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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.
See this image and copyright information in PMC

References

    1. Andersson P., Klein M., Lilliebridge R. A. and Giffard P. M. (2013). Sequences of multiple bacterial genomes and a Chlamydia trachomatis genotype from direct sequencing of DNA derived from a vaginal swab diagnostic specimen. Clinical Microbiology and Infection 19, E405–E408. - PubMed
    1. Arumugam M., Raes J., Pelletier E., Le Paslier D., Yamada T., Mende D. R., Fernandes G. R., Tap J., Bruls T., Batto J. M., Bertalan M., Borruel N., Casellas F., Fernandez L., Gautier L., Hansen T., Hattori M., Hayashi T., Kleerebezem M., Kurokawa K., Leclerc M., Levenez F., Manichanh C., Nielsen H. B., Nielsen T., Pons N., Poulain J., Qin J., Sicheritz-Ponten T., Tims S., Torrents D., Ugarte E., Zoetendal E. G., Wang J., Guarner F., Pedersen O., de Vos W. M., Brunak S., Dore J., Antolin M., Artiguenave F., Blottiere H. M., Almeida M., Brechot C., Cara C., Chervaux C., Cultrone A., Delorme C., Denariaz G., Dervyn R., Foerstner K. U., Friss C., van de Guchte M., Guedon E., Haimet F., Huber W., van Hylckama-Vlieg J., Jamet A., Juste C., Kaci G., Knol J., Lakhdari O., Layec S., Le Roux K., Maguin E., Merieux A., Melo Minardi R., M'rini C., Muller J., Oozeer R., Parkhill J., Renault P., Rescigno M., Sanchez N., Sunagawa S., Torrejon A., Turner K., Vandemeulebrouck G., Varela E., Winogradsky Y., Zeller G., Weissenbach J., Ehrlich S. D. and Bork P. (2011). Enterotypes of the human gut microbiome. Nature 473, 174–180. - PMC - PubMed
    1. Batty E. M., Wong T. H., Trebes A., Argoud K., Attar M., Buck D., Ip C. L., Golubchik T., Cule M., Bowden R., Manganis C., Klenerman P., Barnes E., Walker A. S., Wyllie D. H., Wilson D. J., Dingle K. E., Peto T. E., Crook D. W. and Piazza P. (2013). A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples. PLoS One 8, . - PMC - PubMed
    1. Bos K. I., Schuenemann V. J., Golding G. B., Burbano H. A., Waglechner N., Coombes B. K., McPhee J. B., DeWitte S. N., Meyer M., Schmedes S., Wood J., Earn D. J., Herring D. A., Bauer P., Poinar H. N. and Krause J. (2011). A draft genome of Yersinia pestis from victims of the Black Death. Nature 478, 506–510. - PMC - PubMed
    1. Bouwman A. S., Kennedy S. L., Muller R., Stephens R. H., Holst M., Caffell A. C., Roberts C. A. and Brown T. A. (2012). Genotype of a historic strain of Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences USA 109, 18511–18516. - PMC - PubMed