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Volume 31, Supplement—May 2025

SUPPLEMENT ISSUE
Supplement

Lessons from 5 Years of Routine Whole-Genome Sequencing for Epidemiologic Surveillance of Shiga Toxin–Producing Escherichia coli, France, 2018–2022

Gabrielle JonesComments to Author , Carolina Silva Nodari, Laëtitia Fabre, Henriette de Valk, Harold Noel, Aurélie Cointe, Stéphane Bonacorsi, François-Xavier Weill, and Yann Le Strat
Author affiliation: Santé publique France, Saint-Maurice, France (G. Jones, H. de Valk, H. Noel, Y. Le Strat); Institut Pasteur, Université Paris Cité, Paris, France (C. Silva Nodari, L. Fabre, F.-X. Weill); Centre hospitalier universitaire Robert Debré, Assistance Publique–Hôpitaux de Paris, Paris (A. Cointe, S. Bonacorsi)

Main Article

Figure 5

Single-nucleotide polymorphism–based maximum likelihood phylogenetic tree of 226 080:H2 isolates from 5 years of routine whole-genome sequencing for epidemiologic surveillance of Shiga toxin–producing Escherichia coli, France, 2018–2022. Tree was built based on the sequence alignment of 3,949 single-nucleotide variant sites of the recombination-free core genome of E. coli strain MOD1-EC6881 (GenBank accession no. GCF_002520045.1). Tree was midpoint-rooted and visualized with iTOL (https://itol.embl.de). Bootstrap support values >90% are indicated with red dots on the branches. Branch lengths and corresponding scale bar indicate numbers of single-nucleotide polymorphisms per base of the final alignment. HC5, hierarchical clustering at a threshold of 5 allelic differences.

Figure 5. Single-nucleotide polymorphism–based maximum likelihood phylogenetic tree of 226 080:H2 isolates from 5 years of routine whole-genome sequencing for epidemiologic surveillance of Shiga toxin–producing Escherichia coli, France, 2018–2022. Tree was built based on the sequence alignment of 3,949 single-nucleotide variant sites of the recombination-free core genome of E. coli strain MOD1-EC6881 (GenBank accession no. GCF_002520045.1). Tree was midpoint-rooted and visualized with iTOL (https://itol.embl.de). Bootstrap support values >90% are indicated with red dots on the branches. Branch lengths and corresponding scale bar indicate numbers of single-nucleotide polymorphisms per base of the final alignment. HC5, hierarchical clustering at a threshold of 5 allelic differences.

Main Article

Page created: April 08, 2025
Page updated: May 12, 2025
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