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Review
. 2014 Dec;141(14):1856-62.
doi: 10.1017/S0031182014000134. Epub 2014 Feb 27.

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

M J Pallen  1
Affiliations
Free PMC article
Review

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

M J Pallen. Parasitology. 2014 Dec.
Free PMC article

Abstract

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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Figures

Fig. 1.
Fig. 1.
Comparisons between culture, targeted molecular assays and diagnostic metagenomics.
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