zdorПроблемы здоровья и экологииHealth and Ecology Issues2220-09672708-6011Gomel State Medical University10.51523/2708-6011.2021-18-4-3zdor-2108Research ArticleОБЗОРЫ И ЛЕКЦИИREVIEWS AND LECTURESМетоды секвенирования нового поколения (NGS) и их использование в клинической микробиологии , инфектологии и эпидемиологииNext-generation sequencing (NGS) methods and their application in clinical microbiology, infectology and epidemiologyhttps://orcid.org/0000-0002-0449-5026МицураВ. М.MitsuraV. M.

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

г. Гомель

Viktar M. Mitsura, DMedSc, Associate Professor, Deputy Director for Research; Professor at the Department of Infectious Diseases, Gomel State Medical University

Gomel

mitsura_victor@tut.byРеспубликанский научно-практический центр радиационной медицины и экологии человекаRepublican Research Center for Radiation Medicine and Human Ecology20213012202118426–32Copyright © Мицура В.М., 20212021Мицура В.М.Mitsura V.M.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://journal.gsmu.by/jour/article/view/2108

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.

This review presents basic principles and methods of next-generation sequencing (NGS) and discusses a number of the latest papers on the possibilities, principles and stages of NGS, as well as the application of NGS in medical research, particularly, clinical microbiology and infectious diseases, epidemiology. The development of NGS technologies will allow improving the results of diagnostics, treatment and prevention of infectious diseases and opens up new prospects for personalized medicine.

секвенирование нового поколенияклиническая микробиологияинфектологияэпидемиологияnext-generation sequencingclinical microbiologyinfectologyepidemiologyReferencesYohe 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-RAYohe 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-RAHeather 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.2015.11.003Heather 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.2015.11.003Zhong 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.2021.41.1.25Zhong 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.2021.41.1.25McCombie 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.a036798McCombie 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.a036798Petersen 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/s12863-017-0479-5Petersen 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/s12863-017-0479-5Hayeems 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/s41525-020-00164-7Hayeems 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/s41525-020-00164-7Prokop 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.00046.2018Prokop 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.00046.2018Vincent 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.2016.02.016Vincent 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.2016.02.016Besser 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.2017.10.013Besser 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.2017.10.013Xu 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/s12859-019-2751-3Xu 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/s12859-019-2751-3Natarajan 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/s13059-019-1676-5Natarajan 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/s13059-019-1676-5Esposito S. Infectious Diseases: Pathophysiology, Diagnostics and Prevention. Int J Mol Sci. 2016;17(9):1464. DOI: https://doi.org/10.3390/ijms17091464Esposito S. Infectious Diseases: Pathophysiology, Diagnostics and Prevention. Int J Mol Sci. 2016;17(9):1464. DOI: https://doi.org/10.3390/ijms17091464Deurenberg 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.2016.12.022Deurenberg 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.2016.12.022Leber 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.00730-16Leber 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.00730-16Ellington 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.2016.11.012Ellington 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.2016.11.012Duan 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/s12879-020-05746-5Duan 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/s12879-020-05746-5Chiu CY, Miller SA. Clinical metagenomics. Nature Rev Genetics. 2019;20(6):341-355. DOI: https://doi.org/10.1038/s41576-019-0113-7Chiu CY, Miller SA. Clinical metagenomics. Nature Rev Genetics. 2019;20(6):341-355. DOI: https://doi.org/10.1038/s41576-019-0113-7Miao 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/ciy693Miao 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:S231-40. DOI: https://doi.org/10.1093/cid/ciy693Yu 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.14624Yu 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.14624Zhou 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/s41586-020-2012-7Zhou 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 outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579(7798):270-273. DOI: https://doi.org/10.1038/s41586-020-2012-7Gwinn 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.01967-16Gwinn 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.01967-16Riley 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-0001-2018Riley 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-0001-2018Eybpoosh 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/10.19082/5149Eybpoosh 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/10.19082/5149Стома ИО, Карпов ИА. Микробиом человека. Минск: Доктор-Дизайн, 2018. 120 с.Stoma IO, Karpov IA. Human microbiome. Minsk, Doctor-Design; 2018. 120 p. (In Russ.).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.1809700115Langelier 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.1809700115De 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.2013.10.034De 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.2013.10.034Morgan 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-r79Morgan 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-r79van 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/NEJMoa1205037van 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;368:407-15. DOI: https://doi.org/10.1056/NEJMoa1205037Rapin 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.29Rapin 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

The authors declare that there are no conflicts of interest present.