Zhang Zhen, Tian Lei
Department of Pharmacy, Tongji Hospital, Tongji Medical College,Huazhong University of Science and Technology, Wuhan, Hubei Province, Hubei Province, China.
Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China.
BMC Microbiol. 2025 Mar 28;25(1):173. doi: 10.1186/s12866-025-03908-6.
Interpreting the results of metagenomic next-generation sequencing (mNGS) presents a significant challenge in both clinical and laboratory contexts.
A retrospective analysis was conducted to validate mNGS findings, with a particular emphasis on Mycobacterium tuberculosis, Mycoplasma pneumoniae, and Pneumocystis jirovecii as representative pathogens, examined from both clinical and laboratory perspectives.
Based on a comprehensive clinical analysis, the mNGS demonstrated detection accuracies for M. tuberculosis, M. pneumoniae, and P. jirovecii of 87.0% (60 out of 69; 95% confidence interval [CI], 77.04%-92.99%), 97.6% (81 out of 83; 95% CI, 91.63%-99.34%), and 78.9% (45 out of 57; 95% CI, 66.72%-87.53%), respectively. Conversely, when incorporating laboratory confirmation from a variety of detection methodologies, the accuracy rates for mNGS in identifying M. tuberculosis, M. pneumoniae, and P. jirovecii were 92.7% (51 out of 55; 95% CI, 82.74%-97.14%), 82.3% (51 out of 62; 95% CI, 70.96%-89.80%), and 83.9% (26 out of 31; 95% CI, 67.36%-92.91%), respectively. Additionally, our analysis revealed no statistically significant difference in read counts and relative abundances between mNGS results deemed clinically as false positives and those considered true positives (P < 0.05).
In contemporary clinical practice, the detection of positive results from mNGS is notably high from both laboratory and clinical standpoints. Nonetheless, the interpretation of results with low read counts presents significant challenges for both clinical and laboratory environments under current conditions.
在临床和实验室环境中，解读宏基因组下一代测序（mNGS）结果都面临重大挑战。
进行了一项回顾性分析以验证mNGS的结果，特别着重于结核分枝杆菌、肺炎支原体和耶氏肺孢子菌这三种代表性病原体，从临床和实验室两个角度进行研究。
基于全面的临床分析，mNGS对结核分枝杆菌、肺炎支原体和耶氏肺孢子菌的检测准确率分别为87.0%（69例中的60例；95%置信区间[CI]，77.04%-92.99%）、97.6%（83例中的81例；95%CI，91.63%-99.34%）和78.9%（57例中的45例；95%CI，66.72%-87.53%）。相反，当结合多种检测方法的实验室确认结果时，mNGS识别结核分枝杆菌、肺炎支原体和耶氏肺孢子菌的准确率分别为92.7%（55例中的51例；95%CI，82.74%-97.14%）、82.3%（62例中的51例；95%CI，70.96%-89.80%）和83.9%（31例中的26例；95%CI，67.36%-92.91%）。此外，我们的分析显示，在临床判定为假阳性的mNGS结果与判定为真阳性的结果之间，读取计数和相对丰度没有统计学上的显著差异（P<0.05）。
在当代临床实践中，从实验室和临床角度来看，mNGS检测出阳性结果的比例都相当高。然而，在当前条件下，对于读取计数较低的结果进行解读，在临床和实验室环境中都面临重大挑战。
