<p> Supplementary material</p><p>Rapid detection and evolutionary analysis of Legionella pneumophila serogroup 1 sequence type 47 </p><p>M. Mentasti1, P. Cassier2, S. David1,3, C. Ginevra2,4, L. Gomez-Valero5,6, A. Underwood1, B. Afshar1,7, J. Etienne2, J. Parkhill3, V.</p><p>Chalker1, C. Buchrieser5,6, T. G. Harrison 1 and S. Jarraud2,4; ESCMID Study Group for Legionella Infections (ESGLI).</p><p>1 Public Health England, London, UK; 2 French National Reference Center of Legionella, Hospices Civils de Lyon, France; 3 Wellcome Trust</p><p>Sanger Institute, Cambridge, UK; 4 International Center for Infectiology Research, Inserm, U1111 ; CNRS ; UMR5308, Université Lyon 1 ; École</p><p>Normale Supérieure de Lyon, Lyon, F-69008, France; 5 Institut Pasteur, Unité de Biologie des Bactéries Intracellulaires; 6CNRS UMR 3525, 28,</p><p>Rue du Dr Roux, 75724, Paris, France; 7 The European Programme for Public Health Microbiology Training (EUPHEM), ECDC, Stockholm,</p><p>Sweden Table S1. Bacterial strains tested for in vitro validation of the LPO_1073 real time PCR</p><p>WGS LP0_1073 Name Serogroup ST Further information Strain ID LPO_1073 PCR assay present/absent</p><p>Lab1 Lab2 Lp1 non-ST47 L. pneumophila 1 1 Paris CIP 1076295 Neg NT ND L. pneumophila 1 1 clinical LG 1202 5033 Neg NT ND L. pneumophila 1 1 clinical LG 1209 3009 Neg NT ND L. pneumophila 1 1 clinical LG 0948 4034 Neg NT ND L. pneumophila 1 1 clinical LG 1004 4014 Neg NT ND L. pneumophila 1 1 clinical LG 1009 5093 Neg NT ND L. pneumophila 1 1 clinical LG 1145 2007 Neg NT ND L. pneumophila 1 1 clinical LG 1213 4012 Neg NT ND L. pneumophila 1 1 clinical LG 1222 4017 Neg NT ND L. pneumophila 1 1 clinical LG 1250 2024 Neg NT ND L. pneumophila 1 1 clinical LG 1302 5007 Neg NT ND L. pneumophila 1 1 OLDA NCTC 12008 NT Neg ND L. pneumophila 1 1 Oxford NCTC 12009 NT Neg ND L. pneumophila 1 1 Camperdown NCTC 12098 NT Neg ND L. pneumophila 1 3 Heysham NCTC 12025 NT Neg ND L. pneumophila 1 9 clinical LG 1132 3017 Neg NT ND L. pneumophila 1 9 clinical LG 1229 4013 Neg NT ND L. pneumophila 1 15 Lens CIP 108256 Neg NT ND L. pneumophila 1 15 clinical LG 0944 3023 Neg NT ND L. pneumophila 1 16 clinical LG 0902 4029 Neg NT ND L. pneumophila 1 18 clinical LG 1134 1017 Neg NT ND L. pneumophila 1 18 clinical LG 1140 5007 Neg NT ND L. pneumophila 1 20 clinical LG 1001 2009 Neg NT ND L. pneumophila 1 20 clinical LG 1214 2003 Neg NT ND L. pneumophila 1 22 clinical LG 1206 2007 Neg NT ND L. pneumophila 1 22 clinical LG 0948 5010 Neg NT ND L. pneumophila 1 23 clinical LG 1202 2003 Neg NT ND L. pneumophila 1 23 clinical LG 1206 4014 Neg NT ND L. pneumophila 1 23 clinical LG 0906 4016 Neg NT ND L. pneumophila 1 23 clinical LG 0932 3006 Neg NT ND L. pneumophila 1 23 clinical LG 1004 4017 Neg NT ND ATCC 33152 / L. pneumophila 1 36 Philadelphia-1 Neg Neg ND NCTC 11192 L. pneumophila 1 36 Philadelphia-2 NCTC 11193 NT Neg ND L. pneumophila 1 37 clinical LG 1249 3007 Neg NT ND L. pneumophila 1 37 Kingston-1 NCTC 11378 NT Neg ND L. pneumophila 1 38 clinical LG 1144 1013 Neg NT ND L. pneumophila 1 40 clinical LG 1206 3003 Neg NT ND L. pneumophila 1 40 clinical LG 0932 4002 Neg NT ND L. pneumophila 1 40 clinical LG 1245 5017 Neg NT ND L. pneumophila 1 40 France NCTC 12007 NT Neg ND L. pneumophila 1 42 clinical LG 1006 5003 Neg NT ND L. pneumophila 1 42 clinical LG 1229 4015 Neg NT ND L. pneumophila 1 42 Benidorm NCTC 12006 NT Neg ND L. pneumophila 1 42 W872 NCTC 12821 NT Neg ND L. pneumophila 1 44 clinical LG 1205 4021 Neg NT ND L. pneumophila 1 44 clinical LG 1249 4012 Neg NT ND L. pneumophila 1 44 Allentown NCTC 12024 NT Neg ND L. pneumophila 1 48 clinical LG 1238 1018 Neg NT ND L. pneumophila 1 58 Knoxville-1 NCTC 11286 NT Neg ND L. pneumophila 1 59 clinical LG 1001 4001 Neg NT ND L. pneumophila 1 61 Bellingham NCTC 11404 NT Neg ND L. pneumophila 1 61 Washington NCTC 11201 NT Neg ND L. pneumophila 1 62 clinical LG 0944 3024 Neg NT ND L. pneumophila 1 62 clinical LG 1004 4015 Neg NT ND L. pneumophila 1 62 clinical LG 1132 3016 Neg NT ND L. pneumophila 1 62 clinical LG 1140 5025 Neg NT ND L. pneumophila 1 62 clinical LG 1144 4014 Neg NT ND L. pneumophila 1 62 clinical LG 1145 1030 Neg NT ND L. pneumophila 1 62 clinical LG 1205 5005 Neg NT ND L. pneumophila 1 62 Pontiac-1 NCTC 11191 NT Neg ND L. pneumophila 1 65 clinical LG 1201 5006 Neg NT ND L. pneumophila 1 65 clinical LG 1236 3026 Neg NT ND L. pneumophila 1 65 clinical LG 1246 1004 Neg NT ND L. pneumophila 1 74 clinical H093480402 NT Neg absent L. pneumophila 1 74 clinical H101480488 NT Neg absent L. pneumophila 1 74 clinical H120140563 NT Neg absent L. pneumophila 1 74 clinical H130700140 NT Neg absent L. pneumophila 1 74 clinical H144480100 NT Neg absent L. pneumophila 1 74 clinical H053260229 NT Neg absent L. pneumophila 1 75 clinical LG 1203 5005 Neg NT ND L. pneumophila 1 75 clinical LG 1145 3010 Neg NT ND L. pneumophila 1 82 clinical H053540099 NT Neg absent L. pneumophila 1 82 clinical H083480003 NT Neg absent L. pneumophila 1 82 clinical H143160254 NT Neg absent L. pneumophila 1 82 clinical H143520156 NT Neg absent L. pneumophila 1 82 clinical LG 1207 1029 Neg NT ND L. pneumophila 1 82 clinical LG 0953 3017 Neg NT ND L. pneumophila 1 82 clinical LG 1132 3015 Neg NT ND L. pneumophila 1 82 clinical LG 1238 2009 Neg NT ND L. pneumophila 1 82 clinical LG 1403 5007 Neg NT ND L. pneumophila 1 82 clinical LG 1302 2006 Neg NT ND L. pneumophila 1 82 clinical LG 1329 3007 Neg NT ND L. pneumophila 1 82 clinical LG 1329 2003 Neg NT ND L. pneumophila 1 82 clinical LG 1347 2009 Neg NT ND L. pneumophila 1 82 clinical LG 1236 5002 Neg NT ND L. pneumophila 1 82 clinical LG 1238 3011 Neg NT ND L. pneumophila 1 82 clinical LG 1126 2010 Neg NT ND L. pneumophila 1 82 clinical LG 1127 3020 Neg NT ND L. pneumophila 1 82 clinical LG 1131 2009 Neg NT ND L. pneumophila 1 82 clinical LG 1147 1020 Neg NT ND L. pneumophila 1 82 clinical LG 1027 2002 Neg NT ND L. pneumophila 1 82 clinical LG 0939 3010 Neg NT ND L. pneumophila 1 82 clinical LG 0837 5015 Neg NT ND L. pneumophila 1 82 clinical LG 0813 3016 Neg NT ND L. pneumophila 1 84 clinical LG 1222 4014 Neg NT ND L. pneumophila 1 87 clinical LG 1249 4018 Neg NT ND L. pneumophila 1 93 clinical LG 1229 3033 Neg NT ND L. pneumophila 1 94 clinical LG 1206 1025 Neg NT ND L. pneumophila 1 94 clinical LG 0948 4033 Neg NT ND L. pneumophila 1 94 clinical LG 1004 5004 Neg NT ND L. pneumophila 1 96 clinical LG 1204 3003 Neg NT ND L. pneumophila 1 96 clinical LG 1206 5010 Neg NT ND L. pneumophila 1 96 clinical LG 0918 3011 Neg NT ND L. pneumophila 1 96 clinical LG 0918 3029 Neg NT ND L. pneumophila 1 96 clinical LG 1027 5006 Neg NT ND L. pneumophila 1 96 clinical LG 1250 4013 Neg NT ND L. pneumophila 1 107 clinical LG 1214 4001 Neg NT ND L. pneumophila 1 109 clinical LEG331 NT Pos ND L. pneumophila 1 109 environmental W12-1142 NT Neg ND L. pneumophila 1 109 clinical L08-482 NT Pos ND L. pneumophila 1 109 clinical L10-409 NT Neg ND L. pneumophila 1 109 clinical L10-418 NT Pos ND L. pneumophila 1 109 clinical L15-025 NT Pos ND L. pneumophila 1 109 clinical L15-122 NT Pos ND L. pneumophila 1 109 environmental W15-003 NT Pos ND L. pneumophila 1 109 clinical R7213 NT Pos ND L. pneumophila 1 109 clinical R6323 NT Pos ND L. pneumophila 1 109 clinical LG 0927 5012 Pos Pos present L. pneumophila 1 109 clinical LG 0928 1008 Pos Pos present L. pneumophila 1 109 clinical LG 0933 1003 Pos Pos present L. pneumophila 1 109 clinical LG 1101 4027 Pos Pos present L. pneumophila 1 109 clinical LG 1105 1006 Pos Pos present L. pneumophila 1 109 clinical LG 1106 4019 Pos Pos present L. pneumophila 1 109 clinical LG 1135 3014 Pos Pos present L. pneumophila 1 109 clinical LG 1230 2004 Pos Pos present L. pneumophila 1 109 clinical LG 1334 4009 Pos Pos present L. pneumophila 1 109 clinical 015134851801 NT Pos ND L. pneumophila 1 109 clinical 015172872101 NT Pos ND L. pneumophila 1 109 clinical H053040071 Neg Neg absent L. pneumophila 1 109 clinical H083920183 Neg Neg absent L. pneumophila 1 109 clinical H092380261 Neg Neg absent L. pneumophila 1 109 environmental H092400768 Neg Neg absent L. pneumophila 1 109 clinical H073660663 Neg Neg absent L. pneumophila 1 109 clinical H100640680 Neg Neg absent L. pneumophila 1 109 clinical H144600853 NT Pos ND L. pneumophila 1 109 clinical H150320371 NT Pos ND L. pneumophila 1 109 clinical H150540408 NT Pos ND L. pneumophila 1 109 clinical 080910019001 NT Pos ND L. pneumophila 1 109 clinical 060222019001 NT Pos ND L. pneumophila 1 109 clinical 080912019001 NT Pos ND L. pneumophila 1 109 clinical 090324019001 NT Pos ND L. pneumophila 1 109 clinical 110627019001 NT Pos ND L. pneumophila 1 109 clinical 110729019001 NT Pos ND L. pneumophila 1 109 clinical 120312019001 NT Pos ND L. pneumophila 1 109 clinical H093380154 NT Neg absent L. pneumophila 1 109 clinical H084060004 NT Neg absent L. pneumophila 1 109 clinical D-2466 NT* NT* absent L. pneumophila 1 109 clinical D-4080 NT* NT* ND L. pneumophila 1 109 clinical D-4102 NT* NT* ND L. pneumophila 1 109 clinical D-5342 NT* NT* ND L. pneumophila 1 109 clinical D-5725 NT* NT* ND L. pneumophila 1 117 clinical LG 1129 1010 Neg NT ND L. pneumophila 1 143 clinical LG 1236 3008 Neg NT ND L. pneumophila 1 146 clinical LG 0915 4010 Neg NT ND L. pneumophila 1 146 clinical LG 1129 1011 Neg NT ND L. pneumophila 1 146 clinical LG 1129 3004 Neg NT ND L. pneumophila 1 146 clinical LG 1222 4016 Neg NT ND L. pneumophila 1 152 clinical LG 1036 1001 Neg NT ND L. pneumophila 1 152 clinical LG 1304 4030 Neg NT ND L. pneumophila 1 154 clinical LG 1303 2010 Neg NT ND L. pneumophila 1 205 clinical D-4017 NT* NT* ND L. pneumophila 1 205 clinical D-4328 NT* NT* ND L. pneumophila 1 205 clinical D-5285 NT* NT* ND L. pneumophila 1 205 clinical D-5375 NT* NT* ND L. pneumophila 1 205 clinical D-5466 NT* NT* ND L. pneumophila 1 206 clinical H053620029 NT Neg ND L. pneumophila 1 219 clinical LR1023 NT Neg ND L. pneumophila 1 224 clinical LG 1031 2006 Neg NT ND L. pneumophila 1 259 clinical LG 1205 5009 Neg NT ND L. pneumophila 1 259 clinical LG 0902 4027 Neg NT ND L. pneumophila 1 259 clinical LG 1004 5013 Neg NT ND L. pneumophila 1 259 clinical LG 1129 3010 Neg NT ND L. pneumophila 1 259 clinical LG 1214 3009 Neg NT ND L. pneumophila 1 259 clinical LG 1303 1018 Neg NT ND L. pneumophila 1 277 clinical D-5512 NT* NT* ND L. pneumophila 1 313 clinical LG 1210 5007 Neg NT ND L. pneumophila 1 345 clinical LG 1210 2003 Neg NT ND L. pneumophila 1 346 Cambridge-1 NCTC 11231 NT Neg ND L. pneumophila 1 435 clinical LG 1006 3002 Neg NT ND L. pneumophila 1 436 clinical LG 1004 3006 Neg NT ND L. pneumophila 1 436 clinical LG 1028 2010 Neg NT ND L. pneumophila 1 436 clinical LG 1035 5002 Neg NT ND L. pneumophila 1 444 clinical LG 0902 5001 Neg NT ND L. pneumophila 1 500 clinical LG 1129 3009 Neg NT ND L. pneumophila 1 534 clinical LG 1010 1024 Neg NT ND L. pneumophila 1 534 clinical LG 1304 2006 Neg NT ND L. pneumophila 1 540 clinical LG 1031 2002 Neg NT ND L. pneumophila 1 542 clinical LG 1206 5009 Neg NT ND L. pneumophila 1 579 clinical LG 0938 1004 Neg NT ND L. pneumophila 1 591 clinical H084780287 NT Neg ND L. pneumophila 1 647 clinical LG 0915 3010 Neg NT ND L. pneumophila 1 664 clinical LG 1006 3009 Neg NT ND L. pneumophila 1 664 clinical LG 1129 1026 Neg NT ND L. pneumophila 1 664 clinical LG 1250 3003 Neg NT ND L. pneumophila 1 701 clinical LG 1206 5001 Neg NT ND L. pneumophila 1 701 clinical LG 0944 4016 Neg NT ND L. pneumophila 1 701 clinical LG 1140 2025 Neg NT ND L. pneumophila 1 701 clinical LG 1215 2045 Neg NT ND L. pneumophila 1 702 clinical LG 1212 2009 Neg NT ND L. pneumophila 1 706 clinical LG 1035 5001 Neg NT ND L. pneumophila 1 751 clinical LG 0938 4014 Neg NT ND 107 L. pneumophila 1 clinical LG 1135 1011 4 Neg NT ND 108 L. pneumophila 1 clinical LG 1141 4013 4 Neg NT ND 108 L. pneumophila 1 clinical LG 1442 3007 6 Neg NT ND 114 L. pneumophila 1 clinical LG 1147 4009 7 Neg NT ND 169 L. pneumophila 1 environmental R6928 7 NT Neg ND Lp1 ST47 L. pneumophila 1 47 clinical CIP 108729 Pos NT ND L. pneumophila 1 47 clinical LG 0842 1021 Pos NT ND L. pneumophila 1 47 clinical LG 0742 5012 Pos NT ND L. pneumophila 1 47 clinical LG 1104 2016 Pos NT ND L. pneumophila 1 47 clinical LG 1104 4042 Pos NT ND L. pneumophila 1 47 clinical LG 1105 5013 Pos NT ND L. pneumophila 1 47 clinical LG 1106 3013 Pos NT ND L. pneumophila 1 47 clinical LG 1109 1026 Pos NT ND L. pneumophila 1 47 clinical LG 1110 2014 Pos NT ND L. pneumophila 1 47 clinical LG 1111 2001 Pos NT ND L. pneumophila 1 47 clinical LG 1126 2014 Pos NT ND L. pneumophila 1 47 clinical 98 01 0561 Pos NT ND L. pneumophila 1 47 clinical HL 0227 4033 Pos NT present L. pneumophila 1 47 clinical HL 0231 1034 Pos NT ND L. pneumophila 1 47 clinical HL 0235 1033 Pos NT ND L. pneumophila 1 47 clinical HL 0239 2002 Pos NT present L. pneumophila 1 47 clinical HL 0302 5015 Pos NT ND L. pneumophila 1 47 clinical HL 0303 5006 Pos NT ND L. pneumophila 1 47 clinical HL 0305 3023 Pos NT ND L. pneumophila 1 47 clinical HL 0307 4038 Pos NT ND L. pneumophila 1 47 clinical HL 0334 3052 Pos NT ND L. pneumophila 1 47 clinical HL 0344 3027 Pos NT present L. pneumophila 1 47 clinical HL 0350 3011 Pos NT present L. pneumophila 1 47 clinical HL 0406 4040 Pos NT ND L. pneumophila 1 47 clinical HL 0407 5055 Pos NT present L. pneumophila 1 47 clinical HL 0408 3041 Pos NT ND L. pneumophila 1 47 clinical HL 0426 4021 Pos NT ND L. pneumophila 1 47 clinical LG 1011 2008 Pos NT ND L. pneumophila 1 47 clinical HL 0435 5030 Pos NT ND L. pneumophila 1 47 clinical HL 0436 3019 Pos NT ND L. pneumophila 1 47 clinical HL 0438 2020 Pos NT ND L. pneumophila 1 47 clinical HL 0439 2006 Pos NT ND L. pneumophila 1 47 clinical HL 0440 4025 Pos NT ND L. pneumophila 1 47 clinical HL 0445 5101 Pos NT ND L. pneumophila 1 47 clinical HL 0447 2046 Pos NT ND L. pneumophila 1 47 clinical HL 0447 2047 Pos NT ND L. pneumophila 1 47 clinical LG 10491019 Pos NT ND L. pneumophila 1 47 clinical HL 0535 5024 Pos NT ND L. pneumophila 1 47 clinical HL 0546 5018 Pos NT ND L. pneumophila 1 47 clinical HL 0645 3016 Pos NT ND L. pneumophila 1 47 clinical HL 0603 5032 Pos NT ND L. pneumophila 1 47 clinical HL 0612 3003 Pos NT ND L. pneumophila 1 47 clinical LG 1040 1013 Pos NT ND L. pneumophila 1 47 clinical HL 0645 3023 Pos NT ND L. pneumophila 1 47 clinical HL 0645 3024 Pos NT ND L. pneumophila 1 47 clinical LG1039 1003 Pos NT ND L. pneumophila 1 47 clinical HL 0710 5012 Pos NT ND L. pneumophila 1 47 clinical LG 0731 5014 Pos NT ND L. pneumophila 1 47 clinical LG 1039 1003 Pos NT ND L. pneumophila 1 47 clinical LG 0739 5005 Pos NT ND L. pneumophila 1 47 clinical LG 0751 2016 Pos NT ND L. pneumophila 1 47 environmental LG 0743 5013 Pos NT ND L. pneumophila 1 47 environmental LG 0743 5014 Pos NT ND L. pneumophila 1 47 clinical LG 0802 3006 Pos NT ND L. pneumophila 1 47 clinical LG 0826 4030 Pos NT ND L. pneumophila 1 47 clinical LG 0829 2015 Pos NT ND L. pneumophila 1 47 clinical LG 0835 5011 Pos NT ND L. pneumophila 1 47 clinical LG 0838 4026 Pos NT ND L. pneumophila 1 47 clinical LG 0848 3003 Pos NT ND L. pneumophila 1 47 clinical LG 0909 5008 Pos NT ND L. pneumophila 1 47 clinical LG 0924 1014 Pos NT ND L. pneumophila 1 47 clinical LG 0928 5005 Pos NT ND L. pneumophila 1 47 clinical LG 0927 3014 Pos NT ND L. pneumophila 1 47 clinical LG 0934 4009 Pos NT ND L. pneumophila 1 47 clinical LG 1005 3001 Pos NT ND L. pneumophila 1 47 clinical LG 1026 5004 Pos NT ND L. pneumophila 1 47 clinical LG 1027 5005 Pos NT ND L. pneumophila 1 47 clinical LG 1035 4004 Pos NT ND L. pneumophila 1 47 clinical LG 1039 7001 Pos NT present L. pneumophila 1 47 clinical LG 1042 5016 Pos NT present L. pneumophila 1 47 clinical LG 1050 4011 Pos NT ND L. pneumophila 1 47 clinical LG 1103 5011 Pos NT ND L. pneumophila 1 47 clinical LG 1104 4015 Pos NT ND L. pneumophila 1 47 clinical LG 1102 3009 Pos NT ND L. pneumophila 1 47 clinical LG 1103 1019 Pos NT ND L. pneumophila 1 47 clinical LG 1103 2051 Pos NT ND L. pneumophila 1 47 clinical LG 1103 2052 Pos NT ND L. pneumophila 1 47 clinical LG 1103 3012 Pos NT ND L. pneumophila 1 47 clinical LG 1128 1003 Pos NT ND L. pneumophila 1 47 clinical LG 1129 3001 Pos NT ND L. pneumophila 1 47 clinical LG 1135 3014 Pos NT ND L. pneumophila 1 47 clinical LG 1136 4009 Pos NT ND L. pneumophila 1 47 clinical LG 1140 3003 Pos NT present L. pneumophila 1 47 clinical LG 1141 3009 Pos NT ND L. pneumophila 1 47 clinical LG 1208 1019 Pos NT ND L. pneumophila 1 47 clinical LG 1202 2004 Pos NT ND L. pneumophila 1 47 clinical LG 1203 4018 Pos NT present L. pneumophila 1 47 clinical LG 1208 4002 Pos NT present L. pneumophila 1 47 clinical LG 1211 2005 Pos NT ND L. pneumophila 1 47 clinical LG 1222 3003 Pos NT ND L. pneumophila 1 47 clinical LG 1223 5003 Pos NT ND L. pneumophila 1 47 clinical LG 1227 5006 Pos NT ND L. pneumophila 1 47 clinical LG 1227 2002 Pos NT ND L. pneumophila 1 47 clinical LG 1227 3004 Pos NT ND L. pneumophila 1 47 clinical LG 1227 4009 Pos NT ND L. pneumophila 1 47 clinical LG 1228 2004 Pos NT ND L. pneumophila 1 47 clinical LG 1229 2013 Pos NT ND L. pneumophila 1 47 clinical LG 1230 2002 Pos NT ND L. pneumophila 1 47 clinical LG 1230 3010 Pos NT ND L. pneumophila 1 47 clinical LG 1230 4026 Pos NT ND L. pneumophila 1 47 clinical LG 1232 2006 Pos NT ND L. pneumophila 1 47 clinical LG 1238 4012 Pos NT ND L. pneumophila 1 47 clinical LG 1243 2031 Pos NT ND L. pneumophila 1 47 clinical LG 1302 2003 Pos NT ND L. pneumophila 1 47 clinical LG 1303 4017 Pos NT ND L. pneumophila 1 47 clinical L10-531 NT Pos present L. pneumophila 1 47 clinical L11-078 NT Pos present L. pneumophila 1 47 clinical L12-679 NT Pos present L. pneumophila 1 47 clinical L13-510 NT Pos present L. pneumophila 1 47 clinical H070420012 NT Pos ND Lp non sg 1 ATCC 33154 / L. pneumophila 39 Togus-1 Neg Neg ND 2 NCTC 11230 L. pneumophila 2 39 clinical LG 0735 3006 Neg NT ND L. pneumophila 2 39 clinical LG 0928 2005 Neg NT ND L. pneumophila 2 338 clinical LG 1051 4015 Neg NT ND L. pneumophila 2 948 clinical LG 1209 4023 Neg NT ND 145 L. pneumophila 2 clinical LG 1235 1021 Neg NT ND 5 ATCC 33155 / L. pneumophila 395 Bloomington-2 Neg Neg ND 3 NCTC 11232 L. pneumophila 3 87 clinical LG 0819 5001 Neg NT ND L. pneumophila 3 93 clinical LG 0928 2008 Neg NT ND L. pneumophila 3 93 clinical LG 1002 4012 Neg NT ND L. pneumophila 3 790 clinical LG 1009 4045 Neg NT ND L. pneumophila 3 93 clinical LG 1124 2022 Neg NT ND 134 L. pneumophila 3 clinical LG 1227 3015 Neg NT ND 1 L. pneumophila 3 87 clinical LG 1304 3018 Neg NT ND L. pneumophila subsp. 133 4 Los Angeles NCTC 11233 Neg Neg ND fraseri 4 L. pneumophila 4 378 clinical LG 1201 2012 Neg NT ND L. pneumophila 4 ND clinical LG 1113 1027 Neg NT ND L. pneumophila 4 17 clinical LG 1118 2027 Neg NT ND L. pneumophila 4 ND clinical LG 0929 3017 Neg NT ND L. pneumophila 4 378 clinical LG 0830 1011 Neg NT ND L. pneumophila 5 80 Cambridge-2 NCTC 11417 NT Neg ND L. pneumophila subsp. 130 ATCC 33216 / 5 Dallas-1E Neg Neg ND fraseri 0 NCTC 11405 136 L. pneumophila 5 clinical LG 1203 3016 Neg NT ND 2 135 L. pneumophila 5 clinical LG 1127 3018 Neg NT ND 8 L. pneumophila 5 70 clinical LG 1002 4013 Neg NT ND L. pneumophila 5 ND clinical LG 0902 4050 Neg NT ND 205 L. pneumophila 5 clinical LG 0830 2017 Neg NT ND 9 ATCC 33125 / L. pneumophila 30 Chicago-2 Neg Neg ND 6 NCTC 11406 L. pneumophila 6 60 Oxford NCTC 11287 NT Neg ND L. pneumophila 6 778 clinical LG 1004 4016 Neg NT ND L. pneumophila 6 114 clinical LG 0906 2008 Neg NT ND L. pneumophila 6 114 clinical LG 0930 2019 Neg NT ND 131 ATCC 33823 / L. pneumophila Chicago-8 Neg Neg ND 7 9 NCTC 11984 L. pneumophila 7 451 clinical LG 0751 2019 Neg NT ND 190 L. pneumophila 7 clinical LG 1106 1018 Neg NT ND 4 L. pneumophila 7 ND clinical LG 0942 4021 Neg NT ND 132 ATCC 35096 / L. pneumophila Concord-3 Neg Neg ND 8 0 NCTC 11985 L. pneumophila 8 48 clinical LG 1139 6001 Neg NT ND 133 L. pneumophila 8 clinical LG 1040 1025 Neg NT ND 2 L. pneumophila 8 ND clinical LG 0934 4011 Neg NT ND ATCC 35289 / L. pneumophila 390 IN-23-GI-C2 Neg Neg ND 9 NCTC 11986 ATCC 43283 / L. pneumophila 17 Leiden-1 Neg Neg 10 NCTC 12000 139 L. pneumophila 10 clinical LG 1241 3001 Neg NT ND 2 ATCC 43130 / L. pneumophila NA 797-PA-H Neg Neg ND 11 NCTC 12179 L. pneumophila 11 ND clinical LG 1241 3003 Neg NT ND ATCC 43290 / L. pneumophila 187 570-CO-H Neg Neg ND 12 NCTC 12180 131 ATCC 43736 / L. pneumophila 82A3105 Neg Neg ND 13 8 NCTC 12181 ATCC 73703 / L. pneumophila NA 1169-MN-H Neg Neg ND 14 NCTC 12174 132 L. pneumophila 14 clinical LG 0819 2016 Neg NT ND 4 ATCC 35251 / L. pneumophila 336 Lansing-3 Neg Neg ND 15 LC3330 L. pneumophila 16 378 Jena-1 LC3392 NT Neg ND L. pneumophila subsp. 133 MICU-B NCTC 12271 NT Neg ND pascullei ND 5 L. pneumophila subsp. 133 U7W NCTC 12272 NT Neg ND pascullei ND 5 L. pneumophila subsp. 133 U8W NCTC 12273 NT Neg ND pascullei ND 5 Legionella non- pneumophila CDC 1762- L. adelaidensis NA AUS-E / Neg Neg ND NCTC 12735 ATCC 35290 / L. anisa Neg Neg ND NA NCTC 11974 L. anisa NA CH-47-C3 Neg NT ND L. anisa NA WA-316-C3 Neg NT ND L. beliardensis NA NCTC 13315 NT Neg ND ATCC 73702 / L. birminghamensis NA Neg Neg ND NCTC 12437 ATCC 33217 / L. bozemanii Neg Neg ND 1 NA NCTC 11368 ATCC 35245 / L. bozemanii Neg Neg ND 2 NA NCTC 11975 ATCC 43878 / L. brunensis Neg Neg ND NA NCTC 12240 L. busanensis NA NCTC 13316 NT Neg ND ATCC 35252 / L. cherrii Neg Neg ND NA NCTC 11976 ATCC 43753 / L. cincinnatiensis Neg Neg ND NA NCTC 12438 L. dresdeniensis NA NCTC 13409 NT Neg ND L. drozanskii NA DSM 19890 NT Neg ND ATCC 35280 / L. dumoffii Neg Neg ND NA NCTC 11370 ATCC 35303 / L. erythra Neg Neg ND 1 NA NCTC 11977 L. fairfieldensis NA NCTC 12488 NT Neg ND L. fallonii NA DSM 19889 NT Neg ND L. feeleii 1 NA NCTC 12022 NT Neg ND ATCC 35849 / L. feeleii Neg Neg ND 2 NA NCTC 11978 L. feeleii NA ATCC 700514 Neg NT ND L. geestiana NA NCTC 12373 NT Neg ND ATCC 33297 / L. gormanii Neg Neg ND NA NCTC 11401 ATCC 49413 / L. gratiana Neg Neg ND NA NCTC 12388 ATCC L. gresilensis 700509 / Neg Neg ND NA NCTC 13312 ATCC 35250 / L. hackeliae Neg Neg ND 1 NA NCTC 11979 ATCC 35999 / L. hackeliae Neg Neg ND 2 NA NCTC 11980 L. impletisoli NA DSM 18493 NT Neg ND ATCC 43119 / L. israelensis Neg Neg ND NA NCTC 12010 ATCC 35298 / L. jamestownensis Neg Neg ND NA NCTC 11981 ATCC 33263 / L. jordanis Neg Neg ND NA NCTC 11533 ATCC 49751 / L. lansingensis NT Neg ND NA NCTC 12830 ATCC 49505 / L. londiniensis Neg Neg ND NA NCTC 12931 L. londiniensis NA ATCC 700510 Neg NT ND ATCC 33462 / L. longbeachae Neg Neg ND 1 NA NCTC 11477 ATCC 33484 / L. longbeachae Neg Neg ND 2 NA NCTC 11530 ATCC 35300 / L. maceachernii Neg Neg ND NA NCTC 11982 L. micdadei NA Heba NCTC 11403 NT Neg ND ATCC 33218 / L. micdadei Neg Neg ND NA Tatlock NCTC 11371 ATCC 43877 / L. moravica Neg Neg ND NA NCTC 12239 ATCC L. nagasakii NT Neg ND NA BAA1558 L. nautarum NA ATCC Neg Neg ND 49506 /NCTC 12932</p><p>ATCC L. oakridgensis 700515 / Neg Neg ND NA NCTC 11531 ATCC 35299 / L. parisiensis Neg Neg ND NA NCTC 11983 ATCC 49507 / L. quateirensis Neg Neg ND NA NCTC 12376 L. quinlivanii 1 NA 1448-AUS-E Neg NT ND ATCC 43830 / L. quinlivanii Neg Neg ND 1 NA NCTC 12433 L. quinlivanii 2 NA NCTC 12434 NT Neg ND L. rowbothamii NA ATCC 700991 NT Neg ND ATCC 35304 / L. rubrilucens Neg Neg ND NA NCTC 11987 ATCC 35248 / L. sainthelensi Neg Neg ND 1 NA NCTC 11988 ATCC 49322 / L. sainthelensi Neg Neg ND 2 NA NCTC 12450 L. sainthelensi 2 NA ATCC 700517 Neg NT ND ATCC 35301 / L. santicrucis NA Neg Neg ND NCTC 11989 L. shakespearei NA NCTC 12829 NT Neg ND L. species IBV-3 NA ATCC 700511 Neg NT ND ATCC 35249 / L. spiritensis Neg Neg ND 1 NA NCTC 11990 L. spiritensis 2 NA NCTC 12082 NT Neg ND L. steelei NA ATCC NT Neg ND BAA2169 ATCC 35302 / L. steigerwaltii Neg Neg ND NA NCTC 11991 ATCC L. taurinensis 700508 / Neg Neg ND NA NCTC 13314 ATCC 49180 / L. tucsonensis Neg Neg ND NA NCTC 12439 ATCC 33877 / L. wadsworthii Neg Neg ND NA NCTC 11532 ATCC 51914 / L. waltersii Neg Neg ND NA NCTC 13017 ATCC 49508 / L. worsliensis Neg Neg ND NA NCTC 12377 L. yabuuchiae NA DSM 18492 NT Neg ND non-Legionella spp. Aeromonas hydrophila clinical BE 1236 -1 Neg NT ND Alcaligenes faecalis clinical BE 1236 -2 Neg NT ND Bacillus subtilis ATCC 6633 Neg NT ND Bulkholderia cepacia clinical BE 1236-3 Neg NT ND Clostridium ATCC 19404 NT ND sporogenes Neg Enterobacter clinical BE 1236-3 NT ND aerogenes Neg Escherichia coli clinical BE 1236-4 Neg NT ND Flavobacterium sp. clinical BE 1236-5 Neg NT ND Klebsiella oxytoca clinical BE 1236-6 Neg NT ND Listeria clinical BE 1236-7 NT ND monocytogenes Neg Proteus vulgaris clinical BE 1236-8 Neg NT ND Pseudomonas ATCC 9027 NT ND aeruginosa Neg P. fluorescens clinical BE 1236-9 Neg NT ND P. putida clinical BE 1236-10 Neg NT ND Serratia marcesens clinical BE 1236-11 Neg NT ND Stenotrophomonas clinical BE 1236-12 NT ND maltophila Neg *Tested negative by CDC Atlanta USA Table S2. Legionella pneumophila strains analysed by WGS</p><p>Reference/Accession Isolate name ST Country of isolation Source LPO_1073 number 36 genomes available at the start of the study and used for initial selection of a PCR target Paris 1 France Clinical Absent Cazalet et al. 2004 H034800423/LP423 1 UK Environmental Absent Reuter et al. 2013 EUL 13 5 Scotland Clinical Absent Underwood et al. 2013 Lens 15 France Clinical Absent Cazalet et al. 2004 H063280001 23 UK Clinical Absent Underwood et al. 2013 RR08000134 34 UK Environmental Absent Underwood et al. 2015 Philadelphia 36 USA Clinical Absent Chien et al. 2004 H034680035/EUL 165 37 UK Clinical Absent Underwood et al. 2017 H044540088 42 UK Clinical Absent Underwood et al. 2018 Wadsworth/130b 42 USA Clinical Absent Schroeder et al. 2010 H100260089 44 UK Clinical Absent Underwood et al. 2019 H093620212 46 UK Clinical Absent Underwood et al. 2021 Lorraine 47 France Clinical Present Gomez-Valero et al. 2011 H034700617/LP617 47 UK Clinical Present Reuter et al. 2013 H063920004 47 UK Clinical Present Underwood et al. 2013 Corby 51 UK Environmental Absent Gloeckner et al. 2008 H065000139 54 UK Clinical Absent Underwood et al. 2013 H070840415 59 UK Clinical Absent Underwood et al. 2013 H064180002 62 UK Clinical Absent Underwood et al. 2013 H074360710 68 UK Environmental Absent Underwood et al. 2013 H053260229/EUL 164 74 UK Clinical Absent Underwood et al. 2013 LC6451 78 UK Clinical Absent Underwood et al. 2013 H043940028/EUL 151 84 UK Clinical Absent Underwood et al. 2013 LC6677 87 Spain Clinical Absent Underwood et al. 2013 H074360702 152 UK Environmental Absent Underwood et al. 2013 LC6774 154 UK Environmental Absent Underwood et al. 2013 H093380153 179 UK Clinical Absent Underwood et al. 2013 H044500045 186 UK Clinical Absent Underwood et al. 2013 H075160080 188 UK Environmental Absent Underwood et al. 2013 Lansing-3 336 USA Clinical Absent Underwood et al. 2013 RR08000517 337 UK Environmental Absent Underwood et al. 2014 RR08000760 376 UK Environmental Absent Underwood et al. 2016 H091960011 454 UK Environmental Absent Underwood et al. 2020 Alcoy 578 Spain Clinical Absent D'Auria et al. 2010 H090500162 611 UK Environmental Absent Underwood et al. 2013 H091960009 707 UK Environmental Absent Underwood et al. 2013 423 genomes published since the beginning of this study and used to validate the PCR target EUL 55 1 Spain Clinical Absent David et al. 2016 EUL 88 1 Denmark Clinical Absent David et al. 2016 EUL 93 1 Denmark Clinical Absent David et al. 2016 EUL 10 1 Switzerland Environmental Absent David et al. 2016 EUL 1 1 Switzerland Clinical Absent David et al. 2016 EUL 21 1 GBR Environmental Absent David et al. 2016 EUL 14 5 GBR Clinical Absent David et al. 2016 EUL 16 5 GBR Clinical Absent David et al. 2016 EUL 17 7 GBR Clinical Absent David et al. 2016 EUL 3 1 Switzerland Clinical Absent David et al. 2016 EUL 109 1 Sweden Environmental Absent David et al. 2016 EUL 42 1 Italy Clinical Absent David et al. 2016 EUL 43 1 Italy Clinical Absent David et al. 2016 EUL 44 1 Italy Environmental Absent David et al. 2016 EUL 45 72 Italy Clinical Absent David et al. 2016 EUL 46 1 Italy Environmental Absent David et al. 2016 EUL 110 10 Germany Clinical Absent David et al. 2016 EUL 58 1 Spain Environmental Absent David et al. 2016 EUL 60 1 Greece Clinical Absent David et al. 2016 EUL 62 1 Greece Environmental Absent David et al. 2016 EUL 67 1 Greece Clinical Absent David et al. 2016 EUL 85 1 Denmark Clinical Absent David et al. 2016 EUL 9 1 Switzerland Environmental Absent David et al. 2016 EUL 82 1 Denmark Clinical Absent David et al. 2016 EUL 84 1 Denmark Clinical Absent David et al. 2016 EUL 90 1 Denmark Clinical Absent David et al. 2016 EUL 94 1 Denmark Clinical Absent David et al. 2016 EUL 95 1 Denmark Environmental Absent David et al. 2016 EUL 104 1 Sweden Clinical Absent David et al. 2016 EUL 108 1 Sweden Clinical Absent David et al. 2016 EUL 113 7 Germany Environmental Absent David et al. 2016 EUL 37 1 Italy Clinical Absent David et al. 2016 EUL 114 7 Germany Environmental Absent David et al. 2016 EUL 117 6 Germany Clinical Absent David et al. 2016 EUL 119 1 Germany Clinical Absent David et al. 2016 EUL 53 1 Spain Clinical Absent David et al. 2016 EUL 157 8 GBR Environmental Absent David et al. 2016 OLDA (ATCC43109) 1 USA Clinical Absent David et al. 2016 HL 0036 4001 1 France Clinical Absent David et al. 2016 HL 0230 4015 1 France Clinical Absent David et al. 2016 HL 0311 1005 1 France Environmental Absent David et al. 2016 HL 0337 3012 1 France Environmental Absent David et al. 2016 HL 0416 3014 1 France Clinical Absent David et al. 2016 HL 0701 3004 1 France Environmental Absent David et al. 2016 LG 0919 2006 1 France Clinical Absent David et al. 2016 LG 0940 4015 1 France Clinical Absent David et al. 2016 LG 1019 1002 1 France Clinical Absent David et al. 2016 LG 1020 3012 1 France Environmental Absent David et al. 2016 LG 1101 1012 1 France Environmental Absent David et al. 2016 LG 1105 4025 1 France Environmental Absent David et al. 2016 LG 1118 1044 1 Morocco Environmental Absent David et al. 2016 LG 1139 1124 1 France Environmental Absent David et al. 2016 LP21 1 Sweden Clinical Absent David et al. 2016 LP23 1 Sweden Clinical Absent David et al. 2016 LT 40/04 1 Austria Clinical Absent David et al. 2016 NIIB223 1 Japan Environmental Absent David et al. 2016 NIIB225 1 Japan Environmental Absent David et al. 2016 L 3386/03 1 Austria Environmental Absent David et al. 2016 L 3415/03 1 Austria Environmental Absent David et al. 2016 LG 1014 3009 1 France Clinical Absent David et al. 2016 EUL 8 23 Switzerland Clinical Absent David et al. 2016 EUL 11 23 Switzerland Environmental Absent David et al. 2016 EUL 12 23 Switzerland Environmental Absent David et al. 2016 EUL 41 23 Italy Clinical Absent David et al. 2016 EUL 130 23 Croatia Clinical Absent David et al. 2016 EUL 129 23 Croatia Clinical Absent David et al. 2016 EUL 4 23 Switzerland Clinical Absent David et al. 2016 EUL 28 23 France Clinical Absent David et al. 2016 HL 0127 3027 23 France Clinical Absent David et al. 2016 HL 0236 5014 23 France Clinical Absent David et al. 2016 HL 0236 5015 23 France Clinical Absent David et al. 2016 HL 0302 1012 23 France Clinical Absent David et al. 2016 HL 0339 3028 23 France Clinical Absent David et al. 2016 HL 0437 1017 23 France Clinical Absent David et al. 2016 HL 0443 3031 23 France Clinical Absent David et al. 2016 HL 0506 3005 23 France Clinical Absent David et al. 2016 HL 0532 2037 23 France Environmental Absent David et al. 2016 HL 0541 5018 23 France Clinical Absent David et al. 2016 HL 0604 3045 23 France Clinical Absent David et al. 2016 HL 0637 3021 23 France Clinical Absent David et al. 2016 HL 0709 3017 23 France Clinical Absent David et al. 2016 LG 0751 2008 23 France Clinical Absent David et al. 2016 LG 0834 5006 23 France Clinical Absent David et al. 2016 LG 0839 2025 23 France Clinical Absent David et al. 2016 LG 0915 3012 23 France Environmental Absent David et al. 2016 LG 0935 3013 23 France Environmental Absent David et al. 2016 LG 0940 3015 23 France Clinical Absent David et al. 2016 LG 094 54021 23 France Clinical Absent David et al. 2016 LG 1025 5002 23 France Clinical Absent David et al. 2016 LG 1036 3013 23 France Environmental Absent David et al. 2016 LG 1048 1020 23 France Clinical Absent David et al. 2016 LG 1127 2006 23 France Clinical Absent David et al. 2016 LG 1136 3009 23 France Clinical Absent David et al. 2016 LG 1140 2026 23 France Clinical Absent David et al. 2016 LG 1224 2012 23 France Clinical Absent David et al. 2016 LG 1246 5006 23 France Clinical Absent David et al. 2016 H064240448 37 UK Environmental Absent David et al. 2016 LC0731 37 UK Clinical Absent David et al. 2016 LC0732 37 UK Clinical Absent David et al. 2016 LC0763 37 UK Environmental Absent David et al. 2016 LC5694 37 UK Clinical Absent David et al. 2016 LC5722 37 UK Clinical Absent David et al. 2016 LC5738 37 UK Clinical Absent David et al. 2016 LC5755 37 UK Clinical Absent David et al. 2016 LC5908 37 UK Clinical Absent David et al. 2016 LC6163 37 UK Clinical Absent David et al. 2016 LC6267 37 UK Clinical Absent David et al. 2016 LC6268 37 UK Clinical Absent David et al. 2016 LC6228 37 UK Clinical Absent David et al. 2016 H041380048 37 UK Clinical Absent David et al. 2016 H042960010 37 UK Clinical Absent David et al. 2016 H061140013 37 UK Clinical Absent David et al. 2016 H071880001 37 UK Clinical Absent David et al. 2016 H073060003 37 UK Clinical Absent David et al. 2016 H080820009 37 UK Clinical Absent David et al. 2016 Unknown (travel- LC6058 37 associated) Clinical Absent David et al. 2016 Unknown (travel- LC6293 37 associated) Clinical Absent David et al. 2016 H041640791 37 UK Environmental Absent David et al. 2016 Unknown (travel- LC6788 37 associated) Clinical Absent David et al. 2016 Unknown (travel- H062660463 37 associated) Clinical Absent David et al. 2016 Unknown (travel- H073900557 37 associated) Clinical Absent David et al. 2016 LC1127 37 UK Clinical Absent David et al. 2016 H084760449 37 UK Clinical Absent David et al. 2016 H085020185 37 UK Clinical Absent David et al. 2016 H090320386 37 UK Clinical Absent David et al. 2016 H044260061 37 UK Environmental Absent David et al. 2016 H093140322 37 UK Clinical Absent David et al. 2016 H093160422 37 UK Environmental Absent David et al. 2016 Unknown (travel- H092760433 37 associated) Clinical Absent David et al. 2016 H100940111 37 UK Clinical Absent David et al. 2016 H101760092 37 UK Clinical Absent David et al. 2016 H101820190 37 UK Clinical Absent David et al. 2016 H102020414 37 UK Clinical Absent David et al. 2016 Unknown (travel- H101980130 37 associated) Clinical Absent David et al. 2016 H103820081 37 UK Clinical Absent David et al. 2016 H120240685 37 Slovenia Clinical Absent David et al. 2016 H104320293 37 UK Environmental Absent David et al. 2016 H113180118 37 UK Clinical Absent David et al. 2016 H113340664 37 UK Environmental Absent David et al. 2016 H113280076 37 UK Clinical Absent David et al. 2016 H113660550 37 UK Clinical Absent David et al. 2016 H114740454 37 UK Clinical Absent David et al. 2016 H115040456 37 UK Clinical Absent David et al. 2016 H111580389 37 UK Clinical Absent David et al. 2016 Unknown (travel- H113780240 37 associated) Clinical Absent David et al. 2016 H083920177 37 UK Clinical Absent David et al. 2016 H084140691 37 UK Environmental Absent David et al. 2016 H081180019 37 UK Environmental Absent David et al. 2016 H103260667 37 Greece Environmental Absent David et al. 2016 LC464 37 UK Clinical Absent David et al. 2016 Unknown (travel- LC0512 37 associated) Clinical Absent David et al. 2016 LC0565 37 UK Clinical Absent David et al. 2016 LC0583 37 UK Clinical Absent David et al. 2016 LC0782 37 UK Clinical Absent David et al. 2016 LC0794 37 UK Clinical Absent David et al. 2016 LC0795 37 UK Clinical Absent David et al. 2016 LC0798 37 UK Clinical Absent David et al. 2016 LC0801 37 UK Clinical Absent David et al. 2016 EUL 166/LP056 37 UK Environmental Absent David et al. 2016 EUL 69 37 UK Clinical Absent David et al. 2016 EUL 73 37 UK Clinical Absent David et al. 2016 EUL 78 37 UK Clinical Absent David et al. 2016 EUL 79 37 UK Clinical Absent David et al. 2016 EUL 132 37 UK Clinical Absent David et al. 2016 EUL 133 37 UK Clinical Absent David et al. 2016 EUL 134 37 UK Clinical Absent David et al. 2016 EUL 131 37 UK Clinical Absent David et al. 2016 HL 0131 3013 47 France Clinical Present David et al. 2016 H064160534 47 UK Environmental Present David et al. 2016 H043580159 47 UK Clinical Present David et al. 2016 H043580160 47 UK Clinical Present David et al. 2016 H043660021 47 UK Clinical Present David et al. 2016 H043680663 47 UK Clinical Present David et al. 2016 H043700021 47 UK Clinical Present David et al. 2016 H043790008 47 UK Clinical Present David et al. 2016 H052920051 47 UK Clinical Present David et al. 2016 H053540106 47 UK Clinical Present David et al. 2016 H063660005 47 UK Clinical Present David et al. 2016 H063660006 47 UK Clinical Present David et al. 2016 H063660009 47 UK Clinical Present David et al. 2016 H063680006 47 UK Clinical Present David et al. 2016 H063680007 47 UK Clinical Present David et al. 2016 H063740003 47 UK Clinical Present David et al. 2016 H063740018 47 UK Clinical Present David et al. 2016 H063760006 47 UK Clinical Present David et al. 2016 H063780007 47 UK Clinical Present David et al. 2016 H063780008 47 UK Clinical Present David et al. 2016 H063860003 47 UK Clinical Present David et al. 2016 H063960001 47 UK Clinical Present David et al. 2016 Unknown (travel- LC5759 47 associated) Clinical Present David et al. 2016 H070420013 47 UK Clinical Present David et al. 2016 LC5822 47 UK Clinical Present David et al. 2016 H040260015 47 UK Clinical Present David et al. 2016 H055140095 47 UK Clinical Present David et al. 2016 H060780053 47 UK Clinical Present David et al. 2016 H061120064 47 UK Clinical Present David et al. 2016 H062840608 47 UK Clinical Present David et al. 2016 H062940111 47 UK Clinical Present David et al. 2016 H064320006 47 UK Clinical Present David et al. 2016 H064280005 47 UK Clinical Present David et al. 2016 H064380002 47 UK Clinical Present David et al. 2016 H064380001 47 UK Clinical Present David et al. 2016 H064560527 47 UK Clinical Present David et al. 2016 H064660638 47 UK Clinical Present David et al. 2016 H070160015 47 UK Clinical Present David et al. 2016 H071120010 47 UK Clinical Present David et al. 2016 H071360036 47 UK Clinical Present David et al. 2016 H072740002 47 UK Clinical Present David et al. 2016 H073000045 47 UK Clinical Present David et al. 2016 H073380007 47 UK Clinical Present David et al. 2016 H073600182 47 UK Clinical Present David et al. 2016 H073640185 47 UK Clinical Present David et al. 2016 H074960018 47 UK Clinical Present David et al. 2016 H080780059 47 UK Clinical Present David et al. 2016 H053840008 47 UK Clinical Present David et al. 2016 H072520002 47 UK Clinical Present David et al. 2016 H081340222 47 UK Clinical Present David et al. 2016 H082520613 47 UK Clinical Present David et al. 2016 H083120262 47 UK Clinical Present David et al. 2016 H083620580 47 UK Clinical Present David et al. 2016 H083960064 47 UK Clinical Present David et al. 2016 H084620118 47 UK Clinical Present David et al. 2016 H090140214 47 UK Clinical Present David et al. 2016 H090440226 47 UK Clinical Present David et al. 2016 H040960441 47 UK Clinical Present David et al. 2016 H041120007 47 UK Clinical Present David et al. 2016 Unknown (travel- H093480403 47 associated) Clinical Present David et al. 2016 H094340202 47 UK Clinical Present David et al. 2016 H095060125 47 UK Clinical Present David et al. 2016 H100140151 47 UK Clinical Present David et al. 2016 H100660110 47 UK Clinical Present David et al. 2016 H100700025 47 UK Clinical Present David et al. 2016 H103140121 47 UK Clinical Present David et al. 2016 H103620160 47 UK Clinical Present David et al. 2016 H103660126 47 UK Clinical Present David et al. 2016 H103660121 47 UK Clinical Present David et al. 2016 H104420240 47 UK Clinical Present David et al. 2016 H110480273 47 UK Clinical Present David et al. 2016 H112320437 47 UK Clinical Present David et al. 2016 H112080616 47 UK Clinical Present David et al. 2016 H112380374 47 UK Clinical Present David et al. 2016 H120160499 47 UK Clinical Present David et al. 2016 H120200371 47 UK Clinical Present David et al. 2016 H105140391 47 UK Clinical Present David et al. 2016 H121040204 47 UK Clinical Present David et al. 2016 H121420445 47 UK Clinical Present David et al. 2016 H102240357 47 UK Clinical Present David et al. 2016 H122500497 47 UK Clinical Present David et al. 2016 Unknown (travel- H122820408 47 associated) Clinical Present David et al. 2016 H123620597 47 UK Clinical Present David et al. 2016 H123840629 47 UK Clinical Present David et al. 2016 H123940534 47 UK Clinical Present David et al. 2016 H124920387 47 UK Clinical Present David et al. 2016 H131340777 47 UK Clinical Present David et al. 2016 H131460248 47 UK Clinical Present David et al. 2016 H131480353 47 UK Environmental Present David et al. 2016 H131480354 47 UK Environmental Present David et al. 2016 H131840211 47 UK Environmental Present David et al. 2016 H132140863 47 UK Clinical Present David et al. 2016 EUL 31 47 France Clinical Present David et al. 2016 EUL 70 47 UK Clinical Present David et al. 2016 EUL 168 47 UK Clinical Present David et al. 2016 EUL 170 47 UK Environmental Present David et al. 2016 LG 1208 4002 47 France Clinical Present David et al. 2016 LG 1203 4018 47 France Clinical Present David et al. 2016 LG 1146 3009 47 France Clinical Present David et al. 2016 LG 1141 5002 47 France Clinical Present David et al. 2016 LG 1140 3003 47 France Clinical Present David et al. 2016 LG 1042 5016 47 France Clinical Present David et al. 2016 LG 1039 7001 47 France Clinical Present David et al. 2016 LG 0953 4017 47 France Clinical Present David et al. 2016 LG 0947 1012 47 France Clinical Present David et al. 2016 LG 0839 4013 47 France Clinical Present David et al. 2016 LG 0825 1002 47 France Clinical Present David et al. 2016 HL 0751 2016 47 France Clinical Present David et al. 2016 HL 0705 5011 47 France Clinical Present David et al. 2016 HL 0635 3025 47 France Clinical Present David et al. 2016 HL 0538 3032 47 France Clinical Present David et al. 2016 HL 0537 5017 47 France Clinical Present David et al. 2016 HL 0441 1050 47 France Environmental Present David et al. 2016 HL 0428 4070 47 France Clinical Present David et al. 2016 HL 0407 5055 47 France Clinical Present David et al. 2016 HL 0350 3011 47 France Clinical Present David et al. 2016 HL 0344 3027 47 France Clinical Present David et al. 2016 HL 0239 2002 47 France Clinical Present David et al. 2016 HL 0227 4033 47 France Clinical Present David et al. 2016 Unknown (travel- H043540106 62 associated) Clinical Absent David et al. 2016 H044120014 62 Bulgaria Clinical Absent David et al. 2016 H052780022 62 UK Clinical Absent David et al. 2016 H054280040 62 UK Clinical Absent David et al. 2016 H063680003 62 UK Clinical Absent David et al. 2016 H063840008 62 UK Clinical Absent David et al. 2016 H073660582 62 UK Clinical Absent David et al. 2016 LC5804 62 UK Clinical Absent David et al. 2016 H063760005 62 UK Clinical Absent David et al. 2016 H064240003 62 UK Clinical Absent David et al. 2016 H065040012 62 UK Clinical Absent David et al. 2016 H070140635 62 UK Clinical Absent David et al. 2016 H073020039 62 UK Clinical Absent David et al. 2016 H073320399 62 UK Clinical Absent David et al. 2016 H073440003 62 UK Clinical Absent David et al. 2016 Unknown (travel- LC6009 62 associated) Clinical Absent David et al. 2016 H083140015 62 UK Clinical Absent David et al. 2016 H064180019 62 UK Environmental Absent David et al. 2016 H093400182 62 UK Clinical Absent David et al. 2016 H094760070 62 UK Clinical Absent David et al. 2016 H094800237 62 UK Clinical Absent David et al. 2016 H110480715 62 UK Clinical Absent David et al. 2016 H112840293 62 UK Clinical Absent David et al. 2016 H114100406 62 Greece Clinical Absent David et al. 2016 H120240362 62 UK Clinical Absent David et al. 2016 Unknown (travel- H104640262 62 associated) Clinical Absent David et al. 2016 H123140428 62 UK Environmental Absent David et al. 2016 H123460520 62 UK Clinical Absent David et al. 2016 H124360642 62 UK Clinical Absent David et al. 2016 EUL 54 62 Spain Clinical Absent David et al. 2016 EUL 57 62 Spain Environmental Absent David et al. 2016 EUL 71 62 UK Clinical Absent David et al. 2016 EUL 76 62 UK Clinical Absent David et al. 2016 EUL 77 62 UK Clinical Absent David et al. 2016 EUL 7 18 Switzerland Clinical Absent David et al. 2016 LG 1248 2019 146 France Clinical Absent David et al. 2016 EUL 2 2 Switzerland Clinical Absent David et al. 2016 EUL 6 42 Switzerland Clinical Absent David et al. 2016 EUL 18 26 Scotland Clinical Absent David et al. 2016 EUL 19 9 Scotland Clinical Absent David et al. 2016 EUL 20 28 Scotland Clinical Absent David et al. 2016 EUL 25 44 France Clinical Absent David et al. 2016 EUL 26 22 France Clinical Absent David et al. 2016 EUL 27 42 France Clinical Absent David et al. 2016 EUL 29 20 France Clinical Absent David et al. 2016 EUL 30 38 France Clinical Absent David et al. 2016 EUL 32 16 France Clinical Absent David et al. 2016 EUL 33 40 France Clinical Absent David et al. 2016 EUL 36 21 Italy Clinical Absent David et al. 2016 EUL 38 1 Italy Clinical Absent David et al. 2016 EUL 39 42 Italy Clinical Absent David et al. 2016 EUL 40 12 Italy Clinical Absent David et al. 2016 EUL 48 48 Spain Clinical Absent David et al. 2016 EUL 49 20 Spain Clinical Absent David et al. 2016 EUL 50 42 Spain Clinical Absent David et al. 2016 EUL 51 1156 Spain Clinical Absent David et al. 2016 EUL 52 107 Spain Clinical Absent David et al. 2016 EUL 63 77 Greece Clinical Absent David et al. 2016 EUL 66 77 Greece Clinical Absent David et al. 2016 EUL 68 46 UK Clinical Absent David et al. 2016 EUL 72 4 UK Clinical Absent David et al. 2016 EUL 74 29 UK Clinical Absent David et al. 2016 EUL 75 42 UK Clinical Absent David et al. 2016 EUL 81 53 Denmark Environmental Absent David et al. 2016 EUL 83 50 Denmark Clinical Absent David et al. 2016 EUL 86 46 Denmark Clinical Absent David et al. 2016 EUL 87 2122 Denmark Clinical Absent David et al. 2016 EUL 91 63 Denmark Clinical Absent David et al. 2016 EUL 92 53 Denmark Clinical Absent David et al. 2016 EUL 97 9 Sweden Clinical Absent David et al. 2016 EUL 98 9 Sweden Clinical Absent David et al. 2016 EUL 99 34 Sweden Clinical Absent David et al. 2016 EUL 100 59 Sweden Clinical Absent David et al. 2016 EUL 101 60 Sweden Clinical Absent David et al. 2016 EUL 102 59 Sweden Clinical Absent David et al. 2016 EUL 103 45 Sweden Clinical Absent David et al. 2016 EUL 105 42 Sweden Clinical Absent David et al. 2016 EUL 111 25 Germany Clinical Absent David et al. 2016 EUL 116 42 Germany Clinical Absent David et al. 2016 EUL 118 36 Germany Clinical Absent David et al. 2016 EUL 120 42 Germany Clinical Absent David et al. 2016 EUL 22 9 Scotland Clinical Absent David et al. 2016 EUL 23 9 Scotland Clinical Absent David et al. 2016 EUL 24 9 Scotland Environmental Absent David et al. 2016 EUL 34 40 France Environmental Absent David et al. 2016 EUL 35 40 France Environmental Absent David et al. 2016 EUL 47 12 Italy Environmental Absent David et al. 2016 EUL 56 48 Spain Clinical Absent David et al. 2016 EUL 59 1156 Spain Environmental Absent David et al. 2016 EUL 96 53 Denmark Clinical Absent David et al. 2016 EUL 106 9 Sweden Clinical Absent David et al. 2016 EUL 107 9 Sweden Environmental Absent David et al. 2016 EUL 121 42 Germany Clinical Absent David et al. 2016 LC 202/EUL 153 68 UK Clinical Absent David et al. 2016 LC 206/EUL 158 68 UK Environmental Absent David et al. 2016 LC 569/EUL 154 1326 UK Clinical Absent David et al. 2016 LC 606/EUL 155 1326 UK Environmental Absent David et al. 2016 LC 384/EUL 156 1362 Belgium Clinical Absent David et al. 2016 LC 395/EUL 159 1362 Belgium Environmental Absent David et al. 2016 LC6379-1/EUL 145 78 UK Environmental Absent David et al. 2016 LC6376 78 UK Environmental Absent David et al. 2016 LC6382 78 UK Environmental Absent David et al. 2016 LC6391 78 UK Environmental Absent David et al. 2016 LC6394 78 UK Environmental Absent David et al. 2016 LC6397 78 UK Clinical Absent David et al. 2016 LC6406 78 UK Clinical Absent David et al. 2016 LC6407 78 UK Clinical Absent David et al. 2016 LC6408 78 UK Clinical Absent David et al. 2016 LC6411 78 UK Clinical Absent David et al. 2016 LC6412 78 UK Clinical Absent David et al. 2016 LC6413 78 UK Clinical Absent David et al. 2016 LC6416 78 UK Clinical Absent David et al. 2016 LC6418 78 UK Clinical Absent David et al. 2016 LC6385 78 UK Environmental Absent David et al. 2016 LC6388 78 UK Environmental Absent David et al. 2016 LC6409 78 UK Clinical Absent David et al. 2016 LC6410 78 UK Clinical Absent David et al. 2016 LC230/EUL 122 42 Unknown Clinical Absent David et al. 2016 LC231/EUL 123 42 Unknown Clinical Absent David et al. 2016 LC0462/EUL 124 42 UK Clinical Absent David et al. 2016 LC0463/EUL 125 42 UK Clinical Absent David et al. 2016 Pontiac-1 62 USA Environmental Absent David et al. 2016 EUL 5 114 Switzerland Clinical Absent David et al. 2016 EUL 61 77 Greece Environmental Absent David et al. 2016 EUL 64 77 Greece Environmental Absent David et al. 2016 EUL 115 1362 Germany Clinical Absent David et al. 2016 EUL 140 14 Spain Clinical Absent David et al. 2016 EUL 141 14 Spain Clinical Absent David et al. 2016 EUL 142 14 Spain Environmental Absent David et al. 2016 EUL 143 14 Spain Environmental Absent David et al. 2016 EUL 148 1321 Australia Environmental Absent David et al. 2016 EUL 149 83 UK Clinical Absent David et al. 2016 EUL 150 79 UK Clinical Absent David et al. 2016 EUL 161 75 UK Clinical Absent David et al. 2016 EUL 162 85 UK Clinical Absent David et al. 2016 EUL 163 73 Austria Clinical Absent David et al. 2016 EUL 167/H053540099 82 UK Environmental Absent David et al. 2016 63 strains newly sequenced for this study and used to validate the PCR target CG1_A5_Toronto 47 Canada Clinical Present ERR1470944 CG3_C5_Oshawa 47 Canada Clinical Present ERR1470920 CG3_D5_Hamilton 47 Canada Clinical Present ERR1470919 L13-510 (RR14000643) 47 Germany Clinical Present ERR1470965 L12-679 (RR14000644) 47 Germany Clinical Present ERR1470954 L11-078 (RR14000645) 47 Germany Clinical Present ERR1470953 L10-531 (RR14000646) 47 Germany Clinical Present ERR1470932 H092380261 109 UK Clinical Absent ERR1470913 H092400768 109 UK Environmental Absent ERR1470928 Unknown (travel- LC4339 (2,10,14,28,2,2 0) associated) Clinical Absent ERR1470906 797-PA-H (ATCC43130) (12,17,11,10,5,12,0) USA Clinical Absent ERR1470971 1169-MN-H (ATCC43703) 1324 USA Clinical Absent ERR1470977 H090520323 616 United Arab Emirates Clinical Absent ERR1470900 H095120351 616 United Arab Emirates Clinical Absent ERR1470905 H105120234 616 United Arab Emirates Clinical Absent ERR1470950 H133820072 616 United Arab Emirates Clinical Absent ERR1470959 H141440701 616 United Arab Emirates Clinical Absent ERR1470936 H152720257 616 United Arab Emirates Clinical Absent ERR1470937 H142560153 1554 UK Clinical Absent ERR1470925 H133380070 1554 UK Clinical Absent ERR1470923 H133660138 1554 UK Clinical Absent ERR1470909 H134700259 1554 UK Clinical Absent ERR1470970 H134840204 1554 UK Clinical Absent ERR1470939 H140720439 1554 UK Clinical Absent ERR1470947 H141260453 1554 UK Clinical Absent ERR1470973 H150980398 1554 UK Clinical Absent ERR1470962 H114960442 1327 United Arab Emirates Clinical Absent ERR1470903 H142840244 1327 United Arab Emirates Clinical Absent ERR1470940 Unknown (travel- H150960426 1327 associated) Clinical Absent ERR1470924 Unknown (travel- H152520393 701 associated) Clinical Absent ERR1470914 Unknown (travel- H150680447 487 associated) Clinical Absent ERR1470958 H073160025 1327 Cruise ship Environmental Absent ERR1470943 H073260013 93 Cruise ship Environmental Absent ERR1470955 H073280009 151 Cruise ship Environmental Absent ERR1470951 Novel (28, 21, 33, 19, 41, 1, H073280010 215) Cruise ship Environmental Absent ERR1470976 H073300077 1 Cruise ship Environmental Absent ERR1399519 H073300078 1327 Cruise ship Environmental Absent ERR1470895 H073300079 1 Cruise ship Environmental Absent ERR1399496 Novel ST H073300080 (19,25,25,32,37,28,225) Cruise ship Environmental Absent ERR1470918 Novel ST H073300081 (19,25,25,32,37,28,225) Cruise ship Environmental Absent ERR1470957 H073360657 1 Cruise ship Environmental Absent ERR1399557 H073420011 1327 Cruise ship Environmental Absent ERR1470911 H073420013 93 Cruise ship Environmental Absent ERR1470969 H073420020 93 Cruise ship Environmental Absent ERR1470916 H073420023 1328 Cruise ship Environmental Absent ERR1470901 H073420024 2037 Cruise ship Environmental Absent ERR1470930 H073580013 1327 Cruise ship Environmental Absent ERR1470946 H102700691 341 UK Environmental Absent ERR1470967 H105100860 950 UK Clinical Absent ERR1470927 H105281046 950 UK Clinical Absent ERR1470956 H110280386 1 UK Environmental Absent ERR1470978 H110920414 1261 UK Environmental Absent ERR1470961 RR14000599 Novel ST (6, 9, 2, 5, 3, 17, 213) UK Environmental Absent ERR1470922 RR14000600 710 UK Environmental Absent ERR1470941 Novel ST (2, 10, 5, 13, 33, 14, RR14000601 207) UK Environmental Absent ERR1470972 RR14000603 Novel ST (6, 9, 2, 5, 3, 17, 213) UK Environmental Absent ERR1470896 RR14000604 Novel ST (6, 9, 2, 5, 3, 17, 213) UK Environmental Absent ERR1470974 RR14000605 Novel ST (6, 9, 2, 5, 3, 17, 213) UK Environmental Absent ERR1470912 RR08000296 345 UK Environmental Absent ERR1470966 A32/81 51 UK Environmental Absent ERR1470902 A100/81 59 Australia Environmental Absent ERR1470917 A167/80 (LD8/79) 42 Sweden Clinical Absent ERR1470926 LC32 1 France Clinical Absent ERR1470931 Additional 23 strains newly sequenced for this study and used to investigate the evolutionary relationship of ST47 with closely-related STs H093480402 74 UK Clinical Absent ERR1470945 H101480488 74 UK Clinical Absent ERR1470904 H120140563 74 UK Clinical Absent ERR1470933 H130700140 74 UK Clinical Absent ERR1470907 H144480100 74 UK Clinical Absent ERR1470899 H083480003 82 UK Clinical Absent ERR1470929 H143160254 82 UK Clinical Absent ERR1470949 H143520156 82 UK Clinical Absent ERR1470942 LG 1230 2004 (RR14000702) 109 France Clinical Present ERR1470908 LG 1101 4027 (RR14000703) 109 France Clinical Present ERR1470964 LG 1105 1006 (RR14000704) 109 France Clinical Present ERR1470938 LG 1106 4019 (RR14000705) 109 France Clinical Present ERR1470948 LG 1135 3014 (RR14000706) 109 France Clinical Present ERR1470935 LG 0927 5012 (RR14000707) 109 France Clinical Present ERR1470910 LG 0928 1008 (RR14000708) 109 France Clinical Present ERR1470975 LG 0933 1003 (RR14000709) 109 France Clinical Present ERR1470952 LG 1334 4008 (RR14000710) 109 France Clinical Present ERR1470968 H053040071 109 UK Clinical Absent ERR1470897 H073660663 109 UK Clinical Absent ERR1470915 H083920183 109 UK Clinical Absent ERR1470921 H084060004 109 UK Clinical Absent ERR1470898 H093380154 109 UK Clinical Absent ERR1470963 H100640680 109 UK Clinical Absent ERR1470960 Supplementary Table S3. 21 gene targets evaluated by endpoint PCR </p><p> gene targets Position in Lorraine genome Putative function LPO_0158 173283-174235 replicative DNA helicase LPO_0162 176247-177227 hypothetical protein LPO_0164 177699 - 180173 site-specific DNA-methyltransferase LPO_0165 180182 - 182971 type III restriction enzyme, res subunit LPO_0166 182982 - 184757 hypothetical protein LPO_0280 299833 - 301458 hypothetical protein LPO_0873 898939 - 900165 hypothetical protein LPO_1073 1111323 - 1112222 hypothetical protein LPO_1074 1112315 - 1112821 Unknown function LPO_1139 1174046 - 1176274 hypothetical protein LPO_1380 1418082 - 1419137 flavanone 3-dioxygenase LPO_1575 1612153 - 1614657 hypothetical protein LPO_1576 1614746 - 1615792 hypothetical protein LPO_1577 1615779 - 1617698 hypothetical protein LPO_1578 1617691 - 1618011 hypothetical protein LPO_2473 2597692 - 2598879 hypothetical protein LPO_2485 2607550 - 2608200 hypothetical protein LPO_2487 2610438 - 2610818 hypothetical protein LPO_2516 2629516 - 2630526 fatty acid desaturase LPO_2519 2633413 - 2634288 hypothetical protein LPO_2854 2973368 - 2974312 transposase Table S4. Result comparison of 106 respiratory samples analysed by SBT or nSBT and LPO_1073 PCR </p><p>Other STs SBT or nSBT No SBT ST47 result Full SBT Partial SBT alleles profile profile (1-6 loci) LPO_107 Positive 22 0 0 4 3 Negative 0 54 17 9</p>