基于全基因组测序的我国耐多药结核分枝杆菌耐药突变特征分析

高敏; 杨婷婷; 李桂莲; 陈蓉; 刘海灿; 高谦; 万康林; 奉水东

Abstract

高敏,杨婷婷,李桂莲,陈蓉,刘海灿,高谦,万康林,奉水东.基于全基因组测序的我国耐多药结核分枝杆菌耐药突变特征分析[J].Chinese journal of Epidemiology,2020,41(5):770-775

基于全基因组测序的我国耐多药结核分枝杆菌耐药突变特征分析

Analysis on drug resistance-associated mutations of multi-drug resistant Mycobacterium tuberculosis based on whole-genome sequencing in China

Received:November 11, 2019

DOI：10.3760/cma.j.cn112338-20191111-00800

KeyWord: 结核分枝杆菌耐药全基因组测序

English Key Word: Mycobacterium tuberculosis Drug resistance Whole genome sequencing

FundProject:湖南省自然科学基金（2018JJ2342）；湖南省研究生科研创新项目（CX20190759）；国家科技重大专项（2018ZX10103001-003-012）

Author Name	Affiliation	E-mail
Gao Min	School of Public Health, University of South China, Hengyang 421001, China
Yang Tingting	School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
Li Guilian	State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
Chen Rong	School of Public Health, University of South China, Hengyang 421001, China State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
Liu Haican	State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
Gao Qian	School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
Wan Kanglin	State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China	wankanglin@icdc.cn
Feng Shuidong	School of Public Health, University of South China, Hengyang 421001, China	shuidong_f@hotmail.com

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Abstract:

目的利用全基因组测序数据分析中国耐多药结核分枝杆菌的耐药相关基因突变谱及主要突变类型与菌株基因型的相关性。方法查询并下载NCBI数据库中截至2019年8月公开发表的中国结核分枝杆菌全基因组测序数据，利用全基因组数据预测菌株分子药敏结果，统计不同药物耐药相关基因的突变类型，并分析耐药突变类型与菌株基因型的相关性。结果根据分子药敏结果从2 019株菌株中鉴定出1 024株耐多药菌株，对常用抗结核药物的耐药相关基因主要突变类型分别为katG S315T（73.2%，异烟肼）、rpoB S450L（63.1%，利福平）、rpsL K43R（70.0%，链霉素）、embB M306V（37.4%，乙胺丁醇）、pncA启动子区T（-11）C（7.9%，吡嗪酰胺）、gyrA A90V（32.3%，氟喹诺酮类）、rrs A1401G（67.7%，二线注射类）、fabG1启动子区C（-15）T（87.0%，乙硫异烟胺）、folC I43T（30.4%，对氨基水杨酸）。其中，katG S315T、rpsL K43R、embB M306V、gyrA D94G在L2系菌株中的频率显著高于L4系菌株，folC I43T仅在L2系菌株中发现；katG S315T在古典北京型菌株中比例较高，而rpsL K43R在现代北京基因型菌株中的比例更高，其差异均有统计学意义（均P<0.05）。结论本研究提供了基于全基因组测序的我国耐多药结核分枝杆菌对多种常用抗结核药的耐药相关基因主要突变类型，为研发敏感、特异的快速分子检测方法提供了依据；同时也发现多种耐药相关基因主要突变类型与菌株基因型有关。

English Abstract:

Objective To analyze the resistance mutational profiles of multi-drug resistant Mycobacterium tuberculosis in China and the correlation between major mutation types and genotypes based on the whole-genome sequencing data. Methods Search and download of the genome-wide sequencing data of M. tuberculosis published in China by August 2019 on NCBI database were conducted. Mutation frequency of drug resistance-related gene loci based on whole-genome sequencing was used to predict the molecular susceptibility of strains, and the correlation between mutation types and genotypes was analyzed. Results According to the results of molecular resistance and susceptibility profiles, 1 024 MDR strains were identified from 2 019 M. tuberculosis strains. The major mutation types of resistance-related genes to common drugs were katG S315T (73.2%, isoniazid), rpoB S450L (63.1%, rifampicin), rpsL K43R (70.0%, streptomycin), embB M306V (37.4%, ethambutol), pncA_promoter T (-11)C (7.9%, pyrazinamide), gyrA A90V (32.3%, fluoroquinolones), rrs A1401G (67.7%, second-line injection drugs), fabG1_promoter C (-15) T (87.0%, Ethionamide), folC I43T (30.4%, P-aminosalicylic acid). Among them, the frequencies of katG S315T, embB M306V, rpsL K43R, gyrA A90V in lineage 2 were significantly higher than those in lineage 4, and folC I43T was only found in lineage 2. The proportion of katG S315T was significantly higher in the ancient Beijing genotype compared to the modern genotype, in contrast, the proportion of rpsL K43R was significantly higher in modern Beijing genotype, the differences were significant (all P<0.05). Conclusions The results showed the main mutation types of resistance-related genes of MDR strains to many commonly used anti-tuberculosis drugs in China based on whole-genome sequencing, providing a basis for the development of sensitive and specific rapid molecular detection methods. At the same time, it was also found that the major mutation types of MDR-related genes were related to the genotype of the strains.

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