Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: Identification of genes absent from epidemic strains
Identifieur interne : 002A00 ( Main/Exploration ); précédent : 002999; suivant : 002A01Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: Identification of genes absent from epidemic strains
Auteurs : Audrey J. King [Pays-Bas] ; Tamara Van Gorkom [Pays-Bas] ; Jeroen La Pennings [Pays-Bas] ; Han Gj Van Der Heide [Pays-Bas] ; Qiushui He [Finlande] ; Dimitri Diavatopoulos [Australie] ; Kees Heuvelman [Pays-Bas] ; Marjolein Van Gent [Pays-Bas] ; Karin Van Leeuwen [Pays-Bas] ; Frits R. Mooi [Pays-Bas]Source :
- BMC Genomics [ 1471-2164 ] ; 2008.
Descripteurs français
- KwdFr :
- ADN bactérien (génétique), ADN bactérien (isolement et purification), Allèles, Analyse de profil d'expression de gènes, Analyse de regroupements, Analyse de séquence d'ADN, Bordetella pertussis (), Bordetella pertussis (génétique), Bordetella pertussis (isolement et purification), Coqueluche (microbiologie), Coqueluche (épidémiologie), Fréquence d'allèle, Gènes bactériens, Humains, Hybridation d'acides nucléiques, Hétérogénéité génétique, Modèles génétiques, Mutation ponctuelle, Pays-Bas (épidémiologie), Séquences répétées en tandem (génétique), Séquençage par oligonucléotides en batterie (), Techniques de typage bactérien, Variation génétique, Études rétrospectives, Évolution moléculaire.
- MESH :
- génétique : ADN bactérien, Bordetella pertussis, Séquences répétées en tandem.
- isolement et purification : ADN bactérien, Bordetella pertussis.
- microbiologie : Coqueluche.
- épidémiologie : Coqueluche, Pays-Bas.
- Allèles, Analyse de profil d'expression de gènes, Analyse de regroupements, Analyse de séquence d'ADN, Bordetella pertussis, Fréquence d'allèle, Gènes bactériens, Humains, Hybridation d'acides nucléiques, Hétérogénéité génétique, Modèles génétiques, Mutation ponctuelle, Séquençage par oligonucléotides en batterie, Techniques de typage bactérien, Variation génétique, Études rétrospectives, Évolution moléculaire.
- Wicri :
- geographic : Pays-Bas.
English descriptors
- KwdEn :
- Alleles, Bacterial Typing Techniques, Bordetella pertussis (classification), Bordetella pertussis (genetics), Bordetella pertussis (isolation & purification), Cluster Analysis, DNA, Bacterial (genetics), DNA, Bacterial (isolation & purification), Evolution, Molecular, Gene Expression Profiling, Gene Frequency, Genes, Bacterial, Genetic Heterogeneity, Genetic Variation, Humans, Models, Genetic, Netherlands (epidemiology), Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis (methods), Point Mutation, Retrospective Studies, Sequence Analysis, DNA, Tandem Repeat Sequences (genetics), Whooping Cough (epidemiology), Whooping Cough (microbiology).
- MESH :
- chemical , genetics : DNA, Bacterial.
- geographic , epidemiology : Netherlands.
- classification : Bordetella pertussis.
- epidemiology : Whooping Cough.
- genetics : Bordetella pertussis, Tandem Repeat Sequences.
- isolation & purification : Bordetella pertussis, DNA, Bacterial.
- methods : Oligonucleotide Array Sequence Analysis.
- microbiology : Whooping Cough.
- Alleles, Bacterial Typing Techniques, Cluster Analysis, Evolution, Molecular, Gene Expression Profiling, Gene Frequency, Genes, Bacterial, Genetic Heterogeneity, Genetic Variation, Humans, Models, Genetic, Nucleic Acid Hybridization, Point Mutation, Retrospective Studies, Sequence Analysis, DNA.
Abstract
Whooping cough caused by
We used Multi-Locus Sequence Typing (MLST), Multiple-Locus Variable Number of Tandem Repeat Analysis (MLVA) and microarray-based comparative genomic hybridization (CGH) to characterize the
The presented MLST, MLVA and CGH-analysis identified distinctive characteristics of
Url:
DOI: 10.1186/1471-2164-9-311
PubMed: 18590534
PubMed Central: 2481270
Affiliations:
- Australie, Finlande, Pays-Bas
- Finlande occidentale, Victoria (État)
- Melbourne, Turku
- Université de Melbourne
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Le document en format XML
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King</name><affiliation wicri:level="1"><nlm:aff id="I1">Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven</wicri:regionArea><wicri:noRegion>Bilthoven</wicri:noRegion></affiliation></author><author><name sortKey="Van Gorkom, Tamara" sort="Van Gorkom, Tamara" uniqKey="Van Gorkom T" first="Tamara" last="Van Gorkom">Tamara Van Gorkom</name><affiliation wicri:level="1"><nlm:aff id="I1">Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands</nlm:aff><country 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King</name><affiliation wicri:level="1"><nlm:aff id="I1">Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven</wicri:regionArea><wicri:noRegion>Bilthoven</wicri:noRegion></affiliation></author><author><name sortKey="Van Gorkom, Tamara" sort="Van Gorkom, Tamara" uniqKey="Van Gorkom T" first="Tamara" last="Van Gorkom">Tamara Van Gorkom</name><affiliation wicri:level="1"><nlm:aff id="I1">Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven</wicri:regionArea><wicri:noRegion>Bilthoven</wicri:noRegion></affiliation></author><author><name sortKey="Pennings, Jeroen La" sort="Pennings, Jeroen La" uniqKey="Pennings J" first="Jeroen La" last="Pennings">Jeroen La Pennings</name><affiliation wicri:level="1"><nlm:aff id="I2">Laboratory for Health Protection Research, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Laboratory for Health Protection Research, National Institute for Public Health and the Environment (RIVM), Bilthoven</wicri:regionArea><wicri:noRegion>Bilthoven</wicri:noRegion></affiliation></author><author><name sortKey="Van Der Heide, Han Gj" sort="Van Der Heide, Han Gj" uniqKey="Van Der Heide H" first="Han Gj" last="Van Der Heide">Han Gj Van Der Heide</name><affiliation wicri:level="1"><nlm:aff id="I1">Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven</wicri:regionArea><wicri:noRegion>Bilthoven</wicri:noRegion></affiliation></author><author><name sortKey="He, Qiushui" sort="He, Qiushui" uniqKey="He Q" first="Qiushui" last="He">Qiushui He</name><affiliation wicri:level="3"><nlm:aff id="I3">Pertussis Reference Laboratory, National Public Health Institute, Turku, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Pertussis Reference Laboratory, National Public Health Institute, Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName></affiliation></author><author><name sortKey="Diavatopoulos, Dimitri" sort="Diavatopoulos, Dimitri" uniqKey="Diavatopoulos D" first="Dimitri" last="Diavatopoulos">Dimitri Diavatopoulos</name><affiliation wicri:level="4"><nlm:aff id="I4">Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Microbiology and Immunology, University of Melbourne, Victoria</wicri:regionArea><orgName type="university">Université de Melbourne</orgName><placeName><settlement type="city">Melbourne</settlement><region type="état">Victoria (État)</region></placeName></affiliation></author><author><name sortKey="Heuvelman, Kees" sort="Heuvelman, Kees" uniqKey="Heuvelman K" first="Kees" last="Heuvelman">Kees Heuvelman</name><affiliation wicri:level="1"><nlm:aff id="I1">Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven</wicri:regionArea><wicri:noRegion>Bilthoven</wicri:noRegion></affiliation></author><author><name sortKey="Van Gent, Marjolein" sort="Van Gent, Marjolein" uniqKey="Van Gent M" first="Marjolein" last="Van Gent">Marjolein Van Gent</name><affiliation wicri:level="1"><nlm:aff id="I1">Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven</wicri:regionArea><wicri:noRegion>Bilthoven</wicri:noRegion></affiliation></author><author><name sortKey="Van Leeuwen, Karin" sort="Van Leeuwen, Karin" uniqKey="Van Leeuwen K" first="Karin" last="Van Leeuwen">Karin Van Leeuwen</name><affiliation wicri:level="1"><nlm:aff id="I1">Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven</wicri:regionArea><wicri:noRegion>Bilthoven</wicri:noRegion></affiliation></author><author><name sortKey="Mooi, Frits R" sort="Mooi, Frits R" uniqKey="Mooi F" first="Frits R" last="Mooi">Frits R. Mooi</name><affiliation wicri:level="1"><nlm:aff id="I1">Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Laboratory for Infectious Diseases and Screening (LIS) Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven</wicri:regionArea><wicri:noRegion>Bilthoven</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alleles</term><term>Bacterial Typing Techniques</term><term>Bordetella pertussis (classification)</term><term>Bordetella pertussis (genetics)</term><term>Bordetella pertussis (isolation & purification)</term><term>Cluster Analysis</term><term>DNA, Bacterial (genetics)</term><term>DNA, Bacterial (isolation & purification)</term><term>Evolution, Molecular</term><term>Gene Expression Profiling</term><term>Gene Frequency</term><term>Genes, Bacterial</term><term>Genetic Heterogeneity</term><term>Genetic Variation</term><term>Humans</term><term>Models, Genetic</term><term>Netherlands (epidemiology)</term><term>Nucleic Acid Hybridization</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Point Mutation</term><term>Retrospective Studies</term><term>Sequence Analysis, DNA</term><term>Tandem Repeat Sequences (genetics)</term><term>Whooping Cough (epidemiology)</term><term>Whooping Cough (microbiology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN bactérien (génétique)</term><term>ADN bactérien (isolement et purification)</term><term>Allèles</term><term>Analyse de profil d'expression de gènes</term><term>Analyse de regroupements</term><term>Analyse de séquence d'ADN</term><term>Bordetella pertussis ()</term><term>Bordetella pertussis (génétique)</term><term>Bordetella pertussis (isolement et purification)</term><term>Coqueluche (microbiologie)</term><term>Coqueluche (épidémiologie)</term><term>Fréquence d'allèle</term><term>Gènes bactériens</term><term>Humains</term><term>Hybridation d'acides nucléiques</term><term>Hétérogénéité génétique</term><term>Modèles génétiques</term><term>Mutation ponctuelle</term><term>Pays-Bas (épidémiologie)</term><term>Séquences répétées en tandem (génétique)</term><term>Séquençage par oligonucléotides en batterie ()</term><term>Techniques de typage bactérien</term><term>Variation génétique</term><term>Études rétrospectives</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Bacterial</term></keywords><keywords scheme="MESH" type="geographic" qualifier="epidemiology" xml:lang="en"><term>Netherlands</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Bordetella pertussis</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Whooping Cough</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bordetella pertussis</term><term>Tandem Repeat Sequences</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN bactérien</term><term>Bordetella pertussis</term><term>Séquences répétées en tandem</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Bordetella pertussis</term><term>DNA, Bacterial</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>ADN bactérien</term><term>Bordetella pertussis</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Coqueluche</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Whooping Cough</term></keywords><keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr"><term>Coqueluche</term><term>Pays-Bas</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Alleles</term><term>Bacterial Typing Techniques</term><term>Cluster Analysis</term><term>Evolution, Molecular</term><term>Gene Expression Profiling</term><term>Gene Frequency</term><term>Genes, Bacterial</term><term>Genetic Heterogeneity</term><term>Genetic Variation</term><term>Humans</term><term>Models, Genetic</term><term>Nucleic Acid Hybridization</term><term>Point Mutation</term><term>Retrospective Studies</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Allèles</term><term>Analyse de profil d'expression de gènes</term><term>Analyse de regroupements</term><term>Analyse de séquence d'ADN</term><term>Bordetella pertussis</term><term>Fréquence d'allèle</term><term>Gènes bactériens</term><term>Humains</term><term>Hybridation d'acides nucléiques</term><term>Hétérogénéité génétique</term><term>Modèles génétiques</term><term>Mutation ponctuelle</term><term>Séquençage par oligonucléotides en batterie</term><term>Techniques de typage bactérien</term><term>Variation génétique</term><term>Études rétrospectives</term><term>Évolution moléculaire</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Pays-Bas</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Whooping cough caused by <italic>Bordetella pertussis </italic>in humans, is re-emerging in many countries despite vaccination. Several studies have shown that significant shifts have occurred in the <italic>B. pertussis </italic>population resulting in antigenic divergence between vaccine strains and circulating strains and suggesting pathogen adaptation. In the Netherlands, the resurgence of pertussis is associated with the rise of <italic>B. pertussis </italic>strains with an altered promoter region for pertussis toxin (<italic>ptxP3</italic>).</p></sec><sec><title>Results</title><p>We used Multi-Locus Sequence Typing (MLST), Multiple-Locus Variable Number of Tandem Repeat Analysis (MLVA) and microarray-based comparative genomic hybridization (CGH) to characterize the <italic>ptxP3 </italic>strains associated with the Dutch epidemic. For CGH analysis, we developed an oligonucleotide (70-mers) microarray consisting of 3,581 oligonucleotides representing 94% of the gene repertoire of the <italic>B. pertussis </italic>strain Tohama I. Nine different MLST profiles and 38 different MLVA types were found in the period 1993 to 2004. Forty-three Dutch clinical isolates were analyzed with CGH, 98 genes were found to be absent in at least one of the <italic>B. pertussis </italic>strains tested, these genes were clustered in 8 distinct regions of difference.</p></sec><sec><title>Conclusion</title><p>The presented MLST, MLVA and CGH-analysis identified distinctive characteristics of <italic>ptxP3 B. pertussis </italic>strains -the most prominent of which was a genomic deletion removing about 23,000 bp. We propose a model for the emergence of <italic>ptxP3 </italic>strains.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Australie</li><li>Finlande</li><li>Pays-Bas</li></country><region><li>Finlande occidentale</li><li>Victoria (État)</li></region><settlement><li>Melbourne</li><li>Turku</li></settlement><orgName><li>Université de Melbourne</li></orgName></list><tree><country name="Pays-Bas"><noRegion><name sortKey="King, Audrey J" sort="King, Audrey J" uniqKey="King A" first="Audrey J" last="King">Audrey J. King</name></noRegion><name sortKey="Heuvelman, Kees" sort="Heuvelman, Kees" uniqKey="Heuvelman K" first="Kees" last="Heuvelman">Kees Heuvelman</name><name sortKey="Mooi, Frits R" sort="Mooi, Frits R" uniqKey="Mooi F" first="Frits R" last="Mooi">Frits R. Mooi</name><name sortKey="Pennings, Jeroen La" sort="Pennings, Jeroen La" uniqKey="Pennings J" first="Jeroen La" last="Pennings">Jeroen La Pennings</name><name sortKey="Van Der Heide, Han Gj" sort="Van Der Heide, Han Gj" uniqKey="Van Der Heide H" first="Han Gj" last="Van Der Heide">Han Gj Van Der Heide</name><name sortKey="Van Gent, Marjolein" sort="Van Gent, Marjolein" uniqKey="Van Gent M" first="Marjolein" last="Van Gent">Marjolein Van Gent</name><name sortKey="Van Gorkom, Tamara" sort="Van Gorkom, Tamara" uniqKey="Van Gorkom T" first="Tamara" last="Van Gorkom">Tamara Van Gorkom</name><name sortKey="Van Leeuwen, Karin" sort="Van Leeuwen, Karin" uniqKey="Van Leeuwen K" first="Karin" last="Van Leeuwen">Karin Van Leeuwen</name></country><country name="Finlande"><region name="Finlande occidentale"><name sortKey="He, Qiushui" sort="He, Qiushui" uniqKey="He Q" first="Qiushui" last="He">Qiushui He</name></region></country><country name="Australie"><region name="Victoria (État)"><name sortKey="Diavatopoulos, Dimitri" sort="Diavatopoulos, Dimitri" uniqKey="Diavatopoulos D" first="Dimitri" last="Diavatopoulos">Dimitri Diavatopoulos</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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