Microbial co-infections may contribute to the pulmonary deterioration in COVID-19 patients needing intensive care treatment. The present study portrays the extent of co-infections in COVID-19 ICU patients. Conventional culture, molecular detections for atypical aetiologies, QiaStat-Dx® respiratory panel V2 detecting 21 respiratory pathogens and ribosomal DNA genes 16S/18S amplicon-based microbiome analyses were performed on respiratory samples from 34 COVID-19 patients admitted to the ICU. Potential pathogens were detected in seven patients (21%) by culturing, in four patients (12%) by microbiome analysis and in one patient (3%) by respiratory panel. Among 20 patients receiving antibiotics prior to ICU admission, fungi (3 Candida albicans, 1 C. tropicalis, 1 C. dubliniensis) were cultured in 5 (15%) endotracheal aspirates. Among 14 patients who were antibiotic-naive at ICU admission, two patients (6%) had bacterial respiratory pathogens (Staphylococcus aureus, Streptococcus pseudopneumoniae) cultured in their endotracheal aspirates. Microbiome analysis recognized four potential respiratory pathogens (3 Haemophilus influenza, 1 Fusobacterium necrophorum) isolated in samples from four other patients (12%). QiaStat-Dx® respiratory panel V2 detected adenovirus in one patient (3%). The prevalence of pulmonary microbial co-infections is modest among COVID-19 patients upon admission to ICU. Microbiome analysis complements conventional microbial diagnostics in characterization of respiratory co-infections.

中文翻译：

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危重 COVID-19 患者的广泛微生物呼吸道标本表征

微生物合并感染可能导致需要重症监护治疗的 COVID-19 患者的肺部恶化。本研究描述了 COVID-19 ICU 患者合并感染的程度。常规培养、非典型病因的分子检测、QiaStat-Dx® 呼吸检测试剂盒 V2 检测 21 种呼吸道病原体和核糖体 DNA 基因 对入住 ICU 的 34 名 COVID-19 患者的呼吸道样本进行了基于 16S/18S 扩增子的微生物组分析。在 7 名患者 (21%) 中通过培养检测到潜在病原体，在 4 名患者 (12%) 中通过微生物组分析和 1 名患者 (3%) 通过呼吸面板检测。在 ICU 入院前接受抗生素治疗的 20 名患者中，真菌（3 种白色念珠菌 、 1种 热带念珠菌, 1 ℃。 dubliniensis ) 在 5 个 (15%) 气管内吸出物中培养。在 ICU 入院时未使用过抗生素的 14 名患者中，2 名患者 (6%)在其气管内吸出物中培养出细菌性呼吸道病原体（金黄色葡萄球菌、 假肺炎链球菌）。微生物组分析识别出四种潜在的呼吸道病原体（3种流感嗜血杆菌、1种坏死梭杆菌 ) 从其他四名患者 (12%) 的样本中分离出来。QiaStat-Dx® 呼吸检测试剂盒 V2 在一名患者 (3%) 中检测到腺病毒。入住 ICU 时，COVID-19 患者肺部微生物合并感染的发生率适中。微生物组分析在表征呼吸道合并感染方面补充了传统的微生物诊断方法。