The fungal airway microbiome in cystic fibrosis and non-cystic fibrosis bronchiectasis

Abstract

Background: The prevalence of fungal disease in cystic fibrosis (CF) and non-CF bronchiectasis is increasing and the clinical spectrum is widening. Poor sensitivity and a lack of standard diagnostic criteria renders interpretation of culture results challenging. In order to develop effective management strategies, a more accurate and comprehensive understanding of the airways fungal microbiome is required. The study aimed to use DNA sequences from sputum to assess the load and diversity of fungi in adults with CF and non-CF bronchiectasis. Methods: Next generation sequencing of the ITS2 region was used to examine fungal community composition (n = 176) by disease and underlying clinical subgroups including allergic bronchopulmonary aspergillosis, chronic necrotizing pulmonary aspergillosis, non-tuberculous mycobacteria, and fungal bronchitis. Patients with no known active fungal disease were included as disease controls. Results: ITS2 sequencing greatly increased the detection of fungi from sputum. In patients with CF fungal diversity was lower, while burden was higher than those with non-CF bronchiectasis. The most common operational taxonomic unit (OTU) in patients with CF was Candida parapsilosis (20.4%), whereas in non-CF bronchiectasis sputum Candida albicans (21.8%) was most common. CF patients with overt fungal bronchitis were dominated by Aspergillus spp. , Exophiala spp., Candida parapsilosis or Scedosporium spp. Conclusion: This study provides a framework to more accurately characterize the extended spectrum of fungal airways diseases in adult suppurative lung diseases.

The airway microbiome in COPD, bronchiectasis and bronchiectasis‐COPD overlap

“…60,61 Comparing mycobiome composition between CF and non-CF bronchiectasis, Cuthbertson et al (2020) reported lower diversity with increased fungal burden in CF, with a predominance of Candida in both groups. 62,63 In general, respiratory microbiome studies report that sputum has greater resemblance to that of the upper airway while BAL better represents the lower airway, however, this does not appear the case in bronchiectasis. Limited variability is observed in profiles obtained by sputum and BAL, respectively, in microbial richness, diversity and abundance.…”

One versus Many: Polymicrobial Communities and the Cystic Fibrosis Airway

“…Last, an important caveat to most of the microbiome studies published so far is the strong focus on bacteria; most reports have overlooked the presence of fungi and viruses and their impact on CF airway disease ( 26 , 43 , 44 ). Taken together, these multiple lines of evidence now make it clear that chronic CF lung infections are not restricted to bacteria and that interkingdom interactions involving viruses and fungi have the potential to be major players in CF lung disease.…”

Antimicrobial Resistance in Common Respiratory Pathogens of Chronic Bronchiectasis Patients: A Literature Review

“…Members of this family, most frequently found in NCFB, are Mycobacterium avium complex and Mycobacterium abscessus [ 57 ]. Aspergillus [ 58 ], and Candida [ 59 ] are fungi commonly identified in the respiratory secretions of NCFB patients [ 59 , 60 ]. It can be difficult to determine if these organisms play a pathophysiological role in infectious symptoms or if they are simply bystander organisms in patients with other primary pathogens.…”