Effects of Lumacaftor-Ivacaftor on Airway Microbiota-Mycobiota and Inflammation in Patients with Cystic Fibrosis Appear To Be Linked to Pseudomonas aeruginosa Chronic Colonization

Abstract

Lumacaftor-ivacaftor is a cystic fibrosis transmembrane conductance regulator (CFTR) modulator combination approved for patients with cystic fibrosis (CF) who are homozygous for the F508del allele. This treatment showed significant clinical improvement; however, few studies have addressed the evolution of the airway microbiota-mycobiota and inflammation in patients receiving lumacaftor-ivacaftor treatment. Seventy-five patients with CF aged 12 years or older were enrolled at the initiation of lumacaftor-ivacaftor therapy. Among them, 41 had spontaneously produced sputa collected before and 6 months after treatment initiation. Airway microbiota and mycobiota analyses were performed via high-throughput sequencing. Airway inflammation was assessed by measuring the calprotectin levels in sputum; the microbial biomass was evaluated via quantitative PCR (qPCR). At baseline (n = 75), bacterial alpha-diversity was correlated with pulmonary function. After 6 months of lumacaftor-ivacaftor treatment, a significant improvement in the body mass index and a decreased number of intravenous antibiotic courses were noted. No significant changes in bacterial and fungal alpha- and beta-diversities, pathogen abundances, or calprotectin levels were observed. However, for patients not chronically colonized with Pseudomonas aeruginosa at treatment initiation, calprotectin levels were lower, and a significant increase in bacterial alpha-diversity was observed at 6 months. This study shows that the evolution of the airway microbiota-mycobiota in CF patients depends on the patient's characteristics at lumacaftor-ivacaftor treatment initiation, notably chronic colonization with P. aeruginosa. IMPORTANCE The management of cystic fibrosis has been transformed recently by the advent of CFTR modulators, including lumacaftor-ivacaftor. However, the effects of such therapies on the airway ecosystem, particularly on the microbiota-mycobiota and local inflammation, which are involved in the evolution of pulmonary damage, are unclear. This multicenter study of the evolution of the microbiota under protein therapy supports the notion that CFTR modulators should be started as soon as possible, ideally before the patient is chronically colonized with P. aeruginosa. (This study has been registered at ClinicalTrials.gov under identifier NCT03565692).

Keywords: airway inflammation; airway microbiome; airway mycobiome; cystic fibrosis; inflammation; lumacaftor-ivacaftor; microbiome.

FIG 1

Bacterial composition of sputum at baseline according to lung function. (A) Alpha-diversity indices (Shannon and Simpson) of the microbiota. (B) Beta-diversity (which assesses differences in microbiota compositions between samples) according to lung function at baseline, using a nonmetric multidimensional scaling (NMDS) ordination method with the Bray-Curtis distance metric. (C) Correlation between the ppFEV₁ and the Shannon index. (D) LEfSe method showing ASVs distinguishing patients with a ppFEV₁ of <80% and a ppFEV₁ of ≥80% at baseline.

FIG 2

Sputum calprotectin at baseline, according to patient and disease characteristics. Shown are sputum calprotectin levels at baseline according to age (A), ppFEV₁ (B), bacterial alpha-diversity indices (Shannon [C] and Simpson [D]), qPCR load of P. aeruginosa (E), and chronic colonization with P. aeruginosa (F).

FIG 3

Bacterial and fungal compositions of sputa at baseline according to the P. aeruginosa chronic colonization phenotype. (A and B) Comparison of targeted metagenomics data obtained from sputum samples at baseline (M0) between the patients colonized and those not colonized with P. aeruginosa for alpha- and beta-diversities. Beta-diversity, which assesses differences in microbial compositions between samples using a nonmetric multidimensional scaling (NMDS) ordination method with the Bray-Curtis distance metric of bacterial (A) and fungal (B) communities, is shown to measure the microbiota and mycobiota compositional similarity throughout. Permutational multivariate analysis of variance (PERMANOVA) was used to test sample clustering hypotheses. (C and D) Alpha-diversities of bacterial (C) and fungal (D) communities determined using the Shannon and Simpson indices.

FIG 4

Evolution of bacterial alpha-diversity indices with lumacaftor-ivacaftor treatment according to P. aeruginosa chronic colonization at baseline. Shown is the evolution of bacterial alpha-diversity indices with lumacaftor-ivacaftor treatment in patients without (A and B) and with (C and D) P. aeruginosa chronic colonization at baseline.