宏基因组测序在临床重症感染患者寻找病原体中的应用

Metagenomic Sequencing for Pathogens Detection in a Critically Ill Patient

目的应用宏基因组测序检测重症患者感染病原体,了解在重症患者中的应用对寻找感染病原体的帮助。方法对1例表现为腹痛、逐渐进展至意识障碍合并严重感染的急性重症胰腺炎患者,用传统方法检测病原体的同时应用宏基因组测序。传统方法包括:常规涂片、培养,VitekII Compact全自动微生物鉴定和药敏分析,实时荧光定量PCR检测病毒载量,以及免疫组织化学等病理检查。宏基因组测序则采用基于BGISEQ-100高通量测序平台的二代测序,剔除人类宿主序列后,将保留下来的序列与包含病毒、细菌、真菌和寄生虫基因组序列的微生物基因组数据库进行比对,确定标本中所有的病原体。结果传统检验发现该患者感染了耐甲氧西林的金黄色葡萄球菌、耐碳青霉烯的肺炎克雷伯菌和耐碳青霉烯的鲍曼不动杆菌。宏基因组测序结果不仅检出了前述病原体,还检查出了加重疾病恶化的巨细胞病毒(CMV),耗时约5 d。实时荧光定量PCR补充病毒载量检测证实其CMV载量为189 000 copies/mL。结论在本例重症患者中,宏基因组测序一次性快速准确检出了3种病原菌和1种病毒,可辅助重症患者感染病的快速诊断。

Objective To detect pathogens in a critically ill patient using metagenomic sequencing. Methods A critically ill patient with severe acute pancreatitis suffered from abdominal pain and progressed into unconsciousness. Tissue smear, culture, automated biochemical identification and antibiotic susceptibility test, viral load determination by real-time fluorescence quantitative PCR, and immunohistochemical pathological tests were performed to detect pathogens, in addition to metagenomic sequencing based on the BGISEQ-100 high throughput sequencing platform. The sequences exclusive of host sequences were searched in the microbial genome database including viruses, bacteria, fungi and parasites. Results The patient was infected with methicillin-resistant Staphylococcus aureus, carbapenem-resistant Klebsiella pneumoniae and carbapenem-resistant Acinetobacter baumannii, verified by both the routine methods and the metagenomic sequencing. The metagenomic sequencing also detected cytomegalovirus(CMV) with a turn-around time of 5 days. Real-time fluorescent quantitative PCR confirmed 189 000 copies/mL CMV load. Conclusion In this case, three species of bacteria and one virus were detected by metagenomic sequencing quickly and accurately. Metagenomic sequencing may be helpful for diagnosing infectious diseases in critically ill patients.