应用实时荧光定量PCR方法检测血小板制品细菌污染

目的应用实时荧光定量PCR方法检测血小板制品中细菌的探讨。方法选取金黄色葡萄球菌及大肠埃希氏杆菌,用改良的Chelex-100法抽提细菌基因组DNA,进行荧光定量PCR检测。并应用过滤法去除反应体系中潜在的细菌及其基因组DNA污染。结果针对16srRNA基因保守序列进行扩增的荧光定量PCR方法具有较高的特异性和灵敏度,与人类淋巴细胞及病毒等的基因组无交叉反应。在金黄色葡萄球菌检测中,应用过滤法后最低含菌量组与阴性对照组Ct值有极显著差异(P<0.001)。该方法对金黄色葡萄球菌的最低检出量为0.3CFUs/PCR,与阴性对照Ct值有显著差异(P<0.01),在大肠埃希氏杆菌中该法可检测出0.1CFUs/PCR,与阴性对照Ct值有显著性差异(P<0.01)。结论改良Chelex-100法抽提细菌基因组及后续的荧光定量PCR分析用于检测血小板制品中的细菌污染,检测实验缩短到3-4h,操作简单,灵敏性高,特异性好,为在临床标本大规模检测中的应用提供理论基础和实验数据。     

一种新的实时荧光定量PCR方法对血小板制品细菌污染检测效果的评价

目的建立一种自主研发的针对细菌16 S r DNA基因的实时荧光定量PCR(Real-time PCR)方法并评价该方法对浓缩血小板制品中细菌污染检测的效果。方法设计16S r DNA基因保守区引物,构建SYBR Green Real-time PCR反应体系;然后分别将大肠杆菌、金黄色葡萄球菌、表皮葡萄球菌、蜡样芽孢杆菌和绿脓杆菌以初始浓度为1CFU/m L、10 CFU/m L和100 CFU/m L接种到浓缩血小板中,经22℃保存7 d后,用实时定量荧光PCR方法进行细菌检测。结果细菌污染后的血小板在常规保存条件下,最长保存期7 d,不同接种浓度的细菌生长情况的变化趋势基本一致,所有种类的细菌均在d 1、2表现出迅猛的增殖高峰,d 3以后增殖趋于平缓。结论该Real-time PCR检测体系可定量地检测出血小板的细菌污染的情况,可适用于血小板输注前的快速细菌污染检测。     

Triplex real-time PCR assay for the detection of Streptococcus pneumoniae,Neisseria meningitidis and Haemophilus influenzae directly from clinical specimens without extraction of DNA

This study presents a triplex real-time PCR assay that allows for the direct detection of Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae in one reaction without DNA extraction, with similar sensitivity and specificity to singleplex assays. This approach saves time, specimen volume and reagents while achieving a higher testing throughput.     

Chimeric LNA/DNA probes as a detection system for real-time PCR

OBJECTIVE: Evaluation of the use of short probes as a detection system in real-time PCR. DESIGN AND METHOD: Comparison of results obtained with hybridization probes with and without locked nucleic acid (LNA) residues in the detection of fetal DNA in maternal serum. RESULTS: The use of chimeric LNA/DNA probes led to a slight but significantly higher level of sensitivity as well as a higher level of fluorescence signal. CONCLUSION: Chimeric LNA/DNA probes offer an interesting alternative detection method in real-time PCR.     

Validation and comparison of two quantitative real-time PCR assays for direct detection of DMD/BMD carriers

Objectives

To develop a robust and reliable assay for direct identification of female carriers of deletions in the dystrophin gene.

Design and methods

We compared two quantitative real-time PCR approaches for the detection of the deletions of exons 4, 17, 47, and 50 in DMD/BMD carriers. One hundred and ten individuals from 26 unrelated families, including 8 large pedigrees characterized by having at least two DMD affected males, were studied. Carrier status of the subjects was also evaluated by MLPA.

Results

The results showed the gene dosage ratio of 0.99 ± 0.14 and 1.09 ± 0.19 for normal individuals and 0.48 ± 0.06 and 0.50 ± 0.10 for carriers in SYBR green and TaqMan probe assays, respectively. Carrier status was accurately attributed in 100% of cases and confirmed by MLPA.

Conclusion

Quantitative real-time PCR can be used as a direct method for carrier detection in female relatives of DMD patients with known deletions. The results are comparable to the MLPA data.     

Novel primers and PCR protocols for the specific detection and quantification of Sphingobium suberifaciens in situ

The pathogen causing corky root on lettuce, Sphingobium suberifaciens, is recalcitrant to standard epidemiological methods. Primers were developed from 16S rDNA sequences to be useful for the specific detection and quantification of S. suberifaciens. Quantitative PCR (qPCR) protocols specifically amplified DNA from the type strain of S. suberifaciens (LMG 17323) and other members of this species but not from other members of the Sphingomonadaceae. The detection limit was as little as 100 fg DNA (equivalent to 2 × 10² cells) in the qPCR. Detection was successful from soils inoculated with as little as 1 × 10³ CFU/g soil. DNA isolated from naturally infested soils and diseased lettuce roots was amplified and sequenced fragments were identical or nearly identical to 16S rDNA sequences from S. suberifaciens. In growth chamber experiments, there was a positive correlation between disease severity and S. suberifaciens population levels in roots and soil, as detected by qPCR. Detection levels were below population levels of the pathogen necessary for disease development.     

Validation of a reference control for an SYBR-Green fluorescence assay-based real-time PCR for detection of bovine herpesvirus 5 in experimentally exposed bovine embryos

The objective of this study was to optimize an internal control to improve SYBR-Green-based qPCR to amplify/detect the BoHV-5 US9 gene in bovine embryos produced in vitro and experimentally exposed to the virus. We designed an SYBR-Green-based binding assay that is quick to perform, reliable, easily optimized and compares well with the published assay. Herein we demonstrated its general applicability to detect BoHV-5 US9 gene in bovine embryos produced in vitro experimentally exposed to BoHV-5. In order to validate the assay, three different reference genes were tested; and the histone 2a gene was shown to be the most adequate for normalizing the qPCR reaction, by considering melting and standard curves (p < 0.05). On the other hand, no differences were found in the development of bovine embryos in vitro whether they were exposed to BoHV-5 reference and field strains comparing to unexposed embryos. The developed qPCR assay may have important field applications as it provides an accurate BoHV-5 US9 gene detection using a proven reference gene and is considerably less expensive than the TaqMan qPCR currently employed in sanitary programs.     

p53基因第8外显子实时荧光PCR方法的建立

目的建立实时荧光定量聚合酶链反应(PCR)检测p53基因第8外显子的方法。方法用酚-氯仿抽提法提取云南省中医院的常规体检患者的DNA,应用SYBR GreenⅠ作荧光染料,通过检测PCR产物中荧光讯号的强度来定量p53基因,重复测定该标本18次,以此建立检测p53基因的实时荧光定量PCR方法。结果融解曲线分析表明该方法特异可靠。结论该研究建立了p53基因实时荧光定量PCR检测方法,该方法简便、特异、重复性好、可信度高,为p53基因第8外显子的定量研究提供了理想的检测方法。     

Activity and DNA contamination of commercial polymerase chain reaction reagents for the universal 16S rDNA real-time polymerase chain reaction detection of bacterial pathogens in blood

Universal 16S rRNA gene polymerase chain reaction (PCR) is a promising means of detecting bacteremia. Among other factors, the PCR reagents play a prominent role for obtaining a high sensitivity of detection. The reagents are ideally optimized with respect to the amplifying activity and absence of contaminating DNA. In this study, it was shown in a universal 16S rDNA real-time PCR assay that commercial PCR reagents can vary greatly among each other in these characters. Only 1 of the 5 reagents tested met the criteria of sensitive detection of pathogen DNA with a minimum of false-positive results. The reagent was validated by the detection of pathogens at low titers using bacterial DNA extracted from blood that was spiked with various Gram-positive and Gram-negative bacteria.     

人血浆DNA双重实时荧光定量PCR检测法的建立

目的 建立带有内参照的双重实时荧光定量PCR方法检测血浆DNA含量.方法 构建重组质粒DNA作为内参照物,采用共用下游引物的双重实时荧光定量PCR技术同步扩增人看家基因β-actin和重组质粒载体中人工合成DNA序列,定量检测健康成年人血浆DNA含量.结果 本法能在同一个反应管中对目的基因和内参照进行同步扩增,两者的扩增无相互干扰,特异性好;重组质粒DNA的平均扩增效率达90%,β-actin基因的平均扩增效率接近100%;本法批内变异系数（CV）11%,批间CV17%.结论 成功建立含有内参照的双重实时荧光定量PCR方法,可对血浆DNA进行定量检测.     

荧光定量PCR方法在空肠弯曲菌检测中的应用

空肠弯曲菌是引起人类食源性疾病的主要病原菌之一。快速、特异检测方法的建立对于该病原菌感染的诊断及鉴别诊断具有重要意义。荧光定量PCR方法作为一种快速诊断方法已经广泛应用于空肠弯曲菌的检测及鉴定。本文从荧光定量PCR方法在空肠弯曲菌病原检测中的建立、发展以及应用等方面进行综述。     

Rapid detection of eight causative pathogens for the diagnosis of bacterial meningitis by real-time PCR

We aimed to detect causative pathogens in cerebrospinal fluid (CSF) collected from patients diagnosed with bacterial meningitis by real-time polymerase chain reaction (PCR). In addition to Streptococcus pneumoniae, Haemophilus influenzae, and Mycoplasma pneumoniae described previously, five other pathogens, Neisseria meningitidis, Escherichia coli, Streptococcus agalactiae, Staphylococcus aureus, and Listeria monocytogenes, were targeted, based on a large-scale surveillance in Japan. Results in CSF from neonates and children (n = 150), and from adults (n = 18) analyzed by real-time PCR with molecular beacon probes were compared with those of conventional culturing. The total time from DNA extraction from CSF to PCR analysis was 1.5 h. The limit of detection for these pathogens ranged from 5 copies to 28 copies per tube. Nonspecific positive reactions were not recognized for 37 microorganisms in clinical isolates as a negative control. The pathogens were detected in 72.0% of the samples by real-time PCR, but in only 48.2% by culture, although the microorganisms were completely concordant. With the real-time PCR, the detection rate of H. influenzae from CSF was high, at 45.2%, followed by S. pneumoniae (21.4%), S. agalactiae (2.4%), E. coli (1.8%), L. monocytogenes (0.6%), and M. pneumoniae (0.6%). The detection rate with PCR was significantly better than that with cultures in patients with antibiotic administration (χ² = 18.3182; P = 0.0000). In conclusion, detection with real-time PCR is useful for rapidly identifying the causative pathogens of meningitis and for examining the clinical course of chemotherapy.     

细菌革兰双检荧光定量PCR方法检测新生儿败血症

目的 建立细菌革兰阴、阳性菌双重实时荧光定量检测体系,探讨其检测败血症的临床应用价值.方法 分析细菌16SrRNA基因序列,在高度保守区自行设计通用引物和革兰阴性和阳性分型探针,选取临床较常见的35株菌株进行细菌革兰双检实时荧光定量PCR方法检测;对临床疑为败血症的512例新生患儿分别做细菌革兰双检荧光定量PCR和血培养检测.结果 细菌革兰双检荧光定量PCR具有较好的敏感性和特异性,能稳定检测到10 CFU左右细菌数.35株菌株进行细菌革兰双检荧光定量PCR检测,均为阳性,且革兰阴、阳性菌能正确分型和定量.巨细胞病毒、EB病毒、乙肝病毒、新型隐球菌及白色念珠菌、人基因组DNA及空白对照均为阴性.对临床疑为败血症的512份新生患儿标本中,革兰双检荧光定量PCR检测血标本阳性率8.20%(42/512),血培养阳性率6.25%(32/512),前者明显高于后者,差异具有统计学意义(χ<'2>=8.10,P<0.01),30例非感染性疾病同期患儿血标本革兰双检荧光定量PER及细菌培养均为阴性.若以血培养作为对照,细菌革兰双检荧光定量PCR方法的诊断敏感度为100%,特异度为97.92%,准确性98.05%.结论 建立了用通用引物和分型双荧光探针的细菌革兰双检荧光定量PER方法.其检测快速、准确,具有很大的临床推广价值.     

Comparing the performance of conventional PCR,RTQ-PCR,and droplet digital PCR assays in detection of Shigella

The incidence of foodborne infections caused by Shigella spp. is still very high in every year, which poses a great potential threat to public health. Conventional quantification methods based on culture techniques, biochemical, and serological identification are time-consuming and labor-intensive. To develop a more rapid and efficient detection method of Shigella spp., we compared the sensitivity and specificity of three different polymerase chain reaction (PCR) methods, including conventional PCR, quantitative real-time PCR (RTQ-PCR), and droplet digital PCR (ddPCR). Our results indicated that ddPCR method exhibited higher sensitivity, and the limit of detection was 10⁻⁵ ng/μl for genomic DNA templates, 10⁻¹ cfu/ml for Shigella bacteria culture. In addition, we found that ddPCR was a time-saving method, which required a shorter pre-culturing time. Collectively, ddPCR assay was a reliable method for rapid and effective detection of Shigella spp.     

Applications of real-time PCR in the screening of platelet concentrates for bacterial contamination

Although there have been major improvements over the past few decades in detection methods for blood-borne infectious agents, platelet concentrates are still responsible for most cases of transfusion-transmitted bacterial infections. To date, real-time PCR is an indispensable tool in diagnostic laboratories to detect pathogens in a variety of biological samples. In this article, the applications of this powerful technique in the screening of platelet concentrates for bacterial contamination are discussed. Next to pathogen-specific (real-time) PCR assays, particular attention is directed to the recently developed 16S rDNA real-time PCR. This assay has been proven as a convenient way to detect bacterial contamination of platelet concentrates. The assay is sensitive and enables rapid detection of low initial numbers of bacteria in platelet concentrates. The short turnaround time of this assay allows high-throughput screening and reduction of the risk of transfusion of bacterially contaminated units. As with every method, real-time PCR has its advantages and disadvantages. These and especially limitations inherent to generation of false-positive or -negative results are emphasized. The universal nature of detection of the assay may be suitable for generalized bacterial screening of other blood components, such as red blood cells and plasma. Therefore, it is necessary to adapt and optimize detection in red blood cells and plasma with real-time PCR. Further sophistication, miniaturization and standardization of extraction and amplification methods should improve the total performance and robustness of the assay. Hence, real-time PCR is an attractive method in development as a more rapid screening test than currently used culture methods to detect bacterial contamination in blood components.     

A real-time PCR assay for detection of emerging infectious Elizabethkingia miricola

Elizabethkingia miricola, a Gram-negative bacillus, is emerging as a life-threatening pathogen in both humans and animals. However, no specific and rapid diagnostic method exists to detect E. miricola. Here, we established a real-time PCR assay for the rapid, sensitive, and specific detection of E. miricola with a wide dynamic range of 10⁸ copies/μL to 10² copies/μL. The detection limit of the real-time assay was 145 copies/μL, which was 100 times more sensitive than conventional PCR. All clinical isolates E. miricola from different host species yield very close Tm (80.25 ± 0.25 °C). Additionally, no cross-reaction or false positives were observed in the assay for non-target bacterial species. The performance of this assay was primarily assessed by testing frog tissue samples. Overall, our study provided a real-time PCR assay, which is a rapid, sensitive, and specific diagnostic method that could be used for early diagnosis and epidemiological investigation of E. miricola.     

类志贺邻单胞菌实时荧光TaqMan PCR快速检测体系的建立

目的建立针对类志贺邻单胞菌的高灵敏、高特异的实时荧光TaqMan聚合酶链式反应(PCR)快速检测体系。方法根据类志贺邻单胞菌23S rRNA基因的一段特异性序列设计引物及TaqMan探针,利用实时荧光PCR检测平台探讨该检测体系的灵敏度;用30种其他肠道致病菌及院内感染中常见的致病菌评价该检测体系的特异性。结果实时荧光TaqMan PCR快速检测体系对类志贺邻单胞菌重组质粒的检测灵敏度为1×102拷贝/反应体系;对类志贺邻单胞菌基因组的检测灵敏度为3×10-2pg/反应体系;该检测体系在检测30种其他肠道致病菌及院内感染中常见的致病菌时未出现特异性扩增,整个反应在2 h内完成。结论本研究建立的实时荧光TaqMan PCR检测体系可作为类志贺邻单胞菌灵敏、特异、快速的检测方法。     

Successful use of saliva without DNA extraction for detection of macrolide-resistant Mycoplasma pneumoniae DNA in children using LNA probe-based real-time PCR

It is not known that saliva is useful to diagnose Mycoplasma pneumoniae (M. pneumoniae) infection by PCR. We evaluated prospectively whether crude saliva samples without the DNA extraction process were useful for the detection of M. pneumoniae DNA in a locked nucleic acid (LNA) probe-based real-time PCR assay. Fifty-one clinical specimens (29 sputum, 22 saliva) that were positive by conventional M. pneumoniae-specific PCR were evaluated in this study. We designed an LNA probe-based real-time PCR that could discriminate the mutant strain (A2063G mutation) from the wild-type strain. All the 51 samples treated with DNA extraction were positive using the LNA probe-based real-time PCR. The results of the real-time PCR with DNA extraction were consistent with the sequence analysis. Of the 51 samples without DNA extraction, on the other hand, 41 (80.4 %) were positive by real-time PCR. Of 29 sputum samples without DNA extraction, 23 (79.3 %) were positive by real-time PCR; of the 22 saliva samples without DNA extraction, 18 (81.8 %) were positive by real-time PCR. There was a statistically significant difference in the amplified DNA levels with extraction between the direct real-time PCR-positive samples (mean ± SD, 7.5 ± 1.6 log copies/ml) and PCR-negative samples (4.2 ± 0.8 log copies/ml) (P < 0.001). Saliva was useful for a template for PCR as well as sputum. In addition, crude samples were useful for real-time PCR when the samples had medium or high DNA levels. However, samples with low DNA levels sometimes showed false-negative results in direct real-time PCR.     

TaqMan荧光定量PCR检测新型隐球菌方法的建立

目的建立TaqMan荧光定量PCR方法定量检测新型隐球菌基因组DNA,为检测隐球菌性脑膜炎提供重要方法。方法在国家生物技术信息中心(NCBI)查找新型隐球菌各亚型的ITS-rDNA序列,序列比对后设计特异性引物和探针,扩增片段为114bp,构建质粒标准品,调整质粒浓度为1.42×10~8 copy/μL~1.42×10copy/μL共8个浓度梯度,分别取2μL作为模板,优化反应条件,建立标准曲线,进行敏感性、特异性、重复性评价,并检测临床确诊的15例隐球菌脑膜炎感染菌株。结果建立的荧光定量PCR可以检测2.84×10~2拷贝的质粒DNA,对临床分离的各10例其他真菌、细菌、乙型肝炎病毒DNA和人类基因组DNA均无扩增曲线,重复性良好,3个浓度的批间变异系数分别为2.86%、1.48%、1.36%,可准确检测15例新型隐球菌。结论成功建立检测新型隐球菌的荧光定量PCR方法,敏感性和特异性较高,结果稳定可靠,可早期、快速诊断隐球菌性脑膜炎。     

实时定量PCR检测胃癌组织miR-20a及初步应用

目的建立检测人胃癌组织中miR-20a的实时荧光定量PCR方法。方法建立miR-20a标准曲线,评价该法检测的线性范围及灵敏度;对标准质粒扩增产物进行熔解曲线分析和琼脂糖凝胶电泳检测以分析该法的特异性。取高、中、低3份不同浓度的标准质粒进行批内和日间变异系数(CV)的检测,分析该法的重复性。收集70例胃癌患者手术切除的癌组织和对应的癌旁组织,定量检测组织中miR-20a的表达水平。结果构建的实时荧光定量PCR法的灵敏度为101copies/μL,扩增的线性范围为101～109copies/μL;扩增产物的熔解曲线峰和电泳片段特异;3份不同浓度标准质粒定量检测的批内CV分别为6.33%、4.74%、5.89%,日间CV分别为9.45%、6.29%、7.48%。定量结果显示75.7%(53/70)胃癌组织中miR-20a的表达高于癌旁组织,差异有显著性(Z=-4.427,P<0.01)。结论建立的实时荧光定量PCR检测miR-20a的方法准确、快速、灵敏、特异,可用于胃癌组织中miR-20a的检测。