非结核分枝杆菌基因分型的研究进展
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摘要
非结核分枝杆菌(Nontuberculous mycobacteria,NTM)是除结核分枝杆菌和麻风分枝杆菌以外的所有的分枝杆菌的总称。近年来,非结核分枝杆菌病呈上升趋势,NTM可侵犯以肺部病变为主的全身各部分组织器官。由于非结核分枝杆菌菌种多样,基因型复杂,且不同菌株毒力与耐药性不同。其基因分型将为临床的诊断和治疗提供了有力的依据。目前非结核分枝杆菌基因分型技术主要分为非核酸法(传统方法)和核酸法(分子生物法)。本文就当前主要的核酸分型技术做一综述。
Nontuberculous mycobacteria(NTM) is a generic term for all mycobacteria except Mycobacterium tuberculosis and M. leprae. Over the past few years, non-tuberculous mycobacterial disease has been on the rise, and NTM can invade various tissues and organs of the body, and especially the lungs. Genotyping NTM is complicated because of their diversity, and different strains have differing virulence and drug resistance. Genotyping NTM will provide a powerful basis for clinical diagnosis and treatment. At present, NTM genotyping techniques are mainly divided into non-nucleic acid methods(conventional methods) and nucleic acid methods(molecular biological methods). Nucleic acid typing is the main method for genotyping NTM, and the most widely used are IS6110-RFLP and VNTR techniques. This article reviews the main techniques for nucleic acid typing at this time.
Nontuberculous mycobacteria(NTM) is a generic term for all mycobacteria except Mycobacterium tuberculosis and M. leprae. Over the past few years, non-tuberculous mycobacterial disease has been on the rise, and NTM can invade various tissues and organs of the body, and especially the lungs. Genotyping NTM is complicated because of their diversity, and different strains have differing virulence and drug resistance. Genotyping NTM will provide a powerful basis for clinical diagnosis and treatment. At present, NTM genotyping techniques are mainly divided into non-nucleic acid methods(conventional methods) and nucleic acid methods(molecular biological methods). Nucleic acid typing is the main method for genotyping NTM, and the most widely used are IS6110-RFLP and VNTR techniques. This article reviews the main techniques for nucleic acid typing at this time.
引文
[1] Gupta S, Bandyopadhyay D, Paine SK, et al. Rapid identification of Mycobacterium species with the aid of multiplex polymerase chain reaction (PCR) from clinical isolates[J]. Open Microbiol J, 2010(4): 93-7.
[2] Sinha P, Gupta A, Prakash P, et al. Differentiation of Mycobacterium tuberculosis complex from non-tubercular mycobacteria by nested multiplex PCR targeting IS6110, MTP40 and 32kD alpha antigen encoding gene fragments[J]. BMC Infect Dis, 2016(16): 123.
[3] Nour-Neamatollahie A, Ebrahimzadeh N, Siadat SD, et al. Distribution of non-tuberculosis mycobacteria strains from suspected tuberculosis patients by heat shock protein 65 PCR-RFLP[J]. Saudi J Biol Sci, 2017, 24(6): 1380-6.
[4] 李国利, 庄玉辉, 赵铭, 等. 16S～23SrDNA内转录间隔区序列分析及其在分支杆菌鉴定中的应用价值[J]. 中华结核和呼吸杂志, 2002(3): 41-5.
[5] 黄根成. hsp65-、rpoB-PCR-RFLP用于非结核分枝杆菌菌种鉴定的研究[D]. 扬州大学, 2012.
[6] 李晓亮. 基于rpoB基因的非结核分枝杆菌菌种鉴定PCR-RFLP方法的研究[D]. 扬州大学, 2011.
[7] Mathema B, Kurepina NE, Bifani PJ, et al. Molecular epidemiology of tuberculosis: current insights[J]. Clin Microbiol Rev, 2006, 19(4): 658-85.
[8] Radomski N, Thibault VC, Karoui C, et al. Determination of genotypic diversity of Mycobacterium avium subspecies from human and animal origins by mycobacterial interspersed repetitive-unit-variable-number tandem-repeat and IS1311 restriction fragment length polymorphism typing methods[J]. J Clin Microbiol, 2010, 48(4): 1026-34.
[9] Kremer K, van Soolingen D, Frothingham R, et al. Comparison of methods based on different molecular epidemiological markers for typing of Mycobacterium tuberculosis complex strains: interlaboratory study of discriminatory power and reproducibility[J]. J Clin Microbiol, 1999, 37(8): 2607-18.
[10] Groenen PM, Bunschoten AE, van Soolingen D, et al. Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method[J]. Mol Microbiol, 1993, 10(5): 1057-65.
[11] Mathema B, Bifani PJ, Driscoll J, et al. Identification and evolution of an IS6110 low-copy-number Mycobacterium tuberculosis cluster[J]. J Infect Dis, 2002,185(5): 641-9.
[12] van Embden JD, van Gorkom T, Kremer K, et al. Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria[J]. J Bacteriol, 2000,182(9): 2393-401.
[13] 吴雪琼, 张俊仙, 刘佳文, 等. PCR-SSCP分支杆菌菌种初步鉴定方法的建立及其应用[J]. 中国现代医学杂志, 2000(07): 25-6.
[14] Ali IF, Babak F, Fazlollah MS, et al. Rapid detection of MDR-Mycobacterium tuberculosis using modified PCR-SSCP from clinical Specimens[J]. Asian Pac J Trop Biomed, 2014,4(Suppl 1): S165-S170.
[15] Choi YJ, Kim HJ, Shin HB, et al. Evaluation of peptide nucleic acid probe-based real-time PCR for detection of Mycobacterium tuberculosis complex and nontuberculous mycobacteria in respiratory specimens[J]. Ann Lab Med, 2012, 32(4): 257-63.
[16] 赵建宏, 李雅静, 温海楠, 等. 非结核分枝杆菌感染的分子诊断研究进展[J]. 检验医学, 2012(3): 155-8.
[17] Wong YL, Ong CS, Ngeow YF. Molecular typing of Mycobacterium abscessus based on tandem-repeat polymorphism[J]. J Clin Microbiol, 2012, 50(9): 3084-8.
[18] Inagaki T, Nishimori K, Yagi T, et al. Comparison of a variable-number tandem-repeat (VNTR) method for typing Mycobacterium avium with mycobacterial interspersed repetitive-unit-VNTR and IS1245 restriction fragment length polymorphism typing[J]. J Clin Microbiol, 2009, 47(7): 2156-64.
[19] 胡晓红, 向启云, 韩宇, 等. 基因芯片技术在宜昌地区结核分枝杆菌耐药情况监测中的应用[J]. 中国病原生物学杂志, 2015, 10(4): 351-4.
[20] 欧维正, 厉宁, 蒙俊, 等. Hain和基因芯片技术在结核分枝杆菌异烟肼耐药性检测中的应用评价[J]. 中国病原生物学杂志, 2016, 11(12): 1062-5.
[21] 陈国会, 冯大山, 王秀丽, 等. 应用基因芯片检测系统诊断结核分枝杆菌感染及耐药基因突变的临床研究[J]. 国际检验医学杂志, 2017(5): 638-40.
[22] Srilohasin P, Chaiprasert A, Tokunaga K, et al. Novel DNA chip based on a modified DigiTag2 assay for high-throughput species identification and genotyping of Mycobacterium tuberculosis complex isolates[J]. J Clin Microbiol, 2014, 52(6): 1962-8.
[23] 丁水军. 脉冲场凝胶电泳技术及其在病原菌分子分型中的应用[J]. 中国卫生检验杂志, 2009(4): 962-4.
[24] Candido PH, Nunes LS, Marques EA, et al. Multidrug-resistant nontuberculous mycobacteria isolated from cystic fibrosis patients[J]. J Clin Microbiol, 2014, 52(8): 2990-7.
[25] Park JS, Choi JI, Lim JH, et al. The combination of real-time PCR and HPLC for the identification of non-tuberculous mycobacteria[J]. Ann Lab Med, 2013, 33(5): 349-52.
[26] Sebastian G, Nagaraja SB, Vishwanatha T, et al. Non-Tuberculosis mycobacterium speciation using HPLC under Revised National TB Control Programme (RNTCP) in India[J]. J Appl Microbiol, 2018, 124(1): 267-73.
[2] Sinha P, Gupta A, Prakash P, et al. Differentiation of Mycobacterium tuberculosis complex from non-tubercular mycobacteria by nested multiplex PCR targeting IS6110, MTP40 and 32kD alpha antigen encoding gene fragments[J]. BMC Infect Dis, 2016(16): 123.
[3] Nour-Neamatollahie A, Ebrahimzadeh N, Siadat SD, et al. Distribution of non-tuberculosis mycobacteria strains from suspected tuberculosis patients by heat shock protein 65 PCR-RFLP[J]. Saudi J Biol Sci, 2017, 24(6): 1380-6.
[4] 李国利, 庄玉辉, 赵铭, 等. 16S～23SrDNA内转录间隔区序列分析及其在分支杆菌鉴定中的应用价值[J]. 中华结核和呼吸杂志, 2002(3): 41-5.
[5] 黄根成. hsp65-、rpoB-PCR-RFLP用于非结核分枝杆菌菌种鉴定的研究[D]. 扬州大学, 2012.
[6] 李晓亮. 基于rpoB基因的非结核分枝杆菌菌种鉴定PCR-RFLP方法的研究[D]. 扬州大学, 2011.
[7] Mathema B, Kurepina NE, Bifani PJ, et al. Molecular epidemiology of tuberculosis: current insights[J]. Clin Microbiol Rev, 2006, 19(4): 658-85.
[8] Radomski N, Thibault VC, Karoui C, et al. Determination of genotypic diversity of Mycobacterium avium subspecies from human and animal origins by mycobacterial interspersed repetitive-unit-variable-number tandem-repeat and IS1311 restriction fragment length polymorphism typing methods[J]. J Clin Microbiol, 2010, 48(4): 1026-34.
[9] Kremer K, van Soolingen D, Frothingham R, et al. Comparison of methods based on different molecular epidemiological markers for typing of Mycobacterium tuberculosis complex strains: interlaboratory study of discriminatory power and reproducibility[J]. J Clin Microbiol, 1999, 37(8): 2607-18.
[10] Groenen PM, Bunschoten AE, van Soolingen D, et al. Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method[J]. Mol Microbiol, 1993, 10(5): 1057-65.
[11] Mathema B, Bifani PJ, Driscoll J, et al. Identification and evolution of an IS6110 low-copy-number Mycobacterium tuberculosis cluster[J]. J Infect Dis, 2002,185(5): 641-9.
[12] van Embden JD, van Gorkom T, Kremer K, et al. Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria[J]. J Bacteriol, 2000,182(9): 2393-401.
[13] 吴雪琼, 张俊仙, 刘佳文, 等. PCR-SSCP分支杆菌菌种初步鉴定方法的建立及其应用[J]. 中国现代医学杂志, 2000(07): 25-6.
[14] Ali IF, Babak F, Fazlollah MS, et al. Rapid detection of MDR-Mycobacterium tuberculosis using modified PCR-SSCP from clinical Specimens[J]. Asian Pac J Trop Biomed, 2014,4(Suppl 1): S165-S170.
[15] Choi YJ, Kim HJ, Shin HB, et al. Evaluation of peptide nucleic acid probe-based real-time PCR for detection of Mycobacterium tuberculosis complex and nontuberculous mycobacteria in respiratory specimens[J]. Ann Lab Med, 2012, 32(4): 257-63.
[16] 赵建宏, 李雅静, 温海楠, 等. 非结核分枝杆菌感染的分子诊断研究进展[J]. 检验医学, 2012(3): 155-8.
[17] Wong YL, Ong CS, Ngeow YF. Molecular typing of Mycobacterium abscessus based on tandem-repeat polymorphism[J]. J Clin Microbiol, 2012, 50(9): 3084-8.
[18] Inagaki T, Nishimori K, Yagi T, et al. Comparison of a variable-number tandem-repeat (VNTR) method for typing Mycobacterium avium with mycobacterial interspersed repetitive-unit-VNTR and IS1245 restriction fragment length polymorphism typing[J]. J Clin Microbiol, 2009, 47(7): 2156-64.
[19] 胡晓红, 向启云, 韩宇, 等. 基因芯片技术在宜昌地区结核分枝杆菌耐药情况监测中的应用[J]. 中国病原生物学杂志, 2015, 10(4): 351-4.
[20] 欧维正, 厉宁, 蒙俊, 等. Hain和基因芯片技术在结核分枝杆菌异烟肼耐药性检测中的应用评价[J]. 中国病原生物学杂志, 2016, 11(12): 1062-5.
[21] 陈国会, 冯大山, 王秀丽, 等. 应用基因芯片检测系统诊断结核分枝杆菌感染及耐药基因突变的临床研究[J]. 国际检验医学杂志, 2017(5): 638-40.
[22] Srilohasin P, Chaiprasert A, Tokunaga K, et al. Novel DNA chip based on a modified DigiTag2 assay for high-throughput species identification and genotyping of Mycobacterium tuberculosis complex isolates[J]. J Clin Microbiol, 2014, 52(6): 1962-8.
[23] 丁水军. 脉冲场凝胶电泳技术及其在病原菌分子分型中的应用[J]. 中国卫生检验杂志, 2009(4): 962-4.
[24] Candido PH, Nunes LS, Marques EA, et al. Multidrug-resistant nontuberculous mycobacteria isolated from cystic fibrosis patients[J]. J Clin Microbiol, 2014, 52(8): 2990-7.
[25] Park JS, Choi JI, Lim JH, et al. The combination of real-time PCR and HPLC for the identification of non-tuberculous mycobacteria[J]. Ann Lab Med, 2013, 33(5): 349-52.
[26] Sebastian G, Nagaraja SB, Vishwanatha T, et al. Non-Tuberculosis mycobacterium speciation using HPLC under Revised National TB Control Programme (RNTCP) in India[J]. J Appl Microbiol, 2018, 124(1): 267-73.