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

Rick Conzemius, Yehudit Bergman, Peter Májek, Stephan Beisken, Shawna Lewis, Emily B. Jacobs, Pranita D. Tamma, Patricia J. Simner*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

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% (Illumina) and 88% (ONT) across all antimicrobials, 96% for the prediction of resistance to third-generation cephalosporins for both platforms, and 94% (Illumina) and 91% (ONT) for the prediction of resistance to carbapenems. Carbapenem resistance was overestimated on ONT with a major error of 16%. Sensitivity for the detection of carbapenemases, extended-spectrum β-lactamases, and plasmid-mediated ampC genes was 98, 95, and 70% by ONT compared to the Illumina dataset as the reference. Our results highlight the potential of the ONT platform’s use in clinical microbiology laboratories. When combined with robust bioinformatics methods, WGS-AST predictions may be a future approach to guide effective antimicrobial decision-making.

Original languageAmerican English
Article number973605
JournalFrontiers in Microbiology
Volume13
DOIs
StatePublished - 8 Aug 2022
Externally publishedYes

Bibliographical note

Publisher Copyright:
Copyright © 2022 Conzemius, Bergman, Májek, Beisken, Lewis, Jacobs, Tamma and Simner.

Keywords

  • WGS-AST
  • antimicrobial susceptibility testing
  • carbapenem-resistant Enterobacteriaceae
  • molecular diagnostics
  • nanopore sequencing
  • point-of-care testing
  • whole-genome sequencing

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