82 the Oropharyngeal Microbiome Predicts Need for Respiratory Support among COVID-19 Patients

The clinical course and severity of infection with respiratory viruses such as SARS-CoV-2, the causative agent of COVID-19, are hypothesized to be affected by the microbes colonizing the upper airway, also known as the oropharyngeal microbiome, where they first establish infection. To determine how the oropharyngeal microbiome interacts SARS-CoV-2 and if it affects the clinical course of COVID-19, we carried out a study of the oropharyngeal microbiome of patients presenting to the emergency department or on the admission wards with symptoms of COVID-19. We collected oral swabs and clinical data regarding COVID-19 severity including need for respiratory support and mortality. Nucleic acids were extracted from oral swabs and high- throughput metagenomic sequencing was performed on extracted DNA. Out of a total of 115 enrolled patients with complete data, 51 had a laboratory confirmed diagnosis of acute COVID-19 and 40 went on to require some respiratory support. We analyzed the relative abundance of detected organisms in individuals who were COVID-19+ versus COVID-19- and used mixed-effect random forest modeling to identify microbiota and clinical covariates that associated with the need for respiratory support among COVID-19+ subjects. We found 19 species that were significantly different among COVID-19+/ COVID-19– patients, most notably, several Actinomyces species showed significant increases among COVID-19+ patients. We found that among COVID- 19+ patients, microbiome features were highly correlated with need for respiratory support (F1 score 0.876). The contributions of microbiome features such as relative abundances of Prevotella salivae, Campylobacter concisus, and Veillonella infantium as well as the Shannon Diversity Index this model approximated the importance of clinical factors known to contribute to risk for severe COVID-19 such as body mass index (BMI) and age. The composition of the oropharyngeal microbiome may represent a target for diagnostics in the ED to aid in the determination of who is likely to suffer respiratory failure and require oxygen support.