Direct detection of rifampicin and isoniazid resistance-associated genes in clinical specimens from the patients with tuberculosis using gene chip

doi:10.3969/j.issn.1000-6621.2019.02.004

Abstract

Abstract:

Objective To study the clinical value of direct detection on Mycobacterium tuberculosis (MTB) rifampicin (RFP) and isoniazid (INH) resistance-related genes in clinical specimens from the patients with tuberculosis (TB) by gene chip. Methods A retrospective analysis of 125 clinical specimens identified as MTB by culture using the media with nitrobenzoic acid (PNB) and thiophene-carboxylic acid hydrazide (TCH) was carried out, including sputum specimens (n=90), bronchial lavage fluid (n=12), pus (n=12), pleural effusion (n=6), tissue specimens (n=3), peritoneal effusion (n=1) and urine specimen (n=1). RFP and INH susceptibility tests were performed simultaneously by absolute concentration method, and MTB rpoB, katG and inhA genotypes in clinical specimens were detected directly by gene chip. Using absolute concentration method as control, the sensitivities and specificities of gene chips for detecting RFP, INH resistance and multidrug resistance (MDR) were evaluated, and the consistency of the two methods was compared. Results Of 125 clinical specimens from TB patients, the results of absolute concentration method showed that RFP-, INH- and multidrug-resistant (MDR) rates were respectively 20.0% (25/125) (88.0% (22/25) high level resistance and 12.0% (3/25) low level resistance), 17.6% (22/125) (18.2% (4/22) high level resistance and 81.8% (18/22) low level resistance) and 16.8% (21/125). The detection rates of MDR-MTB were 7.6% (7/92) and 39.4% (13/33) in the clinical specimens from primary and recurrent TB patients, respectively. Compared with absolute concentration method, the sensitivities of detecting RFP-, INH-resistant and MDR-MTB were 72.0% (18/25), 63.6% (14/22) and 61.9% (13/21) by gene chip, respectively. The specificity was 91.0% (91/100), 86.4% (89/103) and 89.4% (93/104), respectively. The consistency rates of the two methods were 87.2% (109/125), 82.4% (103/125) and 84.8% (106/125), respectively. Conclusion MTB, RFP, and INH resistance-related gene mutation detection in clinical samples of TB patients have moderate sensitivities and high specificities by gene chip. It can be used to quickly detect RFP-, INH-resistant, and MDR-MTB to provide experimental basis for early effective chemotherapy.

Key words: Specimen handling, Tuberculosis,multidrug-resistant, Nucleic acid probes, Point mutation, Microbial sensitivity tests, Rifampin, Isoniazid, Comparative study

Xue-juan BAI,Yin-ping LIU,Jun-xian ZHANG,Jie WANG,Xue-qiong WU. Direct detection of rifampicin and isoniazid resistance-associated genes in clinical specimens from the patients with tuberculosis using gene chip[J]. Chinese Journal of Antituberculosis, 2019, 41(2): 138-144. doi: 10.3969/j.issn.1000-6621.2019.02.004

Figures/Tables 5

References 24

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结核病患者	例数	绝对浓度法药敏试验[例数(构成比,%)]
结核病患者	例数	MDR	单耐RFP	单耐INH	对RFP、INH敏感
初治	92	7(7.6)	3(3.3)	1(1.1)	81(88.0)
复治	33	13(39.4)	2(6.1)	0(0.0)	18(54.5)

例数	RFP绝对浓度法药敏试验	RFP基因型(rpoB)	INH绝对浓度法药敏试验	INH基因型
例数	RFP绝对浓度法药敏试验	RFP基因型(rpoB)	INH绝对浓度法药敏试验	katG	inhA
87	敏感	野生型	敏感	野生型	野生型
1	敏感	野生型	敏感	315(AGC>ACC)	野生型
3	敏感	野生型	敏感	野生型	-15(C>T)
1	敏感	531(TCG>TTG)	敏感	野生型	野生型
5	敏感	531(TCG>TTG)	敏感	315(AGC>ACC)	野生型
1	敏感	526(CAC>TAC)	敏感	315(AGC>ACC)	野生型
1	敏感	513(CAA>CCA)	敏感	野生型	-15(C>T)
1	敏感	531(TCG>TTG)	高度耐药	315(AGC>ACC)	-15(C>T)
1	高度耐药	野生型	敏感	野生型	野生型
2	高度耐药	531(TCG>TTG)	敏感	野生型	-15(C>T)
1	高度耐药	516(GAC>TAC),531(TCG>TTG)	敏感	野生型	-15(C>T)
1	高度耐药	531(TCG>TTG)	高度耐药	315(AGC>ACC)	野生型
5	高度耐药	531(TCG>TTG)	低度耐药	315(AGC>ACC)	野生型
1	高度耐药	526(CAC>CGC)	低度耐药	315(AGC>ACC)	野生型
1	高度耐药	526(CAC>TAC)	低度耐药	315(AGC>ACC)	野生型
2	高度耐药	531(TCG>TTG)	低度耐药	野生型	-15(C>T)
1	高度耐药	526(CAC>TAC)	高度耐药	野生型	-15(C>T)
2	低度耐药	531(TCG>TTG)	低度耐药	315(AGC>ACC)	野生型
2	高度耐药	531(TCG>TTG)	低度耐药	野生型	野生型
1	高度耐药	野生型	高度耐药	野生型	野生型
4	高度耐药	野生型	低度耐药	野生型	野生型
1	低度耐药	野生型	低度耐药	野生型	野生型

检测技术	绝对浓度法药敏试验(例)						敏感度 (%)	特异度 (%)	阳性预测值(%)	阴性预测值(%)	一致率 (%)
检测技术	耐RFP (25)	不耐RFP (100)	耐INH (22)	不耐INH (103)	MDR (21)	非MDR (104)	敏感度 (%)	特异度 (%)	阳性预测值(%)	阴性预测值(%)	一致率 (%)
耐药基因芯片检测
耐RFP(27)	18^a	9^b	16	11	15	12	72.0	91.0	66.7	92.9	87.2
不耐RFP(98)	7^c	91^d	6	92	6	92
耐INH(28)	16	12	14^a	14^b	13	15	63.6	86.4	50.0	91.8	82.4
不耐INH(97)	9	88	8^c	89^d	8	89
耐多药(24)	16	8	14	10	13^a	11^b	61.9	89.4	54.2	92.1	84.8
非耐多药(101)	9	92	8	93	8^c	93^d