Whole genome analysis of carbapenem resistant Acinetobacter baumannii isolates from healthcare-associated infections in Dakar, Senegal

Issa Ndiaye; Ousmane Sow; Abdoulaye Cissé; Bissoume Sambe Ba; Farma Thiam; Mouhamadou Moustapha Boye; Baidy Dièye; Cheikh Fall; Yakhya Dieye; Assane Dieng; Amadou Diop; Guillaume Constantin de Magny; Abdoulaye Seck

doi:10.1016/j.nmni.2026.101713

Whole genome analysis of carbapenem resistant Acinetobacter baumannii isolates from healthcare-associated infections in Dakar, Senegal

New Microbes New Infect. 2026 Jan 30:70:101713. doi: 10.1016/j.nmni.2026.101713. eCollection 2026 Apr.

Authors

Issa Ndiaye^{1

2}, Ousmane Sow¹, Abdoulaye Cissé¹, Bissoume Sambe Ba³, Farma Thiam⁴, Mouhamadou Moustapha Boye⁵, Baidy Dièye⁶, Cheikh Fall¹, Yakhya Dieye¹, Assane Dieng⁵, Amadou Diop⁶, Guillaume Constantin de Magny^{7

8}, Abdoulaye Seck^{1

2}

Affiliations

¹ Pôle de Microbiology, Institut Pasteur de Dakar, Senegal.
² Faculté de Médecine, Pharmacie et Odontostomatologie, Université Cheikh Anta Diop, Dakar, Senegal.
³ World Health Organization WCARO, Dakar, Senegal.
⁴ Laboratoire de Biologie Médicale, Hôpital régional de Pikine, Senegal.
⁵ Laboratoire de Bactériologie et Virologie, Hôpital Aristide Le Dantec, Dakar, Senegal.
⁶ Laboratoire de Bactériologie et Virologie, Hôpital Albert Royer, Dakar, Senegal.
⁷ MIVEGEC, Université Montpellier, CNRS, IRD, Montpellier, France.
⁸ MEEDiN, Montpellier Ecology and Evolution of Disease Network, France.

Abstract

Background: Carbapenem resistant Acinetobacter baumannii (CRAB) is considered a top priority pathogen by the World Health Organization and is also considered a leading cause of healthcare-associated infections (HAIs). This study aimed to investigate antimicrobial resistance (AMR) patterns and perform comprehensive whole-genome analysis on CRAB strains isolated from HAIs in Dakar, Senegal.

Methods: CRAB isolates were collected from 2018 to 2021 in two major hospitals in Dakar and subjected to antimicrobial susceptibility tests followed by whole genome sequencing and comprehensive bioinformatic analysis to identify resistance genes, mobile genetic elements (MGEs) and perform phylogeny analysis.

Results: The isolates demonstrated an alarming level of resistance to multiple classes of antibiotics, categorizing them as extremely drug resistant. Genetically, they present 5 distinct sequence types (ST1, ST52, ST85, ST107, and ST164), and an average of 71.9% accessory genes. They also present 30 to 51 genes associated with resistance to numerous classes of antibiotics. These genes included those responsible for resistance to β-lactams (such as bla _OXA-23 , bla _NDM-1 , bla _OXA-51 and bla _CTX-M15 ), to aminoglycosides (ant(3″)-IIa, aph(3″)-Ib, aph(3')-Ia), to fluoroquinolones (such as qnrS1, qnrB17, AdeFGH efflux pump), to fosfomycin (fos2A, fosA6, AbaF), and to tetracyclines (tet(A), tet(B), tet(39)).

Conclusion: This pioneering study offers insight into the molecular mechanisms underlying carbapenem-resistant bacteria associated with HAIs in Senegal. These findings emphasize the critical need to implement surveillance programs particularly for carbapenem-resistant bacteria to gain a comprehensive understanding of their prevalence, propagation, impact on patient health outcomes, and prolonged hospital stays.

Keywords: Carbapenem resistant A. baumannii (CRAB); Healthcare-associated infections (HAIs); Mobile genetic elements (MGEs); Resistance genes.