Extended spectrum beta lactamases and carbapenemase-producing Escherichia coli in humans, animals and the environment in East Africa: a scoping review.

BACKGROUND

Antimicrobial resistance (AMR) is escalating in East Africa through close human-animal-environment interactions. Extended-spectrum beta-lactamases (ESBL) and carbapenemase-producing Escherichia coli are clinically critical pathogens, yet local evidence is limited. This scoping review synthesizes evidence on ESBL and carbapenemase-producing E. coli in East Africa to inform One Health AMR control strategies.

METHODS

Following PRISMA-ScR guidelines, PubMed and Scopus were searched, identifying 279 records published between 2015 and 2025. After removing duplicates and screening, 185 articles were assessed for eligibility; 154 studies spanning human, animal and environmental sources met the inclusion criteria. Two reviewers independently extracted epidemiological, microbiological and molecular data in Covidence, including resistance genes and transmission evidence.

RESULTS

The 154 included studies spanned 11 East African countries, led by Ethiopia (n = 55), Tanzania (n = 39) and Uganda (n = 22). Most studies (85.7%) were cross-sectional and human-focused (68.2%), with only 19 (12.3%) using a multi-sector One Health design. Overall, 21,554 E. coli isolates were recovered from 74,700 samples. ESBL prevalence was reported in 117 studies (76.0%, median 46.8%) and carbapenemase prevalence in 65 (42.2%, median 3.3%), representing heterogeneous study-level estimates. bla CTX-M predominated (89.9%), led by bla CTX-M-15 (26.1%); reported carbapenemase genes included bla NDM, bla OXA-48, bla OXA-181 and bla KPC. Whole-genome sequencing in 30 studies (19.5%) identified high-risk clones ST131, ST10, ST38 and ST410, though animal, food-chain and environmental sectors remained underrepresented.

CONCLUSION

This review maps the current evidence on landscape for ESBL/carbapenemase- producing E. coli in East Africa, highlighting gaps in surveillance that are largely due to heterogeneity of available genomics data and limited longitudinal data within the "One Health" sectors. We recommend scaling up genomic capacity and standardized longitudinal surveillance to better understand national and regional AMR transmission and MDR E. coli infections.