AustralieFrV1, Pmc, Curation, bibRecord, 000E71

High-Throughput Genotyping of Salmonella enterica Serovar Typhi Allowing Geographical Assignment of Haplotypes and Pathotypes within an Urban District of Jakarta, Indonesia ▿ †

Identifieur interne : 000E71 ( Pmc/Curation ); précédent : 000E70; suivant : 000E72

High-Throughput Genotyping of Salmonella enterica Serovar Typhi Allowing Geographical Assignment of Haplotypes and Pathotypes within an Urban District of Jakarta, Indonesia ▿ †

Auteurs : Stephen Baker ; Kathryn Holt ; Esther Van De Vosse ; Philippe Roumagnac ; Sally Whitehead ; Emma King ; Philip Ewels ; Andrew Keniry ; François-Xavier Weill ; Diane Lightfoot ; Jaap T. Van Dissel ; Kenneth E. Sanderson ; Jeremy Farrar ; Mark Achtman ; Panagiotis Deloukas ; Gordon Dougan

Source :

Journal of Clinical Microbiology [ 0095-1137 ] ; 2008.

RBID : PMC:2395080

Abstract

High-throughput epidemiological typing systems that provide phylogenetic and genotypic information are beneficial for tracking bacterial pathogens in the field. The incidence of Salmonella enterica serovar Typhi infection in Indonesia is high and is associated with atypical phenotypic traits such as expression of the j and the z66 flagellum antigens. Utilizing a high-throughput genotyping platform to investigate known nucleotide polymorphisms dispersed around the genome, we determined the haplotypes of 140 serovar Typhi isolates associated with Indonesia. We identified nine distinct serovar Typhi haplotypes circulating in Indonesia for more than 30 years, with eight of these present in a single Jakarta suburb within a 2-year period. One dominant haplotype, H59, is associated with j and z66 flagellum expression, representing a potential pathotype unique to Indonesia. Phylogenetic analysis suggests that H59 z66⁺, j⁺ isolates emerged relatively recently in terms of the origin of serovar Typhi and are geographically restricted. These data demonstrate the potential of high-throughput genotyping platforms for analyzing serovar Typhi populations in the field. The study also provides insight into the evolution of serovar Typhi and demonstrates the value of a molecular epidemiological technique that is exchangeable, that is internet friendly, and that has global utility.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2395080

DOI: 10.1128/JCM.02249-07
PubMed: 18322069
PubMed Central: 2395080

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 Serovar Typhi Allowing Geographical Assignment of Haplotypes and Pathotypes within an Urban District of Jakarta, Indonesia <xref ref-type="fn" rid="fn2">▿</xref>
 <xref ref-type="fn" rid="fn1">†</xref>
 </title>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">High-Throughput Genotyping of <italic>Salmonella enterica</italic>
 Serovar Typhi Allowing Geographical Assignment of Haplotypes and Pathotypes within an Urban District of Jakarta, Indonesia <xref ref-type="fn" rid="fn2">▿</xref>
 <xref ref-type="fn" rid="fn1">†</xref>
 </title>
<author><name sortKey="Baker, Stephen" sort="Baker, Stephen" uniqKey="Baker S" first="Stephen" last="Baker">Stephen Baker</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Holt, Kathryn" sort="Holt, Kathryn" uniqKey="Holt K" first="Kathryn" last="Holt">Kathryn Holt</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Van De Vosse, Esther" sort="Van De Vosse, Esther" uniqKey="Van De Vosse E" first="Esther" last="Van De Vosse">Esther Van De Vosse</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Roumagnac, Philippe" sort="Roumagnac, Philippe" uniqKey="Roumagnac P" first="Philippe" last="Roumagnac">Philippe Roumagnac</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Whitehead, Sally" sort="Whitehead, Sally" uniqKey="Whitehead S" first="Sally" last="Whitehead">Sally Whitehead</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="King, Emma" sort="King, Emma" uniqKey="King E" first="Emma" last="King">Emma King</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Ewels, Philip" sort="Ewels, Philip" uniqKey="Ewels P" first="Philip" last="Ewels">Philip Ewels</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Keniry, Andrew" sort="Keniry, Andrew" uniqKey="Keniry A" first="Andrew" last="Keniry">Andrew Keniry</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Weill, Francois Xavier" sort="Weill, Francois Xavier" uniqKey="Weill F" first="François-Xavier" last="Weill">François-Xavier Weill</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Lightfoot, Diane" sort="Lightfoot, Diane" uniqKey="Lightfoot D" first="Diane" last="Lightfoot">Diane Lightfoot</name>
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</affiliation>
</author>
<author><name sortKey="Van Dissel, Jaap T" sort="Van Dissel, Jaap T" uniqKey="Van Dissel J" first="Jaap T." last="Van Dissel">Jaap T. Van Dissel</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
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<author><name sortKey="Sanderson, Kenneth E" sort="Sanderson, Kenneth E" uniqKey="Sanderson K" first="Kenneth E." last="Sanderson">Kenneth E. Sanderson</name>
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</affiliation>
</author>
<author><name sortKey="Farrar, Jeremy" sort="Farrar, Jeremy" uniqKey="Farrar J" first="Jeremy" last="Farrar">Jeremy Farrar</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Achtman, Mark" sort="Achtman, Mark" uniqKey="Achtman M" first="Mark" last="Achtman">Mark Achtman</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Deloukas, Panagiotis" sort="Deloukas, Panagiotis" uniqKey="Deloukas P" first="Panagiotis" last="Deloukas">Panagiotis Deloukas</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Dougan, Gordon" sort="Dougan, Gordon" uniqKey="Dougan G" first="Gordon" last="Dougan">Gordon Dougan</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
</analytic>
<series><title level="j">Journal of Clinical Microbiology</title>
<idno type="ISSN">0095-1137</idno>
<idno type="eISSN">1098-660X</idno>
<imprint><date when="2008">2008</date>
</imprint>
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<front><div type="abstract" xml:lang="en"><p>High-throughput epidemiological typing systems that provide phylogenetic and genotypic information are beneficial for tracking bacterial pathogens in the field. The incidence of <italic>Salmonella enterica</italic>
 serovar Typhi infection in Indonesia is high and is associated with atypical phenotypic traits such as expression of the j and the z66 flagellum antigens. Utilizing a high-throughput genotyping platform to investigate known nucleotide polymorphisms dispersed around the genome, we determined the haplotypes of 140 serovar Typhi isolates associated with Indonesia. We identified nine distinct serovar Typhi haplotypes circulating in Indonesia for more than 30 years, with eight of these present in a single Jakarta suburb within a 2-year period. One dominant haplotype, H59, is associated with j and z66 flagellum expression, representing a potential pathotype unique to Indonesia. Phylogenetic analysis suggests that H59 z66<sup>+</sup>
, j<sup>+</sup>
 isolates emerged relatively recently in terms of the origin of serovar Typhi and are geographically restricted. These data demonstrate the potential of high-throughput genotyping platforms for analyzing serovar Typhi populations in the field. The study also provides insight into the evolution of serovar Typhi and demonstrates the value of a molecular epidemiological technique that is exchangeable, that is internet friendly, and that has global utility.</p>
</div>
</front>
</TEI>
<pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
  <front><journal-meta><journal-id journal-id-type="nlm-ta">J Clin Microbiol</journal-id>
<journal-id journal-id-type="publisher-id">jcm</journal-id>
<journal-title>Journal of Clinical Microbiology</journal-title>
<issn pub-type="ppub">0095-1137</issn>
<issn pub-type="epub">1098-660X</issn>
<publisher><publisher-name>American Society for Microbiology (ASM)</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">18322069</article-id>
<article-id pub-id-type="pmc">2395080</article-id>
<article-id pub-id-type="publisher-id">2249-07</article-id>
<article-id pub-id-type="doi">10.1128/JCM.02249-07</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Epidemiology</subject>
</subj-group>
</article-categories>
<title-group><article-title>High-Throughput Genotyping of <italic>Salmonella enterica</italic>
 Serovar Typhi Allowing Geographical Assignment of Haplotypes and Pathotypes within an Urban District of Jakarta, Indonesia <xref ref-type="fn" rid="fn2">▿</xref>
 <xref ref-type="fn" rid="fn1">†</xref>
 </article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Baker</surname>
<given-names>Stephen</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="aff" rid="aff1">2</xref>
<xref ref-type="corresp" rid="cor1">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Holt</surname>
<given-names>Kathryn</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>van de Vosse</surname>
<given-names>Esther</given-names>
</name>
<xref ref-type="aff" rid="aff1">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Roumagnac</surname>
<given-names>Philippe</given-names>
</name>
<xref ref-type="aff" rid="aff1">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Whitehead</surname>
<given-names>Sally</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>King</surname>
<given-names>Emma</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ewels</surname>
<given-names>Philip</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Keniry</surname>
<given-names>Andrew</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Weill</surname>
<given-names>François-Xavier</given-names>
</name>
<xref ref-type="aff" rid="aff1">5</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lightfoot</surname>
<given-names>Diane</given-names>
</name>
<xref ref-type="aff" rid="aff1">6</xref>
</contrib>
<contrib contrib-type="author"><name><surname>van Dissel</surname>
<given-names>Jaap T.</given-names>
</name>
<xref ref-type="aff" rid="aff1">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Sanderson</surname>
<given-names>Kenneth E.</given-names>
</name>
<xref ref-type="aff" rid="aff1">7</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Farrar</surname>
<given-names>Jeremy</given-names>
</name>
<xref ref-type="aff" rid="aff1">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Achtman</surname>
<given-names>Mark</given-names>
</name>
<xref ref-type="aff" rid="aff1">8</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Deloukas</surname>
<given-names>Panagiotis</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Dougan</surname>
<given-names>Gordon</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
</contrib-group>
<aff id="aff1">The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom,<label>1</label>
 Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam,<label>2</label>
 Department of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands,<label>3</label>
 Centre National de la Recherche Scientifique, Saint Paul Lez Durance, France,<label>4</label>
 Centre National de Référence des Salmonella, Institut Pasteur, Paris, France,<label>5</label>
 Microbiological Diagnostic Unit-Public Health Laboratory, University of Melbourne, Melbourne, Victoria, Australia,<label>6</label>
 Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada,<label>7</label>
 Environmental Research Institute, University College Cork, Cork, Ireland<label>8</label>
</aff>
<author-notes><fn id="cor1"><label>*</label>
<p>Corresponding author. Mailing address: Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 190 Ben Ham Tu, Quan 5, Ho Chi Minh City, Vietnam. Phone: (84-8) 9 241 761. Fax: (84-8) 9 238 904. E-mail: <email>sbaker@oucru.org</email>
</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><month>5</month>
<year>2008</year>
</pub-date>
<pub-date pub-type="epub"><day>5</day>
<month>3</month>
<year>2008</year>
</pub-date>
<volume>46</volume>
<issue>5</issue>
<fpage>1741</fpage>
<lpage>1746</lpage>
<history><date date-type="received"><day>20</day>
<month>11</month>
<year>2007</year>
</date>
<date date-type="rev-recd"><day>8</day>
<month>2</month>
<year>2008</year>
</date>
<date date-type="accepted"><day>17</day>
<month>2</month>
<year>2008</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2008, American Society for Microbiology</copyright-statement>
</permissions>
<self-uri xlink:title="pdf" xlink:href="zjm00508001741.pdf"></self-uri>
<abstract><p>High-throughput epidemiological typing systems that provide phylogenetic and genotypic information are beneficial for tracking bacterial pathogens in the field. The incidence of <italic>Salmonella enterica</italic>
 serovar Typhi infection in Indonesia is high and is associated with atypical phenotypic traits such as expression of the j and the z66 flagellum antigens. Utilizing a high-throughput genotyping platform to investigate known nucleotide polymorphisms dispersed around the genome, we determined the haplotypes of 140 serovar Typhi isolates associated with Indonesia. We identified nine distinct serovar Typhi haplotypes circulating in Indonesia for more than 30 years, with eight of these present in a single Jakarta suburb within a 2-year period. One dominant haplotype, H59, is associated with j and z66 flagellum expression, representing a potential pathotype unique to Indonesia. Phylogenetic analysis suggests that H59 z66<sup>+</sup>
, j<sup>+</sup>
 isolates emerged relatively recently in terms of the origin of serovar Typhi and are geographically restricted. These data demonstrate the potential of high-throughput genotyping platforms for analyzing serovar Typhi populations in the field. The study also provides insight into the evolution of serovar Typhi and demonstrates the value of a molecular epidemiological technique that is exchangeable, that is internet friendly, and that has global utility.</p>
</abstract>
</article-meta>
</front>
<floats-wrap><fig position="float" id="f1"><label>FIG. 1.</label>
<caption><p>Minimal spanning tree based upon SNPs, demonstrating the relationship of the isolates used in the present study. This illustration is modified from Fig. <xref rid="f1" ref-type="fig">1</xref>
 of Roumagnac et al. (<xref ref-type="bibr" rid="r24">24</xref>
) and demonstrates the relationship of the 161 strains used here. The 18 serovar Typhi control strains with known haplotypes are labeled green and include CT18 (superscript a), Ty2 (superscript b), E00-7866 (superscript c), and AG3 (superscript d). The 140 experimental serovar Typhi strains are distinguished by red clusters, and the three serovar Paratyphi A isolates are colored yellow. The specific haplotype for each cluster is labeled (e.g., H45), and undetected haplotypes are gray. The size of each cluster corresponds to the number of strains identified in each group; this is demonstrated by the key in the bottom right corner.</p>
</caption>
<graphic xlink:href="zjm0050880800001"></graphic>
</fig>
<fig position="float" id="f2"><label>FIG. 2.</label>
<caption><p>Specific locations of serovar Typhi haplotypes isolated in Jatinegara, Jakarta. A map of the Jatinegara area in Eastern Jakarta highlighted to demonstrate the association of the household of the typhoid patient with the haplotype of the serovar Typhi bacteria isolated from the patient. Each specific haplotype corresponds to a colored circle as depicted on the right. H45* demonstrates the location of a household from which serovar Paratyphi A was isolated. The red circle enclosed by a black circle depicts the location of four individual typhoid patients from which H59 serovar Typhi was isolated.</p>
</caption>
<graphic xlink:href="zjm0050880800002"></graphic>
</fig>
<fig position="float" id="f3"><label>FIG. 3.</label>
<caption><p>Association of the <italic>fliC</italic>
 and <italic>fljB</italic>
(z66) flagellin genes with specific haplotypes. (A) Diagram displaying the association of <italic>fliC</italic>
 allele with haplotype of 140 serovar Typhi strains. The strains with harbor the <italic>fliC</italic>
 gene which directs expression of the d antigen are colored gray the strains which harbor the <italic>fliC</italic>
 gene which directs expression of the j antigen are colored white. The specific haplotypes are labeled in association with Fig. <xref rid="f1" ref-type="fig">1</xref>
, and the sizes of the clusters correspond to the number of strains located within each group; this is demonstrated by the key in the bottom right corner. (B) Diagram displaying the association of <italic>fljB</italic>
(z66) gene with haplotype H59 in 140 serovar Typhi strains. The groups of strains lacking the <italic>fljB</italic>
(z66) gene are white, and the strains harboring the <italic>fljB</italic>
(z66) gene are shaded gray. The strains harboring the <italic>fljB</italic>
(z66) gene are further subdivided in to groups carrying the <italic>fliC</italic>
 j allele (solid gray) or the <italic>fliC</italic>
 d allele (broken gray). The specific haplotypes are labeled in association with Fig. <xref rid="f1" ref-type="fig">1</xref>
, and the sizes of the clusters correspond to the number of strains located within each group, as Fig. <xref rid="f3" ref-type="fig">3A</xref>
.</p>
</caption>
<graphic xlink:href="zjm0050880800003"></graphic>
</fig>
</floats-wrap>
</pmc>
</record>

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	Serveur d'exploration sur les relations entre la France et l'Australie
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Serveur d'exploration sur les relations entre la France et l'Australie

High-Throughput Genotyping of Salmonella enterica Serovar Typhi Allowing Geographical Assignment of Haplotypes and Pathotypes within an Urban District of Jakarta, Indonesia ▿ †

High-Throughput Genotyping of Salmonella enterica Serovar Typhi Allowing Geographical Assignment of Haplotypes and Pathotypes within an Urban District of Jakarta, Indonesia ▿ †

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