结核分枝杆菌eis基因突变与氨基糖苷耐药的研究

目的：探讨结核分枝杆菌eis基因突变与氨基糖苷耐药之间的相互关系。方法：以本室保存的35株已确定耐一线药物（异烟肼、利福平、乙胺丁醇、链霉素）的结核分支杆菌为研究对象,应用BECTEC960测定其二线药物（阿米卡星、卡那霉素）的耐药情况,同时应用基因测序的方法测定结核分枝杆菌eis基因突变情况,分析eis基因突变与氨基糖苷耐药之间的相互关系。结果：氨基糖苷耐药的部分结核分杆杆菌中,eis基因487位碱基出现突变,相应的163位氨基酸密码子由CGT突变为CAT,即由缬氨酸变为异亮氨酸。结论：eis基因V163I突变（缬氨酸变为异亮氨酸）可能与结核分枝杆菌耐氨基糖苷类药物有关。     

深圳地区结核分枝杆菌耐利福平株rpoB基因突变分布

目的:调查深圳地区结核分枝杆菌耐利福平(RFP)株rpoB基因突变的分布情况,建立结核分枝杆菌耐药基因快速检测的方法.方法:对55株结核分枝杆菌临床分离株的rpoB基因280个碱基(包括其核心区75个碱基)应用PCR-直接测序法(PCR-DS)测定序列,其中耐利福平株51株,敏感株4株.结果:4株敏感株无突变,92.2%(47/51)耐利福平临床分离株存在rpoB基因突变.基因突变导致531位氨基酸突变率为41.2%(21/51);导致526位氨基酸突变率为29.4%(15/51);导致516位氨基酸突变率为13.7%(7/51).联合突变发生率为2.0%(1/51).未检测到发生缺失或插入碱基突变的菌株.结论:深圳地区结核分枝杆菌耐利福平株发生rpoB基因突变最常见的是531位丝氨酸、526位组氨酸和516位天冬氨酸的基因突变,三者突变率之和为84.3%(43/51).PCR-DS方法可快速测定结核分枝杆菌RFP耐药基因突变.     

结核分枝杆菌耐链霉素和乙胺丁醇分子机制的研究

目的:研究结核分枝杆菌耐链霉素和乙胺丁醇的rpsL和emb B基因突变情况,探讨耐药基因突变与耐药性的关系。方法:通过传统药敏实验和聚合酶链反应(PCR)--单链构象多态性(SSCP)技术初步鉴定62株临床分离株的药敏和rps L、emb B基因。结果:与结核菌标准株H37Rv对照,分析30例TB菌耐链霉素(SM)的rps L基因,发现其突变率为70.0%(21/30),分析29例耐乙胺丁醇(EMB)的emb B基因,该基因的突变率为65.5%(19/29)。结论:部分结核分枝杆菌耐SM和EMB是由于其rps L、emb B基因突变所致,PCR-SSCP银染技术可能成为测定部分结核分枝杆菌耐药的简便、快速的方法。     

空洞型肺结核组织样本耐药菌及相关基因检测的临床研究

目的:比较分析空洞型肺结*核组织样本与痰样本结核分枝杆菌培养的阳性率及检测的一致性,并基于rpoB基因及KatG基因突变检测在诊断耐多药结核分枝杆菌中的重要作用,探讨直接应用肺结核组织样本进行结核分枝杆菌耐药性检测的临床意义.方法:对肺结核实施肺部手术患者,在术前和术后分别进行痰及手术切除组织样本利用BacT ALERT 3D快速培养系统进行分枝杆菌培养,对培养阳性者进行菌种鉴定,对结核分枝杆菌分离株应用绝对浓度法进行异烟肼(H)、利福平(R)药物敏感性测定,比较分析二者的一致性;同时应用特异性引物对手术切除组织样本直接进行分枝杆菌rpoB、KatG基因扩增,并与其培养结果进行比较.结果:62例进入分析的病例中,术前痰培养阳性22例,阳性率35.5%(22/62),药敏试验耐药18例,耐异烟肼16例,耐利福平13例.二者均耐药12例,术中所取结核组织培养阳性34例,阳性率55%(34/62),耐药30例,耐H26例,耐R20例,二者均耐药17例,术中所取结核组织耐药基因检测与INH耐药性相关的KatG基因突变表现有22例,与RFP的耐药性相关的rpoB基因突变18例.二者同时有突变表现的16例.所有培养为结核敏感菌的组织检测中,无上述二基因突变表现.在相关的rpoB基因突变18例病例中有16例同时表现出KatG基因突(89%,16/18).结论:厚壁空洞肺结核患者肺部手术切除组织样本病原学检测与痰样本间具有较好的一致性,且结核菌培养的阳性率明显高于普通痰培养.同时可直接应用组织样本进行结核分枝杆菌rpoB基因、KatG基因检测,可更加及时、准确地用于指导临床术后抗结核的药物治疗.     

新疆南疆MTB临床分离株异烟肼耐药情况及耐药相关基因的突变研究

目的:探索新疆南疆部分地区维吾尔族结核病人群中分离到的结核分枝杆菌基因组中的katG、inhA、kasA、ahpC基因突变与耐异烟肼的关联,揭示新疆肺结核病高患病率、高死亡率的可能原因.方法:收集新疆南疆部分地区维吾尔族结核病患者痰液标本,对MTB进行分离培养后,应用比例法检测其对异烟肼耐药性,运用PCR技术对所分离菌株的上述基因相关片段扩增并进行测序及序列分析.结果:筛选出实验菌株99株,其中敏感株63株,耐异烟肼菌株36株,耐药率为36.4%.耐药株中katG基因突变率为63.9%,315位点突变,突变类型AGC→ACC(Ser→Thr)、AGC→AAC(Ser→Asn);inhA基因突变率为47.2%,有缺失、同义突变和错义突变;kasA基因突变率为41.7%,突变类型为缺失和错义突变;ahpC基因突变率为8.3%,属于错义突变.结论:新疆南疆结核病高患病率、高死亡率的可能原因之一是结核分枝杆菌对INH产生了耐药,结核分枝杆菌对INH耐药机制可能与耐药菌株基因组内katG、inhA、kasA和ahpC基因发生了突变有关.     

结核分枝杆菌三种耐药基因的检测方法

建立3种结核分枝杆菌耐药基因的检测方法,探讨耐药基因突变与耐药性的关系。将58株临床分离株均做聚合酶链反应-单链构象多态性分析(PCR—SSCP)和传统药物敏感试验。结果表明,结核分枝杆菌耐药基因突变与耐药水平有密切联系,绝大多数结核分枝杆菌耐药基因突变发生在高耐药株,少部分在低耐药株发生基因突变。     

结核分枝杆菌katG基因突变的研究

探讨编码过氧化氢-过氧化物酶的katG基因突变与结核分枝杆菌异烟肼(INH)耐药性的相关关系。根据结核分枝杆菌GenBank中的katG序列,自行设计特异性寡聚核苷酸引物,采用聚合酶链反应-单链构象多态性(PCR-SSCP)分析和直接测序法(DS)分析结核分枝杆菌中katG基因突变情况。以HR37Rv标准株为对照。所有23株敏感菌均未有SSCP结果异常;35株耐药菌中,有2株(5．7％)katG基因扩增阴性,且发生在高度耐药菌中。进一步分析发现,SSCP法突变检出23株(65．7％),测序法突变检出24株(68．6％),符合率为95．8％(23／24)。参照测序法对耐药菌突变序列的分析结果,PCR—SSCP敏感、特异,可快速检测结核分枝杆菌katG耐药基因突变,有利于耐药结核分枝杆菌耐药性的快速检测。     

两株超级广泛耐药结核分枝杆菌全基因组比较分析

【目的】结合现有数据,通过对两株临床超级广泛耐药的结核分枝杆菌全基因组的测序和分析,发现其型别相关的突变位点,解释发生广泛耐药的基因组突变机制。【方法】利用Solexa第二代测序技术对两株广泛耐药结核分枝杆菌(FJ05194和GuangZ0019)进行全基因组测序分析。以H37Rv为参考序列得到两株广泛耐药菌株的单核苷酸多态性(SNPs),构建系统发育树鉴定菌株型别,判断突变位点中型别相关和非型别相关的SNPs。定位SNPs所在的基因组区域,对型别相关的突变基因进行KEGG通路的富集分析,对非型别相关的突变基因和间隔区判断是否与耐药相关。【结果】两株广泛耐药菌株分别属于Lineage2和Lineage4型别,两菌株在碱基替换方面存在差异性,Lineage2型别相关的基因功能富集于ABC转运蛋白和核苷酸切除修复的通路。耐药方面,发现了已知的耐药相关基因的突变(rpoB、katG、rpsl、gyrA、gyrB、embB和ethA等),但卷曲霉素和卡那霉素相关的rrs、tlyA和eis启动子区域未发生突变,不足以解释其耐药性的产生。与最新报道的候选耐药基因比较,发现了卷曲霉素和卡那霉素相关的突变(Rv1393c、Rv0265c和narX等)和外排泵相关的pstB、Rv2333c和Rv2687c突变。【结论】结核分枝杆菌Lineage2型别相关的SNPs中含有影响结核分枝杆菌突变率和耐药性的突变。对于两株超级广泛耐药的结核菌,已知的激活药物或药靶相关的单耐药基因突变集合不能完全解释其广泛耐药性,还涉及新候选结核耐药基因、外排泵和补偿等其他潜在机制的相关基因突变。     

结核分枝杆菌利福平耐药性的研究进展

本旨在阐明结核分枝杆菌耐利福平分离株rpoB基因突变的规律,以及rpoB基因突变与利福平最低抑菌浓度(MIC)的关系。结核分枝杆菌的rpoB基因突变是引起利福平耐药性的主要原因,耐利福平分离株的rpoB基因突变主要集中在507～533位密码子的81bp的区域内,约80％的菌株发生531位或526位密码子突变。不同类型rpoB基因突变的结核分枝杆菌对利福平的耐受性也不同,通常发生531位密码子突变的菌株的MIC≥64μg／ml。     

高分辨率熔解曲线分析技术检测结核分枝杆菌的耐药性

目的:探讨高分辨率熔解曲线分析(High resolution melting,HRM)技术检测结核分枝杆菌耐药突变位点的可行性。方法:对218株结核分枝杆菌进行利福平(RFP)和异烟肼(INH)的药物敏感性测定,并进行耐药基因位点的PCR扩增和测序,同时采用HRM方法检测RFP和INH耐药基因位点情况,分析HRM的敏感性和特异性。结果:218株结核分枝杆菌药敏试验结果显示,有106株(48.6%)对RFP耐药,100株(45.9%)对INH耐药,81株(37.4%)对RFP和INH均耐药。测序发现,101株(46.3%)存在RFP耐药基因的突变,107株(49.1%)存在INH耐药基因的突变。HRM检测结果显示,100株(45.9%)存在RFP耐药基因的突变,103株(47.2%)存在INH耐药基因的突变。分别以药敏试验和测序结果为标准,HRM检测RFP耐药的敏感性为94.3%(100/106)和99.0%(100/101);特异性为97.3%(109/112)和100%(117/117);INH耐药的敏感性为97.0%(97/100)和98.1%(103/105);特异性为97.3%(109/112)和100%(113/113)。结论:HRM快速检测结核分枝杆菌耐药具有较高的特异性和灵敏度,能够满足临床需求。     

Comparative analysis of TB-Biochip, Xpert MTB/RIF, and GenoType MTBDRplus test systems for rapid determination of mutations responsible for drug resistance of M. tuberculosis complex (in sputum from patients in Moscow region)

We studied the frequency of occurrence and combinations of mutations in rpoB, katG, inhA, and oxyR-ahpC genes of Mycobacterium tuberculosis (MTB) DNA isolated from patients of Moscow region. In isoniazid monoresistant MTB isolates, Ser315Thr mutation in the katG gene prevails (15.8%), whereas the most frequent mutations in multidrug-resistant MTB isolates were Ser531Leu in the rpoB gene, Ser315Thr in the katG gene (26.3%), and their combination with C(-15)T in the inhA gene (5.3%). The efficiency of TB-Biochip (OOO Biochip-IMB Russia), Xpert MTB/RIF (Cepheid, United States), and GenoType MTBDRplus (Hain Lifescience, Germany) test systems was analyzed and compared with the efficiency of luminescent microscopy and phenotypic drug-susceptibility testing in BACTEC? MGIT? 960 automated system (Becton, Dickinson and Company, United States). Using Xpert MTB/RIF, TB-Biochip, and GenoType MTBDRplus systems, MTB DNA was detected in sputum from patients in 92, 78, and 49% of all culturepositive cases, respectively. Standard cultural data match the test results of the susceptibility of MTB for Xpert MTB/RIF (rifampicin resistance) and for TB-Biochip and GenoType MTBDRplus (resistance to rifampicin and isoniazid) by 100, 97, and 100%, respectively. Thus, Xpert MTB/RIF system is the most efficient in primary MTB DNA detection, and TB-Biochip is the only one sensitive enough for both MTB DNA detection and determination of MTB multidrug resistance in sputum. Multidrug resistance is considered as resistance to both rifampicin and isoniazid.     

Molecular genetics of Mycobacterium tuberculosis resistant to aminoglycosides and cyclic peptide capreomycin antibiotics in Korea

Aminoglycosides are key drugs for the treatment of multidrug-resistant tuberculosis. A total of 97 extensively drug-resistant (XDR) and 29 pan-susceptible Mycobacterium tuberculosis isolates from Korean tuberculosis patients were analyzed to characterize mutations within the rrs, rpsL, gidB, eis and tlyA genes. Thirty (56.6 %) of the 53 streptomycin (STR)-resistant strains had a rpsL mutation and eight strains (15.1 %) had a rrs (514 or 908 site) mutation, whereas 11 (20.8 %) of the 53 STR-resistant strains had a gidB mutation without rpsL or either rrs mutation. Most of the gidB mutations conferred low-level STR resistance, and 22 of these mutations were novel. Mutation at position 1401 in rrs lead to resistance to kanamycin (80/95 = 84.2 %; KAN), amikacin (80/87 = 92.0 %; AMK), and capreomycin (74/86 = 86.0 %; CAP). In this study, 13.7 % (13/95) of KAN-resistant strains showed eis mutations, including 4 kinds of novel mutations. Isolates with eis structural gene mutations were cross-resistant to STR, KAN, CAP, and AMK. Here, 5.8 % (5/86) of the CAP-resistant strains harbored a tlyA mutation that included 3 different novel point mutations. Detection of the A1401G mutation appeared to be 100 % specific for the detection of resistance to KAN and AMK. These data establish the presence of phenotypic XDR strains using molecular profiling and are helpful to understanding of aminoglycoside resistance at the molecular level.     

Web-based access to mouse models of human cancers: the Mouse Tumor Biology (MTB) Database

The Mouse Tumor Biology (MTB) Database serves as a curated, integrated resource for information about tumor genetics and pathology in genetically defined strains of mice (i.e., inbred, transgenic and targeted mutation strains). Sources of information for the database include the published scientific literature and direct data submissions by the scientific community. Researchers access MTB using Web-based query forms and can use the database to answer such questions as 'What tumors have been reported in transgenic mice created on a C57BL/6J background?', 'What tumors in mice are associated with mutations in the Trp53 gene?' and 'What pathology images are available for tumors of the mammary gland regardless of genetic background?'. MTB has been available on the Web since 1998 from the Mouse Genome Informatics web site (http://www.informatics.jax.org). We have recently implemented a number of enhancements to MTB including new query options, redesigned query forms and results pages for pathology and genetic data, and the addition of an electronic data submission and annotation tool for pathology data.     

High Isoniazid Resistance Rates in Rifampicin Susceptible Mycobacterium tuberculosis Pulmonary Isolates from Pakistan

Background

Rapid new diagnostic methods (including Xpert MTB/RIF assay) use rifampicin resistance as a surrogate marker for multidrug resistant tuberculosis. Patients infected with rifampicin susceptible strains are prescribed first line anti-tuberculosis therapy. The roll out of such methods raises a concern that strains with resistance to other first line anti-tuberculosis drugs including isoniazid will be missed and inappropriate treatment given. To evaluate implications of using such methods review of resistance data from high burden settings such as ours is essential.

Objective

To determine resistance to first line anti-tuberculosis drugs amongst rifampicin susceptible pulmonary Mycobacterium tuberculosis (MTB) isolates from Pakistan.

Materials and Methods

Data of pulmonary Mycobacterium tuberculosis strains isolated in Aga Khan University Hospital (AKUH) laboratory (2009–2011) was retrospectively analyzed. Antimicrobial susceptibility profile of rifampicin susceptible isolates was evaluated for resistance to isoniazid, pyrazinamide, ethambutol, and streptomycin.

Results

Pulmonary specimens submitted to AKUH from 2009 to 2011 yielded 7738 strains of Mycobacterium tuberculosis. These included 54% (n 4183) rifampicin susceptible and 46% (n: 3555) rifampicin resistant strains. Analysis of rifampicin susceptible strains showed resistance to at least one of the first line drugs in 27% (n:1133) of isolates. Overall isoniazid resistance was 15.5% (n: 649), with an isoniazid mono-resistance rate of 4% (n: 174). Combined resistance to isoniazid, pyrazinamide, and ethambutol was noted in 1% (n: 40), while resistance to isoniazid, pyrazinamide, ethambutol, and streptomycin was observed in 1.7% (n: 70) of strains.

Conclusions

Our data suggests that techniques (including Xpert MTB/RIF assay) relying on rifampicin susceptibility as an indicator for initiating first line therapy will not detect patients infected with MTB strains resistant to other first line drugs (including isoniazid). The roll out of these techniques must therefore be accompanied by strict monitoring ensuring early resistance detection to increase chances of improved patient outcomes.     

结核分枝杆菌临床株4种耐药基因的检测与分析

结核分枝杆菌Mycobacterium tuberculsis(M.t)4种耐药基因的研究,了解耐药基因突变情况和耐药水平的关系。108例临床痰标本临床分离株均做传统梯度药敏试验和聚合酶链反应多态-单链构象多态性（PCR-SSCP）试验。结果表明耐SM（rpsL）REP(rpoB）INH(katG）EMB（embB）基因突变率分别为78.5%,68.2%,70.5%,48.6%。其中,上海高耐药株基因突变率分别为86.5%,89.3%,84.3%,35.3%。低耐药株分别为28.5%,16.5%,7.1%。EMB在低耐药区无基因突变。M.t的4种耐药基因联合检测的分析,在国内外很少报道。部分M.t的耐药由耐药基因突变所致,M.t耐药基因突变与耐药水平密切相关,且M.t基因突变绝大多数发生在高耐药区中,也有少部分在低耐区株中发生。     

结核分枝杆菌的耐药基因及其相关分子机制

结核分枝杆菌原发性和继发性耐药是当前控帝】和治疗结核病面临的重要问题,随着分子遗传学的发展,已经阐明了结核分枝杆菌耐药的分子基础是染色体的突变,影响了药靶本身或激活了药物前体的细菌酶,造成MTB的耐药。本文主要就MTB对其常用药物的耐药机制展开讨论,以便正确认识MTB对不同药物的耐药机制,建立快速检测耐药结核分枝杆菌基因型的分子生物学方法。     

Whole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan

Improved molecular diagnostic methods for detection drug resistance in Mycobacterium tuberculosis (MTB) strains are required. Resistance to first- and second- line anti-tuberculous drugs has been associated with single nucleotide polymorphisms (SNPs) in particular genes. However, these SNPs can vary between MTB lineages therefore local data is required to describe different strain populations. We used whole genome sequencing (WGS) to characterize 37 extensively drug-resistant (XDR) MTB isolates from Pakistan and investigated 40 genes associated with drug resistance. Rifampicin resistance was attributable to SNPs in the rpoB hot-spot region. Isoniazid resistance was most commonly associated with the katG codon 315 (92%) mutation followed by inhA S94A (8%) however, one strain did not have SNPs in katG, inhA or oxyR-ahpC. All strains were pyrazimamide resistant but only 43% had pncA SNPs. Ethambutol resistant strains predominantly had embB codon 306 (62%) mutations, but additional SNPs at embB codons 406, 378 and 328 were also present. Fluoroquinolone resistance was associated with gyrA 91–94 codons in 81% of strains; four strains had only gyrB mutations, while others did not have SNPs in either gyrA or gyrB. Streptomycin resistant strains had mutations in ribosomal RNA genes; rpsL codon 43 (42%); rrs 500 region (16%), and gidB (34%) while six strains did not have mutations in any of these genes. Amikacin/kanamycin/capreomycin resistance was associated with SNPs in rrs at nt1401 (78%) and nt1484 (3%), except in seven (19%) strains. We estimate that if only the common hot-spot region targets of current commercial assays were used, the concordance between phenotypic and genotypic testing for these XDR strains would vary between rifampicin (100%), isoniazid (92%), flouroquinolones (81%), aminoglycoside (78%) and ethambutol (62%); while pncA sequencing would provide genotypic resistance in less than half the isolates. This work highlights the importance of expanded targets for drug resistance detection in MTB isolates.