The bronchiectasis microbiome

Non-CF bronchiectasis is characterised by dysregulated immunity and impaired airway clearance. Mucus accumulation results in an increased susceptibility to persistent lung infections by pathogens such as Haemophilus influenzae, Pseudomonas aeruginosa and Aspergillus fumigatus. The presence of these microbes within the lower airways contributes to a “vicious circle” of impaired mucociliary function, bronchial inflammation and progressive lung injury. The importance of pathogen detection as a guide to antimicrobial therapy has led to the use of narrowly focused diagnostic practices. However, extended culture techniques and DNA sequencing technologies have revealed a more diverse airway microbiota, including an abundance of species that are refractory to common diagnostic protocols. Interactions that occur between these microbial species can profoundly affect the expression of pathogenicity and virulence by important airway pathogens, such as P. aeruginosa. This chapter sets out current hypotheses regarding the contribution of the respiratory microbiome to non-CF bronchiectasis, and discusses how the insight gained using emerging analytical technologies can inform clinical care.