Antimicrobial resistant E. coli in animals, humans and the environment within household and compound settings: A scoping review

Objective: This scoping review summarizes evidence on the prevalence and potential risk factors of antimicrobial-resistant (AMR) E. coli in animals, humans, and the environment within household and compound settings. Methods: Four databases (CINAHL, PubMed, PubMed Central, and Scopus) were searched for studies published up to October 2024. Results: Most studies (60%, 24/40) reported AMR E. coli in studies involving animals and humans (AH), followed by those included animals, humans, and the environment (AHE) (35%, 14/40). and animals and the environment (AE) (5%, 2/40). AMR E. coli was commonly detected using disk diffusion methods, often combined with PCR, WGS, MIC, or PFGE for genetic relatedness analysis. The estimated overall prevalence was 63%, 36.5%, and 46% at the AH, AHE, and AE categories, respectively. No eligible studies reported AMR E. coli exclusively from humans and the environment. None of the AE studies assessed genetic relatedness between isolates. However, 13 AH studies identified genetically related E. coli strains between animals and humans, particularly extended-spectrum β lactamase and extended-spectrum cephalosporin-resistant. Shared clonal lineages and identical resistance genes were observed among cohabiting animals and humans. Similarly, three AHE category studies reported genetic overlap involving β-lactam, carbapenem, tetracycline, and aminoglycoside resistance. Close human–animal contact, shared living environments, and the presence of multiple animal species were identified as potential contributors to transmission of resistant E.coli between animals and humans. Conclusion: Genetically related AMR E. coli strains are widespread, with strong evidence of genetic relatedness between isolates originating from animals and humans within household and compound settings.