Supplementary Table S1 : Natural E. Coli Isolates Used in This Study1

Supplementary Table S1: Natural E. coli isolates used in this study1

Phylogenetic Commensal or Name Origin Host (Linnaean) Host (common) group pathovar ExPEC 1 IAI16 A France Homo sapiens Human (septicemia) ExPEC 2 IAI18 A France Homo sapiens Human (UPEC) ExPEC 3 IAI21 B1 France Homo sapiens Human (UPEC) ExPEC 4 IAI27 D France Homo sapiens Human (UPEC) ExPEC 5 IAI34 A France Homo sapiens Human (septicemia) ExPEC 6 IAI35 D France Homo sapiens Human (septicemia) ExPEC 7 IAI36 D France Homo sapiens Human (miscellaneous) ExPEC 8 IAI37 A France Homo sapiens Human (miscellaneous) ExPEC 9 IAI38 B2 France Homo sapiens Human (miscellaneous) ExPEC 10 IAI39 D France Homo sapiens Human (UPEC) ExPEC 11 IAI40 A France Homo sapiens Human (UPEC) ExPEC 12 IAI42 A France Homo sapiens Human (UPEC) ExPEC 13 IAI44 A France Homo sapiens Human (UPEC) ExPEC 14 IAI58 D France Homo sapiens Human (UPEC) ExPEC 15 IAI61 B2 France Homo sapiens Human (miscellaneous) ExPEC 16 IAI64 B2 France Homo sapiens Human (UPEC) ExPEC 17 IAI69 B2 France Homo sapiens Human (miscellaneous) ExPEC 18 IAI71 B2 France Homo sapiens Human (UPEC) ExPEC 19 IAI72 B2 France Homo sapiens Human (UPEC) ExPEC 20 IAI73 B2 France Homo sapiens Human (septicemia) ExPEC 21 IAI74 B2 France Homo sapiens Human (UPEC) ExPEC 22 IAI77 B2 France Homo sapiens Human (UPEC) ExPEC 23 IAI79 B2 France Homo sapiens Human (UPEC) 24 G1 B1 Commensal French Guyana Homo sapiens Human 25 G31 B2 Commensal French Guyana Homo sapiens Human 26 G86 D Commensal French Guyana Homo sapiens Human 27 G103 A Commensal French Guyana Homo sapiens Human 28 G109 A Commensal French Guyana Homo sapiens Human 29 17-2 A EAEC Chile Homo sapiens Human 30 H10407 A ETEC Bangladesh Homo sapiens Human 31 DAEC 7 A DAEC Brazil Homo sapiens Human 32 EDL1493 A ETEC ? Homo sapiens Human 33 DEC8b B1 EHEC USA Homo sapiens Human 34 248/1-2 C STEC France Bos taurus Cow 35 DEC12a B1 EPEC UK Homo sapiens Human 36 TX-1 B1 ETEC ? Homo sapiens Human 37 H-19 B1 EHEC UK Homo sapiens Human 38 11097 B1 EAEC Senegal Homo sapiens Human

39 440 B1 ETEC New Caledonia Homo sapiens Human 40 DAECT179 C Commensal France Homo sapiens Human 41 DEC7a C ETEC USA Sus scrofa Pig 42 DEC5d E EPEC Sri Lanka Homo sapiens Human 43 DEC3a E EHEC USA Homo sapiens Human 44 DEC4a E EHEC Argentina Bos taurus Cow 45 DAEC19 D DAEC Brazil Homo sapiens Human Central African 46 56390 D EAEC Homo sapiens Human Republic 47 DAEC141 D DAEC France Homo sapiens Human 48 DAEC162 F DAEC France Homo sapiens Human 49 DAEC9 F DAEC Brazil Homo sapiens Human 50 DEC1a B2 EPEC USA Homo sapiens Human ExPEC 51 RS218 B2 (newborn USA Homo sapiens Human meningitis) 52 DAEC18 B2 DAEC Brazil Homo sapiens Human ExPEC 53 EC7372 B2 USA Homo sapiens Human (UPEC) ExPEC 54 IH11128 B2 Sweden Homo sapiens Human (UPEC) 55 DAEC20 B2 DAEC Brazil Homo sapiens Human 56 C1845 B2 DAEC USA Homo sapiens Human 57 431 A ETEC USA Sus scrofa Pig ExPEC 58 239KH89 C Belgium Bos taurus Cow (septicemia) 59 211 B1 ETEC Belgium Bos taurus Cow 60 86-1390 B1 EPEC Canada Sus scrofa Pig 61 S1191 A EHEC USA Sus scrofa Pig Central African 62 381A B2 EAEC Homo sapiens Human Republic 63 DAEC213 D DAEC France Homo sapiens Human 64 ROAR001 B1 Commensal Antarctic Aptenodytes forsteri Emperor penguin 65 ROAR002 B1 Commensal Antarctic Aptenodytes forsteri Emperor penguin 66 ROAR003 B2 Commensal Antarctic Aptenodytes forsteri Emperor penguin 67 ROAR012 B2 Commensal Gabon Taurotragus oryx Eland 68 ROAR014 D Commensal Gabon Gorilla gorilla Gorilla 69 ROAR016 D Commensal Gabon Cephalophus sylvicultor Yellow-backed Duiker 70 ROAR023 B2 Commensal Gabon Syncerus caffer nanus African buffalo 71 ROAR029 D Commensal Gabon Aepyceros melampus Impala 72 ROAR036 D Commensal Gabon Oryx gazella Gemsbok 73 ROAR037 D Commensal Gabon Oryx gazella Gemsbok 74 ROAR038 B2 Commensal Gabon Antidorcas marsupialis Springbok 75 ROAR044 B2 Commensal Pyrenees mountain Sus scrofa Wild boar 76 ROAR048 B1 Commensal Pyrenees mountain Martes martes Pine marten 77 ROAR051 B1 Commensal Pyrenees mountain Ovis ammon European mouflon sheep 78 ROAR057 B1 Commensal Pyrenees mountain Rupricapra pyrenaica Pyrenean isard 79 ROAR061 B1 Commensal Pyrenees mountain Lepus capensi Domestic rabbit 80 ROAR066 B1 Commensal Pyrenees mountain Lepus capensi Domestic rabbit 81 ROAR083 A Commensal Pyrenees mountain Ursus arctos Brown bear 82 ROAR087 D Commensal Pyrenees mountain Turdus merula Blackbird 83 ROAR094 Clade V Commensal Pyrenees mountain Capreolus capreolus Roe deer 84 ROAR102 B2 Commensal Pyrenees mountain Tetrao urogallus Capercaillie Pyrrhocorax 85 ROAR109 D Commensal Pyrenees mountain Chough pyrrhocorax 86 ROAR110 B1 Commensal Pyrenees mountain Phasianus colchicus Pheasant ROAR111 87 B1 Commensal Fontainebleau Forest Capreolus capreolus Roe deer (Ec111) 88 ROAR113 D Commensal Fontainebleau Forest Sus scrofa Wild boar 89 ROAR122 B2 Commensal Fontainebleau Forest Columba palumbus Wood pigeon 90 ROAR133 D Commensal Fontainebleau Forest Vulpes vulpes Fox 91 ROAR135 B2 Commensal Fontainebleau Forest Capreolus capreolus Roe deer 92 ROAR137 B1 Commensal Fontainebleau Forest Cervus elaphus Common deer 93 ROAR142 B2 Commensal Fontainebleau Forest Cervus elaphus Common deer 94 ROAR150 B2 Commensal Fontainebleau Forest Lepus capensi Domestic rabbit 95 ROAR152 B2 Commensal Fontainebleau Forest Oryctolagus cuniculus Rabbit 96 ROAR157 B2 Commensal Fontainebleau Forest Capreolus capreolus Roe deer 97 ROAR167 B2 Commensal Fontainebleau Forest Sus scrofa Wild boar 98 ROAR172 B1 Commensal Pyrenees farm Ovis aries Sheep 99 ROAR179 B1 Commensal Pyrenees farm Gallus gallus Chicken 100 ROAR183 D Commensal Pyrenees farm Anser anser Geese 101 ROAR192 A Commensal Pyrenees farm Ovis aries Sheep 102 ROAR193 B1 Commensal Pyrenees farm Ovis aries Sheep 103 ROAR194 B1 Commensal Pyrenees farm Ovis aries Sheep 104 ROAR195 D Commensal Pyrenees farm Ovis aries Sheep 105 ROAR206 B1 Commensal Pyrenees farm Sus scrofa domestica Pig 106 ROAR208 C Commensal Pyrenees farm Sus scrofa domestica Pig 107 ROAR212 B1 Commensal Pyrenees farm Equus caballus Horse 108 ROAR248 D Commensal Pyrenees farm Equus caballus Horse 109 ROAR267 B2 Commensal Pyrenees farm Meleagris gallopavo Turkey 110 ROAR272 B1 Commensal Pyrenees farm Sus scrofa domestica Pig ROAR300 111 A Commensal Pyrenees pets Canis familiaris Dog (Ec300) 112 ROAR313 A Commensal Pyrenees pets Canis familiaris Dog 113 ROAR319 A Commensal Pyrenees pets Canis familiaris Dog 114 ROAR324 C Commensal Pyrenees pets Canis familiaris Dog 115 ROAR328 D Commensal Pyrenees pets Canis familiaris Dog 116 ROAR330 B2 Commensal Pyrenees pets Canis familiaris Dog 117 ROAR342 B2 Commensal France Homo sapiens Human 118 ROAR372 B2 Commensal France Homo sapiens Human 119 ROAR373 A Commensal France Homo sapiens Human 120 ROAR377 B2 Commensal France Homo sapiens Human 121 ROAR381 A Commensal France Homo sapiens Human 122 ROAR396 D Commensal France Homo sapiens Human

1Compiled from: (3) (1) (2) (4)

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