A total of 31 isolates (16 E. faecalis, 14 E. faecium, and 1 MRSA) were analyzed by whole‐genome sequencing to further investigate linezolid and vancomycin‐resistant isolates and a few isolates resistant to five or more antimicrobials. Isolate selection was based on the resistance phenotypes, irrespective of the bacterial species, that is all isolates resistant to linezolid (11 E. faecalis and 11 E. faecium) and vancomycin (n = 2 E. faecalis). The remaining isolates (3 E. faecalis, 3 E. faecium, and 1 MRSA) were selected because of their MDR phenotype (resistant to at least five different antimicrobials). Genomic DNA was extracted as detailed in “DNA preparation.” Libraries were prepared using Nextera XT DNA library preparation kit (Illumina) according to the manufacturer's instructions and underwent Illumina sequencing using the MiSeq V3 chemistry (Illumina) for the production of two ×250 bp paired‐end reads. Raw sequenced reads were trimmed with Trimmomatic v0.38 using default settings and de novo assembled with SPAdes v 3.13.0 using default settings (Bankevich et al., 2012 (link)). Identification of AMR genes was assessed with ResFinder 4.1 using default settings (Bortolaia et al., 2020 (link)).
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