Publication: The effects of signal erosion and core genome reduction on the identification of diagnostic markers
Issued Date
2016-09-01
Resource Type
ISSN
21507511
21612129
21612129
Other identifier(s)
2-s2.0-84994416001
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Mahidol University
Rights Holder(s)
SCOPUS
Bibliographic Citation
mBio. Vol.7, No.5 (2016)
Suggested Citation
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. mBio. Vol.7, No.5 (2016). doi:10.1128/mBio.00846-16 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/40702
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Title
The effects of signal erosion and core genome reduction on the identification of diagnostic markers
Author(s)
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
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
Abstract
© 2016 Sahl et al. 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.
