TABLE 5.

Overview of quinolone resistant E. coli and wild type E. coli isolate pairs of the same sequence type (ST).

ST	GyrA	ParC	ParE	Year	Clade shared genome (%)	SNP distance	CIP MIC	Location
752	S83L	S80I		2016	83.4a	2634d	1	K
				2014			0.015	U
10	S83L			2014	80.1b	635e	0.12	R
				2014			0.015	S
602	S83L			2014	86.4	1795	0.25	T
				2014			0.015	V
191	S83L			2014	84.2	40	0.25	U
				2006			0.03	S
355	S83L		D475E	2014	85.4c	66f	0.25	Q
			D475E	2006			0.06	C
117	S83L			2014	88.2	2950	0.25	F
				2017*			0.015	L
115	S83L			2014	85.2	397	0.25	V
				2014			0.015	P

Two isolates are included for each ST, where the topmost isolate in each row is quinolone resistant and the bottom one the wild type isolate. Amino acid substitutions are listed in columns “GyrA,” “ParC,” and “ParE.” The shared genome is calculated based on analysis with ParSNP on the two genomes, with results listed as “Clade shared genome (%).” If the clade was comprised of only the wild type and quinolone resistant isolate, this value is based on the shared genome between those two isolates only. The “SNP distance” column represents the SNP distances between the two respective isolates derived from the core gene alignment. CIP MIC = ciprofloxacin minimum inhibitory concentration. Location represents production site. ^aFor closest resistant and sensitive isolate: 84.0%. ^bFor closest resistant and sensitive isolate: 82.0%. ^cFor closest resistant and sensitive isolate: 84.2%. ^dCore genome SNP distance: 104. ^eCore genome SNP distance: 254. ^fCore genome SNP distance: 100. *Parent flock.