Detection of live and antibiotic-killed bacteria by quantitative real-time PCR of specific fragments of rRNA

Antimicrobial Agents and Chemotherapy

Volumn 50, Issue 6, 2006, Pages 1913-1920

  Aellen, Steve ^a   Que, Yok Ai ^a   Guignard, Bertrand ^b   Haenni, Marisa ^b   Moreillon, Philippe ^b  

^a LAUSANNE UNIVERSITY HOSPITAL   (Switzerland)

^b UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

LEVOFLOXACIN; MOLECULAR MARKER; PENICILLIN DERIVATIVE; POLYNUCLEOTIDE; RIBOSOME RNA; RNA 16S;

ANTIBIOTIC THERAPY; ARTICLE; BACTERIAL COUNT; BACTERIAL GROWTH; BACTERICIDAL ACTIVITY; BACTERIUM CULTURE; BACTERIUM DETECTION; CELL DIFFERENTIATION; CELL KILLING; CELL VIABILITY; COLONY FORMING UNIT; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RNA GENE; STREPTOCOCCUS GORDONII;

ANTI-BACTERIAL AGENTS; COLONY COUNT, MICROBIAL; DNA, BACTERIAL; GENES, BACTERIAL; GENETIC MARKERS; KINETICS; MICROBIAL SENSITIVITY TESTS; MUTATION; OFLOXACIN; PENICILLINS; POLYMERASE CHAIN REACTION; RNA, BACTERIAL; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 16S; STREPTOCOCCUS;

EID: 33744467948     PISSN: 00664804     EISSN: None     Source Type: Journal    
DOI: 10.1128/AAC.00869-05     Document Type: Article

References (38)

1. Anthony, R. M., T. J. Brown, and G. L. French. 2000. Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array. J. Clin. Microbiol. 38:781-788.
2. Birch, L., C. E. Dawson, J. H. Cornett, and J. T. Keer. 2001. A comparison of nucleic acid amplification techniques for the assessment of bacterial viability. Lett. Appl. Microbiol. 33:296-301.
3. Bosshard, P. P., A. Kronenberg, R. Zbinden, C. Ruef, E. C. Bottger, and M. Altwegg. 2003. Etiologic diagnosis of infective endocarditis by broad-range polymerase chain reaction: a 3-year experience. Clin. Infect. Dis. 37:167-172.
4. Branger, S., J. P. Casalta, G. Habib, F. Collard, and D. Raoult. 2003. Streptococcus pneumoniae endocarditis: persistence of DNA on heart valve material 7 years after infectious episode. J. Clin. Microbiol. 41:4435-4437.
5. Brown, D. F. 2001. Detection of methicillin/oxacillin resistance in staphylococci. J. Antimicrob. Chemother. 48(Suppl. 1):65-70.
6. Caldelari, I., B. Loeliger, H. Langen, M. P. Glauser, and P. Moreillon. 2000. Deregulation of the arginine deiminase (arc) operon in penicillin-tolerant mutants of Streptococcus gordonii. Antimicrob. Agents Chemother. 44:2802-2810.
7. Canvin, J. M., S. C. Goutcher, M. Hagig, C. G. Gemmell, and R. D. Sturrock. 1997. Persistence of Staphylococcus aureus as detected by polymerase chain reaction in the synovial fluid of a patient with septic arthritis. Br. J. Rheumatol. 36:203-206.
8. Carpousis, A. J. 2002. The Escherichia coli RNA degradosome: structure, function and relationship in other ribonucleolytic multienzyme complexes. Biochem. Soc. Trans. 30:150-155.
9. Carpousis, A. J., A. Leroy, N. Vanzo, and V. Khemici. 2001. Escherichia coli RNA degradosome. Methods Enzymol. 342:333-345.
10. Entenza, J. M., I. Caldelari, M. P. Glauser, P. Francioli, and P. Moreillon. 1997. Importance of genotypic and phenotypic tolerance in the treatment of experimental endocarditis due to Streptococcus gordonii. J. Infect. Dis. 175:70-76.
11. Entenza, J. M., I. Caldelari, M. P. Glauser, and P. Moreillon. 1999. Efficacy of levofloxacin in the treatment of experimental endocarditis caused by viridans group streptococci. J. Antimicrob. Chemother. 44:775-786.
12. Francois, P., D. Pittet, M. Bento, B. Pepey, P. Vaudaux, D. Lew, and J. Schrenzel. 2003. Rapid detection of methicillin-resistant Staphylococcus aureus directly from sterile or nonsterile clinical samples by a new molecular assay. J. Clin. Microbiol. 41:254-260.
13. Gauduchon, V., L. Chalabreysse, J. Etienne, M. Celard, Y. Benito, H. Lepidi, F. Thivolet-Bejui, and F. Vandenesch. 2003. Molecular diagnosis of infective endocarditis by PCR amplification and direct sequencing of DNA from valve tissue. J. Clin. Microbiol. 41:763-766.
14. Goldenberger, D., A. Kunzli, P. Vogt, R. Zbinden, and M. Altwegg. 1997. Molecular diagnosis of bacterial endocarditis by broad-range PCR amplification and direct sequencing. J. Clin. Microbiol. 35:2733-2739.
15. Hellyer, T. J., L. E. DesJardin, G. L. Hehman, M. D. Cave, and K. D. Eisenach. 1999. Quantitative analysis of mRNA as a marker for viability of Mycobacterium tuberculosis. J. Clin. Microbiol. 37:290-295.
16. Hellyer, T. J., T. W. Fletcher, J. H. Bates, W. W. Stead, G. L. Templeton, M. D. Cave, and K. D. Eisenach. 1996. Strand displacement amplification and the polymerase chain reaction for monitoring response to treatment in patients with pulmonary tuberculosis. J. Infect. Dis. 173:934-941.
17. Hiasa, H., D. O. Yousef, and K. J. Marians. 1996. DNA strand cleavage is required for replication fork arrest by a frozen topoisomerase-quinolone-DNA ternary complex. J. Biol. Chem. 271:26424-26429.
18. Jacobs, W. R., Jr., R. G. Barletta, R. Udani, J. Chan, G. Kalkut, G. Sosne, T. Kieser, G. J. Sarkis, G. F. Hatfull, and B. R. Bloom. 1993. Rapid assessment of drug susceptibilities of Mycobacterium tuberculosis by means of luciferase reporter phages. Science 260:819-822.
19. Josephson, K. L., C. P. Gerba, and I. L. Pepper. 1993. Polymerase chain reaction detection of nonviable bacterial pathogens. Appl. Environ. Microbiol. 59:3513-3515.
20. Keer, J. T., and L. Birch. 2003. Molecular methods for the assessment of bacterial viability. J. Microbiol. Methods 53:175-183.
21. Lindahl, T. 1993. Instability and decay of the primary structure of DNA. Nature 362:709-715.
22. Loeliger, B., I. Caldelari, A. Bizzini, P. Stutzmann Meier, P. A. Majcherczyk, and P. Moreillon. 2003. Antibiotic-dependent correlation between drug-induced killing and loss of luminescence in Streptococcus gordonii expressing luciferase. Microb. Drug Resist. 9:123-131.
23. McCarty, S. C., and R. M. Atlas. 1993. Effect of amplicon size on PCR detection of bacteria exposed to chlorine. PCR Methods Appl. 3:181-185.
24. McKillip, J. L., L. A. Jaykus, and M. Drake. 1998. rRNA stability in heat-killed and UV-irradiated enterotoxigenic Staphylococcus aureus and Escherichia coli O157:H7. Appl. Environ. Microbiol. 64:4264-4268.
25. Nakatomi, Y., and J. Sugiyama. 1998. A rapid latex agglutination assay for the detection of penicillin-binding protein 2′. Microbiol. Immunol. 42:739-743.
26. National Committee for Clinical Laboratory Standards. 1996. Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically. Approved standard M7-T. National Committee for Clinical Laboratory Standards, Wayne, Pa.
27. Oliveira, K., G. W. Procop, D. Wilson, J. Coull, and H. Stender. 2002. Rapid identification of Staphylococcus aureus directly from blood cultures by fluorescence in situ hybridization with peptide nucleic acid probes. J. Clin. Microbiol. 40:247-251.
28. Patel, J. B. 2001. 16S rRNA gene sequencing for bacterial pathogen identification in the clinical laboratory. Mol. Diagn. 6:313-321.
29. Recorbet, G., C. Picard, P. Normand, and P. Simonet. 1993. Kinetics of the persistence of chromosomal DNA from genetically engineered Escherichia coli introduced into soil. Appl. Environ. Microbiol. 59:4289-4294.
30. Romanowski, G., M. G. Lorenz, and W. Wackernagel. 1993. Use of polymerase chain reaction and electroporation of Escherichia coli to monitor the persistence of extracellular plasmid DNA introduced into natural soils. Appl. Environ. Microbiol. 59:3438-3446.
31. Shepard, C. C. 1969. Further experience with the kinetic method for the study of drugs against Mycobacterium leprae in mice. Activities of DDS, DFD, ethionamide, capreomycin and PAM 1392. Int. J. Lepr. Other Mycobact. Dis. 37:389-397.
32. Sheridan, G. E., C. I. Masters, J. A. Shallcross, and B. M. MacKey. 1998. Detection of mRNA by reverse transcription-PCR as an indicator of viability in Escherichia coli cells. Appl. Environ. Microbiol. 64:1313-1318.
33. Tanaka, M., Y. Onodera, Y. Uchida, K. Sato, and I. Hayakawa. 1997. Inhibitory activities of quinolones against DNA gyrase and topoisomerase IV purified from Staphylococcus aureus. Antimicrob. Agents Chemother. 41:2362-2366.
34. van der Heijden, I. M., B. Wilbrink, A. E. Vije, L. M. Schouls, F. C. Breedveld, and P. P. Tak. 1999. Detection of bacterial DNA in serial synovial samples obtained during antibiotic treatment from patients with septic arthritis. Arthritis Rheum. 42:2198-2203.
35. van der Vliet, G. M., S. N. Cho, K. Kampirapap, J. van Leeuwen, R. A. Schukkink, B. van Gemen, P. K. Das, W. R. Faber, G. P. Walsh, and P. R. Klatser. 1996. Use of NASBA RNA amplification for detection of Mycobacterium leprae in skin biopsies from untreated and treated leprosy patients. Int. J. Lepr. Other Mycobact. Dis. 64:396-403.
36. van der Vliet, G. M., P. Schepers, R. A. Schukkink, B. van Gemen, and P. R. Klatser. 1994. Assessment of mycobacterial viability by RNA amplification. Antimicrob. Agents Chemother. 38:1959-1965.
37. Villarino, A., O. M. Bouvet, B. Regnault, S. Martin-Delautre, and P. A. D. Grimont. 2000. Exploring the frontier between life and death in Escherichia coli: evaluation of different viability markers in live and heat- or UV-killed cells. Res. Microbiol. 151:755-768.
38. Williams, D. L., T. L. Pittman, T. P. Gillis, M. Matsuoka, and Y. Kashiwabara. 2001. Simultaneous detection of Mycobacterium leprae and its susceptibility to dapsone using DNA heteroduplex analysis. J. Clin. Microbiol. 39:2083-2088.