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BioMed Research International
Volume 2013 (2013), Article ID 264651, 8 pages
http://dx.doi.org/10.1155/2013/264651
Research Article

Development of a Broad-Range 23S rDNA Real-Time PCR Assay for the Detection and Quantification of Pathogenic Bacteria in Human Whole Blood and Plasma Specimens

1Operative Unit of Clinical Microbiology, St. Orsola-Malpighi University Hospital, 40138 Bologna, Italy
2Department of Haematology and Oncology “L. and A. Seragnoli”, Unit of Clinical Microbiology, Regional Reference Centre for Microbiological Emergencies (CRREM), St. Orsola-Malpighi Hospital, University of Bologna, 9 Via G. Massarenti, 40138 Bologna, Italy
3DIVET, University of Milan, 20100 Milan, Italy
4Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy

Received 17 October 2012; Revised 15 January 2013; Accepted 29 January 2013

Academic Editor: Arun K. Bhunia

Copyright © 2013 Paolo Gaibani et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. J. M. Mylotte and A. Tayara, “Blood cultures: clinical aspects and controversies,” European Journal of Clinical Microbiology and Infectious Diseases, vol. 19, no. 3, pp. 157–163, 2000.
  2. M. Paolucci, M. P. Landini, and V. Sambri, “Conventional and molecular techniques for the early diagnosis of bacteraemia,” International Journal of Antimicrobial Agents, vol. 36, no. 2, pp. S6–S16, 2010. View at Publisher · View at Google Scholar · View at Scopus
  3. P. Gaibani, G. Rossini, S. Ambretti et al., “Blood culture systems: rapid detection: how and why?” International journal of antimicrobial agents, vol. 34, pp. S13–S15, 2009. View at Scopus
  4. R. M. Anthony, T. J. Brown, and G. L. French, “Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array,” Journal of Clinical Microbiology, vol. 38, no. 2, pp. 781–788, 2000. View at Scopus
  5. A. L. Rosey, E. Abachin, G. Quesnes et al., “Development of a broad-range 16S rDNA real-time PCR for the diagnosis of septic arthritis in children,” Journal of Microbiological Methods, vol. 68, no. 1, pp. 88–93, 2007. View at Publisher · View at Google Scholar · View at Scopus
  6. F. Zucol, R. A. Ammann, C. Berger et al., “Real-time quantitative broad-range PCR assay for detection of the 16S rRNA gene followed by sequencing for species identification,” Journal of Clinical Microbiology, vol. 44, no. 8, pp. 2750–2759, 2006. View at Publisher · View at Google Scholar · View at Scopus
  7. W. Jiang, M. M. Lederman, and P. Hunt, “Plasma levels of bacterial DNA correlate with immune activation and the magnitude of immune restoration in persons with antiretroviral-treated HIV infection,” Journal of Infectious Diseases, vol. 199, no. 1177, p. 1185, 2009. View at Scopus
  8. K. Matsuda, H. Tsuji, T. Asahara, Y. Kado, and K. Nomoto, “sensitive quantitative detection of commensal bacteria by rRNA-targeted reverse transcription-PCR,” Applied and Environmental Microbiology, vol. 73, no. 1, pp. 32–39, 2007. View at Publisher · View at Google Scholar · View at Scopus
  9. S. K. Rampini, G. V. Bloemberg, P. M. Keller et al., “Broad-range 16S rRNA gene polymerase chain reaction for diagnosis of culture-negative bacterial infections,” Clinical Infectious Diseases, vol. 53, no. 12, pp. 1245–1251, 2011. View at Publisher · View at Google Scholar
  10. S. Yang, S. Lin, G. D. Kelen et al., “Quantitative multiprobe PCR assay for simultaneous detection and identification to species level of bacterial pathogens,” Journal of Clinical Microbiology, vol. 40, no. 9, pp. 3449–3454, 2002. View at Publisher · View at Google Scholar · View at Scopus
  11. P. Zapater, R. Francés, J. M. González-Navajas et al., “Serum and ascitic fluid bacterial DNA: a new independent prognostic factor in noninfected patients with cirrhosis,” Hepatology, vol. 48, no. 6, pp. 1924–1931, 2008. View at Publisher · View at Google Scholar · View at Scopus
  12. J. E. Clarridge, “Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases,” Clinical Microbiology Reviews, vol. 17, no. 4, pp. 840–862, 2004. View at Publisher · View at Google Scholar · View at Scopus
  13. T. Bacchetti De Gregoris, N. Aldred, A. S. Clare, and J. G. Burgess, “Improvement of phylum- and class-specific primers for real-time PCR quantification of bacterial taxa,” Journal of Microbiological Methods, vol. 86, no. 3, pp. 351–356, 2011. View at Publisher · View at Google Scholar · View at Scopus
  14. A. Cherkaoui, S. Emonet, D. Ceroni et al., “Development and validation of a modified broad-range 16S rDNA PCR for diagnostic purposes in clinical microbiology,” Journal of Microbiological Methods, vol. 79, no. 2, pp. 227–231, 2009. View at Publisher · View at Google Scholar · View at Scopus
  15. E. Ferri, S. Novati, M. Casiraghi et al., “Plasma levels of bacterial DNA in HIV infection: the limits of quantitative polymerase chain reaction,” Journal of Infectious Diseases, vol. 202, no. 1, pp. 176–177, 2010. View at Publisher · View at Google Scholar · View at Scopus
  16. V. Gentili, P. G. Balboni, E. Menegatti et al., “Panbacterial real-time PCR to evaluate bacterial burden in chronic wounds treated with Cutimed Sorbact,” European Journal of Clinical Microbiology and Infectious Diseases, vol. 31, no. 7, pp. 1523–1529, 2011.
  17. E. T. Zemanick, B. D. Wagner, S. D. Sagel, M. J. Stevens, F. J. Accurso, and J. Kirk Harris, “Reliability of quantitative real-time PCR for bacterial detection in cystic fibrosis airway specimens,” PLoS ONE, vol. 5, no. 11, Article ID e15101, 2010. View at Publisher · View at Google Scholar · View at Scopus
  18. Ø. Kommedal, K. Simmon, D. Karaca, N. Langeland, and H. G. Wikera, “Dual priming oligonucleotides for broad-range amplification of the bacterial 16S rRNA gene directly from human clinical specimens,” Journal of Clinical Microbiology, vol. 50, no. 4, pp. 1289–1294, 2012. View at Publisher · View at Google Scholar
  19. D. E. Hunt, V. Klepac-Ceraj, S. G. Acinas, C. Gautier, S. Bertilsson, and M. F. Polz, “Evaluation of 23S rRNA PCR primers for use in phylogenetic studies of bacterial diversity,” Applied and Environmental Microbiology, vol. 72, no. 3, pp. 2221–2225, 2006. View at Publisher · View at Google Scholar · View at Scopus
  20. S. Nikkari, I. J. McLaughlin, W. Bi, D. E. Dodge, and D. A. Relman, “Does blood of healthy subjects contain bacterial ribosomal DNA?” Journal of Clinical Microbiology, vol. 39, no. 5, pp. 1956–1959, 2001. View at Publisher · View at Google Scholar · View at Scopus
  21. R. C. Edgar, “MUSCLE: multiple sequence alignment with high accuracy and high throughput,” Nucleic Acids Research, vol. 32, no. 5, pp. 1792–1797, 2004. View at Publisher · View at Google Scholar · View at Scopus
  22. S. Epis, P. Gaibani, U. Ulissi, B. Chouaia, I. Ricci, et al., “Do mosquito-associated bacteria of the genus Asaia circulate in humans?” European Journal of Clinical Microbiology & Infectious Diseases, vol. 31, pp. 1137–1140, 2012.
  23. K. A. Harris and J. C. Hartley, “Development of broad-range 16S rDNA PCR for use in the routine diagnostic clinical microbiology service,” Journal of Medical Microbiology, vol. 52, no. 8, pp. 685–691, 2003. View at Publisher · View at Google Scholar · View at Scopus
  24. K. Rantakokko-Jalava, S. Nikkari, J. Jalava et al., “Direct amplification of rRNA genes in diagnosis of bacterial infections,” Journal of Clinical Microbiology, vol. 38, no. 1, pp. 32–39, 2000. View at Scopus
  25. B. Vandercam, S. Jeumont, O. Cornu et al., “Amplification-based DNA analysis in the diagnosis of prosthetic joint infection,” Journal of Molecular Diagnostics, vol. 10, no. 6, pp. 537–543, 2008. View at Publisher · View at Google Scholar · View at Scopus
  26. W. Ludwig and K. H. Schleifer, “Bacterial phylogeny based on 16S and 23S rRNA sequence analysis,” FEMS Microbiology Reviews, vol. 15, no. 2-3, pp. 155–173, 1994. View at Scopus
  27. A. Pei, C. W. Nossa, P. Chokshi et al., “Diversity of 23S rRNA genes within individual prokaryotic genomes,” PloS One, vol. 4, no. 5, Article ID e5437, 2009. View at Publisher · View at Google Scholar · View at Scopus
  28. P. P. Banada, S. Chakravorty, D. Shah, M. Burday, F. M. Mazzella, and D. Alland, “Highly sensitive detection of staphylococcus aureus directly from patient blood,” PLoS ONE, vol. 7, no. 2, Article ID e31126, 2012. View at Publisher · View at Google Scholar
  29. I. Gómez-Hurtado, A. Santacruz, G. Peiró et al., “Gut microbiota dysbiosis is associated with inflammation and bacterial translocation in mice with CCl4-Induced fibrosis,” PLoS ONE, vol. 6, no. 7, Article ID e23037, 2011. View at Publisher · View at Google Scholar · View at Scopus
  30. M. Kramski, A. J. Gaeguta, R. Rajasuriar et al., “Novel sensitive real-time PCR for quantification of bacterial 16S rRNA genes in plasma of HIV-infected patients as a marker for microbial translocation,” Journal of Clinical Microbiology, vol. 49, no. 10, pp. 3691–3693, 2011. View at Publisher · View at Google Scholar