"Table S4. Missense mutations in PmrA and PmrB in mcr negative E. coli strains reported as being responsible for colistin resistance in E. coli, K. pneumoniae or Salmonella" Strain ID Abroad hospitalisation history* ST Warwick ST Pasteur Phylogroup Serotype PmrA PmrB ESBL Prediction of the impact of the amino acid substitution Nucleotide change Codon change Amino acid change Nucleotide change Codon change Amino acid change SIFT Polyphen-2 PROVEAN 1197A none 1434 817 A O18ab:H14 281C>A CCG>CAG P94Q deleterious probably damaging deleterious 791A none 540 716 A O9:H30 1245A none 540 716 A O9:H10 476C>T GCG>GTG A159V tolerated probably damaging deleterious 897B none 8153 890 A O174:H26 389A none 165 898 A Unknown:H10 992A Portugal 165 809 A O96:H2 251G>A TAC>CGC C84Y tolerated possibly damaging deleterious 364A none 10 16 A O2:H48 250T>C TGC>CGC C84R tolerated possibly damaging deleterious 1157B none 10 767 A O19:H4 157G>T GGG>TGG G53W tolerated probably damaging deleterious 55A none 5363 889 A O21:H4 251G>A TAC>CGC C84Y tolerated possibly damaging deleterious 807B none 10 2 A O12:H4 392A none 3877 2 A Unknown:H4 1158A none 208 897 A O157:H11 241C>A CGC>AGC R81S deleterious benign deleterious 1093B none 48 132 A O9:H11 156A none 10 2 A O8:H4 blaCTX-M-14 418A Algeria 744 2 A O89:H9 157G>A GGG>AGG G53R tolerated possibly damaging deleterious 1109AB none 227 638 A O9:H4 173A none 93 83 A O11:H4 650A none 1494 900 B1 O9:H21 281C>T CCG>CTG P94L tolerated probably damaging deleterious 984A none 6448 901 B1 O5:H20 476C>T GCG>GTG A159V blaCTX-M-55 tolerated probably damaging deleterious 402A none 3519 891 B1 O116:H48 929B none 58 24 B1 O8:H25 361G>A GAA>AAA E121K deleterious probably damaging deleterious 477A none 58 24 B1 O9:H4 241C>A CGC>AGC R81S deleterious benign deleterious 1043A none 58 24 B1 O9:H11 29T>C CTG>CCG L10P deleterious probably damaging deleterious 534A Tunisia 278 357 B1 O153:H7 157G>T GGG>TGG G53W tolerated probably damaging deleterious 95A foreign trip 210 894 B1 O96:H19 496G>A GAA>AAA E166K deleterious possibly damaging deleteriou 940A none 162 893 B1 O8:H19 496G>A GAA>AAA E166K deleterious possibly damaging deleteriou 641A none 2522 899 B1 O185:H8 157G>T GGG>TGG G53W tolerated probably damaging deleterious 789B none 2008 892 B1 Onovel26:H2 158G>A GGG>GAG G53E tolerated probably damaging deleterious 387A none 348 19 B1 O110:H28 729A none 410 903 C O8:H27 361G>A GAA>AAA E121K deleterious probably damaging deleterious 378A none 88 885 C O8:H19 476C>T GCG>GTG A159V tolerated probably damaging deleterious 884A none 23 7 C O78:H4 361G>A GAA>AAA E121K deleterious probably damaging deleterious 1253A none 88 66 C O9:H9 281C>T CCG>CTG P94L tolerated probably damaging deleterious 467A none 2064 907 E O52:H45 251G>A TAC>CGC C84Y blaCTX-M-15 tolerated possibly damaging deleterious 1200A none 543 864 E O169:H9 157G>A GGG>AGG G53R tolerated possibly damaging deleterious 1219A none 5281 906 E O160:H28 361G>A GAA>AAA E121K deleterious probably damaging deleterious 268A none 3045 888 D O23:H15 476C>T GCG>GTG A159V tolerated probably damaging deleterious 145A none 349 886 D O86:H2 157G>T GGG>TGG G53W tolerated probably damaging deleterious 619A none 38 535 D O7:H18 316A none 38 8 D O153var1:H30 157G>T GGG>TGG G53W blaCTX-M-15 tolerated probably damaging deleterious 892B none 38 8 D O153var1:H18 280C>T CCG>TCG P94S tolerated probably damaging deleterious 411A none 38 8 D O86:H18 blaCTX-M-15 172B none 549 887 D O17:H1 806A none 8172 905 D O15:H18 439A>G ACC>GCC T147A tolerated benign deleterious 699A none 31 511 D O130:H27 157G>T GGG>TGG G53W tolerated probably damaging deleterious 847C none 394 77 D O17:H18 467C>T ACG>ATG T156M deleterious probably damaging deleterious 353A none 394 77 D O17:H18 1171A none 394 77 D O17:H18 157G>T GGG>TGG G53W tolerated probably damaging deleterious 597A none 69 3 D O25b:H4 388A none 69 3 D O15:H1 241C>A CGC>AGC R81S blaCTX-M-14 deleterious benign deleterious 941A none 69 3 D O17:H18 344A none 69 3 D O17:H18 241C>A CGC>AGC R81S deleterious benign deleterious 707B none 69 3 D O45:H7 43G>A GGA>AGA G15R deleterious probably damaging deleterious 749B none 69 3 D O117:H4 281C>T CCG>CTG P94L tolerated probably damaging deleterious 536A none 69 3 D O15:H18 361G>A GAA>AAA E121K deleterious probably damaging deleterious 1160A none 8171 3 D O45:H16 241C>A CGC>AGC R81S deleterious benign deleterious 68A none 69 3 D O15:H6 1086A none 69 3 D O15:H6 476C>T GCG>GTG A159V tolerated probably damaging deleterious 1185A none 69 3 D O15:H18 526B none 69 3 D O15:H18 475G>C GCG>CCG A159P tolerated probably damaging deleterious 715A none 69 3 D O15:H18 476C>T GCG>GTG A159V tolerated probably damaging deleterious 24C none 69 3 D O15:H18 158G>A GGG>GAG G53E tolerated probably damaging deleterious 1194A none 69 3 D O15:H18 158G>T GGG>GTG G53V tolerated probably damaging deleterious 493A none 69 3 D O15:H18 157G>T GGG>TGG G53W tolerated probably damaging deleterious 348A none 69 3 D O15:H18 476C>T GCG>GTG A159V tolerated probably damaging deleterious 370A none 648 NA*** F O153var1:H42 157G>T GGG>TGG G53W tolerated probably damaging deleterious 215A none 648 NA F O1:H6 1171B none 648 NA F O153var1:H6 blaCTX-M-15 142A none 62 757 F O7:H45 200A none 59 34 F O1:H7 561B none 59 34 F O1:H7 29T>C CTG>CCG L10P deleterious probably damaging deleterious 802B none 59 34 F O1:H7 1198A none 59 34 F O1:H7 281C>A CCG>CAG P94Q deleterious probably damaging deleterious 764A none 117 48 F O33:H4 157G>T GGG>TGG G53W tolerated probably damaging deleterious 857A none 738 895 F O146:H28 361G>A GAA>AAA E121K deleterious probably damaging deleterious 921A none 174 896 F Unknown:H34 361G>A GAA>AAA E121K deleterious probably damaging deleterious 916A none 174 896 F Unknown:H34 383A none 5924 880 B2 O18:H4 586A none 428 73 B2 O117:H4 41T>G CTG>CGG L14R deleterious probably damaging deleterious 494A none 538 221 B2 O129:H4 29T>G CTG>CGG L10R deleterious probably damaging deleterious 464A unknown 131 506 B2 O16:H56 361G>C GAA>CAA E121Q blaCTX-M-27 tolerated probably damaging deleterious 1155A none 131 506 B2 O16:H5 blaCTX-M-27 481B none 131 506 B2 O16:H56 29T>C CTG>CCG L10P deleterious probably damaging deleterious 993B none 131 506 B2 O16:H5 "157G>T,159G>C" GGG>TGC G53C tolerated possibly damaging deleterious 945A none 131 506 B2 O16:H5 361G>A GAA>AAA E121K deleterious probably damaging deleterious 1162A none 131 527 B2 O25b:H4 476C>T GCG>GTG A159V tolerated probably damaging deleterious 1140C none 131 43 B2 O25b:H4 242G>T CGC>CTC R81L deleterious benign deleterious 27A none 131 43 B2 O25b:H4 475G>C GCG>CCG A159P blaCTX-M-15 tolerated probably damaging deleterious 381A Mali 131 43 B2 O25b:H4 blaCTX-M-15 309A none 131 43 B2 O25b:H4 29T>G CTG>CGG L10R blaCTX-M-27 deleterious probably damaging deleterious 547A Mali 131 43 B2 O25b:H4 281C>T CCG>CTG P94L blaCTX-M-27 tolerated probably damaging deleterious 130A none 131 43 B2 O25b:H4 250T>C TGC>CGC C84R blaCTX-M-27 tolerated possibly damaging deleterious 455B none 131 43 B2 O25b:H4 242G>T CGC>CTC R81L blaCTX-M-27 deleterious benign deleterious 1163A none 131 43 B2 O25b:H4 361G>A GAA>AAA E121K blaCTX-M-27 deleterious probably damaging deleterious 456A none 136 304 B2 O8:H10 43G>A GGA>AGA G15R deleterious probably damaging deleterious 868A none 567 82 B2 O83:H33 "157G>A,159G>C" GGG>AGC G53S tolerated possibly damaging deleterious 486A none 7295 883 B2 O93:H18 476C>T GCG>GTG A159V tolerated probably damaging deleterious 569A none 491 375 B2 O131:H45 250T>C TGC>CGC C84R tolerated possibly damaging deleterious 477B none 491 375 B2 O54:H45 476C>T GCG>GTG A159V tolerated probably damaging deleterious 962A none 1604 884 B2 O75:H5 988A Algeria 550 6 B2 O75:H5 241C>A CGC>AGC R81S deleterious benign deleterious 809B none 1193 53 B2 O75:H5 952A none 1193 53 B2 O75:H5 280C>G CCG>GCG P94A tolerated probably damaging deleterious 239A none 1193 53 B2 O75:H5 "158G>C,159G>C" GGG>GCC G53A tolerated possibly damaging deleterious 726A none 14 6 B2 O18:H5 86A none 14 6 B2 O18:H5 1279A none 14 6 B2 O18:H5 730B none 404 6 B2 O75:H5 839B none 404 6 B2 O75:H5 431A none 404 6 B2 O75:H5 361G>A GAA>AAA E121K deleterious probably damaging deleterious 1207B none 404 6 B2 O75:H5 953A none 144 55 B2 O16:H6 281C>T CCG>CTG P94L tolerated probably damaging deleterious 131A none 95 1 B2 O18:H7 361G>A GAA>AAA E121K deleterious probably damaging deleterious 61A none 95 1 B2 O1:H7 241C>A CGC>AGC R81S deleterious benign deleterious 393A none 421 70 B2 O1:H7 909A none 95 1 B2 O2:H4 241C>A CGC>AGC R81S blaCTX-M-15 deleterious benign deleterious 787A none 95 1 B2 O1:H7 361G>A GAA>AAA E121K deleterious probably damaging deleterious 365A none 95 1 B2 O1:H7 496G>A GAA>AAA E166K deleterious possibly damaging deleteriou 1233B Tunisia 95 1 B2 O1:H7 746A none 141 10 B2 O2:H6 361G>A GAA>AAA E121K deleterious probably damaging deleterious 1091A none 141 10 B2 O2:H6 29T>C CTG>CCG L10P deleterious probably damaging deleterious 582A none 2015 658 B2 O2:H14 "157G>A,159G>C" GGG>AGC G53S tolerated possibly damaging deleterious 1052A none 706 217 B2 O85:H1 1189A Turkey 127 32 B2 O6:H31 281C>A CCG>CAG P94Q deleterious probably damaging deleterious 372A none 12 879 B2 O4:H5 775A none 12 35 B2 O4:H5 12B none 961 882 B2 O4:H5 1227A none 12 36 B2 O4:H5 241C>A CGC>AGC R81S deleterious benign deleterious 1004A none 968 29 B2 O2:H1 684A none 73 29 B2 O2:H1 1217A none 8151 29 B2 O2:H1 "157G>A,159G>C" GGG>AGC G53S tolerated possibly damaging deleterious 624A none 73 52 B2 O6:H1 878A none 73 902 B2 O22:H1 748A none 73 4 B2 O6:H1 1129A none 8173 4 B2 O6:H1 241C>A CGC>AGC R81S deleterious benign deleterious 982A none 73 4 B2 O18:H1 475G>C GCG>CCG A159P tolerated probably damaging deleterious 678A none 73 4 B2 O18:H1 241C>A CGC>AGC R81S deleterious benign deleterious 960A none 73 4 B2 O25a:H1 241C>A CGC>AGC R81S deleterious benign deleterious 1173A none 73 4 B2 O25a:H1 963B none 73 4 B2 O18:H1 241C>A CGC>AGC R81S deleterious benign deleterious 900B none 73 4 B2 O6:H1 242G>T CGC>CTC R81L deleterious benign deleterious 1141A none 73 4 B2 O6:H1 241C>A CGC>AGC R81S deleterious benign deleterious 633B none 73 4 B2 O6:H1 99A unknown 73 4 B2 O6:H1 330A none 73 4 B2 O6:H1 895B none NP** 904 CladeV O103:H56 * During the previous year ** NP: new profile *** NA: not assignable (uidA gene missing)