Preview

Проблемы здоровья и экологии

Расширенный поиск

Методы секвенирования нового поколения (NGS) и их использование в клинической микробиологии , инфектологии и эпидемиологии

https://doi.org/10.51523/2708-6011.2021-18-4-3

Аннотация

В обзоре представлены сведения об основных принципах и методах генного секвенирования нового поколения (next-generation sequencing, NGS). Обсуждается ряд современных работ, касающихся возможностей, принципов и этапов NGS, а также применения NGS в медицинских исследованиях, в частности: клиническая микробиология и инфекционные болезни, эпидемиология. Развитие NGS-технологий позволит улучшить результаты диагностики, лечения и профилактики инфекционных болезней и открывает новые перспективы персонализованной медицины.

Об авторе

В. М. Мицура
Республиканский научно-практический центр радиационной медицины и экологии человека
Беларусь

Мицура Виктор Михайлович, д.м.н., доцент, заместитель директора по научной работе; профессор кафедры инфекционных болезней, УО «Гомельский государственный медицинский университет»

г. Гомель



Список литературы

1. Yohe S, Thyagarajan B. Review of clinical next-generation sequencing. Arch Pathol Lab Med. 2017;141(11):1544-1557. DOI: https://doi.org/10.5858/arpa.2016-0501-RA

2. Heather JM, Chain B. The sequence of sequencers: The history of sequencing DNA. Genomics. 2016;107(1):1-8. DOI: https://doi.org/10.1016/j.ygeno.2015.11.003

3. Zhong Y, Xu F, Wu J, Schubert J, Li MM. Application of next generation sequencing in laboratory medicine. Ann Lab Med. 2021;41(1):25-43. DOI: https://doi.org/10.3343/alm.2021.41.1.25

4. McCombie WR, McPherson JD, Mardis ER. Next-Generation Sequencing Technologies. Cold Spring Harb Perspect Med. 2019;9(11):a036798. DOI: https://doi.org/10.1101/cshperspect.a036798

5. Petersen BS, Fredrich B, Hoeppner MP, Ellinghaus D, Franke A. Opportunities and challenges of whole-genome and -exome sequencing. BMC Genet. 2017;18(1):14. DOI: https://doi.org/10.1186/s12863-017-0479-5

6. Hayeems RZ, Dimmock D, Bick D, Belmont JW, Green RC, Lanpher B, Jobanputra V, Mendoza R, Kulkarni Sh, Grove ME, Taylor SL, Ashley E, Medical Genome Initiative. Clinical utility of genomic sequencing: a measurement toolkit. Genomic Medicine. 2020;5:56. DOI: https://doi.org/10.1038/s41525-020-00164-7

7. Prokop JW, May T, Strong K, Bilinovich SM, Bupp C, Rajasekaran S, Worthey EA, Lazar J. Genome sequencing in the clinic: the past, present, and future of genomic medicine. Physiol Genomics. 2018 Aug 1;50(8):563-579. DOI: https://doi.org/10.1152/physiolgenomics.00046.2018

8. Vincent AT, Derome N, Boyle B, Culley AI, Charette SJ. Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money. J Microbiol Methods. 2017;138:60-71. DOI: https://doi.org/10.1016/j.mimet.2016.02.016

9. Besser J, Carleton HA, Gerner-Smidt P, Lindsey RL, Trees E. Next-generation sequencing technologies and their application to the study and control of bacterial infections. Clin Microbiol Infect. 2018;24(4):335-341. DOI: https://doi.org/10.1016/j.cmi.2017.10.013

10. Xu Y, Lin Z, Tang C, Tang Y, Cai Y, Zhong H, Wang X, Zhang W, Xu C, Wang J, Wang J, Yang H, Yang L, Gao Q. A new massively parallel nanoball sequencing platform for whole exome research. BMC Bioinformatics. 2019;20(1):153. DOI: https://doi.org/10.1186/s12859-019-2751-3

11. Natarajan KN, Miao Zh, Jiang M, Huang X, Zhou H, Xie J, Wang Ch, et al. Comparative analysis of sequencing technologies for single-cell transcriptomics. Genome Biol. 2019;20:70. DOI: https://doi.org/10.1186/s13059-019-1676-5

12. Esposito S. Infectious Diseases: Pathophysiology, Diagnostics and Prevention. Int J Mol Sci. 2016;17(9):1464. DOI: https://doi.org/10.3390/ijms17091464

13. Deurenberg RH, Bathoorn E, Chlebowicz MA, Couto N, Ferdous M, García-Cobos S, Kooistra-Smid AM, Raangs EC, Rosema S, Veloo AC, Zhou K, Friedrich AW, Rossen JW. Application of next generation sequencing in clinical microbiology and infection prevention. J Biotechnol. 2017;243:16-24. DOI: https://doi.org/10.1016/j.jbiotec.2016.12.022

14. Leber AL, Everhart K, Balada-Llasat JM, Cullison J, Daly J, Holt S, Lephart P, Salimnia H, Schreckenberger PC, DesJarlais S, Reed SL, Chapin KC, LeBlanc L, Johnson JK, Soliven NL, Carroll KC, Miller JA, Dien Bard J, Mestas J, Bankowski M, Enomoto T, Hemmert AC, Bourzac KM. Multicenter Evaluation of BioFire FilmArray Meningitis/Encephalitis Panel for Detection of Bacteria, Viruses, and Yeast in Cerebrospinal Fluid Specimens. J Clin Microbiol. 2016;54(9):2251-2261. DOI: https://doi.org/10.1128/JCM.00730-16

15. Ellington MJ, Ekelund O, Aarestrup FM, Canton R, Doumith M, Giske C, Grundman H, Hasman H, Holden MTG, Hopkins KL, Iredell J, Kahlmeter G, Köser CU, MacGowan A, Mevius D, Mulvey M, Naas T, Peto T, Rolain JM, Samuelsen Ø, Woodford N. The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee. Clin Microbiol Infect. 2017;23(1):2-22. DOI: https://doi.org/10.1016/j.cmi.2016.11.012

16. Duan H, Li X, Mei A, Li P, Liu Y, Li X, Li W, Wang C, Xie S. The diagnostic value of metagenomic next-generation sequencing in infectious diseases. BMC Infect Dis. 2021;21(1):62. DOI: https://doi.org/10.1186/s12879-020-05746-5

17. Chiu CY, Miller SA. Clinical metagenomics. Nature Rev Genetics. 2019;20(6):341-355. DOI: https://doi.org/10.1038/s41576-019-0113-7

18. Miao Q, Ma Y, Wang Q, Pan J, Zhang Y, Jin W, Yao Y, Su Y, Huang Y, Wang M, Li B, Li H, Zhou C, Li C, Ye M, Xu X, Li Y, Hu B. Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical Practice. Clin Infect Dis. 2018;67:S231-240. DOI: https://doi.org/10.1093/cid/ciy693

19. Yu X, Jiang W, Shi Y, Ye H, Lin J. Application of sequencing technology in clinical microbial infection. J Cell Mol Med. 2019;23(11):7143-7150. DOI: https://doi.org/10.1111/jcmm.14624

20. Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, Si HR, Zhu Y, Li B, Huang CL, Chen HD, Chen J, Luo Y, Guo H, Jiang RD, Liu MQ, Chen Y, Shen XR, Wang X, Zheng XS, Zhao K, Chen QJ, Deng F, Liu LL, Yan B, Zhan FX, Wang YY, Xiao GF, Shi ZL. A pneumonia out-break associated with a new coronavirus of probable bat origin. Nature. 2020;579(7798):270-273. DOI: https://doi.org/10.1038/s41586-020-2012-7

21. Gwinn M, MacCannell DR, Khabbaz RF. Integrating advanced molecular technologies into public health. J Clin Microbiol. 2017;55(3):703-714. DOI: https://doi.org/10.1128/JCM.01967-16

22. Riley LW, Blanton RE. Advances in Molecular Epidemiology of Infectious Diseases: Definitions, Approaches, and Scope of the Field. Microbiol Spectr. 2018;6(6):10.1128/microbiolspec.AME-0001-2018. DOI: https://doi.org/10.1128/microbiolspec.AME-0001-2018

23. Eybpoosh S, Haghdoost AA, Mostafavi E, Bahrampour A, Azadmanesh K, Zolala F. Molecular epidemiology of infectious diseases. Electron Physician. 2017;9(8):5149-5158. DOI: https://doi.org/10.19082/5149

24. Стома ИО, Карпов ИА. Микробиом человека. Минск: Доктор-Дизайн, 2018. 120 с.

25. Langelier C, Kalantar KL, Moazed F, Wilson MR, Crawford ED, Deiss T, et al. Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults. Proc Natl Acad Sci USA 2018;115:E12353-E62. DOI: https://doi.org/10.1073/pnas.1809700115

26. De Vlaminck I, Khush KK, Strehl C, Kohli B, Neff NF, Okamoto J, Snyder TM, Weill D, Bernstein D, Valantine HA, Quake SR. Temporal response of the human virome to immunosuppression and antiviral therapy. Cell 2013;155(5):1178-1187. DOI: https://doi.org/10.1016/j.cell.2013.10.034

27. Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, Reyes JA, Shah SA, LeLeiko N, Snapper SB, Bousvaros A, Korzenik J, Sands BE, Xavier RJ, Huttenhower C. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 2012;13:R79. DOI: https://doi.org/10.1186/gb-2012-13-9-r79

28. van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, Visser CE, Kuijper EJ, Joep Bartelsman FWM, Tijssen JGP, Speelman P, Dijkgraaf MGW, Keller JJ. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 2013;368:407-415. DOI: https://doi.org/10.1056/NEJMoa1205037

29. Rapin A, Pattaroni C, Marsland BJ, Harris NL. Microbiota Analysis Using an Illumina MiSeq Platform to Sequence 16S rRNA Genes. Curr Protoc Mouse Biol. 2017;7(2):100-129. DOI: https://doi.org/10.1002/cpmo.29


Рецензия

Для цитирования:


Мицура В.М. Методы секвенирования нового поколения (NGS) и их использование в клинической микробиологии , инфектологии и эпидемиологии. Проблемы здоровья и экологии. 2021;18(4):26–32. https://doi.org/10.51523/2708-6011.2021-18-4-3

For citation:


Mitsura V.M. Next-generation sequencing (NGS) methods and their application in clinical microbiology, infectology and epidemiology. Health and Ecology Issues. 2021;18(4):26–32. https://doi.org/10.51523/2708-6011.2021-18-4-3

Просмотров: 732


Creative Commons License
Контент доступен под лицензией Creative Commons Attribution 4.0 License.


ISSN 2220-0967 (Print)
ISSN 2708-6011 (Online)