Application of next-generation sequencing in the detection of antimicrobial resistance

Antimicrobial resistance (AMR) is increasing on a global scale, necessitating the development of diagnostic tools that are more accurate, comprehensive, and rapid. Traditional phenotypic methods, such as culture-based antimicrobial susceptibility testing, are constrained by low throughput and limited applicability to polymicrobial or non-culturable pathogens. In contrast, Next-Generation Sequencing (NGS) technologies have transformed resistance detection by enabling high-resolution genotyping. This review provides a comprehensive overview of major sequencing strategies and evaluates their clinical applications for detecting drug resistance across diverse pathogens, while critically examining the advantages and limitations of each platform. Despite ongoing challenges including high cost, technical complexity, and imperfect genotype-phenotype correlations, recent advances in artificial intelligence (AI)-assisted analysis, resistance gene databases, and portable sequencing platforms are progressively bridging the gap between research and clinical implementation. NGS-based diagnostics are poised to become indispensable tools for precision antimicrobial therapy and global AMR surveillance.