Introduction and Objectives The microbial communities present in CF sputum are polymicrobial and consist of bacteria, viruses and fungi. Although stratified studies have demonstrated a change in the CF bacterial microbiota with increasing age, individual patients have not been followed longitudinally across stable phases and exacerbation episodes period of time. The aim of this study was to follow CF patients who were either homo- or heterozygous for the F508del mutation over a period of up to 20 months to assess how the bacterial and fungal communities fluctuate over this period to determine whether a shift in the microbiota could be linked with acute pulmonary exacerbations.
Methods Adult CF patients were recruited and spontaneously expectorated sputum samples were collected. DNA was extracted from the samples and PCR-DGGE was used to analyse the bacterial and fungal communities using universal primer sets.
Results Routine microbial culture identified a mean of 1.52 bacterial species and 0.62 fungal species, whereas molecular analysis found a mean of 12.24 bacterial species and 1.41 fungal species across the cohort. The composition of the bacterial communities between patients varied significantly according to gender and being culture positive for P aeruginosa. Patients homozygous for the F508del mutation had more rich fungal communities than heterozygotes. However, a bacterial or fungal community characteristic for pulmonary exacerbations was not observed.
Conclusions Our data clearly demonstrates that bacterial and fungal communities in the CF lower respiratory tract are more diverse than previously thought. Furthermore, the microbial communities in the lower respiratory tract of CF patients are subject are selected by predisposing factors such as gender but still remain unique to individual patients. Monitoring the microbial communities has found that although they are subject to some fluctuation a characteristic community does not assemble to cause acute pulmonary exacerbations. Furthermore, particular bacterial taxa were present throughout the sampling period, suggesting that current antimicrobial therapies are not adequate at removing these taxa.