Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients
Research output: Contribution to journal › Journal article › Research › peer-review
Standard
Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients. / Zhong, Huanzi; Wang, Yanqun; Shi, Zhun; Zhang, Lu; Ren, Huahui; He, Weiqun; Zhang, Zhaoyong; Zhu, Airu; Zhao, Jingxian; Xiao, Fei; Yang, Fangming; Liang, Tianzhu; Ye, Feng; Zhong, Bei; Ruan, Shicong; Gan, Mian; Zhu, Jiahui; Li, Fang; Li, Fuqiang; Wang, Daxi; Li, Jiandong; Ren, Peidi; Zhu, Shida; Yang, Huanming; Wang, Jian; Kristiansen, Karsten; Tun, Hein Min; Chen, Weijun; Zhong, Nanshan; Xu, Xun; Li, Yi-min; Li, Junhua; Zhao, Jincun.
In: Cell Discovery, Vol. 7, 23, 2021.Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
APA
Vancouver
Author
Bibtex
}
RIS
TY - JOUR
T1 - Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients
AU - Zhong, Huanzi
AU - Wang, Yanqun
AU - Shi, Zhun
AU - Zhang, Lu
AU - Ren, Huahui
AU - He, Weiqun
AU - Zhang, Zhaoyong
AU - Zhu, Airu
AU - Zhao, Jingxian
AU - Xiao, Fei
AU - Yang, Fangming
AU - Liang, Tianzhu
AU - Ye, Feng
AU - Zhong, Bei
AU - Ruan, Shicong
AU - Gan, Mian
AU - Zhu, Jiahui
AU - Li, Fang
AU - Li, Fuqiang
AU - Wang, Daxi
AU - Li, Jiandong
AU - Ren, Peidi
AU - Zhu, Shida
AU - Yang, Huanming
AU - Wang, Jian
AU - Kristiansen, Karsten
AU - Tun, Hein Min
AU - Chen, Weijun
AU - Zhong, Nanshan
AU - Xu, Xun
AU - Li, Yi-min
AU - Li, Junhua
AU - Zhao, Jincun
PY - 2021
Y1 - 2021
N2 - 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.
AB - 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.
U2 - 10.1038/s41421-021-00257-2
DO - 10.1038/s41421-021-00257-2
M3 - Journal article
C2 - 33850111
AN - SCOPUS:85104312574
VL - 7
JO - Cell Discovery
JF - Cell Discovery
SN - 2056-5968
M1 - 23
ER -
ID: 261218978