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EcOH: In silico serotyping of E. coli from short read data

Danielle J. Ingle, Mary Valcanis, Alex Kuzevski, Marija Tauschek, Michael Inouye, Tim Stinear, Myron M. Levine, Roy M. Robins-Browne, Kathryn E. Holt
doi: https://doi.org/10.1101/032151
Danielle J. Ingle
1Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria, Australia
2Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
3Centre for Systems Genomics, The University of Melbourne, Victoria, Australia
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  • For correspondence: ingled@student.unimelb.edu.au r.browne@unimelb.edu.au kholt@unimelb.edu.au
Mary Valcanis
4Microbiological Diagnostic Unit Public Health Laboratory, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria, Australia
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Alex Kuzevski
4Microbiological Diagnostic Unit Public Health Laboratory, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria, Australia
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Marija Tauschek
1Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria, Australia
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Michael Inouye
3Centre for Systems Genomics, The University of Melbourne, Victoria, Australia
5School of BioSciences, The University of Melbourne, Victoria, Australia
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Tim Stinear
1Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria, Australia
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Myron M. Levine
6Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD, USA
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Roy M. Robins-Browne
1Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria, Australia
7Murdoch Childrens Research Institute, Royal Children’s Hospital, Victoria
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Kathryn E. Holt
2Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
3Centre for Systems Genomics, The University of Melbourne, Victoria, Australia
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  • For correspondence: ingled@student.unimelb.edu.au r.browne@unimelb.edu.au kholt@unimelb.edu.au
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Abstract

The lipopolysaccharide (O) and flagellar (H) surface antigens of Escherichia coli are targets for serotyping that have traditionally been used to identify pathogenic lineages of E. coli. As serotyping has several limitations, public health reference laboratories are increasingly moving towards whole genome sequencing (WGS) for the rapid characterisation of bacterial isolates. Here we present a method to rapidly and accurately serotype E. coli isolates from raw, short read sequence data, leveraging the known genetic basis for the biosynthesis of O- and H-antigens. Our approach bypasses the need for de novo genome assembly by directly screening WGS reads against a curated database of alleles linked to known E. coli O-groups and H-types (the EcOH database) using the software package SRST2. We validated our approach by comparing in silico results with those obtained via serological phenotyping of 197 enteropathogenic (EPEC) isolates. We also demonstrated the utility of our method to characterise enterotoxigenic E. coli (ETEC) and the uropathogenic E. coli (UPEC) epidemic clone ST131, and for in silico serotyping of foodborne outbreak-related isolates in the public GenomeTrakr database.

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Posted November 18, 2015.
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EcOH: In silico serotyping of E. coli from short read data
Danielle J. Ingle, Mary Valcanis, Alex Kuzevski, Marija Tauschek, Michael Inouye, Tim Stinear, Myron M. Levine, Roy M. Robins-Browne, Kathryn E. Holt
bioRxiv 032151; doi: https://doi.org/10.1101/032151
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EcOH: In silico serotyping of E. coli from short read data
Danielle J. Ingle, Mary Valcanis, Alex Kuzevski, Marija Tauschek, Michael Inouye, Tim Stinear, Myron M. Levine, Roy M. Robins-Browne, Kathryn E. Holt
bioRxiv 032151; doi: https://doi.org/10.1101/032151

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