Analysis of mixed sequencing chromatograms and its application in direct 16S rRNA gene sequencing of polymicrobial samples

Journal of Clinical Microbiology

Volumn 46, Issue 11, 2008, Pages 3766-3771

  Kommedal, Øyvind ^a,b   Karlsen, Bjarte ^c   Sæbø, Øystein ^c  

^a HAUKELAND UNIVERSITY HOSPITAL   (Norway)

^b UNIVERSITY OF BERGEN   (Norway)

^c iSentio Ltd   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ALGORITHM; ARTICLE; CHROMATOGRAPHY; COMPUTER PROGRAM; DNA SEQUENCE; GENETIC DATABASE; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

BACTERIA; COMPUTATIONAL BIOLOGY; DNA, BACTERIAL; DNA, RIBOSOMAL; HUMANS; INTERNET; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS);

EID: 55849101449     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.00213-08     Document Type: Article

References (12)

1. Baker, G. C., J. J. Smith, and D. A. Cowan. 2003. Review and re-analysis of domain-specific 16S primers. J. Microbiol. Methods 55:541-555.
2. Clarridge, J. E., III. 2004. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin. Microbiol. Rev. 17:840-862.
3. Coenye, T., and P. Vandamme. 2003. Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes. FEMS Microbiol. Lett. 228:45-49.
4. Corless, C. E., M. Guiver, R. Borrow, V. Edwards-Jones, E. B. Kaczmarski, and A. J. Fox. 2000. Contamination and sensitivity issues with a real-time universal 16S rRNA PCR. J. Clin. Microbiol. 38:1747-1752.
5. Deutch, S., L. N. Pedersen, L. Podenphant, R. Olesen, M. B. Schmidt, J. K. Moller, and L. Ostergaard. 2006. Broad-range real time PCR and DNA sequencing for the diagnosis of bacterial meningitis. Scand.J. Infect. Dis. 38:27-35.
6. Harris, K. A., and J. C. Hartley. 2003. Development of broad-range 16S rDNA PCR for use in the routine diagnostic clinical microbiology service. J. Med. Microbiol. 52:685-691.
7. Huys, G., T. Vanhoutte, M. Joossens, A. S. Mahious, E. De Brandt, S. Vermeire, and J. Swings. 2008. Coamplification of eukaryotic DNA with 16S rRNA gene-based PCR primers: possible consequences for population fingerprinting of complex microbial communities. Curr. Microbiol. 56:553-557.
8. Kawamura, Y., R. A. Whiley, S. E. Shu, T. Ezaki, and J. M. Hardie. 1999. Genetic approaches to the identification of the mitis group within the genus Streptococcus. Microbiology 145:2605-2613.
9. Petti, C. A. 2007. Detection and identification of microorganisms by gene amplification and sequencing. Clin. Infect. Dis. 44:1108-1114.
10. Poyart, C., G. Quesne, C. Boumaila, and P. Trieu-Cuot. 2001. Rapid and accurate species-level identification of coagulase-negative staphylococci by using the sodA gene as a target. J. Clin. Microbiol. 39:4296-4301.
11. Rantakokko-Jalava, K., S. Nikkari, J. Jalava, E. Eerola, M. Skurnik, O. Meurman, O. Ruuskanen, A. Alanen, E. Kotilainen, P. Toivanen, and P. Kotilainen. 2000. Direct amplification of rRNA genes in diagnosis of bacterial infections. J. Clin. Microbiol. 38:32-39.
12. Schuurman, T., R. F. de Boer, A. M. Kooistra-Smid, and A. A. van Zwet. 2004. 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. 42:734-740.