The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers

ABSTRACT Whole-genome sequence (WGS) data are commonly used to design diagnostic targets for the identification of bacterial pathogens. To do this effectively, genomics databases must be comprehensive to identify the strict core genome that is specific to the target pathogen. As additional genomes a...

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Autores principales:	Jason W. Sahl, Adam J. Vazquez, Carina M. Hall, Joseph D. Busch, Apichai Tuanyok, Mark Mayo, James M. Schupp, Madeline Lummis, Talima Pearson, Kenzie Shippy, Rebecca E. Colman, Christopher J. Allender, Vanessa Theobald, Derek S. Sarovich, Erin P. Price, Alex Hutcheson, Jonas Korlach, John J. LiPuma, Jason Ladner, Sean Lovett, Galina Koroleva, Gustavo Palacios, Direk Limmathurotsakul, Vanaporn Wuthiekanun, Gumphol Wongsuwan, Bart J. Currie, Paul Keim, David M. Wagner
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2016
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/cee03ed17fd64a758eee20d30ac89ba0
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spelling	oai:doaj.org-article:cee03ed17fd64a758eee20d30ac89ba02021-11-15T15:50:15ZThe Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers10.1128/mBio.00846-162150-7511https://doaj.org/article/cee03ed17fd64a758eee20d30ac89ba02016-11-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00846-16https://doaj.org/toc/2150-7511ABSTRACT Whole-genome sequence (WGS) data are commonly used to design diagnostic targets for the identification of bacterial pathogens. To do this effectively, genomics databases must be comprehensive to identify the strict core genome that is specific to the target pathogen. As additional genomes are analyzed, the core genome size is reduced and there is erosion of the target-specific regions due to commonality with related species, potentially resulting in the identification of false positives and/or false negatives. IMPORTANCE A comparative analysis of 1,130 Burkholderia genomes identified unique markers for many named species, including the human pathogens B. pseudomallei and B. mallei. Due to core genome reduction and signature erosion, only 38 targets specific to B. pseudomallei/mallei were identified. By using only public genomes, a larger number of markers were identified, due to undersampling, and this larger number represents the potential for false positives. This analysis has implications for the design of diagnostics for other species where the genomic space of the target and/or closely related species is not well defined.Jason W. SahlAdam J. VazquezCarina M. HallJoseph D. BuschApichai TuanyokMark MayoJames M. SchuppMadeline LummisTalima PearsonKenzie ShippyRebecca E. ColmanChristopher J. AllenderVanessa TheobaldDerek S. SarovichErin P. PriceAlex HutchesonJonas KorlachJohn J. LiPumaJason LadnerSean LovettGalina KorolevaGustavo PalaciosDirek LimmathurotsakulVanaporn WuthiekanunGumphol WongsuwanBart J. CurriePaul KeimDavid M. WagnerAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 7, Iss 5 (2016)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Jason W. Sahl Adam J. Vazquez Carina M. Hall Joseph D. Busch Apichai Tuanyok Mark Mayo James M. Schupp Madeline Lummis Talima Pearson Kenzie Shippy Rebecca E. Colman Christopher J. Allender Vanessa Theobald Derek S. Sarovich Erin P. Price Alex Hutcheson Jonas Korlach John J. LiPuma Jason Ladner Sean Lovett Galina Koroleva Gustavo Palacios Direk Limmathurotsakul Vanaporn Wuthiekanun Gumphol Wongsuwan Bart J. Currie Paul Keim David M. Wagner The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers
description	ABSTRACT Whole-genome sequence (WGS) data are commonly used to design diagnostic targets for the identification of bacterial pathogens. To do this effectively, genomics databases must be comprehensive to identify the strict core genome that is specific to the target pathogen. As additional genomes are analyzed, the core genome size is reduced and there is erosion of the target-specific regions due to commonality with related species, potentially resulting in the identification of false positives and/or false negatives. IMPORTANCE A comparative analysis of 1,130 Burkholderia genomes identified unique markers for many named species, including the human pathogens B. pseudomallei and B. mallei. Due to core genome reduction and signature erosion, only 38 targets specific to B. pseudomallei/mallei were identified. By using only public genomes, a larger number of markers were identified, due to undersampling, and this larger number represents the potential for false positives. This analysis has implications for the design of diagnostics for other species where the genomic space of the target and/or closely related species is not well defined.
format	article
author	Jason W. Sahl Adam J. Vazquez Carina M. Hall Joseph D. Busch Apichai Tuanyok Mark Mayo James M. Schupp Madeline Lummis Talima Pearson Kenzie Shippy Rebecca E. Colman Christopher J. Allender Vanessa Theobald Derek S. Sarovich Erin P. Price Alex Hutcheson Jonas Korlach John J. LiPuma Jason Ladner Sean Lovett Galina Koroleva Gustavo Palacios Direk Limmathurotsakul Vanaporn Wuthiekanun Gumphol Wongsuwan Bart J. Currie Paul Keim David M. Wagner
author_facet	Jason W. Sahl Adam J. Vazquez Carina M. Hall Joseph D. Busch Apichai Tuanyok Mark Mayo James M. Schupp Madeline Lummis Talima Pearson Kenzie Shippy Rebecca E. Colman Christopher J. Allender Vanessa Theobald Derek S. Sarovich Erin P. Price Alex Hutcheson Jonas Korlach John J. LiPuma Jason Ladner Sean Lovett Galina Koroleva Gustavo Palacios Direk Limmathurotsakul Vanaporn Wuthiekanun Gumphol Wongsuwan Bart J. Currie Paul Keim David M. Wagner
author_sort	Jason W. Sahl
title	The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers
title_short	The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers
title_full	The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers
title_fullStr	The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers
title_full_unstemmed	The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers
title_sort	effects of signal erosion and core genome reduction on the identification of diagnostic markers
publisher	American Society for Microbiology
publishDate	2016
url	https://doaj.org/article/cee03ed17fd64a758eee20d30ac89ba0
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The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers

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