Characterization of the Human Oropharyngeal Microbiomes in SARS‐CoV‐2 Infection and Recovery Patients

Abstract

Respiratory tract microbiome is closely related to respiratory tract infections, while characterization of oropharyngeal microbiome in recovered coronavirus disease 2019 (COVID-19) patients is not studied. Herein, oropharyngeal swabs are collected from confirmed cases (CCs) with COVID-19 (73 subjects), suspected cases (SCs) (36), confirmed cases who recovered (21), suspected cases who recovered (36), and healthy controls (Hs) (140) and then completed MiSeq sequencing. Oropharyngeal microbial 𝜶-diversity is markedly reduced in CCs versus Hs. Opportunistic pathogens are increased, while butyrate-producing genera are decreased in CCs versus Hs. The classifier based on eight optimal microbial markers is constructed through a random forest model and reached great diagnostic efficacy in both discovery and validation cohorts. Notably, the classifier successfully diagnosed SCs with positive IgG antibody as CCs and is demonstrated from the perspective of the microbiome. Importantly, several genera with significant differences gradually increase and decrease along with recovery from COVID-19. Forty-four oropharyngeal operational taxonomy units (OTUs) are closely correlated with 11 clinical indicators of SARS-CoV-2 infection and Hs based on Spearman correlation analysis. Together, this research is the first to characterize oropharyngeal microbiota in recovered COVID-19 cases and suspected cases, to successfully construct and validate the diagnostic model for COVID-19 and to depict the correlations between microbial OTUs and clinical indicators.

Characterization of Altered Oropharyngeal Microbiota in Hospitalized Patients With Mild SARS-CoV-2 Infection

“…However, the oral microbiota of mild COVID-19 patients in our research showed coherent decreased richness (Chao1 index, not significant) but increased Shannon biodiversity compared to the HCs, which showed inconformity to previous research (Iebba et al, 2021;Ma et al, 2021). Nonetheless, when we divided SARS-CoV-2 patients into two groups with higher and lower viral burdens, interestingly, a significantly increased trend of alpha richness (Chao1 index) and Shannon biodiversity, although not significant, was found in those patients with higher SARS-CoV-2 viral load, which was inconsistent with previous studies (Gao et al, 2021;Ma et al, 2021;Wu et al, 2021). These results indicated dysbiosis in the oropharyngeal bacteria of patients infected with SARS-CoV-2.…”

Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome

“…The composition of the nasal microbiome has been observed to be altered in several respiratory infections including COVID-19 affecting the course of the disease and clinical outcome ( 44 ). Different metagenomic studies portrayed decrease in the nasopharyngeal microbiome diversity in SARS-CoV-2 infected patients, leading to predominance of a specific microbe that correlated with symptom severity ( 22 , 23 , 45 ).…”

“…Thus, co-infections deserve closer attention to understand and evaluate their role in disease management and patient outcome ( 21 ). Few studies have illustrated the function of respiratory microbiome in SARS-CoV-2 infection, emphasizing the role of co-infecting pathogens as prospective modulators of COVID-19 ( 22 – 25 ).…”

Gut microbiota and COVID-19: A systematic review

“…Other opportunistic pathogenesis of the upper respiratory tract like Haemophilus, Stenotrophomonas, Acinetobacter, Moraxella, Corynebacterium, Gemella, Ralstonia, Pseudomonas [53], Granulicatella [52], Megasphaera [25] were increased in COVID-19 patients which are associated with serious clinical outcomes. Also, in Severe COVID-19 patients, an increase of Megasphaera, and infatal COVID-19 patients increase Rothiadentocariosa, Streptococcus infantis, Veillonelladispar [21] were seen which may be associated with secondary pneumonia due to mechanical ventilation.…”