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预防医学  2020, Vol. 32 Issue (9): 899-903    DOI: 10.19485/j.cnki.issn2096-5087.2020.09.009
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全基因组测序在结核病分子流行病学研究中的应用
郭海萍, 尚媛媛 综述, 李姗姗, 逄宇 审校
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
Whole genome sequencing in the molecular epidemiology of tuberculosis
GUO Haiping, SHANG Yuanyuan, LI Shanshan, PANG Yu
National Clinical Laboratory on Tuberculosis,Beijing Chest Hospital affiliated to Capital Medical University,Beijing 101149,China
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摘要 结核病分子流行病学主要利用分子流行病学分型技术结合流行病学资料研究结核病的传播和流行特点。全基因组测序利用新一代生物信息技术获得物种个体或群体的基因图谱,具有高分辨率、高通量、结果精确和周期短等优势,能弥补传统基因分型技术的不足,已广泛应用于结核病分子流行病学研究。本文对全基因组测序的发展以及在鉴别菌株类型及谱系、鉴定传播方向、疫情追踪和菌株进化等方面的应用进行综述,为结核病的防控和研究提供参考。
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郭海萍
尚媛媛
李姗姗
逄宇
关键词 结核病结核分枝杆菌全基因组测序分子流行病学    
Abstract:Tuberculosis molecular epidemiology mainly applies strain genotyping technology combined with epidemiological data to explore the transmission characteristics. Whole genome sequencing obtains the genomes of species using new biological information technology,whose high resolution,high throughput,high precision and short cycle time can make up for the shortcomings of traditional gene typing technology,and has been widely used in the tuberculosis molecular epidemiology. In this paper,we reviewed the development of whole genome sequencing recently and its application in the identification of strain types and pedigrees,identification of transmission direction,epidemic tracing and strain evolution,so as to provide reference for the control of tuberculosis and related research.
Key wordstuberculosis    Mycobacterium tuberculosis    whole genome sequencing    molecular epidemiology
收稿日期: 2020-04-09      修回日期: 2020-05-28      出版日期: 2020-09-10
中图分类号:  R52  
基金资助:北京市医院管理中心“登峰”人才培养计划(DFL20191601)
作者简介: 郭海萍,硕士在读,主要从事结核流行病学工作
通信作者: 逄宇,E-mail:pangyupound@163.com   
引用本文:   
郭海萍, 尚媛媛, 李姗姗, 逄宇. 全基因组测序在结核病分子流行病学研究中的应用[J]. 预防医学, 2020, 32(9): 899-903.
GUO Haiping, SHANG Yuanyuan, LI Shanshan, PANG Yu. Whole genome sequencing in the molecular epidemiology of tuberculosis. Preventive Medicine, 2020, 32(9): 899-903.
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http://www.zjyfyxzz.com/CN/10.19485/j.cnki.issn2096-5087.2020.09.009      或      http://www.zjyfyxzz.com/CN/Y2020/V32/I9/899
[1] World Health Organisation.Global tuberculosis report 2019 [R]. Geneva:World Health Organisation,2019.
[2] JAJOU R,KOHL T A,WALKER T,et al. Towards standardisation: comparison of five whole genome sequencing (WGS) analysis pipelines for detection of epidemiologically linked tuberculosis cases [J/OL]. Euro Surveill,2019,24(50)[2020-05-28].https://www.researchgate.net/publication/338048151_Towards_standardisation_comparison_of_five_whole_genome_sequencing_WGS_analysis_pipelines_for_detection_of_epidemiologically_linked_tuberculosis_cases.
[3] 李伟,印莉萍. 基因组学相关概念及其研究进展[J]. 生物学通报,2000,35(11):1-3.
[4] 翟俊斌,曹小利. 全基因组测序技术的发展及其在临床微生物实验室的应用前景[J]. 检验医学与临床,2018,15(3):414-417.
[5] 陈欣,孙宇,郭俊,等. 谈精准医学时代“基因组学”在医学研究生培养中的重要性[J]. 中国医药导报,2017,14(1):113-116.
[6] 申晨,申阿东. 抗结核药物基因组学研究进展[J]. 中国防痨杂志,2018,40(9):993-998.
[7] 周子超,何岚,丁月平. 全基因测序(WGS)在肠杆菌科细菌中的应用研究[J]. 智慧健康,2019,5(2):70-72.
[8] MAXAM A M,GILBERT W.A new method for sequencing DNA[J]. Proc Natl Acad Sci U S A,1977,74(2):560-564.
[9] 朱海星,白春学. 全基因组序列分析在肺癌个体化治疗中的研究进展[J]. 中华结核和呼吸杂志,2014,37(9):700-702.
[10] 彭司华,吴智超,孙丹,等. 宏基因组学在抗生素抗性基因鉴定中的应用[J]. 基因组学与应用生物学,2019,38(9):4102-4109.
[11] 陈钰,罗力涵,李莎. 影响结核分枝杆菌全基因组测序结果的因素分析[J]. 中国国境卫生检疫杂志,2018,41(2):144-147.
[12] PETERSEN L M,MARTIN I W,MOSCHETTI W E,et al.Third-generation sequencing in the clinical laboratory:exploring the advantages and challenges of nanopore sequencing[J]. J Clin Microbiol,2019,58(1):e01315-e01319.
[13] COLE S T,BROSCH R,PARKHILL J,et al.Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence[J]. Nature,1998,393(6685):537-544.
[14] CAMUS J C,PRYOY M J,MEDIGUE C,et al.Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv.[J]. Microbiology,2002,148(Pt10):2967-2973.
[15] FLEISCHMANN R D,ALLAND D,EISEN J A,et al.Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains[J]. J Bacteriol,2002,184(19):5479-5490.
[16] TSUI C K M,WONG D,NARULA G,et al. Genome sequences of the Mycobacterium tuberculosis H37Rv-ptkA deletion mutant and its parental strain[J]. Genome Announc,2017,5(44):e01156-e011517.
[17] 罗涛. 中国结核病分子流行病学研究进展[J].寄生虫病与感染性疾病,2019,17(3):133-137.
[18] 陈昕昶,张文宏. 全基因组测序在结核病研究中的应用进展[J].中国防痨杂志,2018,40(2):149-152.
[19] MERKER M,KOHL T A,NIEMANN S,et al.The evolution of strain typing in the Mycobacterium tuberculosis complex[J]. Adv Exp Med Biol,2017(1019):43-78.
[20] 董毅,吴利先. 结核分枝杆菌基因分型技术的研究进展[J].国际流行病学传染病学杂志,2013,40(5):336-339.
[21] RAVANSALAR H,TADAYON K,GHAZVINI K .Molecular typing methods used in studies of Mycobacterium tuberculosis in Iran:a systematic review[J]. Iran J Microbiol,2016,8(5):338-346.
[22] OSEI SEKYERE J,RETA M A,MANINGI N E,et al.Antibiotic resistance of Mycobacterium tuberculosis complex in Africa: a systematic review of current reports of molecular epidemiology,mechanisms and diagnostics[J]. J Infect,2019,79(6):550-571.
[23] 田丽丽,丁北川,祝秉东,等. 结核分枝杆菌基因分型方法及其应用[J].中国防痨杂志,2015,37(8):885-891.
[24] AMLEROVA J,BITAR I,HRABAK J.Genotyping of Mycobacterium tuberculosis using whole genome sequencing[J]. Folia Microbiol (Praha),2018,63(5):537-545.
[25] 李道群,夏雪山,宋玉竹,等. 结核分枝杆菌分子分型技术的研究和应用[J].中国人兽共患病学报,2016,32(1):76-82.
[26] 贺文从,刘东鑫,赵雁林.掌握科学规律是实施科学防治的前提——分子流行病学技术在结核病防治中的应用[J].中国防痨杂志,2017,39(8):789-792.
[27] TAKIFF H E,FEO O.Clinical value of whole-genome sequencing of Mycobacterium tuberculosis[J]. Lancet Infect Dis,2015,15(9):1077-1090.
[28] TULU B,AMENI G. Spoligotyping based genetic diversity of Mycobacterium tuberculosis in Ethiopia: a systematic review [J/OL]. BMC Infect Dis,2018,18(1)[2020-05-28].https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870191.
[29] MAEDA S,HIJIKATA M,HANG N T L,et al. Genotyping of Mycobacterium tuberculosis spreading in Hanoi,Vietnam using conventional and whole genome sequencing methods [J/OL]. Infect,Genet Evo,2020(78)[2020-05-28].http://www.docin.com/p-2326434494.html.
[30] WU W,ZHENG H,ZHANG L,et al.A genome-wide analysis of multidrug-resistant and extensively drug-resistant strains of
Mycobacterium tuberculosis Beijing genotype[J]. Mol Genet Genomics,2013,288(9):425-436.
[31] 武洁,唐利红,杨崇广,等.全基因组测序技术在结核病流行病学调查中的应用[J].中华流行病学杂志,2016,37(12):1644-1646.
[32] DIXIT A,FRESCHI L,VARGAS R,et al. Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting [J/OL]. Sci Rep,2019,9(1)[2020-05-28].https://www.researchgate.net/publication/332174134_Whole_genome_sequencing_identifies_bacterial_factors_affecting_transmission_of_multidrug-resistant_tuberculosis_in_a_high-prevalence_setting_OPEN.
[33] CONCEICAO E C,GUIMARAES A,LOPES M L,et al.Detailed analysis of potential household transmission events of tuberculosis in the city of Belem,Brazil[J]. Tuberculosis(Edinb),2018(113):125-129.
[34] YANG C,LUO T,SHEN X,et al.Transmission of multidrug-resistant Mycobacterium tuberculosis in Shanghai,China: a retrospective observational study using whole-genome sequencing and epidemiological investigation[J]. Lancet Infect Dis,2017,17(3):275-284.
[35] 江琦,武洁,刘艳,等.利用全基因组测序解析耐多药结核病传播路径[J].上海预防医学,2016,28(3):153-156.
[36] GARDY J L,JOHNSTON J C,SUI S J H,et al . Whole-genome sequencing and social-network analysis of a tuberculosis outbreak[J]. N Engl J Med,2011,364(8):730-739.
[37] GUO X J,TAKIFF H E,WANG J,et al.An office building outbreak: the changing epidemiology of tuberculosis in Shenzhen,China[J]. Epidemiol Infect,2020,148:1-22.
[38] YU H,ZHANG Y,CHEN X,et al. Whole-genome sequencing and epidemiological analysis of a tuberculosis outbreak in a high school of southern China [J/OL]. Infect Genet Evol,2020(83)[2020-05-28].http://www.sciencedirect.com/science/article/pii/S156713482030174X.
[39] ROETZER A,DIEL R,KOHL T A,et al. Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study [J/OL]. PLoS Med,2013,10(2)[2020-05-28].https://pubmed.ncbi.nlm.nih.gov/23424287.
[40] DHEDA K,GUMBO T,MAARTENS G,et al.The Lancet Respiratory Medicine Commission: 2019 update: epidemiology,pathogenesis,transmission,diagnosis,and management of multidrug-resistant and incurable tuberculosis[J]. The Lancet Respir Med,2019,7(9):820-826.
[41] ZENG X,KWOK J S,YANG K Y,et al.Whole genome sequencing data of 1 110 Mycobacterium tuberculosis isolates identifies insertions and deletions associated with drug resistance[J]. BMC Genomics,2018,19(1):1-10.
[42] FORD C,YUSIM K,IOERGER T,et al.Mycobacterium tuberculosis-heterogeneity revealed through whole genome sequencing[J]. Tuberculosis (Edinb),2012,92(3):194-201.
[43] FORD C B,LIN P L,CHASE M R,et al.Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection[J]. Nat Genet,2011,43(5):482-486.
[44] HERRANZ M,POLE I,OZERE I,et al.Mycobacterium tuberculosis acquires limited genetic diversity in prolonged infections,reactivations and transmissions involving multiple hosts[J]. Front Microbiol,2017,(8):1-9.
[45] NSOFOR C A,JIANG Q,WU J,et al. Transmission is a noticeable cause of resistance among treated tuberculosis patients in Shanghai,China [J/OL]. Sci Rep,2017,7(1)[2020-05-28].https://pubmed.ncbi.nlm.nih.gov/28794425.
[46] COHEN K A,MANSON A L,DESJARDINS C A,et al. Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress,promise,and challenges [J/OL]. Genome Med,2019,11(1)[2020-05-28].https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6657377.
[47] SATTA G,LIPMAN M,SMITH G P,et al.Mycobacterium tuberculosis and whole-genome sequencing: how close are we to unleashing its full potential?[J]. Clin Microbiol Infect,2018,24(6):604-609.
[48] MEEHAN C J,GOIG G A,KOHL T A,et al.Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues[J]. Nat Rev Microbiol,2019,17(9):533-545.
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