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Background <p>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.</p> Methods <p>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.</p> Results <p>The collection included <i>Staphylococcus aureus</i> (<i>n</i> = 8), <i>Pseudomonas aeruginosa</i> (<i>n</i> = 5), <i>Serratia marcescens</i> (<i>n</i> = 2), <i>Enterobacter hormaechei</i> (<i>n</i> = 1), and <i>Klebsiella pneumoniae</i> (<i>n</i> = 1). SCV phenotypes were observed in 2 <i>S. aureus</i> ST398 isolates. <i>P. aeruginosa</i> strains belonged to diverse STs (ST644, ST2967, ST1228, ST242). The hypervirulent <i>K. pneumoniae</i> ST23-KL1 isolate harbored siderophores (<i>iucA</i>, <i>ybt</i>) and <i>peg-344</i>. All <i>S. aureus</i> ST398 isolates exhibited reduced growth rate and dense colony morphology.</p> Conclusion <p>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 <i>K. pneumoniae</i> lineages. The findings call for regular genomic surveillance in Ukrainian CF cohorts.</p>

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

  • 期刊论文

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  • 发表日期：

    2025年11月5日

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  • Dmytro Stepanskyi,
  • Oksana Ishchenko,
  • Patrick McGann,
  • Yuliia Lapa,
  • Iryna Koshova

摘要

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.