新型宏基因组/宏转录组学技术在反向病原学研究中的应用

王亚丽; 麻锦敏; 陈路; 邹弈君; 江佳富; 陈唯军

doi:10.3784/jbjc.202210270462

新型宏基因组/宏转录组学技术在反向病原学研究中的应用

doi: 10.3784/jbjc.202210270462

王亚丽^1,,
麻锦敏¹,
陈路²,
邹弈君³,
江佳富⁴,
陈唯军^{1, 3, ,}

1.
深圳华大因源医药科技有限公司, 广东深圳 518085
2.
北京宏微特斯生物科技有限公司, 北京 101300
3.
中国科学院大学生命科学学院, 北京 100049
4.
军事医学研究院微生物流行病研究所病原微生物生物安全国家重点实验室, 北京 100071

基金项目: 国家重点研发计划项目（No. 2019YFC1200500，No. 2019YFC1200501）

详细信息

作者简介:
王亚丽，女，江苏省泰州市人，博士，主要从事宏基因组学病原检测技术工作，Email：wangyali1@genomics.cn

通讯作者:
陈唯军，Tel：0755−36382041，Email：chenwj@genomics.cn

中图分类号: R211; R183.5
计量
- 文章访问数: 129
- HTML全文浏览量: 32
- PDF下载量: 11
- 被引次数: 0
出版历程
- 收稿日期: 2022-10-27
- 网络出版日期: 2023-05-08

Application of novel metagenomics/metatranscriptomics technologies in reverse etiology research

Wang Yali^1
,,
Ma Jinmin¹,
Chen Lu²,
Zou Yijun³,
Jiang Jiafu⁴,
Chen Weijun^{1, 3
, ,}

1.
BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen 518085, Guangdong, China
2.
Beijing Macro & micro-test Bio-Tech Co., Ltd., Beijing 101300, China
3.
College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
4.
State Key Laboratory of Pathogens and Biosecurity, Academy of Military Medical Sciences, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China

Funds: This study was supported by the fund for National Key Research and Development Program of China (No. 2019YFC1200500, No. 2019YFC1200501)

More Information

Corresponding author: Chen Weijun, Email: chenwj@genomics.cn

摘要

摘要: 以微生物组学和宏基因组学为基础的新技术的飞跃式发展为新微生物的发现提供了无可比拟的优势。反向病原学理念公开提出后，在指导新发突发传染病的主动防控实践方面也正在发挥越来越多的作用，在公共卫生和疾病防控领域应用越来越广。新型宏基因组/宏转录组学技术进一步支撑和促进反向病原学研究，在发展评估新微生物致病潜力的理论、策略和方法方面有了一定的进展。在此，本综述梳理了新型宏基因组/宏转录组学技术在反向病原学研究中的作用实践、以及面临的挑战，期望促进人们对病原体的认识和理论技术创新。
- 新型宏基因组/宏转录组学技术 /
- 反向病原学 /
- 未来传染病 /
- 新发传染病
Abstract: The rapid development of new technologies based on microbiomes and metagenomics provides unparalleled advantages in the discovery of novel microorganisms. Since the publication of concept of reverse etiology, it has played an increasingly important role in guiding the active prevention and control practice of emerging infectious diseases and has been widely used in the fields of public health and disease prevention and control. New metagenomics/metatranscriptomics technologies have further supported and facilitated reverse etiology research, and some progresses have been made in the development of theories, strategies and methodologies for assessing the pathogenic potentials of novel microorganisms. This paper summarizes the role, application of new metagenomics/metatranscriptomics technologies in reverse etilogy research and the challenges in its application for the purpose of improving the understanding of pathogens and theoretical and technical innovations.
- Novel metagenomics/metatranscriptomics technologies /
- Reverse etiology /
- Future infectious disease /
- Emerging infectious disease

HTML全文

参考文献(27)

[1]	Qin JJ, Li RQ, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing[J]. Nature, 2010, 464(7285): 59–65. DOI: 10.1038/nature08821.
[2]	Wang LH, Lv XJ, Zhai YG, et al. Genomic characterization of a novel virus of the family Tymoviridae isolated from mosquitoes[J]. PLoS One, 2012, 7(7): e39845. DOI: 10.1371/journal.pone.0039845.
[3]	Palacios G, Druce J, Du L, et al. A new arenavirus in a cluster of fatal transplant-associated diseases[J]. N Engl J Med, 2008, 358(10): 991–998. DOI: 10.1056/NEJMoa073785.
[4]	Xu BL, Liu LC, Huang XY, et al. Metagenomic analysis of fever, thrombocytopenia and leukopenia syndrome (FTLS) in Henan province, China: discovery of a new bunyavirus[J]. PLoS Pathog, 2011, 7(11): e1002369. DOI: 10.1371/journal.ppat.1002369.
[5]	Shi M, Lin XD, Tian JH, et al. Redefining the invertebrate RNA virosphere[J]. Nature, 2016, 540(7634): 539–543. DOI: 10.1038/nature20167.
[6]	李沛翰, 李鹏, 宋宏彬. 宏基因组学在传染病防控中的应用进展[J]. 生物技术通报,2018,34(3):43–52. DOI:10.13560/j.cnki.biotech.bull.1985.2017−0787. Li PH, Li P, Song HB. Application of metagenomics in prevention and control of infectious diseases[J]. Biotechnol Bull, 2018, 34(3): 43–52. DOI: 10.13560/j.cnki.biotech.bull.1985.2017−0787.
[7]	徐建国. 反向病原学[J]. 疾病监测,2019,34(7):593–598. DOI:10.3784/j.issn.1003−9961.2019.07.005. Xu JG. Reverse microbial etiology[J]. Dis Surveill, 2019, 34(7): 593–598. DOI: 10.3784/j.issn.1003−9961.2019.07.005.
[8]	Li K, Lin XD, Wang W, et al. Isolation and characterization of a novel arenavirus harbored by rodents and shrews in Zhejiang province, China[J]. Virology, 2015, 476: 37–42. DOI: 10.1016/j.virol.2014.11.026.
[9]	Blasdell KR, Duong V, Eloit M, et al. Evidence of human infection by a new mammarenavirus endemic to Southeastern Asia[J]. eLife, 2016, 5: e13135. DOI: 10.7554/eLife.13135.001.
[10]	Wylie KM, Blanco-Guzman M, Wylie TN, et al. High-throughput sequencing of cerebrospinal fluid for diagnosis of chronic Propionibacterium acnes meningitis in an allogeneic stem cell transplant recipient[J]. Transpl Infect Dis, 2016, 18(2): 227–233. DOI: 10.1111/tid.12512.
[11]	Wilson MR, Naccache SN, Samayoa E, et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing[J]. N Engl J Med, 2014, 370(25): 2408–2417. DOI: 10.1056/NEJMoa1401268.
[12]	Saeb ATM, Abouelhoda M, Selvaraju M, et al. The use of next-generation sequencing in the identification of a fastidious pathogen: a lesson from a clinical setup[J]. Evol Bioinform, 2017, 13: 1–15. DOI: 10.1177/1176934316686072.
[13]	Naccache SN, Peggs KS, Mattes FM, et al. Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing[J]. Clin Infect Dis, 2015, 60(6): 919–923. DOI: 10.1093/cid/ciu912.
[14]	Ruppé E, Lazarevic V, Girard M, et al. Clinical metagenomics of bone and joint infections: a proof of concept study[J]. Sci Rep, 2017, 7(1): 7718. DOI: 10.1038/s41598−017−07546−5.
[15]	Guan HZ, Shen A, Lv X, et al. Detection of virus in CSF from the cases with meningoencephalitis by next-generation sequencing[J]. J Neurovirol, 2016, 22(2): 240–245. DOI: 10.1007/s13365−015−0390−7.
[16]	Wang Q, Li JM, Ji JK, et al. A case of Naegleria fowleri related primary amoebic meningoencephalitis in China diagnosed by next-generation sequencing[J]. BMC Infect Dis, 2018, 18(1): 349. DOI: 10.1186/s12879−018−3261−z.
[17]	Ai JW, Weng SS, Cheng Q, et al. Human endophthalmitis caused by pseudorabies virus infection, China, 2017[J]. Emerg Infect Dis, 2018, 24(6): 1087–1090. DOI: 10.3201/eid2406.171612.
[18]	Wang J, Zhou WM, Ling H, et al. Identification of Histoplasma causing an unexplained disease cluster in Matthews Ridge, Guyana[J]. Biosaf Health, 2019, 1(3): 150–154. DOI: 10.1016/j.bsheal.2019.12.003.
[19]	Liu R, Zhang GL, Yang YH, et al. Genome sequence of Abbey Lake virus, a novel orthobunyavirus isolated from China[J]. Genome Announc, 2014, 2(3). DOI: 10.1128/genomeA.00433-14.
[20]	Xia H, Liu R, Zhao L, et al. Characterization of Ebinur lake virus and its human seroprevalence at the China–Kazakhstan border[J]. Front Microbiol, 2020, 10: 3111. DOI: 10.3389/fmicb.2019.03111.
[21]	Zhang XA, Li H, Jiang FC, et al. A zoonotic henipavirus in febrile patients in China[J]. N Engl J Med, 2022, 387(5): 470–472. DOI: 10.1056/NEJMc2202705.
[22]	Wei R, Liu HB, Jongejan F, et al. Cultivation of Anaplasma ovis in the HL-60 human promyelocytic leukemia cell line[J]. Emerg Microbes Infect, 2017, 6(9): e83. DOI: 10.1038/emi.2017.70.
[23]	Qin XC, Shi M, Tian JH, et al. A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors[J]. Proc Natl Acad Sci USA, 2014, 111(18): 6744–6749. DOI: 10.1073/pnas.1324194111.
[24]	Wang ZD, Wang B, Wei F, et al. A new segmented virus associated with human febrile illness in China[J]. N Engl J Med, 2019, 380(22): 2116–2125. DOI: 10.1056/NEJMoa1805068.
[25]	Liu S, Jin D, Lan RT, et al. Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana[J]. Int J Syst Evol Microbiol, 2015, 65(7): 2130–2134. DOI: 10.1099/ijs.0.000228.
[26]	Sivertsen A, Dyrhovden R, Tellevik MG, et al. Escherichia marmotae—a human pathogen easily misidentified as Escherichia coli[J]. Microbiol Spectr, 2022, 10(2): e0203521. DOI: 10.1128/spectrum.02035−21.
[27]	Shi M, Lin XD, Vasilakis N, et al. Divergent viruses discovered in arthropods and vertebrates revise the evolutionary history of the Flaviviridae and related viruses[J]. J Virol, 2016, 90(2): 659–669. DOI: 10.1128/JVI.02036−15.