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Descriptive studies analysing bacterial and fungal microbiota concomitantly are scarce, especially using both culture and high\u2010throughput\u2010sequencing (HTS).<\/jats:p><\/jats:sec><jats:sec><jats:title>Objectives<\/jats:title><jats:p>We analysed bacterial\u2013fungal microbiota and inter\u2010kingdom correlations in two French CF centres according to clinical parameters and antimicrobial choices.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Forty\u2010eight pwCF with PEx from Creteil (<jats:italic>n<\/jats:italic>\u2009=\u200924) and Lille (<jats:italic>n<\/jats:italic>\u2009=\u200924) CF centres were included over 2\u2009years. Sputa were collected for culture and targeted\u2010HTS (ITS2 and V3\u2010V4 targets). Sequencing and culture data, along with clinical, radiological and treatment data, were analysed. Two\u2010level stratified analysis was performed to study potential confounding factors (age, CF mutation, FEV1 and antibiotics) on the centre factor. Inter\u2010kingdom correlations were analysed.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Significant differences in the bacterial microbiota profile were found between centres (<jats:italic>p<\/jats:italic>\u2010value\u2009=\u20090.03). For mycobiota, the taxonomic distribution and diversity were comparable. HTS provided concordant but more detailed information than culture and increased detection of main CF fungi (&gt;\u200925% more positive samples for <jats:italic>Aspergillus<\/jats:italic> or <jats:italic>Scedosporium<\/jats:italic>). FEV1 and systemic antibiotic before PEx influenced bacterial microbiota, but no clinical association was found with the mycobiota. No inter\u2010kingdom correlation between <jats:italic>Pseudomonas<\/jats:italic> and fungi was found.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Describing concomitant bacterial and fungal communities of pwCF at the beginning of PEx using culture and HTS shows greater diversity in HTS and better detection in case of low microbial load. Interesting inter\u2010kingdom correlations were observed, requiring further research on larger cohorts to understand the potential microbial interactions.<\/jats:p><\/jats:sec>","DOI":"10.1111\/myc.70024","type":"journal-article","created":{"date-parts":[[2025,1,16]],"date-time":"2025-01-16T09:28:48Z","timestamp":1737019728000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Airway Mycobiota\u2014Microbiota During Pulmonary Exacerbation of Cystic Fibrosis Patients: A Culture and Targeted Sequencing Study"],"prefix":"10.1111","volume":"68","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7641-3002","authenticated-orcid":false,"given":"C\u00e9cile","family":"Angebault","sequence":"first","affiliation":[{"name":"Unit\u00e9 de Parasitologie\u2010Mycologie, D\u00e9partement de Pr\u00e9vention, Diagnostic et Traitement Des Infections CHU Henri Mondor, Assistance Publique Des H\u00f4pitaux de Paris (APHP)  Creteil France"},{"name":"UR Dynamyc 7380, Facult\u00e9 de Sant\u00e9, Univ Paris\u2010Est Creteil (UPEC), Ecole Nationale V\u00e9t\u00e9rinaire d'Alfort (ENVA); 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