Cohort Study of Airway Mycobiome in Adult Cystic Fibrosis Patients: Differences in Community Structure between Fungi and Bacteria Reveal Predominance of Transient Fungal Elements

Abstract

The respiratory mycobiome is an important but understudied component of the human microbiota. Like bacteria, fungi can cause severe lung diseases, but their infection rates are much lower. This study compared the bacterial and fungal communities of sputum samples from a large cohort of 56 adult patients with cystic fibrosis (CF) during nonexacerbation periods and under continuous antibiotic treatment. Molecular fingerprinting based on single-strand conformation polymorphism (SSCP) analysis revealed fundamental differences between bacterial and fungal communities. Both groups of microorganisms were taxonomically classified by identification of gene sequences (16S rRNA and internal transcript spacer), and prevalences of single taxa were determined for the entire cohort. Major bacterial pathogens were frequently observed, whereas fungi of known pathogenicity in CF were detected only in low numbers. Fungal species richness increased without reaching a constant level (saturation), whereas bacterial richness showed saturation after 50 patients were analyzed. In contrast to bacteria, a large number of fungal species were observed together with high fluctuations over time and among patients. These findings demonstrated that the mycobiome was dominated by transient species, which strongly suggested that the main driving force was their presence in inhaled air rather than colonization. Considering the high exposure of human airways to fungal spores, we concluded that fungi have low colonization abilities in CF, and colonization by pathogenic fungal species may be considered a rare event. A comprehensive understanding of the conditions promoting fungal colonization may offer the opportunity to prevent colonization and substantially reduce or even eliminate fungus-related disease progression in CF.

Understanding the role of the microbiome in chronic obstructive pulmonary disease: principles, challenges, and future directions

“…A recent analysis of fungal communities in cystic fibrosis sputum observed greater fluctuations in fungal richness, which contrasted with that for bacterial richness (77). Though chronic treatments with antibiotics during this period might have influenced the findings, the investigators nonetheless concluded that fungal elements detected in CF sputum are predominantly transient and likely related to inhaled sources.…”

Mycobiome in the Lower Respiratory Tract – A Clinical Perspective

“…However, the association was mainly derived from two patients with preceding antibiotic therapy and antifungal therapy and the contribution of fungal or bacterial microbiota to lung function could not be distinguished. Despite variable fungal composition in LRT, Candida overall dominated mycobiota in most of the studies including CF patients, lung transplant patients, HIV infected patients and ICU patients (Bousbia et al, 2012; Charlson et al, 2012; Bittinger et al, 2014; Willger et al, 2014; Cui et al, 2015; Kramer et al, 2015a; Krause et al, 2016). In remaining studies with dominating fungi other than Candida methodologies were too weak to draw profound conclusions.…”

“…Observation periods varied between days (ICU patients; Krause et al, 2016), weeks (CF patients; Willger et al, 2014), 3 months to 1 year (CF patients; Delhaes et al, 2012), and months up to 2 years (CF patients; Kramer et al, 2015a). Conclusions are difficult to draw based on low numbers of individuals investigated, different patient groups and differences in time frames elapsing between sampling.…”

“…Whereas high intraindividual differences with changes in Candida abundance were found in one CF study (Delhaes et al, 2012) another CF study found stable results (Willger et al, 2014). The third CF study found differences in number of fungal genera in some patients providing two sputum samples (Kramer et al, 2015a). In ICU patients fungal microbiota were stable in 3 of 4 patients as shown by analysis of first and second BAL sample 4 to 7 days apart (Krause et al, 2016).…”

“…In another study 72 sputum samples were collected from 56 CF patients recruited in an ambulatory center including a subcohort of 13 patients who provided sputum two (10 patients) or three (three patients) times within a 2-years sampling period (Kramer et al, 2015a). Sputum samples were collected in duplicate, stored at -20°C and subsequently analyzed by ITS primer based PCR, preparation of single stranded DNA, single-strand conformation polymorphism electrophoresis and sequencing of individual bands.…”