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<jats:title>ABSTRACT</jats:title> <jats:p>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.</jats:p> <jats:p> <jats:bold>IMPORTANCE</jats:bold> A comparative analysis of 1,130 <jats:italic>Burkholderia</jats:italic> genomes identified unique markers for many named species, including the human pathogens <jats:italic>B. pseudomallei</jats:italic> and <jats:italic>B. mallei</jats:italic> . Due to core genome reduction and signature erosion, only 38 targets specific to <jats:italic>B. pseudomallei</jats:italic> /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. </jats:p>

Original publication

DOI

10.1128/mbio.00846-16

Type

Journal article

Journal

mBio

Publisher

American Society for Microbiology

Publication Date

02/11/2016

Volume

7