Culture-dependent evaluation of the respiratory microbiome in children with cystic fibrosis
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
Lynch, S. V., Bruce, K. D. (2013). The Cystic Fibrosis Airway Microbiome. Cold Spring Harbor Perspectives in Medicine, 3 (3), a009738–a009738. doi: https://doi.org/10.1101/cshperspect.a009738
Gilpin, D., Hoffman, L. R., Ceppe, A., Muhlebach, M. S. (2021). Phenotypic characteristics of incident and chronic MRSA isolates in cystic fibrosis. Journal of Cystic Fibrosis, 20 (4), 692–698. doi: https://doi.org/10.1016/j.jcf.2021.05.015
Cuthbertson, L., Walker, A. W., Oliver, A. E., Rogers, G. B., Rivett, D. W., Hampton, T. H. et. al. (2020). Lung function and microbiota diversity in cystic fibrosis. Microbiome, 8 (1). doi: https://doi.org/10.1186/s40168-020-00810-3
Françoise, A., Héry-Arnaud, G. (2020). The Microbiome in Cystic Fibrosis Pulmonary Disease. Genes, 11(5), 536. doi: https://doi.org/10.3390/genes11050536
Scialo, F., Amato, F., Cernera, G., Gelzo, M., Zarrilli, F., Comegna, M. et. al. (2021). Lung Microbiome in Cystic Fibrosis. Life, 11 (2), 94. doi: https://doi.org/10.3390/life11020094
Burns, J. L., Rolain, J.-M. (2014). Culture-based diagnostic microbiology in cystic fibrosis: Can we simplify the complexity? Journal of Cystic Fibrosis, 13 (1), 1–9. doi: https://doi.org/10.1016/j.jcf.2013.09.004
Royal Brompton Hospital Paediatric Cystic Fibrosis Team. Clinical guidelines: Care of children with cystic fibrosis (2022). Medicines Management Board of Royal Brompton & Harefield NHS Foundation Trust 2020, 311.
Cornaglia, G., Courcol, R., Hermann, J.-L. et. al. (2011). ESCMID: European Manual of Clinical Microbiology.
Yadav, S. K., Singh, S., Gupta, R. (2019). Biomedical Statistics. A Beginner's Guide. Singapore: Springer, 342. doi: http://doi.org/10.1007/978-981-32-9294-9
Sait, L., Galic, M., Strugnell, R. A., Janssen, P. H. (2003). Secretory Antibodies Do Not Affect the Composition of the Bacterial Microbiota in the Terminal Ileum of 10-Week-Old Mice. Applied and Environmental Microbiology, 69 (4), 2100–2109. doi: https://doi.org/10.1128/aem.69.4.2100-2109.2003
Thornton, C. S., Surette, M. G. (2021). Potential Contributions of Anaerobes in Cystic Fibrosis Airways. Journal of Clinical Microbiology, 59 (3). doi: https://doi.org/10.1128/jcm.01813-19
Frayman, K. B., Armstrong, D. S., Grimwood, K., Ranganathan, S. C. (2017). The airway microbiota in early cystic fibrosis lung disease. Pediatric Pulmonology, 52 (11), 1384–1404. doi: https://doi.org/10.1002/ppul.23782
Hardy, B. L., Merrell, D. S. (2021). Friend or Foe: Interbacterial Competition in the Nasal Cavity. Journal of Bacteriology, 203 (5). doi: https://doi.org/10.1128/jb.00480-20
Krishnakumari, V., Guru, A., Adicherla, H., Nagaraj, R. (2018). Effects of increasing hydrophobicity by N‐terminal myristoylation on the antibacterial and hemolytic activities of the C‐terminal cationic segments of human‐β‐defensins 1–3. Chemical Biology & Drug Design, 92 (2), 1504–1513. doi: https://doi.org/10.1111/cbdd.13317
Bhagirath, A. Y., Li, Y., Somayajula, D., Dadashi, M., Badr, S., Duan, K. (2016). Cystic fibrosis lung environment and Pseudomonas aeruginosa infection. BMC Pulmonary Medicine, 16 (1). doi: https://doi.org/10.1186/s12890-016-0339-5
Clunes, M. T., Boucher, R. C. (2007). Cystic fibrosis: the mechanisms of pathogenesis of an inherited lung disorder. Drug Discovery Today: Disease Mechanisms, 4 (2), 63–72. doi: https://doi.org/10.1016/j.ddmec.2007.09.001
Martín-Gómez, M. T. (2020). Taking a look on fungi in cystic fibrosis: More questions than answers. Revista Iberoamericana de Micología, 37 (1), 17–23. doi: https://doi.org/10.1016/j.riam.2019.10.004
Singh, A., Ralhan, A., Schwarz, C., Hartl, D., Hector, A. (2017). Fungal Pathogens in CF Airways: Leave or Treat? Mycopathologia, 183 (1), 119–137. doi: https://doi.org/10.1007/s11046-017-0184-y
Poore, T. S., Hong, G., Zemanick, E. T. (2021). Fungal Infection and Inflammation in Cystic Fibrosis. Pathogens, 10 (5), 618. doi: https://doi.org/10.3390/pathogens10050618
Goddard, A. F., Staudinger, B. J., Dowd, S. E., Joshi-Datar, A., Wolcott, R. D., Aitken, M. L. et. al. (2012). Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota. Proceedings of the National Academy of Sciences, 109 (34), 13769–13774. doi: https://doi.org/10.1073/pnas.1107435109
Hector, A., Jonas, F., Kappler, M., Feilcke, M., Hartl, D., Griese, M. (2009). Novel Method to Process Cystic Fibrosis Sputum for Determination of Oxidative State. Respiration, 80 (5), 393–400. doi: https://doi.org/10.1159/000271607
Sibley, C. D., Grinwis, M. E., Field, T. R., Eshaghurshan, C. S., Faria, M. M., Dowd, S. E. et. al. (2011). Culture Enriched Molecular Profiling of the Cystic Fibrosis Airway Microbiome. PLoS ONE, 6 (7), e22702. doi: https://doi.org/10.1371/journal.pone.0022702
Caballero, J. de D., del Campo, R., Tato, M., Gómez G de la Pedrosa, E., Cobo, M., López-Causapé, C. et. al. (2014). Microbiological diagnostic procedures for respiratory cystic fibrosis samples in Spain: towards standard of care practices. doi: BMC Microbiology, 14 (1). https://doi.org/10.1186/s12866-014-0335-y
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