The first study characterizing the respiratory microbiome in cystic fibrosis patients in Jordan

Main Article Content

Ahmad R Alsayed
Anas Abed
Malek Zihlif
Mahmoud S Abu-Samak
Rana Ahmad Almuhur
Mohammad Alkhatib


Cystic fibrosis, Respiratory, Microbiome , Jordan, Epidemiology


Cystic fibrosis (CF) is most commonly seen in Caucasians and is uncommon in the Middle East. This study, based in Jordan, aimed to describe the association between lung exacerbation in CF patients and the respiratory microbiome composition. Using the 16S rRNA marker-gene sequencing, we investigated the microbiota in sputa during exacerbation (E1) and 14 days after the exacerbation (E2) of two CF patients admitted to the hospital. Detected genera with high abundance in the E1-related sputa of the first patient included Achromobacter and Streptococcus. At E2, Achromobacter and Staphylococcus were the highest abundant genera. Regarding the second patient, Veillonella and Streptococcus, were the highest abundant genera at E1. Whereas, Streptococcus and Veillonella were the highest abundant genera. This is the first study, based in Jordan, to report and describe the respiratory microbiome during and after the exacerbation of CF patients. This study suggests that pulmonary exacerbation in CF patients can result in alterations in their respiratory microbiome. A better knowledge of this link could allow more focused use of antibiotics, especially during exacerbations, improving clinical efficacy and patient outcomes 

Abstract 177 | PDF Downloads 234


1. O’Sullivan BP, Freedman SD. Cystic fibrosis. Lancet. 2009;373(9678):1891-1904.
2. Alsayed AR, Abed A, Khader HA, et al. Molecular Accounting and Profiling of Human Respiratory Microbial Communities: Toward Precision Medicine by Targeting the Respiratory Microbiome for Disease Diagnosis and Treatment. Int J Mol Sci. 
3. Lipuma JJ. The changing microbial epidemiology in cystic fibrosis. Clin Microbiol Rev. 2010;23(2):299-323.
4. Surette MG. The cystic fibrosis lung microbiome. Ann Am Thorac Soc. 2014;11(Suppl 1):S61-S65.
5. Sanders DB, Bittner RC, Rosenfeld M, et al. Failure to recover to baseline pulmonary function after cystic fibrosis pulmonary exacerbation. Am J Respir Crit Care Med. 2010;182(5):627-32.
6. Klepac‐Ceraj V, Lemon KP, Martin TR, et al. Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa. Environmental Microbiology. 2010;12(5):1293-1303. https://doi.
7. Zhao J, Schloss PD, Kalikin LM, et al. Decade-long bacterial community dynamics in cystic fibrosis airways. Proceedings of the National Academy of Sciences. 2012;109(15):5809-5814.
8. Flanagan J, Brodie E, Weng L, et al. Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. Journal of Clinical Microbiology. 2007;45(6):1954-1962.
9. Cox MJ, Allgaier M, Taylor B, et al. Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PloS One. 2010;5(6):e11044.
10. Rawashdeh M, Manal H. Cystic fibrosis in Arabs: a prototype from Jordan. Ann Trop Paediatr. 2000;20(4):283-286.
11. Nazer HM. Early diagnosis of cystic fibrosis in Jordanian children. J Trop Pediatr. 1992;38(3):113-115.
12. Comeau AM, Accurso FJ, White TB, et al. Guidelines for implementation of cystic fibrosis newborn screening programs: Cystic Fibrosis Foundation workshop report. Pediatrics. 2007;119(2):e495-e518.
13. Farrell PM, Rosenstein BJ, White TB, et al. Guidelines for diagnosis of cystic fibrosis in newborns through older adults: Cystic Fibrosis Foundation consensus report. The Journal of Pediatrics. 2008;153(2):S4-s14.
14. De Boeck K, Wilschanski M, Castellani C, et al. Cystic fibrosis: terminology and diagnostic algorithms. Thorax. 2006;61(7):627-635.
15. Flume PA, Mogayzel Jr PJ, Robinson KA, et al. Cystic fibrosis pulmonary guidelines: treatment of pulmonary exacerbations. American Journal of Respiratory and Critical Care Medicine. 2009;180(9):802-808.
16. Al-Dulaimi A, Alsayed AR, Maqbali MA, et al. Investigating the human rhinovirus co-infection in patients with asthma exacerbations and COVID-19. Pharm Pract (Granada). 2022;20(2):2665.
17. Alsayed AR, Talib W, Al-Dulaimi A, et al. The first detection of Pneumocystis jirovecii in asthmatic patients post-COVID-19 in Jordan. Bosn J Basic Med Sci. 2022;22(5):784-790.
18. Alsayed AR, Hasoun L, Khader HA, et al. Co‑infection of COVID-19 patients with atypical bacteria: A study based in Jordan. Pharmacy Practice. 2023;21(1):1-5.
19. Alsayed A, Al-Doori A, Al-Dulaimi A, et al. Influences of bovine colostrum on nasal swab microbiome and viral upper respiratory tract infections - A case report. Respir Med Case Rep. 2020;31:101189.
20. Alsayed AR, Abed A, Jarrar YB, et al. Alteration of the Respiratory Microbiome in Hospitalized Patients with Asthma–COPD Overlap during and after an Exacerbation. Journal of Clinical Medicine. 2023;12(6):2118.
21. Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nature methods. 2010;7(5):335-336.
22. Edgar RC, Haas BJ, Clemente JC, et al. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27(16):2194-2200.
23. Caporaso JG, Bittinger K, Bushman FD, et al. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics. 2009;26(2):266-267.
24. Wang Q, Garrity GM, Tiedje JM, et al. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology. 2007;73(16):5261-5267.
25. Fodor AA, Klem ER, Gilpin DF, et al. The adult cystic fibrosis airway microbiota is stable over time and infection type, and highly resilient to antibiotic treatment of exacerbations. PLoS One. 2012;7(9):e45001.
26. van der Gast CJ, Walker AW, Stressmann FA, et al. Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities. Isme J. 2011;5(5):780-791.
27. Han MK, Huang YJ, Lipuma JJ, et al. Significance of the microbiome in obstructive lung disease. Thorax. May 2012;67(5):456-463.
28. Madan JC, Koestler DC, Stanton BA, et al. Serial analysis of the gut and respiratory microbiome in cystic fibrosis in infancy: interaction between intestinal and respiratory tracts and impact of nutritional exposures. MBio. 2012;3(4): e00251-12. https://
29. O’Neill K, Bradley JM, Johnston E, et al. Reduced bacterial colony count of anaerobic bacteria is associated with a worsening in lung clearance index and inflammation in cystic fibrosis. PloS One. 2015;10(5):e0126980.
30. Sherrard LJ, Graham KA, McGrath SJ, et al. Antibiotic resistance in Prevotella species isolated from patients with cystic fibrosis. Journal of Antimicrobial Chemotherapy. 2013;68(10):2369-2374.
31. Hurst JR, Wilkinson TM, Perera WR, et al. Relationships among bacteria, upper airway, lower airway, and systemic inflammation in COPD. CHEST Journal. 2005;127(4):1219-1226.
32. Rogers G, Carroll M, Serisier D, et al. Use of 16S rRNA gene profiling by terminal restriction fragment length polymorphism analysis to compare bacterial communities in sputum and mouthwash samples from patients with cystic fibrosis. Journal of 
Clinical Microbiology. 2006;44(7):2601-2604.
33. Patel I, Seemungal T, Wilks M, et al. Relationship between bacterial colonisation and the frequency, character, and severity of COPD exacerbations. Thorax. 2002;57(9):759-764.
34. Wilkinson TM, Patel IS, Wilks M, et al. Airway bacterial load and FEV1 decline in patients with chronic obstructive pulmonary disease. American Journal of Respiratory and Critical Care Medicine. 2003;167(8):1090-1095.
35. Tunney MM, Field TR, Moriarty TF, et al. Detection of anaerobic bacteria in high numbers in sputum from patients with cystic fibrosis. American Journal of Respiratory and Critical Care Medicine. 2008;177(9):995-1001.

Most read articles by the same author(s)