Whole genome sequencing for antimicrobial resistance surveillance: A transformative approach to detection, monitoring, and public health response

Background: The global rise of antimicrobial resistance (AMR) demands advanced and precise tools for surveillance, detection, and public health intervention. This review explores the pivotal role of Whole Genome Sequencing (WGS) in enhancing AMR monitoring by offering comprehensive insights into resistance genes, virulence factors, and pathogen phylogenetics in a single assay. Compared to traditional phenotypic and molecular methods, WGS may provide superior resolution and early detection of emerging threats. Through a structured analysis of recent literature, and global surveillance data including initiatives like GLASS and Pathogen Genomics Services, this review highlights that WGS demonstrates up to 97–100% concordance with phenotypic resistance profiles and has reduced outbreak investigation times by 30–50% in hospital settings. Moreover, it has enabled real-time tracking of high-risk clones such as Klebsiella pneumoniae ST258 and the early identification of plasmid-mediated resistance genes like mcr-1. Despite its advantages, the implementation of WGS is challenged by high costs, technical complexity, and the need for standardized workflows and robust bioinformatics support. Nevertheless, the integration of WGS into national and international AMR surveillance systems, alongside advances in portable sequencing technologies and AI-driven analytics, positions it as a transformative tool in global AMR mitigation. Addressing infrastructural disparities and ensuring equitable access to sequencing capabilities will be essential for its widespread adoption and impact.