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Kang M, Jeong E, Kim JY, Yun SA, Jang MA, Jang JH, Kim TY, Huh HJ, Lee NY. Optimization of extraction-free protocols for SARS-CoV-2 detection using a commercial rRT-PCR assay. Sci Rep 2023; 13:20364. [PMID: 37990045 PMCID: PMC10663557 DOI: 10.1038/s41598-023-47645-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023] Open
Abstract
In the ongoing global fight against coronavirus disease 2019 (COVID-19), the sample preparation process for real-time reverse transcription polymerase chain reaction (rRT-PCR) faces challenges due to time-consuming steps, labor-intensive procedures, contamination risks, resource demands, and environmental implications. However, optimized strategies for sample preparation have been poorly investigated, and the combination of RNase inhibitors and Proteinase K has been rarely considered. Hence, we investigated combinations of several extraction-free protocols incorporating heat treatment, sample dilution, and Proteinase K and RNase inhibitors, and validated the effectiveness using 120 SARS-CoV-2 positive and 62 negative clinical samples. Combining sample dilution and heat treatment with Proteinase K and RNase inhibitors addition exhibited the highest sensitivity (84.26%) with a mean increase in cycle threshold (Ct) value of + 3.8. Meanwhile, combined sample dilution and heat treatment exhibited a sensitivity of 79.63%, accounting for a 38% increase compared to heat treatment alone. Our findings highlight that the incorporation of Proteinase K and RNase inhibitors with sample dilution and heat treatment contributed only marginally to the improvement without yielding statistically significant differences. Sample dilution significantly impacts SARS-CoV-2 detection, and sample conditions play a crucial role in the efficiency of extraction-free methods. Our findings may provide insights for streamlining diagnostic testing, enhancing its accessibility, cost-effectiveness, and sustainability.
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Affiliation(s)
- Minhee Kang
- Smart Healthcare Research Institute, Biomedical Engineering Research Center, Samsung Medical Center, Seoul, South Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea
| | - Eunjung Jeong
- Smart Healthcare Research Institute, Biomedical Engineering Research Center, Samsung Medical Center, Seoul, South Korea
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea
| | - Ji-Yeon Kim
- Samsung Biomedical Research Institute, Center for Clinical Medicine, Samsung Medical Center, Seoul, South Korea
| | - Sun Ae Yun
- Samsung Biomedical Research Institute, Center for Clinical Medicine, Samsung Medical Center, Seoul, South Korea
| | - Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Hee Jae Huh
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea.
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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Khera HK, Mishra R. Nucleic Acid Based Testing (NABing): A Game Changer Technology for Public Health. Mol Biotechnol 2023:10.1007/s12033-023-00870-4. [PMID: 37695473 DOI: 10.1007/s12033-023-00870-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023]
Abstract
Timely and accurate detection of the causal agent of a disease is crucial to restrict suffering and save lives. Mere symptoms are often not enough to detect the root cause of the disease. Better diagnostics applied for screening at a population level and sensitive detection assays remain the crucial component of disease surveillance which may include clinical, plant, and environmental samples, including wastewater. The recent advances in genome sequencing, nucleic acid amplification, and detection methods have revolutionized nucleic acid-based testing (NABing) and screening assays. A typical NABing assay consists of three modules: isolation of the nucleic acid from the collected sample, identification of the target sequence, and final reading the target with the help of a signal, which may be in the form of color, fluorescence, etc. Here, we review current NABing assays covering the different aspects of all three modules. We also describe the frequently used target amplification or signal amplification procedures along with the variety of applications of this fast-evolving technology and challenges in implementation of NABing in the context of disease management especially in low-resource settings.
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Affiliation(s)
- Harvinder Kour Khera
- Tata Institute for Genetics and Society, New inStem Building NCBS Campus, GKVK Post, Bellary Road, Bengaluru, 560065, India.
| | - Rakesh Mishra
- Tata Institute for Genetics and Society, New inStem Building NCBS Campus, GKVK Post, Bellary Road, Bengaluru, 560065, India.
- CSIR-Centre for Cellular and Molecular Biology, Uppal Rd, IICT Colony, Habsiguda, Hyderabad, Telangana, 500007, India.
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Huang Z, Lyon CJ, Wang J, Lu S, Hu TY. CRISPR Assays for Disease Diagnosis: Progress to and Barriers Remaining for Clinical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301697. [PMID: 37162202 PMCID: PMC10369298 DOI: 10.1002/advs.202301697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/24/2023] [Indexed: 05/11/2023]
Abstract
Numerous groups have employed the special properties of CRISPR/Cas systems to develop platforms that have broad potential applications for sensitive and specific detection of nucleic acid (NA) targets. However, few of these approaches have progressed to commercial or clinical applications. This review summarizes the properties of known CRISPR/Cas systems and their applications, challenges associated with the development of such assays, and opportunities to improve their performance or address unmet assay needs using nano-/micro-technology platforms. These include rapid and efficient sample preparation, integrated single-tube, amplification-free, quantifiable, multiplex, and non-NA assays. Finally, this review discusses the current outlook for such assays, including remaining barriers for clinical or point-of-care applications and their commercial development.
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Affiliation(s)
- Zhen Huang
- National Clinical Research Center for Infectious DiseasesShenzhen Third People's HospitalSouthern University of Science and Technology29 Bulan RoadShenzhenGuangdong518112China
- Center for Cellular and Molecular DiagnosticsTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
- Department of Biochemistry and Molecular BiologyTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
| | - Christopher J. Lyon
- Center for Cellular and Molecular DiagnosticsTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
- Department of Biochemistry and Molecular BiologyTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
| | - Jin Wang
- Tolo Biotechnology Company Limited333 Guiping RoadShanghai200233China
| | - Shuihua Lu
- National Clinical Research Center for Infectious DiseasesShenzhen Third People's HospitalSouthern University of Science and Technology29 Bulan RoadShenzhenGuangdong518112China
| | - Tony Y. Hu
- Center for Cellular and Molecular DiagnosticsTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
- Department of Biochemistry and Molecular BiologyTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
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Bogožalec Košir A, Lužnik D, Tomič V, Milavec M. Evaluation of DNA Extraction Methods for Reliable Quantification of Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa. BIOSENSORS 2023; 13:bios13040463. [PMID: 37185538 PMCID: PMC10136035 DOI: 10.3390/bios13040463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/25/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023]
Abstract
Detection and quantification of DNA biomarkers relies heavily on the yield and quality of DNA obtained by extraction from different matrices. Although a large number of studies have compared the yields of different extraction methods, the repeatability and intermediate precision of these methods have been largely overlooked. In the present study, five extraction methods were evaluated, using digital PCR, to determine their efficiency in extracting DNA from three different Gram-negative bacteria in sputum samples. The performance of two automated methods (GXT NA and QuickPick genomic DNA extraction kit, using Arrow and KingFisher Duo automated systems, respectively), two manual kit-based methods (QIAamp DNA mini kit; DNeasy UltraClean microbial kit), and one manual non-kit method (CTAB), was assessed. While GXT NA extraction kit and the CTAB method have the highest DNA yield, they did not meet the strict criteria for repeatability, intermediate precision, and measurement uncertainty for all three studied bacteria. However, due to limited clinical samples, a compromise is necessary, and the GXT NA extraction kit was found to be the method of choice. The study also showed that dPCR allowed for accurate determination of extraction method repeatability, which can help standardize molecular diagnostic approaches. Additionally, the determination of absolute copy numbers facilitated the calculation of measurement uncertainty, which was found to be influenced by the DNA extraction method used.
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Affiliation(s)
- Alexandra Bogožalec Košir
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000 Ljubljana, Slovenia
| | - Dane Lužnik
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik 36, 4204 Golnik, Slovenia
| | - Viktorija Tomič
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik 36, 4204 Golnik, Slovenia
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000 Ljubljana, Slovenia
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Abstract
Nearly 40 years have elapsed since the invention of the PCR, with its extremely sensitive and specific ability to detect nucleic acids via in vitro enzyme-mediated amplification. In turn, more than 2 years have passed since the onset of the coronavirus disease 2019 (COVID-19) pandemic, during which time molecular diagnostics for infectious diseases have assumed a larger global role than ever before. In this context, we review broadly the progression of molecular techniques in clinical microbiology, to their current prominence. Notably, these methods now entail both the detection and quantification of microbial nucleic acids, along with their sequence-based characterization. Overall, we seek to provide a combined perspective on the techniques themselves, as well as how they have come to shape health care at the intersection of technologic innovation, pathophysiologic knowledge, clinical/laboratory logistics, and even financial/regulatory factors.
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Hrdy J, Vasickova P. Virus detection methods for different kinds of food and water samples – The importance of molecular techniques. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108764] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Martín G, Rojo-Alba S, Castelló-Abietar C, Abreu-Salinas F, Costales I, Boga JA, Melón S, Álvarez-Argüelles ME. Comparison of in-house SARS-CoV-2 genome extraction procedures. A need for COVID-19 pandemic. J Virol Methods 2022; 300:114415. [PMID: 34902458 PMCID: PMC8662953 DOI: 10.1016/j.jviromet.2021.114415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 10/08/2021] [Accepted: 12/08/2021] [Indexed: 12/28/2022]
Abstract
Among the methods used to diagnose COVID-19, those based on genomic detection by q(RT)-PCR are the most sensitive. To perform these assays, a previous genome extraction of the sample is required. The dramatic increase in the number of SARS-CoV-2 detection assays has increased the demand for extraction reagents hindering the supply of commercial reagents. Homemade reagents and procedures could be an alternative. Nasopharyngeal samples were extracted by seven different methods as well as the automatic method MagNaPure96, to detect SARS-CoV-2. All protocols show sensitivity higher than 87 %, in comparison with reference method, for detecting SARS-CoV-2 as well as human β- globin. Our results support that these procedures, using common and cheap reagents, are effective to extract RNA (from SARS-CoV-2) or DNA (from human β-globin) genome from nasopharyngeal swabs. Furthermore, these procedures could be easily adopted by routine diagnostic laboratories to implement detection methods to help to fight against COVID-19 pandemic.
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Affiliation(s)
- Gabriel Martín
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA) and Grupo de Investigación Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.
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Direct digital polymerase chain reaction chip for the detection of EGFR T790M mutation in plasma. Talanta 2022; 237:122977. [PMID: 34736699 DOI: 10.1016/j.talanta.2021.122977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/11/2021] [Accepted: 10/15/2021] [Indexed: 01/02/2023]
Abstract
Nucleic acid extraction and purification before amplification is considered an essential step for nucleic acid amplification testing. However, this may cause losses or introduce errors that can lead to inaccurate results, especially when using samples with a small nucleic acid concentration. Here, we developed a direct digital chip that enabled us to detect nucleic acid without DNA extraction and purification. We have developed a self-priming liquid-dispensing digital PCR chip that does not require any external power. This is a robust anti-evaporation digital PCR chip with fast sampling and accurate quantification performance. Using this chip, we have established an on-chip direct nucleic acid amplification method that does not require nucleic acid extraction and purification for liquid biopsy samples. In order to verify the feasibility of this chip for clinical samples, we detected the EGFR T790M mutation from plasma. Results showed that EGFR T790M mutation could be detected with an accuracy of 100% and a sensitivity of 0.01%. Without nucleic acid extraction and purification, the assay avoids complex pre-processing, thus saving time and achieving precise quantification. We expect our direct digital PCR chip to have practical applications in diagnosis, screening, and research, especially in resource-deprived regions.
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Stelzl E, Ciesek S, Cornberg M, Maasoumy B, Heim A, Chudy M, Olivero A, Miklau FN, Nickel A, Reinhardt A, Dietzsch M, Kessler HH. Reliable quantification of plasma HDV RNA is of paramount importance for treatment monitoring: A European multicenter study. J Clin Virol 2021; 142:104932. [PMID: 34333392 DOI: 10.1016/j.jcv.2021.104932] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 07/06/2021] [Accepted: 07/14/2021] [Indexed: 01/03/2023]
Abstract
OBJECTIVES Quantification of plasma hepatitis D virus (HDV) RNA is the essential tool for patient management under antiviral therapy. The aim of this European multicenter study was to improve the comparability of quantitative results reported by different laboratories using the CE/IVD-labeled RoboGene HDV RNA Quantification Kit 2.0 (Roboscreen GmbH) with different manual or automated nucleic acid extraction protocols/platforms and amplification/detection devices. METHODS For harmonization of HDV RNA concentrations obtained by different protocols, correction factors (CF) were determined using the 1st WHO International Standard for HDV RNA. The limit of detection (LOD) and accuracy were determined for each protocol by using reference material. Furthermore, clinical samples were analyzed and results compared. RESULTS The CF ranged from 20 to 1,870 depending on the protocol used. The LOD was found between 4 and 450 IU/ml. When accuracy was tested, external quality control (EQC) samples containing low HDV RNA concentrations were not detected by those protocols with higher LODs. For EQC samples, the maximum standard deviation of HDV RNA concentrations was found to be 0.53 log10 IU/ml, for clinical samples 0.87 log10 IU/mL. CONCLUSION To ensure reliability in quantification of HDV RNA, any modification of the extraction and amplification/detection protocol validated by the manufacturer requires revalidation. With the 1st WHO International Standard for HDV RNA, the CF could easily be calculated leading to harmonization of quantitative results. This warrants both accurate monitoring of response to existing anti-HDV treatment and comparability of study results investigating novel anti-HDV drugs.
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Affiliation(s)
- Evelyn Stelzl
- Research Unit Molecular Diagnostics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Austria
| | - Sandra Ciesek
- Institute of Virology, University Hospital Essen, Germany (currently Institute for Medical Virology, University Hospital Frankfurt, Germany)
| | - Markus Cornberg
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Germany
| | - Benjamin Maasoumy
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Germany
| | - Albert Heim
- Department for Virology, Hannover Medical School, Germany
| | - Michael Chudy
- Section of Molecular Virology, Paul-Ehrlich-Institut, Langen, Germany
| | - Antonella Olivero
- University of Torino, Department of Medical Sciences, Laboratory of Molecular Hepatology and Gastroenterology, Torino, Italy
| | - Fabienne N Miklau
- Research Unit Molecular Diagnostics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Austria
| | | | | | | | - Harald H Kessler
- Research Unit Molecular Diagnostics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Austria.
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Sabatier M, Bal A, Destras G, Regue H, Quéromès G, Cheynet V, Lina B, Bardel C, Brengel-Pesce K, Navratil V, Josset L. Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses. Microorganisms 2020; 8:E1539. [PMID: 33036303 PMCID: PMC7601816 DOI: 10.3390/microorganisms8101539] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022] Open
Abstract
Viral metagenomics next-generation sequencing (mNGS) is increasingly being used to characterize the human virome. The impact of viral nucleic extraction on virome profiling has been poorly studied. Here, we aimed to compare the sensitivity and sample and reagent contamination of three extraction methods used for viral mNGS: two automated platforms (eMAG; MagNA Pure 24, MP24) and the manual QIAamp Viral RNA Mini Kit (QIAamp). Clinical respiratory samples (positive for Respiratory Syncytial Virus or Herpes Simplex Virus), one mock sample (including five viruses isolated from respiratory samples), and a no-template control (NTC) were extracted and processed through an mNGS workflow. QIAamp yielded a lower proportion of viral reads for both clinical and mock samples. The sample cross-contamination was higher when using MP24, with up to 36.09% of the viral reads mapping to mock viruses in the NTC (vs. 1.53% and 1.45% for eMAG and QIAamp, respectively). The highest number of viral reads mapping to bacteriophages in the NTC was found with QIAamp, suggesting reagent contamination. Our results highlight the importance of the extraction method choice for accurate virome characterization.
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Affiliation(s)
- Marina Sabatier
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Antonin Bal
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Grégory Destras
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Hadrien Regue
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
| | - Grégory Quéromès
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
| | - Valérie Cheynet
- Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France; (V.C.); (K.B.-P.)
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Claire Bardel
- Université Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, F-69100 Villeurbanne, France;
| | - Karen Brengel-Pesce
- Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France; (V.C.); (K.B.-P.)
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Université Claude Bernard Lyon 1, F-69000 Lyon, France;
- European Virus Bioinformatics Center, Leutragraben 1, D-07743 Jena, Germany
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
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Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin Microbiol Rev 2020; 33:33/4/e00053-19. [PMID: 32907806 DOI: 10.1128/cmr.00053-19] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.
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Matzkies LM, Leitner E, Stelzl E, Assig K, Bozic M, Siebenhofer D, Mustafa ME, Steinmetz I, Kessler HH. Lack of sensitivity of an IVD/CE-labelled kit targeting the S gene for detection of SARS-CoV-2. Clin Microbiol Infect 2020; 26:1417.e1-1417.e4. [PMID: 32652240 PMCID: PMC7345380 DOI: 10.1016/j.cmi.2020.06.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 01/18/2023]
Abstract
OBJECTIVES New molecular tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are being rapidly launched in response to the coronavirus disease 2019 (COVID-19) pandemic. The aim of this study was to evaluate the analytical and clinical performance of the VIASURE SARS-CoV-2 S gene RT-PCR Kit on the BD Max™ system and to compare results with those obtained with the cobas® SARS-CoV-2 test on the cobas® 6800 system. METHODS For testing the analytical performance, reference material was used. Clinical samples (n = 101) obtained from individuals with symptoms compatible with COVID-19 were studied. Oropharyngeal and nasopharyngeal swabs were collected by using either ESwab™ or UTM™ collection systems. RESULTS When the analytical performance was evaluated, the sample containing the lowest SARS-CoV-2 concentration tested negative with the VIASURE test whereas results obtained with the cobas® test were found to be concordant with the results expected. Six out of the 101 clinical samples (5.9%) showed an inhibition with the VIASURE test. When analysing the remaining 95 clinical samples, 27 were found to be negative with both assays. Of 68 samples that were positive with the cobas® test, the VIASURE test missed 21 (30.9 %) samples. All of those 21 samples had shown Ct values ≥ 31 with the cobas® 6800 system. None of the samples tested positive with the VIASURE test and negative with the cobas® test. CONCLUSIONS The VIASURE test was impaired by a lack of sensitivity and a relatively high number of invalid results. When using the VIASURE test for routine testing, a significant number of COVID-19-positive samples would have been missed.
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Affiliation(s)
- L-M Matzkies
- Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - E Leitner
- Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - E Stelzl
- Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - K Assig
- Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - M Bozic
- Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - D Siebenhofer
- Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - M E Mustafa
- Medical-chemical laboratory Dr Mustafa, Dr Richter OG, Salzburg, Austria
| | - I Steinmetz
- Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria.
| | - H H Kessler
- Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
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Pauly MD, Kamili S, Hayden TM. Impact of nucleic acid extraction platforms on hepatitis virus genome detection. J Virol Methods 2019; 273:113715. [PMID: 31419455 DOI: 10.1016/j.jviromet.2019.113715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/07/2019] [Accepted: 08/12/2019] [Indexed: 02/06/2023]
Abstract
Detection and quantification of viral nucleic acids are important for diagnosing current viral infections and monitoring response to antiviral therapy. Automated nucleic acid extraction and purification platforms are routinely used during the first step in these processes in clinical and research laboratories. Here, we compare the extraction efficiencies of four MagNA Pure magnetic bead-based nucleic acid extraction platforms and associated kits using samples positive for nucleic acids from HAV, HBV, HCV, HDV, and HEV. These five hepatitis viruses are diverse in their virion structures and type of nucleic acid that compose their genomes. We found that the most efficient nucleic acid extraction platform and corresponding kit, when averaged across all tested viruses, was the MagNA Pure 96, which yielded twice as much detectable nucleic acid as the other platforms. However, the relative efficiencies of the different platforms varied by virus type, suggesting that an extraction platform that is more efficient for one virus type will not necessarily function better with a different virus type. Our results show that the choice of a nucleic acid extraction platform influences the sensitivity of the methodology and has the potential to generate false-negative results especially in samples with low levels of viral nucleic acids.
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Affiliation(s)
- Matthew D Pauly
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, GA, USA
| | - Saleem Kamili
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, GA, USA
| | - Tonya M Hayden
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, Atlanta, GA, USA.
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14
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Does Size Matter? Comparison of Extraction Yields for Different-Sized DNA Fragments by Seven Different Routine and Four New Circulating Cell-Free Extraction Methods. J Clin Microbiol 2018; 56:JCM.01061-18. [PMID: 30282788 DOI: 10.1128/jcm.01061-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/26/2018] [Indexed: 12/13/2022] Open
Abstract
An element essential for PCR detection of microbial agents in many sample types is the extraction step, designed to purify nucleic acids. Despite the importance of this step, yields have not been extensively compared across methods to determine whether the method used contributes to quantitative differences and the lack of commutability seen with existing clinical methods. This may in part explain why plasma and blood viral load assays have proven difficult to standardize. Also, studies have identified small DNA fragments of <200 bp in plasma (cell-free DNA [cfDNA]), which may include significant quantities of viral DNA. Our study evaluated extraction yields for 11 commercially available extraction methods, including 4 new methods designed to isolate cfDNA. Solutions of DNA fragments with sizes ranging from 50 to 1,500 bp were extracted, and then the eluates were tested by droplet digital PCR to determine the DNA fragment yield for each method. The results demonstrated a wide range of extraction yields across the variety of methods/instruments used, with the 50- and 100-bp fragment sizes showing especially inconsistent quantitative results and poor yields of less than 20%. Slightly higher, more consistent yields were seen with 2 of the 4 circulating cell-free extraction kits. These results demonstrate a significant need for further evaluation of nucleic acid yields across the variety of extraction platforms and highlight the poor extraction yields of small DNA fragments by existing methods. Further work is necessary to determine the impact of this inconsistency across instruments and the relevance of the low yields for smaller DNA fragments in clinical virology testing.
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Hirvonen JJ. Comparison of three multiplex real-time PCR assays for detection of enteric viruses in patients with diarrhea. Eur J Clin Microbiol Infect Dis 2018; 38:241-244. [DOI: 10.1007/s10096-018-3418-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/30/2018] [Indexed: 02/06/2023]
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16
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Harbusch NS, Bozic M, Konrad PM, Winkler M, Kessler HH. Evaluation of a new extraction platform in combination with molecular assays useful for monitoring immunosuppressed patients. J Clin Virol 2018; 108:59-63. [PMID: 30248619 DOI: 10.1016/j.jcv.2018.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/10/2018] [Accepted: 09/09/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND In the immunosuppressed, detection of viral reactivation at the earliest convenience and molecular monitoring are of paramount importance. Nucleic acid extraction has a major impact on the reliability of results obtained from molecular assays. OBJECTIVES The aim of this study was to investigate the accuracy of the new EMAG® nucleic acid extraction platform and to compare the performance of the new platform to that of the standard NucliSENS® easyMAG® instrument in the routine clinical laboratory. STUDY DESIGN For accuracy testing, reference material and for comparison studies, clinical specimens were used. In addition, a lab-flow analysis including estimation of hands-on time and that for automated extraction was performed. RESULTS When accuracy was tested, all 89 results obtained were found to be concordant with the results expected. When 648 clinical results were compared, 85.7% were found to be within ±0.5 log10 unit, 9.5% between ±0.5 and ±1.0 log10 unit, and 4.8% more than ±1.0 log10 unit. The overall time required for nucleic acid extraction of 8 samples in parallel was 94 min for the fully automated extraction mode and 82 min for the partly automated mode with the new platform, and 73 min with the standard instrument. Hands-on time was found to be shorter with the new platform. CONCLUSIONS The extraction performance of both platforms was found to be similar for EDTA whole blood, BAL, and urine specimens. The total turn-around time for nucleic acid extraction was found to be longer with the EMAG® platform, whereas hands-on time was reduced.
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Affiliation(s)
- Nora S Harbusch
- Research Unit Molecular Diagnostics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria
| | - Michael Bozic
- Research Unit Molecular Diagnostics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria
| | - Petra M Konrad
- Research Unit Molecular Diagnostics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria
| | - Michaela Winkler
- Research Unit Molecular Diagnostics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria
| | - Harald H Kessler
- Research Unit Molecular Diagnostics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria.
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Tan JJL, Balne PK, Leo YS, Tong L, Ng LFP, Agrawal R. Persistence of Zika virus in conjunctival fluid of convalescence patients. Sci Rep 2017; 7:11194. [PMID: 28894118 PMCID: PMC5594005 DOI: 10.1038/s41598-017-09479-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 07/26/2017] [Indexed: 11/29/2022] Open
Abstract
A widespread epidemic of Zika fever, caused by Zika virus (ZIKAV) has spread throughout the Pacific islands, the Americas and Southeast Asia. The increased incidences of ocular anomalies observed in ZIKAV-infected infants and adults may be associated with the rapid spread of ZIKAV. The objective of this study was to check if ZIKAV could be detected in human tears after the first week of infection. Twenty-nine patients with PCR confirmed ZIKAV infection during the Singapore August 2016 ZIKAV outbreak were enrolled for the study. Detection and quantification of ZIKAV RNA was performed on conjunctival swabs collected from both eyes of these patients at the late convalescent phase (30 days post-illness). Efficiency of viral isolation from swab samples was confirmed by the limit of detection (as low as 0.1 PFU/µL, equivalent to copy number of 4.9) in spiked swabs with different concentrations of ZIKAV (PFU/µL). Samples from three patients were found positive by qRT-PCR for ZIKAV and the viral RNA copy numbers detected in conjunctival swabs ranged from 5.2 to 9.3 copies respectively. ZIKAV could persist in the tears of infected patients for up to 30 days post-illness, and may therefore possess a potential public health risk of transmission.
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Affiliation(s)
- Jeslin J L Tan
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Praveen K Balne
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
| | - Yee-Sin Leo
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Infectious Disease and Epidemiology, Tan Tock Seng Hospital, Singapore, Singapore
| | - Louis Tong
- Singapore Eye Research Institute, Singapore, Singapore
- Institute of Infectious Disease and Epidemiology, Tan Tock Seng Hospital, Singapore, Singapore
- Singapore National Eye Center, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Lisa F P Ng
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.
| | - Rupesh Agrawal
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore.
- Singapore Eye Research Institute, Singapore, Singapore.
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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18
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Kim H, Hur M, Kim JY, Moon HW, Yun YM, Cho HC. Automated Nucleic Acid Extraction Systems for Detecting Cytomegalovirus and Epstein-Barr Virus Using Real-Time PCR: A Comparison Study Between the QIAsymphony RGQ and QIAcube Systems. Ann Lab Med 2017; 37:129-136. [PMID: 28028999 PMCID: PMC5203990 DOI: 10.3343/alm.2017.37.2.129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/21/2016] [Accepted: 11/17/2016] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Cytomegalovirus (CMV) and Epstein-Barr virus (EBV) are increasingly important in immunocompromised patients. Nucleic acid extraction methods could affect the results of viral nucleic acid amplification tests. We compared two automated nucleic acid extraction systems for detecting CMV and EBV using real-time PCR assays. METHODS One hundred and fifty-three whole blood (WB) samples were tested for CMV detection, and 117 WB samples were tested for EBV detection. Viral nucleic acid was extracted in parallel by using QIAsymphony RGQ and QIAcube (Qiagen GmbH, Germany), and real-time PCR assays for CMV and EBV were performed with a Rotor-Gene Q real-time PCR cycler (Qiagen). Detection rates for CMV and EBV were compared, and agreements between the two systems were analyzed. RESULTS The detection rate of CMV and EBV differed significantly between the QIAsymphony RGQ and QIAcube systems (CMV, 59.5% [91/153] vs 43.8% [67/153], P=0.0005; EBV, 59.0% [69/117] vs 42.7% [50/117], P=0.0008). The two systems showed moderate agreement for CMV and EBV detection (kappa=0.43 and 0.52, respectively). QIAsymphony RGQ showed a negligible correlation with QIAcube for quantitative EBV detection. QIAcube exhibited EBV PCR inhibition in 23.9% (28/117) of samples. CONCLUSIONS Automated nucleic acid extraction systems have different performances and significantly affect the detection of viral pathogens. The QIAsymphony RGQ system appears to be superior to the QIAcube system for detecting CMV and EBV. A suitable sample preparation system should be considered for optimized nucleic acid amplification in clinical laboratories.
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Affiliation(s)
- Hanah Kim
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, Korea
| | - Mina Hur
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, Korea.
| | - Ji Young Kim
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, Korea
| | - Hee Won Moon
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, Korea
| | - Yeo Min Yun
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, Korea
| | - Hyun Chan Cho
- Department of Laboratory Medicine, Hallym University College of Medicine, Seoul, Korea
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Garcia M, Chessa C, Bourgoin A, Giraudeau G, Plouzeau C, Agius G, Lévêque N, Beby-Defaux A. Comparison of eMAG™ versus NucliSENS ® EasyMAG ® performance on clinical specimens. J Clin Virol 2017; 88:52-57. [PMID: 28160729 PMCID: PMC7185493 DOI: 10.1016/j.jcv.2017.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/27/2016] [Accepted: 01/14/2017] [Indexed: 11/28/2022]
Abstract
eMAG™ is a new nucleic acid extraction platform based on magnetic silica technology. Performance of eMAG™ and easyMAG® were compared on various clinical specimens. Agreement for virus detection ranged from 84.6% to 95.9%. Correlation for virus quantitation displayed R2 from 0.802 to 0.995. The two platforms showed comparable performance on the clinical specimens tested.
Background eMAG™ (bioMerieux) is a new nucleic acid extraction platform based on magnetic silica technology, like its predecessor, NucliSENS® easyMAG® (bioMerieux). Using the same reagents and disposables, eMAG™ adds further automation, allowing simultaneous extraction of 48 samples directly from primary tubes, and distribution of nucleic acid extracts on PCR strips or in tubes at the end of the extraction process. Objective To compare the performance of eMAG™ and easyMAG® on various clinical specimens. Study design Respiratory (n = 199), whole blood (n = 50), plasma (n = 25) and urine (n = 25) specimens were extracted in parallel on both platforms. Both qualitative (respiratory virus, cell control, CMV, EBV, HHV6 and BKV detection) and quantitative (respiratory virus and cell control cycle thresolds, and CMV, EBV, HHV6 and BKV viral loads) results were compared. Results Detection of qualitative targets showed good agreement, ranging from 84.6% for whole blood to 95.9% for respiratory specimens. Correlations between quantitative results were good, with R2 ranging from 0.802 to 0.995. Quantitative results showed average overall differences below 0.10 log10 copies/mL between eMAG™ and easyMAG®. Conclusions The two platforms showed comparable performance on the types of clinical specimen tested. With higher automation and throughput than easyMAG®, the eMAG™ platform is likely to be advantageous for laboratories performing a large number of molecular analyses.
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Affiliation(s)
- Magali Garcia
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France; EA4331-LITEC, Université de Poitiers, Poitiers, France
| | - Céline Chessa
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France; EA4331-LITEC, Université de Poitiers, Poitiers, France
| | - Anne Bourgoin
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France
| | - Geneviève Giraudeau
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France
| | - Chloé Plouzeau
- Laboratoire de Bactériologie, CHU de Poitiers, Poitiers, France; Unité de Microbiologie Moléculaire et Séquençage, CHU de Poitiers, Poitiers, France
| | - Gérard Agius
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France
| | - Nicolas Lévêque
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France; EA4331-LITEC, Université de Poitiers, Poitiers, France.
| | - Agnès Beby-Defaux
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France; Unité de Microbiologie Moléculaire et Séquençage, CHU de Poitiers, Poitiers, France
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Inter-laboratory assessment of different digital PCR platforms for quantification of human cytomegalovirus DNA. Anal Bioanal Chem 2017; 409:2601-2614. [PMID: 28124757 PMCID: PMC5359388 DOI: 10.1007/s00216-017-0206-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/04/2017] [Accepted: 01/11/2017] [Indexed: 12/24/2022]
Abstract
Quantitative PCR (qPCR) is an important tool in pathogen detection. However, the use of different qPCR components, calibration materials and DNA extraction methods reduces comparability between laboratories, which can result in false diagnosis and discrepancies in patient care. The wider establishment of a metrological framework for nucleic acid tests could improve the degree of standardisation of pathogen detection and the quantification methods applied in the clinical context. To achieve this, accurate methods need to be developed and implemented as reference measurement procedures, and to facilitate characterisation of suitable certified reference materials. Digital PCR (dPCR) has already been used for pathogen quantification by analysing nucleic acids. Although dPCR has the potential to provide robust and accurate quantification of nucleic acids, further assessment of its actual performance characteristics is needed before it can be implemented in a metrological framework, and to allow adequate estimation of measurement uncertainties. Here, four laboratories demonstrated reproducibility (expanded measurement uncertainties below 15%) of dPCR for quantification of DNA from human cytomegalovirus, with no calibration to a common reference material. Using whole-virus material and extracted DNA, an intermediate precision (coefficients of variation below 25%) between three consecutive experiments was noted. Furthermore, discrepancies in estimated mean DNA copy number concentrations between laboratories were less than twofold, with DNA extraction as the main source of variability. These data demonstrate that dPCR offers a repeatable and reproducible method for quantification of viral DNA, and due to its satisfactory performance should be considered as candidate for reference methods for implementation in a metrological framework.
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The Effect of Nucleic Acid Extraction Platforms and Sample Storage on the Integrity of Viral RNA for Use in Whole Genome Sequencing. J Mol Diagn 2016; 19:303-312. [PMID: 28041870 DOI: 10.1016/j.jmoldx.2016.10.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/20/2016] [Accepted: 10/19/2016] [Indexed: 11/24/2022] Open
Abstract
Extraction of viral RNA and the storage of sample material are extremely important factors in the detection and whole genome sequencing (WGS) of viral pathogens. Although PCR-based detection methods focus on small amplicons, viral WGS applications require RNA of high quality and integrity for adequate sequence coverage and depth. This study examined the fitness of one manual and four automated RNA extraction platforms commonly used in diagnostic laboratories for use in metagenomic sequencing, how the practice of storing sample material in Qiagen buffer AVL before extraction affected the integrity of viral RNA and its suitability for use in amplicon-based WGS methods, and how the addition of Triton X-100 to buffer AVL affected the capability of the extraction platforms and the integrity of viral RNA in stored samples. This study found that the EZ1 platform gave the best performance of the automated platforms and gave comparable results to the frequently used manual Qiagen extraction protocol when extracted viral RNA was used in metagenomics sequencing. To maintain high levels of viral RNA integrity suitable for amplicon-based WGS, nucleic acid should be extracted from samples immediately, because even short storage periods in buffer AVL have a severe effect on integrity, and the addition of Triton X-100 had little effect on the quality of viral material for WGS.
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22
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Abbate I, Piralla A, Calvario A, Callegaro A, Giraldi C, Lunghi G, Gennari W, Sodano G, Ravanini P, Conaldi PG, Vatteroni M, Gaeta A, Paba P, Cavallo R, Baldanti F, Lazzarotto T. Nation-wide measure of variability in HCMV, EBV and BKV DNA quantification among centers involved in monitoring transplanted patients. J Clin Virol 2016; 82:76-83. [DOI: 10.1016/j.jcv.2016.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 06/30/2016] [Accepted: 07/01/2016] [Indexed: 11/28/2022]
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Luchsinger V, Prades Y, Ruiz M, Pizarro R, Rossi P, Lizama L, Garmendia ML, Meza A, Larrañaga C, Avendaño LF. Comparison of Luminex xTAG® RVP fast assay and real time RT-PCR for the detection of respiratory viruses in adults with community-acquired pneumonia. J Med Virol 2016; 88:1173-9. [PMID: 27061405 PMCID: PMC7166572 DOI: 10.1002/jmv.24463] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/26/2015] [Indexed: 11/18/2022]
Abstract
Community‐acquired pneumonia (CAP) is the third cause of death worldwide. Viruses are frequently detected in adult CAP. Highly sensitive diagnostic techniques should be used due to poor viral shedding. Different sampling methods can affect viral detection, being necessary to establish the optimal type of sample for identifying respiratory viruses in adults. The detection rates of respiratory viruses by Luminex xTAG® RVP fast assay, real time RT‐PCR (rtRT‐PCR) (Sacace®), and immunofluorescence assay (IFA) in adult CAP were performed in nasopharyngeal swabs (NPS) and aspirates (NPA) from 179 hospitalized adults. Positivity was 47.5% for Luminex®, 42.5% for rtRT‐PCR (P = 0.3), and 2.7% for IFA (2.7%) (P < 0.0). The sensitivity, specificity, and kappa coefficient of xTAG® RVP compared with rtRT‐PCR were 84.2%, 79.6%, and 0.62%, respectively. Luminex® and rtRT‐PCR detected 65 (58.0%) and 57 (50.9%) viruses in 112 NPA and 35 (34.3%) and 31 (30.4%) in 102 NPS, respectively (P < 0.01). xTAG® RVP is appropriate for detecting respiratory viruses in CAP adults. Both molecular techniques yielded better results with nasopharyngeal aspirate than swabs. J. Med. Virol. 88:1173–1179, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Vivian Luchsinger
- Program of Virology, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Yara Prades
- Program of Virology, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Mauricio Ruiz
- Clinical Hospital of the University of Chile, Santiago, Chile
| | - Rolando Pizarro
- Dr. Lucio Cordova Hospital of Infectious Diseases, Santiago, Chile
| | | | - Luis Lizama
- Program of Virology, Faculty of Medicine, University of Chile, Santiago, Chile
| | | | | | - Carmen Larrañaga
- Program of Virology, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Luis F Avendaño
- Program of Virology, Faculty of Medicine, University of Chile, Santiago, Chile
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Pavšič J, Žel J, Milavec M. Digital PCR for direct quantification of viruses without DNA extraction. Anal Bioanal Chem 2015; 408:67-75. [PMID: 26483186 PMCID: PMC4706837 DOI: 10.1007/s00216-015-9109-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/02/2015] [Accepted: 10/08/2015] [Indexed: 12/30/2022]
Abstract
DNA extraction before amplification is considered an essential step for quantification of viral DNA using real-time PCR (qPCR). However, this can directly affect the final measurements due to variable DNA yields and removal of inhibitors, which leads to increased inter-laboratory variability of qPCR measurements and reduced agreement on viral loads. Digital PCR (dPCR) might be an advantageous methodology for the measurement of virus concentrations, as it does not depend on any calibration material and it has higher tolerance to inhibitors. DNA quantification without an extraction step (i.e. direct quantification) was performed here using dPCR and two different human cytomegalovirus whole-virus materials. Two dPCR platforms were used for this direct quantification of the viral DNA, and these were compared with quantification of the extracted viral DNA in terms of yield and variability. Direct quantification of both whole-virus materials present in simple matrices like cell lysate or Tris-HCl buffer provided repeatable measurements of virus concentrations that were probably in closer agreement with the actual viral load than when estimated through quantification of the extracted DNA. Direct dPCR quantification of other viruses, reference materials and clinically relevant matrices is now needed to show the full versatility of this very promising and cost-efficient development in virus quantification.
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Affiliation(s)
- Jernej Pavšič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.
- Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia.
| | - Jana Žel
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
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Chakupurakal G, Leitzke S, Langerbeins P, Schiller J, Schneider PM, Holtick U, Shimabukuro-Vornhagen A, Theurich S, Chemnitz J, Hallek M, von Bergwelt-Baildon M, Scheid C. Nonmyeloablative allogeneic stem cell transplantation for chronic lymphocytic leukaemia offers the possibility of disease control with minimal morbidity and mortality--a single institution experience. Ann Hematol 2015; 94:1717-25. [PMID: 26259502 DOI: 10.1007/s00277-015-2449-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 07/08/2015] [Indexed: 10/23/2022]
Abstract
Allogeneic stem cell transplantation is a treatment option for patients with poor risk CLL. We conducted a retrospective analysis of all CLL patients allografted at our institution, the University Hospital of Cologne, Germany. Data was collected on 40 patients from 2004 to 2012. The mean age was 54, and the majority were male (75 %). On average, the patients were diagnosed 6 years (range 2-12) prior to transplant with an average of 4 years (range 1-8) from time of first-line therapy to transplant. The remission states at the time of transplant were complete remission (CR) (n = 4), stable disease (n = 10), partial remission (n = 20) and progressive disease (n = 6). Only reduced intensity conditioning regimens were employed. The average CD34(+) cell dose was 4.16 × 10(6)/kg. Neutrophil engraftment was seen by day +17 (range 10-23) post-transplant, and 88 % achieved 95-100 % donor chimerism by day 100. Overall survival, progression-free survival and non-relapse mortality at 2 years post-transplant were 65, 52.5 and 27.5 %, respectively. A total of 51 % of patients were found to be minimal residual disease (MRD)-negative at 1 year post-transplant. Our single-centre experience confirms the valuable role of allogeneic stem cell transplantation (allo-SCT) in the treatment of poor risk CLL patients with promising long-term survival and acceptable transplant-related mortality. The advent of newer therapeutic agents should not hinder the consideration of allo-SCT for this patient cohort as it remains the only curative option for these patients.
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Affiliation(s)
- G Chakupurakal
- Stem Cell Transplantation Program, Department of Internal Medicine, University Hospital of Cologne, Cologne, Germany,
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Verheyen J, Maizus K, Feist E, Tolman Z, Knops E, Saech J, Spengler L, Waterboer T, Burmester GR, Pawlita M, Pfister H, Rubbert-Roth A. Increased frequency of JC-polyomavirus detection in rheumatoid arthritis patients treated with multiple biologics. Med Microbiol Immunol 2015; 204:613-8. [DOI: 10.1007/s00430-015-0390-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 02/02/2015] [Indexed: 11/29/2022]
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Rotary-based platform with disposable fluidic modules for automated isolation of nucleic acids. Biomed Microdevices 2015; 17:18. [DOI: 10.1007/s10544-014-9920-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
BACKGROUND Effective upstream preparation of nucleic acid (NA) is important for molecular techniques that detect unique DNA or RNA sequences. The isolated NA should be extracted efficiently and purified away from inhibitors of a downstream molecular assay. CONTENT Many NA sample preparation techniques and commercial kits are available. Techniques for cell lysis and isolation or purification of NA were discovered in early NA characterization studies, evolved in the 20th century with molecular techniques, and still serve as the foundation for current methods. Advances in solid phase extraction methods with nonhazardous chemicals and automated systems have changed the way NA is prepared. Factors to consider when selecting NA preparation methods for molecular detection include lysis (from sources as diverse as human cells, viruses, bacterial spores, or protozoan oocysts), DNA vs RNA, sample background, appropriate preparation chemicals, and required detection limits. Methods are also selected on the basis of requirements for a particular application, such as sample volume or removal of inhibitors. Sometimes tradeoffs are made. SUMMARY Good automated and manual methods are available to effectively prepare NA for molecular detection in under an hour. Numerous systems are available for various applications, including techniques that are flexible for multiple sample types, are capable of processing large batches, can be performed in <10 min, or that can yield high-purity NA. When methods are selected using the most applicable combination of lysis isolation efficiency and concentration, NA preparation can be very effective, even for molecular detection of multiple targets from the same sample.
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Tan JJL, Capozzoli M, Sato M, Watthanaworawit W, Ling CL, Mauduit M, Malleret B, Grüner AC, Tan R, Nosten FH, Snounou G, Rénia L, Ng LFP. An integrated lab-on-chip for rapid identification and simultaneous differentiation of tropical pathogens. PLoS Negl Trop Dis 2014; 8:e3043. [PMID: 25078474 PMCID: PMC4117454 DOI: 10.1371/journal.pntd.0003043] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 06/10/2014] [Indexed: 01/03/2023] Open
Abstract
Tropical pathogens often cause febrile illnesses in humans and are responsible for considerable morbidity and mortality. The similarities in clinical symptoms provoked by these pathogens make diagnosis difficult. Thus, early, rapid and accurate diagnosis will be crucial in patient management and in the control of these diseases. In this study, a microfluidic lab-on-chip integrating multiplex molecular amplification and DNA microarray hybridization was developed for simultaneous detection and species differentiation of 26 globally important tropical pathogens. The analytical performance of the lab-on-chip for each pathogen ranged from 102 to 103 DNA or RNA copies. Assay performance was further verified with human whole blood spiked with Plasmodium falciparum and Chikungunya virus that yielded a range of detection from 200 to 4×105 parasites, and from 250 to 4×107 PFU respectively. This lab-on-chip was subsequently assessed and evaluated using 170 retrospective patient specimens in Singapore and Thailand. The lab-on-chip had a detection sensitivity of 83.1% and a specificity of 100% for P. falciparum; a sensitivity of 91.3% and a specificity of 99.3% for P. vivax; a positive 90.0% agreement and a specificity of 100% for Chikungunya virus; and a positive 85.0% agreement and a specificity of 100% for Dengue virus serotype 3 with reference methods conducted on the samples. Results suggested the practicality of an amplification microarray-based approach in a field setting for high-throughput detection and identification of tropical pathogens. Tropical diseases consist of a group of debilitating and fatal infections that occur primarily in rural and urban settings of tropical and subtropical countries. While the primary indices of an infection are mostly the presentation of clinical signs and symptoms, outcomes due to an infection with tropical pathogens are often unspecific. Accurate diagnosis is crucial for timely intervention, appropriate and adequate treatments, and patient management to prevent development of sequelae and transmission. Although, multiplex assays are available for the simultaneous detection of tropical pathogens, they are generally of low throughput. Performing parallel assays to cover the detection for a comprehensive scope of tropical infections that include protozoan, bacterial and viral infections is undoubtedly labor-intensive and time consuming. We present an integrated lab-on-chip using microfluidics technology coupled with reverse transcription (RT), PCR amplification, and microarray hybridization for the simultaneous identification and differentiation of 26 tropical pathogens that cause 14 globally important tropical diseases. Such diagnostics capacity would facilitate evidence-based management of patients, improve the specificity of treatment and, in some cases, even allow contact tracing and other disease-control measures.
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Affiliation(s)
- Jeslin J. L. Tan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore
| | - Monica Capozzoli
- CI Group, Molecular Diagnostic Business Unit, Microfluidics Division, ST Microelectronics, Catania, Italy
| | - Mitsuharu Sato
- Veredus Laboratories Pte Ltd, Singapore Science Park, Singapore
| | - Wanitda Watthanaworawit
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Clare L. Ling
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Marjorie Mauduit
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore
| | - Benoît Malleret
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore
| | - Anne-Charlotte Grüner
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore
| | - Rosemary Tan
- Veredus Laboratories Pte Ltd, Singapore Science Park, Singapore
| | - François H. Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Georges Snounou
- Université Pierre et Marie Curie (Paris VI), Centre Hospitalo-Universitaire Pitié-Salpêtrière, Paris, France
- INSERM UMR S 945, Paris, France
| | - Laurent Rénia
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore
- * E-mail: (LR); (LFPN)
| | - Lisa F. P. Ng
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- * E-mail: (LR); (LFPN)
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30
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Evaluation of three automated nucleic acid extraction systems for identification of respiratory viruses in clinical specimens by multiplex real-time PCR. BIOMED RESEARCH INTERNATIONAL 2014; 2014:430650. [PMID: 24868527 PMCID: PMC4020539 DOI: 10.1155/2014/430650] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/14/2014] [Accepted: 04/18/2014] [Indexed: 01/31/2023]
Abstract
A total of 84 nasopharyngeal swab specimens were collected from 84 patients. Viral nucleic acid was extracted by three automated extraction systems: QIAcube (Qiagen, Germany), EZ1 Advanced XL (Qiagen), and MICROLAB Nimbus IVD (Hamilton, USA). Fourteen RNA viruses and two DNA viruses were detected using the Anyplex II RV16 Detection kit (Seegene, Republic of Korea). The EZ1 Advanced XL system demonstrated the best analytical sensitivity for all the three viral strains. The nucleic acids extracted by EZ1 Advanced XL showed higher positive rates for virus detection than the others. Meanwhile, the MICROLAB Nimbus IVD system was comprised of fully automated steps from nucleic extraction to PCR setup function that could reduce human errors. For the nucleic acids recovered from nasopharyngeal swab specimens, the QIAcube system showed the fewest false negative results and the best concordance rate, and it may be more suitable for detecting various viruses including RNA and DNA virus strains. Each system showed different sensitivity and specificity for detection of certain viral pathogens and demonstrated different characteristics such as turnaround time and sample capacity. Therefore, these factors should be considered when new nucleic acid extraction systems are introduced to the laboratory.
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31
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Waggoner JJ, Pinsky BA. Comparison of automated nucleic acid extraction methods for the detection of cytomegalovirus DNA in fluids and tissues. PeerJ 2014; 2:e334. [PMID: 24765569 PMCID: PMC3994632 DOI: 10.7717/peerj.334] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 03/16/2014] [Indexed: 12/17/2022] Open
Abstract
Testing for cytomegalovirus (CMV) DNA is increasingly being used for specimen types other than plasma or whole blood. However, few studies have investigated the performance of different nucleic acid extraction protocols in such specimens. In this study, CMV extraction using the Cell-free 1000 and Pathogen Complex 400 protocols on the QIAsymphony Sample Processing (SP) system were compared using bronchoalveolar lavage fluid (BAL), tissue samples, and urine. The QIAsymphonyAssay Set-up (AS) system was used to assemble reactions using artus CMV PCR reagents and amplification was carried out on the Rotor-Gene Q. Samples from 93 patients previously tested for CMV DNA and negative samples spiked with CMV AD-169 were used to evaluate assay performance. The Pathogen Complex 400 protocol yielded the following results: BAL, sensitivity 100% (33/33), specificity 87% (20/23); tissue, sensitivity 100% (25/25), specificity 100% (20/20); urine, sensitivity 100% (21/21), specificity 100% (20/20). Cell-free 1000 extraction gave comparable results for BAL and tissue, however, for urine, the sensitivity was 86% (18/21) and specimen quantitation was inaccurate. Comparative studies of different extraction protocols and DNA detection methods in body fluids and tissues are needed, as assays optimized for blood or plasma will not necessarily perform well on other specimen types.
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Affiliation(s)
- Jesse J Waggoner
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine , Stanford, CA , USA
| | - Benjamin A Pinsky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine , Stanford, CA , USA ; Department of Pathology, Stanford University School of Medicine , Stanford, CA , USA
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Daher RK, Stewart G, Boissinot M, Bergeron MG. Isothermal Recombinase Polymerase Amplification Assay Applied to the Detection of Group B Streptococci in Vaginal/Anal Samples. Clin Chem 2014; 60:660-6. [DOI: 10.1373/clinchem.2013.213504] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Group B streptococcal infections are the leading cause of sepsis and meningitis in newborns. A rapid and reliable method for the detection of this pathogen at the time of delivery is needed for the early treatment of neonates. Isothermal amplification techniques such as recombinase polymerase amplification have advantages relative to PCR in terms of the speed of reaction and simplicity.
METHODS
We studied the clinical performance of recombinase polymerase amplification for the screening of group B streptococci in vaginal/anal samples from 50 pregnant women. We also compared the limit of detection and the analytical specificity of this isothermal assay to real-time PCR (RT-PCR).
RESULTS
Compared to RT-PCR, the recombinase polymerase amplification assay showed a clinical sensitivity of 96% and a clinical specificity of 100%. The limit of detection was 98 genome copies and the analytical specificity was 100% for a panel of 15 bacterial and/or fungal strains naturally found in the vaginal/anal flora. Time-to-result for the recombinase polymerase amplification assay was <20 min compared to 45 min for the RT-PCR assay; a positive sample could be detected as early as 8 min.
CONCLUSIONS
We demonstrate the potential of isothermal recombinase polymerase amplification assay as a clinically useful molecular diagnostic tool that is simple and faster than PCR/RT-PCR. Recombinase polymerase amplification offers great potential for nucleic acid–based diagnostics at the point of care.
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Affiliation(s)
- Rana K Daher
- Centre de recherche du CHU de Québec, Centre de recherche en infectiologie de l'Université Laval (CRI), Quebec, Canada
- Département de microbiologie-immunologie, faculté de médecine, Université Laval, Quebec, Canada
| | - Gale Stewart
- Centre de recherche du CHU de Québec, Centre de recherche en infectiologie de l'Université Laval (CRI), Quebec, Canada
| | - Maurice Boissinot
- Centre de recherche du CHU de Québec, Centre de recherche en infectiologie de l'Université Laval (CRI), Quebec, Canada
| | - Michel G Bergeron
- Centre de recherche du CHU de Québec, Centre de recherche en infectiologie de l'Université Laval (CRI), Quebec, Canada
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33
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Sun N, Deng C, Zhao X, Zhou Q, Ge G, Liu Y, Yan W, Xia Q. Extraction of total nucleic acid based on silica-coated magnetic particles for RT-qPCR detection of plant RNA virus/viroid. J Virol Methods 2014; 196:204-11. [DOI: 10.1016/j.jviromet.2013.11.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 11/16/2013] [Accepted: 11/20/2013] [Indexed: 10/26/2022]
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Pillet S, Roblin X, Cornillon J, Mariat C, Pozzetto B. Quantification of cytomegalovirus viral load. Expert Rev Anti Infect Ther 2013; 12:193-210. [PMID: 24341395 DOI: 10.1586/14787210.2014.870887] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cytomegalovirus (CMV), a member of the Herpesviridae family, is worldwide distributed. After the primary infection, CMV induces a latent infection with possible reactivation(s). It is responsible for severe to life-threatening diseases in immunocompromised patients and in foetuses and newborns of infected mothers. For monitoring CMV load, classical techniques based on rapid culture or pp65 antigenemia are progressively replaced by quantitative nuclear acid tests (QNAT), easier to implement and standardize. A large variety of QNAT are available from laboratory-developed assays to fully-automated commercial tests. The indications of CMV quantification include CMV infection during pregnancy and in newborns, and viral surveillance of grafted and non-grafted immunocompromised patients, patients with bowel inflammatory diseases and those hospitalised in intensive care unit. A close cooperation between virologists and clinicians is essential for optimizing the benefit of CMV DNA monitoring.
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Affiliation(s)
- Sylvie Pillet
- Faculty of Medicine of Saint-Etienne, University of Lyon, Groupe Immunité des Muqueuses et Agents Pathogènes (GIMAP)-EA3064, 42023 Saint-Etienne, France
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35
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Impact of the New Abbott
m
PLUS Feature on Clinical Laboratory Efficiencies of Abbott RealTi
m
e Assays for Detection of HIV-1, Hepatitis C Virus, Hepatitis B Virus, Chlamydia trachomatis, and Neisseria gonorrhoeae. J Clin Microbiol 2013; 51:4050-4. [DOI: 10.1128/jcm.01672-13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
Diagnostic laboratories are under increasing pressure to improve and expand their services. Greater flexibility in sample processing is a critical factor that can improve the time to results while reducing reagent waste, making laboratories more efficient and cost-effective. The introduction of the Abbott
m
PLUS feature, with the capacity for extended use of amplification reagents, significantly increases the flexibility of the
m
2000 platform and enables laboratories to customize their workflows based on sample arrival patterns. The flexibility in sample batch size offered by
m
PLUS enables significant reductions in processing times. For hepatitis B virus tests, a reduction in sample turnaround times of up to 30% (105 min) was observed for batches of 12 samples compared with those for batches of 24 samples; for
Chlamydia trachomatis
/
Neisseria gonorrhoeae
tests, the ability to run batches of 24 samples reduced the turnaround time by 83% (54 min) compared with that for batches of 48 samples. Excellent correlations between
m
PLUS and
m
2000 standard condition results were observed for all RealTi
m
e viral load assays evaluated in this study, with correlation
r
values of 0.998 for all assays tested. For the qualitative RealTi
m
e
C. trachomatis
/
N. gonorrhoeae
assay, the overall agreements between the two conditions tested were >98% for
C. trachomatis
and 100% for
N. gonorrhoeae
. Comparable precision results were observed for the two conditions tested for all RealTi
m
e assays. The enhanced
m
PLUS capability provides clinical laboratories with increased efficiencies to meet increasingly stringent turnaround time requirements without increased costs associated with discarding partially used amplification reagents.
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Abstract
DNA isolation is a fundamental initial step for molecular genetic studies. Two quite different methodologies are described in this unit: silica spin column and phenol/chloroform extraction. Currently, the most commonly used technique is the silica-based spin column, although phenol/chloroform extraction is still widely used. This unit also presents basic procedures for extraction of DNA from both fresh tissues and formalin-fixed, paraffin-embedded (FFPE) tissue samples.
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Affiliation(s)
- Ximeng Liu
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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37
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Cekin Y, Erman Daloğlu A, Oğünç D, Ozhak Baysan B, Dağlar D, Inan D, Mutlu D, Ongüt G, Colak D. Evaluation of vancomycin resistance 3 multiplexed PCR assay for detection of vancomycin-resistant enterococci from rectal swabs. Ann Lab Med 2013; 33:326-30. [PMID: 24003422 PMCID: PMC3756236 DOI: 10.3343/alm.2013.33.5.326] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/18/2013] [Accepted: 06/04/2013] [Indexed: 11/19/2022] Open
Abstract
Background Active screening for vancomycin-resistant enterococci (VRE) using rectal specimens is recommended to limit the spread of antimicrobial resistance within certain high-risk populations. We evaluated the diagnostic performance of Vancomycin Resistance 3 Multiplexed Tandem PCR assay (AusDiagnostics, Australia), a rapid multiplex real-time PCR assay that detects vanA and/or vanB. Methods Two-hundred-and-eleven rectal swabs from Hematology and Oncology unit were submitted for VRE surveillance via direct detection of vanA and/or vanB by culture and by using Vancomycin Resistance 3 Multiplexed Tandem PCR assay. Enterococci were identified to the species level by using standard biochemical tests and BD Phoenix Automated Microbiology System (BD Diagnostic Systems, USA). Vancomycin susceptibility of enterococci was determined using Etest (BioMerieux, France). Results Compared to the culture method, Vancomycin Resistance 3 Multiplexed Tandem PCR assay had a sensitivity of 84.0%, specificity of 98.8%, positive predictive value (PPV) of 91.3%, and negative predictive value (NPV) of 97.6%. The assay failed to detect 18 (8.5%) specimens because of the presence of PCR inhibitors; of the remaining 193 specimens, 25 (12.9%) were positive, 23 for vanA, and 2 for vanB. Although both sensitivity and specificity for vanA VRE was 100% compared to the culture method, all vanB-positive specimens tested negative by VRE culture. Conclusions Vancomycin Resistance 3 Multiplexed Tandem PCR assay is a rapid and laborsaving option for VRE surveillance for direct use on rectal swabs. However, the high rate of PCR failure owing to the inhibitors in the specimens and the low specificity for vanB should be considered when interpreting the results.
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Affiliation(s)
- Yesim Cekin
- Clinical Microbiology, Antalya Research and Training Hospital, Antalya, Turkey
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38
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Edelmann A, Eichenlaub U, Lepek S, Krüger DH, Hofmann J. Performance of the MagNA Pure 96 system for cytomegalovirus nucleic acid amplification testing in clinical samples. J Clin Microbiol 2013; 51:1600-1. [PMID: 23467597 PMCID: PMC3647938 DOI: 10.1128/jcm.03289-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 02/25/2013] [Indexed: 11/20/2022] Open
Abstract
This report shows the performance of MagNA Pure 96 automated nucleic acid extraction for the quantitative detection of cytomegalovirus DNA in clinical samples by real-time PCR. The obtained results demonstrate that this workflow is characterized by high sensitivity and linearity and ensures reliable, reproducible clinical diagnostics.
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Affiliation(s)
- A Edelmann
- Labor Berlin-Charité Vivantes GmbH, Virology, Berlin, Germany.
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39
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Roeber F, Jex AR, Gasser RB. Comparative evaluation of two DNA isolation techniques for PCR-based diagnosis of gastrointestinal nematode infections in sheep. Mol Cell Probes 2013; 27:153-7. [PMID: 23524142 DOI: 10.1016/j.mcp.2013.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 03/05/2013] [Accepted: 03/05/2013] [Indexed: 11/16/2022]
Abstract
The specific diagnosis of gastrointestinal parasite infections in livestock is central to their control. PCR assays have been developed for routine diagnosis and to overcome limitations of classical methods. Central to the performance of such assays is the effective isolation of the nucleic acids from samples and the elimination of components that are inhibitory to PCR. Here, we directly compared two techniques for the isolation of DNA from strongylid nematode eggs from faecal samples from sheep, and assessed their performance in relation to the sensitivity and specificity of PCR, time required for DNA isolation and ease of use. The results showed differences in the performance of the two isolation techniques, subsequently effecting the PCR results. The main differences related to the time required for DNA isolation, and the elimination of inhibitory substances from the DNA isolated by one technique but not the other.
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Affiliation(s)
- Florian Roeber
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Alvarez WA, Gibbons PM, Rivera S, Archer LL, Childress AL, Wellehan JF. Development of a quantitative PCR for rapid and sensitive diagnosis of an intranuclear coccidian parasite in Testudines (TINC), and detection in the critically endangered Arakan forest turtle (Heosemys depressa). Vet Parasitol 2013; 193:66-70. [DOI: 10.1016/j.vetpar.2012.11.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Revised: 11/13/2012] [Accepted: 11/24/2012] [Indexed: 11/25/2022]
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Stals A, Mathijs E, Baert L, Botteldoorn N, Denayer S, Mauroy A, Scipioni A, Daube G, Dierick K, Herman L, Van Coillie E, Thiry E, Uyttendaele M. Molecular detection and genotyping of noroviruses. FOOD AND ENVIRONMENTAL VIROLOGY 2012; 4:153-67. [PMID: 23412888 DOI: 10.1007/s12560-012-9092-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 10/06/2012] [Indexed: 05/13/2023]
Abstract
Noroviruses (NoVs) are a major cause of gastroenteritis worldwide in humans and animals and are known as very infectious viral agents. They are spread through feces and vomit via several transmission routes involving person-to-person contact, food, and water. Investigation of these transmission routes requires sensitive methods for detection of NoVs. As NoVs cannot be cultivated to date, detection of these viruses relies on the use of molecular methods such as (real-time) reverse transcriptase polymerase chain reaction (RT-PCR). Regardless of the matrix, detection of NoVs generally requires three subsequent steps: a virus extraction step, RNA purification, and molecular detection of the purified RNA, occasionally followed by molecular genotyping. The current review mainly focused on the molecular detection and genotyping of NoVs. The most conserved region in the genome of human infective NoVs is the ORF1/ORF2 junction and has been used as a preferred target region for molecular detection of NoVs by methods such as (real-time) RT-PCR, NASBA, and LAMP. In case of animal NoVs, broad range molecular assays have most frequently been applied for molecular detection. Regarding genotyping of NoVs, five regions situated in the polymerase and capsid genes have been used for conventional RT-PCR amplification and sequencing. As the expected levels of NoVs on food and in water are very low and inhibition of molecular methods can occur in these matrices, quality control including adequate positive and negative controls is an essential part of NoV detection. Although the development of molecular methods for NoV detection has certainly aided in the understanding of NoV transmission, it has also led to new problems such as the question whether low levels of human NoV detected on fresh produce and shellfish could pose a threat to public health.
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Affiliation(s)
- Ambroos Stals
- Laboratory of Food Microbiology and Food Preservation, Faculty of Bioscience Engineering, Department of Food Safety and Food Quality, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
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Pérez-Ruiz M, Pedrosa-Corral I, Sanbonmatsu-Gámez S, Navarro-Marí M. Laboratory detection of respiratory viruses by automated techniques. Open Virol J 2012; 6:151-9. [PMID: 23248735 PMCID: PMC3522051 DOI: 10.2174/1874357901206010151] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 09/11/2012] [Accepted: 09/20/2012] [Indexed: 12/26/2022] Open
Abstract
Advances in clinical virology for detecting respiratory viruses have been focused on nucleic acids amplification techniques, which have converted in the reference method for the diagnosis of acute respiratory infections of viral aetiology. Improvements of current commercial molecular assays to reduce hands-on-time rely on two strategies, a stepwise automation (semi-automation) and the complete automation of the whole procedure. Contributions to the former strategy have been the use of automated nucleic acids extractors, multiplex PCR, real-time PCR and/or DNA arrays for detection of amplicons. Commercial fully-automated molecular systems are now available for the detection of respiratory viruses. Some of them could convert in point-of-care methods substituting antigen tests for detection of respiratory syncytial virus and influenza A and B viruses. This article describes laboratory methods for detection of respiratory viruses. A cost-effective and rational diagnostic algorithm is proposed, considering technical aspects of the available assays, infrastructure possibilities of each laboratory and clinic-epidemiologic factors of the infection.
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Affiliation(s)
- Mercedes Pérez-Ruiz
- Laboratorio de Referencia de Salud Pública para Enfermedades con Sospecha de Etiología Vírica en Andalucía (Consejería de Salud), Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Avda, Fuerzas Armadas, 2, 18014 Granada, Spain
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König K, Vogeser M. Sample preparation for measurement of plasma mycophenolic acid concentrations using chromatographically functionalized magnetic micro-particles. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2012; 18:413-417. [PMID: 23221116 DOI: 10.1255/ejms.1197] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Utilizing chromatographically modified magnetic micro-particles is an innovative principle of sample preparation for quantitative analysis of small molecules in complex biomedical samples by liquid chromatography tandem mass spectrometry. Since no vacuum or pressure has to be applied-in contrast to cartridge based solid phase extraction protocols-the principle's main characteristics are potentially straightforward automation and a high extraction performance (in terms of µg of extraction material per µL of sample). Following first descriptions of the approach, this article reports, the validation of a magnetic particle-based, analytical method for the quantification of the immunosuppressant mycophenolic acid in plasma. This sample preparation technology has shown a good performance for this clinically relevant analyte. As a result, we conclude that further work towards the implementation of this technology in a multi- analyte approach on robotic systems, aiming towards a fully automated process, is justified.
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Affiliation(s)
- Katrin König
- Institute of Laboratory Medicine, University of Munich, München, Germany.
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