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Using a Systems Biology Approach To Study Host-Pathogen Interactions

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  • Authors: Amy Yeung1, Christine Hale2, Simon Clare3, Sophie Palmer4, Josefin Bartholdson Scott5, Stephen Baker6,7, Gordon Dougan8
  • Editors: Pascale Cossart9, Craig R. Roy10, Philippe Sansonetti11
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom; 2: Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom; 3: Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom; 4: Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, United Kingdom; 5: Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, United Kingdom; 6: Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, United Kingdom; 7: Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam; 8: Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, United Kingdom; 9: Institut Pasteur, Paris, France; 10: Yale University School of Medicine, New Haven, Connecticut; 11: Institut Pasteur, Paris, France
  • Source: microbiolspec April 2019 vol. 7 no. 2 doi:10.1128/microbiolspec.BAI-0021-2019
  • Received 16 October 2018 Accepted 10 January 2019 Published 05 April 2019
  • Gordon Dougan, [email protected]
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  • Abstract:

    The rapid development of genomics and other “-omics” approaches has significantly impacted how we have investigated host-pathogen interactions since the turn of the millennium. Technologies such as next-generation sequencing, stem cell biology, and high-throughput proteomics have transformed the scale and sensitivity with which we interrogate biological samples. These approaches are impacting experimental design in the laboratory and transforming clinical management in health care systems. Here, we review this area from the perspective of research on bacterial pathogens.

  • Citation: Yeung A, Hale C, Clare S, Palmer S, Bartholdson Scott J, Baker S, Dougan G. 2019. Using a Systems Biology Approach To Study Host-Pathogen Interactions. Microbiol Spectrum 7(2):BAI-0021-2019. doi:10.1128/microbiolspec.BAI-0021-2019.

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/content/journal/microbiolspec/10.1128/microbiolspec.BAI-0021-2019
2019-04-05
2019-08-19

Abstract:

The rapid development of genomics and other “-omics” approaches has significantly impacted how we have investigated host-pathogen interactions since the turn of the millennium. Technologies such as next-generation sequencing, stem cell biology, and high-throughput proteomics have transformed the scale and sensitivity with which we interrogate biological samples. These approaches are impacting experimental design in the laboratory and transforming clinical management in health care systems. Here, we review this area from the perspective of research on bacterial pathogens.

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Figures

Image of FIGURE 1
FIGURE 1

Potential pathways to the functional analysis and exploitation of pathogen whole-genome sequence information. A reference genome (complete and annotated) provides a blueprint for further analysis. The sequencing of populations of related bacteria can be exploited to map sequence variation back onto the reference, providing a map of natural genetic variation on the population. This variation can then be built into phylogeny, providing the evolutionary background of the population. The data can then be collectively used to drive experimental analysis (functional genomics and phenotyping).

Source: microbiolspec April 2019 vol. 7 no. 2 doi:10.1128/microbiolspec.BAI-0021-2019
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Image of FIGURE 2
FIGURE 2

How genomics can empower a clinical sample. It is possible to collect whole-genome or targeted genetic data directly from a clinical sample. This can provide information on the pathogen (TaqMan arrays can cover ∼200 pathogens and provide data in hours) or for metagenomics. Metagenomics and 16S analysis can provide data on the microbiota. RNA-seq and other approaches can provide data on the host.

Source: microbiolspec April 2019 vol. 7 no. 2 doi:10.1128/microbiolspec.BAI-0021-2019
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