BackgroundHigh bacterial burden in lung microbiota predicts progression of idiopathic pulmonary fibrosis (IPF). Azithromycin (AZT) is a macrolide antibiotic known to alter the lung microbiota in several chronic pulmonary diseases and observational studies have shown a positive effect of azithromycin on mortality and hospitalization rate in IPF. However, the effect of AZT on lung microbiota in IPF remains unknown.MethodsWe sought to determine the impact of a three-month course of AZT on lung microbiota in IPF. We assessed sputum and oropharyngeal swab specimens from 24 adults with IPF included in a randomized controlled cross-over trial of a thrice-weekly 500 mg oral AZT. 16S rRNA gene amplicon sequencing and quantitative polymerase chain reaction (qPCR) were performed to assess bacterial communities. Antibiotic resistance genes (ARG) were assessed using real-time qPCR.ResultsAZT significantly decreased community diversity with a stronger and more persistent effect in lower airways (sputum). AZT treatment altered the temporal kinetics of the upper (oropharyngeal swab) and lower airway microbiota, increasing community similarity between the two sites for one month after macrolide cessation.Patients with an increase in ARG carriage had lower bacterial density and enrichment of the genusStreptococcus. In contrast, patients with more stable ARG carriage had higher bacterial density and enrichment inPrevotella.ConclusionsAZT caused sustained changes in the diversity and composition of the upper and lower airway microbiota in IPF, with effects on the temporal and spatial dynamics between the two sites.