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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/.

SUBMITTER: Waters NR

PROVIDER: S-EPMC7656184 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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

Waters Nicholas R NR Abram Florence F Brennan Fiona F Holmes Ashleigh A Pritchard Leighton L

Access microbiology 20200619 9

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 enabl ...[more]

PMID: 33195978

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