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Deep sequencing approach for investigating infectious agents causing fever. Eur J Clin Microbiol Infect Dis 2016; 35:1137-49. [PMID: 27180244 PMCID: PMC4902837 DOI: 10.1007/s10096-016-2644-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/01/2016] [Indexed: 11/29/2022]
Abstract
Acute undifferentiated fever (AUF) poses a diagnostic challenge due to the variety of possible aetiologies. While the majority of AUFs resolve spontaneously, some cases become prolonged and cause significant morbidity and mortality, necessitating improved diagnostic methods. This study evaluated the utility of deep sequencing in fever investigation. DNA and RNA were isolated from plasma/sera of AUF cases being investigated at Cairns Hospital in northern Australia, including eight control samples from patients with a confirmed diagnosis. Following isolation, DNA and RNA were bulk amplified and RNA was reverse transcribed to cDNA. The resulting DNA and cDNA amplicons were subjected to deep sequencing on an Illumina HiSeq 2000 platform. Bioinformatics analysis was performed using the program Kraken and the CLC assembly-alignment pipeline. The results were compared with the outcomes of clinical tests. We generated between 4 and 20 million reads per sample. The results of Kraken and CLC analyses concurred with diagnoses obtained by other means in 87.5 % (7/8) and 25 % (2/8) of control samples, respectively. Some plausible causes of fever were identified in ten patients who remained undiagnosed following routine hospital investigations, including Escherichia coli bacteraemia and scrub typhus that eluded conventional tests. Achromobacter xylosoxidans, Alteromonas macleodii and Enterobacteria phage were prevalent in all samples. A deep sequencing approach of patient plasma/serum samples led to the identification of aetiological agents putatively implicated in AUFs and enabled the study of microbial diversity in human blood. The application of this approach in hospital practice is currently limited by sequencing input requirements and complicated data analysis.
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202
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García‐Arroyo L, Prim N, Martí N, Roig MC, Navarro F, Rabella N. Benefits and drawbacks of molecular techniques for diagnosis of viral respiratory infections. Experience with two multiplex PCR assays. J Med Virol 2016; 88:45-50. [PMID: 26100363 PMCID: PMC7166422 DOI: 10.1002/jmv.24298] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2015] [Indexed: 11/08/2022]
Abstract
Molecular techniques have represented a major step forward in the diagnosis of viral respiratory infections. They are considered highly sensitive and specific compared to conventional techniques. In this study two nucleic acid amplification tests (NAATs) were compared to conventional methods (immunofluorescence and viral culture). The aim of this work was to discuss the clinical interpretation of the results obtained by NAATs on the basis of the two-decade experience of our group and the literature. Eighty nasopharyngeal aspirates were collected from children under six years attended for acute respiratory illness at the pediatric emergency room of a third level Hospital. Both NAATs tested (Seeplex(®) and Clart(®)) showed an overall higher performance regarding sensitivity (76% and 90%, respectively). Compared to Seeplex(®), the Clart(®) system tripled the number of multiple detections (8 by Seeplex(®) vs. 25 by Clart(®)). In some specimens both NAATs detected different viruses. Given these discrepancies and the fact that detection of viral nucleic acids is not necessarily related to the current clinical syndrome, the interpretation of molecular results may not always be so straightforward. The pros and cons of NAATs should always be taken into account when giving a result.
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Affiliation(s)
| | - Núria Prim
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
| | - Neus Martí
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
| | - Maria Carme Roig
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
| | - Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
- Departament de Genètica i de MicrobiologiaUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - Núria Rabella
- Servei de Microbiologia, Hospital de la Santa Creu i Sant PauBarcelonaSpain
- Departament de Genètica i de MicrobiologiaUniversitat Autònoma de BarcelonaBarcelonaSpain
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203
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Raj A, Singh N, Gupta KB, Chaudhary D, Yadav A, Chaudhary A, Agarwal K, Varma-Basil M, Prasad R, Khuller GK, Mehta PK. Comparative Evaluation of Several Gene Targets for Designing a Multiplex-PCR for an Early Diagnosis of Extrapulmonary Tuberculosis. Yonsei Med J 2016; 57:88-96. [PMID: 26632387 PMCID: PMC4696977 DOI: 10.3349/ymj.2016.57.1.88] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 03/21/2015] [Accepted: 05/02/2015] [Indexed: 11/27/2022] Open
Abstract
PURPOSE Diagnosis of extrapulmonary tuberculosis (EPTB) poses serious challenges. A careful selection of appropriate gene targets is essential for designing a multiplex-polymerase chain reaction (M-PCR) assay. MATERIALS AND METHODS We compared several gene targets of Mycobacterium tuberculosis, including IS6110, devR, and genes encoding MPB-64 (mpb64), 38kDa (pstS1), 65kDa (hsp65), 30kDa (fbpB), ESAT-6 (esat6), and CFP-10 (cfp10) proteins, using PCR assays on 105 EPTB specimens. From these data, we chose the two best gene targets to design an M-PCR. RESULTS Among all gene targets tested, mpb64 showed the highest sensitivity (84% in confirmed cases and 77.5% in clinically suspected cases), followed by IS6110, hsp65, 38kDa, 30kDa, esat6, cfp10, and devR. We used mpb64+IS6110 for designing an M-PCR assay. Our M-PCR assay demonstrated a high sensitivity of 96% in confirmed EPTB cases and 88.75% in clinically suspected EPTB cases with a high specificity of 100%, taking clinical diagnosis as the gold standard. CONCLUSION These M-PCR results along with the clinical findings may facilitate an early diagnosis of EPTB patients and clinical management of disease.
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Affiliation(s)
- Ankush Raj
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Netrapal Singh
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Krishna B Gupta
- Department of TB & Respiratory Medicine, Postgraduate Institute of Medical Sciences (PGIMS), Rohtak, India
| | - Dhruva Chaudhary
- Department of Pulmonary and Critical Care Medicine, Postgraduate Institute of Medical Sciences (PGIMS), Rohtak, India
| | - Aparna Yadav
- Department of Microbiology, Postgraduate Institute of Medical Sciences (PGIMS), Rohtak, India
| | - Anil Chaudhary
- Rajan Babu Institute of Pulmonary Medicine and Tuberculosis (RBIPMT), Delhi, India
| | - Kshitij Agarwal
- Rajan Babu Institute of Pulmonary Medicine and Tuberculosis (RBIPMT), Delhi, India
| | | | - Rajendra Prasad
- Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Gopal K Khuller
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Promod K Mehta
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India.
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204
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Park KT, Cho DG, Park JW, Hong S, Hwang J. Detection of airborne viruses using electro-aerodynamic deposition and a field-effect transistor. Sci Rep 2015; 5:17462. [PMID: 26642822 PMCID: PMC4672335 DOI: 10.1038/srep17462] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/23/2015] [Indexed: 11/09/2022] Open
Abstract
We report a technique for the detection of aerosolized viruses. Conventional field-effect-transistor (FET)-based techniques use solution-based processes, thus require antibody binding to the detection region of the FET prior to the supply of the analyte. With the method described here, virus-antibody-bound particles are delivered to the FET during detection; therefore, neither a pre-treatment antibody binding step on the FET channel nor washing process for virus-antibody-binding are necessary. Our method is based on the concept that virus-antibody-bound particles are larger than the virus or antibody alone, and thus have larger charge numbers following aerosol charging. When these particles are charged by negative ions and electro-aerodynamically deposited on a substrate, there exists a location on the substrate where neither lone virus nor antibody particles land, and where only virus-antibody-bound particles are deposited. If this location coincides with the channel of the FET, the resulting variation in the current can be used to indicate the existence of a virus. By aerosolizing a mixed solution of the virus and the antibody, only the virus-antibody-bound particles were transported to the swCNT-FET, and the electric current in the swCNT-FET decreased to 30% of that measured with no deposited particles.
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Affiliation(s)
- Kyu-Tae Park
- School of Mechanical Engineering, Yonsei University, Seoul 120-749, Korea
| | - Dong-Guk Cho
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul 151-747, Korea
| | - Ji-Woon Park
- School of Mechanical Engineering, Yonsei University, Seoul 120-749, Korea
| | - Seunghun Hong
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul 151-747, Korea
| | - Jungho Hwang
- School of Mechanical Engineering, Yonsei University, Seoul 120-749, Korea
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205
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Kim JE, Seo Y, Jeong Y, Hwang MP, Hwang J, Choo J, Hong JW, Jeon JH, Rhie GE, Choi J. A novel nanoprobe for the sensitive detection of Francisella tularensis. JOURNAL OF HAZARDOUS MATERIALS 2015; 298:188-194. [PMID: 26057442 DOI: 10.1016/j.jhazmat.2015.05.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 04/23/2015] [Accepted: 05/23/2015] [Indexed: 06/04/2023]
Abstract
Francisella tularensis is a human zoonotic pathogen and the causative agent of tularemia, a severe infectious disease. Given the extreme infectivity of F. tularensis and its potential to be used as a biological warfare agent, a fast and sensitive detection method is highly desirable. Herein, we construct a novel detection platform composed of two units: (1) Magnetic beads conjugated with multiple capturing antibodies against F. tularensis for its simple and rapid separation and (2) Genetically-engineered apoferritin protein constructs conjugated with multiple quantum dots and a detection antibody against F. tularensis for the amplification of signal. We demonstrate a 10-fold increase in the sensitivity relative to traditional lateral flow devices that utilize enzyme-based detection methods. We ultimately envision the use of our novel nanoprobe detection platform in future applications that require the highly-sensitive on-site detection of high-risk pathogens.
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Affiliation(s)
- Ji-eun Kim
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, South Korea
| | - Youngmin Seo
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, South Korea
| | - Yoon Jeong
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, South Korea
| | - Mintai P Hwang
- Center for Biomaterials, Korea Institute of Science and Technology, Seoul 136-791, South Korea
| | - Jangsun Hwang
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, South Korea
| | - Jaebum Choo
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, South Korea; Department of Bionano Engineering, Hanyang University ERICA, Ansan 426-791, South Korea
| | - Jong Wook Hong
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, South Korea; Department of Bionano Engineering, Hanyang University ERICA, Ansan 426-791, South Korea
| | - Jun Ho Jeon
- Division of High-risk Pathogen Research, Center for Infectious Disease, Korea National Institute of Health, Cheongju 363-951, South Korea
| | - Gi-eun Rhie
- Division of High-risk Pathogen Research, Center for Infectious Disease, Korea National Institute of Health, Cheongju 363-951, South Korea
| | - Jonghoon Choi
- Department of Bionano Technology, Graduate School, Hanyang University, Seoul 133-791, South Korea; Department of Bionano Engineering, Hanyang University ERICA, Ansan 426-791, South Korea.
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206
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Lee JH, Seo HJ, Park JY, Kim SH, Cho YS, Kim YJ, Cho IS, Jeoung HY. Detection and differentiation of Schmallenberg, Akabane and Aino viruses by one-step multiplex reverse-transcriptase quantitative PCR assay. BMC Vet Res 2015; 11:270. [PMID: 26497392 PMCID: PMC4619357 DOI: 10.1186/s12917-015-0582-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 10/14/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Schmallenberg virus (SBV), Akabane virus (AKAV) and Aino virus (AINV) are members of the Simbu serogroup within the genus Orthobunyavirus, family Bunyaviridae, which can cause reproductive disorders including abortion, stillbirth and congenital malformation in ruminants. Because, the clinical signs are similar, confirmatory diagnosis requires viral detection to differentiate infection between these three viruses. METHODS In this study, a one-step multiplex reverse-transcriptase quantitative PCR (one-step mRT-qPCR) was developed for the simultaneous detection and differentiation of SBV, AKAV and AINV. RESULTS The detection limit of the one-step mRT-qPCR for SBV, AKAV and AINV were 2.4 copies (10 (0.6) TCID 50/ml), 96.2 copies (10 (1.5) TCID 50/ml) and 52.3 copies (10 (1.2) TCID 50/ml), respectively. Various field samples such as bovine serum, bovine whole blood, bovine brain, goat serum and Culicoides were analyzed using the one-step mRT-qPCR and compared with previously published RT-qPCRs. The test results of the field samples were identical for the one-step mRT-qPCR and RT-qPCRs, which showed all samples to be negative for SBV, AKAV and AINV, except for one bovine brain sample (1/123) that was positive for AKAV. CONCLUSION The one-step mRT-qPCR allows for the simultaneous detection of three viral pathogens (SBV, AKAV and AINV) that cause reproductive failure.
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Affiliation(s)
- Ji-Hye Lee
- Animal and Plant Quarantine Agency, Anyang, Gyeonggi-do, 430-824, Republic of Korea.
| | - Hyun-Ji Seo
- Animal and Plant Quarantine Agency, Anyang, Gyeonggi-do, 430-824, Republic of Korea.
| | - Jee-Yong Park
- Animal and Plant Quarantine Agency, Anyang, Gyeonggi-do, 430-824, Republic of Korea.
| | - Sung-Hee Kim
- Animal and Plant Quarantine Agency, Anyang, Gyeonggi-do, 430-824, Republic of Korea.
| | - Yun Sang Cho
- Animal and Plant Quarantine Agency, Anyang, Gyeonggi-do, 430-824, Republic of Korea.
| | - Yong-Joo Kim
- Animal and Plant Quarantine Agency, Anyang, Gyeonggi-do, 430-824, Republic of Korea.
| | - In-Soo Cho
- Animal and Plant Quarantine Agency, Anyang, Gyeonggi-do, 430-824, Republic of Korea.
| | - Hye-Young Jeoung
- Animal and Plant Quarantine Agency, Anyang, Gyeonggi-do, 430-824, Republic of Korea.
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207
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Aubry F, Nougairède A, de Fabritus L, Piorkowski G, Gould EA, de Lamballerie X. "ISA-Lation" of Single-Stranded Positive-Sense RNA Viruses from Non-Infectious Clinical/Animal Samples. PLoS One 2015; 10:e0138703. [PMID: 26407018 PMCID: PMC4583506 DOI: 10.1371/journal.pone.0138703] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/02/2015] [Indexed: 01/25/2023] Open
Abstract
Isolation of viral pathogens from clinical and/or animal samples has traditionally relied on either cell cultures or laboratory animal model systems. However, virus viability is notoriously susceptible to adverse conditions that may include inappropriate procedures for sample collection, storage temperature, support media and transportation. Using our recently described ISA method, we have developed a novel procedure to isolate infectious single-stranded positive-sense RNA viruses from clinical or animal samples. This approach, that we have now called "ISA-lation", exploits the capacity of viral cDNA subgenomic fragments to re-assemble and produce infectious viral RNA in susceptible cells. Here, it was successfully used to rescue enterovirus, Chikungunya and Tick-borne encephalitis viruses from a variety of inactivated animal and human samples. ISA-lation represents an effective option to rescue infectious virus from clinical and/or animal samples that may have deteriorated during the collection and storage period, but also potentially overcomes logistic and administrative difficulties generated when complying with current health and safety and biosecurity guidelines associated with shipment of infectious viral material.
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Affiliation(s)
- Fabien Aubry
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13385, Marseille, France
- * E-mail:
| | - Antoine Nougairède
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13385, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Lauriane de Fabritus
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13385, Marseille, France
| | - Géraldine Piorkowski
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13385, Marseille, France
| | - Ernest A. Gould
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13385, Marseille, France
| | - Xavier de Lamballerie
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13385, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
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208
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Choi KY, Lee TK, Sul WJ. Metagenomic Analysis of Chicken Gut Microbiota for Improving Metabolism and Health of Chickens - A Review. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1217-25. [PMID: 26323514 PMCID: PMC4554860 DOI: 10.5713/ajas.15.0026] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 02/23/2015] [Accepted: 03/31/2015] [Indexed: 02/01/2023]
Abstract
Chicken is a major food source for humans, hence it is important to understand the mechanisms involved in nutrient absorption in chicken. In the gastrointestinal tract (GIT), the microbiota plays a central role in enhancing nutrient absorption and strengthening the immune system, thereby affecting both growth and health of chicken. There is little information on the diversity and functions of chicken GIT microbiota, its impact on the host, and the interactions between the microbiota and host. Here, we review the recent metagenomic strategies to analyze the chicken GIT microbiota composition and its functions related to improving metabolism and health. We summarize methodology of metagenomics in order to obtain bacterial taxonomy and functional inferences of the GIT microbiota and suggest a set of indicator genes for monitoring and manipulating the microbiota to promote host health in future.
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Affiliation(s)
- Ki Young Choi
- Department of Environmental Engineering, Yonsei University, Wonju 220-710, Korea
| | - Tae Kwon Lee
- Department of Environmental Engineering, Yonsei University, Wonju 220-710, Korea
| | - Woo Jun Sul
- Department of Environmental Engineering, Yonsei University, Wonju 220-710, Korea
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209
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Glushakova LG, Sharma N, Hoshika S, Bradley AC, Bradley KM, Yang Z, Benner SA. Detecting respiratory viral RNA using expanded genetic alphabets and self-avoiding DNA. Anal Biochem 2015; 489:62-72. [PMID: 26299645 PMCID: PMC4733849 DOI: 10.1016/j.ab.2015.08.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 08/07/2015] [Accepted: 08/13/2015] [Indexed: 11/23/2022]
Abstract
Nucleic acid (NA)-targeted tests detect and quantify viral DNA and RNA (collectively xNA) to support epidemiological surveillance and, in individual patients, to guide therapy. They commonly use polymerase chain reaction (PCR) and reverse transcription PCR. Although these all have rapid turnaround, they are expensive to run. Multiplexing would allow their cost to be spread over multiple targets, but often only with lower sensitivity and accuracy, noise, false positives, and false negatives; these arise by interactions between the multiple nucleic acid primers and probes in a multiplexed kit. Here we offer a multiplexed assay for a panel of respiratory viruses that mitigates these problems by combining several nucleic acid analogs from the emerging field of synthetic biology: (i) self-avoiding molecular recognition systems (SAMRSs), which facilitate multiplexing, and (ii) artificially expanded genetic information systems (AEGISs), which enable low-noise PCR. These are supplemented by “transliteration” technology, which converts standard nucleotides in a target to AEGIS nucleotides in a product, improving hybridization. The combination supports a multiplexed Luminex-based respiratory panel that potentially differentiates influenza viruses A and B, respiratory syncytial virus, severe acute respiratory syndrome coronavirus (SARS), and Middle East respiratory syndrome (MERS) coronavirus, detecting as few as 10 MERS virions in a 20-μl sample.
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Affiliation(s)
| | - Nidhi Sharma
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Andrea C Bradley
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Steven A Benner
- Firebird Biomolecular Sciences, Alachua, FL 32615, USA; Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA.
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210
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Liu ZM, Xu YG, Luo J, Qu M, Mo CS, Li SL. Target-Enriched Multiplex PCR (Tem-PCR) Assay for Simultaneous Detection of S
almonella
spp., L
isteria Monocytogenes
and E
scherichia Coli
O157:H7 in Food. J Food Saf 2015. [DOI: 10.1111/jfs.12225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Zhong-Mei Liu
- Technology Center; Heilongjiang Entry-Exit Inspection and Quarantine Bureau; Harbin 150001 China
| | - Yi-Gang Xu
- Technology Center; Heilongjiang Entry-Exit Inspection and Quarantine Bureau; Harbin 150001 China
- College of Veterinary Medicine; Northeast Agricultural University; Harbin 150030 China
| | - Jia Luo
- Technology Center; Liaoning Entry-Exit Inspection and Quarantine Bureau; Dalian China
| | - Min Qu
- College of Food Engineering; Harbin University of Commerce; Harbin China
| | - Chun-Sheng Mo
- College of Food Engineering; Harbin University of Commerce; Harbin China
| | - Su-Long Li
- Technology Center; Heilongjiang Entry-Exit Inspection and Quarantine Bureau; Harbin 150001 China
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211
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Jang JP, Baek IC, Choi EJ, Kim TG. Multiplex genotyping of cytokine gene SNPs using fluorescence bead array. PLoS One 2015; 10:e0118008. [PMID: 25689696 PMCID: PMC4331502 DOI: 10.1371/journal.pone.0118008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/05/2015] [Indexed: 01/02/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) of genes that affect cytokine production and function are known to influence the susceptibility and progression of immune-related conditions such as infection, autoimmune diseases, transplantation, and cancer. We established a multiplex genotyping method to analyze the SNPs of cytokine genes by combining the multiplex PCR and bead array platform. Thirteen cytokine gene regions, including 20 SNPs, were amplified, and allele-specific primer extension was performed in a single tube. High-quality allele-specific primers were selected for signals greater than 1000 median fluorescence intensity (MFI) for positive alleles, and less than 500 MFI for negative alleles. To select and improve the extension primers, modifications for the reverse direction, length or refractory were performed. 24 primers in the forward or reverse direction step and 12 primers in length or refractory modifications were selected and showed high concordance with results by nucleotide sequencing. Among the 13 candidate cytokine genes, the SNPs of 12 cytokine genes, including IL-1α, IL-1R, IL-1RA, IL-1β, IL-2, IL-4, IL-4Rα, IL-6, IL-10, IL-12, TGF-β1, and TNF-α, were successfully defined with the selected allele-specific primers in healthy Korean subjects. Our genotyping system provides a fast and accurate detection for SNPs of multiple cytokine genes to investigate their association with immune-related diseases and transplantation outcomes.
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Affiliation(s)
- Jung-Pil Jang
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - In-Cheol Baek
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eun-Jeong Choi
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Tai-Gyu Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Korea
- * E-mail:
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212
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High-throughput multiplexed xMAP Luminex array panel for detection of twenty two medically important mosquito-borne arboviruses based on innovations in synthetic biology. J Virol Methods 2015; 214:60-74. [PMID: 25680538 DOI: 10.1016/j.jviromet.2015.01.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 01/25/2015] [Accepted: 01/26/2015] [Indexed: 11/23/2022]
Abstract
Mosquito-borne arboviruses are emerging world-wide as important human and animal pathogens. This makes assays for their accurate and rapid identification essential for public health, epidemiological, ecological studies. Over the past decade, many mono- and multiplexed assays targeting arboviruses nucleic acids have been reported. None has become established for the routine identification of multiple viruses in a "single tube" setting. With increasing multiplexing, the detection of viral RNAs is complicated by noise, false positives and negatives. In this study, an assay was developed that avoids these problems by combining two new kinds of nucleic acids emerging from the field of synthetic biology. The first is a "self-avoiding molecular recognition system" (SAMRS), which enables high levels of multiplexing. The second is an "artificially expanded genetic information system" (AEGIS), which enables clean PCR amplification in nested PCR formats. A conversion technology was used to place AEGIS component into amplicon, improving their efficiency of hybridization on Luminex beads. When Luminex "liquid microarrays" are exploited for downstream detection, this combination supports single-tube PCR amplification assays that can identify 22 mosquito-borne RNA viruses from the genera Flavivirus, Alphavirus, Orthobunyavirus. The assay differentiates between closely-related viruses, as dengue, West Nile, Japanese encephalitis, and the California serological group. The performance and the sensitivity of the assay were evaluated with dengue viruses and infected mosquitoes; as few as 6-10 dengue virions can be detected in a single mosquito.
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213
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An Y, Toyoda A, Zhao C, Fujiyama A, Agata K. A colony multiplex quantitative PCR-Based 3S3DBC method and variations of it for screening DNA libraries. PLoS One 2015; 10:e0116997. [PMID: 25646755 PMCID: PMC4315571 DOI: 10.1371/journal.pone.0116997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 12/18/2014] [Indexed: 11/18/2022] Open
Abstract
A DNA library is a collection of DNA fragments cloned into vectors and stored individually in host cells, and is a valuable resource for molecular cloning, gene physical mapping, and genome sequencing projects. To take the best advantage of a DNA library, a good screening method is needed. After describing pooling strategies and issues that should be considered in DNA library screening, here we report an efficient colony multiplex quantitative PCR-based 3-step, 3-dimension, and binary-code (3S3DBC) method we used to screen genes from a planarian genomic DNA fosmid library. This method requires only 3 rounds of PCR reactions and only around 6 hours to distinguish one or more desired clones from a large DNA library. According to the particular situations in different research labs, this method can be further modified and simplified to suit their requirements.
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Affiliation(s)
- Yang An
- Department of Biophysics, Kyoto University, Kyoto, Kyoto, Japan
- * E-mail: (KA); (YA)
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Chen Zhao
- School of Pharmacy, Fudan University, Shanghai, China
| | - Asao Fujiyama
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kiyokazu Agata
- Department of Biophysics, Kyoto University, Kyoto, Kyoto, Japan
- * E-mail: (KA); (YA)
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214
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Mirmajlessi SM, Destefanis M, Gottsberger RA, Mänd M, Loit E. PCR-based specific techniques used for detecting the most important pathogens on strawberry: a systematic review. Syst Rev 2015; 4:9. [PMID: 25588564 PMCID: PMC4320524 DOI: 10.1186/2046-4053-4-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 01/02/2015] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Strawberry diseases are a major limiting factor that severely impact plant agronomic performance. Regarding limitations of traditional techniques for detection of pathogens, researchers have developed specific DNA-based tests as sensitive and specific techniques. The aim of this review is to provide an overview of polymerase chain reaction (PCR)-based methods used for detection or quantification of the most widespread strawberry pathogens, such as Fusarium oxysporum f.sp. fragariae, Phytophthora fragariae, Colletotrichum acutatum, Verticillium dahliae, Botrytis cinerea, Macrophomina phaseolina, and Xanthomonas fragariae. An updated and detailed list of published PCR protocols is presented and discussed, aimed at facilitating access to information that could be particularly useful for diagnostic laboratories in order to develop a rapid, cost-effective, and reliable monitoring technique. METHODS The study design was a systematic review of PCR-based techniques used for detection and quantification of strawberry pathogens. Using appropriate subject headings, AGRICOLA, AGRIS, BASE, Biological Abstracts, CAB Abstracts, Google Scholar, Scopus, Web of Knowledge, and SpringerLink databases were searched from their inception up to April 2014. Two assessors independently reviewed the titles, abstracts, and full articles of all identified citations. Selected articles were included if one of the mentioned strawberry pathogens was investigated based on PCR methods, and a summary of pre-analytical requirements for PCR was provided. RESULTS A total of 259 titles and abstracts were reviewed, of which 22 full texts met all the inclusion criteria. Our systematic review identified ten different protocols for X. fragariae, eight for P. fragariae, four for B. cinerea, six for C. acutatum, three for V. dahlia, and only one for F. oxysporum. The accuracy and sensitivity of PCR diagnostic methods is the focus of most studies included in this review. However, a large proportion of errors in laboratories occur in the pre-analytical phase of the testing process. Due to heterogeneity, results could not be meta-analyzed. CONCLUSIONS From a systematic review of the currently available published literature, effective detection assays to detect the major strawberry pathogens have been developed. These assays can function as a basis for clinical labs, regulatory personnel, and other diagnosticians to adapt or implement for detection of these six important strawberry pathogens.
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Affiliation(s)
- Seyed Mahyar Mirmajlessi
- />Department of Field Crops and Grassland Husbandry, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Marialaura Destefanis
- />Pesticides, Plant Health and Seed Testing Laboratories, Department of Agriculture, Food and the Marine, Backweston Campus, Celbridge, Co. Kildare Ireland
| | - Richard Alexander Gottsberger
- />Department for Molecular Diagnostics of Plant Diseases, Institute for Sustainable Plant Production, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Marika Mänd
- />Department of Plant Protection, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Evelin Loit
- />Department of Field Crops and Grassland Husbandry, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
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215
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Behzadi P, Ranjbar R, Alavian SM. Nucleic Acid-based approaches for detection of viral hepatitis. Jundishapur J Microbiol 2014; 8:e17449. [PMID: 25789132 PMCID: PMC4350052 DOI: 10.5812/jjm.17449] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/14/2014] [Accepted: 06/14/2014] [Indexed: 12/12/2022] Open
Abstract
CONTEXT To determining suitable nucleic acid diagnostics for individual viral hepatitis agent, an extensive search using related keywords was done in major medical library and data were collected, categorized, and summarized in different sections. RESULTS Various types of molecular biology tools can be used to detect and quantify viral genomic elements and analyze the sequences. These molecular assays are proper technologies for rapidly detecting viral agents with high accuracy, high sensitivity, and high specificity. Nonetheless, the application of each diagnostic method is completely dependent on viral agent. CONCLUSIONS Despite rapidity, automation, accuracy, cost-effectiveness, high sensitivity, and high specificity of molecular techniques, each type of molecular technology has its own advantages and disadvantages.
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Affiliation(s)
- Payam Behzadi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
- Corresponding author: Reza Ranjbar, Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran. Tel: +98-21-88039883, E-mail:
| | - Seyed Moayed Alavian
- Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
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216
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Al Ahmad M, Mustafa F, Ali LM, Rizvi TA. Virus detection and quantification using electrical parameters. Sci Rep 2014; 4:6831. [PMID: 25355078 PMCID: PMC4213776 DOI: 10.1038/srep06831] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 10/06/2014] [Indexed: 01/31/2023] Open
Abstract
Here we identify and quantitate two similar viruses, human and feline immunodeficiency viruses (HIV and FIV), suspended in a liquid medium without labeling, using a semiconductor technique. The virus count was estimated by calculating the impurities inside a defined volume by observing the change in electrical parameters. Empirically, the virus count was similar to the absolute value of the ratio of the change of the virus suspension dopant concentration relative to the mock dopant over the change in virus suspension Debye volume relative to mock Debye volume. The virus type was identified by constructing a concentration-mobility relationship which is unique for each kind of virus, allowing for a fast (within minutes) and label-free virus quantification and identification. For validation, the HIV and FIV virus preparations were further quantified by a biochemical technique and the results obtained by both approaches corroborated well. We further demonstrate that the electrical technique could be applied to accurately measure and characterize silica nanoparticles that resemble the virus particles in size. Based on these results, we anticipate our present approach to be a starting point towards establishing the foundation for label-free electrical-based identification and quantification of an unlimited number of viruses and other nano-sized particles.
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Affiliation(s)
- Mahmoud Al Ahmad
- Department of Electrical Engineering, College of Engineering, United Arab Emirates University, Al Ain, UAE
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, UAE
| | - Lizna M Ali
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, UAE
| | - Tahir A Rizvi
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, UAE
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217
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Tian Y, Zhao Y, Xu R, Liu F, Hu B, Walcott RR. Simultaneous Detection of Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola in Rice Seed Using a Padlock Probe-Based Assay. PHYTOPATHOLOGY 2014; 104:1130-7. [PMID: 25207482 DOI: 10.1094/phyto-10-13-0274-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Based on 16S-23S internal transcribed spacer ribosomal DNA sequence data, two padlock probes (PLPs), P-Xoo and P-Xoc, were designed and tested to detect Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola, respectively. These PLPs were combined with dot-blot hybridization to detect X. oryzae pv. oryzae and X. oryzae pv. oryzicola individually in rice seed. Using this technique, a detection sensitivity of 1 pg of X. oryzae pv. oryzae genomic DNA was observed. The technique also facilitated the detection of X. oryzae pv. oryzae in rice seedlots with 2% artificially infested seed. With regards to X. oryzae pv. oryzicola a detection threshold of 1 pg genomic DNA was observed and the pathogen was successful detected in rice seedlots with 0.2% artificially infested seed. The PLP assays detected X. oryzae pv. oryzae and X. oryzae pv. oryzicola in 39.3% (13 of 33) and 21.3% (10 of 47) of naturally infested commercial rice seedlots, respectively. In contrast, conventional polymerase chain reaction using OSF1/OSR1 and XoocF/XoocR primers sets detected X. oryzae pv. oryzae and X. oryzae pv. oryzicola in 9.1% (3 of 33) and 8.5% (4 of 47) of the same rice seedlots, respectively. We also detected both pathogens simultaneously in two seedlots, which successfully proved that PLPs (P-Xoo and P-Xoc) combined with reverse dotblot hybridization can be used to simultaneously detect multiple pathogens in naturally infested commercial rice seedlots. This approach has the potential to be an important tool for detecting multiple pathogens in seed and thereby preventing the spread of important pathogens.
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218
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Sahore V, Fritsch I. Redox-magnetohydrodynamics, flat flow profile-guided enzyme assay detection: toward multiple, parallel analyses. Anal Chem 2014; 86:9405-11. [PMID: 25171501 DOI: 10.1021/ac502014t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A proof-of-concept superparamagnetic microbead-enzyme complex was integrated with microfluidics pumped by redox-magneto-hydrodynamics (MHD) to take advantage of the magnet (0.56 T) beneath the chip and the uniform flat flow profile, as a first step toward developing multiple, parallel chemical analyses on a chip without the need for independent channels. The superparamagnetic beads were derivatized with alkaline phosphatase (a common enzyme label for biochemical assays) and magnetically immobilized at three different locations on the chip with one directly on the path to the detector and the other two locations adjacent to, but off the path, by a distance >5 times the detector diameter. Electroactive p-aminophenol, enzymatically generated at the bead-enzyme complex from its electroinactive precursor p-aminophenyl phosphate in a solution containing a redox species [Ru(NH3)6](3+/2+) for pumping and Tris buffer, was transported by redox-MHD and detected with square wave voltammetry at a 312 μm diameter gold microdisk stationed 2 mm downstream from the bead-complex on the flow path. Oppositely biased pumping electrodes, consisting of 2.5 cm long gold bands and separated by 5.6 mm, flanked the active flow region containing the bead-enzyme complex and detection site. The signal from adjacent paths was only 20% of that for the direct path and ≤8% when pumping electrodes were inactive.
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Affiliation(s)
- Vishal Sahore
- Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States
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219
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Wang Y, Wang Z, Zhang Y, Bai L, Zhao Y, Liu C, Ma A, Yu H. Polymerase chain reaction-based assays for the diagnosis of human brucellosis. Ann Clin Microbiol Antimicrob 2014; 13:31. [PMID: 25082566 PMCID: PMC4236518 DOI: 10.1186/s12941-014-0031-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 07/09/2014] [Indexed: 12/14/2022] Open
Abstract
Polymerase chain reaction (PCR) is an in vitro technique for the nucleic acid amplification, which is commonly used to diagnose infectious diseases. The use of PCR for pathogens detection, genotyping and quantification has some advantages, such as high sensitivity, high specificity, reproducibility and technical ease. Brucellosis is a common zoonosis caused by Brucella spp., which still remains as a major health problem in many developing countries around the world. The direct culture and immunohistochemistry can be used for detecting infection with Brucella spp. However, PCR has the potential to address limitations of these methods. PCR are now one of the most useful assays for the diagnosis in human brucellosis. The aim of this review was to summarize the main PCR techniques and their applications for diagnosis and follow-up of patients with brucellosis. Moreover, advantages or limitation of the different PCR methods as well as the evaluation of PCR results for treatment and follow-up of human brucellosis were also discussed.
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220
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Han JI, Kang SY, Yoon KJ, Na KJ. Nucleic acid-based differential diagnostic assays for feline coronavirus. J Virol Methods 2014; 208:21-5. [PMID: 25088974 PMCID: PMC7113662 DOI: 10.1016/j.jviromet.2014.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 07/08/2014] [Accepted: 07/11/2014] [Indexed: 11/19/2022]
Abstract
A multiplex RT-PCR assay was developed to detect feline coronavirus. To improve primer binding, inosine was used for primer design. The assay could detect and differentiate FCoV, CCoV, and TGEV precisely.
Feline coronavirus (FCoV) is a pleomorphic, enveloped, positive-sense single-stranded RNA virus. Owing to the differences in its genotype, FCoV belongs to a separate clade along with other viruses, such as transmissible gastroenteritis virus (TGEV) and canine coronavirus (CCoV), which can be isolated from cats. In this study, a PCR assay was developed to differentiate these coronaviruses concurrently. Multiplex differential RT-PCR was performed with primers based on the highly conserved coronavirus membrane protein. Three primer sets were designed: a primer pair (S1 and S2) that can bind to conserved sequences in all target coronaviruses, a CCoV-specific primer (S3), and a TGEV-specific primer (S4). Because of the high sequence homology among FCoV, CCoV, and TGEV, a nucleotide preceding the last pair of dissimilar nucleotides in S3 and S4 was substituted with an inosine to allow primer binding. This assay could detect and differentiate FCoV (n = 7), CCoV (n = 4), and TGEV (n = 8) precisely and did not show any cross-reactivity with other pathogens. These results suggest that this molecular approach provides a rapid and reliable way to detect FCoV, especially in feline clinical specimens.
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Affiliation(s)
- Jae-Ik Han
- College of Veterinary Medicine, Chungbuk National University, Cheongju 361-763, South Korea; Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Shien-Young Kang
- College of Veterinary Medicine, Chungbuk National University, Cheongju 361-763, South Korea
| | - Kyoung-Jin Yoon
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Ki-Jeong Na
- College of Veterinary Medicine, Chungbuk National University, Cheongju 361-763, South Korea.
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221
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Lim S, Nan H, Lee MJ, Kang SH. Fast on-site diagnosis of influenza A virus by Palm PCR and portable capillary electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 963:134-9. [PMID: 24956080 DOI: 10.1016/j.jchromb.2014.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 05/17/2014] [Accepted: 06/02/2014] [Indexed: 11/19/2022]
Abstract
A method combining Palm polymerase chain reaction (PCR) and portable capillary electrophoresis (CE) was developed for rapid on-site analysis of influenza A (H1N1) virus. The portable CE system was suitable for rapid diagnosis which was able to detect a sample in ∼4 min after sample loading, while the 'Palm PCR' system allowed for high-speed nucleic acid amplification in ∼16 min. The analysis time from DNA sample to analysis of amplified target DNA molecule was only ∼20 min, which was significantly less than slab gel electrophoresis with other commercially available PCR machine. When the 100-bp DNA ladder was separated, the relative standard deviation values (n=5) for the migration times and peak areas of the 100 and 200-bp DNA molecules were 0.26 and 8.9%. The detection limits were 6.3 and 7.2 pg/μL, respectively. The combined method was also able to identify two influenza A-associated genes (the HA and NP genes of the novel H1N1 influenza). CE separation was achieved with a sieving matrix of 1% poly(vinylpyrrolidone) (Mr=1,300,000) in 1× TBE buffer (pH 8.45). The combined Palm PCR-portable CE system should provide an improved, fast on-site molecular genetic diagnostic method.
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Affiliation(s)
- Seoyeon Lim
- Department of Applied Chemistry, College of Applied Science, Kyung Hee University, Yongin-si, Gyunggi-do 446-701, Republic of Korea
| | - He Nan
- Department of Applied Chemistry, College of Applied Science, Kyung Hee University, Yongin-si, Gyunggi-do 446-701, Republic of Korea
| | - Min-Jun Lee
- Ahram Biosystems Inc., Seoul 133-120, Republic of Korea
| | - Seong Ho Kang
- Department of Applied Chemistry, College of Applied Science, Kyung Hee University, Yongin-si, Gyunggi-do 446-701, Republic of Korea.
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222
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Lee H, Park JE, Nam JM. Bio-barcode gel assay for microRNA. Nat Commun 2014; 5:3367. [PMID: 24569571 DOI: 10.1038/ncomms4367] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 02/03/2014] [Indexed: 12/17/2022] Open
Abstract
MicroRNA has been identified as a potential biomarker because expression level of microRNA is correlated with various cancers. Its detection at low concentrations would be highly beneficial for cancer diagnosis. Here, we develop a new type of a DNA-modified gold nanoparticle-based bio-barcode assay that uses a conventional gel electrophoresis platform and potassium cyanide chemistry and show this assay can detect microRNA at aM levels without enzymatic amplification. It is also shown that single-base-mismatched microRNA can be differentiated from perfectly matched microRNA and the multiplexed detection of various combinations of microRNA sequences is possible with this approach. Finally, differently expressed microRNA levels are selectively detected from cancer cells using the bio-barcode gel assay, and the results are compared with conventional polymerase chain reaction-based results. The method and results shown herein pave the way for practical use of a conventional gel electrophoresis for detecting biomolecules of interest even at aM level without polymerase chain reaction amplification.
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Affiliation(s)
- Hyojin Lee
- 1] Department of Chemistry, Seoul National University, Seoul 151-747, South Korea [2]
| | - Jeong-Eun Park
- 1] Department of Chemistry, Seoul National University, Seoul 151-747, South Korea [2]
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, Seoul 151-747, South Korea
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223
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Comparison of a transplant multiplex viral panel on the ICEPlex system with real-time PCR for detection of cytomegalovirus, Epstein-Barr virus, and BK virus in clinical specimens. J Clin Microbiol 2014; 52:1711-3. [PMID: 24554746 DOI: 10.1128/jcm.00358-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
We compared a multiplex viral transplant panel on the ICEPlex system to real-time PCR for the detection of cytomegalovirus (CMV), Epstein-Barr virus (EBV), and BK virus (BKV). The sensitivities of the ICEPlex were 83.3%, 95.5%, and 65.5% for the detection of CMV, EBV, and BKV, respectively. Interestingly, the multiplex assay detected dual infections in 16/280 (5.7%) samples tested.
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224
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Poritz MA, Ririe KM. Getting things backwards to prevent primer dimers. J Mol Diagn 2014; 16:159-62. [PMID: 24457120 DOI: 10.1016/j.jmoldx.2014.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 12/30/2013] [Accepted: 01/09/2014] [Indexed: 02/04/2023] Open
Abstract
This Commentary highlights the article by Satterfield that describes a new class of primer technology-cooperative primers, which prevent primer-dimer amplification.
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225
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Takei F, Nakatani K. The Chemistry of Polymerase Chain Reaction^|^mdash;Development of the PCR Method Using New Modified Primers^|^mdash;. J SYN ORG CHEM JPN 2014. [DOI: 10.5059/yukigoseikyokaishi.72.370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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226
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Grigorenko E, Fisher C, Patel S, Chancey C, Rios M, Nakhasi HL, Duncan RC. Multiplex Screening for Blood-Borne Viral, Bacterial, and Protozoan Parasites using an OpenArray Platform. J Mol Diagn 2014; 16:136-44. [DOI: 10.1016/j.jmoldx.2013.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 08/13/2013] [Accepted: 08/22/2013] [Indexed: 02/02/2023] Open
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227
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Liu T, Sin MLY, Pyne JD, Gau V, Liao JC, Wong PK. Electrokinetic stringency control in self-assembled monolayer-based biosensors for multiplex urinary tract infection diagnosis. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2014; 10:159-66. [PMID: 23891989 PMCID: PMC3858494 DOI: 10.1016/j.nano.2013.07.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 06/24/2013] [Accepted: 07/05/2013] [Indexed: 11/30/2022]
Abstract
Rapid detection of bacterial pathogens is critical toward judicious management of infectious diseases. Herein, we demonstrate an in situ electrokinetic stringency control approach for a self-assembled monolayer-based electrochemical biosensor toward urinary tract infection diagnosis. The in situ electrokinetic stringency control technique generates Joule heating induced temperature rise and electrothermal fluid motion directly on the sensor to improve its performance for detecting bacterial 16S rRNA, a phylogenetic biomarker. The dependence of the hybridization efficiency reveals that in situ electrokinetic stringency control is capable of discriminating single-base mismatches. With electrokinetic stringency control, the background noise due to the matrix effects of clinical urine samples can be reduced by 60%. The applicability of the system is demonstrated by multiplex detection of three uropathogenic clinical isolates with similar 16S rRNA sequences. The results demonstrate that electrokinetic stringency control can significantly improve the signal-to-noise ratio of the biosensor for multiplex urinary tract infection diagnosis. FROM THE CLINICAL EDITOR Urinary tract infections remain a significant cause of mortality and morbidity as secondary conditions often related to chronic diseases or to immunosuppression. Rapid and sensitive identification of the causative organisms is critical in the appropriate management of this condition. These investigators demonstrate an in situ electrokinetic stringency control approach for a self-assembled monolayer-based electrochemical biosensor toward urinary tract infection diagnosis, establishing that such an approach significantly improves the biosensor's signal-to-noise ratio.
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Affiliation(s)
- Tingting Liu
- Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ, USA
| | - Mandy L Y Sin
- Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ, USA; Department of Urology, Stanford University, Stanford, CA, USA
| | - Jeff D Pyne
- Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ, USA
| | | | - Joseph C Liao
- Department of Urology, Stanford University, Stanford, CA, USA; Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| | - Pak Kin Wong
- Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ, USA.
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228
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Mamedov IZ, Britanova OV, Zvyagin IV, Turchaninova MA, Bolotin DA, Putintseva EV, Lebedev YB, Chudakov DM. Preparing unbiased T-cell receptor and antibody cDNA libraries for the deep next generation sequencing profiling. Front Immunol 2013; 4:456. [PMID: 24391640 PMCID: PMC3870325 DOI: 10.3389/fimmu.2013.00456] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 11/30/2013] [Indexed: 11/25/2022] Open
Abstract
High-throughput sequencing has the power to reveal the nature of adaptive immunity as represented by the full complexity of T-cell receptor (TCR) and antibody (IG) repertoires, but is at present severely compromised by the quantitative bias, bottlenecks, and accumulated errors that inevitably occur in the course of library preparation and sequencing. Here we report an optimized protocol for the unbiased preparation of TCR and IG cDNA libraries for high-throughput sequencing, starting from thousands or millions of live cells in an investigated sample. Critical points to control are revealed, along with tips that allow researchers to minimize quantitative bias, accumulated errors, and cross-sample contamination at each stage, and to enhance the subsequent bioinformatic analysis. The protocol is simple, reliable, and can be performed in 1–2 days.
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Affiliation(s)
- Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia ; CEITEC, Masaryk University , Brno , Czech Republic
| | - Olga V Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Ivan V Zvyagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia ; CEITEC, Masaryk University , Brno , Czech Republic
| | - Maria A Turchaninova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Dmitriy A Bolotin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Ekaterina V Putintseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Yuriy B Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia ; CEITEC, Masaryk University , Brno , Czech Republic
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Shang Y, Zhu P, Xu W, Guo T, Tian W, Luo Y, Huang K. Single universal primer multiplex ligation-dependent probe amplification with sequencing gel electrophoresis analysis. Anal Biochem 2013; 443:243-8. [PMID: 24050969 DOI: 10.1016/j.ab.2013.09.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 09/06/2013] [Accepted: 09/09/2013] [Indexed: 10/26/2022]
Abstract
In this study, a novel single universal primer multiplex ligation-dependent probe amplification (SUP-MLPA) technique that uses only one universal primer to perform multiplex polymerase chain reaction (PCR) was developed. Two reversely complementary common sequences were designed on the 5' or 3' end of the ligation probes (LPs), which allowed the ligation products to be amplified through only a single universal primer (SUP). SUP-MLPA products were analyzed on sequencing gel electrophoresis with extraordinary resolution. This method avoided the high expenses associated with capillary electrophoresis, which was the commonly used detection instrument. In comparison with conventional multiplex PCR, which suffers from low sensitivity, nonspecificity, and amplification disparity, SUP-MLPA had higher specificity and sensitivity and a low detection limit of 0.1 ng for detecting single crop species when screening the presence of genetically modified crops. We also studied the effect of different lengths of stuffer sequences on the probes for the first time. Through comparing the results of quantitative PCR, the LPs with different stuffer sequences did not affect the ligation efficiency, which further increased the multiplicity of this assay. The improved SUP-MLPA and sequencing gel electrophoresis method will be useful for food and animal feed identification, bacterial detection, and verification of genetic modification status of crops.
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Affiliation(s)
- Ying Shang
- Laboratory of Food Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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230
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Sanjuan-Jimenez R, Morata P, Bermúdez P, Bravo MJ, Colmenero JD. Comparative clinical study of different multiplex real time PCR strategies for the simultaneous differential diagnosis between extrapulmonary tuberculosis and focal complications of brucellosis. PLoS Negl Trop Dis 2013; 7:e2593. [PMID: 24349599 PMCID: PMC3861180 DOI: 10.1371/journal.pntd.0002593] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 11/01/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Both brucellosis and tuberculosis are chronic-debilitating systemic granulomatous diseases with a high incidence in many countries in Africa, Central and South America, the Middle East and the Indian subcontinent. Certain focal complications of brucellosis and extrapulmonary tuberculosis are very difficult to differentiate clinically, biologically and radiologically. As the conventional microbiological methods for the diagnosis of the two diseases have many limitations, as well as being time-consuming, multiplex real time PCR (M RT-PCR) could be a promising and practical approach to hasten the differential diagnosis and improve prognosis. METHODOLOGY/PRINCIPAL FINDINGS We designed a SYBR Green single-tube multiplex real-time PCR protocol targeting bcsp31 and the IS711 sequence detecting all pathogenic species and biovars of Brucella genus, the IS6110 sequence detecting Mycobacterium genus, and the intergenic region senX3-regX3 specifically detecting Mycobacterium tuberculosis complex. The diagnostic yield of the M RT-PCR with the three pairs of resultant amplicons was then analyzed in 91 clinical samples corresponding to 30 patients with focal complications of brucellosis, 24 patients with extrapulmonary tuberculosis, and 36 patients (Control Group) with different infectious, autoimmune or neoplastic diseases. Thirty-five patients had vertebral osteomyelitis, 21 subacute or chronic meningitis or meningoencephalitis, 13 liver or splenic abscess, eight orchiepididymitis, seven subacute or chronic arthritis, and the remaining seven samples were from different locations. Of the three pairs of amplicons (senX3-regX3+ bcsp3, senX3-regX3+ IS711 and IS6110+ IS711) only senX3-regX3+ IS711 was 100% specific for both the Brucella genus and M. tuberculosis complex. For all the clinical samples studied, the overall sensitivity, specificity, and positive and negative predictive values of the M RT-PCR assay were 89.1%, 100%, 85.7% and 100%, respectively, with an accuracy of 93.4%, (95% CI, 88.3-96.5%). CONCLUSIONS/SIGNIFICANCE In this study, a M RT-PCR strategy with species-specific primers based on senX3-regX3+IS711 sequences proved to be a sensitive and specific test, useful for the highly efficient detection of M. tuberculosis and Brucella spp in very different clinical samples. It thus represents an advance in the differential diagnosis between some forms of extrapulmonary tuberculosis and focal complications of brucellosis.
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Affiliation(s)
- Rocio Sanjuan-Jimenez
- Biochemistry, Molecular Biology and Immunology Department, Faculty of Medicine, University of Malaga, Malaga, Spain
| | - Pilar Morata
- Biochemistry, Molecular Biology and Immunology Department, Faculty of Medicine, University of Malaga, Malaga, Spain
| | - Pilar Bermúdez
- Microbiology Service, Carlos Haya University Hospital, Malaga, Spain
| | - M. José Bravo
- Biochemistry, Molecular Biology and Immunology Department, Faculty of Medicine, University of Malaga, Malaga, Spain
| | - Juan D. Colmenero
- Infectious Diseases Service, Carlos Haya University Hospital, Malaga, Spain
- * E-mail:
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231
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Application of the ASLP technology to a novel platform for rapid and noise-free multiplexed SNP genotyping. Biosens Bioelectron 2013; 54:687-94. [PMID: 24362043 DOI: 10.1016/j.bios.2013.10.071] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 10/30/2013] [Accepted: 10/30/2013] [Indexed: 11/30/2022]
Abstract
A novel multiplexing method, which relies on universal amplification of separated ligation-dependent probes (ASLP), has been developed to genotype single-nucleotide polymorphisms (SNPs). The ASLP technique employs two allele-specific oligonucleotides (ASO), modified with universal forward primer sequences at the 5'-end and a common locus-specific oligonucleotide (LSO) extended with a universal separation (US) sequence at the 3'-end. In the process, allele-specific ligation first takes place when target genomic DNA is hybridized by perfectly matching the ASO together with the LSO. A separation probe, which consists of a universal reverse primer sequence labeled with biotin at the 5'-end and complementary sequence of US at the 3'-end, is then applied to the resulting ligation product. During the extension reaction of the separation probe, the ligated probes dissociate from target genomic DNA in the form of a double-stranded DNA and are separated from the reaction mixture, which includes genomic DNA and unligated probes, by simply using streptavidin-coated magnetic beads. PCR amplification of the separated ligation products is then carried out by using universal primers and the PCR products are hybridized on a DNA microarray using the RecA protein. The advantageous features of the new method were demonstrated by using it to genotype 15 SNP markers for cultivar identification of pepper in a convenient and correct manner.
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232
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Development and padronization of three multiplex PCRs for the diagnosis of Chlamydia trachomatis, Toxoplasma gondii, herpes simplex viruses 1 and 2, and Cytomegalovirus. Mol Biotechnol 2013; 54:1004-9. [PMID: 23436027 DOI: 10.1007/s12033-013-9652-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
To develop multiplex PCRs (mPCRs) that allows simultaneous diagnosis of the infectious agents Chlamydia trachomatis, Toxoplasma gondii, HSV 1/2, and Cytomegalovirus (CMV). The study included patients with clinical suspicion of these agents, and clinical samples were blood, cerebrospinal fluid, urine, vaginal swabs, and amniotic fluid. After the extraction of DNA, this was used as a template in amplification by PCR of selected genes. The following conditions were tested: primer concentration, MgCl2 concentration, and annealing temperature. Three mPCRs were developed: multiplex I (CMV, HSV 1/2), multiplex II (CMV, HSV 1/2, T. gondii), and multiplex III (C. trachomatis, T. gondii, HSV 1/2, and CMV). The primer pairs used were shown to be specific for each infectious agent, and the specificity of mPCR assays was 100 %. Both the reactions of the monoplex PCR and mPCR produced a detection limit of 2 × 10(-5) to 6 × 10(-7) ng/μl of different DNAs. Upon conclusion, amplified products of expected size were obtained in 3 different reactions, and all the infectious agents were detected simultaneously in each mPCR. The concordant results of the study suggest that mPCR can be a powerful tool to improve the diagnostics of infectious diseases.
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233
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Development and application of a multiplex PCR method for rapid differential detection of subgroup A, B, and J avian leukosis viruses. J Clin Microbiol 2013; 52:37-44. [PMID: 24131697 DOI: 10.1128/jcm.02200-13] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Avian leukosis virus (ALV) subgroups A, B, and J are very common in poultry flocks and have caused serious economic losses in recent years. A multiplex PCR (mPCR) method for the detection of these three subgroups was developed and optimized in this study. We first designed a common forward primer, PF, and three downstream primers, AR, BR, and JR, which can amplify 715 bp for subgroup A, 515 bp for subgroup B, and 422 bp for subgroup J simultaneously in one reaction. The mPCR method produced neither cross-reactions with other subgroups of ALVs nor nonspecific reactions with other common avian viruses. The detection limit of the mPCR was as low as 1 × 10(3) viral DNA copies of each of the three subgroups. In animal experiments, the mPCR detected ALVs 2 to 4 days earlier than did virus isolation from whole-blood samples and cloaca swabs. Furthermore, a total of 346 clinical samples (including 127 tissue samples, 86 cloaca swabs, 59 albumen samples, and 74 whole-blood samples) from poultry flocks with suspected ALV infection were examined by mPCR, routine PCR, and virus isolation. The positive sample/total sample ratios for ALV-A, ALV-B, and ALV-J were 48% (166/346) as detected by mPCR and 48% (166/346) as detected by routine PCR. However, the positive sample/total sample ratio detected by virus isolation was 40% (138/346). The results of the mPCR and routine PCR were confirmed by sequencing the specific fragments. These results indicate that the mPCR method is rapid, specific, sensitive, and convenient for use in epidemiological studies of ALV, clinical detection of ALV, and ALV eradication programs.
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234
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Bai J, Baldwin E, Liao HL, Zhao W, Kostenyuk I, Burns J, Irey M. Extraction of DNA from orange juice, and detection of bacterium Candidatus Liberibacter asiaticus by real-time PCR. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:9339-9346. [PMID: 24047134 DOI: 10.1021/jf402364y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Orange juice processed from Huanglongbing (HLB) affected fruit is often associated with bitter taste and/or off-flavor. HLB disease in Florida is associated with Candidatus Liberibacter asiaticus (CLas), a phloem-limited bacterium. The current standard to confirm CLas for citrus trees is to take samples from midribs of leaves, which are rich in phloem tissues, and use a quantitative real-time polymerase chain reaction (qPCR) test to detect the 16S rDNA gene of CLas. It is extremely difficult to detect CLas in orange juice because of the low CLas population, high sugar and pectin concentration, low pH, and possible existence of an inhibitor to DNA amplification. The objective of this research was to improve extraction of DNA from orange juice and detection of CLas by qPCR. Homogenization using a sonicator increased DNA yield by 86% in comparison to mortar and pestle extraction. It is difficult to separate DNA from pectin; however, DNA was successfully extracted by treating the juice with pectinase. Application of an elution column successfully removed the unidentified inhibitor to DNA amplification. This work provided a protocol to extract DNA from whole orange juice and detect CLas in HLB-affected fruit.
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Affiliation(s)
- Jinhe Bai
- USDA , ARS, USHRL, 2001 South Rock Road, Ft. Pierce, Florida 34945, United States
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235
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Reisberg K, Selim AM, Gaede W. Simultaneous detection of Chlamydia spp., Coxiella burnetii, and Neospora caninum in abortion material of ruminants by multiplex real-time polymerase chain reaction. J Vet Diagn Invest 2013; 25:614-9. [DOI: 10.1177/1040638713497483] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Chlamydia spp., Coxiella burnetii, and Neospora caninum are responsible for reproductive diseases and are closely linked with high abortion rates in ruminants. Furthermore, C. burnetii and Chlamydia spp. have zoonotic potential. A real-time polymerase chain reaction (PCR) assay was developed for the simultaneous detection of Chlamydia spp., C. burnetii, and N. caninum. The detection of beta-actin as internal control in the same PCR reaction provides additional information about sample quality by detecting the presence of PCR inhibitors. The multiplex real-time PCR developed in the current study shows a greater sensitivity compared to previously used single-target PCR reactions with a reproducible detection limit of 0.13 plasmid copies per PCR for each target. Additional parallel amplification of all detectable pathogens did not adversely impact sensitivity. This new multiplex PCR allows the highly sensitive, cost-effective, and rapid detection of 3 important pathogens and has the potential to be a useful time-saving tool in the routine diagnosis of abortion cases in ruminants.
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Affiliation(s)
- Kerstin Reisberg
- State Institute for Consumer Protection of Saxony-Anhalt, Department of Veterinary Medicine, Stendal, Germany (Reisberg, Gaede)
- Department of Animal Medicine, Faculty of Veterinary Medicine, Benha University, Moshtohor Toukh, Egypt (Selim)
| | - Abdelfattah M. Selim
- State Institute for Consumer Protection of Saxony-Anhalt, Department of Veterinary Medicine, Stendal, Germany (Reisberg, Gaede)
- Department of Animal Medicine, Faculty of Veterinary Medicine, Benha University, Moshtohor Toukh, Egypt (Selim)
| | - Wolfgang Gaede
- State Institute for Consumer Protection of Saxony-Anhalt, Department of Veterinary Medicine, Stendal, Germany (Reisberg, Gaede)
- Department of Animal Medicine, Faculty of Veterinary Medicine, Benha University, Moshtohor Toukh, Egypt (Selim)
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236
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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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237
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Usability application of multiplex polymerase chain reaction in the diagnosis of microorganisms isolated from urine of patients treated in cancer hospital. Radiol Oncol 2013; 47:296-303. [PMID: 24133395 PMCID: PMC3794886 DOI: 10.2478/raon-2013-0044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 05/11/2013] [Indexed: 11/21/2022] Open
Abstract
Background The objective of this study was: i) to compare the results of urine culture with polymerase chain reaction (PCR) -based detection of microorganisms using two commercially available kits, ii) to assess antimicrobial susceptibility of urine isolates from cancer patients to chosen antimicrobial drugs and, if necessary, to update the recommendation of empirical therapy. Materials and methods. A one-year hospital-based prospective study has been conducted in Greater Poland Cancer Centre and Genetic Medicine Laboratory CBDNA Research Centre in 2011. Urine cultures and urine PCR assay from 72 patients were examined Results Urine cultures and urine PCR assay from 72 patients were examined. Urine samples were positive for 128 strains from which 95 (74%) were identical in both tests. The most frequently isolated bacteria in both culture and PCR assay were coliform organisms and Enterococcus spp. The Gram negative bacilli were most resistant to cotrimoxazol. 77.2% of these bacilli and 100% of E. faecalis and S. agalactiae were sensitive to amoxicillin-clavulanic acid. 4.7% of Gram positive cocci were resistant to nitrofurantoin. Conclusions The PCR method quickly finds the causative agent of urinary tract infection (UTI) and, therefore, it can help with making the choice of the proper antimicrobial therapy at an early stage. It appears to be a viable alternative to the recommendations made in general treatment guidelines, in cases where diversified sensitivity patterns of microorganisms have been found.
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238
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Development and validation of a multiplex, real-time RT PCR assay for the simultaneous detection of classical and African swine fever viruses. PLoS One 2013; 8:e71019. [PMID: 23923045 PMCID: PMC3724773 DOI: 10.1371/journal.pone.0071019] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/28/2013] [Indexed: 11/19/2022] Open
Abstract
A single-step, multiplex, real-time polymerase chain reaction (RT-PCR) was developed for the simultaneous and differential laboratory diagnosis of Classical swine fever virus (CSFV) and African swine fever virus (ASFV) alongside an exogenous internal control RNA (IC-RNA). Combining a single extraction methodology and primer and probe sets for detection of the three target nucleic acids CSFV, ASFV and IC-RNA, had no effect on the analytical sensitivity of the assay and the new triplex RT-PCR was comparable to standard PCR techniques for CSFV and ASFV diagnosis. After optimisation the assay had a detection limit of 5 CSFV genome copies and 22 ASFV genome copies. Analytical specificity of the triplex assay was validated using a panel of viruses representing 9 of the 11 CSFV subgenotypes, at least 8 of the 22 ASFV genotypes as well as non-CSFV pestiviruses. Positive and negative clinical samples from animals infected experimentally, due to field exposure or collected from the UK which is free from both swine diseases, were used to evaluate the diagnostic sensitivity and specificity for detection of both viruses. The diagnostic sensitivity was 100% for both viruses whilst diagnostic specificity estimates were 100% for CSFV detection and 97.3% for ASFV detection. The inclusion of a heterologous internal control allowed identification of false negative results, which occurred at a higher level than expected. The triplex assay described here offers a valuable new tool for the differential detection of the causative viruses of two clinically indistinguishable porcine diseases, whose geographical occurrence is increasingly overlapping.
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239
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Wang Q, Zhou Y, Li S, Zhuo C, Xu S, Huang L, Yang L, Liao K. Real-time fluorescence loop mediated isothermal amplification for the detection of Acinetobacter baumannii. PLoS One 2013; 8:e66406. [PMID: 23843955 PMCID: PMC3699609 DOI: 10.1371/journal.pone.0066406] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 05/06/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Detection of Acinetobacter baumannii has been relying primarily on bacterial culture that often fails to return useful results in time. Although DNA-based assays are more sensitive than bacterial culture in detecting the pathogen, the molecular results are often inconsistent and challenged by doubts on false positives, such as those due to system- and environment-derived contaminations. In addition, these molecular tools require expensive laboratory instruments. Therefore, establishing molecular tools for field use require simpler molecular platforms. The loop-mediated isothermal amplification method is relatively simple and can be improved for better use in a routine clinical bacteriology laboratory. A simple and portable device capable of performing both the amplification and detection (by fluorescence) of LAMP in the same platform has been developed in recent years. This method is referred to as real-time loop-mediated isothermal amplification. In this study, we attempted to utilize this method for rapid detection of A. baumannii. METHODOLOGY AND SIGNIFICANT FINDINGS Species-specific primers were designed to test the utility of this method. Clinical samples of A. baumannii were used to determine the sensitivity and specificity of this system compared to bacterial culture and a polymerase chain reaction method. All positive samples isolated from sputum were confirmed to be the species of Acinetobacter by 16S rRNA gene sequencing. The RealAmp method was found to be simpler and allowed real-time detection of DNA amplification, and could distinguish A. baumannii from Acinetobacter calcoaceticus and Acinetobacter genomic species 3. DNA was extracted by simple boiling method. Compared to bacterial culture, the sensitivity and specificity of RealAmp in detecting A. baumannii was 98.9% and 75.0%, respectively. CONCLUSION The RealAmp assay only requires a single unit, and the assay positivity can be verified by visual inspection. Therefore, this assay has great potential of field use as a molecular tool for detection of A. baumannii.
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Affiliation(s)
- Qinqin Wang
- Department of Respiratory Medicine, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Institute of Respiratory Diseases, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yanbin Zhou
- Department of Respiratory Medicine, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Institute of Respiratory Diseases, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail:
| | - Shaoli Li
- Department of Respiratory Medicine, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Institute of Respiratory Diseases, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Chao Zhuo
- State Key Laboratory of Respiratory Diseases, Guangzhou Medical College, Guangzhou, Guangdong, China
| | - Siqi Xu
- Department of Respiratory Medicine, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Institute of Respiratory Diseases, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lixia Huang
- Department of Respiratory Medicine, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
- Institute of Respiratory Diseases, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ling Yang
- State Key Laboratory of Respiratory Diseases, Guangzhou Medical College, Guangzhou, Guangdong, China
| | - Kang Liao
- Department of Clinical Laboratory, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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Meng W, McElroy JP, Volinia S, Palatini J, Warner S, Ayers LW, Palanichamy K, Chakravarti A, Lautenschlaeger T. Comparison of microRNA deep sequencing of matched formalin-fixed paraffin-embedded and fresh frozen cancer tissues. PLoS One 2013; 8:e64393. [PMID: 23696889 PMCID: PMC3655971 DOI: 10.1371/journal.pone.0064393] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 04/13/2013] [Indexed: 01/07/2023] Open
Abstract
MicroRNAs regulate several aspects of tumorigenesis and cancer progression. Most cancer tissues are archived formalin-fixed and paraffin-embedded (FFPE). While microRNAs are a more stable form of RNA thought to withstand FFPE-processing and degradation there is only limited evidence for the latter assumption. We examined whether microRNA profiling can be successfully conducted on FFPE cancer tissues using SOLiD ligation based sequencing. Tissue storage times (2-9 years) appeared to not affect the number of detected microRNAs in FFPE samples compared to matched frozen samples (paired t-test p>0.7). Correlations of microRNA expression values were very high across microRNAs in a given sample (Pearson's r = 0.71-0.95). Higher variance of expression values among samples was associated with higher correlation coefficients between FFPE and frozen tissues. One of the FFPE samples in this study was degraded for unknown reasons with a peak read length of 17 nucleotides compared to 21 in all other samples. The number of detected microRNAs in this sample was within the range of microRNAs detected in all other samples. Ligation-based microRNA deep sequencing on FFPE cancer tissues is feasible and RNA degradation to the degree observed in our study appears to not affect the number of microRNAs that can be quantified.
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Affiliation(s)
- Wei Meng
- Department of Radiation Oncology, Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard L. Solove Research Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Joseph P. McElroy
- Center for Biostatistics, The Ohio State University, Columbus, Ohio, United States of America
| | - Stefano Volinia
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Jeff Palatini
- Microarray Shared Resource, Arthur G. James Comprehensive Cancer Center and Richard L. Solove Research Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Sarah Warner
- Microarray Shared Resource, Arthur G. James Comprehensive Cancer Center and Richard L. Solove Research Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Leona W. Ayers
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Kamalakannan Palanichamy
- Department of Radiation Oncology, Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard L. Solove Research Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Arnab Chakravarti
- Department of Radiation Oncology, Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard L. Solove Research Institute, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (AC); (TL)
| | - Tim Lautenschlaeger
- Department of Radiation Oncology, Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard L. Solove Research Institute, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (AC); (TL)
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241
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Adzitey F, Huda N, Ali GRR. Molecular techniques for detecting and typing of bacteria, advantages and application to foodborne pathogens isolated from ducks. 3 Biotech 2013; 3:97-107. [PMID: 28324565 PMCID: PMC3597138 DOI: 10.1007/s13205-012-0074-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 05/23/2012] [Indexed: 01/18/2023] Open
Abstract
In recent times, several foodborne pathogens have become important and a threat to public health. Surveillance studies have provided data and a better understanding into the existence and spread of foodborne pathogens. The application of molecular techniques for detecting and typing of foodborne pathogens in surveillance studies provide reliable epidemiological data for tracing the source of human infections. A wide range of molecular techniques (including pulsed field gel electrophoresis, multilocus sequence typing, random amplified polymorphism deoxyribonucleic acid, repetitive extragenic palindromic, deoxyribonucleic acid sequencing, multiplex polymerase chain reaction and many more) have been used for detecting, speciating, typing, classifying and/or characterizing foodborne pathogens of great significance to humans. Farm animals including chickens, cattle, sheep, goats and pigs, and others (such as domestic and wild animals) have been reported to be primary reservoirs for foodborne pathogens. The consumption of contaminated poultry meats or products has been considered to be the leading source of human foodborne infections. Ducks like other farm animals are important source of foodborne pathogens and have been implicated in some human foodborne illnesses and deaths. Nonetheless, few studies have been conducted to explore the potential of ducks in causing foodborne outbreaks, diseases and its consequences. This review highlights some common molecular techniques, their advantages and those that have been applied to pathogens isolated from ducks and their related sources.
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Affiliation(s)
- Frederick Adzitey
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia
- Animal Science Department, University for Development Studies, Box TL 1882, Tamale, Ghana
| | - Nurul Huda
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia
| | - Gulam Rusul Rahmat Ali
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia.
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242
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Whale AS, Cowen S, Foy CA, Huggett JF. Methods for applying accurate digital PCR analysis on low copy DNA samples. PLoS One 2013; 8:e58177. [PMID: 23472156 PMCID: PMC3589384 DOI: 10.1371/journal.pone.0058177] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 01/31/2013] [Indexed: 01/09/2023] Open
Abstract
Digital PCR (dPCR) is a highly accurate molecular approach, capable of precise measurements, offering a number of unique opportunities. However, in its current format dPCR can be limited by the amount of sample that can be analysed and consequently additional considerations such as performing multiplex reactions or pre-amplification can be considered. This study investigated the impact of duplexing and pre-amplification on dPCR analysis by using three different assays targeting a model template (a portion of the Arabidopsis thaliana alcohol dehydrogenase gene). We also investigated the impact of different template types (linearised plasmid clone and more complex genomic DNA) on measurement precision using dPCR. We were able to demonstrate that duplex dPCR can provide a more precise measurement than uniplex dPCR, while applying pre-amplification or varying template type can significantly decrease the precision of dPCR. Furthermore, we also demonstrate that the pre-amplification step can introduce measurement bias that is not consistent between experiments for a sample or assay and so could not be compensated for during the analysis of this data set. We also describe a model for estimating the prevalence of molecular dropout and identify this as a source of dPCR imprecision. Our data have demonstrated that the precision afforded by dPCR at low sample concentration can exceed that of the same template post pre-amplification thereby negating the need for this additional step. Our findings also highlight the technical differences between different templates types containing the same sequence that must be considered if plasmid DNA is to be used to assess or control for more complex templates like genomic DNA.
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Affiliation(s)
- Alexandra S Whale
- Molecular and Cell Biology Team, LGC Ltd, Teddington, United Kingdom.
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243
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Søe MJ, Rohde M, Mikkelsen J, Warthoe P. IsoPCR: An Analytically Sensitive, Nested, Multiplex Nucleic Acid Amplification Method. Clin Chem 2013; 59:436-9. [DOI: 10.1373/clinchem.2012.193664] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND
Nucleic acid tests that can simultaneously detect multiple targets with high sensitivity, specificity, and speed are highly desirable. To meet this need, we developed a new approach we call the isoPCR method.
METHODS
The isoPCR method is a 2-stage nested-like nucleic acid amplification method that combines a single multiplex preamplification PCR with subsequent distinct detection of specific targets by use of isothermal amplification. We compared isoPCR to nested quantitative PCR (qPCR), loop-mediated isothermal amplification (LAMP), and nested LAMP (PCR followed by LAMP), for detection of DNA from Candida glabrata. We evaluated the method's multiplex capability for detecting low copy numbers of pathogens commonly involved in sepsis.
RESULTS
IsoPCR provided detection of 1 copy of Candida glabrata, an LOD that was 5-fold lower than a nested qPCR assay (5 copies), while the amplification time was simultaneously halved. Similarly, the LOD for isoPCR was lower than that for a LAMP assay (1000 copies) and a nested LAMP assay (5 copies). IsoPCR required recognition of 6 regions for detection, thereby providing a theoretically higher specificity compared to nested qPCR (4 regions). The isoPCR multiplexing capability was demonstrated by simultaneous detection of 4 pathogens with individual LODs of 10 copies or fewer. Furthermore, the specificity of isoPCR was demonstrated by successful pathogen detection from samples with more than 1 pathogen present.
CONCLUSIONS
IsoPCR provides a molecular diagnostic tool for multiplex nucleic acid detection, with an LOD down to 1 copy, high theoretical specificity, and halving of the amplification time compared to a nested qPCR assay.
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Affiliation(s)
| | - Mikkel Rohde
- Danish Cancer Society Research Center, Cell Death and Metabolism, Copenhagen, Denmark
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244
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Single-tube multiplexed molecular detection of endemic porcine viruses in combination with background screening for transboundary diseases. J Clin Microbiol 2013; 51:938-44. [PMID: 23303496 DOI: 10.1128/jcm.02947-12] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Detection of several pathogens with multiplexed real-time quantitative PCR (qPCR) assays in a one-step setup allows the simultaneous detection of two endemic porcine and four different selected transboundary viruses. Reverse transcription (RT)-qPCR systems for the detection of porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2), two of the most economically important pathogens of swine worldwide, were combined with a screening system for diseases notifiable to the World Organization of Animal Health, namely, classical and African swine fever, foot-and-mouth disease, and Aujeszky's disease. Background screening was implemented using the identical fluorophore for all four different RT-qPCR assays. The novel multiplex RT-qPCR system was validated with a large panel of different body fluids and tissues from pigs and other animal species. Both reference samples and clinical specimens were used for a complete evaluation. It could be demonstrated that a highly sensitive and specific parallel detection of the different viruses was possible. The assays for the notifiable diseases were even not affected by the simultaneous amplification of very high loads of PRRSV- and PCV2-specific sequences. The novel broad-spectrum multiplex assay allows in a unique form the routine investigation for endemic porcine pathogens with exclusion diagnostics of the most important transboundary diseases in samples from pigs with unspecific clinical signs, such as fever or hemorrhages. The new system could significantly improve early detection of the most important notifiable diseases of swine and could lead to a new approach in syndromic surveillance.
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245
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Targeting herpetic keratitis by gene therapy. J Ophthalmol 2012; 2012:594869. [PMID: 23326647 PMCID: PMC3541562 DOI: 10.1155/2012/594869] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 11/30/2012] [Indexed: 01/15/2023] Open
Abstract
Ocular gene therapy is rapidly becoming a reality. By November 2012, approximately 28 clinical trials were approved to assess novel gene therapy agents. Viral infections such as herpetic keratitis caused by herpes simplex virus 1 (HSV-1) can cause serious complications that may lead to blindness. Recurrence of the disease is likely and cornea transplantation, therefore, might not be the ideal therapeutic solution. This paper will focus on the current situation of ocular gene therapy research against herpetic keratitis, including the use of viral and nonviral vectors, routes of delivery of therapeutic genes, new techniques, and key research strategies. Whereas the correction of inherited diseases was the initial goal of the field of gene therapy, here we discuss transgene expression, gene replacement, silencing, or clipping. Gene therapy of herpetic keratitis previously reported in the literature is screened emphasizing candidate gene therapy targets. Commonly adopted strategies are discussed to assess the relative advantages of the protective therapy using antiviral drugs and the common gene therapy against long-term HSV-1 ocular infections signs, inflammation and neovascularization. Successful gene therapy can provide innovative physiological and pharmaceutical solutions against herpetic keratitis.
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246
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Nolte O. Nucleic Acid Amplification Based Diagnostic of Lyme (Neuro-)borreliosis - Lost in the Jungle of Methods, Targets, and Assays? Open Neurol J 2012; 6:129-39. [PMID: 23230454 PMCID: PMC3514706 DOI: 10.2174/1874205x01206010129] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Revised: 06/22/2012] [Accepted: 07/02/2012] [Indexed: 11/30/2022] Open
Abstract
Laboratory based diagnosis of infectious diseases usually relies on culture of the disease causing micro-organism, followed by identification and susceptibility testing. Since Borrelia burgdorferi sensu lato, the etiologic agent of Lyme disease or Lyme borreliosis, requires very specific culture conditions (e.g. specific liquid media, long term cul-ture) traditional bacteriology is often not done on a routine basis. Instead, confirmation of the clinical diagnosis needs ei-ther indirect techniques (like serology or measurement of cellular activity in the presence of antigens) or direct but culture independent techniques, like microscopy or nucleic acid amplification techniques (NAT), with polymerase chain reaction (PCR) being the most frequently applied NAT method in routine laboratories. NAT uses nucleic acids of the disease causing micro-organism as template for amplification, isolated from various sources of clinical specimens. Although the underlying principle, adoption of the enzymatic process running during DNA duplication prior to prokaryotic cell division, is comparatively easy, a couple of ‘pitfalls’ is associated with the technique itself as well as with interpretation of the results. At present, no commercial, CE-marked and sufficiently validated PCR assay is available. A number of homebrew assays have been published, which are different in terms of target (i.e. the gene targeted by the amplification primers), method (nested PCR, PCR followed by hybridization, real-time PCR) and validation criteria. Inhibitory compounds may lead to false negative results, if no appropriate internal control is included. Carry-over of amplicons, insufficient handling and workflow and/or insufficiently validated targets/primers may result in false positive results. Different targets may yield different analytical sensitivity, depending, among other factors, of the redundancy of a target gene in the genome. Per-formance characteristics (e.g. analytical sensitivity and specificity, clinical sensitivity and specificity, reproducibility, etc.) are, if available, only applicable to a specific assay, running in a specific laboratory. Finally, not only the NAT/PCR method itself, but also the process of DNA isolation from the specimen, is highly diverse and may have fundamental im-pact on the (expected) PCR result. Of concern are distribution effects of DNA, in particular, if only low numbers of bacte-ria/genomes are present in a sample, as it is the case for instance in cerebrospinal fluids. For the ordering physician and for the patient requesting PCR analysis, these ‘pitfalls’ are usually invisible. As a conse-quence, the reported result (i.e. PCR negative or positive for B. burgdorferi) is hard to interpret, especially, if the reported PCR result is contradictory to the clinical diagnosis or other laboratory findings. Moreover, due to the high number of dif-ferent assays in use, two laboratories, testing the same specimen, might come to different PCR results. The current paper wants to summarize the available PCR/NAT assays for the detection of B. burgdorferi DNA in clinical specimens, with special attention to neurologic disorders, and to discuss the difficulties in PCR analysis and result inter-pretation, associated thereof. In view of growing numbers of patients who are diagnosed of having Lyme disease, and ac-knowledging a substantial growth in knowledge regarding other tick- or vector-borne pathogens, which might be able to induce symptoms comparable to Lyme (neuro-)borreliosis, efforts are urgently needed to standardize and harmonize methods for B. burgdorferi nucleic acid amplification.
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Affiliation(s)
- Oliver Nolte
- Labor Dr. Brunner, Mainaustrabe 48 a/b, DE-78464, Konstanz, Germany
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247
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Multiplex bead suspension array for screening Neisseria gonorrhoeae antibiotic resistance genetic determinants in noncultured clinical samples. J Mol Diagn 2012; 15:116-29. [PMID: 23159594 DOI: 10.1016/j.jmoldx.2012.08.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 08/15/2012] [Accepted: 08/24/2012] [Indexed: 11/22/2022] Open
Abstract
The increasing threat of antibiotic-resistant Neisseria gonorrhoeae highlights the need for new diagnostic options. A high-throughput multiplex bead suspension array assay was developed for profiling 29 N. gonorrhoeae genomic mutations and 2 plasmid genes conferring resistance to 6 antimicrobial agents: penicillin, ciprofloxacin, cefixime, tetracycline, azithromycin, and spectinomycin. The three steps of this assay include amplification of 12 N. gonorrhoeae chromosomal and plasmid loci, multiplex allele-specific primer extension reaction, and multiplex bead suspension array detection. Antibiotic resistance genetic determinants were identified successfully in 239 cervicovaginal N. gonorrhoeae-positive noncultured swab samples. This molecular assay can be used for detection of gonococci in clinical specimens, molecular typing, mutation profiling, and predictive assessment of N. gonorrhoeae susceptibility to antibiotics without the need for culture.
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248
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Quintero-Vásquez GA, Bazán-Tejeda ML, Martínez-Peñafiel E, Kameyama-Kawabe L, Bermúdez-Cruz RM. Multiplex PCR to detect four different tomato-infecting pathogens. Folia Microbiol (Praha) 2012; 58:269-76. [PMID: 23135900 DOI: 10.1007/s12223-012-0206-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 10/23/2012] [Indexed: 01/26/2023]
Abstract
This work was aimed to develop a multiplex PCR assay to detect infectious agents such as Clavibacter michiganensis subsp. michiganensis, Fusarium sp, Leveillula taurica, and begomoviruses in tomato (Solanum lycopersicum) plants. Specific primer sets of each pathogen were designed based on intergenic ribosomal RNA sequences for the first three, whereas for begomoviruses, primers were designed based on conserved regions. The design also considered that the length (200-800 bp) of the PCR products was resolvable by electrophoresis; thus 296, 380, 457, and 731 bp fragments for Clavibacter, Fusarium, Leveillula, and begomoviruses, respectively, were considered. PCR conditions were optimized to amplify all the products in a single tube from genomic DNA and circumvent PCR inhibitors from infected plants. Finally, when the multiplex PCR assay was tested with tomato plants infected with any of the four pathogens, specific PCR products confirmed the presence of the pathogens. Optimized PCR multiplex allowed for the accurate and simultaneous detection of Clavibacter, Fusarium, Leveillula, and begomoviruses in infected plants or seeds from tomato.
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Affiliation(s)
- Gabriela Alejandra Quintero-Vásquez
- Genetics and Molecular Biology Department, Centro de Investigaciones y Estudios Avanzados del IPN, Av IPN 2508. Delegación Gustavo A, Madero, Federal District, México
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249
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Liu L, Wu Y. Development of a genome-wide multiple duplex-SSR protocol and its applications for the identification of selfed progeny in switchgrass. BMC Genomics 2012; 13:522. [PMID: 23031617 PMCID: PMC3533973 DOI: 10.1186/1471-2164-13-522] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 10/01/2012] [Indexed: 12/01/2022] Open
Abstract
Background Switchgrass (Panicum virgatum) is a herbaceous crop for the cellulosic biofuel feedstock development in the USA and Europe. As switchgrass is a naturally outcrossing species, accurate identification of selfed progeny is important to producing inbreds, which can be used in the production of heterotic hybrids. Development of a technically reliable, time-saving and easily used marker system is needed to quantify and characterize breeding origin of progeny plants of targeted parents. Results Genome-wide screening of 915 mapped microsatellite (simple sequence repeat, SSR) markers was conducted, and 842 (92.0%) produced clear and scorable bands on a pooled DNA sample of eight switchgrass varieties. A total of 166 primer pairs were selected on the basis of their relatively even distribution in switchgrass genome and PCR amplification quality on 16 tetraploid genotypes. Mean polymorphic information content value for the 166 markers was 0.810 ranging from 0.116 to 0.959. From them, a core set of 48 loci, which had been mapped on 17 linkage groups, was further tested and optimized to develop 24 sets of duplex markers. Most of (up to 87.5%) targeted, but non-allelic amplicons within each duplex were separated by more than 10-bp. Using the established duplex PCR protocol, selfing ratio (i.e., selfed/all progeny x100%) was identified as 0% for a randomly selected open-pollinated ‘Kanlow’ genotype grown in the field, 15.4% for 22 field-grown plants of bagged inflorescences, and 77.3% for a selected plant grown in a growth chamber. Conclusions The study developed a duplex SSR-based PCR protocol consisting of 48 markers, providing ample choices of non-tightly-linked loci in switchgrass whole genome, and representing a powerful, time-saving and easily used method for the identification of selfed progeny in switchgrass. The protocol should be a valuable tool in switchgrass breeding efforts.
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Affiliation(s)
- Linglong Liu
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, 74078-6028, USA
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250
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Faltin B, Wadle S, Roth G, Zengerle R, von Stetten F. Mediator probe PCR: a novel approach for detection of real-time PCR based on label-free primary probes and standardized secondary universal fluorogenic reporters. Clin Chem 2012; 58:1546-56. [PMID: 22923452 DOI: 10.1373/clinchem.2012.186734] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND The majority of established techniques for monitoring real-time PCR amplification involve individual target-specific fluorogenic probes. For analysis of numerous different targets the synthesis of these probes contributes to the overall cost during assay development. Sequence-dependent universal detection techniques overcome this drawback but are prone to detection of unspecific amplification products. We developed the mediator probe PCR as a solution to these problems. METHODS A set of label-free sequence-specific primary probes (mediator probes), each comprising a target-specific region and a standardized mediator tag, is cleaved upon annealing to its target sequence by the polymerases' 5' nuclease activity. Release of a mediator triggers signal generation by cleavage of a complementary fluorogenic reporter probe. RESULTS Real-time PCR amplification of human papillomavirus 18 (HPV18), Staphylococcus aureus, Escherichia coli, and Homo sapiens DNA dilution series showed exceptional linearity when detected either by novel mediator probes (r(2) = 0.991-0.999) or state-of-the-art hydrolysis probes (TaqMan probes) (r(2) = 0.975-0.993). For amplification of HPV18 DNA the limits of detection were 78.3 and 85.1 copies per 10-μL reaction when analyzed with the mediator probe and hydrolysis probe, respectively. Duplex amplification of HPV18 target DNA and internal standard had no effects on back calculation of target copy numbers when quantified with either the mediator probe PCR (r(2) = 0.998) or the hydrolysis probe PCR (r(2) = 0.988). CONCLUSIONS The mediator probe PCR has equal performance to hydrolysis probe PCR and has reduced costs because of the use of universal fluorogenic reporters.
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Affiliation(s)
- Bernd Faltin
- Laboratory for MEMS Applications, Department of Microsystems Engineering-IMTEK, University of Freiburg, Freiburg, Germany
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