Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients

Cell Discovery

Weijun Chen¹  Xun Xu²  Fangming Yang²  Zhun Shi²  Jiandong Li²  Huanming Yang²  Daxi Wang²  Peidi Ren²  Shida Zhu²  Jian Wang²  Huanzi Zhong²  Jiahui Zhu²  Huahui Ren²  Karsten Kristiansen²  Fuqiang Li²  Tianzhu Liang²  Junhua Li²  Fei Xiao³  Hein Min Tun⁴  Lu Zhang⁵  Mian Gan⁶  Airu Zhu⁶  Feng Ye⁶  Jingxian Zhao⁶  Nanshan Zhong⁶  Yi-min Li⁶  Yanqun Wang⁶  Zhaoyong Zhang⁶  Weiqun He⁶  Jincun Zhao⁶  Fang Li⁶  Bei Zhong⁷  Shicong Ruan⁸ 

[1] BGI Education Center, University of Chinese Academy of Sciences;BGI-Shenzhen;Department of Infectious Diseases, Guangdong Provincial Key Laboratory of Biomedical Imaging, Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University;HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong;Institute of Infectious disease, Guangzhou Eighth People’s Hospital of Guangzhou Medical University;State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University;The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital;Yangjiang People’s Hospital;

DOI  :  10.1038/s41421-021-00257-2

来源: DOAJ

【 摘 要 】

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of Coronavirus disease 2019 (COVID-19). However, the microbial composition of the respiratory tract and other infected tissues as well as their possible pathogenic contributions to varying degrees of disease severity in COVID-19 patients remain unclear. Between 27 January and 26 February 2020, serial clinical specimens (sputum, nasal and throat swab, anal swab and feces) were collected from a cohort of hospitalized COVID-19 patients, including 8 mildly and 15 severely ill patients in Guangdong province, China. Total RNA was extracted and ultra-deep metatranscriptomic sequencing was performed in combination with laboratory diagnostic assays. We identified distinct signatures of microbial dysbiosis among severely ill COVID-19 patients on broad spectrum antimicrobial therapy. Co-detection of other human respiratory viruses (including human alphaherpesvirus 1, rhinovirus B, and human orthopneumovirus) was demonstrated in 30.8% (4/13) of the severely ill patients, but not in any of the mildly affected patients. Notably, the predominant respiratory microbial taxa of severely ill patients were Burkholderia cepacia complex (BCC), Staphylococcus epidermidis, or Mycoplasma spp. (including M. hominis and M. orale). The presence of the former two bacterial taxa was also confirmed by clinical cultures of respiratory specimens (expectorated sputum or nasal secretions) in 23.1% (3/13) of the severe cases. Finally, a time-dependent, secondary infection of B. cenocepacia with expressions of multiple virulence genes was demonstrated in one severely ill patient, which might accelerate his disease deterioration and death occurring one month after ICU admission. Our findings point to SARS-CoV-2-related microbial dysbiosis and various antibiotic-resistant respiratory microbes/pathogens in hospitalized COVID-19 patients in relation to disease severity. Detection and tracking strategies are needed to prevent the spread of antimicrobial resistance, improve the treatment regimen and clinical outcomes of hospitalized, severely ill COVID-19 patients.

【 授权许可】

Unknown