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Original article
Use of culture and molecular analysis to determine the effect of antibiotic treatment on microbial community diversity and abundance during exacerbation in patients with cystic fibrosis
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  1. M M Tunney1,
  2. E R Klem2,
  3. A A Fodor3,
  4. D F Gilpin1,
  5. T F Moriarty1,
  6. S J McGrath1,
  7. M S Muhlebach4,
  8. R C Boucher2,5,
  9. C Cardwell6,
  10. G Doering7,
  11. J S Elborn6,
  12. M C Wolfgang2,8
  1. 1School of Pharmacy, Queen's University Belfast, UK
  2. 2Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
  3. 3Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
  4. 4Department of Paediatrics, University of North Carolina at Chapel, Chapel Hill, North Carolina, USA
  5. 5Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
  6. 6Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, UK
  7. 7Eberhard-Karls-Universtät, Hygiene-Institut, Department of General and Environmental Hygiene, Wilhelmstrasse, Tübingen, Germany
  8. 8Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
  1. Correspondence to Michael M Tunney, School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; m.tunney{at}qub.ac.uk

Abstract

Background Anaerobic bacteria are increasingly regarded as important in cystic fibrosis (CF) pulmonary infection. The aim of this study was to determine the effect of antibiotic treatment on aerobic and anaerobic microbial community diversity and abundance during exacerbations in patients with CF.

Methods Sputum was collected at the start and completion of antibiotic treatment of exacerbations and when clinically stable. Bacteria were quantified and identified following culture, and community composition was also examined using culture-independent methods.

Results Pseudomonas aeruginosa or Burkholderia cepacia complex were detected by culture in 24/26 samples at the start of treatment, 22/26 samples at completion of treatment and 11/13 stable samples. Anaerobic bacteria were detected in all start of treatment and stable samples and in 23/26 completion of treatment samples. Molecular analysis showed greater bacterial diversity within sputum samples than was detected by culture; there was reasonably good agreement between the methods for the presence or absence of aerobic bacteria such as P aeruginosa (κ=0.74) and B cepacia complex (κ=0.92), but agreement was poorer for anaerobes. Both methods showed that the composition of the bacterial community varied between patients but remained relatively stable in most individuals despite treatment. Bacterial abundance decreased transiently following treatment, with this effect more evident for aerobes (median decrease in total viable count 2.3×107 cfu/g, p=0.005) than for anaerobes (median decrease in total viable count 3×106 cfu/g, p=0.046).

Conclusion Antibiotic treatment targeted against aerobes had a minimal effect on abundance of anaerobes and community composition, with both culture and molecular detection methods required for comprehensive characterisation of the microbial community in the CF lung. Further studies are required to determine the clinical significance of and optimal treatment for these newly identified bacteria.

  • Cystic fibrosis
  • anaerobe
  • infection
  • molecular detection
  • exacerbation
  • bacterial infection
  • bronchiectasis
  • cystic fibrosis
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Footnotes

  • Linked article 157875.

  • MMT, JSE and MCW contributed equally to this study.

  • Funding Supported by a UK Cystic Fibrosis Trust grant (PJ533) and a grant from the US National Institutes of Health (HL084934). MMT was supported by a Health and Social Care Research and Development, Public Health Agency, Northern Ireland-funded UK National Institute for Health Research Career Scientist Award.

  • Competing interests None.

  • Ethics approval This study was conducted with the approval of the Office for Research Ethics Northern Ireland.

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

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