Antibiotic resistance determination using Enterococcus faecium whole-genome sequences: a diagnostic accuracy study...

Area of Science:

• Genomics
• Microbiology
• Infectious Diseases

Background:

• Antibiotic resistance in Enterococcus faecium poses a significant global health threat.
• Traditional in vitro antibiotic susceptibility testing (AST) can be time-consuming.
• DNA sequencing offers a potential alternative for rapid detection of resistance genes.

Purpose of the Study:

• To assess and enhance the accuracy of predicting antibiotic resistance in E. faecium using whole-genome sequencing data.
• To develop a comprehensive catalogue of genetic markers associated with antibiotic resistance in E. faecium.
• To support the use of genomic data for diagnosing and surveilling antimicrobial resistance.

Main Methods:

• A retrospective diagnostic accuracy study involving a literature search for resistance genes.
• Evaluation of 4382 E. faecium isolates with whole-genome sequences and AST phenotypes.
• Development of a bioinformatics pipeline for genotypic resistance prediction and comparison with existing tools.

Main Results:

• A curated catalogue of 228 genetic markers for 12 antibiotics was established.
• High accuracy was achieved for predicting resistance to ampicillin, ciprofloxacin, vancomycin, and linezolid.
• The developed database demonstrated superior sensitivity and specificity compared to other tools for several antibiotics.

Conclusions:

• Whole-genome sequencing provides accurate predictions of antibiotic resistance in E. faecium.
• The findings facilitate the adoption of WGS for antimicrobial resistance diagnosis and surveillance.
• Further research is needed to characterize resistance to last-line antibiotics and improve genotypic prediction accuracy.