Abstract
BackgroundFusobacterium nucleatum (F. n) is an important opportunistic pathogen causing oral and gastrointestinal disease. Faecalibacterium prausnitzii (F. p) is a next-generation probiotic and could serve as a biomarker of gut eubiosis/dysbiosis to some extent. Alterations in the human oral and gut microbiomes are associated with viral respiratory infection. The aim of this study was to characterise the oral and fecal bacterial biomarker (i.e., F. n and F. p) in COVID-19 patients by qPCR and investigate the pharyngeal microbiome of COVID-19 patients through metagenomic next-generation sequencing (mNGS).ResultsPharyngeal F. n was significantly increased in COVID-19 patients, and it was higher in male than female patients. Increased abundance of pharyngeal F. n was associated with a higher risk of a positive SARS-CoV-2 test (adjusted OR = 1.32, 95% CI = 1.06 ~ 1.65, P < 0.05). A classifier to distinguish COVID-19 patients from the healthy controls based on the pharyngeal F. n was constructed and achieved an area under the curve (AUC) of 0.843 (95% CI = 0.688 ~ 0.940, P < 0.001). However, the level of fecal F. n and fecal F. p remained unaltered between groups. Besides, mNGS showed that the pharyngeal swabs of COVID-19 patients were dominated by opportunistic pathogens.ConclusionsPharyngeal but not fecal F. n was significantly increased in COVID-19 patients, clinicians should pay careful attention to potential coinfection. Pharyngeal F. n may serve as a promising candidate indicator for COVID-19.
Highlights
Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) is highly transmissible and pathogenic and has caused a pandemic coronavirus disease 2019 (COVID19), which threatens human health and public safety
Moderate illness accounted for the largest proportion of all the enrolled cases (66.67% ~ 70.43%), which was consistent with observed tendency [42, 43]
Retrospective cohort studies indicate that clinical course provides an objective basis for the egregation of patients into groups, and 7 days is an time node of great clinical importance [5, 43, 44]
Summary
Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) is highly transmissible and pathogenic and has caused a pandemic coronavirus disease 2019 (COVID19), which threatens human health and public safety. The pharynx is one of the main entrance into the gastrointestinal tract for microorganisms Both the pharynx and gastrointestinal tract are recognised as crucial sites for the pathogenesis of SARS-CoV-2 infection [7, 8]. SARS-CoV-2 infection and invasion in these sites may cause local microbiome dysbiosis and lead to secondary bacterial infection [9,10,11]. Alterations in the human oral and gut microbiomes are associated with viral respiratory infection. The aim of this study was to characterise the oral and fecal bacterial biomarker (i.e., F. n and F. p) in COVID-19 patients by qPCR and investigate the pharyngeal microbiome of COVID-19 patients through metagenomic next-generation sequencing (mNGS)
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