Short-term clinical evolution of Enterococcus faecium
Long-read isolate genome sequencing of hospital-endemic Enteroccus faecium and Enterococcus faecalis lineages over several years reveals the activity of Insertion Sequences and their role in short-term evolution. Long-read metagenomic sequencing of longitudinal patient stool samples tracks gut-resident E. faecium's population dynamics and genomic structural variation over time. IS-mediated structural variation contributes to E. faecium's success as a clinical pathogen.