Table 1.

The 27 Escherichia coli and Shigella genomes used in this study. NCBI, National Center for Biotechnology Information.

genome	NCBI identifier	clinical condition and/or pathotypea	reference(s)
E. coli SE11	NC_011415	commensal	[18]
E. coli IAI1	NC_011741	commensal	[14]
E. coli 55989	NC_011748	diarrhoea (EAEC)	[14]
E. coli E24377A	NC_009801	diarrhoea (ETEC)	[19]
Shigella boydii Sb227	NC_007613	shigellosis	[20]
Shigella boydii CDC 3083 94	NC_010658	shigellosis	[21]
Shigella sonnei Ss046	NC_007384	shigellosis	[20]
Shigella flexneri 2a 2457T	NC_004741	shigellosis	[22]
Shigella flexneri 2a	NC_004337	shigellosis	[23]
Shigella flexneri 5 8401	NC_008258	shigellosis	[24]
E. coli C ATCC 8739	NC_010468	commensal	[25]
E. coli HS	NC_009800	commensal	[19]
E. coli K12 substr MG1655	NC_000913	commensal	[26]
E. coli K12 substr W3110	AC_000091	commensal	[27]
E. coli 0157 : H7 EDL933	NC_002655	diarrhoea (EHEC)	[28]
E. coli O157 : H7	NC_002695	diarrhoea (EHEC)	[29]
Shigella dysenteriae	NC_007606	shigellosis	[20]
E. coli UMN026	NC_011751	cystitis (ExPEC)	[14]
E. coli APEC O1	NC_008563	colisepticaemia (ExPEC, APEC)	[30]
E. coli S88	NC_011742	newborn meningitis (ExPEC)	[14]
E. coli UTI89	NC_007946	cystitis (ExPEC, UPEC)	[31]
E. coli ED1a	NC_011745	healthy subject	[14]
E. coli 536	NC_008253	pyelonephritis (ExPEC, UPEC)	[32,33]
E. coli CFT073	NC_004431	pyelonephritis (ExPEC, UPEC)	[34]
E. coli 0127 H6 E2348 69	NC_011601	diarrhoea (EPEC)	[35]
E. coli IAI39	NC_011750	pyelonephritis (ExPEC)	[14]
E. coli SMS 3 5	NC_010498	environmental strain	[36]

^aEAEC, enteroaggregative E. coli; ETEC, enterotoxigenic E. coli; EHEC, enterohemorrhagic E. coli; ExPEC, extraintestinal pathogenic E. coli; APEC, avian pathogenic E. coli; UPEC, uropathogenic E. coli; EPEC, enteropathogenic E. coli.