Evidence map›Paper›PMID 33236030›Full record

ArticlemedRxiv : the preprint server for health sciences2020

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

Clarisse Marotz, Pedro Belda-Ferre, Farhana Ali, Promi Das, Shi Huang, Kalen Cantrell, Lingjing Jiang, Cameron Martino, Rachel E Diner, Gibraan Rahman and 25 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in medRxiv : the preprint server for health sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

35 authors.

Clarisse MarotzDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Pedro Belda-FerreDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Farhana AliDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Promi DasDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Shi HuangDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Kalen CantrellCenter for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA.
Lingjing JiangCenter for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA.
Cameron MartinoDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Rachel E DinerDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Gibraan RahmanDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Daniel McDonaldDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
George ArmstrongDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Sho KoderaDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Sonya DonatoMicrobiome Core, School of Medicine, University of California San Diego, La Jolla, California, USA.
Gertrude Ecklu-MensahDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Neil GottelDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Mariana C Salas GarciaDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Leslie Y ChiangDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Rodolfo A SalidoDepartment of Bioengineering, University of California San Diego, La Jolla, California, USA.
Justin P ShafferDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
MacKenzie BryantDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Karenina SandersDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Greg HumphreyDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Gail AckermannDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Niina HaiminenIBM, T.J Watson Research Center, Yorktown Heights, New York, USA.
Kristen L BeckAI and Cognitive Software, IBM Research-Almaden, San Jose, California, USA.
Ho-Cheol KimAI and Cognitive Software, IBM Research-Almaden, San Jose, California, USA.
Anna Paola CarrieriAI and Cognitive Software, IBM Research-Almaden, San Jose, California, USA.
Laxmi ParidaAI and Cognitive Software, IBM Research-Almaden, San Jose, California, USA.
Yoshiki Vázquez-BaezaCenter for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA.
Francesca J TorrianiInfection Prevention and Clinical Epidemiology Unit at UC San Diego Health, Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego, San Diego CA, USA.
Rob KnightDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Jack A GilbertDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.
Daniel A SweeneyDivision of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California San Diego, La Jolla, California, USA.
Sarah M AllardDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.

Funding

UCSD/SDSU IRACDAK12GM068524 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI TREJO, JOANN · 2003 to 2025
$24.4M
San Diego Digestive Diseases Research CenterP30DK120515 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Bernd G. Schnabl · 2019 to 2026
$10.8M
Mapping host-microbe-metabolite interactions in 3D to find diet-derived enhancers of immunityDP1AT010885 · NCCIH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI KNIGHT, ROB · 2019 to 2023
$5.5M
NCCIH NIH HHS DP1 AT010885NIDDK NIH HHS P30 DK120515NIGMS NIH HHS K12 GM068524
6 · The paper itself

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.

Identifiers

PMID33236030
PMCPMC7685343

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.