Genomic epidemiology of carbapenemase-producing Klebsiella pneumoniae circulating in a Chilean tertiary-care hospital (2021–2022): Molecular characterization, resistance-virulence convergence, and clinical associations

Abstract Klebsiella pneumoniae (Kp) is a Gram-negative bacillus responsible for approximately 10% of nosocomial bacterial infections and one-third of Gram-negative bacterial infections in hospitalized patients. The rise of multidrug-resistant and hypervirulent strains makes it a significant public health issue. This study characterized carbapenem-resistant Kp (CR-Kp) strains isolated at the Hospital Clínico Universidad de Chile (HCUCH) 2021–2022 and explored associations with clinical characteristics. 45 CR-Kp strains from 29 patients in critical care units were analyzed. Mass spectrometry was used for species identification, and antimicrobial susceptibility was assessed by Kirby-Bauer disk diffusion. Clonality was determined using pulsed-field gel electrophoresis (PFGE), and multiplex PCR detected resistance and virulence genes. Clonal strains underwent whole-genome sequencing. PCR revealed the high prevalence of carbapenemase genes and extended-spectrum β -lactamases. PFGE identified nine clones, corresponding to sequence types ST25, ST45, ST307, and ST1161. Frequent virulence factors included siderophores and adhesins, while the capsular serotype K2 was present in 44% of isolates. No classical hypervirulence markers were detected. The presence of blaKPC correlated with more extended hospitalization. These findings reveal convergence between multidrug resistance and adaptive virulence traits rather than classical hypervirulence, highlighting evolving pathogenic strategies in high-risk CR-Kp clones circulating in Chile and emphasizing the need for enhanced molecular surveillance and infection protocols in critical care settings.