Forensic Genetic Analysis of Microorganisms: Overview of Some Important Technical Concepts and Selected Genetic Typing Methods

Microbial Forensics

Volumn , Issue , 2005, Pages 233-249

  Cooke, Charles L ^a  

^a DEFENSE THREAT REDUCTION AGENCY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33744522021     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-012088483-4/50015-9     Document Type: Chapter

References (46)

1. SP Lane, TJ Beugelsdijk and CKN Patel (Eds) (2001) Firepower in the Lab: Automation in the Fight Against Infectious Disease Washington, DC: Joseph Henry Press 203-213
2. RA Falkenrath, RD Newman and BA Thayer (Eds) (1999) America's Achilles' Heel: Nuclear, Biological and Chemical Terrorism and Covert Attack Cambridge, Massachusetts: The MIT Press 261-336
3. D Brown (1993) The Secret of Life: Untwisting Genetic Mysteries. Washington Post B1. September 25
4. Editorial (1997) Dealing with Dolly. Washington Post A24. May 22
5. CA Cummings and DA Relman (2002) Microbial forensics-“cross examining pathogens”. Science 296 1976-1979
6. B Budowle, J Smith, T Moretti and J DiZinno (2000) DNA Typing Protocols: Molecular Biology and Forensic Analysis. Biotechniques Books, Eaton Publishing
7. A Van Belkum, M Struelens, A De Visser, H Verbrugh and M Tibayrenc (2001) Role of genomic typing in taxonomy, evolutionary genetics and microbial epidemiology. Clin Microbiol Rev 14 547-560
8. L Dijkshoorn, B Ursing and J Ursing (2000) Strain, clone and species: Comments on three basic concepts of bacteriology. J Med Microbiol 49 397-401
9. R Lan and P Reeves (2001) When does a clone deserve a name? A perspective on bacterial species based on population genetics. Trends in Microbiol 9 419-424
10. W Fitch, W Brisse, J Stevens and M Tibayrenc (2000) Infectious diseases and the golden age of phylogenetics: An E-debate. Infection, Genetics and Evolution 1 69-74
11. P Tenover, R Arbeit, R Goering, P Mickelsen, B Murray, D Persing and B Swaminathan (1995) Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: Criteria for bacterial strain typing. J Clin Microbiol 33 2233-2239
12. J Giesecke (2002) Modern Infectious Disease Epidemiology. 2nd ed. New York, NY: Arnold Publishing 160-175
13. H Lodish, A Berk, S Zipursky, P Matsudaira, D Baltimore and J Darnell (2000) Mol Cell Biol. 4th ed. New York, NY: W.H. Freeman
14. A Van Belkum, S Scherer, L Van Alphen and H Verbrugh (1998) Short-sequence DNA repeats in prokaryotic genomes. Micro Mol Biol Rev 62 275-293
15. S Flint, L Enquist, R Krug, V Racaniello and A Skalka (2000) Principles of Virology: Molecular Biology, Pathogenesis and Control. Washington, DC: ASM Press
16. R Lewis (2002) SNPs as windows on evolution. The Scientist 16 16-18
17. T Read, S Salzberg, M Pop, M Shumway, L Umayam, L Jiang, E Holtzapple, J Busch, K Smith, J Schupp, D Solomon, P Keim and C Fraser (2002) Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 296 2028-2033
18. L Snyder and W Champness (2003) Molecular Genetics of Bacteria. 2nd ed. Washington, DC: ASM Press
19. B Glick and J Pasternak (1998) Molecular Biotechnology: Principles and Applications of Recombinant DNA Technology. 2nd ed. Washington, DC: ASM Press
20. K Mullis, F Faloona, S Scharf, R Saiki, G Horn and H Erlich (1986) Specific enzymatic amplification of DNA in vitro: The polymerase chain reaction. Cold Spring Harbor Symp Quant Bio 51 263-273
21. RK Saiki, DH Gelfand, S Stoffel, SJ Scharf, R Higuchi, GT Horn, KB Mullis and HA Erlich (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239 487-491
22. M Nei and S Kumar (2000) Molecular Evolution and Phylogenetics. New York, NY: Oxford University Press
23. M Maiden, J Bygraves, E Feil, G Morelli, J Russell, R Urwin, Q Zhang, J Zhou, K Zurth, D Caugant, I Feavers, M Achtman and B Spratt (1998) Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95 3140-3145
24. C Salcedo, L Arreaza, B Alcala, L De La Fuente and J Vazquez (2003) Development of a multilocus sequence typing method for analysis of Listeria monocytogenes clones. J Clin Microbiol 41 757-762
25. A Noller, M McEllistrem, O Stine, J Morris, D Boxrud, B Dixon and L Harrison (2003) Multilocus sequence typing reveals lack of diversity among Escherichia coli O157:H7 isolates that are distinct by pulsed-field gel electrophoresis. J Clin Microbiol 41 675-679
26. H Grundmann, S Hori, M Enright, C Webster, A Tami, E Feil and T Pitt (2002) Determining the genetic structure of the natural population of Staphlococcus aureus: A comparison of multilocus sequence typing with pulsed-field gel electrophoresis, randomly amplified polymorphic DNA analysis and phage typing. J Clin Microbiol 40 4544-4546
27. L Price, M Hugh-Jones, P Jackson and P Keim (1999) Genetic diversity in the protectice antigen gene of Bacillus anthracis. J Bacteriol 181 2358-2362
28. B Swaminathan, T Barret, S Hunter and R Tauxe CDC PulseNet Task Force (2001) PulseNet: The molecular subtyping network for foodborne bacterial disease surveillance, United States. Emerg Infect Dis 7 382-389
29. J Cole, B Chai, T Marsh, R Farris, Q Wang, S Kulman, S Chandra, D McGarrell, T Schmidt, G Garrity and J Tiedje (2003) The Ribosomal Database Project (RDP-II): Previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31 442-443
30. K Aarnisalo, T Autio, A Sjoberg, J Lunden, H Korkeala and M Suihko (2003) Typing of Listeria monocytogenes isolates originating from the food processing industry with automated ribotyping and pulsed-field gel electrophoresis. J Food Prot 66 249-255
31. B Schalch, L Bader, H Schau, R Bergmann, A Rometsch, G Maydl and S Kessler (2003) Molecular typing of Chlostridium perfringens from a food-borne disease outbreak in a nursing home: Ribotyping versus pulsed-field gel electrophoresis. J Clin Microbiol 41 892-895
32. C Clark, T Kruk, L Bryden, Y Hirvi, R Ahmed and F Rodgers (2003) Subtyping of Salmonella enterica serotype Enteritidis strains by manual and automated PstI-SphI ribotyping. J Clin Microbiol 41 27-33
33. P Vos, R Hogers, M Bleeker, M Reijans, T van de Lee, A Frijters, J Pot, J Peleman, M Kuiper and M Zabeau (1995) AFLP: A new technique for DNA fingerprinting. Nucleic Acids Res 23 4407-4414
34. P Keim, A Kalif, J Schupp, K Hill, S Travis, D Richmond, M Adair, M Hugh-Jones, C Kuske and P Jackson (1997) Molecular evolution and diversity in Bacillus anthracis as detected by amplified fragment length polymorphism markers. J Bacteriol 179 818-824
35. P Jackson, K Hill, M Laker, L Ticknor and P Keim (1999) Genetic comparison of Bacillus anthracis and its close relatives using amplified fragment length polymorphism and polymerase chain reaction analysis. J Appl Microbiol 87 263-269
36. P Keim, L Price, A Klevytska, L Price, G Zinser, K Smith, M Hugh-Jones, R Okinaka, K Hill and P Jackson (1999) Molecular diversity in Bacillus anthracis. J Appl Microbiol 87 215-217
37. L Ticknor, A Koltso, K Hill, P Keim, M Laker, M Tonks and P Jackson (2001) Fluorescent amplified fragment length polymorphism analysis of Norwegian Bacillus cereus and Bacillus thuringiensis soil isolates. Appl Environ Microbiol 67 4863-4873
38. S Jiang, V Louis, N Choopun, A Sharma, A Huq and R Colwell (2000) Genetic diversity of Vibrio cholerae in Chesapeake Bay determined by amplified fragment length polymorphism fingerprinting. Appl Environ Microbiol 66 140-147
39. J Coopman, G Huys, J Swings, M Bleeker, P Vos, M Zabeau and K Kersters (1996) Evaluation of the DNA fingerprinting method AFLP as an new tool in bacterial taxonomy. Microbiol 142 1881-1893
40. P Keim, L Price, A Klevytska, K Smith, J Schupp, R Okinaka, P Jackson and M Hugh-Jones (2000) Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis. J Bacteriol 182 2928-2936
41. A Klevytska, L Price, J Schupp, P Worsham, J Wong and P Keim (2001) Identification and characterization of variable-number tandem repeats in the Yersinia pestis genome. J Clin Microbiol 39 3179-3185
42. J Farlow, K 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 3186-3192
43. M Arens (1999) Methods for subtyping and molecular comparison of human viral genomes. Clin Microbiol Rev 12 612-626
44. D Sol (2000) The ins and outs of DNA fingerprinting the infectious fungi. Clin Microbiol Rev 13 332-370
45. J Taylor, D Geiser, A Burt and V Koufopanou (1999) The evolutionary biology and population genetics underlying fungal strain typing. Clin Microbiol Rev 12 126-146
46. A Constans (2003) The state of the microarray. The Scientist 17 34-39