Molecular Detection and Antibiotic Susceptibility Pattern of Shiga Toxin Producing Escherichia coli among Children with Diarrhea in Addis Ababa, Gondar, and Harar, Ethiopia

Introduction: Shiga toxin-producing Escherichia coli (STEC) is a major cause of pediatric diarrhea globally, yet its burden, molecular characteristics, and antibiotic resistance patterns remain underexplored in low-resource settings like Ethiopia. This study aimed to assess the molecular detection and antibiotic susceptibility pattern of STEC among children with diarrhea in Ethiopia. Methods: A cross-sectional study was conducted between October 2021 and November 2022 in Ethiopia (Addis Ababa, Gondar, and Harar) among 568 children under 15 years of age. Socio-demographic and clinical data were collected using a standardized questionnaire and REDCap software. Stool samples were screened for STEC using ChromSTEC agar. Shiga toxin (stx) and intimin (eae) genes were detected using polymerase chain reaction (PCR). The antibiotic susceptibility profile was determined using the Phoenix M50 machine. Data analysis was performed using R version 4.3.2 for descriptive statistics and logistic regression analysis. Results: The overall prevalence of STEC among children with diarrhea was 12.15% [95% CI: 9.71-15.09], with the higher prevalence among children aged two to five years and those with bloody diarrhea. STEC isolates showed high antimicrobial resistance (AMR), with 46.38% showing multidrug resistance (MDR) and 2.90% classified as extensively drug-resistant (XDR). Additionally, 21.74% of STEC isolates were extended-spectrum beta lactamase (ESBL) producers, including 12.50% of those harboring the eae gene. Conclusions: This study provides one of the first comprehensive assessments of STEC across pediatric age groups and multiple regions in Ethiopia, revealing high prevalence and antibiotic resistance with regional and seasonal variations. These findings highlight the urgent need for enhanced infection prevention and strengthened antimicrobial stewardship.