Guide to the various phylogenetic classification schemes for Escherichia coli and the correspondence among schemes.
Identifieur interne : 002D33 ( PubMed/Curation ); précédent : 002D32; suivant : 002D34Guide to the various phylogenetic classification schemes for Escherichia coli and the correspondence among schemes.
Auteurs : Olivier Clermont [France] ; David Gordon ; Erick Denamur [France]Source :
- Microbiology (Reading, England) [ 1465-2080 ] ; 2015.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Escherichia coli Proteins.
- classification : Escherichia coli.
- genetics : Escherichia coli.
- Genome-Wide Association Study, Multilocus Sequence Typing, Phylogeny, Polymerase Chain Reaction.
Abstract
Numerous tools allowing the rapid and universal identification of the clones/clonal complexes/phylogroups of Escherichia coli have been developed, as it is a commensal of the vertebrate gut, a major pathogen in veterinary and human medicine, and a bacterial indicator of faecal contamination. The ability to identify clones/clonal complexes/phylogroups is crucial, as a strain's ecological niche, lifestyle and propensity to cause disease vary with its phylogenetic origins. There are currently three multi-locus sequence typing (MLST) schemes for E. coli, as well as several PCR-based assays for determining a strain's phylogroup or clonal complex. In this work, we present data that will enable investigators to determine the correspondence between the PCR-based assays and the three MLST schemes, and provide the means for assigning a sequence type (ST) to a phylogroup when no other data on the strain phylogroup membership are available. Such information will help the scientific community to accurately identify the E. coli clones reported in various publications. Although whole-genome sequencing will replace classical MLST and most alternative PCR-based methods, the ST nomenclature of the MLST scheme hosted at the University of Warwick will largely persist.
DOI: 10.1099/mic.0.000063
PubMed: 25714816
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :002E09
Links to Exploration step
pubmed:25714816Curation
No country items
David Gordon<affiliation><nlm:affiliation>Division of Evolution, Ecology & Genetics, Research School of Biology, Australian National University, Canberra, ACT 0200 Australia.</nlm:affiliation>
<wicri:noCountry code="subField">ACT 0200 Australia</wicri:noCountry>
</affiliation>
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Guide to the various phylogenetic classification schemes for Escherichia coli and the correspondence among schemes.</title>
<author><name sortKey="Clermont, Olivier" sort="Clermont, Olivier" uniqKey="Clermont O" first="Olivier" last="Clermont">Olivier Clermont</name>
<affiliation wicri:level="1"><nlm:affiliation>INSERM, IAME, UMR 1137, F-75018 Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France.</nlm:affiliation>
<country xml:lang="fr">France</country>
<wicri:regionArea>INSERM, IAME, UMR 1137, F-75018 Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Gordon, David" sort="Gordon, David" uniqKey="Gordon D" first="David" last="Gordon">David Gordon</name>
<affiliation><nlm:affiliation>Division of Evolution, Ecology & Genetics, Research School of Biology, Australian National University, Canberra, ACT 0200 Australia.</nlm:affiliation>
<wicri:noCountry code="subField">ACT 0200 Australia</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Denamur, Erick" sort="Denamur, Erick" uniqKey="Denamur E" first="Erick" last="Denamur">Erick Denamur</name>
<affiliation wicri:level="1"><nlm:affiliation>INSERM, IAME, UMR 1137, F-75018 Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France erick.denamur@inserm.fr.</nlm:affiliation>
<country wicri:rule="url">France</country>
<wicri:regionArea>INSERM, IAME, UMR 1137, F-75018 Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris</wicri:regionArea>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2015">2015</date>
<idno type="RBID">pubmed:25714816</idno>
<idno type="pmid">25714816</idno>
<idno type="doi">10.1099/mic.0.000063</idno>
<idno type="wicri:Area/PubMed/Corpus">002E09</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002E09</idno>
<idno type="wicri:Area/PubMed/Curation">002D33</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002D33</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Guide to the various phylogenetic classification schemes for Escherichia coli and the correspondence among schemes.</title>
<author><name sortKey="Clermont, Olivier" sort="Clermont, Olivier" uniqKey="Clermont O" first="Olivier" last="Clermont">Olivier Clermont</name>
<affiliation wicri:level="1"><nlm:affiliation>INSERM, IAME, UMR 1137, F-75018 Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France.</nlm:affiliation>
<country xml:lang="fr">France</country>
<wicri:regionArea>INSERM, IAME, UMR 1137, F-75018 Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Gordon, David" sort="Gordon, David" uniqKey="Gordon D" first="David" last="Gordon">David Gordon</name>
<affiliation><nlm:affiliation>Division of Evolution, Ecology & Genetics, Research School of Biology, Australian National University, Canberra, ACT 0200 Australia.</nlm:affiliation>
<wicri:noCountry code="subField">ACT 0200 Australia</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Denamur, Erick" sort="Denamur, Erick" uniqKey="Denamur E" first="Erick" last="Denamur">Erick Denamur</name>
<affiliation wicri:level="1"><nlm:affiliation>INSERM, IAME, UMR 1137, F-75018 Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France erick.denamur@inserm.fr.</nlm:affiliation>
<country wicri:rule="url">France</country>
<wicri:regionArea>INSERM, IAME, UMR 1137, F-75018 Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris</wicri:regionArea>
</affiliation>
</author>
</analytic>
<series><title level="j">Microbiology (Reading, England)</title>
<idno type="eISSN">1465-2080</idno>
<imprint><date when="2015" type="published">2015</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Escherichia coli (classification)</term>
<term>Escherichia coli (genetics)</term>
<term>Escherichia coli Proteins (genetics)</term>
<term>Genome-Wide Association Study</term>
<term>Multilocus Sequence Typing</term>
<term>Phylogeny</term>
<term>Polymerase Chain Reaction</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Escherichia coli ()</term>
<term>Escherichia coli (génétique)</term>
<term>Phylogénie</term>
<term>Protéines Escherichia coli (génétique)</term>
<term>Réaction de polymérisation en chaîne</term>
<term>Typage par séquençage multilocus</term>
<term>Étude d'association pangénomique</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Escherichia coli Proteins</term>
</keywords>
<keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Escherichia coli</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Escherichia coli</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Escherichia coli</term>
<term>Protéines Escherichia coli</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Genome-Wide Association Study</term>
<term>Multilocus Sequence Typing</term>
<term>Phylogeny</term>
<term>Polymerase Chain Reaction</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Escherichia coli</term>
<term>Phylogénie</term>
<term>Réaction de polymérisation en chaîne</term>
<term>Typage par séquençage multilocus</term>
<term>Étude d'association pangénomique</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Numerous tools allowing the rapid and universal identification of the clones/clonal complexes/phylogroups of Escherichia coli have been developed, as it is a commensal of the vertebrate gut, a major pathogen in veterinary and human medicine, and a bacterial indicator of faecal contamination. The ability to identify clones/clonal complexes/phylogroups is crucial, as a strain's ecological niche, lifestyle and propensity to cause disease vary with its phylogenetic origins. There are currently three multi-locus sequence typing (MLST) schemes for E. coli, as well as several PCR-based assays for determining a strain's phylogroup or clonal complex. In this work, we present data that will enable investigators to determine the correspondence between the PCR-based assays and the three MLST schemes, and provide the means for assigning a sequence type (ST) to a phylogroup when no other data on the strain phylogroup membership are available. Such information will help the scientific community to accurately identify the E. coli clones reported in various publications. Although whole-genome sequencing will replace classical MLST and most alternative PCR-based methods, the ST nomenclature of the MLST scheme hosted at the University of Warwick will largely persist.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25714816</PMID>
<DateCreated><Year>2015</Year>
<Month>06</Month>
<Day>04</Day>
</DateCreated>
<DateCompleted><Year>2016</Year>
<Month>02</Month>
<Day>24</Day>
</DateCompleted>
<DateRevised><Year>2015</Year>
<Month>06</Month>
<Day>04</Day>
</DateRevised>
<Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1465-2080</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>161</Volume>
<Issue>Pt 5</Issue>
<PubDate><Year>2015</Year>
<Month>May</Month>
</PubDate>
</JournalIssue>
<Title>Microbiology (Reading, England)</Title>
<ISOAbbreviation>Microbiology (Reading, Engl.)</ISOAbbreviation>
</Journal>
<ArticleTitle>Guide to the various phylogenetic classification schemes for Escherichia coli and the correspondence among schemes.</ArticleTitle>
<Pagination><MedlinePgn>980-8</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1099/mic.0.000063</ELocationID>
<Abstract><AbstractText>Numerous tools allowing the rapid and universal identification of the clones/clonal complexes/phylogroups of Escherichia coli have been developed, as it is a commensal of the vertebrate gut, a major pathogen in veterinary and human medicine, and a bacterial indicator of faecal contamination. The ability to identify clones/clonal complexes/phylogroups is crucial, as a strain's ecological niche, lifestyle and propensity to cause disease vary with its phylogenetic origins. There are currently three multi-locus sequence typing (MLST) schemes for E. coli, as well as several PCR-based assays for determining a strain's phylogroup or clonal complex. In this work, we present data that will enable investigators to determine the correspondence between the PCR-based assays and the three MLST schemes, and provide the means for assigning a sequence type (ST) to a phylogroup when no other data on the strain phylogroup membership are available. Such information will help the scientific community to accurately identify the E. coli clones reported in various publications. Although whole-genome sequencing will replace classical MLST and most alternative PCR-based methods, the ST nomenclature of the MLST scheme hosted at the University of Warwick will largely persist.</AbstractText>
<CopyrightInformation>© 2015 The Authors.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Clermont</LastName>
<ForeName>Olivier</ForeName>
<Initials>O</Initials>
<AffiliationInfo><Affiliation>INSERM, IAME, UMR 1137, F-75018 Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Gordon</LastName>
<ForeName>David</ForeName>
<Initials>D</Initials>
<AffiliationInfo><Affiliation>Division of Evolution, Ecology & Genetics, Research School of Biology, Australian National University, Canberra, ACT 0200 Australia.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Denamur</LastName>
<ForeName>Erick</ForeName>
<Initials>E</Initials>
<AffiliationInfo><Affiliation>INSERM, IAME, UMR 1137, F-75018 Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France erick.denamur@inserm.fr.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<GrantList CompleteYN="Y"><Grant><Agency>Biotechnology and Biological Sciences Research Council</Agency>
<Country>United Kingdom</Country>
</Grant>
</GrantList>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2015</Year>
<Month>02</Month>
<Day>24</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>England</Country>
<MedlineTA>Microbiology</MedlineTA>
<NlmUniqueID>9430468</NlmUniqueID>
<ISSNLinking>1350-0872</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D029968">Escherichia coli Proteins</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D004926" MajorTopicYN="N">Escherichia coli</DescriptorName>
<QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D029968" MajorTopicYN="N">Escherichia coli Proteins</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D055106" MajorTopicYN="N">Genome-Wide Association Study</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D058885" MajorTopicYN="N">Multilocus Sequence Typing</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D010802" MajorTopicYN="Y">Phylogeny</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016133" MajorTopicYN="N">Polymerase Chain Reaction</DescriptorName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year>
<Month>10</Month>
<Day>27</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2015</Year>
<Month>02</Month>
<Day>19</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez"><Year>2015</Year>
<Month>2</Month>
<Day>26</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed"><Year>2015</Year>
<Month>2</Month>
<Day>26</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2016</Year>
<Month>2</Month>
<Day>26</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">25714816</ArticleId>
<ArticleId IdType="pii">mic.0.000063</ArticleId>
<ArticleId IdType="doi">10.1099/mic.0.000063</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Asie/explor/AustralieFrV1/Data/PubMed/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002D33 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd -nk 002D33 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Wicri/Asie |area= AustralieFrV1 |flux= PubMed |étape= Curation |type= RBID |clé= pubmed:25714816 |texte= Guide to the various phylogenetic classification schemes for Escherichia coli and the correspondence among schemes. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Curation/RBID.i -Sk "pubmed:25714816" \ | HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd \ | NlmPubMed2Wicri -a AustralieFrV1
![]() | This area was generated with Dilib version V0.6.33. | ![]() |