SRST2 is a read mapping-based tool designed for rapid and accurate detection of genes, alleles, and multi-locus sequence types (MLST) from whole genome sequencing (WGS) data. The tool addresses the challenges of routine WGS use in public health and hospital microbiology labs, such as the lack of efficient methods for extracting informative data from raw sequence data. SRST2 outperforms assembly-based methods in terms of gene detection and allele assignment, demonstrating high accuracy using over 900 genomes of common pathogens. It includes validation within a public health laboratory and is shown to be useful for microbial genome surveillance in hospital settings. SRST2 is particularly valuable in the context of rising antimicrobial resistance and emerging virulence, providing a powerful tool for extracting clinically useful information from raw WGS data. The source code is available at http://katholt.github.io/srst2/.SRST2 is a read mapping-based tool designed for rapid and accurate detection of genes, alleles, and multi-locus sequence types (MLST) from whole genome sequencing (WGS) data. The tool addresses the challenges of routine WGS use in public health and hospital microbiology labs, such as the lack of efficient methods for extracting informative data from raw sequence data. SRST2 outperforms assembly-based methods in terms of gene detection and allele assignment, demonstrating high accuracy using over 900 genomes of common pathogens. It includes validation within a public health laboratory and is shown to be useful for microbial genome surveillance in hospital settings. SRST2 is particularly valuable in the context of rising antimicrobial resistance and emerging virulence, providing a powerful tool for extracting clinically useful information from raw WGS data. The source code is available at http://katholt.github.io/srst2/.