Optimizing multiplex SNP-based data analysis for genotyping of Mycobacterium tuberculosis isolates

BMC Genomics

Table 1 Comparison of MLPA lineage types and spoligotypes

	Lineage type by spoligotyping
Lineage type by MLPA	Beijing	H1	H3	LAM1	LAM5	LAM9	T5-RUS1 (LAM)^a	T5-RUS1	MANU2	T1	T1-RUS2	T2	T3	T4	T5	Ural-1^b	Unknown	Unknown (LAM)^a	Not reported before	Not-interpretable
Beijing K1 (n = 28)	28
Beijing V+/CHIN + (n = 5)	5
Beijing SA-/CHIN- (n = 1)	1
Beijing V- (n = 1)																	1
MTB4 other than LAM or Haarlem (n = 40)			1						1	8	1		1	1	1	9	13		4
LAM (n = 16)				3	1	1	2	3				1					3	1	1
Haarlem (n = 8)		2	6
Non-interpretable (n = 1)																				1
Total (100 isolates)	34	2	7	3	1	1	2	3	1	8	1	1	1	1	1	9	17	1	5	1

Lineage types were obtained from spoligotyping using the SITVITWEB database. a, isolates were identified as T5-RUS1 or Unknown according to SITVITWEB but LAM according to their spoligotype identification type [41]; b, isolates were identified as Ural-1 on the basis of their SIT according to [42]; Numbers in bold indicate disagreement between MLPA and spoligotyping.

ISSN: 1471-2164