Elexacaftor-tezacaftor-ivacaftor (ETI) has transformed cystic fibrosis (CF) care, but individual responses remain variable. Although longitudinal studies indicate that ETI reshapes lung and gut microbiota, the contribution of direct drug-microbe interactions remains unclear. We used an in vitro pharmacomicrobiomics approach to screen bidirectional interactions between individual cystic fibrosis transmembrane conductance regulator (CFTR) modulators and CF-relevant bacteria from pulmonary and intestinal niches.

Thirty-five Gram-positive and Gram-negative strains (15 reference strains, 20 pulmonary clinical isolates) were selected according to their frequency in CF lung and gut microbiota. Bacteria were grown in brain-heart infusion or M9 medium with or without elexacaftor, tezacaftor or ivacaftor. Growth was assessed by OD600 and CFU counts, and residual parent-drug concentrations were quantified by validated liquid chromatography-tandem mass spectrometry. Logistic growth models were fitted to OD600 data.

Elexacaftor modestly increased growth of Pseudomonas aeruginosa and Escherichia coli reference strains, but not clinical P. aeruginosa isolates, suggesting strain-dependent effects. Ivacaftor inhibited all Staphylococcus aureus strains, including methicillin-resistant S. aureus , and several anaerobic commensals, while leaving P. aeruginosa and E. coli largely unaffected. Tezacaftor had no detectable effect on growth. In sterile media, all three modulators remained relatively stable. In bacteria-exposed cultures, parent-drug concentrations decreased by approximately 60–70%, with several pathogens and commensals showing high-depleting phenotypes.

CFTR modulators and CF-associated microbiota interact bidirectionally in vitro . Elexacaftor and ivacaftor exert compound-, species- and strain-dependent effects on bacterial growth independent of their canonical role in restoring CFTR function, while multiple bacterial species decrease detectable parent-drug concentrations in culture supernatants.