呼吸系统感染发病率高，早期明确感染的病原体是提高治愈率、降低死亡率的关键。目前病原体培养仍是临床病原学诊断的主要方式，但其敏感性低、耗时较长，不利于早期诊断和治疗。宏基因组学测序技术具有覆盖病原体广泛、快速、无偏倚、无需特异性扩增的优势，在鉴定罕见、混合感染、免疫抑制患者感染和常规检测方法难以检测到病原体的诊断中有较高的临床应用价值；但其也有特异性较低、公认判读标准缺乏、测序结果与治疗关系不明确、耐药基因检测困难、价格较高等不足。在临床应用中，宏基因组学测序与传统微生物检测技术具有相互补充的作用，两者结合使用能够提高临床诊断效能。本文就近年来宏基因组学测序方法在临床的应用进展进行综述。

The incidence of respiratory infections is high, and early identification of infectious pathogens is the key to improving clinical results. Metagenomics next-generation sequencing (mNGS) has the advantages of being whole spectrum, time saving, no specific amplification of pathogens, and has high clinical application value in the identification of rare infections, mixed infections, immunosuppressive patient infection and the diagnosis of pathogens that are difficult to be detected by conventional methods. However, mNGS results of some cases have low specificity, lack recognized interpretation standards, have unclear relationships between sequencing results and treatment, and have difficulties testing drug-resistant genes. In clinical application present, mNGS and traditional microbial detection technology have a complementary effect and the combination of the two can improve the clinical diagnosis efficiency.