The importance of virulence prediction and gene networks in microbial risk assessment

Human and Ecological Risk Assessment

Volumn 13, Issue 2, 2007, Pages 254-268

  Wassenaar, Trudy M ^a   Gamieldien, Junaid ^a   Shatkin, Joanne ^b   Luber, Petra ^c   Moyer, Nelson ^b   Carpenter, Tom ^d   Ussery, David W ^e  

^a Molecular Microbiology and Genomics Consultants   (Germany)

^b Cadmus Group Inc   (United States)

^c Federal Office of Consumer Protection and Food Safety   (Germany)

^d U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

^e TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

Emerging pathogens; Gene networks; Pathogenicity; Virulence gene recognition

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 33947370322     PISSN: 10807039     EISSN: 15497860     Source Type: Journal    
DOI: 10.1080/10807030701226855     Document Type: Review

References (45)

1. Alm RA, Ling LS, Moir DT, et al. 1999. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397:176-80
2. Altschul SF, Gish W, Miller W, et al. 1990. Basic local alignment search tool. J Mol Biol 215:403-10
3. Azad RK and Borodovsky M. 2004. Probabilistic methods of identifying genes in prokaryotic genomes: Connections to the HMM theory. Brief Bioinform 5:118-30
4. Becker D, Selbach M, Rollenhagen C, et al. 2006. Robust Salmonella metabolism limits possibilities for new antimicrobials. Nature 440:303-7
5. Bendtsen JD, Binnewies TT, Hallin PF, et al. 2005. Genome update: Prediction of secreted proteins in 225 bacterial proteomes. Microbiology 151:1725-7
6. Benton BM, Zhang JP, Bond S, et al. 2004. Large-scale identification of genes required for full virulence of Staphylococcus aureus. J Bacteriol 186:8478-89
7. Boerlin P, McEwen SA, Boerlin-Petzold F, et al 1999. Associations between virulence factors of Shiga toxin-producingEscherichia coli and disease in humans. J Clin Microbiol 37:497-503
8. Cassin MH, Lammerding AM, Todd ECD, et al. 1998. Quantitative risk assessment for Es-cherichia coli O157:H7 in ground beef hamburgers. IntJ Food Microbiol 41:21-44
9. Chain P, Kurtz S, Ohlebusch E, et al. 2003. An applications-focused review of comparative genomics tools: Capabilities, limitations and future challenges. Brief Bioinform 4:105-23
10. Davis MA, Hancock DD, and Besser TE. 2002. Multiresistant clones of Salmonella enterica: The importance of dissemination. J Lab Clin Med 140:135-41
11. Dorman CJ. 2004. H-NS: A universal regulator for a dynamic genome. Nat Rev Microbiol 2:391-400
12. Dougan G, Hormaeche CE, and Maskell DJ. 1987. Live oral Salmonella vaccines: Potential use of attenuated strains as carriers of heterologous antigens to the immune system. Parasite Immunol 9:151-60
13. Falkow S. 1988. Molecular Koch's postulates applied to microbial pathogenicity. Rev Infect Dis 10:S274-6
14. Field D and Hughes J. 2005. Cataloguing our current, genome collection. Microbiology 151:1016-9
15. Finlay BB and Falkow S. 1989. Common themes in microbial pathogenicity. Microbiol Rev 53:210-30
16. Finlay BB and Falkow S. 1997. Common themes in microbial pathogenicity revisited. Microbiol Mol Biol Rev 61:136-69
17. Fleischmann RD, Adams MD, White O, et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512
18. Fouts DE, Mongodin EF, Mandrell RE, et al. 2005. Major structural differences and novel potential virulence mechanisms from the genomes of multiple Campylobacter species PLoS Biol 3:e15
19. Fraser CM, Casjens S, Huang WM, et al. 1997. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390:580-6
20. Gaynor EC, Cawthraw S, Manning G, et al. 2004. The genome-sequenced variant of Campylobacter jejuni NCTC 11168 and the original clonal clinical isolate differ markedly in colonization, gene expression, and virulence-associated phenotypes. J Bacteriol 186:503-17; Erratum in: J Bacteriol 2004 186:8159
21. Goodner B, Hinkle G, Gattung S, et al. 2001. Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 294:2323-8
22. Harrison A, Dyer DW, Gillaspy A, et al. 2005. Genomic sequence of an otitis media isolate of nontypeable Haemophilus influenzae: Comparative study with H. influenzae serotyped, strain KW20. J Bacteriol 187:4627-36
23. Hayashi T, Makino K, Ohnishi M, et al. 2001. Complete genome sequence of enterohemorrhagic Eschetichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res 8:11-22
24. Hussein HS and Sakuma T. 2005. Prevalence of shiga toxin-producing Escherichia coli in dairy cattle and their products. J Dairy Sci 88:450-5
25. Jaffe JD, Stange-Thomann N, Smith C, et al 2004. The complete genome and proteome of Mycoplasma mobile. Genome Res 14:1447-61
26. Jenkins TM, Scott TM, Cole JR, et al. 2004. Assessment of virulence-factor activity relationships (VFARs) for waterborne diseases. Water Sci Technol 50:309-14
27. Kill K, Binnewies TT, Sicheritz-Ponten T, Willenbrock H, et al. 2005. Genome update: Sigma factors in 240 bacterial genomes. Microbiology 151:3147-5
28. Kirschner D, DeRita V, and Flynn J. 2005. Overcoming math anxiety: Matlthus meets Koch. ASM News 71:357-62
29. Maurelli AT, Fernández RE, Block CA, et al 1998. "Black holes" and bacterial pathogenicity: A large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli. Proc Natl Acad Sci USA 95:3943-8
30. Newell DG. 2001. Animal models of Campylobacter jejuni colonization and disease and the lessons to be learned from similar Helicobacter pylon models. Symp Ser Soc Appl Microbiol 30:57S-67S
31. Palmer SR, Gully PR, White JM, et al. 1983. Water-borne outbreak of Campylobader gastroenteritis. Lanceti (8319):287-90
32. Parkhill J, Wren BW, Mungall K, et al. 2000. The genome sequence of the food-borne pathogen Campylobader jejuni reveals hypervariable sequences. Nature 403:665-8
33. Perna NT, Plunkett G, Burland V, et al. 2001. Genome sequence of enterohaemorrhagic Escherichia coli. O157:H7. Nature 409:529-33. Erratum in: Nature 2001, 410:240
34. Pichon C and Felden B. 2005. Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains. Proc Natl Acad Sci USA 102:14249-54
35. Roberts A, Chan Y, and Wiedmann M. 2005. Definition of genetically distinct attenuation mechanisms in naturally virulence-attenuated Listeria monocytogenes by comparative cell culture and molecular characterization. Appl Environ Microbiol 71:3900-10
36. Rosenquist H, Nielsen NL, Sommer HM, et al. 2003. Quantitative risk assessment of human campylobacteriosis associated with thermophilic Campylobacter species in chickens. Int J Food Microbiol 83:87-103
37. Schattner P, Brooks AN, and Lowe TM. 2005. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 1 (33) [Web Server issue]: W686-9
38. Schlundt J. 2000. Comparison of microbial risk assessment studies published. Int J Food Microbiol 58:197-202
39. Tomb J-F, White O, Kerlavage AR, et al. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388:539-47
40. Ussery DW and Hallin PF. 2004. Genome update: Annotation quality in sequenced microbial genomes. Microbiology 150:2015-7
41. Wassenaar TM. 2004. Risk assessment prediction from genome sequences, promises and dreams. J Food Protect 67:2053-7
42. Wassenaar TM and Gaastra W. 2001. Bacterial virulence, where to draw a line? FEMS Microbiol Lett 201:1-7
43. Wassenaar TM and Meinersmann RJ. 2003. The TGA stop codon and the phylogeny of the selenocysteine pathway. Genome Lett 2:127-38
44. Welch RA, Burland V, Plunkett G, et al. 2002. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escheiichia coli. Proc Natl Acad Sci USA 99:17020-4
45. Wong HC, Shen CT, Chang CN, et al. 2004. Biochemical and virulence characterization of viable but nonculturable cells of Vibrio parahaemolyticus. J Food Prot 67:2430-5