High-throughput sequencing is being adopted to characterize microbial pathogens and track their evolution and spread.
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References
Loman, N.J. et al. Nat. Rev. Microbiol. 10, 599–606 (2012).
Bashir, A. et al. Nat. Biotechnol. 30, 701–707 (2012).
Koren, S. et al. Nat. Biotechnol. 30, 693–700 (2012).
Harris, S.R. et al. Science 327, 469–474 (2010).
Hendriksen, R.S. et al. mBio 2, e00157–11 (2011).
Mutreja, A. et al. Nature 477, 462–465 (2011).
Rasko, D.A. et al. N. Engl. J. Med. 365, 709–717 (2011).
Rohde, H. et al. N. Engl. J. Med. 365, 718–724 (2011).
Chin, C.-S. et al. N. Engl. J. Med. 364, 33–42 (2011).
Baker, S. et al. Open Biol. 1, 110008 (2011).
Gardy, J.L. et al. N. Engl. J. Med. 364, 730–739 (2011).
McAdam, P.R. et al. Proc. Natl. Acad. Sci. USA 109, 9107–9112 (2012).
Eyre, D.W. et al. BMJ Open 2, e001124 (2012).
Köser, C.U. et al. N. Engl. J. Med. 366, 2267–2275 (2012).
Lewis, T. et al. J. Hosp. Infect. 75, 37–41 (2010).
Nadell, C.D., Xavier, J.B. & Foster, K.R. FEMS Microbiol. Rev. 33, 206–224 (2009).
Rogers, G.B., Carroll, M.P. & Bruce, K.D. J. Med. Microbiol. 58, 1401–1418 (2009).
Hall-Stoodley, L., Costerton, J.W. & Stoodley, P. Nat. Rev. Microbiol. 2, 95–108 (2004).
Cho, I. & Blaser, M.J. Nat. Rev. Genet. 13, 260–270 (2012).
Rogers, G.B. et al. Gut Microbes 1, 85–93 (2010).
Stecher, B. & Hardt, W.-D. Trends Microbiol. 16, 107–114 (2008).
de Sablet, T. et al. Infect. Immun. 77, 783–790 (2009).
Ubeda, C. et al. J. Clin. Invest. 120, 4332–4341 (2010).
Sen, C.K. et al. Wound Repair Regen. 17, 763–771 (2009).
Tuttle, M.S. et al. J. Clin. Microbiol. 49, 3812–3819 (2011).
Wolcott, R.D., Gontcharova, V., Sun, Y., Zischakau, A. & Dowd, S.E. J. Wound Care 18, 317–323 (2009).
Greninger, A.L. et al. PLoS ONE 5, e13381 (2010).
Yang, J. et al. J. Clin. Microbiol. 49, 3463–3469 (2011).
Lieberman, T.D. et al. Nat. Genet. 43, 1275–1280 (2011).
Croucher, N.J. et al. Science 331, 430–434 (2011).
Hornsey, M. et al. J. Antimicrob. Chemother. 66, 1499–1503 (2011).
Feng, J. et al. Genome Res. 19, 1214–1223 (2009).
Kos, V.N. et al. mBio 3, e00112–12 (2012).
Fournier, P.-E. & Raoult, D. Annu. Rev. Microbiol. 65, 169–188 (2011).
Pallen, M.J., Loman, N.J. & Penn, C.W. Curr. Opin. Microbiol. 13, 625–631 (2010).
Raoult, D., Fournier, P.E. & Drancourt, M. Nat. Rev. Microbiol. 2, 151–159 (2004).
The NIH HMP Working Group et al. Genome Res. 19, 2317–2323 (2009).
Li, K., Bihan, M., Yooseph, S. & Methé, B.A. PLoS ONE 7, e32118 (2012).
Wylie, K.M. et al. PLoS ONE 7, e35294 (2012).
The Human Microbiome Project Consortium. Nature 486, 207–214 (2012).
Sergeant, M.J., Constantinidou, C., Cogan, T., Penn, C.W. & Pallen, M.J. PLoS ONE 7, e38094 (2012).
Azhikina, T.L. et al. Biotechniques 48, 139–144 (2010).
Nocker, A. & Camper, A.K. FEMS Microbiol. Lett. 291, 137–142 (2009).
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M.J.P. was a winner of an Ion Torrent Personal Genome Machine in the European PGM grant program.
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Chan, JM., Pallen, M., Oppenheim, B. et al. Genome sequencing in clinical microbiology. Nat Biotechnol 30, 1068–1071 (2012). https://doi.org/10.1038/nbt.2410
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DOI: https://doi.org/10.1038/nbt.2410
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