MIRU-VNTR genotyping and clustering of Mycobacterium tuberculosis isolates in Yichang

doi:10.3969/j.issn.1000-6621.2019.03.012

Abstract

Abstract:

Objective To determine the genotypes and clustering patterns of Mycobacterium tuberculosis in Yichang and provide evidence for use in the prevention and treatment of tuberculosis.Methods Sputum samples determined to be positive for Mycobacterium tuberculosis using gene microarrays were collected in Yichang from December 2016 to May 2017. After culturing in Roche medium, 367 Mycobacterium tuberculosis isolates were genotyped using the internationally recognised 24 locus MIRU-VNTR system, and the resolution and variation of the MIRU locus was evaluated using the Hunter-Gaston index (HGI) and genetic difference value (h). MIRU-VNTR results were analyzed using BioNumerics 5.0 software to calculate recent transmission rates. The study population of 367 strains, isolated from 367 patients, was subdivided into 321 strains isolated from new TB cases and 46 strains from relapsed cases. Clustering rates were analysed separately for each set of strains. The clustering rates for new and retreated cases were compared using the chi-square test. P<0.05 was considered statistically significant.Results Genotyping of the 367 M.tuberculosis strains using the 24 locus MIRU-VNTR system gave an HGI value of 0.999. The locus with the highest genetic diversity was QUB11b, with an h value of 0.79, and that with the lowest genetic diversity was MIRU24, with an h value of 0.03. A total of 324 genotypes were identified, polymorphisms being evident. Results from clustering analysis indicated that 90 strains formed 39 clusters, with a clustering rate of 24.52% (90/367) and the recent transmission rate of 13.90% (51/367). The clustering rate of strains from relapsed cases (21.74%, 10/46) was not significantly different from that for strains isolated from new cases (24.92%, 80/321) (χ²=0.220, P=0.639).Conclusion Tuberculosis cases in the Yichang area showed high genetic diversity and low transmission rates. Clustering rates were not linked to whether cases were new or relapsed cases.Results suggest that the majority of tuberculosis cases in Yichang are due to endogenous activation. There is also a limited amount of local transmission. Greater attention should be paid to tuberculosis prevention and control in Yichang.

Key words: Mycobacterium tuberculosis, Genotype, Tandem repeat sequences, Sequence tagged sites, Cluster analysis

Xiao-jun LIU,Feng-hua YU,Yun-fang YU,L-yu JI,Pan ZHOU,Yan-lin ZHAO. MIRU-VNTR genotyping and clustering of Mycobacterium tuberculosis isolates in Yichang[J]. Chinese Journal of Antituberculosis, 2019, 41(3): 308-314. doi: 10.3969/j.issn.1000-6621.2019.03.012

Figures/Tables 6

References 21

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位点	h值	HGI值
MIRU02	0.043	0.042
Mtub04	0.065	0.064
ETRC	0.072	0.071
MIRU04	0.294	0.293
MIRU40	0.536	0.535
MIRU10	0.536	0.535
MIRU16	0.473	0.472
Mtub21	0.791	0.790
MIRU20	0.264	0.263
位点	h值	HGI值
QUB11b	0.791	0.790
Mtub29	0.512	0.511
Mtub29	0.086	0.085
Mtub30	0.453	0.452
ETRB	0.287	0.286
MIRU23	0.072	0.071
MIRU24	0.032	0.031
MIRU26	0.735	0.734
MIRU27	0.258	0.257
Mtub34	0.082	0.081
MIRU31	0.554	0.553
Mtub39	0.082	0.081
QUB26	0.635	0.634
QUB4156	0.311	0.310
MIRU39	0.516	0.515
总分辨率	-	0.999

患者类别	菌株数	成簇菌株数	OR(95%CI)值	χ²值	P值
复治	46	10(21.74)	1.000	0.220	0.639
初治	321	80(24.92)	1.195(0.567~2.517)
合计	367	90(24.52)