Article
Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli.
Microbial genomics - 1 Dec 2023
Davies Timothy J, Swann Jeremy, Sheppard Anna E, Pickford Hayleigh, Lipworth Samuel, AbuOun Manal, Ellington Matthew J, Fowler Philip W, Hopkins Susan, Hopkins Katie L, Crook Derrick W, Peto Timothy E A, Anjum Muna F, Walker A Sarah, Stoesser Nicole
Abstract excerpt
Several bioinformatics genotyping algorithms are now commonly used to characterize antimicrobial resistance (AMR) gene profiles in whole-genome sequencing (WGS) data, with a view to understanding AMR epidemiology and developing resistance prediction workflows using WGS in clinical settings. Accurately evaluating AMR in Enterobacterales, particularly Escherichia coli, is of major importance, because this is a...
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