Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics

Authors

Patricia Buendia, Lifetime Omics, Miami, FL, United States.
Krystal Fernandez, Lifetime Omics, Miami, FL, United States.
Castle Raley, The George Washington University Genomics Core, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States.
Ali Rahnavard, Department of Biostatistics and Bioinformatics, Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States.
Keith A. Crandall, The George Washington University Genomics Core, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States.
Jose Guillermo Castro, Division of Infectious Diseases, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, United States.

Document Type

Journal Article

Publication Date

1-1-2024

Journal

Frontiers in microbiology

Volume

15

DOI

10.3389/fmicb.2024.1346762

Keywords

COVID-19; Candida albicans (C. albicans); Staphylococcus aureus (S. aureus); broad-spectrum antibiotics; hospital antimicrobial stewardship; saliva microbiome; sepsis

Abstract

INTRODUCTION: During the COVID-19 Delta variant surge, the CLAIRE cross-sectional study sampled saliva from 120 hospitalized patients, 116 of whom had a positive COVID-19 PCR test. Patients received antibiotics upon admission due to possible secondary bacterial infections, with patients at risk of sepsis receiving broad-spectrum antibiotics (BSA). METHODS: 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 outcomes were known, patients were classified based on their COVID-19 disease severity and the antibiotics they received. RESULTS: Our study reveals that BSA regimens differentially impacted the human salivary microbiome and disease progression. 12 patients died and all of them received BSA. Significant associations were found between the composition of the COVID-19 saliva microbiome and BSA use, between SARS-CoV-2 genome coverage and severity of disease. We also found significant associations between the non-bacterial microbiome and severity of disease, with detected most frequently in critical patients. For patients who did not receive BSA before saliva sampling, our study suggests as a potential risk factor for sepsis. DISCUSSION: Our results indicate that the course of the infection may be explained by both monitoring antibiotic treatment and profiling a patient's salivary microbiome, establishing a compelling link between microbiome and the specific antibiotic type and timing of treatment. This approach can aid with emergency room triage and inpatient management but also requires a better understanding of and access to narrow-spectrum agents that target pathogenic bacteria.

APA Citation

Buendia, Patricia; Fernandez, Krystal; Raley, Castle; Rahnavard, Ali; Crandall, Keith A.; and Castro, Jose Guillermo, "Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics" (2024). GW Authored Works. Paper 4299.
https://hsrc.himmelfarb.gwu.edu/gwhpubs/4299

Department

Biostatistics and Bioinformatics