Extraintestinal pathogenic Escherichia coli (ExPEC) are a leading cause of urinary tract and bloodstream infections. Several pandemic multidrug resistant (MDR) ExPEC clones have emerged recently, with the exemplar being fluoroquinolone resistant ST131. The antimicrobial resistance (AMR) and virulence profiles of these lineages differ markedly, in concert with the mobile genetic elements (MGEs) on which AMR and virulence genes reside. The biological fitness factors determining their success are mostly undetermined, however much can be learnt from studying the emergence of new clones. E. coli ST101 is an emerging MDR, pathogenic lineage associated with the carriage of blaNDM-1, conferring resistance to carbapenems, a last-resort antibiotic. We analysed the genomes of seven ST101 isolates sequenced with Pacific Biosciences Single Molecule Real Time (SMRT) Sequencing. This technology enabled complete resolution of MGEs including plasmids, and definition of the genome-wide complement of DNA methylation. When considered together with publicly available genome data for 263 ST101 isolates, we determined how MGEs are major drivers of the evolution of the ST101 lineage. E. coli ST101 are monophyletic within the B1 phylogroup and cluster in two major clades. Remarkably, extensive MDR to at least 9 different antimicrobial classes was restricted to a single sub-lineage within Clade 1. This sub-lineage showed clonal expansion following the acquisition of chromosomal mutations conferring fluoroquinolone resistance, blaCTX-M-15 and blaNDM-1. We also found complex acquisition and dissemination pathways for blaNDM-1 and MDR depending on the plasmid type. For IncC plasmids, acquisition was primarily due to dynamic recombination within the antibiotic resistance island (ARI-A). However, for F-type plasmids, we found evidence for acquisition of a blaNDM-1 resistance island on one plasmid, followed by transposition to another. Lastly, we revealed how recombination events and the acquisition of a genomic island result in global methylome changes within the lineage. This work highlights the benefits of SMRT sequencing in revealing the dynamic evolutionary events and epigenetic heterogeneity that is driving the evolution of this emerging, pathogenic clone.