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

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...

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Detalles Bibliográficos
Autores principales: Waters, Nicholas R., Abram, Florence, Brennan, Fiona, Holmes, Ashleigh, Pritchard, Leighton
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Microbiology Society 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7656184/
https://www.ncbi.nlm.nih.gov/pubmed/33195978
http://dx.doi.org/10.1099/acmi.0.000143
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author Waters, Nicholas R.
Abram, Florence
Brennan, Fiona
Holmes, Ashleigh
Pritchard, Leighton
author_facet Waters, Nicholas R.
Abram, Florence
Brennan, Fiona
Holmes, Ashleigh
Pritchard, Leighton
author_sort Waters, Nicholas R.
collection PubMed
description 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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spelling pubmed-76561842020-11-12 Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool Waters, Nicholas R. Abram, Florence Brennan, Fiona Holmes, Ashleigh Pritchard, Leighton Access Microbiol Method 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/. Microbiology Society 2020-06-19 /pmc/articles/PMC7656184/ /pubmed/33195978 http://dx.doi.org/10.1099/acmi.0.000143 Text en © 2020 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License.
spellingShingle Method
Waters, Nicholas R.
Abram, Florence
Brennan, Fiona
Holmes, Ashleigh
Pritchard, Leighton
Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool
title Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool
title_full Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool
title_fullStr Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool
title_full_unstemmed Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool
title_short Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool
title_sort easy phylotyping of escherichia coli via the ezclermont web app and command-line tool
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7656184/
https://www.ncbi.nlm.nih.gov/pubmed/33195978
http://dx.doi.org/10.1099/acmi.0.000143
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