PERSPECTIVE article
Front. Public Health
Sec. Infectious Diseases: Epidemiology and Prevention
Volume 13 - 2025 | doi: 10.3389/fpubh.2025.1650925
This article is part of the Research TopicLeveraging Real-Time Genomic Surveillance to Combat Infectious Diseases and Antimicrobial ResistanceView all 9 articles
NEXT GENERATION SEQUENCING AS A PANACEA FOR ANTIBIOTIC SUSCEPTIBILITY TESTING: YEA OR NAY?
Provisionally accepted
- Independent Microbiol Advisor, RIJNSBURG, Netherlands
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Practical next generation sequencing (NGS) technologies are entering the high-throughput diagnostic clinical microbiology laboratory. Bacterial whole genome sequences (WGS) can be used for detection and identification of species and their (relative) quantification. Genomic relatedness and epidemiological spread of strains of microorganisms can be traced, in parallel with detection of virulence genes as well as genes involved in antimicrobial resistance (AMR). The latter potentially facilitates genomic antimicrobial susceptibility testing (gAST). AMR mechanisms and the genes involved are diverse and require dedicated supporting databases in order to be accurately detected by microbial genomics. The present document assesses the current position of NGS and gAST assays in the clinical microbiology laboratory and discusses their role in establishing a clinically actionable antibiogram which defines the spectrum of antibiotics to which a given microbial strain is susceptible or resistant. Key question is whether or not gAST has added value as compared to current AST methodologies.
Keywords: antibiotic susceptibility testing, next generation sequencing, antimicrobial resistance, Critical assessment, in vitro diagnostics regulation
Received: 20 Jun 2025; Accepted: 01 Aug 2025.
Copyright: © 2025 Van Belkum. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Alex Van Belkum, Independent Microbiol Advisor, RIJNSBURG, Netherlands
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