Molecular characterization of the whole genome in clinical multidrug-resistant strains of Klebsiella pneumoniae

Abstract

Introduction: Antimicrobial resistance (AMR) is a major public health concern. The spread of AMR-encoding genes between enterobacteria, especially in Klebsiella pneumoniae strains, lead to failure in the treatment of most individuals. The aim of this study was to characterize multi-drug resistant (MDR) clinical K. pneumoniae isolates that produce extended-spectrum β-lactamases (ESBLs) from Algeria.

Methodology: The isolates were identified using biochemical tests, and the identification was confirmed by mass spectrometry using VITEK® MS (BioMerieux, Marcy l’Etoile, France). Antibiotic susceptibility testing was assessed by the disk diffusion method. Molecular characterization was performed by whole genome sequencing (WGS) using Illumina technology. Sequenced raw reads were processed using bioinformatics parameters: FastQC, ARIBA, and Shovill-Spades. Multilocus sequence typing (MLST) was used to estimate the evolutionary relationship between isolate strains.

Results: Molecular analysis resulted in the first detection of blaNDM-5 encoding K. pneumoniae in Algeria. Other resistance genes were blaTEM, blaSHV, blaCTX-M, aac(6')-Ib-cr, qnrB1, qnrB4, qnrB19, qnrS1, gyrA and parC variants.

Conclusions: Our data demonstrated a very high level of resistance in clinical K. pneumoniae strains which were resistant to most common antibiotic families. This was the first detection of K. pneumoniae with the blaNDM-5 gene in Algeria. Surveillance of antibiotic use and measures for control should be implemented to reduce occurrence of AMR in clinical bacteria.