Journal article
The effects of signal erosion and core genome reduction on the identification of diagnostic markers
mBio, Vol.7(5), e00846-16
2016
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.
Details
- 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 StatesA J Vazquez (Author) - Northern Arizona University, United StatesC M Hall (Author) - Northern Arizona University, United StatesJ D Busch (Author) - Northern Arizona University, United StatesA Tuanyok (Author) - University of Florida, United StatesM Mayo (Author) - Menzies School of Health ResearchJ M Schupp (Author) - Translational Genomics Research Institute, United StatesM Lummis (Author) - Northern Arizona University, United StatesT Pearson (Author) - Northern Arizona University, United StatesK Shippy (Author) - Northern Arizona University, United StatesR E Colman (Author) - Translational Genomics Research Institute, United StatesC J Allender (Author) - Northern Arizona University, United StatesV Theobald (Author) - Menzies School of Health ResearchDerek S Sarovich (Author) - Menzies School of Health ResearchErin P Price (Author) - Menzies School of Health ResearchA Hutcheson (Author) - University of Michigan, United StatesJ Korlach (Author) - University of Michigan, United StatesJ J LiPuma (Author) - University of Michigan, United StatesJ Ladner (Author) - USAMRIID, United StatesS Lovett (Author) - USAMRIID, United StatesG Koroleva (Author) - USAMRIID, United StatesG Palacios (Author) - USAMRIID, United StatesD Limmathurotsakul (Author) - Mahidol University, ThailandV Wuthiekanun (Author) - Mahidol University, ThailandG Wongsuwan (Author) - Mahidol University, ThailandB J Currie (Author) - Menzies School of Health ResearchP Keim (Author) - Northern Arizona University, United StatesD 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
- 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
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