Dataset Information

Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment.

ABSTRACT: Synergistic effects of bacteria on viral stability and transmission are widely documented but remain unclear in the context of SARS-CoV-2. We collected 972 samples from hospitalized ICU patients with coronavirus disease 2019 (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 contextualized the massive microbial diversity in this dataset in a meta-analysis of over 20,000 samples. Sixteen percent of surfaces from COVID-19 patient rooms were positive, with the highest prevalence in floor samples next to patient beds (39%) and directly outside their rooms (29%). Although bed rail samples increasingly resembled the patient microbiome throughout their stay, SARS-CoV-2 was less frequently detected there (11%). Despite surface contamination in almost all patient rooms, no health care workers providing COVID-19 patient care contracted the disease. SARS-CoV-2 positive samples had higher bacterial phylogenetic diversity across human and surface samples, and higher biomass in floor samples. 16S microbial community profiles allowed for 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 was highly predictive of SARS-CoV-2 across sample types, and had higher prevalence in positive surface and human samples, even when comparing to samples from patients in another intensive care unit prior to the COVID-19 pandemic. These results suggest that bacterial communities contribute to viral prevalence both in the host and hospital environment.

SUBMITTER: Marotz C

PROVIDER: S-EPMC7685343 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment.

Marotz Clarisse C Belda-Ferre Pedro P Ali Farhana F Das Promi P Huang Shi S Cantrell Kalen K Jiang Lingjing L Martino Cameron C Diner Rachel E RE Rahman Gibraan G McDonald Daniel D Armstrong George G Kodera Sho S Donato Sonya S Ecklu-Mensah Gertrude G Gottel Neil N Garcia Mariana C Salas MCS Chiang Leslie Y LY Salido Rodolfo A RA Shaffer Justin P JP Bryant MacKenzie M Sanders Karenina K Humphrey Greg G Ackermann Gail G Haiminen Niina N Beck Kristen L KL Kim Ho-Cheol HC Carrieri Anna Paola AP Parida Laxmi L Vázquez-Baeza Yoshiki Y Torriani Francesca J FJ Knight Rob R Gilbert Jack A JA Sweeney Daniel A DA Allard Sarah M SM

medRxiv : the preprint server for health sciences 20201122

Synergistic effects of bacteria on viral stability and transmission are widely documented but remain unclear in the context of SARS-CoV-2. We collected 972 samples from hospitalized ICU patients with coronavirus disease 2019 (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 contextualized the massive microbial diversity in th ...[more]

PMID: 33236030

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Project description: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. Video Abstract.

Project description:BackgroundRacial and ethnic minority groups experience a disproportionate burden of SARS-CoV-2 illness and studies suggest that cancer patients are at a particular risk for severe SARS-CoV-2 infection.AimsThe objective of this study was examine the association between neighborhood characteristics and SARS-CoV-2 infection among patients with cancer.Methods and resultsWe performed a cross-sectional study of New York City residents receiving treatment for cancer at a tertiary cancer center. Patients were linked by their address to data from the US Census Bureau's American Community Survey and to real estate tax data from New York's Department of City Planning. Models were used to both to estimate odds ratios (ORs) per unit increase and to predict probabilities (and 95% CI) of SARS-CoV2 infection. We identified 2350 New York City residents with cancer receiving treatment. Overall, 214 (9.1%) were infected with SARS-CoV-2. In adjusted models, the percentage of Hispanic/Latino population (aOR = 1.01; 95% CI, 1.005-1.02), unemployment rate (aOR = 1.10; 95% CI, 1.05-1.16), poverty rates (aOR = 1.02; 95% CI, 1.0002-1.03), rate of >1 person per room (aOR = 1.04; 95% CI, 1.01-1.07), average household size (aOR = 1.79; 95% CI, 1.23-2.59) and population density (aOR = 1.86; 95% CI, 1.27-2.72) were associated with SARS-CoV-2 infection.ConclusionAmong cancer patients in New York City receiving anti-cancer therapy, SARS-CoV-2 infection was associated with neighborhood- and building-level markers of larger household membership, household crowding, and low socioeconomic status.Novelty and impactWe performed a cross-sectional analysis of residents of New York City receiving treatment for cancer in which we linked subjects to census and real estate date. This linkage is a novel way to examine the neighborhood characteristics that influence SARS-COV-2 infection. We found that among patients receiving anti-cancer therapy, SARS-CoV-2 infection was associated with building and neighborhood-level markers of household crowding, larger household membership, and low socioeconomic status. With ongoing surges of SARS-CoV-2 infections, these data may help in the development of interventions to decrease the morbidity and mortality associated with SARS-CoV-2 among cancer patients.

Dataset Information

Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment.

Publications

Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment.

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