Culture-dependent evaluation of the respiratory microbiome in children with cystic fibrosis

Keywords: cystic fibrosis, microbiome, minor colony variants, mucoid phenotype, resistance


The study aimed to assess the regional peculiarities of the respiratory profile of children with cystic fibrosis (CF) in the Dnipro region (Ukraine).

Methods. Children living in the Dnipro region and aged younger than 18 years old with molecular-genetic confirmation of CF were enrolled in the study. Lung colonization was evaluated using a culture-dependent method. Sputum, mucus from the posterior pharyngeal wall and bronchoalveolar lavage fluid (BALF) were utilized.

Results. The Firmicutes phylum was the most common and occupied 54.00 % of the general proportion. On the other hand, the Proteobacteria phylum demonstrated overexpression in CF airways and kept the second rank with 28.87 %.

Sorensen's species similarity coefficient showed an allied affinity between the microbial burden of oropharyngeal samples with nasopharyngeal and sputum, QS = 0.61 and 0.91, respectively. However, the species composition within the nasal cavity was distinct from sputum and BALF (QS=0.47).

The primary pathogens in childhood were S. aureus, H. influenza, P. aeruginosa and A. fumigatus. In contrast to gram-negative non-fermenters (GNNF), the prevalence of S. aureus isolates by age had a non-linear character. The commensal microbiota changed negatively with age. Among children under 12 years, the Streptococcus genus was identified in 23.08 % of the samples, but among the age category older than 15 – only in 9.22 %.

11.06 % of S. aureus had small colony variants (SCVs) morphotypes. Isolates of P. aeruginosa with the properties of SCVs were also found in children who underwent prolonged antimicrobial treatment. However, the most prominent was the mucoid phenotype – 34.31 % of isolates.

Conclusions. Along with conventional microbiological properties, obligate pathobionts in children with CF exhibited changes, resulting in difficulties in identification. These included auxotrophic modification into SCVs and mucoid transformation.

The culture-dependent technique gives crucial data about the profile of pathogens usually associated with CF, although it is sufficiently limited


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Author Biographies

Oksana Ishchenko, Dnipro State Medical University

Department of Microbiology, Virology, Immunology and Epidemiology

Iryna Koshova, Dnipro State Medical University

Department of Microbiology, Virology, Immunology and Epidemiology

Tetiana Krushinska, Dnipro State Medical University

Department of Microbiology, Virology, Immunology and Epidemiology

Iryna Kolesnikova, Bogomolets National Medical University

Department of Epidemiology

Dmytro Stepanskyi, Dnipro State Medical University

Department of Microbiology, Virology, Immunology and Epidemiology


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Culture-dependent evaluation of the respiratory microbiome in children with cystic fibrosis

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How to Cite
Ishchenko, O., Koshova, I., Krushinska, T., Kolesnikova, I., & Stepanskyi, D. (2022). Culture-dependent evaluation of the respiratory microbiome in children with cystic fibrosis. EUREKA: Health Sciences, (4), 39-49.
Medicine and Dentistry