近日，来自英国东安格利亚大学的Justin O’Grady研究组，开发了可用于快速诊断临床下呼吸道细菌感染的纳米孔宏基因组测序技术。2019年7月出版的国际学术期刊《自然—生物技术》发表了这一最新研究成果。

研究人员开发了一个用于下呼吸道感染细菌诊断的宏基因组方法，这个方法能够高效去除宿主DNA并通过纳米孔技术进行测序。这个方法在40个样品上进行了测试，并在优化后进一步测试了41个样品。优化后的方法从样本到结果仅需6小时，与培养的方式比起来，其检测病原体达到了96.6%的灵敏度和41.7%的特异性，甚至还能准确地检测到耐抗生素基因。通过qPCR以及病原微生物特有基因分析的验证，这个方法的特异性和灵敏度能够提升到100%。因此，纳米孔宏基因组测序技术能够快速并准确地鉴别下呼吸道细菌感染，并有可能降低广谱抗生素的使用。

研究人员表示，临床诊断下呼吸道细菌感染的金标准是通过病原体培养，但这种方法的灵敏度较低并且对于及时指导抗菌治疗而言太慢。宏基因组测序技术能够比培养更快地鉴别病原体类型，但在这项技术变得可行之前需要去除样本中大量的人类DNA信号。

附：英文原文

Title: Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection

Author: Themoula Charalampous, Gemma L. Kay, Hollian Richardson, Alp Aydin, Rossella Baldan, Christopher Jeanes, Duncan Rae, Sara Grundy, Daniel J. Turner, John Wain, Richard M. Leggett, David M. Livermore, Justin OGrady

Issue&Volume:Volume37 Issue7

Abstract: The gold standard for clinical diagnosis of bacterial lower respiratory infections (LRIs) is culture, which has poor sensitivity and is too slow to guide early, targeted antimicrobial therapy. Metagenomic sequencing could identify LRI pathogens much faster than culture, but methods are needed to remove the large amount of human DNA present in these samples for this approach to be feasible. We developed a metagenomics method for bacterial LRI diagnosis that features efficient saponin-based host DNA depletion and nanopore sequencing. Our pilot method was tested on 40 samples, then optimized and tested on a further 41 samples. Our optimized method (6h from sample to result) was 96.6% sensitive and 41.7% specific for pathogen detection compared with culture and we could accurately detect antibiotic resistance genes. After confirmatory quantitative PCR and pathobiont-specific gene analyses, specificity and sensitivity increased to 100%. Nanopore metagenomics can rapidly and accurately characterize bacterial LRIs and might contribute to a reduction in broad-spectrum antibiotic use.

DOI: 10.1038/s41587-019-0156-5

Source: https://www.nature.com/articles/s41587-019-0156-5