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

Autor: 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., Chung M; Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA., 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., 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., 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., Yeung ST; Department of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA., 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., 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., Duerr R; Department of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA., 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., Thannickal SA; Department of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA., 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., 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., 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., 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., Wang C; Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, USA., Banakis S; Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA., 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., Shen G; Department of Pathology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA., Jour G; Department of Pathology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA., Meyn P; Division of Pediatrics, Longhua Hospital affiliated to Shanghai University of Chinese Medicine, Shanghai, China., 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., 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., 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., 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., 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., 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., 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., 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., 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., 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., 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., 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., 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., 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., 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., Evans L; Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA., Uyeki TM; Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA., Clemente JC; Department of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA., 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., 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., Shopsin B; Division of Infectious Diseases, Department of Medicine, New York University School of Medicine, NYU Langone Health, New York, NY, USA., Desvignes L; Department of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA., Wang C; Department of Population Health, New York University School of Medicine, NYU Langone Health, New York, NY, USA., Li H; Department of Population Health, New York University School of Medicine, NYU Langone Health, New York, NY, USA., 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., 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., 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., Stapleford KA; Department of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA., 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., 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., 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.
Jazyk: angličtina
Zdroj: Nature microbiology [Nat Microbiol] 2021 Oct; Vol. 6 (10), pp. 1245-1258. Date of Electronic Publication: 2021 Aug 31.
DOI: 10.1038/s41564-021-00961-5
Abstrakt: 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.
(© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)
Databáze: MEDLINE
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