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"last-update": "2019-05-02T15:45:41",
"secondary-accession": "ERP114688",
"centre-name": "UNIVERSITY OF ZURICH, Institute of Molecular Life Sciences",
"public-release-date": null,
"study-abstract": "Cystic fibrosis (CF) is a life-threatening genetic disorder accompanied by chronic lung infections and respiratory complications that arise from the accumulation of viscous mucus in the airways. In the clinic, cultures of microbes isolated from the coughed-up lung sputum are used to decide on the CF management strategy. The approach, however, frequently misses non-typical microbes and provides limited strain-level resolution. In the study, we applied an unbiased sequencing approach to lung sputum samples in order to gain a more complete picture of the lung microbiome. We explored changes in the lung microbiome composition over time, particularly during exacerbations and antibiotic treatments. Moreover, we distinguished between evolution of internal strains and introduction of external strains from the environment. To do this, we followed four CF patients displaying extreme clinical phenotypes over the course of two years. During each exacerbation or routine clinical visit, the lung sputum from these patients was taken for shotgun sequencing. Reads not mapping to the host were subjected to assembly, taxonomic profiling, strain typing, and variant analysis. Sequencing revealed the presence of several microbes missed by culture, particularly anaerobes. It allowed us to identify dominant strains of abundant microbes, and to correct mistakes in taxonomic assignment from culture. Finally, after analysing variation on the genome level, we describe multiple events such as a battle for dominance between multiple strains of Pseudomonas aeruginosa in the same patient. This study provides a first insight into the advantages of assessing the complete lung microbiome over time.",
"study-name": "Strain-Level Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis",
"data-origination": "SUBMITTED"
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