{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T07:33:50Z","timestamp":1781163230834,"version":"3.54.1"},"reference-count":96,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2025,8,28]],"date-time":"2025-08-28T00:00:00Z","timestamp":1756339200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"German Research Foundation (DFG)","doi-asserted-by":"publisher","award":["390874280"],"award-info":[{"award-number":["390874280"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation (DFG)","doi-asserted-by":"publisher","award":["210879364"],"award-info":[{"award-number":["210879364"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"J\u00fcrgen Manchot Stiftung to RN","award":["390874280"],"award-info":[{"award-number":["390874280"]}]},{"name":"J\u00fcrgen Manchot Stiftung to RN","award":["210879364"],"award-info":[{"award-number":["210879364"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JoF"],"abstract":"<jats:p>Patients with cystic fibrosis (CF) are frequently exposed to antibiotic treatments, which can alter the fungal communities (mycobiome) across their mucosal sites. This pilot study investigated the impact of antibiotic exposure on the mycobiome by analyzing fungal community dynamics in the upper respiratory- (nasal lavage) and gastrointestinal- (stool samples) tracts of 12 patients with CF following (a) long-term antibiotic treatment over a three-year period and (b) short-term antibiotic therapy during acute pulmonary exacerbations. Mycobiome profiles of the samples obtained from 38 healthy individuals were also analyzed and used for comparison purposes. The ITS1 region of the fungal rRNA gene cluster was sequenced to characterize and quantify the fungal community composition in both cohorts. Compared to healthy controls, samples from the patients with CF who had undergone long-term antibiotic treatment revealed a significantly increased fungal biomass in both sino-nasal and stool samples. Moreover, diversity metrics revealed significant differences in nasal lavage samples, whereas the stool samples showed no significant variation. Candida spp. was significantly enriched in both nasal and stool samples from CF patients. Further analyses demonstrated a strong positive correlation between the relative abundance of Candida spp. and the cumulative antibiotic intake over the three-year period in sino-nasal samples, but not in stool samples. Acute antibiotic treatment during a pulmonary exacerbation episode also led to a marked increase in the abundance of Candida spp. in sino-nasal samples. These findings highlight the increased sensitivity of the sino-nasal mycobiome to both chronic and acute antibiotic exposure in CF patients, as characterized by a site-specific fungal overgrowth, particularly of Candida spp.<\/jats:p>","DOI":"10.3390\/jof11090631","type":"journal-article","created":{"date-parts":[[2025,8,29]],"date-time":"2025-08-29T08:01:01Z","timestamp":1756454461000},"page":"631","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Impact of Antibiotic Therapy on the Upper Respiratory Tract and Gut Mycobiome in Patients with Cystic Fibrosis"],"prefix":"10.3390","volume":"11","author":[{"given":"Cristina","family":"Zubiria-Barrera","sequence":"first","affiliation":[{"name":"Department of Respiratory Medicine and Infectious Diseases, Medical School Hannover (MHH), German Center for Lung Research (DZL), Research Network \u201cBREATH\u201d, 30625 Hannover, Germany"},{"name":"Dynamics of Respiratory Infections, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany"},{"name":"Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Stra\u00dfe 1, 30625 Hannover, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Malena","family":"Bos","sequence":"additional","affiliation":[{"name":"Department of Respiratory Medicine and Infectious Diseases, Medical School Hannover (MHH), German Center for Lung Research (DZL), Research Network \u201cBREATH\u201d, 30625 Hannover, Germany"},{"name":"Dynamics of Respiratory Infections, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany"},{"name":"Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Stra\u00dfe 1, 30625 Hannover, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Neubert","sequence":"additional","affiliation":[{"name":"Department of Respiratory Medicine and Infectious Diseases, Medical School Hannover (MHH), German Center for Lung Research (DZL), Research Network \u201cBREATH\u201d, 30625 Hannover, Germany"},{"name":"Dynamics of Respiratory Infections, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany"},{"name":"Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Stra\u00dfe 1, 30625 Hannover, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6691-3561","authenticated-orcid":false,"given":"Jenny","family":"Fiebig","sequence":"additional","affiliation":[{"name":"Department of Respiratory Medicine and Infectious Diseases, Medical School Hannover (MHH), German Center for Lung Research (DZL), Research Network \u201cBREATH\u201d, 30625 Hannover, Germany"},{"name":"Dynamics of Respiratory Infections, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6153-2068","authenticated-orcid":false,"given":"Michael","family":"Lorenz","sequence":"additional","affiliation":[{"name":"Department of Pediatric Pulmonology\/Allergology, Section Cystic Fibrosis Centre for Children and Adults, University Hospital Jena, 07747 Jena, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Hartmann","sequence":"additional","affiliation":[{"name":"Hospital Pharmacy, University Hospital Jena, 07747 Jena, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3780-7759","authenticated-orcid":false,"given":"Jochen G.","family":"Mainz","sequence":"additional","affiliation":[{"name":"Cystic Fibrosis Center, Klinikum Westbrandenburg, Brandenburg Medical School (MHB) University, 16816 Neuruppin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hortense","family":"Slevogt","sequence":"additional","affiliation":[{"name":"Department of Respiratory Medicine and Infectious Diseases, Medical School Hannover (MHH), German Center for Lung Research (DZL), Research Network \u201cBREATH\u201d, 30625 Hannover, Germany"},{"name":"Dynamics of Respiratory Infections, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany"},{"name":"Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Stra\u00dfe 1, 30625 Hannover, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4502-5450","authenticated-orcid":false,"given":"Tilman E.","family":"Klassert","sequence":"additional","affiliation":[{"name":"Department of Respiratory Medicine and Infectious Diseases, Medical School Hannover (MHH), German Center for Lung Research (DZL), Research Network \u201cBREATH\u201d, 30625 Hannover, Germany"},{"name":"Dynamics of Respiratory Infections, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany"},{"name":"Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Stra\u00dfe 1, 30625 Hannover, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,8,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1992","DOI":"10.1056\/NEJMra043184","article-title":"Mechanisms of disease: Cystic fibrosis","volume":"352","author":"Steven","year":"2005","journal-title":"N. Eng. J. Med."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.nut.2018.03.052","article-title":"Cystic fibrosis, body composition, and health outcomes: A systematic review","volume":"55","author":"Calella","year":"2018","journal-title":"Nutrition"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1128\/CMR.00068-09","article-title":"The changing microbial epidemiology in cystic fibrosis","volume":"23","author":"LiPuma","year":"2010","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1468","DOI":"10.1513\/AnnalsATS.201510-678OC","article-title":"The multiple faces of non\u2013cystic fibrosis bronchiectasis. A cluster Analysis approach","volume":"13","author":"Vendrell","year":"2016","journal-title":"Ann. Am. Thorac. Soc."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1002\/ppul.21434","article-title":"Bronchoscopy in cystic fibrosis infants diagnosed by newborn screening","volume":"46","author":"Stafler","year":"2011","journal-title":"Pediatr. Pulmonol."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"de Dios Caballero, J., Cant\u00f3n, R., Ponce-Alonso, M., Garc\u00eda-Clemente, M.M., G\u00f3mez, G., de la Pedrosa, E., L\u00f3pez-Campos, J.L., M\u00e1iz, L., Del Campo, R., and Mart\u00ednez-Garc\u00eda, M.\u00c1. (2022). The human mycobiome in chronic respiratory diseases: Current situation and future perspectives. Microorganisms, 10.","DOI":"10.3390\/microorganisms10040810"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1136\/thx.2006.060889","article-title":"Exacerbations in cystic fibrosis 1: Epidemiology and pathogenesis","volume":"62","author":"Goss","year":"2007","journal-title":"Thorax"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1183\/09031936.00159111","article-title":"Effect of pulmonary exacerbations on long-term lung function decline in cystic fibrosis","volume":"40","author":"Waters","year":"2012","journal-title":"Eur. Respir. J."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1809","DOI":"10.1056\/NEJMoa1908639","article-title":"Elexacaftor\u2013tezacaftor\u2013ivacaftor for cystic fibrosis with a single Phe508del allele","volume":"381","author":"Middleton","year":"2019","journal-title":"N. Engl. J. Med."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1183\/09059180.00006512","article-title":"Treatment of pulmonary exacerbations in cystic fibrosis","volume":"22","author":"Bhatt","year":"2013","journal-title":"Eur. Respir. Rev."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"190041","DOI":"10.1183\/16000617.0041-2019","article-title":"Influence of the lung microbiome on antibiotic susceptibility of cystic fibrosis pathogens","volume":"28","author":"Vandeplassche","year":"2019","journal-title":"Eur. Respir. Rev."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Vitiello, A., Blasi, F., Sabbatucci, M., Zovi, A., Miele, F., Ponzo, A., Langella, R., and Boccellino, M. (2024). The Impact of Antimicrobial Resistance in cystic fibrosis. J. Clin. Med., 13.","DOI":"10.3390\/jcm13061711"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.jcf.2018.11.003","article-title":"The lung and gut microbiome: What has to be taken into consideration for cystic fibrosis?","volume":"18","author":"Boutin","year":"2019","journal-title":"J. Cyst. Fibros."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Souza, V.G., Forder, A., Pewarchuk, M.E., Telkar, N., de Araujo, R.P., Stewart, G.L., Vieira, J., Reis, P.P., and Lam, W.L. (2023). The complex role of the microbiome in non-small cell lung cancer development and progression. Cells, 12.","DOI":"10.3390\/cells12242801"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2900","DOI":"10.1128\/JCM.01094-15","article-title":"Cohort study of airway mycobiome in adult cystic fibrosis patients: Differences in community structure between fungi and bacteria reveal predominance of transient fungal elements","volume":"53","author":"Kramer","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1097\/MCP.0000000000000316","article-title":"Development of the respiratory tract microbiota in cystic fibrosis","volume":"22","author":"Bogaert","year":"2016","journal-title":"Curr. Opin. Pulm. Med."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Fran\u00e7oise, A., and H\u00e9ry-Arnaud, G. (2020). The microbiome in cystic fibrosis pulmonary disease. Genes, 11.","DOI":"10.3390\/genes11050536"},{"key":"ref_18","first-page":"OA1601","article-title":"A study of the airway mycobiome in COPD patients and controls","volume":"54","author":"Martinsen","year":"2019","journal-title":"Eur. Respir. Soc."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"e36519","DOI":"10.1097\/MD.0000000000036519","article-title":"Changes in the airway microbiome in patients with bronchiectasis","volume":"102","author":"Lu","year":"2023","journal-title":"Medicine"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1513\/pats.200908-086AL","article-title":"Allergic bronchopulmonary aspergillosis","volume":"7","author":"Patterson","year":"2010","journal-title":"Proc. Am. Thorac. Soc."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Kanj, A.N., and Skalski, J.H. (2024). Gut mycobiome and asthma. J. Fungi, 10.","DOI":"10.3390\/jof10030192"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Boutin, S., Graeber, S.Y., Weitnauer, M., Panitz, J., Stahl, M., Clausznitzer, D., Kaderali, L., Einarsson, G., Tunney, M.M., and Elborn, J.S. (2015). Comparison of microbiomes from different niches of upper and lower airways in children and adolescents with cystic fibrosis. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0116029"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1016\/j.jcf.2020.12.022","article-title":"Relationship between airway dysbiosis, inflammation and lung function in adults with cystic fibrosis","volume":"20","author":"Frey","year":"2021","journal-title":"J. Cyst. Fibros."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1007\/s12281-016-0268-z","article-title":"Pathogenesis of fungal infections in cystic fibrosis","volume":"10","author":"Williams","year":"2016","journal-title":"Curr. Fungal Infect. Rep."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1093\/mmy\/myaa003","article-title":"Clinical relevance of Scedosporium spp. and Exophiala dermatitidis in patients with cystic fibrosis: A nationwide study","volume":"58","author":"Slabbers","year":"2020","journal-title":"Med. Mycol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"56","DOI":"10.3109\/13693780802716532","article-title":"Persistence of Candida species in the respiratory tract of cystic fibrosis patients","volume":"48","author":"Muthig","year":"2010","journal-title":"Med. Mycol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1002\/(SICI)1099-0496(199601)21:1<6::AID-PPUL1>3.0.CO;2-R","article-title":"Clinical significance of the recovery of Aspergillus species from the respiratory secretions of cystic fibrosis patients","volume":"21","author":"Milla","year":"1996","journal-title":"Pediatr. Pulmonol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1082","DOI":"10.1002\/ppul.23302","article-title":"Association of chronic Candida albicans respiratory infection with a more severe lung disease in patients with cystic fibrosis","volume":"50","author":"Shoseyov","year":"2015","journal-title":"Pediatr. Pulmonol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1007\/s11046-024-00887-6","article-title":"Metagenomics Applied to the Respiratory Mycobiome in Cystic Fibrosis","volume":"189","author":"Angebault","year":"2024","journal-title":"Mycopathologia"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1111\/myc.12338","article-title":"Candida albicans chronic colonisation in cystic fibrosis may be associated with inhaled antibiotics","volume":"58","author":"Noni","year":"2015","journal-title":"Mycoses"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"652","DOI":"10.1136\/thoraxjnl-2012-202412","article-title":"Intravenous antibiotics reduce the presence of Aspergillus in adult cystic fibrosis sputum","volume":"68","author":"Baxter","year":"2013","journal-title":"Thorax"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.jim.2013.12.003","article-title":"Influences of nasal lavage collection-, processing-and storage methods on inflammatory markers\u2014Evaluation of a method for non-invasive sampling of epithelial lining fluid in cystic fibrosis and other respiratory diseases","volume":"404","author":"Hentschel","year":"2014","journal-title":"J. Immunol. Methods"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1002\/ppul.22982","article-title":"Non-invasive assessment of upper and lower airway infection and inflammation in CF patients","volume":"49","author":"Fischer","year":"2014","journal-title":"Pediatr. Pulmonol."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Hoggard, M., Vesty, A., Wong, G., Montgomery, J.M., Fourie, C., Douglas, R.G., Biswas, K., and Taylor, M.W. (2018). Characterizing the human mycobiota: A comparison of small subunit rRNA, ITS1, ITS2, and large subunit rRNA genomic targets. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.02208"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"D259","DOI":"10.1093\/nar\/gky1022","article-title":"The UNITE database for molecular identification of fungi: Handling dark taxa and parallel taxonomic classifications","volume":"47","author":"Nilsson","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_38","first-page":"347","article-title":"CF lung disease-a German S3 guideline: Module 2: Diagnostics and treatment in chronic infection with Pseudomonas aeruginosa","volume":"72","author":"Schwarz","year":"2018","journal-title":"Pneumologie"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"932","DOI":"10.1164\/rccm.201409-1583OC","article-title":"Topographic diversity of the respiratory tract mycobiome and alteration in HIV and lung disease","volume":"191","author":"Cui","year":"2015","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Belvoncikova, P., Splichalova, P., Videnska, P., and Gardlik, R. (2022). The human mycobiome: Colonization, composition and the role in health and disease. J. Fungi, 8.","DOI":"10.3390\/jof8101046"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"iqae009","DOI":"10.1093\/oxfimm\/iqae009","article-title":"The airway mycobiome and interactions with immunity in health and chronic lung disease","volume":"5","author":"Katsoulis","year":"2024","journal-title":"Oxf. Open Immunol."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Su, J., Liu, H.-y., Tan, X.-l., Ji, Y., Jiang, Y.-x., Prabhakar, M., Rong, Z.-h., Zhou, H.-w., and Zhang, G.-x. (2015). Sputum bacterial and fungal dynamics during exacerbations of severe COPD. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0130736"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/j.jcf.2020.05.013","article-title":"The fungal airway microbiome in cystic fibrosis and non-cystic fibrosis bronchiectasis","volume":"20","author":"Cuthbertson","year":"2021","journal-title":"J. Cyst. Fibros."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1183\/09031936.04.00097503","article-title":"Normal nasal mucociliary clearance in CF children: Evidence against a CFTR-related defect","volume":"24","author":"McShane","year":"2004","journal-title":"Eur. Respir. J."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Delhaes, L., Monchy, S., Fr\u00e9alle, E., Hubans, C., Salleron, J., Leroy, S., Prevotat, A., Wallet, F., Wallaert, B., and Dei-Cas, E. (2012). The airway microbiota in cystic fibrosis: A complex fungal and bacterial community\u2014Implications for therapeutic management. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0036313"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/2049-2618-2-40","article-title":"Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis","volume":"2","author":"Willger","year":"2014","journal-title":"Microbiome"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1186","DOI":"10.1378\/chest.09-2996","article-title":"Sputum Candida albicans presages FEV1 decline and hospital-treated exacerbations in cystic fibrosis","volume":"138","author":"Chotirmall","year":"2010","journal-title":"Chest"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Willis, J.R., Saus, E., Iraola-Guzm\u00e1n, S., Cabello-Yeves, E., Ksiezopolska, E., Cozzuto, L., Bejarano, L.A., Andreu-Somavilla, N., Alloza-Trabado, M., and Blanco, A. (2021). Citizen-science based study of the oral microbiome in Cystic fibrosis and matched controls reveals major differences in diversity and abundance of bacterial and fungal species. J. Oral Microbiol., 13.","DOI":"10.1080\/20002297.2021.1897328"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1177\/194589240501900108","article-title":"Presence of fungus in sinus cultures of cystic fibrosis patients","volume":"19","author":"Wise","year":"2005","journal-title":"Am. J. Rhinol."},{"key":"ref_50","first-page":"AB70","article-title":"Prevalence of esophageal candidiasis induced by inhaled corticosteroids","volume":"125","author":"Aun","year":"2010","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref_51","first-page":"189","article-title":"Candida albicans the main opportunistic pathogenic fungus in humans","volume":"55","year":"2023","journal-title":"Rev. Argent. Microbiol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"S114","DOI":"10.3109\/13693786.2010.503320","article-title":"Candida species in cystic fibrosis: A road less travelled","volume":"48","author":"Chotirmall","year":"2010","journal-title":"Sabouraudia"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1178","DOI":"10.4314\/ahs.v17i4.27","article-title":"Intestinal candidiasis and antibiotic usage in children: Case study of Nsukka, South Eastern Nigeria","volume":"17","author":"Ezeonu","year":"2017","journal-title":"Afr. Health Sci."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Azevedo, M.M., Teixeira-Santos, R., Silva, A.P., Cruz, L., Ricardo, E., Pina-Vaz, C., and Rodrigues, A.G. (2015). The effect of antibacterial and non-antibacterial compounds alone or associated with antifugals upon fungi. Front. Microbiol., 6.","DOI":"10.3389\/fmicb.2015.00669"},{"key":"ref_55","unstructured":"Sarmento, B. (2016). Fernanda Tissue-based in vitro and ex vivo models for pulmonary permeability studies. Concepts and Models for Drug Permeability Studies, Woodhead Publishing."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1128\/9781555818883.ch11","article-title":"Bacterial metabolism in the host environment: Pathogen growth and nutrient assimilation in the mammalian upper respiratory tract","volume":"3","author":"Armstrong","year":"2015","journal-title":"Metab. Bact. Pathog."},{"key":"ref_57","first-page":"449","article-title":"The role of long-acting antibiotics in the clinical practice: A narrative review","volume":"31","author":"Micheli","year":"2023","journal-title":"Le Infez. Med."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Finazzi, S., Luci, G., Olivieri, C., Langer, M., Mandelli, G., Corona, A., Viaggi, B., and Di Paolo, A. (2022). Tissue penetration of antimicrobials in intensive care unit patients: A systematic review\u2014Part I. Antibiotics, 11.","DOI":"10.3390\/antibiotics11091164"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1016\/j.it.2012.05.003","article-title":"Antibiotics, microbiota, and immune defense","volume":"33","author":"Ubeda","year":"2012","journal-title":"Trends Immunol."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1007\/s40262-015-0250-x","article-title":"Clinical pharmacokinetics of inhaled antimicrobials","volume":"54","author":"Stockmann","year":"2015","journal-title":"Clin. Pharmacokinet."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1111\/jam.14949","article-title":"Biofilm of Candida albicans: Formation, regulation and resistance","volume":"131","author":"Pereira","year":"2021","journal-title":"J. Appl. Microbiol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1128\/IAI.00475-17","article-title":"Candida albicans and Pseudomonas aeruginosa interact to enhance virulence of mucosal infection in transparent zebrafish","volume":"85","author":"Bergeron","year":"2017","journal-title":"Infect. Immun."},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Zhang, K., Huang, Y., Jiang, Y., Liu, T., Kong, J., Cai, S., Wen, Z., and Chen, Y. (2025). Effect of Candida albicans\u2019 supernatant on biofilm formation and virulence factors of Pseudomonas aeruginosa through las\/rhl System. BMC Microbiol., 25.","DOI":"10.1186\/s12866-024-03604-x"},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Lopez-Medina, E., Fan, D., Coughlin, L.A., Ho, E.X., Lamont, I.L., Reimmann, C., Hooper, L.V., and Koh, A.Y. (2015). Candida albicans inhibits Pseudomonas aeruginosa virulence through suppression of pyochelin and pyoverdine biosynthesis. PLoS Pathog., 11.","DOI":"10.1371\/journal.ppat.1005129"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1465-9921-10-68","article-title":"Candida soluble cell wall \u03b2-glucan facilitates ovalbumin-induced allergic airway inflammation in mice: Possible role of antigen-presenting cells","volume":"10","author":"Inoue","year":"2009","journal-title":"Respir. Res."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12931-016-0352-5","article-title":"\u03b2-Glucan exacerbates allergic airway responses to house dust mite allergen","volume":"17","author":"Hadebe","year":"2016","journal-title":"Respir. Res."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"e969","DOI":"10.1016\/S2666-5247(22)00203-8","article-title":"The gut mycobiome in health, disease, and clinical applications in association with the gut bacterial microbiome assembly","volume":"3","author":"Zhang","year":"2022","journal-title":"Lancet Microbe"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"100057","DOI":"10.1016\/j.medmic.2022.100057","article-title":"Intestinal dysbiosis and inflammation in cystic fibrosis impacts gut and multi-organ axes","volume":"13","author":"Ooi","year":"2022","journal-title":"Med. Microecol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"1930871","DOI":"10.1080\/19490976.2021.1930871","article-title":"Inter-kingdom relationships in Crohn\u2019s disease explored using a multi-omics approach","volume":"13","author":"Frau","year":"2021","journal-title":"Gut Microbes"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"e00092-18","DOI":"10.1128\/mSphere.00092-18","article-title":"Investigating colonization of the healthy adult gastrointestinal tract by fungi","volume":"3","author":"Auchtung","year":"2018","journal-title":"MSphere"},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Strati, F., Di Paola, M., Stefanini, I., Albanese, D., Rizzetto, L., Lionetti, P., Calabr\u00f2, A., Jousson, O., Donati, C., and Cavalieri, D. (2016). Age and gender affect the composition of fungal population of the human gastrointestinal tract. Front. Microbiol., 7.","DOI":"10.3389\/fmicb.2016.01227"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"e0098622","DOI":"10.1128\/msystems.00986-22","article-title":"Host factors associated with gut mycobiome structure","volume":"8","author":"Handschuh","year":"2023","journal-title":"MSystems"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1111\/j.1567-1364.2009.00559.x","article-title":"The antagonistic effect of Saccharomyces boulardii on Candida albicans filamentation, adhesion and biofilm formation","volume":"9","author":"Krasowska","year":"2009","journal-title":"FEMS Yeast Res."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"2302290","DOI":"10.1183\/13993003.02290-2023","article-title":"The longitudinal microbial and metabolic landscape of infant cystic fibrosis: The gut\u2013lung axis","volume":"63","author":"Frayman","year":"2024","journal-title":"Eur. Respir. J."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1016\/j.jcf.2024.05.002","article-title":"Impact of extended Elexacaftor\/Tezacaftor\/Ivacaftor therapy on the gut microbiome in cystic fibrosis","volume":"23","author":"Marsh","year":"2024","journal-title":"J. Cyst. Fibros."},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Pallenberg, S.T., Pust, M.-M., Rosenboom, I., Hansen, G., Wiehlmann, L., Dittrich, A.-M., and T\u00fcmmler, B. (2022). Impact of elexacaftor\/tezacaftor\/ivacaftor therapy on the cystic fibrosis airway microbial metagenome. Microbiol. Spectr., 10.","DOI":"10.1128\/spectrum.01454-22"},{"key":"ref_77","doi-asserted-by":"crossref","unstructured":"Mainz, J.G., Arnold, C., Wittstock, K., Hipler, U.-C., Lehmann, T., Zagoya, C., Duckstein, F., Ellemunter, H., and Hentschel, J. (2021). Ivacaftor reduces inflammatory mediators in upper airway lining fluid from cystic fibrosis patients with a G551D mutation: Serial non-invasive home-based collection of upper airway lining fluid. Front. Immunol., 12.","DOI":"10.3389\/fimmu.2021.642180"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1159\/000543009","article-title":"The proof of the pudding is in the eating: Real-life intra-and extrapulmonary impact of elexacaftor\/tezacaftor\/ivacaftor","volume":"104","author":"Vincken","year":"2025","journal-title":"Respiration"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"e71038","DOI":"10.1002\/ppul.71038","article-title":"Impact of Elexacaftor\/Tezacaftor\/Ivacaftor on Microbiology and Antibiotic Utilization in People With Cystic Fibrosis","volume":"60","author":"Williams","year":"2025","journal-title":"Pediatr. Pulmonol."},{"key":"ref_80","unstructured":"(2022, June 30). AmoClav. Available online: https:\/\/www.gelbe-liste.de\/produkte\/beipackzettel_Amoclav-875-mg-125-mg-Filmtabletten.pdf\/734afd5c-d352-4103-a592-2680a646f542."},{"key":"ref_81","unstructured":"(2022, June 30). AmoClavliquid. Available online: https:\/\/www.gelbe-liste.de\/produkte\/beipackzettel_Amoclav-Trockensaft-125-31-25-mg-5-ml-Pulver-zur-Herstellung-einer-Suspension-zum-Einnehmen.pdf\/720da084-17f1-4ace-8c31-ae5b951554e5."},{"key":"ref_82","unstructured":"(2022, June 30). AmoClavLiquid400. Available online: https:\/\/www.gelbe-liste.de\/produkte\/beipackzettel_Amoclav-400-57-mg-5-ml-Trockensaft-Pulver-zur-Herstellung-einer-Suspension-zum-Einnehmen.pdf\/467f2d27-bf0d-4b05-8d3f-52d1aa2068b7."},{"key":"ref_83","unstructured":"(2022, June 30). Infectomox. Available online: https:\/\/data-storage.live\/data\/unsec\/pb-infectomox-750saft.pdf."},{"key":"ref_84","unstructured":"Bodmann, K.-F., Grabein, B., and Kresken, M. (2020). S2k guideline \u201cCalculated parenteral initial treatment of bacterial infections in adults\u2013update 2018\u201d, 2nd updated version: Foreword. GMS Infect. Dis., 8."},{"key":"ref_85","unstructured":"(2022, June 30). Cefpodoxime. Available online: https:\/\/www.gelbe-liste.de\/produkte\/beipackzettel_Cefpodoxim-HEXAL-40-mg-5-ml-Pulver-zur-Herstellung-einer-Suspension-zum-Einnehmen.pdf\/4497845f-4832-4ec5-aacd-d0a80e717cff."},{"key":"ref_86","first-page":"590","article-title":"S3-Leitlinie \u201cLungenerkrankung bei Mukoviszidose\u201d","volume":"6","author":"Bend","year":"2015","journal-title":"Monatsschrift Kinderheilkd."},{"key":"ref_87","unstructured":"(2022, June 30). AzythromycinLiquid. Available online: https:\/\/www.fachinfo.de\/static\/lib\/pdfjs\/web\/viewer.html?file=\/fi\/pdf\/010322\/azithromycin-ratiopharm-r-200-mg-5-ml#zoom=auto."},{"key":"ref_88","unstructured":"(2022, June 30). Erythromycin200. Available online: https:\/\/data-storage.live\/data\/unsec\/pb-infectomycin-200saft.pdf."},{"key":"ref_89","unstructured":"(2022, June 30). Erythromycin400. Available online: https:\/\/data-storage.live\/data\/unsec\/pb-infectomycin-400saft.pdf."},{"key":"ref_90","unstructured":"(2022, June 30). Erythromycin600. Available online: https:\/\/data-storage.live\/data\/unsec\/pb-infectomycin-600saft.pdf."},{"key":"ref_91","unstructured":"(2022, June 30). Clarithromycin125. Available online: https:\/\/www.gelbe-liste.de\/produkte\/beipackzettel_Clarithromycin-1-A-Pharma-125-mg-5-ml-Granulat-zur-Herstellung-einer-Suspension-zum-Einnehmen.pdf\/4964180c-d861-44b6-9a1a-1f5908d42803."},{"key":"ref_92","unstructured":"(2022, June 30). Clarithromycin250. Available online: https:\/\/www.gelbe-liste.de\/produkte\/beipackzettel_Clarithromycin-1-A-Pharma-250-mg-5-ml-Granulat-zur-Herstellung-einer-Suspension-zum-Einnehmen.pdf\/4ebf2a16-a9a6-4132-b36c-63f17b6f8dfb."},{"key":"ref_93","unstructured":"(2022, June 30). Co-trimoxazole. Available online: https:\/\/www.gelbe-liste.de\/produkte\/beipackzettel_Cotrim-forte-ratiopharm-800-mg-160-mg-Tabletten.pdf\/df28ec3a-8477-4d1e-92dd-5d9de40e0182."},{"key":"ref_94","unstructured":"(2022, June 30). Co-trimoxazoleLiquid200. Available online: https:\/\/www.gelbe-liste.de\/produkte\/beipackzettel_Cotrim-K-ratiopharm-200-mg-5-ml-40-mg-5-ml-Suspension-zum-Einnehmen.pdf\/a8af7b7e-939f-4128-b794-9aca49946070."},{"key":"ref_95","unstructured":"(2022, June 30). Co-trimoxazoleLiquid400. Available online: https:\/\/www.gelbe-liste.de\/produkte\/beipackzettel_Cotrim-E-ratiopharm-400-mg-5-ml-80-mg-5-ml-Suspension-zum-Einnehmen.pdf\/0ded57e2-8b70-40f8-954b-72ac38c8a911."},{"key":"ref_96","unstructured":"(2022, June 30). Doxycycline. Available online: https:\/\/www.gelbe-liste.de\/produkte\/beipackzettel_Doxycyclin-100-1-A-Pharma-100-mg-Tabletten.pdf\/0b91d543-6238-46d1-bc72-fae79e25b93d."}],"container-title":["Journal of Fungi"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2309-608X\/11\/9\/631\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:34:55Z","timestamp":1760034895000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2309-608X\/11\/9\/631"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,28]]},"references-count":96,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2025,9]]}},"alternative-id":["jof11090631"],"URL":"https:\/\/doi.org\/10.3390\/jof11090631","relation":{},"ISSN":["2309-608X"],"issn-type":[{"value":"2309-608X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,8,28]]}}}