Cystic Fibrosis Airway Microbiome: Overturning the Old, Opening the Way for the New

Abstract

The genetic disease cystic fibrosis (CF) is associated with chronic airway infections that are a proximal cause of death in many patients with this affliction. Classic microbiology studies focusing on canonical pathogens resulted in the development of a common set of views regarding the nature of the airway infections associated with this disease, and these ideas have influenced everything from the way infections are treated to how clinical trials for new CF-targeted antibiotics are designed and the focus of CF-related research topics. Recent culture-independent studies have prompted us to rethink, and in some cases discard, some of these long-held views. In this piece, I argue that an updated view of the complicated chronic infections associated with CF, thanks in large part to culture-independent studies of sputum and bronchoalveolar lavage fluid samples, should be leveraged to develop new strategies to treat these recalcitrant infections.

Keywords: airway; cystic fibrosis; infection; microbiome; sputum.

FIG 1

Role of culture-independent approaches for studying the microbiology of the CF airway. Sputum and BAL fluid, in most cases, are the sources of material used for elucidating the microbiology of the CF airway. New culture-independent methods have built on and complemented classical microbiology approaches. The culture-independent methods (largely 16S rRNA gene sequencing) have provided new insight into the nature of these infections.