新疆维吾尔自治区南疆地区结核分枝杆菌ESX-4分泌系统基因突变特征分析

杨淑柳; 向煜; 王泉; 武娅宁; 肖开提·米吉提; 王瑞欢; 高晓平; 赵秀芹; 李马超; 王冕; 万康林; 李桂莲; 刘海灿; 袁秀琴

doi:10.3784/jbjc.202311300656

新疆维吾尔自治区南疆地区结核分枝杆菌ESX-4分泌系统基因突变特征分析

Analysis on mutations in the genes of ESX-4 secretion system of Mycobacterium tuberculosis isolated from Southern Xinjiang

摘要

摘要:
目的比较不同家系及耐药性结核分枝杆菌临床分离株ESX-4分泌系统7个毒力基因突变的差异，探讨临床菌株中 ESX-4基因的多态性特征。
方法纳入新疆南疆地区807株结核分枝杆菌临床株，进行全基因组测序。利用TB-profiler软件及C++脚本程序检测不同临床菌株ESX-4基因的突变、家系和药物敏感性结果。对数据进行描述性分析、χ²检验及logistics回归分析。
结果在807株结核分枝杆菌中共发现119个单核苷酸多态性位点和12种不同的插入/缺失。非同义突变率排在前3位的基因是Rv3446c（43.12%）、esxU（40.02%）以及eccC4和eccD4基因（均为23.30%）。家系中Lineage 2（L2）占62.70%（506/807），L3占19.46%（157/807），L4占17.84%（144/807）；敏感株占39.41%（318/807），耐药株占60.59%（489/807）；利福平耐药占34.08%（275/807），异烟肼耐药占28.50%（230/807），喹诺酮类耐药占12.14%（98/807）。 L3家系中eccC4和esxT基因的突变率均显著高于L2或L4家系。多因素logistics回归模型分析发现：L2家系和异烟肼耐药是esxU和Rv3446c基因发生突变的危险因素［均比值比（OR）>1，均P<0.001］；多耐药则是Rv3446c突变的又一危险因素［OR=1.94，95%置信区间（CI）：1.12～3.37］。
结论本研究发现了结核分枝杆菌ESX-4分泌系统中与L2、L3家系及耐药性相关的基因突变，为进一步研究结核分枝杆菌的传播、耐药和致病机制提供基础科学依据。

Abstract:
Objectives To compare the mutation differences of the virulence genes of ESX-4 system in clinical isolates of Mycobacterium tuberculosis in different lineages and with different drug resistance, and explore the polymorphisms of ESX-4 system gene in clinical isolates.
Methods Whole-genome sequencing (WGS) was performed on 807 M. tuberculosis clinical isolates in southern Xinjiang. The mutation profiles of the ESX-4 system virulence genes as well as the lineages and drug susceptibility results were detected using TB-profiler software and C++ Script program. Descriptive analysis method, the χ² test and logistics regression model were performed on the data.
Results A total of 119 single nucleotide polymorphic sites and 12 different insertions/deletions were found in 807 M. tuberculosis isolates. The genes with top three non-synonymous mutation rates were Rv3446c (43.12%), esxU (40.02%), and eccC4 both eccD4 genes (both 23.30%). Lineage 2(L2) isolates accounted for 62.70% (506/807), L3 isolates accounted for 19.45% (157/807) and L4 isolates were 17.84% (144/807). In addition, the susceptible isolates accounted for 39.41% (318/807), drug-resistant isolates accounted for 60.59% (489/807); and the rifampicin resistant rate was 34.08% (275/807), isoniazid resistant rate was 28.50% (230/807), quinolones resistant rate was 12.14% (98/807). The mutation rates of both eccC4 and esxT genes were significantly higher in the L3 isolates than in L2 or L4 isolates. Multivariate logistic regression model analysis revealed that L2 and isoniazid resistance were risk factors for mutations in esxU and Rv3446c genes (all OR>1, all P<0.001), and MDR was an additional risk factor for Rv3446c mutation (OR=1.94, 95%CI: 1.12–3.37).
Conclusion Our results identified gene mutations associated with L2、L3 isolates and drug resistance in the ESX-4 secretion system of M. tuberculosis, which provided basic scientific evidence for further research on the transmission, drug resistance and pathogenic mechanism of M. tuberculosis.

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