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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
doi: https://doi.org/10.1101/006627
Michael Inouye
1Medical Systems Biology, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
2Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
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Harriet Dashnow
3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
4Victorian Life Sciences Computation Initiative, The University of Melbourne, 187 Grattan Street Carlton, Melbourne, Victoria, Australia
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Lesley Raven
1Medical Systems Biology, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
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Mark B. Schultz
3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
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Bernard J. Pope
4Victorian Life Sciences Computation Initiative, The University of Melbourne, 187 Grattan Street Carlton, Melbourne, Victoria, Australia
5Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria, Australia
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Takehiro Tomita
2Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
6Microbiological Diagnostic Unit, The University of Melbourne, Parkville, Victoria, Australia
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Justin Zobel
5Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria, Australia
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Kathryn E. Holt
3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
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  • For correspondence: kholt@unimelb.edu.au
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Abstract

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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 26, 2014.
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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
bioRxiv 006627; doi: https://doi.org/10.1101/006627
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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
bioRxiv 006627; doi: https://doi.org/10.1101/006627

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