Table 1.
C. pseudotuberculosis isolates included in this study for whole genome sequencing (WGS).
Table 2.
Comparison of the number of genetic differences of isolates from horses by cgMLST and SNP analysis.
Table 3.
Comparison of the number of genetic differences of several isolates by cgMLST and SNP analysis.
Fig 1.
cgMLST result of 187 C. pseudotuberculosis genomes displayed graphically as minimum spanning tree (MST).
1,577 core genome targets were used. For distance calculation of the MST, the "pairwise ignore missing values" parameter was utilized. The distance between allelic genotypes is represented by the linkage between two MST nodes. The data on biotypes were retrieved from the NCBI GenBank and from our own investigations (21 CPS isolates). (A) Colors represent the different host animals of the isolates used. (B) Colors represent the three genotypes identified in this study, based on the detection of (intact) genes of the narKGHJI operon. (C) Colors represent the different geographic origins of the isolates.
Fig 2.
Phylogenetic trees of C. pseudotuberculosis genomic data.
Phylogenetic trees of genomic data from of 187 C. pseudotuberculosis isolates. Biovars are represented by colors. Biovar Ovis in green, Biovar Equi with narKGHJI operon in blue. If no information on the biovar was included in the metadata, the biovar was determined based on the presence of the narKGHJI operon. The data sets with indel in the genes of the narKGHJI operon are marked in red and labeled as Biovar Ovis genomovar camelid. (A) Neighbor-joining tree based on cgMLST allelic profiles of 1,577 core genome targets. The "pairwise ignore missing values" parameter within Ridom SeqSphere+ was utilized for distance calculation. (B) DNA sequences of the ABC transporter substrate-binding protein CDS gene CpMEX29_RS07510, extracted from the whole genomes, were aligned by Clustal Omega. The tree was generated through the use of FastTree from the alignments, using an approximately-maximum-likelihood approach.