Characterization of Carbapenemase-producing Enterobacterales isolated from patients returning from Sub-Saharan Africa, France, 2015–2022

Abstract Objectives The rise of carbapenemase-producing Enterobacterales (CPE) represents a major public health threat, as highlighted in numerous reports from international health organizations. However, a significant data gap remains for certain regions, particularly Sub-Saharan Africa (SSA). The aim of this study is to characterize CPE isolates from patients returning from SSA at both phenotypic and genomic levels. Methods This retrospective study analysed 408 CPE received at the French National Reference Center between 2015 and 2022 and collected from patients returning from SSA. Antibiotic susceptibility testing and WGS were performed to assess phenotypic and genomic diversity. Results Among 408 isolates collected from 29 countries, 55.1% produced oxacillinase-48 (OXA-48)-like carbapenemases, predominantly OXA-181, while 46.3% produced NDM (New Delhi metallo-β-lactamase), with NDM-5 being the major variant despite regional disparities. Temporal analysis revealed a trend shifting from OXA-48-like producers to NDM producers. Ceftazidime-avibactam was effective against 100% of non-metallo-β-lactamase producers. Cefiderocol, amikacin and colistin were effective on 73%, 86.7% and 98.4% of all CPEs respectively. Genomic analysis revealed a polyclonal dissemination among K. pneumoniae strains, whereas three E. coli clonal complexes were dominant (CC410, CC167, CC448). Conclusion This study provides a comprehensive characterization of CPE isolated from patients returning from SSA. WGS allowed the identification of major circulating clones, their associated resistance genes, and their susceptibility to last-resort antibiotics.