Genetic analysis and attribution of microbial forensics evidence

Critical Reviews in Microbiology

Volumn 31, Issue 4, 2005, Pages 233-254

  Budowle, Bruce ^a   Johnson, Martin D ^b   Fraser, Claire M ^c   Leighton, Terrance J ^d   Murch, Randall S ^e   Chakraborty, Ranajit ^f  

^a FBI LABORATORY   (United States)

^b APPLIED BIOSYSTEMS   (United States)

^c J CRAIG VENTER INSTITUTE   (United States)

^d CHILDREN S HOSPITAL OAKLAND RESEARCH INSTITUTE   (United States)

^e VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

^f UNIVERSITY OF CINCINNATI COLLEGE OF MEDICINE   (United States)

Author keywords

Attribution; Genetic Markers; Microarrays; Microbial Forensics; MLST; MLVA; PCR; Real Time PCR; Sequencing

Indexed keywords

ARTICLE; ASEXUAL REPRODUCTION; BACILLUS ANTHRACIS; BIOLOGICAL WARFARE; CONTROLLED STUDY; DNA MICROARRAY; FORENSIC IDENTIFICATION; GENE DELETION; GENE INSERTION; GENE SEQUENCE; GENE TARGETING; GENETIC ANALYSIS; GENETIC TRANSFECTION; NONHUMAN; PATHOGENESIS; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; THERMUS AQUATICUS;

BACTERIAL TYPING TECHNIQUES; BIOTERRORISM; DNA, BACTERIAL; FORENSIC MEDICINE; HUMANS; MICROBIOLOGICAL TECHNIQUES; MICROBIOLOGY; NUCLEIC ACID AMPLIFICATION TECHNIQUES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SEQUENCE ANALYSIS, DNA;

BACILLUS ANTHRACIS; THERMUS AQUATICUS;

EID: 28844459028     PISSN: 1040841X     EISSN: None     Source Type: Journal    
DOI: 10.1080/10408410500304082     Document Type: Article

References (212)

1. Adams, J. 2004. Microbial evolution in laboratory environments. Res. Microbiol. 155, 311-318.
2. Alm, E.W., Oerther, D.B., Larsen, N., Stahl, D.A., and Raskin, L. 1996. The oligonucleotide probe database. Appl. Environ. Microbiol. 62, 3557-3559.
3. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
4. Altshuler, D., Pollara, V.J., Cowles, C.R., Van Etten, W.J., Baldwin, J., Linton, L., and Lander, E.S. 2000. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407, 513-516.
5. Amann, R.I., Ludwig, W., and Schleifer, K.H. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbial Rev. 59, 143-169.
6. Anderson, I.C., Campbell, C.D., and Prosser, J.I. 2003. Potential bias of fungal 18S rDNA and internal transcribed spacer polymerase chain reaction primers for estimating fungal biodiversity in soil. Environ. Microbiol. 5, 36-47.
7. Anderson, I.C., and Cairney, J.W.G. 2004. Diversity and ecology of soil fungal communities: Increased understanding through the application of molecular techniques. Environ. Microbiol. 6, 769-779.
8. Anderson, R.P., and Roth, J.R. 1977. Tandem genetic duplications in phage and bacteria. Ann. Rev. Microbiol. 31, 473-505.
9. Anisimova, M., Nielsen, R., and Yang, Z. 2003. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid level. Genetics 164, 1229-1236.
10. Arber, W. 2004. Biological evolution: Lessons to be learned from microbiology population biology and genetics. Res. Microbiol. 155, 297-300.
11. Ball, L.M., Bes, M.A., Theelen, B., Boekhout, T., Egeler, R.M., and Kuijper, E.J. 2004. Significance of amplified fragment length polymorphism in identification and epidemiological examination of Candida species colonization in children undergoing allogeneic stem cell transplantation. J. Clin. Microbiol. 42, 1673-1679.
12. Bassler, H.A., Flood, S.J., Livak, K.J., Marmaro, J., Knorr, R., and Batt, C.A. 1995. Use of a fluorogenic probe in a PCR-based assay for the detection of Listeria monocytogenes. Appl. Environ. Microbol. 61, 3724-3728.
13. Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffiths-Jones, S., Howe, K.L., Marshall, M., and Sonnhammer, E.L. 2000. The Pfam protein families database. Nuc. Acids Res. 30, 276-280.
14. Bell, C.A., Uhl, J.R., Hadfield, T.L., David, J.C., Meyer, R.F., Smith, T.F., and Cockerill III, F.R. 2002. Detection of Bacillus anthracis by Light-Cycler PCR. J. Clin. Microbiol. 40, 2897-2902.
15. Bhattacharjee, J.K., and Janssen, G.R. 2005. Priority for "Biodefense" research grants: Security or misguided microbiology? Amer. Soc. Microbiol. News, 75, 209.
16. Boles, B.R., Thoendel, M., and Singh, P.K. 2004. Self-generated diversity produces "insurance effects" in biofilm communities. Proc. Natl. Acad. Sci. U.S.A. 101, 16630-16635.
17. Borneman, J., and Hartin, R.J. 2000. PCR primers that amplify fungal rRNA genes from environmental samples. Appl. Environ. Microbiol. 66, 4356-4360.
18. Borst, A., Theelen, B., Reinders, E., Boekhout, T., Fluit, A.C., and Savelkout, P.H.M. 2003. Use of amplified fragment length polymorphism analysis to identify medically important Candida species, including C. dubliniensis. J. Clin. Microbiol. 41, 1357-1362.
19. Bos, D.H., and Posada, D. 2005. Using models of nucleotide evolution to build phylogenetic trees. Dev. Compar. Immunol. 29, 211-227.
20. Bottger, E.C. 1989. Rapid determination of bacterial ribosomal RNA sequences by direct sequencing of enzymatically amplified DNA. FEMS Microbiol. Lett. 65, 171-176.
21. Bridge, P., and Spooner, B. 2001. Soil fungi: Diversity and detection. Plant Soil 232, 147-154.
22. Brown, E.W., Kotewicz, M.L., and Cebula, T.A. 2002. Detection of recombination among Salmonella enterica strains using the incongruence length difference test. Mol. Phylogen. Evol. 24, 102-120.
23. Brown, E.W., LeClerc, J.E., Li, B., Payne, W.L., and Cebula, T.A. 2001a. Phylogenetic evidence for horizontal transfer of mutS alleles among naturally occurring Escherichia coli strains. J. Bacteriol. 183, 1631-1644.
24. Brown, E.W., LeClerc, J.E., Kotewicz, M.L., and Cebula, T.A. 2001b. Three R's of bacterial evolution: How replication, repair, and recombination frame the origin of species. Environ. Mol. Mutagen. 38, 248-260.
25. Budowle, B. 2004. Genetics and attribution issues that confront the microbial forensics field. Forens. Sci. Int. 146 Suppl, S185-S188.
26. Budowle, B., and Brown, B.L. 2001. The use of DNA typing for forensic identification. Forensica 1, 9-37.
27. Budowle, B., and Chakraborty, R. 2004. Genetic considerations for interpreting molecular microbial forensic evidence. In Progress in Forensic Genetics 10, Doutremepuich, C., and Morling, N., Eds., Elsevier, Amsterdam, 56-58.
28. Budowle, B., Murch, R.S., and Chakraborty, R. 2005a. Microbial forensics: The next forensic challenge. Int. J. Leg. Med. (in press).
29. Budowle, B., Planz, J., Campbell, R., and Eisenberg, A. 2004. SNPs and microarray technology in forensic genetics: Development and application to mitochondrial DNA. Forens. Sci. Rev. 16, 22-36.
30. Budowle, B., Schutzer, S.E., Ascher, M.S., Atlas, R.M., Burans, J.P., Chakraborty, R., Dunn, J.J., Fraser, C.M., Franz, D.R., Leighton, T.J., Morse, S.A., Murch, R.S., Ravel, J., Rock, D.L., Slezak, T.R., Velsko, S.P., Walsh, A.C., and Walters, R.A. 2005b. Towards a system of microbial forensics: From sample collection to interpretation of evidence. Applied and Environmental Microbiology 71, 2209-2213.
31. Budowle, B., Schutzer, S.E., Einseln, A., Kelley, L.C., Walsh, A.C., Smith, J.A.L., Marrone, B.L., Robertson, J., and Campos, J. 2003. Building microbial forensics as a response to Bioterrorism. Science 301, 1852-1853.
32. Budowle, B., and SWGMGF Member. 2003. Quality assurance guidelines for laboratories performing microbial forensic work. Forens. Science Communications October 5(4), www.fbi.gov/hq/lab/fsc/current/2003_10_guide01.htm.
33. Chandler, M., and Mahillon, J. 1998. Insertion sequences. Microbiol. Mol. Biol. Rev. 62, 725-774.
34. Chee, M., Yang, R., Hubbell, E., Berno, A., Huang, X.C., Stern. D., Winkler, J., Lockhart, D.J., Morris, M.S., and Fodor, S.P.A. 1996. Accessing genetic information with high-density DNA arrays. Science 274, 610-614.
35. Chen, Z., Rerai, M., Fu, L., Herrero, R., DeSalle, R., and Burk, R.D. 2005. Diversifying selection in human papillomavirus type 16 lineages based on complete genome analyses. J. Virol. 79, 7014-7023.
36. Ciesielski, C., Marianos, D., Ou, C.Y., Dumbaugh, R., Witte, J., Berkelman, R., Gooch, B., Myers, G., Luo, C.C., Schochetman, G. et al. 1992. Transmission of human immunodeficiency virus in a dental practice. Ann. Intern. Med. 116, 798-805.
37. Cockerill III, F.R 2003. Rapid detection of pathogens and antimicrobial resistance in intensive care patients using nucleic acid-based techniques. Scand. J. Clin. Lab. Invest. 63, 34-46.
38. Cockerill III, F.R., and Smith, T.F. 2004. Response to the clinical microbiology laboratory to emerging (new) and reemerging infectious diseases. J. Clin. Microbiol. 42, 2359-2365.
39. Costerton, J.W., Geesey, G.G., and Cheng, K.J. 1978. How bacteria stick. Sci. Amer. 238, 86-95.
40. Costerton, J.W., Stewart, P.S., and Greenberg, E.P. 1999. Bacterial biofilms: A common cause of persistent infections. Science 284, 1318-1322.
41. Cox, E.C. 1976. Bacterial mutator genes and the control of spontaneous mutation. Annu. Rev. Genet. 10, 135-156.
42. Cristina, J., Lopez, F., Moratorio, G., Lopez, L., Vasquez, S., Garcia-Aguirre, L., and Chunga, A. 2005. Hepatitis C virus protein sequence reveals a lack of functional constraints and a variable pattern of amino acid substitution. J. Gen. Virol. 86, 115-120.
43. Curtis, T.P., and Sloan, W.T. 2004. Prokaryotic diversity and its limits: Microbial community structure in nature and implications for microbial ecology. Curr. Opinion Microbiol. 7, 221-226.
44. Cvitkovitch, D.G., Li, Y.H., and Ellen, R.P. 2003. Quorum sensing and biofilm formation in Streptococcal infections. J. Clin. Invest. 112, 1626-1632.
45. Daubin, V., Moran, N.A., and Ochman, H. 2003. Phylogenetics and cohesion of bacterial genomes. Science 301, 829-832.
46. Davies, D.G., Parsek, M.R., Pearson, J.P., Iglewski, B.H., Costerton, J.W., and Greenberg, E.P. 1998. The involvement of cell-to-cell signals in the development of a bacterial biofilm. Science 280, 295-298.
47. De Baere, T., Van Keerberghen, A., Van Hauwe, P., De Beenhouwer, H., Boel, A., Verschraegen, G., Claeys, G., and Vaneechoutte, M. 2005. An interlaboratory comparison of ITS2-PCR for the identification of yeasts, using the ABI Prism 310 and CEQ8000 capillary electrophoresis systems. BMC Microbiology 5, 14.
48. de Bruijn, F.J. 1992. Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergenic consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. Appl. Environ. Microbiol. 58, 2180-2187.
49. De Kievit, T.R., Gillis, R., Marx, S., Brown, C., and Iglewski B.H. 2001. Quorum-sensing genes in Pseudomonas aeruginosa biofilms: Their role and expression patterns. Appl. Environ. Microbiol. 67, 1865-1873.
50. Delcher, A.L., Kasif, S., Fleischmann, R.D., Peterson, J., White, O., and Salzberg, S.L. 1999. Alignment of whole genomes. Nuc. Acids Res. 27, 2369-2376.
51. Delcher, A.L., Phillippy, A. Carlton, J., Salzberg, S.L. 2002. Fast algorithms for large-scale genome alignment and comparison. Nuc. Acids Res. 30, 2478-2483.
52. Delgrange, O., and Rivals, E. 2004. STAR: An algorithm to search for tandem approximate repeats. Bioinformatics 16, 1812-2820.
53. DeLong, E.F. 2002a. Microbial population genomics and ecology. Curr. Opin. Microbiol. 5, 520-524.
54. DeLong, E.F. 2002b. Towards microbial systems science: Integrating microbial perspective, from genomes to biomes. Environ. Microbiol. 4, 9-10.
55. DeLong, E.F., Wickham, G.S., and Pace, N.R. 1989. Phylogenetic stains: Ribosomal RNA-based probes for the identification of single cells. Science 243, 1360-1363.
56. Dore, J., Sghir, A., Hannequart-Gramet, G., Corthier, G., and Pochart, P. 1998. Design and evaluation of a 16S rRNA-targeted oligonucleotide probe for specific detection and quantitation of human faecal Bacteroides populations. Syst. Appl. Microbiol. 21, 65-71.
57. Drake, J.W., Charlesworth, B., Charlesworth, D., and Crow, J.F. 1998. Rates of spontaneous mutation. Genetics 148, 1667-1686.
58. Drancourt, M., Bollet, C., Carlioz, A., Martelin, R., Gayral, J.P., and Raoult, D. 2000. 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J. Clin. Microbiol. 38, 3623-3630.
59. Dunbar, J., Takala, S., Barns, S.M., Davis, J.A., and Kuske, C.R. 1999. Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl. Environ. Microbiol. 65, 1662-1669.
60. Dunham, M.J., Badrane, H., Ferea, T., Adams, I., Brown, P.O., Rosenzweig, R.F., and Botsein, D. 2002. Characteristic genome rearrangements accompany experimental evolution of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 99, 16144-16149.
61. Eddy, S.R. 1998. Profile hidden Markov models. Bioinformatics 14, 755-763.
62. Elena, S.F., Cooper, V.S., and Lenski, R.E. 1996. Punctuated evolution caused by selection of rare beneficial mutations. Science 272, 1802-1804.
63. Ewing, B., Hillier, L., Wendl, M.C., and Green, P. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175-185.
64. Feil, E.J., Holmes, E.C., Bessen, D.E., Chan, M.S., Day, N.P., Enright, M.C., Goldstein, R., Hood, D.W., Kalia, A., Moore, C.E., Zhou, J., and Spratt, B.G. 2001. Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences. Proc. Natl. Acad. Sci. U.S.A. 98, 182-187.
65. Feil, E.J., Maiden, C.J., Achtman, M., and Spratt, B.G. 1999. The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitidis. Mol. Biol. Evol. 16, 1496-1502.
66. Feil, E.J., Maynard Smith, J., Enright, M.C., and Spratt, B.G. 2000. Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data. Genetics 154, 1439-1450.
67. Feil, E.J., and Spratt, B.G. 2001. Recombination and the population structures of bacterial pathogens. Annu. Rev. Microbiol. 55, 561-590.
68. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17, 368-376.
69. Fitch, W.M. 1970. Toward defining the course of evolution: Minimal change for a specific tree topology. Syst. Zool. 20, 406-416.
70. Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., Bult, C.J., Tomb, J.F., Dougherty, B.A., Merrick, J.M., et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 269, 496-512.
71. Fodor, S.P.A., Rava, R.P., Huang, X.C., Pease, A.C., Holmes, C.P., and Adams, C.L. 1993. Multiplexed biochemical assays with biological chips. Science 364, 555-556.
72. Fodor, S.P.A., Read, J.L., Pirrung, M.C., Stryerm, L., Lu, A.T., and Solas, D. 1991. Light-directed, spatially addressable parallel chemical synthesis. Science 251, 767-773.
73. Fox, G.E., Peckman, K., and Woese, C.R. 1977. Comparative cataloging of 16S ribosomal ribonucleic acid: Molecular approach to prokaryotic systematics. Int. J. Syst. Bacteriol. 27, 44-57.
74. Fraser, C.M., and Fleischmann, R.D. 1997. Strategies for whole microbial genome sequencing and analysis. Electrophoresis 18, 1207-1216.
75. Gardes, M., and Bruns, T.D. 1993. ITS primers with enhanced specificity for basidiomycets: Application to the identification of mycorrhizae and rusts. Mol. Ecol. 2, 113-118.
76. Gibson, T.C., Scheppe, E.C., and Cox, E.C. 1970. Fitness of an Escherichia coli mutator gene. Science 169, 686-688.
77. Gilson, E., Clement, J.M., Brutlag, D., and Hofnung, M. 1984. A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli. EMBO J. 3, 1417-1421.
78. Gu, X., and Li, W.-H. 1996. A general additive distance with time-reversibility and rate variation among nucleotide sites. Proc. Natl. Acd. Sci. U.S.A. 93, 4671-4676.
79. Gutler, V., and Stanisich, V.A. 1996. New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142, 3-16.
80. Haft, D.H., Selengut, J.D., and White, O. 2003. The TIGRFAMs database of protein families. Nuc. Acids Res. 31, 371-373.
81. Harayama, S., Kasai, Y., and Hara, A. 2004. Microbial communities in oil-contaminated seawater. Curr. Opinion Biotech. 15, 205-214.
82. Harmsen, D., and Karch, H. 2004. 16S rDNA for diagnosing pathogens: A living tree. ASM News 70, 19-24.
83. Hathout, Y., Setlow, B., Cabrera-Martinez, R.M., Fenselau, C., and Setlow, P. 2003. Small, acid-soluble proteins as biomarkers in mass spectrometry analysis of Bacillus spores. Appl. Environ. Microbiol. 69, 1100-1107.
84. Haugland, R.P. 2002. Molecular Probes Handbook of Fluorescent Probes and Research Products, Ninth Edition, Gregory, J., Ed., Molecular Probes, Inc. Eugene, Oregon, catalog number H-19999.
85. Hausner, M., and Wuertz, S. 1999. High rates of conjugation in bacterial biofilms as determined by quantitative in situ analysis. Appl. Environ. Microbiol. 65, 3710-3713.
86. Higgins, J.S., Ezzel, J., Hinnebusch, B.J., Shipley, M., Henchal, E.A., and Ibrahim, S.S. 1998. 5′ nuclease PCR assay to detect Yersinia pestis. J. Clin. Microbiol. 36, 2284-2288.
87. Higuchi, R., Dollinger G., Walsh, P.S., and Griffith, R. 1992. Simultaneous amplification and detection of specific DNA sequences. Biotechnology 10, 413-417.
88. Hill, K.K., Ticknor, L.O., Okinaka, R.T., Asay, M., Blair, H., Bliss, K.A., Laker, M., Pardington, P.E., Richardson, A.P., Tonks, M., Beecher, D.J., Kemp, J.D., Kolsto, A.B., Wong, A.C., Keim, P., and Jackson, P.J. 2004. Fluorescent amplified fragment length polymorphism analysis of Bacillusanthracis, Bacillus cereus, and Bacillus thuringiensis isolates. Appl. Environ. Microbiol. 70, 1068-1080.
89. Hoiby, N., Krogh Johansen, H., Moser, C., Song, Z., Ciofu, O., and Kharazmi, A. 2001. Pseudomonas aeruginosa and the in vitro and in vivo biofilm mode of growth. Microbes Infect. 3, 23-35.
90. Holland, P.M., Abramson, R.D., Watson, R., and Gelfand, D.H. 1991. Detection of specific polymerase chain reaction products by utilizing the 5-3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proc. Natl. Acad. Sci. U.S.A. 88, 7276-7280.
91. Horner, D.S., and Pesole, G. 2003. The estimation of relative site variability among aligned homologous protein sequences. Bioinformatics 19, 600-606.
92. Horner-Devine, M.C., Lage, M., Hughes, J.B., and Bohannan, B.J. 2004. A taxa-area relationship for bacteria. Nature 432, 750-753.
93. Huang, X., Ye, L., Chou, H.H., Yang, I.H., and Chao, K.M. 2004. Efficient combination of multiple word models for improved sequence comparison. Bioinformatics 16, 2529-2533.
94. Huelsenbeck, J.P. 1995. The robustness of two phylogenetic methods: Four-taxon simulations reveal a slight superiority of the maximum likelihood over neighbor joining. Mol. Biol. Evol. 12, 843-849.
95. Huelsenbeck, J.P., Larget, B., and Swofford, D. 2000. A compound poisson process for relaxing the molecular clock. Genetics 154, 1879-1892.
96. Hugenholtz, P., and Pace, N.R. 1996. Identifying microbial diversity in the natural environment: A molecular phylogenetic approach. Trends Biotechnol. 14, 190-197.
97. Iwen, P.C., Hinrichs, S.H., and Rupp, M.E. 2002. Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens. Med. Mycol. 40, 87-109.
98. Jackson, R.J., Ramsay, A.J., Christensen, C.D., Beaton, S., Hall, D.E., Ramshaw, I.A. 2001. Expression of mouse interleukin-4 by a recombinant Ectromelia virus suppresses cytolytic lymphocyte responses and overcomes genetic resistance to mousepox. J. Virology 75, 1205-1210.
99. Jefferson, K.K. 2004. What drives bacteria to produce a biofilm? FEMS Microbiol. Lett. 236, 163-173.
100. Joyce, E.A., Chan, K., Salama, N.R., and Falkow, S. 2003. Redefining bacterial populations: A post-genomic reformation. Nat. Rev. Genet. 3, 462-473.
101. Keim, P., Price, L.B., Klevytska, A.M., Smith, K.L., Schupp, J.M., Okinaka, R., Jackson, P.J., and Hugh-Jones, M.E. 2000. Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis. J. Bacteriol. 182, 2928-2936.
102. Keim, P., Smith, K.L., Keys, C., Takahashi, H., Kurata, T., and Kaufmann, A. 2001. Molecular investigation of the Aum Shinrikyo anthrax release in Kameido, Japan. J. Clin. Microbiol. 39, 4566-4567.
103. Keim, P., Van Ert, M.N., Pearson, T., Vogler, A.J., Huynh, L.Y., and Wagner, D.M. 2004, Anthrax molecular epidemiology and forensics: Using the appropriate marker for different evolutionary scales. Infect. Genet. Evol. 4, 205-213.
104. Kent, W.J. 2002. BLAT - the BLAST-like alignment tool. Genome Res. 12, 656-664.
105. Kim, K., Seo, J., Wheeler, K., Park, C., Kim, D., Park, S., Kim, W., Chung, S.I., and Leighton, T. 2005. Rapid genotypic detection of Bacillus anthracis and the Bacillus cereus group by multiplex real-time PCR melting curve analysis. FEMS Immunol. Med. Microbiol. 43, 301-310.
106. Kimura, M. 1983. The Neutral Theory of Molecular Evolution, Cambridge University Press, Cambridge.
107. Kitamura, K., Torii, Y., Matsuoka, C., and Yamamoto, K. 1995. DNA sequence changes in mutations in the tonB gene on the chromosome of Escherichia coli K-12: Insertion elements dominate the spontaneous spectra. Jpn. J. Genet. 70, 35-16.
108. Klerks, M.M., Zijlstra, C., and van Bruggen, A.H.C. 2004. Comparison of real-time PCR methods for detection of Salmonella enterica and Escherichia coli O157:H7, and introduction of a general internal amplification control. J. Microbiol. Meth. 59, 337-349.
109. Klevytska AM, Price, L.B., Schupp, J.M., Worsham, P.L., Wong, J., and Keim, P. 2001. Identification and characterization of variable-number tandem repeats in the Yersinia pestis genome. J. Clin. Microbiol. 39, 3179-3185.
110. Kolbert, C.P., and Persing, D.H. 1999. Ribosomal DNA sequencing as a tool for identification of bacterial pathogens. Curr. Opin. Microbiol. 2, 299-305.
111. Kotewicz, M.L., Brown, E.W., LeClerc, J.E., and Cebula, T.A. 2003. Genomic variability among enteric pathogens: The case of the mutS-ipoS intergenic region. Trends Microbiol. 11, 2-6.
112. Kotewicz, M.L., Li, B., Levy, D.D., LeClerc, J.E., Shifflet, A.W., and Cebula, T.A. 2002. Evolution of multi-gene segments in the mutS-ipoS intergenic region of Salmonella enterica serovar Typhimurium LT2. Microbiology 148, 2531-2540.
113. Kuhner, M.K., and Felsenstein, J. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11, 459-468.
114. Kurtz, S., and Schleiermacher, C. 1999. REPuter-fast computation of maximal repeats in complete genomes. Bioinformatics 15, 426-427.
115. Kutyavin, I.V., Afonina, I.A., Mills, A., Gorn, V.V., Lukhtanov, E.A., Belousov, E.S., Singer, M.J., Walburger, D.K., Lokhov, S.G., Gall, A.A., Dempcy, R., Reed, M.W., Meyer, R.B., and Hedgpeth, I. 2000. 3′ minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures. Nuc. Acids Res. 28, 655-661.
116. Larena, I., Salazar, O., Gonzalez, V., Julian, M.C., and Rubio, V. 1999. Design of a primer for ribosomal DNA internal transcribed spacer with enhanced specificity for ascomycetes. J. Biotechnol. 75, 187-194.
117. Larget, B., and Simon, D. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16, 750-759.
118. LeClerc, J.E., Li, B.G., Payne, W.L., and Cebula, T.A. 1996. High mutation frequencies among Escherichia coli and Salmonella pathogens. Science 274, 1208-1211.
119. Lee, L.G., Connell, C.R., and Bloch, W. 1993. Allelic discrimination by nick-translation PCR with fluorogenic probes. Nuc. Acids Res. 21, 3761-3766.
120. Lee Ligon, B. 2004. Monkeypox: A review of the history and emergence in the Western Hemisphere. Pediatric Infect. Dis. 15, 280-287.
121. Lewis, K. 2001. Riddle of biofilm resistance. Antimicrob. Agents Chemother. 45. 999-1007.
122. Li, M., Ma, B., Kisman, D., and Tromp, J. 2004. Patternhunter II: Highly sensitive and fast homology search. J. Bioinform. Comput. Biol. 2, 417-439.
123. Li, W.H., Tanimura, M., and Sharp, P. 1998. Rates and dates of divergence between AIDS virus nucleotide sequences. Mol. Biol. Evol. 5, 313-330.
124. Lipshutz, R.J., Fodor, S.P., Gingeras, T.R., and Lockhart, D.J. 1999. High density synthetic oligonucleotide arrays. Nat. Genet. (1 suppl), 20-24.
125. Lopez, P., Casane, D., and Philippe, H. 2002. Heterotachy, an important process of protein evolution. Mol. Biol. Evol. 19, 1-7.
126. Lord, N.S., Kaplan, C.W., Shank, P., Kitts, C.L., and Elrod, S.L. 2002. Assessment of fungal diversity using terminal restriction fragment (TRF) pattern analysis: Comparison of 18S and ITS ribosomal regions. FEMS Microbiol. Ecol. 42, 327-337.
127. Lowe, T.M., and Eddy, S.R. 1997. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nuc. Acids Res. 25, 955-964.
128. Lukhtanov, E.A., Metcalf, M., and Reed, M.W. 2001. Fluorogenic DNA probes for multicolor hybridization assays. Amer. Biotech. Lab. 19, 68-69.
129. Lupski, J.R., and Weinstock, G.M. 1992. Short, interspersed repetitive DNA sequences in prokaryotic genomes. J. Bacteriol. 174, 4525-4529.
130. Maiden, M.C., Bygraves, J.A., Feil, E., Morelli, G., Russell, J.E., Urwin, R., Zhang, Q., Zhou, J., Zurth, K., Caugant, D.A., Feavers, I.M., Achtman, M., and Spratt, B.G. 1998. Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. U.S.A. 95, 3140-3145.
131. Makino, S., and Cheun, H.I. 2003. Application of the real-time PCR for the detection of airborne microbial pathogens in reference to the anthrax spores. J. Microbiol. Meth. 53, 141-147.
132. Metzker, M.L., Mindell, D.P., Liu, X., Ptak, R.G., Gibbs, R.A., and Hillis, D.M. 2002. Molecular evidence of HIV-1 transmission in a criminal case. Proc. Natl. Acad. Sci. U.S.A. 99, 14292-14297.
133. Moxon, E.R., Rainey, P.B., Nowak, M.A., and Lenski, R.E. 1994. Adaptive evolution of highly mutable loci in pathogenic bacteria. Curr. Biol. 4, 24-33.
134. Myers, E.W. 1995. Toward simplifying and accurately formulating fragment assembly. J. Comput. Biol. 2, 275-290.
135. Myers, E.W., Suttton, G.G., Delcher, A.L., Dew, I.M., Fasulo, D.P., Flanigan, M.J., Kravitz. S.A., Mobarry, C.M., Reinert, K.H., Remington, K.A., Anson, E.L., Bolanos, R.A., Chou, H.H., Jordan, C.M., Halpern, A.L., Lonardi, S., Beasley, E.M., Brandon, R.C., Chen, L., Dunn, P.J., Lai, Z., Liang, Y., Nusskern, D.R., Zhan, M., Zhang, Q., Zheng, X., Rubin, G.M., Adams, M.D., and Venter, J.C. 2000. A whole-genome assembly of Drosophila. Science 287, 2196-2204.
136. Naas, T., Blot, M., Fitch, W.M., and Arber, W. 1994. Insertion sequence-related genetic variation in resting Escherichia coli K-12. Genetics 136, 721-730.
137. Narayanan, S. 2004. Molecular epidemiology of tuberculosis. Ind. J. Med. Res. 120, 233-247.
138. National Research Council II Report. The Evaluation of Forensic Evidence. National Academy Press, Washington, D.C., 1996.
139. Nei, M., and Kumar, S. 2000. Molecular Evolution and Phylogenetics, Oxford University Press Oxford, UK.
140. Neumann, A.U., Lam, N.P., Dahari, H., Gretch, D.R., Wiley, T.E., Layden, T.J., and Perelson, A.S. 1988. Hepatitis C dynamics in vivo and the antiviral efficacy of interferon-α therapy. Science 282, 103-107.
141. Ning, Z., Cox, A.J., and Mullikin, J.C. 2001. SSAHA: A fast search method for large DNA databases. Genome Res. 11, 1725-1729.
142. Nuwaysir, E.F., Huang, W., Albert, T.J., Singh, J., Nuwaysir, K., Pitas, A., Richmond, T., Gorski, T., Berg, J.P., Ballin, J., McCormick, M., Norton, J., Pollock, T., Sumwalt, T., Butcher, L., Porter, D., Molla, M., Hall, C., Blattner, F., Sussman, M.R., Wallace, R.L., Cerrina, F., and Green, R.D. 2002. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 12, 1749-1755.
143. O'Neil, P.K., Sun, G., Yu, H., Ron, Y., Dougherty, J.P., and Preston, B.D. 2002. Mutational analysis of HIV-1 long terminal repeats to explore the relative contribution of reverse transcriptase and RNA polymerase II to viral mutagenesis. J. Biol. Chem. 277, 38053-38061.
144. Ovcharenko, I., Loots, G.G., Giardine, B.M., Hou, M., Ma, J., Hardison, R.C., Stubbs, L., and Miller, W. 2005. Mulan: Multiple sequence alignment and visualization for studying function and evolution. Genome Res. 15, 184-189.
145. Pace, N.R. 1997. A molecular view of microbial diversity and the biosphere. Science 276, 734-740.
146. Palys, T., Nakamura, L.K., and Cohan, F.M. 1997. Discovery and classification of ecological diversity in the bacterial world: The role of DNA sequence data. Int. J. Syst. Bacteriol. 47, 1145-1156.
147. Parsek, M.R., and Singh, P.K. 2003. Bacterial biofilms: An emerging link to disease pathogenesis. Annu. Rev. Microbiol. 57, 677-701.
148. Pearson, T., Busch, J.D., Ravel, J., Read, T.D., Rhoton, S.D., U'Ren, J.M., Simonson, T.S., Kachur, S.M., Leadem, R.R., Cardon, M.L., Van Ert, M.N., Huynh, L.Y., Fraser, C.M., and Keim, P. 2004. Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing. Proc. Natl. Acad. Sci. U.S.A. 101, 13536-13541.
149. Pearson, W.R., and Lipman, D. 1998. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U.S.A. 85, 2444-2448.
150. Peters, R.P., van Agtmael, M.A., Danner, S.A., Savelkoul, P.H., and Vandenbroucke-Grauls, C.M. 2004. New developments in the diagnosis of bloodstream infections. The Lancet 4, 751-760.
151. Popovic, T., and Glass, M. 2003. Laboratory aspects of bioterrorism-related anthrax - from identification to molecular subtyping to microbial forensics. Croat. Med. J. 44, 336-341.
152. Posada, D., and Crandall, K.A. 2002. The effect of recombination on the accuracy of phylogeny estimation. J. Mol. Evol. 54, 396-402.
153. Preston, B.D., Poiesz, B.J., and Loeb, L.A. 1988. Fidelity of HIV-1 reverse transcriptase. Science 242, 1168-1171.
154. Ranjard, L., Poly, F., and Nazaret, S. 2000. Monitoring complex bacterial communities using culture-independent molecular techniques: Application to soil environment. Res. Microbiol. 151, 167-177.
155. Read, T.D., Salzberg, S.L., Pop, M., Shumway, M., Umayam, L., Jiang, L., Holtzapple, E., Busch, J.D., Smith, K.L., Schupp, J.M., Solomon, D., Keim, P., and Fraser, C.M. 2002. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 296, 2028-2033.
156. Reid, A.H., Taubenberger, J.K., and Fanning, T.G. 2004. Evidence of an absence: The genetic origins of the 1918 pandemic influenza virus. Nat. Rev. 2, 909-914.
157. Robbins, K.E., Weidle, P.J., Brown, T.M., Saekhou, A.M., Coles, B., Holmberg, S.D., Folks, T.M., and Kalish, M.L. 2002. Molecular analysis in support of an investigation of a cluster of HIV-1-infected women. AIDS Res. Hum. Retroviruses 18, 1157-1161.
158. Roberts, A.P., Pratten, J., Wilson, M., and Mullany, P. 1999. Transfer of a conjugative transposon Tn 5397 in a model oral biofilm. FEMS Microbiol. Lett. 177, 63-66.
159. Ronquist, F., and Huelsenbeck, J.P. 2003. MrBayes3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574.
160. Roth, A., Fischer, M., Hamid, M.E., Michalke, S., Ludwig, W., and Mauch, H. 1998. Differentiation of phylogenetically related slowly growing mycobacteria based on 16S-23S rRNA gene internal transcribed spacer sequences. J. Clin. Microbiol. 36, 139-147.
161. Saiki, R.K., Scharf, S., Faloona, F., Mullis, K.B., Horn, G.T., Erlich, H.A., and Arnheim, N. 1985. Enzymatic amplification of beta-globin genomic sequences and restriction analysis for diagnosis of sickle cell anemia. Science 230, 1350-1354.
162. Saitou, N., and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
163. Sala, M., and Wain-Hobson, S. 2000. Are RNA viruses adapting or merely changing? J. Mol. Evol. 51, 12-20.
164. Salzberg, S.L., Delcher, A.L., Kasif, S., and White, O. 1998. Microbial gene identification using interpolated Markov models. Nuc. Acids Res. 26, 544-548.
165. Sampath, R., Hofstadler, S.A., Blyn, L.B., Eshoo, M.W., Hall, T.A., Massire, C., Levene, H.M., Hannis, J.C., Harrell, P.M., Neuman, B., Buchmeier, M.J., Jiang, Y., Ranken, R., Drader, J.J., Samant, V., Griffey, R.H., McNeil, J.A., Crooke, S.T., and Ecker, D.J. 2005. Rapid identification of emerging pathogens: Coronavirus. Emerg. Infect. Dis. 11, 373-379.
166. Sanger, F., Nicklen, S., and Coulson, A.R. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. U.S.A. 74, 5463-5467.
167. Schierup, M.H., and Hein, J. 2000. Consequences of recombination on traditional phylogenetic analysis. Genetics 156, 879-891.
168. Schmidt, T.M., DeLong, E.F., and Pace, N.R. 1991. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol. 173, 4371-4378.
169. Schneeberger, C., Speiser, P., Kury, F., and Zeillenger, R. 1995. Quantitative detection of reverse transcriptase-PCR products by means of a novel and sensitive DNA stain. PCR Methods Appl. 4, 234-238.
170. Schneider, D., and Lenski, R.E. 2004. Dynamics of insertion sequence elements during experimental evolution of bacteria. Res. Microbiol. 155, 319-327.
171. Simmonds, P. 2004. Genetic diversity and evolution of hepatitis C virus - 15 years on. J. Gen. Virol. 85, 3173-3188.
172. Singh-Gasson, S., Green, R.D., Yue, Y., Nelson, C., Blattner, F., Sussman, M.R., and Cerrina, F. 1999. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat. Biotechnol. 17, 974-978.
173. Sniegowski, P.D., Gerrish, P.J., and Lenski, R.E. 1997. Evolution of high mutation rates in experimental populations of Escherichia coli. Nature 387, 703-705.
174. Snow, J. 1936. On the mode of communication of cholera. In: Snow on Cholera. The Commonwealth Fund, New York, 1-175.
175. Spratt, B.G. 1999. Multilocus sequence typing: Molecular typing of bacterial pathogens in an era of rapid DNA sequencing and the Internet. Curr. Opin. Microbiol. 2, 312-316.
176. Stackebrandt, E., and Goebel, B.M. 1994. Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44, 846-849.
177. Stern, M.J., Ames, G.F., Smith, N.H., Robinson, E.C., and Higgins, C.F. 1984. Repetitive extragenic palindromic sequences: A major component of the bacterial genome. Cell 37, 1015-1026.
178. Suau, A., Bonnet, R., Sutren, M., Godon, J., Gibson, G., Collins, M., and Dore, J. 1999. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 65, 4799-4807.
179. Suffin, C.S., Carnes, W.H., and Kaufmann, A.F. 1978. Inhalational anthrax in a home craftsman. Hum. Pathol. 9, 594-597.
180. Sutton, G., White, O., Adams, M., and Kerlavage, A.R. 1995. TIGR Assembler: A new tool for assembling large shotgun sequencing projects. Genome Sci. Technol. 1, 9-19.
181. Svarovskaia, E.S., Cheslock, S.R., Zhang, W.H., Hu, W.S., and Pathak, V.K. 2003. Retroviral mutation rates and reverse transcriptase fidelity. Front. Biosci. 8, d117-d134.
182. Swiecicka, I. 2003. Molecular typing by pulsed-field gel electrophoresis of Bacillus thuringiensis from root voles. Current Microbiol. 46, 256-260.
183. Syvanen, A.C. 1999. From gels to chips: Minisequencing primer extension for analysis of point mutation and single nucleotide polymorphisms. Hum. Mut. 13, 1-10.
184. Syvanen, A.C., Aalto-Setala, K., Harju, L., Kontula, K., and Soderlund, H.A. 1990. A primer-guided nucleotide incorporation assay in genotyping of apolipoprotein E. Genomics 8, 684-692.
185. Tang, H., and Lewontin, R.C. 1999. Locating regions of differential variability in DNA and protein sequences. Genetics 153, 485-495.
186. Torsvik, V., Goksoyr, J., and Daae, F.L. 1990. High diversity in DNA of sou bacteria. Appl. Environ. Microbiol. 56, 782-787.
187. Troesch, A., Nguyen, H., Miyada, C.G., Desvarenne, S., Gingeras, T.R., Kaplan, P.M., Cros, P., and Mabilat, C. 1999. Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays. J. Clin. Microbiol. 37, 49-55.
188. Turenne, C.Y., Sanche, S.E., Hoban, D.J., Karlowsky, J.A., and Kabani, A.M. 1999. Rapid identification of fungi by using the ITS2 genetic region and an automated fluorescent capillary electrophoresis system. J. Clin. Microbiol. 37, 1846-1851.
189. Ussery, D.W., Binnewiesm T.T., Gouveia-Oliveira, R., Jarmer, H., and Hallin, P.F. 2004. Genome update: DNA repeats in bacterial genomes. Microbiology 150, 3519-3521.
190. Van Ert, M.N., Hofstadler, S.A., Jiang, Y., Busch, J.D., Wagner, D.M., Drader, J.J., Ecker, D.J., Hannis, J.C., Huynh, L.Y., Schupp, J.M., Simonson, T.S., and Keim, P. 2004. Mass spectrometry provides accurate characterization of two genetic marker types in Bacillus anthracis. Biotechniques 37, 642-651.
191. Venter, J.C., Adams, M.D,, Sutton, G.G., Kerlavage, A.R., Smith, H.O., and Hunkapiller, M. 1998. Shotgun sequencing of the human genome. Science 280, 1540-1542.
192. Venter, J.C., Smith, H.O., and Hood, L. 1996. A new strategy for genome sequencing. Nature 381, 364-366.
193. Versalovic, J., Koeuth, T., and Lupski, J.R. 1991. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nuc. Acids Res. 19, 6823-6831.
194. Vetsigian, K., and Goldenfeld, N. 2005. Global divergence of microbial genome sequences mediated by propagating fronts. Proc. Natl. Acad. Sci. USA. 17, 7332-7337.
195. Volfovsky, N., Haas, B.J., and Salzberg, S.L. 2001. A clustering method for repeat analysis in DNA sequences. Genome Biol. 2, RESEARCH0027.
196. White, T.J., Bruns, T.D., Lee, S., and Taylor, J. 1990. Analysis of phylogenetic relationships by amplification and direct sequencing of ribosomal RNA genes. In PCR Protocols: A Guide to Methods and Applications, Gelfand, M.A., Sninsky, J.J., and White, T.J., Eds., Academic press, New York, 315-322.
197. Whitman, W.B., Coleman, D.C., and Wiebe, W.J. 1998. Prokaryotes: The unseen majority. Proc. Natl. Acad. Sci. U.S.A. 95, 6578-6583.
198. Wilson, K.H., Blitchington, R., and Greene, R.C. 1990. Amplification of bacterial 16S rRNA sequences with polymerase chain reaction. J. Clin. Microbiol. 28, 1942-1946.
199. Wilson, K.H., Wilson, W.J., Radosevich, J.L., DeSantis, T.Z., Viswanathan, V.S., Kuczmarski, T.A., and Andersen, G.L. 2002. High-density microarray of small-subunit ribosomal DNA probes. Appl. Environ. Microbiol. 68, 2535-2541.
200. Wilson, W.J., Strout, C.L., DeSantis, T.Z., Stilwell, J.L., Carrano, A.V., and Andersen, G.L. 2004. Sequence-specific identification of 18 pathogenic microorganisms using microarray technology. Nuc. Acids Res. 32, 1848-1856.
201. Woese, C.R. 1987. Bacterial evolution. Microbiol. Rev. 51, 221-271.
202. Woese, C.R., Olsen, G.J., Ibba, M., and Soll, D. 2000. Comparisons of complete genome sequences allow the most objective and comprehensive descriptions possible of a lineage's evolution. Microbiol. Mol. Biol. Rev. 64, 202-236.
203. Woese, C.R., Stackebrandt, E., Macke, T.J., and Fox, G.E. 1985. A phylogenetic definition of the major eubacterial taxa. Syst. Appl. Microbiol. 6, 143-151.
204. Wong, C.W., Albert, T.J., Vega, V.B., Norton, J.E., Cutler, D.J., Richmond, T.A., Stanton, L.W., Liu, E.T., and Miller, L.D. 2004. Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays. Genome Res. 14, 398-405.
205. Yang, Z. 1994. Statistical properties of the maximum likelihood method of phylogenetic estimation and comparison with distance matrix methods. Syst. Biol. 43, 329-342.
206. Yang, Z. 1996. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol. 11, 367-372.
207. Zak, J.C., and Visser, S. 1996. An appraisal of soil fungal biodiversity: The crossroads between taxonomic and functional biodiversity. Biodivers. Conserv. 5, 169-183.
208. Zhang, J., and Gu, X. 1998. Correlation between the substitution rate and rate variation among sites in protein evolution. Genetics 149, 1615-1625.
209. Zhang, Z., Schwartz, S., Wagner, L., and Miller, W. 2000. A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 7, 203-214.
210. Zheng, D., Alm, E., Stahl, D., and Raskin, L. 1996. Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Appl. Environ. Microbiol. 62, 4504-4513.
211. Zheng, Y., Roberts, R.J., and Kasif, S. 2004. Identification of genes with fast-evolving regions in microbial genomes. Nuc. Acids Res. 32, 6347-6357.
212. Zwick, M.E., Mcafee, F., Cutler, D.J., Read, T.D., Ravel, J., Bowman, G.R., Galloway, D.R., and Mateczun, A. 2004. Microarray-based resequencing of multiple Bacillus anthracis isolates. Genome Biology 6, R10.1-R10.13.