Microarray for molecular typing of Salmonella enterica serovars.
Identifieur interne : 002101 ( PubMed/Curation ); précédent : 002100; suivant : 002102Microarray for molecular typing of Salmonella enterica serovars.
Auteurs : Joy Scaria [États-Unis] ; Raghavan U M. Palaniappan ; David Chiu ; Julie Ann Phan ; Lalit Ponnala ; Patrick Mcdonough ; Yrjo T. Grohn ; Steffen Porwollik ; Michael Mcclelland ; Chien-Shun Chiou ; Chishih Chu ; Yung-Fu ChangSource :
- Molecular and cellular probes [ 0890-8508 ] ; 2008.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , classification : DNA Probes.
- chemical , genetics : DNA Probes.
- genetics : Salmonella enterica.
- methods : Oligonucleotide Array Sequence Analysis.
- Cluster Analysis, Substrate Specificity.
Abstract
We describe the development of a spotted array for the delineation of the most common 14 disease-causing Salmonella serovars in the United States. Our array consists of 414 70 mers targeting core genes of Salmonella enterica, subspecies I specific genes, fimbrial genes, pathogenicity islands, Gifsy elements and other variable genes. Using this array we were able to identify a unique gene presence/absence profile for each of the targeted serovar which was used as the serovar differentiating criteria. Based on this profile, we developed a Matlab programme that compares the profile of an unknown sample to all 14 reference serovar profiles and give out the closest serovar match. Since we have included probes targeting most of the virulence genes and variable genes in Salmonella, in addition to using for serovar detection this array could also be used for studying the virulence gene content and also for evaluating the genetic relation between different isolates of Salmonella.
DOI: 10.1016/j.mcp.2008.04.002
PubMed: 18554865
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Palaniappan</name></author><author><name sortKey="Chiu, David" sort="Chiu, David" uniqKey="Chiu D" first="David" last="Chiu">David Chiu</name></author><author><name sortKey="Phan, Julie Ann" sort="Phan, Julie Ann" uniqKey="Phan J" first="Julie Ann" last="Phan">Julie Ann Phan</name></author><author><name sortKey="Ponnala, Lalit" sort="Ponnala, Lalit" uniqKey="Ponnala L" first="Lalit" last="Ponnala">Lalit Ponnala</name></author><author><name sortKey="Mcdonough, Patrick" sort="Mcdonough, Patrick" uniqKey="Mcdonough P" first="Patrick" last="Mcdonough">Patrick Mcdonough</name></author><author><name sortKey="Grohn, Yrjo T" sort="Grohn, Yrjo T" uniqKey="Grohn Y" first="Yrjo T" last="Grohn">Yrjo T. Grohn</name></author><author><name sortKey="Porwollik, Steffen" sort="Porwollik, Steffen" uniqKey="Porwollik S" first="Steffen" last="Porwollik">Steffen Porwollik</name></author><author><name sortKey="Mcclelland, Michael" sort="Mcclelland, Michael" uniqKey="Mcclelland M" first="Michael" last="Mcclelland">Michael Mcclelland</name></author><author><name sortKey="Chiou, Chien Shun" sort="Chiou, Chien Shun" uniqKey="Chiou C" first="Chien-Shun" last="Chiou">Chien-Shun Chiou</name></author><author><name sortKey="Chu, Chishih" sort="Chu, Chishih" uniqKey="Chu C" first="Chishih" last="Chu">Chishih Chu</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">Molecular and cellular probes</title><idno type="ISSN">0890-8508</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Cluster Analysis</term><term>DNA Probes (classification)</term><term>DNA Probes (genetics)</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Salmonella enterica (genetics)</term><term>Substrate Specificity</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de regroupements</term><term>Salmonella enterica (génétique)</term><term>Sondes d'ADN ()</term><term>Sondes d'ADN (génétique)</term><term>Spécificité du substrat</term><term>Séquençage par oligonucléotides en batterie ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="classification" xml:lang="en"><term>DNA Probes</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA Probes</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Salmonella enterica</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Salmonella enterica</term><term>Sondes d'ADN</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Cluster Analysis</term><term>Substrate Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de regroupements</term><term>Sondes d'ADN</term><term>Spécificité du substrat</term><term>Séquençage par oligonucléotides en batterie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We describe the development of a spotted array for the delineation of the most common 14 disease-causing Salmonella serovars in the United States. Our array consists of 414 70 mers targeting core genes of Salmonella enterica, subspecies I specific genes, fimbrial genes, pathogenicity islands, Gifsy elements and other variable genes. Using this array we were able to identify a unique gene presence/absence profile for each of the targeted serovar which was used as the serovar differentiating criteria. Based on this profile, we developed a Matlab programme that compares the profile of an unknown sample to all 14 reference serovar profiles and give out the closest serovar match. Since we have included probes targeting most of the virulence genes and variable genes in Salmonella, in addition to using for serovar detection this array could also be used for studying the virulence gene content and also for evaluating the genetic relation between different isolates of Salmonella.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18554865</PMID><DateCompleted><Year>2008</Year><Month>10</Month><Day>31</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0890-8508</ISSN><JournalIssue CitedMedium="Print"><Volume>22</Volume><Issue>4</Issue><PubDate><Year>2008</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Molecular and cellular probes</Title><ISOAbbreviation>Mol. Cell. Probes</ISOAbbreviation></Journal><ArticleTitle>Microarray for molecular typing of Salmonella enterica serovars.</ArticleTitle><Pagination><MedlinePgn>238-43</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.mcp.2008.04.002</ELocationID><Abstract><AbstractText>We describe the development of a spotted array for the delineation of the most common 14 disease-causing Salmonella serovars in the United States. Our array consists of 414 70 mers targeting core genes of Salmonella enterica, subspecies I specific genes, fimbrial genes, pathogenicity islands, Gifsy elements and other variable genes. Using this array we were able to identify a unique gene presence/absence profile for each of the targeted serovar which was used as the serovar differentiating criteria. Based on this profile, we developed a Matlab programme that compares the profile of an unknown sample to all 14 reference serovar profiles and give out the closest serovar match. Since we have included probes targeting most of the virulence genes and variable genes in Salmonella, in addition to using for serovar detection this array could also be used for studying the virulence gene content and also for evaluating the genetic relation between different isolates of Salmonella.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Scaria</LastName><ForeName>Joy</ForeName><Initials>J</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>Palaniappan</LastName><ForeName>Raghavan U M</ForeName><Initials>RU</Initials></Author><Author ValidYN="Y"><LastName>Chiu</LastName><ForeName>David</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Phan</LastName><ForeName>Julie Ann</ForeName><Initials>JA</Initials></Author><Author ValidYN="Y"><LastName>Ponnala</LastName><ForeName>Lalit</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>McDonough</LastName><ForeName>Patrick</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Grohn</LastName><ForeName>Yrjo T</ForeName><Initials>YT</Initials></Author><Author ValidYN="Y"><LastName>Porwollik</LastName><ForeName>Steffen</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>McClelland</LastName><ForeName>Michael</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Chiou</LastName><ForeName>Chien-Shun</ForeName><Initials>CS</Initials></Author><Author ValidYN="Y"><LastName>Chu</LastName><ForeName>Chishih</ForeName><Initials>C</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>N01 AI030054</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH 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Jul;38(7):2465-7</Citation><ArticleIdList><ArticleId IdType="pubmed">10878026</ArticleId></ArticleIdList></Reference><Reference><Citation>J Microbiol Methods. 2007 Aug;70(2):261-71</Citation><ArticleIdList><ArticleId IdType="pubmed">17555834</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2001 Oct 25;413(6858):852-6</Citation><ArticleIdList><ArticleId IdType="pubmed">11677609</ArticleId></ArticleIdList></Reference><Reference><Citation>Trends Microbiol. 2002 Feb;10(2):94-9</Citation><ArticleIdList><ArticleId IdType="pubmed">11827811</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2002 Nov 26;99(24):15687-92</Citation><ArticleIdList><ArticleId IdType="pubmed">12429852</ArticleId></ArticleIdList></Reference><Reference><Citation>J Bacteriol. 2003 Jan;185(2):553-63</Citation><ArticleIdList><ArticleId IdType="pubmed">12511502</ArticleId></ArticleIdList></Reference><Reference><Citation>J Bacteriol. 2004 Mar;186(6):1678-82</Citation><ArticleIdList><ArticleId IdType="pubmed">14996798</ArticleId></ArticleIdList></Reference><Reference><Citation>Clin Infect Dis. 2004 Apr 15;38 Suppl 3:S127-34</Citation><ArticleIdList><ArticleId IdType="pubmed">15095181</ArticleId></ArticleIdList></Reference><Reference><Citation>J Bacteriol. 2004 Sep;186(17):5883-98</Citation><ArticleIdList><ArticleId IdType="pubmed">15317794</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 1986 May;51(5):873-84</Citation><ArticleIdList><ArticleId IdType="pubmed">2425735</ArticleId></ArticleIdList></Reference><Reference><Citation>J Clin Microbiol. 1993 Feb;31(2):233-7</Citation><ArticleIdList><ArticleId IdType="pubmed">8432808</ArticleId></ArticleIdList></Reference><Reference><Citation>J Gen Microbiol. 1993 Oct;139(10):2409-14</Citation><ArticleIdList><ArticleId IdType="pubmed">8254310</ArticleId></ArticleIdList></Reference><Reference><Citation>J Clin Microbiol. 1996 Oct;34(10):2440-3</Citation><ArticleIdList><ArticleId IdType="pubmed">8880496</ArticleId></ArticleIdList></Reference><Reference><Citation>Emerg Infect Dis. 1999 Sep-Oct;5(5):607-25</Citation><ArticleIdList><ArticleId IdType="pubmed">10511517</ArticleId></ArticleIdList></Reference><Reference><Citation>APMIS. 2004 Nov-Dec;112(11-12):908-29</Citation><ArticleIdList><ArticleId IdType="pubmed">15638843</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 2005 Mar;71(3):1616-25</Citation><ArticleIdList><ArticleId IdType="pubmed">15746367</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2005;33(5):1690-8</Citation><ArticleIdList><ArticleId IdType="pubmed">15781495</ArticleId></ArticleIdList></Reference><Reference><Citation>J Clin Microbiol. 2005 Aug;43(8):4092-106</Citation><ArticleIdList><ArticleId IdType="pubmed">16081956</ArticleId></ArticleIdList></Reference><Reference><Citation>Infect Immun. 2005 Dec;73(12):7894-905</Citation><ArticleIdList><ArticleId IdType="pubmed">16299280</ArticleId></ArticleIdList></Reference><Reference><Citation>J Clin Microbiol. 2006 Apr;44(4):1495-501</Citation><ArticleIdList><ArticleId IdType="pubmed">16597882</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Cell Probes. 2007 Feb;21(1):56-65</Citation><ArticleIdList><ArticleId IdType="pubmed">17029709</ArticleId></ArticleIdList></Reference><Reference><Citation>J Microbiol Methods. 2007 Apr;69(1):23-36</Citation><ArticleIdList><ArticleId IdType="pubmed">17208323</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2001 Oct 25;413(6858):848-52</Citation><ArticleIdList><ArticleId IdType="pubmed">11677608</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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