Whole genome analysis of MDR Klebsiella pneumoniae strains isolated from Hospital acquired infections in tertiary hospitals in Dakar, Senegal.
Background: Klebsiella pneumoniae is widely recognized as an opportunistic pathogen in both hospital and community settings. It is a key member of the ESKAPE group, which comprises priority microorganisms of major concern owing to their antibiotic resistance. The resistance of K. pneumoniae, particularly related to extended-spectrum ß-lactamases (ESBLs), poses a significant global public health challenge. The combination of its multidrug resistance (MDR) phenotype and various pathogenicity factors increases its potential to cause severe clinical infections. Methods: Biofilm formation was assessed via a semiquantitative microtiter technique. We employed various bioinformatics tools to analyze the antimicrobial resistance (AMR), virulence factors, plasmid replicons, and genomic diversity of the CRKP isolates. Results: The isolates predominantly produced strong biofilms (n = 21), with some exhibiting moderate (n = 1) or weak (n = 2) biofilm production. An alarming level of resistance to multiple classes of antibiotics was correlated with the presence of various resistance genes, including those for ß-lactams (blaOXA-48, blaOXA-181, blaCTX-M15, blaTEM and blaSHV), aminoglycosides (aph(6)-Id, aac(3)-IIe, aadA2, ant(3'')-IIa, aph(3')-Ia and aac(6')-Ib-cr), and quinolones (qnrA, qnrB, qnrS, CRP, and emrR). Various efflux pumps, such as KpnGH, oqxAB, acrAB, acrD, and KpnEF, are ubiquitously distributed across MDR K. pneumoniae strains. Several virulence-associated genes encoding type 1 fimbriae (fimH), type 3 fimbriae (mrkA), efflux pumps (acrAB, oqxAB), enterobactin (entA, entB, fepC), and yersiniabactin (irp1, irp2, ytbA, ybtE, ybtP, ybtQ, ytbT, ytbU, ytbX) have been identified. Genetically, the isolates presented high diversity, with 18 sequence types (STs) and an average of 50.7% accessory genes. On the basis of SNP distance and pairwise ANI analysis, the majority of K. pneumoniae isolates were grouped into one clade, with one strain (KP8) being relatively distant. Conclusion: The high plasticity of K. pneumoniae in the acquisition of an MDR phenotype, combined with the phenotypic and genotypic factors described in this report, underscores the challenges in achieving effective clinical therapy with the available antibiotics. The findings also emphasize the critical need for the surveillance of multidrug-resistant pathogens in clinical settings in Senegal, as well as the need to evaluate their prevalence, propagation, and impact on patient health outcomes.