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Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections

  • M. J. PALLEN (a1)

Summary

The term ‘shotgun metagenomics’ is applied to the direct sequencing of DNA extracted from a sample without culture or target-specific amplification or capture. In diagnostic metagenomics, this approach is applied to clinical samples in the hope of detecting and characterizing pathogens. Here, I provide a conceptual overview, before reviewing several recent promising proof-of-principle applications of metagenomics in virus discovery, analysis of outbreaks and detection of pathogens in contemporary and historical samples. I also evaluate future prospects for diagnostic metagenomics in the light of relentless improvements in sequencing technologies.

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The online version of this article is published within an Open Access environment subject to the conditions of the Creative Commons Attribution licence

Corresponding author

*Corresponding author: Division of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK. E-mail: m.pallen@warwick.ac.uk

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Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections

  • M. J. PALLEN (a1)

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