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

• DOI: 10.1038/s41564-021-00961-5
• Publication Date: 2021-08-31T10:03:02Z
• Authors: Imran Sulaiman; Matthew Chung; Luis Angel; Jun-Chieh J. Tsay; Benjamin G. Wu; Stephen T. Yeung; Kelsey Krolikowski; Yonghua Li; Ralf Duerr; Rosemary Schluger; Sara A. Thannickal; Akiko Koide; Samaan Rafeq; Clea Barnett; Radu Postelnicu; Chang Wang; Stephanie Banakis; Lizzette Pérez-Pérez; Guomiao Shen; George Jour; Peter Meyn; Joseph Carpenito; Xiuxiu Liu; Kun Ji; Destiny Collazo; Anthony Labarbiera; Nancy Amoroso; Shari Brosnahan; Vikramjit Mukherjee; David Kaufman; Jan Bakker; Anthony Lubinsky; Deepak Pradhan; Daniel H. Sterman; Michael Weiden; Adriana Heguy; Laura Evans; Timothy M. Uyeki; Jose C. Clemente; Emmie de Wit; Ann Marie Schmidt; Bo Shopsin; Ludovic Desvignes; Chan Wang; Huilin Li; Bin Zhang; Christian V. Forst; Shohei Koide; Kenneth A. Staple...; Kamal M. Khanna; Elodie Ghedin; Leopoldo N. Segal
• Keywords: Respiratory tract

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 poor outcome of a prospective, observational cohort 589 critically ill adults, all whom required mechanical ventilation. For subset 142 patients who underwent bronchoscopy, we quantified SARS-CoV-2 viral load, analysed the tract microbiome using metagenomics and metatranscriptomics profiled host immune response. Acquisition hospital-acquired pathogen was not fatal Poor enrichment an oral commensal (Mycoplasma salivarium). Increased abundance, low anti-SARS-CoV-2 antibody response distinct transcriptome profile airways most predictive mortality. Our data provide evidence that secondary do drive management strategies should prioritize reducing replication maximizing responses SARS-CoV-2. Analysis mechanically ventilated rules out role for as drivers