TABLE 1.

E. faecium isolates and their genomes used in this study

Group	Strain	Isolation origin(s)	MLSTa	Countryb (state)	Yrb	GenBank accession no.	Genome sizec (kb)	Reference(s)
NC	Com12	Human, healthy volunteer, feces	ST107	USA (MA)	2006	ACBC00000000	2,685	48
NC	Com15	Human, healthy volunteer, feces	ST583	USA (MA)	2006	ACBD00000000	2,771	48
NC	E1039	Human, healthy volunteer, feces	ST42	Netherlands	1998	ACOS00000000	2,503	39
NC	E1071	Human, hospital patient, not related to enterococcal infection outbreak, feces	ST32	Netherlands	2000	ABQI00000000	2,701	39
NC	E4452	Dog, community, ampicillin-resistant enterococcus, rectal swabs	ST266	Netherlands	2008	AEOU00000000	2,769	49
NC	E4453	Dog, community, ampicillin-resistant enterococcus, rectal swabs	ST192	Netherlands	2008	AEDZ00000000	2,819	49
NC	E980	Human, healthy volunteer, feces	ST94	Netherlands	1998	ABQA00000000	2,793	39
NC	NRRL B-2354	Food, milk	ST860d	USA	≤1947	CP004063 and CP004064	2,850	50
NC	PC4.1	Food, Mongolian yogurt (tarag)	ST720		≤2010	ADMM00000000	2,811	51
NC	TX1330	Human, healthy community volunteer, feces	ST107	USA (TX)	1994	ACHL00000000	2,721	52
CL	1,141,733	Human, clinical isolate, hospitalized patient, blood culture	ST327			ACAZ00000000	2,865	48
CL	1,230,933	Human, clinical isolate, hospitalized patient, wound swab	ST18			ACAS00000000	2,952	48
CL	1,231,408	Human, clinical isolate, hospitalized patient, blood culture	ST582			ACBB00000000	2,889	48
CL	1,231,410	Human, clinical isolate, skin and soft tissue infection	ST17			ACBA00000000	2,944	48
CL	1,231,501	Human, clinical isolate, hospitalized patient, blood culture	ST52			ACAY00000000	2,799	48
CL	1,231,502	Human, clinical isolate, hospitalized patient, blood culture	ST203			ACAX00000000	2,926	48
CL	Aus0004	Human, liver transplant recipient, blood	ST17	Australia	1998	CP003351 to CP003354	3,020	47
CL	C68	Human, clinical isolate, hospitalized patient, blood culture	ST16	USA (OH)	1998	ACJQ00000000	2,941	53
CL	D344SRF	Human, isolation site not specified	ST25	France	1985	ACZZ00000000	2,745	3
CL	DO	Human, endocarditis infection	ST18	USA (TX)	1994	CP003583 to CP003586	3,053	4
CL	E1162	Human, clinical isolate, hospitalized patient, blood culture	ST17	France	1997	ABQJ00000000	2,711	39
CL	E1636	Human, clinical isolate, hospitalized patient, blood culture	ST106	Netherlands	1961	ABRY00000000	2,838	39
CL	E1679	Human, clinical isolate, vascular catheter tip	ST114	Brazil	1998	ABSC00000000	2,928	39
CL	TX0082	Human, clinical isolate, endocarditis, blood	ST17	USA (TX)	1999	AEBU00000000	2,691	52
CL	TX0133A	Human, clinical isolate, blood	ST17	USA (TX)	2006	AECH00000000	2,930	52
CL	TX0133a01	Human, clinical isolate, in the inhibition zone, blood	ST17	USA (TX)		AECJ00000000	3,073
CL	TX0133a04	Human, clinical isolate, outside the inhibition zone, blood	ST17	USA (TX)		AEBC00000000	2,922	52, 54
CL	TX0133B	Human, clinical isolate, blood	ST17	USA (TX)	2006	AECI00000000	2,927	52, 54
CL	TX0133C	Human, clinical isolate, blood	ST17	USA (TX)	2006	AEBG00000000	2,907	52, 54
CL	U0317	Human, clinical isolate, urinary tract infection (urine)	ST78	Netherlands	2005	ABSW00000000	2,893	39
	TC6	Colonizing transconjugant between C68 and D344SRF	ST25	USA (OH)		ACOB00000000	2,884	19

^aMLST were assigned according to each genome sequence used in this study. MLST of 24 isolates assigned by us were compared to the reported MLST. Twenty-three MLST were the same as the reported MLST, but that of D344SRF (ST25) was different from the reported MLST (ST21). MLST of 5 strains were assigned for the first time in this study.

^bInformation on isolation country and year (4).

^cGenome sizes were calculated as the total length of contigs for each genome.

^dNew sequence type assigned during the course of this study (http://efaecium.mlst.net/).