| Popis: |
During the COVID-19 Delta variant surge, the CLAIRE cross-sectional study sampled saliva from 120 hospitalized patients, 116 of them with a positive COVID-19 PCR test. Patients received antibiotics upon admission due to possible secondary bacterial infections, with patients at risk of sepsis receiving more potent antibiotics. The saliva samples were analyzed with shotgun DNA metagenomics and respiratory RNA virome sequencing. Medical records for the period of hospitalization were obtained for all patients. Once hospitalization outcome was known, patients were classified based on their COVID-19 disease severity and their sepsis-related antibiotic treatment. 12 patients passed away with all 12 having received sepsis treatment. Significant associations were found between the composition of the COVID-19 saliva microbiome and broad-spectrum antibiotic use, between SARS-CoV-2 genome coverage and severity of disease, and between the non-bacterial microbiome and severity of disease, with Candida albicans, the most significantly elevated fungus in critical patients. Our results suggest a use of the saliva microbiome as a biomarker that aids with emergency room triage and suggests the need to develop narrow-spectrum agents that target pathogenic bacteria. |
