RT Journal Article SR Electronic(1) A1 Ludden, Catherine A1 Decano, Arun Gonzales A1 Jamrozy, Dorota A1 Pickard, Derek A1 Morris, Dearbhaile A1 Parkhill, Julian A1 Peacock, Sharon J. A1 Cormican, Martin A1 Downing, TimYR 2020 T1 Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones JF Microbial Genomics, VO 6 IS 4 OP SP e000352 DO https://doi.org/10.1099/mgen.0.000352 PB Microbiology Society, SN 2057-5858, AB Escherichia coli sequence type 131 (ST131) is a pandemic clone that is evolving rapidly with increasing levels of antimicrobial resistance. Here, we investigated an outbreak of E. coli ST131 producing extended spectrum β-lactamases (ESBLs) in a long-term care facility (LTCF) in Ireland by combining data from this LTCF (n=69) with other Irish (n=35) and global (n=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, de novo 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 fimH41, B with fimH22, C with fimH30), and was associated with the presence of different ESBL alleles, diverse plasmids and transposable elements. Clade C was estimated to have emerged in c. 1985 and subsequently acquired different ESBL gene variants (bla CTX-M-14 vs bla CTX-M-15 ). An ISEcp1-mediated transposition of the bla 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 bla CTX-M-15 at the mppA 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., UL https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000352