Introduction: This study determined changes in the antimicrobial resistome and airway microbiota following treatment with tobramycin inhalation powder (TIP) or placebo in the iBEST study.

Methods: DNA was extracted from sputum collected at baseline and at day 29 (Day 1 vs Day 29) following treatment with TIP (224mg daily; n=11 patients) or placebo (n=5 patients). Shotgun-metagenomic sequencing (sgNGS) was performed on the Illumina Novaseq platform. P. aeruginosa density was determined by both total viable count (TVC) and qPCR of the oprL gene with total bacterial density measured by qPCR of the 16S rRNA gene. Resistome profiles were determined by mapping reads to the Comprehensive Antibiotic Resistance gene Database (CARD).

Results: Using sgNGS sequences, reads mapped to 62 different resistance genes. Differences in resistance gene prevalence for multiple targets were observed pre- and post-treatment and were primarily associated with samples from patients receiving TIP. Limited or no difference was observed for those receiving placebo. Differences in resistome profiles were strongly aligned with a decrease in P. aeruginosa density determined by TVC (Day 1 vs. Day 29; TIP: p<0.001; Placebo: p=0.222) and qPCR (Day 1 vs. Day 29; TIP: p=0.001; Placebo: p=0.421). No difference was seen in total bacterial density (16S rRNA) for either treatment group (p=0.193 and p=0.841, respectively).   

Conclusion: Treatment with TIP reduced the number of resistance genes detected. This was mainly due to a decrease in P. aeruginosa density within the community.

Supported by EU/EFPIA IMI iABC grant no° 115721