Development of a multiplex polymerase chain reaction assay for detection of hepatitis C virus,hepatitis B virus,and human immunodeficiency virus 1

BACKGROUND Hepatitis C virus(HCV),hepatitis B virus(HBV),and human immunodeficiency virus 1(HIV-1)are the most epidemic blood-borne viruses,posing threats to human health and causing economic losses to nations for combating the infection transmission.The diagnostic methodologies that depend on the detection of viral nucleic acids are much more expensive,but they are more accurate than sero-logical testing.AIM To develop a rapid,cost-effective,and accurate diagnostic multiplex polymerase chain reaction(PCR)assay for simultaneous detection of HCV,HBV,and HIV-1.METHODS The design of the proposed PCR assay targets the amplification of a short conserved region featured with a distinguishable melting profile and electro-phoretic molecular weight inside each viral genome.Therefore,this diagnostic method will be appropriate for application in both conventional(combined with electrophoresis)and real-time PCR facilities.Confirmatory in silico investigations were conducted to prove the capability of the approached PCR assay to detect variants of each virus.Then,Egyptian isolates of each virus were subjected to the wet lab examination using the given diagnostic assay.RESULTS The in silico investigations confirmed that the PCR primers can match many viral variants in a multiplex PCR assay.The wet lab experiment proved the efficiency of the assay in distinguishing each viral type through high-resolution melting analysis.Compared to related published assays,the proposed assay in the current study is more sensitive and competitive with many expensive PCR assays.CONCLUSION This study provides a simple,cost-effective,and sensitive diagnostic PCR assay facilitating the detection of the most epidemic blood-borne viruses;this makes the proposed assay promising to be substitutive for the mistakable and cheap serological-based assays.

Human papillomavirus 16 physical status detection in preinvasive and invasive cervical carcinoma by multiplex real-time polymerase chain reaction

Objective: To explore an ideal approach for detecting the physical status of HPV-16 in clinic use and to investigate the integrated HPV-16 in CINs and cervical cancer. Methods: Multiplex real-time PCR method was established to quantify the copy numbers of E2 and E6 genes (E2/E6) for analysis of the physical status of HPV-16 DNA and this assay was compared to Southern blot analysis. HPV-16-containing paraffin-embedded tissues including 49 CINs and 51 cervical squamous cancers were detected using the method. Results: (1) The cutoff ratio of E2/E6 to distinguish pure episomal from mixed HPV-16, was 0.81 in the multiplex real-time PCR; (2) The agreement rate between multiplex real-time PCR and Southern blot was 81.5% (the Kappa statistic was 0.844, P<0.001); (3) HPV-16 DNA existed in an episomal form in 57.1% and mixed form in 42.9% of CIN I lesions; The concomitant form of HPV-16 (>70%) constituted the majority in CIN II and CIN III; HPV-16 DNA mostly integrated into the host chromosome (s) in squamous cervical cancers (68.6%); (4) The incidence of HPV-16 integration was increased with the degree of cervical lesions; (5) The frequency of pure integrated HPV-16 in stage II+III (88%) was signifi- cantly higher than that in stage I (33.3%). Conclusion: (1) Mutiplex real-time PCR provides a rapid, sensitive and reliable method for clinic detection of the physical state of HPV-16 DNA; (2) The integration of the HPV-16 DNA is a very early and important event in the progression from preinvasive to invasive cervical cancer; (3) The pure integrated status of HPV-16 in cervical cancer may be associated with poor prognosis of cervical cancer, but further study will be needed to prove its prog- nostic significance.

DETECTION OF PATHOGENS CAUSING GENITAL ULCER DISEASE BY MULTIPLEX POLYMERASE CHAIN REACTION

Objective To establish a multiplex polymerase chain reaction (M-PCR) assay for simultaneous detection of pathogens causing genital ulcer disease (GUD). Methods Based on the gene-specific region of the following pathogens: Chlamydia trachomatis omp1/ompb, herpes simplex virus (HSV) DNA polymerase, Treponema pallidum tpp47, Haemophilus ducreyi 16s rRNA, four sets of primers were designed and an M-PCR assay was developed to detect four pathogens in one test. The assay was evaluated with diagnostic result of golden standard for each pathogen. Results Of the 51 clinical samples, M-PCR showed slightly higher positive rate (47.1%) of HSV than cell culture (23.6%).Meanwhile, the positive rate of T. pallidum detected by M-PCR and dark-field microscopy was 19.6% (10/51) and 15.7% (8/51), respectively. Only one sample was positive for H. ducreyi and no sample was positive for C. trachomatis detected by both M-PCR assay and culture. Conclusion This primary study indicated that M-PCR assay can simultaneously and rapidly detect the four etiologic pathogens causing GUD.

Efficacy of stool multiplex polymerase chain reaction assay in adult patients with acute infectious diarrhea

BACKGROUND Recently,stool multiplex polymerase chain reaction(PCR)tests have been developed for identifying diarrhea-causing bacterial pathogens.Furthermore,fecal calprotectin is a well-known effective marker for intestinal mucosal inflammation.AIM To evaluate the efficacy of stool multiplex PCR and fecal calprotectin in acute infectious diarrhea.METHODS Overall,400 patients with acute infectious diarrhea were enrolled from Kangdong Sacred Heart Hospital(January 2016 to December 2018).Multiplex PCR detected 7 enteropathogenic bacteria including Salmonella,Campylobacter,Shigella,Escherichia coli O157:H7,Aeromonas,Vibrio,and Clostridium difficile.We reviewed clinical and laboratory findings using stool multiplex PCR.RESULTS Stool multiplex PCR test detected considerably more bacterial pathogens than stool culture(49.2%vs 5.2%),with Campylobacter as the most common pathogen(54%).Patients with positive stool PCR showed elevated fecal calprotectin expression compared to patients with negative stool PCR(1124.5±816.9 mg/kg vs 609±713.2 mg/kg,P=0.001).C-reactive protein(OR=1.01,95%CI:1.001-1.027,P=0.034)and sigmoidoscopy-detected colitis(OR=4.76,95%CI:1.101-20.551,P=0.037)were independent factors in stool PCR-based detection of bacterial pathogens.Sensitivity and specificity of calprotectin were evaluated to be 70.5%and 60.9%,respectively(adjusted cut-off value=388 mg/kg).CONCLUSION Stool multiplex PCR test has increased sensitivity in detecting pathogens than conventional culture,and it is correlated with calprotectin expression.Stool multiplex PCR and calprotectin may be effective in predicting clinical severity of infectious diarrhea.

4种植物源性成分多重real-time PCR检测方法的建立及其在食用淀粉中的应用

建立一种可同时快速检测红薯、木薯、马铃薯、玉米源性成分的多重实时聚合酶链式反应(real-time polymerase chain reaction,real-time PCR)方法。分别以红薯g3pdh基因、木薯g3pdh基因、马铃薯UGPase基因、玉米zSSIIb基因为靶基因设计特异性引物和TaqMan探针,以18S rRNA基因为内参基因,建立多重real-time PCR方法,开展方法学验证,并对不同掺入比例模拟样品和实际淀粉样品进行检测。结果显示,该方法具有高通量、特异性强、灵敏度高等优点。与15种非目标源性均无交叉反应;对目标DNA的检测灵敏度可达到3×10^(-3) ng/μL,且具有良好的线性关系和扩增效率;对淀粉样品的检出限可达0.1%,对50份实际样品进行检测,结果与参比方法一致,说明建立的多重real-time PCR法可用于食用淀粉种类掺假鉴别检测。

多重PCR毛细管电泳细菌快速鉴定方法的建立和临床应用研究

目的针对引起人类感染的常见病原菌建立一种基于多重PCR毛细管电泳技术的快速细菌鉴定方法,评估其临床应用价值。方法建立23种常见病原菌的多重PCR毛细管电泳检测体系。收集150例临床微生物检测标本,分别用多重PCR毛细管电泳法(以下简称多重PCR法)、培养法进行检测。对两种方法的检测结果进行比较,评价多重PCR法的检测效能。结果150例标本中多重PCR法检出15种病原菌、培养法检出14种病原菌。多重PCR法检测阳性率为73.3%,培养法为70.0%,差异无统计学意义(P>0.05)。多重PCR法对肺炎链球菌的检出率为16.0%,培养法为6.0%,差异有统计学意义(P<0.05)。多重PCR法对混合菌标本的检出率为15.3%,培养法未检出混合菌标本。多重PCR法与培养法检测结果的符合率为79.3%。多重PCR法检测时间为3~6 h,培养法为2~4 d。结论与培养法比较,多重PCR法具有较高的时效性,对肺炎链球菌及混合菌标本具有较高的检出率,可满足临床标本病原微生物快速初筛的需求。

Diagnosis of the accurate genotype of HKαα carriers in patients with thalassemia using multiplex ligation-dependent probe amplification combined with nested polymerase chain reaction

Background:Patients carrying the HongKongαα(HKαα)allele and-α3.7/αααanti-4.2 could be misdiagnosed as-α3.7/ααby the current conventional thalassemia detection methods,leading to inaccurate genetic counseling and an incorrect prenatal diagnosis.This study was aimed to accurately analyze the genotypes of HKααcarriers and-α3.7/αααanti-4.2.Methods::Samples were collected in our hospital from July 2017 to October 2019.Twenty-four common types of Chinese thalassemia were screened by gap-polymerase chain reaction(Gap-PCR)and reverse dot blot(RDB).Anti-4.2 multiplex-PCR was used to confirm carriers of theαααanti-4.2 duplication with-α3.7 deletion.Two-round nested PCR and multiplex ligation-dependent probe amplification(MLPA)were applied to accurately identify and confirm their genotypes.For data analysis,we used descriptive statistics and Fisher’s exact tests.Results::Two thousand five hundred and forty-four cases were identified as thalassemia in 5488 peripheral blood samples.The results showed thatα,β,andαβcompound thalassemia were identified in 1190(46.78%),1286(50.55%),and 68(2.67%)cases,respectively.A total of 227 samples from thalassemia patients were identified as-α3.7/ααby Gap-PCR,and the genotypes of two samples were uncertain.There was a difference between Gap-PCR and combined groups(Gap-PCR combined with nested PCR and MLPA)in detecting HKαα(P<0.05).Among the 229 patients,20 patients were identified as HKααcarriers and one was identified as-α3.7/ααα anti-4.2 by two-round nested PCR and MLPA,including 15 patients with HKαα/αα,three with HKαα/αα and β-thalassemia coinheritance,one with HKαα/-SEA,one with HKαα/-α4.2 andβ-thalassemia coinheritance,and one with-α3.7/αααanti-4.2 and β-thalassemia coinheritance.Conclusions::αααanti-4.2 and HKααgenotypes of patients carrying-α3.7 need to be detected to reduce the misdiagnosis rate of patients carrying HKααand-α3.7/αααanti-4.2 alleles.More accurate genetic counseling can be provided in the clinic using nested PCR combined with MLPA.

Rapid prenatal diagnosis of trisomy 21 by fluorescent quantitative multiplex polymerase chain reaction

Trisomy 21, also named Down syndrome was the most frequent autosomal aneuploidy and the most common cause of mental retardation. Fifty percent patients had congenital heart malformation. Every 20 minutes one case of trisomy 21 was born, and the incidence rate was 1 in 600 to 800 newborns in China.1 In two thirds of cases with trisomy 21, there was a spontaneous abortion, so the actual incidence was higher than that obtained postnatally.

Forensic Identification of Four Indian Snake Species Using Single Multiplex Polymerase Chain Reaction

Among different endangered animal species,snakes are the most neglected creature looked at with apathy and therefore,are ruthlessly killed,illegally trafficked,and poached for their venom,lucrative skin,meat,and bones for manufacturing of medicines,accessories,and food items.Establishing the identity of the endangered snake species is important for punishing the offenders under Wildlife Protection Act(WPA)(1972)but morphological characters fail to establish identity as they are often altered.The technique of identification of snake species at molecular level holds very effective conclusion in punishing offender.Here,we have constructed and demonstrated a novel multiplexing polymerase chain reaction technique,using 16S rRNA and C-mos gene for identification of four Indian snake species,namely Ptyas mucosa,Daboia russellii,Naja naja,and Xenochrophis piscator.They are listed in Appendix-II and III of convention on international trade in endangered species of wild fauna and flora and Schedule II;Part II of Indian WPA,1972.Therefore,it may be considered a functional tool for establishing species-specific identity of four Indian snake species and promising to be useful for their conservation.

市售食品21种动植物过敏原成分的检测分析

为进一步明确市售食品动植物过敏原标注情况,该研究建立一种可同时检测21种动植物过敏原成分的多重连接依赖性探针扩增(MLPA)技术,并对其进行灵敏度实验,并结合实时荧光定量聚合酶链式反应(RT-fqPCR)检测技术对38种市售预包装食品中动植物过敏原成分进行比较分析。结果表明,采用MLPA检测技术可同时对21种动植物过敏原成分进行检测,扩增峰之间不存在交叉干扰,扩增峰实际大小和理论大小相差≤3 bp,检出最低脱氧核糖核酸(DNA)质量浓度为1 ng/μL;RT-fqPCR、MLPA技术检测标注过敏原成分食品的检出率分别为51.5%、44.1%,此外,MLPA检测法检出了6个标注可能含有过敏原成分样品中的过敏原成分,10个样品中未标记的过敏原成分。因此,采用MLPA技术检测21种动植物过敏原成分的灵敏度更高。

Multiplex RT-PCR-based detections of CEA, CK20 and EGFR in colorectal cancer patients

AIM: To develop a multiplex reverse transcription polymerase chain reaction (RT-PCR) method detecting cir-culating tumor cells in the peripheral blood of colorectal cancer (CRC) patients. METHODS: Peripheral blood samples were collected from 88 CRC patients and 40 healthy individuals from the blood donors' clinic and subsequently analyzed by multiplex RT-RCR for the expression of carcinoembryonic antigen (CEA), cytokeratin 20 (CK20) and epidermal growth factor receptor (EGFR) mRNA. The analysis involved determining the detection rates of CEA, CK20 and EGFR transcripts vs disease stage and overall survival. Median follow-up period was 19 mo (range 8-28 mo). RESULTS: Rates of CEA, CK20 and EGFR detection in CRC patients were 95.5%, 78.4% and 19.3%, respectively. CEA transcripts were detected in 3 healthy volunteer samples (7.5%), whereas all control samples were tested negative for CK20 and EGFR transcripts. The increasing number of positive detections for CEA, CK20 and EGFR transcripts in each blood sample was positively correlated with Astler-Coller disease stage (P< 0.001) and preoperative serum levels of CEA (P=0.029) in CRC patients. Data analysis using Kaplan-Meier estimator documented signif icant differences in the overall survival of the different CRC patient groups as formed according to the increasing number of positivity for CEA, CK20 and EGFR transcripts. CONCLUSION: These data suggest that multiplex RTPCR assay can provide useful information concerning disease stage and overall survival of CRC patients.

Dual-priming oligonucleotide-based multiplex PCR using tissue samples in rapid urease test in the detection of Helicobacter pylori infection

AIM:To investigate whether tissue samples processed by the rapid urease test(RUT)kit are suitable for dualpriming oligonucleotide-based multiplex polymerase chain reaction(DPO-PCR)to detect Helicobacter pylori(H.pylori).METHODS:A total of 54 patients with specific gastrointestinal symptom were enrolled in this study.During endoscopy,gastric biopsy specimens were taken for histology,RUT,and DPO-PCR.DPO-PCR was performed on gastric biopsy samples and tissue samples that were analyzed by RUT at 2 separate institutes.In detecting H.pylori,the concordance rate of the DPO-PCR tests between the tissue samples that had been submitted to RUT and the gastric biopsy samples was investigated.RESULTS:H.pylori co-occurred with 76.0%(19/25)of gastric ulcers,64.3%(9/14)of duodenal ulcers,and 33.3%(4/12)of gastritis cases.H.pylori infection was found in 100%(3/3)of the patients with both gastric and duodenal ulcers.Overall,H.pylori was detected in 35 of 54(64.8%)patients.The diagnostic sensitivities of histology,RUT,and DPO-PCR were85.7%(30/35),74.3%(26/35),and 97.1%(34/35),respectively(P=0.02).The positive predictive value(PPV)of DPO-PCR was 94.4%,whereas the negative predictive value(NPV)was 94.7%.In the rapid urease test(CLOtest)-negative cases,the frequency of positive DPO-PCR and histologic results was 20.0%(7/35).The concordance rate of the DPO-PCR tests between the tissue samples from the RUT kit and the gastric biopsy samples was 94.4%(51/54).The rate of DPOPCR and silver stain positivity in the RUT-negative cases was 20.0%(7/35).CONCLUSION:In diagnosing H.pylori infection,DPO-PCR can be performed on tissue samples that have been processed by the RUT kit.Particularly,in patients with RUT-negative results,DPO-PCR on these tissue samples could be helpful in detecting of H.pylori infection.

Establishment of a Multiplex PCR System to Diagnose Tuberculosis and Other Bacterial Infections

In order to rapidly diagnose and differentiate tuberculosis from other bacterial infections, a 16S rRNA gene (16s rDNA)-directed multiplex PCR system was developed. In this system, a pair of universal primers and a tubercle bacillus (Tb)-specific primer were designed based on highly con- served regions and Tb species-specific variable region of bacterial 16s rDNA. A 360bp fragment was detected in all bacteria tested, and a 210bp fragment was found only in Tb. 19 species of known bac- teria including Tb were used for evaluating specificity, universality and sensitivity of the PCR. Candi- da albicans and human diploid cell served as controls. It was found that both 210bp and 360bp frag- ments were amplified only in Tb, and only 360 bp fragment was detected in other 18 species of gener- al bacteria. Candida albicans and human cells were negative for both 360bp and 2l0bp fragments. The lowest detectable level of the PCR was 10 fg of DNA for Escherichia coli and 100 fg of DNA for Tb. The results indicated that this multiplex PCR system for the simultaneous detection of Tb and other common bacteria had higher specificity and sensitivity, as well as good universality and might be useful to rapidly diagnose bacterial infections and effectively distinguish tuberculosis from other bacterial involvement.

4种动物源性成分多重real-time PCR检测方法的建立及其在驴肉制品检测中的应用

建立一种同时快速检测驴、马、猪及鸭源性成分的四重实时聚合酶链式反应(real-time polymerase chain reaction,real-time PCR)方法。分别以4种源性成分的Nad5、ATpase6、ATP8、cytb基因为靶基因设计特异性引物和TaqMan探针,以18S rRNA基因为内参基因,建立多重real-time PCR方法,并对该方法进行方法学验证,同时对不同掺入比例模拟样品、不同加工工艺模拟样品和实际驴肉样品进行检测。结果显示,该方法具有高通量、特异性强、灵敏度高等优点。当Ct值≤35.0时,方法对16种非目标源性具有良好特异性;灵敏度可检测到质量浓度为2×10^(-4)ng/μL的模板DNA;对生肉的检出限为肉含量的0.001%,对熟肉制品的检出限为肉含量的0.01%;对100份实际样品进行检测,结果与标准方法一致,说明建立的多重real-time PCR法可用于肉及肉制品中常见掺假源性成分的检测。

Clinical Application of Multiplex PCR Assay for the Diagnosis of the Etiology of Genital Ulcer Disease Among Patients Attending STD Clinics in Guangzhou, China

Objectives: To develop a method of simultaneous PCRdetection of Haemophilus ducreyi, Treponema pallidum, andHerpes Simplex Virus Types 1 and 2 from genital ulcersamong patients attending STD clinics in Guangzhou, China;and evaluate the clinical application of multiplex PCR (M-PCR) assay for diagnosing the etiology of genital ulcerdiseases (GUD). Methods: 244 patients with a genital ulcer were evaluated.Clinical etiology of GUD was based on physical appearanceand microbiologic evaluations that included dark fieldmicroscopy examination (D-F) and serology test for syphilis(STS). Swabs of each genital ulcer were tested for HSVantigen by enzyme immunoassay (EIA) and processed in anM-PCR assay for simultaneous detection of T. pallidum, HSVand H. ducreyi. Results: The standard strains of T. pallidum, HSV and H.ducreyi were amplified by M-PCR, producing amplifiedproducts of 260bp,432bp,170bp, respectively. The sensitivityof M-PCR is 102pg DNA. M-PCR assay for T. pallidum, HSVand H. ducreyi showed good agreement when compared withD-F detection for T. pallidum, STS, H. ducreyi culture and EIAfor HSV antigen (Kappa scores are 0.774,0.704,0.793,0.756,respectively). Conclusions: The M-PCR is a convenient, accurate andreliable assay for the detection of T. pallidum, HSV and H.ducreyi from genital ulcers, and can be used as a method of diagnosing the etiology of GUD.

多重聚合酶链式反应技术检测罗非鱼5种常见食源性致病菌

目的 建立一种可同时检测无乳链球菌(Streptococcus agalactiae)、嗜水气单胞菌(Aeromonas hydrophila)、霍乱弧菌(Vibrio cholerae)、大肠杆菌(Escherichia coli)和沙门菌(Salmonella) 5种罗非鱼常见食源性致病菌的多重聚合酶链式反应(polymerase chain reaction,PCR)方法。方法 根据5种致病菌特异性基因片段设计并合成引物,优化多重PCR体系条件,并对多重PCR体系的特异性、灵敏度以及人工模拟样品进行检测。结果 建立的多重PCR方法可同时扩增5种目的菌株的特异性条带,且不与非靶标细菌发生交叉反应。敏感性实验结果显示,该方法对无乳链球菌、嗜水气单胞菌、沙门菌、霍乱弧菌、大肠杆菌纯培养物基因组DNA的检出限均为0.4 ng/μL。人工模拟样品检测结果显示,该方法可以快速且准确地检测上述5种食源性致病菌,且检出限可达到2×10^(1)CFU/g。结论 本研究建立了一种可同时检测无乳链球菌、嗜水气单胞菌、霍乱弧菌、大肠杆菌和沙门菌5种罗非鱼常见食源性致病菌的多重PCR检测方法。该方法的建立为罗非鱼常见食源性致病菌的快速检测提供了重要的技术手段。

海南不同地区红火蚁社会型鉴定

为明确海南部分地区红火蚁的社会型,通过多重PCR(Multiplex Polymerase Chain Reaction)技术及Gp-9^(b)等位基因扩增2种方法,鉴定分析了采集自海南万宁、琼海、海口、陵水、文昌、屯昌和儋州7个不同地区的红火蚁的社会型。鉴定结果表明,采自7个地区的不同蚁巢社会型均为多蚁后型。本研究对海南地区科学监测红火蚁具有重大意义,同时为增强红火蚁的防治效果提供理论依据。

通用多重不对称PCR联合基因芯片实现下呼吸道病原菌及耐药基因快速检测

目的 建立一种基于通用多重不对称聚合酶链反应(PCR)联合基因芯片的下呼吸道病原菌及耐药基因检测方法,同步实现6种下呼吸道常见病原菌(大肠埃希菌、鲍曼不动杆菌、肺炎克雷伯菌、金黄色葡萄球菌、肺炎链球菌、卡他莫拉菌)和两种碳青霉烯酶基因(blaKPC、blaVIM)快速检测。方法 针对待检病原菌及耐药基因的保守序列设计特异性引物与探针,并制备相应的基因芯片。优化多重PCR的反应体系和杂交参数,分析其特异度、灵敏度,并通过临床标本进行方法应用评价。结果 本研究建立的检测方法特异性强、稳定性好,能在4 h内特异性地鉴别单一或多重靶标。检测大肠埃希菌纯培养物的灵敏度为104copy/mL,鲍曼不动杆菌、肺炎克雷伯菌及碳青霉烯酶基因(blaKPC、blaVIM)的灵敏度均为103copy/mL,金黄色葡萄球菌、肺炎链球菌、卡他莫拉菌的灵敏度均为102copy/mL。与产酸克雷伯菌、黏质沙雷菌、奇异变形杆菌、表皮葡萄球菌、唾液链球菌、流感嗜血杆菌等6种病原菌无交叉反应。结论 基于通用多重不对称PCR结合基因芯片的下呼吸道病原菌及耐药基因检测方法特异性强、灵敏度高,为快速、灵敏地鉴定下呼吸道病原菌及耐药基因提供了一种有效的检测手段。