SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
Michael Inouye, Harriet Dashnow, Lesley-Ann Raven, Mark B Schultz, Bernard J Pope, Takehiro Tomita, Justin Zobel, Kathryn E Holt
GENOME MEDICINE | BMC | Published : 2014
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 read mapping-based tool for fast and accurate detection of genes, alleles and multi-locus sequence types (MLST) from WGS data. Using >900 genomes from common pathogens, we show SRST2 is highly accurate and outperforms assembly-based methods in terms of both gene detection and allele assignment. We include validation of SRST2 within a public health laboratory, and demonstrate its use for microbial genome surveillance in the hospital setting. In the..View full abstract
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Awarded by NHMRC of Australia
Awarded by Victorian Life Sciences Computation Initiative (VLSCI)
This work was supported by the NHMRC of Australia (grant #1043830; fellowships #1061409 (KEH) and #1061435 (MI, co-funded with the Australian Heart Foundation)) and the Victorian Life Sciences Computation Initiative (VLSCI) (grant #VR0082).