1 Morens D M, Folkers G K, Fauci A S. The challenge of emerging and re-emerging infectious diseases. Nature, 2004, 430: 242-249？？
[2]
2 Lun Z R, Wang Q P, Chen X G, et al. Streptococcus suis: an emerging zoonotic pathogen. Lancet Infect Dis, 2007, 7: 201-209？？
[3]
3 Yang S, Rothman R E. PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings.Lancet Infect Dis, 2004, 4: 337-348？？
[4]
4 Tang Y W, Procop G W, Persing D H. Molecular diagnostics of infectious diseases. Clin Chem, 1997, 43: 2021-2038
[5]
5 Muldrew K L. Molecular diagnostics of infectious diseases. Curr Opin Pediatr, 2009, 21: 102-111？？
[6]
6 Vandamme P, Pot B, Gillis M, et al. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev, 1996, 60:407-438
[7]
7 Clarke S C. Nucleotide sequence-based typing of bacteria and the impact of automation. Bioessays, 2002, 24: 858-862？？
[8]
8 Fox G E, Pechman K R, Woese C R. Comparative cataloging of 16S ribosomal ribonucleic acid: molecular aproach to procaryoticsystematics. Int J Syst Bacteriol, 1977, 27: 44-57？？
[9]
9 Urwin R, Maiden M C. Multi-locus sequence typing: a tool for global epidemiology. Trends Microbiol, 2003, 11: 479-487？？
[10]
10 Maiden M C. Multilocus sequence typing of bacteria. Annu Rev Microbiol, 2006, 60: 561-588？？
[11]
11 Lindstedt B A. Multiple-locus variable number tandem repeatsanalysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis,2005, 26: 2567-2582？？
[12]
12 Konstantinidis K T, Tiedje J M. Towards a genome-based taxonomy for prokaryotes. J Bacteriol, 2005, 187: 6258-6264？？
[13]
13 Tindall B J, Rossello-Mora R, Busse H J, et al. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst EvolMicrobiol, 2010, 60: 249-266？？
[14]
14 Moran N A. Microbial minimalism: genome reduction in bacterial pathogens. Cell, 2002, 108: 583-586？？
[15]
15 Khalturin K, Hemmrich G, Fraune S, et al. More than just orphans: are taxonomically-restricted genes important in evolution? Trends Genet,2009, 25: 404-413
[16]
16 中华人民共和国卫生部. 人间传染的病原微生物名录, 2006
[17]
17 Altschul S F, Gish W, Miller W, et al. Basic local alignment search tool. J Mol Biol, 1990, 215: 403-410
[18]
18 Tatusov R L, Galperin M Y, Natale D A, et al. The COG database: a tool for genome-scale analysis of protein functions and evolution.Nucleic Acids Res, 2000, 28: 33-36？？
[19]
19 Lemee L, Bourgeois I, Ruffin E, et al. Multilocus sequence analysis and comparative evolution of virulence-associated genes andhousekeeping genes of Clostridium difficile. Microbiology, 2005, 151: 3171-3180？？
[20]
20 Spurgiesz R S, Quitugua T N, Smith K L, et al. Molecular typing of Mycobacterium tuberculosis by using nine novel variable-numbertandem repeats across the Beijing family and low-copy-number IS6110 isolates. J Clin Microbiol, 2003, 41: 4224-4230？？
[21]
21 Ahmed N. A flood of microbial genomes-do we need more? PLoS One, 2009, 4: e5831
[22]
22 Blaxter M L. The promise of a DNA taxonomy. Philos Trans R Soc Lond B Biol Sci, 2004, 359: 669-679？？
[23]
23 Vieites J M, Guazzaroni M E, Beloqui A, et al. Metagenomics approaches in systems microbiology. FEMS Microbiol Rev, 2009, 33:236-255？？
[24]
24 Tringe S G, Rubin E M. Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet, 2005, 6: 805-814？？
[25]
25 Metzker M L. Sequencing technologies-the next generation. Nat Rev Genet, 2010, 11: 31-46？？
[26]
26 Streit W R, Schmitz R A. Metagenomics-the key to the uncultured microbes. Curr Opin Microbiol, 2004, 7: 492-498？？
[27]
27 Tringe S G, Von M C, Kobayashi A, et al. Comparative metagenomics of microbial communities. Science, 2005, 308: 554-557？？
