Chapter 10 : Pathogenomics of Bacterial Biothreat Agents

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

Pathogenomics of Bacterial Biothreat Agents, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555815530/9781555814519_Chap10-1.gif /docserver/preview/fulltext/10.1128/9781555815530/9781555814519_Chap10-2.gif


The idea of "pathogenomics" encompasses every aspect of microbial pathogenesis. Before genome sequences for biothreat pathogens became available, the types of whole-genome approaches applied today were unimaginable to investigators. This chapter therefore revolves around a period of transition in the study of pathogen biology in general and of biothreat agents in particular, much of it stemming from the recent biodefense funding impetus. In discussing the genome biology of classical biothreat pathogens, several common themes emerge. The chapter provides an overview of these ideas before discussing the specific pathogenomics of each agent. The study of genomics emphasizes the similarities of the major themes in biology and allows advances that occur in one field to be quickly transferred to others. The enormity of the impact of horizontal gene transfer (HGT) on the genome content of bacterial species is gradually coming to light. In a postgenomic study, comparative proteomics of the secretomes performed with two-dimensional gel electrophoresis between fully virulent , pXO1/pXO2 and pXO1/pXO2 was performed. The pathobiology of , stimulated by the genome sequence, is a highly active field. As knowledge of biothreat pathogenesis grows, so does the possibility of identifying common pathways in the host. For instance, many of the bacteria described in the chapter invade macrophages at some point when causing disease.

Citation: Read T, Thomason B. 2007. Pathogenomics of Bacterial Biothreat Agents, p 232-266. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch10
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of FIGURE 1

Dampening of macrophage immune response genes after treatment with anthrax lethal toxin measured by DNA microarray. Bars indicate the level of induction relative to expression in untreated cells, as measured by DNA microarray. For each gene indicated, induction levels are shown for cells treated with lipopolysaccharide (LPS) and cells treated with LPS and lethal toxin (LeTx). TNF, tumor necrosis factor; MMP-9, matrix metalloproteinase 9; IL, interleukin. From reference .

Citation: Read T, Thomason B. 2007. Pathogenomics of Bacterial Biothreat Agents, p 232-266. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch10
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2

The nonpathogenic yersiniae gain the virulence plasmid pYV to form the predecessor of pathogenic yersinae. diverges from and forms three lineages: 1A, Old World, and New World. gains the ability to parasitize insects and to form biofilms in hosts before evolving into through the acquisition of plasmids pPla and pMT1, genome mixing, and decay. Hms, hemin storage; HPI and HPI*, high-pathogenicity islands; IS, insertion sequence. Reprinted by permission from Macmillan Publishers Ltd.: ( ), copyright 2004.

Citation: Read T, Thomason B. 2007. Pathogenomics of Bacterial Biothreat Agents, p 232-266. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch10
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Abramova, F. A.,, L. M. Grinberg,, O. V. Yampolskaya, and, D. H. Walker. 1993. Pathology of inhalational anthrax in 42 cases from the Sverdlovks outbreak of 1979. Proc. Natl. Acad. Sci. USA 90: 22912294.
2. Agaisse, H.,, M. Gominet,, O. A. Okstad,, A. B. Kolsto, and, D. Lereclus. 1999. PlcR is a pleiotropic regulator of extracellular virulence factor gene expression in Bacillus thuringiensis. Mol. Microbiol. 32: 10431053.
3. Akporiaye, E. T.,, J. D. Rowatt,, A. A. Aragon, and, O. G. Baca. 1983. Lysosomal response of a murine macrophage-like cell line persistently infected with Coxiella burnetii. Infect. Immun. 3: 11551162.
4. Albert, T. J.,, D. Dailidiene,, G. Dailide,, J. E. Norton,, A. Kalia,, T. A. Richmond,, M. Molla,, J. Singh,, R. D. Green, and, D. E. Berg. 2005. Mutation discovery in bacterial genomes: metro-nidazole resistance in Helicobacter pylori. Nat. Methods 2: 951953.
5. Albrink, W. S.,, S. M. Brooks,, R. E. Biron, and, M. Kopel. 1960. Human inhalation anthrax: a report of three fatal cases. Am. J. Pathol. 36: 457471.
6. Amlie-Lefond, C.,, D. A. Paz,, M. P. Connelly,, G. B. Huffnagle,, K. S. Dunn,, N. T. Whelan, and, H. T. Whelan. 2005. Innate immunity for biodefense: a strategy whose time has come. J. Allergy Clin. Immunol. 116: 13341342.
7. Arenas, G. N.,, A. S. Staskevich,, A. Aballay, and, L. S. Mayorga. 2000. Intracellular trafficking of Brucella abortus in J774 macrophages. Infect. Immun. 68: 42554263.
8. Ariel, N.,, A. Zvi,, H. Grosfeld,, O. Gat,, Y. Inbar,, B. Velan,, S. Cohen, and, A. Shaffer-man. 2002. Search for potential vaccine candidate open reading frames in the Bacillus anthracis virulence plasmid pXO1: in silico and in vitro screening. Infect. Immun. 70: 68176827.
9. Ariel, N.,, A. Zvi,, K. S. Makarova,, T. Chitlaru,, E. Elhanany,, B. Velan,, S. Cohen,, A. M. Fried-lander, and, A. Shafferman. 2003. Genome-based bioinformatic selection of chromosomal Bacillus anthracis putative vaccine candidates coupled with proteomic identification of surface-associated antigens. Infect. Immun. 71: 45634579.
10. Aronson, A. I.,, C. Bell, and, B. Fulroth. 2005. Plasmid-encoded regulator of extracellular proteases in Bacillus anthracis. J. Bacteriol. 187: 31333138.
11. Arun, S.,, H. Neubauer,, A. Gurel,, G. Ayyildiz,, B. Kuscu,, T. Yesildere,, H. Meyer, and, W. Hermanns. 1999. Equine glanders in Turkey. Vet. Rec. 144: 255258.
12. Ascenzi, P.,, P. Visca,, G. Ippolito,, A. Spallarossa,, M. Bolognesi, and, C. Montecucco. 2002. Anthrax toxin: a tripartite lethal combination. FEBS Lett. 531: 384388.
13. Baca, O. G.,, Y.-P. Li, and, H. Kumar. 1994. Survival of the Q fever agent Coxiella burnetii in the phagolysosome. Trends. Microbiol. 2: 476480.
14. Baillie, L.,, S. Hibbs,, P. Tsai,, G. L. Cao, and, G. M. Rosen. 2005. Role of superoxide in the germination of Bacillus anthracis endospores. FEMS Microbiol. Lett. 245: 3338.
15. Beare, P. A.,, S. F. Porcella,, R. Seshadri,, J. E. Samuel, and, R. A. Heinzen. 2005. Preliminary assessment of genome differences between the reference Nine Mile Isolate and two human endocarditis isolates of Coxiella burnetii. Ann. N. Y. Acad. Sci. 1063: 6467.
16. Bergman, N. H.,, K. D. Passalacqua,, R. Gaspard,, L. M. Shetron-Rama,, J. Quackenbush, and, P. C. Hanna. 2005. Murine macrophage transcriptional responses to Bacillus anthracis infection and intoxication. Infect. Immun. 73: 10691080.
17. Bode, E.,, W. Hurtle, and, D. Norwood. 2004. Real-time PCR assay for a unique chromosomal sequence of Bacillus anthracis. J. Clin. Microbiol. 42: 58255831.
18. Bordenstein, S. R., and, W. S. Reznikoff. 2005. Mobile DNA in obligate intracellular bacteria. Nat. Rev. Microbiol. 3: 688699.
19. Borio, L.,, T. Inglesby,, C. J. Peters,, A. L. Schmaljohn,, J. M. Hughes,, P. B. Jahrling,, T. Ksiazek,, K. M. Johnson,, A. Meyerhoff,, T. O’Toole,, M. S. Ascher,, J. Bartlett,, J. G. Breman,, E. M. Eitzen, Jr.,, M. Hamburg,, J. Hauer,, D. A. Henderson,, R. T. Johnson,, G. Kwik,, M. Layton,, S. Lillibridge,, G. J. Nabel,, M. T. Osterholm,, T. M. Perl,, P. Russell, and, K. Tonat. 2002. Hemorrhagic fever viruses as biological weapons: medical and public health management. JAMA 287: 23912405.
20. Brachman, P. S.,, A. F. Kaufman, and, F. G. Dalldorf. 1966. Industrial inhalation anthrax. Bacteriol. Rev. 30: 646659.
21. Bradaric, N., and, V. Punda-Polic. 1992. Cutaneous anthrax due to penicillin-resistant Bacillus anthracis transmitted by an insect bite. Lancet 340: 306307.
22. Breitbart, M.,, I. Hewson,, B. Felts,, J. M. Mahaffy,, J. Nulton,, P. Salamon, and, F. Rohwer. 2003. Metagenomic analyses of an uncultured viral community from human feces. J. Bacteriol. 185: 62206223.
23. Broekhuijsen, M.,, P. Larsson,, A. Johansson,, M. Bystrom,, U. Eriksson,, E. Larsson,, R. G. Prior,, A. Sjostedt,, R. W. Titball, and, M. Forsman. 2003. Genome-wide DNA microarray analysis of Francisella tularensis strains demonstrates extensive genetic conservation within the species but identifies regions that are unique to the highly virulent F. tularensis subsp. tularensis. J. Clin. Micro-biol. 41: 29242931.
24. Brossier, F., and, M. Mock. 2001. Toxins of Bacillus anthracis. Toxicon 39: 17471755.
25. Brown, P. O., and, D. Botstein. 1999. Exploring the new world of the genome with DNA microarrays. Nat. Genet. 21: 3337.
26. Brunsing, R. L.,, C. La Clair,, S. Tang,, C. Chiang,, L. E. Hancock,, M. Perego, and, J. A. Hoch. 2005. Characterization of sporulation histidine kinases of Bacillus anthracis. J. Bacteriol. 187: 69726981.
27. Brussow, H.,, C. Canchaya, and, W. D. Hardt. 2004. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev. 68: 560602.
28. Buchrieser, C.,, C. Rusniok,, L. Frangeul,, E. Couve,, A. Billault,, F. Kunst,, E. Carniel, and, P. Glaser. 1999. The 102-kilobase pgm locus of Yersinia pestis: sequence analysis and comparison of selected regions among different Yersinia pestis and Yersinia pseudotuberculosis strains. Infect. Immun. 67: 48514861.
29. Candela, T., and, A. Fouet. 2005. Bacillus anthracis CapD, belonging to the gamma-glutamyl-transpeptidase family, is required for the covalent anchoring of capsule to peptidoglycan. Mol. Microbiol. 57: 717726.
30. C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 20122018.
31. Celli, J.,, C. de Chastellier,, D.-M. Franchini,, J. Cerda-Pizarro,, E. Moreno, and, J.-P. Gorvel. 2006. Brucella evades macrophage killing via VirB-dependent sustained interactions with the endoplasmic reticulum. J. Exp. Med. 198: 545556.
32. Cello, J.,, A. V. Paul, and, E. Wimmer. 2002. Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science 297: 10161018.
33. Cendrowski, S.,, W. MacArthur, and, P. Hanna. 2004. Bacillus anthracis requires side-rophore biosynthesis for growth in macrophages and mouse virulence. Mol. Microbiol. 51: 407417.
34. Chain, P. S.,, E. Carniel,, F. W. Larimer,, J. Lamerdin,, P. O. Stoutland,, W. M. Regala,, A. M. Georgescu,, L. M. Vergez,, M. L. Land,, V. L. Motin,, R. R. Brubaker,, J. Fowler,, J. Hinnebusch,, M. Marceau,, C. Medigue,, M. Simonet,, V. Chenal-Francisque,, B. Souza,, D. Dacheux,, J. M. Elliott,, A. Derbise,, L. J. Hauser, and, E. Garcia. 2004. Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. USA 101: 1382613831.
35. Chain, P. S.,, D. J. Comerci,, M. E. Tolmasky,, F. W. Larimer,, S. A. Malfatti,, L. M. Vergez,, F. Aguero,, M. L. Land,, R. A. Ugalde, and, E. Garcia. 2005. Whole-genome analyses of speciation events in pathogenic Brucellae. Infect. Immun. 73: 83538361.
36. Chaowagul, W.,, N. J. White,, D. A. Dance,, Y. Wattanagoon,, P. Naigowit,, T. M. Davis,, S. Looareesuwan, and, N. Pitakwatchara. 1989. Melioidosis: a major cause of community-acquired septicemia in northeastern Thailand. J. Infect. Dis. 159: 890899.
37. Chow, K. Y.,, C. C. Hon,, R. K. Hui,, R. T. Wong,, C. W. Yip,, F. Zeng, and, F. C. Leung. 2003. Molecular advances in severe acute respiratory syndrome-associated coronavirus (SARS-CoV). Genomics Proteomics Bioinformatics 1: 247262.
38. Chromy, B. A.,, J. Perkins,, J. L. Heidbrink,, A. D. Gonzales,, G. A. Murphy,, J. P. Fitch, and, S. L. McCutchen-Maloney. 2004. Proteomic characterization of host response to Yersinia pestis and near neighbors. Biochem. Biophys. Res. Commun. 320: 474479.
39. Clemens, D. L.,, B. Y. Lee, and, M. A. Horwitz. 2004. Virulent and avirulent strains of Fran-cisella tularensis prevent acidification and maturation of their phagosomes and escape into the cytoplasm of human macrophages. Infect. Immun. 74: 32043217.
40. Coenye, T., and, J. J. LiPuma. 2003. Molecular epidemiology of Burkholderia species. Front. Biosci. 8: e55e67.
41. Cole, S. T.,, K. Eiglmeier,, J. Parkhill,, K. D. James,, N. R. Thomson,, P. R. Wheeler,, N. Honore,, T. Garnier,, C. Churcher,, D. Harris,, K. Mungall,, D. Basham,, D. Brown,, T. Chill-ingworth,, R. Connor,, R. M. Davies,, K. Devlin,, S. Duthoy,, T. Feltwell,, A. Fraser,, N. Hamlin,, S. Holroyd,, T. Hornsby,, K. Jagels,, C. Lacroix,, J. Maclean,, S. Moule,, L. Murphy,, K. Oliver,, M. A. Quail,, M. A. Rajandream,, K. M. Rutherford,, S. Rutter,, K. Seeger,, S. Simon,, M. Simmonds,, J. Skelton,, R. Squares,, S. Squares,, K. Stevens,, K. Taylor,, S. White-head,, J. R. Woodward, and, B. G. Barrell. 2001. Massive gene decay in the leprosy bacillus. Nature 409: 10071011.
42. Collier, R. J., and, J. A. T. Young. 2003. Anthrax toxin. Ann. Rev. Cell. Dev. Biol. 19: 4570.
43. Comer, J. E.,, C. L. Galindo,, A. K. Chopra, and, J. W. Peterson. 2005. GeneChip analyses of global transcriptional responses of murine macrophages to the lethal toxin of Bacillus anthracis. Infect. Immun. 73: 18791885.
44. Crouzet, J.,, L. Naudin,, C. Orsini,, E. Vigne,, L. Ferrero,, A. Le Roux,, P. Benoit,, M. Latta,, C. Torrent,, D. Branellec,, P. Denefle,, J. F. Mayaux,, M. Perricaudet, and, P. Yeh. 1997. Recombinational construction in Escherichia coli of infectious adenoviral genomes. Proc. Natl. Acad. Sci. USA 94: 14141419.
45. Cummings, C. A., and, D. A. Relman. 2002. Genomics and microbiology. Microbial forensics—”cross-examining pathogens.” Science 296: 19761979.
46. Day, W. A., Jr.,, R. E. Fernandez, and, A. T. Maurelli. 2001. Pathoadaptive mutations that enhance virulence: genetic organization of the cadA regions of Shigella spp. Infect. Immun. 69: 74717480.
47. DelVecchio, V. G.,, V. Kapatral,, P. Elzer,, G. Patra, and, C. V. Mujer. 2002. The genome of Brucella melitensis. Vet. Microbiol. 90: 587592.
48. DelVecchio, V. G.,, V. Kapatral,, R. J. Redkar,, G. Patra,, C. Mujer,, T. Los,, N. Ivanova,, I. Anders,, A. Bhattacharyya,, W. Lykidis,, G. Reznik,, L. Jablonski,, N. Larsen,, M. D’Souza,, A. Bernal,, M. Mazur,, E. Goltsman,, E. Selkov,, P. H. Elzer,, S. Hagius,, D. O’Callaghan,, J.-J. Letesson,, R. Haselkorn,, N. Kyrpides, and, R. Overbeek. 2002. The genome sequence of the facultative intracellular pathogen Brucella melitensis. Proc. Natl. Acad. Sci. USA 99: 443448.
49. Deng, W.,, V. Burland,, G. Plunkett III,, A. Boutin,, G. F. Mayhew,, P. Liss,, N. T. Perna,, D. J. Rose,, B. Mau,, S. Zhou,, D. C. Schwartz,, J. D. Fetherston,, L. E. Lindler,, R. R. Brubaker,, G. V. Plano,, S. C. Straley,, K. A. McDonough,, M. L. Nilles,, J. S. Matson,, F. R. Blattner, and, R. D. Perry. 2002. Genome sequence of Yersinia pestis KIM. J. Bacteriol. 184: 46014611.
50. Dennis, D. T.,, T. V. Inglesby,, D. A. Henderson,, J. G. Bartlett,, M. S. Ascher,, E. Eitzen,, A. D. Fine,, A. M. Friedlander,, J. Hauer,, M. Layton,, S. R. Lillibridge,, J. E. McDade,, M. T. Osterholm,, T. O’Toole,, G. Parker,, T. M. Perl,, P. K. Russell, and, K. Tonat. 2001. Tularemia as a biological weapon. JAMA 285: 27632773.
51. Dixon, T. C.,, A. A. Fadl,, T. M. Koehler,, J. A. Swanson, and, P. C. Hanna. 2000. Early Bacillus anthracis–macrophage interactions: intracellular survival and escape. Cell. Microbiol. 2: 453463.
52. Dixon, T. C.,, M. Meselson,, J. Guilemin, and, P. C. Hanna. 1999. Anthrax. N. Engl. J. Med. 341: 815826.
53. Dornand, J.,, Gross, A.,, Lafont, V.,, Liautard, J.,, Oliaro, J., and, Liautard, J.-P. 2002. The innate immune response against Brucella in humans. Vet. Microbiol. 90: 383394.
54. Draghici, S.,, P. Khatri,, Y. Liu,, K. J. Chase,, E. A. Bode,, D. A. Kulesh,, L. P. Wasieloski,, D. A. Norwood, and, J. Reifman. 2005. Identification of genomic signatures for the design of assays for the detection and monitoring of anthrax threats. Pac. Symp. Biocomput. 2005: 248259.
55. Dricot, A.,, J.-F. Rual,, P. Lamesch,, N. Bertin,, D. Dupuy,, T. Hao,, C. Lambert,, R. Hallez,, J.-M. Delroisse,, J. Vandenhaute,, I. Lopez-Goñi,, I. Moriyon,, J. M. Garcia-Lobo,, F. J. Sangari,, A. P. MacMillan,, S. J. Cutler,, A. M. Whatmore,, S. Bozak,, R. Sequerra,, L. Doucette-Stamm,, M. Vidal,, D. E. Hill,, J.-J. Letesson, and, X. De Bolle. 2006. Generation of the Brucella melatensis ORFeome version 1.1. Genome Res. 10B: 22012206.
56. Drysdale, M.,, A. Bourgogne, and, T. M. Koehler. 2005. Transcriptional analysis of the Bacillus anthracis capsule regulators. J. Bacteriol. 187: 51085114.
57. Drysdale, M.,, S. Heninger,, J. Hutt,, Y. Chen,, C. R. Lyons, and, T. M. Koehler. 2005. Capsule synthesis by Bacillus anthracis is required for dissemination in murine inhalation anthrax. EMBO J. 24: 221227.
58. Duesbery, N. S.,, C. P. Webb,, S. H. Leppla,, V. M. Gordon,, K. R. Klimpel,, T. D. Copeland,, N. G. Ahn,, M. K. Oskarsson,, K. Fikasawa,, K. D. Paull, and, G. P. Vande Woude. 1998. Proteolytic inactivation of MAP-kinase-kinase by anthrax lethal factor. Science 280: 734737.
59. Ecker, D. J.,, R. Sampath,, P. Willett,, J. R. Wyatt,, V. Samant,, C. Massire,, T. A. Hall,, K. Hari,, J. A. McNeil,, C. Buchen-Osmond, and, B. Budowle. 2005. The Microbial Rosetta Stone Database: a compilation of global and emerging infectious microorganisms and bioterrorist threat agents. BMC Microbiol. 5: 19.
60. Edwards, J. S.,, M. Covert, and, B. Palsson. 2002. Metabolic modelling of microbes: the flux-balance approach. Environ. Microbiol. 4: 133140.
61. Ellis, J.,, P. C. F. Oyston,, M. Green, and, R. Titball. 2002. Tularemia. Clin. Microbiol. Rev. 15: 631646.
62. Elvin, S. J.,, J. E. Eyles,, K. A. Howard,, E. Ravichandran,, S. Somavarappu,, H. O. Alpar, and, E. D. Williamson. 2006. Protection against bubonic and pneumonic plague with a single dose microencapsulated sub-unit vaccine. Vaccine 15: 44334439.
63. Etienne-Toumelin, I.,, J. C. Sirard,, E. Duflot,, M. Mock, and, A. Fouet. 1995. Characterization of the Bacillus anthracis S-layer: clongin and sequence of the structural gene. J. Bacteriol. 177: 614620.
64. Ezzell, J. W. J., and, T. G. Abshire. 1988. Immunological analysis of cell-associated antigens of Bacillus anthracis. Infect. Immun. 56: 349356.
65. Farlow, J.,, K. L. Smith,, J. Wong,, M. Abrams,, M. Lytle, and, P. Keim. 2001. Francisella tularensis strain typing using multiple-locus, variable-number tandem repeat analysis. J. Clin. Microbiol. 39: 31863192.
66. Fernandez-Moreia, E., and, M. S. Swanson. 2002. A microbial strategy to multiply in macrophages: the pregnant pause. Traffic 3: 170177.
67. Flashner, Y.,, E. Mamroud,, A. Tidhar,, R. Ber,, M. Aftalion,, D. Gur,, S. Lazar,, A. Zvi,, T. Bino,, N. Ariel,, B. Velan,, A. Shafferman, and, S. Cohen. 2004. Generation of Yersinia pestis attenuated strains by signature-tagged mutagenesis in search of novel vaccine candidates. Infect. Immun. 72: 908915.
68. Fleischmann, R. D.,, M. D. Adams,, O. White,, R. A. Clayton,, E. F. Kirkness,, A. R. Kerlavage,, C. J. Bult,, J.-F. Tomb,, B. A. Dougherty,, J. M. Merrick,, K. McKenny,, G. Sutton,, W. Fitzhugh,, C. Fields,, J. D. Gocayne,, J. Scott,, R. Shirley,, L.-I. Liu,, A. Glodek,, J. M. Kelley,, J. F. Wiedman,, C. A. Phillips,, T. Spriggs,, E. Hedblom,, M. D. Cotton,, T. R. Utterback,, M. C. Hanna,, D. T. Nquyen,, D. M. Saudek,, R. C. Brandon,, L. D. Fine,, J. L. Fritchman,, J. L. Fuhrman,, N. S. M. Geoghagen,, C. L. Gnehm,, L. A. McDonald,, K. V. Small,, C. M. Fraser,, H. O. Smith, and, J. C. Venter. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496512.
69. Forde, C. E.,, J. M. Rocco,, J. P. Fitch, and, S. L. McCutchen-Maloney. 2004. Real-time characterization of virulence factor expression in Yersinia pestis using a GFP reporter system. Biochem. Biophys. Res. Commun. 324: 795800.
70. Freer, E.,, J. Pizarro-Cerda,, A. Weintraub,, J. A. Bengoechea,, I. Moriyon,, K. Hultenby,, J. P. Grovel, and, E. Moreno. 1999. The outer membrane of Brucella ovis shows increased permeability to hydrophobic probes and is more susceptible to cationic peptides than are the outer membranes of mutant rough Brucella abortus strains. Infect. Immun. 67: 61816186.
71. Friedlander, A. M.,, S. L. Welkos,, M. L Pitt,, J. W. Ezzell,, P. L. Worsham,, K. J. Rose,, B. E. Ivins,, J. R. Lowe,, G. B Howe,, P. Mikesell, and, W. B. Lawrence. 1993. Postexposure prophylaxis against experimental inhalation antharx. J. Infect. Dis. 167: 12391243.
72. Galloway, C. S.,, P. Wang,, D. Winstanley, and, I. M. Jones. 2005. Comparison of the bacterial Enhancin-like proteins from Yersinia and Bacillus spp. with a baculovirus Enhancin. J. Invertebr. Pathol. 90: 134137.
73. Garbom, S.,, A. Forsberg,, H. Wolf-Watz, and, B. M. Kihlberg. 2004. Identification of novel virulence-associated genes via genome analysis of hypothetical genes. Infect. Immun. 72: 13331340.
74. Godoy, D.,, G. Randle,, A. J. Simpson,, D. M. Aanensen,, T. L. Pitt,, R. Kinoshita, and, B. G. Spratt. 2003. Multilocus sequence typing and evolutionary relationships among the causative agents of melioidosis and glanders, Burkholderia pseudomallei and Burkholderia mallei. J. Clin. Micro-biol. 41: 20682079.
75. Golovliov, I.,, V. Baranov,, Z. Krocova,, H. Kovarova, and, A. Sjostedt. 2006. An attenuated strain of the facultative intracellular bacterium Francisella tularensis can escape the phagosome of monocytic cells. Infect. Immun. 71: 59405950.
76. Guidi-Rontani, C. 2002. The alveolar macrophage: the Trojan horse of Bacillus anthracis. Trends Microbiol. 10: 405409.
77. Guidi-Rontani, C.,, M. Levy,, H. Ohayon, and, M. Mock. 2001. Fate of germinated Bacillus anthracis spores in primary murine macrophages. Mol. Microbiol. 42: 931938.
78. Guidi-Rontani, C.,, Y. Pereira,, S. Ruffie,, J. C. Sirard,, M. Weber-Levy, and, M. Mock. 1999. Identification and characterization of a germination operon on the virulence plasmid pXO1 of Bacillus anthracis. Mol. Microbiol. 33: 407414.
79. Hacker, J.,, G. Blum-Oehler,, I. Muhldorfer, and, H. Tschape. 1997. Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol. Microbiol. 23: 10891097.
80. Hacker, J.,, B. Hochhut,, B. Middendorf,, G. Schneider,, C. Buchrieser,, G. Gottschalk, and, U. Dobrindt. 2004. Pathogenomics of mobile genetic elements of toxigenic bacteria. Int. J. Med. Microbiol. 293: 453461.
81. Halling, S. M.,, B. D. Peterson-Burch,, B. J. Bricker,, R. L. Zuerner,, Z. Qing,, L. L. Li,, V. Kapur,, D. P. Alt, and, S. C. Olsen. 2005. Completion of the genome sequence of Brucella abortus and comparison to the highly similar genomes of Brucella melitensis and Brucella suis. J. Bacteriol. 187: 27152726.
82. Han, Y.,, D. Zhou,, X. Pang,, L. Zhang,, Y. Song,, Z. Tong,, J. Bao,, E. Dai,, J. Wang,, Z. Guo,, J. Zhai,, Z. Du,, X. Wang,, J. Wang,, P. Huang, and, R. Yang. 2005. Comparative transcriptome analysis of Yersinia pestis in response to hyperosmotic and high-salinity stress. Res. Micro-biol. 156: 403415.
83. Han, Y.,, D. Zhou,, X. Pang,, L. Zhang,, Y. Song,, Z. Tong,, J. Bao,, E. Dai,, J. Wang,, Z. Guo,, J. Zhai,, Z. Du,, X. Wang,, J. Wang,, P. Huang, and, R. Yang. 2005. DNA microarray analysis of the heat- and cold-shock stimulons in Yersinia pestis. Microbes Infect. 7: 335348.
84. Hanna, P. 1998. Anthrax pathogenesis and host response. Curr. Top. Microbiol. Immunol. 225: 1335.
85. Harb, O. S.,, L. Y. Gao, and, Y. Abu Kwaik. 2000. From protozoa to mammalian cells: a new paradigm in the life cycle of intracellular bacterial pathogens. Environ. Microbiol. 2: 251265.
86. Heinzen, R. A.,, Hackstadt, T., and, Samuel, J. E. 1999. Developmental biology of Coxiella burnetii. Trends Microbiol. 7: 149154.
87. Hensel, M.,, J. E. Shea,, C. Gleeson,, M. D. Jones,, E. Dalton, and, D. W. Holden. 1995. Simultaneous identification of bacterial virulence genes by negative selection. Science 269: 400403.
88. Hinchliffe, S. J.,, K. E. Isherwood,, R. A. Stabler,, M. B. Prentice,, A. Rakin,, R. A. Nichols,, P. C. Oyston,, J. Hinds,, R. W. Titball, and, B. W. Wren. 2003. Application of DNA microar-rays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis. Genome Res. 13: 20182029.
89. Hinnebusch, B. J. 2005. The evolution of flea-borne transmission in Yersinia pestis. Curr. Issues Mol. Biol. 7: 197212.
90. Hoffmaster, A. R.,, J. Ravel,, D. A. Rasko,, G. D. Chapman,, M. D. Chute,, C. K. Marston,, B. K. De,, C. T. Sacchi,, C. Fitzgerald,, L. W. Mayer,, M. C. Maiden,, F. G. Priest,, M. Barker,, L. Jiang,, R. Z. Cer,, J. Rilstone,, S. N. Peterson,, R. S. Weyant,, D. R. Galloway,, T. D. Read,, T. Popovic, and, C. M. Fraser. 2004. Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax. Proc. Natl. Acad. Sci. USA 101: 84498454.
91. Holden, M. T.,, R. W. Titball,, S. J. Peacock,, A. M. Cerdeno-Tarraga,, T. Atkins,, L. C. Crossman,, T. Pitt,, C. Churcher,, K. Mungall,, S. D. Bentley,, M. Sebaihia,, N. R. Thomson,, N. Bason,, I. R. Beacham,, K. Brooks,, K. A. Brown,, N. F. Brown,, G. L. Challis,, I. Cherevach,, T. Chillingworth,, A. Cronin,, B. Crossett,, P. Davis,, D. DeShazer,, T. Feltwell,, A. Fraser,, Z. Hance,, H. Hauser,, S. Holroyd,, K. Jagels,, K. E. Keith,, M. Maddison,, S. Moule,, C. Price,, M. A. Quail,, E. Rabbi-nowitsch,, K. Rutherford,, M. Sanders,, M. Simmonds,, S. Songsivilai,, K. Stevens,, S. Tumapa,, M. Vesaratchavest,, S. Whitehead,, C. Yeats,, B. G. Barrell,, P. C. Oyston, and, J. Parkhill. 2004. Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudo-mallei. Proc. Natl. Acad. Sci. USA 101: 1424014245.
92. Holty, J.-E. C.,, D. M. Bravata,, H. Liu,, R. A. Olshen,, K. M. McDonald, and, D. K. Owens. 2006. Systematic review: a century of inhalational anthrax cases from 1900 to 2005. Ann. Intern. Med. 144: 270280.
93. Hong, P. C.,, R. M. Tsolis, and, T. A. Ficht. 2000. Identification of genes required for chronic persistence of Brucella abortus in mice. Infect. Immun. 90: 281297.
94. Inglesby, T. V.,, D. T. Dennis,, D. A. Henderson,, J. G. Bartlett,, M. S. Ascher,, E. Eitzen,, A. D. Fine,, A. M. Friedlander,, J. Hauer,, J. F. Koerner,, M. Layton,, J. McDade,, M. T. Osterholm,, T. O’Toole,, G. Parker,, T. M. Perl,, P. K. Russell,, M. Schoch-Spana, and, K. Tonat. 2000. Plague as a biological weapon: medical and public health management. Working Group on Civilian Biodefense. JAMA 283: 22812290.
95. Inglesby, T. V.,, D. A. Henderson,, J. G. Bartlett,, M. S. Ascher,, E. Eitzen,, A. M. Friedlander,, J. Hauer,, J. McDade,, M. T. Osterholm,, T. O’Toole,, G. Parker,, T. M. Perl,, P. K. Russell, and, K. Tonat. 1999. Anthrax as a biological weapon: medical and public health management. Working Group on Civilian Bio-defense. JAMA 281: 17351745.
96. Inglis, T. J.,, P. Rigby,, T. A. Robertson,, N. S. Dutton,, M. Henderson, and, B. J. Chang. 2000. Interaction between Burkholderia pseudo-mallei and Acanthamoeba species results in coiling phagocytosis, endamebic bacterial survival, and escape. Infect. Immun. 68: 16811686.
97. Inglis, T. J.,, T. Robertson,, D. E. Woods,, N. Dutton, and, B. J. Chang. 2003. Flagellum-mediated adhesion by Burkholderia pseudomallei precedes invasion of Acanthamoeba astronyxis. Infect. Immun. 71: 22802282.
98. Inglis, T. J. J. 2004. Mellioidosis in man and other animals: epidemiology, ecology and pathogenesis. Vet. Bull. 74: 39N48N.
99. Ireland, J. A., and, P. C. Hanna. 2002. Macrophage-enhanced germination of Bacillus anthracis endospores requires gerS. Infect. Immun. 70: 58705872.
100. Ivanova, N.,, A. Sorokin,, I. Anderson,, N. Galleron,, B. Candelon,, V. Kapatral,, A. Bhattacharyya,, G. Reznik,, N. Mikhailova,, A. Lapidus,, L. Chu,, M. Mazur,, E. Goltsman,, N. Larsen,, M. D’Souza,, T. Walunas,, Y. Grechkin,, G. Pusch,, R. Haselkorn,, M. Fonstein,, S. D. Ehrlich,, R. Overbeek, and, N. Kyrpides. 2003. Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature 423: 8791.
101. Jackson, P. J.,, M. E. Hugh-Jones,, D. M. Adair,, G. Green,, K. K. Hill,, C. R. Kuske,, L. M. Grinberg,, F. A. Abramova, and, P. Keim. 1998. PCR analysis of tissue samples from the 1979 Sverdlovsk anthrax victims: the presence of multiple Bacillus anthracis strains in different victims. Proc. Natl. Acad. Sci. USA 95: 12241229.
102. Jackson, R. J.,, A. J. Ramsay,, C. D. Christensen,, S. Beaton,, D. F. Hall, and, I. A. Ramshaw. 2001. Expression of mouse inter-leukin-4 by a recombinant ectromelia virus suppresses cytolytic lymphocyte responses and overcomes genetic resistance to mousepox. J. Virol. 75: 12051210.
103. Jeddeloh, J. A.,, D. L. Fritz,, D. M. Waag,, J. M. Hartings, and, G. P. Andrews. 2003. Biodefense-driven murine model of pneumonic melioidosis. Infect. Immun. 71: 584587.
104. Jensen, G. B.,, B. M. Hansen,, J. Eilenberg, and, J. Mahillon. 2003. The hidden lifestyles of Bacillus cereus and relatives. Environ. Microbiol. 5: 631640.
105. Jernigan, D. B.,, P. L. Raghunathan,, B. P. Bell,, R. Brechner,, E. A. Bresnitz,, J. C. Butler,, M. Cetron,, M. Choen,, T. Doyel,, M. Fisher,, C. Greene,, K. S. Griffith,, J. Guarner,, J. L. Hadler,, J. A. Hayslett,, R. Meyer,, L. R. Petersen,, M. Phillips,, R. Pinner,, T. Popovic,, C. P. Quinn,, J. Reefhuis,, D. Reissman,, N. Rosenstein,, A. Schuchat,, W. J. Shieh,, L. Siegal,, D. L. Swerdlow,, F. C. Tenover,, M. Traeger,, J. W. Ward,, I. Weisfurse,, S. Wiersma,, K. Yeskey,, S. Zaki,, D. A. Ashford,, B. A. Perkins,, S. Ostroff,, J. Hughes,, D. Fleming,, J. P. Koplan,, J. L. Gerberding, and, the National Anthrax Epidemiologic Investigation Team. 2002. Investigation of bioterrorism-related anthrax, United States, 2001: epidemiologic findings. Emerg. Infect. Dis. 8: 10191028.
106. Jiménez de Bagüés, M. P.,, S. Dudal,, J. Dornand, and, A. Gross. 2005. Cellular bioterrorism: how Brucella corrupts macrophage physiology to promote invasion and proliferation. Clin. Immunol. 114: 227238.
107. Karlin, S.,, M. J. Barnett,, A. M. Campbell,, R. F. Fisher, and, J. Mrazek. 2003. Predicting gene expression levels from codon biases in alpha-proteobacterial genomes. Proc. Natl. Acad. Sci. USA 100: 73137318.
108. Kau, J. H.,, D. S. Sun,, W. J. Tsai,, H. F. Shyu,, H. H. Huang,, H. C. Lin, and, H. H. Chang. 2005. Antiplatelet activities of anthrax lethal toxin are associated with suppressed p42/44 and p38 mitogen-activated protein kinase pathways in the platelets. J. Infect. Dis. 192: 14651474.
109. Kavanagh, K., and, E. P. Reeves. 2004. Exploiting the potential of insects for in vivo pathogenicity testing of microbial pathogens. FEMS Microbiol. Rev. 28: 101112.
110. Kazar, J. 2005. Coxiella burnetii infection. Ann. N.Y. Acad. Sci. 1063: 105114.
111. Keim, P.,, A. M. Klevytska,, L. B. Price,, J. M. Schupp,, G. Zinser,, K. L. Smith,, M. E. Hugh-Jones,, R. Okinaka,, K. K. Hill, and, P. J. Jackson. 1999. Molecular diversity in Bacillus anthracis. J. Appl. Microbiol. 87: 215217.
112. Kerschen, E. J.,, D. A. Cohen,, A. M. Kaplan, and, S. C. Straley. 2004. The plague virulence protein YopM targets the innate immune response by causing a global depletion of NK cells. Infect. Immun. 72: 45894602.
113. Kespichayawattana, W.,, S. Rattanachetkul,, T. Wanun,, P. Utaisincharoen, and, S. Sirisinha. 2000. Burkholderia pseudomallei induces cell fusion and actin-associated membrane protrusion: a possible mechanism for cell-to-cell spread. Infect. Immun. 68: 53775384.
114. Khan, A. S.,, C. V. Mujer,, T. G. Alefantis,, J. P. Connolly,, U. B. Mayr,, P. Walcher,, W. Lubitz, and, V. G. Delvecchio. 2006. Proteomics and bioinformatics strategies to design countermeasures against infectious threat agents. J. Chem. Inf. Model 46: 111115.
115. Kim, H. S.,, M. A. Schell,, Y. Yu,, R. L. Ulrich,, S. H. Sarria,, W. C. Nierman, and, D. DeShazer. 2005. Bacterial genome adaptation to niches: divergence of the potential virulence genes in three Burkholderia species of different survival strategies. BMC Genomics 6: 174.
116. Klein, F.,, J. S. Walker,, D. F. Fitzpatrick,, R. E. Lincoln,, B. G. Mahlandt,, W. I. Jones, Jr.,, J. P. Dobbs, and, K. J. Hendrix. 1966. Pathophysiology of anthrax. J. Infect. Dis. 116: 123138.
117. Klimpel, K. R.,, N. Arora, and, S. H. Leppla. 1994. Anthrax toxin lethal factor contains a zinc metalloprotease consensus sequence which is required for lethal toxin activity. Mol. Microbiol. 13: 10931100.
118. Kohler, S.,, V. Foulongne,, S. Ouahrani-Bettache,, G. Bourg,, J. Teyssier,, M. Ramuz, and, J. P. Liautard. 2002. The analysis of the intramacrophage virulome of Brucella suis deciphers the environment encountered by the pathogen inside the macrophage host cell. Proc. Natl. Acad. Sci. USA 99: 1571115716.
119. Konstantinidis, K. T., and, J. M. Tiedje. 2004. Trends between gene content and genome size in prokaryotic species with larger genomes. Proc. Natl. Acad. Sci. USA 101: 31603165.
120. Kotetishvili, M.,, A. Kreger,, G. Wauters,, J. G. Morris, Jr.,, A. Sulakvelidze, and, O. C. Stine. 2005. Multilocus sequence typing for studying genetic relationships among Yersinia species. J. Clin. Microbiol. 43: 26742684.
121. Lamonica, J. M.,, M. Wagner,, M. Eschen-brenner,, L. E. Williams,, T. L. Miller,, G. Patra, and, V. G. DelVecchio. 2005. Comparative secretome analyses of three Bacillus anthracis strains with variant plasmid contents. Infect. Immun. 73: 36463658.
122. Larsson, P.,, P. C. Oyston,, P. Chain,, M. C. Chu,, M. Duffield,, H. H. Fuxelius,, E. Garcia,, G. Halltorp,, D. Johansson,, K. E. Isher-wood,, P. D. Karp,, E. Larsson,, Y. Liu,, S. Michell,, J. Prior,, R. Prior,, S. Malfatti,, A. Sjostedt,, K. Svensson,, N. Thompson,, L. Vergez,, J. K. Wagg,, B. W. Wren,, L. E. Lindler,, S. G. Andersson,, M. Forsman, and, R. W. Titball. 2005. The complete genome sequence of Francisella tularensis, the causative agent of tularemia. Nat. Genet. 37: 153159.
123. Lathem, W. W.,, S. D. Crosby,, V. L. Miller, and, W. E. Goldman. 2005. Progression of primary pneumonic plague: a mouse model of infection, pathology, and bacterial transcriptional activity. Proc. Natl. Acad. Sci. USA 102: 1778617791.
124. Lavigne, J. P.,, A. C. Vergunst,, G. Bourg, and, D. O’Callaghan. 2005. The IncP island in the genome of Brucella suis 1330 was acquired by site-specific integration. Infect. Immun. 73: 77797783.
125. Lawrence, J. G. 2005. Common themes in the genome strategies of pathogens. Curr. Opin. Genet. Dev. 15: 584588.
126. Leamon, J. H.,, W. L. Lee,, K. R. Tartaro,, J. R. Lanza,, G. J. Sarkis,, A. D. deWinter,, J. Berka,, M. Weiner,, J. M. Rothberg, and, K. L. Lohman. 2003. A massively parallel PicoTiter-Plate based platform for discrete picoliter-scale polymerase chain reactions. Electrophoresis 24: 37693777.
127. Lederberg, J. 1975. DNA splicing: will fear rob us of its benefits? Prism 3: 3337.
128. Le Fleche, P.,, I. Jacques,, M. Grayon,, S. Al Dahouk,, P. Bouchon,, F. Denoeud,, K. Nockler,, H. Neubauer,, L. A. Guilloteau, and, G. Vergnaud. 2006. Evaluation and selection of tandem repeat loci for a Brucella MLVA typing assay. BMC Microbiol. 6: 9.
129. Lepore, L. S.,, P. R. Roelvink, and, R. R. Granados. 1996. Enhancin, the granulosis virus protein that facilitates nucleopolyhedrovirus (NPV) infections, is a metalloprotease. J. Invertebr. Pathol. 68: 131140.
130. Leppla, S. H. 1982. Anthrax toxin edema factor: a bacterial adenylate cyclase that increases cyclic AMP concentrations in eukaryotic cells. Proc. Natl. Acad. Sci. USA 79: 31623166.
131. Leppla, S. H. 1984. Bacillus anthracis calmodulin-dependent adenylate cyclase: chemical and enzymatic properties and interactions with eucaryotic cells. Adv. Cyclic Nucleotide Protein Phosphorylation Res. 17: 189198.
132. Leppla, S. H. 1991. The Anthrax Toxin Complex. Academic Press, London.
133. Lerat, E.,, V. Daubin,, H. Ochman, and, N. A. Moran. 2005. Evolutionary origins of genomic repertoires in bacteria. PLoS Biol. 3: e130.
134. Lerat, E., and, H. Ochman. 2004. Psi-Phi: exploring the outer limits of bacterial pseudo-genes. Genome Res. 14: 22732278.
135. Lesic, B.,, S. Bach,, J. M. Ghigo,, U. Dobrindt,, J. Hacker, and, E. Carniel. 2004. Excision of the high-pathogenicity island of Yersinia pseudo-tuberculosis requires the combined actions of its cognate integrase and Hef, a new recombination directionality factor. Mol. Microbiol. 52: 13371348.
136. Lesic, B., and, E. Carniel. 2005. Horizontal transfer of the high-pathogenicity island of Yersinia pseudotuberculosis. J. Bacteriol. 187: 33523358.
137. Li, B.,, L. Jiang,, Q. Song,, J. Yang,, Z. Chen,, Z. Guo,, D. Zhou,, Z. Du,, Y. Song,, J. Wang,, H. Wang,, S. Yu,, J. Wang, and, R. Yang. 2005. Protein microarray for profiling antibody responses to Yersinia pestis live vaccine. Infect. Immun. 73: 37343739.
138. Li, Z. N.,, S. N. Mueller,, L. Ye,, Z. Bu,, C. Yang,, R. Ahmed, and, D. A. Steinhauer. 2005. Chimeric influenza virus hemagglutinin proteins containing large domains of the Bacillus anthracis protective antigen: protein characterization, incorporation into infectious influenza viruses, and antigenicity. J. Virol. 79: 1000310012.
139. Lin, B.,, Z. Wang,, G. J. Vora,, J. A. Thornton,, J. M. Schnur,, D. C. Thach,, K. M. Blaney,, A. G. Ligler,, A. P. Malanoski,, J. Santiago,, E. A. Walter,, B. K. Agan,, D. Metzgar,, D. Seto,, L.T. Daum,, R. Kruzelock,, R. K. Rowley,, E. H. Hanson,, C. Tibbetts, and, D. A. Stenger. 2006. Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays. Genome Res. 16: 527535.
140. Liu, H.,, N. H. Bergman,, B. Thomason,, S. Shallom,, A. Hazen,, J. Crossno,, D. A. Rasko,, J. Ravel,, T. D. Read,, S. N. Peterson,, J. Yates III, and, P. C. Hanna. 2004. Formation and composition of the Bacillus anthracis endospore. J. Bacteriol. 186: 164178.
141. Liu, Y.,, P. M. Harrison,, V. Kunin, and, M. Gerstein. 2004. Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes. Genome Biol. 5: R64.
142. Lopez, J.,, J. Copps,, C. Wilhelmsen,, R. Moore,, J. Kubay,, M. St.-Jacques,, S. Halayko,, C. Kranendonk,, S. Toback,, D. DeShazer,, D. L. Fritz,, M. Tom, and, D. E. Woods. 2003. Characterization of experimental equine glanders. Microbes Infect. 5: 11251131.
143. Lu, Q.,, W. Wei,, P. E. Kowalski,, A. C. Chang, and, S. N. Cohen. 2004. EST-based genome-wide gene inactivation identifies ARAP3 as a host protein affecting cellular susceptibility to anthrax toxin. Proc. Natl. Acad. Sci. USA 101: 1724617251.
144. Mahan, M. J.,, J. M. Slauch, and, J. J. Mekalanos. 1993. Selection of bacterial virulence genes that are specifically induced in host tissues. Science 259: 686688.
145. Maiden, M. C.,, J. A. Bygraves,, E. Feil,, G. Morelli,, J. E. Russell,, R. Urwin,, Q. Zhang,, J. Zhou,, K. Zurth,, D. A. Caugant,, I. M. Feavers,, M. Achtman, and, B. G. Spratt. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95: 31403145.
146. Manchee, R. J.,, M. G. Broster,, R. M. Henstridge,, A. J. Stagg, and, J. Melling. 1982. Anthrax island. Nature 296: 598.
147. Marketon, M. M.,, R. W. DePaolo,, K. L. DeBord,, B. Jabri, and, O. Schneewind. 2005. Plague bacteria target immune cells during infection. Science 309: 17391741.
148. Masui, S.,, S. Kamoda,, T. Sasaki, and, H. Ishikawa. 1999. The first detection of the insertion sequence ISW1 in the intracellular reproductive parasite Wolbachia. Plasmid 42: 1319.
149. Maurin, M., and, D. Raoult. 1999. Q fever. Clin. Microbiol. Rev. 12: 518553.
150. McCaul, T. F., and, J. C. Williams. 1981. Developmental cycle of Coxiella burnetii: structure and morphogenesis of vegetative and sporogenic differentiations. J. Bacteriol. 147: 10631076.
151. McDonald, W. H., and, J. R. Yates III. 2002. Shotgun proteomics and biomarker discovery. Dis. Markers 18: 99105.
152. Meselson, M.,, J. Guillemin,, M. Hugh-Jones,, A. Langmuir,, I. Popova,, A. Shelokov, and, O. Yampolskaya. 1994. The Svedlovsk anthrax outbreak of 1979. Science 266: 12021208.
153. Mignot, T.,, B. Denis,, E. Couture-Tosi,, A. B. Kolsto,, M. Mock, and, A. Fouet. 2001. Distribution of S-layers on the surface of Bacillus cereus strains: phylogenetic origin and ecological pressure. Environ. Microbiol. 3: 493501.
154. Mignot, T.,, M. Mock,, D. Robichon,, A. Landier,, D. Lereclus, and, A. Fouet. 2001. The incompatibility between the PlcR- and AtxA-controlled regulons may have selected a nonsense mutation in Bacillus anthracis. Mol. Microbiol. 42: 11891198.
155. Mikesell, P.,, B. E. Ivins,, J. D. Ristroph, and, T. M. Dreier. 1983. Evidence for plasmid-mediated toxin production in Bacillus anthracis. Infect. Immun. 39: 371376.
156. Miller, J. M.,, J. G. Hair,, M. Hebert,, L. Hebert,, F. J. Roberts, Jr., and, R. S. Weyant. 1997. Fulminating bacteremia and pneumonia due to Bacillus cereus. J. Clin. Microbiol. 35: 504507.
157. Minakhin, L.,, E. Semenova,, J. Liu,, A. Vasilov,, E. Severinova,, T. Gabisonia,, R. Inman,, A. Mushegian, and, K. Severinov. 2005. Genome sequence and gene expression of Bacillus anthracis bacteriophage Fah. J. Mol. Biol. 354: 115.
158. Moens, S., and, J. Vanderleyden. 1996. Functions of bacterial flagella. Crit. Rev. Microbiol. 22: 67100.
159. Mogridge, J.,, K. Cunningham,, D. B. Lacy,, M. Mourez, and, R. J. Collier. 2002. The lethal and edema factors of anthrax toxin bind only to oligomeric forms of the protective antigen. Proc. Natl. Acad. Sci. USA 99: 70457048.
160. Moore, R. A.,, S. Reckseidler-Zenteno,, H. Kim,, W. Nierman,, Y. Yu,, A. Tuanyok,, J. Warawa,, D. DeShazer, and, D. E. Woods. 2004. Contribution of gene loss to the pathogenic evolution of Burkholderia pseudomallei and Burkholderia mallei. Infect. Immun. 72: 41724187.
161. Motin, V. L.,, A. M. Georgescu,, J. P. Fitch,, P. P. Gu,, D. O. Nelson,, S. L. Mabery,, J. B. Garnham,, B. A. Sokhansanj,, L. L. Ott,, M.A. Coleman,, J. M. Elliott,, L. M. Kegelmeyer,, A. J. Wyrobek,, T. R. Slezak,, R. R. Brubaker, and, E. Garcia. 2004. Temporal global changes in gene expression during temperature transition in Yersinia pestis. J. Bacteriol. 186: 62986305.
162. Nano, F. E.,, N. Zhang,, S. C. Cowley,, K. E. Klose,, K. K. Cheung,, M. J. Roberts,, J. S. Ludu,, G. W. Letendre,, A. I. Meierovics,, G. Stephens, and, K. L. Elkins. 2004. A Fran-cisella tularensis pathogenicity island required for intramacrophage growth. J. Bacteriol. 186: 64306436.
163. Naroeni, A.,, N. Jouy,, S. Ouahrani-Bettache,, J. P. Liautard, and, F. Porte. 2001. Brucella suis– impaired specific recognition of phagosomes by lysosomes due to phagosomal membrane modifications. Infect. Immun. 69: 486493.
164. Ngauy, V.,, Y. Lemeshev,, L. Sadkowski, and, G. Crawford. 2005. Cutaneous melioidosis in a man who was taken as a prisoner of war by the Japanese during World War II. J. Clin. Microbiol. 43: 970972.
165. Nierman, W. C.,, D. DeShazer,, H. S. Kim,, H. Tettelin,, K. E. Nelson,, T. Feldblyum,, R. L. Ulrich,, C. M. Ronning,, L. M. Brinkac,, S. C. Daugherty,, T. D. Davidsen,, R. T. Deboy,, G. Dimitrov,, R. J. Dodson,, A. S. Durkin,, M. L. Gwinn,, D. H. Haft,, H. Khouri,, J. F. Kolonay,, R. Madupu,, Y. Mohammoud,, W. C. Nelson,, D. Radune,, C. M. Romero,, S. Sarria,, J. Selengut,, C. Shamblin,, S. A. Sullivan,, O. White,, Y. Yu,, N. Zafar,, L. Zhou, and, C. M. Fraser. 2004. Structural flexibility in the Burkholderia mallei genome. Proc. Natl. Acad. Sci. USA 101: 1424614251.
166. Nordberg, B. K.,, C. G. Schmiterlow, and, H. J. Hansen. 1961. Pathophysiological investigations into the terminal course of experimental anthrax in the rabbit. Acta Pathol. Microbiol. Scand. 53: 295318.
167. Ogata, H.,, P. Renesto,, S. Audic,, C. Robert,, G. Blanc,, P.-E. Fournier,, H. Parinello,, J.-M. Claverie, and, D. Raoult. 2005. The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite. PLoS Biol. 3: e248.
168. Okinaka, R. T.,, K. Cloud,, O. Hampton,, A. R. Hoffmaster,, K. K. Hill,, P. Keim,, T. M. Koehler,, G. Lamke,, S. Kuman,, J. Mahillon,, D. Manter,, Y. Martinez,, D. Ricke,, R. Svensson, and, P. J. Jackson. 1999. Sequence and organization of pXO1, the large Bacillus anthracis plasmid harboring the anthrax toxin genes. J. Bacteriol. 181: 65096515.
169. Ong, C.,, C. H. Ooi,, D. Wang,, H. Chong,, K. C. Ng,, F. Rodrigues,, M. A. Lee, and, P. Tan. 2004. Patterns of large-scale genomic variation in virulent and avirulent Burkholderia species. Genome Res. 14: 22952307.
170. Ou, K.,, C. Ong,, S. Y. Koh,, F. Rodrigues,, S. H. Sim,, D. Wong,, C. H. Ooi,, K. C. Ng,, H. Jikuya,, C. C. Yau,, S.Y. Soon,, D. Kesuma,, M. A. Lee, and, P. Tan. 2005. Integrative genomic, transcriptional, and proteomic diversity in natural isolates of the human pathogen Burkholderia pseudomallei. J. Bacteriol. 187: 42764285.
171. Pal, C.,, B. Papp, and, M. J. Lercher. 2005. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat. Genet. 37: 13721375.
172. Parkhill, J.,, B. W. Wren,, N. R. Thomson,, R. W. Titball,, M. T. Holden,, M. B. Prentice,, M. Sebaihia,, K. D. James,, C. Churcher,, K. L. Mungall,, S. Baker,, D. Basham,, S. D. Bentley,, K. Brooks,, A. M. Cerdeno-Tarraga,, T. Chillingworth,, A. Cronin,, R. M. Davies,, P. Davis,, G. Dougan,, T. Feltwell,, N. Hamlin,, S. Holroyd,, K. Jagels,, A. V. Karlyshev,, S. Leather,, S. Moule,, P. C. Oyston,, M. Quail,, K. Rutherford,, M. Simmonds,, J. Skelton,, K. Stevens,, S. Whitehead, and, B. G. Barrell. 2001. Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413: 523527.
173. Paulsen, I. T.,, R. Seshadri,, K. E. Nelson,, J. A. Eisen,, J. F. Heidelberg,, T. D. Read,, R. J. Dodson,, L. Umayam,, L. M. Brinkac,, M. J. Beanan,, S. C. Daugherty,, R. T. Deboy,, A. S. Durkin,, J. F. Kolonay,, R. Madupu,, W. C. Nelson,, B. Ayodeji,, M. Kraul,, J. Shetty,, J. Malek,, S. E. Van Aken,, S. Riedmuller,, H. Tettelin,, S. R. Gill,, O. White,, S. L. Salzberg,, D. L. Hoover,, L. E. Lindler,, S. M. Halling,, S. M. Boyle, and, C. M. Fraser. 2002. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc. Natl. Acad. Sci. USA 99: 1314813153.
174. Pearson, T.,, J. D. Busch,, J. Ravel,, T. D. Read,, S. D. Rhoton,, J. M. U’Ren,, T. S. Simonson,, S. M. Kachur,, R. R. Leadem,, M. L. Cardon,, M. N. Van Ert,, L. Y. Huynh,, C. M. Fraser, and, P. Keim. 2004. Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing. Proc. Natl. Acad. Sci. USA 101: 1353613541.
175. Pellizzari, R.,, C. Guidi-Rontani,, G. Vitale,, M. Mock, and, C. Montecucco. 1999. Anthrax lethal factor cleaves MKK3 in macrophages and inhibits the LPS/IFN gammainduced release of NO and TNF alpha. FEBS Lett. 462: 199204.
176. Perry, R. D., and, J. D. Fetherston. 1997. Yersinia pestis—etiologic agent of plague. Clin. Microbiol. Rev. 10: 3566.
177. Plotkin, S. A.,, P. S. Brachman,, M. Utell,, F. H. Bumford, and, M. M. Stechinson. 2002. An epidemic of inhalation anthrax, the first in the twentieth century: I. Clinical features. Am. J. Med. 112: 412.
178. Price, M. N.,, K. H. Huang,, E. J. Alm, and, A. P. Arkin. 2005. A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res. 33: 880892.
179. Pucci, M. J. 2006. Use of genomics to select antibacterial targets. Biochem. Pharmacol. 71: 10661072.
180. Pujol, C., and, J. B. Bliska. 2005. Turning Yersinia pathogenesis outside in: subversion of macrophage function by intracellular yersiniae. Clin. Immunol. 114: 216226.
181. Pujol, C.,, J. P. Grabenstein,, R. D. Perry, and, J. B. Bliska. 2005. Replication of Yersinia pestis in interferon gamma-activated macrophages requires ripA, a gene encoded in the pigmentation locus. Proc. Natl. Acad. Sci. USA 102: 1290912914.
182. Qiu, J.,, D. Zhou,, Y. Han,, L. Zhang,, Z. Tong,, Y. Song,, E. Dai,, B. Li,, J. Wang,, Z. Guo,, J. Zhai,, Z. Du,, X. Wang, and, R. Yang. 2005. Global gene expression profile of Yersinia pestis induced by streptomycin. FEMS Microbiol. Lett. 243: 489496.
183. Rajashekara, G.,, J. D. Glasner,, D. A. Glover, and, G. A. Splitter. 2004. Comparative wholegenome hybridization reveals genomic islands in Brucella species. J. Bacteriol. 186: 50405051.
184. Rasko, D. A.,, M. R. Altherr,, C. S. Han, and, J. Ravel. 2005. Genomics of the Bacillus cereus group of organisms. FEMS Microbiol. Rev. 29: 303329.
185. Rasko, D. A.,, J. Ravel,, O. A. Okstad,, E. Helgason,, R. Z. Cer,, L. Jiang,, K. A. Shores,, D. E. Fouts,, N. J. Tourasse,, S. V. Angiuoli,, J. Kolonay,, W. C. Nelson,, A. B. Kolsto,, C. M. Fraser, and, T. D. Read. 2004. The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucleic Acids Res. 32: 977988.
186. Ratner, A. J.,, K. R. Hippe,, J. L. Aguilar,, M. H. Bender,, A. L. Nelson, and, J. N. Weiser. 2006. Epithelial cells are sensitive detectors of bacterial pore-forming toxins. J. Biol. Chem. 281: 1299412998.
187. Read, T. D.,, S. N. Peterson,, N. Tourasse,, L. W. Baillie,, I. T. Paulsen,, K. E. Nelson,, H. Tettelin,, D. E. Fouts,, J. A. Eisen,, S. R. Gill,, E. K. Holtzapple,, O. A. Okstad,, E. Helga-son,, J. Rilstone,, M. Wu,, J. F. Kolonay,, M. J. Beanan,, R. J. Dodson,, L. M. Brinkac,, M. Gwinn,, R. T. DeBoy,, R. Madpu,, S. C. Daugherty,, A. S. Durkin,, D. H. Haft,, W. C. Nelson,, J. D. Peterson,, M. Pop,, H. M. Khouri,, D. Radune,, J. L. Benton,, Y. Mahamoud,, L. Jiang,, I. R. Hance,, J. F. Weidman,, K. J. Berry,, R. D. Plaut,, A. M. Wolf,, K. L. Watkins,, W. C. Nierman,, A. Hazen,, R. Cline,, C. Redmond,, J. E. Thwaite,, O. White,, S. L. Salzberg,, B. Thomason,, A. M. Fried-lander,, T. M. Koehler,, P. C. Hanna,, A. B. Kolsto, and, C. M. Fraser. 2003. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423: 8186.
188. Read, T. D.,, S. L. Salzberg,, M. Pop,, M. Shumway,, L. Umayam,, L. Jiang,, E. Holtzapple,, J. D. Busch,, K. L. Smith,, J. M. Schupp,, D. Solomon,, P.