Nasopharyngeal microbiome

The influence of SARS-CoV-2 on the nasopharyngeal microbiome, or vice-verse, is unclear. Nasopharyngeal DNA from Dutch healthcare workers (N=257) and hospital outpatients with respiratory symptoms (N=143), leftover after SARS-CoV-2 testing in 2020-2021, were 16S rRNA amplicon sequenced and tested for respiratory viruses by multiplex PCR panel. The healthcare workers were younger and much healthier than the patients, and experienced less severe viral infections. In the healthcare workers, log10 estimated concentrations (ECs) of Corynebacterium were slightly increased in samples with SARS-CoV-2 versus no virus detected, regardless of symptomatology (adjusted regression coefficient 0.52, p=0.042) but no other bacterial ECs differed. Corynebacterium and Dolosigranulum ECs were higher in very mild/asymptomatic SARS-CoV-2 episodes compared to very mild/asymptomatic episodes with no viruses detected, but lower in mild compared to very mild/asymptomatic SARS-CoV-2 episodes (-1.07, p=0.015, and -1.37, p=0.011, respectively). In the patients, similar but non-significant trends by SARS-CoV-2 severity (fatal, severe, moderate versus mild) were seen for Dolosigranulum, but not for Corynebacterium. In this population, the largest nasopharyngeal microbiome composition differences were seen by the presence and severity of comorbidities. These findings suggest that the Dolosigranulum EC decreases with increasing SARS-CoV-2 severity, but the clinical relevance of this finding is unclear.

严重急性呼吸综合征冠状病毒2（SARS-CoV-2）对鼻咽微生物组（nasopharyngeal microbiome）的影响，反之亦然，目前尚不明确。本研究使用2020-2021年SARS-CoV-2检测后剩余的鼻咽DNA样本，受试者包括荷兰医护人员（N=257）以及伴有呼吸道症状的医院门诊患者（N=143），对上述样本进行16S rRNA扩增子测序（16S rRNA amplicon sequencing），并通过多重PCR检测面板（multiplex PCR panel）检测呼吸道病毒。医护人员相较于门诊患者更为年轻，健康状况更佳，且病毒感染的病情严重程度更低。在医护人员群体中，相较于未检测到病毒的样本，棒杆菌属（Corynebacterium）的log₁₀估算浓度（estimated concentrations, ECs）在SARS-CoV-2阳性样本中略有升高，且不受症状状态影响（校正回归系数为0.52，p=0.042）；其余细菌的估算浓度均无显著差异。相较于未检测到病毒的极轻度/无症状感染，棒杆菌属与欺骗杆菌属（Dolosigranulum）的估算浓度在极轻度/无症状的SARS-CoV-2感染中更高，但在轻度SARS-CoV-2感染中则低于极轻度/无症状感染（分别为-1.07，p=0.015与-1.37，p=0.011）。在患者群体中，欺骗杆菌属的估算浓度随SARS-CoV-2感染严重程度（致命、重度、中度相较于轻度）呈现相似但无统计学显著性的变化趋势，而棒杆菌属则未观察到此关联。在本研究队列中，鼻咽微生物组组成的最大差异与合并症（comorbidities）的存在及严重程度密切相关。上述结果表明，欺骗杆菌属的估算浓度随SARS-CoV-2感染严重程度升高而降低，但该发现的临床相关性尚不明确。