Molecular genetic markers of resistance and virulence of invasive Klebsiella pneumoniae strains according to whole genome sequencing data

Abstract

Objective. To evaluate genetic mechanisms of antibiotic resistance and virulence of invasive strains of Klebsiella pneumoniae isolated from inpatients using whole genome sequencing.Materials and methods. For two carbapenem-resistant multiple-antibiotic-resistant invasive strains of K.pneumoniae, as well as two carbapenem-sensitive invasive strains of K.pneumoniae, sequencing was performed using the MiSeq genomic sequencer (Illumina). Genomic sequences were assembled and annotated. Sequence type determination, search for plasmids and virulence factors, antibiotic resistance genes, and efflux mechanisms were performed.Results. K.pneumoniae strains belonged to sequence types ST395, ST101, ST111, and ST512 s and had a hypermucoid phenotype. The iutA aerobactin genes were detected in both sensitive and carbapenem-resistant strains. Virulence genes fimH, fyuA, and irp2 were detected in one strain isolated from blood. Carbapenemase genes (blaKPC, blaNDM) were detected in two strains. Aminoglycosides and fluoroquinolones resistance genes were detected in 3 of 4 strains. All strains showed the presence of different systems of active antibiotic elimination from the microbial cell.Conclusion. The possibility of identifying hypervirulent strains of K.pneumoniae using a complex phenotypic test along with hvKp genotyping is shown. The results of full-genome sequencing reflect significant resistance of hypervirulent K.pneumoniae strains isolated from blood to most antibiotics, including β-lactams, aminoglycosides, fluoroquinolones, phosphomycin, chloramphenicol and polymyxins.