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Accuracy of different bioinformatics methods in detecting antibiotic resistance and virulence factors from Staphylococcus aureus whole genome sequences

Abstract:
Background: In principle, whole genome sequencing (WGS) can predict phenotypic resistance directly from genotype, replacing laboratory-based tests. However, the contribution of different bioinformatics methods to genotype-phenotype discrepancies has not been systematically explored to date. Methods: We compared three WGS-based bioinformatics methods (Genefinder (read-based), Mykrobe (de Bruijn graph-based) and Typewriter (BLAST-based)) for predicting presence... Expand abstract
Publication status:
Published
Peer review status:
Peer reviewed
Version:
Accepted Manuscript

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Publisher copy:
10.1128/JCM.01815-17

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Institution:
University of Oxford
Division:
Medical Sciences Division
Department:
NDM
Role:
Author
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Institution:
University of Oxford
Division:
Medical Sciences Division
Department:
NDM; NDM Experimental Medicine
Role:
Author
More by this author
Institution:
University of Oxford
Division:
Medical Sciences Division
Department:
NDM; Human Genetics Wt Centre
Role:
Author
More by this author
Institution:
University of Oxford
Division:
Medical Sciences Division
Department:
NDM; NDM Experimental Medicine
Role:
Author
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Publisher:
American Society for Microbiology Publisher's website
Journal:
Journal of Clinical Microbiology Journal website
Volume:
56
Issue:
9
Pages:
e01815-17
Publication date:
2018-06-20
Acceptance date:
2018-05-04
DOI:
EISSN:
1098-660X
ISSN:
0095-1137
Pubs id:
pubs:846355
URN:
uri:522263b5-04bf-44fa-8573-275cef918237
UUID:
uuid:522263b5-04bf-44fa-8573-275cef918237
Local pid:
pubs:846355

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