Bacterial diversity in sputum samples from phase 2B clinical trials of OligoG CF-5/20 in CF patients colonised with Pseudomonas aeruginosa (NCT02157922) or Burkholderia cepacia complex bacteria (NCT02453789)

Culture-independent microbiota analysis is becoming increasingly used in translational studies and clinical trials. In cystic fibrosis (CF), microbiota analysis has revealed that infection is polymicrobial and consists of microorganisms previously unidentified by culture. Studies have used this analysis to follow changes in bacterial lung infections during antibiotic treatment, CF modulator therapies and pulmonary exacerbations.We report the microbiota (PCR, qPCR and 16S rRNA gene sequencing) analysis that accompanied two phase 2B clinical trials of the novel, non-antibiotic CF therapy OligoG CF-5/20, and discuss the value and application of culture-independent methods in this context.Microbiota analysis identified that paired sputum samples taken within 2 hours had highly concordant bacterial diversity profiles. Both trials had recruited heterogeneous groups of patients with respect to lung infection communities, even though culture had identified them as dominant for either Pseudomonas or Burkholderia. Microbiota profiles were patient-specific and stable over the course of the trials. Patients carrying Burkholderia were either colonised with B. cenocepacia or B. multivorans, and the species determined the overall community structure; B. cenocepacia was always found as the dominant pathogen, whereas B. multivorans could be at high or low abundance.The sputum microbiota is stable over a short time-frame and community profiles could guide patient stratification for future clinical trials. Microbiota analysis is useful for the identification of trends that would not otherwise be found by culture-based approaches, but has it's limitations. Other studies are starting to address these by exploring bacterial, fungal and viral diversity, and infer community functions.