Strategies for integrating whole-genome sequencing into antimicrobial resistance surveillance

Antimicrobial resistance (AMR) poses a significant global public health challenge requiring improved diagnostic procedures and strategic surveillance. Such surveillance is imperative for monitoring resistance trends, formulating clinical and public health strategies and guiding stewardship interventions. Culture-based susceptibility testing and targeted gene amplification-based molecular methods remain conventional surveillance techniques. However, the limitations of labour and time requirements and narrow resolution make whole-genome sequencing (WGS) a powerful complement, enabling the high-resolution detection of resistance determinants, virulence factors and mobile genetic elements. The integration of WGS into surveillance systems is restricted by bioinformatics capacity, standardisation and interpretability. This review introduces key bioinformatics tools across five domains, i.e. pathogen identification, molecular epidemiology, resistance gene detection, virulence profiling and mobile genetic element analysis, offering structured workflows tailored for both web-based and locally installed environments. By demonstrating the utility and complementarity of WGS-based approaches, we propose a practical and scalable framework for the genomics-based surveillance of AMR. The widespread implementation of these tools, along with advanced user-friendly interfaces and automation, can help bolster pathogen monitoring efforts and enhance the global capacity to combat AMR.