The next-generation sequencing technology for diagnosis of pulmonary tuberculosis and pulmonary nontuberculous mycobacterial diseases: two cases report and literature review_Chinese Journal of Respiratory and Critical Care Medicine

Authors：

HUANG Changyu ¹ , HU Ruicheng ¹ ,  ZHANG Youzhi ² , LI Shengqing ²

1. Department of Respiratory Medicine, Hunan Provincial People’s Hospital, Changsha, Hunan 410016, P. R. China;
2. Department of Respiratory Medicine, Huashan Hospital Affiliated to Fudan University, Shanghai 200040, P. R. China;

Corresponding?author：

ZHANG Youzhi, Email: zhyouzhi1977@163.com

Keywords：

Mycobacterium tuberculosis; Non-tuberculous mycobacteria; Infection; Next-generation sequencing

DOI：

10.7507/1671-6205.201803032

Video：

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Objective To explore application value of next-generation sequencing (NGS) technology in diagnosis of pathogenic microorganism infection through two cases report and literature review.Methods The NGS technology was used to make clear diagnosis of two cases of suspected pulmonary tuberculosis and pulmonary nontuberculous mycobacterial diseases. Bronchoalveolar lavage fluid of these two patients was collected for gene detection of pathogens using the NGS technology. A systematic literature review was performed for similar published cases in WanFang and CNKI database, using the keywords (next-generation sequencing) OR (NGS) AND (microorganism OR infection) from January 2000 to January 2018, using the PubMed database to retrieve the English literature before January 2018 with the " NGS, infectious diseases, China” as keywords.Results One case of Mycobacterium tuberculosis and one case of non-tuberculous Mycobacteria were detected respectively. A total of 221 Chinese literatures and 3 English literatures were retrieved, excluding dissertations, conferences and newspapers. Finally, 10 articles were published in the infectious diseases and respiratory diseases subjects. The role of NGS technology in the diagnosis and study of related pathogens is proposed.Conclusion The NGS method is expected to achieve precision medical purposes, such as early diagnosis of infectious diseases, transmission control, accurate treatment, good prognosis and so on.

Citation： HUANG Changyu, HU Ruicheng, ZHANG Youzhi, LI Shengqing. The next-generation sequencing technology for diagnosis of pulmonary tuberculosis and pulmonary nontuberculous mycobacterial diseases: two cases report and literature review. Chinese Journal of Respiratory and Critical Care Medicine, 2019, 18(1): 21-25. doi: 10.7507/1671-6205.201803032 Copy

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2.	Brode SK, Daley CL, Marras TK. The epidemiologic relationship between tuberculosis and non-tuberculous mycobacterial disease: a systematic review. Int J Tuberc Lung Dis, 2014, 18(11): 1370-1377.
3.	O’Brien RJ, Geiter LJ, snider DE Jr. The epidemiology of nontuberculous mycobacterial diseases in the United States. Results from a national survey. Am Rev Respir Dis, 1987, 135(5): 1007-1014.
4.	Marras TK, Mendelson D, Marchand-Austin A, et al. Pulmonary nontuberculous mycobacterial disease, Ontario, Canada, 1998-2010. Emerg Infect Dis, 2013, 19(11): 1889-1891.
5.	Cox MJ, Cookson WO, Moffatt MF. Sequencing the human microbiome in health and disease. Hum Mol Genet, 2013, 22(R1): R88-R94.
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7.	潘陽, 張奕, 楊鵬, 等. 32 例甲型 H3N2 流感病毒感染嚴重急性呼吸道感染病例病毒全基因組分析. 國際檢驗醫學雜志, 2017, 38(17): 2367-2370.
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9.	金嘉琳, 胡越凱, 徐斌, 等. 非人類免疫缺陷病毒感染馬爾尼菲青霉病 9 例臨床特征分析及文獻復習. 微生物與感染, 2017, 12(6): 333-339.
10.	Lasker BA. Nucleotide sequence-based analysis for determining the molecular epidemiology of Penicillium marneffei. J Clin Microbiol, 2006, 44(9): 3145-3153.
11.	季曉偉, 肖雯, 裴家平, 等. HCV F 蛋白和 APC 基因甲基化與慢性 HCV 感染的相關研究. 中華疾病控制雜志, 2017, 21(4): 327-331.
12.	吳衍恒, 師舞陽, 林金思, 等. 一株人感染 H9N2 禽流感病毒高通量測序及序列分析. 中華疾病控制雜志, 2016, 20(11): 1131-1143.
13.	孫英偉, 于丹梅, 陳君, 等. 遼寧省丹東市兩例間日瘧病例報告疫情分析. 中國公共衛生, 2017, 33(2): 314-316.
14.	何片紅, 熊建斌. 解脲脲原體對環丙沙星耐藥機制的探討. 醫學臨床研究, 2007, 24(6): 898-901.
15.	楊柳, 王瑞, 余伍忠, 等. 111 例新疆柯爾克孜族乙型肝炎患者 HBV 基因分型與基因變異的分析. 中國優生與遺傳雜志, 2016, 24(10): 17-20.
16.	陳勁峰, 張復春, 胡鳳玉, 等. 中國首例甲型 H1N1 流感二代病例的臨床特征. 熱帶醫學雜志, 2009, 9(10): 1099-1129.
17.	朱小娟, 郭喜玲, 趙康辰, 等. 腺病毒 55 型感染肺炎患者的病原學鑒定及全基因序列分析. 中國病原生物學雜志, 2017, 12(3): 209-213.
18.	Chen GQ, Zhuang QY, Wang KC, et al. Identification and survey of a novel avian coronavirus in ducks. PLoS One, 2013, 8(8): e72918.
19.	Yao M, Zhou J, Zhu Y, et al. Detection of Listeria monocytogenes in CSF from three patients with meningoencephalitis by next-generation sequencing. J Clin Neurol, 2016, 12(4): 446-451.
20.	Steuernagel B, Taudien S, Gundlach H, et al. De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley. BMC Genomics, 2009, 21(10): 547.
21.	K?ser CU, Ellington MJ, Cartwright EJ, et al. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog, 2012, 8(8): e1002824.
22.	Didelot X, Bowden R, Wilson DJ, et al. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet, 2012, 13(9): 601-612.

1. Eurosurveillance editorial team. WHO publishes global tuberculosis report 2013. Euro Surveill, 2013, 18(43): 20615.
2. Brode SK, Daley CL, Marras TK. The epidemiologic relationship between tuberculosis and non-tuberculous mycobacterial disease: a systematic review. Int J Tuberc Lung Dis, 2014, 18(11): 1370-1377.
3. O’Brien RJ, Geiter LJ, snider DE Jr. The epidemiology of nontuberculous mycobacterial diseases in the United States. Results from a national survey. Am Rev Respir Dis, 1987, 135(5): 1007-1014.
4. Marras TK, Mendelson D, Marchand-Austin A, et al. Pulmonary nontuberculous mycobacterial disease, Ontario, Canada, 1998-2010. Emerg Infect Dis, 2013, 19(11): 1889-1891.
5. Cox MJ, Cookson WO, Moffatt MF. Sequencing the human microbiome in health and disease. Hum Mol Genet, 2013, 22(R1): R88-R94.
6. Morgan XC, Huttenhower C. Chapter 12: human microbiome analysis. PLoS Comput Biol, 2012, 8(12): e1002808.
7. 潘陽, 張奕, 楊鵬, 等. 32 例甲型 H3N2 流感病毒感染嚴重急性呼吸道感染病例病毒全基因組分析. 國際檢驗醫學雜志, 2017, 38(17): 2367-2370.
8. 孫晝, 邱曉楓, 任曉賓, 等. 2015 年杭州市首例本地感染登革熱病例病原溯源調查. 疾病監測, 2017, 32(2): 132-134.
9. 金嘉琳, 胡越凱, 徐斌, 等. 非人類免疫缺陷病毒感染馬爾尼菲青霉病 9 例臨床特征分析及文獻復習. 微生物與感染, 2017, 12(6): 333-339.
10. Lasker BA. Nucleotide sequence-based analysis for determining the molecular epidemiology of Penicillium marneffei. J Clin Microbiol, 2006, 44(9): 3145-3153.
11. 季曉偉, 肖雯, 裴家平, 等. HCV F 蛋白和 APC 基因甲基化與慢性 HCV 感染的相關研究. 中華疾病控制雜志, 2017, 21(4): 327-331.
12. 吳衍恒, 師舞陽, 林金思, 等. 一株人感染 H9N2 禽流感病毒高通量測序及序列分析. 中華疾病控制雜志, 2016, 20(11): 1131-1143.
13. 孫英偉, 于丹梅, 陳君, 等. 遼寧省丹東市兩例間日瘧病例報告疫情分析. 中國公共衛生, 2017, 33(2): 314-316.
14. 何片紅, 熊建斌. 解脲脲原體對環丙沙星耐藥機制的探討. 醫學臨床研究, 2007, 24(6): 898-901.
15. 楊柳, 王瑞, 余伍忠, 等. 111 例新疆柯爾克孜族乙型肝炎患者 HBV 基因分型與基因變異的分析. 中國優生與遺傳雜志, 2016, 24(10): 17-20.
16. 陳勁峰, 張復春, 胡鳳玉, 等. 中國首例甲型 H1N1 流感二代病例的臨床特征. 熱帶醫學雜志, 2009, 9(10): 1099-1129.
17. 朱小娟, 郭喜玲, 趙康辰, 等. 腺病毒 55 型感染肺炎患者的病原學鑒定及全基因序列分析. 中國病原生物學雜志, 2017, 12(3): 209-213.
18. Chen GQ, Zhuang QY, Wang KC, et al. Identification and survey of a novel avian coronavirus in ducks. PLoS One, 2013, 8(8): e72918.
19. Yao M, Zhou J, Zhu Y, et al. Detection of Listeria monocytogenes in CSF from three patients with meningoencephalitis by next-generation sequencing. J Clin Neurol, 2016, 12(4): 446-451.
20. Steuernagel B, Taudien S, Gundlach H, et al. De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley. BMC Genomics, 2009, 21(10): 547.
21. K?ser CU, Ellington MJ, Cartwright EJ, et al. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog, 2012, 8(8): e1002824.
22. Didelot X, Bowden R, Wilson DJ, et al. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet, 2012, 13(9): 601-612.

Chinese Journal of Respiratory and Critical Care Medicine

The next-generation sequencing technology for diagnosis of pulmonary tuberculosis and pulmonary nontuberculous mycobacterial diseases: two cases report and literature review

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