The effects of signal erosion and core genome reduction on the identification of diagnostic markers

J W Sahl; A J Vazquez; C M Hall; J D Busch; A Tuanyok; M Mayo; J M Schupp; M Lummis; T Pearson; K Shippy; R E Colman; C J Allender; V Theobald; Derek S Sarovich; Erin P Price; A Hutcheson; J Korlach; J J LiPuma; J Ladner; S Lovett; G Koroleva; G Palacios; D Limmathurotsakul; V Wuthiekanun; G Wongsuwan; B J Currie; P Keim; D M Wagner

doi:10.1128/mBio.00846-16

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The effects of signal erosion and core genome reduction on the identification of diagnostic markers

Journal article

Open access

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The effects of signal erosion and core genome reduction on the identification of diagnostic markers

J W Sahl, A J Vazquez, C M Hall, J D Busch, A Tuanyok, M Mayo, J M Schupp, M Lummis, T Pearson, K Shippy, …

mBio, Vol.7(5), e00846-16

2016

DOI: https://doi.org/10.1128/mBio.00846-16

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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. © 2016 Sahl et al.

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Title: The effects of signal erosion and core genome reduction on the identification of diagnostic markers
Authors: J W Sahl (Author) - Northern Arizona University, United States
A J Vazquez (Author) - Northern Arizona University, United States
C M Hall (Author) - Northern Arizona University, United States
J D Busch (Author) - Northern Arizona University, United States
A Tuanyok (Author) - University of Florida, United States
M Mayo (Author) - Menzies School of Health Research
J M Schupp (Author) - Translational Genomics Research Institute, United States
M Lummis (Author) - Northern Arizona University, United States
T Pearson (Author) - Northern Arizona University, United States
K Shippy (Author) - Northern Arizona University, United States
R E Colman (Author) - Translational Genomics Research Institute, United States
C J Allender (Author) - Northern Arizona University, United States
V Theobald (Author) - Menzies School of Health Research
Derek S Sarovich (Author) - Menzies School of Health Research
Erin P Price (Author) - Menzies School of Health Research
A Hutcheson (Author) - University of Michigan, United States
J Korlach (Author) - University of Michigan, United States
J J LiPuma (Author) - University of Michigan, United States
J Ladner (Author) - USAMRIID, United States
S Lovett (Author) - USAMRIID, United States
G Koroleva (Author) - USAMRIID, United States
G Palacios (Author) - USAMRIID, United States
D Limmathurotsakul (Author) - Mahidol University, Thailand
V Wuthiekanun (Author) - Mahidol University, Thailand
G Wongsuwan (Author) - Mahidol University, Thailand
B J Currie (Author) - Menzies School of Health Research
P Keim (Author) - Northern Arizona University, United States
D M Wagner (Corresponding Author) - Northern Arizona University, United States
Publication details: mBio, Vol.7(5), e00846-16
Publisher: American Society for Microbiology
Date published: 2016
DOI: 10.1128/mBio.00846-16
ISSN: 2161-2129; 2150-7511; 2161-2129
Copyright note: Copyright © 2016 Sahl et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
Organisation Unit: University of the Sunshine Coast, Queensland; Centre for Bioinnovation
Language: English
Record Identifier: 99451267102621
Output Type: Journal article
Research Statement: false

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Web Of Science research areas: Microbiology

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