)