TABLE 1.

List of strains and sequences included in the study

Species	Strain	Serogroup	GenBank assembly accession no.a	Strain included in phylogeny?
				Core genome SNP	ctxAB	tcpA
Vibrio cholerae	2010EL-1786	O1	GCA_000166455.2	Yes	Yes	Yes
	2016V-1085	O141	GCA_021308775.1	Yes	Yes	Yes
	3528-08	NAG	GCA_009762895.1	Yes	Yes	Yes
	3566-08	O141	GCA_009763105.1	Yes	Yes	Yes
	3569-08	O1	GCA_009762985.1	Yes	Yes	Yes
	BX 330286	O1	GCA_000174335.1	Yes	Yes	No
	2011V-1043	O75	GCA_009764135.1	Yes	Yes	Yes
	MJ1236	O1	GCA_000022585.1	Yes	No	No
	N16961	O1	GCA_900205735.1	Yes	Yes	No
	O395	O1	GCA_000021625.1	Yes	Yes	Yes
	V51	O141	GCA_000152465.2	Yes	Yes	Yes
	V52	O37	GCA_001857545.1	Yes	Yes	Yes
	3541-04	O75	GCA_009763045.1	Yes	Yes	Yes
	E506	O1	GCA_001887475.1	Yes	Yes	No
	F9993	O139	GCA_009763825.1	Yes	No	No
	IEC224	O1	GCA_000250855.1	Yes	No	No
	MS6	O1	GCA_000829215.1	Yes	No	No
	K2802	O141	GCA_009763985.1	Yes	No	No
	2470-80	O1	GCA_001683415.1	Yes	No	No
	365-96b,c	O27	NA	No	Yes	Yes
	ATCC 25872 (280 NAG)	O37	GCA_018336415.1	No	No	Yes
	CIRS101	O1	GCA_000175695.1	No	Yes	No
Vibrio mimicus	M1567 (523-80)d	NA	NA	No	No	Yes
	06-2455	NA	GCA_009764005.1	No	No	Yes
	2011V-1073	NA	GCA_009665195.1	No	No	Yes

^aNA, not available.

^bThe GenBank accession number for the 365-96 ctxAB sequence is AF390572.1.

^cThe GenBank accession number for the 365-96 tcpA sequence is AF390571.1.

^dThe GenBank accession number for the M1567 (523-80) tcpA sequence is FJ209007.1.