SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

Abstract

Background SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic and antagonistic effects of specific bacterial taxa on viral prevalence and infectivity. We set out to test whether specific bacterial communities predict SARS-CoV-2 occurrence in a hospital setting. Methods We collected 972 samples from hospitalized patients with COVID-19, their health care providers, and hospital surfaces before, during, and after admission. We screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities using 16S rRNA gene amplicon sequencing, and used these bacterial profiles to classify SARS-CoV-2 RNA detection with a random forest model. Results Sixteen percent of surfaces from COVID-19 patient rooms had detectable SARS-CoV-2 RNA, although infectivity was not assessed. The highest prevalence was in floor samples next to patient beds (39%) and directly outside their rooms (29%). Although bed rail samples more closely resembled the patient microbiome compared to floor samples, SARS-CoV-2 RNA was detected less often in bed rail samples (11%). SARS-CoV-2 positive samples had higher bacterial phylogenetic diversity in both human and surface samples and higher biomass in floor samples. 16S microbial community profiles enabled high classifier accuracy for SARS-CoV-2 status in not only nares, but also forehead, stool, and floor samples. Across these distinct microbial profiles, a single amplicon sequence variant from the genus Rothia strongly predicted SARS-CoV-2 presence across sample types, with greater prevalence in positive surface and human samples, even when compared to samples from patients in other intensive care units prior to the COVID-19 pandemic. Conclusions These results contextualize the vast diversity of microbial niches where SARS-CoV-2 RNA is detected and identify specific bacterial taxa that associate with the viral RNA prevalence both in the host and hospital environment.

Dysbiosis and structural disruption of the respiratory microbiota in COVID-19 patients with severe and fatal outcomes

“…Additionally, we found Rothia dentocariosa very abundant in deceased patients. This bacteria has been found as a causative agent of secondary pneumonia in H1N1 infection 33 and more recently has been associated with disease progression in previous studies characterizing the respiratory microbiota of COVID-19, proposing it as a biomarker for the disease 26 , 42 .…”

Analysis of the upper respiratory tract microbiota in mild and severe COVID-19 patients

“…In [13] this genus was described as a major taxon in one of the throat microbial community types represented in patients but not in healthy controls. In another study, ASV identical to 16S rRNA of Rothia dentocariosa was found to be overrepresented in samples from COVID-19 patients [41]. There is also at least one published work describing the lower abundance of Rothia species in COVID-19 patients [42].…”

Analysis of SARS-CoV-2 RNA Persistence across Indoor Surface Materials Reveals Best Practices for Environmental Monitoring Programs

“…Viral signatures have been demonstrated to persist up to 4 weeks in bulk floor dust collected from a room with a quarantined individual ( 6 ). Previous environmental monitoring studies have detected SARS-CoV-2 on surfaces contaminated by infected individuals in hospitals and congregate care facilities ( 6 – 10 ). Thus, indoor surface sampling can be valuable for detection of infected persons indoors, where transmission risk is highest ( 11 ).…”