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Abstract Background Fungi are increasingly recognized for their potential role in contributing to pulmonary damage in Cystic Fibrosis (CF). We therefore designed a prospective international study aimed at (i) determining the prevalence of fungi isolated from sputum samples collected from a large CF population, (ii) comparing the performance of different media used for fungal culture, and (iii) proposing a standardized protocol suitable for CF routine microbiology. Methods An international, consensually designed prospective study was set up (https://www.ecfs.eu/special-projects/mucofong-international-project). All centers worked according to the same protocol approved by Lille Ethical Committee. CF sputa were inoculated onto eight semi-selective media incubated at 37 °C or 25 °C–30 °C for 15 days, and inspected twice weekly for fungal growth. Results A total of 469 sputa were collected from patients at 18 European and one Australian CF centers. Positive cultures for fungal growth were significantly associated with patient ages. Aspergillus fumigatus was the most frequently isolated mold. We identified a growing European North-to-South gradient of Scedosporium prevalence, while yeasts, Aspergillus section Fumigati , Cladosporium and Penicillium were significantly more prevalent in the Northern regions. Conclusions According to the CHi-squared Automatic Interaction Detector method, we propose a consensual protocol based on two media (YPDA or Sabouraud medium, and B(+) medium) to detect the main opportunistic molds in CF context; the use of an additional medium being recommended according to the patient's clinical status. This standardized protocol allows us to have an accurate overview of the respiratory mycobiome on the culturomic side in CF. [ABSTRACT FROM AUTHOR]

Fungal respiratory colonization of cystic fibrosis (CF) patients emerges as a new concern; however, the heterogeneity of mycological protocols limits investigations. We first aimed at setting up an efficient standardized protocol for mycological analysis of CF sputa that was assessed during a prospective, multicenter study: 'MucoFong' program (PHRC-06/1902). Sputa from 243 CF patients from seven centers in France were collected over a 15-month period and submitted to a standardized protocol based on 6 semi-selective media. After mucolytic pretreatment, sputa were plated in parallel on cycloheximide-enriched (ACT37), erythritol-enriched (ERY37), benomyl dichloran-rose bengal (BENO37) and chromogenic (CAN37) media incubated at 37 °C and on Sabouraud-chloramphenicol (SAB27) and erythritol-enriched (ERY27) media incubated at 20-27 °C. Each plate was checked twice a week during 3 weeks. Fungi were conventionally identified; time for detection of fungal growth was noted for each species. Fungal prevalences and media performances were assessed; an optimal combination of media was determined using the Chi-squared automatic interaction detector method. At least one fungal species was isolated from 81% of sputa. Candida albicans was the most prevalent species (58.8%), followed by Aspergillus fumigatus (35.4%). Cultivation on CAN37, SAB27, ACT37 and ERY27 during 16 days provided an optimal combination, detecting C. albicans, A. fumigatus, Scedosporium apiospermum complex and Exophiala spp. with sensitivities of 96.5, 98.8, 100 and 100%. Combination of these four culture media is recommended to ensure the growth of key fungal pathogens in CF respiratory specimens. The use of such consensual protocol is of major interest for merging results from future epidemiological studies. [ABSTRACT FROM AUTHOR]

The historical hypothesis of sterility of the lungs was invalidated over a decade ago when studies demonstrated the existence of sparse but very diverse bacterial populations in the normal lung and the association between pulmonary dysbiosis and chronic respiratory diseases. Under mechanical ventilation, dysbiosis occurs rapidly with a gradual decline in diversity over time and the progressive predominance of a bacterial pathogen (mainly Proteobacteria) when lung infection occurs. During acute respiratory distress syndrome, an enrichment in bacteria of intestinal origin, mainly Enterobacteriaceae, is observed. However, the role of this dysbiosis in the pathogenesis of ventilator-associated pneumonia and acute respiratory distress syndrome is not yet fully understood. The lack of exploration of other microbial populations, viruses (eukaryotes and prokaryotes) and fungi is a key issue. Further analysis of the interaction between these microbial kingdoms and a better understanding of the host−microbiome interaction are necessary to fully elucidate the role of the microbiome in the pathogenicity of acute diseases. The validation of a consensual and robust methodology in order to make the comparison of the different studies relevant is also required. Filling these different gaps should help develop preventive and therapeutic strategies for both acute respiratory distress syndrome and ventilator-associated pneumonia. [ABSTRACT FROM AUTHOR]