Establishment of a duplex SYBR green I-based real-time polymerase chain reaction assay for the rapid detection of canine circovirus and canine astrovirus

The similar clinical characteristics of canine circovirus (CaCV) and canine astrovirus (CaAstV) infections and high frequency of co-infection make diagnosis difficult. In this study, a duplex SYBR Green I-based real-time polymerase chain reaction (PCR) assay was established for the rapid, simultaneous detection of CaCV and CaAstV. Two pairs of specific primers were designed based on the Rep gene of CaCV and the Cap gene of CaAstV. By using the real-time PCR assay method, the two viruses can be distinguished by the difference in melting temperatures, 79 °C and 86 °C for CaCV and CaAstV, respectively. This assay had high specificity, showing no cross-reaction with other common canine viruses, as well as high sensitivity, with minimum detection limits of 9.25 × 10¹ copies/μL and 6.15 × 10¹ copies/μL for CaCV and CaAstV, respectively. Based on the mean coefficient of variation, the method had good reproducibility and reliability. In a clinical test of 57 fecal samples, the rates of positive detection by real-time PCR were 14.04% (8/57) and 12.28% (7/57) for CaCV and CaAstV, respectively, and the rate of co-infection was 8.77% (5/57). In conclusion, the newly established duplex SYBR Green I-based real-time PCR assay is sensitive, specific, reliable, and rapid and is an effective tool for the detection of co-infections with CaCV and CaAstV.     

Development and preliminary testing of a probe-based duplex real-time PCR assay for the detection of African swine fever virus

An outbreak of African swine fever (ASF) in China in 2018 caused substantial economic losses to the swine industry. To accurately diagnose clinical infection with ASF virus (ASFV), we developed a TaqMan probe-based duplex real-time PCR that simultaneously detected two discontinuous genes in the virus genome, thereby preventing the inaccurate results obtained with only one reaction. Two sets of ASFV gene-specific primers, along with two fluorescent TaqMan probes were designed to target conserved regions of the B646L and B438L genes. This method had high sensitivity and specificity, with a limit of detection of 10 copies/μL, and it did not cross-react with the genomes of other viral pathogens that affect pigs (i.e., CSFV, PRRSV, PEDV, PRV, PPV and PCV2). Overall, 180 clinical samples from ASFV-infected pig farms were used to compare this method with a commercial kit, which yielded excellent consistency (98.3%). This new diagnostic method should greatly improve the efficiency of ASFV surveillance and reduce economic losses, providing benefits for both animal and public health.     

TaqMan MGB 探针实时荧光定量-聚合酶链反应检测人粒细胞无形体Msp2基因方法的建立

目的 建立敏感、特异、实时荧光定量-聚合酶链反应(real-time fluorescence quantitative, FQ-PCR)方法, 用于人粒细胞无形体病的检测。 方法 根据无形体特异外膜蛋白 Msp2基因为靶基因设计引物以及TaqMan MGB探针, 建立FQ-PCR方法,并对湖北省随州和河北省张家口地区的蜱标本进行了检测。 结果 本研究建立的TaqMan MGB探针具有良好的特异性,建立的FQ-PCR标准曲线的循环阈值(Ct)与模板拷贝数呈良好的线性关系(r=0.99),灵敏性评估发现每个20 μl PCR反应管中只要有35个拷贝的目的基因即可被检测到,即最低检出浓度为2拷贝/μl,并且具有较好的重复性。共检测蜱标本426只,其中豪猪血蜱253只,共49组,阳性7份。 结论 本研究建立的FQ-PCR方法具有很高的特异性和敏感性, 可用于人粒细胞无形体感染的快速检测。进一步证实了豪猪血蜱可能是粒细胞无形体的媒介宿主。     

Evaluation of Seeplex® STD6 ACE Detection kit for the diagnosis of six bacterial sexually transmitted infections

Traditionally, the diagnosis of bacterial sexually transmitted infection (STI) has been dependent on the isolation of the causative pathogens by culturing endocervical or urethral swab specimens on selective media. While such procedures typically provide excellent diagnostic accuracy, they are often time-consuming and expensive. A multiplex polymerase chain reaction (PCR) assay, based on a semi-automated detection system, was evaluated for the detection of six STI causative organisms. The Seeplex^® STD6 ACE (auto-capillary electrophoresis) Detection assay employed six pairs of dual priming oligonucleotide (DPO?) primers specifically targeted to unique genes of Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, Ureaplasma urealyticum, Mycoplasma hominis, and Trichomonas vaginalis. A total of 739 specimens (304 cervical swabs and 435 urine samples) collected for 4 months were tested, and results were compared to those obtained with a combined monoplex PCR. The concordance between the multiplex PCR and monoplex PCR assay was 100% for both sensitivity and specificity. We also tested for the presence of two pathogenic bacteria (C. trachomatis and N. gonorrhoeae) and compared the results obtained with the multiplex PCR and BD ProbeTec duplex strand displacement amplification (SDA). The results of the multiplex PCR and duplex SDA were 99.7% concordant for C. trachomatis and 100% concordant for N. gonorrhoeae. The multiplex PCR assay using the Seeplex^® STD6 ACE Detection kit proved to be a novel cost-effective and fast diagnostic tool with high sensitivity and specificity for the simultaneous detection of six STI pathogens.     

Performance evaluation of five commercial real-time PCR reagent systems using TaqMan assays for B. anthracis detection

BackgroundReal-time PCR assay sensitivity is affected by the choice and concentrations of reaction mix constituents among other factors such as primers, probes, and analytical assay platforms. Commercially available reagent mixes facilitate PCR assay set-up with fewer steps and timeliness. However, determination of analytical assay framework is important for ready-to-use real-time PCR reagent systems for rapid, quantitative and accurate detection of bioterror pathogens such as Bacillus anthracis.MethodsIn this study, performance characteristics of five commercially available quantitative PCR reagent mixes were evaluated using TaqMan-based real-time PCR. The reagent systems were tested for compatibility on the ABI 7000 assay platform and compared for their distinctive analytical characteristics using the B. anthracis rpoB and pag gene real-time PCR assays.Results and conclusionsKnowledge of distinctive assay performance characteristics of commercially available qPCR reagent mixes is critical for carefully designing analytical assay systems. The ABI, ABgene and Eppendorf reagent systems performed consistently overall for the two TaqMan assays for B. anthracis detection that were used in the current study. However, the use of Eppendorf reagent system requires shorter thermal cycling time. In addition, while the ABI and Eppendorf systems have similar assay sensitivity for both the rpoB and pag assays, the Eppendorf system achieves the same with lower C_T values.     

应用TaqMan实时荧光-聚合酶链反应方法快速检测粪便标本空肠弯曲菌的研究

目的建立空肠弯曲菌TaqMan实时荧光-PCR方法,用于粪便标本的直接检测。方法根据空肠弯曲菌特异性基因hipO和mapA分别设计引物和探针,在对2组引物和探针进行灵敏度、特异性和重复性评价的基础上,对45例临床腹泻患者粪便标本提取DNA之后,荧光PCR检测,同时进行分离培养。 结果两组引物和探针能准确检测空肠弯曲菌菌株2株,检测限可达到10~20 cfu/ml,并与其他肠道致病菌无交叉反应。检测45份腹泻病例粪便标本,该方法检测到3份为阳性,同时进行的传统培养方法仅从该3份标本中的两份中分离到空肠弯曲菌。 结论本研究建立的TaqMan荧光PCR检测粪便标本中所携带的空肠弯曲菌灵敏度高,特异性好,能够提高粪便中空肠弯曲菌的阳性检出率和缩短检测时限。     

Multiplex real-time polymerase chain reaction for rapid detection of β-lactamase–negative,ampicillin-resistant Haemophilus influenzae

We evaluated a multiplex real-time quantitative polymerase chain reaction (PCR) method for quantification of Haemophilus influenzae and rapid detection of β-lactam–resistant strains. We designed 5 PCR primer sets to simultaneously detect the β-lactam–resistant genes and quantify the pathogen. To demonstrate the validity of this assay, we used 191 clinical isolates, including 141 H. influenzae strains, and 100 purulent sputum samples, including 30 samples from which H. influenzae had been isolated. This assay showed 92.9% sensitivity and 91.8% specificity for detecting β-lactam–resistant genes, relative to the conventional phenotypic method, and this assay correlated well with conventional quantitative culture counts. By using this assay, we could quantify H. influenzae and identify β-lactam susceptibility in only 3 h and with only one tube. This method will be helpful for the rapid detection of H. influenzae infections and the selection of appropriate antibiotics.     

新型二聚体突变荧光引物定量检测沙眼衣原体

目的 以二聚体突变荧光引物技术为基础建立对沙眼衣原体进行定量检测的新方法.方法 以沙眼衣原体主要外膜蛋白(MOMP)基因构建重组质粒作为DNA标准品,设计二聚体突变荧光引物,优化定量PCR体系并进行性能评价;同时对148例临床生殖道标本进行检测.结果 建立的二聚体突变荧光引物的定量PCR方法,其线性范围为101～109...     

A highly sensitive semi-nested real-time PCR utilizing oligospermine-conjugated degenerate primers for the detection of diverse strains of small ruminant lentiviruses

Small ruminant lentiviruses (SRLVs) are highly diverse retroviruses infecting sheep and goats. Although PCR-based testing is being utilized for diagnostics, its application is hampered by various factors. These include, among others, the exceptionally high genetic variability of SRLVs, as well as the low number of infected blood monocytes. For this reason, a highly sensitive and specific semi-nested real-time PCR for proviral DNA detection and quantification was developed. The method is innovative in that a) its design is based on selecting the preferred codon usage in the targeted conserved genomic regions and b) oligospermine-conjugated degenerate primers with increased Tm were utilized. Modifications permitted primer/template duplex formation in the cases of mismatches due to sporadic nucleotide polymorphisms in a number of variant SRLV strains and consequently, the detection of highly diverse SRLV strains. The potential loss of analytical sensitivity and specificity was counterbalanced by including a semi-nested step in combination with LNA probes. An in silico procedure for the evaluation of hybridization efficiency of the designed oligonucleotides to all known targeted variants was also implemented. The method presents a linear range of quantification over a 3-log₁₀ range and a limit of detection of 3.9 proviral dsDNA copies per reaction. Its diagnostic performance was evaluated by testing field samples from seropositive and seronegative animals, followed by phylogenetic analysis of the strains detected. To further increase the diagnostic sensitivity, a DNA extraction protocol for blood leukocytes was developed and evaluated. A minimum of 500 ng input DNA is recommended for PCR-based detection of SRLV proviral DNA, given the low numbers of infected blood monocytes. The developed methodology may serve as a useful tool, which can be adjusted for the quantitative detection of viruses exhibiting high genetic variability.     

新型二聚体突变荧光引物定量PCR方法的建立及其在检测HCV中的应用

目的 开发新型二聚体突变荧光引物技术,建立一种能广泛应用于临床检测HCv的实时PCR方法.方法 构建重组质粒pMD18-T-HCV 5′NCR作为标准品,设计二聚体突变荧光引物,优化定量PCR体系,并进行方法学评价.将本法应用于临床确诊的30份HCV阳性患者、30份其他病毒性肝炎患者和30份健康志愿者血清标本的检测,定量结果与商品化TaqMan HCv定量试剂盒的定量结果进行比较.结果 建立了利用二聚体突变荧光引物的实时PCR方法,检测的线性范围为20～109IU/ml;批内CV在1.37%～4.59%之间,批间CV在1.58%～4.81%之间;对所有其他病毒性肝炎患者和健康志愿者血清HCV的检测结果均阴性,检测特异性为100%(60/60);对临床确诊的HCV感染患者血清标本全部检出HCV阳性,定量结果与商品化TaqMan HCV定量试剂盒的定量结果具有很好的相关性,相关系数R2=0.9501.结论 建立的以二聚体突变荧光引物为平台的HCV实时PCR检测方法,具有快速、价廉、准确、结果可靠等特点,可为HCV感染的诊断、治疗监测和流行病学调查提供较好的技术支持.     

Multiplex real-time PCR assay for detection of pathogenic Vibrio parahaemolyticus strains

Foodborne disease caused by pathogenic Vibrio parahaemolyticus has become a serious public health problem in many countries. Rapid diagnosis and the identification of pathogenic V. parahaemolyticus are very important in the context of public health. In this study, an EvaGreen-based multiplex real-time PCR assay was established for the detection of pathogenic V. parahaemolyticus. This assay targeted three genetic markers of V. parahaemolyticus (species-specific gene toxR and virulence genes tdh and trh). The assay could unambiguously identify pathogenic V. parahaemolyticus with a minimum detection limit of 1.4 pg genomic DNA per reaction (concentration giving a positive multiplex real-time PCR result in 95% of samples). The specificity of the assay was evaluated using 72 strains of V. parahaemolyticus and other bacteria. A validation of the assay with clinical samples confirmed its sensitivity and specificity. Our data suggest the newly established multiplex real-time PCR assay is practical, cost-effective, specific, sensitive and capable of high-throughput detection of pathogenic V. parahaemolyticus.     

氨基糖苷类药物耐药基因armA实时荧光定量聚合酶链反应检测方法的建立

目的建立一种快速、准确检测细菌中arm A耐药基因的Taq Man实时荧光定量-聚合酶链反应(real-time fluorescence quantitative-polymerase chain reaction,real-time PCR)方法。方法根据arm A基因设计特异的引物及探针,在多种常见致病菌中检测其特异性;使用阳性质粒标准品评价该方法的灵敏度;使用粪便模拟标本验证该方法的应用性。结果本方法特异性好,建立的arm A耐药基因real-time PCR方法标准曲线,确定其对质粒标准品的灵敏度为4.07×101拷贝/ml。应用该方法对粪便模拟标本进行检测,其检测下限为1.3×104cfu/ml。结论本研究建立了arm A耐药基因荧光定量PCR检测方法,有望在耐药基因监测中推广使用。     

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.     

Rapid and specific detection of the Mycobacterium tuberculosis complex using fluorogenic probes andreal-time PCR

A rapid and sensitive strategy for the specific identification of Mycobacterium tuberculosis (TB) was designed and evaluated using crude mycobacterial lysates. The speed of real-time polymerase chain reaction (PCR) was combined with the sensitivity of fluorogenic probes to confirm the presence of mycobacteria as well as specifically identify the presence of members of the mycobacteria tuberculosis complex (MTC) in a single-tube assay. Oligonucleotides were designed to amplify the internal transcribed spacer (ITS) from several mycobacterial species. Specific fluorogenic probes were included in the PCR reaction for the identification of TB as well as Mycobacterium bovia and Mycobacterium africanum in bacterial lysates. The combination of TB-specific fluorogenic probes with real-time PCR formed an approach determined to be fast (less than 40 min), sensitive (less than 800 copies of DNA) and reliable for the specific detection of the MTC. Our data demonstrate the use of real-time PCR and fluorogenic probes in a rapid and sensitive assay to distinguish members of the MTC from other mycobacterial species.     

双重荧光定量RT-PCR快速检测甲型和甲型H1N1流感病毒

目的建立双重荧光RT-PCR快速检测方法,用于甲型和甲型H1N1流感病毒的同时检测和鉴别诊断。方法针对甲型流感病毒M基因和甲型H1N1流感病毒NA基因的保守区序列分别设计特异性引物和Taqman探针,建立优化双重荧光RT-PCR反应体系,评价所建双重RT-PCR反应体系的特异性、敏感性和稳定性,并应用于疑似流感或甲型H1N1流感含漱液标本检测。结果该方法对甲型、甲型H1N1流感病毒检测具有高度特异性,检出限分别为0.01 TCID50和0.1 TCID50,具有较好的稳定性。可从疑似流感或甲型H1N1流感患者含漱液中直接检测到流感病毒核酸。结论本研究建立的双重荧光定量RT-PCR可以同时准确检测甲型和甲型H1N1流感病毒,灵敏度高,稳定性好,是一种快速检测流感病毒的新方法。     

Development of multiplexed real-time quantitative polymerase chain reaction assay for detecting human adenoviruses

Adenoviruses (AdVs) have been associated with a wide variety of human disease and are increasingly recognized as viral pathogens that can cause significant morbidity and mortality in immunocompromised patients. Early detection of AdV DNA in plasma and sterile fluids has been shown to be useful for identifying patients at risk for invasive AdV disease. Because of the large number of existing Adv types, few real-time quantitative AdV polymerase chain reaction (PCR) assays published effectively cover all AdV types. We designed a series of AdV PCR primers and probes and empirically multiplexed them into 2 separate real-time PCR assays to quantitatively detect all 49 serotypes of human AdV (types 1–49) available from American Type Culture Collection. We then subsequently multiplexed all the primers and probes into 1 reaction. The sensitivity of these assays was determined to be less than 10 copies per reaction (500 copies/mL plasma). In a retrospective evaluation, we detected all 84 clinical AdV isolates isolated in cell culture from patients undergoing hematopoietic stem cell transplantation between 1981 and 1987. Prospective analysis of 46 consecutive clinical samples submitted for AdV testing showed greater sensitivity and equal specificity of the AdV PCR than viral culture. This real-time PCR assay allows rapid, sensitive, and specific quantification of all currently defined AdVs into either 2 or 1 multiplex assay for clinical samples.     

副溶血弧菌TaqMan双重实时-聚合酶链反应检测方法的建立

目的建立副溶血弧菌TaqMan实时-PCR和毒力基因TaqMan双重实时-PCR筛检的实验室检测方法。方法根据副溶血弧菌ItoxR/I基因的保守序列设计引物和TaqMan探针,建立检测副溶血弧菌的实时-PCR方法;根据副溶血弧菌耐热直接溶血素（thermostable direct hemolysin, Itdh/I）和耐热相关溶血素（thermostable related hemolysin, Itrh/I）基因的保守序列设计引物和探针,建立检测致病性副溶血弧菌毒力基因的双重TaqMan实时-PCR方法。对所建立的副溶血弧菌实时-PCR检测方法进行灵敏度和特异度评价。结果副溶血弧菌的检测下限为10sup2/sup拷贝/l,Itdh/I和Itrh/I双重实时PCR的检测下限为10sup2/sup拷贝/l。针对ItoxR/I基因建立的副溶血弧菌实时-PCR方法对11种其他弧菌和肠道细菌的染色体无扩增。结论建立的方法能够特异和敏感地检测副溶血弧菌,并能确定致病性副溶血弧菌的毒力基因,能作为副溶血弧菌的灵敏和快速检测方法。     

Development of a duplex SYBR GreenⅠ based real-time PCR assay for detection of porcine epidemic diarrhea virus and porcine bocavirus3/4/5

The duplex real-time PCR assay based on SYBR Green І was developed for detection of porcine epidemic diarrhea virus (PEDV) and porcine bocavirus (PBoV) 3/4/5 genotypes simultaneously. Two pairs of specific primers were designed targeting the N gene sequence of PEDV and VP1 gene sequence of PBoV3/4/5. PEDV and PBoV3/4/5 could be distinguished by their different melting temperatures (Tm) in one sample. The Tm value of PEDV was 83.5 °C, and the Tm value of PBoV3/4/5 was 78.5 °C, while other swine pathogens showed no specific melting peaks. The detection limits of this assay were 10 copies/μL for both PEDV and PBoV3/4/5. A total of sixty-three intestinal tissue samples were collected from piglets suffering from diarrhea, and the viral nucleic acids detected and identified by the real-time PCR assay and conventional PCR assay. The duplex real-time PCR detection results showed that the prevalence of PEDV and PBoV3/4/5 was 85.7% and 46%, respectively, and the co-infection rate of the two viruses was 28.6%. These results indicated that this duplex real-time PCR assay was a sensitive, specific and reproducible method for differentiating PEDV and PBoV3/4/5 or their co-infection.     

Rapid and specific detection of section Fumigati and Aspergillus fumigatus in human samples using a new multiplex real-time PCR

Invasive aspergillosis is an opportunistic infection caused primarily by Aspergillus fumigatus. However, other common fungal pathogens belonging to section Fumigati are often misidentified as A. fumigatus. Thus, we have developed a multiplex real-time PCR (qPCR) assay with primers and specific TaqMan probes based on internal transcribed spacer regions or benA gene to discriminate, in less than 3 h, species of section Fumigati and, specifically, A. fumigatus. The multiplex qPCR showed a limit of detection of 20 and 50 fg of DNA for section Fumigati and A. fumigatus, respectively. Moreover, it enabled detection of a single germinated conidia. The inclusion of some PCR facilitators together with the dilution of samples makes it possible to completely avoid PCR inhibitions in all bronchoalveolar lavage (BAL) samples assayed. This technique may be a useful complementary tool in the diagnosis of invasive pulmonary aspergillosis caused by A. fumigatus using BAL fluid.     

实时荧光定量PCR检测血中曲霉菌基因的实验研究

目的：建立并评价从血标本中检测曲霉菌基因的real-time PCR方法。方法：用自行设计的高效率引物探针对标准菌株及临床疑似病人血标本进行检测,对方法的敏感性、特异性进行评价。结果检测出曲霉菌基因敏感性达10拷贝ITS I基因,相当于5～10CFU／ml,与人类基因组、其他真菌及细菌无交叉反应。29例临床疑似标本阳性率为69％,与临床诊断符合率为86％。结论：real-time PCR检测血中曲霉菌基因有较高的敏感性、特异性,有一定的临床应用前景。