下一代测序(NGS)彻底改变了临床微生物学,特别是在诊断呼吸道传染病和进行流行病学调查方面。这篇叙述性综述总结了常规呼吸道感染诊断的常规方法,包括文化,涂片显微镜,免疫测定,图像技术以及聚合酶链反应(PCR)。与传统方法相比,有一种新的检测技术,测序技术,在这里,我们主要关注下一代测序NGS,尤其是宏基因组NGS(mNGS)。NGS提供优于传统方法的显著优势。首先,mNGS消除了对病原体的假设,导致更快,更准确的结果,从而减少诊断时间。其次,它允许对已知和新的病原体进行公正的鉴定,提供广谱覆盖。第三,mNGS不仅可以识别病原体,还可以表征微生物群,分析人类宿主的反应,并检测抗性基因和毒力因子。它可以补充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,由于血浆中病原体DNA的延长存活,mNGS受到的影响较小,扩大其适用性。然而,完全融入临床实践的障碍仍然存在,主要是由于成本限制以及灵敏度和周转时间的限制。尽管面临这些挑战,正在进行的改进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基石技术。
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.