Use of multiple-displacement amplification and checkerboard DNA-DNA hybridization to examine the microbiota of endodontic infections

Journal of Clinical Microbiology

Volumn 45, Issue 9, 2007, Pages 3039-3049

  Brito, L C N ^b   Teles, F R ^a,c   Teles, R P ^a   Franca E C ^b   Ribeiro Sobrinho, A P ^b   Haffajee, A D ^a   Socransky, S S ^a  

^a FORSYTH INSTITUTE   (United States)

^b FEDERAL UNIVERSITY OF MINAS GERAIS   (Brazil)

^c HARVARD SCHOOL OF DENTAL MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACINETOBACTER BAUMANNII; ADOLESCENT; ADULT; AGED; ARTICLE; BACTERIAL COLONIZATION; BACTERIAL GENOME; BACTERIUM IDENTIFICATION; BRAZIL; CHECKERBOARD DNA DNA HYBRIDIZATION; DIAGNOSTIC VALUE; DNA DNA HYBRIDIZATION; DNA PROBE; GENE AMPLIFICATION; HUMAN; MAJOR CLINICAL STUDY; MULTIPLE DISPLACEMENT AMPLIFICATION; NONHUMAN; PREVOTELLA ORIS; PREVOTELLA TANNERAE; PRIORITY JOURNAL; SCHOOL CHILD; SPECIES IDENTIFICATION; TAXON; TOOTH INFECTION; WILCOXON SIGNED RANKS TEST;

ADOLESCENT; ADULT; AGED; AGED, 80 AND OVER; BACTERIA; BACTERIAL INFECTIONS; BACTERIOLOGICAL TECHNIQUES; BIODIVERSITY; CHILD; COLONY COUNT, MICROBIAL; HUMANS; MIDDLE AGED; NUCLEIC ACID AMPLIFICATION TECHNIQUES; NUCLEIC ACID HYBRIDIZATION; TOOTH DISEASES;

ACINETOBACTER BAUMANNII; BACTERIA (MICROORGANISMS); PREVOTELLA ORIS; PREVOTELLA TANNERAE;

EID: 34548703815     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.02618-06     Document Type: Article

References (64)

1. Aas, J. A., B. J. Paster, L. N. Stokes, I. Olsen, and F. E. Dewhirst. 2005. Defining the normal bacterial flora of the oral cavity. J. Clin. Microbiol. 43:5721-5732.
2. Afzal-Shah, M., and D. M. Livermore. 1998. Worldwide emergence of carbapenem-resistant Acinetobacter spp. J. Antimicrob. Chemother. 41:576-577.
3. Andres, O., A. C. Ronn, A. Ferrando, M. Bosch, and X. Domingo-Roura. 2006. Sequence quality is maintained after multiple displacement amplification of non-invasively obtained macaque semen DNA. Biotechnol. J. 1:466-469.
4. Baumgartner, J. C., and W. A. Falkler, Jr. 1991. Bacteria in the apical 5 mm of infected root canals. J. Endod. 17:380-383.
5. Baumgartner, J. C., S. U. Khemaleelakul, and T. Xia. 2003. Identification of spirochetes (treponemes) in endodontic infections. J. Endod. 29:794-797.
6. Bradshaw, D. J., P. D. Marsh, G. K. Watson, and C. Allison. 1998. Role of Fusobacterium nucleatum and coaggregation in anaerobe survival in planktonic and biofilm oral microbial communities during aeration. Infect. Immun. 66:4729-4732.
7. Cisneros, J. M., M. J. Reyes, J. Pachon, B. Becerril, F. J. Caballero, J. L. Garcia-Garmendia, C. Ortiz, and A. R. Cobacho. 1996. Bacteremia due to Acinetobacter baumannii: epidemiology, clinical findings, and prognostic features. Clin. Infect. Dis. 22:1026-1032.
8. Conrads, G., S. E. Gharbia, K. Gulabivala, F. Lampert, and H. N. Shah. 1997. The use of a 16s rDNA directed PCR for the detection of endodontopathogenic bacteria. J. Endod. 23:433-438.
9. Corbella, X., M. Pujol, M. A. Dominguez, J. Ayats, M. J. Argerich, F. Garrigosa, J. Ariza, and F. Gudiol. 2000. Emergence and rapid spread of carbapenem resistance during a large and sustained hospital outbreak of multiresistant Acinetobacter baumannii. J. Clin. Microbiol. 38:4086-4095.
10. da Silva, G. J., G. J. Leltao, and L. Peixe. 1999. Emergence of carbapenem-hydrolyzing enzymes in Acinetobacter baumannii clinical isolates. J. Clin. Microbiol. 37:2109-2110.
11. Dean, F. B., S. Hosono, L. Fang, X. Wu, A. F. Faruqi, P. Bray-Ward, Z. Sun, Q. Zong, Y. Du, J. Du, M. Driscoll, W. Song, S. F. Kingsmore, M. Egholm, and R. S. Lasken. 2002. Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl. Acad. Sci. USA 99:5261-5266.
12. de Souza, C. A., R. P. Teles, R. Souto, M. A. Chaves, and A. P. Colombo. 2005. Endodontic therapy associated with calcium hydroxide as an intracanal dressing: microbiologic evaluation by the checkerboard DNA-DNA hybridization technique. J. Endod. 31:79-83.
13. Dewhirst, F. E., M. A. Tamer, R. E. Ericson, C. N. Lau, V. A. Levanos, S. K. Boches, J. L. Galvin, and B. J. Paster. 2000. The diversity of periodontal spirochetes by 16S rRNA analysis. Oral Microbiol. Immunol. 15:196-202.
14. Didilescu, A. C., N. Skaug, C. Marica, and C. Didilescu. 2005. Respiratory pathogens in dental plaque of hospitalized patients with chronic lung diseases. Clin. Oral Investig. 9:141-147.
15. Dymock, D., A. J. Weightman, C. Scully, and W. G. Wade. 1996. Molecular analysis of microflora associated with dentoalveolar abscesses. J. Clin. Microbiol. 34:537-542.
16. Farber, P. A., and S. Seltzer. 1988. Endodontic microbiology. I. Etiology. J. Endod. 14:363-371.
17. Feinberg, A. P., and B. Vogelstein. 1983. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132:6-13.
18. Foschi, F., J. Izard, H. Sasaki, V. Sambri, C. Prati, R. Muller, and P. Stashenko. 2006. Treponema denticola in disseminating endodontic infections. J. Dent. Res. 85:761-765.
19. Fouad, A. F., J. Barry, M. Caimano, M. Clawson, Q. Zhu, R. Carver, K. Hazlett, and J. D. Radolf. 2002. PCR-based identification of bacteria associated with endodontic infections. J. Clin. Microbiol. 40:3223-3231.
20. Gatti, J. J., J. M. Dobeck, C. Smith, R. R. White, S. S. Socransky, and Z. Skobe. 2000. Bacteria of asymptomatic periradicular endodontic lesions identified by DNA-DNA hybridization. Endod. Dent. Traumatol. 16:197-204.
21. Go, E. S., C. Urban, J. Burns, B. Kreiswirth, W. Eisner, N. Mariano, K. Mosinka-Snipas, and J. J. Rahal. 1994. Clinical and molecular epidemiology of acinetobacter infections sensitive only to polymyxin B and sulbactam. Lancet 344:1329-1332.
22. Gomes, B. P., R. C. Jacinto, E. T. Pinheiro, E. L. Sousa, A. A. Zaia, C. C. Ferraz, and F. J. Souza-Filho. 2005. Porphyromonas gingivalis, Porphyromonas endodontalis, Prevotella intermedia and Prevotella nigrescens in endodontic lesions detected by culture and by PCR. Oral Microbiol. Immunol. 20:211-215.
23. Gomes, B. P., E. T. Pinheiro, C. R. Gade-Neto, E. L. Sousa, C. C. Ferraz, A. A. Zaia, F. B. Teixeira, and F. J. Souza-Filho. 2004. Microbiological examination of infected dental root canals. Oral Microbiol. Immunol. 19:71-76.
24. Haapasalo, M. 1989. Bacteroides spp. in dental root canal infections. Endod. Dent. Traumatol. 5:1-10.
25. Haffajee, A. D., A. Bogren, H. Hasturk, M. Feres, N. J. Lopez, and S. S. Socransky. 2004. Subgingival microbiota of chronic periodontitis subjects from different geographic locations. J. Clin. Periodontol. 31:996-1002.
26. Haffajee, A. D., M. A. Cugini, S. Dibart, C. Smith, R. L. Kent, Jr., and S. S. Socransky. 1997. The effect of SRP on the clinical and microbiological parameters of periodontal diseases. J. Clin. Periodontol. 24:324-334.
27. Hsueh, P. R., M. L. Chen, C. C. Sun, W. H. Chen, H. J. Pan, L. S. Yang, S. C. Chang, S. W. Ho, C. Y. Lee, W. C. Hsieh, and K. T. Luh. 2002. Antimicrobial drug resistance in pathogens causing nosocomial infections at a university hospital in Taiwan, 1981-1999. Emerg. Infect. Dis. 8:63-68.
28. Jung, I. Y., B. Choi, K. Y. Kum, Y. J. Yoo, T. C. Yoon, S. J. Lee, and C. Y. Lee. 2001. Identification of oral spirochetes at the species level and their association with other bacteria in endodontic infections. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 92:329-334.
29. Kolenbrander, P. E., N. Ganeshkumar, F. J. Cassels, and C. V. Hughes. 1993. Coaggregation: specific adherence among human oral plaque bacteria. FASEB J. 7:406-413.
30. Lana, M. A., A. P. Ribeiro-Sobrinho, R. Stehling, G. D. Garcia, B. K. Silva, J. S. Hamdan, J. R. Nicoli, M. A. Carvalho, and L. M. Farias. 2001. Microorganisms isolated from root canals presenting necrotic pulp and their drug susceptibility in vitro. Oral Microbiol. Immunol. 16:100-105.
31. Metzger, Z., L. G. Featherstone, W. W. Ambrose, M. Trope, and R. R. Arnold. 2001. Kinetics of coaggregation of Porphyromonas gingivalis with Fusobacterium nucleatum using an automated microtiter plate assay. Oral Microbiol. Immunol. 16:163-169.
32. Möller, A. J. 1966. Microbiological examination of root canals and periapical tissues of human teeth. Methodological studies. Odontol. Tidskr. 74(Suppl.):1-380.
33. Nelson, J. R., Y. C. Cai, T. L. Giesler, J. W. Farchaus, S. T. Sundaram, M. Ortiz-Rivera, L. P. Hosta, P. L. Hewitt, J. A. Mamone, C. Palaniappan, and C. W. Fuller. 2002 TempliPhi, phi29 DNA polymerase based rolling circle amplification of templates for DNA sequencing. BioTechniques June-(Suppl.):44-47.
34. Paster, B. J., S. K. Boches, J. L. Galvin, R. E. Ericson, C. N. Lau, V. A. Levanos, A. Sahasrabudhe, and F. E. Dewhirst. 2001. Bacterial diversity in human subgingival plaque. J. Bacteriol. 183:3770-3783.
35. Rocas, I. N., I. Y. Jung, C. Y. Lee, and J. F. Siqueira, Jr. 2004. Polymerase chain reaction identification of microorganisms in previously root-filled teeth in a South Korean population. J. Endod. 30:504-508.
36. Roças, I. N., J. F. Siqueira, Jr., K. R. Santos, and A. M. Coelho. 2001. "Red complex" (Bacteroides forsythus, Porphyromonas gingivalis, and Treponema denticola) in endodontic infections: a molecular approach. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 91:468-471.
37. Sedgley, C., A. Nagel, G. Dahlen, C. Reit, and A. Molander. 2006. Real-time quantitative polymerase chain reaction and culture analyses of Enterococcus faecalis in root canals. J. Endod. 32:173-177.
38. Seol, J. H., B. H. Cho, C. P. Chung, and K. S. Bae. 2006. Multiplex polymerase chain reaction detection of black-pigmented bacteria in infections of endodontic origin. J. Endod. 32:110-114.
39. Shaniztki, B., D. Hurwitz, N. Smorodinsky, N. Ganeshkumar, and E. I. Weiss. 1997. Identification of a Fusobacterium nucleatum PK1594 galactose-binding adhesin which mediates coaggregation with periopathogenic bacteria and hemagglutination. Infect. Immun. 65:5231-5237.
40. Siqueira, J. F., I. Y. Jung, I. N. Rocas, and C. Y. Lee. 2005. Differences in prevalence of selected bacterial species in primary endodontic infections from two distinct geographic locations. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 99:641-647.
41. Siqueira, J. F., Jr., and I. N. Rocas. 2002. Dialister pneumosintes can be a suspected endodontic pathogen. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 94:494-498.
42. Siqueira, J. F., Jr., and I. N. Rocas. 2003. Detection of Filifactor alocis in endodontic infections associated with different forms of periradicular diseases. Oral Microbiol. Immunol. 18:263-265.
43. Siqueira, J. F., Jr., and I. N. Rocas. 2004. Simultaneous detection of Dialister pneumosintes and Filifactor alocis in endodontic infections by 16S rDNA-directed multiplex PCR. J. Endod. 30:851-854.
44. Siqueira, J. F., Jr., and I. N. Rocas. 2005. Exploiting molecular methods to explore endodontic infections. Part 1 - current molecular technologies for microbiological diagnosis. J. Endod. 31:411-423.
45. Siqueira, J. F., Jr., I. N. Rocas, F. R. Alves, and K. R. Santos. 2004. Selected endodontic pathogens in the apical third of infected root canals: a molecular investigation. J. Endod. 30:638-643.
46. Siqueira, J. F., Jr., I. N. Rocas, A. Favieri, and K. R. Santos. 2000. Detection of Treponema denticola in endodontic infections by 16S rRNA gene-directed polymerase chain reaction. Oral Microbiol. Immunol. 15:335-337.
47. Siqueira, J. F., Jr., I. N. Rocas, and H. P. Lopes. 2002. Patterns of microbial colonization in primary root canal infections. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 93:174-178.
48. Siqueira, J. F., Jr., I. N. Rocas, J. C. Oliveira, and K. R. Santos. 2001. Molecular detection of black-pigmented bacteria in infections of endodontic origin. J. Endod. 27:563-566.
49. Siqueira, J. F., Jr., I. N. Rocas, R. Souto, M. de Uzeda, and A. P. Colombo. 2000. Checkerboard DNA-DNA hybridization analysis of endodontic infections. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 89:744-748.
50. Siqueira, J. F., Jr., I. N. Rocas, R. Souto, M. Uzeda, and A. P. Colombo. 2001. Microbiological evaluation of acute periradicular abscesses by DNA-DNA hybridization. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 92:451-457.
51. Smith, G. L., S. S. Socransky, and C. Smith. 1989. Rapid method for the purification of DNA from subgingival microorganisms. Oral Microbiol. Immunol. 4:47-51.
52. Socransky, S. S., A. D. Haffajee, M. A. Cugini, C. Smith, and R. L. Kent, Jr. 1998. Microbial complexes in subgingival plaque. J. Clin. Periodontol. 25:134-144.
53. Socransky, S. S., A. D. Haffajee, C. Smith, and S. Dibart. 1991. Relation of counts of microbial species to clinical status at the sampled site. J. Clin. Periodontol. 18:766-775.
54. Socransky, S. S., A. D. Haffajee, C. Smith, L. Martin, J. A. Haffajee, N. G. Uzel, and J. M. Goodson. 2004. Use of checkerboard DNA-DNA hybridization to study complex microbial ecosystems. Oral Microbiol. Immunol. 19:352-362.
55. Socransky, S. S., C. Smith, L. Martin, B. J. Paster, F. E. Dewhirst, and A. E. Levin. 1994. "Checkerboard" DNA-DNA hybridization. BioTechniques 17:788-792.
56. Sunde, P. T., L. Tronstad, E. R. Eribe, P. O. Lind, and I. Olsen. 2000. Assessment of periradicular microbiota by DNA-DNA hybridization. Endod. Dent. Traumatol. 16:191-196.
57. Sundqvist, G. 1992. Associations between microbial species in dental root canal infections. Oral Microbiol. Immunol. 7:257-262.
58. Sundqvist, G. 1992. Ecology of the root canal flora. J. Endod. 18:427-430.
59. Tankovic, J., P. Legrand, G. De Gatines, V. Chemineau, C. Brun-Buisson, and J. Duval. 1994. Characterization of a hospital outbreak of imipenem-resistant Acinetobacter baumannii by phenotypic and genotypic typing methods. J. Clin. Microbiol. 32:2677-2681.
60. Teles, F., A. D. Haffajee, and S. S. Socransky. 2007. Multiple displacement as an aid in checkerboard DNA-DNA hybridization. Oral Microbiol. Immunol. 22:118-125.
61. Tronstad, L., and P. T. Sunde. 2003. The evolving new understanding of endodontic infections. Endod. Topics 6:57-77.
62. Xia, T., J. C. Baumgartner, and L. L. David. 2000. Isolation and identification of Prevotella tannerae from endodontic infections. Oral Microbiol. Immunol. 15:273-275.
63. Yan, J., J. Feng, S. Hosono, and S. S. Sommer. 2004. Assessment of multiple displacement amplification in molecular epidemiology. BioTechniques 37:136-143.
64. Yokouchi, H., Y. Fukuoka, D. Mukoyama, R. Calugay, H. Takeyama, and T. Matsunaga. 2006. Whole-metagenome amplification of a microbial community associated with scleractinian coral by multiple displacement amplification using phi29 polymerase. Environ. Microbiol. 8:1155-1163.