送检脑脊液病原宏基因组第二代测序技术客观标准再探讨

doi:10.3969/j.issn.1672-6731.2021.05.004

中国现代神经疾病杂志 ›› 2021, Vol. 21 ›› Issue (5): 350-357. doi: 10.3969/j.issn.1672-6731.2021.05.004

• 中枢神经系统感染性疾病 • 上一篇下一篇

2 送检脑脊液病原宏基因组第二代测序技术客观标准再探讨

刘磊¹, 张景晓¹, 狄晓萌¹, 谢竹霄¹, 王佳伟^1,2

1 100730 首都医科大学附属北京同仁医院神经内科;
2 100730 首都医科大学附属北京同仁医院中心实验室

收稿日期:2021-05-13 出版日期:2021-05-25 发布日期:2021-05-28
通讯作者: 王佳伟,Email:wangjwcq@163.com
基金资助:
国家自然科学基金资助项目（项目编号：81771313）；国家自然科学基金青年科学基金资助项目（项目编号：81301029）；北京市自然科学基金资助项目（项目编号：7192040）；北京市医院管理局“青苗”计划专项经费资助项目（项目编号：QML20150206）；北京市科技计划课题“首都特色”项目（项目编号：Z171100001017039）；首都卫生发展科研专项项目（项目编号：首发2020-2-2056）

Discussion on objective inclusion criteria for sending cerebrospinal fluid pathogen metagenomic next-generation sequencing

LIU Lei¹, ZHANG Jing-xiao¹, DI Xiao-meng¹, XIE Zhu-xiao¹, WANG Jia-wei^1,2

1 Department of Neurology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China;
2 Medical Research Center, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China

Received:2021-05-13 Online:2021-05-25 Published:2021-05-28
Supported by:
This study was supported by the National Natural Science Foundation of China (No. 81771313), the National Natural Science Foundation for Young Scientists of China (No. 81301029), Beijing Municipal Natural Science Foundation (No. 7192040), Beijing Hospitals Authority Youth Program (No. QML20150206), Beijing Science and Technology Project Characteristics of the Capital Project (No. Z171100001017039), and Key Project of Capital Medical Development (No. 2020-2-2056).

摘要/Abstract

摘要：

目的对比分析脑脊液病原宏基因组第二代测序技术（mNGS）、传统病原学检测与临床最终诊断中枢神经系统感染的符合程度，探讨脑脊液病原mNGS测序的送检标准。方法 2017年3月至2020年4月首都医科大学附属北京同仁医院对35例需排除中枢神经系统感染的患者送检脑脊液标本，同时行脑脊液病原mNGS测序和传统病原学检测，分别计算两种检测方法的灵敏度、特异度和Youden指数；绘制受试者工作特征（ROC）曲线并计算曲线下面积（AUC），比较两种检测方法的诊断效能。根据送检脑脊液病原mNGS测序的客观标准进行评分（满足1项计为1），计算不同评分下mNGS测序的阳性符合率。结果 35例患者中19例临床最终诊断为中枢神经系统感染。有18例脑脊液病原mNGS测序呈阳性，总阳性率为51.43%（18/35）；有17例传统病原学检测呈阳性，总阳性率约48.57%（17/35）。临床最终诊断为中枢神经系统感染的患者中17例mNGS测序呈阳性，其诊断灵敏度为17/19、特异度为15/16，Youden指数为0.832；14例传统病原学检测呈阳性，其诊断灵敏度为14/19、特异度为13/16，Youden指数为0.612。ROC曲线显示，脑脊液病原mNGS测序的曲线下面积为0.916（95% CI：0.822~1.000，P=0.000）；传统病原学检测的曲线下面积为0.806（95% CI：0.674~0.938，P=0.000）；二者诊断效能差异无统计学意义（Z=1.245，P=0.213）。根据送检脑脊液病原mNGS测序的客观标准评分，mNGS测序的阳性符合率分别是0为0/4、1为0/2、2为1/8、3为3/4、4为4/6、5为3/4、6为6/7，随着评分的增加，mNGS测序阳性符合率呈升高趋势，其中评分≥ 3组mNGS测序阳性符合率高于评分< 3组（16/21对1/14；Fisher确切概率法：P=0.000）。结论脑脊液病原mNGS测序可以辅助明确诊断中枢神经系统感染，进一步按照基于临床和常规辅助检查的客观标准送检脑脊液可以提高mNGS测序的阳性符合率。

关键词: 中枢神经系统感染, 脑脊髓液, 宏基因组, 序列分析, DNA, ROC曲线

Abstract:

Objective By comparing consistency of metagenomic next-generation sequencing (mNGS) results and final clinical diagnoses of central nervous system infection, we discuss the objective inclusion criteria for suspected central nervous system infection patients sending CSF pathogen mNGS. Methods From March 2017 to April 2020, Department of Neurology, Beijing Tongren Hospital, Capital Medical University sent CSF of 35 patients for pathogen mNGS and conventional pathogen testing to exclude central nervous system infection. Sensitivities, specificities and Youden's index of mNGS as well as conventional pathogen testing were calculated and compared. We also drew receiver operating characteristic (ROC) curves and calculated areas under the curve (AUC) to compared diagnostic efficacies of two methods. All patients were then scored according to objective inclusion criteria for sending samples (one score for one item). Positive coincidence rates of CSF pathogen mNGS and final clinical diagnoses of central nervous system infection of each score were also calculated. Results Nineteen of 35 patients enrolled were finally clinical diagnosed as central nervous system infection. Eighteen cases were positive by CSF pathogen mNGS, with positive rate 51.43% (18/35). Seventeen cases were positive by conventional pathogen testing with positive rate 48.57% (17/35). Seventeen cases of clinical diagnosed central nervous system infection were CSF pathogen mNGS positive, with diagnostic sensitivity 17/19, specificity 15/16 and Youden index 0.832. Fourteen cases of clinical diagnosed central nervous system infection were conventional pathogen testing positive, with diagnostic sensitivity 14/19, specificity 13/16 and Youden index 0.612. ROC curve showed the AUC of CSF pathogen mNGS was 0.916 (95%CI:0.822-1.000, P=0.000), and AUC of conventional pathogen testing was 0.806 (95%CI:0.674-0.938, P=0.000). There was no difference in diagnostic efficacies between CSF pathogen mNGS and conventional pathogen testing (Z=1.245, P=0.213). According to objective inclusion criteria for sending pathogen mNGS of CBF, the positive coincidence rates of mNGS were 0 score (0/4), 1 score (0/2), 2 scores (1/8), 3 scores (3/4), 4 scores (4/6), 5 scores (3/4), 6 scores (6/7). The positive coincidence rates of mNGS showed an overall trend of increase with scores, and notably cases ≥ 3 scores had higher positive coincidence rates than cases < 3 scores (Fisher exact probability:P=0.000). Conclusions CSF pathogen mNGS can assist in accurate diagnosis of central nervous system infection. Sending CSF according to objective inclusion criteria based on clinical and routine auxiliary examination results can improve positive coincidence rate of pathogen mNGS.

Key words: Central nervous system infections, Cerebrospinal fluid, Metagenome, Sequence analysis, DNA, ROC curve

刘磊, 张景晓, 狄晓萌, 谢竹霄, 王佳伟. 送检脑脊液病原宏基因组第二代测序技术客观标准再探讨[J]. 中国现代神经疾病杂志, 2021, 21(5): 350-357.

LIU Lei, ZHANG Jing-xiao, DI Xiao-meng, XIE Zhu-xiao, WANG Jia-wei. Discussion on objective inclusion criteria for sending cerebrospinal fluid pathogen metagenomic next-generation sequencing[J]. Chinese Journal of Contemporary Neurology and Neurosurgery, 2021, 21(5): 350-357.

http://journal11.magtechjournal.com/cjcnn/CN/Y2021/V21/I5/350

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