Broad-range PCR: Past, present, or future of bacteriology?

Medecine et Maladies Infectieuses

Volumn 43, Issue 8, 2013, Pages 322-330

  Renvoise A ^a   Brossier, F ^a   Sougakoff, W ^a   Jarlier, V ^a   Aubry, A ^a  

^a SORBONNE UNIVERSITÉ   (France)

Author keywords

16S ribosomal RNA; Broad range PCR; Molecular diagnosis

Indexed keywords

BACTERIAL DNA; RNA 16S;

ASCITES; BACTERIAL STRAIN; BACTERIOLOGY; DNA EXTRACTION; GENE TARGETING; GENETIC CODE; INTESTINE LIPODYSTROPHY; MICROBIOLOGY; NONHUMAN; PHENOTYPE; POLYMERASE CHAIN REACTION; PROTEOMICS; REVIEW;

16S RIBOSOMAL RNA; ARN RIBOSOMAL 16S; BROAD-RANGE PCR; DIAGNOSTIC MOLÉCULAIRE; MOLECULAR DIAGNOSIS; PCR UNIVERSELLE;

BACTERIA; BACTERIAL INFECTIONS; BACTERIOLOGY; DNA, BACTERIAL; DNA, RIBOSOMAL; FALSE POSITIVE REACTIONS; FORECASTING; HUMANS; MASS SPECTROMETRY; POLYMERASE CHAIN REACTION; RIBOTYPING; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY; SPECIES SPECIFICITY;

EID: 84883304945     PISSN: 0399077X     EISSN: 17696690     Source Type: Journal    
DOI: 10.1016/j.medmal.2013.06.003     Document Type: Review

References (49)

1. Clarridge J.E. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 2004, 17:840-862.
2. Petti C.A. Detection and identification of microorganisms by gene amplification and sequencing. Clin Infect Dis 2007, 44:1108-1114.
3. Woese C.R. Bacterial evolution. Microbiol Rev 1987, 51:221-271.
4. Janda J.M., Abbott S.L. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol 2007, 45:2761-2764.
5. Kiratisin P., Li L., Murray P.R., Fischer S.H. Identification of bacteria recovered from clinical specimens by 16S rRNA gene sequencing. Eur J Clin Microbiol Infect Dis 2003, 22:628-631.
6. Schlaberg R., Simmon K.E., Fisher M.A. A systematic approach for discovering novel, clinically relevant bacteria. Emerg Infect Dis 2012, 18:422-430.
7. Woo P.C.Y., Ng K.H.L., Lau S.K.P., Yip K.T., Fung A.M.Y., Leung K.W., et al. Usefullness of the MicroSeq 500 16S ribosomal DNA-based bacterial identification system for identification of clinically significant bacterial isolates with ambiguous biochemical profiles. J Clin Microbiol 2003, 41:1996-2001.
8. Sontakke S., Cadenas M.B., Maggi R.G., Diniz P.P., Breitschwerdt E.B. Use of broad range16S rDNA PCR in clinical microbiology. J Microbiol Methods 2009, 76:217-225.
9. Petti C.A., Polage C.R., Schreckenberger P. The role of 16S rRNA gene sequencing in identification of microorganisms misidentified by conventional methods. J Clin Microbiol 2005, 43:6123-6125.
10. Mignard S., Flandrois J.P. 16S rRNA sequencing in routine bacterial identification: a 30-month experiment. J Microbiol Methods 2006, 67:574-581.
11. Bosshard P.P., Abels S., Zbinden R., Bottger E.C., Altwegg M. Ribosomal DNA sequencing for identification of aerobic gram-positive rods in the clinical laboratory (an 18-month evaluation). J Clin Microbiol 2003, 41:4134-4140.
12. Petti C.A., Bosshard P.P., Brandt M.E., Clarridge J.E., Feldblyum T.V., Foxall P., et al. Interpretive criteria for identification of bacteria and fungi by DNA target sequencing; approved guideline 2008, CLSI.
13. Gevers D., Cohan F.M., Lawrence J.G., Spratt B.G., Coenye T., Feil E.J., et al. Re-evaluating prokaryotic species. Nat Rev Microbiol 2005, 3:733-739.
14. Stackebrandt E., Frederiksen W., Garrity G.M., Grimont P.A.D., Kampfer P., Maiden M.C.J., et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002, 52:1043-1047.
15. Drancourt M., Berger P., Raoult D. Systematic 16S rRNA gene sequencing of atypical clinical isolates identified 27 new bacterial species associated with humans. J Clin Microbiol 2004, 42:2197-2202.
16. Rampini S.K., Bloemberg G.V., Keller P.M., Buchler A.C., Dollenmaier G., Speck R.F., et al. Broad-range 16S rRNA gene polymerase chain reaction for diagnosis of culture-negative bacterial infections. Clin Infect Dis 2011, 53:1245-1251.
17. Rafi W., Chandramuki A., Mani R., Satishchandra P., Shankar S.K. Rapid diagnosis of acute bacterial meningitis: role of a broad range 16S rRNA polymerase chain reaction. J Emerg Med 2010, 38:225-230.
18. Al Masalma M., Armougom F., Scheld W.M., Dufour H., Roche P.H., Drancourt M., et al. The expansion of the microbiological spectrum of brain abscesses with use of multiple 16S ribosomal DNA sequencing. Clin Infect Dis 2009, 48:1169-1178.
19. Fournier P.E., Thuny F., Richet H., Lepidi H., Casalta J.P., Arzouni J.P., et al. Comprehensive diagnostic strategy for blood culture-negative endocarditis: a prospective study of 819 new cases. Clin Infect Dis 2010, 51:131-140.
20. Greub G., Lepidi H., Rovery C., Casalta J.P., Habib G., Collard F., et al. Diagnosis of infectious endocarditis in patients undergoing valve surgery. Am J Med 2005, 118:230-238.
21. Goldenberger D., Kunzli A., Vogt P., Zbinden R., Altwegg M. Molecular diagnosis of bacterial endocarditis by broad-range PCR amplification and direct sequencing. J Clin Microbiol 1997, 35:2733-2739.
22. Gauduchon V., Chalabreysse L., Etienne J., Celard M., Benito Y., Lepidi H., et al. Molecular diagnosis of infective endocarditis by PCR amplification and direct sequencing of DNA from valve tissue. J Clin Microbiol 2003, 41:763-766.
23. Podglajen I., Bellery F., Poyart C., Coudol P., Buu-Hoi A., Bruneval P., et al. Comparative molecular and microbiologic diagnosis of bacterial endocarditis. Emerg Infect Dis 2003, 9:1543-1547.
24. Lang S., Watkin R.W., Lambert P.A., Bonser R.S., Littler W.A., Elliott T.S. Evaluation of PCR in the molecular diagnosis of endocarditis. J Infect 2004, 48:269-275.
25. Vondracek M., Sartipy U., Aufwerber E., Julander I., Lindblom D., Westling K. 16S rDNA sequencing of valve tissue improves microbiological diagnosis in surgically treated patients with infective endocarditis. J Infect 2011, 62:472-478.
26. Rovery C., Greub G., Lepidi H., Casalta J.P., Habib G., Collart F., et al. PCR detection of bacteria on cardiac valves of patients with treated bacterial endocarditis. J Clin Microbiol 2005, 43:163-167.
27. Schuurman T., de Boer R.F., Kooistra-Smid A.M., van Zwet A.A. Prospective study of use of PCR amplification and sequencing of 16S ribosomal DNA from cerebrospinal fluid for diagnosis of bacterial meningitis in a clinical setting. J Clin Microbiol 2004, 42:734-740.
28. Welinder-Olsson C., Dotevall L., Hogevik H., Jungnelius R., Trollfors B., Wahl M., et al. Comparison of broad-range bacterial PCR and culture of cerebrospinal fluid for diagnosis of community-acquired bacterial meningitis. Clin Microbiol Infect 2007, 13:879-886.
29. Srinivasan L., Pisapia J.M., Shah S.S., Halpern C.H., Harris M.C. Can Broad-range 16S ribosomal ribonucleic acid gene polymerase chain reactions improve the diagnosis of bacterial meningitis? A systematic review and meta-analysis. Ann Emerg Med 2012, 60:609-620.
30. Saravolatz L.D., Manzor O., VanderVelde N., Pawlak J., Belian B. Broad-range bacterial polymerase chain reaction for early detection of bacterial meningitis. Clin Infect Dis 2003, 36:40-45.
31. Zarrouk V., Leflon-Guibout V., Robineaux S., Kalamarides M., Nicolas-Chanoine M.H., Sterkers O., et al. Broad-range 16S rRNA PCR with cerebrospinal fluid may be unreliable for management of postoperative aseptic meningitis. J Clin Microbiol 2010, 48:3331-3333.
32. Fenollar F., Roux V., Stein A., Drancourt M., Raoult D. Analysis of 525 samples to determine the usefulness of PCR amplification and sequencing of the 16S rRNA gene for diagnosis of bone and joint infections. J Clin Microbiol 2006, 44:1018-1028.
33. Fenollar F., Levy P.Y., Raoult D. Usefulness of broad-range PCR for the diagnosis of osteoarticular infections. Curr Opin Rheumatol 2008, 20:463-470.
34. Fuursted K., Arpi M., Lindblad B.E., Pedersen L.N. Broad-range PCR as a supplement to culture for detection of bacterial pathogens in patients with a clinically diagnosed spinal infection. Scand J Infect Dis 2008, 40:772-777.
35. Marin M., Garcia-Lechuz J.M., Alonso P., Villanueva M., Alcala L., Gimeno M., et al. Role of universal 16S rRNA gene PCR and sequencing in diagnosis of prosthetic joint infection. J Clin Microbiol 2012, 50:583-589.
36. Ince A., Rupp J., Frommelt L., Katzer A., Gille J., Lohr J.F. Is "aseptic" loosening of the prosthetic cup after total hip replacement due to nonculturable bacterial pathogens in patients with low-grade infection?. Clin Infect Dis 2004, 39:1599-1603.
37. Rudkjobing V.B., Thomsen T.R., Alhede M., Kragh K.N., Nielsen P.H., Johansen U.R., et al. True microbiota involved in chronic lung infection of cystic fibrosis patients found by culturing and 16S rRNA gene analysis. J Clin Microbiol 2011, 49:4352-4355.
38. Hebb J.K., Cohen C.R., Astete S.G., Bukusi E.A., Totten P.A. Detection of novel organisms associated with salpingitis, by use of 16S rDNA polymerase chain reaction. J Infect Dis 2004, 190:2109-2120.
39. Drancourt M., Berger P., Terrada C., Bodaghi B., Conrath J., Raoult D., et al. High prevalence of fastidious bacteria in 1520 cases of uveitis of unknown etiology. Medicine (Baltimore) 2008, 87:167-176.
40. Levy P.Y., Fournier P.E., Charrel R., Metras D., Habib G., Raoult D. Molecular analysis of pericardial fluid: a 7-year experience. Eur Heart J 2006, 27:1942-1946.
41. Such J., Frances R., Munoz C., Zapater P., Casellas J.A., Cifuentes A., et al. Detection and identification of bacterial DNA in patients with cirrhosis and culture-negative, nonneutrocytic ascites. Hepatology 2002, 36:135-141.
42. Rogers G.B., Russell L.E., Preston P.G., Marsh P., Collins J.E., Saunders J., et al. Characterisation of bacteria in ascites--reporting the potential of culture-independent, molecular analysis. Eur J Clin Microbiol Infect Dis 2010, 29:533-541.
43. Mancini N., Carletti S., Ghidoli N., Cichero P., Burioni R., Clementi M. The era of molecular and other non-culture-based methods in diagnosis of sepsis. Clin Microbiol Rev 2010, 23:235-251.
44. Pichlmaier M., Marwitz V., Kuhn C., Niehaus M., Klein G., Bara C., et al. High prevalence of asymptomatic bacterial colonization of rhythm management devices. Europace 2008, 10:1067-1072.
45. Relman D.A., Loutit J.S., Schmidt T.M., Falkow S., Tompkins L.S. The agent of bacillary angiomatosis. An approach to the identification of uncultured pathogens. N Engl J Med 1990, 323:1573-1580.
46. Seng P., Drancourt M., Gouriet F., La S.B., Fournier P.E., Rolain J.M., et al. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 2009, 49:543-551.
47. Bizzini A., Jaton K., Romo D., Bille J., Prod'hom G., Greub G. Matrix-assisted laser desorption ionization-time of flight mass spectrometry as an alternative to 16S rRNA gene sequencing for identification of difficult-to-identify bacterial strains. J Clin Microbiol 2011, 49:693-696.
48. Croxatto A., Prod'hom G., Greub G. Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol Rev 2012, 36:380-407.
49. Clifford R.J., Milillo M., Prestwood J., Quintero R., Zurawski D.V., Kwak Y.I., et al. Detection of bacterial 16S rRNA and identification of four clinically important bacteria by real-time PCR. PLoS One 2012, 7:e48558.