Prognostic biomarkers of disease severity for patients infected with coronavirus covid-19

SESSION TITLE: Chest Infections COVID 19: Adding Salt to the Wound SESSION TYPE: Original Investigations PRESENTED ON: 10/08/2023 08:15 am - 09:15 am PURPOSE: Identifying patients at risk for severe complications (i.e., respiratory failure, shock, or multiorgan dysfunction) following COVID-19 infection represents a critical challenge. Emerging evidence suggests that the microbiota in various body sites, including the oropharynx, upper airways, and gut, play a critical role in the development and progression of these complications. We hypothesize that understanding the shift in microbial populations in the oropharynx, upper airways, and gut of patients with severe coronavirus infection has the potential to identify pathways involved in the development of more severe complications of viral infection and predict disease severity. METHODS: Stool, oral, and nasal samples collected from COVID-19 patients admitted at the University of Maryland Medical Center between January 2021-June 2021 were characterized using whole community shotgun metagenomic sequencing on Illumina HiSeq NovaSeq 4000 6000 platform. Clinical factors including ICU status, survival, and use of ventilator were correlated with microbiome characteristics. MetaPhlAn was used to profile the composition and structure of the microbiome of the samples at high taxonomic resolution. The PhyloSeq R package was employed to evaluate community alpha diversity, and LEfSe DESeq2 was used to determine biomarkers significantly different by clinical features. RESULTS: The stool samples of patients with severe cases, admitted to the ICU, had significantly more Parasutterella, Odoribacter, Staphylococcus, and Sellimonas, all of which have been previously implicated in dysbiotic conditions. The oral microbiome of patients who required mechanical ventilation demonstrated increased abundance of Staphylococcus and Enterococcus, both of which generally attach to skin and mucous membranes but also can be aerosolized. Patients with COVID pneumonia requiring supplemental oxygen demonstrated significantly lower community biodiversity in both the GI tract and oral cavity. CONCLUSIONS: Patients admitted with severe COVID infection had lower microbiome diversity and significantly altered microbial community composition and structure. Our data indicates COVID-19 infection imposes a systemic influence on the body and changes in the gut and oral microbiome may represent an indicator of disease severity. CLINICAL IMPLICATIONS: Our study has the potential to identify biomarkers of disease progression and severity, that also promote local immune activation and contribute to the high rates of death in COVID patients. These results allow us to plan tests of microbiota-based actionable targets for diagnostic applications and guide new treatments for patients with severe disease. DISCLOSURES: No relevant relationships by Etse Gebru No relevant relationships by Bing Ma No relevant relationships by Jay Magaziner No disclosure on file for Dean Mann No relevant relationships by Uday Nanavaty No relevant relationships by Alice Ryan No relevant relationships by Jawad Shabani No relevant relationships by Matthew Simpson No relevant relationships by Dalwinder Singh-Basra No disclosure on file for Yang Song No relevant relationships by Michael Terrin No relevant relationships by Irina Timofte No relevant relationships by Anu Varghese No relevant relationships by Yuji Zhang