Table 1

Movement of MDR strains around the globe

MDR-defining node	Lineage	Spoligotype	Bootstrap value	Total # MDR strains	# Strains per country (# XDR)		# Strains per UN region		# Strains per dataset		min SNP dist. bt. countries
(A) Movement of MDR strains between UN geographic regions. This table lists MDR clades with >1 UN geographic region represented.
1	LIN-4	T2	1.00	3	Uganda	2	E. Africa	2	Clark et al, 2013	2	Uganda-Sweden 4
1					Sweden	1	N. Europe	1	TB-ARC Sweden	1
2	LIN-1	EAI1-SOM	1.00	3	South Africa	2	S. Africa	2	Cohen et al, 2015	2	South Africa-Sweden 5
2					Sweden	1	N. Europe	1	TB-ARC Sweden	1
3	LIN-2	Beijing	0.99	8	Russia	1	E. Europe	1	Casali et al, 2014	1	Russia-Uzbekistan 11
3					Uzbekistan	7	Central Asia	7	Merket et al., 2015	7
4	LIN-2	Beijing	0.88	5	Russia	2	E. Europe	3	TB-ARC Moldova	1	Russia-Moldova 12
					Moldova	1			Merker et al., 2015	3	Russia-Georgia 14
					Georgia	2	W. Asia	2	Casali et al., 2014	1	Moldova-Georgia 20
5	LIN-2	Beijing	0.99	23	Russia	19	E. Europe	21	Merker et al., 2015	1	Russia-Sweden 13
					Belarus	2 (2)			Casali et al., 2014	19	Russia-Georgia 17
					Sweden	1	N. Europe	1	TB-ARC Belarus	2	Russia-Belarus 20
					Georgia	1	W. Asia	1	TB-ARC Sweden	1	Belarus-Georgia 26
											Belarus-Sweden 29
											Sweden-Georgia 32
6	LIN-2	Beijing	1.00	3	UK	1 (1)	N. Europe	2	TB-ARC Moldova	1	UK-Moldova 14
					Sweden	1			Casali et al., 2014	1	UK-Sweden 19
					Moldova	1	E. Europe	1	TB-ARC Sweden	1	Sweden-Moldova 24
7	LIN-4	LAM9	0.92	3	Russia	1	E. Europe	1	Casali et al, 2014	1	Russia-Sweden 14
7					Sweden	2 (2)	N. Europe	2	TB-ARC Sweden	2
8	LIN-2	Beijing	0.99	2	Russia	1	E. Europe	1	Casali et al, 2014	1	Russia-Iran 14
8					Iran	1 (1)	S. Asia	1	TB-ARC Iran	1
9	LIN-4	LAM9	0.99	3	Sweden	1	N. Europe	1	TB-ARC Moldova	2	Sweden-Moldova 15
9					Moldova	2	E. Europe	2	TB-ARC Sweden	1
10	LIN-2	Beijing	0.86	6	UK	1 (1)	N. Europe	1	Bryant et al, 2013	1	UK-Russia 16
					Russia	4	E. Europe	4	Casali et al, 2014	5	Russia-Netherlands 16
					Netherlands	1	W. Europe	1			UK-Netherlands 17
11	LIN-2	Beijing	0.84	7	Russia	2	E. Europe	2	Merker et al, 2015	1	Iran-Azerbaijan 17
					Iran	4 (4)	S. Asia	4	Casali et al, 2014	2	Russia-Azerbaijan 24
					Azerbaijan	1	W. Asia	1	TB-ARC Iran	4	Russia-Iran 30
12	LIN-4	T2	1.00	2	Uganda	1	N. Europe	1	Clark et al, 2013	1	Uganda-Sweden 17
12					Sweden	1	E. Africa	1	TB-ARC Sweden	1
13	LIN-4	LAM9	1.00	2	Russia	1	N. Europe	1	Casali et al, 2014	1	Russia-Sweden 17
13					Sweden	1	E. Europe	1	TB-ARC Sweden	1
14	LIN-2	Beijing	0.94	37	Russia	32 (6)	E. Europe	35	Merker et al, 2015	1	Russia-Iran 19
					Belarus	3 (2)		1	Casali et al, 2014	32	Russia-Germany 19
					Germany	1	W. Europe		TB-ARC Iran	1	Iran-Germany 19
					Iran	1	S. Asia	1	TB-ARC Belarus	3	Russia-Belarus 25
											Iran-Belarus 27
											Belarus-Germany 30
15	LIN-2	Beijing	0.88	52	Russia	1	E. Europe	51	Merker et al, 2015	2	Russia-Belarus 20
					Belarus	50 (27)			TB-ARC Belarus	50	Turkmenistan-Belarus 30
					Turkmenistan	1	Central Asia	1			Russia-Turkmenistan 34
16	LIN-4	S	0.97	3	Sweden	1	N. Europe	1	TB-ARC Romania	2	Sweden-Romania 21
16					Romania	2	E. Europe	2	TB-ARC Sweden	1
17	LIN-2	Beijing	0.82	3	Russia	2 (1)	E. Europe	2	Merker et al, 2015	3	Russia-Uzbekistan 22
17					Uzbekistan	1	Central Asia	1
18	LIN-2	Beijing	0.96	5	South Africa	4	S. Africa	4	Cohen et al, 2015	2	South Africa-Sweden 27
									TB-ARC MRC	2
					Sweden	1 (1)	N. Europe	1	TB-ARC Sweden	1
19	LIN-2	Beijing	0.88	4	Sweden	3	N. Europe	3	TB-ARC Iran	1	Sweden-Iran 33
19					Iran	1	S. Asia	1	TB-ARC Sweden	3
20	LIN-2	Beijing	0.95	2	Russia	1	E. Europe	1	Merker et al, 2015	1	Russia-Georgia 33
20					Georgia	1	W. Asia	1	Casali et al, 2014	1
21	LIN-2	Beijing	0.99	10	Sweden	2	N. Europe	2	TB-ARC Sweden	2	Sweden-Belarus 36
21					Belarus	8 (3)	E. Europe	8	TB-ARC Belarus	8
22	LIN-2	Beijing	1.00	7	Russia	5	N. Europe	2	Casali et al, 2014	5	Russia-Sweden 39
22					Sweden	2	E. Europe	5	TB-ARC Sweden	2
(B) Movement of MDR strains between countries within a UN geographical region. This table lists MDR clades found in a single UN geographic region, but in >1 country.
23	LIN-4	S	1.00	37	South Africa	36	S. Africa	37	Cohen et al, 2015	18	South Africa-Swaziland 1
23					Swaziland	1			TB-ARC MRC	19
24	LIN-4	T1	1.00	22	Russia	1	E. Europe	22	Casali et al, 2014	1	Russia-Belarus 7
24					Belarus	21 (3)			TB-ARC Belarus	21
25	LIN-2	Beijing	0.99	5	Russia	4 (1)	E. Europe	5	TB-ARC Moldova	1	Russia-Moldova 9
25					Moldova	1			Casali et al, 2014	4
26	LIN-4	T1	0.91	19	South Africa	18 (1)	S. Africa	19	Cohen et al, 2015	7	South Africa-Swaziland 13
26					Swaziland	1			TB-ARC MRC	12
27	LIN-4	H3	0.91	14	Russia	12	E. Europe	14	TB-ARC Moldova	2	Russia-Moldova 16
27					Moldova	2			Casali et al, 2014	12
28	LIN-2	Beijing	1.00	4	UK	1 (1)	N. Europe	4	Bryant et al, 2013	3	UK-Estonia 16
28					Estonia	3 (1)			Casali et al, 2014	1
29	LIN-2	Beijing	0.91	4	Belarus	1	E. Europe	4	TB-ARC Moldova	3	Belarus-Moldova 17
29					Moldova	3			TB-ARC Belarus	1
30	LIN-2	Beijing	0.83	3	Russia	1	E. Europe	3	Casali et al, 2014	1	Russia-Belarus 22
30					Belarus	2 (2)			TB-ARC Belarus	2
31	LIN-2	Beijing	0.98	2	Russia	1 (1)	E. Europe	2	TB-ARC Moldova	1	Russia-Moldova 27
31					Moldova	1			Casali et al, 2014	1
32	LIN-4	H3	1.00	3	Russia	2	E. Europe	3	Casali et al, 2014	2	Russia-Belarus 116
32					Belarus	1			TB-ARC Belarus	1

For each unique MDR clade in the phylogeny, defined as the set of descendants from a single node where MDR arose in our parsimony-based analysis (see Methods section), we calculated the number of countries and UN geographic regions represented. For each MDR-defining node, the table provides lineage and spoligotype designations for descendent strains, the level of statistical confidence for each node in the phylogenetic tree (figure 3), the total number of descendent strains as well as by country, UN geographic region and dataset, and the minimum SNP distance between isolates from each country pair, defined as the minimum distance between all pairs of strains from each two countries contained in a single MDR clade. WHO high burden countries are indicated in red.
MDR, multidrug-resistant; SNP, single nucleotide polymorphism; XDR, extensively drug-resistant.