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

Thorax. 2011 Jul;66(7):579-84. doi: 10.1136/thx.2010.137281. Epub 2011 Jan 26.


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 2.3×10(7) cfu/g, p=0.005) than for anaerobes (median decrease in total viable count 3×10(6) 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Anti-Bacterial Agents / pharmacology*
  • Anti-Bacterial Agents / therapeutic use
  • Bacteria / classification
  • Bacteria / drug effects*
  • Bacteria / isolation & purification
  • Bacteria, Aerobic / classification
  • Bacteria, Aerobic / drug effects
  • Bacteria, Aerobic / isolation & purification
  • Bacteria, Anaerobic / classification
  • Bacteria, Anaerobic / drug effects
  • Bacteria, Anaerobic / isolation & purification
  • Bacterial Infections / complications
  • Bacterial Infections / drug therapy*
  • Colony Count, Microbial
  • Cystic Fibrosis / complications
  • Cystic Fibrosis / microbiology*
  • Cystic Fibrosis / physiopathology
  • Female
  • Forced Expiratory Volume
  • Humans
  • Male
  • Opportunistic Infections / complications
  • Opportunistic Infections / drug therapy*
  • Polymorphism, Restriction Fragment Length
  • Sputum / microbiology
  • Young Adult


  • Anti-Bacterial Agents