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

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.