Characteristics of the anaerobic microbiota of the respiratory tract of children with cystic fibrosis

The study of the potential role of anaerobic bacteria in CF and their involvement in the pathophysiology of CF is important for understanding the influence of anaerobic flora on the damage to the bronchopulmonary system in cystic fibrosis. Objective: to determine the anaerobic diversity of the respiratory tract microbiota and its role in CF, to determine the resistance of anaerobic bacterial strains to antibacterial drugs. Materials and methods Sputum samples from 65 pediatric patients with cystic fibrosis were examined for anaerobic flora, a total of 86 samples of discharge from the lower respiratory tract were taken. Group 1 without anaerobic flora culture amounted to 56/86.2% of people, group 2 with anaerobic flora culture - 9/13.84% of people. To assess the effect of anaerobic flora on lung function, two groups of patients were identified - a group with Pseudomonas aeruginosa culture - 31/47.7% patients and a group of patients with Pseudomonas aeruginosa culture and anaerobic flora - 9/13.84%. Results: long-term persistence of anaerobic flora in severe patients and re-infection with anaerobic bacteria, including new species, were shown. Fusobacterium necrophorum isolated from one patient with cystic fibrosis had complete resistance to 7 antibacterial drugs, and sensitivity in increased concentrations to 4 antibacterial drugs, including metronidazole. The addition of anaerobic flora significantly aggravates the course of the chronic bronchopulmonary process, which is shown in the study with statistically significant differences in nutritional status indicators - patients with anaerobic flora culture had worse indicators M ± SD BMI per 21.5 ± 15.49 compared to the group of patients without anaerobic flora culture 35.43 ± 27.96 (p2-3 = 0.03), FEV1 57.60 ± 24.99, without AnM culture 82.69 ± 23.24 (p2.3 = 0.036), FVC 67.40 ± 15.63, in the group without AnM culture 87.62 ± 23.71 (p2.3 = 0.049), and including when comparing groups with an increase in P. aeruginosa and the group with the growth of P. aeruginosa in association with anaerobic flora - FEV1 57.60% ± 24.99 of the expected value in the group with the growth of anaerobes and 77.44 ± 22.89% of the expected value in the group with the growth of only P. aeruginosa (p = 0.033), FVC - 67.40 ± 15.63% of the expected value versus 85.43 ± 18.66% of the expected value, respectively (p = 0.041). Conclusion. The addition of anaerobic flora significantly aggravates the course of the chronic bronchopulmonary process, the possible long-term persistence of anaerobic flora in severe patients is shown, it is necessary to examine patients with CF during an exacerbation for the presence of anaerobic flora. It is necessary to include antimicrobial drugs with activity against anaerobic bacteria in the treatment of exacerbations in the absence of an effect from antimicrobial therapy.

cystic fibrosis, bacterial pathogen, anaerobic bacteria, microbiota, Pseudomonas aeruginosa, respiratory function

1. Tunney M.M., Field T.R., Moriarty T.F. et al. Detection of anaerobic bacteria in high numbers in sputum from patients with cystic fibrosis. Am J Respir Crit Care Med. 2008 May 1;177(9):995-1001. doi: 10.1164/rccm.200708-1151OC.

2. Wellinghausen N., Köthe J., Wirths B. et al. Superiority of molecular techniques for identification of Gram-negative, oxidase-positive rods, including morphologically nontypical Pseudomonas aeruginosa, from patients with cystic fibrosis. J Clin Microbiol. 2005;43(8):4070-5. doi: 10.1128/jcm.43.8.4070-4075.2005.

3. Muhlebach M.S., Hatch J.E., Einarsson G.G. et al. Anaerobic bacteria cultured from cystic fibrosis airways correlate to milder disease: a multisite study. Eur Respir J. 2018 Jul 11;52(1):1800242. doi: 10.1183/13993003.00242-2018.

4. Nguyen M., Sharma A., Wu W., Gomi R., Sung B., Hospodsky D., Angenent L.T., Worgall S. The fermentation product 2,3-butanediol alters P. aeruginosa clearance, cytokine response and the lung microbiome. ISME J. 2016 Dec;10(12):2978-2983. doi: 10.1038/ismej.2016.76.

5. Phan J., Gallagher T., Oliver A., England W.E., Whiteson K. Fermentation products in the cystic fibrosis airways induce aggregation and dormancy-associated expression profiles in a CF clinical isolate of Pseudomonas aeruginosa. FEMS Microbiol Lett. 2018 May 1;365(10): fny082. doi: 10.1093/femsle/fny082.

6. Ulrich M., Beer I., Braitmaier P. et al. Relative contribution of Prevotella intermedia and Pseudomonas aeruginosa to lung pathology in airways of patients with cystic fibrosis. Thorax. 2010 Nov;65(11):978-84. doi: 10.1136/thx.2010.137745.

7. Polikarpova S.V., Zhilina S.V., Kondratenko O.V., Lyamin A.V., Borzova Yu.V., Zhestkov A.V. Guidelines for the microbiological diagnosis of respiratory tract infections in patients with cystic fibrosis, Moscow, 2019, 127 p. (in Russ.) ISBN 978-5-94789-905-4

8. Practical recommendations for laboratory diagnostics of anaerobic infection Practical recommendations of the association. FLM Moscow. 2021. (in Russ.) Available at: https://fedlab.ru/upload/iblock/c99/Практические%20рекомендации%20по%20диагностики%20анаэробной%20инфекции%20%20Финал.pdf (Accessed: 01.11.2024)@@ Практические рекомендации по лабораторной диагностике анаэробной инфекции Практические рекомендации ассоциации. ФЛМ Москва 2021. URL: https://fedlab.ru/upload/iblock/c99/Практические%20рекомендации%20по%20диагностики%20анаэробной%20инфекции%20%20Финал.pdf

9. CLSI. Methods for Antimicrobial Susceptibility Testing of Anaerobic Bacteria. 9th ed. CLSI standard M11. Wayne, PA: Clinical and Laboratory Standards Institute; 2018, Volume 38, Number 19. ISBN 978-1-68440-021-8

10. Cowley E.S., Kopf S.H., LaRiviere A., Ziebis W., Newman D.K. Pediatric Cystic Fibrosis Sputum Can Be Chemically Dynamic, Anoxic, and Extremely Reduced Due to Hydrogen Sulfide Formation. mBio. 2015 Jul 28;6(4): e00767. doi: 10.1128/mBio.00767-15.

11. Rogers G.B., Carroll M.P., Serisier D.J., Hockey P.M., Jones G., Bruce K.D. characterization of bacterial community diversity in cystic fibrosis lung infections by use of 16s ribosomal DNA terminal restriction fragment length polymorphism profiling. J Clin Microbiol. 2004 Nov;42(11):5176-83. doi: 10.1128/JCM.42.11.5176-5183.2004.

12. Zemanick E.T., Wagner B.D., Sagel S.D., Stevens M.J., Accurso F.J., Harris J.K. Reliability of quantitative real-time PCR for bacterial detection in cystic fibrosis airway specimens. PLoS One. 2010 Nov 30;5(11): e15101. doi: 10.1371/journal.pone.0015101.

13. Tunney M.M., Klem E.R., Fodor A.A. et al. Use of culture and molecular analysis to determine the effect of antibiotic treatment on microbial community diversity and abundance during exacerbation in patients with cystic fibrosis. Thorax. 2011 Jul;66(7):579-84. doi: 10.1136/thx.2010.137281.

14. Zemanick E.T., Harris J.K., Wagner B.D. et al. Inflammation and airway microbiota during cystic fibrosis pulmonary exacerbations. PLoS One. 2013 Apr 30;8(4): e62917. doi: 10.1371/journal.pone.0062917.

15. Hauser P.M., Bernard T., Greub G., Jaton K., Pagni M., Hafen G.M. Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing. PLoS One. 2014 Mar 5;9(3): e90934. doi: 10.1371/journal.pone.0090934.

16. Carmody L.A., Caverly L.J., Foster B.K. et al. Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis. PLoS One. 2018 Mar 9;13(3): e0194060. doi: 10.1371/journal.pone.0194060.

17. Flynn J.M., Niccum D., Dunitz J.M., Hunter R.C. Evidence and Role for Bacterial Mucin Degradation in Cystic Fibrosis Airway Disease. PLoS Pathog. 2016 Aug 22;12(8): e1005846. doi: 10.1371/journal.ppat.1005846.

18. Sherrard L.J., McGrath S.J., McIlreavey L. et al. Production of extended-spectrum β-lactamases and the potential indirect pathogenic role of Prevotella isolates from the cystic fibrosis respiratory microbiota.Int J Antimicrob Agents. 2016 Feb;47(2):140-5. doi: 10.1016/j.ijantimicag.2015.12.004.

19. Quinn R.A., Whiteson K., Lim Y.W., Salamon P. et al. A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation. ISME J. 2015 Mar 17;9(4):1052. doi: 10.1038/ismej.2014.266.