Genomics of Enterococcus faecium in cirrhosis patients
We performed comprehensive metagenomic sequencing on ascites and urine samples collected from 209 hospitalized patients with liver cirrhosis. Metagenome assembly and binning efforts reconstructed Enterococcus faecium genomes from these specimens, revealing that a large proportion harbored known daptomycin-resistance–associated mutations. Comparative genomic analysis demonstrated that E. faecium strains recovered from different patients shared over 99.7% average nucleotide identity and clustered tightly in phylogenetic trees. This high degree of similarity indicates locally disseminated, phylogenetically linked lineages of noscomially transmitted E. faecium within the patient cohort.