Genomic surveillance of <i>Escherichia coli</i> ST131 identifies local expansion and serial replacement of subclones.

<i>Escherichia coli</i> sequence type 131 (ST131) is a pandemic clone that is evolving rapidly with increasing levels of antimicrobial resistance. Here, we investigated an outbreak of <i>E. coli</i> ST131 producing extended spectrum β-lactamases (ESBLs) in a long-term care facility (LTCF) in Ireland by combining data from this LTCF (<i>n</i>=69) with other Irish (<i>n</i>=35) and global (<i>n</i>=690) ST131 genomes to reconstruct the evolutionary history and understand changes in population structure and genome architecture over time. This required a combination of short- and long-read genome sequencing, <i>de novo</i> assembly, read mapping, ESBL gene screening, plasmid alignment and temporal phylogenetics. We found that Clade C was the most prevalent (686 out of 794 isolates, 86 %) of the three major ST131 clades circulating worldwide (A with <i>fimH41</i>, B with <i>fimH22</i>, C with <i>fimH30</i>), and was associated with the presence of different ESBL alleles, diverse plasmids and transposable elements. Clade C was estimated to have emerged in <i>c</i>. 1985 and subsequently acquired different ESBL gene variants (<i>bla</i> _CTX-M-14 vs <i>bla</i> _CTX-M-15). An ISEcp<i>1-</i>mediated transposition of the <i>bla</i> _CTX-M-15 gene further increased the diversity within Clade C. We discovered a local clonal expansion of a rare C2 lineage (C2_8) with a chromosomal insertion of <i>bla</i> _CTX-M-15 at the <i>mppA</i> gene. This was acquired from an IncFIA plasmid. The C2_8 lineage clonally expanded in the Irish LTCF from 2006, displacing the existing C1 strain (C1_10), highlighting the potential for novel ESBL-producing ST131 with a distinct genetic profile to cause outbreaks strongly associated with specific healthcare environments.