Despite the importance of
pneumonia to public health, little is known about the composition of the lung microbiome during
infectious diseases, such as
pneumonia, and how it evolves during
antibiotic therapy. To study the possible relation of the pulmonary microbiome to the severity and outcome of this respiratory disease, we analyzed the dynamics of the pathogen and the human lung microbiome during
persistent infections caused by the bacterium Legionella pneumophila and their evolution during antimicrobial treatment. We collected 10 bronchoalveolar lavage fluid samples from three patients during long-term hospitalization due to
pneumonia and performed a unique longitudinal study of the interkingdom microbiome, analyzing the samples for presence of bacteria, archaea, fungi, and protozoa by high-throughput Illumina sequencing of marker genes. The lung microbiome of the patients was characterized by a strong predominance of the pathogen, a low diversity of the bacterial fraction, and an increased presence of opportunistic microorganisms. The fungal fraction was more stable than the bacterial fraction. During long-term treatment, no genomic changes or antibiotic resistance-associated mutations that could explain the
persistent infection occurred, according to whole-genome sequencing analyses of the pathogen. After
antibiotic treatment, the microbiome did not recover rapidly but was mainly constituted of
antibiotic-resistant species and enriched in bacteria, archaea, fungi, or protozoa associated with pathogenicity. The lung microbiome seems to contribute to nonresolving Legionella
pneumonia, as it is strongly disturbed during
infection and enriched in opportunistic and/or
antibiotic-resistant bacteria and microorganisms, including fungi, archaea, and protozoa that are often associated with
infections.IMPORTANCE The composition and dynamics of the lung microbiome during
pneumonia are not known, although the lung microbiome might influence the severity and outcome of this
infectious disease, similar to what was shown for the microbiome at other body sites. Here we report the findings of a comprehensive analysis of the lung microbiome composition of three patients with long-term
pneumonia due to L. pneumophila and its evolution during
antibiotic treatment. This work adds to our understanding of how the microbiome changes during disease and
antibiotic treatment and points to microorganisms and their interactions that might be beneficial. In addition to bacteria and fungi, our analyses included archaea and eukaryotes (protozoa), showing that both are present in the pulmonary microbiota and that they might also play a role in the response to the microbiome disturbance.