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Article: Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients

TitleCharacterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients
Authors
Issue Date2021
PublisherNature Publishing Group: Open Access Journals. The Journal's web site is located at http://www.nature.com/celldisc/
Citation
Cell Discovery, 2021, v. 7, p. article no.23 How to Cite?
AbstractSevere 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.
Persistent Identifierhttp://hdl.handle.net/10722/301151
ISSN
2023 Impact Factor: 13.0
2023 SCImago Journal Rankings: 4.198
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorZhong, H-
dc.contributor.authorWang, Y-
dc.contributor.authorShi, Z-
dc.contributor.authorZhang, L-
dc.contributor.authorRen, H-
dc.contributor.authorHe, W-
dc.contributor.authorZhang, Z-
dc.contributor.authorZhu, A-
dc.contributor.authorZhao, J-
dc.contributor.authorXiao, F-
dc.contributor.authorYang, F-
dc.contributor.authorLiang, T-
dc.contributor.authorYe, F-
dc.contributor.authorZhong, B-
dc.contributor.authorRuan, S-
dc.contributor.authorGan, M-
dc.contributor.authorZhu, J-
dc.contributor.authorLi, F-
dc.contributor.authorLi, F-
dc.contributor.authorWang, D-
dc.contributor.authorLi, J-
dc.contributor.authorRen, P-
dc.contributor.authorZhu, S-
dc.contributor.authorYang, H-
dc.contributor.authorWang, J-
dc.contributor.authorKristiansen, K-
dc.contributor.authorTun, HM-
dc.contributor.authorChen, W-
dc.contributor.authorZhong, N-
dc.contributor.authorXu, X-
dc.contributor.authorLi, Y-
dc.contributor.authorLi, J-
dc.contributor.authorZhao, J-
dc.date.accessioned2021-07-27T08:06:53Z-
dc.date.available2021-07-27T08:06:53Z-
dc.date.issued2021-
dc.identifier.citationCell Discovery, 2021, v. 7, p. article no.23-
dc.identifier.issn2056-5968-
dc.identifier.urihttp://hdl.handle.net/10722/301151-
dc.description.abstractSevere 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.-
dc.languageeng-
dc.publisherNature Publishing Group: Open Access Journals. The Journal's web site is located at http://www.nature.com/celldisc/-
dc.relation.ispartofCell Discovery-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.titleCharacterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients-
dc.typeArticle-
dc.identifier.emailTun, HM: heinmtun@hku.hk-
dc.identifier.authorityTun, HM=rp02389-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1038/s41421-021-00257-2-
dc.identifier.pmid33850111-
dc.identifier.pmcidPMC8043102-
dc.identifier.scopuseid_2-s2.0-85104312574-
dc.identifier.hkuros323444-
dc.identifier.volume7-
dc.identifier.spagearticle no.23-
dc.identifier.epagearticle no.23-
dc.identifier.isiWOS:000640368400001-
dc.publisher.placeUnited Kingdom-

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