Exploring the Cystic Fibrosis Lung Microbiome: Making the Most of a Sticky Situation

Abstract

Chronic lower respiratory tract infections are a leading contributor to morbidity and mortality in persons with cystic fibrosis (pwCF). Traditional respiratory tract surveillance culturing has focused on a limited range of classic pathogens; however, comprehensive culture and culture-independent molecular approaches have demonstrated complex communities highly unique to each individual. Microbial community structure evolves through the lifetime of pwCF and is associated with baseline disease state and rates of disease progression including occurrence of pulmonary exacerbations. While molecular analysis of the airway microbiome has provided insight into these dynamics, challenges remain including discerning not only “who is there” but “what they are doing” in relation to disease progression. Moreover, the microbiome can be leveraged as a multi-modal biomarker for both disease activity and prognostication. In this article, we review our evolving understanding of the role these communities play in pwCF and identify challenges in translating microbiome data to clinical practice.

Evaluating Sinus Microbiology by Transplant Status in Persons With Cystic Fibrosis: A Matched Cohort Study

“…Finally, our study was the first to associate sinus microbiome compositional structure with sinonasal clinical outcomes by transplant status in PwCF as noted by patient reported questionnaires. Not surprisingly, those with greater microbial diversity had improved symptom scores consistent with earlier findings 25 . Finally, we did not observe a significant association with LM scores and microbiome composition and were likely limited by sample size similar to others 26,27 …”

“…Not surprisingly, those with greater microbial diversity had improved symptom scores consistent with earlier findings. 25 Finally, we did not observe a significant association with LM scores and microbiome composition and were likely limited by sample size similar to others. 26,27 Previous studies have demonstrated the sinonasal cavity as an initial site of bacterial colonization, including canonical pathogens such as P. aeruginosa, with development of a microbial reservoir that can then seed the lungs of PwCF.…”

Early nasal microbiota and subsequent respiratory tract infections in infants with cystic fibrosis

“…The respiratory microbiota profile is altered in infants with CF, independent of the presence of pathogens detected with culture-based techniques [14][15][16][17] . Early microbial development is characterized by early dominance and persistence of Staphylococcus aureus in infants with CF, shifting to Corynebacterium spp.…”

Using metabolic potential within the airway microbiome as predictors of clinical state in persons with cystic fibrosis

“…Additionally, many external genetic factors and genotypic variants of CF contribute to the disease phenotype of the CF individual that make it very difficult to create a universal treatment solely based on host genotype or phenotype (5). Beyond CFTR modulators and broad antibiotic treatments directed at common CF airway pathogens, insights may be gained in observing the variation in the CF airway microbiome across clinical states (6)(7)(8)(9). More recent work also suggests that the metabolome could be used to predict or diagnose pulmonary exacerbation (10,11).…”