Differentiation of Escherichia coli pathotypes by oligonucleotide spotted array.
Identifieur interne : 002261 ( PubMed/Corpus ); précédent : 002260; suivant : 002262Differentiation of Escherichia coli pathotypes by oligonucleotide spotted array.
Auteurs : Raghavan U M. Palaniappan ; Yu Zhang ; David Chiu ; Alfonso Torres ; Chobi Debroy ; Thomas S. Whittam ; Yung-Fu ChangSource :
- Journal of clinical microbiology [ 0095-1137 ] ; 2006.
English descriptors
- KwdEn :
- DNA, Bacterial (analysis), DNA, Bacterial (genetics), Escherichia coli (classification), Escherichia coli (genetics), Escherichia coli (isolation & purification), Escherichia coli (pathogenicity), Escherichia coli Infections (diagnosis), Gene Expression Profiling, Oligonucleotide Array Sequence Analysis (methods), Oligonucleotide Probes, Virulence.
- MESH :
- chemical , analysis : DNA, Bacterial.
- chemical , genetics : DNA, Bacterial.
- classification : Escherichia coli.
- diagnosis : Escherichia coli Infections.
- genetics : Escherichia coli.
- isolation & purification : Escherichia coli.
- methods : Oligonucleotide Array Sequence Analysis.
- pathogenicity : Escherichia coli.
- Gene Expression Profiling, Oligonucleotide Probes, Virulence.
Abstract
To accurately determine the pathotypes of Escherichia coli strains, a comprehensive assessment of each strain that targets multiple genes is required. A new approach to the identification and characterization of E. coli pathotypes was developed by constructing gene-specific probes (70-mers) for not only the virulence genes associated with each E. coli pathotype but also the O157-, CFT073-, and K-12-specific and common genes of each pathotype. Analysis of oligonucleotide probes with reference and clinical isolates of E. coli pathotypes indicated that the array could differentiate the pathotypes on the basis of their virulence and specific gene patterns. Probes targeting common genes of E. coli were present in all the reference and clinical strains. Salmonella enterica subsp. enterica-specific genes and Salmonella core genes were used as negative controls. The entire E. coli pathotype showed reactivity to only 4 of the 81 Salmonella-specific gene probes. Characterization of the genetic and virulence profiles of a single strain by using probes for virulence factors and specific and common genes in the spotted array is an ideal diagnostic tool for determination of E. coli pathotypes and could also have a significant impact on the epidemiological analysis of E. coli infections.
DOI: 10.1128/JCM.44.4.1495-1501.2006
PubMed: 16597882
Links to Exploration step
pubmed:16597882Le document en format XML
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Palaniappan</name><affiliation><nlm:affiliation>Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Yu" sort="Zhang, Yu" uniqKey="Zhang Y" first="Yu" last="Zhang">Yu Zhang</name></author><author><name sortKey="Chiu, David" sort="Chiu, David" uniqKey="Chiu D" first="David" last="Chiu">David Chiu</name></author><author><name sortKey="Torres, Alfonso" sort="Torres, Alfonso" uniqKey="Torres A" first="Alfonso" last="Torres">Alfonso Torres</name></author><author><name sortKey="Debroy, Chobi" sort="Debroy, Chobi" uniqKey="Debroy C" first="Chobi" last="Debroy">Chobi Debroy</name></author><author><name sortKey="Whittam, Thomas S" sort="Whittam, Thomas S" uniqKey="Whittam T" first="Thomas S" last="Whittam">Thomas S. Whittam</name></author><author><name sortKey="Chang, Yung Fu" sort="Chang, Yung Fu" uniqKey="Chang Y" first="Yung-Fu" last="Chang">Yung-Fu Chang</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2006">2006</date><idno type="RBID">pubmed:16597882</idno><idno type="pmid">16597882</idno><idno type="doi">10.1128/JCM.44.4.1495-1501.2006</idno><idno type="wicri:Area/PubMed/Corpus">002261</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002261</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Differentiation of Escherichia coli pathotypes by oligonucleotide spotted array.</title><author><name sortKey="Palaniappan, Raghavan U M" sort="Palaniappan, Raghavan U M" uniqKey="Palaniappan R" first="Raghavan U M" last="Palaniappan">Raghavan U M. Palaniappan</name><affiliation><nlm:affiliation>Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Yu" sort="Zhang, Yu" uniqKey="Zhang Y" first="Yu" last="Zhang">Yu Zhang</name></author><author><name sortKey="Chiu, David" sort="Chiu, David" uniqKey="Chiu D" first="David" last="Chiu">David Chiu</name></author><author><name sortKey="Torres, Alfonso" sort="Torres, Alfonso" uniqKey="Torres A" first="Alfonso" last="Torres">Alfonso Torres</name></author><author><name sortKey="Debroy, Chobi" sort="Debroy, Chobi" uniqKey="Debroy C" first="Chobi" last="Debroy">Chobi Debroy</name></author><author><name sortKey="Whittam, Thomas S" sort="Whittam, Thomas S" uniqKey="Whittam T" first="Thomas S" last="Whittam">Thomas S. Whittam</name></author><author><name sortKey="Chang, Yung Fu" sort="Chang, Yung Fu" uniqKey="Chang Y" first="Yung-Fu" last="Chang">Yung-Fu 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>DNA, Bacterial (analysis)</term><term>DNA, Bacterial (genetics)</term><term>Escherichia coli (classification)</term><term>Escherichia coli (genetics)</term><term>Escherichia coli (isolation & purification)</term><term>Escherichia coli (pathogenicity)</term><term>Escherichia coli Infections (diagnosis)</term><term>Gene Expression Profiling</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Oligonucleotide Probes</term><term>Virulence</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>DNA, Bacterial</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Bacterial</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Escherichia coli</term></keywords><keywords scheme="MESH" qualifier="diagnosis" xml:lang="en"><term>Escherichia coli Infections</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Escherichia coli</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Escherichia coli</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" qualifier="pathogenicity" xml:lang="en"><term>Escherichia coli</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Profiling</term><term>Oligonucleotide Probes</term><term>Virulence</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">To accurately determine the pathotypes of Escherichia coli strains, a comprehensive assessment of each strain that targets multiple genes is required. A new approach to the identification and characterization of E. coli pathotypes was developed by constructing gene-specific probes (70-mers) for not only the virulence genes associated with each E. coli pathotype but also the O157-, CFT073-, and K-12-specific and common genes of each pathotype. Analysis of oligonucleotide probes with reference and clinical isolates of E. coli pathotypes indicated that the array could differentiate the pathotypes on the basis of their virulence and specific gene patterns. Probes targeting common genes of E. coli were present in all the reference and clinical strains. Salmonella enterica subsp. enterica-specific genes and Salmonella core genes were used as negative controls. The entire E. coli pathotype showed reactivity to only 4 of the 81 Salmonella-specific gene probes. Characterization of the genetic and virulence profiles of a single strain by using probes for virulence factors and specific and common genes in the spotted array is an ideal diagnostic tool for determination of E. coli pathotypes and could also have a significant impact on the epidemiological analysis of E. coli infections.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16597882</PMID><DateCompleted><Year>2006</Year><Month>11</Month><Day>14</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0095-1137</ISSN><JournalIssue CitedMedium="Print"><Volume>44</Volume><Issue>4</Issue><PubDate><Year>2006</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Journal of clinical microbiology</Title><ISOAbbreviation>J. Clin. Microbiol.</ISOAbbreviation></Journal><ArticleTitle>Differentiation of Escherichia coli pathotypes by oligonucleotide spotted array.</ArticleTitle><Pagination><MedlinePgn>1495-501</MedlinePgn></Pagination><Abstract><AbstractText>To accurately determine the pathotypes of Escherichia coli strains, a comprehensive assessment of each strain that targets multiple genes is required. A new approach to the identification and characterization of E. coli pathotypes was developed by constructing gene-specific probes (70-mers) for not only the virulence genes associated with each E. coli pathotype but also the O157-, CFT073-, and K-12-specific and common genes of each pathotype. Analysis of oligonucleotide probes with reference and clinical isolates of E. coli pathotypes indicated that the array could differentiate the pathotypes on the basis of their virulence and specific gene patterns. Probes targeting common genes of E. coli were present in all the reference and clinical strains. Salmonella enterica subsp. enterica-specific genes and Salmonella core genes were used as negative controls. The entire E. coli pathotype showed reactivity to only 4 of the 81 Salmonella-specific gene probes. Characterization of the genetic and virulence profiles of a single strain by using probes for virulence factors and specific and common genes in the spotted array is an ideal diagnostic tool for determination of E. coli pathotypes and could also have a significant impact on the epidemiological analysis of E. coli infections.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Palaniappan</LastName><ForeName>Raghavan U M</ForeName><Initials>RU</Initials><AffiliationInfo><Affiliation>Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Yu</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Chiu</LastName><ForeName>David</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Torres</LastName><ForeName>Alfonso</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Debroy</LastName><ForeName>Chobi</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Whittam</LastName><ForeName>Thomas S</ForeName><Initials>TS</Initials></Author><Author ValidYN="Y"><LastName>Chang</LastName><ForeName>Yung-Fu</ForeName><Initials>YF</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>N01AI30054</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Clin 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