Nature Microbiology

, volume 6 , issue 10 , pages 1245-1258

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

Imran Sulaiman ^{1, 2}

Matthew Chung ³

Luis F. Angel ^{1, 2}

S. B. Koralov ^{1, 2, 4}

Benjamin G. Wu ^{1, 2, 4}

Stephen T Yeung ⁵

Kelsey Krolikowski ^{1, 2}

Yonghua Li ^{1, 2}

Ralf Duerr ⁵

Rosemary Schluger ^{1, 2}

Sara A Thannickal ⁵

Akiko Koide ^{2, 6}

Samaan Rafeq ^{1, 2}

Clea Barnett ^{1, 2}

Radu Postelnicu ^{1, 2}

Chang Wang ⁷

Stephanie Banakis ³

Lizzette Pérez Pérez ⁸

Guomiao Shen ⁹

George Jour ⁹

Peter Meyn ¹⁰

Joseph Carpenito ^{1, 2}

Xiuxiu Liu ^{1, 10}

Kun Ji ^{1, 11}

Destiny Collazo ^{1, 2}

Anthony Labarbiera ^{1, 2}

Nancy Amoroso ^{1, 2}

Shari B. Brosnahan ^{1, 2}

Vikramjit Mukherjee ^{1, 2}

David Kaufman ^{1, 2}

Jan Bakker ^{1, 2}

Anthony Lubinsky ^{1, 2}

Deepak Pradhan ^{1, 2}

Daniel H. Sterman ^{1, 2}

Michael Weiden ^{1, 2}

Adriana Heguy ^{9, 12}

Laura Evans ¹³

Timothy M. Uyeki ¹⁴

Jose C. Clemente ¹⁵

E. A. de Wit ⁸

Ann Marie Schmidt ¹⁶

Bo Shopsin ¹⁷

Ludovic Desvignes ⁵

Chan Wang ¹⁸

Huilin Li ¹⁸

Bin Zhang ¹⁹

Christian V. Forst ¹⁹

S. Koide ^{6, 20}

Kenneth A Stapleford ⁵

Kamal M Khanna ^{5, 6}

Elodie Ghedin ^{3, 7}

Leopoldo N Segal ^{1, 2, 6}

Hide authors affiliations Show authors affiliations: 20 affiliations

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

Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, USA |

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

⁴

Division of Pulmonary and Critical Care Medicine, VA New York Harbor Healthcare System, New York, USA |

⁵

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

⁶

Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, USA |

⁷

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

⁸

Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health Rocky Mountain Laboratories, Hamilton, USA |

⁹

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

¹⁰

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

¹¹

Dongfang Hospital affiliated to Beijing University of Traditional Chinese Medicine, Beijing, China |

¹²

NYU Langone Genome Technology Center, New York University Grossman School of Medicine, NYU Langone Health, New York, USA |

¹³

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

¹⁴

Influenza Division, Centers for Disease Control and Prevention, Atlanta, USA |

¹⁵

Department of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, USA |

¹⁶

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

¹⁷

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

¹⁸

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

¹⁹

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

²⁰

Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, NYU Langone Health, New York, USA |

Publication type: Journal Article

Publication date: 2021-08-31

Springer Nature

Nature Microbiology

scimago Q1

wos Q1

SJR: 6.893

CiteScore: 27.6

Impact factor: 19.4

ISSN: 20585276

DOI: 10.1038/s41564-021-00961-5

Copy DOI

PubMed ID: 34465900

Cell Biology

Genetics

Microbiology (medical)

Microbiology

Applied Microbiology and Biotechnology

Immunology

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. Analysis of lower respiratory tract microbiome of mechanically ventilated COVID-19 patients rules out a role for secondary respiratory infections as drivers of increased mortality.

Found

1 citation

Pena-Lopez Yolanda

32 publications, 424 citations

h-index: 11

University of Texas Southwestern Medical Center

Vall d'Hebron University Hospital

Vall d'Hebron Research Institute

Research interests

Critical care

Microbiome

1 citation

Yan Zheng-Zheng

13 publications, 565 citations, 3 reviews

h-index: 11

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GOST Copy

Sulaiman I. et al. Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome // Nature Microbiology. 2021. Vol. 6. No. 10. pp. 1245-1258.

GOST all authors (up to 50) Copy

RIS |

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RIS Copy

TY - JOUR

DO - 10.1038/s41564-021-00961-5

UR - https://doi.org/10.1038/s41564-021-00961-5

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

T2 - Nature Microbiology

AU - Sulaiman, Imran

AU - Chung, Matthew

AU - Angel, Luis F.

AU - Koralov, S. B.

AU - Wu, Benjamin G.

AU - Yeung, Stephen T

AU - Krolikowski, Kelsey

AU - Li, Yonghua

AU - Duerr, Ralf

AU - Schluger, Rosemary

AU - Thannickal, Sara A

AU - Koide, Akiko

AU - Rafeq, Samaan

AU - Barnett, Clea

AU - Postelnicu, Radu

AU - Wang, Chang

AU - Banakis, Stephanie

AU - Pérez Pérez, Lizzette

AU - Shen, Guomiao

AU - Jour, George

AU - Meyn, Peter

AU - Carpenito, Joseph

AU - Liu, Xiuxiu

AU - Ji, Kun

AU - Collazo, Destiny

AU - Labarbiera, Anthony

AU - Amoroso, Nancy

AU - Brosnahan, Shari B.

AU - Mukherjee, Vikramjit

AU - Kaufman, David

AU - Bakker, Jan

AU - Lubinsky, Anthony

AU - Pradhan, Deepak

AU - Sterman, Daniel H.

AU - Weiden, Michael

AU - Heguy, Adriana

AU - Evans, Laura

AU - Uyeki, Timothy M.

AU - Clemente, Jose C.

AU - de Wit, E. A.

AU - Schmidt, Ann Marie

AU - Shopsin, Bo

AU - Desvignes, Ludovic

AU - Wang, Chan

AU - Li, Huilin

AU - Zhang, Bin

AU - Forst, Christian V.

AU - Koide, S.

AU - Stapleford, Kenneth A

AU - Khanna, Kamal M

AU - Ghedin, Elodie

AU - Segal, Leopoldo N

PY - 2021

DA - 2021/08/31

PB - Springer Nature

SP - 1245-1258

IS - 10

VL - 6

PMID - 34465900

SN - 2058-5276

ER -

BibTex |

Cite this

BibTex (up to 50 authors) Copy

@article{2021_Sulaiman,

author = {Imran Sulaiman and Matthew Chung and Luis F. Angel and S. B. Koralov and Benjamin G. Wu and Stephen T Yeung and Kelsey Krolikowski and Yonghua Li and Ralf Duerr and Rosemary Schluger and Sara A Thannickal and Akiko Koide and Samaan Rafeq and Clea Barnett and Radu Postelnicu and Chang Wang and Stephanie Banakis and Lizzette Pérez Pérez and Guomiao Shen and George Jour and Peter Meyn and Joseph Carpenito and Xiuxiu Liu and Kun Ji and Destiny Collazo and Anthony Labarbiera and Nancy Amoroso and Shari B. Brosnahan and Vikramjit Mukherjee and David Kaufman and Jan Bakker and Anthony Lubinsky and Deepak Pradhan and Daniel H. Sterman and Michael Weiden and Adriana Heguy and Laura Evans and Timothy M. Uyeki and Jose C. Clemente and E. A. de Wit and Ann Marie Schmidt and Bo Shopsin and Ludovic Desvignes and Chan Wang and Huilin Li and Bin Zhang and Christian V. Forst and S. Koide and Kenneth A Stapleford and Kamal M Khanna and others},

title = {Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome},

journal = {Nature Microbiology},

year = {2021},

volume = {6},

publisher = {Springer Nature},

month = {aug},

url = {https://doi.org/10.1038/s41564-021-00961-5},

number = {10},

pages = {1245--1258},

doi = {10.1038/s41564-021-00961-5}

}

MLA

Cite this

MLA Copy

Sulaiman, Imran, et al. “Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome.” Nature Microbiology, vol. 6, no. 10, Aug. 2021, pp. 1245-1258. https://doi.org/10.1038/s41564-021-00961-5.

Publisher

Springer Nature

Journal

Nature Microbiology

scimago Q1

wos Q1

SJR

6.893

CiteScore

27.6

Impact factor

19.4

ISSN

20585276 (Electronic)