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Platforms and Analytical Tools Used in Nucleic Acid Sequence-Based Microbial Genotyping Procedures *

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  • Author: Duncan MacCannell1
  • Editors: Lee W. Riley2, Ronald E. Blanton3
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Office of Advanced Molecular Detection, National Center for Zoonotic and Emerging Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333; 2: Divisions of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA; 3: Center for Global Health & Diseases, Case Western Reserve University, Cleveland, OH
  • Source: microbiolspec February 2019 vol. 7 no. 1 doi:10.1128/microbiolspec.AME-0005-2018
  • Received 25 July 2018 Accepted 28 November 2018 Published 08 February 2019
  • Duncan MacCannell, [email protected]
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  • Abstract:

    In the decade and a half since the introduction of next-generation sequencing (NGS), the technical feasibility, cost, and overall utility of sequencing have changed dramatically, including applications for infectious disease epidemiology. Massively parallel sequencing technologies have decreased the cost of sequencing by more than 6 orders or magnitude over this time, with a corresponding increase in data generation and complexity. This review provides an overview of the basic principles, chemistry, and operational mechanics of current sequencing technologies, including both conventional Sanger and NGS approaches. As the generation of large amounts of sequence data becomes increasingly routine, the role of bioinformatics in data analysis and reporting becomes all the more critical, and the successful deployment of NGS in public health settings requires careful consideration of changing information technology, bioinformatics, workforce, and regulatory requirements. While there remain important challenges to the sustainable implementation of NGS in public health, in terms of both laboratory and bioinformatics capacity, the impact of these technologies on infectious disease surveillance and outbreak investigations has been nothing short of revolutionary. Understanding the important role that NGS plays in modern public health laboratory practice is critical, as is the need to ensure appropriate workforce, infrastructure, facilities, and funding consideration for routine NGS applications, future innovation, and rapidly scaling NGS-based infectious disease surveillance and outbreak response activities.

    *This article is part of a curated collection.

  • Citation: MacCannell D. 2019. Platforms and Analytical Tools Used in Nucleic Acid Sequence-Based Microbial Genotyping Procedures * . Microbiol Spectrum 7(1):AME-0005-2018. doi:10.1128/microbiolspec.AME-0005-2018.

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2019-02-08
2019-02-23

Abstract:

In the decade and a half since the introduction of next-generation sequencing (NGS), the technical feasibility, cost, and overall utility of sequencing have changed dramatically, including applications for infectious disease epidemiology. Massively parallel sequencing technologies have decreased the cost of sequencing by more than 6 orders or magnitude over this time, with a corresponding increase in data generation and complexity. This review provides an overview of the basic principles, chemistry, and operational mechanics of current sequencing technologies, including both conventional Sanger and NGS approaches. As the generation of large amounts of sequence data becomes increasingly routine, the role of bioinformatics in data analysis and reporting becomes all the more critical, and the successful deployment of NGS in public health settings requires careful consideration of changing information technology, bioinformatics, workforce, and regulatory requirements. While there remain important challenges to the sustainable implementation of NGS in public health, in terms of both laboratory and bioinformatics capacity, the impact of these technologies on infectious disease surveillance and outbreak investigations has been nothing short of revolutionary. Understanding the important role that NGS plays in modern public health laboratory practice is critical, as is the need to ensure appropriate workforce, infrastructure, facilities, and funding consideration for routine NGS applications, future innovation, and rapidly scaling NGS-based infectious disease surveillance and outbreak response activities.

*This article is part of a curated collection.

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Figures

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FIGURE 1

Principal steps of a generic NGS workflow.

Source: microbiolspec February 2019 vol. 7 no. 1 doi:10.1128/microbiolspec.AME-0005-2018
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Tables

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TABLE 1

Summary characteristics of most common NGS commercial systems

Source: microbiolspec February 2019 vol. 7 no. 1 doi:10.1128/microbiolspec.AME-0005-2018

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