Whole-genome sequencing analysis of clinical carbapenemase-producing bacteria isolated in Dakar, Senegal

ABSTRACT Antimicrobial resistance, particularly to carbapenems, represents a major global public health threat. In Senegal, the increasing prevalence of carbapenem-resistant Gram-negative bacilli compromises the management of severe infections. This study, conducted between October 2022 and March 2024 at the Centre Hospitalier National Universitaire de Fann and the Institut Pasteur de Dakar, investigated 50 carbapenem-resistant bacterial isolates. Species identification was performed using Vitek 2 and MALDI-TOF MS, and antimicrobial susceptibility was assessed by disk diffusion testing. Whole-genome sequencing enabled the detection of resistance genes, plasmid replicons, and clonal lineages through MLST analysis. Among the 50 isolates, 35 (70%) carried at least one carbapenemase gene. The bla NDM-5 gene was the most frequent (15/35; 42.9%), followed by bla OXA-181 (20.0%), bla NDM-1 (14.3%), and bla OXA-484 (11.4%). Co-occurrences of carbapenemase genes were observed (17.1%), including bla NDM-5 + blaOXA OXA-181 , bla OXA-23 + blaOXA OXA-68 , and bla OXA-70 + blaOXA OXA-420 . These isolates extensively co-harbored other resistance determinants, most notably the bla CTX-M-15 extended-spectrum β-lactamase (ESBL) gene. Genes conferring high-level resistance to aminoglycosides ( rmtB, armA ) and quinolones [ aac(6′)-Ib-cr, qnrA, qnrB ] were also identified. The predominant plasmid types were IncF (91.4%) and Col (62.9%). MLST analysis showed that, in this study collection ( n = 35), Escherichia coli ST410 (7/35; 20.0%) and ST648 (3/35; 8.6%), as well as Klebsiella pneumoniae ST307 (3/35; 8.6%) and ST147 (2/35; 5.7%), were the most frequently detected sequence types. Notably, this study reports the first detection of the bla VEB-6 gene in Senegal. These findings highlight the circulation of multidrug-resistant clones harboring carbapenemase genes and underscore the urgent need to strengthen surveillance and infection control measures in Senegalese hospitals. IMPORTANCE Carbapenem resistance among Gram-negative bacilli represents a global public health emergency, particularly in resource-limited settings where therapeutic options are scarce. In Senegal, data on the genetic mechanisms underlying this resistance remain limited. This study is among the few that have employed whole-genome sequencing to characterize carbapenemase-producing bacteria. The identification of high-risk clones, such as Escherichia coli ST410 and Klebsiella pneumoniae ST307, along with the first detection of the bla VEB-6 gene in Senegal, highlights the local spread of multidrug-resistant lineages. By combining phenotypic and genomic analyses, this research provides essential insights to strengthen genomic surveillance, optimize antibiotic use, and improve infection prevention and control strategies in Senegalese hospitals.