Strain Diversity of Mycobacterium tuberculosis Isolates from Pulmonary Tuberculosis Patients in Afar Pastoral Region of Ethiopia

Table 2

Description of 35 shared-types (SITs; 𝑛=96 isolates) and corresponding spoligotyping defined lineages/sublineages starting from a total of 105 M. tuberculosis strains isolated in Addis Ababa (Ethiopia).

SIT*	Spoligotype description	Octal number	Nb (%) in study	% in study versus database	Lineage**	Clustered versus unique patterns***
10		477777277413771	1 (0.95)	1.14	EAI8-MDG	Unique
20		677777607760771	2 (1.9)	0.24	LAM1	Clustered
25		703777740003171	4 (3.81)	0.64	CAS1-Delhi	Clustered
26		703777740003771	4 (3.81)	0.26	CAS1-Delhi	Clustered
34		776377777760771	1 (0.95)	0.12	S	Unique
37		777737777760771	10 (9.52)	2.04	T3	Clustered
41		777777404760771	1 (0.95)	0.21	LAM7-TUR	Unique
50		777777777720771	1 (0.95)	0.03	H3	Unique
52		777777777760731	6 (5.71)	0.65	T2	Clustered
53		777777777760771	9 (8.57)	0.14	T1	Clustered
54		777777777763771	9 (8.57)	3.56	Manu2	Clustered
100		777777777773771	1 (0.95)	1.22	Manu1	Unique
119		777776777760771	3 (2.86)	0.28	X1	Clustered
121		777777775720771	3 (2.86)	5.77	H3	Clustered
149		777000377760771	10 (9.52)	2.07	T3-ETH	Clustered
241		777777777760411	1 (0.95)	3.7	T1	Unique
247		703777740003471	2 (1.9)	5.13	CAS1-Delhi	Clustered
289		703777740003571	2 (1.9)	15.38	CAS1-Delhi	Clustered
336		777776777760731	2 (1.9)	1.71	X1	Clustered
523		777777777777771	3 (2.86)	6.25	Manu_ancestor	Clustered
804		477777777760771	1 (0.95)	3.85	T1	Unique
1264		703777740000000	1 (0.95)	4.35	CAS1-Delhi	Unique
1338		777777777777671	1 (0.95)	16.67	Unknown	Unique
1967		703777740000031	2 (1.9)	28.57	CAS	Clustered
2693		703763740003771	1 (0.95)	11.11	CAS1-Delhi	Unique
2781		777777777767771	1 (0.95)	11.11	Unknown	Unique
2820		777777767760731	1 (0.95)	14.29	T2	Unique
3896*		777737777760000	1 (0.95)	50	T3	Unique
3897*		777347777763671	3 (2.86)	75	Manu2	Clustered
3898*		677777077413771	1 (0.95)	50	EAI2	Unique
3899*		703777700001771	1 (0.95)	50	CAS	Unique
3900*		777347777763771	2 (1.9)	66.67	Manu2	Clustered
3901*		000773777777600	2 (1.9)	66.67	BOV	Clustered
3902*		777777457413771	2 (1.9)	66.67	EAI6-BGD1	Clustered
3903*		677777407760771	1 (0.95)	50	LAM1	Unique

∗A total of 27/35 SITs containing 83 isolates matched a preexisting shared-type in the database, whereas 8/35 SITs (𝑛=13 isolates) were newly created. A total of 19/35 SITs containing 80 isolates were clustered within this study (2 to 10 isolates per cluster) while 16/35 SITs containing 16 strains were unique (for total unique strains, one should add to this number the 9 orphan strains which brings the number of unclustered isolates in this study to 25/105 (23.81%) and clustered isolates to 80/105 (76.19%)). 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: 3896* this study 𝑛=1. DEU 𝑛=1; 3897* this study 𝑛=3. USA 𝑛=1; 3898* this study 𝑛=1. AUS 𝑛=1; 3899* this study 𝑛=1. NPL 𝑛=1; 3900* this study 𝑛=2. CHN 𝑛=1; 3901* this study 𝑛=2. FXX 𝑛=1; 3902* this study 𝑛=2. MYS 𝑛=1; 3903* this study 𝑛=1. BRA 𝑛=1.
**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 1).