Endotypes of Pseudomonas Aeruginosa Infection in Bronchiectasis are Associated with Inhaled Antibiotic Response

Abstract

Background: Replicate phase 3 trials of inhaled antibiotics in patients with bronchiectasis have given inconsistent results. We hypothesized that patients with chronic Pseudomonas aeruginosa infection would demonstrate different microbial and inflammatory endotypes linked to antibiotic response.

Methods: ORBIT-3 and ORBIT-4 were phase III trials of inhaled liposomal ciprofloxacin compared with placebo in bronchiectasis patients with chronic P. aeruginosa infections. Baseline sputum samples collected during the trials were analysed by 16S rRNA sequencing (LoopSeq)(n=377), proteomics(n=164), and Olink®(n=116). Relationships with clinical features and frequency of exacerbations during the trial were analysed.

Findings: Patients with P. aeruginosa infections demonstrated heterogenous 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 commensals including Rothia and B-cell responses. Regional differences were observed, with increased microbiota diversity and decreased neutrophilic inflammation in central Europe. Candidate biomarkers for treatment response were identified including IL-7, neutrophil elastase, LSP1 and Rothia. Prior to 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]). Following linear discriminant analysis to adjust for microbiota profile and 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.

Interpretation: 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 regional differences and baseline microbiota.

Funding: Supported by the Innovative Medicines Initiative and The European Federation of Pharmaceutical Industries and Associations companies under the European Commission–funded Horizon 2020 Framework Program and by Inhaled Antibiotic for Bronchiectasis and Cystic Fibrosis (grant 115721). EMBARC3 is funded by the European Respiratory Society through the EMBARC3 clinical research collaboration. EMBARC3 is supported by project partners Armata, AstraZeneca, Boehringer Ingelheim, Chiesi, CSL Behring, Glaxosmithkline, Grifols, Insmed, Lifearc, Roche, Verona Pharma and Zambon. J.D.C. is supported by the GlaxoSmithKline/Asthma and Lung UK Chair of Respiratory Research.

Declaration of Interest: M.M. Tunney reports grants from Novartis, Spexis, Shionogi and NIHR EME, outside the submitted work. C.S. Haworth reports payment or honoraria for lectures, presentations, manuscript writing or educational events from 30 Technology, CSL Behring, Chisi, Insmed, Janssen, LifeArc, Meiji, Mylan, Pneumagen, Shionogi, Vertex and Zambon. J.D. Chalmers reports grants or contracts from AstraZeneca, Boehringer Ingelheim, Genentech, Gilead Sciences, GlaxoSmithKline, Grifols, Insmed, LifeArc and Novartis, and consulting fees from AstraZeneca, Chiesi, GlaxoSmithKline, Insmed, Grifols, Novartis, Boehringer Ingelheim, Pfizer, Janssen, Antabio and Zambon. All other authors report no conflicts of interest.

Ethical Approval: The studies were done in accordance with the principles of the Declaration of Helsinki, International Conference on Harmonisation Guideline for Good Clinical Practice, and applicable local regulations. The trial protocols were approved at each site by an ethics committee or institutional review board. Patients provided written informed consent at enrolment.

Keywords: Pseudomonas aeruginosa, bronchiectasis, ciprofloxacin, microbiota, inflammation