Table 3. Distribution of Spoligotype International Types (SIT) in this study.
| SIT* | Spoligotype pattern (Octal format) | Number in study (%) | % in study vs. Database | Lineage** | Unique or Clustered SIT*** |
|---|---|---|---|---|---|
| 1 | 000000000003771 | 12 (4.1) | 0.11 | Beijing | Clustered |
| 4 | 000000007760771 | 1 (0.34) | 0.26 | Unknown | Unique |
| 8 | 400037777413771 | 12 (4.1) | 6 | EAI5 | Clustered |
| 10 | 477777277413771 | 1 (0.34) | 1.12 | EAI8-MDG | Unique |
| 21 | 703377400001771 | 76 (25.94) | 15.97 | CAS1-Kili | Clustered |
| 22 | 703777400001771 | 1 (0.34) | 1.08 | CAS1-Delhi | Unique |
| 25 | 703777740003171 | 3 (1.02) | 0.45 | CAS1-Delhi | Clustered |
| 26 | 703777740003771 | 14 (4.78) | 0.8 | CAS1-Delhi | Clustered |
| 34 | 776377777760771 | 1 (0.34) | 0.11 | S | Unique |
| 36 | 777737777720771 | 1 (0.34) | 0.63 | H3 | Unique |
| 37 | 777737777760771 | 4 (1.37) | 0.73 | T3 | Clustered |
| 42 | 777777607760771 | 6 (2.05) | 0.17 | LAM9 | Clustered |
| 48 | 777777777413731 | 1 (0.34) | 0.22 | EAI1-SOM | Unique |
| 50 | 777777777720771 | 3 (1.02) | 0.07 | H3 | Clustered |
| 53 | 777777777760771 | 15 (5.12) | 0.23 | T1 | Clustered |
| 59 | 777777606060771 | 22 (7.51) | 4.54 | LAM11-ZWE | Clustered |
| 62 | 777777774020731 | 1 (0.34) | 0.17 | H1 | Unique |
| 64 | 777777607560771 | 2 (0.68) | 0.48 | LAM6 | Clustered |
| 73 | 777737777760731 | 1 (0.34) | 0.34 | T | Unique |
| 126 | 477777777413771 | 18 (6.14) | 12.08 | EAI5 | Clustered |
| 128 | 637775777760730 | 3 (1.02) | 8.57 | T2-uganda | Clustered |
| 135 | 777777777760730 | 4 (1.37) | 11.43 | T2-uganda | Clustered |
| 137 | 777776777760601 | 1 (0.34) | 0.1 | X2 | Unique |
| 149 | 777000377760771 | 4 (1.37) | 0.82 | T3-ETH | Clustered |
| 244 | 777777777760601 | 5 (1.71) | 4.03 | T1 | Clustered |
| 245 | 777777777760671 | 1 (0.34) | 4.55 | T1 | Unique |
| 281 | 777775777760771 | 1 (0.34) | 3.13 | T1 | Unique |
| 288 | 700377740003771 | 2 (0.68) | 1.27 | CAS2 | Clustered |
| 345 | 777000377760731 | 7 (2.39) | 33.33 | T3-ETH | Clustered |
| 420 | 637774777760730 | 6 (2.05) | 24 | T2-uganda | Clustered |
| 458 | 777777777403771 | 1 (0.34) | 2.7 | EAI5 | Unique |
| 486 | 703777740000371 | 1 (0.34) | 1.75 | CAS | Unique |
| 522 | 777777777760770 | 1 (0.34) | 6.25 | T1 | Unique |
| 523 | 777777777777771 | 1 (0.34) | 1.69 | Manu_ancestor | Unique |
| 702 | 700775747413771 | 1 (0.34) | 2.86 | EAI6-BGD1 | Unique |
| 727 | 777737774020731 | 1 (0.34) | 2.44 | H1 | Unique |
| 815 | 777777606060731 | 2 (0.68) | 1.34 | LAM11-ZWE | Clustered |
| 891 | 777777607660771 | 2 (0.68) | 6.67 | LAM9 | Clustered |
| 1090 | 077777777413771 | 2 (0.68) | 22.22 | EAI5 | Clustered |
| 1192 | 777777677763771 | 1 (0.34) | 10 | Manu2 | Unique |
| 1369 | 477777777413671 | 1 (0.34) | 12.5 | EAI5 | Unique |
| 1549 | 775777606060731 | 2 (0.68) | 18.18 | LAM11-ZWE | Clustered |
| 1765 | 703337400001771 | 1 (0.34) | 14.29 | CAS1-Kili | Unique |
| 1801 | 777777777413730 | 1 (0.34) | 25 | EAI1-SOM | Unique |
| 1824 | 760377777760701 | 2 (0.68) | 25 | T1 | Clustered |
| 1957 | 477777777013771 | 1 (0.34) | 6.67 | EAI5 | Unique |
| 2196 | 777775606060731 | 6 (2.05) | 30 | LAM11-ZWE | Clustered |
| 2267 | 701377400001771 | 1 (0.34) | 25 | CAS | Unique |
| 2269 | 703377400000771 | 1 (0.34) | 20 | CAS | Unique |
| 2364 | 703601740003771 | 1 (0.34) | 25 | CAS1-Delhi | Unique |
| 2391 | 703377400003771 | 1 (0.34) | 11.11 | CAS1-Kili | Unique |
| 2484 | 737377677760771 | 1 (0.34) | 25 | T1 | Unique |
| 2736 | 777777777760741 | 1 (0.34) | 25 | T1 | Unique |
| 3880 | 437774777760730 | 2 (0.68) | 50 | T2-uganda | Clustered |
| 4056* | 477777777413411 | 2 (0.68) | 100 | EAI5 | Clustered |
| 4057* | 777017777760771 | 1 (0.34) | 50 | T1 | Unique |
| 4058* | 477777777413371 | 1 (0.34) | 50 | EAI5 | Unique |
* A total of 54/57 SITs containing 264 isolates matched a preexisting shared-type in the database, whereas 3/57 SITs (n = 4 isolates) were newly created. A total of 27/57 SITs containing 238 isolates were clustered within this study (2 to 76 isolates per cluster) while 30/57 SITs containing 30 isolates were unique (for total unique strains, one should add to this number the 25 orphan strains, which brings the number of unclustered isolates in this study to 55/293 or 18.77%, and clustered isolates to 238/293 or 81.23%). 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: 4056* this study n = 2; 4057* this study n = 1, SDN n = 1; 4058* this study n = 1, NLD n = 1.
** Lineage designations according to SITVIT2; “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”.