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Updated: Jan 12, 2026
Growing a Cystic Fibrosis-Relevant Polymicrobial Biofilm to Probe Community Phenotypes
Published on: April 19, 2024
Genomic and phenotypic characterization of respiratory pathogens from CF pediatric patients from Dnipro, Ukraine
Dmytro Stepanskyi1, Oksana Ishchenko2, Patrick McGann3
1Department of Microbiology, Virology, Immunology, Epidemiology and Biomedical Physics and Informatics, Dnipro State Medical University, Dnipro, Ukraine. dstepanskiy@gmail.com.
Insights
Chronic infections in cystic fibrosis patients are complex. This study identified specific bacterial strains, including small colony variants (SCVs) of Staphylococcus aureus ST398, and hypervirulent Klebsiella pneumoniae, highlighting the need for genomic surveillance.
Area of Science:
- Microbiology
- Genomics
- Clinical Medicine
Background:
- Chronic infections in cystic fibrosis (CF) patients are driven by adaptive, drug-resistant bacterial lineages.
- Understanding bacterial sequence types (STs) and phenotypic adaptations like small colony variants (SCVs) is crucial for effective CF patient management.
Purpose of the Study:
- To characterize the genetic and phenotypic diversity of respiratory bacterial pathogens in pediatric CF patients from Ukraine.
- To identify specific sequence types (STs) and antimicrobial resistance (AMR) genes.
- To investigate the emergence of small colony variants (SCVs) and hypervirulent strains.
Main Methods:
- Whole genome sequencing (WGS) and Multi-Locus Sequence Typing (MLST) were used to analyze 17 bacterial isolates from 12 pediatric CF patients.
- Phenotypic traits, including SCV morphology, and AMR genes were characterized.
- Isolates included Staphylococcus aureus, Pseudomonas aeruginosa, Serratia marcescens, Enterobacter hormaechei, and Klebsiella pneumoniae.
Main Results:
- Staphylococcus aureus ST398 isolates (n=2) exhibited SCV phenotypes, reduced growth rates, and dense colony morphology.
- Diverse STs were identified in Pseudomonas aeruginosa strains.
- A hypervirulent Klebsiella pneumoniae ST23-KL1 isolate harbored specific virulence factors (siderophores, peg-344).
Conclusions:
- The study reveals significant genetic and phenotypic complexity in respiratory pathogens affecting Ukrainian CF children.
- Emergence of ST398 SCVs and introduction of hypervirulent Klebsiella pneumoniae lineages were noted.
- Regular genomic surveillance is recommended for Ukrainian CF cohorts to guide clinical management.
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.
