SRST2 is a read mapping-based tool for rapid and accurate detection of genes, alleles, and multi-locus sequence types (MLST) from whole genome sequencing (WGS) data. It outperforms assembly-based methods in terms of gene detection and allele assignment. SRST2 was validated in a public health laboratory and demonstrated its utility for microbial genome surveillance in hospital settings. It is designed to extract clinically useful information from raw WGS data, particularly in the face of rising antimicrobial resistance and emerging virulence. The tool is named after its predecessor, SRST, but uses different algorithms and is more stable and robust. It allows for simultaneous typing of MLST, resistance genes, and virulence genes. SRST2 performs fast and accurate detection of genes and alleles directly from WGS reads, using any sequence database. It calculates combinatorial sequence types defined in MLST-style databases. SRST2 is used for routine molecular typing in public health and hospital laboratories via automated MLST and typing of virulence, antimicrobial resistance, and plasmid genes. It is faster and more reliable than SRST for MLST analysis. SRST2 is available as open-source software and can be used for genomic epidemiology. It is designed to handle large numbers of bacterial isolates and is suitable for both routine surveillance and outbreak investigation. The tool is particularly useful for detecting antimicrobial resistance genes and virulence genes. It has been validated for use in public health laboratories and has been shown to be effective in identifying resistant clones and tracking outbreaks. SRST2 is a powerful tool for rapid genomic surveillance in public health and hospital microbiology labs.SRST2 is a read mapping-based tool for rapid and accurate detection of genes, alleles, and multi-locus sequence types (MLST) from whole genome sequencing (WGS) data. It outperforms assembly-based methods in terms of gene detection and allele assignment. SRST2 was validated in a public health laboratory and demonstrated its utility for microbial genome surveillance in hospital settings. It is designed to extract clinically useful information from raw WGS data, particularly in the face of rising antimicrobial resistance and emerging virulence. The tool is named after its predecessor, SRST, but uses different algorithms and is more stable and robust. It allows for simultaneous typing of MLST, resistance genes, and virulence genes. SRST2 performs fast and accurate detection of genes and alleles directly from WGS reads, using any sequence database. It calculates combinatorial sequence types defined in MLST-style databases. SRST2 is used for routine molecular typing in public health and hospital laboratories via automated MLST and typing of virulence, antimicrobial resistance, and plasmid genes. It is faster and more reliable than SRST for MLST analysis. SRST2 is available as open-source software and can be used for genomic epidemiology. It is designed to handle large numbers of bacterial isolates and is suitable for both routine surveillance and outbreak investigation. The tool is particularly useful for detecting antimicrobial resistance genes and virulence genes. It has been validated for use in public health laboratories and has been shown to be effective in identifying resistant clones and tracking outbreaks. SRST2 is a powerful tool for rapid genomic surveillance in public health and hospital microbiology labs.