Dynamics of the Upper Respiratory Tract Microbiota and Its Association with Mortality in COVID-19

Ren, Lili; Wang, Yeming; Zhong, Jiaxin; Li, Xia; Xiao, Yan; Li, Jie; Yang, Jing; Fan, Guohui; Guo, Li; Shen, Zijie; Kang, Lu; Shi, Leisheng; Li, Qiong; Li, Jizhou; Lin, Dachuan; Li, Haibo; Wang, Conghui; Wang, Ying; Wang, Xinming; Zou, Xiaohui; Rao, Jian Yu; Zhang, Li; Wang, Jianbin; Huang, Yanyi; Cao, Bin; Wang, Jianwei; Li, Mingkun

doi:10.1164/rccm.202103-0814oc

Cited by 66 publications

(88 citation statements)

References 49 publications

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“…The available evidence suggests a potential role of microbiota in susceptibility to SARS-CoV-2 infection and COVID-19 severity, but longitudinal studies evaluating the microbiota as a prognostic factor for severity of disease progression are lacking [19] , [20] , [21] , [22] . The data regarding the association between nasopharyngeal microbiota features and disease severity are scarce and limited in terms of showing a decrease in α diversity or identifying specific genera with relevance to critical illness [ 23 , 24 ].…”

Section: Introductionmentioning

confidence: 99%

Nasopharyngeal Microbiota as an early severity biomarker in COVID-19 hospitalised patients

Ventero

Moreno-Pérez

Molina-Pardines

et al. 2022

Journal of Infection

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This study aimed to analyse the diversity and taxonomic composition of the nasopharyngeal microbiota, to determine its association with COVID-19 clinical outcome. To study the microbiota, we utilized 16S rRNA sequencing of 177 samples that came from a retrospective cohort of COVID-19 hospitalized patients. Raw sequences were processed by QIIME2. The associations between microbiota, invasive mechanical ventilation (IMV), and all-cause mortality were analysed by multiple logistic regression, adjusted for age, gender, and comorbidity. The microbiota α diversity indexes were lower in patients with a fatal outcome, whereas the β diversity analysis showed a significant clustering in these patients. After multivariate adjustment, the presence of Selenomonas spp., Filifactor spp., Actinobacillus spp., or Chroococcidiopsis spp., was associated with a reduction of more than 90% of IMV. Higher diversity and the presence of certain genera in the nasopharyngeal microbiota seem to be early biomarkers of a favourable clinical evolution in hospitalized COVID-19 patients.

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Section: Introductionmentioning

confidence: 99%

Nasopharyngeal Microbiota as an early severity biomarker in COVID-19 hospitalised patients

Ventero

Moreno-Pérez

Molina-Pardines

et al. 2022

Journal of Infection

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“…Other studies focused on microbiota factors that were associated with COVID-19 severity and outcomes. For example, Mycoplasma salivarium enrichment in the lung microbiota was described as a marker for disease severity and Streptococcus abundance in the oropharyngeal microbiota was indicated as a marker for survival until discharge [25,26]. However, as Lloréns-Rico and colleagues demonstrate in their analysis based on 58 upper and 35 lower respiratory tract microbiota samples from well defined COVID-19 patients, intensive care stay including antibiotic courses and mechanical ventilation strongly confounds microbiota composition changes attributed to SARS-CoV-2 infection, hampering interpretation of results found in severely ill COVID-19 patients [27 ▪ ].…”

Section: Resultsmentioning

confidence: 99%

Section: Key Pointsmentioning

confidence: 99%

The microbiota in respiratory tract infections: from association to intervention

Koenen

Piters

Bogaert

et al. 2022

Current Opinion in Infectious Diseases

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Purpose of reviewThe respiratory microbiota has a role in respiratory tract infection (RTI) pathogenesis. On the mucosa, the respiratory microbiota interacts with potential pathogenic viruses, bacteria and the host immune system, including secretory IgA (sIgA). This review discusses the role of the respiratory microbiota and its interaction with the (mucosal) immune system in RTI susceptibility, as well as the potential to exploit the microbiota to promote health and prevent RTIs. Recent findingsRecent studies confirm that specific microbiota profiles are associated with RTI susceptibility and during susceptibility and found accompanying RTIs, although clear associations have not yet been found for SARS-CoV-2 infection. sIgA plays a central role in RTI pathogenesis: it stands under control of the local microbiota, while at the same time influencing bacterial gene expression, metabolism and defense mechanisms. Respiratory microbiota interventions are still newly emerging but promising candidates for probiotics to prevent RTIs, such as Corynebacterium and Dolosigranulum species, have been identified.

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“…A study analyzing oropharyngeal, nasopharyngeal, and endotracheal samples from hospitalized COVID-19 patients using 16S rRNA sequencing reported respiratory tract bacterial dysbiosis in patients with COVID-19; microbial signatures were also associated with COVID-19 severity and systemic immune response (12). Recent studies have also reported lower airway microbial signatures associated with poor clinical outcome of COVID-19 and upper respiratory microbiota associated with mortality and COVID-19 severity (18,19). These early findings suggest that the airway microbiome may be an important factor in indicating and influencing COVID-19 clinical outcomes and should be investigated further.…”

Section: Introductionmentioning

confidence: 99%

The salivary and nasopharyngeal microbiomes are associated with SARS-CoV-2 infection and disease severity

Kim

Rauseo

et al. 2022

Preprint

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Oral and upper respiratory microbiota play important roles in modulating host immune responses to viral infection. As emerging evidence suggests the host microbiome may be involved in the pathophysiology of COVID-19, we aimed to investigate associations between the oral and nasopharyngeal microbiome and COVID-19 severity. We collected saliva (n = 78) and nasopharyngeal swab (n = 66) samples from a COVID-19 cohort and characterized the microbiomes using 16S ribosomal RNA gene sequencing. We also examined associations between the salivary and nasopharyngeal microbiome and age, COVID-19 symptoms, and blood cytokines. SARS-CoV-2 infection status, but not COVID-19 severity, was associated with community-level differences in the oral and nasopharyngeal microbiomes. Salivary and nasopharyngeal microbiome alpha diversity negatively correlated with age and were associated with fever and diarrhea. Several bacterial genera were differentially abundant by COVID-19 severity, including oral Bifidobacterium, Lactobacillus, and Solobacterium, all of which were depleted in patients with severe COVID-19. Nasopharyngeal Paracoccus was depleted while nasopharyngeal Proteus, Cupravidus, and Lactobacillus were increased in patients with severe COVID-19. Further analysis revealed that the abundance of oral Bifidobacterium was negatively associated with plasma concentrations of known COVID-19 biomarkers interleukin 17F (IL-17F) and monocyte chemoattractant protein-1 (MCP-1). In conclusion, our results suggest COVID-19 disease severity is associated with the relative abundance of certain bacterial taxa.

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Dynamics of the Upper Respiratory Tract Microbiota and Its Association with Mortality in COVID-19

Abstract: Impact: This study demonstrates the association between the upper respiratory tract microbiota and the prognosis in COVID-19. A higher abundance of Streptococcus on admission predicts a lower mortality rate. The upper respiratory tract microbiota may reflect

Cited by 66 publications

References 49 publications

Nasopharyngeal Microbiota as an early severity biomarker in COVID-19 hospitalised patients

Nasopharyngeal Microbiota as an early severity biomarker in COVID-19 hospitalised patients

The microbiota in respiratory tract infections: from association to intervention

The salivary and nasopharyngeal microbiomes are associated with SARS-CoV-2 infection and disease severity

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