TABLE 2.
Islands predicted by IslandViewer and/or genomic comparison to E. coli K12 from sequenced strains belonging to pathotypes UPEC (536, CFT073, UMNO26, and UTI89), NMEC (RS218, IHE3034, CE10, and S88), APEC (APECO1) and AIEC (LF82, NRG857C, and UM146) and commensal strains (ED1a and HS).
| PAI name (alternatives) | Chromosomal insertion site | Size (kb) | %GC | Virulence/fitness factors within islands (≥4kb) | Position |
| UPEC strain 536 (Genbank accession number: NC_008253, 4938920-bp) | |||||
| PAI-536-thrW (III536) | thrW | 77 | 47 | S pilus, Salmochelin, Ag43, Vat | 294409.371141 |
| PAI-536-icd | icd | 47 | 50 | Iss, Sit system | 1187870.1235252 |
| PAI-536-serU (VII536) | serU | 22 | 38 | TcpC | 1947667.1969721 |
| PAI-536-asnT (IV536, HPI) | asnT | 30 | 57 | Yersiniabactin | 1971318.2001603 |
| PAI-536-asnW (VI536) | asnW | 54 | 53 | Colibactin | 2015441.2068949 |
| PAI-536-cobU | cobU | 43 | 49 | Hma, Fbp system | 2075300.2116007 |
| PAI-536-pheV (V536) | pheV | 80 | 48 | Pix pilus, Ag43, K15 capsule | 3128357.3208357 |
| PAI-536-selC (I536) | selC | 77 | 46 | α-Hemolysin, PapX, F17-like pilus, CS12-like pilus | 3948173.4025637 |
| PAI-536-leuX (II536) | leuX | 102 | 46 | Hek, P pilus, α-Hemolysin, CdiAB, DsdA | 4735418.4840138 |
| UPEC strain CFT073 (Genbank accession number: NC_004431, 5231428-bp) | |||||
| PAI-CFT073-aspV (IIICFT073) | aspV | 100 | 47 | Pic, Hma, TosA, fbp system | 248751.348573 |
| PAI-CFT073-serX | serX | 113 | 49 | S pilus, Salmochelin, Ag43 | 1127702-1241149 |
| PAI-CFT073-icd | icd | 54 | 50 | Sit system | 1397370.1450849 |
| PAI-CFT073-serU | serU | 22 | 38 | TcpC | 2194512.2216563 |
| PAI-CFT073-asnT (HPI) | asnT | 32 | 57 | Yersiniabactin | 2218159.2250547 |
| PAI-CFT073-asnW | asnW | 54 | 53 | Colibactin | 2262986.2316960 |
| PAI-CFT073-cobU | cobU | 43 | 49 | Hma, Fbp system | 2322324.2365760 |
| PAI-CFT073-argW | argW | 17 | 44 | IpuA, IpuB, DsdA | 2747237.2764564 |
| PAI-CFT073-pheV (ICFT073) | pheV | 123 | 47 | α-Hemolysin, P pilus, Iha, Sat, Aerobactin, Ag43, K2 capsule | 3406498.3529292 |
| PAI-CFT073-pheU (IICFT073) | pheU | 52 | 48 | P pilus, IreA | 4919569.4971387 |
| UPEC strain UMNO26 (Genbank accession number: NC_011751, 5202090-bp) | |||||
| PAI-UMNO26-icd | icd | 46 | 50 | Iss, Sit system | 1411940.1457673 |
| PAI-UMNO26-asnT (HPI) | asnT | 66 | 52 | Yersiniabactin, T4SS | 2277413.2343149 |
| PAI-UMNO26-pheV | pheV | 116 | 47 | P pilus, Iha, Sat, Aerobactin, Ag43, K5 capsule | 3445979.3561885 |
| PAI-UMNO26-selC | selC | 17 | 48 | eaeX | 4301079.4320994 |
| PAI-UMNO26-fecI | fecI | 26 | 50 | Ag43 | 5031002.5057400 |
| UPEC strain UTI89 (Genbank accession number: NC_007946, 5065741-bp) | |||||
| PAI-UTI89-serX | serX | 62 | 48 | S pilus, Salmochelin, Ag43 | 1080842.1142536 |
| PAI-UTI89-icd | icd | 47 | 50 | Iss, Sit system | 1242292.1288830 |
| PAI-UTI89-asnT | asnT | 31 | 57 | Yersiniabactin | 2069935.2101331 |
| PAI-UTI89-asnW | asnW | 54 | 53 | Colibactin | 2113982.2168375 |
| PAI-UTI89-cobU | cobU | 42 | 49 | Hma, Fbp system | 2173987.2216153 |
| PAI-UTI89-pheV | pheV | 18 | 40 | K1 capsule | 3288044. 3306044 |
| PAI-UTI89-leuX | leuX | 122 | 46 | Hek, P pilus, F17-like pilus, CNF1, α-Hemolysin, CdiB, DsdA | 4779711.4900870 |
| PAI-UTI89-iraD | iraD | 20 | 46 | IbeA | 4919657.4940004 |
| NMEC strain RS218 (Genbank accession number: CP007149, 5087638-bp) | |||||
| PAI-RS218-serX | serX | 62 | 48 | S pilus, Salmochelin, Ag43 | 1060280.1123164 |
| PAI-RS218-icd | icd | 49 | 50 | Iss, Sit system | 1219583.1268928 |
| PAI-RS218-asnT (HPI) | asnT | 31 | 57 | Yersiniabactin | 2089060.2120469 |
| PAI-RS218-asnW | asnW | 54 | 53 | Colibactin | 2133298.2134569 |
| PAI-RS218-cobU | cobU | 43 | 49 | Hma, Fbp system | 2191418.2235286 |
| PAI-RS218-pheV | pheV | 18 | 40 | K1 capsule | 3307311.3325311 |
| PAI-RS218-leuX | leuX | 123 | 46 | Hek, P pilus, F17-like pilus, CNF1, α-Hemolysin, CdiB, DsdA | 4841086.4963833 |
| PAI-RS218-iraD (GimA) | iraD | 21 | 46 | IbeA | 4982442.5003432 |
| NMEC strain IHE3034 (Genbank accession number: NC_017628, 5108383-bp) | |||||
| PAI-IHE3034-argU | argU | 50 | 50 | Iss, ompT | 559677.609271 |
| PAI-IHE3034-serX | serX | 62 | 48 | S pilus, Salmochelin, Ag43 | 1123943.1185632 |
| PAI-IHE3034-icd | icd | 48 | 50 | Iss, Sit system | 1285251.1331958 |
| PAI-IHE3034-asnT (HPI) | asnT | 31 | 57 | Yersiniabactin | 2148149.2179443 |
| PAI-IHE3034-cobU | cobU | 43 | 49 | Hma, Fbp system | 2252158.2294325 |
| PAI-IHE3034-pheV | pheV | 18 | 46 | K1 capsule | 3441108.3459812 |
| PAI-IHE3034-iraD (GimA) | iraD | 21 | 46 | IbeA | 4964058 4984404 |
| NMEC strain CE10 (Genbank accession number: NC_017646, 5313531-bp) | |||||
| PAI-CE10-ybcQ | ybcQ | 32 | 52 | Iss | 574012.606099 |
| PAI-CE10-icd | icd | 56 | 52 | Sit system | 1285000.1341381 |
| PAI-CE10-asnT (HPI) | asnT | 31 | 57 | Yersiniabactin | 2259714.2291113 |
| PAI-CE10-cobU | cobU | 27 | 47 | Hma | 2309373.2336831 |
| PAI-CE10-pheV | pheV | 63 | 46 | P pilus, Aerobactin, Sat, Iha, K1 capsule | 3487305.3550576 |
| PAI-CE10-selC | argW | 10 | 42 | IpuA, IpuB (DsdA) | 4303582.4357800 |
| PAI-CE10-pheU | pheU | 20 | 47 | Hek, P pilus | 4961804.4982152 |
| PAI-CE10-leuX | leuX | 42 | 49 | Fec, VirK, MsbB2 | 5127122.5169094 |
| NMEC strain S88 (Genbank accession number: NC_011742, 5032268 bp-bp) | |||||
| PAI-S88-argU | argU | 38 | 52 | ompT | 574349.612629 |
| PAI-S88-icd | icd | 48 | 50 | Iss, Sit system | 1183142.1229738 |
| PAI-S88-asnT (HPI) | asnT | 31 | 57 | Yersiniabactin | 1998347.2029756 |
| PAI-S88-pheV | pheV | 74 | 45 | Hek, P pilus, IreA, K1 capsule | 3219875.3293447 |
| PAI-S88-pheU | pheU | 64 | 48 | PapX | 4621378.4684940 |
| PAI-S88-leuX | leuX | 39 | 50 | Fec, Ag43 | 4821000.4862061 |
| APEC strain APECO1 (Genbank accession number: NC_008563, 5082025-bp) | |||||
| PAI-APECO1-thrW | thrW | 20 | 41 | Tsh | 295124.315041 |
| PAI-APCEO1-icd | icd | 49 | 50 | Iss, Sit system | 1179544.1226126 |
| PAI-APECO1-asnT | asnT | 31 | 57 | Yersiniabactin | 2090794.2122085 |
| PAI-APECO1-pheV | pheV | 73 | 44 | Hek, P pilus, IreA, K1 capsule | 3305091.3378655 |
| PAI-APECO1-iraD (GimA) | iraD | 21 | 46 | IbeA | 4935886.4956233 |
| AIEC strain LF82 (Genbank accession number: NC_011993, 4773108-bp) | |||||
| PAI_LF82-icd | icd | 49 | 50 | Iss, Sit system | 1174302 1223227 |
| PAI-LF82-asnT | asnT | 31 | 57 | Yersiniabactin | 2007750 2039203 |
| PAI-LF82-pheV | pheV | 18 | 42 | K5 capsule | 3110301 3128705 |
| PAI-LF82-iraD (GimA) | iraD | 21 | 46 | IbeA | 4673091 4693405 |
| AIEC strain NRG857C (Genbank accession number: NC_017634, 4747819-bp) | |||||
| PAI-NRG857C-icd | Icd | 61 | 50 | Iss, Sit system | 1171022 1231985 |
| PAI-NRG857C-asnT | asnT | 31 | 57 | Yersiniabactin | 2014814 2046266 |
| PAI-NRG857C-pheV | pheV | 18 | 42 | K5 capsule | 3084523 3102935 |
| PAI-NRG857C-iraD (GimA) | iraD | 21 | 46 | IbeA | 4648143 4668457 |
| AIEC strain UM146 (Genbank accession number: NC_017632, 4993013-bp) | |||||
| PAI-UM146-pheV | pheV | 28 | 46 | K1 capsule | 326687 354390 |
| PAI-UM146-cobU | cobU | 42 | 49 | Hma, Fbp system | 1426242 1468411 |
| PAI-UM146-asnW | asnW | 54 | 53 | Colibactin | 1474024 1529464 |
| PAI-UM146-asnT | asnT | 31 | 57 | Yersiniabactin | 1541958 1573422 |
| PAI-UM146-icd | icd | 29 | 53 | Sit system | 2353562 2382356 |
| PAI-UM146-serX | serX | 62 | 48 | S pilus, Salmochelin, Ag43 | 2499854 2561497 |
| PAI-UM146-thrW | thrW | 20 | 41 | Tsh | 3301638 3321999 |
| PAI-UM146-leuX | leuX | 121 | 46 | Hek, P pilus, F17-like pilus, CNF-1, α-Hemolysin, CdiA, DsdA | 4520979 4642133 |
| PAI-UM146-iraD (GimA) | iraD | 20 | 46 | IbeA | 4660918 4681265 |
| Commensal strain ED1a (Genbank accession number: NC_011745, 5209548-bp) | |||||
| PAI-ED1a-icd | icd | 12 | 49 | Sit system | 1282697.1294467 |
| PAI-ED1a-asnT (HPI) | asnT | 31 | 57 | Yersiniabactin | 2164139.2222325 |
| PAI-ED1a-pheU | pheU | 44 | 48 | Iha, Aerobactin | 4837580 4881090 |
| PAI-ED1a-leuX | leuX | 57 | 50 | MsbB2, VirK, fec, Ag43 | 5065910.5122732 |
| Commensal strain HS (Genbank accession number: NC_009800, 4643538-bp) | |||||
| PAI-HS-hisF | hisI | 39 | 47 | Klebsiella-related LPS and capsule determinants | 2143083.2181967 |