Host Strain Source of Isolate Host Sex Disease Status Age ST 12-1-TI12 Terminal Ileum Biopsy Male Non IBD 61 127 12-2-TI13 Terminal Ileum Biopsy Male Non IBD 61 127 18-3 TI5 Terminal Ileum Biopsy Male Non IBD 21 73 18-4 TI12 Terminal Ileum Biopsy Male Non IBD 21 73 33-1-TI5 Terminal Ileum Biopsy Male Crohn's Disease 53 131 36-1-TI13 Terminal Ileum Biopsy Male Crohn's Disease 49 429 39-2-TI18 Terminal Ileum Biopsy Female Crohn's Disease 28 95 41-2-TI13 Terminal Ileum Biopsy Female Crohn's Disease 69 720 46-1-TI2 Terminal Ileum Biopsy Male Ulcerative Colitis 30 95 52-1-TI3 Terminal Ileum Biopsy Female Non IBD 29 95 52-2-TI10 Terminal Ileum Biopsy Female Non IBD 29 550 54-1-TI6 Terminal Ileum Biopsy Female Crohn's Disease 33 1919 55-1-AU4 Apthous Ulcer Biopsy Female Crohn's Disease 34 131 55-1-TI19 Terminal Ileum Biopsy Female Crohn's Disease 34 131 57-3-TI5 Terminal Ileum Biopsy Male Crohn's Disease 60 537 60-1-TI1 Terminal Ileum Biopsy Female Ulcerative Colitis 32 80 61-1-TI1 Terminal Ileum Biopsy Female Ulcerative Colitis 45 95 62-2-TI6 Terminal Ileum Biopsy Male Ulcerative Colitis 24 95 63-1-TI1 Terminal Ileum Biopsy Male Non IBD 43 963 69-1 AU1 Apthous Ulcer Biopsy Male Crohn's Disease 20 569 69-1-TI1 Terminal Ileum Biopsy Male Crohn's Disease 20 569 70-2-TI12 Terminal Ileum Biopsy Male Crohn's Disease 21 569 72-6-Ti12 Terminal Ileum Biopsy Male Ulcerative Colitis 52 569 CD 1IM 3 Terminal Ileum Resection Male Crohn's Disease 15 2622 CD 34 LN Lymph Node Female Crohn's Disease 27 95 CD 62 LN Lymph Node Male Crohn's Disease 20 95 H001 Bloodstream Male Sepsis 73 681 H020 Bloodstream Female Sepsis 47 73 H223 Bladder Male UTI 141 H252 Faecal Female Non IBD 56 95 H263 Faecal Male Non IBD 33 95 H296 Faecal Female Non IBD 96 95 H305 Faecal Female Non IBD 0.2 95 H397 Faecal Male Non IBD 95 H413 Faecal Male Non IBD 95 H461 Faecal Female Non IBD 3 95 H504 Faecal Male Non IBD 95 H588 Bloodstream Female Sepsis 63 126 H660 Faecal Female Non IBD 4 95 LF82 135 ED1A 452 Sequencing Serotype Platform Coverage % number of Contigs # genes Phenotype O6: H31 HiSeQ 2000 63 224 4777 AIEC O6: H31 HiSeQ 2000 99 100 4795 non AIEC O25:H1 HiSeQ 2000 57 128 4956 non AIEC O25:H1 HiSeQ 2000 85 139 4948 non AIEC O16:H5 HiSeQ 2000 48 188 4707 AIEC O83:H4 HiSeQ 2000 49 142 4849 non AIEC No O or H genes found HiSeQ 2000 72 209 5049 non AIEC O17/O77:H41 HiSeQ 2000 76 114 4743 non AIEC O1:H7 HiSeQ 2000 82 101 4988 non AIEC O18:H7 HiSeQ 2000 101 127 4964 AIEC O75:H5 HiSeQ 2000 106 148 5124 non AIEC O110:H27 HiSeQ 2000 126 55 4589 non AIEC O25:H4 HiSeQ 2000 34 70 5191 non AIEC O25:H4 HiSeQ 2000 85 68 5028 non AIEC O75:H5 HiSeQ 2000 112 80 4570 AIEC O75:H7 HiSeQ 2000 82 130 4819 AIEC O18:H7 HiSeQ 2000 70 159 4925 AIEC O1:H7 HiSeQ 2000 98 117 5208 non AIEC O50O2:H18 HiSeQ 2000 20 453 5139 non AIEC O46:H31 HiSeQ 2000 50 79 4662 non AIEC O46:H31 HiSeQ 2000 51 54 4664 non AIEC O46:H31 HiSeQ 2000 62 93 4663 non AIEC O46:H31 HiSeQ 2000 46 58 4659 non AIEC O83:H6 HiSeQ 2000 128 52 4493 non AIEC O1:H7 HiSeQ 2000 98 62 4861 non AIEC O2:H4 HiSeQ 2000 31 155 4936 AIEC O8:H10 454 15 123 4708 non AIEC O22:H1 MiSeQ 37 375 5424 non AIEC O2:H6 454 18 155 4687 AIEC O1:H7 454 19 112 4984 non AIEC O2:H7 454 34 165 4872 non AIEC O2:H7 454 13 190 4951 non AIEC O18:H7 454 14 176 4870 AIEC O1:H7 454 19 120 5028 non AIEC O18:H7 454 13 98 4770 non AIEC O18:H7 454 22 99 4927 non AIEC O18ac:H7 454 20 101 4875 AIEC :H5 454 22 36 4374 non AIEC O1:H7 454 15 168 4936 non AIEC O83:H1 4330 AIEC O81:H27 4638 non AIEC Strain Phenotype Adhesion Invasion Replication Log10 Adhesion 12-1-TI12 AIEC 3.81375 0.3725 310.6001875 0.581352221 12-2-TI13 non AIEC 5.6125 0.71625 50.23961395 0.749156354 18-3 TI5 non AIEC 0.25075 0.036 179.301746 -0.600759058 18-4 TI12 non AIEC 0.475 0.041875 143.0926795 -0.32330639 33-1-TI5 AIEC 6.675 0.10125 867.08843 0.82445127 36-1-TI13 non AIEC 0.38575 0.01175 402.4522855 -0.413694065 39-2-TI18 non AIEC 0.068 0.012 1241.089152 -1.167491087 41-2-TI13 non AIEC 0.6825 0.03425 410.2941121 -0.165897344 46-1-TI2 non AIEC 0.197 0.015 707.9799699 -0.705533774 52-1-TI3 AIEC 34.25 1.4975 934.2769366 1.534660576 52-2-TI10 non AIEC 0.113 0.013875 153.105794 -0.946921557 54-1-TI6 non AIEC 9.3 0.0645 408.3595742 0.968482949 55-1-AU4 non AIEC 0.10925 0.034125 162.9219308 -0.961578554 55-1-TI19 non AIEC 0.0509625 0.0255 325.7437458 -1.292749276 57-3-TI5 AIEC 2.7325 0.1405 723.5493255 0.436560171 60-1-TI1 AIEC 7.075 0.127375 333.2508761 0.849726444 61-1-TI1 AIEC 54.625 1.89 869.8991073 1.73739145 62-2-TI6 non AIEC 1.235 0.138875 90.7346411 0.091666958 63-1-TI1 non AIEC 1.43375 0.033375 158.2170393 0.156473431 69-1 AU1 non AIEC 0.65875 0.073875 79.01965897 -0.181279372 69-1-TI1 non AIEC 0.60125 0.097125 91.36887633 -0.220944911 70-2-TI12 non AIEC 1.22125 0.062625 45.49219179 0.086804577 72-6-Ti12 non AIEC 1.046666667 0.025 73.81516784 0.019808393 CD 1IM 3 non AIEC 3.466666667 0.017 1163.704283 0.539912085 CD 34 LN non AIEC 0.138 0.018375 458.4854843 -0.860120914 CD 62 LN AIEC 4.67625 0.32625 1686.325907 0.669897721 H001 non AIEC 1.191666667 0.018333333 708.1241622 0.076154791 H020 non AIEC 1.33 0.083166667 1009.197879 0.123851641 H223 AIEC 9.033333333 0.455 435.2265658 0.955848036 H252 non AIEC 3.466666667 0.089833333 74.23443389 0.539912085 H263 non AIEC 0.296 0.006333333 398.5140018 -0.528708289 H296 non AIEC 0.451166667 0.003666667 792.3299621 -0.345662995 H305 AIEC 27.51666667 0.63 730.6493507 1.439595823 H397 non AIEC 0.418833333 0.004833333 245.2223816 -0.377958762 H413 non AIEC 0.912666667 0.021 717.9204615 -0.039687811 H461 non AIEC 0.403833333 0.008166667 73.6013249 -0.393797836 H504 AIEC 3.281666667 0.283333333 320.6272282 0.516094466 H588 non AIEC 3.381666667 0.034666667 1141.506148 0.529130797 H660 non AIEC 0.521166667 0.007166667 701.5574897 -0.283023369 LF82 AIEC 62.83333333 12.23333333 227.8140881 1.7981901 ED1A non AIEC 0.245375 0.049625 68.33726762 -0.610169687 Log10Invasion Log10 Replication -0.428873723 2.492201714 -0.144935365 1.701046294 -1.443697499 2.253584519 -1.37804518 2.155617416 -0.994604968 2.938063391 -1.929962133 2.604714398 -1.920818754 3.09380298 -1.465339424 2.613095285 -1.823908741 2.850020971 0.175366831 2.970475628 -1.857767008 2.184991626 -1.190440285 2.611042742 -1.46692734 2.211979548 -1.59345982 2.512876086 -0.852323676 2.859468143 -0.894915803 2.5227713 0.276461804 2.939468885 -0.857375928 1.957773126 -1.476578726 2.199253253 -1.131502506 1.897735151 -1.012668968 1.960798284 -1.203252261 1.657936861 -1.602059991 1.868145612 -1.769551079 3.065842633 -1.735772652 2.661325591 -0.48644948 3.226941512 -1.736758565 2.850109413 -1.080050705 3.003976329 -0.341988603 2.638715396 -1.046562485 1.870605401 -2.198367654 2.600443585 -2.43572857 2.898906079 -0.200659451 2.863709003 -2.315753252 2.389560106 -1.677780705 2.856076331 -2.08795517 1.866885632 -0.547702329 2.506000401 -1.460087915 3.057478255 -2.144682795 2.846063265 1.08754481 2.357580578 -1.30429948 1.83465761 CRISPR id 62-2 ti6 H252 H263 H296 39-2 ti18 46-1 ti2 H660 tmp_1_Crispr_1 1 tmp_1_Crispr_2 1 1 1 tmp_1_Crispr_3 1 1 1 tmp_1_Crispr_4 1 tmp_1_Crispr_5 1 tmp_1_Crispr_6 1 1 tmp_1_Crispr_9 1 tmp_1_PossibleCrispr_1 1 1 1 tmp_1_PossibleCrispr_2 1 tmp_1_PossibleCrispr_3 1 tmp_1_PossibleCrispr_4 1 1 1 tmp_1_PossibleCrispr_5 1 1 1 tmp_1_PossibleCrispr_6 1 1 tmp_1_PossibleCrispr_7 1 1 1 1 tmp_1_PossibleCrispr_8 1 1 1 1 tmp_1_PossibleCrispr_9 1 1 tmp_1_PossibleCrispr_10 1 tmp_1_PossibleCrispr_11 1 tmp_2_Crispr_2 tmp_2_Crispr_3 tmp_2_PossibleCrispr_1 tmp_3_PossibleCrispr_1 tmp_5_Crispr_1 1 tmp_5_Crispr_2 tmp_5_Crispr_3 tmp_5_PossibleCrispr_1 tmp_6_Crispr_1 1 tmp_6_Crispr_2 1 tmp_7_Crispr_2 tmp_7_Crispr_3 tmp_7_PossibleCrispr_1 tmp_8_Crispr_2 1 tmp_8_Crispr_3 1 tmp_8_PossibleCrispr_1 1 tmp_10_Crispr_1 1 tmp_10_Crispr_2 1 tmp_10_Crispr_3 tmp_10_PossibleCrispr_1 tmp_10_PossibleCrispr_3 1 tmp_12_PossibleCrispr_1 tmp_14_Crispr_1 tmp_14_Crispr_2 tmp_25_PossibleCrispr_1 tmp_25_PossibleCrispr_2 tmp_32_PossibleCrispr_1 tmp_35_PossibleCrispr_1 tmp_37_PossibleCrispr_1 tmp_70_PossibleCrispr_1 tmp_91_PossibleCrispr_1 total confirmed CRISPRs 2 2 5 2 2 3 3 total possible CRISPRs 1 6 4 7 1 0 8 CD 34 LN H397 H461 H413 H305 H504 52-1 ti3 61-1 ti1 CD 62 LN 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 2 2 2 2 3 2 2 2 2 3 2 4 3 3 5 2 2 2 All ST95 strains 1 AIEC 4 Non-AIEC 5 4 2 2 1 6 3 2 3 5 5 5 4 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 1 2 1 2 1 1 1 1 1 1 1 1 1 1 1 38 53 IL-6 manip 1 manip 2 manip 3 Avg SD LF82 3969.30 3633.93 2627.94 3410.39 403.02 K12 C600 927.50 1053.57 1223.53 1068.20 85.77 70-2 ti12 2732.46 732.50 1998.53 1821.16 584.11 54-1 ti6 1706.14 565.00 2389.71 1553.62 532.24 55-1-AU4 1899.12 487.50 2222.06 1536.23 532.59 CD 62 LN 2372.81 770.00 2386.76 1843.19 536.61 18-3 ti5 970.00 412.50 557.35 646.62 167.01 55-1-ti19 1907.89 1037.50 3016.18 1987.19 572.57 61-1-ti1 605.00 287.50 298.53 397.01 104.04 63-1-ti1 1513.16 800.00 2280.88 1531.35 427.59 62-2-ti6 1451.75 772.50 1913.24 1379.16 331.30 CD 34 LN 1179.82 747.50 1380.88 1102.74 186.86 ED1a 1609.65 767.50 1010.29 1129.15 250.27 39-2-ti18 2811.40 1633.93 2310.29 2251.88 341.16 69-1-AU1 1267.54 607.50 2172.06 1349.03 453.48 60-1-ti1 975.00 745.00 1963.24 1227.75 373.69 52-2-ti10 1062.50 750.00 2036.76 1283.09 387.49 12-1-ti12 907.50 330.00 751.47 662.99 172.48 18-4-ti12 932.50 297.50 819.12 683.04 195.53 57-3-ti5 827.50 455.00 1357.35 879.95 261.80 46-1-ti2 1250.00 1162.50 2616.18 1676.23 470.65 69-1-ti1 1171.05 552.50 1645.59 1123.05 316.46 12-2-ti13 515.00 640.00 -39.71 371.76 208.88 33-1-ti5 4460.53 4196.43 2227.94