Molecular epidemiological exploration of carbapenem-resistant Enterobacteriaceae in Africa from One Health perspective: A systematic review

Abstract

Carbapenem‑resistant Enterobacteriaceae (CRE) are associated with high morbidity and mortality in humans due to very limited therapeutic options. This systematic review examines the prevalence and geographic distribution of CRE, as well as the associated genetic factors at the human-animal-environment interface in Africa. To extract information for this study, the Medical Subject Headings (MeSH) technique was used to identify studies that employed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) reporting guidelines, with a focus on original research articles. Additionally, this systematic review employed the CoCoPop (conditions, context, and population) framework to identify relevant articles. Search engines used to retrieve articles included Web of Science, Google Scholar, Scopus, ResearchGate, and PubMed. By August 2025, only eight articles from Africa met the search criteria and were included in the analysis. The observed prevalence of CRE across the heterogeneous studies was 18.58%. The animal domain exhibited the highest CRE prevalence (9.89%), followed by the human (6.06%) and environmental (2.63%) domains. Escherichia coli (58.35%) and Klebsiella pneumoniae (28.28%) were the predominant spp. among the reported CRE isolates. The highest gene prevalence was observed for blaOXA-48 (42%), followed by blaKPC (33%) and blaOXA-66 (9.78%). Geographically, North Africa had the highest prevalence (55.78%), followed by Eastern Africa (29.82%), whereas Southern Africa had the lowest prevalence (3.08%). Our study emphasizes the significant burden of CRE infections and genes, as well as their spread across human, animal, and environmental sectors in Africa. The simultaneous presence of CRE in these areas indicates potential interfaces, but current evidence does not permit a definitive assignment of specific transmission routes. Surveillance programs, research, infection prevention, and control measures from a One Health perspective should be implemented to inform interventions.