Tchoupou Saha Ornella la Fortune, Dubourg Grégory, Yacouba Abdourahamane, Bossi Vincent, Raoult Didier, Lagier Jean-Christophe
Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.
IHU Méditerranée Infection, Marseille, France.
Front Microbiol. 2022 May 17;13:871627. doi: 10.3389/fmicb.2022.871627. eCollection 2022.
While populations at risk for severe SARS-CoV-2 infections have been clearly identified, susceptibility to the infection and its clinical course remain unpredictable. As the nasopharyngeal microbiota may promote the acquisition of several respiratory infections and have an impact on the evolution of their outcome, we studied the nasopharyngeal microbiota of COVID-19 patients in association with baseline disease-related clinical features compared to that of patients tested negative. We retrospectively analyzed 120 nasopharyngeal pseudonymized samples, obtained for diagnosis, divided into groups (infected patients with a favorable outcome, asymptomatic, and deceased patients) and patients tested negative for SARS-CoV-2, by using Illumina-16S ribosomal ribonucleic acid (rRNA) sequencing and specific polymerase chain reaction (PCR) targeting pathogens. We first found a depletion of anaerobes among COVID-19 patients, irrespective of the clinical presentation of the infection ( < 0.029). We detected 9 taxa discriminating patients tested positive for SARS-CoV-2 from those that were negative including ( ≤ 0.05), ( ≤ 0.05), ( ≤ 0.01), ( ≤ 0.05), subsp. ( ≤ 0.001), and ( ≤ 0.001) with 16S rRNA sequencing, and ( ≤ 0.01), ( ≤ 0.01), and ( ≤ 0.05) using real-time PCR. By designing a specific real-time PCR, we also demonstrated that is decreased in asymptomatic individuals compared to other SARS-CoV 2 positive patients. These findings indicate that the nasopharyngeal microbiota as in any respiratory infection plays a role in the clinical course of the disease. Further studies are needed to elucidate the potential role in the clinical course of the disease of , and more specifically in order to include them as predictors of the severity of COVID-19.
虽然已明确确定了感染严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的高危人群，但对该感染的易感性及其临床病程仍不可预测。由于鼻咽微生物群可能促进多种呼吸道感染的发生，并对其病情演变产生影响，我们研究了新冠肺炎患者的鼻咽微生物群，并将其与基线疾病相关临床特征进行关联，同时与检测结果为阴性的患者进行比较。我们回顾性分析了120份用于诊断的匿名鼻咽样本，这些样本通过Illumina-16S核糖体核糖核酸（rRNA）测序和针对病原体的特异性聚合酶链反应（PCR），分为几组（预后良好的感染患者、无症状患者和死亡患者）以及SARS-CoV-2检测结果为阴性的患者。我们首先发现，无论感染的临床表现如何，新冠肺炎患者中的厌氧菌数量均减少（<0.029）。我们检测到9个分类群可区分SARS-CoV-2检测呈阳性的患者和阴性患者，包括（≤0.05）、（≤0.05）、（≤0.01）、（≤0.05）、亚种（≤0.001）和（≤0.001）（通过16S rRNA测序），以及（≤0.01）、（≤0.01）和（≤0.05）（使用实时PCR）。通过设计一种特异性实时PCR，我们还证明，与其他SARS-CoV-2阳性患者相比，无症状个体中的数量减少。这些发现表明，与任何呼吸道感染一样，鼻咽微生物群在该疾病的临床病程中发挥作用。需要进一步研究以阐明在该疾病临床病程中的潜在作用，更具体地说是的作用，以便将它们纳入新冠肺炎严重程度的预测指标。
