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. 2021 Sep 26;13(10):686. doi: 10.3390/toxins13100686

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© 2021 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

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SNP-Phylogeny and hierarchical clustering of 93 strains belonging to the clonal complex CC165, isolated from various sources and countries throughout the world between 1980 and 2020. Caption: A maximum-likelihood tree based on 37,956 core SNPs within all 93 genomes retrieved from EnteroBase was built. Clonal complex (CC) 165 is divided into three STs (ST165, ST189, and ST301), as indicated by the colored rectangle on the left side of the figure. ST301 is split into two groups, A and B. The origin of the strain (country, year, and source of isolation) is represented, if available, by the suitable abbreviation (BE, Belgium; CN, China; DE, Germany; DK, Denmark; EC, Ecuador; ES, Spain; FR, France; GW, Guinea-Bissau; IT, Italy; JP, Japan; KR, Korea; NL, Netherlands; NO, Norway; UK, United Kingdom; US, USA) and symbols for human, animal (picture, W for wild animal or haystack for a feed animal), and water for environmental source. The strain serotype is represented by a colored circle to the left of the name of the strain. The presence of intimin (eae) and Shiga toxin (stx) genes are represented by a colored square, depending on the nature of the subtype. The presence of virulence genes or the cryptic plasmid (pR444_B) is indicated by a black square. The genomes were also assigned to hierarchical clusters (HCs) based on core genome MLST to assess their genomic relatedness. Common HCs are represented by a number highlighted in the same color, indicating that the strains are closely related. For example, two strains sharing the same HC10 means they have links that are no more than 10 alleles apart. * signifies that the name of the strain has been shortened for the figure (n = 7). The complete names are as follows: Escherichia_coli_200708-sc-2012-01-13T20:11:28Z-1332516, Escherichia_coli_201589-sc-2012-01-13T20:11:52Z-1332550, Escherichia_coli_201488-sc-2012-01-13T20:11:51Z-1332549, Escherichia_coli_102366-sc-2012-01-13T20:11:47Z-1332544, Escherichia_coli_402248-sc-2012-01-13T20:11:08Z-1332489, Escherichia_coli_503028-sc-2012-01-13T20:11:16Z-1332499, and Escherichia_coli_403726-sc-2012-01-13T20:11:40Z-1332534.

SNP-Phylogeny and hierarchical clustering of 93 strains belonging to the clonal complex CC165, isolated from various sources and countries throughout the world between 1980 and 2020. Caption: A maximum-likelihood tree based on 37,956 core SNPs within all 93 genomes retrieved from EnteroBase was built. Clonal complex (CC) 165 is divided into three STs (ST165, ST189, and ST301), as indicated by the colored rectangle on the left side of the figure. ST301 is split into two groups, A and B. The origin of the strain (country, year, and source of isolation) is represented, if available, by the suitable abbreviation (BE, Belgium; CN, China; DE, Germany; DK, Denmark; EC, Ecuador; ES, Spain; FR, France; GW, Guinea-Bissau; IT, Italy; JP, Japan; KR, Korea; NL, Netherlands; NO, Norway; UK, United Kingdom; US, USA) and symbols for human, animal (picture, W for wild animal or haystack for a feed animal), and water for environmental source. The strain serotype is represented by a colored circle to the left of the name of the strain. The presence of intimin (eae) and Shiga toxin (stx) genes are represented by a colored square, depending on the nature of the subtype. The presence of virulence genes or the cryptic plasmid (pR444_B) is indicated by a black square. The genomes were also assigned to hierarchical clusters (HCs) based on core genome MLST to assess their genomic relatedness. Common HCs are represented by a number highlighted in the same color, indicating that the strains are closely related. For example, two strains sharing the same HC10 means they have links that are no more than 10 alleles apart. * signifies that the name of the strain has been shortened for the figure (n = 7). The complete names are as follows: Escherichia_coli_200708-sc-2012-01-13T20:11:28Z-1332516, Escherichia_coli_201589-sc-2012-01-13T20:11:52Z-1332550, Escherichia_coli_201488-sc-2012-01-13T20:11:51Z-1332549, Escherichia_coli_102366-sc-2012-01-13T20:11:47Z-1332544, Escherichia_coli_402248-sc-2012-01-13T20:11:08Z-1332489, Escherichia_coli_503028-sc-2012-01-13T20:11:16Z-1332499, and Escherichia_coli_403726-sc-2012-01-13T20:11:40Z-1332534.