Global Microbial Identifier

Peter Wielinga, Rene S. Hendriksen, Frank Møller Aarestrup, Ole Lund, Saskia L. Smits, Marion Koopmans, Jørgen Schlundt

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

Abstract

Human and animal populations are increasingly confronted with emerging and re-emerging infections and often such infections are exchanged between these populations, e.g. through food. A more effective and uniform approach to the prevention of these microbial threats is essential. The technological advances in the next generation sequencing field and decreasing costs of these tests provide novel opportunities in understanding the dynamics of infection—even in real time—through the analysis of microbial genome diversity. The projected significant increase in whole (microbial) genome sequencing (WGS) will likely also enable a much better understanding of the pathogenesis of the infection and the molecular basis of the host response to infection. But the full potential of these advances will only transpire if the data in this area become transferable and thereby comparable, preferably in open-source systems. There is therefore an obvious need to develop a global system of whole microbial genome databases to aggregate, share, mine and use microbiological genomic data, to address global public health and clinical challenges, and most importantly to identify and diagnose infectious diseases. The global microbial identifier (GMI) initiative, aims to build a database of whole microbial genome sequencing data linked to relevant metadata, which can be used to identify microorganisms, their communities and the diseases they cause. It would be a platform for storing whole genome sequencing (WGS) data of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect outbreaks and emerging pathogens. To harness the full potential of WGS, a shared global database of genomes linked to relevant metadata and the necessary software tools needs to be generated, hence the global microbial identifier (GMI) initiative. This tool will ideally be used in amongst others in the diagnosis of infectious diseases in humans and animals, in the identification of microorganisms in food and environment, and to track and trace microbial agents in all arenas globally. This will require standardization and extensive investments in computational analytical tools. In addition, the wider introduction of WGS in clinical diagnostics can accelerate developments in health care in many poor countries. This overview describes the growing network of stakeholders behind GMI, the contours of the database, and the IT structures needed to serve the GMI user community. It discusses what essentially can be done by a global GMI tool and how the GMI organization could help achieve these goals.
Original languageEnglish
Title of host publicationApplied Genomics of Foodborne Pathogens
Place of PublicationSwitzerland
PublisherSpringer
Publication date2017
Pages13-31
Chapter2
ISBN (Electronic)978-3-319-43751-4
DOIs
Publication statusPublished - 2017

Keywords

  • Life Sciences
  • Food Microbiology
  • Food Science
  • Bioinformatics
  • Microbial Genetics and Genomics
  • Applied Microbiology
  • DNA sequencing
  • Microbiology
  • Global DNA database
  • Whole genome sequence
  • Infectious disease
  • Open-source

Cite this

Wielinga, P., Hendriksen, R. S., Aarestrup, F. M., Lund, O., Smits, S. L., Koopmans, M., & Schlundt, J. (2017). Global Microbial Identifier. In Applied Genomics of Foodborne Pathogens (pp. 13-31). Switzerland: Springer. https://doi.org/10.1007/978-3-319-43751-4_2
Wielinga, Peter ; Hendriksen, Rene S. ; Aarestrup, Frank Møller ; Lund, Ole ; Smits, Saskia L. ; Koopmans, Marion ; Schlundt, Jørgen. / Global Microbial Identifier. Applied Genomics of Foodborne Pathogens. Switzerland : Springer, 2017. pp. 13-31
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Wielinga, P, Hendriksen, RS, Aarestrup, FM, Lund, O, Smits, SL, Koopmans, M & Schlundt, J 2017, Global Microbial Identifier. in Applied Genomics of Foodborne Pathogens. Springer, Switzerland, pp. 13-31. https://doi.org/10.1007/978-3-319-43751-4_2

Global Microbial Identifier. / Wielinga, Peter; Hendriksen, Rene S.; Aarestrup, Frank Møller; Lund, Ole; Smits, Saskia L.; Koopmans, Marion; Schlundt, Jørgen.

Applied Genomics of Foodborne Pathogens. Switzerland : Springer, 2017. p. 13-31.

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

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AU - Koopmans, Marion

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AB - Human and animal populations are increasingly confronted with emerging and re-emerging infections and often such infections are exchanged between these populations, e.g. through food. A more effective and uniform approach to the prevention of these microbial threats is essential. The technological advances in the next generation sequencing field and decreasing costs of these tests provide novel opportunities in understanding the dynamics of infection—even in real time—through the analysis of microbial genome diversity. The projected significant increase in whole (microbial) genome sequencing (WGS) will likely also enable a much better understanding of the pathogenesis of the infection and the molecular basis of the host response to infection. But the full potential of these advances will only transpire if the data in this area become transferable and thereby comparable, preferably in open-source systems. There is therefore an obvious need to develop a global system of whole microbial genome databases to aggregate, share, mine and use microbiological genomic data, to address global public health and clinical challenges, and most importantly to identify and diagnose infectious diseases. The global microbial identifier (GMI) initiative, aims to build a database of whole microbial genome sequencing data linked to relevant metadata, which can be used to identify microorganisms, their communities and the diseases they cause. It would be a platform for storing whole genome sequencing (WGS) data of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect outbreaks and emerging pathogens. To harness the full potential of WGS, a shared global database of genomes linked to relevant metadata and the necessary software tools needs to be generated, hence the global microbial identifier (GMI) initiative. This tool will ideally be used in amongst others in the diagnosis of infectious diseases in humans and animals, in the identification of microorganisms in food and environment, and to track and trace microbial agents in all arenas globally. This will require standardization and extensive investments in computational analytical tools. In addition, the wider introduction of WGS in clinical diagnostics can accelerate developments in health care in many poor countries. This overview describes the growing network of stakeholders behind GMI, the contours of the database, and the IT structures needed to serve the GMI user community. It discusses what essentially can be done by a global GMI tool and how the GMI organization could help achieve these goals.

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KW - Microbial Genetics and Genomics

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KW - Global DNA database

KW - Whole genome sequence

KW - Infectious disease

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Wielinga P, Hendriksen RS, Aarestrup FM, Lund O, Smits SL, Koopmans M et al. Global Microbial Identifier. In Applied Genomics of Foodborne Pathogens. Switzerland: Springer. 2017. p. 13-31 https://doi.org/10.1007/978-3-319-43751-4_2