TableĀ 1.

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

genomeNCBI identifierclinical condition and/or pathotypeareference(s)
E. coli SE11NC_011415commensal[18]
E. coli IAI1NC_011741commensal[14]
E. coli 55989NC_011748diarrhoea (EAEC)[14]
E. coli E24377ANC_009801diarrhoea (ETEC)[19]
Shigella boydii Sb227NC_007613shigellosis[20]
Shigella boydii CDC 3083 94NC_010658shigellosis[21]
Shigella sonnei Ss046NC_007384shigellosis[20]
Shigella flexneri 2a 2457TNC_004741shigellosis[22]
Shigella flexneri 2aNC_004337shigellosis[23]
Shigella flexneri 5 8401NC_008258shigellosis[24]
E. coli C ATCC 8739NC_010468commensal[25]
E. coli HSNC_009800commensal[19]
E. coli K12 substr MG1655NC_000913commensal[26]
E. coli K12 substr W3110AC_000091commensal[27]
E. coli 0157 : H7 EDL933NC_002655diarrhoea (EHEC)[28]
E. coli O157 : H7NC_002695diarrhoea (EHEC)[29]
Shigella dysenteriaeNC_007606shigellosis[20]
E. coli UMN026NC_011751cystitis (ExPEC)[14]
E. coli APEC O1NC_008563colisepticaemia (ExPEC, APEC)[30]
E. coli S88NC_011742newborn meningitis (ExPEC)[14]
E. coli UTI89NC_007946cystitis (ExPEC, UPEC)[31]
E. coli ED1aNC_011745healthy subject[14]
E. coli 536NC_008253pyelonephritis (ExPEC, UPEC)[32,33]
E. coli CFT073NC_004431pyelonephritis (ExPEC, UPEC)[34]
E. coli 0127 H6 E2348 69NC_011601diarrhoea (EPEC)[35]
E. coli IAI39NC_011750pyelonephritis (ExPEC)[14]
E. coli SMS 3 5NC_010498environmental 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.