脓肿分枝杆菌舒达吡啶耐药菌株单核苷酸多态性功能注释及耐药相关通路分析

doi:10.19982/j.issn.1000-6621.20250346

中国防痨杂志 ›› 2026, Vol. 48 ›› Issue (2): 264-273.doi: 10.19982/j.issn.1000-6621.20250346

脓肿分枝杆菌舒达吡啶耐药菌株单核苷酸多态性功能注释及耐药相关通路分析

尚园园¹, 王雪钰², 王宇津², 于霞³, 黄海荣³(), 聂文娟²()

¹ 首都医科大学附属北京友谊医院老年医学科, 北京 100050
² 首都医科大学附属北京胸科医院/北京市结核病胸部肿瘤研究所结核一科, 北京 101149
³ 首都医科大学附属北京胸科医院/国家结核病临床实验室, 北京 101149

收稿日期:2025-08-25 出版日期:2026-02-10 发布日期:2026-02-03
通信作者: 聂文娟,Email:94642975@qq.com;黄海荣,Email:nclhuang@ccmu.edu.cn
作者简介:注:尚园园、王雪钰与王宇津对本文有同等贡献,为并列第一作者
基金资助:
北京市卫健委研究型病房卓越临床研究计划(BRWEP2024W042160109);北京市医管中心扬帆3.0项目(ZLRK202331);首都医科大学临床专科学院(系)培养基金开放课题(CCMU2024ZKYXY011)

Functional annotation of single nucleotide polymorphisms and analysis of drug resistance-related pathways in Mycobacterium abscessus strains resistant to Sudapyridine

Shang Yuanyuan¹, Wang Xueyu², Wang Yujin², Yu Xia³, Huang Hairong³(), Nie Wenjuan²()

¹ Department of Geriatrics, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
² Department Ⅰ of Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
³ National Clinical Laboratory on Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China

Received:2025-08-25 Online:2026-02-10 Published:2026-02-03
Contact: Nie Wenjuan, Email: 94642975@qq.com;Huang Hairong, Email: nclhuang@ccmu.edu.cn
Supported by:
Beijing Municipal Health Commission Research Ward Excellent Clinical Research Program(BRWEP2024W042160109);Clinical Medicine Development Special Project “Sailing” Plan Project(ZLRK202331);Training Fund for Open Projects at Clinical Institutes and Departments of Capital Medical University(CCMU2024ZKYXY011)

摘要/Abstract

摘要：

目的: 诱导脓肿分枝杆菌标准株ATCC19977对舒达吡啶(sudapyridine,WX-081)的耐药菌株,对其耐药单核苷酸多态性(single nucleotide polymorphism,SNP)基因功能注释及相关通路进行初步研究。方法: 选取单克隆脓肿分枝杆菌标准株ATCC19977,采用2倍WX-081药物递增液体培养方法筛选耐药菌株。将获得耐WX-081菌株提取DNA并进行全基因组测序,检测SNP。随后,使用BLAST软件将所有基因(包含新基因和原有注释基因)与非监督直系群(evolutionary genealogy of genes: non-supervised orthologous,eggNOG)、基因本体(gene ontology,GO)、京都基因与基因组百科全书(kyoto encyclopedia of genes and genomes,KEGG)、非冗余数据库(non-redundant, Nr)、蛋白质家族(protein families,Pfam)和注释的蛋白质序列(swiss-prot protein sequence,swiss-prot)等数据库进行序列比对,获得基因的注释信息,建立相应的GO、eggNOG和KEGG数据库。结果: ATCC19977标准株与WX-081耐药ATCC19977菌株相比,编码区共检测到187个SNP,其中62个满足质量标准,43个为纯合SNP,包括12个同义突变和31个错义突变。编码区SNP占9.14%(187/2047),其中获得性终止密码子比例最低,仅为0.05%(1/2047)。非编码区SNP占90.86%(1860/2047),其中基因下游区域、基因上游区域产生SNP占比分别达51.83%(1061/2047)、39.03%(799/2047)。GO注释结果显示,生物学过程(BP)8条,细胞组分(CC)5条,分子功能(MF)4条。eggNOG功能预测显示,7个差异基因功能未知,3个参与氨基酸转运及代谢,1个与核苷酸代谢及转运相关,2个参与脂转运和代谢,1个与转录相关,2个参与细胞壁/细胞膜/包膜生物合成,1个参与翻译后修饰、蛋白质降解、分子伴侣,2个参与无机离子运输与代谢,2个参与次级代谢物生物合成、运输与降解,1个与信号传导功能相关。KEGG通路注释显示,细胞膜转运、氨基酸代谢、碳水化合物代谢、全局和总览图谱、脂代谢相关通路分别有1条、1条、1条、3条、4条。结论: 耐WX-081脓肿分枝杆菌的基因组变异以非编码区SNP为主,编码区31个错义突变可能直接参与耐药。代谢通路分析显示,脂代谢、细胞壁合成及氨基酸转运相关基因显著富集,提示膜/壁结构重塑和代谢重编程是耐药关键机制。耐WX-081脓肿分枝杆菌基因组分析显示,其代谢调控与膜结构相关通路中SNP显著富集。

关键词: 分枝杆菌属, 舒达吡啶, 抗药性, 多态性, 单核苷酸

Abstract:

Objective: To induce Mycobacterium abscessus strain ATCC 19977 resistant to sudapyridine (WX-081) and to perform the functional annotation of resistance-associated single nucleotide polymorphism (SNP) along with related pathways. Methods: The standard strain Mycobacterium abscessus ATCC19977 was subjected to incrementally increasing WX-081 exposure in liquid medium to select resistant mutants. Genomic DNA was extracted from the WX-081-resistant strains for whole-genome sequencing to identify SNP. Sequence alignment was performed using BLAST against multiple databases, such as evolutionary genealogy of genes: non-supervised orthologous (eggNOG), gene ontology (GO), kyoto encyclopedia of genes and genomes (KEGG), non-redundant (Nr), protein families (Pfam), swiss-prot protein sequence (swiss-prot) for functional annotation, followed by GO, eggNOG, and KEGG pathway enrichment analyses. Results: Comparative genomic analysis identified 187 SNP in coding regions between the parental ATCC19977 and WX-081-resistant strains, of which 62 met quality thresholds. Among these, 43 were homozygous SNP (12 synonymous and 31 missense mutations). SNP in the coding regions accounted for 9.14% (187/2047), of the total, with stop-gained variants (nonsense mutations) being the least frequent (0.05%, 1/2047). In contrast, 90.86% (1860/2047) of SNP were located in non-coding regions, predominantly in downstream (51.83%, 1061/2047) and upstream (39.03%, 799/2047) regions.GO annotation identified 8 biological processes (BP), 5 cellular components (CC), and 4 molecular functions (MF). eggNOG functional prediction classified the variant genes as follows: 7 with unknown function, 3 involved in amino acid transport and metabolism, 1 in nucleotide transport and metabolism, 2 in lipid transport and metabolism, 1 in transcription, 2 in cell wall/membrane and/envelope biogenesis, 1 in post-translational modification, protein turnover, chaperones, 2 in inorganic ion transport and metabolism, 2 in secondary metabolite biosynthesis, transport and catabolism, and 1 in signal transduction mechanisms. KEGG pathway analysis identified 1 pathway each related to membrane transport, amino acid metabolism, and carbohydrate metabolism, 3 pathways in global and overview maps, and 4 pathways associated with lipid metabolism. Conclusion: The genome of WX-081-resistant Mycobacterium abscessus exhibited predominantly non-coding SNP, while 31 missense mutations in coding regions may directly contribute to drug resistance. Metabolic pathway analysis revealed significant enrichment of genes related to lipid metabolism, cell wall synthesis, and amino acid transport, suggesting that membrane/wall structural remodeling and metabolic reprogramming are key resistance mechanisms.

Key words: Mycobacterium, Sudapyridine, Drug resistance, Polymorphism, single nucleotide

中图分类号:

S852.61+8

尚园园, 王雪钰, 王宇津, 于霞, 黄海荣, 聂文娟. 脓肿分枝杆菌舒达吡啶耐药菌株单核苷酸多态性功能注释及耐药相关通路分析[J]. 中国防痨杂志, 2026, 48(2): 264-273. doi: 10.19982/j.issn.1000-6621.20250346

Shang Yuanyuan, Wang Xueyu, Wang Yujin, Yu Xia, Huang Hairong, Nie Wenjuan. Functional annotation of single nucleotide polymorphisms and analysis of drug resistance-related pathways in Mycobacterium abscessus strains resistant to Sudapyridine[J]. Chinese Journal of Antituberculosis, 2026, 48(2): 264-273. doi: 10.19982/j.issn.1000-6621.20250346

图/表 6

图1

表1

WX-081耐药脓肿分枝杆菌菌株纯合SNP位点结果注释

基因名称	突变类型	变异在cDNA中的位置(X/Y)	变异在蛋白质中的位置(A/B)	变异点
Control_00084_gene	同义突变	12/951	4/316	c.12TG
xapB	同义突变	597/1284	199/427	c.597T>C
xapB	错义突变	576/1284	192/427	c.576G>C
Control_00164_gene	错义突变	985/1221	329/406	c.985T>C
Control_00578_gene	错义突变	330/339	110/112	c.330A>C
Control_00659_gene	错义突变	28/1248	10/415	c.28G>A
rhtB	同义突变	504/642	168/213	c.504T>C
rhtB	错义突变	488/642	163/213	c.488C>T
rhtB	错义突变	476/642	159/213	c.476T>C
rhtB	同义突变	471/642	157/213	c.471T>C
dagK	错义突变	187/879	63/292	c.187C>G
dagK	错义突变	160/879	54/292	c.160T>C
Control_00820_gene	错义突变	518/1407	173/468	c.518T>G
Control_00820_gene	错义突变	503/1407	168/468	c.503G>T
Control_01036_gene	错义突变	250/342	84/113	c.250C>G
Control_01038_gene	错义突变	767/1353	256/450	c.767T>G
Control_01038_gene	错义突变	757/1353	253/450	c.757G>A
Control_01038_gene	同义突变	747/1353	249/450	c.747A>C
rhtA_2	同义突变	88/807	30/268	c.88T>C
Control_01935_gene	错义突变	565/681	189/226	c.565C>A
Control_02156_gene	错义突变	1105/1440	369/479	c.1105T>C
Control_02216_gene	错义突变	680/1080	227/359	c.680C>A
Control_02216_gene	错义突变	691/1080	231/359	c.691A>G
dap4	错义突变	761/2238	254/745	c.761C>A
dap4	错义突变	767/2238	256/745	c.767A>G
dap4	错义突变	778/2238	260/745	c.778T>C
Control_03110_gene	错义突变	69/1230	23/409	c.69G>C
Control_03877_gene	错义突变	362/1554	121/517	c.362C>T
pcaB_1	错义突变	827/999	276/332	c.827G>C
leuA	同义突变	1821/1824	607/607	c.1821T>C
leuA	错义突变	1814/1824	605/607	c.1814T>C
Control_04429_gene	错义突变	47/666	16/221	c.47G>C
Control_04459_gene	错义突变	490/624	164/207	c.490G>A
Control_04459_gene	错义突变	511/624	171/207	c.511A>C
Control_04459_gene	同义突变	516/624	172/207	c.516T>C
mviN	错义突变	643/3435	215/1144	c.643A>C
mviN	错义突变	611/3435	204/1144	c.611A>C
dcd_2	错义突变	1097/1947	366/648	c.1097G>T
dcd_2	错义突变	1109/1947	370/648	c.1109G>A
pstC2_1	错义突变	17/1053	6/350	c.17C>A
pstC2_1	同义突变	30/1053	10/350	c.30T>C
mmpL4_16	同义突变	2538/2904	846/967	c.2538T>C
Control_05039_gene	错义突变	372/744	124/247	c.372C>A
Control_00084_gene	同义突变	12/951	4/316	c.12T>G

表1

表2

图2

图3

图4

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脓肿分枝杆菌舒达吡啶耐药菌株单核苷酸多态性功能注释及耐药相关通路分析

Functional annotation of single nucleotide polymorphisms and analysis of drug resistance-related pathways in Mycobacterium abscessus strains resistant to Sudapyridine

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突变类型	SNP数量	占比(%)
编码区突变	187	9.14
基因间区	31	1.51
错义变异	92	4.49
非编码转录本变异	2	0.10
获得性终止密码子	1	0.05
同义变异	61	2.98
非编码区突变	1860	90.86
上游基因突变	799	39.03
下游基因突变	1061	51.83

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