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 182 body fluids from 160 patients with acute 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 12 patients 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.

我们开发了一种宏基因组下一代测序 (mNGS) 测试，使用来自体液的无细胞 DNA 来识别病原体。与使用培养、16S 细菌 PCR 和/或 28S-内部转录核糖体基因间隔区 (28S-ITS) 真菌 PCR 的微生物测试相比，使用两个测序平台评估了 mNGS 对 160 名急性疾病患者的 182 份体液的检测性能。通过 Illumina 测序，细菌的检测灵敏度和特异性分别为 79% 和 91%，真菌为 91% 和 89%；通过纳米孔测序，细菌分别为 75% 和 81%，真菌分别为 91% 和 100%。在 12 名体液培养/PCR 阴性但最终确诊感染的患者的病例系列中，有 7 名 (58%) mNGS 阳性。实时计算分析能够通过纳米孔测序在平均 50 分钟的测序时间和 6 小时的样本到应答时间内识别病原体。快速 mNGS 检测是诊断未知体液感染的很有前途的工具。