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Availability of data and materials Scripts used to align sequences and construct the phylogenetic tree are stored in Abbreviations ANI: Average nucleotide identity CA: Community associated CC: Clonal complex CFU: Colony forming units cgMLST: Core genome multi-locus sequence type CNS: Central nervous system CRISPR: Clustered regularly interspaced short palindromic repeats DNA: Deoxyribonucleic acid DRE: Daptomycin resistant Enterococci FDA: Food and drug administration FMT: Faecal microbiota transplantation GI: Genomic island GIT: Gastrointestinal tract HA: Hospital associated HAI: Hospital associated infection HGT: Horizontal gene transfer IS: Insertion sequence LAB: Lactic acid bacteria LGG: Lacticaseibacillus rhamnosus GG MDR: Multi-drug resistant MGE: Mobile genetic element MIC: Minimum inhibitory concentration MLST: Multi locus sequence type MRSA: Methicillin resistant Staphylococcus aureus NSG: Niche specific genes PFGE: Pulsed field gel electrophoresis PTS: Phosphotransferase systems RV: Reverse vaccinology SCV: Small colony variant ST: Sequence type UTI: Urinary tract infection VF: Virulence factor VRCD: Vancomycin resistant Clostridium difficile VRE: Vancomycin resistant Enterococci VREfm: Vancomycin-resistant Enterococcus faecium VREfs: Vancomycin-resistant Enterococcus faecalis VRSA: Vancomycin resistant Staphylococcus aureus VSEfm: Vancomycin susceptible Enterococcus faecium VSEfs: Vancomycin susceptible Enterococcus faecalis WGS: Whole-genome sequencing References Garca-Solache M, Rice LB

We employed the Science Citation Index Expanded (SCI-EXPANDED), part of the Web of Science Core Collection (WoSCC), recognized for its extensive and inclusive coverage of scientific literature