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Table 1 Mycobacterium tuberculosis complex lineages and sub-lineages across the 35,298 isolates

From: Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies

Lineage No. training (test) No. countries train (test) % MDR-TB No. transmission [clusters] Potential barcoding SNPs* Robust SNPs**
1 2162 (1203) 25 (42) 7.8 354 [130] 344 17
1.1 1487 (530) 19 (36) 5.5 218 [82] 23 2
1.1.1 706 (170) 8 (16) 3.8 60 [25] 41 5
1.1.1.1 358 (120) 5 (9) 2.1 28 [11] 52 3
1.1.2 459 (278) 15 (25) 9.0 83 [31] 109 3
1.1.3 299 (80) 11 (16) 3.2 73 [25] 42 2
1.1.3.1 84 (31) 7 (13) 3.5 10 [4] 68 2
1.1.3.2 155 (33) 7 (7) 1.1 57 [18] 113 6
1.1.3.3 32 (7) 5 (4) 10.3 4 [2] 36 2
1.2 309 (550) 13 (21) 7.5 40 [16] 60 2
1.2.1 28 (44) 3 (7) 6.9 6 [2] 78 5
1.2.2 277 (505) 13 (18) 7.5 34 [14] 159 8
1.2.2.1 244 (453) 12 (18) 6.9 34 [14] 34 1
1.3 366 (122) 16 (19) 18.0 96 [32] 71 2
1.3.1 88 (25) 7 (11) 10.6 20 [7] 50 4
1.3.2 278 (97) 16 (17) 20.3 76 [25] 83 4
2 4556 (4322) 45 (56) 36.2 1778 [413] 72 4
2.1 95 (41) 6 (9) 19.8 27 [10] 172 4
2.2 4461 (4281) 45 (56) 36.5 1751 [403] 79 17
2.2.1 4239 (4007) 45 (56) 35.1 1632 [389] 17 2
2.2.1.1 338 (443) 19 (18) 28.0 98 [40] 6 2
2.2.1.2 29 (21) 6 (9) 36.0 10 [3] 5 1
2.2.2 222 (273) 16 (15) 59.0 119 [14] 54 4
3 2654 (1271) 24 (31) 13.4 847 [242] 166 8
3.1 715 (362) 15 (22) 9.5 372 [80] 1 1
3.1.1 387 (280) 11 (16) 6.2 243 [43] 17 2
3.1.2 295 (69) 13 (8) 14.3 124 [35] 8 2
3.1.2.1 98 (25) 8 (7) 19.5 25 [12] 15 7
3.1.2.2 48 (0) 3 (0) 0 36 [2] 85 6
3.2 89 (31) 6 (9) 10.0 31 [7] 85 2
4 8320 (9883) 44 (99) 18.5 3109 [731] 94 3
4.1 2594 (2325) 35 (64) 18.5 1043 [191] 58 3
4.1.1 889 (482) 20 (27) 18.1 403 [72] 30 13
4.1.1.1 210 (158) 14 (16) 9.5 92 [20] 39 2
4.1.1.2 55 (44) 4 (6) 2.0 33 [3] 92 2
4.1.1.3 579 (247) 18 (23) 22.4 266 [44] 58 3
4.1.1.3.1 207 (13) 3 (3) 9.6 158 [5] 46 3
4.1.2 1612 (1743) 32 (61) 17.3 622 [113] 13 1
4.1.2.1 1383 (1087) 32 (60) 22.5 563 [96] 49 3
4.1.2.1.1 231 (18) 1 (1) 97.6 221 [2] 73 3
4.1.3 28 (70) 7 (10) 57.1 4 [2] 124 3
4.1.4 24 (12) 8 (7) 38.9 10 [2] 60 4
4.2 481 (532) 23 (26) 28.0 87 [32] 116 8
4.2.1 206 (240) 13 (20) 28.3 34 [13] 26 2
4.2.1.1 54 (148) 9 (10) 6.9 2 [1] 36 2
4.2.2 274 (288) 20 (18) 28.1 53 [19] 20 2
4.2.2.1 74 (41) 10 (6) 45.2 22 [7] 26 2
4.2.2.2 120 (139) 11 (14) 27.8 15 [7] 31 10
4.3 2507 (2928) 30 (75) 23.1 993 [244] 38 2
4.3.1 58 (67) 7 (15) 6.4 40 [3] 28 1
4.3.1.1 37 (2) 3 (1) 0.0 36 [1] 52 2
4.3.2 409 (1200) 16 (21) 7.2 75 [32] 75 1
4.3.2.1 291 (917) 6 (7) 3.7 50 [23] 55 4
4.3.3 648 (810) 25 (57) 41.3 210 [66] 33 1
4.3.4 1366 (807) 23 (45) 24.1 664 [142] 8 1
4.3.4.1 194 (170) 14 (30) 28.9 49 [14] 19 4
4.3.4.2 1170 (635) 22 (34) 23.1 614 [128] 26 1
4.3.4.2.1 877 (287) 13 (18) 5.6 457 [103] 11 1
4.4 560 (1059) 24 (29) 15.7 190 [63] 37 2
4.4.1 420 (861) 22 (25) 16.0 149 [48] 38 4
4.4.1.1 379 (755) 21 (24) 17.8 136 [44] 16 1
4.4.1.1.1 75 (206) 5 (4) 19.6 22 [9] 60 3
4.4.1.2 39 (106) 8 (6) 1.4 13 [4] 95 9
4.4.2 112 (181) 7 (9) 14.7 33 [13] 7 2
4.5 293 (357) 17 (17) 15.7 49 [22] 50 1
4.6 340 (442) 21 (25) 22.1 139 [39] 12 1
4.6.1 73 (296) 9 (12) 29.8 24 [8] 53 3
4.6.1.1 29 (126) 6 (7) 1.3 14 [3] 22 1
4.6.1.2 40 (154) 9 (11) 54.6 10 [5] 37 1
4.6.2 164 (89) 16 (17) 15.4 65 [20] 22 1
4.6.2.1 2 (0) 1 (0) 0 2 [1] 45 2
4.6.2.2 150 (89) 14 (17) 15.9 60 [18] 106 6
4.6.3 23 (9) 3 (4) 0 20 [3] 135 3
4.6.4 23 (7) 5 (4) 50.0 10 [2] 49 1
4.6.5 23 (18) 5 (5) 19.5 9 [3] 8 2
4.7 158 (200) 18 (23) 10.3 56 [20] 10 3
4.8 1051 (1807) 29 (55) 7.8 419 [88] 17 1
4.8.1 63 (90) 7 (4) 22.2 21 [5] 46 3
4.8.2 116 (5) 3 (2) 0 113 [1] 42 2
4.8.3 21 (3) 1 (1) 0 19 [1] 34 1
4.9 243 (141) 14 (22) 12.5 114 [24] 37 3
4.9.1 74 (15) 6 (3) 5.6 44 [1] 49 3
5 26 (255) 6 (12) 14.6 2 [1] 460 13
6 32 (135) 6 (13) 3.6 5 [2] 214 10
7 38 (26) 3 (2) 0 3 [1] 837 38
8 2 (0) 1 (0) 0 0 [0] 888 43
9 3 (0) 1 (0) 0 0 [0] 160 5
M. bovis 81 (281) 9 (12) 0.8 42 [11] 93 3
M. caprae 3 (7) 2 (3) 0 0 [0] 225 5
M. orygis 26 (12) 4 (4) 0 0 [0] 743 28
Totals 17,903 (17,395) 165 (269) 21.0 6140 [1531] 8128 421
  1. Bolded are changes from the barcode in reference [1]—either new sub-lineages or new barcoding SNPs; MDR-TB multidrug-resistant TB, which is resistant to at least rifampicin and isoniazid drugs. *All potential barcoding SNPs (FST = 1). **Final robust SNP set, based on synonymous changes in essential and non-drug resistance genes only (except 12 sub-lineages which had no informative SNPs in essential genes; see Additional file 1: Table S2)