Background: The chronic suppurative lung diseases, CF and non-CF bronchiectasis (BX) are characterised by polymicrobial airways infection. The prevalence of fungal airways isolates and clinical spectrum of associated disease are increasing in CF, however poor sensitivity of traditional detection methods and lack of consensus diagnostic criteria renders clinical interpretation challenging. Recent culture-independent investigations have profiled complex and diverse bacterial lower airways microbiota in both diseases. By contrast, comparatively little has been established regarding the fungal composition, or mycobiota therein.
Aims: The aims of this thesis are i) to establish fungal airways isolate prevalence, biodiversity and clinical associations in UK adults with CF, ii) to investigate the fungal biodiversity as determined by conventional and enhanced mycological diagnostic techniques and iii) to develop a culture-independent method of characterising the fungal airways mycobiota in CF and non-CF BX.
Methods, Results & Conclusions: The epidemiological study of the UK CF Registry established that fungal airways isolates have increased in prevalence and biodiversity over six years, with associated measures of increased disease burden with emerging fungal pathogens.
The enhanced mycological diagnostic study revealed significant improvement in detection sensitivity for non-Aspergillus fungal isolates which are known to be emerging pathogens in CF airways disease.
Characterisation of the fungal airways mycobiome by a novel, next generation sequencing assay, targeting the Internal Transcribed Spacer-2 (ITS2) region of ribosomal RNA gene in both CF and non-CF BX sputa, revealed complex fungal communities of which 97% of taxa were undetected by conventional culture techniques, and where fungi were found in all samples regardless of their isolation in culture. Compared with non-CF BX, CF airways were significantly less diverse and showed distinct airways mycobiome characteristics according to dominance by emerging fungal pathogens highlighting the proposed diagnostic category of ‘Fungal bronchitis’.