Contributors: Biologie des Bactéries intracellulaires - Biology of Intracellular Bacteria; Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047); Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS); Centre National de Référence des Légionelles (CNR); Centre International de Recherche en Infectiologie (CIRI); École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL); Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS); This work was supported by the Institut Pasteur, and the Agence National de Recherche grant numbers ANR-15-CE17-0014-03 and ANR-10-LABX-62-IBEID to C.B. A.E.P.-C. was financed by ANR-10-LABX-62-IBEID. Work in the S.J. laboratory is financed by the Agence Nationale de la Recherche grant number ANR-15-CE17-0014-01, the DGOS, and Santé Publique France. A.E.P.-C. is a recipient of a Grant for the Attraction of Talent within the Community of Madrid (grant No. 2019-T2/BMD-12874). We thank the Institut Pasteur Biomics pole (Christiane Bouchier and Laurence Ma) for sequencing the samples reported in this study.; A.E.P.-C. and C.B. designed the experiments. A.E.P.-C. conducted the experiments. A.E.P.-C. and C.R. analyzed and interpreted the data. C.G. and S.J. contributed to sample and metadata collection. The manuscript was written by A.E.P.-C. and C.B. with input from co-authors. The project was conceived, planned, and supervised by C.B.; ANR-15-CE17-0014,ProgLegio,Biomarqueurs bactériens et humains d'intérêt pronostic pour les légionelloses sévères(2015); ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010)
نبذة مختصرة : International audience ; 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.
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