Background: Carbapenem-resistant Enterobacterales (CRE) are a major global health threat. Carbapenem resistance in Enterobacteriaceae poses a major threat to public health in West Africa. In Senegal, although the presence of classic carbapenemase genes (blaOXA-48, blaNDM) has been documented, the emergence of rare variants remains poorly understood.

In West Africa, the molecular epidemiology of CRE remains largely uncharacterized. This study aimed to investigate the genetic mechanisms of carbapenem resistance in clinical isolates of Enterobacterales from Dakar, Senegal.

Methods: A total of 434 Enterobacterales isolates were collected from clinical samples at the Centre Hospitalier National Universitaire (CHNU) de Fann, Dakar, between 2021 and 2022. Among these, 137 were identified as extended-spectrum β-lactamase (ESBL) producers, and 22 were resistant to carbapenems. These 22 CRE isolates were subjected to whole-genome sequencing (WGS) for molecular characterization at the Institute Pasteur of Dakar.

Results: Among the 22 CRE isolates, Escherichia coli was predominant (16/22, 72.7%), while the other species were Enterobacter hormaechei (3/22, 13.6%), Klebsiella pneumoniae, Klebsiella oxytoca and Klebsiella aerogenes (1 isolate each). WGS analysis revealed a diverse array of carbapenem resistance mechanisms. blaNDM-5 was detected in 6 isolates (27.3%), and blaOXA-244 was identified in one E. coli ST6359 isolate (4.5%), representing the first report of this variant in Senegal The ompC R195L mutation was found in one isolate (4.5%), a first report in West Africa. Notably, 9 isolates (40.9%) did not harbor any major carbapenemase genes, suggesting the presence of alternative resistance mechanisms.

Conclusions: This study provides the first comprehensive genomic analysis of CRE in Senegal, revealing a complex molecular epidemiology. The first description of blaOXA-244 and the ompC R195L mutation in Senegal highlights the urgent need for enhanced genomic surveillance to monitor the emergence and spread of novel resistance mechanisms. These findings underscore the importance of implementing robust infection control measures and antimicrobial stewardship programs in the region.