Name	Dataset Description	Bioproject	Bioproject_link	Reference Genome Biosample	Reference
C. difficile #3	Clinical infection isolates	PRJNA594943	https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA594943	SAMEA1705932	19
C. difficile #4	Clinical infection isolates	PRJNA561087	https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA561087	SAMEA1705932	20
E. faecium #1	Healthcare-associated colonization isolates	PRJNA435617	https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA435617	SAMN10039001	"21, 22"
E. faecalis #1	Healthcare-associated colonization isolates	PRJNA435617	https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA435617	SAMN10039299	"21, 22"
K. pneumoniae #1	Healthcare-associated clinical isolates	PRJNA415194	https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA415194	SAMN01057611	23
L. crispatus #1	Publicly available genomes	"PRJNA547620, PRJNA50051, PRJNA50173, PRJNA50057, PRJNA50067, PRJNA50165, PRJNA50167, PRJNA50053, PRJNA52107, PRJNA52105, PRJNA222257, PRJNA272101, PRJEB8104, PRJNA316969, PRJNA379934, PRJEB22112"	"https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA547620, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA50051, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA50173, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA50057, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA50067, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA50165, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA50167, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA50053, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA52107, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA52105, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA222257, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA272101, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB8104, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA316969, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA379934, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB22112"	SAMEA2272191	"24, 25"
S. aureus #1	MRSA jail colonization isolates	PRJNA530184	https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA530184	SAMN00253845	26
S. aureus #2	Healthcare-associated colonization isolates	PRJNA435617	https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA435617	SAMN10038895	"21, 22"
S. maltophilia #1	Publicly available genomes	"PRJDB3841, PRJNA267549, PRJNA231221, PRJNA164599, PRJNA380601, PRJNA350620, PRJNA390523, PRJNA483996, PRJNA489399, PRJNA268101, PRJNA344912"	"https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJDB3841, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA267549, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA231221, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA164599, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA380601, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA350620, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA390523, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA483996, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA489399, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA268101, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA344912"	SAMEA1705934	27-30