Array-based identification of species of the genera Abiotrophia, Enterococcus, Granulicatella, and Streptococcus.
Identifieur interne : 002D49 ( Main/Exploration ); précédent : 002D48; suivant : 002D50Array-based identification of species of the genera Abiotrophia, Enterococcus, Granulicatella, and Streptococcus.
Auteurs : Sheng Kai Tung [Belgique] ; Lee Jene Teng ; Mario Vaneechoutte ; Hung Mo Chen ; Tsung Chain ChangSource :
- Journal of clinical microbiology [ 0095-1137 ] ; 2006.
Descripteurs français
- KwdFr :
- ADN bactérien (), ADN bactérien (génétique), Analyse de séquence d'ADN, Bactéries à Gram positif (), Bactéries à Gram positif (génétique), Bactéries à Gram positif (isolement et purification), Données de séquences moléculaires, Enterococcus (), Enterococcus (génétique), Enterococcus (isolement et purification), Espaceur de l'ADN ribosomique (génétique), Humains, Hybridation d'acides nucléiques, Infections bactériennes à Gram positif (microbiologie), Réaction de polymérisation en chaîne, Sang (microbiologie), Sensibilité et spécificité, Sondes oligonucléotidiques, Streptococcus (), Streptococcus (génétique), Streptococcus (isolement et purification), Séquençage par oligonucléotides en batterie, Techniques bactériologiques.
- MESH :
- génétique : ADN bactérien, Bactéries à Gram positif, Enterococcus, Espaceur de l'ADN ribosomique, Streptococcus.
- isolement et purification : Bactéries à Gram positif, Enterococcus, Streptococcus.
- microbiologie : Infections bactériennes à Gram positif, Sang.
- ADN bactérien, Analyse de séquence d'ADN, Bactéries à Gram positif, Données de séquences moléculaires, Enterococcus, Humains, Hybridation d'acides nucléiques, Réaction de polymérisation en chaîne, Sensibilité et spécificité, Sondes oligonucléotidiques, Streptococcus, Séquençage par oligonucléotides en batterie, Techniques bactériologiques.
English descriptors
- KwdEn :
- Bacteriological Techniques, Blood (microbiology), DNA, Bacterial (chemistry), DNA, Bacterial (genetics), DNA, Ribosomal Spacer (genetics), Enterococcus (classification), Enterococcus (genetics), Enterococcus (isolation & purification), Gram-Positive Bacteria (classification), Gram-Positive Bacteria (genetics), Gram-Positive Bacteria (isolation & purification), Gram-Positive Bacterial Infections (microbiology), Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Oligonucleotide Probes, Polymerase Chain Reaction, Sensitivity and Specificity, Sequence Analysis, DNA, Streptococcus (classification), Streptococcus (genetics), Streptococcus (isolation & purification).
- MESH :
- chemical , chemistry : DNA, Bacterial.
- chemical , genetics : DNA, Bacterial, DNA, Ribosomal Spacer.
- classification : Enterococcus, Gram-Positive Bacteria, Streptococcus.
- genetics : Enterococcus, Gram-Positive Bacteria, Streptococcus.
- isolation & purification : Enterococcus, Gram-Positive Bacteria, Streptococcus.
- microbiology : Blood, Gram-Positive Bacterial Infections.
- Bacteriological Techniques, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Oligonucleotide Probes, Polymerase Chain Reaction, Sensitivity and Specificity, Sequence Analysis, DNA.
Abstract
Some species of enterococci and streptococci are difficult to differentiate by phenotypic traits. The feasibility of using an oligonucleotide array for identification of 11 viridans group streptococci was previously established. The aim of this study was to expand the array to identify species of Abiotrophia (1 species), Enterococcus (18 species), Granulicatella (3 species), and Streptococcus (31 species and 6 subspecies). The method consisted of PCR amplification of the ribosomal DNA intergenic spacer (ITS) regions, followed by hybridization of the digoxigenin-labeled PCR products to a panel of oligonucleotide probes (16- to 30-mers) immobilized on a nylon membrane. Probes could be divided into three categories: species specific, group specific, and supplemental probes. All probes were designed either from the ITS regions or from the 3' ends of the 16S rRNA genes. A collection of 312 target strains (162 reference strains and 150 clinical isolates) and 73 nontarget strains was identified by the array. Most clinical isolates were isolated from blood cultures or deep abscesses, and only those strains having excellent species identification with the Rapid ID 32 STREP system (bioMérieux Vitek, Taipei, Taiwan) were used for array testing. The test sensitivity and specificity of the array were 100% (312/312) and 98.6% (72/73), respectively. The whole procedure of array hybridization took about 8 h, starting from isolated colonies, and the hybridization patterns could be read by the naked eye. The oligonucleotide array is accurate for identification of the above microorganisms and could be used as a reliable alternative to phenotypic identification methods.
DOI: 10.1128/JCM.01712-06
PubMed: 17065265
Affiliations:
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Le document en format XML
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Hospital</wicri:noRegion></affiliation></author><author><name sortKey="Teng, Lee Jene" sort="Teng, Lee Jene" uniqKey="Teng L" first="Lee Jene" last="Teng">Lee Jene Teng</name></author><author><name sortKey="Vaneechoutte, Mario" sort="Vaneechoutte, Mario" uniqKey="Vaneechoutte M" first="Mario" last="Vaneechoutte">Mario Vaneechoutte</name></author><author><name sortKey="Chen, Hung Mo" sort="Chen, Hung Mo" uniqKey="Chen H" first="Hung Mo" last="Chen">Hung Mo Chen</name></author><author><name sortKey="Chang, Tsung Chain" sort="Chang, Tsung Chain" uniqKey="Chang T" first="Tsung Chain" last="Chang">Tsung Chain Chang</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2006">2006</date><idno type="RBID">pubmed:17065265</idno><idno type="pmid">17065265</idno><idno type="doi">10.1128/JCM.01712-06</idno><idno type="wicri:Area/PubMed/Corpus">002216</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" 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last="Tung">Sheng Kai Tung</name><affiliation wicri:level="1"><nlm:affiliation>Department of Medical Laboratory Science and Biotechnology, School of Medicine, National Cheng Kung University, Tainan, Taiwan, Republic of China, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Medical Laboratory Science and Biotechnology, School of Medicine, National Cheng Kung University, Tainan, Taiwan, Republic of China, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital</wicri:regionArea><wicri:noRegion>Ghent University Hospital</wicri:noRegion></affiliation></author><author><name sortKey="Teng, Lee Jene" sort="Teng, Lee Jene" uniqKey="Teng L" first="Lee Jene" last="Teng">Lee Jene Teng</name></author><author><name sortKey="Vaneechoutte, Mario" sort="Vaneechoutte, Mario" uniqKey="Vaneechoutte M" first="Mario" last="Vaneechoutte">Mario Vaneechoutte</name></author><author><name sortKey="Chen, Hung Mo" sort="Chen, Hung Mo" uniqKey="Chen H" first="Hung Mo" last="Chen">Hung Mo Chen</name></author><author><name sortKey="Chang, Tsung Chain" sort="Chang, Tsung Chain" uniqKey="Chang T" first="Tsung Chain" last="Chang">Tsung Chain Chang</name></author></analytic><series><title level="j">Journal of clinical microbiology</title><idno type="ISSN">0095-1137</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bacteriological Techniques</term><term>Blood (microbiology)</term><term>DNA, Bacterial (chemistry)</term><term>DNA, Bacterial (genetics)</term><term>DNA, Ribosomal Spacer (genetics)</term><term>Enterococcus (classification)</term><term>Enterococcus (genetics)</term><term>Enterococcus (isolation & purification)</term><term>Gram-Positive Bacteria (classification)</term><term>Gram-Positive Bacteria (genetics)</term><term>Gram-Positive Bacteria (isolation & purification)</term><term>Gram-Positive Bacterial Infections (microbiology)</term><term>Humans</term><term>Molecular Sequence Data</term><term>Nucleic Acid Hybridization</term><term>Oligonucleotide Array Sequence Analysis</term><term>Oligonucleotide Probes</term><term>Polymerase Chain Reaction</term><term>Sensitivity and Specificity</term><term>Sequence Analysis, DNA</term><term>Streptococcus (classification)</term><term>Streptococcus (genetics)</term><term>Streptococcus (isolation & purification)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN bactérien ()</term><term>ADN bactérien (génétique)</term><term>Analyse de séquence d'ADN</term><term>Bactéries à Gram positif ()</term><term>Bactéries à Gram positif (génétique)</term><term>Bactéries à Gram positif (isolement et purification)</term><term>Données de séquences moléculaires</term><term>Enterococcus ()</term><term>Enterococcus (génétique)</term><term>Enterococcus (isolement et purification)</term><term>Espaceur de l'ADN ribosomique (génétique)</term><term>Humains</term><term>Hybridation d'acides nucléiques</term><term>Infections bactériennes à Gram positif (microbiologie)</term><term>Réaction de polymérisation en chaîne</term><term>Sang (microbiologie)</term><term>Sensibilité et spécificité</term><term>Sondes oligonucléotidiques</term><term>Streptococcus ()</term><term>Streptococcus (génétique)</term><term>Streptococcus (isolement et purification)</term><term>Séquençage par oligonucléotides en batterie</term><term>Techniques bactériologiques</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA, Bacterial</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Bacterial</term><term>DNA, Ribosomal Spacer</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Enterococcus</term><term>Gram-Positive Bacteria</term><term>Streptococcus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Enterococcus</term><term>Gram-Positive Bacteria</term><term>Streptococcus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN bactérien</term><term>Bactéries à Gram positif</term><term>Enterococcus</term><term>Espaceur de l'ADN ribosomique</term><term>Streptococcus</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Enterococcus</term><term>Gram-Positive Bacteria</term><term>Streptococcus</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Bactéries à Gram positif</term><term>Enterococcus</term><term>Streptococcus</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Infections bactériennes à Gram positif</term><term>Sang</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Blood</term><term>Gram-Positive Bacterial Infections</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Bacteriological Techniques</term><term>Humans</term><term>Molecular Sequence Data</term><term>Nucleic Acid Hybridization</term><term>Oligonucleotide Array Sequence Analysis</term><term>Oligonucleotide Probes</term><term>Polymerase Chain Reaction</term><term>Sensitivity and Specificity</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN bactérien</term><term>Analyse de séquence d'ADN</term><term>Bactéries à Gram positif</term><term>Données de séquences moléculaires</term><term>Enterococcus</term><term>Humains</term><term>Hybridation d'acides nucléiques</term><term>Réaction de polymérisation en chaîne</term><term>Sensibilité et spécificité</term><term>Sondes oligonucléotidiques</term><term>Streptococcus</term><term>Séquençage par oligonucléotides en batterie</term><term>Techniques bactériologiques</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Some species of enterococci and streptococci are difficult to differentiate by phenotypic traits. The feasibility of using an oligonucleotide array for identification of 11 viridans group streptococci was previously established. The aim of this study was to expand the array to identify species of Abiotrophia (1 species), Enterococcus (18 species), Granulicatella (3 species), and Streptococcus (31 species and 6 subspecies). The method consisted of PCR amplification of the ribosomal DNA intergenic spacer (ITS) regions, followed by hybridization of the digoxigenin-labeled PCR products to a panel of oligonucleotide probes (16- to 30-mers) immobilized on a nylon membrane. Probes could be divided into three categories: species specific, group specific, and supplemental probes. All probes were designed either from the ITS regions or from the 3' ends of the 16S rRNA genes. A collection of 312 target strains (162 reference strains and 150 clinical isolates) and 73 nontarget strains was identified by the array. Most clinical isolates were isolated from blood cultures or deep abscesses, and only those strains having excellent species identification with the Rapid ID 32 STREP system (bioMérieux Vitek, Taipei, Taiwan) were used for array testing. The test sensitivity and specificity of the array were 100% (312/312) and 98.6% (72/73), respectively. The whole procedure of array hybridization took about 8 h, starting from isolated colonies, and the hybridization patterns could be read by the naked eye. The oligonucleotide array is accurate for identification of the above microorganisms and could be used as a reliable alternative to phenotypic identification methods.</div></front></TEI><affiliations><list><country><li>Belgique</li></country></list><tree><noCountry><name sortKey="Chang, Tsung Chain" sort="Chang, Tsung Chain" uniqKey="Chang T" first="Tsung Chain" last="Chang">Tsung Chain Chang</name><name sortKey="Chen, Hung Mo" sort="Chen, Hung Mo" uniqKey="Chen H" first="Hung Mo" last="Chen">Hung Mo Chen</name><name sortKey="Teng, Lee Jene" sort="Teng, Lee Jene" uniqKey="Teng L" first="Lee Jene" last="Teng">Lee Jene Teng</name><name sortKey="Vaneechoutte, Mario" sort="Vaneechoutte, Mario" uniqKey="Vaneechoutte M" first="Mario" last="Vaneechoutte">Mario Vaneechoutte</name></noCountry><country name="Belgique"><noRegion><name sortKey="Tung, Sheng Kai" sort="Tung, Sheng Kai" uniqKey="Tung S" first="Sheng Kai" last="Tung">Sheng Kai Tung</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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