Resonance Energy Transfer Hybridization Probes Research Articles

Performance Comparison of Multiplexed Fluorescent Resonance Emission Transfer Hybridization Probes Across Roche LightCycler® Real-Time PCR Systems for the Detection of Bartonella species

Abstract Introduction/Objective Molecular assays for Bartonella species are important in diagnosing infection and expediting patient treatment. Real time polymerase chain reaction (RT-PCR) using fluorescent resonance energy transfer (FRET) hybridization probes can be used to detect Bartonella species in blood and fresh/fixed tissue biopsies in RT-PCR instruments. Over time, new technologies and reagents are introduced and existing PCR primers and FRET probes must be re-validated on new platforms. This study aimed to compare the performance of a Bartonella RT-PCR assay using the sunsetting Roche LightCycler® 2.0 (Roche Diagnostics, Indianapolis, IN) and newer LightCycler® 480 RT- PCR instruments. Methods/Case Report DNA was extracted from 132 historically positive, whole organism spiked, and historically negative whole blood and formalin fixed paraffin embedded (FFPE) samples. Samples were run on the LightCycler® 2.0 using instrument specific LightCycler® FastStart DNA Master HybProbe enzyme and compared to results generated using the LightCycler® 480 and its instrument specific LightCycler® 480 Genotyping Master enzyme. During optimization, MgCl2 concentrations and thermocycling profiles were adjusted. Accuracy, specificity, inclusivity, and limit of detection studies were performed. Crossing point (Cp), melting temperature (Tm), fluorescent peak and fluorescent background values were compared between the two instruments. Results (if a Case Study enter NA) The agreement in accuracy between the LightCycler® 2.0 and the LightCycler® 480 was 100% for whole blood samples. For historically positive FFPE samples, LightCycler® 2.0 sensitivity and LightCycler® 480 sensitivity were 86% and 100%, respectively. Specificity and inclusivity of the assay were identical between the two instruments. The limit of detection in whole blood was 5-fold lower on the LightCycler® 480 (50 copies/µL) compared to the LightCycler® 2.0 (250 copies/µL). Mean Cp and fluorescent peak intensity values increased by 5.1% and 65-fold, respectively. Conclusion The study demonstrates similar performance and improved limit of detection for the Bartonella FRET hybridization probe RT-PCR assay on the LightCycler® 480 compared to the LightCycler® 2.0.

Evaluation of the GENE-UP®Salmonella Method for the Detection of Salmonella Species in a Broad Range of Foods and Select Environmental Surfaces: Collaborative Study, First Action 2020.02.

The GENE-UP®Salmonella assay (Performance Tested MethodSM [PTM] 121802) is a PCR detection method that utilizes fluorescence resonance energy transfer (FRET) hybridization probes for the rapid detection of Salmonella species in foods and on environmental surfaces. The purpose of this validation was to evaluate the method's interlaboratory performance for submission to AOAC INTERNATIONAL for adoption as First Action Official Method of AnalysisSM. The GENE-UP method was evaluated in a multi-laboratory study using unpaired test portions for one food matrix, raw ground beef (80% lean). The candidate method was compared to the US Department of Agriculture (USDA), Food Safety Inspection Service, Microbiology Laboratory Guidebook (MLG) 4.10 reference method. An alternative confirmation procedure, using ASAP™ and CHROMID®Salmonella chromogenic agars, was included in the validation study. Fifteen collaborators from 14 laboratories participated. Three levels of contamination were evaluated: a non-inoculated control level (0 CFU/test portion), a low contamination level (∼0.7 CFU/test portion), and a high contamination level (∼2 CFU/test portion). Data were analyzed using the probability of detection (POD) statistical model. The dLPODC values with 95% confidence interval for the GENE-UP Salmonella method, with either alternative or traditional confirmation, were: 0.00 (-0.03, 0.03), -0.02 (-0.15, 0.12), and 0.02 (-0.03, 0.09) for the non-inoculated, low, and high contamination levels respectively. The dLPODC results demonstrate no difference in performance between the candidate method and reference method for the matrix evaluated. The GENE-UP Salmonella method, with ASAP and CHROMID Salmonella, provides industry with a simplified, rapid, and accurate workflow for the detection of Salmonella in a broad range of foods and select environmental surfaces.

Evaluation of the GENE-UP ®E. coli O157:H7 Method for the Detection of E. coli O157:H7 in Select Foods: Collaborative Study, 2019.03.

The GENE-UP®E. coli O157:H7 2 (ECO 2) assay (Performance Tested MethodSM 121805) incorporates Fluorescence Resonance Energy Transfer hybridization probes into its proprietary PCR technology for the rapid detection of E. coli O157:H7 in select foods. The purpose of this validation was to evaluate the method's interlaboratory performance and submit the result to AOAC INTERNATIONAL for adoption as First Action Official MethodSM for the detection of E. coli O157:H7 in select foods. The GENE-UP® method was evaluated in a multi-laboratory study as part of the MicroVal validation process using unpaired test portions for one food matrix, raw milk cheese (Comté, 34% fat, 0.8% salt). The candidate method was compared to the ISO 16654:2001 reference method. Fourteen participants from 13 laboratories throughout the European Union participated. Three levels of contamination were evaluated: a non-inoculated control level (0 colony-forming units (CFU)/test portion), a low contamination level (∼5 CFU/test portion), and a high contamination level (∼10 CFU/test portion). Data from that study were analyzed according to the Probability of Detection (POD) statistical model as presented in the AOAC validation guidelines. The difference in laboratory POD (dLPODC) values with 95% confidence interval across collaborators was calculated for each level between the candidate and reference method results, and between the candidate presumptive and confirmed results. The dLPODC values with 95% confidence interval were; 0.00 (-0.04, 0.04), 0.27 (0.04, 0.49), and 0.17 (0.01, 0.33) for the non-inoculated, low and high contamination levels respectively. The dLPODC results indicate a significant difference between the candidate method and the reference method for both the low and high contamination levels, with the candidate method producing higher recovery of the target organism at both levels. The GENE-UP E. coli O157:H7 assay provides industry with a rapid, accurate detection method for E. coli O157:H7 in a broad range of foods.

VAL34LEU POLYMORPHISM DETECTION BY REAL TIME PCR ASSAY USING

Factor XIII (FXIII) Val34Leu is the most important polymorphism of the A subunit in factor XIII gene. The aim of the present study was to develop an efficient method based on real time PCR with Fluorescence resonance energy transfer (FRET) detection and melting curve analysis for the detection of Val34Leu polymorphism. Specific primers were used to amplify the relevant fragment of the factor XIII-A gene and fluorescence resonance energy transfer hybridization probes were used for detection in a Rotor-Gene Q 5Plex HRM platform. Melting temperature (Tm) for the wild type was at 68.8, while Tm for homozygote mutant was at 63.8; heterozygote demonstrated both peaks. Our results showed that primers and probes propoesd in this study demonstrated a high specificity to identify wild type , heterozygous and homozygous mutantgenotypes. Due to the increasing molecular diagnosis in developing countries and the importance of identifying polymorphisms, this real time PCR assay is of great importance. An important advantage of this approach is the high sensitivity and specificity.

Real-time PCR assay for rapid qualitative and quantitative detection of Entamoeba histolytica

Simple real-time PCR assay with one set of primer and probe for rapid, sensitive qualitative and quantitative detection of Entamoeba histolytica has been used. Consensus sequences were used to amplify a species-specific region of the 16S rRNA gene, and fluorescence resonance energy transfer hybridization probes were used for detection in a LightCycler platform (Roche). The anchor probe sequence was designed to be a perfect match for the 16S rRNA gene of Entamoeba species, while the acceptor probe sequence was designed for Entamoeba histolytica, which allowed differentiation. The performed characteristics of the real-time PCR assay were compared with ELISA antigen and microscopical detection from 77 samples of individuals with suspected clinical diagnosis of imported E. histolytica infection. Stool and liver abscess pus samples were examined with analytical sensitivity of 5 parasites per PCR reaction. The melting curve means Tms (standard deviation) in clinical isolates were 54°C. The real-time assay was 100% sensitive and specific for differentiation of Entamoeba histolytica, compared with conventional ELISA or microscopy. This real-time PCR assay with melting curve analysis is rapid, and specific for the detection and differentiation of Entamoeba histolytica. The suitability for routine use of this assay in clinical diagnostic laboratories is discussed.

Real-time PCR improve detection of Trichomonas vaginalis compared to conventional techniques

Trichomonas vaginalis is the cause of one of the most common types of vaginitis, trichomoniasis. Clinical manifestations of symptomatic women are generally nonspecific, but include vaginal discharge, vaginitis and irritation. T. vaginalis infection has also been linked to the increased risk of human immunodeficiency virus transmission. The aim of the study was to compare a real-time polymerase chain reaction (PCR) assay with culture and wet-mount examination for the detection of T. vaginalis. This is a descriptive analytical study. Vaginal swabs from 504 female patients with suspected vaginitis were included in the study. They were subjected to culture, wet-mount microscopic examination (WM), and real-time PCR. Real-time fluorescence resonance energy transfer hybridization probe PCR assays were used in this study to test for T. vaginalis DNA, targeting the b-tubulin genes. The result of the PCR was compared with culture and wet-mount microscopy. WM were positive for T. vaginalis in 60/504 cases (11.9%) and cultures were positive for T. vaginalis in 116/504 cases (23%). Real-time PCR was done on 50/504 specimens which was randomly chosen, 33/50 (66%) cases were positive for T. vaginalis (78% sensitivity), 25/50 (50%) of them were culture and wet-mount examination positive. Of them, 1/33 (3%) were culture positive and wet examination negative, 7/33 (21%) real-time positive were negative by culture while 17/50 (34%) real-time PCR negative cases were also negative by both techniques. The time taken for PCR assay was 4 to 8 h whereas positive protozoal cultures took up to 4 days. The Real-time PCR done in this study, provide a rapid, sensitive and specific diagnosis of T. vaginalis infection.

Real-Time Qualitative PCR for 57 Human Adenovirus Types from Multiple Specimen Sources

Human adenoviruses (HAdVs) are ubiquitous double-stranded DNA viruses that cause a wide array of diseases in humans including pharyngitis, pneumonia, gastroenteritis, hemorrhagic cystitis, and keratoconjunctivitis. They also cause life-threatening opportunistic infections in immunocompromised individuals and are responsible for outbreaks in certain populations. Diagnosis is traditionally by cell culture or antigen detection methods. However, some HAdVs can take up to 4 weeks to isolate, and diarrheagenic types 40 and 41 will not grow in routine cell culture. Therefore, the goal of this study was to design a rapid, real-time PCR assay to detect all known 57 HAdV types from multiple different specimen sources. Primers and fluorescence resonance energy transfer hybridization probes were designed to target a 185-bp region of the penton base gene of HAdV. The analytical sensitivity was determined to be 10 copies/μl for HAdV types showing exact primer/probe homology in specimen matrix. Using whole-virus strains, the analytical sensitivity for representative HAdV types ranged from 10(-1) to 10(3) 50% tissue culture infective dose (TCID(50))/ml. The assay demonstrated 100% sensitivity and 99% specificity. This real-time PCR assay provides a rapid method for the detection of all 57 known HAdV types from respiratory specimens, blood, stool, urine, and ocular swabs.

Detection of Blastomyces dermatitidis and Histoplasma capsulatum from Culture Isolates and Clinical Specimens by Use of Real-Time PCR

Blastomyces dermatitidis and Histoplasma capsulatum are dimorphic fungi that often cause self-limited respiratory infections. However, they may also cause severe disseminated disease, depending on the level of the exposure to the organism and the host immune status. In addition, patients with infections caused by these fungi may have very similar clinical presentations. Although microbiologic culture is a standard method for detecting these pathogens, their recovery may require days to weeks, and the manipulation of cultures presents a significant safety hazard to laboratory personnel. Therefore, the goal of this study was to design a rapid, real-time PCR assay to detect and differentiate B. dermatitidis and H. capsulatum from culture isolates and directly from clinical specimens. Primers and fluorescence resonance energy transfer hybridization probes were designed to target the histidine kinase and glyceraldehyde-3-phosphate dehydrogenase genes of B. dermatitidis and H. capsulatum, respectively. The analytical sensitivity of the assay was determined to be 100 copies/μl for both fungi. From culture isolates, the assay demonstrated 100% specificity and 100% sensitivity for B. dermatitidis and 100% specificity and 94% sensitivity for H. capsulatum. Detection directly from 797 clinical specimens demonstrated specificities and sensitivities of 99% and 86% for B. dermatitidis and 100% and 73% for H. capsulatum compared with the results for culture. This real-time PCR assay provides a rapid method for the detection of B. dermatitidis and H. capsulatum from culture isolates and directly from clinical specimens.

Rapid Detection and Molecular Differentiation of Toxigenic Corynebacterium diphtheriae and Corynebacterium ulcerans Strains by LightCycler PCR

The systemic symptoms of diphtheria are caused by the tox-encoded diphtheria toxin (DT) which is produced by toxigenic Corynebacterium spp. Besides the classical agent C. diphtheriae, the zoonotic pathogen C. ulcerans has increasingly been reported as an emerging pathogen for diphtheria. The reliable detection of toxigenic Corynebacterium spp. is of substantial importance for both diphtheria surveillance in the public health sector and the clinical workup of a patient with diphtherialike symptoms. Since the respective tox genes of C. diphtheriae and C. ulcerans differ from each other in both DNA and amino acid sequence, both tox genes should be covered by novel real-time PCR methods. We describe the development and validation of a LightCycler PCR assay which reliably recognizes tox genes from both C. diphtheriae and C. ulcerans and differentiates the respective target genes by fluorescence resonance energy transfer (FRET) hybridization probe melting curve analysis.

Molecular detection of Mycobacterium tuberculosis in formalin-fixed, paraffin-embedded tissues and biopsies of gastrointestinal specimens using real-time polymerase chain reaction system

We aimed to perform the molecular detection of Mycobacterium tuberculosis in formalin-fixed, paraffin-embedded tissues and biopsies of gastrointestinal specimens using real-time polymerase chain reaction system. The study included three groups: (A) control (n=24), with no previous signs of M. tuberculosis complex (MTBC), (B) patients (n=28) with known TB origin and (C) patients (n=50) with clinical and histopathological signs of TB but who were culture- and acid-fast bacilli (AFB)-negative. The samples were obtained from the Medical and Surgical Gastroenterology Departments of Bhopal Memorial Hospital and Research Centre. We extracted DNA using DNeasy Blood & Tissue kit (QIAGEN, Germany) and performed realtime assay using Roche LightCycler 2.0 with fluorescence resonance energy transfer (FRET) hybridization probes obtained from Roche Molecular Diagnostics (USA) for the specific amplification of the 159 bp region of the mycobacterium genome. All the samples (n=24) of Group A were found to be negative, while in Group B, 27 out of the 28 cases studied were found to be positive by LightCycler real-time polymerase chain reaction (LC PCR). In Group C, 18 out of the 50 cases studied were found to be positive, showing a positivity of 36%. The overall positive and negative predictive values of the test for clinical TB (Group C) were 100% and 96.9%, respectively. Results of our investigation demonstrated that the real-time detection technology using FRET probes has much higher sensitivity for the detection of MTBC DNA in tissue biopsy samples and formalin-fixed paraffin-embedded surgically resected tissues of the gastrointestinal tract.

P30 Preimplantation genetic diagnosis of β-thalassemia using real-time polymerase chain reaction with fluorescence resonance energy transfer hybridization probes

P30 Preimplantation genetic diagnosis of β-thalassemia using real-time polymerase chain reaction with fluorescence resonance energy transfer hybridization probes

Diagnosis of gastrointestinal tuberculosis: Using cytomorphological, microbiological, immunological and molecular techniques — A study from Central India

The present study included three groups: (A) age and gender matched control (n=24) with no previous signs of M. tuberculosis complex (MTBC) infection, (B) patients (n=28) diagnosed with gastro-intestinal TB (GITB), (C) patients (n=50) with clinical and histo-pathological signs of GITB, but were culture and AFB negative. Real time assay performed using fluorescence resonance energy transfer hybridization probes showed a positivity index of 36 % in group C, i.e. 18 were found reactive from the total 50 cases studied. In addition, immune characterization of these 18 cases showed depleted CD(4) (+) count and increased levels of IFN-γ and TNF-α cytokines. No positive case was found in group A, while in group B, out of total 28 cases studied 27 were found positive. A combinatorial diagnostic approach for rapid detection and characterization of GITB might provide specific therapeutic strategies for prevention and treatment of the infection in future.

A novel multiplex real-time RT-PCR assay with FRET hybridization probes for the detection and quantitation of 13 respiratory viruses

Quantitative multiplex real-time RT-PCR assays utilizing fluorescence resonance energy transfer (FRET) hybridization probes were developed for the detection of 13 respiratory viruses, including well recognized viral causes (respiratory syncytial virus, influenza viruses A and B, parainfluenza viruses types 1, 2, and 3, adenovirus) as well as viruses described recently as causes of acute respiratory tract infections (human coronaviruses NL63, HKU1, 229E, and OC43, human bocavirus, and human metapneumovirus). FRET probes have an improved toleration for single base mismatches than other probe chemistries, reducing the chances of missing highly variable RNA viruses. The assay could detect 2.5–25 DNA/RNA copies/μl (2.5 × 10 3–2.5 × 10 4 copies/ml). Validation on 91 known positive respiratory specimens indicated similar specificity as commercial direct immunofluorescence assays (IFA) or single-round PCRs used in initial identification. Screening of 270 IFA negative respiratory specimens identified new viruses in 40/270 (14.8%) cases and additional 79/270 (29.3%) well recognized viruses missed by routine diagnostic assays including 6.7% co-infections. All viruses could be detected in the clinical screening panel. The assays demonstrates an improved sensitivity and scope of detecting respiratory viruses relative to routine antigen detection assays while the quantitative utility may facilitate investigation of the role of co-infections and viral load in respiratory virus pathogenesis.

Preimplantation genetic diagnosis of β-thalassemia using real-time polymerase chain reaction with fluorescence resonance energy transfer hybridization probes

Preimplantation genetic diagnosis (PGD) is employed increasingly to allow transfer of embryos to the uterus in assisted reproduction procedures. There are three stages of biopsy: polar bodies, one or two blastomeres from the cleavage-stage embryos, and trophectoderm cells (∼5 cells) from the blastocyst-stage embryos. Validation of polymerase chain reaction (PCR)-based assays are challenging because only limited genetic material can be obtained for PGD. In the current study, we modified a valid single-cell PCR protocol for PGD using real-time PCR assay with fluorescence resonance energy transfer (FRET) hybridization probes followed by melting curve analysis. We optimized and clinically applied the protocol, permitting molecular genetic analysis to amplify a specific region on the beta-globin ( HBB) gene for a couple, carriers of two mutations: c.-78A>G and c.52A>T. Among a total of eight embryos obtained after ovarian stimulation, a single blastomere per embryo at the six- to eight-cell stage was biopsied. This PGD method showed that four embryos were unaffected, two embryos were selected for transfer, and one pregnancy was achieved. Finally, a healthy male baby was delivered at 38 weeks’ gestation. The results obtained using the new method, FRET hybridization probes, were compared with findings using an existing method, primer extension minisequencing.

Diagnosis of Gastrointestinal Tuberculosis: Combining Cytology, Immunology and Molecular Techniques - A Study From Central India

Purpose: The diagnosis of gastrointestinal tuberculosis still remains a major challenge. Molecular and immunological methods open a way for rapid and specific identification of gastrointestinal tuberculosis. Methods: The present study included three groups (A) control (n=24) with no previous signs of M. tuberculosis complex (B) patients (n=30) with known TB origin (C) patients (n=48) with clinical suspicion of TB but was culture and AFB negative. The inclusion criteria of the patients in group C was chosen according to the presence of certain symptoms, namely, abdominal pain, dyspepsia, weight loss, fever, anorexia, nausea and vomiting, constipation, rectal bleeding, chronic or bloody diarrhea, change in bowel habits, mal-absorption, and additional suspicious lesions. Real time assay using Roche Light Cycler 2.0 with fluorescence resonance energy transfer hybridization probes was performed for the specific amplification of 159 bp region of mycobacterium genome. Later immuno-phenotyping and Th1/Th2 cytokine profiling was performed using flow cytometry. Results: All the samples (n=24) of group A were found to be negative while in group B out of total 30 cases studied 29 were found to be positive by LC PCR. In group C out of total 48 cases studied 16 were found to be positive showing a positivity of 33%. The overall positive predictive value of the test was 98.95% and the negative predictive value was 95.19%. Immune characterization showed depleted CD4+ count and increased levels of IFN-gamma and TNF-alfa. Conclusion: A combinatorial diagnostic approach for rapid detection and characterization of gastrointestinal tuberculosis might provide specific therapeutic strategies for prevention and treatment of the infection in the future.

Improved detection of JC virus in AIDS patients with progressive multifocal leukoencephalopathy by T‐antigen specific fluorescence resonance energy transfer hybridization probe real‐time PCR: Evidence of diverse JC virus genotypes associated with progressive multifocal leukoencephalopathy in Southern Africa

JC virus (JCV) causes progressive multifocal leukoencephalopathy under conditions of immunosuppression, especially associated with HIV. Despite the high prevalence of HIV-1 infection, few cases of progressive multifocal leukoencephalopathy have been reported and only a small number of JCV strains have been characterized in AIDS patients in Southern Africa. Diagnosis of progressive multifocal leukoencephalopathy through PCR detection of JCV DNA in CSF may result in false negative results if variable regions of the genome are targeted. Characterization of circulating JCV genotypes in Southern Africa may assist with designing appropriate diagnostic assays and characterizing the molecular epidemiology of JCV in African AIDS patients. In this study, a new real-time PCR using fluorescence resonance energy transfer hybridization probes targeting the conserved large T-antigen was developed and compared to a conventional nested PCR targeting the variable VP1 region. Validation against known JCV positive specimens confirmed its specificity while amplification of a serial dilution of JCV control DNA suggests that the new real-time PCR can detect lower concentrations of JCV than the VP1 nested PCR. Investigation of CSF specimens from 44 suspected progressive multifocal leukoencephalopathy patients suggest that the new assay is more sensitive being able to detect JCV in 12 specimens versus 5 specimens with the VP1 nested PCR. Sequence analysis confirmed that the T-antigen region is completely conserved while phylogenetic analysis of the five VP1 products identified two genotype 3, one genotype 1 and two genotype 4 strains, the latter two identified for the first time in South African AIDS patients.

Real-Time FRET PCR Assay forSalmonella entericaSerotype Detection in Food

Salmonella enterica subsp. enterica serotypes are leading etiological agents of food-borne gastroenteritis. Traditional identification is laborious and time intensive. Faster molecular methods may allow early identification in contaminated food products. We developed a real-time, fluorescence resonance energy transfer hybridization probe polymerase chain reaction (PCR) assay for S. enterica serotypes on the basis of the exclusive presence of the apeE gene in Salmonella Typhimurium. Assay sensitivity for 12 S. enterica serotypes was as low as 1.87 x 10(2) genomic equivalents per milliliter. PCR efficiency was 94% and the dynamic range was linear over six orders of magnitude from 10(0) to 10(6) copies. The lower limit of detection for 12 different food matrices was between 1.5 x 10(2) and 1.5 x 10(5) CFU/mL without pre-enrichment. When combined with high-throughput automated DNA extraction, 32 food specimens were processed and assayed in less than 2 hours, allowing rapid, specific, sensitive detection of S. enterica serotypes in food products.

Role of PCR in the diagnosis of pertussis infection in infants: 5 years' experience of provision of a same-day real-time PCR service in England and Wales from 2002 to 2007

As part of an enhanced surveillance programme for pertussis in England and Wales, a real-time PCR service for the detection of Bordetella pertussis was introduced for infants aged <or=6 months admitted to a paediatric intensive care unit or paediatric ward with a respiratory illness compatible with pertussis. Two real-time fluorescent resonance energy transfer hybridization probe LightCycler (Roche Diagnostics) PCR assays were used. One (designed in-house) targeted the pertussis toxin S1 promoter (ptxA-pr), and included an internal process control to test for sample inhibition and reagent performance. The other (already published) targeted the insertion element IS481. The analytical sensitivities of the assays were 100 and 10 fg per reaction for the ptxA-pr and IS481 PCRs, respectively. The ptxA-pr assay was specific for B. pertussis, whilst the IS481 PCR also showed some cross-reactivity with Bordetella holmesii and the type strain of Bordetella parapertussis. From April 2002 to March 2007, 848 samples were received from 774 patients and DNA was extracted. Of 824 samples that were suitable for testing, 183 (22.2 %) had evidence of Bordetella infection (18.9 % ptxA-pr and IS481; 3.3 % IS481 only), 621 (75.4 %) were negative and 20 (2.4 %) were inhibitory for the PCR. Within the targeted age group of <or=6 months, most patients (130/138) with evidence of Bordetella spp. by PCR were <or=3 months old. The overall percentage increase in laboratory-confirmed cases due to PCR compared with culture for the 5 year period described ranged from 9 to 26 % per year (mean 19 %). Real-time PCR is an invaluable tool both for enhanced epidemiological surveillance and for the provision of a rapid diagnosis of pertussis where results can affect patient and contact management.

Detection of Cytomegalovirus in Whole Blood Using Three Different Real-Time PCR Chemistries

Several different primer-probe chemistries have been produced commercially for real-time PCR detection and quantification of cytomegalovirus, but there are few studies evaluating their relative performance. We assessed three such commercial reagents with respect to analytical and clinical operating characteristics. The samples included 149 clinical whole blood specimens that were de-identified and assayed in parallel with all primer-probe systems. Individual methods used TaqMan, dual fluorescence resonance energy transfer hybridization probes, and labeled primer chemistries. Method comparability was determined both qualitatively, based on pair-wise assessment of concordance, and quantitatively, based on pair-wise linear regression analysis. Analytical sensitivity and the lower end of the linear dynamic range reached 10 target copies per reaction for the TaqMan and labeled primer systems and 100 target copies per reaction for the dual fluorescence resonance energy transfer probe system. Quantitative linearity reached an upper limit of 10(5) copies per reaction for all methods. No assay cross-reactivity was seen with other common viral pathogens (100% analytical specificity). Pair-wise analysis of qualitative results from clinical samples showed no significant differences in sensitivity between the three sets of reagents, and linear regression analysis indicated that the quantitative values achieved were comparable in all positive specimens. The findings demonstrate that similar analytical and clinical performance characteristics can be demonstrated for quantitative detection of cytomegalovirus in clinical whole blood extracts using a wide variety of real-time PCR chemistries.

Detection and differentiation of human papillomavirus genotypes HPV-6 and HPV-11 by FRET-based real-time PCR

A real-time PCR (RT-PCR) assay was developed based on fluorescence resonance energy transfer (FRET) hybridization probe technology, allowing very sensitive and specific detection of HPV-6 and HPV-11, reliable differentiation of HPV-6 and HPV-11, as well as prototypic and non-prototypic HPV-6 genomic variants, in a single PCR reaction. The primers and probe were designed on the basis of multiple alignments of 74 HPV-6 E2 gene sequences and 20 HPV-11 E2 gene sequences. Testing on defined plasmid standards showed that the RT-PCR allowed simple and reliable identification of HPV-6 and HPV-11 using type specific amplification followed by probe-specific post-amplification dissociation analysis. Sensitivity, assessed by probit analysis at a 95% detection level, was 42.9, 43.4, and 25.3 DNA copies per assay for prototypic and non-prototypic HPV-6 variants and HPV-11, respectively. The results obtained by the developed assay on 51 HPV DNA-negative samples and 149 HPV DNA-positive samples, including 81 HPV-6 positive samples (19 prototypic and 62 non-prototypic HPV-6 variants), 28 HPV-11 positive samples, 10 samples of HPV-44 and HPV-74 (the closest relatives of HPV-6 and HPV-11) and 30 samples of 15 other important alpha HPV, showed complete agreement with those obtained with the INNO-LiPA human papillomavirus (HPV) Genotyping Assay and HPV-6 E2 and E6 gene sequencing.