Epidemiology and genomic characteristics of carbapenem-resistant Klebsiella pneumoniae in intensive care unit from 2021 to 2024

The primary aim of this research was to elucidate the clinical epidemiology and genetic traits of carbapenem-resistant Klebsiella pneumoniae (CRKP) infection and colonization within the intensive care unit (ICU) of a tertiary care teaching hospital in China, spanning the period from 2021 to 2024. All CRKP isolates were obtained from patients in the ICU, and relevant clinical data pertaining to these patients were collected. The whole genome sequencing was conducted for all isolates, followed by downstream genomic analyses. The study identified 29 non-duplicate CRKP strains, completely isolated from ICU, with sputum as the most common anal swab sample. Patients with factors including a prior ICU stay, use of a central venous catheter and antibiotic treatment were found to be associated with CRKP infection. Our collected CRKP isolates demonstrated multidrug resistance, with additional resistance to cephalosporins. Further virulence assays revealed that these isolates exhibited strong serum survival capabilities despite lacking the mucoid phenotype. Molecular epidemiology indicated that all strains harbored the blaKPC-2 gene and belonged to the KL64-O2v1 serotype. Although all isolates lacked the regulator of mucoid phenotype (rmpA) gene, they carried the colibactin (clb) and yersiniabactin (ybt) genes. These findings suggest a complex interplay between resistance and virulence factors that contribute to the pathogenicity of these CRKP strains. This study provided insights into the molecular epidemiology of CRKP within ICUs from 2021 to 2024, identifying potential factors associated with CRKP infections. Our findings underscore the critical importance of monitoring CRKP and implementing robust antimicrobial stewardship programs to limit the spread of CRKP infections.