Automated identification of medically important bacteria by 16S rRNA gene sequencing using a novel comprehensive database, 16SpathDB

Journal of Clinical Microbiology

Volumn 49, Issue 5, 2011, Pages 1799-1809

  Woo, Patrick C Y ^a,b   Teng, Jade L L ^b   Yeung, Juilian M Y ^b   Tse, Herman ^a,b   Lau, Susanna K P ^a,b   Yuen, Kwok Yung ^a,b  

^a THE UNIVERSITY OF HONG KONG   (Hong Kong)

^b UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; NUCLEOTIDE; RNA 16S;

16SPATH DATABASE; ACCURACY; ARTICLE; AUTOMATION; BACTERIAL GENE; BACTERIAL INFECTION; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; CLINICAL LABORATORY; GENE SEQUENCE; GENETIC DATABASE; GORDONIBACTER PAMELAEAE; MICROBIOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

BACTERIA; BACTERIAL INFECTIONS; DATABASES, NUCLEIC ACID; DNA, BACTERIAL; DNA, RIBOSOMAL; HUMANS; RNA, RIBOSOMAL, 16S;

BACTERIA (MICROORGANISMS);

EID: 79955546432     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.02350-10     Document Type: Article

References (35)

1. Benson, D. A., I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler. 2008. GenBank. Nucleic Acids Res. 36:D25-D30.
2. Cole, J. R., et al. 2005. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33:D294-D296. (Pubitemid 40207881)
3. Cole, J. R., et al. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37:D141-D145.
4. Harmsen, D., J. Rothganger, M. Frosch, and J. Albert. 2002. RIDOM: Ribosomal Differentiation of Medical Micro-organisms Database. Nucleic Acids Res. 30:416-417. (Pubitemid 34679601)
5. Harmsen, D., J. Rothganger, C. Singer, J. Albert, and M. Frosch. 1999. Intuitive hypertext-based molecular identification of micro-organisms. Lancet 353:291. (Pubitemid 29088124)
6. Harmsen, D., et al. 2001. Diagnostics of neisseriaceae and moraxellaceae by ribosomal DNA sequencing: ribosomal differentiation of medical microorganisms. J. Clin. Microbiol. 39:936-942.
7. Lau, S. K., et al. 2006. Usefulness of the MicroSeq 500 16S rDNA bacterial identification system for identification of anaerobic Gram positive bacilli isolated from blood cultures. J. Clin. Pathol. 59:219-222.
8. Lau, S. K., et al. 2006. Bacteremia caused by Solobacterium moorei in a patient with acute proctitis and carcinoma of the cervix. J. Clin. Microbiol. 44:3031-3034.
9. Lau, S. K., et al. 2004. Anaerobic, non-sporulating, Gram-positive bacilli bacteraemia characterized by 16S rRNA gene sequencing. J. Med. Microbiol. 53:1247-1253.
10. Lau, S. K., et al. 2004. Characterization of Haemophilus segnis, an important cause of bacteremia, by 16S rRNA gene sequencing. J. Clin. Microbiol. 42:877-880.
11. Lau, S. K., et al. 2004. Eggerthella hongkongensis sp. nov. and Eggerthella sinensis sp. nov., two novel Eggerthella species, account for half of the cases of Eggerthella bacteremia. Diagn. Microbiol. Infect. Dis. 49:255-263.
12. Lau, S. K., P. C. Woo, T. C. Yim, A. P. To, and K. Y. Yuen. 2003. Molecular characterization of a strain of group A streptococcus isolated from a patient with a psoas abscess. J. Clin. Microbiol. 41:4888-4891.
13. Maidak, B. L., et al. 1999. A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res. 27:171-173. (Pubitemid 29209430)
14. Murray, P. R., E. J. Baron, J. H. Jorgensen, M. R. Louise, and M. A. Pfaller (ed.). 2007. Manual of clinical microbiology, 9th ed. American Society for Microbiology, Washington, DC.
15. Patel, J. B., et al. 2000. Sequence-based identification of Mycobacterium species using the MicroSeq 500 16S rDNA bacterial identification system. J. Clin. Microbiol. 38:246-251.
16. Simmon, K. E., A. C. Croft, and C. A. Petti. 2006. Application of SmartGene IDNS software to partial 16S rRNA gene sequences for a diverse group of bacteria in a clinical laboratory. J. Clin. Microbiol. 44:4400-4406.
17. Tang, Y. W., et al. 2000. Identification of coryneform bacterial isolates by ribosomal DNA sequence analysis. J. Clin. Microbiol. 38:1676-1678.
18. Tse, H., et al. 2010. Complete genome sequence of Staphylococcus lugdunensis strain HKU09-01. J. Bacteriol. 192:1471-1472.
19. Woo, P. C., et al. 2007. In silico analysis of 16S ribosomal RNA gene sequencing-based methods for identification of medically important anaerobic bacteria. J. Clin. Pathol. 60:576-579.
20. Woo, P. C., et al. 2009. First report of Tsukamurella keratitis: association between T. tyrosinosolvens and T. pulmonis and ophthalmologic infections. J. Clin. Microbiol. 47:1953-1956.
21. Woo, P. C., et al. 2003. Granulicatella adiacens and Abiotrophia defectiva bacteraemia characterized by 16S rRNA gene sequencing. J. Med. Microbiol. 52:137-140.
22. Woo, P. C., A. M. Fung, S. K. Lau, E. Hon, and K. Y. Yuen. 2002. Diagnosis of pelvic actinomycosis by 16S ribosomal RNA gene sequencing and its clinical significance. Diagn. Microbiol. Infect. Dis. 43:113-118.
23. Woo, P. C., A. M. Fung, S. S. Wong, H. W. Tsoi, and K. Y. Yuen. 2001. Isolation and characterization of a Salmonella enterica serotype Typhi variant and its clinical and public health implications. J. Clin. Microbiol. 39:1190-1194.
24. Woo, P. C., et al. 2005. Clostridium bacteraemia characterised by 16S ribosomal RNA gene sequencing. J. Clin. Pathol. 58:301-307.
25. Woo, P. C., et al. 2007. Surgical site abscess caused by Lactobacillus fermentum identified by 16S ribosomal RNA gene sequencing. Diagn. Microbiol. Infect. Dis. 58:251-254.
26. Woo, P. C., S. K. Lau, J. L. Teng, H. Tse, and K. Y. Yuen. 2008. Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin. Microbiol. Infect. 14:908-934.
27. Woo, P. C., et al. 2009. The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats. PLoS Genet. 5:e1000416.
28. Woo, P. C., et al. 2004. Bacteremia due to Clostridium hathewayi in a patient with acute appendicitis. J. Clin. Microbiol. 42:5947-5949.
29. Woo, P. C., D. M. Tam, S. K. Lau, A. M. Fung, and K. Y. Yuen. 2004. Enterococcus cecorum empyema thoracis successfully treated with cefotaxime. J. Clin. Microbiol. 42:919-922.
30. Woo, P. C., et al. 2010. First report of Gordonibacter pamelaeae bacteremia. J. Clin. Microbiol. 48:319-322.
31. Woo, P. C., et al. 2003. Analysis of a viridans group strain reveals a case of bacteremia due to Lancefield group G alpha-hemolytic Streptococcus dysgalactiae subsp. equisimilis in a patient with pyomyositis and reactive arthritis. J. Clin. Microbiol. 41:613-618.
32. Woo, P. C., et al. 2009. Guidelines for interpretation of 16S rRNA gene sequence-based results for identification of medically important aerobic Gram-positive bacteria. J. Med. Microbiol. 58:1030-1036.
33. Woo, P. C., et al. 2004. "Streptococcus milleri" endocarditis caused by Streptococcus anginosus. Diagn. Microbiol. Infect. Dis. 48:81-88.
34. Woo, P. C., et al. 2005. Life-threatening invasive Helcococcus kunzii infections in intravenous-drug users and ermA-mediated erythromycin resistance. J. Clin. Microbiol. 43:6205-6208.
35. Woo, P. C., G. K. Woo, S. K. Lau, S. S. Wong, and K. Yuen. 2002. Single gene target bacterial identification. groEL gene sequencing for discriminating clinical isolates of Burkholderia pseudomallei and Burkholderia thailandensis. Diagn. Microbiol. Infect. Dis. 44:143-149.