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Identification of clinically important anaerobic bacteria by an oligonucleotide array

Yu Tzu Lin, Mario Vaneechoutte UGent, Ay Huey Huang, Lee Jene Teng, Hung-Mo Chen, Shu-Li Su and Tsung Chain Chang (2010) JOURNAL OF CLINICAL MICROBIOLOGY. 48(4). p.1283-1290
abstract
Anaerobic bacteria can cause a wide variety of infections, and some of these infections can be serious. Conventional identification methods based on biochemical tests are often lengthy and can produce inconclusive results. An oligonucleotide array based on the 16S-23S rRNA intergenic spacer (ITS) sequences was developed to identify 28 species of anaerobic bacteria and Veillonella. The method consisted of PCR amplification of the ITS regions with universal primers, followed by hybridization of the digoxigenin-labeled PCR products to a panel of 35 oligonucleotide probes (17- to 30-mers) immobilized on a nylon membrane. The performance of the array was determined by testing 310 target strains (strains which we aimed to identify), including 122 reference strains and 188 clinical isolates. In addition, 98 nontarget strains were used for specificity testing. The sensitivity and the specificity of the array for the identification of pure cultures were 99.7 and 97.1%, respectively. The array was further assessed for its ability to detect anaerobic bacteria in 49 clinical specimens. Two species (Finegoldia magna and Bacteroides vulgatus) were detected in two specimens by the array, and the results were in accordance with those obtained by culture. The whole procedure of array hybridization took about 8 h, starting with the isolated colonies. The array can be used as an accurate alternative to conventional methods for the identification of clinically important anaerobes.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
BACTEROIDES-FRAGILIS GROUP, POLYMERASE-CHAIN-REACTION, ACINETOBACTER-BAUMANNII COMPLEX, FUSOBACTERIUM-NUCLEATUM, RAPID IDENTIFICATION, MULTICENTER SURVEY, GENUS VEILLONELLA, SEQUENCE-ANALYSIS, SPACER REGION, BLOOD CULTURES
journal title
JOURNAL OF CLINICAL MICROBIOLOGY
J. Clin. Microbiol.
volume
48
issue
4
pages
1283 - 1290
Web of Science type
Article
Web of Science id
000276153200036
JCR category
MICROBIOLOGY
JCR impact factor
4.22 (2010)
JCR rank
20/103 (2010)
JCR quartile
1 (2010)
ISSN
0095-1137
DOI
10.1128/JCM.01620-09
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1016486
handle
http://hdl.handle.net/1854/LU-1016486
date created
2010-08-02 11:00:14
date last changed
2016-12-19 15:43:02
@article{1016486,
  abstract     = {Anaerobic bacteria can cause a wide variety of infections, and some of these infections can be serious. Conventional identification methods based on biochemical tests are often lengthy and can produce inconclusive results. An oligonucleotide array based on the 16S-23S rRNA intergenic spacer (ITS) sequences was developed to identify 28 species of anaerobic bacteria and Veillonella. The method consisted of PCR amplification of the ITS regions with universal primers, followed by hybridization of the digoxigenin-labeled PCR products to a panel of 35 oligonucleotide probes (17- to 30-mers) immobilized on a nylon membrane. The performance of the array was determined by testing 310 target strains (strains which we aimed to identify), including 122 reference strains and 188 clinical isolates. In addition, 98 nontarget strains were used for specificity testing. The sensitivity and the specificity of the array for the identification of pure cultures were 99.7 and 97.1\%, respectively. The array was further assessed for its ability to detect anaerobic bacteria in 49 clinical specimens. Two species (Finegoldia magna and Bacteroides vulgatus) were detected in two specimens by the array, and the results were in accordance with those obtained by culture. The whole procedure of array hybridization took about 8 h, starting with the isolated colonies. The array can be used as an accurate alternative to conventional methods for the identification of clinically important anaerobes.},
  author       = {Lin, Yu Tzu and Vaneechoutte, Mario and Huang, Ay Huey and Teng, Lee Jene and Chen, Hung-Mo and Su, Shu-Li and Chang, Tsung Chain},
  issn         = {0095-1137},
  journal      = {JOURNAL OF CLINICAL MICROBIOLOGY},
  keyword      = {BACTEROIDES-FRAGILIS GROUP,POLYMERASE-CHAIN-REACTION,ACINETOBACTER-BAUMANNII COMPLEX,FUSOBACTERIUM-NUCLEATUM,RAPID IDENTIFICATION,MULTICENTER SURVEY,GENUS VEILLONELLA,SEQUENCE-ANALYSIS,SPACER REGION,BLOOD CULTURES},
  language     = {eng},
  number       = {4},
  pages        = {1283--1290},
  title        = {Identification of clinically important anaerobic bacteria by an oligonucleotide array},
  url          = {http://dx.doi.org/10.1128/JCM.01620-09},
  volume       = {48},
  year         = {2010},
}

Chicago
Lin, Yu Tzu, Mario Vaneechoutte, Ay Huey Huang, Lee Jene Teng, Hung-Mo Chen, Shu-Li Su, and Tsung Chain Chang. 2010. “Identification of Clinically Important Anaerobic Bacteria by an Oligonucleotide Array.” Journal of Clinical Microbiology 48 (4): 1283–1290.
APA
Lin, Y. T., Vaneechoutte, M., Huang, A. H., Teng, L. J., Chen, H.-M., Su, S.-L., & Chang, T. C. (2010). Identification of clinically important anaerobic bacteria by an oligonucleotide array. JOURNAL OF CLINICAL MICROBIOLOGY, 48(4), 1283–1290.
Vancouver
1.
Lin YT, Vaneechoutte M, Huang AH, Teng LJ, Chen H-M, Su S-L, et al. Identification of clinically important anaerobic bacteria by an oligonucleotide array. JOURNAL OF CLINICAL MICROBIOLOGY. 2010;48(4):1283–90.
MLA
Lin, Yu Tzu, Mario Vaneechoutte, Ay Huey Huang, et al. “Identification of Clinically Important Anaerobic Bacteria by an Oligonucleotide Array.” JOURNAL OF CLINICAL MICROBIOLOGY 48.4 (2010): 1283–1290. Print.