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

Microbiome

Ho-Cheol Kim¹  Kristen L. Beck¹  Yoshiki Vázquez-Baeza²  Kalen Cantrell³  Lingjing Jiang⁴  Mac Kenzie Bryant⁵  Karenina Sanders⁵  Greg Humphrey⁵  Gail Ackermann⁵  Leslie Y. Chiang⁵  Daniel McDonald⁵  Justin P. Shaffer⁵  Farhana Ali⁵  Gibraan Rahman⁶  Pedro Belda-Ferre⁷  Shi Huang⁷  George Armstrong⁸  Cameron Martino⁸  Rob Knight⁹  Gertrude Ecklu-Mensah^1,10  Rachel E. Diner^1,10  Sho Kodera^1,10  Neil Gottel^1,10  Clarisse Marotz^1,10  Mariana C. Salas Garcia^1,10  Promi Das^1,10  Sarah M. Allard^1,10  Jack Gilbert^1,11  Daniel A. Sweeney^1,12  Anna Paola Carrieri^1,13  Laxmi Parida^1,14  Niina Haiminen^1,14  Francesca J. Torriani^1,15  Rodolfo A. Salido^1,15  Sonya Donato^1,16 

[1] AI and Cognitive Software, IBM Research-Almaden, San Jose, CA, USA;Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA;Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA;Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA;Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA;Division of Biostatistics, University of California, San Diego, La Jolla, CA, USA;Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA;Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA;Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA;Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA;Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA;Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA;Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA;Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA;Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA;Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA;Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA;Department of Bioengineering, University of California San Diego, La Jolla, CA, USA;Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA;Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA;Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA;Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA;Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA;Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California San Diego, La Jolla, CA, USA;IBM Research UK, The Hartree Centre, Warrington, UK;IBM, T.J Watson Research Center, Yorktown Heights, New York, USA;Infection 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;Microbiome Core, School of Medicine, University of California San Diego, La Jolla, CA, USA;

关键词: Built environment;    SARS-CoV-2;    16S rRNA;    Microbiome;    COVID-19;   

DOI  :  10.1186/s40168-021-01083-0

来源: Springer

【 摘 要 】

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 Abstract

【 授权许可】

CC BY