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Yan S, Lan H, Wu Z, Sun Y, Tu M, Pan D. Cleavable molecular beacon-based loop-mediated isothermal amplification assay for the detection of adulterated chicken in meat. Anal Bioanal Chem 2022; 414:8081-8091. [PMID: 36152037 DOI: 10.1007/s00216-022-04342-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/30/2022]
Abstract
A simple, sensitive, specific and fast method based on the loop-mediated isothermal amplification (LAMP) technique and cleavable molecular beacon (CMB) was developed for chicken authentication detection. LAMP and CMB were used for DNA amplification and amplicon analysis, respectively. Targeting the mitochondrial cytochrome b gene of chickens, five primers and one CMB probe were designed, and their specificity was validated against nine other animal species. The structure of CMB and concentrations of dNTPs, MgSO4, betaine, RNase H2, primers and CMB were optimized. The CMB-LAMP assay was completed within 17 min, and its limit of detection for chicken DNA was 1.5 pg μL-1. Chicken adulteration as low as 0.5% was detected in beef, and no cross-reactivity was observed. Finally, this assay was successfully applied to 20 commercial meat products. When combined with our developed DNA extraction method (the extraction time was 1 min: lysis for 10 s, washing for 20 s and elution for 30 s), the entire process (from DNA extraction to results analysis) was able to be completed within 20 min, which is at least 10 min shorter than other LAMP-based methods. Our method showed great potential for the on-site detection of chicken adulteration in meat.
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Affiliation(s)
- Song Yan
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.,Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang Province and College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China
| | - Hangzhen Lan
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China. .,Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang Province and College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China.
| | - Zhen Wu
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.,Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang Province and College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China
| | - Yangying Sun
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.,Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang Province and College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China
| | - Maolin Tu
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.,Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang Province and College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China
| | - Daodong Pan
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China. .,Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang Province and College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China. .,National R&D Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang, 330022, Jiangxi, China.
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2
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El Wahed AA, Patel P, Maier M, Pietsch C, Rüster D, Böhlken-Fascher S, Kissenkötter J, Behrmann O, Frimpong M, Diagne MM, Faye M, Dia N, Shalaby MA, Amer H, Elgamal M, Zaki A, Ismail G, Kaiser M, Corman VM, Niedrig M, Landt O, Faye O, Sall AA, Hufert FT, Truyen U, Liebert UG, Weidmann M. Suitcase Lab for Rapid Detection of SARS-CoV-2 Based on Recombinase Polymerase Amplification Assay. Anal Chem 2021; 93:2627-2634. [PMID: 33471510 PMCID: PMC7839158 DOI: 10.1021/acs.analchem.0c04779] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/11/2021] [Indexed: 12/30/2022]
Abstract
In March 2020, the SARS-CoV-2 virus outbreak was declared as a world pandemic by the World Health Organization (WHO). The only measures for controlling the outbreak are testing and isolation of infected cases. Molecular real-time polymerase chain reaction (PCR) assays are very sensitive but require highly equipped laboratories and well-trained personnel. In this study, a rapid point-of-need detection method was developed to detect the RNA-dependent RNA polymerase (RdRP), envelope protein (E), and nucleocapsid protein (N) genes of SARS-CoV-2 based on the reverse transcription recombinase polymerase amplification (RT-RPA) assay. RdRP, E, and N RT-RPA assays required approximately 15 min to amplify 2, 15, and 15 RNA molecules of molecular standard/reaction, respectively. RdRP and E RT-RPA assays detected SARS-CoV-1 and 2 genomic RNA, whereas the N RT-RPA assay identified only SARS-CoV-2 RNA. All established assays did not cross-react with nucleic acids of other respiratory pathogens. The RT-RPA assay's clinical sensitivity and specificity in comparison to real-time RT-PCR (n = 36) were 94 and 100% for RdRP; 65 and 77% for E; and 83 and 94% for the N RT-RPA assay. The assays were deployed to the field, where the RdRP RT-RPA assays confirmed to produce the most accurate results in three different laboratories in Africa (n = 89). The RPA assays were run in a mobile suitcase laboratory to facilitate the deployment at point of need. The assays can contribute to speed up the control measures as well as assist in the detection of COVID-19 cases in low-resource settings.
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Affiliation(s)
- Ahmed Abd El Wahed
- Institute
of Animal Hygiene and Veterinary Public Health, University of Leipzig, 04103 Leipzig, Germany
- Division
of Microbiology and Animal Hygiene, Georg-August-University, 37077 Goettingen, Germany
| | - Pranav Patel
- Expert
Molecular Diagnostics, 82256Fürstenfeldbruck, Germany
| | - Melanie Maier
- Institute
of Medical Microbiology and VirologyLeipzig
University Hospital, 04103 Leipzig, Germany
| | - Corinna Pietsch
- Institute
of Medical Microbiology and VirologyLeipzig
University Hospital, 04103 Leipzig, Germany
| | - Dana Rüster
- Institute
of Animal Hygiene and Veterinary Public Health, University of Leipzig, 04103 Leipzig, Germany
| | - Susanne Böhlken-Fascher
- Division
of Microbiology and Animal Hygiene, Georg-August-University, 37077 Goettingen, Germany
| | - Jonas Kissenkötter
- Division
of Microbiology and Animal Hygiene, Georg-August-University, 37077 Goettingen, Germany
| | - Ole Behrmann
- Institute
of Microbiology & Virology, Brandenburg Medical School, 01968 Senftenberg, Germany
| | - Michael Frimpong
- Kumasi Centre
for Collaborative Research in Tropical Medicine, Department of Molecular
Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Martin Faye
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Ndongo Dia
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Mohamed A. Shalaby
- Virology
Department, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
| | - Haitham Amer
- Virology
Department, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
| | - Mahmoud Elgamal
- Virology
Department, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
| | - Ali Zaki
- Department
of Medical Microbiology and Immunology, Faculty of Medicine, Ain Shams University, 11591 Cairo, Egypt
| | - Ghada Ismail
- Department
of Clinical Pathology, Faculty of Medicine, Ain Shams University, 11591 Cairo, Egypt
| | - Marco Kaiser
- GenExpress Gesellschaft für Proteindesign, 12103 Berlin, Germany
| | - Victor M. Corman
- Charité−Universitätsmedizin
Berlin, Institute
of Virology, Berlin, Germany
- German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | | | | | - Ousmane Faye
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Amadou A. Sall
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Frank T. Hufert
- Institute
of Microbiology & Virology, Brandenburg Medical School, 01968 Senftenberg, Germany
| | - Uwe Truyen
- Institute
of Animal Hygiene and Veterinary Public Health, University of Leipzig, 04103 Leipzig, Germany
| | - Uwe G. Liebert
- Institute
of Medical Microbiology and VirologyLeipzig
University Hospital, 04103 Leipzig, Germany
| | - Manfred Weidmann
- Institute
of Microbiology & Virology, Brandenburg Medical School, 01968 Senftenberg, Germany
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Burdukiewicz M, Spiess AN, Blagodatskikh KA, Lehmann W, Schierack P, Rödiger S. Algorithms for automated detection of hook effect-bearing amplification curves. BIOMOLECULAR DETECTION AND QUANTIFICATION 2018; 16:1-4. [PMID: 30560061 PMCID: PMC6287529 DOI: 10.1016/j.bdq.2018.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 07/12/2018] [Accepted: 08/20/2018] [Indexed: 12/16/2022]
Abstract
Amplification curves from quantitative Real-Time PCR experiments typically exhibit a sigmoidal shape. They can roughly be divided into a ground or baseline phase, an exponential amplification phase, a linear phase and finally a plateau phase, where in the latter, the PCR product concentration no longer increases. Nevertheless, in some cases the plateau phase displays a negative trend, e.g. in hydrolysis probe assays. This cycle-to-cycle fluorescence decrease is commonly referred to in the literature as the hook effect. Other detection chemistries also exhibit this negative trend, however the underlying molecular mechanisms are different. In this study we present two approaches to automatically detect hook effect-like curvatures based on linear (hookreg) and nonlinear regression (hookregNL). As the hook effect is typical for qPCR data, both algorithms can be employed for the automated identification of regular structured qPCR curves. Therefore, our algorithms streamline quality control, but can also be used for assay optimization or machine learning.
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Affiliation(s)
| | | | | | | | - Peter Schierack
- Institute of Biotechnology, Brandenburg University of Technology Cottbus – Senftenberg, Senftenberg, Germany
| | - Stefan Rödiger
- Institute of Biotechnology, Brandenburg University of Technology Cottbus – Senftenberg, Senftenberg, Germany
- Corresponding author.
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Martinez-Serra J, Robles J, Nicolàs A, Gutierrez A, Ros T, Amat JC, Alemany R, Vögler O, Abelló A, Noguera A, Besalduch J. Fluorescence resonance energy transfer-based real-time polymerase chain reaction method without DNA extraction for the genotyping of F5, F2, F12, MTHFR, and HFE. J Blood Med 2014; 5:99-106. [PMID: 25028568 PMCID: PMC4077787 DOI: 10.2147/jbm.s64976] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Blood samples are extensively used for the molecular diagnosis of many hematological diseases. The daily practice in a clinical laboratory of molecular diagnosis in hematology involves using a variety of techniques, based on the amplification of nucleic acids. Current methods for polymerase chain reaction (PCR) use purified genomic DNA, mostly isolated from total peripheral blood cells or white blood cells (WBC). In this paper we describe a real-time fluorescence resonance energy transfer-based method for genotyping directly from blood cells. Our strategy is based on an initial isolation of the WBCs, allowing the removal of PCR inhibitors, such as the heme group, present in the erythrocytes. Once the erythrocytes have been lysed, in the LightCycler® 2.0 Instrument, we perform a real-time PCR followed by a melting curve analysis for different genes (Factors 2, 5, 12, MTHFR, and HFE). After testing 34 samples comparing the real-time crossing point (CP) values between WBC (5×106 WBC/mL) and purified DNA (20 ng/μL), the results for F5 Leiden were as follows: CP mean value for WBC was 29.26±0.566 versus purified DNA 24.79±0.56. Thus, when PCR was performed from WBC (5×106 WBC/mL) instead of DNA (20 ng/μL), we observed a delay of about 4 cycles. These small differences in CP values were similar for all genes tested and did not significantly affect the subsequent analysis by melting curves. In both cases the fluorescence values were high enough, allowing a robust genotyping of all these genes without a previous DNA purification/extraction.
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Affiliation(s)
- Jordi Martinez-Serra
- Department of Hematology, Hospital Universitary Son Espases, Palma de Mallorca, Spain
| | - Juan Robles
- Department of Clinical Analysis, Hospital Universitary Son Espases, Palma de Mallorca, Spain
| | | | - Antonio Gutierrez
- Department of Hematology, Hospital Universitary Son Espases, Palma de Mallorca, Spain
| | - Teresa Ros
- Department of Hematology, Hospital Universitary Son Espases, Palma de Mallorca, Spain
| | - Juan Carlos Amat
- Department of Hematology, Hospital Universitary Son Espases, Palma de Mallorca, Spain
| | - Regina Alemany
- Department of Cell Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Oliver Vögler
- Department of Cell Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Aina Abelló
- Department of Clinical Analysis, Hospital Universitary Son Espases, Palma de Mallorca, Spain
| | - Aina Noguera
- Department of Clinical Analysis, Hospital Universitary Son Espases, Palma de Mallorca, Spain
| | - Joan Besalduch
- Department of Hematology, Hospital Universitary Son Espases, Palma de Mallorca, Spain
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5
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Stellrecht KA. Nucleic acid amplification technology for the diagnosis of genital herpes infection. Expert Rev Mol Diagn 2014; 4:485-93. [PMID: 15225096 DOI: 10.1586/14737159.4.4.485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Nucleic acid amplification technologies are well-characterized methods for the rapid and sensitive diagnosis of a wide variety of infectious diseases. Herpes simplex virus amplification is no exception, demonstrating as much as a ninefold enhancement in sensitivity over viral culture in some settings. Currently, there are no US Food and Drug Administration-approved systems for herpes simplex virus amplification; hence, most laboratories utilize in-house-developed PCR-based systems. Unfortunately, the utilization of herpes simplex virus amplification has been confined to the investigations of suspected herpes simplex virus encephalitis, largely due to cost and the need for appropriately trained technical staff. Recent methodological advances will help to render herpes simplex virus nucleic acid amplification technologies more applicable to routine practice. However, the use of nucleic acid amplification technologies for the diagnosis of genital herpes infection remains highly controversial.
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Affiliation(s)
- Kathleen A Stellrecht
- Albany Medical Center, Center for Immunology and Microbial Diseases, 43 New Scotland Ave., Albany, NY 12208, USA.
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Faltin B, Zengerle R, von Stetten F. Current methods for fluorescence-based universal sequence-dependent detection of nucleic acids in homogenous assays and clinical applications. Clin Chem 2013; 59:1567-82. [PMID: 23938456 DOI: 10.1373/clinchem.2013.205211] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Specific and sensitive nucleic acid (NA) testing in research and clinical diagnostics is usually performed by use of labeled oligonucleotide probes. However, the use of target-specific fluorogenic probes increases the cost of analysis. Therefore, universal sequence-dependent (USD) NA detection methods have been developed to facilitate cost-effective target detection using standardized reagents. CONTENT We provide a comprehensive review of the current methods for fluorescence-based USD NA detection. Initially, we focus on the emergence of these methods as a means to overcome the shortcomings of common NA detection methods, such as hydrolysis probes and molecular beacons. Thereafter, we provide a critical evaluation of the individual detection methods. These methods include (a) target amplification with bipartite primers introducing a universal detection tag to the amplicon (UniPrimer PCR, universal fluorescence energy transfer probe PCR, attached universal duplex probe PCR, and universal strand displacement amplification) or combined with bipartite probes comprising a universal detection region (mediator probe PCR, universal strand displacement amplification, universal quenching probe PCR) and (b) amplification-independent assays employing either a universal variant of the invader assay or universal NA hybridization sensors. We discuss differences between the methods and review clinical applications. SUMMARY The current methods for USD NA testing are cost-effective and flexible and have concordant analytical performance in comparison with common probe-based techniques. They can detect any target sequence by the simple use of a label-free, low-cost primer or probe combined with a universal fluorogenic reporter. The methods differ in the number of target specificities, capability of multiplexing, and incubation requirements (isothermal/thermocycling). Extensive clinical applications comprise detection of single-nucleotide polymorphisms, study of gene expression, in situ PCR, and quantification of pathogen load.
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7
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Martinez-Serra J, Gutiérrez A, Marcús TF, Soverini S, Amat JC, Navarro-Palou M, Ros T, Bex T, Ballester C, Bauça JM, SanFelix S, Novo A, Vidal C, Santos C, Besalduch J. Four-channel asymmetric Real-Time PCR hybridization probe assay: a rapid pre-screening method for critical BCR-ABL kinase domain mutations. Clin Biochem 2012; 45:345-51. [PMID: 22266405 DOI: 10.1016/j.clinbiochem.2011.12.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2011] [Revised: 12/28/2011] [Accepted: 12/31/2011] [Indexed: 11/30/2022]
Abstract
OBJECTIVES Within the laboratory protocols, used for the study of BCR-ABL resistance mutations in chronic myeloid leukemia patients treated with Imatinib, direct sequencing remains the reference method. Since the incidence of patients with a mutation-related loss of response is not very high, it is very useful in the routine laboratory to perform a fast pre-screening method. DESIGN AND METHODS With this in mind, we have designed a new technique, based on a single Real-Time FRET-based PCR, followed by a study of melting peaks. This new tool, developed in a LightCycler 2.0, combines four different fluorescence channels for the simultaneous detection, in a single close tube, of critical mutations within the ABL kinase domain. RESULTS Assay evaluation performed on 33 samples, previously genotyped by sequentiation, resulted in full concordance of results. CONCLUSIONS This new methodology detects in a few steps the presence of critical mutations associated to Imatinib resistance.
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Affiliation(s)
- Jordi Martinez-Serra
- Department of Hematology, University Hospital of Son Espases, Carretera Valldemossa no. 79, Palma de Mallorca, Spain.
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The Hybrid II assay: a sensitive and specific real-time hybridization assay for the diagnosis ofTheileria parvainfection in Cape buffalo (Syncerus caffer) and cattle. Parasitology 2011; 138:1935-44. [DOI: 10.1017/s0031182011001454] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
SUMMARYCorridor disease is an acute, fatal disease of cattle caused by buffalo-adaptedTheileria parva. This is a nationally controlled disease in South Africa and strict control measures apply for the movement of buffalo, which includes mandatory testing for the presence ofT. parvaand other controlled diseases. Accurate diagnosis of theT. parvacarrier state in buffalo using the official real-time hybridization PCR assay (Sibekoet al.2008), has been shown to be affected by concurrent infection withT.sp. (buffalo)-like parasites. We describe the Hybrid II assay, a real-time hybridization PCR method, which compares well with the official hybridization assay in terms of specificity and sensitivity. It is, however, not influenced by mixed infections ofT.sp. (buffalo)-like parasites and is as such a significant improvement on the current hybridization assay.
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Tani H, Miyata R, Ichikawa K, Morishita S, Kurata S, Nakamura K, Tsuneda S, Sekiguchi Y, Noda N. Universal quenching probe system: flexible, specific, and cost-effective real-time polymerase chain reaction method. Anal Chem 2009; 81:5678-85. [PMID: 19530673 DOI: 10.1021/ac900414u] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed a flexible, specific, and cost-effective real-time polymerase chain reaction (PCR) method. In this technique, a quenching probe (QProbe) and a nonfluorescent 3'-tailed probe are used. The QProbe is a singly labeled oligonucleotide bearing a fluorescent dye that is quenched via electron transfer between the dye and a guanine base at a particular position. The nonfluorescent 3'-tailed probe consists of two parts: one is the target-specific sequence on the 5' side, and the other is complementary to the QProbe on the 3' side. When the QProbe/nonfluorescent 3'-tailed probe complex hybridizes with the target in PCR, the fluorescence of the dye is quenched. Fluorescence quenching efficiency is proportional to the amount of the target. We called this method the universal QProbe system. This method substantially reduces the cost of real-time PCR setup because the same QProbe can be used for different target sequences. Moreover, this method allows accurate quantification even in the presence of nonspecific PCR products because the use of nonfluorescent 3'-tailed probe significantly increases specificity. Our results demonstrate that this method can accurately and reproducibly quantify specific nucleic acid sequences in crude samples, comparable with conventional TaqMan chemistry. Furthermore, this method is also applicable to single-nucleotide polymorphism (SNP) genotyping.
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Affiliation(s)
- Hidenori Tani
- Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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New real-time PCR-based method for the joint genotyping of JAK2 (V617F) with inherited thrombophilic F5 and F2 mutations. Clin Chim Acta 2009; 410:59-63. [PMID: 19778528 DOI: 10.1016/j.cca.2009.09.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 08/10/2009] [Accepted: 09/09/2009] [Indexed: 11/21/2022]
Abstract
BACKGROUND During the last years the appearance of the acquired V617F mutation of the Janus Kinase 2 gene (JAK2) in patients suffering different thrombotic events has been described. We decided to develop a new and rapid multiplex real-time Polymerase Chain Reaction (PCR) in order to detect the V617F mutation together with the inherited prothrombotic mutations of factors F5 and F2. DESIGN AND METHODS The method was carried out on the LightCycler 2.0 (Roche Diagnostics, Mannheim, Germany) and consisted in a first step of simultaneous amplification by real-time PCR of the three genes to be genotyped, in a 20microl closed tube, using a primer pair together with the correspondent FRET-hybridization probes for each gene. RESULTS We assayed 41 samples in the multiplex PCR reaction, 19 were positive (46.34%) for V617F mutation. From the V617F positive samples we found 1 sample heterozygous for F2 (5.26%) and 1 sample heterozygous for F5 (5.26%), so a 10.52% of the samples tested combine V617F mutation with inherited thrombophilic mutations. Results were clear, rapid and reliable allowing a significant time saving. CONCLUSIONS The technique presented in this manuscript is a new achievement in the field of the molecular diagnosis that combines the genotyping of F5 and F2 with the assessment of the JAK2 (V617F) mutation load.
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Martínez-Serra J, Gutierrez A, Amat J, Galmés B, Vila A, Julia M, López H, Bautista A, Truyols C, Ros T, Navarro M, Canaro M, Díaz M, Besalduch J. Rapid triplex asymmetric real-time PCR hybridization probe assay for the joint genotyping of F2, F5 and F12. Clin Biochem 2009; 42:1317-24. [DOI: 10.1016/j.clinbiochem.2009.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2009] [Revised: 04/06/2009] [Accepted: 04/24/2009] [Indexed: 10/20/2022]
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12
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YANG HY, XI T, LIANG C, CHEN ZY, XU DB, ZHOU Guo H. Preparation of Single-Stranded DNA for Pyrosequencing by Linear-after-the-Exponential-Polymerase Chain Reaction. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2009. [DOI: 10.1016/s1872-2040(08)60095-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Real-time PCR detection of gyrA and parC mutations in Streptococcus pneumoniae. Antimicrob Agents Chemother 2008; 52:4155-8. [PMID: 18725440 DOI: 10.1128/aac.00082-08] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Fluoroquinolone resistance in Streptococcus pneumoniae mainly involves stepwise mutations predominantly in the parC and gyrA genes. We have developed a single-run real-time PCR assay for detection of the four most common mutations in the quinolone resistance-determining regions of these genes. This assay provides a useful tool for both clinical and epidemiological use.
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14
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A duplex Neisseria gonorrhoeae real-time polymerase chain reaction assay targeting the gonococcal porA pseudogene and multicopy opa genes. Diagn Microbiol Infect Dis 2008; 61:6-12. [PMID: 18248938 DOI: 10.1016/j.diagmicrobio.2007.12.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 12/03/2007] [Accepted: 12/05/2007] [Indexed: 11/23/2022]
Abstract
Cross-reactions of gonococcal nucleic acid amplification tests (NAATs) with commensal Neisseria strains are well documented. Recent data now indicate that sequence-related false-negative results can occur in gonococcal NAATs, whereby target sequences either are absent or contain several mutations. In this study, a duplex Neisseria gonorrhoeae real-time polymerase chain reaction (PCR) (NGduplex) assay targeting the gonococcal porA pseudogene and multicopy opa genes was developed. The NGduplex was evaluated by testing 596 clinical specimens, including 292 urogenital specimens and 304 throat swab specimens. The results were compared with those obtained using a consensus reference standard comprising 3 monoplex real-time PCR assays. The results show that the NGduplex assay is highly suitable for routine screening for gonorrhea, providing an overall clinical sensitivity and specificity of 100% and 99.3%, respectively, for both urogenital and throat swab specimens. In addition, the 2-target system of the NGduplex assay decreases the potential for sequence-related false-negative results and can provide simultaneous confirmation of positive results.
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15
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Vernel-Pauillac F, Merien F. A novel real-time duplex PCR assay for detecting penA and ponA genotypes in Neisseria gonorrhoeae: Comparison with phenotypes determined by the E-test. Clin Chem 2006; 52:2294-6. [PMID: 17053151 DOI: 10.1373/clinchem.2006.075309] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND For many years, the pathogenic bacterium Neisseria gonorrhoeae, the etiologic agent of gonorrhea, was generally susceptible to penicillin, until the emergence of resistant strains. Well-characterized genetic variations in the penicillin resistance-determining region correlate with decreased susceptibility to penicillin. At least 5 genes (penA, penB, mtrR, ponA, and penC) are involved in the chromosomally mediated resistance to this antibiotic. To date, no development of multiplex PCR assays targeting a range of gonococcal genes and variations as a means of predicting antibiotic resistance has been reported. METHODS The aim of this study was to develop a duplex assay using DNA from isolated strains. We describe the development and evaluation on the LightCycler platform of a real-time duplex PCR assay (hybridization probe format) for rapid and specific detection of ponA and penA variations, predicting penicillin susceptibilities. RESULTS The real-time duplex PCR assay successfully detected variations in ponA and penA genes by use of distinct melting temperatures from a total of 120 Neisseria gonorrhoeae isolates. Moreover, the variation profiles obtained with the real-time PCR and the melting analysis showed good correlation with the pattern of penicillin susceptibility generated with classical antibiograms. Nucleotide sequencing data were in complete agreement with multiplex assay results. CONCLUSIONS The presented assay is suitable for the detection of chromosomally mediated resistant strains of Neisseria gonorrhoeae in genotyping studies and could be valuable in the effective antimicrobial strategy to gonococci.
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Faner R, Casamitjana N, Coll J, Caro P, Pujol-Borrell R, Palou E, Juan M. Real-Time PCR Using Fluorescent Resonance Emission Transfer Probes for HLA-B Typing. Hum Immunol 2006; 67:374-85. [PMID: 16720220 DOI: 10.1016/j.humimm.2006.02.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Indexed: 12/01/2022]
Abstract
HLA genotyping by polymerase chain reaction (PCR) has some inherent labor-intensive and effort-demanding limitations. To overcome them, we have developed a real-time PCR with hybridization probes approach able to obtain a medium-low resolution HLA-B genotyping with fewer tubes and probes and with a shorter time requirement. Our strategy used 18 simultaneous reactions amplifying HLA-B alleles and an internal control. Monitorization of both amplifications in each tube is performed by the simultaneous application of two fluorescent resonance emission transfer probes: the first probe, different for each tube, is specific for the HLA-B locus and the second probe detects the control gene. A medium-low resolution (300 HLA-B allelic groups) typing is obtained for each sample by analyzing the melting curve patterns. Because some alleles may be determined without using the complete set of reactions, we present an alternative strategy: a first round of seven reactions and, according to the result, a second (or third) round of PCRs to solve the ambiguities. This method was validated in pretyped clinical samples and the results were completely concordant. Moreover, fewer ambiguous results were obtained. In summary, we present a new, faster, and more accurate method than currently used PCR techniques to type HLA-B alleles.
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Affiliation(s)
- Rosa Faner
- Laboratory of Immunobiology Research and Applications to Diagnosis, Banc de Sang i Teixits, Barcelona, Spain
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Whiley DM, Sloots TP. Comparison of three in-house multiplex PCR assays for the detection of Neisseria gonorrhoeae and Chlamydia trachomatis using real-time and conventional detection methodologies. Pathology 2005; 37:364-70. [PMID: 16194847 DOI: 10.1080/00313020500254552] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AIMS To develop and evaluate multiplex PCR assays for Chlamydia trachomatis and Neisseria gonorrhoeae, using real-time and conventional PCR detection methodologies. METHODS Two real-time multiplex PCR assays, using nuclease (TaqMan-ABI7500) and hybridisation (LightCycler) probe formats, and a third assay using conventional PCR with solid-phase hybridisation and colour detection, were developed. The porA pseudogene was targeted for N. gonorrhoeae, and the major outer membrane protein gene for C. trachomatis. A total of 145 urogenital specimens were tested in all assays, and the results were compared with the Roche Cobas Amplicor assay. RESULTS There was little difference in clinical sensitivity and specificity, result discrimination and test cost for the three in-house assays. Our results showed that competitive inhibition of the PCR occurred in some samples that were positive for both organisms. CONCLUSIONS These results highlight the suitability and versatility of three multiplex PCR methods for the detection of C. trachomatis and N. gonorrhoeae.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Brisbane, Queensland, Australia.
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Szilvási A, Andrikovics H, Kalmár L, Bors A, Tordai A. Asymmetric PCR increases efficiency of melting peak analysis on the LightCycler. Clin Biochem 2005; 38:727-30. [PMID: 15982647 DOI: 10.1016/j.clinbiochem.2005.04.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2004] [Revised: 04/01/2005] [Accepted: 04/08/2005] [Indexed: 11/20/2022]
Abstract
OBJECTIVES To systematically analyze the effects of asymmetric PCR on LightCycler melting analyses of four different allelic-discrimination systems and to reduce an inconsistent non-specific melting peak observed during factor V Leiden genotyping. DESIGN AND METHODS PCR amplifications and melting analyses were carried out with various oligonucleotide concentrations and ratios. To monitor the efficiency, calculated peak area values were compared after melting analyses. RESULTS Peak area values increased by a mean of 11.2-fold (range: 6 to 17) in case of an amplification primer ratio of 1:6.7 asymmetric PCR compared to symmetric primer conditions in four different SNP-genotyping systems. Using a complementary hybridization probe set for factor V Leiden genotyping, a converse amplification primer ratio was necessary for similar results. CONCLUSIONS Asymmetric PCR resulting in the formation of higher amounts of target strands significantly increases the efficiency of LightCycler allelic-discrimination.
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Affiliation(s)
- Anikó Szilvási
- Laboratory of Molecular Genetics, Institute of Hematology and Immunology, National Medical Center, Diószegi út 64, Budapest H-1113, Hungary
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Mackay IM, Arden KE, Nitsche A. Real-time Fluorescent PCR Techniques to Study Microbial-Host Interactions. METHODS IN MICROBIOLOGY 2004; 34:255-330. [PMID: 38620210 PMCID: PMC7148886 DOI: 10.1016/s0580-9517(04)34010-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
This chapter describes how real-time polymerase chain reaction (PCR) performs and how it may be used to detect microbial pathogens and the relationship they form with their host. Research and diagnostic microbiology laboratories contain a mix of traditional and leading-edge, in-house and commercial assays for the detection of microbes and the effects they impart upon target tissues, organs, and systems. The PCR has undergone significant change over the last decade, to the extent that only a small proportion of scientists have been able or willing to keep abreast of the latest offerings. The chapter reviews these changes. It discusses the second-generation of PCR technology-kinetic or real-time PCR, a tool gaining widespread acceptance in many scientific disciplines but especially in the microbiology laboratory.
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Affiliation(s)
- Ian M Mackay
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Qld, Australia
- Clinical Medical Virology Centre, University of Queensland, Brisbane, Qld, Australia
| | - Katherine E Arden
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Qld, Australia
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Whiley DM, Crisante ME, Syrmis MW, Mackay IM, Sloots TP. Detection of Neisseria Meningitidis in clinical samples by a duplex real-time PCR targeting the porA and ctrA genes. ACTA ACUST UNITED AC 2004; 7:141-5. [PMID: 15068383 DOI: 10.1007/bf03260030] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
BACKGROUND In recent years PCR has proven to be a highly sensitive and specific method for the diagnosis of infections caused by Neisseria meningitidis. STUDY DESIGN We developed and evaluated a N. meningitidis LightCycler real-time duplex PCR (NM-LCdPCR) capable of simultaneously detecting and distinguishing between two separate genes on the N. meningitidis genome. METHODS The NM-LCdPCR was developed on the LightCycler platform (Roche Diagnostics, Castle Hill, NSW, Australia) and comprised two primer pairs and two hybridization probe sets, enabling the detection of both the porA and ctrA genes within the same reaction mix. To distinguish between the fluorescence emitted by each hybridization probe set, each downstream probe was labeled with a different fluorophore (either LC-Red640 or LC-Red705). The results obtained by the NM-LCdPCR were then compared with the results obtained by a mono-specific LightCycler assay targeting the porA gene only (porA-LCPCR). PATIENTS One-hundred and forty-eight clinical samples from patients with suspected meningococcal infection were evaluated. RESULTS The results of the NM-LCdPCR and porA-LCPCR gave 100% agreement; N. meningitidis DNA was detected in 25 samples whereas 123 samples were negative by both assays. The breakdown of the NM-LCdPCR results show that both genes were detected in 26 of the 28 positive samples. DISCUSSION By targeting two separate N. meningitidis genes, the NM-LCdPCR has the potential to prevent the false-positive results which may arise from sequence variation. In addition, the ability to detect and discriminate between the two different N. meningitidis genes within the same reaction mix offers a rapid means for confirming the presence of N. meningitidis DNA in clinical samples, thereby reducing the need for subsequent confirmatory assays to be performed. CONCLUSIONS The sensitivity and specificity of the NM-LCdPCR assay, combined with its ability to detect and discriminate both the N. meningitidis porA and ctrA genes, make it suitable for the diagnosis of N. meningitidis infections in the routine clinical laboratory.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Herston, and Clinical Medical Virology Centre, University of Queensland, Brisbane, Queensland, Australia
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Whiley DM, Mackay IM, Syrmis MW, Witt MJ, Sloots TP. Detection and differentiation of herpes simplex virus types 1 and 2 by a duplex LightCycler PCR that incorporates an internal control PCR reaction. J Clin Virol 2004; 30:32-8. [PMID: 15072751 DOI: 10.1016/j.jcv.2003.08.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2003] [Revised: 08/12/2003] [Accepted: 08/15/2003] [Indexed: 11/27/2022]
Abstract
BACKGROUND In recent years polymerase chain reaction (PCR) has proven to be a highly sensitive and specific method for the diagnosis of herpes simplex virus (HSV) infections. The advent of real-time HSV PCR protocols now enables rapid result turnaround times with minimal hands-on time. OBJECTIVES In this study, we developed a real-time duplex PCR assay (HSVgD-dPCR) comprising of HSV and internal control PCR reactions. STUDY DESIGN Using the LightCycler, the HSVgD-dPCR targeted the HSV glycoprotein D gene and HSV typing was performed by melting curve analysis. The internal control PCR reaction targeted sequences of the DNA of the human endogenous retrovirus (ERV-3). In total, 300 swab specimens, from patients with suspected HSV infection, were tested by the HSVgD-dPCR assay. The results were then compared to the results obtained by another HSV LightCycler assay, which utilized published primer and probe sequences targeting the HSV DNA polymerase gene (Dpol-HSV-LCPCR). RESULTS Overall, 91 (30.3%) specimens were positive and 204 (68.0%) specimens were negative for HSV by both LightCycler assays. In addition, four (1.3%) specimens were positive by Dpol-HSV-LCPCR and negative by HSVgD-dPCR, whereas one (0.3%) specimen was positive by HSVgD-dPCR and negative by Dpol-HSV-LCPCR. The presence of HSV in these five specimens was confirmed by conventional PCR. Melting curve analysis by the HSVgD-dPCR assay enabled all HSV positive specimens to be typed, whereas sequence variation prevented three HSV positive specimens from being typed by the Dpol-HSV-LCPCR. Using the ERV-3 PCR, 5% specimens were found to contain inhibitory substances. CONCLUSIONS By developing the HSVgD-dPCR we have enhanced the diagnostic utility of real-time detection of HSV by incorporating an internal control reaction and by accurately typing a greater proportion of HSV positive specimens.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital & Health Service District, Herston Road, Herston, Queensland 4029, Australia
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Faner R, Casamitjana N, Colobran R, Ribera A, Pujol-Borrell R, Palou E, Juan M. HLA-B27 genotyping by Fluorescent Resonance Emission Transfer (FRET) probes in real-time PCR. Hum Immunol 2004; 65:826-38. [PMID: 15336784 DOI: 10.1016/j.humimm.2004.05.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2004] [Revised: 05/10/2004] [Accepted: 05/19/2004] [Indexed: 11/28/2022]
Abstract
Several polymerase chain reaction (PCR)-based human leukocyte antigen (HLA) genotyping methods are in use, but none is fully satisfactory. The introduction of real-time PCR (rt-PCR) with fluorescence resonance energy transfer (FRET) probes provides a powerful tool to overcome the drawbacks of current methods such as the long processing time and the requirement for post-PCR manual procedures. Here we present evidence that the FRET-fluorotyping principle may resolve HLA-B27 variants, providing a higher resolution in less time than the techniques currently in use. The protocol uses between one and three consecutive amplification reactions depending on the resolution required. The first reaction, aimed at detecting HLA-B27-positive samples, uses beta-globin coamplification as control. The second reaction, aimed at resolving most frequent B27 alleles, uses two hybridization probes whose melting temperatures curves allow the classification of HLA-B27 alleles into eight groups. By adding a third reaction, even the rarest alleles associated and not associated to ankylosing spondylitis (AS) may be discriminated. The technique was blindly tested on 60 samples from individuals previously typed and confirmed by standard PCR sequence-specific oligoprobes-PCR sequence and PCR-based typing PCR-SBT (30 B27+, 30 non-B27). There was a complete concordance rate, thus confirming the potential of this new technique for clinical HLA-B27 typing and for HLA typing in general.
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Affiliation(s)
- Rosa Faner
- Laboratory of Immunobiology Research and Applications to Diagnosis (LIRAD), Serveis Sanitaris de Referència-Centre de Transfusió i Banc de Teixits (SSR-CTBT), Badalona, Barcelona, Spain
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Anderson TP, Werno AM, Beynon KA, Murdoch DR. Failure to genotype herpes simplex virus by real-time PCR assay and melting curve analysis due to sequence variation within probe binding sites. J Clin Microbiol 2003; 41:2135-7. [PMID: 12734260 PMCID: PMC154719 DOI: 10.1128/jcm.41.5.2135-2137.2003] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Real-time PCR with melting curve analysis of PCR products is a rapid procedure for detecting and genotyping herpes simplex virus (HSV). When testing mucocutaneous samples for HSV by a real-time PCR assay targeting the DNA polymerase gene, we found that some PCR products had atypical melting curves that did not conform to the expected melting temperatures for HSV type 1 or 2. Sequence analysis showed that these strains had base-pair mismatches over the probe binding sites. An alternative assay is required to type such atypical isolates.
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MESH Headings
- Base Pair Mismatch
- Base Sequence
- Binding Sites/genetics
- DNA Probes/genetics
- DNA-Directed DNA Polymerase/genetics
- Genes, Viral
- Genetic Variation
- Genotype
- Herpesvirus 1, Human/classification
- Herpesvirus 1, Human/enzymology
- Herpesvirus 1, Human/genetics
- Herpesvirus 1, Human/isolation & purification
- Herpesvirus 2, Human/classification
- Herpesvirus 2, Human/enzymology
- Herpesvirus 2, Human/genetics
- Herpesvirus 2, Human/isolation & purification
- Humans
- Molecular Sequence Data
- Nucleic Acid Denaturation
- Polymerase Chain Reaction/methods
- Sequence Homology, Nucleic Acid
- Simplexvirus/classification
- Simplexvirus/enzymology
- Simplexvirus/genetics
- Simplexvirus/isolation & purification
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Affiliation(s)
- Trevor P Anderson
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand.
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