Genomic and phenotypic characterization of respiratory pathogens from CF pediatric patients from Dnipro, Ukraine.

BACKGROUND

Chronic infections in cystic fibrosis (CF) patients are often driven by adaptive and drug-resistant bacterial lineages. Understanding sequence types (STs) and phenotypic adaptations such as small colony variants (SCVs) can guide more effective clinical management.

METHODS

Seventeen bacterial isolates from respiratory specimens of 12 pediatric CF patients (Dnipro, Ukraine, Sept 2022-Sept 2024) were characterized via culture-based diagnostics and whole genome sequencing (WGS). Multi-Locus Sequence Typing (MLST) was applied to determine sequence types, while phenotypic traits, including SCV morphology, were recorded and antimicrobial resistance (AMR) genes profiled.

RESULTS

The collection included Staphylococcus aureus (n = 8), Pseudomonas aeruginosa (n = 5), Serratia marcescens (n = 2), Enterobacter hormaechei (n = 1), and Klebsiella pneumoniae (n = 1). SCV phenotypes were observed in 2 S. aureus ST398 isolates. P. aeruginosa strains belonged to diverse STs (ST644, ST2967, ST1228, ST242). The hypervirulent K. pneumoniae ST23-KL1 isolate harbored siderophores (iucA, ybt) and peg-344. All S. aureus ST398 isolates exhibited reduced growth rate and dense colony morphology.

CONCLUSION

This study highlights the genetic and phenotypic complexity of respiratory pathogens in Ukrainian CF children, emphasizing the emergence of ST398 SCVs and the introduction of hypervirulent K. pneumoniae lineages. The findings call for regular genomic surveillance in Ukrainian CF cohorts.