Antibiotic pressure does not uncover intra-host heterogeneity of Pseudomonas aeruginosa in patients with chronic lung disease

Pseudomonas aeruginosa colonization and infection in patients with chronic obstructive pulmonary disease (COPD) or non-cystic fibrosis bronchiectasis (NCFBE) are associated with increased airway inflammation and mortality. Pseudomonas-active antibiotic therapy is a frequent therapeutic intervention in acute bacteria-driven exacerbation or when eradication of P. aeruginosa colonization is intended. However, the impact of intra-patient heterogeneity of P. aeruginosa on eradication outcomes remains unclear.We enrolled 30 patients receiving inpatient care for COPD and/or NCFBE exacerbation with known or newly detected P. aeruginosa colonization into an observational study. The analysis cohort consisted of 22 participants receiving in-hospital antibiotic eradication therapy, from whom a total of 91 lower respiratory tract samples were collected prior to, during, and after antibiotic therapy. To explore intra-host clonal heterogeneity, a maximum of 10 randomly selected P. aeruginosa isolates were collected from all patient samples containing Pseudomonas.P. aeruginosa-positive cultures were detected in 11 of 22 patients at baseline or during antibiotic therapy. Among these patients, short-term microbiological eradication, defined as a Pseudomonas-negative culture during or at the conclusion of antibiotic treatment, was achieved in 10 of 11 cases (90.9%). Extended antimicrobial susceptibility testing was performed on all isolates and indicated low levels of resistance in isolates obtained from patients before the initiation of eradication therapy and overall limited intra-host phenotypic resistance variability. Whole-genome sequencing of isolates from four patients with at least three longitudinal P. aeruginosa-positive samples confirmed colonization by a single clonal lineage in each case.While concordance between phenotypic resistance and detected genetic resistance determinants was limited, overall resistance levels were low. Our data suggest that P. aeruginosa colonization in our cohort of COPD/NCFBE patients was predominantly associated with a single clonal lineage and with limited intra-host resistance heterogeneity. These findings, based on a small sample size, suggest that susceptibility testing of a single isolate could inform eradication therapy in selected patients. The high rate of short-term eradication success is consistent with the effectiveness of current antibiotic regimens. Yet, more comprehensive longitudinal studies with larger patient numbers and more diverse patient backgrounds are warranted to clarify persistence and re-infection dynamics.Trial registrationGerman Clinical Trials Register (DRKS), DRKS00023975. Registered 28 December 2020. Retrospectively registered.