Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper airway specimens can misrepresent infecting populations

Amanda F. Goddard, Ben J. Staudinger, Scot E. Dowd, Amruta Datar, Randy D. Wolcott, Moira L. Aitken, Corrine L. Fligner, and Pradeep K. Singh, Recent work suggests that the airways of cystic fibrosis (CF) patients harbor a vast array of bacteria not previously implicated in CF infections. These data have fundamentally altered understanding of this disease. However, sampling lung secretions in living subjects involves expectorated specimens, or passing collection devices pass through the oropharynx, which contains a high degree of microbial diversity. Thus, contamination could confound results. Here we directly sampled CF lungs removed at the time of transplantation and compared non-culture based analysis of lung secretions, to throat and sputum samples obtained several hours earlier. We found that CF lungs with advanced disease contained relatively homogenous populations of typical CF pathogens, whereas upper airway specimens from the same patients showed markedly higher levels of microbial diversity. Furthermore, soutum samples exhibited significant day-to-day variation in microbial composition, consistent with varying levels of oro-pharyngeal contamination. These findings highlight the importance of sampling procedures for microbiome studies, and suggest that new methods are needed to validate data when DNA-based methods are used on specimens prone to contamination.