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

Microbiome
Clarisse MarotzSarah M Allard

Abstract

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. 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. 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 ...Continue Reading

References

Apr 2, 2003·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·M BoudewijnsR Cartuyvels
May 12, 2007·Journal of the Formosan Medical Association = Taiwan Yi Zhi·Chin-Ying YangLi-Min Huang
Dec 17, 2009·BMC Microbiology·Egija ZauraWim Crielaard
Feb 26, 2010·The ISME Journal·Melissa L Wos-OxleyDietmar H Pieper
Jul 19, 2011·Nature Methods·Dan KnightsScott T Kelley
Mar 22, 2014·PloS One·Jens KeilwagenJan Grau
Apr 30, 2016·Science·Gwen FalonyJeroen Raes
Sep 8, 2016·MSphere·Daniel McDonaldPaul E Wischmeyer
May 26, 2017·Science Translational Medicine·Simon LaxJack A Gilbert
Nov 2, 2017·Nature·Luke R ThompsonUNKNOWN Earth Microbiome Project Consortium
Dec 7, 2017·PLoS Pathogens·Angela K BergerBernardo A Mainou
Jan 2, 2018·Cell Host & Microbe·Andrea K EricksonJulie K Pfeiffer
Apr 21, 2018·MicrobiologyOpen·Sylvia I PavlovaLin Tao
May 26, 2018·MSystems·Daniel McDonaldRob Knight
Aug 22, 2018·Nature Reviews. Microbiology·Jack A Gilbert, Brent Stephens
Sep 7, 2018·Frontiers in Microbiology·Imen NouiouiMarkus Göker
Sep 22, 2018·Molecular Ecology Resources·Laura M BergnerDaniel G Streicker
Oct 3, 2018·Nature Methods·Antonio GonzalezRob Knight
Nov 1, 2018·Nature Methods·Daniel McDonaldRob Knight
Feb 13, 2019·ELife·Thomas Sb SchmidtPeer Bork
Feb 26, 2019·MSystems·Cameron MartinoKarsten Zengler
May 28, 2019·BioTechniques·Clarisse MarotzRob Knight
Jul 26, 2019·Nature Biotechnology·Evan BolyenJ Gregory Caporaso
Nov 9, 2019·BMC Biology·Christina KumpitschChristine Moissl-Eichinger
Jan 30, 2020·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Victor M CormanChristian Drosten
Mar 7, 2020·Infection Control and Hospital Epidemiology : the Official Journal of the Society of Hospital Epidemiologists of America·Vincent C C ChengKwok-Yung Yuen
Mar 18, 2020·The New England Journal of Medicine·Neeltje van DoremalenVincent J Munster
May 4, 2020·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·E Durante-MangoniR Zampino
May 4, 2020·The Journal of Infection·Guangming YeXinghuan Wang
May 6, 2020·World Journal of Clinical Cases·Shi-Yan RenRong-Ding Gao
May 15, 2020·American Journal of Infection Control·Songjie WuYiping Mao
May 15, 2020·Nature·Sin Fun SiaHui-Ling Yen
May 16, 2020·Frontiers in Public Health·Jian-Min JinJin-Kui Yang
May 31, 2020·Nature Communications·Po Ying ChiaUNKNOWN Singapore 2019 Novel Coronavirus Outbreak Research Team
Jun 5, 2020·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Silan GuLanjuan Li

❮ Previous
Next ❯

Software Mentioned

CFX384 Real - Time System ( BIO - RAD )
R caret package
SourceTracker2
crossRanger
R ranger package
PERMANOVA
R PRROC
RDA
EMPress

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

MedRxiv : the Preprint Server for Health Sciences
Clarisse MarotzSarah M Allard
International Journal of Environmental Research and Public Health
Hana MlejnkovaEva Juranova
© 2021 Meta ULC. All rights reserved