Antibiotic resistance determination using Enterococcus faecium whole-genome sequences: a diagnostic accuracy study using genotypic and phenotypic data
Published in The Lancet Microbe, 2024
Recommended citation: Coll F, Gouliouris T, Blane B, et al. Antibiotic resistance determination using Enterococcus faecium whole-genome sequences: a diagnostic accuracy study using genotypic and phenotypic data. January 11, 2024. The Lancet Microbe. DOI: 10.1016/S2666-5247(23)00297-5 https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4345808
This work represents the largest evaluation to date on the accuracy of antibiotic resistance predictions from E. faecium genomes, using a dataset of 4,382 genomes with available culture-based AST phenotypes. I curated a catalogue of 228 genetic markers involved in resistance to 12 different antibiotics in E. faecium, and developed a bioinformatics pipeline to predict antibiotic resistance from E. faecium genomes, with important improvements in the accuracy of predictions. Given the mortality burden of antibiotic-resistant E. faecium and the increasingly routine use of WGS in clinical microbiology labs, these results and resources will facilitate the adoption of WGS as a tool for the diagnosis and surveillance of AMR in E. faecium.
Recommended citation: Coll F, Gouliouris T, Blane B, et al. Antibiotic resistance determination using Enterococcus faecium whole-genome sequences: a diagnostic accuracy study using genotypic and phenotypic data. January 11, 2024. The Lancet Microbe. DOI: 10.1016/S2666-5247(23)00297-5