Escherichia coli evolution fimbrial Genome infection plasmid ST131. Abbreviations: AMR antimicrobial resistance CTX-M cefotaximase ESBL extended-spectrum beta-lactamase ExPEC extra-intestinal pathogenic E. coli HGT horizontal gene transfer HMP Human Microbiome Project Inc incompatibility MGE mobile genetic element SIAS Sequence Identity and Similarity SNP single nucleotide polymorphism ST sequence type TDA topological data analysis UTI urinary tract infection