Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool

Nicholas R. Waters; Florence Abram; Fiona Brennan; Ashleigh Holmes; Leighton Pritchard

doi:10.1099/acmi.0.000143

Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool

Nicholas R. Waters, Florence Abram, Fiona Brennan, Ashleigh Holmes, Leighton Pritchard (Lead / Corresponding author)

DArcy Thompson Unit

Research output: Contribution to journal › Article › peer-review

77 Citations (Scopus)

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Abstract

The Clermont PCR method for phylotyping Escherichia coli remains a useful classification scheme even though genome sequencing is now routine, and higher-resolution sequence typing schemes are now available. Relating present-day whole-genome E. coli classifications to legacy phylotyping is essential for harmonizing the historical literature and understanding of this important organism. Therefore, we present EzClermont - a novel in silico Clermont PCR phylotyping tool to enable ready application of this phylotyping scheme to whole-genome assemblies. We evaluate this tool against phylogenomic classifications, and an alternative software implementation of Clermont typing. EzClermont is available as a web app at www.ezclermont.org, and as a command-line tool at https://nickp60.github.io/EzClermont/.

Original language	English
Article number	000143
Number of pages	5
Journal	Access Microbiology
Volume	2
Issue number	9
DOIs	https://doi.org/10.1099/acmi.0.000143
Publication status	Published - 19 Jun 2020

Keywords

ECOR, Escherichia coli Reference Collection
MLST, multilocus sequence typing

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10.1099/acmi.0.000143Licence: CC BY

Final Published VersionFinal published version, 1.71 MBLicence: CC BY

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title = "Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool",

abstract = "The Clermont PCR method for phylotyping Escherichia coli remains a useful classification scheme even though genome sequencing is now routine, and higher-resolution sequence typing schemes are now available. Relating present-day whole-genome E. coli classifications to legacy phylotyping is essential for harmonizing the historical literature and understanding of this important organism. Therefore, we present EzClermont - a novel in silico Clermont PCR phylotyping tool to enable ready application of this phylotyping scheme to whole-genome assemblies. We evaluate this tool against phylogenomic classifications, and an alternative software implementation of Clermont typing. EzClermont is available as a web app at www.ezclermont.org, and as a command-line tool at https://nickp60.github.io/EzClermont/.",

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AU - Holmes, Ashleigh

AU - Pritchard, Leighton

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N2 - The Clermont PCR method for phylotyping Escherichia coli remains a useful classification scheme even though genome sequencing is now routine, and higher-resolution sequence typing schemes are now available. Relating present-day whole-genome E. coli classifications to legacy phylotyping is essential for harmonizing the historical literature and understanding of this important organism. Therefore, we present EzClermont - a novel in silico Clermont PCR phylotyping tool to enable ready application of this phylotyping scheme to whole-genome assemblies. We evaluate this tool against phylogenomic classifications, and an alternative software implementation of Clermont typing. EzClermont is available as a web app at www.ezclermont.org, and as a command-line tool at https://nickp60.github.io/EzClermont/.

AB - The Clermont PCR method for phylotyping Escherichia coli remains a useful classification scheme even though genome sequencing is now routine, and higher-resolution sequence typing schemes are now available. Relating present-day whole-genome E. coli classifications to legacy phylotyping is essential for harmonizing the historical literature and understanding of this important organism. Therefore, we present EzClermont - a novel in silico Clermont PCR phylotyping tool to enable ready application of this phylotyping scheme to whole-genome assemblies. We evaluate this tool against phylogenomic classifications, and an alternative software implementation of Clermont typing. EzClermont is available as a web app at www.ezclermont.org, and as a command-line tool at https://nickp60.github.io/EzClermont/.

KW - ECOR, Escherichia coli Reference Collection

KW - MLST, multilocus sequence typing

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JO - Access Microbiology

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Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool

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