Objectives Severe or critical COVID-19 is associated with intensive care unit admission, increased secondary infection rate, and would lead to significant worsened prognosis. Risks and characteristics relating to secondary infections in severe COVID-19 have not been described. Methods Severe and critical COVID-19 patients from Shanghai were included. We collected lower respiratory, urine, catheters, and blood samples according to clinical necessity and culture and mNGS were performed. Clinical and laboratory data were archived. Results We found 57.89% (22/38) patients developed secondary infections. The patient receiving invasive mechanical ventilation or in critical state has a higher chance of secondary infections (P<0.0001). The most common infections were respiratory, blood-stream and urinary infections, and in respiratory infections, the most detected pathogens were gram-negative bacteria (26, 50.00%), following by gram-positive bacteria (14, 26.92%), virus (6, 11.54%), fungi (4, 7.69%), and others (2, 3.85%). Respiratory Infection rate post high flow, tracheal intubation, and tracheotomy were 12.90% (4/31), 30.43% (7/23), and 92.31% (12/13) respectively. Secondary infections would lead to lower discharge rate and higher mortality rate. Conclusion Our study originally illustrated secondary infection proportion in severe and critical COVID-19 patients. Culture accompanied with metagenomics sequencing increased pathogen diagnostic rate. Secondary infections risks increased after receiving invasive respiratory ventilations and intravascular devices, and would lead to a lower discharge rate and a higher mortality rate.

目标严重或危重的 COVID-19 与入住重症监护室、继发感染率增加有关，并会导致预后显着恶化。尚未描述与严重 COVID-19 继发感染相关的风险和特征。方法纳入上海市重症和危重症COVID-19患者。我们根据临床需要收集了下呼吸道、尿液、导管和血液样本，并进行了培养和 mNGS。临床和实验室数据已存档。结果我们发现 57.89% (22/38) 的患者发生继发感染。接受有创机械通气或处于危重状态的患者继发感染的机会较高（P<0.0001)。最常见的感染是呼吸道、血流和泌尿系统感染，在呼吸道感染中，检出最多的病原体是革兰氏阴性菌（26, 50.00%），其次是革兰氏阳性菌（14, 26.92%）、病毒（ 6, 11.54%)、真菌 (4, 7.69%) 和其他 (2, 3.85%)。高流量、气管插管和气管切开后的呼吸道感染率分别为 12.90% (4/31)、30.43% (7/23) 和 92.31% (12/13)。继发感染会导致出院率降低和死亡率升高。结论我们的研究最初说明了严重和危重 COVID-19 患者的继发感染比例。伴随宏基因组测序的培养提高了病原体诊断率。接受有创呼吸通气和血管内装置后继发感染风险增加，并导致出院率降低和死亡率升高。