Impact of Antibiotic Therapy on the Upper Respiratory Tract and Gut Mycobiome in Patients with Cystic Fibrosis
Abstract
1. Introduction
2. Materials and Methods
2.1. Study Population and Sample Collection
2.2. DNA Extraction and ITS1 Region Copy Number Quantification
2.3. ITS1 Library Construction and Sequencing
2.4. ITS1 Amplicon Sequencing Analyses
2.5. Antibiotic Equivalent Dose Calculation
2.6. Correlation Analysis and Statistics
3. Results
3.1. Increase Fungal Biomass and Distinct Microbiome Diversities in CF Nasal Lavage and Stool Samples Compared to Healthy Individuals
3.2. Significant Increased Relative Abundance of Candida spp. in CF Samples Compared to the Healthy Cohort
3.3. Long-Term Effect of Cumulative Antibiotic Intake Correlates with the Presence of Candida spp. in CF Nasal Lavage Samples
3.4. Prolonged Antibiotic Exposure Promotes Nasal Site-Specific Candida spp. Colonization in Patients with CF, Linked to the Mode of Antibiotic Administration
3.5. Increased RA of Candida spp. in CF Nasal Lavage Samples After a Short Course of Antibiotics During Pulmonary Exacerbation
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
CF | cystic fibrosis |
AED | Antibiotic Equivalent Dose |
CFTR | CF transmembrane conductance regulator |
spp. | several species |
BMI | body mass index |
FEV1% | Forced expiratory volume in one second as a percentage |
rec. | recommended |
d | days |
ASVs | amplicon sequence variants |
PCoA | principal coordinates analysis |
RA | relative abundance |
iv | intravenous |
po | per os |
beforeAB | before antibiotic treatment |
afterAB | after antibiotic treatment |
HEMT | Highly Effective Triple-Combination Therapy |
ETI | elexacaftor/tezacaftor/ivacaftor |
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Nasal Lavage Samples | Candida spp. RA | ||
---|---|---|---|
Antibiotic Equivalent Dose (over 3 years) | Correlation coefficient | 0.674 | |
Sig. (2-tailed) | 0.016 * | ||
N | 12 | ||
Corticoids (over 3 years) | Correlation coefficient | 0.620 | |
Sig. (2-tailed) | 0.031 * | ||
N | 12 | ||
Modulator (double/single) | Correlation coefficient | 0.230 | |
Sig. (2-tailed) | 0.472 | ||
N | 12 | ||
FEV1% | Correlation coefficient | 0.280 | |
Sig. (2-tailed) | 0.404 | ||
N | 11 | ||
Shannon index | Correlation coefficient | −0.743 | |
Sig. (2-tailed) | 0.006 ** | ||
N | 12 | ||
P. aeruginosa chronic lower airway colonization | Correlation coefficient | 0.285 | |
Sig. (2-tailed) | 0.369 | ||
N | 12 | ||
S. aureus chronic lower airway colonization | Correlation coefficient | 0.275 | |
Sig. (2-tailed) | 0.388 | ||
N | 12 |
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Zubiria-Barrera, C.; Bos, M.; Neubert, R.; Fiebig, J.; Lorenz, M.; Hartmann, M.; Mainz, J.G.; Slevogt, H.; Klassert, T.E. Impact of Antibiotic Therapy on the Upper Respiratory Tract and Gut Mycobiome in Patients with Cystic Fibrosis. J. Fungi 2025, 11, 631. https://doi.org/10.3390/jof11090631
Zubiria-Barrera C, Bos M, Neubert R, Fiebig J, Lorenz M, Hartmann M, Mainz JG, Slevogt H, Klassert TE. Impact of Antibiotic Therapy on the Upper Respiratory Tract and Gut Mycobiome in Patients with Cystic Fibrosis. Journal of Fungi. 2025; 11(9):631. https://doi.org/10.3390/jof11090631
Chicago/Turabian StyleZubiria-Barrera, Cristina, Malena Bos, Robert Neubert, Jenny Fiebig, Michael Lorenz, Michael Hartmann, Jochen G. Mainz, Hortense Slevogt, and Tilman E. Klassert. 2025. "Impact of Antibiotic Therapy on the Upper Respiratory Tract and Gut Mycobiome in Patients with Cystic Fibrosis" Journal of Fungi 11, no. 9: 631. https://doi.org/10.3390/jof11090631
APA StyleZubiria-Barrera, C., Bos, M., Neubert, R., Fiebig, J., Lorenz, M., Hartmann, M., Mainz, J. G., Slevogt, H., & Klassert, T. E. (2025). Impact of Antibiotic Therapy on the Upper Respiratory Tract and Gut Mycobiome in Patients with Cystic Fibrosis. Journal of Fungi, 11(9), 631. https://doi.org/10.3390/jof11090631