Observational studyNature microbiology2021
Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome.
Open access · bronzeAbstract readMulticenter StudyObservational Study
In one paragraph
Observational study in Nature microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 118 papers, 2 of them syntheses that pooled it.
0numbers the graph read from it
0cells of the map it votes in
118citing papers in PubMed, 2 pooled it
24.1field-weighted citation impact, top 1% of its field
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
118 citing papers in PubMed, 2 syntheses or guidelines pooled it, 189 citations in OpenAlex.
- Antimicrobial resistance in patients with COVID-19: a systematic review and meta-analysis.The Lancet. Microbe · 2023Pooled it
- Impact of asthma on COVID-19 mortality in the United States: Evidence based on a meta-analysis.International immunopharmacology · 2022Pooled it
- The role of the respiratory microbiome in acute and chronic respiratory diseases.Nature reviews. Microbiology · 2026Review
- The Role of the Respiratory Microbiome in Pneumonia.Clinics in chest medicine · 2026Review
- A diagnostic model based on pulmonary microbiota and host gene expression to distinguish colonization from pneumonia.Scientific reports · 2026Article
- Indole-acetaldehyde from Rothia mucilaginosa activates the PXR/NRF2 axis to enhance alveolar macrophage phagocytosis and protect against ARDS.Respiratory research · 2026Article
- SARS-CoV-2 Infection disrupts lower respiratory tract microbiome function and interactions.BMC microbiology · 2026Article
- Ventilation-Associated Differences in Lower Airway Microbial Signatures and Peripheral Blood Transcriptome Among Critically Ill COVID-19 Patients.Infection and drug resistance · 2026Article
- Respiratory epithelial cells as central mediators of immune crosstalk in SARS-CoV-2 infection.Frontiers in immunology · 2026Review
- Multi-omics to study chronic respiratory diseases and viral infections.European respiratory review : an official journal of the European Respiratory Society · 2026Review
- Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression.Cell host & microbe · 2025Article
- Bronchoalveolar lavage fluid metagenomic datasets: a multidimensional clinical biomolecular resource.Scientific data · 2025Article
- Unravelling distinct patterns of metagenomic surveillance and respiratory microbiota between two P1 genotypes ofEmerging microbes & infections · 2025Article
- Extensive diversity of unusual microorganisms associated with severe pneumonia in kidney transplant recipients.PLoS pathogens · 2025Article
- Metagenomic fingerprints in bronchoalveolar lavage differentiate pulmonary diseases.NPJ digital medicine · 2025Article
- Effect of Diet Compositions on Colony Strength Parameters, and the Enzymatic Activity ofInsects · 2025Article
- Enrichment of Streptococcus oralis in respiratory microbiome enhance innate immunity and protects against influenza infection.Signal transduction and targeted therapy · 2025Article
- Microbial contribution to metabolic niche formation varies across the respiratory tract.Cell host & microbe · 2025Article
- Ethanol Inhalation for Respiratory Infections due to Enveloped Viruses.Infectious diseases and therapy · 2025Review
- Nerve- and airway-associated interstitial macrophages mitigate SARS-CoV-2 pathogenesis via type I interferon signaling.Immunity · 2025Article
58 more citing papers are in PubMed but not listed here.
Corrections and comments
- Update of
- Update of
Authors and funding
52 authors at 9 institutions in 2 countries.
Imran SulaimanDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.ORCID http://orcid.org/0000-0003-1992-0280
Matthew ChungSystems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Luis AngelDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.ORCID http://orcid.org/0000-0002-5045-9712
Jun-Chieh J TsayDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.ORCID http://orcid.org/0000-0002-2282-2510
Benjamin G WuDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Stephen T YeungDepartment of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Kelsey KrolikowskiDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Yonghua LiDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Ralf DuerrDepartment of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.ORCID http://orcid.org/0000-0001-9569-9237
Rosemary SchlugerDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Sara A ThannickalDepartment of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.ORCID http://orcid.org/0000-0002-7028-3507
Akiko KoideDepartment of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Samaan RafeqDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Clea BarnettDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Radu PostelnicuDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Chang WangCenter for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, USA.
Stephanie BanakisSystems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Lizzette Pérez-PérezLaboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health Rocky Mountain Laboratories, Hamilton, MT, USA.ORCID http://orcid.org/0000-0001-5881-4363
Guomiao ShenDepartment of Pathology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
George JourDepartment of Pathology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Peter MeynDivision of Pediatrics, Longhua Hospital affiliated to Shanghai University of Chinese Medicine, Shanghai, China.
Joseph CarpenitoDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Xiuxiu LiuDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Kun JiDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Destiny CollazoDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Anthony LabarbieraDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Nancy AmorosoDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Shari BrosnahanDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.ORCID http://orcid.org/0000-0002-2092-3633
Vikramjit MukherjeeDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
David KaufmanDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Jan BakkerDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.ORCID http://orcid.org/0000-0003-2236-7391
Anthony LubinskyDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Deepak PradhanDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Daniel H StermanDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Michael WeidenDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Adriana HeguyDepartment of Pathology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Laura EvansPulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA.
Timothy M UyekiInfluenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA.
Jose C ClementeDepartment of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.ORCID http://orcid.org/0000-0002-3970-9856
Emmie de WitLaboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health Rocky Mountain Laboratories, Hamilton, MT, USA.ORCID http://orcid.org/0000-0002-9763-7758
Ann Marie SchmidtDiabetes 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 ShopsinDivision of Infectious Diseases, Department of Medicine, New York University School of Medicine, NYU Langone Health, New York, NY, USA.
Ludovic DesvignesDepartment of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Chan WangDepartment of Population Health, New York University School of Medicine, NYU Langone Health, New York, NY, USA.
Huilin LiDepartment of Population Health, New York University School of Medicine, NYU Langone Health, New York, NY, USA.
Bin ZhangDepartment 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 ForstDepartment of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.ORCID http://orcid.org/0000-0003-0229-9459
Shohei KoideLaura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY, USA.ORCID http://orcid.org/0000-0001-5473-4358
Kenneth A StaplefordDepartment of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Kamal M KhannaDepartment of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
Elodie GhedinSystems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. elodie.ghedin@nih.gov.ORCID http://orcid.org/0000-0002-1515-725X
Leopoldo N SegalDivision of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA. Leopoldo.Segal@nyumc.org.ORCID http://orcid.org/0000-0003-3559-9431
New York University · USNational Institutes of Health · USNYU Langone Health · USIcahn School of Medicine at Mount Sinai · USShanghai University of Traditional Chinese Medicine · CNVA NY Harbor Healthcare System · USBeijing Hospital of Traditional Chinese Medicine · CNCenters for Disease Control and Prevention · USUniversity of Washington · US
Funding
Vaccine FacilityP30CA016087 · NCI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI Richard Lewis Possemato · 1985 to 2026
$83.1MLocal microbiota signatures of pro-tumor immunity and checkpoint inhibition susceptibility in lung cancerR37CA244775 · NCI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI Leopoldo Nicolas Segal · 2020 to 2026
$4.7MTraining Program in Immunology and Inflammation.T32AI100853 · NIAID · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI Susan Ruth Schwab · 2012 to 2026
$4.5MThe Oral Microbiome and Upper Aerodigestive Squamous Cell CancerR01CA159036 · NCI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI AHN, JIYOUNG, HAYES, RICHARD BERNARD · 2011 to 2024
$3.5MMechanisms of MRSA intestinal colonizationR01AI140754 · NIAID · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI SHOPSIN, BO · 2020 to 2024
$3.5MProject 2P20CA252728 · NCI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI MILLER, GEORGE · 2020 to 2022
$3.4MNovel lung resident interstitial macrophage subset with distinct localization and polarizationR01AI143861 · NIAID · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI KHANNA, KAMAL MOHAN · 2019 to 2023
$3.3MHost-pathogen interactions during hospital adaptation of MRSAR01AI137336 · NIAID · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI SHOPSIN, BO, YANAI, ITAI · 2019 to 2022
$3.3MMicrobial triggers and molecular mechanisms of Th17 mediated airway inflammation-Resubmission-1R01HL125816 · NHLBI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI KORALOV, SERGEI BORISOVICH · 2015 to 2019
$3.3MNovel Statistical Methods in Analyzing Microbiome Data for Longitudinal StudyR01DK110014 · NIDDK · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI LI, HUILIN · 2016 to 2019
$1.5MAccurate prediction of neutralization capacity from deep mining of SARS-CoV-2 serologyR21AI158997 · NIAID · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI KOIDE, SHOHEI · 2020 to 2020
$466kNCI NIH HHS P20 CA252728NCI NIH HHS P30 CA016087NCI NIH HHS R01 CA159036NCI NIH HHS R37 CA244775NHLBI NIH HHS R01 HL125816NIAID NIH HHS R01 AI137336NIAID NIH HHS R01 AI140754NIAID NIH HHS R01 AI143861NIAID NIH HHS R21 AI158997NIAID NIH HHS T32 AI100853NIDDK NIH HHS R01 DK110014
Abstract
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.
Indexed as
Respiration, ArtificialAdaptive ImmunityAdultAgedBacteriaBacterial LoadBronchoalveolar Lavage FluidCOVID-19Critical IllnessFemaleHospitalizationHumansImmunity, InnateMaleMicrobiotaMiddle Aged
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