SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

Michael Inouye, Harriet Dashnow, Lesley Raven, Mark B Schultz, Bernard J Pope, Takehiro Tomita, Justin Zobel, Kathryn E Holt

Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (WGS) for these purposes poses significant challenges. Here we present SRST2, a tool for fast and accurate detection of genes, alleles and multi-locus sequence types from WGS data, which outperforms assembly-based methods. Using >900 genomes from common pathogens, we demonstrate SRST2’s utility for rapid genome surveillance in public health laboratory and hospital infection control settings.