Mutation analysis of mycobacterial rpoB genes and rifampin resistance using recombinant Mycobacterium smegmatis

Rifampin is a major drug used to treat leprosy and tuberculosis. The rifampin resistance of Mycobacterium leprae and Mycobacterium tuberculosis results from a mutation in the rpoB gene, encoding the β subunit of RNA polymerase. A method for the molecular determination of rifampin resistance in these two mycobacteria would be clinically valuable, but the relationship between the mutations and susceptibility to rifampin must be clarified before its use. Analyses of mutations responsible for rifampin resistance using clinical isolates present some limitations. Each clinical isolate has its own genetic variations in some loci other than rpoB, which might affect rifampin susceptibility. For this study, we constructed recombinant strains of Mycobacterium smegmatis carrying the M. leprae or M. tuberculosis rpoB gene with or without mutation and disrupted their own rpoB genes on the chromosome. The rifampin and rifabutin susceptibilities of the recombinant bacteria were measured to examine the influence of the mutations. The results confirmed that several mutations detected in clinical isolates of these two pathogenic mycobacteria can confer rifampin resistance, but they also suggested that some mutations detected in M. leprae isolates or rifampin-resistant M. tuberculosis isolates are not involved in rifampin resistance.     

武汉地区耐利福平结核分枝杆菌rpoB基因突变分析

摘要：目的：探讨武汉地区结核分枝杆菌（MTB）利福平耐药株rpoB基因的突变特征。 方法：对76例MTB临床分离株包括rpoB核心区域81 bp碱基在内的428 bp碱基进行PCR测定,并进行DNA序列分析。 结果：76例临床分离MTB中利福平耐药株56例,敏感株20例。耐药株中92.9%（52/56）存在突变,共涉及10个密码子的18种突变类型。 531、526为常见突变位点,其突变率分别为57.7%(30/52)、19.2%(10/52);联合突变率为13.5%（7/52）;同时发现了509位（AGC→AGA）新的突变类型和国内少见的517位CAG缺失类型。 结论：rpoB基因突变在武汉地区利福平耐药MTB中广泛存在,并存在新的突变位点。     

耐利福平结核分枝杆菌rpoB基因序列研究

目的 研究杭州地区结核分枝杆菌（Mycobacterium tuberculosis）对利福平（RFP）的耐受与rpoB基因突变的关系。方法 随机挑选了90例结核杆菌感染的病例。选择了利福平作为主要的药物进行药敏实验，PCR扩增39株耐RFP结核分支杆菌的rpoB基因片段（580bp）；测定扩增片段的序列。并与美国国立生物信息中心（www．ncbi．nlm．nih．gov／nucleotide）检索获得结核杆菌野生株（利福平敏感株）序列（登陆号：AJ749948）作对比分析。结果 结果显示PCR结核测序方法得到了39例结核杆菌耐药株。51例敏感株，与药敏实验的方法检测的结果完全一致。测定的11株临床分离的耐药株中，526位或531位有突变，其中526位有突变的有7株，占耐药测定株63．6%，531位突变的有4株。占耐药测定株36．4％。未见两位点同时突变。检测的11株敏感株，未见526位或531位有突变。结论 杭州地区结核分支杆菌耐利福平的发生与rpoB基因的526位或531位突变密切相关，与国外的报告基本相似。但526位突变占耐药测定株高达63．6％。如此高比例目前国内外未见相似报道。PCR扩增和产物测序将是临床检测结核分支杆菌耐利福平和耐多药的一种迅速、准确的方法。     

PCR—SSCP快速检测结核分枝杆菌耐利福平rpoB基因的研究

目的探讨PCR—SSCP技术检测结核分枝杆菌耐利福平rpoB基因作为新的分子药敏试验方法的价值。方法应用PCR—SSCP技术检测结核分枝杆菌耐利福平rpoB基因核心区的突变，同时对片段长度为215bp的PCR扩增产物进行测序分析。受试菌为23株利福平敏感结核分枝杆菌以72．35株利福平抗性结核分枝杆菌。结果23株利福平敏感结核分枝杆菌分别用PCR—SSCP和PCR扩增片段测序均没有检测到巾0B碱基突变。而在35株利福平抗性菌株中，PCR—SSCP检测到31株与H37Rv标准株不同的带谱，PCR—SSCP检测基因突变的敏感度和特异度分别为88．6％（31／35）和100％（23／23）。对35株利福平抗性菌株PCR扩增产物进行测序分析，在其中32株中检出了基因突变。测序分析检测基因突变的敏感度和特异度分别为91．4％（32／35）和100％（23／23）。卡方检验，PCR—SSCP和PCR扩增片段测序两种方法的敏感度之间没有显著性差异（P〉0．05）。若以DNA测序为标准，则PCR—SSCP检测基因突变的准确度、敏感度和特异度分别为93．1％（54／58），96．9％（31／32）和100％（23／23）。结论PCR—SSCP检测结核分枝杆菌耐利福平rpoB基因突变可用于利福平药物敏感度的快速测定。     

Characterization of rifampin-resistance in pathogenic mycobacteria.

The emergence of rifampin-resistant strains of pathogenic mycobacteria has threatened the usefulness of this drug in treating mycobacterial diseases. Critical to the treatment of individuals infected with resistant strains is the rapid identification of these strains directly from clinical specimens. It has been shown that resistance to rifampin in Mycobacterium tuberculosis and Mycobacterium leprae apparently involves mutations in the rpoB gene encoding the beta-subunit of the RNA polymerases of these species. DNA sequences were obtained from a 305-bp fragment of the rpoB gene from 110 rifampin-resistant and 10 rifampin-susceptible strains of M. tuberculosis from diverse geographical regions throughout the world. In 102 of 110 rifampin-resistant strains 16 mutations affecting 13 amino acids were observed. No mutations were observed in rifampin-susceptible strains. No association was found between particular mutations in the rpoB gene and drug susceptibility patterns of multidrug-resistant M. tuberculosis strains. Drug-resistant M. tuberculosis strains from the same outbreak and exhibiting the same IS6110 DNA fingerprint and drug susceptibility pattern contained the same mutation in the rpoB gene. However, mutations are not correlated with IS6110 profiling outside of epidemics. The evolution of rifampin resistance as a consequence of mutations in the rpoB gene was documented in a patient who developed rifampin resistance during the course of treatment. Rifampin-resistant strains of M. leprae, Mycobacterium avium, and Mycobacterium africanum contained mutations in the rpoB gene similar to that documented for M. tuberculosis. This information served as the basis for developing a rapid DNA diagnostic assay (PCR-heteroduplex formation) for the detection of rifampin susceptibility of M. tuberculosis.     

DNA芯片快速检测耐利福平结核分枝杆菌rpoB基因突变

目的 开发快速检测耐利福平结核分枝杆菌(结核菌)rpoB基因突变的DNA芯片。方法 根据结核菌rpoB基因序列设计探针并制作基因芯片，从临床样品中分离出结核菌的基因组DNA，PCR扩增含有rpoB基因突变位点的特异DNA片段，荧光标记后与芯片上含有的检测特异突变位点的寡核苷酸探针进行杂交，同时与DNA直接测序法测定序列比较。结果 35株耐利福平结核菌中有91．4％(32／35)用直接测序法检测出存在rpoB基因突变，DNA芯片的检测效率为71．4％(25／35)。结论 用DNA芯片检测结核菌对利福平的耐药性具有较高的特异性和敏感性，可用于临床结核菌耐药性检测。     

Pyrosequencing-based approach for rapid detection of rifampin-resistant Mycobacterium tuberculosis

Rifampin resistance in Mycobacterium tuberculosis could be determined within 2 h by using pyrosequencing-based approach. Pyrosequencing results of rifampin-resistant (n = 21) and rifampin-susceptible (n = 20) M. tuberculosis isolates were concordant with those based on drug susceptibility testing and conventional DNA sequencing. Results showed pyrosequencing-based approach is a rapid, sensitive, and efficient detection method of rifampin-resistant M. tuberculosis.     

The rpoB gene of Mycobacterium tuberculosis.

A portion of the Mycobacterium tuberculosis gene encoding the beta subunit of RNA polymerase (rpoB) was amplified by PCR using degenerate oligonucleotides and used as a hybridization probe to isolate plasmid clones carrying the entire rpoB gene of M. tuberculosis H37Rv, a virulent, rifampin-susceptible strain. Sequence analysis of a 5,084-bp SacI genomic DNA fragment revealed a 3,534-bp open reading frame encoding an 1,178-amino-acid protein with 57% identity with the Escherichia coli beta subunit. This SacI fragment also carried a portion of the rpoC gene located 43 bp downstream from the 3' end of the rpoB open reading frame; this organization is similar to that of the rpoBC operon of E. coli. The M. tuberculosis rpoB gene was cloned into the shuttle plasmid pMV261 and electroporated into the LR223 strain of Mycobacterium smegmatis, which is highly resistant to rifampin (MIC > 200 micrograms/ml). The resulting transformants were relatively rifampin susceptible (MIC = 50 micrograms/ml). Using PCR mutagenesis techniques, we introduced a specific rpoB point mutation (associated with clinical strains of rifampin-resistant M. tuberculosis) into the cloned M. tuberculosis rpoB gene and expressed this altered gene in the LR222 strain of M. smegmatis, which is susceptible to rifampin (MIC = 25 micrograms/ml). The resulting transformants were rifampin resistant (MIC = 200 micrograms/ml). The mutagenesis and expression strategy of the cloned M. tuberculosis rpoB gene that we have employed in this study will allow us to determine the rpoB mutations that are responsible for rifampin resistance in M. tuberculosis.     

Characterization of rpoB mutations in rifampin-resistant clinical Mycobacterium tuberculosis isolates from Kuwait and Dubai

Mutations conferring resistance to rifampin in rifampin-resistant clinical Mycobacterium tuberculosis isolates occur mostly in the 81 bp rifampin-resistance-determining region (RRDR) of the rpoB gene. In this study, 29 rifampin-resistant and 12 -susceptible clinical M. tuberculosis isolates were tested for characterization of mutations in the rpoB gene by line probe (INNO-LiPA Rif. TB) assay and the results were confirmed and extended by DNA sequencing of the PCR amplified target DNA. The line probe assay identified all 12 susceptible strains as rifampin-sensitive and the DNA sequence of RRDR in the amplified rpoB gene from two isolates matched perfectly with the wild-type sequence. The line probe assay identified 28 resistant isolates as rifampin-resistant with specific detection of mutation in 22 isolates including one isolate that exhibited hetro-resistance containing both the wild-type pattern as well as a specific mutation within RRDR while one of the rifampin-resistant strain was identified as rifampin-susceptible. DNA sequencing confirmed these results and, in addition, led to the specific detection of mutations in 5 rifampin-resistant isolates in which specific base changes within RRDR could not be determined by the line probe assay. These analyses identified 8 different mutations within RRDR of the rpoB gene including one novel mutation (S522W) that has not been reported so far. The genotyping performed on the isolates carrying similar mutations showed that majority of these isolates were unique as they exhibited varying DNA banding patterns. Correlating the ethnic origin of the infected TB patients with the occurrence of specific mutations at three main codon positions (516, 526 and 531) in the rpoB gene showed that most patients (11 of 15) from South Asian region contained mutations at codon 526 while majority of isolates from patients (6 of 11) of Middle Eastern origin contained mutations at codon 531.     

Molecular Analysis of Codon 548 in the rpoB Gene Involved in Mycobacterium tuberculosis Resistance to Rifampin

Most Mycobacterium tuberculosis rifampin-resistant strains have been associated with mutations in an 81-bp rifampin resistance-determining region (RRDR) in the gene rpoB. However, if this region alone were targeted, rifampin-resistant strains with mutations outside the RRDR would not be detected. In this study, among 51 rifampin-resistant clinical isolates analyzed by sequencing 1,681-bp-long DNA fragments containing the RRDR, 47 isolates contained mutations within the RRDR, three isolates contained mutations both within and outside the RRDR, and only one isolate had a single missense mutation (Arg548His) located outside the RRDR. A drug susceptibility test of recombinant Mycobacterium smegmatis and M. tuberculosis isolates carrying mutated rpoB (Arg548His) showed an increased MIC for rifampin compared to that of the control strains. Modeling of the Arg548His mutant RpoB-DNA complex revealed that the His548 side chain formed a more stable hydrogen bond structure than did Arg548, reducing the flexibility of the rifampin-resistant cluster II region of RpoB, suggesting that the RpoB Arg548His mutant does not effectively interact with rifampin and results in bacterial resistance to the drug. This is the first report on the relationship between the mutation in codon 548 of RpoB and rifampin resistance in tuberculosis. The novel mutational profile of the rpoB gene described here will contribute to the comprehensive understanding of rifampin resistance patterns and to the development of a useful tool for simple and rapid drug susceptibility tests.     

Solid-phase sequence scanning for drug resistance detection in tuberculosis

DNA chip arrays hold considerable promise for diagnostic sequencing of polymerase chain reaction (PCR) products. To date, however, arrays have been relatively expensive, complex to use and difficult to interpret, preventing their adaptation to the clinical lab. A moderate density array method has been developed that enables efficient, easy-to-interpret and robust solid-phase PCR product sequencing. Here, the results of Mycobacterium tuberculosis rifampin resistance mutation detection by primer-extension-based sequence scanning of the rpo B gene of M. tuberculosis are presented. Rifampin resistant clinical isolates were identified in as little as 1 h post PCR amplification with visual results detection.     

Capillary electrophoresis-based heteroduplex analysis with a universal heteroduplex generator for detection of point mutations associated with rifampin resistance in tuberculosis.

BACKGROUND: Slab gel heteroduplex analysis (HDA), a popular scanning method for genetic mutations, uses DNA fragments typically generated by PCR to create homo- and heteroduplex molecules with conformational differences and sequence-dependent electrophoretic profiles. Use of a universal heteroduplex generator (UHG) enhances the subtle variations caused by single-base substitutions. METHODS: The HDA-UHG slab gel format was modified for an efficient capillary-based method. The effect of staining dyes TOPRO5 and YOPRO1 on the analysis of heteroduplexes was studied, as well as ultraviolet absorbance and laser-induced fluorescence (LIF) detection methods. In addition, the entangled polymers hydroxyethyl cellulose, methyl cellulose, and linear polyacrylamide were evaluated as separation matrices. RESULTS: This assay was able to detect the presence of Mycobacterium tuberculosis and its rifampin susceptibility directly from clinical specimens in dramatically reduced analysis time (30 min vs 2.5 h). Optimized conditions included 0.3% methyl cellulose as the separation matrix, on-line staining using 1 micromol/L YOPRO1, and LIF detection for quantitative and reproducible analysis of single-base substitutions in the rifampin resistance-determining region of rpoB that give rise to the rifampin-resistant phenotype of M. tuberculosis. We generated 95% confidence limits using the wild-type sequence and used these limits to determine rifampin susceptibility in samples. CONCLUSIONS: Capillary electrophoresis, combined with the HDA-UHG technique, may be of value for rapid and efficient clinical diagnosis of rifampin-resistant tuberculosis strains.     

Rifampin resistance in Mycobacterium kansasii is associated with rpoB mutations

Rifampin is the most potent drug used in the treatment of disease due to Mycobacterium kansasii. A 69-bp fragment of rpoB, the gene that encodes the beta subunit of the bacterial RNA polymerase, was sequenced and found to be identical in five rifampin-susceptible clinical isolates of M. kansasii. This sequence showed 87% homology with the Mycobacterium tuberculosis gene, with an identical deduced amino acid sequence. In contrast, missense mutations were detected in the same fragment amplified from five rifampin-resistant isolates. A rifampin-resistant strain generated in vitro also harbored an rpoB gene missense mutation that was not present in the parent isolate. All mutations detected (in codons 513, 526, and 531) have previously been described in rifampin-resistant M. tuberculosis isolates. Rifampin MICs determined by E-test were <1 mg/liter for all rifampin-susceptible isolates and >256 mg/liter for all rifampin-resistant ones. In addition, four of the five rifampin-resistant isolates were also resistant to rifabutin. We have thus shown a strong association between rpoB gene missense mutations and rifampin resistance in M. kansasii. Although our results are derived from a small number of isolates and confirmation with larger numbers would be useful, they strongly suggest that mutations within rpoB form the molecular basis of rifampin resistance in this species.     

结核分枝杆菌利福平耐药基因的检测

以药物敏感试验为标准，应用聚合酶链反应－单链构象多态性分析方法对６８例利福平耐药菌株和２０例利福平敏感菌株进行测定，结果８８例结核分枝杆菌均扩增出目标ＤＮＡ条带，１０例非结核分枝杆菌和８例非分枝杆菌未出现目标ＤＮＡ条带，所用引物扩增ｒｐｏＢ基因２１５ｂｐ片段为结核分枝杆菌复合群异性的。     

Characterization of rpoB mutations in rifampin-resistant Mycobacterium tuberculosis isolates from the Middle East

The nature and frequency of mutations in the rpoB gene of rifampin-resistant clinical Mycobacterium tuberculosis isolates vary considerably according to geographical locations. There is no information on the prevalence of specific mutations in clinical M. tuberculosis strains isolated from patients in Middle-Eastern countries. In this study, 13 rifampin-resistant and 6 susceptible clinical M. tuberculosis isolates were tested for identification and characterization of mutations in the rpoB gene by INNO-LiPA Rif. TB kit and DNA sequencing of the PCR amplified target DNA. The kit identified all six susceptible strains as rifampin-sensitive and the DNA sequence of the amplified rpoB gene in the target region matched perfectly with the wild-type sequence. The kit identified 12 resistant isolates as rifampin-resistant with specific detection of mutations in 8 isolates while one of the rifampin-resistant strain was identified as rifampin-susceptible. DNA sequencing confirmed these results and, in addition, led to the specific detection of mutations in 4 rifampin-resistant isolates in which specific base changes within the target region could not be determined by the INNO-LiPA Rif. TB kit. The majority (8 of 13) of resistant isolates involved base changes at codon 531 of the rpoB gene. Mutations at codon position 531 within the rpoB gene have also been reported in majority of rifampin-resistant strains from Greece and St. Petersburg, Russia but not from other geographical locations.     

Rapid direct detection of multiple rifampin and isoniazid resistance mutations in Mycobacterium tuberculosis in respiratory samples by real-time PCR

Rapid detection of resistance in Mycobacterium tuberculosis can optimize the efficacy of antituberculous therapy and control the transmission of resistant M. tuberculosis strains. Real-time PCR has minimized the time required to obtain the susceptibility pattern of M. tuberculosis strains, but little effort has been made to adapt this rapid technique to the direct detection of resistance from clinical samples. In this study, we adapted and evaluated a real-time PCR design for direct detection of resistance mutations in clinical respiratory samples. The real-time PCR was evaluated with (i) 11 clinical respiratory samples harboring bacilli resistant to isoniazid (INH) and/or rifampin (RIF), (ii) 10 culture-negative sputa spiked with a set of strains encoding 14 different resistance mutations in 10 independent codons, and (iii) 16 sputa harboring susceptible strains. The results obtained with this real-time PCR design completely agreed with DNA sequencing data. In all sputa harboring resistant M. tuberculosis strains, the mutation encoding resistance was successfully detected. No mutation was detected in any of the susceptible sputa. The test was applied only to smear-positive specimens and succeeded in detecting a bacterial load equivalent to 10(3) CFU/ml in sputum samples (10 acid-fast bacilli/line). The analytical specificity of this method was proved with a set of 14 different non-M. tuberculosis bacteria. This real-time PCR design is an adequate method for the specific and rapid detection of RIF and INH resistance in smear-positive clinical respiratory samples.     

结核分枝杆菌耐利福平基因变异株的体外最小抑菌浓度研究

目的：研究结核分枝杆菌（MTB）耐利福平临床分离株基因突变对其体外最小抑菌浓度（MIC）测定结果的影响。方法用基因芯片对临床分离的对利福平耐药的175株 MTB及对利福平敏感的48株 MTB进行耐药基因检测;并对所有标本进行利福平的 MIC测定,比较不同变异株的 MIC测定结果。结果对利福平耐药的 MTB 临床分离株基因突变以531、526、516、533位点单突变为主;531位点单突变的利福平耐药变异株 MIC 高于526位点单突变的耐药变异株,差异有统计学意义（t′＝2．2237,t′α＝2．0449,P＜0．05）;526位点单突变的利福平耐药变异株 MIC高于516位点单突变的耐药变异株,差异有统计学意义（t＝2．2056,P＝0．0329,P＜0．05）。双突变者均有较高的 MIC测定值。结论合理的基因芯片设计能检出95．0％以上的对利福平耐药 MTB变异株;对利福平耐药的 MTB变异株有不同的基因突变模式,且不同突变模式的 MTB耐药程度不同,可以为临床用药提供参考。     

Genotypic analysis of Mycobacterium tuberculosis in two distinct populations using molecular beacons: implications for rapid susceptibility testing

Past genotypic studies of Mycobacterium tuberculosis may have incorrectly estimated the importance of specific drug resistance mutations due to a number of sampling biases including an overrepresentation of multidrug-resistant (MDR) isolates. An accurate assessment of resistance mutations is crucial for understanding basic resistance mechanisms and designing genotypic drug resistance assays. We developed a rapid closed-tube PCR assay using fluorogenic reporter molecules called molecular beacons to detect reportedly common M. tuberculosis mutations associated with resistance to isoniazid and rifampin. The assay was used in a comparative genotypic investigation of two different study populations to determine whether these known mutations account for most cases of clinical drug resistance. We analyzed samples from a reference laboratory in Madrid, Spain, which receives an overrepresentation of MDR isolates similar to prior studies and from a community medical center in New York where almost all of the resistant isolates and an equal number of susceptible controls were available. The ability of the molecular beacon assay to predict resistance to isoniazid and rifampin was also assessed. The overall sensitivity and specificity of the assay for isoniazid resistance were 85 and 100%, respectively, and those for rifampin resistance were 98 and 100%, respectively. Rifampin resistance mutations were detected equally well in isolates from both study populations; however, isoniazid resistance mutations were detected in 94% of the isolates from Madrid but in only 76% of the isolates from New York (P = 0.02). In New York, isoniazid resistance mutations were significantly more common in the MDR isolates (94%) than in single-drug-resistant isolates (44%; P < 0.001). No association between previously described mutations in the kasA gene and isoniazid resistance was found. The first mutations that cause isoniazid resistance may often occur in sequences that have not been commonly associated with isoniazid resistance, possibly in other as yet uncharacterized genes. The molecular beacon assay was simple, rapid, and highly sensitive for the detection of rifampin-resistant M. tuberculosis isolates and for the detection of isoniazid resistance in MDR isolates.     

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.     

Comparative antimycobacterial activities of rifampin, rifapentine, and KRM-1648 against a collection of rifampin-resistant Mycobacterium tuberculosis isolates with known rpoB mutations.

A collection of 24 rifampin-resistant clinical isolates of Mycobacterium tuberculosis with characterized RNA polymerase beta-subunit (rpoB) gene mutations was tested against the antimycobacterial agents rifampin, rifapentine, and KRM-1648 to correlate levels of resistance with specific rpoB genotypes. The results indicate that KRM-1648 is more active in vitro than rifampin and rifapentine, and its ability to overcome rifampin resistance in strains with four different genetic alterations may prove to be useful in understanding structure-function relationships.