Identification of clinically important anaerobic bacteria by an oligonucleotide array.
Identifieur interne : 001F70 ( PubMed/Curation ); précédent : 001F69; suivant : 001F71Identification of clinically important anaerobic bacteria by an oligonucleotide array.
Auteurs : Yu Tzu Lin [Taïwan] ; Mario Vaneechoutte ; Ay Huey Huang ; Lee Jene Teng ; Hung-Mo Chen ; Shu-Li Su ; Tsung Chain ChangSource :
- Journal of clinical microbiology [ 1098-660X ] ; 2010.
Descripteurs français
- KwdFr :
- ADN bactérien (), ADN bactérien (génétique), Amorces ADN (génétique), Analyse de séquence d'ADN, Bactéries anaérobies (), Bactéries anaérobies (génétique), Bactéries anaérobies (isolement et purification), Données de séquences moléculaires, Espaceur de l'ADN ribosomique (), Espaceur de l'ADN ribosomique (génétique), Humains, Hybridation d'acides nucléiques, Infections bactériennes (diagnostic), Infections bactériennes (microbiologie), Réaction de polymérisation en chaîne (), Sensibilité et spécificité, Séquençage par oligonucléotides en batterie (), Techniques bactériologiques ().
- MESH :
- diagnostic : Infections bactériennes.
- génétique : ADN bactérien, Amorces ADN, Bactéries anaérobies, Espaceur de l'ADN ribosomique.
- isolement et purification : Bactéries anaérobies.
- microbiologie : Infections bactériennes.
- ADN bactérien, Analyse de séquence d'ADN, Bactéries anaérobies, Données de séquences moléculaires, Espaceur de l'ADN ribosomique, Humains, Hybridation d'acides nucléiques, Réaction de polymérisation en chaîne, Sensibilité et spécificité, Séquençage par oligonucléotides en batterie, Techniques bactériologiques.
English descriptors
- KwdEn :
- Bacteria, Anaerobic (classification), Bacteria, Anaerobic (genetics), Bacteria, Anaerobic (isolation & purification), Bacterial Infections (diagnosis), Bacterial Infections (microbiology), Bacteriological Techniques (methods), DNA Primers (genetics), DNA, Bacterial (chemistry), DNA, Bacterial (genetics), DNA, Ribosomal Spacer (chemistry), DNA, Ribosomal Spacer (genetics), Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis (methods), Polymerase Chain Reaction (methods), Sensitivity and Specificity, Sequence Analysis, DNA.
- MESH :
- chemical , chemistry : DNA, Bacterial, DNA, Ribosomal Spacer.
- chemical , genetics : DNA Primers, DNA, Bacterial, DNA, Ribosomal Spacer.
- classification : Bacteria, Anaerobic.
- diagnosis : Bacterial Infections.
- genetics : Bacteria, Anaerobic.
- isolation & purification : Bacteria, Anaerobic.
- methods : Bacteriological Techniques, Oligonucleotide Array Sequence Analysis, Polymerase Chain Reaction.
- microbiology : Bacterial Infections.
- Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Sensitivity and Specificity, Sequence Analysis, DNA.
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.
DOI: 10.1128/JCM.01620-09
PubMed: 20129959
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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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">20129959</PMID><DateCompleted><Year>2010</Year><Month>06</Month><Day>15</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1098-660X</ISSN><JournalIssue CitedMedium="Internet"><Volume>48</Volume><Issue>4</Issue><PubDate><Year>2010</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Journal of clinical microbiology</Title><ISOAbbreviation>J. Clin. Microbiol.</ISOAbbreviation></Journal><ArticleTitle>Identification of clinically important anaerobic bacteria by an oligonucleotide array.</ArticleTitle><Pagination><MedlinePgn>1283-90</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1128/JCM.01620-09</ELocationID><Abstract><AbstractText>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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Lin</LastName><ForeName>Yu Tzu</ForeName><Initials>YT</Initials><AffiliationInfo><Affiliation>Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vaneechoutte</LastName><ForeName>Mario</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Huang</LastName><ForeName>Ay Huey</ForeName><Initials>AH</Initials></Author><Author ValidYN="Y"><LastName>Teng</LastName><ForeName>Lee Jene</ForeName><Initials>LJ</Initials></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Hung-Mo</ForeName><Initials>HM</Initials></Author><Author ValidYN="Y"><LastName>Su</LastName><ForeName>Shu-Li</ForeName><Initials>SL</Initials></Author><Author ValidYN="Y"><LastName>Chang</LastName><ForeName>Tsung Chain</ForeName><Initials>TC</Initials></Author></AuthorList><Language>eng</Language><DataBankList 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