Molecular Epidemiology and Genotyping of Mycobacterium tuberculosis Isolated in Baghdad
Table 3
Description of 64 shared types (SITs; isolates) and corresponding spoligotyping defined lineages/sublineages starting from a total of 270 M. tuberculosis strains isolated from Iraqi patients.
SIT*
Spoligotype description
Octal number
Nb in study
% in study
% in study versus database
Lineage**
Clustered versus unique patterns***
4
000000007760771
1
0.37
0.28
Unknown
Unique
20
677777607760771
1
0.37
0.12
LAM1
Unique
22
703777400001771
8
2.96
10.26
CAS1-Delhi
Clustered
25
703777740003171
10
3.7
1.77
CAS1-Delhi
Clustered
26
703777740003771
12
4.44
0.87
CAS1-Delhi
Clustered
34
776377777760771
1
0.37
0.12
S
Unique
41
777777404760771
1
0.37
0.21
LAM7-TUR
Unique
42
777777607760771
1
0.37
0.03
LAM9
Unique
47
777777774020771
1
0.37
0.07
H1
Unique
50
777777777720771
6
2.22
0.18
H3
Clustered
53
777777777760771
5
1.85
0.08
T1
Clustered
54
777777777763771
8
2.96
3.31
Manu2
Clustered
64
777777607560771
1
0.37
0.28
LAM6
Unique
75
777767777720771
6
2.22
8.7
H3
Clustered
117
777767777760731
2
0.74
8
T2
Clustered
118
777767777760771
6
2.22
3.9
T1
Clustered
124
777777777700771
1
0.37
1.54
Unknown
Unique
127
577777777420771
6
2.22
3.08
H4 (Ural-2)
Clustered
141
703767740003771
9
3.33
28.13
CAS1-Delhi
Clustered
186
777767404760771
1
0.37
8.33
LAM7-TUR
Unique
247
703777740003471
3
1.11
8.11
CAS1-Delhi
Clustered
284
037637777760771
9
3.33
5.11
T1
Clustered
309
703767740003171
17
6.3
80.95
CAS1-Delhi
Clustered
485
703777400003771
1
0.37
4
CAS1-Delhi
Unique
516
777777777360771
1
0.37
5.56
T1
Unique
568
777767477760771
1
0.37
20
T-H37Rv
Unique
610
777767774020731
1
0.37
14.29
H1
Unique
831
776367777760771
1
0.37
7.69
S
Unique
878
777776777760571
1
0.37
4
X1
Unique
954
703677740003771
1
0.37
6.67
CAS1-Delhi
Unique
1088
777767777763771
4
1.48
33.33
Manu2
Clustered
1144
777777600760771
17
6.3
41.46
T1
Clustered
1198
703737740003171
4
1.48
10.53
CAS1-Delhi
Clustered
1318
577767777760771
2
0.74
25
T1
Clustered
1470
777776607760771
2
0.74
10
LAM9
Clustered
1547
777727777760771
3
1.11
27.27
T3
Clustered
1630
777777601760771
1
0.37
16.67
T1
Unique
1638
577767777763771
1
0.37
33.33
Manu2
Unique
1655
777723777760771
1
0.37
2.7
T3
Unique
1679
777767737760771
2
0.74
20
T1
Clustered
1913
777767757760771
1
0.37
25
T5
Unique
2032
037627777760771
1
0.37
20
T1
Unique
2230
777700077760771
1
0.37
16.67
Unknown
Unique
2359
703677740003171
1
0.37
4.55
CAS1-Delhi
Unique
2686
703767740003471
4
1.48
66.67
CAS1-Delhi
Clustered
2691
037737777760771
1
0.37
20
T3
Unique
2707
701767740003671
1
0.37
33.33
CAS
Unique
2728
577767777420771
3
1.11
50
H4 (Ural-2)
Clustered
3275*
700037777760731
1
0.37
50
T2
Unique
3346*
777767600760771
11
4.07
100
T1
Clustered
3497*
703767400001771
8
2.96
100
CAS
Clustered
3708*
703767740003761
3
1.11
100
CAS1-Delhi
Clustered
3789*
777777740763771
2
0.74
66.67
Manu2
Clustered
3790*
777767600360771
4
1.48
100
T1
Clustered
3791*
703727740003171
4
1.48
100
CAS1-Delhi
Clustered
3792*
703767640003771
2
0.74
66.67
CAS1-Delhi
Clustered
3793*
557767777763771
1
0.37
50
Manu2
Unique
3794*
703767740000771
1
0.37
50
CAS
Unique
3795*
277767607760771
1
0.37
50
LAM1
Unique
3796*
703767740000371
1
0.37
50
CAS
Unique
3797*
777777774120771
1
0.37
50
H3
Unique
3798*
777717777760371
1
0.37
50
T1
Unique
3799*
777767614760771
1
0.37
50
T1
Unique
3800*
703767400003771
2
0.74
100
CAS
Clustered
A total of 48/64 SITs containing 173 isolates matched a preexisting shared type in the database, whereas 16/64 SITs ( isolates) were newly created. A total of 31/64 SITs containing 184 isolates were clustered within this study (2 to 17 isolates per cluster) while 33/64 SITs containing 33 strains were unique (for total unique strains, one should add to this number the 53 orphan strains, which brings the number of unclustered isolates in this study to 86/270 or 31.85% and clustered isolates to 184/270 or 68.15%). 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: 3275* this study , FXX ; 3346* this study ; 3497* this study ; 3708* this study ; 3789* this study , IRQ ; 3790* this study ; 3791* this study ; 3792* this study , IND ; 3793* this study , IND ; 3794* this study , IND ; 3795* this study , BRA ; 3796* this study , PAK ; 3797* this study , MEX ; 3798* this study , IRQ ; 3799* this study , BRA ; 3800* this study .
**Lineage designations according to SITVIT2 using revised SpolDB4 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 2).
