Core genome sequencing and genotyping of Leptospira interrogans in clinical samples by target capture sequencing

Grillova, Linda; Cokelaer, Thomas; Mariet, Jean-François; da Fonseca, Juliana Pipoli; Picardeau, Mathieu

doi:10.1186/s12879-023-08126-x

Table 1 Samples used in this study and identification of the infecting Leptospira strain

From: Core genome sequencing and genotyping of Leptospira interrogans in clinical samples by target capture sequencing

ID	Source	Patient	Sex	Age	Ct value^a	Days^b	Nreads^c	Bacteria (%)^d	Species^e	Serogroup^e	Serovar^e	Strain^e	Reference genome (id)^f	Number of SNPs
1	Blood	A	M	60	31	Unknown	11,223,500	30	L. interrogans	Icterohaemorrhagiae	Copenhageni	L1-130	246	4
2	Urine	B	M	61	30	6	9,523,661	72	L. interrogans	Icterohaemorrhagiae	Copenhageni	L1-130	246	4
3	Blood	C	M	41	33	Unknown	11,662,248	20	L. interrogans	Icterohaemorrhagiae	Copenhageni	L1-130	246	2
4	Blood	D	M	42	20	2	19,405,989	99	L. interrogans	Icterohaemorrhagiae	Copenhageni	L1-130	246	3
5	Blood	E	M	49	34	2	2,817,867	21	L. interrogans	Pyrogenes	Zanoni	LT2156	228	1272
6	Serum	F	M	40	34	4	6,936,356	13	L. kirschneri	Grippotyphosa	Grippotyphosa	201402975	117	6
7	Blood	G	M	54	27	4	13,037,685	90	L. kirschneri	Grippotyphosa	Grippotyphosa	201402975	117	15
8	Blood	H	M	20	32	Unknown	8,739,223	65	L. interrogans	Icterohaemorrhagiae	Copenhageni	L1-130	246	4
9	Blood	I	M	69	29	3	12,665,561	65	L. interrogans	Icterohaemorrhagiae	Copenhageni	L1-130	246	6
10	Blood	J	M	74	28	0	12,989,647	94	L. interrogans	Icterohaemorrhagiae	Copenhageni	L1-130	246	3
11	Blood	K	M	36	32	4	9,589,816	90	L. interrogans	Icterohaemorrhagiae	Copenhageni	L1-130	246	5
12	Urine	L	M	24	31	Unknown	10,827,346	65	L. interrogans	Icterohaemorrhagiae	Copenhageni	L1-130	246	4
13	Urine	M	M	73	31	5	11,947,042	90	L. interrogans	Icterohaemorrhagiae	Copenhageni	L1-130	246	7
14	Urine	N	M	39	35	8	29,832,813	33	L. interrogans	Icterohaemorrhagiae	Copenhageni	L1-130	246	3
15	Urine	O	M	59	34	Unknown	12,556,161	29	L. interrogans	Icterohaemorrhagiae	Copenhageni	L1-130	246	4
16	Blood	P	M	52	37	3	10,420,132	62	L. interrogans	Icterohaemorrhagiae	Copenhageni	L1-130	246	6
17	Blood	Q	M	44	25	5	1,350,830	98	L. interrogans	Icterohaemorrhagiae	Copenhageni	L1-130	246	4
18	Blood	R	M	22	38	4	1,0980,69	13	L. kirschneri	NA	NA	NA	NA	NA
19	Urine	S	M	33	35	5	1,124,989	35	L. interrogans	Icterohaemorrhagiae	Icterohaemorrhagiae	Verdun	106	0
20	Urine	T	M	28	32	4	1,776,330	64	L. interrogans	Icterohaemorrhagiae	Copenhageni	L1-130	246	2

NA non applicable
^aCt value (real-time PCR Lfb1)
^bDays of sample collection since symptom onset
^cNumber of illumina reads
^dProportion of reads from bacteria (%), other reads correspond to human reads
^eIdentification of the infecting strain based on the closest homologue of reference genomes
^fIdentification number (id) of the reference genome in BIGSdb (www.bigsdb.pasteur.fr)

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ISSN: 1471-2334

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