Table 1. Description of 55 shared-types (SITs; n = 198 isolates) and corresponding spoligotyping defined lineages/sublineages starting from a total of 220 M. tuberculosis strains isolated in Malaysia.
| SIT a | Spoligotype Description | Octal Number | Nb (%) in study | % in study vs. Database | Clade b | Unique or Clustered SIT c |
| 1 | □□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□▪▪▪▪▪▪▪▪▪ | 000000000003771 | 56 (25.45) | 0.54 | Beijing | Clustered |
| 11 | ▪□□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪□▪▪□□□▪▪▪▪ | 477777777413071 | 1 (0.45) | 0.15 | EAI3-IND | Unique |
| 19 | ▪▪□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□▪▪▪▪▪▪▪□□□□▪□▪▪▪▪▪▪▪▪▪ | 677777477413771 | 9 (4.09) | 0.99 | EAI2-Manila | Clustered |
| 26 | ▪▪▪□□□□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□□□□□□□□□▪▪▪▪▪▪▪▪▪ | 703777740003771 | 1 (0.45) | 0.06 | CAS1-Delhi | Unique |
| 34 | ▪▪▪▪▪▪▪▪□□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪▪▪▪▪▪▪ | 776377777760771 | 1 (0.45) | 0.12 | S | Unique |
| 48 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪□▪▪▪▪▪□▪▪▪ | 777777777413731 | 1 (0.45) | 0.22 | EAI1-SOM | Unique |
| 50 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□▪□□□□▪▪▪▪▪▪▪ | 777777777720771 | 3 (1.36) | 0.08 | H3 | Clustered |
| 51 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪▪▪□□□□ | 777777777760700 | 2 (0.91) | 0.64 | T1 | Clustered |
| 53 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪▪▪▪▪▪▪ | 777777777760771 | 1 (0.45) | 0.02 | T1 | Unique |
| 54 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□▪▪▪▪▪▪▪▪▪ | 777777777763771 | 1 (0.45) | 0.39 | Manu2 | Unique |
| 89 | ▪▪□▪▪▪▪□□□□□□□□□□□□□□□□□□▪▪▪□□□□▪□▪▪▪▪▪▪▪▪▪ | 674000003413771 | 5 (2.27) | 4.42 | EAI2-nonthaburi | Clustered |
| 126 | ▪□□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪□▪▪▪▪▪▪▪▪▪ | 477777777413771 | 1 (0.45) | 0.81 | EAI5 | Unique |
| 236 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪□▪▪▪▪▪▪▪▪▪ | 777777777413771 | 10 (4.55) | 5.65 | EAI5 | Clustered |
| 250 | □□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□▪▪▪▪▪▪ | 000000000000371 | 2 (0.91) | 5.26 | Beijing | Clustered |
| 256 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪□▪▪▪▪□▪▪▪▪ | 777777777413671 | 12 (5.45) | 18.18 | EAI5 | Clustered |
| 260 | □□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□▪▪□□▪▪▪▪▪ | 000000000003171 | 1 (0.45) | 10 | Beijing | Unique |
| 298 | ▪□□▪▪▪▪▪▪▪▪▪▪▪□▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪□▪▪□□□▪▪▪▪ | 477767777413071 | 1 (0.45) | 2.33 | EAI3-IND | Unique |
| 340 | ▪□□▪▪▪▪□□□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪□▪▪▪▪▪▪▪▪▪ | 474377777413771 | 1 (0.45) | 2.13 | EAI5 | Unique |
| 349 | ▪▪▪▪▪▪▪▪▪▪▪▪□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪□▪▪▪▪▪□▪▪▪ | 777737777413731 | 1 (0.45) | 3.45 | EAI1-SOM | Unique |
| 374 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□□□□□□□▪▪▪▪▪▪▪ | 777777776000771 | 1 (0.45) | 11.11 | Unknown | Unique |
| 429 | ▪▪▪□□□□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□□□□□□□□□▪▪▪▪▪□▪▪▪ | 703777740003731 | 1 (0.45) | 3.33 | CAS1-Delhi | Unique |
| 483 | ▪▪□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□▪▪▪▪▪▪▪□□□□▪□▪▪▪▪▪□□□▪ | 677777477413701 | 1 (0.45) | 5 | EAI2-Manila | Unique |
| 581 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□▪▪▪▪▪▪▪□▪▪▪□□□□▪▪□▪▪▪▪ | 777777677560671 | 1 (0.45) | 25 | T1 | Unique |
| 591 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□▪▪▪▪▪□□□□▪□▪▪▪▪▪▪▪▪▪ | 777777757413771 | 13 (5.91) | 14.77 | EAI6-BGD1 | Clustered |
| 623 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪ | 777777757777771 | 1 (0.45) | 7.14 | Unknown | Unique |
| 655 | ▪□□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□▪□□□□▪▪▪▪▪▪▪ | 477777777720771 | 2 (0.91) | 4.17 | H3 | Clustered |
| 733 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□▪▪▪▪▪□□▪▪▪▪□□□□▪□▪▪▪▪▪▪▪▪▪ | 777775747413771 | 1 (0.45) | 12.5 | EAI6-BGD1 | Unique |
| 745 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪□▪▪□□▪□▪▪▪ | 777777777413131 | 33 (15) | 54.1 | EAI1-SOM | Clustered |
| 939 | ▪▪▪▪▪▪▪□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪□▪▪▪▪▪▪▪▪▪ | 775777777413771 | 1 (0.45) | 20 | EAI5 | Unique |
| 944 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□□□□□□□□□□□▪▪▪▪ | 777777774000071 | 1 (0.45) | 20 | Unknown | Unique |
| 946 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□□□□□□▪□□□□▪▪▪▪▪▪▪ | 777777740020771 | 1 (0.45) | 4.76 | H | Unique |
| 951 | ▪▪▪▪▪▪▪□□□□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪□▪▪▪▪▪▪▪▪▪ | 774177777413771 | 1 (0.45) | 4 | EAI5 | Unique |
| 962 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪□▪▪□□□□▪▪▪ | 777777777413031 | 1 (0.45) | 11.11 | EAI5 | Unique |
| 1183 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪□▪▪□▪▪□▪▪▪ | 777777777413331 | 1 (0.45) | 25 | EAI1-SOM | Unique |
| 1184 | □□□□□□□□□□□□□□□□▪□□□□□□□□□□□□□□□□□▪▪▪▪▪▪▪▪▪ | 000002000003771 | 1 (0.45) | 11.11 | Unknown | Unique |
| 1243 | ▪▪▪▪▪▪▪▪▪□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□▪□□□□▪▪▪▪▪▪▪ | 777377777720771 | 1 (0.45) | 5.88 | H3 | Unique |
| 1268 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□□□□▪□▪▪▪▪▪▪▪▪▪□□□□▪▪▪▪▪▪▪ | 777760057760771 | 1 (0.45) | 11.11 | T5 | Unique |
| 1372 | ▪▪▪▪▪▪▪▪▪▪□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪□▪▪▪▪▪▪▪▪▪ | 777577777413771 | 1 (0.45) | 20 | EAI5 | Unique |
| 1395 | ▪□□▪▪▪▪□□□▪▪▪▪▪▪▪▪▪▪▪▪▪□▪▪▪▪□□□□▪□▪▪▪▪▪▪▪▪▪ | 474377767413771 | 1 (0.45) | 16.67 | EAI5 | Unique |
| 1490 | ▪▪□▪▪▪▪▪▪▪▪▪▪▪□▪▪▪▪□□▪▪▪▪▪▪▪□□□□▪□▪▪▪▪▪▪▪▪▪ | 677767477413771 | 1 (0.45) | 16.67 | EAI2-Manila | Unique |
| 1494 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□▪▪▪▪▪□▪▪▪▪▪□□□□▪▪▪▪▪▪▪ | 777777676760771 | 1 (0.45) | 16.67 | T1 | Unique |
| 1512 | ▪▪□▪□▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□▪▪▪▪▪▪▪□□□□▪□▪▪▪▪▪□□□▪ | 657777477413701 | 1 (0.45) | 16.67 | EAI2-Manila | Unique |
| 1651 | □□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□▪▪▪▪□▪▪□▪ | 000000000003661 | 2 (0.91) | 12.5 | Beijing | Clustered |
| 2383 | ▪▪▪▪□▪▪▪▪▪▪▪□▪▪▪▪▪▪▪□□□□▪▪▪▪▪▪▪▪□□□□▪▪▪▪▪▪▪ | 757737607760771 | 1 (0.45) | 16.67 | LAM5 | Unique |
| 2428 | ▪▪□▪▪▪▪□□□□□□□▪▪▪▪▪▪□□□□▪▪▪▪▪▪▪▪□□□□▪▪▪▪▪▪▪ | 674017607760771 | 1 (0.45) | 16.67 | LAM3 | Unique |
| 2610 | □□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□□▪▪▪▪▪▪▪▪□ | 000000000003770 | 2 (0.91) | 28.57 | Beijing | Clustered |
| 3143 | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪▪▪□□□□ | 777767777760700 | 1 (0.45) | 33.33 | T1 | Unique |
| 3484 | ▪▪▪□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□▪▪▪▪▪□□□□▪□▪▪▪▪▪▪▪▪▪ | 737777757413771 | 1 (0.45) | 33.33 | EAI6-BGD1 | Unique |
| 3949 | ▪□□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪□▪▪□□□□□□▪ | 477777777413001 | 1 (0.45) | 33.33 | EAI5 | Unique |
| 3993* | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪□□□□□□□▪▪▪ | 777777777410031 | 1 (0.45) | 50 | EAI5 | Unique |
| 3994* | ▪▪▪▪▪▪▪▪▪▪▪▪□▪▪▪▪▪▪▪▪▪▪▪▪□▪▪□□□□▪□▪▪▪▪▪□▪▪▪ | 777737775413731 | 2 (0.91) | 66.67 | EAI1-SOM | Clustered |
| 3995* | ▪▪▪▪▪▪▪▪□▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪□▪▪▪▪▪▪▪▪▪ | 776777777413771 | 2 (0.91) | 100 | EAI5 | Clustered |
| 3996* | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□▪▪▪□□□□□□□□□□□□□□▪▪▪▪ | 777777634000071 | 2 (0.91) | 100 | Unknown | Clustered |
| 3997* | ▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪▪□□□□▪□▪▪□□▪□□□▪ | 777777777413101 | 2 (0.91) | 100 | EAI5 | Clustered |
| 3998* | ▪▪▪▪□□□□□□□□▪▪▪▪▪▪▪▪▪▪□▪▪▪▪▪□□□□▪□▪▪▪▪▪▪▪▪▪ | 740077757413771 | 2 (0.91) | 100 | EAI6-BGD1 | Clustered |
Description of 55 shared-types (SITs; n = 198 isolates): 49/55 SITs containing 187 isolates matched a preexisting shared-type in the database, whereas 6/55 SITs (n = 11 isolates) were newly created. A total of 18/55 SITs containing 161 isolates were clustered within this study (2 to 56 isolates per cluster) while 37/55 SITs containing 37 strains were unique (for total unique strains, one should add to this number the 22 orphan strains, which brings the number of unclustered isolates in this study to 59/220 or 26.82%, and clustered isolates to 161/220 or 73.18%). Note that SITs followed by an asterisk indicates "newly created” SITs due to 2 or more strains belonging to an identical new pattern within this study or after a match with an orphan in the database; SIT designations followed by number of strains: 3993* this study n = 1, MYS n = 1; 3994* this study n = 2, MYS n = 1; 3994* this study n = 2; 3995* this study n = 2; 3996* this study n = 2; 3997* this study n = 2; 3998* this study n = 2.
Lineage designations according to SITVITWEB rules; “Unknown” designates patterns with signatures that do not belong to any of the major lineages described in the database.
Clustered strains correspond to a similar spoligotype pattern shared by 2 or more strains “within this study”; as opposed to unique strains harboring a spoligotype pattern that does not match with another strain from this study. Unique strains matching a preexisting pattern in the SITVIT2 database are classified as SITs, whereas in case of no match, they are designated as “orphan” (see Table 1).