Characterization of Altered Oropharyngeal Microbiota in Hospitalized Patients With Mild SARS-CoV-2 Infection.
Characterization of Altered Oropharyngeal Microbiota in Hospitalized Patients With Mild SARS-CoV-2 Infection.
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DOI：
10.3389/fcimb.2022.824578
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发表时间：
2022
影响因子：
5.7
通讯作者：
Huang SH
中科院分区：
文献类型：
--
作者：
Shi YL;He MZ;Han MZ;Gui HY;Wang P;Yu JL;Ge YL;Sun Y;Huang SH
2019冠状病毒病（COVID-19）仍然是一个严重的全球性卫生问题，人们对口咽共生微生物在感染易感性和严重程度中的作用知之甚少。在这里，我们通过NANOPORE平台对10名轻度COVID-19患者和10名健康对照者的口咽拭子标本进行全长16S rRNA基因测序，鉴定了口咽微生物群特征。我们的研究结果显示，在轻度COVID-19患者中，口咽微生物群组成明显不同，其特征是条件致病菌如厌氧胃链球菌和斯图氏假单胞菌富集，而亚布氏鞘单胞菌、sullaagrobacterium和veronii假单胞菌减少。基于物种水平口咽微生物群的相对丰度，我们建立了一个微生物分类器来区分COVID-19患者和健康对照，其中鉴定出P. veronii、假单胞菌fragi和S. yabuuchiae是它们在COVID-19组中消耗最显著的特征。弯曲杆菌属的几种成员，特别是胎儿弯曲杆菌和直弯曲杆菌，在COVID-19病毒载量较高的患者中高度富集，并与疾病状态和多项临床常规血液指标存在显著相关性，提示在面临病毒感染的挑战时，几种细菌可能在COVID-19患者中转化为机会致病菌。我们还在疾病患者网络中发现了潜水分类群血管链球菌和溶乳酸链球菌，这表明这些口咽部微生物群的改变可能通过影响微生物关联模式来影响COVID-19的严重程度。综上所述，本研究中SARS-CoV-2感染患者的样本量较低（n = 10），因此这些结果是初步的；然而，我们提供了总体特征，即安徽省口咽微生物群改变和微生物相关模式与COVID-19严重程度相关。
Coronavirus disease 2019 (COVID-19) remains a serious emerging global health problem, and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity. Here, we present the oropharyngeal microbiota characteristics identified by full-length 16S rRNA gene sequencing through the NANOPORE platform of oropharynx swab specimens from 10 mild COVID-19 patients and 10 healthy controls. Our results revealed a distinct oropharyngeal microbiota composition in mild COVID-19 patients, characterized by enrichment of opportunistic pathogens such as Peptostreptococcus anaerobius and Pseudomonas stutzeri and depletion of Sphingomonas yabuuchiae, Agrobacterium sullae, and Pseudomonas veronii. Based on the relative abundance of the oropharyngeal microbiota at the species level, we built a microbial classifier to distinguish COVID-19 patients from healthy controls, in which P. veronii, Pseudomonas fragi, and S. yabuuchiae were identified as the most prominent signatures for their depletion in the COVID-19 group. Several members of the genus Campylobacter, especially Campylobacter fetus and Campylobacter rectus, which were highly enriched in COVID-19 patients with higher severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and showed a significant correlation with disease status and several routine clinical blood indicators, indicate that several bacteria may transform into opportunistic pathogen in COVID-19 patients when facing the challenges of viral infection. We also found the diver taxa Streptococcus anginosus and Streptococcus alactolyticus in the network of disease patients, suggesting that these oropharynx microbiota alterations may impact COVID-19 severity by influencing the microbial association patterns. In conclusion, the low sample size of SARS-CoV-2 infection patients (n = 10) here makes these results tentative; however, we have provided the overall characterization that oropharyngeal microbiota alterations and microbial correlation patterns were associated with COVID-19 severity in Anhui Province.
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