ArticleCell discovery2021
Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients.
Article in Cell discovery, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 67 citations in OpenAlex.
- Probiotics and Bacteriocins Against SARS-CoV-2: Therapeutic Frontiers and Mechanistic Insights.Probiotics and antimicrobial proteins · 2026Review
- Live AirwayEnvironment & health (Washington, D.C.) · 2026Article
- Integrated multiplex PCR and metatranscriptomics reveal upper-lower airway microbial landscapes in pediatric respiratory infections.Virologica Sinica · 2026Article
- Nanobiosensors: A Potential Tool to Decipher the Nexus Between SARS-CoV-2 Infection and Gut Dysbiosis.Sensors (Basel, Switzerland) · 2026Review
- Bacterial colonization of the respiratory tract in COVID-19 patients: potential source of bacterial infection.BMC infectious diseases · 2026Article
- SARS-CoV-2 infection and gut-lung axis: the potential role of rifaximin.Inflammopharmacology · 2026Review
- African swine fever virus infection enhances CD14-dependent phagocytosis of porcine alveolar macrophages to promote bacterial uptake and apoptotic body-mediated viral transmission.Journal of virology · 2025Article
- Design and Synthesis of Hybrid Compounds for Potential Treatment of Bacterial Co-Infections: In Vitro Antibacterial and In Silico Studies.Antibiotics (Basel, Switzerland) · 2025Article
- Diversity in the composition of pleural cavity and oral cavity microbiota in different bacterial empyema.Frontiers in microbiology · 2025Article
- Optimizing the Antimicrobial Effects by using Natural Compounds in COVID-19 Management.Current medicinal chemistry · 2025Review
- Article
- Insights into the Naso-Oropharyngeal Bacterial Composition in Suspected SARS-CoV-2 Cases.Pathogens (Basel, Switzerland) · 2024Article
- Total Infectome Characterization of Respiratory Infections during the 2022-23 COVID-19 Outbreak in China Revealed Extensive Coinfections with Links to SARS-CoV-2 Status, Age, and Disease Severity.Pathogens (Basel, Switzerland) · 2024Article
- Potential Beneficial Effects of Naringin and Naringenin on Long COVID-A Review of the Literature.Microorganisms · 2024Review
- Article
- Infection with the multidrug-resistant Klebsiella pneumoniae New Delhi metallo-B-lactamase strain in patients with COVID-19:Frontiers in cellular and infection microbiology · 2024Article
- Microbial infection among SARS-COV-2-infected patients in a COVID-19-dedicated tertiary care hospital of Bangladesh: a cross-sectional study.Access microbiology · 2024Article
- Gut bacteria: an etiological agent in human pathological conditions.Frontiers in cellular and infection microbiology · 2024Review
- Metatranscriptome of human lung microbial communities in a cohort of mechanically ventilated COVID-19 Omicron patients.Signal transduction and targeted therapy · 2023Article
- Interaction Between SARS-CoV-2 and Pathogenic Bacteria.Current microbiology · 2023Review
Corrections and comments
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Authors and funding
33 authors at 6 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.