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