Research progress of high-throughput sequencing technology in the diagnosis and treatment of osteoarticular tuberculosis

doi:10.19982/j.issn.1000-6621.20240358

Abstract

Abstract:

Osteoarticular tuberculosis constitutes approximately 10% of all extrapulmonary tuberculosis cases. Traditional diagnostic methods, such as mycobacterial culture and immunological assays, are hindered by low sensitivity and high rates of misdiagnosis and missed diagnosis. The GeneXpert MTB/RIF molecular diagnostic technology has been pivotal in diagnosing osteoarticular tuberculosis; however, it has notable limitations, including an inability to detect non-tuberculous pathogens and reduced sensitivity in extrapulmonary samples. In contrast, high-throughput sequencing (HTS) technology provides a rapid, highly accurate method for pathogen detection, and it holds substantial promise for guiding treatment strategies and identifying drug resistance in osteoarticular tuberculosis. The review aims to explore the advancements in HTS technology applications in diagnosing and managing osteoarticular tuberculosis, offering new perspectives to improve disease control.

Key words: Tuberculosis, osteoarticular, High-throughput sequencing technology, Drug resistance

CLC Number:

R37
R529.2

Xu Zian, Pu Feifei, Feng Jing, Xia Ping. Research progress of high-throughput sequencing technology in the diagnosis and treatment of osteoarticular tuberculosis[J]. Chinese Journal of Antituberculosis, 2025, 47(2): 224-230. doi: 10.19982/j.issn.1000-6621.20240358

Figures/Tables 1

References 51

[1]	舒薇, 刘宇红. 世界卫生组织《2023年全球结核病报告》解读. 结核与肺部疾病杂志, 2024, 5(1): 15-19. doi:10.19983/j.issn.2096-8493.2024006.
[2]	Kumar V, Neradi D, Sherry B, et al. Tuberculosis of the spine and drug resistance: a review article. Neurosurg Rev, 2022, 45(1):217-229. doi:10.1007/s10143-021-01595-1.
[3]	Wang G, Long J, Zhuang Y, et al. Application of metagenomic next-generation sequencing in the detection of pathogens in spinal infections. Spine J, 2023, 23(6):859-867. doi:10.1016/j.spinee.2023.02.001. pmid: 36773890
[4]	Rufai SB, Singh A, Singh J, et al. Diagnostic usefulness of Xpert MTB/RIF assay for detection of tuberculous meningitis using cerebrospinal fluid. J Infect, 2017, 75(2):125-131. doi:10.1016/j.jinf.2017.04.010. pmid: 28501491
[5]	Simner PJ, Miller S, Carroll KC. Understanding the Promises and Hurdles of Metagenomic Next-Generation Sequencing as a Diagnostic Tool for Infectious Diseases. Clin Infect Dis, 2018, 66(5):778-788. doi:10.1093/cid/cix881. pmid: 29040428
[6]	Goldberg B, Sichtig H, Geyer C, et al. Making the Leap from Research Laboratory to Clinic: Challenges and Opportunities for Next-Generation Se-quencing in Infectious Disease Diagnostics. mBio, 2015, 6(6):e01888-15. doi:10.1128/mBio.01888-15.
[7]	高通量测序共识专家组. 高通量测序技术在分枝杆菌病诊断中的应用专家共识. 中华传染病杂志, 2023, 41(3):175-182. doi:10.3760/cma.j.cn311365-20221203-00492.
[8]	Pareek CS, Smoczynski R, Tretyn A. Sequencing technologies and genome sequencing. J Appl Genet, 2011, 52(4):413-435. doi:10.1007/s13353-011-0057-x. pmid: 21698376
[9]	谭聃, 欧铜. 第三代测序技术的研究进展与临床应用. 生物工程学报, 2022, 38(9):3121-3130. doi:10.13345/j.cjb.220063.
[10]	van Dijk EL, Jaszczyszyn Y, Naquin D, et al. The Third Revolution in Sequencing Technology. Trends Genet, 2018, 34(9):666-681. doi:10.1016/j.tig.2018.05.008. pmid: 29941292
[11]	Li Y, Yao XW, Tang L, et al. Diagnostic efficiency of metagenomic next-generation sequencing for suspected spinal tuberculosis in China: A multicenter prospective study. Front Microbiol, 2022,13:1018938. doi:10.3389/fmicb.2022.1018938.
[12]	姚黎明, 姚晓伟, 董昭良, 等. 宏基因组二代测序技术对髋/膝关节结核的诊断价值. 中国防痨杂志, 2023, 45(3):292-296. doi:10.19982/j.issn.1000-6621.20220451.
[13]	Zhao M, Tang K, Liu F, et al. Metagenomic Next-Generation Sequencing Improves Diagnosis of Osteoarticular Infections From Abscess Specimens: A Multicenter Retrospective Study. Front Microbiol, 2020, 11:2034. doi:10.3389/fmicb.2020.02034. pmid: 33042033
[14]	牛宁奎, 费骏, 贺西京, 等. 脊柱感染性疾病的规范诊断与治疗. 中华骨科杂志, 2022, 42(15):968-980. doi:10.3760/cma.j.cn121113-20220210-00058.
[15]	Tsantes AG, Papadopoulos DV, Vrioni G, et al. Spinal Infections: An Update. Microorganisms, 2020, 8(4):476. doi:10.3390/microorganisms8040476.
[16]	Yee DK, Samartzis D, Wong YW, et al. Infective spondylitis in Southern Chinese: a descriptive and comparative study of ninety-one cases. Spine (Phila Pa 1976), 2010, 35(6):635-641. doi:10.1097/BRS.0b013e3181cff4f6.
[17]	Tan YZ, Yuan T, Tan L, et al. Lumbar infection caused by Mycobacterium paragordonae: A case report. World J Clin Cases, 2021, 9(29):8879-8887. doi:10.12998/wjcc.v9.i29.8879.
[18]	Lv H, Zhou JH, Guo Y, et al. Mycobacterium Avium Complex Infection of the Spine in a Patient Without Acquired Immune Deficiency Syndrome: A Case Report and Literature Review. Orthop Surg, 2023, 15(6):1707-1715. doi:10.1111/os.13736.
[19]	Dai L, Wu Y, Zhou X, et al. Multiple Bone Destruction Secondary to Mycobacterium kansasii Pulmonary Disease: A Case Report. Diagnostics (Basel), 2023, 13(11):1970. doi:10.3390/diagnostics13111970.
[20]	Huang H, Shi J, Zheng M, et al. Pathogen detection in suspected spinal infection: metagenomic next-generation sequencing versus culture. Eur Spine J, 2023, 32(12):4220-4228. doi:10.1007/s00586-023-07707-3. pmid: 37237239
[21]	Huang ZD, Zhang ZJ, Yang B, et al. Pathogenic Detection by Metagenomic Next-Generation Sequencing in Osteoarticular Infections. Front Cell Infect Microbiol, 2020,10:471. doi:10.3389/fcimb.2020.00471.
[22]	姚晓伟, 刘树仁, 景艳色, 等. 二代测序技术在骨关节结核临床诊断中的应用价值. 结核与肺部疾病杂志, 2024, 5(1):37-43. doi:10.19983/j.issn.2096-8493.20230094.
[23]	Sun Q, Wang S, Dong W, et al. Diagnostic value of Xpert MTB/RIF Ultra for osteoarticular tuberculosis. J Infect, 2019, 79(2):153-158. doi:10.1016/j.jinf.2019.06.006. pmid: 31207324
[24]	郭超峰, 张广, 胡小江, 等. 宏基因二代测序技术对脊柱感染的诊断效率及预后的影响. 中南大学学报(医学版), 2022, 47(7):865-871. doi:10.11817/j.issn.1672-7347.2022.220163.
[25]	Wang C, Hu J, Gu Y, et al. Application of next-generation metagenomic sequencing in the diagnosis and treatment of acute spinal infections. Heliyon, 2023, 9(3):e13951. doi:10.1016/j.heliyon.2023.e13951.
[26]	黄海荣. 世界卫生组织《应用新一代靶向测序技术检测耐药结核病:快速通告,2023》解读. 中国防痨杂志, 2023, 45(10):921-924. doi:10.19982/j.issn.1000-6621.20230311.
[27]	刘芳, 刘小娟. 分子诊断技术在结核分枝杆菌检测中的应用. 实用医院临床杂志, 2023, 20(5):22-25. doi:10.3969/j.issn.1672-6170.2023.05.006.
[28]	Schwab TC, Perrig L, Göller PC, et al. Targeted next-generation sequencing to diagnose drug-resistant tuberculosis: a systematic review and meta-analysis. Lancet Infect Dis, 2024, 24(10):1162-1176. doi:10.1016/S1473-3099(24)00263-9. pmid: 38795712
[29]	Zhang G, Zhang H, Zhang Y, et al. Targeted next-generation sequencing technology showed great potential in identifying spinal tuberculosis and predicting the drug resistance. J Infect, 2023, 87(6):e110-e112. doi:10.1016/j.jinf.2023.10.018.
[30]	Pawar UM, Kundnani V, Agashe V, et al. Multidrug-resis-tant tuberculosis of the spine--is it the beginning of the end? A study of twenty-five culture proven multidrug-resistant tuberculosis spine patients. Spine (Phila Pa 1976), 2009, 34(22):E806-E810. doi:10.1097/BRS.0b013e3181af7797.
[31]	Meehan CJ, Goig GA, Kohl TA, et al. Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nat Rev Microbiol, 2019, 17(9):533-545. doi:10.1038/s41579-019-0214-5. pmid: 31209399
[32]	Quan TP, Bawa Z, Foster D, et al. Evaluation of Whole-Genome Sequencing for Mycobacterial Species Identification and Drug Susceptibility Testing in a Clinical Setting: a Large-Scale Prospective Assessment of Performance against Line Probe Assays and Phenotyping. J Clin Microbiol, 2018, 56(2):e01480-17. doi:10.1128/JCM.01480-17.
[33]	Clark TG, Mallard K, Coll F, et al. Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing. PLoS One, 2013, 8(12):e83012. doi:10.1371/journal.pone.0083012.
[34]	Ngcelwane M, Omar SV, Said M, et al. New Horizons in the Diagnosis of Tuberculosis of the Spine: The Role of Whole Genome Sequencing. Asian Spine J, 2023, 17(3):511-517. doi:10.31616/asj.2022.0247. pmid: 37194130
[35]	Doyle RM, Burgess C, Williams R, et al. Direct Whole-Genome Sequencing of Sputum Accurately Identifies Drug-Resistant Mycobacterium tuberculosis Faster than MGIT Culture Sequencing. J Clin Microbiol, 2018, 56(8):e00666-18. doi:10.1128/JCM.00666-18.
[36]	Brown AC, Bryant JM, Einer-Jensen K, et al. Rapid Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates Directly from Clinical Samples. J Clin Microbiol, 2015, 53(7):2230-2237. doi:10.1128/JCM.00486-15.
[37]	Wang B, Wang Q, Li M, et al. Diagnostic Role of Metagenomic Next-Generation Sequencing in Tubercular Orthopedic Implant-Associated Infection. Infect Drug Resist, 2024, 17:1951-1960. doi:10.2147/IDR.S441940. pmid: 38774035
[38]	Shi T, Chen H, Liu Y, et al. Clinical applications of metagenomic next-generation sequencing in the identification of pathogens in periprosthetic joint infections: a retrospective study. J Orthop Surg Res, 2024, 19(1):301. doi:10.1186/s13018-024-04745-5. pmid: 38760817
[39]	Zhang C, Hu T, Xiu L, et al. Use of Ultra-Deep Sequencing in a Patient with Tuberculous Coxitis Shows Its Limitations in Extrapulmonary Tuberculosis Diagnostics: A Case Report. Infect Drug Resist, 2019, 12:3739-3743. doi:10.2147/IDR.S226518. pmid: 31819556
[40]	王怡婷, 孟祥莉, 付茵, 等. 宏基因组测序应用于结核病防治的研究进展. 中国防痨杂志, 2024, 46(8):976-981. doi:10.19982/j.issn.1000-6621.20240111.
[41]	Hasan MR, Rawat A, Tang P, et al. Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing. J Clin Microbiol, 2016, 54(4):919-927. doi:10.1128/JCM.03050-15. pmid: 26763966
[42]	Langelier C, Zinter MS, Kalantar K, et al. Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients. Am J Respir Crit Care Med, 2018, 197(4):524-528. doi:10.1164/rccm.201706-1097LE.
[43]	Lindgreen S, Adair KL, Gardner PP. An evaluation of the accuracy and speed of metagenome analysis tools. Sci Rep, 2016,6:19233. doi:10.1038/srep19233.
[44]	Afshinnekoo E, Chou C, Alexander N, et al. Precision Metagenomics: Rapid Metagenomic Analyses for Infectious Disease Diagnostics and Public Health Surveillance. J Biomol Tech, 2017, 28(1):40-45. doi:10.7171/jbt.17-2801-007. pmid: 28337072
[45]	Satam H, Joshi K, Mangrolia U, et al. Next-Generation Sequencing Technology: Current Trends and Advancements. Biology (Basel), 2023, 12(7):997. doi:10.3390/biology12070997.
[46]	Negi S, Pahari S, Bashir H, et al. Gut Microbiota Regulates Mincle Mediated Activation of Lung Dendritic Cells to Protect Against Mycobacterium tuberculosis. Front Immunol, 2019,10:1142. doi:10.3389/fimmu.2019.01142.
[47]	Bergot AS, Giri R, Thomas R. The microbiome and rheumatoid arthritis. Best Pract Res Clin Rheumatol, 2019, 33(6):101497. doi:10.1016/j.berh.2020.101497.
[48]	Nikanjam M, Kato S, Kurzrock R. Liquid biopsy: current technology and clinical applications. J Hematol Oncol, 2022, 15(1):131. doi:10.1186/s13045-022-01351-y.
[49]	Liu H, Ji S, Fang Y, et al. Microbiome Alteration in Lung Tissues of Tuberculosis Patients Revealed by Metagenomic Next-Generation Sequencing and Immune-Related Transcriptional Profile Identified by Transcriptome Sequencing. ACS Infect Dis, 2023, 9(12):2572-2582. doi:10.1021/acsinfecdis.3c00416. pmid: 37975314
[50]	Li M, Hu Y, Zhao B, et al. A next generation sequencing combined genome-wide association study identifies novel tuberculosis susceptibility loci in Chinese population. Genomics, 2021, 113(4):2377-2384. doi:10.1016/j.ygeno.2021.05.035. pmid: 34052317
[51]	Dohál M, Dvořáková V, Šperková M, et al. Whole genome sequencing of multidrug-resistant Mycobacterium tuberculosis isolates collected in the Czech Republic, 2005-2020. Sci Rep, 2022, 12(1):7149. doi:10.1038/s41598-022-11287-5.

测序方法	特点	优点	缺点	应用场景
宏基因组测序	无偏性测序,可检测样本中的所有病原体	高敏感度和特异度;不依赖培养;快速	易受到背景细菌干扰;成本较高;数据分析复杂	病原体鉴定;复杂感染病例;未知病原体检测
全基因组测序	对整个基因组进行测序	可获得完整的基因组信息;适用于药物敏感性分析	成本高;依赖于结核分枝杆菌培养;需要生物信息学专业知识	耐药性分析;流行病学研究;菌株进化研究
靶向测序	综合PCR扩增和高通量测序	可检测多种抗结核药物耐药基因;敏感度和特异度高	不能检测所有病原体;需要特定的靶标区	耐药性基因检测;快速耐药筛查;小范围基因组分析