Development and validation of a Burkholderia pseudomallei core genome multilocus sequence typing scheme to facilitate molecular surveillance
release_np63yrgldbdzlgxouamw4o4aja
by
Sabine Lichtenegger,
Trung T. Trinh,
Karoline Assig,
Karola Prior,
Dag Harmsen,
Julian Pesl,
Andrea Zauner,
Michaela Lipp,
Tram A. Que,
Beatrice Mutsam,
Barbara Kleinhappl,
Ivo Steinmetz
(+1 others)
2021 Volume 59, Issue 8, e0009321
Abstract
<jats:bold><jats:italic>Objectives:</jats:italic></jats:bold> <jats:italic>Burkholderia pseudomallei</jats:italic> causes the severe disease melioidosis. Whole genome-sequencing (WGS) based typing methods currently offer the highest resolution for molecular investigations of this genetically diverse pathogen. Still, its routine application in diagnostic laboratories is limited by the need for high computing power, bioinformatic skills and variable bioinformatic approaches, the latter affecting the results. We therefore aimed to establish and validate a WGS-based core genome multilocus sequence typing (cgMLST) scheme, applicable in routine diagnostic settings.
<jats:bold><jats:italic>Methods:</jats:italic></jats:bold> A soft defined core genome was obtained by challenging the <jats:italic>B. pseudomallei</jats:italic> reference genome K96243 with 469 environmental and clinical genomes, resulting in 4,221 core and 1,359 accessory targets. The scheme was validated with 320 WGS datasets. We compared our novel typing scheme with single nucleotide polymorphism based-approaches investigating closely and distantly related strains. Finally, we applied our scheme for tracking the environmental source of a recent infection.
<jats:bold><jats:italic>Results:</jats:italic></jats:bold> The validation of the scheme detected >95% good cgMLST target genes in 98.4% of the genomes. Comparison with existing typing methods revealed very good concordance. Our scheme proved to be applicable to investigate not only closely related strains, but also the global <jats:italic>B. pseudomallei</jats:italic> population structure. We successfully utilized our scheme to identify a sugar cane field as the presumable source of a recent melioidosis case.
<jats:bold><jats:italic>Conclusion:</jats:italic></jats:bold> We developed a robust cgMLST typing scheme which integrates high resolution, maximized standardization and fast analysis for the non-bioinformatician. Our typing scheme has the potential to serve as a routinely applicable classification system in <jats:italic>B. pseudomallei</jats:italic> molecular epidemiology.
In application/xml+jats
format
Archived Files and Locations
application/pdf
2.3 MB
file_hrbf4a7dejfsllnpnxr7vgp6zy
|
jcm.asm.org (publisher) web.archive.org (webarchive) |
access all versions, variants, and formats of this works (eg, pre-prints)
Crossref Metadata (via API)
Worldcat
SHERPA/RoMEO (journal policies)
wikidata.org
CORE.ac.uk
Semantic Scholar
Google Scholar