Genomic and functional approaches point to potential determinants of neonatal K. pneumoniae sepsis

Neonatal sepsis remains a major cause of global mortality, yet the contribution of pathogen-level traits to clinical outcomes is poorly understood. We combined whole-genome sequencing with phenotypic and functional assays to evaluate whether genomic features of Klebsiella pneumoniae, particularly the stealth siderophore yersiniabactin (ybt), are associated with clinical outcomes in neonates. Thirty-three bloodstream isolates were profiled for antimicrobial resistance (AMR), virulence genes, and sequence type. Phenotypic assays assessed antimicrobial susceptibility and biofilm formation, and host-pathogen interactions were examined using a human airway epithelial cell (A549) model. Ybt-positive isolates showed increased adhesion and intracellular proliferation in A549 cells compared to ybt-negative isolates and were enriched among isolates recovered from non-surviving neonates. Genomic clustering revealed frequent co-occurrence of ybt with multidrug resistance determinants in high-risk sequence types, such as ST14 and ST231. Traditional phenotypes, such as AST and biofilm formation, did not segregate by outcome, whereas ybt presence showed a stronger association with outcome in this cohort. These findings suggest that siderophore-mediated iron acquisition may enhance epithelial fitness and contribute to adverse outcomes in neonatal sepsis. Our study highlights the value of integrating genomic and functional bacterial features into neonatal sepsis research and illustrates the potential of pathogen-based markers to complement host-focused prognostic strategies.IMPORTANCENeonatal sepsis caused by Klebsiella pneumoniae remains a major clinical challenge, yet the pathogen traits that contribute to fatal outcomes are poorly understood. In this study, we analyzed bloodstream isolates from 33 neonates, including 13 who did not survive, and identified genomic features enriched in strains from non-survivors. The siderophore yersiniabactin (ybt), which enables iron acquisition and helps bacteria withstand host immune defenses, was consistently present in these isolates. By integrating genomic profiling with laboratory phenotypes and epithelial cell infection assays, we show that ybt-positive strains exhibit enhanced epithelial fitness and are associated with adverse clinical outcomes in this cohort. These findings highlight the importance of incorporating pathogen genomic and functional markers into neonatal sepsis research, surveillance, and future risk-stratification strategies.