Discrimination between biothreat agents and ‘near neighbor’ species using a resequencing array
Abstract Timely identification of biothreat organisms from large numbers of clinical or environmental samples in potential outbreak or attack scenario is critical for effective diagnosis and treatment. This study aims to evaluate the potential of resequencing arrays for this purpose. Albeit suboptim...
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| Veröffentlicht in: | FEMS immunology and medical microbiology 2008-12, Vol.54 (3), p.356-364 |
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| creator | Taitt, Chris R. Malanoski, Anthony P. Lin, Baochuan Stenger, David A. Ligler, Frances S. Kusterbeck, Anne W. Anderson, George P. Harmon, Sue E. Shriver-Lake, Lisa C. Pollack, Steven K. Lennon, Denise M. Lobo-Menendez, Fe Wang, Zheng Schnur, Joel M. |
| description | Abstract
Timely identification of biothreat organisms from large numbers of clinical or environmental samples in potential outbreak or attack scenario is critical for effective diagnosis and treatment. This study aims to evaluate the potential of resequencing arrays for this purpose. Albeit suboptimal, this report demonstrated that respiratory pathogen microarray version 1 can identify Bacillus anthracis, Francisella tularensis, Yersinia pestis and distinguish them from benign ‘near neighbor’ species in a single assay. Additionally, the sequence information can discriminate strains and possibly the sources of the strains. With further development, it is possible to use resequencing microarrays for biothreat surveillance. |
| doi_str_mv | 10.1111/j.1574-695X.2008.00486.x |
| format | Article |
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Timely identification of biothreat organisms from large numbers of clinical or environmental samples in potential outbreak or attack scenario is critical for effective diagnosis and treatment. This study aims to evaluate the potential of resequencing arrays for this purpose. Albeit suboptimal, this report demonstrated that respiratory pathogen microarray version 1 can identify Bacillus anthracis, Francisella tularensis, Yersinia pestis and distinguish them from benign ‘near neighbor’ species in a single assay. Additionally, the sequence information can discriminate strains and possibly the sources of the strains. With further development, it is possible to use resequencing microarrays for biothreat surveillance.</description><identifier>ISSN: 0928-8244</identifier><identifier>EISSN: 1574-695X</identifier><identifier>EISSN: 2049-632X</identifier><identifier>DOI: 10.1111/j.1574-695X.2008.00486.x</identifier><identifier>PMID: 19049648</identifier><language>eng</language><publisher>Oxford, UK: Blackwell Publishing Ltd</publisher><subject><![CDATA[Anthrax - diagnosis ; Anthrax - microbiology ; Arrays ; Bacillus anthracis ; Bacillus anthracis - classification ; Bacillus anthracis - genetics ; Bacillus anthracis - isolation & purification ; Bacillus cereus - classification ; Bacillus cereus - genetics ; Bacillus cereus - isolation & purification ; Bacterial Typing Techniques ; Bacteriology ; Biological and medical sciences ; Bioterrorism - prevention & control ; biothreat ; Double-Blind Method ; Francisella - classification ; Francisella - genetics ; Francisella - isolation & purification ; Francisella tularensis ; Francisella tularensis - classification ; Francisella tularensis - genetics ; Francisella tularensis - isolation & purification ; Fundamental and applied biological sciences. Psychology ; Humans ; Microbiology ; Miscellaneous ; Oligonucleotide Array Sequence Analysis - methods ; Plague - diagnosis ; Plague - microbiology ; Polymorphism, Single Nucleotide ; resequencing microarray ; Sequence Analysis, DNA - methods ; single nucleotide polymorphism ; Species Specificity ; Strains (organisms) ; Tularemia - diagnosis ; Tularemia - microbiology ; Yersinia - classification ; Yersinia - genetics ; Yersinia - isolation & purification ; Yersinia pestis ; Yersinia pestis - classification ; Yersinia pestis - genetics ; Yersinia pestis - isolation & purification]]></subject><ispartof>FEMS immunology and medical microbiology, 2008-12, Vol.54 (3), p.356-364</ispartof><rights>2008 Federation of European Microbiological Societies. 2008</rights><rights>Journal compilation © 2008 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original US government works</rights><rights>2008 INIST-CNRS</rights><rights>2008 Federation of European Microbiological Societies.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5496-bab79c31b19085d36bcc86485e2d2f9072066f7c71f418425af6d88fdc96f92b3</citedby><cites>FETCH-LOGICAL-c5496-bab79c31b19085d36bcc86485e2d2f9072066f7c71f418425af6d88fdc96f92b3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1574-695X.2008.00486.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1574-695X.2008.00486.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27903,27904,45553,45554</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=20853000$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19049648$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Taitt, Chris R.</creatorcontrib><creatorcontrib>Malanoski, Anthony P.</creatorcontrib><creatorcontrib>Lin, Baochuan</creatorcontrib><creatorcontrib>Stenger, David A.</creatorcontrib><creatorcontrib>Ligler, Frances S.</creatorcontrib><creatorcontrib>Kusterbeck, Anne W.</creatorcontrib><creatorcontrib>Anderson, George P.</creatorcontrib><creatorcontrib>Harmon, Sue E.</creatorcontrib><creatorcontrib>Shriver-Lake, Lisa C.</creatorcontrib><creatorcontrib>Pollack, Steven K.</creatorcontrib><creatorcontrib>Lennon, Denise M.</creatorcontrib><creatorcontrib>Lobo-Menendez, Fe</creatorcontrib><creatorcontrib>Wang, Zheng</creatorcontrib><creatorcontrib>Schnur, Joel M.</creatorcontrib><title>Discrimination between biothreat agents and ‘near neighbor’ species using a resequencing array</title><title>FEMS immunology and medical microbiology</title><addtitle>FEMS Immunol Med Microbiol</addtitle><description>Abstract
Timely identification of biothreat organisms from large numbers of clinical or environmental samples in potential outbreak or attack scenario is critical for effective diagnosis and treatment. This study aims to evaluate the potential of resequencing arrays for this purpose. Albeit suboptimal, this report demonstrated that respiratory pathogen microarray version 1 can identify Bacillus anthracis, Francisella tularensis, Yersinia pestis and distinguish them from benign ‘near neighbor’ species in a single assay. Additionally, the sequence information can discriminate strains and possibly the sources of the strains. With further development, it is possible to use resequencing microarrays for biothreat surveillance.</description><subject>Anthrax - diagnosis</subject><subject>Anthrax - microbiology</subject><subject>Arrays</subject><subject>Bacillus anthracis</subject><subject>Bacillus anthracis - classification</subject><subject>Bacillus anthracis - genetics</subject><subject>Bacillus anthracis - isolation & purification</subject><subject>Bacillus cereus - classification</subject><subject>Bacillus cereus - genetics</subject><subject>Bacillus cereus - isolation & purification</subject><subject>Bacterial Typing Techniques</subject><subject>Bacteriology</subject><subject>Biological and medical sciences</subject><subject>Bioterrorism - prevention & control</subject><subject>biothreat</subject><subject>Double-Blind Method</subject><subject>Francisella - classification</subject><subject>Francisella - genetics</subject><subject>Francisella - isolation & purification</subject><subject>Francisella tularensis</subject><subject>Francisella tularensis - classification</subject><subject>Francisella tularensis - genetics</subject><subject>Francisella tularensis - isolation & purification</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Humans</subject><subject>Microbiology</subject><subject>Miscellaneous</subject><subject>Oligonucleotide Array Sequence Analysis - methods</subject><subject>Plague - diagnosis</subject><subject>Plague - microbiology</subject><subject>Polymorphism, Single Nucleotide</subject><subject>resequencing microarray</subject><subject>Sequence Analysis, DNA - methods</subject><subject>single nucleotide polymorphism</subject><subject>Species Specificity</subject><subject>Strains (organisms)</subject><subject>Tularemia - diagnosis</subject><subject>Tularemia - microbiology</subject><subject>Yersinia - classification</subject><subject>Yersinia - genetics</subject><subject>Yersinia - isolation & purification</subject><subject>Yersinia pestis</subject><subject>Yersinia pestis - classification</subject><subject>Yersinia pestis - genetics</subject><subject>Yersinia pestis - isolation & purification</subject><issn>0928-8244</issn><issn>1574-695X</issn><issn>2049-632X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkdFqFDEUhoModq2-ggRE72ZMMjOZBLyR1mqh4o2CdyHJnGxnmc2syQzt3vUx9PX6JJ7tLhUU0dycE_L9yZ_zE0I5Kzmu16uSN21dSN18LQVjqmSsVrK8fkAW9wcPyYJpoQol6vqIPMl5xZDSjD0mR1xjJ2u1IO60zz716z7aqR8jdTBdAWDtx-kygZ2oXUKcMrWxo7c33yPYRCP0y0s3ptubHzRvwPeQ6Zz7uKSWJsjwbYbo77Yp2e1T8ijYIcOzQz0mX87efT75UFx8en9-8vai8A2aKZx1rfYVd2hONV0lnfcKPTYgOhE0awWTMrS-5aHmqhaNDbJTKnRey6CFq47Jq_29mzSigzyZNf4NhsFGGOdspMbr6lb9E-Ra6Uo1DMEXv4GrcU4RP2FExaRo20rVSKk95dOYc4JgNjhQm7aGM7OLy6zMLhWzS8Xs4jJ3cZlrlD4_PDC7NXS_hId8EHh5AGz2dgjJ4mDzPSdwUhXGitybPXfVD7D9bwPm7PwjNiiv9vJx3vxFXPzp_id8TMHI</recordid><startdate>200812</startdate><enddate>200812</enddate><creator>Taitt, Chris R.</creator><creator>Malanoski, Anthony P.</creator><creator>Lin, Baochuan</creator><creator>Stenger, David A.</creator><creator>Ligler, Frances S.</creator><creator>Kusterbeck, Anne W.</creator><creator>Anderson, George P.</creator><creator>Harmon, Sue E.</creator><creator>Shriver-Lake, Lisa C.</creator><creator>Pollack, Steven K.</creator><creator>Lennon, Denise M.</creator><creator>Lobo-Menendez, Fe</creator><creator>Wang, Zheng</creator><creator>Schnur, Joel M.</creator><general>Blackwell Publishing Ltd</general><general>Blackwell</general><general>Oxford University Press</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7T7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>K9.</scope><scope>P64</scope><scope>7QL</scope><scope>7T5</scope><scope>H94</scope><scope>7X8</scope></search><sort><creationdate>200812</creationdate><title>Discrimination between biothreat agents and ‘near neighbor’ species using a resequencing array</title><author>Taitt, Chris R. ; Malanoski, Anthony P. ; Lin, Baochuan ; Stenger, David A. ; Ligler, Frances S. ; Kusterbeck, Anne W. ; Anderson, George P. ; Harmon, Sue E. ; Shriver-Lake, Lisa C. ; Pollack, Steven K. ; Lennon, Denise M. ; Lobo-Menendez, Fe ; Wang, Zheng ; Schnur, Joel M.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5496-bab79c31b19085d36bcc86485e2d2f9072066f7c71f418425af6d88fdc96f92b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Anthrax - diagnosis</topic><topic>Anthrax - microbiology</topic><topic>Arrays</topic><topic>Bacillus anthracis</topic><topic>Bacillus anthracis - classification</topic><topic>Bacillus anthracis - genetics</topic><topic>Bacillus anthracis - isolation & purification</topic><topic>Bacillus cereus - classification</topic><topic>Bacillus cereus - genetics</topic><topic>Bacillus cereus - isolation & purification</topic><topic>Bacterial Typing Techniques</topic><topic>Bacteriology</topic><topic>Biological and medical sciences</topic><topic>Bioterrorism - prevention & control</topic><topic>biothreat</topic><topic>Double-Blind Method</topic><topic>Francisella - classification</topic><topic>Francisella - genetics</topic><topic>Francisella - isolation & purification</topic><topic>Francisella tularensis</topic><topic>Francisella tularensis - classification</topic><topic>Francisella tularensis - genetics</topic><topic>Francisella tularensis - isolation & purification</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Humans</topic><topic>Microbiology</topic><topic>Miscellaneous</topic><topic>Oligonucleotide Array Sequence Analysis - methods</topic><topic>Plague - diagnosis</topic><topic>Plague - microbiology</topic><topic>Polymorphism, Single Nucleotide</topic><topic>resequencing microarray</topic><topic>Sequence Analysis, DNA - methods</topic><topic>single nucleotide polymorphism</topic><topic>Species Specificity</topic><topic>Strains (organisms)</topic><topic>Tularemia - diagnosis</topic><topic>Tularemia - microbiology</topic><topic>Yersinia - classification</topic><topic>Yersinia - genetics</topic><topic>Yersinia - isolation & purification</topic><topic>Yersinia pestis</topic><topic>Yersinia pestis - classification</topic><topic>Yersinia pestis - genetics</topic><topic>Yersinia pestis - isolation & purification</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Taitt, Chris R.</creatorcontrib><creatorcontrib>Malanoski, Anthony P.</creatorcontrib><creatorcontrib>Lin, Baochuan</creatorcontrib><creatorcontrib>Stenger, David A.</creatorcontrib><creatorcontrib>Ligler, Frances S.</creatorcontrib><creatorcontrib>Kusterbeck, Anne W.</creatorcontrib><creatorcontrib>Anderson, George P.</creatorcontrib><creatorcontrib>Harmon, Sue E.</creatorcontrib><creatorcontrib>Shriver-Lake, Lisa C.</creatorcontrib><creatorcontrib>Pollack, Steven K.</creatorcontrib><creatorcontrib>Lennon, Denise M.</creatorcontrib><creatorcontrib>Lobo-Menendez, Fe</creatorcontrib><creatorcontrib>Wang, Zheng</creatorcontrib><creatorcontrib>Schnur, Joel M.</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Immunology Abstracts</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>FEMS immunology and medical microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Taitt, Chris R.</au><au>Malanoski, Anthony P.</au><au>Lin, Baochuan</au><au>Stenger, David A.</au><au>Ligler, Frances S.</au><au>Kusterbeck, Anne W.</au><au>Anderson, George P.</au><au>Harmon, Sue E.</au><au>Shriver-Lake, Lisa C.</au><au>Pollack, Steven K.</au><au>Lennon, Denise M.</au><au>Lobo-Menendez, Fe</au><au>Wang, Zheng</au><au>Schnur, Joel M.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Discrimination between biothreat agents and ‘near neighbor’ species using a resequencing array</atitle><jtitle>FEMS immunology and medical microbiology</jtitle><addtitle>FEMS Immunol Med Microbiol</addtitle><date>2008-12</date><risdate>2008</risdate><volume>54</volume><issue>3</issue><spage>356</spage><epage>364</epage><pages>356-364</pages><issn>0928-8244</issn><eissn>1574-695X</eissn><eissn>2049-632X</eissn><abstract>Abstract
Timely identification of biothreat organisms from large numbers of clinical or environmental samples in potential outbreak or attack scenario is critical for effective diagnosis and treatment. This study aims to evaluate the potential of resequencing arrays for this purpose. Albeit suboptimal, this report demonstrated that respiratory pathogen microarray version 1 can identify Bacillus anthracis, Francisella tularensis, Yersinia pestis and distinguish them from benign ‘near neighbor’ species in a single assay. Additionally, the sequence information can discriminate strains and possibly the sources of the strains. With further development, it is possible to use resequencing microarrays for biothreat surveillance.</abstract><cop>Oxford, UK</cop><pub>Blackwell Publishing Ltd</pub><pmid>19049648</pmid><doi>10.1111/j.1574-695X.2008.00486.x</doi><tpages>9</tpages><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 0928-8244 |
| ispartof | FEMS immunology and medical microbiology, 2008-12, Vol.54 (3), p.356-364 |
| issn | 0928-8244 1574-695X 2049-632X |
| language | eng |
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| source | MEDLINE; Wiley Online Library Journals Frontfile Complete; Oxford University Press Journals All Titles (1996-Current) |
| subjects | Anthrax - diagnosis Anthrax - microbiology Arrays Bacillus anthracis Bacillus anthracis - classification Bacillus anthracis - genetics Bacillus anthracis - isolation & purification Bacillus cereus - classification Bacillus cereus - genetics Bacillus cereus - isolation & purification Bacterial Typing Techniques Bacteriology Biological and medical sciences Bioterrorism - prevention & control biothreat Double-Blind Method Francisella - classification Francisella - genetics Francisella - isolation & purification Francisella tularensis Francisella tularensis - classification Francisella tularensis - genetics Francisella tularensis - isolation & purification Fundamental and applied biological sciences. Psychology Humans Microbiology Miscellaneous Oligonucleotide Array Sequence Analysis - methods Plague - diagnosis Plague - microbiology Polymorphism, Single Nucleotide resequencing microarray Sequence Analysis, DNA - methods single nucleotide polymorphism Species Specificity Strains (organisms) Tularemia - diagnosis Tularemia - microbiology Yersinia - classification Yersinia - genetics Yersinia - isolation & purification Yersinia pestis Yersinia pestis - classification Yersinia pestis - genetics Yersinia pestis - isolation & purification |
| title | Discrimination between biothreat agents and ‘near neighbor’ species using a resequencing array |
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