Phylogenomic Analysis of Extraintestinal Pathogenic Escherichia coli Sequence Type 1193, an Emerging Multidrug-Resistant Clonal Group

Phylogenetic distribution of accessory traits in representative ST1193 and non-ST1193 STc14 isolates. Squares, colored by trait category, represent the presence of a trait examined. Mutations refer to mutations conferring fluoroquinolone resistance. Year (green to red, older to recent) and ST are categorically colored for comparison. Plasmid mapping refers to the presence of a region (>95% similarity and >80% length) relative to plasmid p1ESCUM.

Mapping of sequencing reads from ST1193 and non-ST1193 STc14 isolates against plasmid pNMEC-O75A in the context of F-plasmid replicon. In the sequencing maps, black peaks indicate regions with exact matches, colored peaks indicate matching regions with nucleotide variation, and white regions indicate areas with no mapping of reads.

Time-scaled phylogenetic analysis of 111 ST1193 isolates collected in the U.S. between 2008 and 2018. Red node bars indicate the 95% highest posterior density interval of the node position. Purple circles indicate nodes with at least 70% posterior support. Brown bars at the right indicate the presence of capsular types K1 and K5, and purple bars at right indicate presence of F plasmid alleles.

Heatmap presence or absence of non-core-predicted proteins across STc14 isolates sequenced in this study. Red, presence of predicted protein presence; cream, absence of predicted protein. Heatmap was generated using Ward two-way hierarchical clustering with the Euclidean distance method.

Enterobase GrapeTree of 484 STc14 isolates, generated using core genome multilocus sequence typing (cgMLST). Using the Achtman 7-gene MLST scheme in Enterobase, a search for ST14 with a mismatch setting of 1 allele resulted in a database of 483 STc14 strains. cgMLST was used in the experimental data setting to generate GrapeTree (minimal spanning tree) images. The upper image is colored according to ST, and the lower image is colored according to predicted serogroup. In the keys, the numbers in brackets represent number of isolates.