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

• DOI: 10.1186/s40168-021-01083-0
• Publication Date: 2021-06-08T15:03:05Z
• Authors: Clarisse Marotz; Pedro Belda-Ferre; Farhana Ali; Promi Das; Shi Huang; Kalen Cantrell; Lingjing Jiang; Cameron Martino; Rachel E. Diner; Gibraan Rahman; Daniel McDonald; George Armstrong; Sho Kodera; Sonya Donato; Gertrude Ecklu-Me...; Neil Gottel; Mariana C. Salas ...; Leslie Y. Chiang; Rodolfo A. Salido; Justin P. Shaffer; Mac Kenzie Bryant; Karenina Sanders; Greg Humphrey; Gail Ackermann; Niina Haiminen; Kristen L. Beck; Ho-Cheol Kim; Anna Paola Carrieri; Laxmi Parida; Yoshiki Vázquez-B...; Francesca J. Torr...; Rob Knight; Jack Gilbert; Daniel A. Sweeney; Sarah M. Allard
• Keywords: Infectivity; Amplicon sequencing; Amplicon

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 antagonistic effects of specific bacterial taxa on viral prevalence infectivity. We set out to test whether communities predict occurrence a hospital setting.We collected 972 samples from hospitalized patients with COVID-19, their health care providers, surfaces before, during, after admission. screened using RT-qPCR, characterized 16S rRNA gene amplicon sequencing, used these profiles classify detection random forest model.Sixteen percent COVID-19 patient rooms had detectable RNA, although infectivity was not assessed. The highest floor next beds (39%) directly outside (29%). Although bed rail more closely resembled microbiome compared samples, detected less often (11%). positive higher phylogenetic diversity human surface biomass samples. community enabled high classifier accuracy status only nares, but also forehead, stool, Across distinct profiles, single sequence variant genus Rothia strongly predicted presence across sample types, greater even when other intensive units prior pandemic.These results contextualize vast niches where identify that associate host environment. Video Abstract.