Molecular assessment of carbapenem-resistant and ESBL Klebsiella pneumoniae clinical isolates to decipher the correlation of antimicrobial resistance with virulence traits

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Klebsiella pneumoniae is a nosocomial pathogen that poses a serious concern due to the high prevalence of extended-spectrum beta-lactamases (ESBL) and carbapenem-resistant K. pneumoniae (CRKP) strains. However, the data on the prevalence of contributing virulence determinants are limited in the Pakistani population. The study aims to characterize clinical isolates of K. pneumoniae to understand clonal relationships and determine the relationship of antibiotic resistance with different virulence factors (i.e., biofilm, capsular polysaccharide, hemolysis, efflux pump, and outer membrane porins). The clinical strains were collected from the diagnostic facility of two public sector hospitals in Karachi. The resistance and virulence profile of the isolates were evaluated via antibiotic susceptibility test, double disk synergy test (DDST), ChromAgar, string test, blood hemolysis, and biofilm assay. Genotypically, the isolates were identified by 16S rRNA and rpoB gene, and further characterized for the presence of ESBL, CRKP, biofilm, efflux pump, and outer membrane porins genes. The clonal lineage among isolates was established by Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC PCR). The antibiotic susceptibility test was analyzed through the Multiple Antibiotic Resistance (MAR) index, which revealed 90.2 % (n = 102) strains were MDR. Whereas, the genetic diversity was revealed through ERIC PCR and clade wise data revealed genetic variations due to ESBL (85 %), carbapenem resistance (73 %), biofilm (97 %), efflux pump (40-53 %), outer membrane porins (38-49 %), and hypermucoidity (6 %). The Pearson correlation analysis revealed a strong relationship of MDR strains with biofilm (r = 0.99), efflux pump (r = 0.92), and outer membrane porins (r = 0.88). The study highlighted the prevalence of MDR K. pneumonia with the plethora of virulence factors in the local clinical setting, necessitating stringent screening to develop national policies to tackle further antimicrobial resistance development and outbreaks.