Endotypes of Pseudomonas aeruginosa Infection in Bronchiectasis Are Associated with Inhaled Antibiotic Response: Results from Two Randomized, Double-Blind, Placebo-controlled Phase III Trials (ORBIT 3 and ORBIT 4)

Abstract Rationale Replicate phase III trials of inhaled antibiotics in patients with bronchiectasis have produced inconsistent results. Objectives This study investigated if different microbial and inflammatory endotypes are linked to antibiotic response in patients with chronic Pseudomonas aeruginosa infection. Methods ORBIT-3 and ORBIT-4 were phase III trials of inhaled liposomal ciprofloxacin compared with placebo in patients with bronchiectasis with chronic P. aeruginosa infections. Baseline sputum from the trials were analyzed by 16S rRNA sequencing (LoopSeq) (n = 377), proteomics (n = 164), and Olink (n = 117). Relationships with clinical features and frequency of exacerbations during the trials were analyzed. Measurements and Main Results Patients with P. aeruginosa infections demonstrated heterogeneous endotypes. Reduced microbiota diversity was associated with exacerbation frequency (P = 0.021) and quality of life (P = 0.012). Increased exacerbations were associated with increased Pseudomonas abundance and neutrophilic inflammation; decreases in the relative abundance of commensals, including Rothia; and B-cell responses. Geographical differences were observed, with increased microbiota diversity and decreased neutrophilic inflammation in Central Europe. Candidate biomarkers for treatment response were identified, including neutrophil elastase, LSP1, and Rothia relative abundance. Before adjustment, treatment estimates of the two trials varied (ORBIT-3 rate ratio [RR], 0.85 [0.65–1.12], ORBIT-4 RR, 0.63 [0.48–0.82]). After linear discriminant analysis to adjust for microbiota profile and geographical region, the treatment estimates of ORBIT-3 (RR, 0.81 [0.54–1.22]) and ORBIT-4 (RR, 0.82 [0.56–1.22]) were similar and consistent with previous meta-analyses of inhaled antibiotics in bronchiectasis. Conclusions Patients with chronic P. aeruginosa have heterogeneous microbiota and inflammatory profiles, influencing antibiotic treatment responses in bronchiectasis. Future trials could be improved by patient stratification, including accounting for geographical differences and biomarkers to represent microbiota differences.