美国加州大学旧金山分校Charles Y. Chiu团队取得最新进展。他们通过宏基因组学二代测序（mNGS）对感染的体液进行快速病原体检测。相关论文于2020年11月9日发表在《自然-医学》杂志上。

他们使用体液中的无细胞DNA进行了mNGS测试，以鉴定病原体。使用两种测序平台对160名急性病患者的182种体液的mNGS测试性能进行了评估，并与使用培养物、16S细菌PCR和/或28S-内部转录核糖体基因间隔子（28S-ITS）真菌PCR的微生物学测试进行对比。

通过Illumina测序，细菌的检测灵敏度和检测特异性分别为79％和91％，真菌为91％和89％；通过纳米孔测序，细菌分别为75％和81％，真菌为91％和100％。在12例培养/ PCR阴性体液但最终被确诊为感染的患者中，有7例（58％）是mNGS阳性。实时计算分析可通过中值50分钟测序和6小时样品到应答时间的纳米孔测序实现病原体鉴定。

据悉，快速的mNGS测试是诊断体液未知感染的潜在工具。

附：英文原文

Title: Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids

Author: Wei Gu, Xianding Deng, Marco Lee, Yasemin D. Sucu, Shaun Arevalo, Doug Stryke, Scot Federman, Allan Gopez, Kevin Reyes, Kelsey Zorn, Hannah Sample, Guixia Yu, Gurpreet Ishpuniani, Benjamin Briggs, Eric D. Chow, Amy Berger, Michael R. Wilson, Candace Wang, Elaine Hsu, Steve Miller, Joseph L. DeRisi, Charles Y. Chiu

Issue&Volume: 2020-11-09

Abstract: We developed a metagenomic next-generation sequencing (mNGS) test using cell-free DNA from body fluids to identify pathogens. The performance of mNGS testing of 182body fluids from 160patients withacute illness was evaluated using two sequencing platforms in comparison to microbiological testing using culture, 16S bacterial PCR and/or 28S–internal transcribed ribosomal gene spacer (28S–ITS) fungal PCR. Test sensitivity and specificity of detection were 79 and 91% for bacteria and 91 and 89% for fungi, respectively, by Illumina sequencing; and 75 and 81% for bacteria and 91 and 100% for fungi, respectively, by nanopore sequencing. In a case series of 12patients with culture/PCR-negative body fluids but for whom an infectious diagnosis was ultimately established, seven (58%) were mNGS positive. Real-time computational analysis enabled pathogen identification by nanopore sequencing in a median 50-min sequencing and 6-h sample-to-answer time. Rapid mNGS testing is a promising tool for diagnosis of unknown infections from body fluids.

DOI: 10.1038/s41591-020-1105-z

Source: https://www.nature.com/articles/s41591-020-1105-z