基因芯片技术检测环境中常见致病菌的初步研究

目的：为了快速，准确地检测环境中存在的致病菌，建立一种采用基因芯片技术对环境中常见致病检测和鉴定的实验方法。方法：采用合成后点样的方法把自行设计合成的一系列寡核苷酸探针固定在经过醛基化修饰的显微镜载玻片上，制成用于致病菌检测的基因芯片。结果：在相同的条件下，扩增了涉及12个菌属的151株细菌的165rDNA基因片段并与基因芯片杂交，经Scan-Array3000芯片阅读仪扫描得到特异性的交杂图，归纳这些杂交图，得到一套属（种）特异的典型杂交图谱。待检的样品菌与基因芯片进行杂交，得到的杂交结果与典型图谱比对即可判断出样品的种类。用这样的方法对从实际样品中分离的细菌进行检测，准确率表达了96．2％（25／26）。结论：该项技术的建立为今后更大规模的检测研究奠定了基础，可以推广应用于感染性疾病诊断，环境监测，食品卫生监督，商品检验检疫等领域。     

PCR结合寡核苷酸探针杂交检测临床常见真菌的实验研究

目的 建立PCR结合生物标记的寡核甘酸探针斑点杂交技术,鉴定临床常见的真菌。方法 首先用真菌通用引物扩增白念球菌、热带念球菌、假热带念球菌、近平滑念球菌、光滑念球菌、解脂念球菌、克鲁斯念球菌、季也蒙念球菌、黄曲 霉、烟曲霉的核糖体大亚单位基因的保守区序列,然后用生物素标记的种特异性寡核苷酸探针与扩增产物杂交,并将此方法用于临床标本和临床分离菌株的检测。结果 通用引物可以扩增上述11种临床常见真菌的DNA,扩增片段长度在260bp左右。9种特异性探针分别与11种真菌标准菌株的PCR扩增产物杂交,结果表明每种探针都具有高度特异性。斑点杂交法和Southerm杂交法检测敏感性相同,为100fg;琼脂糖凝胶电泳法检测敏感性为1pg。通过69例临床标本和31例临床分析菌株的检测,PCR－杂交法的结果和真菌培养法的结果基本一致。结论 PCR结合生物素标记的寡核苷酸探针杂交技术可将9种临床常见真菌鉴定到种,方法快速、敏感、特异。     

通用型病毒检测芯片在三种人类致病病毒属检测中的应用

目的 研究制备对人类有致病作用的38个属的病毒寡核苷酸（oligo）基因芯片对三种人类致病病毒的检测能力。方法 应用生物信息学软件设计70-mer oligo探针，固定于玻片载体制备成基因芯片。以痘苗病毒天坛株、甲肝病毒、乙肝病毒作为检测样本，提取病毒核酸，经随机引物扩增、荧光标记，用于芯片杂交，清洗和干燥后对芯片进行扫描和数据分析。结果 芯片上oligo探针能与相应病毒的PCR扩增样品杂交，呈现阳性荧光信号。结论 建立的病毒寡核苷酸基因芯片能够检出和区分三种检测病毒，为进行未知病毒的基因芯片筛查方法的建立奠定了基础。     

DNA芯片检测乙型肝炎病毒基因多态性

目的　建立DNA芯片检测乙型肝炎病毒 (hepatitisBvirus,HBV)基因多态性的研究方法并对实验条件进行优化。方法　设计多条寡核苷酸探针 ,在硅烷化芯片的特定位置上 ,用点样仪将探针固定 ,并与PCR扩增的HBV基因相应区段杂交 ,杂交结果影印至硝酸纤维素膜 ,经BCIP NBT避光显色 ,用放大镜观察杂交信号呈暗紫色圆点 ,根据特定位置上杂交信号的有无和与之相应的探针序列来判定基因突变的类型。结果　通过 1次杂交反应可检测HBV前C C区 (nt 1896 1814 )、BCP区 (nt1762 1764)和P区 (nt 52 8 552 )等多个位点的变异 ,与测序分析结果完全一致 ,具有较好的检测灵敏度和重复性。结论　DNA芯片检测HBV基因常见突变位点多态性 ,操作简便易行 ,技术要求不高 ,具有临床推广应用价值 ,而且可以方便地通过向寡核苷酸探针阵列中添加相应探针 ,扩大基因芯片的检测应用范围 ,为临床检测提供了新的方法     

基因芯片技术在关节软骨研究中的应用进展

基因芯片通常指DNA芯片,其基本原理是将指大量寡核苷酸分子嗣定于支持物上,然后与标记的样品进行杂交,通过芯片扫描检测杂交信号的强弱进而判断样品中靶分子的数量。基因芯片能对微量样品中的核苷酸序列进行检测和分析,其高通量、快速、并行化采集生物信息的特点均优于其他传统基因检测技术,故已广泛应用于医学各领域研究。将近年来基因芯片技术在关节软骨生物学特性、形成及发育、损伤与修复、退变及再生等领域的应用进行综述：     

自行构建人类白细胞抗原DQA1位点基因分型寡核苷酸芯片性能评价:100例样本与PCR-SSP法的比较

背景:人类白细胞抗原等位基因分型对器官移植和法医鉴定等有重要意义。目前的分型方法难以实现高通量和集成化,准确性和重复性也不理想。目的:比较自行构建的寡核苷酸芯片与序列特异性引物-聚合酶链反应(polymerase chain reaction with sequence-specific primers,PCR-SSP)两种方法用于人类白细胞抗原DQA1基因分型的结果,以评价寡核苷酸芯片的性能。方法:纳入2006-01/2009-03于中国医科大学附属第一医院血液科门诊就诊的患者100例。分别用等位基因特异的PCR-SSP和自行构建的寡核苷酸芯片对患者的人类白细胞抗原DQA1进行分型。寡核苷酸芯片分型采用荧光标记的组间特异性引物扩增基因组DNA,扩增后的产物与分型芯片的探针杂交,由杂交产生的荧光信号确定人类白细胞抗原DQA1位点基因型。比较两种方法分型所获得的结果,不吻合的样本经第三方测序验证。结果与结论:100例临床样本经寡核苷酸芯片和PCR-SSP分型全部成功。分型结果的吻合率为94%。不吻合样本6例,其中4例PCR-SSP定型为杂合子,芯片分型全部为纯合子。经第三方验证,证实芯片的分型全部正确。另外2例不吻合的样本经测序,证实SSP分型错误1例,芯片分型错误1例。芯片的重复率为95%。说明自行构建的寡核苷酸芯片的特异性和灵敏度都能满足基因分型的需要,且稳定性较好。     

人类白细胞抗原-A基因芯片分型研究

目的 探索人类白细胞抗原-A（HLA-A）基因芯片分型，为器官移植临床配型服务。方法 根据中国汉族南方人常见的HLA-A位点基因及其多态性的独特序列，设计并合成48条特异性的寡核苷酸分型探针，将其点在玻片上，制成芯片。基因组DNA通过组间特异性引物扩增，并用荧光素Cy5标记。标记后的产物与结合在芯片上的探针进行杂交，通过荧光扫描仪获得杂交产生的荧光信号值，再经过计算机软件自动分析，确定样品的HLA-A基因亚型。用该方法对120份样本进行HLA-A基因分型。结果 120份待检样本，其中6份因PER无产物，不能分型。1份信号杂乱，不能分型。其余113份样本分型成功。实际检出A抗原特异性结果为A2（含A203）：56；A11（含A1101）：52；A24：33；Al：8；A30（含A3001）：7；A33：21；A26：1；A29：2；A31：3；A68：2；A3：9；A32：1。未检出A＊3002基因型。整个检测耗时约4．5h。芯片检测的重复率为100％。结论 HLA-A基因芯片是一种理想的分型方法，具有特异性高、重复性好、操作简便、所需样本量少、结果判读容易、一次可作多份样本的优点，适合临床器官移植配型应用。     

一种新型基因芯片技术在人乳头瘤病毒(HPV)高通量基因分型检测的应用研究

目前应用比较多的采用反向点杂交/线性杂交方法的人乳头瘤病毒(HPV)基因分型检测方法,操作比较繁琐.该文通过设计针对29种HPV基因型的引物对和特异性探针,对HPV样品进行PCR扩增后,将反向引物生物素标记的PCR产物与固定在HPV基因芯片上的HPV DNA探针杂交、清洗和酶标显色,再对芯片进行图像分析转化为数字信号、确定HPV型别,建立HPV高通量基因分型方法(HPG).HPV基因芯片大小为0.36 cm2,每个芯片可在96孔板内的小孔中进行杂交和显色.与HCII方法检测的203例样本比较,对13种高危型检测的结果表明,HPG和HCII方法的一致性较好(kappa值0.663),HPG的分析灵敏度更高.显示了高通量快速检测的在大规模流行病调查、疫苗试验和常规诊断的临床应用前景.     

聚合酶链反应结合反向线点杂交技术在检测及鉴定真菌性鼻窦炎常见致病曲霉菌中的应用

目的 探讨聚合酶链反应结合反向线点杂交(PCR/RLB)技术在检测和鉴定真菌性鼻窦炎(FS)常见致病曲霉菌中应用的可行性.方法 收集首都医科大学附属北京同仁医院2009年5月至2010年2月住院手术的FS患者活检石蜡包埋组织26例和活检新鲜组织8例,全部病例进行了病理学真菌检查、真菌培养及真菌ITS2区测序;提取各标本中真菌的DNA,用真菌特异性引物行PCR扩增,针对真菌的ITS2区设计曲霉菌种特异性探针,用5根曲霉菌种特异性探针与PCR产物进行反向线点杂交;将PCR/RLB与ITS2区测序、真菌培养及病理学检查的结果进行比较.阳性对照为5株曲霉菌株,阴性对照为真菌培养为非曲霉的石蜡包埋组织.结果 活检标本病理学检查均可见菌丝;真菌培养14例阳性(41.2％);测序16例(47.1％)得到结果;PCR/RLB鉴定34例均得出鉴定结果:黄曲霉14例,烟曲霉10例,黑曲霉4例,构巢曲霉1例,黄曲霉和烟曲霉同时阳性3例,烟曲霉与黑曲霉同时阳性2例.结论 PCR/RLB技术可以对FS常见致病曲霉菌进行检测及鉴定,与病理组织学检查、真菌培养及DNA测序方法相比较,具有经济省时、敏感性高、特异性强、高通量等优势.     

HBV DNA及BCP、Pre-C突变株基因芯片检测方法的构建

目的　构建HBVDNA及BCP、Pre C突变株的基因芯片检测方法。方法　该基因芯片检测方法使用了PCR、寡核苷酸芯片二项技术 ,包含了对nt1896、nt 1899、nt186 2、nt176 4、nt176 2五个突变热点的检测 ,并用DNA测序法对该基因芯片进行验证。结果　该基因芯片检测HBVDNA方面结果与DNA测序法 10 0 %相符 ;检测突变株方面 14 6个位点两种方法结果相符 ,4个位点结果不相符 ,P >0 0 5。结论　该基因芯片具有便捷、高通量的特点 ,能同时检测多个BCP、Pre C突变位点。结果提示该基因芯片和DNA测序法检测结果阳性率相等 ,特异性与DNA测序法相当 ,检测混合株有更大优势 ,可用于临床检测。     

High-throughput identification of clinical pathogenic fungi by hybridization to an oligonucleotide microarray

Here we report the development of an oligonucleotide microarray method that can identify fungal pathogens in a single reaction. Specific oligonucleotide probes targeted to internal transcribed spacer 2 were designed and synthesized. Fungal DNA was amplified by universal primers, and the PCR product was hybridized with the oligonucleotide microarray. A series of specific hybridization profiles corresponding to species were obtained. The 122 strains of fungal pathogens, including standard and clinically isolated strains, used to test the specificity, stability, and sensitivity of the microarray system belonged to 20 species representing 8 genera. We found that the microarray system can successfully discriminate among the fungal pathogens to the species level, with high specificity and stability. The sensitivity was 15 pg/ml of DNA. This oligonucleotide microarray system represents a rapid, simple, and reliable alternative to conventional methods of identifying common clinical fungal isolates.     

Simultaneous analysis of foodborne pathogenic bacteria by an oligonucleotide microarray assay

A rapid and accurate method for simultaneous identification of foodborne infectious pathogens was developed based on oligonucleotide microarray technology. The proposed identification method is based on PCR amplification of the target region of the groEL genes with degenerate primers, followed by the PCR products hybridization with oligonucleotide probes specific for species. The groEL gene amplification products of seventeen species of pathogenic bacteria were hybridized to the oligonucleotide array. Hybridization results were analyzed with digoxigenin-linked enzyme reaction. Results indicated that fifteen species of pathogenic bacteria showed high sensitivity and specificity for the oligonucleotide array, while two other species gave cross-reaction with the E. coli. Our results suggested that microarray analysis of foodborne infectious pathogens might be very useful for simultaneous identification of bacterial pathogens. The oligonucleotide array can also be applied to samples collected in clinical settings of foodborne infections. The superiority of oligonucleotide array over other tests lies on its rapidity, accuracy and efficiency in the diagnosis, treatment and control of foodborne infections.     

Development of a DNA microarray for detection and identification of fungal pathogens involved in invasive mycoses

Invasive fungal infections have emerged as a major cause of morbidity and mortality in immunocompromised patients. Conventional identification of pathogenic fungi in clinical microbiology laboratories is time-consuming and, therefore, often imperfect for the early initiation of an adequate antifungal therapy. We developed a diagnostic microarray for the rapid and simultaneous identification of the 12 most common pathogenic Candida and Aspergillus species. Oligonucleotide probes were designed by exploiting the sequence variations of the internal transcribed spacer (ITS) regions of the rRNA gene cassette to identify Candida albicans, Candida dubliniensis, Candida krusei, Candida glabrata, Candida tropicalis, Candida parapsilosis, Candida guilliermondii, Candida lusitaniae, Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, and Aspergillus terreus. By using universal fungal primers (ITS 1 and ITS 4) directed toward conserved regions of the 18S and 28S rRNA genes, respectively, the fungal ITS target regions could be simultaneously amplified and fluorescently labeled. To establish the system, 12 pre-characterized fungal strains were analyzed; and the method was validated by using 21 clinical isolates as blinded samples. As the microarray was able to detect and clearly identify the fungal pathogens within 4 h after DNA extraction, this system offers an interesting potential for clinical microbiology laboratories.     

Identification of medically important molds by an oligonucleotide array

Infections caused by fungi have increased in recent years. Accurate and rapid identification of fungal pathogens is important for appropriate treatment with antifungal agents. On the basis of the internal transcribed spacer 1 (ITS 1) and ITS 2 sequences of the rRNA genes, an oligonucleotide array was developed to identify 64 species (32 genera) of clinically important filamentous (or dimorphic) fungi. These 64 species included fungi causing superficial, cutaneous, subcutaneous, and invasive infections. The method consisted of PCR amplification of the ITS regions using a pair of universal primers, followed by hybridization of the digoxigenin-labeled PCR products to a panel of species- or group-specific oligonucleotides immobilized on a nylon membrane. Of 397 fungal strains (290 target and 107 nontarget strains) tested, the sensitivity and specificity of the array was 98.3% (285/290) and 98.1% (105/107), respectively. Misidentified strains were usually those belonging to the same genus of the target species or having partial homology with oligonucleotide probes on the membrane. The whole procedure can be finished within 24 h starting from isolated colonies; reproductive structures, which are essential for the conventional identification methods, are not needed. In conclusion, the present array is a powerful tool for identification of clinically important filamentous fungi and may have the potential to be continually extended by adding further oligonucleotides to the array without significantly increasing the cost or complexity.     

Molecular probes for diagnosis of fungal infections.

We have developed 21 specific nucleic acid probes which target the large subunit rRNA genes from Aspergillus flavus, Aspergillus fumigatus, Aspergillus glaucus, Aspergillus niger, Aspergillus terreus, Blastomyces dermatitidis, Candida albicans, Candida (Torulopsis) glabrata, Candida guilliermondii, Candida kefyr, Candida krusei, Candida lusitaniae, Candida parapsilosis, Candida tropicalis, Coccidioides immitis, Cryptococcus neoformans var. gattii, Cryptococcus neoformans var. neoformans, Filobasidiella neoformans var. bacillispora, Filobasidiella neoformans var. neoformans, Histoplasma capsulatum, Pseudallescheria boydii, and Sporothrix schenckii. A section of the 28S rRNA gene from approximately 100 fungi, representing about 50 species of pathogens and commonly encountered saprophytes, was sequenced to develop universal PCR primers and species-specific oligonucleotide probes. Each step in the process of detection and identification was standardized to a common set of conditions applicable without modification to all fungi of interest and all types of clinical specimens. These steps consist of DNA extraction by boiling specimens in an alkaline guanidine-phenol-Tris reagent, amplification of a variable region of the 28S rRNA gene with universal primers, and amplicon identification by probe hybridization or DNA sequencing performed under conditions identical for all fungi. The results obtained by testing a panel of fungal isolates and a variety of clinical specimens indicate a high level of specificity.     

Evaluation of commercially available acridinium ester-labeled chemiluminescent DNA probes for culture identification of Blastomyces dermatitidis, Coccidioides immitis, Cryptococcus neoformans, and Histoplasma capsulatum.

Four commercially available acridinium ester-labeled DNA probes directed against rRNA were evaluated for their ability to identify Blastomyces dermatitidis, Coccidioides immitis, Histoplasma capsulatum, and Cryptococcus neoformans in culture. rRNA was extracted by sonication of 1- to 2-mm2 portions of cultures of fungi in two chaotropic reagents with glass beads. Following a heat inactivation step, the extracts were hybridized in solution with probes specific for each pathogen. The acridinium ester reporter moiety of nonhybridized probe was selectively hydrolyzed, and chemiluminescence of specific DNA:RNA hybrids was quantitated in relative light units with a luminometer. A positive identification required a relative light unit value of > or = 50,000. Sensitivity and specificity of the probes were determined by probing cultures of the respective pathogenic fungi (target) and nontarget fungi. Both mycelial and yeast forms of the dimorphic fungi (B. dermatitidis and H. capsulatum) were tested. For B. dermatitidis, sensitivity and specificity were 87.8 and 100%, respectively (74 target and 219 nontarget fungi tested). For C. immitis, sensitivity and specificity were 99.2 and 100%, respectively (122 target and 164 nontarget fungi tested). For H. capsulatum, sensitivity and specificity were 100 and 100%, respectively (86 target and 154 nontarget fungi tested). For C. neoformans, sensitivity and specificity were 97 and 100%, respectively (100 target and 230 nontarget fungi tested). For B. dermatitidis, C. immitis, and C. neoformans, repeat testing increased the respective sensitivities to 97.3, 100, and 100%. The high sensitivities and specificities of the probes, the relatively short time (less than 1 h) required to perform the assay, and the availability of standardized reagent kits make the acridinium ester-labeled DNA probes well suited to laboratories in need of a rapid method to identify these fungal pathogens. Further, use of the probes to identify pathogenic fungi as soon as colonies appear on primary recovery media significantly shortens the time to reporting.     

Development of an Oligonucleotide Array for Direct Detection of Fungi in Sputum Samples from Patients with Cystic Fibrosis

Cystic fibrosis (CF) is the most common inherited genetic disease in Caucasian populations. Besides bacteria, many species of fungi may colonize the respiratory tract of these patients, sometimes leading to true respiratory infections. In this study, an oligonucleotide array capable of identifying 20 fungal species was developed to directly detect fungi in the sputum samples of CF patients. Species-specific oligonucleotide probes were designed from the internal transcribed spacer (ITS) regions of the rRNA operon and immobilized on a nylon membrane. The fungal ITS regions were amplified by PCR and hybridized to the array for species identification. The array was validated by testing 182 target strains (strains which we aimed to identify) and 141 nontarget strains (135 species), and a sensitivity of 100% and a specificity of 99.2% were obtained. The validated array was then used for direct detection of fungi in 57 sputum samples from 39 CF patients, and the results were compared to those obtained by culture. For 16 sputum samples, the results obtained by the array corresponded with those obtained by culture. For 33 samples, the array detected more fungal species than culture did, while the reverse was found for eight samples. The accuracy of the array for fungal detection in sputum samples was confirmed (or partially confirmed) in some samples by cloning and resequencing the amplified ITS fragments. The present array is a useful tool for both the simultaneous detection of multiple fungal species present in the sputa of CF patients and the identification of fungi isolated from these patients.     

Fluorescent In situ hybridization allows rapid identification of microorganisms in blood cultures

Using fluorescent in situ hybridization (FISH) with rRNA-targeted fluorescently labelled oligonucleotide probes, pathogens were rapidly detected and identified in positive blood culture bottles without cultivation and biotyping. In this study, 115 blood cultures with a positive growth index as determined by a continuous-reading automated blood culture system were examined by both conventional laboratory methods and FISH. For this purpose, oligonucleotide probes that allowed identification of approximately 95% of those pathogens typically associated with bacteremia were produced. The sensitivity and specificity of these probes were 100%. From all 115 blood cultures, microorganisms were grown after 1 day and identification to the family, genus, or species level was achieved after 1 to 3 days while 111 samples (96.5%) were similarly identified by FISH within 2.5 h. Staphylococci were identified in 62 of 62 samples, streptococci and enterococci were identified in 19 of 20 samples, gram-negative rods were identified in 28 of 30 samples, and fungi were identified in two of two samples. Thus, FISH is an appropriate method for identification of pathogens grown in blood cultures from septicemic patients.     

Simultaneous detection of marine fish pathogens by using multiplex PCR and a DNA microarray

We coupled multiplex PCR and a DNA microarray to construct an assay suitable for the simultaneous detection of five important marine fish pathogens (Vibrio vulnificus, Listonella anguillarum, Photobacterium damselae subsp. damselae, Aeromonas salmonicida subsp. salmonicida, and Vibrio parahaemolyticus). The array was composed of nine short oligonucleotide probes (25-mer) complementary to seven chromosomal loci (cyt, rpoN, gyrB, toxR, ureC, dly, and vapA) and two plasmid-borne loci (fatA and A.sal). Nine primer sets were designed to amplify short fragments of these loci (100 to 177 bp) in a multiplex PCR. PCR products were subsequently labeled by nick translation and hybridized to the microarray. All strains of the five target species (n = 1 to 21) hybridized to at least one species-specific probe. Assay sensitivities ranged from 100% for seven probes to 83 and 67% for the two remaining probes. Multiplex PCR did not produce any nonspecific amplification products when tested against 23 related species of bacteria (n = 40 strains; 100% specificity). Using purified genomic DNA, we were able to detect PCR products with < 20 fg of genomic DNA per reaction (equivalent to four or five cells), and the array was at least fourfold more sensitive than agarose gel electrophoresis for detecting PCR products. In addition, our method allowed the tentative identification of virulent strains of L. anguillarum serotype O1 based on the presence of the fatA gene (67% sensitivity and 100% specificity). This assay is a sensitive and specific tool for the simultaneous detection of multiple pathogenic bacteria that cause disease in fish and humans.