Chen Jingyuan, Qin Zhen, Jia Zhongwei
Department of Global Health, School of Public Health, Peking University, Beijing, China.
School of Public Health, Peking University, Beijing, China.
Infection. 2024 Dec;52(6):2169-2181. doi: 10.1007/s15010-024-02360-4. Epub 2024 Aug 16.
Next-generation sequencing (NGS) has revolutionized clinical microbiology, particularly in diagnosing respiratory infectious diseases and conducting epidemiological investigations. This narrative review summarizes conventional methods for routine respiratory infection diagnosis, including culture, smear microscopy, immunological assays, image techniques as well as polymerase chain reaction(PCR). In contrast to conventional methods, there is a new detection technology, sequencing technology, and here we mainly focus on the next-generation sequencing NGS, especially metagenomic NGS(mNGS). NGS offers significant advantages over traditional methods. Firstly, mNGS eliminates assumptions about pathogens, leading to faster and more accurate results, thus reducing diagnostic time. Secondly, it allows unbiased identification of known and novel pathogens, offering broad-spectrum coverage. Thirdly, mNGS not only identifies pathogens but also characterizes microbiomes, analyzes human host responses, and detects resistance genes and virulence factors. It can complement targeted sequencing for bacterial and fungal classification. Unlike traditional methods affected by antibiotics, mNGS is less influenced due to the extended survival of pathogen DNA in plasma, broadening its applicability. However, barriers to full integration into clinical practice persist, primarily due to cost constraints and limitations in sensitivity and turnaround time. Despite these challenges, ongoing advancements aim to improve cost-effectiveness and efficiency, making NGS a cornerstone technology for global respiratory infection diagnosis.
下一代测序（NGS）彻底改变了临床微生物学，尤其是在诊断呼吸道传染病和开展流行病学调查方面。这篇叙述性综述总结了常规呼吸道感染诊断的传统方法，包括培养、涂片显微镜检查、免疫测定、影像技术以及聚合酶链反应（PCR）。与传统方法不同，出现了一种新的检测技术，即测序技术，在此我们主要关注下一代测序（NGS），特别是宏基因组NGS（mNGS）。NGS相对于传统方法具有显著优势。首先，mNGS无需对病原体进行假设，可得出更快、更准确的结果，从而缩短诊断时间。其次，它能够无偏差地鉴定已知和新型病原体，提供广谱覆盖。第三，mNGS不仅能鉴定病原体，还能对微生物群落进行表征、分析人类宿主反应以及检测耐药基因和毒力因子。它可以补充针对细菌和真菌分类的靶向测序。与受抗生素影响的传统方法不同，mNGS受影响较小，因为病原体DNA在血浆中的存活时间延长，拓宽了其适用性。然而，全面融入临床实践仍存在障碍，主要是由于成本限制以及灵敏度和周转时间方面的局限性。尽管存在这些挑战，但正在进行的进展旨在提高成本效益和效率，使NGS成为全球呼吸道感染诊断的一项基石技术。
