Department of Microbiology and Physiological Systems; Program of Microbiome Dynamics; Department of Medicine, Division of Infectious Diseases and Immunology; Department of Internal Medicine; Department of Pediatrics; School of Medicine; Graduate School of Biomedical Sciences
Bacteria | Environmental Public Health | Immunology of Infectious Disease | Immunopathology | Infectious Disease | Medical Microbiology | Microbiology | Virus Diseases
The reason for the striking differences in clinical outcomes of SARS-CoV-2 infected patients is still poorly understood. While most recover, a subset of people become critically ill and succumb to the disease. Thus, identification of biomarkers that can predict the clinical outcomes of COVID-19 disease is key to help prioritize patients needing urgent treatment. Given that an unbalanced gut microbiome is a reflection of poor health, we aim to identify indicator species that could predict COVID-19 disease clinical outcomes. Here, for the first time and with the largest COVID-19 patient cohort reported for microbiome studies, we demonstrated that the intestinal and oral microbiome make-up predicts respectively with 92% and 84% accuracy (Area Under the Curve or AUC) severe COVID-19 respiratory symptoms that lead to death. The accuracy of the microbiome prediction of COVID-19 severity was found to be far superior to that from training similar models using information from comorbidities often adopted to triage patients in the clinic (77% AUC). Additionally, by combining symptoms, comorbidities, and the intestinal microbiota the model reached the highest AUC at 96%. Remarkably the model training on the stool microbiome found enrichment of Enterococcus faecalis, a known pathobiont, as the top predictor of COVID-19 disease severity. Enterococcus faecalis is already easily cultivable in clinical laboratories, as such we urge the medical community to include this bacterium as a robust predictor of COVID-19 severity when assessing risk stratification of patients in the clinic.
SARS-CoV-2, biomarkers, intestinal and oral microbiome, COVID-19 severity, Enterococcus faecalis, predictor, risk stratification, microbiome prediction
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DOI of Published Version
medRxiv 2021.01.05.20249061; doi: https://doi.org/10.1101/2021.01.05.20249061. Link to preprint on medRxiv.
Ward DV, Bhattarai S, Rojas-Correa M, Purkayastha A, Holler D, Qu M, Mitchell WG, Yang JD, Fountain S, Zeamer A, Forconi C, Fujimori G, Odwar B, Cawley C, McCormick BA, Moormann AM, Wessolossky M, Bucci V, Maldonado-Contreras A. (2021). The Intestinal and Oral Microbiomes Are Robust Predictors of COVID-19 Severity the Main Predictor of COVID-19-related Fatality [preprint]. UMass Chan Medical School Faculty Publications. https://doi.org/10.1101/2021.01.05.20249061. Retrieved from https://escholarship.umassmed.edu/faculty_pubs/1889
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