Identification and characterization of microorganisms: DNA-fingerprinting methods

Songklanakarin Journal of Science and Technology

Volumn 35, Issue 4, 2013, Pages

  Fakruddin, Md ^a   Bin Mannan, Khanjada Shahnewaj ^b   Mohammad Mazumdar, Reaz ^c   Chowdhury, Abhijit ^a   Nur Hossain, Md ^a  

^a Bangladesh Council of Scientific and Industrial Research   (Bangladesh)

^b INTERNATIONAL CENTRE FOR DIARRHOEAL DISEASE RESEARCH   (Bangladesh)

^c Bangladesh Council of Scientific and Industrial Research   (Bangladesh)

Author keywords

Fingerprinting; MLST; PFGE; RAPD; RFLP; SSCP

Indexed keywords

EID: 84883343293     PISSN: 01253395     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (67)

1. Ahmed, N., Bal, A., Khan, A. A. et al. 2002. Whole genome fingerprinting and genotyping of multiple drug resistant (MDR) isolates of Pseudomonas aeruginosa from endophthalmitis patients in India. Infect. Genet. Evol. 1, 237-242.
2. Alam, S., Brailsford, S. R., Whiley, R. A. and Beighton, D. 1999. PCR-based methods for genotyping viridans group streptococci. J. Clin. Mimobiol. 37, 2772-2776.
3. Andrighetto, C., Dea, P. D. and Lombardi, A. et al. 1998. Molecular Identification and cluster analysis of homofermantative lactobacilli isolated from Diary products. Res. Microbiol. 149, 631-643.
4. Appuhamy, S., Parton, R., Coote, J. G. and Gibbs, H. A. 1997. Genomic fingerprinting of Haemophilus somnus by a combination of PCR methods. J. Clin. Microbiol. 35, 288-291.
5. Arnold, C., Metherell, L., Clewley, J. P. and Stanley, J. 1999. Predictive fluorescent amplified length polyrnorphism analysis of Esherichia coli: high-resolution typing method with phylogenetic significance. J. Clin. Microbiol. 37, 1274-1279.
6. Busse, H. J., Denner, E. B. M. and Lubitz, W. 1996. Classification and identification of bacteria: current approaches to an old problem. Overview of methods used in bacterial systematics. J. Biotech. 47, 3-38.
7. Cockerill, F. R., Uhl, J. R., Temesg, Z. et al. 1995. Rapid identification of a point mutation of the Mycobacterium tuberculosis catalase-peroxidase (katG) gene associated with isoniazid resistance. J. Infect. Dis. 171, 240-245.
8. Cocolin, L., Manzano, M., Cantoni, C. and Comi, G. 2000. Development of a rapid method for the identification of Lactobacillus spp. isolated from naturally fermented Italian sausages using a polymerase chain reactiontemperature gradient gel electrophoresis. Lett. App. Microbiol. 30, 126-129.
9. Czajka, J., Bsat, N., Piana M. et al. 1993. Differentiation of Listeria monocytogenes and Listeria innocua by 16S genes and intraspecies discrimination of Listeria monocytogenes strains by random amplified polymorphic DNA polymorphisms. Appl. Environ. Microbiol. 59, 304-308.
10. Daly, M., Power, E., Bjorkroth, J. et al. 1999. Molecular analysis of Pseudomonas aeruginosa epidemiological investigation of mastitis outbreaks in Irish dairy herds. Appl Environ Microbiol. 65, 2723-2729.
11. De Bruijn, F. J. 1992. Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergenic consbnsus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. Appl. Environ. Microbiol. 58, 2180-2187.
12. Enright, M. C. and Spratt, B. G. 1998. A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Microbiology. 144, 3049-3060.
13. Enright, M. C., Fenoll, A., Griffiths, D. and Spratt, B. G. 1999. The three major Spanish clones penicillin-resistant Streptococcus pneumoniae are the most common clones recovered recent cases of meningitis in Spain. J. CIin. Microbiol. 37, 3210-3216.
14. Fornasini, M., Reeves, R. R., Murray B. E. et al. 1992. Trimethoprim resistant Escherichia coli in households of children attending day care centers. J. Infect Dis. 166, 326-330.
15. Garcia, J. A., Dominguez, L., Larsen, J. L. and Pedersen, K. 1998. Ribotyping and plasmid profiling of Yersinia ruckeri. J. Appl. Microbiol. 85, 949-955
16. Gibson, J. R., Slater, E., Xery, J., Tompkins, D. S. and Owen, R. J. 1998. Use of an amplified fragment length polymorphism technique to fingerprint and differentiate isolates of Helicobacter pylori. J. Clin. Microbiol. 36, 2580-2585.
17. Goulding, J. N., Stanley, J., Saunders, N., and Arnold, C. 2000. Genome-sequence-based fluorescent amplified fragment length polymorphism analysis of Mycobacterium tuberculosis. J Clin Microbiol. 38, 1121-1126
18. Grimont, F., Verger, J. M., Cornelis, P. et al. 1992. Molecular typing of Brucella with cloned DNA probes. Res. Microbiol. 143, 55-65.
19. Gurtler, 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
20. Hamill, R. J., Houston, E. D., Georghiou, P. R. et al. 1995. An outbreak of Burkholderia (formerly pseudomonas) cepacia respiratory tract colonization and infection associated with nebulized albuterol therapy. Ann. Intern. Med. 122, 762-766
21. Hulton, C. S. J., Higgins, C. F. and Sharp, P. M. 1991. ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium, and other enterobacteria. Mol. Microbiol. 5, 825-834.
22. Janssen, P., Coopman, R., Huys, G. et al. 1996. Evaluation of the DNA fingerprinting method AFLP as a new tool in bacterial taxonomy. Microbiology. 142, 1881-1893
23. Janssen, P., Maquelin, K., Coopman R. et al. 1997. Discrimination of Acinetobocter genomic species by AFLP fingerprinting. Int. J. Syst. Bacteriol. 47, 1119-1187.
24. Jersek, B., Gilot, P., Gubina, M. et al. 1999. Typing of Listeria monocytogenes strains by repetitive elements sequence-based PCR. J. CIin. Microbiol. 37, 103-109
25. Jordens, J. Z. and Leaves, N. I. 1997. Source of variation detected in ribotyping patterns of Haemophilus influenzae comparison of traditional ribotyping, PCRribotyping and rDNA restriction analysis. J. Med Microbiol. 46, 763-772
26. Kim, B. J., Kim, S. Y., Park B. H. et al. 1997. Mutations in the rpoB gene of Mycobacterium tuberculosis that interfere with PCR-single strand conformation polymorphism analysis for rifampicin susceptibility testing. J Clin. Microbiol. 35, 492-494
27. Koeleman, J. G. M., Stoof, J., Biesmans, D. J. et al. 1998. Comparison of amplified ribosomal DNA restriction analysis, random amplified polymorphic DNA analysis and amplified fragment length polymorphism fingerprinting for identification of Acinetobacter genomic species and typing of Acinetobacter baumannii. J. CIin. Microbiol. 36, 2522-2529.
28. Kostman, J. R., Alden, M. B., Mair M. et al. 1995. A universal approach to bacterial molecular epidemiology by polymerase chain reaction ribotyping. J. Infect. Dis. 171, 204-208.
29. Kumar, A., Dietrich, S., Schneider, W. et al. 1997. Genetic relatedness of Burkholderia (Pseudomonas) cepacia isolates from five cystic fibrosis centers in Michigan. Respiratory Med. 9l, 485-492.
30. Lagatolla, C., Dolzani, L., Tonin, E. et al. 1996. PCR ribotyping for isolates of different serotypes. J. Clin. Microbiol. 34, 2440-2443
31. Lobato, M. J., Landeras, E., Gonzalez-Hevia, M. A. and Mendoza, M. C. 1998. Genetic heterogeneity of clinical strains of Yersinia enterocolitica traced by ribotyping and relationships between ribotypes, serotypes and biotypes. J. CIin. Microbiol. 36, 3297-3302
32. Loutit, J. S. and Tompkins, L. S. 1991. Restriction enzyme and Southern hybridization analyses of Pseudomonas aeruginosa strains from patients with cystic fibrosis. J. Clin. Microbiol. 29, 2897-2900.
33. Madden, R. H., Moran L. and Scates, P. 1996. Sub-typing of animal and human Campylobacter spp. using RAPD. Lett. App. Microbiol. 23, 167-170.
34. Maiden, M. C. J., Bygrives, J. A., Feil, E. et al. 1998. Muitilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl Acad. Sci. USA. 95, 3140-3145.
35. Marshall, S., Clark, C. G., Wang G. et al. 1999. Comparison of molecular methods for typing Vibrio parahaemolyticus. J. Clin. Microbiol. 37, 2473-2478.
36. Najdenski, H., Iteman, L. and Carniel, F. 1994. Efficient subtlping of pathogenic Yersinia enterocolitica strains by Pulsed-field Gel Electrophoresis, J. CIin. Microbiol. 32, 2913-2920.
37. Newcombe, J., Dyer, S., Blackwell L. et al. 1997. PCR-singlestranded conformational polymorphism analysis for non-culture-based subtyping of meningococcal strains in clinical specimens, J. Clin. Microbiol. 35, 1809-1812.
38. Owen, R. J., Fitzgerald, C., Sutherland, K. and Borman, P. 1994. Flaggellin qene polymorphism analysis of Campylobacter jejuni infecting man and other host and comparison with biotyping and somatic antigen serotyping. Epidemiol. Infect. 113, 221-234
39. Pfaller, M. A., Wakefield, D. S., Hollis, R. et al. 1991. The clinical microbiology laboratory as an aid in infection control. The application of molecular techniques in epidemiologic studies of methicillin resistant Staphylococcus aureus. Diagn. Microbiol. Infect. Dis. 14, 209-214
40. Poh, C. L. and Lau, Q. C. 1993. Subtyping of Neisseria gonorrhoeae auxotype-serovar groups by pulsedfield gel electrophoresis. J. Med. Microbiol. 38, 366-370.
41. Ragimberbeau, C., Salvat, G., Colin, P. and Ermel, G. 1998. Development of a multiplex PCR gene fingerprinting method using gyrA and pflA polymorphisms to identify genotypic relatedness within Campylobacter jejuni species. J. Appl. Microbiol. 85, 829-838
42. Reboli, A. C., Houston, E. D., Monteforte, J. S., Wood, C. A. and Hamill, R. J. 1994. Discrimination of epidemic and sporadic isolates of. Acinetobacter baumannii by repetitive element PCR mediated DNA fingerprinting. J. Clin. Microbiol. 32, 2635-2640.
43. Sambrook, J., Fritsch, E. F. and Maniatis, T. 1989. Molecular Cloning-A Laboratory Manual. 2nd ed, Cold Spring Harbor, NY: Cold Spring Harbor Press.
44. Savelkoul, P. H. M., Aarts, H. J. M., Haas J. D. et al. 1999. Amplified-length fragment polyrnorphism: the state of an art. J. Clin. Microbiol. 37, 3083-3091.
45. Schaberg, D. R., Tompkins, L. S. and Falkow, S. 1981. Use of agarose gel electrophoresis of plasmid deoxyribonucleic acid to fingerprint gram-negative bacilli. J. Clin. Microbiol. 13, 1105-1110
46. Schmitz, F. J., Steiert, M., Tichy, H. V. et al. 1998. Typing of methicillin-resistant Staphylococcus aureus isolates from Dusseldorf by six genotypic methods. J. Med. Microbiol. 47, 341-351.
47. Schwartz, D. C., and Cantor, C. R. 1984. Separation of yeast chromosome sized DNAs by pulsed field gradient gel electrophoresis. Cell 37, 67-15.
48. Sharples, G. J. and Lloyd, R. G. 1990. A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes. Nucleic Acids Res. 18, 6503-6508
49. Shi, Z. Y., Liu, PY-F., Lau Y-J. et al. 1997. Use of pulsed-field gel electrophoresis to investigate an outbreak of Serratia marcescens. J. Clin. Microbiol. 35, 325-327.
50. Stern, M. J., Ames, G. F. L., 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.
51. Stubbs, S. L., Brazier, J. S., O'Neill, G. L. and Duerden, B. I. 1999. PCR targeted to the 16S-23S rRNA gene intergenic spacer region of Clostridium difficile and construction of a library consisting of 116 different PCR ribotypes. J. Clin. Microbiol. 37, 461-463
52. Talukder, K. A., Dutta, D. and Albert, M. J. 1999. Evaluation of pulsed-field gel electrophoresis for typing of Shigella dysenteriae type 1. J. Med. Microbiol. 48, 78l-784.
53. Tannock, G. W., Timisjarvi, A. T. and Rodtong, S. 1999. Identification of Lactobacillus isolates from the gastrointestinal tract, silage and yoghurt by 16S-23S rRNA gene intergenic spacer region sequence comparisons. App. Environ. Microbiol. 65(9), 4264-4267.
54. Tenover, F. C. 1985. Plasmid fingerprinting a tool for bacterial strain identification and surveillance of nosocomial and community acquired infections. Clin. Lab Med. 5, 413-436.
55. Tram, C., Simonet, M., Nicolas, M. H. et al. 1990. Molecular typing of nosocomial isolates of Legionella pneumophilia serogroup 3. J. Clin. Microbiol. 28, 242-245.
56. Tyler, K. D., Wang, G., Tyler, S. D. and Johnson, W. M. 1997. Factors affecting relability and reproducibility of amplification-based DNA fingerprinting of representative bacterial pathogens. J. Clin. Microbiol. 35, 339-346.
57. van Belkum, A., Maas, H., Verbrugh, H. and Van Leeuwen, N. 1996. Serotyping, ribotyping, PCR mediated ribosomal 16S-23S spacer analysis and arbitrarily primed PCR for epidemiological studies on Legionella pneumophila. Microbiology. l47, 405-413.
58. van Embden, J. D. A., Cave, M. D., Craufort, J.T. et al. 1993. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J. Clin. Microbiol. 31, 406-409
59. Versalovic, J., Koeuth, T. and Lupski, J. R. 1991. Distribution of repetitive of DNA sequences in Eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 19, 6823-6831.
60. Vos, P., Hogers, R., Bleeker, M. et al. 1995. AFLP: a new concept for DNA fingerprinting. Nucleic Acids Res. 21, 4407-4414
61. Warner, J. M. and Oliver, J. D. 1999. Randomly amplified polymorphic DNA analysis of clinical and environmental isolates of Vibrio vulnificus and other Vibrio species. App. Environ. Microbiol. 65, 1141-1144.
62. Welsh, J. and McClelland, M. 1990. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 18, 7213-7218.
63. Welsh, J. and McClelland, M. 1993. The characterization of pathogenic microorganisms by genomic fingerprinting using arbitrarily primed polymerase chain reaction (AP-PCR). In Diagnostic Molecular Microbiology (eds. Persing D. H. et al.) washington: ASM press. pp. 595-602.
64. Williams, J. G. K., Kubelik, A. R., Lival, K. J. et al. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18, 6531-6535.
65. Woods, C. R., Versalovic, J., Koeuth, T. and Lupski, J. R. 1992. Analysis of relationships among isolates of Citrobacter diversus by using DNA fingerprints generated by repetitive sequence based primers in polymerase chain reaction. J. CIin. Microbiol. 30, 2921-2929.
66. Yakubu, D. E. and Pennigton, T. H. 1995. Epidemiological evaluation of Neisseria meningitidis serogroup B by pulse-field gel electrophoresis. FEMS Immunol. Med. Microbiol. 10, 185-189.
67. Young, K. A., Power, E. G., Dryden, M. S. et al. 1994. RAPD typing of clinical isolates of Staphylococcus haemolyticus. Lett. Appl. Microbiol. 18, 86-89.