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


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.

SUBMITTER: Sulaiman I 

PROVIDER: S-EPMC8484067 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature

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

Sulaiman Imran I   Chung Matthew M   Angel Luis L   Tsay Jun-Chieh J JJ   Wu Benjamin G BG   Yeung Stephen T ST   Krolikowski Kelsey K   Li Yonghua Y   Duerr Ralf R   Schluger Rosemary R   Thannickal Sara A SA   Koide Akiko A   Rafeq Samaan S   Barnett Clea C   Postelnicu Radu R   Wang Chang C   Banakis Stephanie S   Pérez-Pérez Lizzette L   Shen Guomiao G   Jour George G   Meyn Peter P   Carpenito Joseph J   Liu Xiuxiu X   Ji Kun K   Collazo Destiny D   Labarbiera Anthony A   Amoroso Nancy N   Brosnahan Shari S   Mukherjee Vikramjit V   Kaufman David D   Bakker Jan J   Lubinsky Anthony A   Pradhan Deepak D   Sterman Daniel H DH   Weiden Michael M   Heguy Adriana A   Evans Laura L   Uyeki Timothy M TM   Clemente Jose C JC   de Wit Emmie E   Schmidt Ann Marie AM   Shopsin Bo B   Desvignes Ludovic L   Wang Chan C   Li Huilin H   Zhang Bin B   Forst Christian V CV   Koide Shohei S   Stapleford Kenneth A KA   Khanna Kamal M KM   Ghedin Elodie E   Segal Leopoldo N LN  

Nature microbiology 20210831 10


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 resp  ...[more]

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