Genomic Dissection of Virulence, Resistance, and Evolution in Colonizing versus Infected Klebsiella pneumoniae Isolates

Objective: To compare the genomic and phenotypic characteristics of colonized and infected Klebsiella pneumoniae (KP) isolates and to explore molecular features associated with progression from colonization to infection. Methods: From October 2020 to September 2023, we prospectively collected pharyngeal swabs from patients scheduled for cardiac surgery at a tertiary hospital in Northeast China. KP isolates from patients without evidence of infection were classified as the colonization group. Concurrently, KP isolates from sterile-site infections (blood, cerebrospinal fluid, joint fluid) diagnosed during the same period and at the same hospital were classified as the infection group. All isolates underwent string testing, antimicrobial susceptibility testing, and whole-genome sequencing. In addition, 55 publicly available KP genomes were retrieved from the NCBI database for phylogenetic context. Results: Among 2052 preoperative pharyngeal swabs, 940 yielded pathogenic isolates; KP was the most frequently detected organism (19.40%, 398/2052). After applying inclusion and exclusion criteria, 32 colonizing and 36 infection isolates were selected for genomic analysis. Both groups were largely susceptible to commonly tested antibiotics. String-test positivity did not differ between groups ((χ2=0.767, P =0.381). However, the infection group had a higher prevalence of sequence type 23 (58.33% vs. 25.00%; χ2=7.696, P =0.006), capsular serotype K1 (61.11% vs. 25.00%; χ2= 8.961, P =0.003), wzi 1 (52.78% vs. 25.00%; χ2=5.460, P =0.020), and the virulence regulator rmpA2 (χ2=4.600, P =0.032). The proportion of hypervirulent KP (hvKP) was also higher in the infection group (75.0% vs. 50.0%; χ2=4.554, P =0.033). Phylogenetic analysis showed that colonizing and infection isolates shared clonal backgrounds. Inclusion of public genomes further demonstrated that the ST23-K1 clone, prevalent in China, is strongly associated with invasive infections such as liver abscess and endophthalmitis. Conclusion: KP was the predominant nasopharyngeal colonizer in preoperative cardiac surgery patients. Infection isolates were enriched for hvKP-associated features, particularly ST23-K1 and rmpA2 . These findings support the hypothesis that colonizing and infecting KP isolates share evolutionary origins, and they highlight the importance of surveillance for high-risk colonizing clones in patients undergoing major surgery. Whether targeted decolonization reduces subsequent infection requires prospective intervention studies.