Microbial signatures in the lower airways of mechanically ventilated COVID19 patients associated with poor clinical outcome

• DOI: 10.1101/2021.02.23.21252221
• Publication Date: 2021-02-24T10:30:41Z
• 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 Perez-Perez; George Jour; Guomiao Shen; 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 Hegu; 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: Infectivity; Rhinovirus

Abstract Mortality among patients with COVID-19 and respiratory failure is high there are no known lower airway biomarkers that predict clinical outcome. We investigated whether bacterial infections viral load were associated poor outcome host immune tone. obtained fungal culture data from 589 critically ill subjects requiring mechanical ventilation. On a subset of the underwent bronchoscopy, we also quantified SARS-CoV-2 load, analyzed microbiome airways by metagenome metatranscriptome analyses profiled response. found isolation hospital-acquired pathogen was not fatal However, enrichment microbiota an oral commensal ( Mycoplasma salivarium ), while burden, anti-SARS-CoV-2 antibody response, together unique transcriptome profile most predictive mortality. Collectively, these support hypothesis 1) extent infectivity drives mortality in severe COVID-19, therefore 2) management strategies targeting replication responses to should be prioritized.