Abstract
BackgroundSARS-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.MethodsWe 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.ResultsSixteen 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.ConclusionsThese 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.2dzjuyGksUvQmCNGvHhZ1uVideo
Highlights
SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic
Marotz et al Microbiome (2021) 9:132. 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
To exclude the possibility that this Rothia amplicon sequence variants (ASV) was associated with sick patients generally, we examined the prevalence of this ASV in an intensive care unit microbiome study that was performed in 2016 [29] and found that high prevalence of this Rothia ASV is specific to SARS-CoV-2 positive patient samples (Fig. 4D)
Summary
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. Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) is the causative agent of a novel infectious disease, COVID-19, that has reached pandemic proportions. This pandemic has been characterized by sustained human to human transmission and has caused more than 91 million cases and nearly 2 million deaths worldwide (as of 15 January 2020, WHO report). Viruses exist in complex microbial environments, and specific virus-bacterium interactions have been increasingly documented in host-associated contexts. Prevalent bacteria in the human microbiome have been demonstrated to alter the human glycocalyx, thereby modulating the ability of SARS-CoV2 to bind host cells [7]
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