Automated antimicrobial susceptibility testing and antimicrobial resistance genotyping using Illumina and Oxford Nanopore Technologies sequencing data among Enterobacteriaceae.

ABSTRACT: Whole-genome sequencing (WGS) enables the molecular characterization of bacterial pathogens. We compared the accuracy of the Illumina and Oxford Nanopore Technologies (ONT) sequencing platforms for the determination of AMR classes and antimicrobial susceptibility testing (AST) among 181 clinical Enterobacteriaceae isolates. Sequencing reads for each isolate were uploaded to AREScloud (Ares Genetics) to determine the presence of AMR markers and the predicted WGS-AST profile. The profiles of both sequencing platforms were compared to broth microdilution (BMD) AST. Isolates were delineated by resistance to third-generation cephalosporins and carbapenems as well as the presence of AMR markers to determine clinically relevant AMR classes. The overall categorical agreement (CA) was 90% (I

SUBMITTER: Conzemius R 

PROVIDER: S-EPMC9393496 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature