Limitations in predicting reduced susceptibility to third generation cephalosporins in Escherichia coli based on whole genome sequence data.

ABSTRACT: Prediction of antibiotic resistance from whole genome sequence (WGS) data has been proposed. However, the performance of WGS data analysis for this matter may be influenced by the resistance mechanism's biology. This study compared traditional antimicrobial susceptibility testing with whole genome sequencing for identification of extended-spectrum beta-lactamases (ESBL) in a collection of 419 Escherichia coli isolates. BLASTn-based prediction and read mapping with srst2 gave matching results, and in 381/419 (91%) isolates WGS was congruent with phenotypic testing. Incongruent results were grouped by potential explanations into biological-related and sequence analysis-related results. Biological-related explanations included weak ESBL-enzyme activity (n = 4), inconclusive phenotypic ESBL-te

SUBMITTER: Heydecke A 

PROVIDER: S-EPMC10688838 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature