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. 2020 Dec 17;10:22135. doi: 10.1038/s41598-020-79123-2

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© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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The RT106 clade may harbor up to three novel genomic islands. (a) Genetic islands GI1, GI2, and GI3 associated with RT106 are at three different locations in the genome. GV364, used as a representative genome, contains GI1 and GI3. Outer ring: Insertion site (green) of GI2 is shown relative to GI1 and GI3 locations; Blue indicate CDS (protein-coding DNA sequences). Inner ring: Purple denotes lower % GC compared to the overall % GC of the genome; Green denotes higher % GC compared to the overall % GC of the genome. Artemis DNA Plotter was used to generate genome circular map. (b) A composition vector tree of 1425 publicly available C. difficile and 38 RT106 genome sequences shows that RT106 strains clade together with 56 other strains (highlighted in red). (c) The relatedness of the 94 strains within the RT106 clade is shown in the maximum likelihood tree (log likelihood = − 29,380.67) based on the 3306 core SNPs identified using Panseq. Tree scale: 0.01 represents 0.01 substitutions per nucleotide site. Our clinical isolates are designated as “GV”, whereas pediatric isolates from Chicago, Illinois²⁷ are designated “DH or ST”. All 94 strains within the RT106 clade harbor the complete GI1. GI2 is present in 7 RT106 strains (green). Thirteen strains harboring GI3 (yellow) belong to 2 different subclades. (d) Gene arrangement, size and functions of GI1, GI2 and GI3. Functions of genes within GI1 and GI3 are named either via GO term or gene name. Genes within GI2 were previously identified and reported²⁷.