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Profiling of bacterial communities in chronic obstructive pulmonary disease

Introduction: It is hypothesized that bacteria are important in the pathogenesis of COPD and exacerbations. Most bacteriological research in COPD has utilised culture based methods. Novel molecular approaches enable detailed evaluation of the airway microbiome that may better inform the role of bacteria in COPD. This project aimed to characterise the microbial community in COPD at stable state and during acute exacerbations through assessment of serial sputa at stable (S), exacerbation (E), follow up (F) and recovery (R) visits. Methods: Sputum from 145 clinical trial COPD patients was collected at multiple stable visits and at each exacerbation (E, F and R visit) over 12 months. Real-time quantitative PCR (qPCR) was performed on sputum DNA using universal 16S gene primers and specific gene targets to quantify total bacterial load and the specific pathogens H. influenzae, S. pneumoniae, M. catarrhalis and S. aureus. In a subgroup of 30 exacerbating patients, 454 high-throughput pyrosequencing of 16S rDNA amplicons was performed at each of the 4 visits. Results: There was no significant difference in total bacterial load or any specific pathogen between longitudinal stable and exacerbation samples. 454 pyrosequencing identified Proteobacteria and Firmicutes to be the dominant groups contributing >80% of the sequence reads at phylum level. Haemophilus, Moraxella and Streptococcus were the dominant groups at genus level. No significant within-subject change in the microbial community was observed across visits. Cluster analysis, based on the ratio of Proteobacteria to Firmicutes (P:F) characterised three subgroups. The high P:F subgroup was characterised by a significant increase in P:F from S to E visits, associated with raised blood CRP and sputum IL-1β levels, suggesting a role for bacteria in exacerbation pathogenesis for this subgroup. Conclusions: Molecular profiling identifies heterogeneity in the airway microbiome of COPD patients, with a role for bacteria suggested in a subgroup.
Date January 2015
CreatorsHaldar, Kairabi Sadhu
ContributorsBarer, Michael; Rajakumar, Kumar
PublisherUniversity of Leicester
Source SetsEthos UK
Detected LanguageEnglish
TypeElectronic Thesis or Dissertation

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