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

Underwood, Anthony P; Jones, Garan; Mentasti, Massimo; Fry, Norman K; Harrison, Timothy G

doi:10.1186/1471-2180-13-302

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

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.

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ISSN: 1471-2180

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