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Long-term cultivation-independent microbial diversity analysis demonstrates that bacterial communities infecting the adult cystic fibrosis lung show stability and resilience
  1. Franziska Anne Stressmann1,
  2. Geraint B Rogers1,
  3. Christopher J van der Gast2,
  4. Peter Marsh3,
  5. Louic S Vermeer4,
  6. Mary P Carroll5,
  7. Lucas Hoffman6,
  8. Thomas W V Daniels5,
  9. Nilesh Patel7,
  10. Benjamin Forbes1,
  11. Kenneth Deans Bruce1
  1. 1Molecular Microbiology Research Laboratory, Institute of Pharmaceutical Science, King's College London, London, UK
  2. 2NERC Centre for Ecology and Hydrology, Wallingford, UK
  3. 3Health Protection Agency South East, Southampton General Hospital, Southampton, UK
  4. 4Institute of Pharmaceutical Science, King's College London, London, UK
  5. 5Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Southampton, UK
  6. 6Department of Pediatrics, University of Washington, Seattle, Washington, USA
  7. 7Department of Pharmacy, Kingston University, Kingston, UK
  1. Correspondence to Dr Geraint Rogers, Molecular Microbiology Research Laboratory, Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, Franklin-Wilkins Building, London SE1 9NH, UK;{at}


Background Culture-independent analysis of the respiratory secretions of people with cystic fibrosis (CF) has identified many bacterial species not previously detected using culture in this context. However, little is known about their clinical significance or persistence in CF airways.

Methods The authors characterised the viable bacterial communities in the sputum collected from 14 patients at monthly intervals over 1 year using a molecular community profiling technique—terminal restriction fragment length polymorphism. Clinical characteristics were also collected, including lung function and medications. Ecological community measures were determined for each sample. Microbial community change over time within subjects was defined using ecological analytical tools, and these measures were compared between subjects and to clinical features.

Results Bacterial communities were stable within subjects over time but varied between subjects, despite similarities in clinical course. Antibiotic therapy temporarily perturbed these communities which generally returned to pretreatment configurations within 1 month. Species usually considered CF pathogens and those not previously regarded as such exhibited similar patterns of persistence. Less diverse sputum bacterial communities were correlated to lung disease severity and relative abundance of Pseudomonas aeruginosa.

Conclusion Whilst not true in all cases, the microbial communities that chronically infect the airways of patients with CF can vary little over a year despite antibiotic perturbation. The species present tended to vary more between than within subjects, suggesting that each CF airway infection is unique, with relatively stable and resilient bacterial communities. The inverse relationship between community richness and disease severity is similar to findings reported in other mucosal infections.

  • Bacterial infection
  • cystic fibrosis
  • respiratory infection
  • lung cancer
  • bronchiectasis
  • COPD mechanisms
  • opportunist lung infections
  • pneumonia
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  • Funding This work was supported by the Anna Trust (grant number KB2008) and the Seattle Children's Hospital Center for Clinical and Translational Research.

  • Competing interests None.

  • Patient consent Detail has been removed from this case description/these case descriptions to ensure anonymity. The editors and reviewers have seen the detailed information available and are satisfied that the information backs up the case the authors are making.

  • Ethics approval Ethics approval was provided by Southampton and South West Hampshire Research Ethics Committee.

  • Provenance and peer review Not commissioned; externally peer reviewed.

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