CF airway shotgun metagenomics

Cystic fibrosis (CF) is an inherited genetic disorder, which manifests primarily in airway disease. Recent advances in molecular technologies have unearthed the diverse polymicrobial nature of the CF airway. Numerous studies have characterised the genus-level composition of this airway community using targetted 16S rRNA sequencing. Here we employed shotgun metagenomics to provide a more comprehensive understanding of the early CF airway microbiome. We collected 48 sputum samples from 11 adolescents and children with CF over a 12-month period and performed shotgun metagenomics on the Illumina NextSeq platform. We performed functional and taxonomic analysis of the lung microbiome at the species and strain levels. Correlations between diversity measures and independent demographic and clinical variables were performed. As expected, shotgun metagenomics detected greater diversity of bacteria than culture. A large proportion of the top 25 most dominant species were anaerobes. Samples dominated by Staphylococcus aureus and Prevotella melaninogenica had significantly higher microbiome diversity while no CF pathogen was associated with reduced diversity. Reduced microbiome diversity and higher abundance of Stenotrophomonas maltophilia and P. aeruginosa were associated with reduced lung function while several anaerobes were associated with higher lung function. There was a diverse resistome present in all samples in this study with 66% agreement between shotgun metagenomics and culture-based methods for detection of resistance. Pathogenic sequence types (STs) of S. aureus, P. aeruginosa, Haemophilus influenzae and S. maltophilia were observed to persist in young CF patients while STs of S. aureus were both persistent and shared between patients. This study provides new insight into the temporal changes in strain level composition of the microbiome and the landscape of the resistome in young people with CF.