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Table 3 Details of Legionella pneumophila strains used in the study

From: Comparison of the Legionella pneumophilapopulation structure as determined by sequence-based typing and whole genome sequencing

ST sequenced BAPS cluster Represen-tative ST Strain Reason for selection Strain significance Sequence source/technology Mean Illumina read coverage ENA accession number or reference
46 1 45 H093620212 closest to centroid fairly common clinical strain - assumed to be virulent NGS mate paired Illumina 169 ERR315646
74* 1 45 H053260229 second of cluster fairly common clinical strain - assumed to be virulent NGS 454   ERR315647
15* 2 15 Lens already published caused a big outbreak in France GenBank (NC_006369.1)   [31]
84 2 15 H043940028 closest available to centroid only one available from this cluster NGS paired end Illumina 283 ERR315648
47 3 16 H063920004 internationally significant in top six strains that cause disease NGS 454, paired end Illumina and mate paired Illumina paired end 211 mate paired 227 ERR315649
47 3 16 Lorraine already published in top six strains that cause disease GenBank(NC_018139.1)   [23]
47 3 16 LP_617 already published in top six strains that cause disease EMBLBank(ERS166047)   [32]
54* 3 16 H065000139 closest to centroid uncommon strain nothing known NGS paired end Illumina 161 ERR315650
62 3 16 H064180002 internationally significant in top six strains that cause disease NGS 454   ERR315651
611 4 124 H090500162 only one in cluster unique environmental isolate NGS mate paired Illumina 276 ERR315652
87 5 17 LC6677 second of cluster common serogroup 3 strain - does cause disease NGS paired end Illumina 490 ERR315653
376 5 17 RR08000760 closest to centroid unique environmental isolate NGS mate paired Illumina 235 ERR315654
1* 6 1 Paris already published   GenBank (NC_006368.1)   [31]
1 6 1 LP_423 already published   EMBLBank(ERS166048)   [32]
5 6 1 EUL00013 (83/41091) on an interesting branch of ST001 only three in database - all from small outbreak in Glasgow NGS mate paired Illumina 304 ERR315655
152 6 1 H074360702 closest to centroid uncommon - mainly environmental NGS mate paired Illumina 180 ERR315656
179 7 130 H093380153 closest to centroid uncommon but causes disease NGS paired end Illumina 32 ERR315657
337 7 130 RR08000517 second of cluster uncommon strain appears to be phenotypically variable NGS mate paired Illumina 161 ERR315658
42 8 14 130b (Wadsworth) already published in top six strains that cause disease - globally distributed. Isolated in USA in ~1980 GenBank (FR687201.1)   [33]
42 8 14 H044540088 internationally significant as above but isolated in UK in 2004 - assumed to be virulent NGS 454   ERR315659
44 8 14 H100260089 closest to centroid similar to ST42 but not so common NGS paired end Illumina 346 ERR315660
154* 9 12 LC677 4 closest to centroid seen in Canada and UK as a cause of nosocomial LD NGS mate paired Illumina 84 ERR315661
336* 9 12 Lansing-3 (sgp15TS) second of cluster Representative of L. pneumophila subsp fraseri NGS paired end Illumina 150 ERR315662
23 10 19 H063280001 closest to centroid in top six strains that cause disease NGS paired end Illumina 265 ERR315663
78* 10 19 LC6451 second of cluster unique strain - caused a major outbreak in Barrow in 2002. NGS 454   ERR315664
51 11 2 Corby already published/closest to centroid uncommon but well characterised - virulent in animal model and protozoa GenBank (NC_009494.2)   [34]
454 11 2 H091960011 second of cluster unique environmental strain (from Roman baths in Bath) NGS mate paired Illumina 268 ERR315665
578 11 2 Alcoy already published responsible for a very big outbreak in Spain GenBank (NC_014125.1)   [35]
59 12 25 H070840415 closest to centroid quite common environmental strain - a few cases of LD. NGS mate paired Illumina 246 ERR315666
188 12 25 H075160080 second of cluster no particular data NGS paired end Illumina 298 ERR315667
36 13 9 Philadelphia already published/closest to centroid the type strain - well characterised caused the Philadelphia outbreak. GenBank (NC_002942.5)   [36]
37 13 9 H034680035 internationally significant in top six strains that cause disease NGS 454   ERR315668
186 13 9 H044500045 second of cluster unique clinical isolate NGS paired end Illumina 375 ERR315669
34 14 34 RR08000134 closest available to centroid no particular significance NGS paired end Illumina 301 ERR315670
68 14 34 H074360710 second of cluster no particular significance NGS mate paired Illumina 179 ERR315671
707* 15 71 H091960009 only one in cluster unique environmental strain (from Roman baths in Bath) NGS paired end Illumina and mate paired Illumina Paired end 136 Mate paired 50 ERR315672
  1. Asterisks designate strains that are likely to have plasmids based on the analysis described in the methods section of this manuscript. The sequence data described can be obtained using the European Nucleotide Archive accession number listed in the table.