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

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 Candida albicans detected most frequently in critical patients. For patients who did not receive BSA before saliva sampling, our study suggests Staphylococcus aureus 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.

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

FIGURE 1

Alpha and Beta diversity associated with broad-spectrum sepsis antibiotics (BSA). (A) Alpha diversity boxplots for the COVID-19 groups, moderate (M) and critical (C) COVID-19 groups stratified by BSA timing [BSA before or same day as saliva sampling: Yes (Y), No (N)]. (B) Beta diversity with COVID-19 groups, as before, stratified by BSA timing. (C) Phyla abundance plot.

FIGURE 2

Alpha diversity and clinical characteristics. (A) Associations between alpha diversity and sample clinical information (x-axis) and statistical significance (–log(p-value)–y-axis) with a horizontal red line showing the –log(0.05) cutoff for significance. With age, BSA and early BSA showing significance, we show alpha diversity against the categorizations of each of these clinical variables, namely, (B) Age, (C) BSA, and (D) early BSA.

FIGURE 3

Bacterial associations across COVID-19 groups, FP, Controls. (A) Top bacteria found in a comparison of the bacterial microbiome composition between the two COVID-19 groups (severe, moderate), the False Positives (FP), and the control group (healthy individuals) using control as reference. (B–E) Show specific significance tests for those bacterial species found to be significantly different between controls and our three case groups.

FIGURE 4

Accuracy of predicting disease severity by microbial species. (A) Random forest analysis of the decrease in accuracy (x-axis) of predicting disease severity with the removal of individual species (y-axis). A higher mean decrease accuracy value indicates the importance of that species in predicting severity of disease (moderate vs. critical). (B) Because Candida albicans was the most important species with respect to disease prediction, we further examined this taxon via a Box and Whisker plot to show individual data points.

FIGURE 5

Antimicrobial resistance for specific antibiotics by broad-spectrum sepsis antibiotic (BSA) timing. Heatmap of samples with antimicrobial resistance to single drug classes grouped by BSA timing.

FIGURE 6

Analysis of broad-spectrum sepsis antibiotic (BSA) classification by bacterial functional group. Significant pathways identified through bacterial functional analysis relative to BSA status with y-axis length or area of each colored segment showing the relative abundance of a taxonomic group in the given pathway: (A) L-methionine biosynthesis II pathway that was preferentially enriched in the Early BSA samples. (B) L-cysteine biosynthesis VI pathways were also enriched in the Early BSA samples.