Distribution and Frequency of rpoB Mutations Detected by Xpert MTB/RIF Assay Among Beijing and Non-Beijing Rifampicin Resistant Mycobacterium tuberculosis Isolates in Bangladesh

Figures & data

Table 1 Association of Demographic Profile and Mutations at Different Probe Sites Among the RR-TB Cases

Category	Probe Type									Total (%)
	A	B	C	D	E	AB	AD	AE	BE
Sex
Male	5	24	5	20	78*	1	2	0	1	136 (66.3)
Female	1	7	0	5	55	0	0	1	0	69 (33.7)
Treatment history
New cases	0	0	0	0	3	0	0	0	0	3 (1.5)
Previously treated	6	31	5	25	130	1	2	1	1	202 (98.5)
Age (years)
≤15	0	0	0	1	1	0	0	0	0	2 (0.9)
15–24	1	10	0	7	54*	0	0	1	1	74 (36.1)
25–34	2	8	1	3	40*	0	1	0	0	55 (26.8)
35–44	0	8	2	6	16*	0	0	0	0	32 (15.6)
45–54	3	1	1	2	13	0	1	0	0	21 (10.3)
≥55	0	4	1	6	9	1	0	0	0	21(10.3)

Note: *Significant at p≤0.001.

Table 2 Pattern of Probe Dropouts in Xpert Assay Among Beijing and Non-Beijing RR-TB Isolates

Probe Dropout	No. (%) of Isolates		p-value
	Beijing (n= 84)	Non-Beijing (n= 121)
A	3 (3.6)	3 (2.5)	0.36
B	16 (19.0)	15 (12.4)
C	1 (1.2)	4(3.3)
D	9 (10.7)	16 (13.2)
E	52 (61.9)	81 (66.9)
A, D	0 (0)	2 (1.7)
A, E	1 (1.2)	0 (0)
B, E	1 (1.2)	0 (0)
A, B	1 (1.2)	0 (0)

Table 3 Detection of Probe Dropout Among Different Lineages in RR-TB Cases

Probe Dropout	Spoligotypes n (%)
	CAS	EAI	LAM	T1	Orphan	Others*
A	0	1 (5.6)	0	0	2 (7.7)	0
B	6 (27.2)	0	0	6 (17.2)	3 (11.5)	0
C	0	3 (16.6)	0	1 (2.8)	0	0
D	2 (9.1)	5 (27.8)	1 (5.6)	4 (11.4)	4 (15.4)	0
E	14 (63.7)	9 (50)	17 (94.4)	22 (62.9)	17 (65.4)	2 (100)
A, D	0	0	0	2 (5.7)	0	0
Total (121)	22 (100)	18 (100)	18 (100)	35 (100)	26 (100)	2 (100)

Note: *Indicates H3 and S genotypes.

Table 4 Frequency of Specific Mutations Based on MTBDRplus Probe Binding Among the Beijing and Non-Beijing Isolates (n=205)

Specific Mutation in MTBDRplus	WT Failure/MUT Probe Binding	Beijing	Non-Beijing	Frequency
		n (%)	n (%)	n (%)
F505L/T508A/S509T	WT1	1(1.2)	0	1(0.5)
E510H/L511P	WT2	1(1.2)	3 (2.5)	4(1.9)
Q513L/Q513P/	WT2/3	4 (4.7)	0 (0.82)	4(1.9)
D516V	WT3/4, MUT 1	12 (14.3)	11(9.0)	23 (11.2)
N518I	WT4/5	0	0	0
S522L, S522Q	WT5/6	1(1.2)	4 (3.3)	5 (2.4)
H526D	WT7, MUT 2B	2 (2.4)	15 (12.4)	17 (8.3)
H526Y	WT7, MUT 2A	10 (11.9)	4 (3.3)	14 (6.8)
S531L	WT8, MUT 3	53 (63.0)	84 (69.4)	137 (66.8)
Total		84 (100)	121 (100)	205 (100)

Table 5 Comparison of Specific Probe Mutations Based on Xpert and MTBDRplus Assay Among the Beijing and Non-Beijing Isolates (n=200)

Xpert Probes (Codons)	MTBDRplus WT/MUT Probes	Beijing n (%)		Non-Beijing n (%)		Overall n (%)
		Concordance	Discordance	Concordance	Discordance	Concordance	Discordance
Probe A (507–512)	WT1/WT2	2 (66.7)	1 (33.3)	3 (100)	0	5 (83.3)	1 (16.7)
Probe B (512–517)	WT2/3, WT3/4, MUT1	14 (87.5)	2 (12.5)	10 (66.7)	5 (33.3)	24 (77.4)	7 (22.6)
Probe C (518–522)	WT4/5, WT5/6	1 (100)	0	4 (100)	0	5(100)	0
Probe D (523–528)	WT7/MUT2A/2B	8 (88.8)	1 (11.2)	16 (100)	0	24 (96.0)	1 (4.0)
Probe E (528–533)	WT8/MUT3	50 (96.1)	2 (3.9)	80 (98.7)	1 (1.3)	130 (97.7)	3 (2.3)
Total		75 (92.6)	6 (7.4)	113 (94.1)	6 (5.9)	188 (93.7)	12 (6.3)

Figure 1 Geographical distribution of probe mutations detected by Xpert assay among the Beijing and non-Beijing MTB isolates. Individual shape with different color denoted as different probe mutation among Beijing and non-Beijing isolates. Different colors on the map indicate seven divisions of Bangladesh.