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

ABSTRACT: 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 th

SUBMITTER: Ludden C 

PROVIDER: S-EPMC7276707 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature