Characterization of polybacterial clinical samples using a set of group-specific broad-range primers targeting the 16S rRNA gene followed by DNA sequencing and RipSeq analysis

Journal of Medical Microbiology

Volumn 60, Issue 7, 2011, Pages 927-936

  Kommedal, Øyvind ^a   Lekang, Katrine ^a   Langeland, Nina ^a   Wiker, Harald G ^a,b  

^a UNIVERSITY OF BERGEN   (Norway)

^b HAUKELAND UNIVERSITY HOSPITAL   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ACTINOMYCES; ARTICLE; BACTERIAL GENETICS; CHROMATOGRAPHY; CONTROLLED STUDY; CROSS REACTION; DNA DETERMINATION; DNA SEQUENCE; ESCHERICHIA COLI; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROPIONIBACTERIUM; STAPHYLOCOCCUS;

BACTERIA; BACTERIAL INFECTIONS; CLONING, MOLECULAR; DNA PRIMERS; DNA, BACTERIAL; HUMANS; REPRODUCIBILITY OF RESULTS; RNA, RIBOSOMAL, 16S; SELF-SUSTAINED SEQUENCE REPLICATION;

EID: 79959499390     PISSN: 00222615     EISSN: None     Source Type: Journal    
DOI: 10.1099/jmm.0.028373-0     Document Type: Article

References (21)

1. Al Masalma, M., Armougom, F., Scheld, W. M., Dufour, H., Roche, P.-H., Drancourt, M. & Raoult, D. (2009). The expansion of the microbiological spectrum of brain abscesses with use of multiple 16S ribosomal DNA sequencing. Clin Infect Dis 48, 1169-1178.
2. Altman, D. G. (1991). Non-parametric analysis. In Practical Statistics for Medical Research, 1st edn, pp. 203-205. London: Chapman & Hall.
3. Baker, G. C., Smith, J. J. & Cowan, D. A. (2003). Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55, 541-555.
4. Bosshard, P. P., Zbinden, R. & Altwegg, M. (2002). Turicibacter sanguinis gen. nov., sp. nov., a novel anaerobic, Gram-positive bacterium. Int J Syst Evol Microbiol 52, 1263-1266.
5. Bosshard, P. P., Abels, S., Zbinden, R., Böttger, E. C. & Altwegg, M. (2003). Ribosomal DNA sequencing for identification of aerobic gram-positive rods in the clinical laboratory (an 18-month evaluation). J Clin Microbiol 41, 4134-4140.
6. Bosshard, P. P., Abels, S., Altwegg, M., Böttger, E. C. & Zbinden, R. (2004). Comparison of conventional and molecular methods for identification of aerobic catalase-negative gram-positive cocci in the clinical laboratory. J Clin Microbiol 42, 2065-2073.
7. de Vries, J. J., Arents, N. L. & Manson, W. L. (2008). Campylobacter species isolated from extra-oro-intestinal abscesses: a report of four cases and literature review. Eur J Clin Microbiol Infect Dis 27, 1119-1123.
8. Di Giusto, D. A. & King, G. C. (2004). Strong positional preference in the interaction of LNA oligonucleotides with DNA polymerase and proofreading exonuclease activities: implications for genotyping assays. Nucleic Acids Res 32, e32.
9. Edwards, U., Rogall, T., Blöcker, H., Emde, M. & Böttger, E. C. (1989). Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 17, 7843-7853.
10. Goldenberger, D., Künzli, A., Vogt, P., Zbinden, R. & Altwegg, M. (1997). Molecular diagnosis of bacterial endocarditis by broad-range PCR amplification and direct sequencing. J Clin Microbiol 35, 2733-2739.
11. Harris, K. A. & Hartley, J. C. (2003). Development of broad-range 16S rDNA PCR for use in the routine diagnostic clinical microbiology service. J Med Microbiol 52, 685-691.
12. Hartmeyer, G. N. & Justesen, U. S. (2010). Direct 16S rRNA gene sequencing of polymicrobial culture-negative samples with analysis of mixed chromatograms. J Med Microbiol 59, 486-488.
13. Johnson, C. C., Reinhardt, J. F., Edelstein, M. A. C., Mulligan, M. E., George, W. L. & Finegold, S. M. (1985). Bacteroides gracilis, an important anaerobic bacterial pathogen. J Clin Microbiol 22, 799-802.
14. Kommedal, Ø., Karlsen, B. & Saebø, Ø. (2008). Analysis of mixed sequencing chromatograms and its application in direct 16S rRNA gene sequencing of polymicrobial samples. J Clin Microbiol 46, 3766-3771.
15. Kommedal, Ø., Kvello, K., Skjåstad, R., Langeland, N. & Wiker, H. G. (2009). Direct 16S rRNA gene sequencing from clinical specimens, with special focus on polybacterial samples and interpretation of mixed DNA chromatograms. J Clin Microbiol 47, 3562-3568.
16. Petti, C. A., Bosshard, P. P., Brandt, M. E., Clarridge, J. E., III, Feldblyum, T. V., Foxall, P., Furtado, M. R., Pace, N. & Procop, G. (2008a). Interpretive Criteria for Identification of Bacteria and Fungi by DNA Target Sequencing, Approved Guideline Document MM18-A, 28. Wayne, PA: Clinical and Laboratory Standards Institute.
17. Petti, C. A., Simmon, K. E., Bender, J., Blaschke, A., Webster, K. A., Conneely, M. F., Schreckenberger, P. C., Origitano, T. C. & Challapalli, M. (2008b). Culture-negative intracerebral abscesses in children and adolescents from Streptococcus anginosus group infection: a case series. Clin Infect Dis 46, 1578-1580.
18. Rupp, J., Solbach, W. & Gieffers, J. (2006). Single-nucleotidepolymorphism-specific PCR for quantification and discrimination of Chlamydia pneumoniae genotypes by use of a ''locked'' nucleic acid. Appl Environ Microbiol 72, 3785-3787.
19. Schuurman, T., de Boer, R. F., Kooistra-Smid, A. M. D. & van Zwet, A. A. (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.
20. Senn, L., Franciolli, M., Raoult, D., Moulin, A., Von Segesser, L., Calandra, T. & Greub, G. (2005). Coxiella burnetii vascular graft infection. BMC Infect Dis 5, 109.
21. Wellinghausen, N., Kochem, A.-J., Disqué, C., Mühl, H., Gebert, S., Winter, J., Matten, J. & Sakka, S. G. (2009). Diagnosis of bacteremia in whole-blood samples by use of a commercial universal 16S rRNA genebased PCR and sequence analysis. J Clin Microbiol 47, 2759-2765.