Molecular endotyping in people with bronchiectasis based on response to antibiotic treatment
Introduction: quantitative polymerase chain reaction (qPCR) and next-generation sequencing (NGS) could potentially be used to measure microbiological efficacy in response to antibiotic treatment, improve understanding of the role of the airway microbiome in determining response to therapy and stratify treatment approaches in people with bronchiectasis.  Objectives: To determine if qPCR and NGS could measure change in P. aeruginosa density following treatment with tobramycin inhalation powder (TIP), assess longitudinal change in the airway microbiota and test the hypothesis that TIP treatment results in a shift to healthier community structures with lower inflammatory endotypes. Methods: qPCR and NGS were performed on sputum samples collected longitudinally from 83 patients with bronchiectasis recruited to the iBEST study. The relationship between ecological metrics and clinical and inflammatory biomarkers were determined.  Results: There was a significant reduction in P. aeruginosa density, measured by qPCR, between Days 1 and 29 for participants in the TIP treatment (p<0.0001) but not placebo group (p>0.05). Based on change in P. aeruginosa density from Day 1 to Day 29, participants receiving TIP were defined as either responders ( =2Log10; n=26) or non-responders (<2Log10; n=37) with a significant shift in community structure (ß-diversity) from Day 1 to Day 29 apparent in the responder group. Lung function (FEV1 %Predicted) was significantly higher (p=0.005) at Day 1 in responders (µ ?median=64.6%) vs. non-responders (µ ?median=50.3%) and independently predicted response to treatment with TIP (p=0.013).  Conclusions: using qPCR, bronchiectasis patients were stratified into responder and non-responder theratypes which may inform a more personalised approach to antimicrobial treatment.