The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia

Bacterial pneumonia is a considerable problem worldwide. Here, we follow the inter-kingdom respiratory tract microbiome (RTM) of a unique cohort of 38 hospitalized patients (n = 97 samples) with pneumonia caused by Legionella pneumophila. The RTM composition is characterized by diversity drops early in hospitalization and ecological species replacement. RTMs with the highest bacterial and fungal loads show low diversity and pathogen enrichment, suggesting high biomass as a biomarker for secondary and/or co -infections. The RTM structure is defined by a commensalcluster associated with a healthy RTM and a pathogenenriched one, suggesting that the cluster equilibrium drives the microbiome to recovery or dysbiosis. Legionella biomass correlates with disease severity and co-morbidities, while clinical interventions influence the RTM dynamics. Fungi, archaea, and protozoa seem to contribute to progress of pneumonia. Thus, the interplay of the RTM equilibrium, the pathogen load dynamics, and clinical interventions play a critical role in patient recovery.

Automated summary

This study examines the respiratory tract microbiome (RTM) of 38 patients with pneumonia caused by Legionella pneumophila. The composition of the RTM changes early in hospitalization, with a decrease in diversity and replacement of species. RTMs with higher bacterial and fungal loads show lower diversity and pathogen enrichment, suggesting that high biomass may be a biomarker for secondary and/or co-infections. The structure of the RTM is defined by a commensal cluster associated with a healthy RTM and a pathogen-enriched cluster, indicating that the balance between these clusters plays a critical role in patient recovery.