Review and Analysis of the Overlapping Threats from Carbapenem and Colistin Resistant Enterobacteriaceae in Africa
Carbapenem-resistant Enterobacteriaceae (CRE) are among the most serious antimicrobial resistance (AMR) threats. Emerging resistance to polymyxins raises the specter of untreatable CRE infections. To better understand these risks we analyzed and mapped available data on polymyxin and carbapenem resistance in E. coli and Klebsiella throughout Africa. Our analysis yielded 1341 data reports documenting carbapenem resistance in 40 of 54 African nations. For nations with at least 100 representative isolates since 2010, estimated resistance among E. coli was high (>5%) in 3, moderate (1-5%) in 8 and low (<1 %) in 14. In 9 additional nations, resistance was present but with insufficient isolates to support estimates. Carbapenem resistance was generally higher among Klebsiella: high in 10 nations, moderate in 6 and low in 6, and present in 11 others with insufficient isolates for estimates. While less information was available concerning polymyxins, we found 341 data reports from 33 of 54 nations, documenting polymyxin resistance in 23. Resistance among E. coli was estimated as high in 2 nations, moderate in 1 and low in 6, while present in 10 with insufficient isolates for estimates. Among Klebsiella, resistance was low in 8 nations and present in 8 others with insufficient isolates for estimates. The most widespread resistance associated genotypes were, for carbapenems, OXA-48, NDM-1 and OXA-181 and, for polymyxins, mcr-1, mgrB, and PhoPQ/PmrAB. Overlapping resistance was documented in 24 nations. While numerous data gaps remain, carbapenem resistance, often significant, is now widespread in Africa and polymyxin resistance also widely distributed, indicating the need to support robust AMR surveillance, antimicrobial stewardship and infection control. The Supplementary Spreadsheet 1 contains all study data and data elements extracted for analyses.