宏基因二代测序技术对非结核分枝杆菌肺病的诊断价值

doi:10.19982/j.issn.1000-6621.20220298

摘要/Abstract

摘要：

目的: 探讨宏基因二代测序技术(metagenomic next-generation sequencing,mNGS)在非结核分枝杆菌肺病(nontuberculous mycobacterial pulmonary disease,NTM-PD)中的诊断价值。方法: 回顾性搜集2020年1月至2022年2月浙江大学医学院附属杭州市胸科医院结核病诊疗中心收治的123例疑似NTM-PD患者的资料。根据诊断标准,123例疑似NTM-PD患者最终诊断为NTM-PD患者(NTM-PD组;74例)和非NTM-PD患者(非NTM-PD组;49例)。123例患者肺泡灌洗液、痰液、肺组织同时进行mNGS、PCR荧光探针法、BACTEC MGIT 960分枝杆菌全自动快速液体培养(简称“液体培养”),比较3种方法的诊断效能。结果: 以最终临床诊断结果为标准,mNGS、液体培养及PCR荧光探针法检测NTM-PD的敏感度分别为83.8%(62/74)、78.4%(58/74)、67.6%(50/74),特异度分别为65.3%(32/49)、91.8%(45/49)、87.8%(43/49),诊断一致率分别为76.4%(94/123)、83.7%(103/123)、75.6%(93/123),Kappa值分别为0.524、0.647、0.521。以液体培养结果为标准,mNGS和PCR荧光探针法检测NTM-PD的敏感度分别为87.1%(54/62)和75.8%(47/62),特异度分别为59.0%(36/61)和85.2%(52/61),诊断一致率分别为73.2%(90/123)和80.5%(99/123),Kappa值分别为0.462和0.587。对74例NTM-PD患者菌株进行mNGS及基因芯片法菌种鉴定,以基因芯片法为菌种鉴定标准,mNGS检测的准确率为63.8%(37/58)。结论: 在NTM-PD的诊断中,mNGS检测的敏感度较高,可直接鉴定至菌种水平,但特异度较低,应重点提高检测特异度,以更好地服务于临床工作。

关键词: 基因组学, 分枝杆菌,非典型性, 诊断技术和方法, 对比研究

Abstract:

Objective: To investigate the diagnostic value of metagenomic next-generation sequencing (mNGS) in nontuberculous mycobacterial pulmonary disease (NTM-PD). Methods: The data of 123 patients with suspected NTM-PD admitted to the Tuberculosis Diagnosis and Treatment Center of Hangzhou Chest Hospital, Zhejiang University School of Medicine from January 2020 to February 2022 were retrospectively selected. According to the diagnostic criteria, 123 suspected NTM-PD patients were finally diagnosed as NTM-PD patients (NTM-PD group; n=74) and non-NTM-PD patients (non-NTM-PD group; n=49). All the patients underwent mNGS, PCR-fluorescence probe and mycobacterial culture in alveolar lavage fluid, sputum and lung tissue simultaneously. The sensitivity and specificity of the three methods were compared. Results: Based on the final clinical diagnosis, the sensitivities of mNGS, liquid culture and PCR fluorescence probe for NTM-PD detection were 83.8% (62/74), 78.4% (58/74) and 67.6% (50/74), respectively, the specificities were 65.3% (32/49), 91.8% (45/49) and 87.8% (43/49), respectively, the consistencies in diagnosis were 76.4% (94/123), 83.7% (103/123) and 75.6% (93/123), respectively, with Kappa values of 0.524, 0.647 and 0.521, respectively. Using liquid culture results as the standard, of mNGS and PCR fluorescence probe for NTM-PD detection, the sensitivities were 87.1% (54/62) and 75.8% (47/62), and specificities were 59.0% (36/61) and 85.2% (52/61), respectively, the consistencies in diagnosis were 73.2% (90/123) and 80.5% (99/123), and the Kappa values were 0.462 and 0.587, respectively. The strains of 74 NTM-PD patients were identified by mNGS and gene chip method, and the concordance rate of two detecting methods was 63.8% (37/58) with gene chip method as the standard for strain identification. Conclusion: For the diagnosis of NTM-PD, of mNGS detection, the sensitivity is high, it can directly identify the strains; however, the specificity is low, the specificity should be focused on improving, to better serve the clinic.

Key words: Genomics, Mycobacteria, atypical, Diagnostic techniques and procedures, Comparative study

中图分类号:

R563

孔娇, 陈园园, 蔡青山, 赵亚芳, 喻义杭. 宏基因二代测序技术对非结核分枝杆菌肺病的诊断价值[J]. 中国防痨杂志, 2022, 44(11): 1135-1140. doi: 10.19982/j.issn.1000-6621.20220298

Kong Jiao, Chen Yuanyuan, Cai Qingshan, Zhao Yafang, Yu Yihang. Diagnostic value of metagenomic next-generation sequencing in nontuberculous mycobacterial pulmonary disease[J]. Chinese Journal of Antituberculosis, 2022, 44(11): 1135-1140. doi: 10.19982/j.issn.1000-6621.20220298

图/表 4

表1

两组患者一般资料及临床特征的比较

指标	NTM-PD组(74例)	非NTM-PD组(49例)	统计检验值	P值
年龄(岁, $x ¯$ ±s)	58.91±13.57	57.49±10.90	t=0.868	0.093
性别[例(构成比,%)]			χ²=0.036	0.499
男性	41(55.4)	28(57.1)
女性	33(44.6)	21(42.9)
样本类型[例(构成比,%)]
肺泡灌洗液	63(85.1)	43(87.8)	χ²=0.170	0.448
痰液^a	7(9.5)	3(6.1)	χ²=0.106	0.380
肺穿刺组织^a	4(5.4)	2(4.1)	χ²=0.000	0.548
胸腔积液^a	0(0.0)	1(2.0)	χ²=0.043	0.398
合并基础疾病[例(发生率,%)]
支气管扩张	17(23.0)	12(24.5)	χ²=0.038	0.506
慢性阻塞性肺疾病	12(16.2)	8(16.3)	χ²=0.000	0.588
肺结核病史	14(18.9)	10(20.4)	χ²=0.042	0.507
实体肿瘤^a	5(6.8)	3(6.1)	χ²=0.000	0.600
自身免疫性疾病^a	5(6.8)	2(4.1)	χ²=0.053	0.420

表1

表2

表3

表4

参考文献 13

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检测方法	临床诊断(例)		敏感度 (%,95%CI)	特异度 (%,95%CI)	阳性预测值 (%,95%CI)	阴性预测值 (%,95%CI)	一致率 (%,95%CI)	Kappa值 (95%CI)
检测方法	阳性	阴性	敏感度 (%,95%CI)	特异度 (%,95%CI)	阳性预测值 (%,95%CI)	阴性预测值 (%,95%CI)	一致率 (%,95%CI)	Kappa值 (95%CI)
mNGS			83.8 (74.0~91.3)	65.3 (50.4~78.3)	78.5 (67.8~86.9)	72.7 (57.2~85.0)	76.4 (66.9~80.2)	0.524 (0.338~0.652)
阳性	62	17
阴性	12	32
液体培养			78.4 (67.2~87.1)	91.8 (80.4~97.7)	93.6 (84.3~98.2)	73.8 (60.9~84.2)	83.7 (77.2~90.2)	0.647 (0.550~0.802)
阳性	58	4
阴性	16	45
PCR荧光探针			67.6 (55.6~78.0)	87.8 (75.2~95.3)	89.3 (78.1~95.9)	64.2 (51.5~75.5)	75.6 (68.0~83.2)	0.521 (0.376~0.663)
阳性	50	6
阴性	24	43

检测方法	液体培养(例)		敏感度 (%,95%CI)	特异度 (%,95%CI)	阳性预测值 (%,95%CI)	阴性预测值 (%,95%CI)	一致率 (%,95%CI)	Kappa值 (95%CI)
检测方法	阳性	阴性	敏感度 (%,95%CI)	特异度 (%,95%CI)	阳性预测值 (%,95%CI)	阴性预测值 (%,95%CI)	一致率 (%,95%CI)	Kappa值 (95%CI)
mNGS			87.1 (76.1~94.2)	59.0 (45.6~71.4)	68.4 (56.9~78.3)	81.8 (67.2~91.8)	73.2 (65.4~81.0)	0.462 (0.313~0.611)
阳性	54	25
阴性	8	36
PCR荧光探针法			75.8 (63.2~85.7)	85.2 (73.8~93.0)	83.9 (71.6~92.3)	77.6 (65.7~86.8)	80.5 (73.4~87.5)	0.587 (0.460~0.740)
阳性	47	9
阴性	15	52

菌种	基因芯片法		宏基因二代测序技术
菌种	例数	构成比(%)	例数	构成比(%)
胞内分枝杆菌	38	65.5	25	39.0
鸟分枝杆菌	9	15.5	18	28.1
堪萨斯分枝杆菌	6	10.3	5	7.8
龟-脓肿分枝杆菌	4	7.0	10	15.6
戈登分枝杆菌	1	1.7	0	0.0
副胞内分枝杆菌	0	0.0	4	6.3
蟾蜍分枝杆菌	0	0.0	1	1.6
马萨分枝杆菌	0	0.0	1	1.6

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