Table 1.

Overview of the 59 whole genome sequenced Fth strains from Switzerland used in this study.

Sample ID	Alternative ID	Source, year	Clade	Sequencing institute/Sample provider	Length of assembly	Contigs	N50	Accession number
FT 29	JF5340a	Human, 2012	B.33	SL/IVB	1798068	102	26695	SAMN08108654	PKBF00000000
FT 31	JF5370a	Human, 2012	B.33	SL/IVB, ADMED	1794649	100	27062	SAMN08108656	PKBD00000000
FT 65	JF5405a	Hare, 2012	B.33	SL/IVB	1802560	102	27621	SAMN08108682	PKAE00000000
FT 66	JF5468a	Hare, 2013	B.33	SL/IVB	1823931	98	27394	SAMN08108683	PKAD00000000
FT 70	JF5609	Monkey, 2014	B.33	SL/IVB	1823454	96	27316	SAMN08108687	PJZZ00000000
FT 22	JF4456a	Human, 2008	B.45	SL/IVB	1801181	95	27456	SAMN08108648	PKBL00000000
FT 32b		Human, 2012	B.45	SL/IVB	1812310	95	27658	SAMN03774932	PKAX00000000
FT 41	FT6_D12	Tick, 2012	B.45	SL	1782791	96	26944	SAMN08108662	PKAK00000000
FT 56	JF5353a	Marten, 2012	B.45	SL/IVB	1818006	97	27313	SAMN08108675	PKAC00000000
FT 67	JF5487	Hare, 2013	B.45	SL/IVB	1822695	96	27391	SAMN08108684	PJZY00000000
FT 71	JF5611	Hare, 2014	B.45	SL/IVB	1812653	98	27006	SAMN08108688	PKBP00000000
FT 14	JF3829	Lion Tamarin, 2004	B.46	SL/IVB	1801041	95	27712	SAMN08108642	PKBR00000000
FT 17	JF4128/FDC304b	Human, 2008	B.46	SL/IVB	1778390	101	24282	SAMN08108644	PKBH00000000
FT 27	JF5141	Human, 2011	B.46	SL/IVB	1807038	109	26708	SAMN08108652	PKBG00000000
FT 28	JF5338	Human, 2012	B.46	SL/IVB	1788115	102	26847	SAMN08108653	PKBT00000000
FT 11	JF3821	Hare, 1997	B.49	SL/IVB	1801451	95	27456	SAMN08108640	PKBQ00000000
FT 16	JF4092	Hare	B.49	SL/IVB	1801566	95	27456	SAMN08108643	PKAQ00000000
FT 50		Human 2014	B.49	SL	1823626	96	27535	SAMN08108669	PKBO00000000
FT 18	JF4212/FDC305b	Human, 2008	B.53	SL/IVB	1801159	95	27712	SAMN03773856	PKBB00000000
FT 36		Human, 2014	B.53	SL	1817604	96	27313	SAMN08108658	PKAS00000000
FT 48		Human, 2014	B.53	SL	1817319	96	27313	SAMN08108667	PKAJ00000000
FT 57	JF5369a	Hare, 2012	B.53	SL/IVB	1809350	97	27005	SAMN08108676	PKAW00000000
FT 38	FT9C_G7b	Tick, 2012	B.59	SL	1811355	96	27676	SAMN03774936	PKAU00000000
FT 42	FT11_B4	Tick, 2012	B.59	SL	1783150	96	26974	SAMN08108663	PKBI00000000
FT 45	FT8_F4	Tick, 2012	B.59	SL	1814235	96	27658	SAMN03774935	PKAO00000000
FT 46	FT8_B3	Tick, 2012	B.59	SL	1780077	95	26974	SAMN08108665	PKAN00000000
FT 26	JF5142	Human, 2011	B.61	SL/IVB	1800278	102	27104	SAMN08108651	PKAM00000000
FT 52	FT21_C4	Tick, 2013	B.61	SL	1801053	95	27456	SAMN08108671	PKAH00000000
FT 53	FT22_F9	Tick, 2013	B.61	SL	1801183	95	27456	SAMN08108672	PKBA00000000
FT 54	FT22_H4	Tick, 2013	B.61	SL	1801200	95	27456	SAMN08108673	PKAZ00000000
FT 59	JF5375a	Hare, 2012	B.61	SL/IVB	1819651	97	27313	SAMN08108678	PKAY00000000
FT 37	FT14_F1	Tick, 2012	B.62	SL	1779923	96	26888	SAMN08108659	PKAV00000000
FT 39	FT14_C4	Tick, 2012	B.62	SL	1780016	96	26888	SAMN08108660	PKAT00000000
FT 40	FT17_C9	Tick, 2012	B.62	SL	1782242	96	26888	SAMN08108661	PJZW00000000
FT 43	FT16_B1b	Tick, 2012	B.62	SL	1805387	95	27658	SAMN03774942	PKBU00000000
FT 44	FT16_E6	Tick, 2012	B.62	SL	1795991	96	27077	SAMN08108664	PKBV00000000
FT 47	FT16_G8b	Tick, 2012	B.62	SL	1781679	96	26888	SAMN08108666	PKBS00000000
FT 75		Human, 2015	B.62	SL	1797368	95	27019	SAMN08108690	PKBM00000000
FT 08		Human, 2003	B.85	SL/IVB	1775380	133	21731	SAMN08108638	PKAG00000000
FT 10	JF3820a	Hare, 1998	B.85	SL/IVB	1772027	102	23187	SAMN08108639	PKAB00000000
FT 13	JF3826a	Marmoset, 1996	B.85	SL/IVB	1801174	95	27456	SAMN08108641	PKBK00000000
FT 20	JF4429/FDC310b	Human, 2008	B.85	SL/IVB	1814653	96	27257	SAMN03773858	PKAP00000000
FT 60	JF5380a	Hare, 2012	B.85	SL/IVB	1801233	95	27456	SAMN08108679	PKAL00000000
FT 68	JF5525	Hare, 2014	B.85	SL/IVB	1818684	96	27313	SAMN08108685	PKBY00000000
FT 24	JF5002	Human, 2011	B.87	SL/IVB	1786520	97	26974	SAMN08108649	PKBW00000000
FT 51		Human, 2014	B.87	SL	1820050	96	27535	SAMN08108670	PKBJ00000000
FT 55	JF5345	Mouse, 2012	B.87	SL/IVB	1825678	100	27313	SAMN08108674	PKBE00000000
FT 64	JF5410a	Mouse, 2012	B.87	SL/IVB	1819162	96	27313	SAMN08108681	PJZX00000000
FT 07		Human, 2008	B.88	SL	1782483	96	26925	SAMN08108637	PKBN00000000
FT 25	JF5048	Human, 2011	B.88	SL/IVB	1797415	97	27104	SAMN08108650	PKBC00000000
FT 30	JF53461	Human, 2012	B.88	SL/IVB	1783341	96	27105	SAMN08108655	PKBX00000000
FT 19	JF4242/FDC306b	Hare	B.89	SL/IVB	1801171	95	27712	SAMN03773857	PKAI00000000
FT 33		Human, 2013	B.89	SL	1820901	96	27535	SAMN08108657	PKAF00000000
FT 73		Human, 2015	B.89	SL	1797389	95	27712	SAMN08108689	PKAR00000000
FT 05		Human, 2008	B.90	SL/IVB	1797365	95	27456	SAMN08108636	PKAA00000000
FT 58	JF5374a	Hare, 2014	B.90	SL/IVB	1819228	96	27313	SAMN08108677	MQVE00000000
FT 63	JF5393a	Hare, 2012	B.90	SL/IVB	1824976	96	27435	SAMN08108680	MQVC00000000
FT 49		Human, 2014	B.91	SL	1822738	96	27535	SAMN08108668	MQVF00000000
FT 69	JF5597	Hare, 2014	B.91	SL/IVB	1818326	96	27313	SAMN08108686	MQVD00000000

SL, Spiez laboratory, Spiez, Switzerland; IVB, Institute of Veterinary Bacteriology, Bern, Switzerland; ADMED, Analyses et Diagnostics Medicaux, La Chaux de Fonds, Switzerland.

^aOriggi et al. (2014).

^bDwibedi et al. (2016).