Comparison of Stool Microbiome in Children with Cystic Fibrosis Treated with and Without Elexacaftor–Tezacaftor–Ivacaftor—A Pilot Study

Prior studies in people with cystic fibrosis (CF) demonstrated a positive impact of ivacaftor on the stool microbiome. However, studies evaluating the impact of elexacaftor–tezacaftor–ivacaftor (ETI) on gut dysbiosis are limited. In this prospective, observational study, we evaluated the differences in stool microbiome in children (aged 2–17 years) with CF who were treated with ETI for at least two months and compared with children with CF who did not receive ETI. We also included healthy siblings as controls. There were no significant differences in the demographics between the groups. There were no significant differences in alpha diversity between the groups for both bacteriome and mycobiome. Alpha diversity showed a negative trend with the duration of ETI therapy for both bacteriome and mycobiome. Firmicutes and Proteobacteria were the most abundant phyla and core members across all samples, regardless of disease status or treatment. Ascomycota and Basidiomycota were the most abundant and core members across all samples, regardless of disease status or treatment. Alpha diversity showed a negative trend with the duration of ETI therapy for both bacteriome and mycobiome in children with CF treated with ETI. Future studies are needed to confirm or refute our preliminary findings.