Preliminary study on genotype of Mycobacterium tuberculosis in some areas of Xinjiang by the multiple locus VNTR analysis

doi:10.3877/cma.j.issn.1674-6902.2017.03.013

Abstract

Abstract:

Objective

To explore the multiple locus VNTR analysis (MLVA) of Mycobacterium tuberculosis.

Methods

It was selected that the data of the fifth TB epidemiological sampling survey in Xinjiang Uygur Autonomously Region from 2010 to 2011, and the genotyping was carried out by the classic 24 site method. The genetic clustering was analyzed by the BioNumerics5.0 database. The original strains of Mycobacterium tuberculosis, the annulus were dissolved and suspended bacterium in 400 μl TE, 80 ℃ 1 h inactivated, 12 000 r/min, the centrifugal 10 min, abandon supernatant, suspended bacterium in 600 μl TE again; multiple site tandem repeat sequence analysis.

Results

There were two genetic groups in Xinjiang: gene group Ⅰ and gene group Ⅱ, 66 strains in genetic group Ⅰ (66.7%), and 33 strains in gene strain Ⅱ (33.3%). gene growp I was Beijing genotype strains 65 different genotype from gene group of 66 strains of Mycobacterium tuberculosis Ⅰ, 2 strains of Mycobacterium tuberculosis belong to the same cluster, clusters rate was 1.5%, It was different that the gene group of Ⅱ 33 of Mycobacterium tuberculosis strain of MLVA pictures, clusters rate was 0.

Conclusion

Mycobacterium tuberculosis strains exist obvious gene polymorphism in Xinjiang, with the majority of Beijing genotype strains, and a certain proportion of strains are not Beijing genotype, we should strengthen the monitoring and management for major epidemic strains.

Key words: Tuberculosis, Mycobacterium tuberculosis, Multiple locus VNTR analysis, Gene polymorphism, Xinjiang areas

Xinji Gong, Yuehua Li, Lidan Yao, Mokomti Aynur·, Nianqiang Liu, Le Wang, Jing Wang. Preliminary study on genotype of Mycobacterium tuberculosis in some areas of Xinjiang by the multiple locus VNTR analysis[J]. Chinese Journal of Lung Diseases(Electronic Edition), 2017, 10(03): 304-308.

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References 34

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位点	H37RV片段长度	H37RV侧翼长度	H37RV重复长度	H37RV重复数	常见重复次数
QUB-11b	412bp	67bp	69bp	5次	3～7
Mtub21	206bp	92bp	57bp	2次	1～6
QUB-26	718bp	163bp	111bp	5次	3～10
QUB-4156	681bp	563bp	59bp	2次	1～5
MIRU26	438bp	285bp	51bp	3次	3～9
Mtub04	639bp	537bp	51bp	2次	2～5
ETRA	420bp	195bp	75bp	3次	2～4
MIRU40	408bp	354bp	54bp	1次	1～4
Mtub39	562bp	272bp	58bp	5次	1～6
MIRU31，ETRE	651bp	492bp	53bp	3次	4～6
MIRU10	643bp	484bp	53bp	3次	1～3
MIRU4，ETRD	353bp	122bp	77bp	3次	0～3
ETRC	382bp	150bp	58bp	4次	2～6
MIRU16	671bp	565bp	53bp	2次	2～4
Mtub30	363bp	247bp	58bp	2次	2～5
Mtub29	563bp	335bp	57bp	4次	2～4
MIRU39	646bp	540bp	53bp	2次	2～4
MIRU27，QUB-5	657bp	498bp	53bp	3次	2～3
ETRB	518bp	347bp	57bp	3次	1～2
Mtub34	488bp	326bp	54bp	3次	3～4
MIRU23	465bp	147bp	53bp	6次	5～6
MIRU20	591bp	437bp	77bp	2次	1～2
MIRU2	508bp	402bp	53bp	2次	2
MIRU24	447bp	339bp	54bp	1次	1

位点	H37RV片段长度	H37RV侧翼长度	H37RV重复长度	H37RV重复数	常见重复次数
QUB-11b	412bp	67bp	69bp	5次	3～7
Mtub21	206bp	92bp	57bp	2次	1～6
QUB-26	718bp	163bp	111bp	5次	3～10
QUB-4156	681bp	563bp	59bp	2次	1～5
MIRU26	438bp	285bp	51bp	3次	3～9
Mtub04	639bp	537bp	51bp	2次	2～5
ETRA	420bp	195bp	75bp	3次	2～4
MIRU40	408bp	354bp	54bp	1次	1～4
Mtub39	562bp	272bp	58bp	5次	1～6
MIRU31，ETRE	651bp	492bp	53bp	3次	4～6
MIRU10	643bp	484bp	53bp	3次	1～3
MIRU4，ETRD	353bp	122bp	77bp	3次	0～3
ETRC	382bp	150bp	58bp	4次	2～6
MIRU16	671bp	565bp	53bp	2次	2～4
Mtub30	363bp	247bp	58bp	2次	2～5
Mtub29	563bp	335bp	57bp	4次	2～4
MIRU39	646bp	540bp	53bp	2次	2～4
MIRU27，QUB-5	657bp	498bp	53bp	3次	2～3
ETRB	518bp	347bp	57bp	3次	1～2
Mtub34	488bp	326bp	54bp	3次	3～4
MIRU23	465bp	147bp	53bp	6次	5～6
MIRU20	591bp	437bp	77bp	2次	1～2
MIRU2	508bp	402bp	53bp	2次	2
MIRU24	447bp	339bp	54bp	1次	1

位点名称	引物序列	碱基	位点名称	引物序列	碱基
MIRU4-a(上游)	5′-gCgCgAgAgCCCgAACTgC-3′	19	Mtub21-a	5′-AgATCCCAgTTgTCgTCgTC-3′	20
MIRU4-b(下游)	5′-gCgCAgCAgAAACgCCAgC-3′	19	Mtub21-b	5′-CAACATCgCCTggTTCTgTA-3′	20
MIRU26-a	5′-TAggTCTACCgTCgAAATCTgTgAC-3′	25	QUB-26-a	5′-AACgCTCAgCTgTCggAT-3′	18
MIRU26-b	5′-CATAggCgACCAggCgAATAg-3′	21	QUB-26-b	5′-CggCCgTgCCggCCAggTCCTTCCCgAT-3′	28
MIRU40-a	5′-gggTTgCTggATgACAACgTgT-3′	22	MIRU2-a	5′-TggACTTgCAgCAATggACCAACT-3′	24
MIRU40-b	5′-gggTgATCTCggCgAAATCAgATA-3′	24	MIRU2-b	5′-TACTCggACgCCggCTCAAAAT-3′	22
MIRU10-a	5′-gTTCTTgACCAACTgCAgTCgTCC-3′	24	MIRU23-a	5′-CTgTCgATggCCgCAACAAAACg-3′	23
MIRU10-b	5′-gCCACCTTggTgATCAgCTACCT-3′	23	MIRU23-b	5′-AgCTCAACgggTTCgCCCTTTTgTC-3′	25
MIRU16-a	5′-TCggTgATCgggTCCAgTCCAAgTA-3′	25	MIRU39-a	5′-CgCATCgACAAACTggAgCCAAAC-3′	24
MIRU16-b	5′-CCCgTCgTgCAgCCCTggTAC-3′	21	MIRU39-b	5′-CggAAACgTCTACgCCCCACACAT-3′	24
MIRU31-a	5′-ACTgATTggCTTCATACggCTTTA-3′	24	MIRU20-a	5′-TCggAgAgATgCCCTTCgAgTTAg-3′	24
MIRU31-b	5′-gTgCCgACgTggTCTTgAT-3′	19	MIRU20-b	5′-ggAgACCgCgACCAggTACTTgTA-3′	24
Mtub04-a	5′-CTTggCCggCATCAAgCgCATTATT-3′	25	MIRU24-a	5′-CgACCAAgATgTgCAggAATACAT-3′	24
Mtub04-b	5′-ggCAgCAgAgCCCgggATTCTTC-3′	23	MIRU24-b	5′-gggCgAgTTgAgCTCACAgAA-3′	21
ETRC-a	5′-CgAgAgTggCAgTggCggTTATCT-3′	24	MIRU27-a	5′-TCgAAAgCCTCTgCgTgCCAgTAA-3′	24
ETRC-b	5′-AATgACTTgAACgCgCAAATTgTgA-3′	25	MIRU27-b	5′-gCgATgTgAgCgTgCCACTCAA-3′	22
ETRA-a	5′-AAATCggTCCCATCACCTTCTTAT-3′	24	Mtub29-a	5′-gCCAgCCgCCgTgCATAAACCT-3′	22
ETRA-b	5′-CgAAgCCTggggTgCCCgCgATTT-3′	24	Mtub29-b	5′-AgCCACCCggTgTgCCTTgTATgAC-3′	25
Mtub30-a	5′-CTTgAAgCCCCggTCTCATCTgT-3′	23	ETRB-a	5′-ATggCCACCCgATACCgCTTCAgT-3′	24
Mtub30-b	5′-ACTTgAACCCCCACgCCCATTAgTA-3′	25	ETRB-b	5′-CgACgggCCATCTTggATCAgCTAC-3′	25
Mtub39-a	5′-CggTggAggCgATgAACgTCTTC-3′	23	Mtub34-a	5′-ggTgCgCACCTgCTCCAgATAA-3′	22
Mtub39-b	5′-TAgAgCggCACgggggAAAgCTTAg-3′	25	Mtub34-b	5′-ggCTCTCATTgCTggAgggTTgTAC-3′	25
QUB-4156-a	5′-ggATTTAgCAggCTgACCAC-3′	20	QUB-11b-a	5′-CgTAAgggggATgCgggAAATAgg-3′	24
QUB-4156-b	5′-TTACCACCCgggCAgTTTAC-3′	20	QUB-11b-b	5′-CgAAgTgAATggTggCAT-3′	18

位点名称	引物序列	碱基	位点名称	引物序列	碱基
MIRU4-a(上游)	5′-gCgCgAgAgCCCgAACTgC-3′	19	Mtub21-a	5′-AgATCCCAgTTgTCgTCgTC-3′	20
MIRU4-b(下游)	5′-gCgCAgCAgAAACgCCAgC-3′	19	Mtub21-b	5′-CAACATCgCCTggTTCTgTA-3′	20
MIRU26-a	5′-TAggTCTACCgTCgAAATCTgTgAC-3′	25	QUB-26-a	5′-AACgCTCAgCTgTCggAT-3′	18
MIRU26-b	5′-CATAggCgACCAggCgAATAg-3′	21	QUB-26-b	5′-CggCCgTgCCggCCAggTCCTTCCCgAT-3′	28
MIRU40-a	5′-gggTTgCTggATgACAACgTgT-3′	22	MIRU2-a	5′-TggACTTgCAgCAATggACCAACT-3′	24
MIRU40-b	5′-gggTgATCTCggCgAAATCAgATA-3′	24	MIRU2-b	5′-TACTCggACgCCggCTCAAAAT-3′	22
MIRU10-a	5′-gTTCTTgACCAACTgCAgTCgTCC-3′	24	MIRU23-a	5′-CTgTCgATggCCgCAACAAAACg-3′	23
MIRU10-b	5′-gCCACCTTggTgATCAgCTACCT-3′	23	MIRU23-b	5′-AgCTCAACgggTTCgCCCTTTTgTC-3′	25
MIRU16-a	5′-TCggTgATCgggTCCAgTCCAAgTA-3′	25	MIRU39-a	5′-CgCATCgACAAACTggAgCCAAAC-3′	24
MIRU16-b	5′-CCCgTCgTgCAgCCCTggTAC-3′	21	MIRU39-b	5′-CggAAACgTCTACgCCCCACACAT-3′	24
MIRU31-a	5′-ACTgATTggCTTCATACggCTTTA-3′	24	MIRU20-a	5′-TCggAgAgATgCCCTTCgAgTTAg-3′	24
MIRU31-b	5′-gTgCCgACgTggTCTTgAT-3′	19	MIRU20-b	5′-ggAgACCgCgACCAggTACTTgTA-3′	24
Mtub04-a	5′-CTTggCCggCATCAAgCgCATTATT-3′	25	MIRU24-a	5′-CgACCAAgATgTgCAggAATACAT-3′	24
Mtub04-b	5′-ggCAgCAgAgCCCgggATTCTTC-3′	23	MIRU24-b	5′-gggCgAgTTgAgCTCACAgAA-3′	21
ETRC-a	5′-CgAgAgTggCAgTggCggTTATCT-3′	24	MIRU27-a	5′-TCgAAAgCCTCTgCgTgCCAgTAA-3′	24
ETRC-b	5′-AATgACTTgAACgCgCAAATTgTgA-3′	25	MIRU27-b	5′-gCgATgTgAgCgTgCCACTCAA-3′	22
ETRA-a	5′-AAATCggTCCCATCACCTTCTTAT-3′	24	Mtub29-a	5′-gCCAgCCgCCgTgCATAAACCT-3′	22
ETRA-b	5′-CgAAgCCTggggTgCCCgCgATTT-3′	24	Mtub29-b	5′-AgCCACCCggTgTgCCTTgTATgAC-3′	25
Mtub30-a	5′-CTTgAAgCCCCggTCTCATCTgT-3′	23	ETRB-a	5′-ATggCCACCCgATACCgCTTCAgT-3′	24
Mtub30-b	5′-ACTTgAACCCCCACgCCCATTAgTA-3′	25	ETRB-b	5′-CgACgggCCATCTTggATCAgCTAC-3′	25
Mtub39-a	5′-CggTggAggCgATgAACgTCTTC-3′	23	Mtub34-a	5′-ggTgCgCACCTgCTCCAgATAA-3′	22
Mtub39-b	5′-TAgAgCggCACgggggAAAgCTTAg-3′	25	Mtub34-b	5′-ggCTCTCATTgCTggAgggTTgTAC-3′	25
QUB-4156-a	5′-ggATTTAgCAggCTgACCAC-3′	20	QUB-11b-a	5′-CgTAAgggggATgCgggAAATAgg-3′	24
QUB-4156-b	5′-TTACCACCCgggCAgTTTAC-3′	20	QUB-11b-b	5′-CgAAgTgAATggTggCAT-3′	18

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