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中国防痨杂志 ›› 2022, Vol. 44 ›› Issue (11): 1126-1134.doi: 10.19982/j.issn.1000-6621.20220224

• 论著 • 上一篇    下一篇

浙江省结核分枝杆菌耐药突变特征及其与基因型相关性分析

吴坤阳1, 陆烨玮2, 张明五1, 朱业蕾1, 李相辰2, 潘军航1, 王晓萌1, 王蔚3, 江敏敏4, 彭小军2, 王炜欣2, 高俊顺2, 柳正卫1()   

  1. 1浙江省疾病预防控制中心结核病预防控制所结核病实验室,杭州 310051
    2杭州广科安德生物科技有限公司生物信息部,杭州 311215
    3嘉兴市第一医院检验科,嘉兴 314001
    4嘉善县第一人民医院检验科,嘉兴 314199
  • 收稿日期:2022-06-08 出版日期:2022-11-10 发布日期:2022-11-03
  • 通信作者: 柳正卫 E-mail:zhwliu@cdc.zj.cn
  • 基金资助:
    浙江省医药卫生科技计划项目(2020keyan512)

Analysis on characteristic of drug resistance-associated gene mutations and the correlation with genotypes among Mycobacterium tuberculosis isolates in Zhejiang Province

Wu Kunyang1, Lu Yewei2, Zhang Mingwu1, Zhu Yelei1, Li Xiangchen2, Pan Junhang1, Wang Xiaomeng1, Wang Wei3, Jiang Minmin4, Peng Xiaojun2, Wang Weixin2, Gao Junshun2, Liu Zhengwei1()   

  1. 1Laboratory for Department of TB Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
    2Department of Bioinformatics, Cosmos Wisdom Biotech Co., Ltd., Hangzhou 311215, China
    3Department of Clinical Laboratory, the First Hospital of Jiaxing, Jiaxing 314001, China
    4Department of Clinical Laboratory, the First People’s Hospital of Jiashan, Jiaxing 314199, China
  • Received:2022-06-08 Online:2022-11-10 Published:2022-11-03
  • Contact: Liu Zhengwei E-mail:zhwliu@cdc.zj.cn
  • Supported by:
    Zhejiang Provincial Medical and Health Science and Technology Plan Project(2020keyan512)

摘要:

目的: 评价全基因组测序(whole-genome sequencing,WGS)对浙江省结核分枝杆菌(Mycobacterium tuberculosis,MTB)耐药相关基因突变特征及其与基因型相关性的耐药分析和检测效能。方法: 对2018—2019年浙江省第五次结核病耐药监测项目收集的808株MTB菌株进行14种抗结核药物的WGS分析。鉴定菌株的基因型及耐药相关基因突变,并对二者相关性,以及WGS检测异烟肼的药物敏感性试验(简称“药敏试验”)结果与表型药敏试验结果的一致性进行分析。结果: 808株MTB菌株中,153株对11种抗结核药物(异烟肼、利福平、乙胺丁醇、吡嗪酰胺、链霉素、氟喹诺酮类、阿米卡星、卡那霉素、卷曲霉素、乙硫异烟胺、对氨基水杨酸)发生了耐药相关基因突变,总突变率为18.9%。主要耐药突变类型分别为katG-315-S/T[异烟肼,60.0%(45/75)]、rpoB-450-S/L[利福平,57.1%(16/28)]、embB-306-M/V[乙胺丁醇,43.8%(7/16)]、rpsL-43-K/R[链霉素,65.5%(36/55)]、gyrA-94-D/G[氟喹诺酮类,36.6%(15/41)]、rrs-1402-C/A(阿米卡星,3/3)、rrs-1402-C/A(卡那霉素,3/4)、rrs-1402-C/A(卷曲霉素,3/3)、inhA-15-C/T[乙硫异烟胺,65.0%(13/20)]、thyA-75-H/N(对氨基水杨酸,7/8)。rpsL基因和katG-315位点在北京基因型中的耐药突变率[均为6.8%(40/586)]均明显高于二者在非北京基因型中的突变率[0.0%(0/222)和3.2%(7/222)],差异均有统计学意义(χ2=15.943,P=0.000;χ2=3.964,P=0.046)。WGS耐药性分析对于异烟肼的检测敏感度、特异度、阳性预测值、阴性预测值、一致率和Kappa值分别为87.5%(49/56)、98.0%(680/694)、77.8%(49/63)、99.0%(680/687)、97.2%(729/750)和0.808。结论: 浙江省MTB菌株对11种抗结核药物耐药相关基因突变以katGrpoBembBpncArpsLgyrArrsthyAinhA基因上的突变为主,其中rpsL基因、katG-315和rpsL-43位点突变与北京基因型相关。WGS耐药性分析对于异烟肼具有全面的耐药检测性能,但对个别基因突变位点的检测性能较弱。

关键词: 分枝杆菌,结核, 抗药物性, 序列分析,DNA, 突变, 基因型

Abstract:

Objective: To evaluate the drug resistance analysis and detection performance of whole-genome sequencing (WGS) on the characteristic of drug resistance-associated gene mutations and its correlation with genotypes among Mycobacterium tuberculosis (MTB) isolates in Zhejiang Province. Methods: WGS analysis of 14 drugs was performed on 808 MTB strains collected from the fifth tuberculosis drug resistance surveillance project in Zhejiang Province from 2018 and 2019. MTB genotypes and drug resistance-related gene mutations were identified, meanwhile, their relationship and the consistency of WGS drug susceptibility test results and phenotypic drug susceptibility test results of isoniazid were analyzed. Results: Of the 808 MTB strains, 153 were identified with drug-resistant gene mutations related to 11 anti-tuberculosis drugs (isoniazid, rifampicin, ethambutol, pyrazinamide, streptomycin, fluoroquinolones, amikacin, kanamycin, capreomycin, ethionamide, para-aminosalicylic acid) and the overall mutation rate was 18.9%. The major drug resistance-associated gene mutation types were katG-315-S/T (isoniazid, 60.0% (45/75)), rpoB-450-S/L (rifampicin, 57.1% (16/28)), embB-306-M/V (ethambutol, 43.8% (7/16)), rpsL-43-K/R (streptomycin, 65.5% (36/55)), gyrA-94-D/G (fluoroquinolones, 36.6% (15/41)), rrs-1402-C/A (amikacin, 3/3), rrs-1402-C/A (kanamycin, 3/4), rrs-1402-C/A (capreomycin, 3/3), inhA-15-C/T (ethionamide, 65.0% (13/20)) and thyA-75-H/N (para-aminosalicylic acid, 7/8). Drug resistance-associated mutations on rpsL gene were detected only in Beijing genotype strains (6.8% (40/586) vs. 0.0% (0/222), χ2=15.943, P=0.000). The mutation rate of katG-315 was higher in Beijing genotype strains (6.8% (40/586)) than non-Beijing genotype strains (3.2% (7/222)) and the difference was statistically significant (χ2=3.964, P=0.046). The sensitivity, specificity, positive predictive value, negative predictive value, consistency rate and Kappa value of the WGS drug resistance profiling method for isoniazid were 87.5% (49/56), 98.0% (680/694), 77.8% (49/63), 99.0% (680/687), 97.2% (729/750) and 0.808, respectively. Conclusion: The major drug resistance-associated gene mutations of 11 drugs were on katG, rpoB, embB, pncA, rpsL, gyrA, rrs, thyA and inhA among Zhejiang Province MTB strains. Mutations on rpsL, katG-315 and rpsL-43 were related with Beijing genotypes. The WGS drug resistance profiling method has comprehensive detection performance for isoniazid, but the performance of some drug-resistant gene mutations is poor.

Key words: Mycobacterium tuberculosis, Drug resistance,bacterial, Sequence analysis,DNA, Mutation, Genotype

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