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Balaban Hanoglu S, Harmanci D, Evran S, Timur S. Detection strategies of infectious diseases via peptide-based electrochemical biosensors. Bioelectrochemistry 2024; 160:108784. [PMID: 39094447 DOI: 10.1016/j.bioelechem.2024.108784] [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: 04/30/2024] [Revised: 07/21/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
Infectious diseases have threatened human life for as long as humankind has existed. One of the most crucial aspects of fighting against these infections is diagnosis to prevent disease spread. However, traditional diagnostic methods prove insufficient and time-consuming in the face of a pandemic. Therefore, studies focusing on detecting viruses causing these diseases have increased, with a particular emphasis on developing rapid, accurate, specific, user-friendly, and portable electrochemical biosensor systems. Peptides are used integral components in biosensor fabrication for several reasons, including various and adaptable synthesis protocols, long-term stability, and specificity. Here, we discuss peptide-based electrochemical biosensor systems that have been developed over the last decade for the detection of infectious diseases. In contrast to other reports on peptide-based biosensors, we have emphasized the following points i) the synthesis methods of peptides for biosensor applications, ii) biosensor fabrication approaches of peptide-based electrochemical biosensor systems, iii) the comparison of electrochemical biosensors with other peptide-based biosensor systems and the advantages and limitations of electrochemical biosensors, iv) the pros and cons of peptides compared to other biorecognition molecules in the detection of infectious diseases, v) different perspectives for future studies with the shortcomings of the systems developed in the past decade.
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Affiliation(s)
- Simge Balaban Hanoglu
- Department of Biochemistry, Faculty of Science, Ege University, Bornova, Izmir 35100, Turkey.
| | - Duygu Harmanci
- Central Research Test and Analysis Laboratory, Application and Research Center, Ege University, Bornova, Izmir 35100, Turkey
| | - Serap Evran
- Department of Biochemistry, Faculty of Science, Ege University, Bornova, Izmir 35100, Turkey
| | - Suna Timur
- Department of Biochemistry, Faculty of Science, Ege University, Bornova, Izmir 35100, Turkey; Central Research Test and Analysis Laboratory, Application and Research Center, Ege University, Bornova, Izmir 35100, Turkey.
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2
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Paniz-Mondolfi AE, Ramírez JD. FDA's proposed rule and its regulatory impact on emerging and reemerging neglected tropical diseases in the United States. PLoS Negl Trop Dis 2024; 18:e0012116. [PMID: 38722919 PMCID: PMC11081280 DOI: 10.1371/journal.pntd.0012116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024] Open
Abstract
Diagnosing infectious diseases significantly influences patient care, aiding in outbreak identification, response, and public health monitoring. However, the range of FDA-approved molecular tests remains notably limited, especially concerning neglected tropical diseases (NTDs). Drawing upon our experience as one of the largest healthcare networks in the greater New York metropolitan area, this viewpoint manuscript aims to spotlight the existing diagnostic landscape and unmet clinical needs for 4 emerging NTDs increasingly prevalent in the United States, additionally, it delves into the possible adverse effects of the FDA's Proposed Rule on Laboratory-Developed Tests for these clinical conditions and the broader spectrum of NTDs.
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Affiliation(s)
- Alberto E. Paniz-Mondolfi
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Juan David Ramírez
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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3
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Leta S, Chibssa TR, Paeshuyse J. CRISPR-Cas12/Cas13: Bibliometric analysis and systematic review of its application in infectious disease detection. J Infect Public Health 2024; 17:741-747. [PMID: 38518680 DOI: 10.1016/j.jiph.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/29/2024] [Accepted: 03/03/2024] [Indexed: 03/24/2024] Open
Abstract
BACKGROUND Infectious diseases impose a significant burden on the global public health and economy, resulting in an estimated 15 million deaths out of 57 million annually worldwide. This study examines the current state of CRISPR-Cas12/Cas13 research, focusing on its applications in infectious disease detection and its evolutionary trajectory. METHODS A bibliometric analysis and systematic review were conducted by retrieving CRISPR-Cas12/Cas13-related articles published between January 1, 2015 to December 31, 2022, from the Web of Science database. The research protocol was registered with International Platform of Registered Systematic Review and Meta-analysis Protocols (INPLASY202380062). RESULTS Our search identified 1987 articles, of which, 1856 were included in the bibliometric analysis and 445 were used in qualitative analysis. The study reveals a substantial increase in scientific production on CRISPR-Cas12/Cas13, with an annual growth rate of 104.5%. The United States leads in the number of published articles. The systematic review identified 580 different diagnostic assays targeting 170 pathogens, with SARS-CoV-2 dominating with 158 assays. Recombinase polymerase amplification (RPA)/reverse transcription-RPA (RT-RPA) emerged as the predominant amplification method, while lateral flow assay was the most common readout method. Approximately 72% of the diagnostic assays developed are suitable for point-of-care testing. CONCLUSION The rapid increase in research on CRISPR-Cas12/Cas13 between 2015 and 2022 suggests promising potential for advancements in infectious disease diagnosis. Given the numerous advantages of CRISPR-Cas technology for disease detection over other methods, and the dedicated efforts of scientists from around the world, it is reasonable to anticipate that CRISPR-Cas technology may emerge as a formidable alternative, offering the possibility of expedited point-of-care testing in the not-too-distant future.
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Affiliation(s)
- Samson Leta
- Laboratory of Host Pathogen Interaction in Livestock, Division of Animal and Human Health Engineering, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium; Department of Biomedical Sciences, College of Veterinary Medicine and Agriculture, Addis Ababa University, P.O. Box 34, Bishoftu, Ethiopia
| | | | - Jan Paeshuyse
- Laboratory of Host Pathogen Interaction in Livestock, Division of Animal and Human Health Engineering, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium.
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de Stigter Y, van der Veer HJ, Rosier BJHM, Merkx M. Bioluminescent Intercalating Dyes for Ratiometric Nucleic Acid Detection. ACS Chem Biol 2024; 19:575-583. [PMID: 38315567 PMCID: PMC10877566 DOI: 10.1021/acschembio.3c00755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/07/2024]
Abstract
Rapid and sensitive DNA detection methods that can be conducted at the point of need may aid in disease diagnosis and monitoring. However, translation of current assays has proven challenging, as they typically require specialized equipment or probe-specific modifications for every new target DNA. Here, we present Luminescent Multivalent Intercalating Dye (LUMID), off-the-shelf bioluminescent sensors consisting of intercalating dyes conjugated to a NanoLuc luciferase, which allow for nonspecific detection of double-stranded DNA through a blue-to-green color change. Through the incorporation of multiple, tandem-arranged dyes separated by positively charged linkers, DNA-binding affinities were improved by over 2 orders of magnitude, detecting nanomolar DNA concentrations with an 8-fold change in green/blue ratio. We show that LUMID is easily combined with loop-mediated isothermal amplification (LAMP), enabling sequence-specific detection of viral DNA with attomolar sensitivity and a smartphone-based readout. With LUMID, we have thus developed a tool for simple and sensitive DNA detection that is particularly attractive for point-of-need applications.
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Affiliation(s)
- Yosta de Stigter
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Harmen J. van der Veer
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Bas J. H. M. Rosier
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
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5
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Bothra A, Perry ML, Wei E, Moayeri M, Ma Q, Biamonte MA, Siirin M, Leppla SH. S9.6-based hybrid capture immunoassay for pathogen detection. Sci Rep 2023; 13:22562. [PMID: 38110611 PMCID: PMC10728093 DOI: 10.1038/s41598-023-49881-w] [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: 10/20/2023] [Accepted: 12/13/2023] [Indexed: 12/20/2023] Open
Abstract
The detection of pathogens is critical for clinical diagnosis and public health surveillance. Detection is usually done with nucleic acid-based tests (NATs) and rapid antigen tests (e.g., lateral flow assays [LFAs]). Although NATs are more sensitive and specific, their use is often limited in resource-poor settings due to specialized requirements. To address this limitation, we developed a rapid DNA-RNA Hybrid Capture immunoassay (HC) that specifically detects RNA from pathogens. This assay utilizes a unique monoclonal antibody, S9.6, which binds DNA-RNA hybrids. Biotinylated single-stranded DNA probes are hybridized to target RNAs, followed by hybrid capture on streptavidin and detection with S9.6. The HC-ELISA assay can detect as few as 104 RNA molecules that are 2.2 kb in length. We also adapted this assay into a LFA format, where captured Bacillus anthracis rpoB RNA of 3.5 kb length was detectable from a bacterial load equivalent to 107 CFU per 100 mg of mouse tissue using either HC-ELISA or HC-LFA. Importantly, we also demonstrated the versatility of HC by detecting other pathogens, including SARS-CoV-2 and Toxoplasma gondii, showing its potential for broad pathogen detection. Notably, HC does not require amplification of the target nucleic acid and utilizes economical formats like ELISA and LFA, making it suitable for use in sentinel labs for pathogen detection or as a molecular tool in basic research laboratories. Our study highlights the potential of HC as a sensitive and versatile method for RNA-based pathogen detection.
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Affiliation(s)
- Ankur Bothra
- Microbial Pathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA.
| | - Megan L Perry
- Microbial Pathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Elena Wei
- Microbial Pathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Mahtab Moayeri
- Microbial Pathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Qian Ma
- Microbial Pathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | | | - Marina Siirin
- Drugs and Diagnostics for Tropical Diseases, San Diego, CA, USA
| | - Stephen H Leppla
- Microbial Pathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
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6
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Hemmateenejad B, Rafatmah E, Shojaeifard Z. Microfluidic paper and thread-based separations: Chromatography and electrophoresis. J Chromatogr A 2023; 1704:464117. [PMID: 37300912 DOI: 10.1016/j.chroma.2023.464117] [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: 04/06/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
Paper and thread are widely used as the substrates for fabricating low-cost, disposable, and portable microfluidic analytical devices used in clinical, environmental, and food safety monitoring. Concerning separation methods including chromatography and electrophoresis, these substrates provide unique platforms for developing portable devices. This review focuses on summarizing recent research on the miniaturization of the separation techniques using paper and thread. Preconcentration, purification, desalination, and separation of various analytes are achievable using electrophoresis and chromatography methods integrated with modified or unmodified paper/thread wicking channels. A variety of 2D and 3D designs of paper/thread platforms for zone electrophoresis, capillary electrophoresis, and modified/unmodified chromatography are discussed with emphasis on their limitation and improvements. The current progress in the signal amplification strategies such as isoelectric focusing, isotachophoresis, ion concentration polarization, isoelectric focusing, and stacking methods in paper-based devices are reviewed. Different strategies for chromatographic separations based on paper/thread will be explained. The separation of target species from complex samples and their determination by integration with other analytical methods like spectroscopy and electrochemistry are well-listed. Furthermore, the innovations for plasma and cell separation from blood as an important human biofluid are presented, and the related paper/thread modification methods are explored.
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7
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Belov A, Yang H, Forshee RA, Whitaker BI, Eder AF, Chancey C, Anderson SA. Modeling the Risk of HIV Transfusion Transmission. J Acquir Immune Defic Syndr 2023; 92:173-179. [PMID: 36219691 DOI: 10.1097/qai.0000000000003115] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 09/19/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND Blood donations are routinely screened for HIV to prevent an infectious unit from being released to the blood supply. Despite improvements to blood screening assays, donations from infected donors remain undetectable during the window period (WP), when the virus has not yet replicated above the lower limit of detection (LOD) of a screening assay. To aid in the quantitative risk assessments of WP donations, a dose-response model describing the probability of transfusion-transmission of HIV over a range of viral RNA copies was developed. METHODS An exponential model was chosen based on data fit and parsimony. A data set from a HIV challenge study using a nonhuman primate model and another data set from reported human blood transfusions associated with HIV infected donors were separately fit to the model to generate parameter estimates. A Bayesian framework using No-U-Turn Sampling (NUTS) and Monte Carlo simulations was performed to generate posterior distributions quantifying uncertainty in parameter estimation and model predictions. RESULTS The parameters of the exponential model for both nonhuman primate and human data were estimated with a mean (95% credible intervals) of 2.70 × 10 -2 (7.74 × 10 -3 , 6.06 × 10 -2 ) and 7.56 × 10 -4 (3.68 × 10 -4 , 1.31 × 10 -3 ), respectively. The predicted ID 50 for the animal and human models was 26 (12, 90) and 918 (529, 1886) RNA copies transfused, respectively. CONCLUSION This dose-response model can be used in a quantitative framework to estimate the probability of transfusion-transmission of HIV through WP donations. These models can be especially informative when assessing risk from blood components with low viral load.
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Affiliation(s)
- Artur Belov
- Office of Biostatistics & Epidemiology, Center for Biologics Evaluation and Research, US FDA; and
| | - Hong Yang
- Office of Biostatistics & Epidemiology, Center for Biologics Evaluation and Research, US FDA; and
| | - Richard A Forshee
- Office of Biostatistics & Epidemiology, Center for Biologics Evaluation and Research, US FDA; and
| | - Barbee I Whitaker
- Office of Biostatistics & Epidemiology, Center for Biologics Evaluation and Research, US FDA; and
| | - Anne F Eder
- Office of Blood Research and Review, Center for Biologics Evaluation and Research, US FDA
| | - Caren Chancey
- Office of Blood Research and Review, Center for Biologics Evaluation and Research, US FDA
| | - Steven A Anderson
- Office of Biostatistics & Epidemiology, Center for Biologics Evaluation and Research, US FDA; and
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8
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Arizti-Sanz J, Bradley A, Zhang YB, Boehm CK, Freije CA, Grunberg ME, Kosoko-Thoroddsen TSF, Welch NL, Pillai PP, Mantena S, Kim G, Uwanibe JN, John OG, Eromon PE, Kocher G, Gross R, Lee JS, Hensley LE, MacInnis BL, Johnson J, Springer M, Happi CT, Sabeti PC, Myhrvold C. Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants. Nat Biomed Eng 2022; 6:932-943. [PMID: 35637389 PMCID: PMC9398993 DOI: 10.1038/s41551-022-00889-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/01/2022] [Indexed: 02/03/2023]
Abstract
The widespread transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) call for rapid nucleic acid diagnostics that are easy to use outside of centralized clinical laboratories. Here we report the development and performance benchmarking of Cas13-based nucleic acid assays leveraging lyophilised reagents and fast sample inactivation at ambient temperature. The assays, which we named SHINEv.2 (for 'streamlined highlighting of infections to navigate epidemics, version 2'), simplify the previously reported RNA-extraction-free SHINEv.1 technology by eliminating heating steps and the need for cold storage of the reagents. SHINEv.2 detected SARS-CoV-2 in nasopharyngeal samples with 90.5% sensitivity and 100% specificity (benchmarked against the reverse transcription quantitative polymerase chain reaction) in less than 90 min, using lateral-flow technology and incubation in a heat block at 37 °C. SHINEv.2 also allows for the visual discrimination of the Alpha, Beta, Gamma, Delta and Omicron SARS-CoV-2 variants, and can be run without performance losses by using body heat. Accurate, easy-to-use and equipment-free nucleic acid assays could facilitate wider testing for SARS-CoV-2 and other pathogens in point-of-care and at-home settings.
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Affiliation(s)
- Jon Arizti-Sanz
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, USA
| | - A'Doriann Bradley
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Yibin B Zhang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Chloe K Boehm
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Catherine A Freije
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Michelle E Grunberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - Nicole L Welch
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Priya P Pillai
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Sreekar Mantena
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Gaeun Kim
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Jessica N Uwanibe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Oluwagboadurami G John
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Philomena E Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Gregory Kocher
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Frederick, MD, USA
| | - Robin Gross
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Frederick, MD, USA
| | - Justin S Lee
- Biotechnology Cores Facility Branch, Division of Scientific Resources, National Center for Emerging and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lisa E Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Frederick, MD, USA
| | - Bronwyn L MacInnis
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jeremy Johnson
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Christian T Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Pardis C Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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Liu D, Rodriguez GD, Zhou HY, Cheng YX, Li X, Tang W, Prasad N, Chen CC, Singh V, Konadu E, James KK, Bahamon MF, Chen Y, Segal-Maurer S, Wu A, Rodgers WH. SARS-CoV-2 Continuous Genetic Divergence and Changes in Multiplex RT-PCR Detection Pattern on Positive Retesting Median 150 Days after Initial Infection. Int J Mol Sci 2022; 23:ijms23116254. [PMID: 35682933 PMCID: PMC9181733 DOI: 10.3390/ijms23116254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Being in the epicenter of the COVID-19 pandemic, our lab tested 193,054 specimens for SARS-CoV-2 RNA by diagnostic multiplex reverse transcription polymerase chain reaction (mRT-PCR) starting in March 2020, of which 17,196 specimens resulted positive. To investigate the dynamics of virus molecular evolution and epidemiology, whole genome amplification (WGA) and Next Generation Sequencing (NGS) were performed on 9516 isolates. 7586 isolates with a high quality were further analyzed for the mutation frequency and spectrum. Lastly, we evaluated the utility of the mRT-PCR detection pattern among 26 reinfected patients with repeat positive testing three months after testing negative from the initial infection. Our results show a continuation of the genetic divergence in viral genomes. Furthermore, our results indicate that independent mutations in the primer and probe regions of the nucleocapsid gene amplicon and envelope gene amplicon accumulate over time. Some of these mutations correlate with the changes of detection pattern of viral targets of mRT-PCR. Our data highlight the significance of a continuous genetic divergence on a gene amplification-based assay, the value of the mRT-PCR detection pattern for complementing the clinical diagnosis of reinfection, and the potential for WGA and NGS to identify mutation hotspots throughout the entire viral genome to optimize the design of the PCR-based gene amplification assay.
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Affiliation(s)
- Dakai Liu
- Department of Pathology and Clinical Laboratories, NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA; (D.L.); (V.S.); (E.K.); (K.K.J.); (M.F.B.); (Y.C.)
| | - George D. Rodriguez
- Division of Infectious Disease, NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA; (N.P.); (S.S.-M.)
- Correspondence: (G.D.R.); (A.W.); (W.H.R.)
| | - Hang-Yu Zhou
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China; (H.-Y.Z.); (Y.-X.C.)
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Ye-Xiao Cheng
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China; (H.-Y.Z.); (Y.-X.C.)
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Xiaofeng Li
- National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 510182, China;
| | - Wenwen Tang
- Vascular Biology and Therapeutics Program, Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA;
| | - Nishant Prasad
- Division of Infectious Disease, NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA; (N.P.); (S.S.-M.)
| | - Chun-Cheng Chen
- Department of Surgery, NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA;
| | - Vishnu Singh
- Department of Pathology and Clinical Laboratories, NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA; (D.L.); (V.S.); (E.K.); (K.K.J.); (M.F.B.); (Y.C.)
| | - Eric Konadu
- Department of Pathology and Clinical Laboratories, NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA; (D.L.); (V.S.); (E.K.); (K.K.J.); (M.F.B.); (Y.C.)
| | - Keither K. James
- Department of Pathology and Clinical Laboratories, NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA; (D.L.); (V.S.); (E.K.); (K.K.J.); (M.F.B.); (Y.C.)
| | - Maria F. Bahamon
- Department of Pathology and Clinical Laboratories, NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA; (D.L.); (V.S.); (E.K.); (K.K.J.); (M.F.B.); (Y.C.)
| | - Yvonne Chen
- Department of Pathology and Clinical Laboratories, NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA; (D.L.); (V.S.); (E.K.); (K.K.J.); (M.F.B.); (Y.C.)
| | - Sorana Segal-Maurer
- Division of Infectious Disease, NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA; (N.P.); (S.S.-M.)
| | - Aiping Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China; (H.-Y.Z.); (Y.-X.C.)
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
- Correspondence: (G.D.R.); (A.W.); (W.H.R.)
| | - William Harry Rodgers
- Department of Pathology and Clinical Laboratories, NewYork-Presbyterian Queens, 56-45 Main Street Flushing, New York, NY 11355, USA; (D.L.); (V.S.); (E.K.); (K.K.J.); (M.F.B.); (Y.C.)
- Department of Pathology and Laboratory Medicine, Weil Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
- Correspondence: (G.D.R.); (A.W.); (W.H.R.)
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10
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O'Bryant SC, Momin Z, Camp E, Jones J, Meskill S. Longitudinal evaluation of pediatric respiratory infections. J Clin Virol 2022; 148:105084. [DOI: 10.1016/j.jcv.2022.105084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/06/2022] [Accepted: 01/24/2022] [Indexed: 12/01/2022]
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11
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Santiago-McRae E, Oh SW, Carlo AM, Bar O, Guan E, Zheng D, Grgicak C, Fu J. Rapid Nucleic Acid Reaction Circuits for Point-Of-Care Diseases Diagnosis. Curr Top Med Chem 2022; 22:686-698. [PMID: 35139798 DOI: 10.2174/1570163819666220207114148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/28/2021] [Accepted: 01/05/2022] [Indexed: 11/22/2022]
Abstract
An urgent need exists for a rapid, cost-effective, facile, and reliable nucleic acid assay for mass screening to control and prevent the spread of emerging pandemic diseases. This urgent need is not fully met by current diagnostic tools. In this review, we summarize the current state-of-the-art research in novel nucleic acid amplification and detection that could be applied to point-of-care (POC) diagnosis and mass screening of diseases. The critical technological breakthroughs will be discussed for their advantages and disadvantages. Finally, we will discuss the future challenges of developing nucleic acid-based POC diagnosis.
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Affiliation(s)
| | - Sung Won Oh
- Center for Computational and Integrative Biology,Camden, NJ 08102, USA.,Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Anthony Monte Carlo
- Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Omri Bar
- Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | | | - Doris Zheng
- Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Catherine Grgicak
- Center for Computational and Integrative Biology,Camden, NJ 08102, USA.,Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Jinglin Fu
- Center for Computational and Integrative Biology,Camden, NJ 08102, USA.,Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
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12
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Chukwudi CU. Consolidating and Upscaling Molecular Research Capacity in Nigeria: On Who's Account? Front Res Metr Anal 2022; 6:788673. [PMID: 35071971 PMCID: PMC8766846 DOI: 10.3389/frma.2021.788673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 12/02/2021] [Indexed: 11/25/2022] Open
Abstract
Molecular research and researchers engage in studies that seek to understand the structures, functions, and interactions of biomolecules as the basis for cellular and systemic effects in living organisms. This research approach was made possible by considerable technological advancements that equip researchers with tools to view biomolecules. Although molecular research holds great promises for improving lives and living, the technological requirements and equipment to undertake molecular research are quite expensive, often requiring a heavy start-up capital or investment. In developing countries such as Nigeria, where the majority of the population lives below the poverty line and research funding is abysmally low, such heavy investments into research that do not provide immediate solutions to societal problems are difficult. This is mostly due to limited resources available to tackle many urgent and pressing needs, and limited perspective and understanding of policymakers, leading to infrastructural and skilled personnel deficit to support molecular research. Despite all these, the field of molecular research continues to grow exponentially globally, hence, funding and investments into this critical life science research area have become imperative. With the rich biodiversity of humans, animals, and plants in Nigeria, and the huge burden of infectious diseases in the country or region, global advances in genomics and proteomics studies will be incomplete without adequate contribution from Nigeria and sub-Saharan Africa region. This paper examines the progression and challenges of undertaking molecular research in Nigeria, and how Nigerian molecular research scientists are tackling these issues, with recommendations for improved molecular research capacity and output in the country or region.
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13
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Kuroki A, Tay J, Lee GH, Yang YY. Broad-Spectrum Antiviral Peptides and Polymers. Adv Healthc Mater 2021; 10:e2101113. [PMID: 34599850 DOI: 10.1002/adhm.202101113] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/13/2021] [Indexed: 12/18/2022]
Abstract
As the human cost of the pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still being witnessed worldwide, the development of broad-spectrum antiviral agents against emerging and re-emerging viruses is seen as a necessity to hamper the spread of infections. Various targets during the viral life-cycle can be considered to inhibit viral infection, from viral attachment to viral fusion or replication. Macromolecules represent a particularly attractive class of therapeutics due to their multivalency and versatility. Although several antiviral macromolecules hold great promise in clinical applications, the emergence of resistance after prolonged exposure urges the need for improved solutions. In the present article, the recent advancement in the discovery of antiviral peptides and polymers with diverse structural features and antiviral mechanisms is reviewed. Future perspectives, such as, the development of virucidal peptides/polymers and their coatings against SARS-CoV-2 infection, standardization of antiviral testing protocols, and use of artificial intelligence or machine learning as a tool to accelerate the discovery of antiviral macromolecules, are discussed.
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Affiliation(s)
- Agnès Kuroki
- Yong Loo Lin School of Medicine National University of Singapore Singapore 117597 Singapore
- Institute of Bioengineering and Bioimaging 31 Biopolis Ways, The Nanos Singapore 138669 Singapore
| | - Joyce Tay
- Institute of Bioengineering and Bioimaging 31 Biopolis Ways, The Nanos Singapore 138669 Singapore
| | - Guan Huei Lee
- Yong Loo Lin School of Medicine National University of Singapore Singapore 117597 Singapore
| | - Yi Yan Yang
- Institute of Bioengineering and Bioimaging 31 Biopolis Ways, The Nanos Singapore 138669 Singapore
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14
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Bustin S, Kirvell S, Huggett JF, Nolan T. RT-qPCR Diagnostics: The "Drosten" SARS-CoV-2 Assay Paradigm. Int J Mol Sci 2021; 22:ijms22168702. [PMID: 34445406 PMCID: PMC8395416 DOI: 10.3390/ijms22168702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 07/31/2021] [Accepted: 08/11/2021] [Indexed: 12/23/2022] Open
Abstract
The reverse transcription quantitative polymerase chain reaction (RT-qPCR) is an established tool for the diagnosis of RNA pathogens. Its potential for automation has caused it to be used as a presence/absence diagnostic tool even when RNA quantification is not required. This technology has been pushed to the forefront of public awareness by the COVID-19 pandemic, as its global application has enabled rapid and analytically sensitive mass testing, with the first assays targeting three viral genes published within days of the publication of the SARS-CoV-2 genomic sequence. One of those, targeting the RNA-dependent RNA polymerase gene, has been heavily criticised for supposed scientific flaws at the molecular and methodological level, and this criticism has been extrapolated to doubts about the validity of RT-qPCR for COVID-19 testing in general. We have analysed this assay in detail, and our findings reveal some limitations but also highlight the robustness of the RT-qPCR methodology for SARS-CoV-2 detection. Nevertheless, whilst our data show that some errors can be tolerated, it is always prudent to confirm that the primer and probe sequences complement their intended target, since, when errors do occur, they may result in a reduction in the analytical sensitivity. However, in this case, it is unlikely that a mismatch will result in poor specificity or a significant number of false-positive SARS-CoV-2 diagnoses, especially as this is routinely checked by diagnostic laboratories as part of their quality assurance.
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Affiliation(s)
- Stephen Bustin
- Medical Technology Research Centre, Faculty of Health, Education, Medicine and Social Care, Anglia Ruskin University Chelmsford, Chelmsford CM1 1SQ, UK; (S.K.); (T.N.)
- Correspondence:
| | - Sara Kirvell
- Medical Technology Research Centre, Faculty of Health, Education, Medicine and Social Care, Anglia Ruskin University Chelmsford, Chelmsford CM1 1SQ, UK; (S.K.); (T.N.)
| | - Jim F. Huggett
- National Measurement Laboratory, LGC, Queens Rd, Teddington, London TW11 0LY, UK;
| | - Tania Nolan
- Medical Technology Research Centre, Faculty of Health, Education, Medicine and Social Care, Anglia Ruskin University Chelmsford, Chelmsford CM1 1SQ, UK; (S.K.); (T.N.)
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15
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Zhou F, Shum E, Moreira AL. Molecular cytology of the respiratory tract and pleura. Cytopathology 2021; 33:14-22. [PMID: 34333812 DOI: 10.1111/cyt.13045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/06/2021] [Accepted: 07/24/2021] [Indexed: 01/01/2023]
Abstract
There is growing evidence that molecular testing is feasible on all types of cytological preparation, which is fortunate as more diagnostic markers and biomarkers for targeted therapies are discovered for use in pulmonary and pleural malignancies. In this article we will discuss the pre-analytic, analytic, and post-analytic (interpretive) considerations for successful implementation of molecular tests for diagnostic and predictive markers in respiratory and pleural cytology. The vast majority of laboratories are familiar with, and have validated their molecular protocols for, formalin-fixed paraffin-embedded surgical specimens, which are not directly applicable to cytology specimens. Thus, rigorous validation must be performed for each type of fixative and cytology preparation before it is implemented in the clinical setting.
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Affiliation(s)
- Fang Zhou
- Department of Pathology, New York University Langone Health, New York, NY, USA
| | - Elaine Shum
- Division of Hematology and Medical Oncology, Department of Medicine, New York University Langone Health, New York, NY, USA
| | - Andre L Moreira
- Department of Pathology, New York University Langone Health, New York, NY, USA
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16
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Manyana S, Gounder L, Pillay M, Manasa J, Naidoo K, Chimukangara B. HIV-1 Drug Resistance Genotyping in Resource Limited Settings: Current and Future Perspectives in Sequencing Technologies. Viruses 2021; 13:1125. [PMID: 34208165 PMCID: PMC8230827 DOI: 10.3390/v13061125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 12/14/2022] Open
Abstract
Affordable, sensitive, and scalable technologies are needed for monitoring antiretroviral treatment (ART) success with the goal of eradicating HIV-1 infection. This review discusses use of Sanger sequencing and next generation sequencing (NGS) methods for HIV-1 drug resistance (HIVDR) genotyping, focusing on their use in resource limited settings (RLS). Sanger sequencing remains the gold-standard method for detecting HIVDR mutations of clinical relevance but is mainly limited by high sequencing costs and low-throughput. NGS is becoming a more common sequencing method, with the ability to detect low-abundance drug-resistant variants and reduce per sample costs through sample pooling and massive parallel sequencing. However, use of NGS in RLS is mainly limited by infrastructure costs. Given these shortcomings, our review discusses sequencing technologies for HIVDR genotyping, focusing on common in-house and commercial assays, challenges with Sanger sequencing in keeping up with changes in HIV-1 treatment programs, as well as challenges with NGS that limit its implementation in RLS and in clinical diagnostics. We further discuss knowledge gaps and offer recommendations on how to overcome existing barriers for implementing HIVDR genotyping in RLS, to make informed clinical decisions that improve quality of life for people living with HIV.
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Affiliation(s)
- Sontaga Manyana
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Lilishia Gounder
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Melendhran Pillay
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Justen Manasa
- Department of Laboratory Medicine and Investigative Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe;
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa;
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban 4013, South Africa
| | - Benjamin Chimukangara
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa;
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17
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Kim H, Huh HJ, Park E, Chung DR, Kang M. Multiplex Molecular Point-of-Care Test for Syndromic Infectious Diseases. BIOCHIP JOURNAL 2021; 15:14-22. [PMID: 33613852 PMCID: PMC7883532 DOI: 10.1007/s13206-021-00004-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 12/17/2022]
Abstract
Point-of-care (POC) molecular diagnostics for clinical microbiology and virology has primarily focused on the detection of a single pathogen. More recently, it has transitioned into a comprehensive syndromic approach that employs multiplex capabilities, including the simultaneous detection of two or more pathogens. Multiplex POC tests provide higher accuracy to for actionable decisionmaking in critical care, which leads to pathogen-specific treatment and standardized usages of antibiotics that help prevent unnecessary processes. In addition, these tests can be simple enough to operate at the primary care level and in remote settings where there is no laboratory infrastructure. This review focuses on state-of-the-art multiplexed molecular point-of-care tests (POCT) for infectious diseases and efforts to overcome their limitations, especially related to inadequate throughput for the identification of syndromic diseases. We also discuss promising and imperative clinical POC approaches, as well as the possible hurdles of their practical applications as front-line diagnostic tests.
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Affiliation(s)
- Hanbi Kim
- Biomedical Engineering Research Center, Smart Healthcare Research Institute, Samsung Medical Center, Seoul, 06351 South Korea.,Department of Medical Device Management and Research, SAIHST (Samsung Advanced Institute for Health Sciences & Technology), Sungkyunkwan University, Seoul, 06355 South Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351 South Korea
| | - Eunkyoung Park
- Biomedical Engineering Research Center, Smart Healthcare Research Institute, Samsung Medical Center, Seoul, 06351 South Korea.,Department of Medical Device Management and Research, SAIHST (Samsung Advanced Institute for Health Sciences & Technology), Sungkyunkwan University, Seoul, 06355 South Korea
| | - Doo-Ryeon Chung
- Center for Infection Prevention and Control, Samsung Medical Center, Seoul, 06351 South Korea.,Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, 06367 South Korea.,Division of Infectious Diseases, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351 South Korea
| | - Minhee Kang
- Biomedical Engineering Research Center, Smart Healthcare Research Institute, Samsung Medical Center, Seoul, 06351 South Korea.,Department of Medical Device Management and Research, SAIHST (Samsung Advanced Institute for Health Sciences & Technology), Sungkyunkwan University, Seoul, 06355 South Korea
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18
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Deviaene M, Weigel KM, Wood RC, Luabeya AKK, Jones-Engel L, Hatherill M, Cangelosi GA. Sample adequacy controls for infectious disease diagnosis by oral swabbing. PLoS One 2020; 15:e0241542. [PMID: 33125422 PMCID: PMC7598519 DOI: 10.1371/journal.pone.0241542] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/16/2020] [Indexed: 12/22/2022] Open
Abstract
Oral swabs are emerging as a non-invasive sample type for diagnosing infectious diseases including Ebola, tuberculosis (TB), and COVID-19. To assure proper sample collection, sample adequacy controls (SACs) are needed that detect substances indicative of samples collected within the oral cavity. This study evaluated two candidate SACs for this purpose. One detected representative oral microbiota (Streptococcus species DNA) and the other, human cells (human mitochondrial DNA, mtDNA). Quantitative PCR (qPCR) assays for the two target cell types were applied to buccal swabs (representing samples collected within the oral cavity) and hand swabs (representing improperly collected samples) obtained from 51 healthy U.S. volunteers. Quantification cycle (Cq) cutoffs that maximized Youden’s index were established for each assay. The streptococcal target at a Cq cutoff of ≤34.9 had 99.0% sensitivity and specificity for oral swab samples, whereas human mtDNA perfectly distinguished between hand and mouth swabs with a Cq cutoff of 31.3. The human mtDNA test was then applied to buccal, tongue, and gum swabs that had previously been collected from TB patients and controls in South Africa, along with “air swabs” collected as negative controls (total N = 292 swabs from 71 subjects). Of these swabs, 287/292 (98%) exhibited the expected Cq values. In a paired analysis the three oral sites yielded indistinguishable amounts of human mtDNA, however PurFlockTM swabs collected slightly more human mtDNA than did OmniSwabsTM (p = 0.012). The results indicate that quantification of human mtDNA cannot distinguish swabs collected from different sites within the mouth. However, it can reliably distinguish oral swabs from swabs that were not used orally, which makes it a useful SAC for oral swab-based diagnosis.
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Affiliation(s)
- Meagan Deviaene
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Kris M. Weigel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Rachel C. Wood
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Angelique K. K. Luabeya
- Department of Pathology, South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease & Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Lisa Jones-Engel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Mark Hatherill
- Department of Pathology, South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease & Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Gerard A. Cangelosi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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19
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Implementation and Validation of the Roche Light Cycler 480 96-Well Plate Platform as a Real-Time PCR Assay for the Quantitative Detection of Cytomegalovirus (CMV) in Clinical Specimens Using the Luminex MultiCode ASRs System. Med Sci (Basel) 2020; 8:medsci8010014. [PMID: 32168800 PMCID: PMC7151591 DOI: 10.3390/medsci8010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/03/2020] [Accepted: 03/07/2020] [Indexed: 11/16/2022] Open
Abstract
Allogenic stem-cell therapies benefit patients in the treatment of multiple diseases; however, the side effects of stem-cell therapies (SCT) derived from the concomitant use of immune suppression agents often include triggering infection diseases. Thus, analysis is required to improve the detection of pathogen infections in SCT. We develop a polymerase chain reaction (PCR)-based methodology for the qualitative real-time DNA detection of cytomegalovirus (CMV), with reference to herpes simplex virus types 1 (HSVI), Epstein–Barr virus (EBV), and varicella-zoster virus (VZV) in blood, urine, solid tissues, and cerebrospinal fluid. This real-time PCR of 96-well plate format provides a rapid framework as required by the Food and Drug Administration (FDA) for clinical settings, including the processing of specimens, reagent handling, special safety precautions, quality control criteria and analytical accuracy, precisely reportable range (analyst measurement range), reference range, limit of detection (LOD), analytical specificity established by interference study, and analyte stability. Specifically, we determined the reportable range (analyst measurement range) with the following criteria: CMV copies ≥200 copies/mL; report copy/mL value; CMV copies ≤199 copies/mL; report detected but below quantitative range; CMV copies = 0 with report <200 copies/mL. That is, with reference range, copy numbers (CN) per milliliter (mL) of the LOD were determined by standard curves that correlated Ct value and calibrated standard DNA panels. The three repeats determined that the measuring range was 1E2~1E6 copies/mL. The standard curves show the slopes were within the range −2.99 to −3.65 with R2 ≥ 0.98. High copy (HC) controls were within 0.17–0.18 log differences of DNA copy numbers; (2) low copy (LC) controls were within 0.17–0.18 log differences; (3) LOD was within 0.14–0.15 log differences. As such, we set up a fast, simple, inexpensive, sensitive, and reliable molecular approach for the qualitative detection of CMV pathogens. Conclusion: This real-time PCR of the 96-well plate format provides a rapid framework as required by the FDA for clinical settings.
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20
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Abstract
Purpose of Review Major technologic advances in two main areas of molecular infectious disease diagnostics have resulted in accelerated adoption or ordering, outpacing implementation, and clinical utility studies. Physicians must understand the limitations to and appropriate utilization of these technologies in order to provide cost-effective and well-informed care for their patients. Recent Findings Rapid molecular testing and, to a lesser degree, clinical metagenomics are now being routinely used in clinical practice. While these tests allow for a breadth of interrogation not possible with conventional microbiology, they pose new challenges for diagnostic and antimicrobial stewardship programs. This review will summarize the most recent literature on these two categories of technologic advances and discuss the few studies that have looked at utilization and stewardship approaches. This review also highlights the future directions for both of these technologies. Summary The appropriate utilization of rapid molecular testing and clinical metagenomics has not been well established. More studies are needed to assess their prospective impacts on patient management and antimicrobial stewardship efforts as the future state of infectious disease diagnostics will see continued expansion of these technologic advances.
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21
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Zehnbauer BA. The Journal of Molecular Diagnostics: 20 Years Defining Professional Practice. J Mol Diagn 2019; 21:938-942. [PMID: 31635797 DOI: 10.1016/j.jmoldx.2019.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 01/09/2023] Open
Abstract
This editorial highlights 20 years of JMD defining professional practice.
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Affiliation(s)
- Barbara A Zehnbauer
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia (Editor-in-Chief).
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22
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Aretzweiler G, Leuchter S, Simon CO, Marins E, Frontzek A. Generating timely molecular diagnostic test results: workflow comparison of the cobas® 6800/8800 to Panther. Expert Rev Mol Diagn 2019; 19:951-957. [PMID: 31526152 DOI: 10.1080/14737159.2019.1665999] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Background: Molecular diagnostic tests for HBV, HCV and HIV-1 and other pathogens are widely used for clinical management. Practical issues related to workflow and labor requirements need to be characterized to inform selection of the most appropriate system. Research design and methods: We compared the workflow of two high-throughput systems: cobas 6800 (Roche) and Panther (Hologic), using average mid-size laboratory test volumes for five different assays (HIV-1, HBV, HCV, HPV or TV, and CT/NG). Results: Set-up time, time to first results, time to last results, and total hands-on time for cobas 6800 was 0.40, 2.47, 7.12, and 0.98 hours, respectively; on the Panther system, these times were 0.75, 2.7, 9.1, and 1.48 hours. Fifty-seven samples had results available at the first time point on cobas 6800 compared to 5 samples on the Panther system. The Panther system required more manual steps including several with potential risks of contamination or error. The number of reagents items required was 5 for cobas 6800 and 40 for the Panther system. Conclusions: Both systems provided a high level of automation. The cobas 6800 platform had shorter start up, time to first result, time to last result and hands-on times than the Panther system.
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Affiliation(s)
- Gudrun Aretzweiler
- Department of Molecular Diagnostics, Labor Stein , Monchengladbach , Germany
| | - Susanne Leuchter
- Department of Molecular Diagnostics, Labor Stein , Monchengladbach , Germany
| | | | - Ed Marins
- Roche Molecular Systems , Pleasanton , CA , USA
| | - Andre Frontzek
- Department of Molecular Diagnostics, Labor Stein , Monchengladbach , Germany
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23
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Qiu X, Hildebrandt N. A clinical role for Förster resonance energy transfer in molecular diagnostics of disease. Expert Rev Mol Diagn 2019; 19:767-771. [DOI: 10.1080/14737159.2019.1649144] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Xue Qiu
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, France
| | - Niko Hildebrandt
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, France
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24
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Aretzweiler G, Leuchter S, García-Álvarez M, Simon C, Marins E, Paxinos E, Canchola J, Delgado R, Frontzek A. Analytical performance of four molecular platforms used for HIV-1, HBV and HCV viral load determinations. Expert Rev Mol Diagn 2019; 19:941-949. [PMID: 31159598 DOI: 10.1080/14737159.2019.1624162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background: Viral load (VL) quantification is important for the management of HBV, HCV, and HIV-1-infected patients. Several semi- or fully automated systems and assays are available that can be used to measure VL for these and other targets. Research design and methods: We assessed the accuracy, genotype/subtype inclusivity, and precision of four VL assays for three viral targets: cobas 4800 (Roche), cobas 6800 (Roche), Aptima (Hologic) and VERIS (Beckman), using WHO standards, cell culture supernatants and clinical samples. Results: Most results were close to expected values, except for significant under-quantification of HIV-1 group O, HBV genotype C, and D at high VL, and HCV genotype 3 by Aptima, and of HIV-1 CRF01_AE and group N and HCV genotype 3 by VERIS. Precision was comparable between tests except for VERIS HCV, which showed more variability. Aptima and cobas 6800 results agreed well with each other except HBV VL at lower VL (<10,000 IU/mL) where Aptima results tended to be higher. Conclusions: Results from different VL assays may not always agree in certain subsets of patients. Clinicians should we aware of these findings when making treatment decisions.
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Affiliation(s)
- Gudrun Aretzweiler
- Department of Molecular Diagnostics, Labor Stein , Monchengladbach , Germany
| | - Susanne Leuchter
- Department of Molecular Diagnostics, Labor Stein , Monchengladbach , Germany
| | - Mónica García-Álvarez
- Department of Microbiology, Instituto de Investigación Hospital 12 de Octubre (imas 12) , Madrid , Spain
| | - Christian Simon
- Department of Molecular Diagnostics, Roche Molecular Systems , Pleasanton , CA , USA
| | - Ed Marins
- Department of Molecular Diagnostics, Roche Molecular Systems , Pleasanton , CA , USA
| | - Ellen Paxinos
- Department of Molecular Diagnostics, Roche Molecular Systems , Pleasanton , CA , USA
| | - Jesse Canchola
- Department of Molecular Diagnostics, Roche Molecular Systems , Pleasanton , CA , USA
| | - Rafael Delgado
- Department of Microbiology, Instituto de Investigación Hospital 12 de Octubre (imas 12) , Madrid , Spain
| | - Andre Frontzek
- Department of Molecular Diagnostics, Labor Stein , Monchengladbach , Germany
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25
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Cretich M, Gori A, D'Annessa I, Chiari M, Colombo G. Peptides for Infectious Diseases: From Probe Design to Diagnostic Microarrays. Antibodies (Basel) 2019; 8:E23. [PMID: 31544829 PMCID: PMC6640701 DOI: 10.3390/antib8010023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 02/28/2019] [Accepted: 03/04/2019] [Indexed: 01/03/2023] Open
Abstract
Peptides and peptidomimetics have attracted revived interest regarding their applications in chemical biology over the last few years. Their chemical versatility, synthetic accessibility and the ease of storage and management compared to full proteins have made peptides particularly interesting in diagnostic applications, where they proved to efficiently recapitulate the molecular recognition properties of larger protein antigens, and were proven to be able to capture antibodies circulating in the plasma and serum of patients previously exposed to bacterial or viral infections. Here, we describe the development, integration and application of strategies for computational prediction and design, advanced chemical synthesis, and diagnostic deployment in multiplexed assays of peptide-based materials which are able to bind antibodies of diagnostic as well as therapeutic interest. By presenting successful applications of such an integrated strategy, we argue that they will have an ever-increasing role in both basic and clinical realms of research, where important advances can be expected in the next few years.
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Affiliation(s)
- Marina Cretich
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
| | - Alessandro Gori
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
| | - Ilda D'Annessa
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
| | - Marcella Chiari
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
| | - Giorgio Colombo
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco 9, 20131 Milano, Italy.
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 12, 27100 Pavia, Italy.
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Avery RK, Yen-Lieberman B. Viral Diagnostics. PRINCIPLES AND PRACTICE OF TRANSPLANT INFECTIOUS DISEASES 2019. [PMCID: PMC7115029 DOI: 10.1007/978-1-4939-9034-4_49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
This chapter discusses recent developments in diagnostics for cytomegalovirus (CMV), Epstein-Barr virus (EBV), BK virus (BKV), community respiratory viruses (CRVs), parvovirus, hepatitis viruses, HIV, and other viral agents of importance in solid organ and hematopoietic stem cell transplantation.
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27
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Ellipilli S, Phillips JD, Heemstra JM. Synthesis of comb-shaped DNA using a non-nucleosidic branching phosphoramidite. Org Biomol Chem 2018; 16:4659-4664. [PMID: 29881861 DOI: 10.1039/c8ob00626a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Branched DNAs (bDNAs) having comb-like structures have found wide utility in molecular diagnostics and DNA nanotechnology. bDNAs can be generated either by designing and assembling linear DNA molecules into rigid non-covalent structures or by using an orthogonally protected branching unit to synthesize covalently linked structures. Despite the advantages of the covalently linked structures, use of this motif has been hampered by the challenging synthesis of appropriately protected branching monomers. We report the facile synthesis of a branching monomer having orthogonal DMT and Lev protecting groups using readily available δ-velarolactone and 1,3-diaminopropan-2-ol. Using this branching monomer, a comb-shaped bDNA was synthesized having three different DNA arms. The synthesis and hybridization capability of the bDNA was assessed by fluorescence microscopy using fluorescently labeled complementary and mismatched DNA probes. Convenient access to an orthogonally protected branching monomer is anticipated to accelerate applications of bDNAs in applications including diagnostics, biosensing, gene-profiling, DNA computing, multicolor imaging, and nanotechnology.
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Affiliation(s)
- Satheesh Ellipilli
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA.
| | - John D Phillips
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah 84112, USA
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA.
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28
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Gürtler C, Laible M, Schwabe W, Steinhäuser H, Li X, Liu S, Schlombs K, Sahin U. Transferring a Quantitative Molecular Diagnostic Test to Multiple Real-Time Quantitative PCR Platforms. J Mol Diagn 2018; 20:398-414. [DOI: 10.1016/j.jmoldx.2018.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/16/2018] [Accepted: 02/28/2018] [Indexed: 12/22/2022] Open
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29
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De Neuter N, Bartholomeus E, Elias G, Keersmaekers N, Suls A, Jansens H, Smits E, Hens N, Beutels P, Van Damme P, Mortier G, Van Tendeloo V, Laukens K, Meysman P, Ogunjimi B. Memory CD4 + T cell receptor repertoire data mining as a tool for identifying cytomegalovirus serostatus. Genes Immun 2018; 20:255-260. [PMID: 29904098 DOI: 10.1038/s41435-018-0035-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/18/2018] [Accepted: 04/25/2018] [Indexed: 12/17/2022]
Abstract
Pathogens of past and current infections have been identified directly by means of PCR or indirectly by measuring a specific immune response (e.g., antibody titration). Using a novel approach, Emerson and colleagues showed that the cytomegalovirus serostatus can also be accurately determined by using a T cell receptor repertoire data mining approach. In this study, we have sequenced the CD4+ memory T cell receptor repertoire of a Belgian cohort with known cytomegalovirus serostatus. A random forest classifier was trained on the CMV specific T cell receptor repertoire signature and used to classify individuals in the Belgian cohort. This study shows that the novel approach can be reliably replicated with an equivalent performance as that reported by Emerson and colleagues. Additionally, it provides evidence that the T cell receptor repertoire signature is to a large extent present in the CD4+ memory repertoire.
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Affiliation(s)
- Nicolas De Neuter
- Department of Mathematics and Computer Science, Adrem Data Lab, University of Antwerp, Antwerp, Belgium. .,Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium. .,AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.
| | - Esther Bartholomeus
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Center for Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - George Elias
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Nina Keersmaekers
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Centre for Health Economics Research and Modeling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Arvid Suls
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Center for Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - Hilde Jansens
- Department of Laboratory Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Evelien Smits
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium.,Center for Cell Therapy and Regenerative Medicine, Antwerp University Hospital, Edegem, Belgium.,Center for Oncological Research Antwerp, University of Antwerp, Antwerp, Belgium
| | - Niel Hens
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Centre for Health Economics Research and Modeling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium.,Interuniversity Institute for Biostatistics and statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium.,Centre for the Evaluation of Vaccination (CEV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Philippe Beutels
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Centre for Health Economics Research and Modeling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Pierre Van Damme
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Centre for the Evaluation of Vaccination (CEV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Geert Mortier
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Center for Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - Viggo Van Tendeloo
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Department of Mathematics and Computer Science, Adrem Data Lab, University of Antwerp, Antwerp, Belgium.,Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium.,AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- Department of Mathematics and Computer Science, Adrem Data Lab, University of Antwerp, Antwerp, Belgium.,Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium.,AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Centre for Health Economics Research and Modeling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium.,Department of Paediatrics, Antwerp University Hospital, Edegem, Belgium
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Urogenital Chlamydia trachomatis multilocus sequence types and genovar distribution in chlamydia infected patients in a multi-ethnic region of Saratov, Russia. PLoS One 2018; 13:e0195386. [PMID: 29641543 PMCID: PMC5895025 DOI: 10.1371/journal.pone.0195386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 03/21/2018] [Indexed: 11/19/2022] Open
Abstract
Background This is the first report to characterize the prevalence and genovar distribution of genital chlamydial infections among random heterosexual patients in the multi-ethnic Saratov Region, located in Southeast Russia. Methods Sixty-one clinical samples (cervical or urethral swabs) collected from a random cohort of 856 patients (7.1%) were C. trachomatis (CT) positive in commercial nucleic acid amplification tests (NAATs) and duplex TaqMan PCRs. Results Sequence analysis of the VDII region of the ompA gene revealed seven genovars of C. trachomatis in PCR-positive patients. The overall genovars were distributed as E (41.9%), G (21.6%), F (13.5%), K (9.5%), D (6.8%), J (4.1%), and H (2.7%). CT-positive samples were from males (n = 12, 19.7%), females (n = 42, 68.8%), and anonymous (n = 7, 11.5%) patients, with an age range of 19 to 45 years (average 26.4), including 12 different ethnic groups representative of this region. Most patients were infected with a single genovar (82%), while 18% were co-infected with either two or three genovars. The 1156 bp-fragment of the ompA gene was sequenced in 46 samples to determine single nucleotide polymorphisms (SNP) among isolates. SNP-based subtyping and phylogenetic reconstruction revealed the presence of 13 variants of the ompA gene, such as E (E1, E2, E6), G (G1, G2, G3, G5), F1, K, D (D1, Da2), J1, and H2. Differing genovar distribution was identified among urban (E>G>F) and rural (E>K) populations, and in Slavic (E>G>D) and non-Slavic (E>G>K) ethnic groups. Multilocus sequence typing (MLST) determined five sequences types (STs), such as ST4 (56%, 95% confidence interval, CI, 70.0 to 41.3), ST6 (10%, 95% CI 21.8 to 3.3), ST9 (22%, 95% CI 35.9 to 11.5), ST10 (2%, 95% CI 10.7 to 0.05) and ST38 (10%, 95% CI 21.8 to 3.3). Thus, the most common STs were ST4 and ST9. Conclusion C. trachomatis is a significant cause of morbidity among random heterosexual patients with genital chlamydial infections in the Saratov Region. Further studies should extend this investigation by describing trends in a larger population, both inside and outside of the Saratov Region to clarify some aspects for the actual application of C. trachomatis genotype analysis for disease control.
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Comparison of Workflow, Maintenance, and Consumables in the GeneXpert Infinity 80 and Panther Instruments While Testing for Chlamydia trachomatis and Neisseria gonorrhoeae. Sex Transm Dis 2017; 43:377-81. [PMID: 27196259 DOI: 10.1097/olq.0000000000000444] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND The 2015 Sexually Transmitted Diseases Treatment Guidelines from the Centers for Disease Control and Prevention recommend testing for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) using nucleic acid amplification tests, and prompt treatment of infected persons on site under direct observation. Faster time to results may enable treatment and management outcomes. METHODS Workflow parameters for processing 1, 10, 48, 96, and 192 tests were determined in the GeneXpert Infinity 80 (Cepheid) and Panther (Hologic) instruments. RESULTS In an Xpert CT/NG cartridge, the time to first results on the Infinity 80 was 1 hour 30 minutes for single or multiple tests and final results for 10, 48, 96, and 192 tests were available at 1 hour 37 minutes, 1 hour 54 minutes, 3 hour 17 minutes, and 5 hour 7 minutes, respectively. With the Aptima CT/GC assay on the Panther, the respective times were 3 hr 45 min for the first test result, and 3 hour 51 minutes, 4 hour 38 minutes, 5 hour 26 minutes, and 7 hour 4 minutes to final results. The Panther required more time for maintenance and consumed a greater variety of plastics and reagents but required less hands-on time when testing larger numbers of specimens. CONCLUSIONS The Infinity 80 is a versatile instrument for continuous random access testing of small or large numbers of clinical specimens and may provide diagnostic results, in some settings, in time for treatment of CT and NG infections.
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Abstract
Since the Human Genome Project completed in 2000, the sequencing of the first genome, massive progress has been made by medical science in the early diagnosis and personalized therapies based on nucleic acids (NA) analysis. To allow the extensive use of these molecular methods in medical practice, scientific research is nowadays strongly focusing on the development of new miniaturized and easy-to-use technologies and devices allowing fast and low cost NA analysis in decentralized environments. It is now the era of so-called genetic "Point-of-Care" (PoC). These systems must integrate and automate all steps necessary for molecular analysis such as sample preparation (extraction and purification of NA) and detection based on PCR (Polymerase Chain Reaction) technology in order to perform, by unskilled personnel, in vitro genetic analysis near the patient (in hospital, in the physician office, clinic, or home), with rapid answers and low cost. In this review, the recent advances in genetic PoC technologies are discussed, including the extraction and PCR amplification chemistry suitable for PoC use and the new frontiers of research in this field.
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Affiliation(s)
| | - Sabrina Conoci
- STMicroelectronics, Stradale Primosole 50, 95121 Catania, Italy
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Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, Myhrvold C, Bhattacharyya RP, Livny J, Regev A, Koonin EV, Hung DT, Sabeti PC, Collins JJ, Zhang F. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 2017; 356:438-442. [PMID: 28408723 PMCID: PMC5526198 DOI: 10.1126/science.aam9321] [Citation(s) in RCA: 1883] [Impact Index Per Article: 269.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/05/2017] [Indexed: 12/14/2022]
Abstract
Rapid, inexpensive, and sensitive nucleic acid detection may aid point-of-care pathogen detection, genotyping, and disease monitoring. The RNA-guided, RNA-targeting clustered regularly interspaced short palindromic repeats (CRISPR) effector Cas13a (previously known as C2c2) exhibits a "collateral effect" of promiscuous ribonuclease activity upon target recognition. We combine the collateral effect of Cas13a with isothermal amplification to establish a CRISPR-based diagnostic (CRISPR-Dx), providing rapid DNA or RNA detection with attomolar sensitivity and single-base mismatch specificity. We use this Cas13a-based molecular detection platform, termed Specific High-Sensitivity Enzymatic Reporter UnLOCKing (SHERLOCK), to detect specific strains of Zika and Dengue virus, distinguish pathogenic bacteria, genotype human DNA, and identify mutations in cell-free tumor DNA. Furthermore, SHERLOCK reaction reagents can be lyophilized for cold-chain independence and long-term storage and be readily reconstituted on paper for field applications.
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Affiliation(s)
- Jonathan S Gootenberg
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Omar O Abudayyeh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jeong Wook Lee
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Patrick Essletzbichler
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Aaron J Dy
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Julia Joung
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Vanessa Verdine
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nina Donghia
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Nichole M Daringer
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Catherine A Freije
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Cameron Myhrvold
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Jonathan Livny
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - James J Collins
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Fedorova VA, Sultanakhmedov ES, Saltykov YV, Utz SR, Motin VL. Improvement of laboratory diagnostics of urogenital chlamydial infection in patients with impaired reproductive functions found to be infected with Chlamydia trachomatis. VESTNIK DERMATOLOGII I VENEROLOGII 2017. [DOI: 10.25208/0042-4609-2017-93-2-34-44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
The dominant role in human infertility has been attributed to sexually transmitted infections (STIs) with a leading contribution of urogenital chlamydial infection (UGCI) caused by Chlamydia trachomatis (CT). the two variants of this pathogen are represented by the wild-type (wtCT) and new Swedish (nvCT) strains containing 377 bp deletion within the cryptic plasmid orf1 gene. Objective. The purpose of the study was investigation of the clinical specimens obtained from the urogenital tract of couples coping with infertility for the presence of genetic material of wtCT and nvCT. Material and methods. Clinical samples (scrapings from the urethra and cervix) obtained from 25 to 41 years old couples (n = 14) were tested for the presence of identifiable wtCT and nvCT chlamydia DNA by monoplex and duplex PCR, specific antigens C. trachomatis in elementary bodies by using immunofluorescence analysis (IFA), while detection of anti-chlamydia antibodies in sera was determined by immunoenzymatic assay (IEA). Results. The nvCT variant with typical deletion of 377 bp within the orf1 gene that belongs to the genovar e subtype E1 was detected in 100% of couples with infertility. The negative results of DNA testing for wtcT were registered in 87.5% of patients from this group, while one individual (12.5%) was likely coinfected with nvCT and wtCT of E1 and D genovars, respectively. The wtCT strains of genovar E (subtypes E1, E2, E6), g (subtypes G1, G2), F (subtypes F1), and K were identified in control group among patients with UGCI. The study revealed difficulties in detection of nvCT by nucleic acid amplification test (NAAT), IFA, and IEA; data on comparison of the efficacy of these methods are presented. Conclusion. Chronic UGCI in patients with reproductive dysfunctions can be caused by nvCT alone or as result of co-infection with nvCT and wtCT. The negative results in NAAT may not 100% correlate with the absence of UGCI that requires further confirmation in tests allowing detection of all known variants of C. trachomatis.
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Strategies for Optimizing the Diagnostic Predictive Value of Clostridium difficile Molecular Diagnostics. J Clin Microbiol 2017; 55:1244-1248. [PMID: 28275072 DOI: 10.1128/jcm.00147-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Because nucleic acid amplification tests (NAATs) do not distinguish Clostridium difficile infection (CDI) and asymptomatic C. difficile carriage, the diagnostic predictive value of NAATs is limited when used in patients with a low probability of CDI. In this issue of the Journal of Clinical Microbiology, Truong et al. (J. Clin. Microbiol., 55:1276-1284, 2017, https://doi.org/10.1128/JCM.02319-16) report significant reductions in hospital-onset CDI and oral vancomycin utilization at their institution following implementation of a novel intervention that leveraged their clinical bioinformatics resources to prevent C. difficile testing of stools from patients without clinically significant diarrhea and in patients with recent laxative use.
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36
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Das S, Shibib DR, Vernon MO. The new frontier of diagnostics: Molecular assays and their role in infection prevention and control. Am J Infect Control 2017; 45:158-169. [PMID: 28159066 PMCID: PMC7115290 DOI: 10.1016/j.ajic.2016.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 08/19/2016] [Accepted: 08/19/2016] [Indexed: 01/05/2023]
Abstract
Recent advances in technology over the last decade have propelled the microbiology laboratory into a pivotal role in infection prevention and control. The rapid adaptation of molecular technologies to the field of clinical microbiology now greatly influences infectious disease management and significantly impacts infection control practices. This review discusses recent developments in molecular techniques in the diagnosis of infectious diseases. It describes the basic concepts of molecular assays, discusses their advantages and limitations, and characterizes currently available commercial assays with respect to cost, interpretive requirements, and clinical utility.
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Meskill SD, Revell PA, Chandramohan L, Cruz AT. Prevalence of co-infection between respiratory syncytial virus and influenza in children. Am J Emerg Med 2016; 35:495-498. [PMID: 28012809 DOI: 10.1016/j.ajem.2016.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/29/2016] [Accepted: 12/04/2016] [Indexed: 10/20/2022] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) and influenza have varying degree of seasonal overlap. OBJECTIVE To determine the prevalence of co-infection of RSV and influenza compared to the prevalence of those infections independently when both are in season. METHODS This was a retrospective cross-sectional study of children evaluated between July 2010 and June 2013 for viral respiratory infection using multiplex PCR. Seasonality was defined retrospectively as weeks when >2% of the total annual positive tests were obtained and was calculated for influenza A, influenza B, and RSV independently. Periods of overlapping seasonality of RSV and influenza A and RSV and influenza B were identified. The expected incidences of co-infection were modeled as the product of the incidences of the individual viruses. RESULTS 13,664 specimens were sent for PCR during the study period. Over all 3 seasons, RSV overlapped with influenza A and B for 22 and 18weeks, respectively; in 2011-12, RSV overlapped with neither influenza A nor B. Based on modeling, there were 6-7 fold fewer cases of RSV/influenza co-infection observed than expected: RSV/influenza A 77 vs. 12, (p≤0.001; RSV/influenza B 76 vs. 11 (p≤0.001). CONCLUSIONS The observed incidence of co-infectivity of RSV and influenza was significantly less than the expected incidence even when both were co-circulating. In light of these data, it may be reasonable to forgo rapid influenza testing or empiric antiviral treatment for children whom rapid RSV testing is positive and who are at low risk of influenza-related complications, especially in times of antiviral therapy shortages.
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Affiliation(s)
- Sarah D Meskill
- Sections of Emergency Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
| | - Paula A Revell
- Department of Pathology, Baylor College of Medicine, Houston, TX, USA
| | - Lakshmi Chandramohan
- Biopharma Division, NeoGenomics Laboratories, 2575 West Bellfort St, Houston 77054 United States
| | - Andrea T Cruz
- Sections of Emergency Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Sections of Infectious Diseases, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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Perner A, Gordon AC, De Backer D, Dimopoulos G, Russell JA, Lipman J, Jensen JU, Myburgh J, Singer M, Bellomo R, Walsh T. Sepsis: frontiers in diagnosis, resuscitation and antibiotic therapy. Intensive Care Med 2016; 42:1958-1969. [PMID: 27695884 DOI: 10.1007/s00134-016-4577-z] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/25/2016] [Indexed: 01/28/2023]
Abstract
Sepsis is a major growing global burden and a major challenge to intensive care clinicians, researchers, guideline committee members and policy makers, because of its high and increasing incidence and great pathophysiological, molecular, genetic and clinical complexity. In spite of recent progress, short-term mortality remains high and there is growing evidence of long-term morbidity and increased long-term mortality in survivors of sepsis both in developed and developing countries. Further improvement in the care of patients with sepsis will impact upon global health. In this narrative review, invited experts describe the expected challenges and progress to be made in the near future. We focus on diagnosis, resuscitation (fluids, vasopressors, inotropes, blood transfusion and hemodynamic targets) and infection (antibiotics and infection biomarkers), as these areas are key, if initial management and subsequent outcomes are to be improved in patients with sepsis.
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Affiliation(s)
- Anders Perner
- Department of Intensive Care, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
| | - Anthony C Gordon
- Section of Anaesthetics, Pain Medicine and Intensive Care, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Daniel De Backer
- Department of Intensive Care, CHIREC Hospitals, Université Libre de Bruxelles, Brussels, Belgium
| | - George Dimopoulos
- Department of Critical Care, University Hospital ATTIKON, Medical School, University of Athens, Athens, Greece
| | - James A Russell
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey Lipman
- Royal Brisbane and Women's Hospital, The University of Queensland, Brisbane, QLD, Australia
| | - Jens-Ulrik Jensen
- CHIP and PERSIMUNE, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - John Myburgh
- The George Institute for Global Health, University of Sydney, Sydney, NSW, Australia
| | - Mervyn Singer
- Division of Medicine, Bloomsbury Institute of Intensive Care Medicine, University College London, London, WC1E 6BT, UK
| | - Rinaldo Bellomo
- School of Medicine, The University of Melbourne, Melbourne, VIC, Australia
| | - Timothy Walsh
- Anaesthetics, Critical Care, and Pain Medicine, Edinburgh University, Edinburgh, Scotland, UK
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Khodakov D, Wang C, Zhang DY. Diagnostics based on nucleic acid sequence variant profiling: PCR, hybridization, and NGS approaches. Adv Drug Deliv Rev 2016; 105:3-19. [PMID: 27089811 DOI: 10.1016/j.addr.2016.04.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/21/2016] [Accepted: 04/06/2016] [Indexed: 12/22/2022]
Abstract
Nucleic acid sequence variations have been implicated in many diseases, and reliable detection and quantitation of DNA/RNA biomarkers can inform effective therapeutic action, enabling precision medicine. Nucleic acid analysis technologies being translated into the clinic can broadly be classified into hybridization, PCR, and sequencing, as well as their combinations. Here we review the molecular mechanisms of popular commercial assays, and their progress in translation into in vitro diagnostics.
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Abstract
Central nervous system (CNS) infections are potentially life threatening if not diagnosed and treated early. The initial clinical presentations of many CNS infections are non-specific, making a definitive etiologic diagnosis challenging. Nucleic acid in vitro amplification-based molecular methods are increasingly being applied for routine microbial detection. These methods are a vast improvement over conventional techniques with the advantage of rapid turnaround and higher sensitivity and specificity. Additionally, molecular methods performed on cerebrospinal fluid samples are considered the new gold standard for diagnosis of CNS infection caused by pathogens, which are otherwise difficult to detect. Commercial diagnostic platforms offer various monoplex and multiplex PCR assays for convenient testing of targets that cause similar clinical illness. Pan-omic molecular platforms possess potential for use in this area. Although molecular methods are predicted to be widely used in diagnosing and monitoring CNS infections, results generated by these methods need to be carefully interpreted in combination with clinical findings. This review summarizes the currently available armamentarium of molecular assays for diagnosis of central nervous system infections, their application, and future approaches.
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Fitchett EJA, Seale AC, Vergnano S, Sharland M, Heath PT, Saha SK, Agarwal R, Ayede AI, Bhutta ZA, Black R, Bojang K, Campbell H, Cousens S, Darmstadt GL, Madhi SA, Meulen AST, Modi N, Patterson J, Qazi S, Schrag SJ, Stoll BJ, Wall SN, Wammanda RD, Lawn JE. Strengthening the Reporting of Observational Studies in Epidemiology for Newborn Infection (STROBE-NI): an extension of the STROBE statement for neonatal infection research. THE LANCET. INFECTIOUS DISEASES 2016; 16:e202-e213. [PMID: 27633910 DOI: 10.1016/s1473-3099(16)30082-2] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 01/14/2016] [Accepted: 04/28/2016] [Indexed: 12/22/2022]
Abstract
Neonatal infections are estimated to account for a quarter of the 2·8 million annual neonatal deaths, as well as approximately 3% of all disability-adjusted life-years. Despite this burden, few data are available on incidence, aetiology, and outcomes, particularly regarding impairment. We aimed to develop guidelines for improved scientific reporting of observational neonatal infection studies, to increase comparability and to strengthen research in this area. This checklist, Strengthening the Reporting of Observational Studies in Epidemiology for Newborn Infection (STROBE- NI), is an extension of the STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) statement. STROBE-NI was developed following systematic reviews of published literature (1996-2015), compilation of more than 130 potential reporting recommendations, and circulation of a survey to relevant professionals worldwide, eliciting responses from 147 professionals from 37 countries. An international consensus meeting of 18 participants (with expertise in infectious diseases, neonatology, microbiology, epidemiology, and statistics) identified priority recommendations for reporting, additional to the STROBE statement. Implementation of these STROBE-NI recommendations, and linked checklist, aims to improve scientific reporting of neonatal infection studies, increasing data utility and allowing meta-analyses and pathogen-specific burden estimates to inform global policy and new interventions, including maternal vaccines.
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Affiliation(s)
| | - Anna C Seale
- MARCH Centre, London School of Hygiene & Tropical Medicine, London, UK; The Farr Institute of Health Informatics Research, University College London, London, UK
| | - Stefania Vergnano
- Paediatric Infectious Disease Research Group, St George's University of London, London, UK
| | - Michael Sharland
- Paediatric Infectious Disease Research Group, St George's University of London, London, UK
| | - Paul T Heath
- Paediatric Infectious Disease Research Group, St George's University of London, London, UK
| | - Samir K Saha
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Ramesh Agarwal
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Adejumoke I Ayede
- Department of Paediatrics, College Of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Zulfiqar A Bhutta
- Center of Excellence in Women and Child Health, The Aga Khan University, Karachi, Pakistan; Centre for Global Child Health, The Hospital for Sick Children, Toronto, Canada
| | - Robert Black
- Institute for International Programs, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kalifa Bojang
- Medical Research Council, The Gambia Unit, Banjul, The Gambia
| | - Harry Campbell
- Centre for Global Health Research, University of Edinburgh, Edinburgh, UK
| | - Simon Cousens
- MARCH Centre, London School of Hygiene & Tropical Medicine, London, UK
| | - Gary L Darmstadt
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Shabir A Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit & DST/NRF Vaccine Preventable Diseases, Faculty Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Neena Modi
- Royal College of Paediatrics and Child Health, London, UK; Department of Medicine, Section of Neonatal Medicine, Imperial College London, London, UK
| | - Janna Patterson
- Maternal, Newborn, and Child Health, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Shamim Qazi
- Department of Maternal Newborn Child and Adolescent Health, WHO, Geneva, Switzerland
| | - Stephanie J Schrag
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Barbara J Stoll
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Stephen N Wall
- Saving Newborn Lives, Save the Children, Washington, DC, USA
| | - Robinson D Wammanda
- Department of Paediatrics, Ahmadu Bello University Teaching Hospital, Ahmadu Bello University, Zaria, Nigeria
| | - Joy E Lawn
- MARCH Centre, London School of Hygiene & Tropical Medicine, London, UK.
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Inzaule SC, Ondoa P, Peter T, Mugyenyi PN, Stevens WS, de Wit TFR, Hamers RL. Affordable HIV drug-resistance testing for monitoring of antiretroviral therapy in sub-Saharan Africa. THE LANCET. INFECTIOUS DISEASES 2016; 16:e267-e275. [PMID: 27569762 DOI: 10.1016/s1473-3099(16)30118-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 04/28/2016] [Accepted: 05/05/2016] [Indexed: 12/19/2022]
Abstract
Increased provision of antiretroviral therapy in sub-Saharan Africa has led to a growing number of patients with therapy failure and acquired drug-resistant HIV, driving the demand for more costly further lines of antiretroviral therapy. In conjunction with accelerated access to viral load monitoring, feasible and affordable technologies to detect drug-resistant HIV could help maximise the durability and rational use of available drug regimens. Potential low-cost technologies include in-house Sanger and next-generation sequencing in centralised laboratories, and point mutation assays and genotype-free systems that predict response to antiretroviral therapy at point-of-care. Strengthening of centralised high-throughput laboratories, including efficient systems for sample referral and results delivery, will increase economies-of-scale while reducing costs. Access barriers can be mitigated by standardisation of in-house assays into commercial kits, use of polyvalent instruments, and adopting price-reducing strategies. A stepwise rollout approach should improve feasibility, prioritising WHO-recommended population-based surveillance and management of complex patient categories, such as patients failing protease inhibitor-based antiretroviral therapy. Implementation research, adaptations of existing WHO guidance, and political commitment, will be key to support the appropriate investments and policy changes. In this Personal View, we discuss the potential role of HIV drug resistance testing for population-based surveillance and individual patient management in sub-Saharan Africa. We review the strengths and challenges of promising low-cost technologies and how they can be implemented.
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Affiliation(s)
- Seth C Inzaule
- Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Pascale Ondoa
- Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Trevor Peter
- African Society for Laboratory Medicine, Addis Abeba, Ethiopia; Clinton Health Access Initiative, Gaborone, Botswana
| | | | - Wendy S Stevens
- Department of Molecular Medicine and Haematology, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa
| | - Tobias F Rinke de Wit
- Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Raph L Hamers
- Department of Global Health and Department of Internal Medicine, Division of Infectious Diseases, Academic Medical Center of the University of Amsterdam, Amsterdam, Netherlands; Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands.
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Henihan G, Schulze H, Corrigan DK, Giraud G, Terry JG, Hardie A, Campbell CJ, Walton AJ, Crain J, Pethig R, Templeton KE, Mount AR, Bachmann TT. Label- and amplification-free electrochemical detection of bacterial ribosomal RNA. Biosens Bioelectron 2016; 81:487-494. [PMID: 27016627 DOI: 10.1016/j.bios.2016.03.037] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/09/2016] [Accepted: 03/17/2016] [Indexed: 01/13/2023]
Abstract
Current approaches to molecular diagnostics rely heavily on PCR amplification and optical detection methods which have restrictions when applied to point of care (POC) applications. Herein we describe the development of a label-free and amplification-free method of pathogen detection applied to Escherichia coli which overcomes the bottleneck of complex sample preparation and has the potential to be implemented as a rapid, cost effective test suitable for point of care use. Ribosomal RNA is naturally amplified in bacterial cells, which makes it a promising target for sensitive detection without the necessity for prior in vitro amplification. Using fluorescent microarray methods with rRNA targets from a range of pathogens, an optimal probe was selected from a pool of probe candidates identified in silico. The specificity of probes was investigated on DNA microarray using fluorescently labeled 16S rRNA target. The probe yielding highest specificity performance was evaluated in terms of sensitivity and a LOD of 20 pM was achieved on fluorescent glass microarray. This probe was transferred to an EIS end point format and specificity which correlated to microarray data was demonstrated. Excellent sensitivity was facilitated by the use of uncharged PNA probes and large 16S rRNA target and investigations resulted in an LOD of 50 pM. An alternative kinetic EIS assay format was demonstrated with which rRNA could be detected in a species specific manner within 10-40min at room temperature without wash steps.
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Affiliation(s)
- Grace Henihan
- Division of Infection and Pathway Medicine, College of Medicine and Veterinary Medicine, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, Scotland, UK
| | - Holger Schulze
- Division of Infection and Pathway Medicine, College of Medicine and Veterinary Medicine, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, Scotland, UK
| | - Damion K Corrigan
- Division of Infection and Pathway Medicine, College of Medicine and Veterinary Medicine, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, Scotland, UK; School of Chemistry, The University of Edinburgh, Joseph Black Building, The King's Buildings, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK
| | - Gerard Giraud
- School of Physics and Astronomy, The University of Edinburgh, The King's Buildings, West Mains Road, Edinburgh EH9 3JZ, Scotland, UK
| | - Jonathan G Terry
- Institute for Integrated Micro and Nano Systems, School of Engineering, The University of Edinburgh, Alexander Crum Brown Road, Edinburgh EH9 3FF, Scotland, UK
| | - Alison Hardie
- Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, Scotland, UK
| | - Colin J Campbell
- School of Chemistry, The University of Edinburgh, Joseph Black Building, The King's Buildings, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK
| | - Anthony J Walton
- Institute for Integrated Micro and Nano Systems, School of Engineering, The University of Edinburgh, Alexander Crum Brown Road, Edinburgh EH9 3FF, Scotland, UK
| | - Jason Crain
- School of Physics and Astronomy, The University of Edinburgh, The King's Buildings, West Mains Road, Edinburgh EH9 3JZ, Scotland, UK; National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, UK
| | - Ronald Pethig
- Institute for Integrated Micro and Nano Systems, School of Engineering, The University of Edinburgh, Alexander Crum Brown Road, Edinburgh EH9 3FF, Scotland, UK
| | - Kate E Templeton
- Division of Infection and Pathway Medicine, College of Medicine and Veterinary Medicine, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, Scotland, UK; Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, Scotland, UK
| | - Andrew R Mount
- School of Chemistry, The University of Edinburgh, Joseph Black Building, The King's Buildings, West Mains Road, Edinburgh EH9 3JJ, Scotland, UK
| | - Till T Bachmann
- Division of Infection and Pathway Medicine, College of Medicine and Veterinary Medicine, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, Scotland, UK.
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Bejhed RS, Tian B, Eriksson K, Brucas R, Oscarsson S, Strömberg M, Svedlindh P, Gunnarsson K. Magnetophoretic Transport Line System for Rapid On-Chip Attomole Protein Detection. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:10296-10302. [PMID: 26309059 DOI: 10.1021/acs.langmuir.5b01947] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A lab-on-a-chip traveling wave magnetophoresis approach for sensitive and rapid protein detection is reported. In this method, a chip-based magnetic microarray comprising lines of micrometer-sized thin film magnetic elements was used to control the movement of magnetic beads (MBs). The MBs and the chip were functionalized, forming a sandwich-type assay. The MBs were transported across a detection area, and the presence of target molecules resulted in the immobilization of MBs within this area. Target quantification was accomplished by MB counting in the detection area using an optical microscope. In order to demonstrate the versatility of the microarray, biotinylated antiavidin was selected as the target protein. In this case, avidin-functionalized MBs and an avidin-functionalized detection area were used. With a total assay time of 1 to 1.5 h (depending on the labeling approach used), a limit of detection in the attomole range was achieved. Compared to on-chip surface plasmon resonance biodetection systems, our method has a larger dynamic range and is about a factor of 500 times more sensitive. Furthermore, our MB transportation system can operate in any chip-based biosensor platform, thereby significantly improving traditional biosensors.
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Affiliation(s)
- Rebecca S Bejhed
- Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University , Box 534, SE-751 21 Uppsala, Sweden
| | - Bo Tian
- Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University , Box 534, SE-751 21 Uppsala, Sweden
| | - Kristofer Eriksson
- Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University , Box 534, SE-751 21 Uppsala, Sweden
| | - Rimantas Brucas
- Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University , Box 534, SE-751 21 Uppsala, Sweden
| | - Sven Oscarsson
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
| | - Mattias Strömberg
- Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University , Box 534, SE-751 21 Uppsala, Sweden
| | - Peter Svedlindh
- Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University , Box 534, SE-751 21 Uppsala, Sweden
| | - Klas Gunnarsson
- Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University , Box 534, SE-751 21 Uppsala, Sweden
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Rogers-Broadway KR, Karteris E. Amplification efficiency and thermal stability of qPCR instrumentation: Current landscape and future perspectives. Exp Ther Med 2015; 10:1261-1264. [PMID: 26622475 PMCID: PMC4578049 DOI: 10.3892/etm.2015.2712] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 05/01/2015] [Indexed: 11/16/2022] Open
Abstract
Quantitative polymerase chain reaction (qPCR) is a method of amplifying and detecting small samples of genetic material in real time and is in routine use across many laboratories. Speed and thermal uniformity, two important factors in a qPCR test, are in direct conflict with one another in conventional peltier-driven thermal cyclers. To overcome this, companies are developing novel thermal systems for qPCR testing. More recently, qPCR technology has developed to enable its use in point-of-care testing (POCT), where the test is administered and results are obtained in a single visit to a health provider, particularly in developing countries. For a system to be suitable for POCT it must be rapid and reliable. In the present study, the speed and thermal uniformity of four qPCR thermal cyclers currently available were compared, two of which use the conventional peltier/block heating method and two of which use novel heating and cooling methods. The time required to complete 40 cycles varied between 12 and 58 min, and the Ct values were comparable, ranging between 13.6 and 16.8. Therefore, the novel technologies investigated in the present study for qPCR instrumentation performed equally well compared with conventional qPCR instruments, in terms of amplification efficiency and thermal uniformity.
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Humphrey B, McLeod N, Turner C, Sutton JM, Dark PM, Warhurst G. Removal of Contaminant DNA by Combined UV-EMA Treatment Allows Low Copy Number Detection of Clinically Relevant Bacteria Using Pan-Bacterial Real-Time PCR. PLoS One 2015; 10:e0132954. [PMID: 26172943 PMCID: PMC4501569 DOI: 10.1371/journal.pone.0132954] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 06/21/2015] [Indexed: 01/12/2023] Open
Abstract
Background More than two decades after its discovery, contaminant microbial DNA in PCR reagents continues to impact the sensitivity and integrity of broad-range PCR diagnostic techniques. This is particularly relevant to their use in the setting of human sepsis, where a successful diagnostic on blood samples needs to combine universal bacterial detection with sensitivity to 1-2 genome copies, because low levels of a broad range of bacteria are implicated. Results We investigated the efficacy of ethidium monoazide (EMA) and propidium monoazide (PMA) treatment as emerging methods for the decontamination of PCR reagents. Both treatments were able to inactivate contaminating microbial DNA but only at concentrations that considerably affected assay sensitivity. Increasing amplicon length improved EMA/PMA decontamination efficiency but at the cost of assay sensitivity. The same was true for UV exposure as an alternative decontamination strategy, likely due to damage sustained by oligonucleotide primers which were a significant source of contamination. However, a simple combination strategy with UV-treated PCR reagents paired with EMA-treated primers produced an assay capable of two genome copy detection and a <5% contamination rate. This decontamination strategy could have important utility in developing improved pan-bacterial assays for rapid diagnosis of low pathogen burden conditions such as in the blood of patients with suspected blood stream infection.
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Affiliation(s)
- Bruce Humphrey
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom
- Infection, Injury & inflammation Research Group, Salford Royal NHS Foundation Trust, Salford, United Kingdom
- * E-mail:
| | - Neil McLeod
- Public Health England, Microbiology Services Division, Porton Down, Salisbury, United Kingdom
| | - Carrie Turner
- Public Health England, Microbiology Services Division, Porton Down, Salisbury, United Kingdom
| | - J. Mark Sutton
- Public Health England, Microbiology Services Division, Porton Down, Salisbury, United Kingdom
| | - Paul M. Dark
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom
- Infection, Injury & inflammation Research Group, Salford Royal NHS Foundation Trust, Salford, United Kingdom
| | - Geoffrey Warhurst
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom
- Infection, Injury & inflammation Research Group, Salford Royal NHS Foundation Trust, Salford, United Kingdom
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Engstrom-Melnyk J, Rodriguez PL, Peraud O, Hein RC. Clinical Applications of Quantitative Real-Time PCR in Virology. METHODS IN MICROBIOLOGY 2015; 42:161-197. [PMID: 38620180 PMCID: PMC7148891 DOI: 10.1016/bs.mim.2015.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Since the invention of the polymerase chain reaction (PCR) and discovery of Taq polymerase, PCR has become a staple in both research and clinical molecular laboratories. As clinical and diagnostic needs have evolved over the last few decades, demanding greater levels of sensitivity and accuracy, so too has PCR performance. Through optimisation, the present-day uses of real-time PCR and quantitative real-time PCR are enumerable. The technique, combined with adoption of automated processes and reduced sample volume requirements, makes it an ideal method in a broad range of clinical applications, especially in virology. Complementing serologic testing by detecting infections within the pre-seroconversion window period and infections with immunovariant viruses, real-time PCR provides a highly valuable tool for screening, diagnosing, or monitoring diseases, as well as evaluating medical and therapeutic decision points that allows for more timely predictions of therapeutic failures than traditional methods and, lastly, assessing cure rates following targeted therapies. All of these serve vital roles in the continuum of care to enhance patient management. Beyond this, quantitative real-time PCR facilitates advancements in the quality of diagnostics by driving consensus management guidelines following standardisation to improve patient outcomes, pushing for disease eradication with assays offering progressively lower limits of detection, and rapidly meeting medical needs in cases of emerging epidemic crises involving new pathogens that may result in significant health threats.
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Affiliation(s)
- Julia Engstrom-Melnyk
- Medical and Scientific Affairs, Roche Diagnostic Corporation, Indianapolis, Indiana, USA
| | - Pedro L Rodriguez
- Medical and Scientific Affairs, Roche Diagnostic Corporation, Indianapolis, Indiana, USA
| | - Olivier Peraud
- Medical and Scientific Affairs, Roche Diagnostic Corporation, Indianapolis, Indiana, USA
| | - Raymond C Hein
- Medical and Scientific Affairs, Roche Diagnostic Corporation, Indianapolis, Indiana, USA
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Weidemaier K, Carrino J, Curry A, Connor JH, Liebmann-Vinson A. Advancing rapid point-of-care viral diagnostics to a clinical setting. Future Virol 2015. [DOI: 10.2217/fvl.14.117] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
ABSTRACT We discuss here critical factors in ensuring the success of a viral diagnostic at the point of care. Molecular and immunoassay approaches are reviewed with a focus on their ability to meet the infrastructure and workflow limitations in clinical settings in both the developed and developing world. In addition to being low cost, easy-to-use, accurate and adapted for the intended laboratory and healthcare environment, viral diagnostics must also provide information that appropriately directs clinical treatment decisions. We discuss the challenges and implications of linking diagnostics to clinical decision-making at the point of care using three examples: respiratory viruses in the developed world, differential fever diagnosis in the developing world and HPV detection in resource-limited settings.
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Affiliation(s)
- Kristin Weidemaier
- Diagnostic Sciences Department, BD Technologies, 21 Davis Drive, Research Triangle Park, NC 27709, USA
| | - John Carrino
- BD Diagnostics, 10865 Road to the Cure, Suite 200, San Diego, CA 92121, USA
| | - Adam Curry
- Diagnostic Sciences Department, BD Technologies, 21 Davis Drive, Research Triangle Park, NC 27709, USA
| | - John H Connor
- Department of Microbiology, Boston University School of Medicine, 620 Albany Street, Boston, MA 02118, USA
| | - Andrea Liebmann-Vinson
- Diagnostic Sciences Department, BD Technologies, 21 Davis Drive, Research Triangle Park, NC 27709, USA
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Comparative performance of the GeneXpert C. difficile PCR assay and C. diff Quik Chek Complete kit assay for detection of Clostridium difficile antigen and toxins in symptomatic community-onset infections. Int J Infect Dis 2014; 29:244-8. [DOI: 10.1016/j.ijid.2014.10.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 09/12/2014] [Accepted: 10/06/2014] [Indexed: 11/22/2022] Open
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Kelley SO, Mirkin CA, Walt DR, Ismagilov RF, Toner M, Sargent EH. Advancing the speed, sensitivity and accuracy of biomolecular detection using multi-length-scale engineering. NATURE NANOTECHNOLOGY 2014; 9:969-80. [PMID: 25466541 PMCID: PMC4472305 DOI: 10.1038/nnano.2014.261] [Citation(s) in RCA: 273] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 10/13/2014] [Indexed: 05/05/2023]
Abstract
Rapid progress in identifying disease biomarkers has increased the importance of creating high-performance detection technologies. Over the last decade, the design of many detection platforms has focused on either the nano or micro length scale. Here, we review recent strategies that combine nano- and microscale materials and devices to produce large improvements in detection sensitivity, speed and accuracy, allowing previously undetectable biomarkers to be identified in clinical samples. Microsensors that incorporate nanoscale features can now rapidly detect disease-related nucleic acids expressed in patient samples. New microdevices that separate large clinical samples into nanocompartments allow precise quantitation of analytes, and microfluidic systems that utilize nanoscale binding events can detect rare cancer cells in the bloodstream more accurately than before. These advances will lead to faster and more reliable clinical diagnostic devices.
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Affiliation(s)
- Shana O. Kelley
- Department of Pharmaceutical Sciences and Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 3M2, Canada
- Correspondence should be addressed to S.O.K.,
| | - Chad A. Mirkin
- Department of Chemistry, International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, USA
| | - David R. Walt
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA
| | - Rustem F. Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Mehmet Toner
- Center for Bioengineering in Medicine, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Edward H. Sargent
- Department of Computer and Electrical Engineering, University of Toronto, Toronto, Ontario M5S 1A4, Canada
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