Antimicrobial resistance of Klebsiella pneumoniae strains isolated from COVID-19 patients: genetic analysis and phenotypic characterization

Introduction. Klebsiella pneumoniae is one of the most significant opportunistic pathogens, causing a wide range of infections in hospitalized patients and characterized by a high capacity to accumulate antimicrobial resistance genes. Aim: analysis of the phenotypic resistance profile to antimicrobials and molecular characteristics (resistance and virulence genes) in clinical К. pneumoniae strains isolated from COVID-19 patients, and a comparative assessment of the relationship between the studied genetic and phenotypic traits. Materials and methods. A total of 102 COVID-19 patients were examined. Nasopharyngeal swabs were analyzed using classical bacteriological methods. Phenotypic antimicrobial susceptibility testing was conducted using the disk-diffusion method. Whole-genome sequencing was performed on 9 K. pneumoniae isolates, followed by bioinformatics analysis of genetic profiles for antimicrobial resistance (AMR) and virulence. Results. The analysis revealed that the predominant resistance mechanism in the studied K. pneumoniae strains was antimicrobial inactivation (42.4%), highlighting the significance of enzymatic inactivation as a primary resistance mechanism. A substantial proportion of genetic determinants were associated with efflux pumps (36.3%), indicating their role in conferring resistance to a broad spectrum of antimicrobials. Smaller fractions of genes were linked to target modification (9.1%), target protection (6.1%), and reduced permeability (6.1%); however, their coexistence suggests a multifactorial AMR profile in K. pneumoniae. Phenotypically, all strains exhibited resistance to at least two antimicrobials, with 67% of isolates resistant to all tested agents. Comparative analysis of virulence factor genes and AMR determinants revealed statistically significant differences (p 0.001). Correlation analysis demonstrated a statistically significant inverse correlation (p = 0.034) between these two parameters. Conclusions. The phenotypic susceptibility of K. pneumoniae to antimicrobials, despite the presence of resistance genes, may result from the complex interplay of regulatory mechanisms, genetic element stability, and environmental conditions. The findings suggest a pronounced trend toward reduced prevalence of virulence factor genes with increasing AMR gene abundance.