(191) CFTR Potentiator (Ivacaftor) has Minimal Effects on Gut Microbiome Composition in People with Cystic Fibrosis and Gating Mutations

Background: Cystic fibrosis (CF) is associated with gut microbiota dysbiosis. The etiology of microbiota differences in CF is likely multifactorial, and includes impaired bicarbonate secretion and low pH, abnormal gastrointestinal motility, inspissated intestinal stool and mucous, fat malabsorption, lack of endogenous pancreatic enzymes, high fat diet, and frequent antibiotic use. Prior studies have demonstrated altered microbiota composition in individuals with CF. The impact of highly effective CFTR modulator therapy on the microbiota is largely unknown. Here we compare microbiota composition in individuals with CF and gating mutations at baseline and 3 months after initiation of the CFTR potentiator, ivacaftor, compared with healthy controls.

Methods: Subjects with gating mutations were recruited from CF Centers in the US and Italy. Stool samples were collected at baseline and 3 months after initiation of ivacaftor treatment. Age-matched healthy subjects were included from two previously published cohorts. [1.2] Microbiome composition was assessed using shotgun metagenomic sequencing using the DNeasy PowerSoil Kit (Qiagen, Germantown, MD) for extraction, the NexteraXT DNA Library Preparation Kit (Illumina, San Diego, CA), and an Illumina HiSeq 2500 using 2x125 bp chemistry. Data were processed using the Sunbeam, abundance of bacteria was estimated using Kraken, and analysis was conducted in R. Dysbiosis score was calculated as the median Bray-Curtis distance to the healthy participants.

Results: 18 individuals with CF (7M/11F, median age 15.3y) completed the study, 13 of whom had exocrine pancreatic insufficiency, and 5 with pancreatic sufficiency. While there were no differences in alpha diversity between healthy vs. CF subjects using either richness or Shannon’s index, CF subjects had higher dysbiosis scores (p< 0.001) and a distinct microbiota composition (beta diversity) compared to healthy controls (Figure 1, PERMANOVA p< 0.01). These differences in composition corresponded to an increase in the relative abundance of Enterobacteriaceae, Escherichia coli, and Veillonella parvula in subjects with CF and decreases in ten Bacteroidetes taxa, Eubacterium rectale, Faecalibacterium prausnitzii, and Akkermansia muciniphila (all fdr< 0.05). By contrast, treatment with ivacaftor for 3 months did not lead to statistically significant differences in alpha diversity (richness or Shannon’s diversity index), beta diversity (Bray-Curtis distances), or the relative abundance of specific bacterial taxa.

Conclusions: Altered microbiome composition was found in subjects with CF compared to healthy participants, consistent with previously reported results. We observed no statistically significant effects of ivacaftor treatment on gut microbiota composition; however, this was a small cohort with multiple confounders including antibiotics use and differences in exocrine pancreatic function.

Acknowledgements: This work was supported by 1) Penn Center for Nutritional Science and Medicine, 2) Vertex Pharmaceuticals, 3) NIH/NCATS (UL1TR001878, UL1RR024134, UL1TR000003), The authors acknowledge JN Brownell for his contributions.

References: [1] Bushman FD et al. Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease. Cell Host Microbe. 2020 Sep 9;28(3):422-433.e7.
[2] Tanes C et al. Role of dietary fiber in the recovery of the human gut microbiome and its metabolome. Cell Host Microbe. 2021 Mar 10;29(3):394-407.e5.