Improved real-time PCR for rapid detection of rifampin and isoniazid resistance in Mycobacterium tuberculosis clinical isolates

In this study we designed two pairs of probes for the detection of rifampin and isoniazid resistance in Mycobacterium tuberculosis with real-time PCR procedures. One pair of probes spans the region between codon 510 and 528 of the rpoB gene, and the other one screens for mutation at the regulatory region of the inhA gene. We have evaluated these probes in combination with two other pairs of probes previously described to detect mutations in 20 susceptible and 53 unique resistant M. tuberculosis clinical isolates. We were able to detect nine different mutations affecting five codons of the rpoB gene, two different mutations at codon 315 of the katG gene and a nucleotide substitution (C209T) in the regulatory region of the inhA gene within two hours turnaround.     

反相斑点杂交快速检测结核分枝杆菌rpoB基因突变

目的 建立以聚合酶链反应(PCR)为基础的寡核甘酸探针反相斑点杂交方法快速检测对利福平耐药的结核菌相关的rpoB基因突变，并评价其临床应用价值。方法 应用PCR-反相斑点杂交方法对利福平耐药的62株结核菌和对其敏感的40株结核菌进行检测，所得结果与传统药敏试验结果以及102株结核菌的直接测序结果进行比较。结果 62株对利福平耐药的菌株中，54株碱基突变被准确鉴定，灵敏度为87．1％(54／62)，阳性预测值为：100％；40株对利福平敏感的菌株均被准确鉴定，特异性为100％，阴性预测值为83．3％(40／48)；准确度为92．2％(94／102)。与测序法结果符合率为99％。结论 以PCR为基础的反相斑点杂交方法其敏感度和特异性均高，无假阳性结果，因此适用于大批量结核菌对利福平耐药性的初筛。     

Direct detection in clinical samples of multiple gene mutations causing resistance of Mycobacterium tuberculosis to isoniazid and rifampicin using fluorogenic probes

BACKGROUND: This study evaluates a method based on real-time PCR for direct detection in clinical samples of the common mutations responsible for isoniazid and rifampicin resistance of Mycobacterium tuberculosis. METHODS: Six pairs of fluorogenic 5' exonuclease probes (Taqman), mutated and wild-type, were designed for six targets: codon 315 of katG, substitution C209T in the regulatory region of inhA, and codons 513, 516, 526 and 531 of rpoB. RESULTS: A total of 98 clinical samples harbouring resistant bacilli from 55 patients and 126 samples harbouring susceptible bacilli from 126 patients were processed. The isolates from samples were tested for drug susceptibility with the radiometric method and sequenced for the same genetic targets. Among the samples, 93 harboured isoniazid-resistant bacilli. According to the sequencing results, 30 had mutations in katG, 30 in inhA and 33 (35.4%) had no mutations in these targets. All 27 clinical specimens harbouring rifampicin-resistant bacilli showed mutations in rpoB. The detection threshold of this method in detecting target genes in serial dilutions of artificial samples was 1.5 x 10(3) cfu/mL. In clinical samples, the sensitivity ranged from 30.4 to 35.3% for smear-negative samples and from 95.1 to 99.2% for smear-positive samples, with a specificity of 100%. In this study, the overall sensitivity in detecting patients having the target mutations was 74.3%. CONCLUSIONS: The main advantage of the described method is the possibility of detecting rifampicin and isoniazid resistance within 48-72 h after sample collection, with a sensitivity of nearly 100% in smear-positive samples if the chosen target is responsible for the resistance.     

Evaluation of the CombiChip Mycobacteria Drug-Resistance detection DNA chip for identifying mutations associated with resistance to isoniazid and rifampin in Mycobacterium tuberculosis

The CombiChip Mycobacteriatrade mark Drug-Resistance Detection DNA chip, recently developed by GeneIn (Pusan, South Korea), is an oligonucleotide microchip coupled with polymerase chain reaction for the detection of mutations associated with resistance to isoniazid (INH) and rifampin (RIF). This oligonucleotide chip was compared with DNA sequencing and phenotypic drug susceptibility testing with 69 INH- and/or RIF-resistant and 27 all tested drug-susceptible Mycobacterium tuberculosis isolates. Two selected codons (the katG codon 315 and inhA15) allowed identification of 84.1% of INH-resistant isolates and 100% of RIF resistance were detected by screening for 7 codons: rpoB511, rpoB513, rpoB516, rpoB522, rpoB526, rpoB531, and rpoB533. The overall specificity of this oligonucleotide chip for detecting INH and RIF resistance were 100 and 95.3%, respectively. This level of sensitivity and specificity is concordant with that from the determination of M. tuberculosis drug resistance by DNA sequencing. This oligonucleotide chip is a rapid and reliable genotypic method capable of detecting multiple mutations associated with INH and RIF resistance simultaneously in a single microchip slide.     

焦磷酸测序技术检测结核分枝杆菌四种药物耐药性

目的 利用焦磷酸测序技术检测结核分枝杆菌对利福平、异烟肼、氧氟沙星、阿米卡星的耐药性,并对其临床应用进行评价.方法 收集上海市肺科医院2008-2009年临床确诊的肺结核患者的痰标本培养阳性结核分枝杆菌89株.所有菌株按<结核病诊断实验室检验规程>进行分枝杆菌培养、菌种鉴定.另外10株已知药敏结果的结核分枝杆菌来自上海市肺科医院菌株库.利用焦磷酸测序技术,以10株已知药敏结果和经直接测序已知耐药基因突变情况的结核分枝杆菌为试验菌株,探索焦磷酸测序检测结核分枝杆菌rpoB、katG、gyrA、rrs耐药基因的最佳模式,并用该条件检测89株结核分枝杆菌临床分离株,检测结果与Bactec 960药敏法进行比较.结果 rpoB、gyrA基因检测宜采用焦磷酸测序序列分析模式,katG、rrs基因检测宜采用焦磷酸测序单核苷酸多态性模式.以Bactec 960药敏法测定结果为判断标准,则焦磷酸测序法检测89株结核分枝杆菌临床分离株对利福平、异烟肼、氧氟沙星、阿米卡星耐药性的敏感度分别为98.0%、64.1%、79.5%、78.3%,特异度分别为97.5%、100.0%、90.0%、100.0%,准确性分别为97.8%、77.5%、85.4%、94.4%,该法检测利福平、氧氟沙星、阿米卡星的检测结果与Bactec 960药敏检测结果一致性较好,Kappa值均≥0.7.结论 焦磷酸测序技术检测结核分枝杆菌对利福平、异烟肼、氧氟沙星、阿米卡星耐药性具有快速、准确、高通量的优点,是一种可对结核分枝杆菌多种药物耐药性进行快速检测的方法.

Abstract：

Objective To develop an assay to determine Mycobacterium tuberculosis resistance to rifampin, isoniazid, ofloxacin and amikacin by pyrosequencing and evaluate the value of this method in clinical application. Methods Eighty-nine clinical isolates of Mycobacterium tuberculosis from tuberculosis patients were collected from Shanghai Pulmonary Hospital during 2008 to 2009. All strains were isolated from decontaminated sputum, cultured on Lowenstein-Jensen media and identified by traditional biochemical tests with standard methods. Ten Mycobacterium tuberculosis were selected from the strain bank of Shanghai Pulmonary Hospital. The optimal conditions of detection of rpoB, katG, gyrA and rrs gene by pyroseuencing were determined, using the 10 Mycobacterium tuberculosis strains whose drug susceptibility of Bactec 960 and sequence of rpoB, katG, gyrA, rrs gene were known. Then the drug susceptibility of 89 Mycobacterium tuberculosis clinical isolate strains were detected by pyrosequencing using this conditions and the results were compared with that of the Bactec 960 methods. Results The pyrosequencing program of sequence analysis was suitable for the detection of the mutations of rpoB and gyrA genes, and the program of single nucleotide polymorphism was suitable for katG and rrs genes. Among the 89 Mycobacterium tuberculosis clinical isolates,when using the drug susceptibility of Bactec 960 as the standard, the sensitivity of rifampin, isoniazid,ofloxacin and amikacin is 98.0%, 64. 1%, 79.5%, 78. 3% respectively, the specificity is 97.5%,100. 0%, 90. 0%, 100. 0% respectively, the accuracy is 97.8%, 77. 5%, 85.4%, 94. 4% respectively,tested by pyrosequencing. The results of the detection of resistance to rifampin, isoniazid, ofloxacin and amikacin in Mycobacterium tuberculosis using pyrosequencing technique were almost the same with that of Bactec 960, and Kappa ≥0. 7 in each detection. Conclusion Pyrosequencing is thus a rapid, accurate and high throughput method for detecting Mycobacterium tuberculosis resistance to these four drugs.     

显色法芯片检测结核分枝杆菌利福平与异烟肼耐药基因的临床应用

目的观察离心柱法抽提、显色法芯片检测结核分枝杆菌(MTB)利福平(RIF)与异烟肼(INH)耐药基因的临床应用价值。方法离心柱法直接抽提痰液中MTBDNA,显色法芯片检测69例结核患者、30例非结核患者痰液和H37Rv标准MTB株DNArpoB、katG、inhA和ahpC4个基因片段多态性。结果42例RIF耐药组rpoB区基因总突变率为90.4%,rpoB511、513、516、526、531位点突变率分别为9.5%、9.5%、7.1%、40.4%、38.0%,有1例未检出芯片信号;46例INH耐药组katG、inhA、ahpC区域突变率分别为58.6%、19.5%、6.5%,有4例未检出芯片信号;30例非结核病人痰液芯片检测结果均为阴性,H37Rv标准株为野生型。结论离心柱法抽提、显色法芯片检测结核分枝杆菌RIF和INH耐药基因方法灵敏、特异、简便,无需特殊仪器,对指导临床用药价值较大。     

焦磷酸测序技术快速检测结核分枝杆菌利福平耐药性研究

目的利用焦磷酸测序技术，建立一种高通量结核分枝杆菌利福平耐药性快速基因检测方法。方法应用生物素标记的引物扩增rpoB基因片段，经链亲和素标记的磁珠分离制备单链模板，设计2个测序引物在焦磷酸测序仪上检测rpoB基因耐药突变区的81bp序列突变情况，与H。Rv序列比对后判断耐药结果。结果通过建立的基于焦磷酸测序技术的结核分枝杆菌rpoB基因突变检测平台，32株利福平耐药株均在rpoB基因片段上检测到突变，22株利福平敏感株未检测到突变，检测结果与直接测序符合率达100％。结论本方法可快速、准确、高通量检测结核分枝杆菌耐利福平rpoB基因突变。     

分子信标荧光探针检测结核分枝杆菌的临床应用

目的:探讨分子信标荧光探针检测结核分枝杆菌的临床应用价值。方法:应用设置内参照的分子信标荧光探针检测178例肺结核标本,并与痰涂片和培养结果进行比较。结果:肺结核组分子信标荧光探针阳性率显著高于痰涂片和培养,检出率分别为56.2%(100/178),34.8%(62/178)、34.8%(62/178)。结论:分子信标荧光探针具有较高的灵敏度和特异度,对结核病的辅助诊断有一定的临床意义。     

RIFO杂交和限制性片段长度多态性检测耐利福平和异烟肼的结核分枝杆菌

目的评价利福平寡核苷酸探针杂交技术（RIFO杂交）和PCR-限制性片段长度多态性（PCR-RFLP）在结核分枝杆菌（MTB）耐利福平（RIF）和异烟肼（INH）快速检测中的应用价值。方法选取121株北京地区MTB菌株，分别采用RIFO杂交技术和PCR—RFLP检测RIF耐药相关基因rpoB核心区和INH耐药相关基因katG315位点突变，并对所有菌株的rpoB基因核心区进行测序验证。结果RIFO杂交检测发现，91，5％（65／71）的RIF耐药株和92．9％（52／56）的耐多药菌株（至少对RIF和INH耐药）存在rpoB基因核心区突变，而RIF敏感株中未发现突变；RIFO杂交与测序结果完全一致，测序结果中有突变的位点在RIFO杂交中均有相应的野生型杂交信号缺失；PCR-RFLP结果显示，INH耐药株中katG315突变率为60.6％（40／66）。结论rpoB基因核心区可作为RIF耐药检测的分子标志及耐多药的筛选指标；RIFO杂交技术是检测MTB耐RIF的快速、准确的实验方法，具有推广及潜在的临床应用价值；PCR—RFLP可检测出大部分INH耐药株，可作为临床INH耐药性检测的辅助手段。     

应用多重PCR-单链构象多态性分析同时检测耐异烟肼和利福平的结核分枝杆菌

目的 探讨应用多重PCR-单链构象多态性分析(multiplexpulymerase chain reaction-single strand conformation polymorphism,multi-PCR-SSCP)方法快速、特异地同时快速检测结核分枝杆菌对异烟肼和利福平耐药性的效能.方法 根据结核分枝杆菌的inhA序列、katG序列、rpoB序列,分别设计出3对特异性寡聚核苷酸引物.采用multi-PCR-SSCP技术,一次性检出耐异烟肼和利福平的结核分枝杆菌.新方法的有效性通过116株临床分离株(70株耐异烟肼,66株耐利福平)的验证.结果 名 Multi-PCR-SSCP方法检测临床分离株基因突变的有效性,以细菌培养和药敏试验结果为金标准.116株临床分离株和H37Rv标准株中除了4株katG缺失突变,其余菌株3个基因katG、inhA和rpoB在单基因PCR中都扩增成功.与H37Rv标准株相比,46株katG基因突变,14株inhA基因突变,58株rpoB基因突变.38株katG和rpoB,4株inhA和rpoB,4株inhA和katG同时突变,还有2株3个基因都有突变.multi-PCR-SSCP对于耐异烟肼和利福平的结核分枝杆菌检出的敏感度分别为80%、82%,特异度分别为100%和92%.结论 multi-PCR-SSCP方法敏感、特异,能同时快速有效地检测耐多药结核分枝杆菌,有望成为临床指导用药的好方法,为深入研究耐药基凶检测奠定了良好的基础.     

结核分枝杆菌对利福平和异烟肼耐药基因突变快速检测方法的建立

目的建立结核分枝杆菌对利福平和异烟肼耐药基因突变的快速检测方法。方法根据结核分枝杆菌标准株H37Rv序列，自行设计覆盖rpoB、katG、inhA基因突变区的系列寡核苷酸探针，并检测临床样品中结核分枝杆菌的基因突变情况，以此来判断耐药结果。结果在56个利福平耐药菌株中，有50个菌株都在rpoB基因上榆出有突变，利福平耐药突变检出率为89．3％（50／56）；有30个利福平敏感菌株rpoB基因上都未检出突变。有58个异烟肼培养的耐药菌株中有47个在katG或inhA基因上检出有突变，异烟肼耐药突变检出率为81．0％（47／58）；有30个异烟肼敏感菌株katG或inhA基因上未检出突变。结论用膜芯片检测结核分枝杆菌对利福平和异烟肼的耐药性，具有较高的特异性和敏感性，可用于临床结核分枝杆菌耐药性的检测。     

Effect of rpoB mutations conferring rifampin resistance on fitness of Mycobacterium tuberculosis

Rifampin is a major drug used in the treatment of tuberculosis infections, and increasing rifampin resistance represents a worldwide clinical problem. Resistance to rifampin is caused by mutations in the rpoB gene, encoding the beta-subunit of RNA polymerase. We examined the effect of three different rpoB mutations on the fitness of Mycobacterium tuberculosis. Rifampin-resistant mutants were isolated from a virulent clinical isolate of M. tuberculosis (strain Harlingen) in vitro at a mutation frequency of 2.3 x 10(-8). Mutations in the rpoB gene were identified, and the growth rates of three defined mutants were measured by competition with the susceptible parent strain in laboratory medium and by single cultures in a macrophage cell line and in laboratory medium. All of the mutants showed a decreased growth rate in the three assays. The relative fitness of the mutants varied between 0.29 and 0.96 (that of the susceptible strain was set to 1.0) depending on the specific mutant and assay system. Unexpectedly, the relative fitness ranking of the mutants differed between the different assays. In conclusion, rifampin resistance is associated with a cost that is conditional.     

Rapid, sensitive, and specific detection of Mycobacterium tuberculosis complex by real-time PCR on paraffin-embedded human tissues

The detection of Mycobacterium tuberculosis complex (MTB) in clinical specimens is important for diagnosing and caring for patients in whom tuberculosis is clinically suspected. We collected 129 FFPE specimens, including 56 nontuberculosis cases, 63 MTB cases, and 10 nontuberculous mycobacteria (NTM) cases determined by acid-fast bacilli (AFB) culture. We performed AFB staining; nested MTB PCR, targeting the IS6110 gene; and real-time MTB PCR, targeting the senX3-regX3 intergenic region in the 129 FFPE specimens. The sensitivity and specificity of AFB staining were 37.0% and 98.2%, respectively, using AFB culture results as the reference standard. The sensitivity and specificity of detecting MTB were 68.3% and 98.5%, respectively, by nested PCR; and 74.6% and 98.5% by real-time PCR, respectively. Among the 129 specimens, four were positive by AFB staining but negative by nested or real-time PCR. NTM grew in all four of these cases by AFB culture. AFB density in FFPE tissue sections significantly correlated with MTB DNA load. Thus, real-time PCR is a useful diagnostic tool for rapid and sensitive MTB detection in FFPE specimens, whereas NTM should be included in differential diagnoses of cases positive by AFB staining but negative by PCR.     

Rapid detection of specific gene mutations associated with isoniazid or rifampicin resistance in Mycobacterium tuberculosis clinical isolates using non-fluorescent low-density DNA microarrays

BACKGROUND: A new, fast 'low cost and density' DNA microarray (LCD array), designed for the detection of mutations that confer isoniazid or rifampicin resistance in Mycobacterium tuberculosis isolates, has been developed and was evaluated using 46 resistant clinical isolates from Barcelona. METHODS: LCD chips are pre-structured polymer supports using a non-fluorescent detection principle based on the precipitation of a clearly visible dark substrate. One LCD chip consists of eight identical microarrays, designed to detect mutations within the 90 bp rpoB region, codon 315 in the katG gene and the mabA-inhA regulatory region. A total of 22 strains with a katG 315 mutation, 19 strains with alterations in the mabA-inhA regulatory region and 16 strains with mutations in the rpoB region, characterized previously, were studied. RESULTS: The identification of S315T and S315N mutations using the LCD was 100% concordant with the sequencing data. A strain with the S315R mutation, which is not tiled on the LCD array, was detected by the absence of hybridization using the wild-type probe. Of 19 strains with low-level isoniazid resistance related to the mabA-inhA regulatory region, 18 were identified correctly. The detection of mutations in the rpoB region was 93.8% concordant with the sequencing data. One mabA-inhA and rpoB mutated strain showed a cross-hybridization. CONCLUSIONS: The LCD array protocol takes 45 min (15 min 'hands-on' time) after prior PCR amplification. Only minimal laboratory equipment is required. LCD arrays provide a rapid and economical method to characterize mutations in codon 315 of the katG gene, in the mabA-inhA regulatory region and in the rpoB gene.     

Concentration-dependent Mycobacterium tuberculosis killing and prevention of resistance by rifampin

Rifampin is a cornerstone of modern antituberculosis therapy. However, rifampin's half-life of 3 h is believed to limit its utility for intermittent therapy, so new congeners with long half-lives are being developed. Using an in vitro pharmacokinetic-pharmacodynamic model of tuberculosis, we examined the relationships between rifampin exposure, microbial killing of log-phase-growth Mycobacterium tuberculosis, and suppression of resistance. Rifampin's microbial killing was linked to the area under the concentration-time curve-to-MIC ratio. The suppression of resistance was associated with the free peak concentration (C(max))-to-MIC ratio and not the duration that the rifampin concentration was above MIC. Rifampin prevented resistance to itself at a free C(max)/MIC ratio of > or =175. The postantibiotic effect duration was > or =5.2 days and was most closely related to the C(max)/MIC ratio (r(2) = 0.96). To explain rifampin's concentration-dependent effect, we examined the kinetics of rifampin entry into M. tuberculosis. Rifampin achieved concentration-dependent intracellular steady-state concentrations within 15 min. Our results suggest that doses of rifampin higher than those currently employed would optimize the effect of rifampin, if patients could tolerate them. Another major implication is that in the design of new rifampin congeners for intermittent therapy, the important properties may include (i) the efficient entry of the rifamycin into M. tuberculosis, (ii) the achievement of a free C(max)/MIC of >175 that can be tolerated by patients, and (iii) a long postantibiotic effect duration.     

Population genetics study of isoniazid resistance mutations and evolution of multidrug-resistant Mycobacterium tuberculosis

The molecular basis for isoniazid resistance in Mycobacterium tuberculosis is complex. Putative isoniazid resistance mutations have been identified in katG, ahpC, inhA, kasA, and ndh. However, small sample sizes and related potential biases in sample selection have precluded the development of statistically valid and significant population genetic analyses of clinical isoniazid resistance. We present the first large-scale analysis of 240 alleles previously associated with isoniazid resistance in a diverse set of 608 isoniazid-susceptible and 403 isoniazid-resistant clinical M. tuberculosis isolates. We detected 12 mutant alleles in isoniazid-susceptible isolates, suggesting that these alleles are not involved in isoniazid resistance. However, mutations in katG, ahpC, and inhA were strongly associated with isoniazid resistance, while kasA mutations were associated with isoniazid susceptibility. Remarkably, the distribution of isoniazid resistance-associated mutations was different in isoniazid-monoresistant isolates from that in multidrug-resistant isolates, with significantly fewer isoniazid resistance mutations in the isoniazid-monoresistant group. Mutations in katG315 were significantly more common in the multidrug-resistant isolates. Conversely, mutations in the inhA promoter were significantly more common in isoniazid-monoresistant isolates. We tested for interactions among mutations and resistance to different drugs. Mutations in katG, ahpC, and inhA were associated with rifampin resistance, but only katG315 mutations were associated with ethambutol resistance. There was also a significant inverse association between katG315 mutations and mutations in ahpC or inhA and between mutations in kasA and mutations in ahpC. Our results suggest that isoniazid resistance and the evolution of multidrug-resistant strains are complex dynamic processes that may be influenced by interactions between genes and drug-resistant phenotypes.     

聚合酶链反应-单链构象多态性技术快速筛选结核杆菌的利福平耐药性

目的：探讨利用分子生物学方法直接快速检测结核分枝杆菌利福平（RFP）药物敏感性的可行性。方法：应用聚合酶链反应-单链构象多态性（PCR-SSCP）技术分别检测了40株RFP药物敏感及耐药的结核分枝杆菌临床分离株。先用PCR扩增rpoB基因，随后用SSCP方法鉴定其扩增产物有无突变，并与药敏试验结果作对照分析。结果：所有临床分离株均观察到rpoB基因PCR扩增产物。40株RFP敏感的临床分离株SSCP带谱与结核分枝杆菌H37RV标准株相同，40株RFP耐药株中37株检测到突变图谱。与Bactec结果对照，用PCR-SSCP技术检测结核分枝杆菌RFP耐药性的敏感性为93％，特异性为100％。结论：结核分枝杆菌耐RFP是其rpoB基因突变所致。PCR-SSCP技术可用于结核分枝杆菌RFP药物敏感性的直接快速检测。     

应用聚合酶链反应-寡核苷酸探针快速检测结核菌耐药基因突变

目的应用聚合酶链反应(PCR)-寡核苷酸探针快速检测结核菌耐药基因突变，建立一种新的分子药敏试验方法。方法以传统药敏试验、PCR-单链构象多态性和PCR-直接测序方法为对照，对利福平、链霉素(SM)和乙胺丁醇耐药的结核菌基因rpoB、rpsL、ITS和embB的寡核苷酸探针，通过反向斑点杂交检测78株结核菌临床分离株PCR产物。结果18株结核菌药物敏感株的4种耐药基因均为野生型。60株结核菌耐药分离株中，59株为耐RFP株，rpoB基因突变率为93．2％，最常见的突变位点为531位和526位密码子，33株为耐SM株，rpsL基因突变率为75．8％，均为43位密码子AAD AGG突变，ITS基因突变率为9．1％，均为513位A→C突变，rpsL和ITS基因总突变率为84．8％；43株为耐EMB株，embB基因突变率为58．1％，均为306位密码子突变。结论应用PCR一寡核苷酸探针反向斑点杂交技术可简便、快速、准确地分析大多数结核菌耐药基因突变，检测其耐药性。