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

Access Microbiol. 2020 Jun 19;2(9):acmi000143. doi: 10.1099/acmi.0.000143. eCollection 2020.

Authors

Nicholas R Waters^{1

2}, Florence Abram¹, Fiona Brennan^{1

3}, Ashleigh Holmes⁴, Leighton Pritchard^{2

5}

Affiliations

¹ Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland.
² Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland.
³ Soil and Environmental Microbiology, Environmental Research Centre, Teagasc, Johnstown Castle, Wexford, Ireland.
⁴ Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland.
⁵ Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, Scotland.

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/.

Keywords: Escherichia coli; bioinformatics; classification; genomics; phylogroups web app.