尽管Omicron变体与上呼吸道的更大传播性和向性有关,在中国爆发疫情期间感染Omicron变异型的患者的临床和致病特征尚不清楚.回顾性研究了来自广州七个医疗中心的COVID-19成人,中国,以及临床信息和标本(BALF,痰,和喉咙拭子)从参与者收集。常规检测方法,宏基因组学下一代测序(mNGS),和其他方法用于检测下呼吸道样本中的病原体。从2022年12月至2023年1月,我们招募了836例COVID-19患者,其中56.7%的患者患有严重/危重症。约91.4%的患者感染了Omicron菌株(BA.5.2)。mNGS对可能合并感染病原体的检出率为53.4%,包括肺炎克雷伯菌(16.3%),烟曲霉(12.2%),铜绿假单胞菌(11.8%)。合并感染率为19.5%,常见病原体为肺炎链球菌(11.5%),流感嗜血杆菌(9.2%),和腺病毒(6.9%)。重复感染率为75.4%,常见病原菌如肺炎克雷伯菌(26.1%)和铜绿假单胞菌(19.4%)。肺炎克雷伯菌(27.1%对6.1%,P<0.001),烟曲霉(19.6%vs5.3%,P=0.001),鲍曼不动杆菌(18.7%vs4.4%,P=0.001),铜绿假单胞菌(16.8%vs7.0%,P=0.024),金黄色葡萄球菌(14.0%vs5.3%,P=0.027),和肺炎链球菌(0.9%对10.5%,P=0.002)在重症病例中更为常见。细菌和真菌的共感染和重复感染在与Omicron变异感染相关的重症肺炎患者中很常见。测序方法可能有助于病原体的诊断和鉴别诊断。
目的:我们的研究分析了广州Omicron菌株暴发期间合并或重复感染的下呼吸道的临床特征和病原体谱,特别是在中国放松了疫情防控策略之后。这项研究可能会促使对具体问题进行进一步的研究,这将有利于临床实践。
Although the Omicron variant has been associated with greater transmissibility and tropism of the upper respiratory tract, the clinical and pathogenic features of patients infected with the Omicron variant during an outbreak in
China have been unclear. Adults with COVID-19 were retrospectively enrolled from seven medical centers in Guangzhou,
China, and clinical information and specimens ( BALF, sputum, and throat swabs) from participants were collected. Conventional detection methods, metagenomics next-generation sequencing (mNGS), and other methods were used to detect pathogens in lower respiratory tract samples. From December 2022 to January 2023, we enrolled 836 patients with COVID-19, among which 56.7% patients had severe/critical illness. About 91.4% of patients were infected with the Omicron strain (BA.5.2). The detection rate of possible co-infection pathogens was 53.4% by mNGS, including Klebsiella pneumoniae (16.3%), Aspergillus fumigatus (12.2%), and Pseudomonas aeruginosa (11.8%). The co-infection rate was 19.5%, with common pathogens being Streptococcus pneumoniae (11.5%), Haemophilus influenzae (9.2%), and Adenovirus (6.9%). The
superinfection rate was 75.4%, with common pathogens such as Klebsiella pneumoniae (26.1%) and Pseudomonas aeruginosa (19.4%). Klebsiella pneumoniae (27.1%% vs 6.1%, P < 0.001), Aspergillus fumigatus (19.6% vs 5.3%, P = 0.001), Acinetobacter baumannii (18.7% vs 4.4%, P = 0.001), Pseudomonas aeruginosa (16.8% vs 7.0%, P = 0.024), Staphylococcus aureus (14.0% vs 5.3%, P = 0.027), and Streptococcus pneumoniae (0.9% vs 10.5%, P = 0.002) were more common in severe cases. Co-infection and
superinfection of bacteria and fungi are common in patients with severe pneumonia associated with Omicron variant infection. Sequencing methods may aid in the diagnosis and differential diagnosis of pathogens.
OBJECTIVE: Our study has analyzed the clinical characteristics and pathogen spectrum of the lower respiratory tract associated with co-infection or superinfection in Guangzhou during the outbreak of the Omicron strain, particularly after the relaxation of the epidemic prevention and control strategy in
China. This study will likely prompt further research into the specific issue, which will benefit clinical practice.