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

Ana Elena Pérez-Cobas (1) , Christophe Ginevra (2, 3) , Christophe Rusniok (1) , Sophie Jarraud (2, 3) , Carmen Buchrieser (1)

1 Biologie des Bactéries intracellulaires - Biology of Intracellular Bacteria
2 CNR - Centre National de Référence des Légionelles
3 CIRI - Centre International de Recherche en Infectiologie

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 "commensal" cluster associated with a healthy RTM and a "pathogen" enriched 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.

Keywords: Legionella pneumophila; biomass; microbial ecology; pneumonia; respiratory tract microbiome; severity

Domains: Microbiology and Parasitology; Genomics [q-bio.GN]

Ana Elena Pérez-Cobas, Christophe Ginevra, Christophe Rusniok, Sophie Jarraud, Carmen Buchrieser. The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia. Cell Reports Medicine, 2023, 4 (9), pp.101167. ⟨10.1016/j.xcrm.2023.101167⟩. ⟨pasteur-04558958⟩