Lung microbiome evolution during Legionella-associated pneumonia and antibiotic therapy

We analyzed the lung microbiome composition including bacteria, archaea, fungi and amoeba of bronchoalveolar lavage (BAL) samples collected during hospitalization of three patients with long-term pneumonia due to L. pneumophila and antibiotic treatment. Using high-throughput sequencing of marker genes we show that the pulmonary microbiome is highly disturbed during pneumonia and by the antibiotic treatment whereas the mycobiome is less affected.