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. 2023 Sep 18;370:fnad091. doi: 10.1093/femsle/fnad091

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© The Author(s) 2023. Published by Oxford University Press on behalf of FEMS.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 1. — Phylogenetic tree showing five clades (1, 2, 3, 4, and 5) and three cryptic clades (C-I, C-II, and C-III) of C. difficile isolates examined based on core genome comparison. Maximum likelihood tree was constructed based on the core genes of 11 strains examined in this study (*) and 78 other reference C. difficile using PhyML as described previously. Single nucleotide polymorphisms (SNPs) in core genes were utilized for the phylogeny, and recombination was accounted for with clonalframeML. Tree visualized in an iTOL software v6.4.3.