Phenotypic and Molecular Characterization of Multi-drug Resistant Klebsiella spp. Isolates Recovered from Clinical Settings

Abstract

Klebsiella pneumoniae is a Gram-negative bacterium that colonizes the gastrointestinal tract and nasopharynx with the vast majority associated with hospitalization and causing human nosocomial infections. Extended-spectrum β-lactamases (ESBL)-producing and carbapenem-resistant K. pneumoniae is recognized by the World Health Organization (WHO) as a serious public health concern. In this study, whole-genome sequencing (WGS) – based analysis was performed to understand the molecular epidemiology of multi-drug resistant Klebsiella spp. clinical isolates. Genome comparison, multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and whole-genome-SNP-based phylogenetic analysis (wg-SNP) were used to determine the relatedness of the isolates. in silico typing was used to determine the resistance genes, virulence factors, Inc groups, and capsular types. All except one isolate were non-susceptible to meropenem and 89% were non-susceptible to ertapenem and imipenem. blaNDM, blaOXA-48, and blaKPC were the carbapenemase-linked genes with blaNDM-1 being detected in half of the sequenced isolates. Resistance to colistin was detected in one and was correlated to mutations in ccrB, pmrB, and pmrC genes. The most common plasmid type was IncFIB followed by IncR, and the Type 3 fimbriae, chromosomally encoded by the mrkABCDF operon, was conserved among the sequenced Klebsiella spp. The most common sequence (ST) and K-type detected were ST147 and K64. A nosocomial outbreak linked to a carbapenem-resistant ST147 K. pneumoniae supported by SNPs-based analysis, PFGE clustering, and genome comparison was also detected. This study provides crucial insights into antimicrobial resistance and the virulence of an increasingly important global pathogen. It also confirms that whole-genome sequencing data should be integrated into routine and targeted pathogen surveillance, outbreak detection, and infection control.