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. 2017 Sep 18;67(10):1793–1804. doi: 10.1136/gutjnl-2017-313863

Table 1.

Deletions and insertions in Helicobacter pylori strains B128 and 7.13, and in vivo-adapted strains isolated from gerbils maintained on iron-depleted or iron-replete diets

Deletions B128 single colonies 7.13 single colonies 7.13 iron-depleted single colonies 7.13 iron-replete single colonies
Location Gene HPB8 locus a b c a b c D1 a D1 b D1
C		 D2 a D2 b D2 c D3 a D3 b D3 c R1 a R1 b R1 c R2 a R2 b R2 c R3 a R3 b R3 c
 88333 Intergenic 43 26 26 29 31 29 26 31 33 39
 132884 tonB1 138 27* 44.3–
46.2
 132889 tonB1 138 27.1–
27.5
 132892 tonB1 138 26
 132907 tonB1 138 27*
 132926 tonB1 138 85 90 79.7–
81.4		 80.6–
81.6		 77 92 75 76
 365607 Intergenic 94
 378215 galE 409 96*
 410076 cheA 442 61.0–
74.5*
 410076 cheA 442 63.8–
71.3
 410080 cheA 442 63*
 693451 cagY 716 100 100
 693465 cagY 716 30* 36* 56*
 819621 oipA 838 93*
 919030 sabA 930 92* 91* 87* 81* 88*
 1065100 Intergenic 25 44
 1098589 hsdR5 1120 96*
 1171489 1200 99* 97*
 1197192 Intergenic 26
 1316726 radA 1343 32* 31* 38* 29* 29* 32* 26* 36* 28* 32* 26* 28* 38*
 1445365 hrgA 1474 78
 1492146 Intergenic 28 43
 1533081 1561 38* 36* 42*
 1533085 1561 38 36 42
 1533088 1561 38* 36* 42*
 1539253 Intergenic 98
 1584758 hopZ 1616 91* 91* 90* 81* 90* 89* 90* 86* 89* 90* 87* 86* 88* 89*
 1584759 hopZ 1616 94* 100* 93* 89* 97* 90* 91* 88* 93*
 1585383 hopZ 1616 92 89 90
 1621918 1665 88.2-
94.4		 89.9–
97.5		 94.1–
99.0
 1621918 1665 98* 96* 97* 98* 98* 97* 99* 94* 96* 98* 99* 98* 97* 99* 99* 98*
 1621919 1665 97* 100* 99* 99*
Insertions B128 single colonies 7.13 single colonies 7.13 iron-depleted single colonies 7.13 iron-replete single colonies
Location Gene HPB8 locus a b c a b c D1 a D1 b D1
C		 D2 a D2 b D2 c D3 a D3 b D3 c R1 a R1 b R1 c R2 a R2 b R2 c R3 a R3 b R3 c
 88333 Intergenic 46 40 38 37 33 40 42 45 38 42 38 55 45 40 31 34 31 33 40
 88334 Intergenic 49 46 54 52
 102469 Intergenic 75
 132300 Intergenic 70 65 63 58 55 52 62 66 50
 149625 Intergenic 52
 210808 Intergenic 50
 236057 268 96*
 293971 Intergenic 98 94 95 91 95 91 94 94 96 93 96 93 92 96 96 95 93 95 97 95 92 95
 397298 fucT1 427 25* 35* 26*
 471641 Intergenic 100 95 97 81 97 93 95 92 92 93 98 93 95 94 95 90 94 95 94 93 94 86 93 91
 607701 Intergenic 63
 628559 Intergenic 28 28
 631022 Intergenic 85 69 82 77 84 85 96 91 93 89 94 81 79 100 84 76 78
 631033 Intergenic 90 80 77 83 95 62 73 96 86 78 89 87 87 75 87 78 82 78 96 91 79 84
 666812 nudT14 691 94* 93* 99*
 759720 Intergenic 68 66 65 74 72 74 63 63 70
 819619 oipA 838 67* 70*
 833169 fucT7 854 63* 66* 65*
 883216 hyuA1 895 93* 99* 98*
 8 83 595 hyuA1 895 100* 96* 97*
 1064308 katA 1087 100*
 1082193 1103 92* 97*
 1197192 Intergenic 42 49 54
 1197193 Intergenic 50 59 57 59 56 48 57 51 52 54 52 55 55 57 51 57 62 55 62
 1217501 Intergenic 58 53 46 44 53
 1332440 Intergenic 45 50 44 48 47 50 46 48 53 57 44
 1332612 1358 79* 69* 83.7-
84.8*		 75* 80* 77* 71.6–
72.5*		 74* 63* 77* 79* 74.4–
75.6*		 81* 87* 80* 84* 73* 85* 66* 73* 75*
 1414196 1447 87*
 1458196 1484 56 60 60
 1566403 Intergenic 43 38 36 43 38 37 37 44
 1566404 Intergenic 58 54 60 45 48 44 59 46 45 53 55 55 47 44 57 51 49 47 58 57 39 59 53
 1621919 1665 83*
 1657270 Intergenic 66 74 65 80 62 73 61 72
 1657271 Intergenic 79 76 76 63 60 70 70 67 60 68 70 63 62 60 69

D1-3 and R1-3 designate independent gerbils maintained on either iron-depleted (n=3) or iron-replete (n=3) diets, respectively, while a-c designate different single colonies isolated from each gerbil. Colour-coded regions within each single colony represent deletions or insertions that were present in each isolate, and the number in each box represents the percentage of reads that contained each single nucleotide polymorphism. When a percentage range is shown, this represents multinucleotide polymorphisms present.

*Deletion or insertion results in a frameshift mutation.