Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome.

Adaptive Immunity Adult Aged Bacteria / classification Bacterial Load Bronchoalveolar Lavage Fluid / immunology COVID-19 / immunology Critical Illness Female Hospitalization Humans Immunity, Innate Male Microbiota Middle Aged Odds Ratio Prognosis Prospective Studies Respiration, Artificial Respiratory System / immunology SARS-CoV-2 / immunology Viral Load

Journal

Nature microbiology
ISSN: 2058-5276
Titre abrégé: Nat Microbiol
Pays: England
ID NLM: 101674869

Informations de publication

Date de publication:
10 2021
Historique:
received: 17 03 2021
accepted: 10 08 2021
pubmed: 2 9 2021
medline: 9 10 2021
entrez: 1 9 2021
Statut: ppublish

Résumé

Respiratory failure is associated with increased mortality in COVID-19 patients. There are no validated lower airway biomarkers to predict clinical outcome. We investigated whether bacterial respiratory infections were associated with poor clinical outcome of COVID-19 in a prospective, observational cohort of 589 critically ill adults, all of whom required mechanical ventilation. For a subset of 142 patients who underwent bronchoscopy, we quantified SARS-CoV-2 viral load, analysed the lower respiratory tract microbiome using metagenomics and metatranscriptomics and profiled the host immune response. Acquisition of a hospital-acquired respiratory pathogen was not associated with fatal outcome. Poor clinical outcome was associated with lower airway enrichment with an oral commensal (Mycoplasma salivarium). Increased SARS-CoV-2 abundance, low anti-SARS-CoV-2 antibody response and a distinct host transcriptome profile of the lower airways were most predictive of mortality. Our data provide evidence that secondary respiratory infections do not drive mortality in COVID-19 and clinical management strategies should prioritize reducing viral replication and maximizing host responses to SARS-CoV-2.

Identifiants

DOI: 10.1038/s41564-021-00961-5 PMID: 34465900 PMC: PMC8484067
pubmed: 34465900
doi: 10.1038/s41564-021-00961-5
pii: 10.1038/s41564-021-00961-5
pmc: PMC8484067
mid: NIHMS1734100
doi:

Types de publication

Journal Article Multicenter Study Observational Study Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

1245-1258

Subventions

Organisme : NCI NIH HHS
ID : R01 CA159036
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA016087
Pays : United States
Organisme : NIDDK NIH HHS
ID : R01 DK110014
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI143861
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL125816
Pays : United States
Organisme : NIAID NIH HHS
ID : R21 AI158997
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI140754
Pays : United States
Organisme : NCI NIH HHS
ID : R37 CA244775
Pays : United States
Organisme : NCI NIH HHS
ID : P20 CA252728
Pays : United States
Organisme : NIAID NIH HHS
ID : T32 AI100853
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI137336
Pays : United States

Commentaires et corrections

Type : UpdateOf
Type : UpdateOf

Informations de copyright

© 2021. The Author(s), under exclusive licence to Springer Nature Limited.

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Auteurs

Imran Sulaiman (I)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
ORCID: 0000-0003-1992-0280

Matthew Chung (M)

Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.

Luis Angel (L)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
ORCID: 0000-0002-5045-9712

Jun-Chieh J Tsay (JJ)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Division of Pulmonary and Critical Care Medicine, VA New York Harbor Healthcare System, New York, NY, USA.
ORCID: 0000-0002-2282-2510

Benjamin G Wu (BG)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Division of Pulmonary and Critical Care Medicine, VA New York Harbor Healthcare System, New York, NY, USA.

Stephen T Yeung (ST)

Department of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Kelsey Krolikowski (K)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Yonghua Li (Y)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Ralf Duerr (R)

Department of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
ORCID: 0000-0001-9569-9237

Rosemary Schluger (R)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Sara A Thannickal (SA)

Department of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
ORCID: 0000-0002-7028-3507

Akiko Koide (A)

Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY, USA.

Samaan Rafeq (S)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Clea Barnett (C)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Radu Postelnicu (R)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Chang Wang (C)

Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, USA.

Stephanie Banakis (S)

Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.

Lizzette Pérez-Pérez (L)

Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health Rocky Mountain Laboratories, Hamilton, MT, USA.
ORCID: 0000-0001-5881-4363

Guomiao Shen (G)

Department of Pathology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

George Jour (G)

Department of Pathology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Peter Meyn (P)

Division of Pediatrics, Longhua Hospital affiliated to Shanghai University of Chinese Medicine, Shanghai, China.

Joseph Carpenito (J)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Xiuxiu Liu (X)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Division of Pediatrics, Longhua Hospital affiliated to Shanghai University of Chinese Medicine, Shanghai, China.

Kun Ji (K)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Dongfang Hospital affiliated to Beijing University of Traditional Chinese Medicine, Beijing, China.

Destiny Collazo (D)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Anthony Labarbiera (A)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Nancy Amoroso (N)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Shari Brosnahan (S)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
ORCID: 0000-0002-2092-3633

Vikramjit Mukherjee (V)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

David Kaufman (D)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Jan Bakker (J)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
ORCID: 0000-0003-2236-7391

Anthony Lubinsky (A)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Deepak Pradhan (D)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Daniel H Sterman (DH)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Michael Weiden (M)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Adriana Heguy (A)

Department of Pathology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
NYU Langone Genome Technology Center, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Laura Evans (L)

Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA.

Timothy M Uyeki (TM)

Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA.

Jose C Clemente (JC)

Department of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
ORCID: 0000-0002-3970-9856

Emmie de Wit (E)

Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health Rocky Mountain Laboratories, Hamilton, MT, USA.
ORCID: 0000-0002-9763-7758

Ann Marie Schmidt (AM)

Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Bo Shopsin (B)

Division of Infectious Diseases, Department of Medicine, New York University School of Medicine, NYU Langone Health, New York, NY, USA.

Ludovic Desvignes (L)

Department of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Chan Wang (C)

Department of Population Health, New York University School of Medicine, NYU Langone Health, New York, NY, USA.

Huilin Li (H)

Department of Population Health, New York University School of Medicine, NYU Langone Health, New York, NY, USA.

Bin Zhang (B)

Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Christian V Forst (CV)

Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
ORCID: 0000-0003-0229-9459

Shohei Koide (S)

Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY, USA.
Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
ORCID: 0000-0001-5473-4358

Kenneth A Stapleford (KA)

Department of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.

Kamal M Khanna (KM)

Department of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY, USA.

Elodie Ghedin (E)

Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. elodie.ghedin@nih.gov.
Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, USA. elodie.ghedin@nih.gov.
ORCID: 0000-0002-1515-725X

Leopoldo N Segal (LN)

Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA. Leopoldo.Segal@nyumc.org.
Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA. Leopoldo.Segal@nyumc.org.
Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY, USA. Leopoldo.Segal@nyumc.org.
ORCID: 0000-0003-3559-9431

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