101
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Jeon H, Jundi B, Choi K, Ryu H, Levy BD, Lim G, Han J. Fully-automated and field-deployable blood leukocyte separation platform using multi-dimensional double spiral (MDDS) inertial microfluidics. LAB ON A CHIP 2020; 20:3612-3624. [PMID: 32990714 DOI: 10.1039/d0lc00675k] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A fully-automated and portable leukocyte separation platform was developed based on a new type of inertial microfluidic device, multi-dimensional double spiral (MDDS) device, as an alternative to centrifugation. By combining key innovations in inertial microfluidic device designs and check-valve-based recirculation processes, highly purified and concentrated WBCs (up to >99.99% RBC removal, ∼80% WBC recovery, >85% WBC purity, and ∼12-fold concentrated WBCs compared to the input sample) were achieved in less than 5 minutes, with high reliability and repeatability (coefficient of variation, CV < 5%). Using this, one can harvest up to 0.4 million of intact WBCs from 50 μL of human peripheral blood (50 μL), without any cell damage or phenotypic changes in a fully-automated operation. Alternatively, hand-powered operation is demonstrated with comparable separation efficiency and speed, which eliminates the need for electricity altogether for truly field-friendly sample preparation. The proposed platform is therefore highly deployable for various point-of-care applications, including bedside assessment of the host immune response and blood sample processing in resource-limited environments.
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Affiliation(s)
- Hyungkook Jeon
- Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. and Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Bakr Jundi
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Kyungyong Choi
- Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Hyunryul Ryu
- Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
| | - Bruce D Levy
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Geunbae Lim
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jongyoon Han
- Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA and Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
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102
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Qiu X, Jiang H, Zhang X, Li K, Ge S, Xia N, Mauk MG. A plasma separator with a multifunctional deformable chamber equipped with a porous membrane for point-of-care diagnostics. Analyst 2020; 145:6138-6147. [PMID: 32869771 DOI: 10.1039/d0an01014f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Traditionally, plasma is extracted from whole blood using centrifuges in clinical laboratories, which is unsuitable for on-site testing. For point-of-care diagnostics, for example in HIV tests, to ensure the detection sensitivity for low-abundance analytical targets, a relatively large volume of plasma needs to be extracted from milliliters of blood with a simpler and easier-to-operate method than centrifugation. We report the development of a membrane-assisted, sedimentation-facilitated plasma separator with a multifunctional deformable chamber, which is able to perform plasma separation from undiluted whole blood in a short time. Multiple steps related to plasma separation, including cell sedimentation, cell filtration, and plasma driving and discharging, are all performed in or through the multifunctional deformable chamber equipped with a top-layer porous membrane, which significantly reduces the device complexity. Assisted by a simple jig or even hands, plasma separation can be conveniently performed upon mechanical actuation of the deformable chamber. Within 8 min, ∼130 μL of plasma can be conveniently extracted with the described device from 2.3 mL of whole blood. It has been demonstrated that HIV antibodies or virus spiked in whole blood can be successfully detected with reasonable sensitivity from the extracted plasma with the described pump-free device.
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Affiliation(s)
- Xianbo Qiu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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103
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Kolenda T, Guglas K, Baranowski D, Sobocińska J, Kopczyńska M, Teresiak A, Bliźniak R, Lamperska K. cfRNAs as biomarkers in oncology - still experimental or applied tool for personalized medicine already? Rep Pract Oncol Radiother 2020; 25:783-792. [PMID: 32904167 PMCID: PMC7451588 DOI: 10.1016/j.rpor.2020.07.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/13/2020] [Accepted: 07/31/2020] [Indexed: 02/07/2023] Open
Abstract
Currently, the challenges of contemporary oncology are focused mainly on the development of personalized medicine and precise treatment, which could be achieved through the use of molecular biomarkers. One of the biological molecules with great potential are circulating free RNAs (cfRNAs) which are present in various types of body fluids, such as blood, serum, plasma, and saliva. Also, different types of cfRNA particles can be distinguished depending on their length and function: microRNA (miRNA), PIWI-interacting RNA (piRNA), tRNA-derived RNA fragments (tRFs), circular RNA (circRNA), long non-coding RNA (lncRNA), and messenger RNA (mRNA). Moreover, cfRNAs occur in various forms: as a free molecule alone, in membrane vesicles, such as exosomes, or in complexes with proteins and lipids. One of the modern approaches for monitoring patient's condition is a "liquid biopsy" that provides a non-invasive and easily available source of circulating RNAs. Both the presence of specific cfRNA types as well as their concentration are dependent on many factors including cancer type or even reaction to treatment. Despite the possibility of using circulating free RNAs as biomarkers, there is still a lack of validated diagnostic panels, defined protocols for sampling, storing as well as detection methods. In this work we examine different types of cfRNAs, evaluate them as possible biomarkers, and analyze methods of their detection. We believe that further research on cfRNA and defining diagnostic panels could lead to better and faster cancer identification and improve treatment monitoring.
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Affiliation(s)
- Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warszawa, Poland
| | - Dawid Baranowski
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Joanna Sobocińska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Magda Kopczyńska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
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104
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Chu Z, Zhang W, You Q, Yao X, Liu T, Liu G, Zhang G, Gu X, Ma Z, Jin W. A Separation‐Sensing Membrane Performing Precise Real‐Time Serum Analysis During Blood Drawing. Angew Chem Int Ed Engl 2020; 59:18701-18708. [PMID: 32648353 DOI: 10.1002/anie.202008241] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Indexed: 12/29/2022]
Affiliation(s)
- Zhenyu Chu
- State Key Laboratory of Materials-Oriented Chemical Engineering College of Chemical Engineering Nanjing Tech University NO.30 Puzhu Road(S) Nanjing 211816 China
| | - Wei Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering College of Chemical Engineering Nanjing Tech University NO.30 Puzhu Road(S) Nanjing 211816 China
- Nanjing Drum Tower Hospital The Affiliated Hospital of Nanjing University Medical School Nanjing 210008 P. R. China
| | - Qiannan You
- State Key Laboratory of Materials-Oriented Chemical Engineering College of Chemical Engineering Nanjing Tech University NO.30 Puzhu Road(S) Nanjing 211816 China
| | - Xiaoyue Yao
- State Key Laboratory of Materials-Oriented Chemical Engineering College of Chemical Engineering Nanjing Tech University NO.30 Puzhu Road(S) Nanjing 211816 China
| | - Tao Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering College of Chemical Engineering Nanjing Tech University NO.30 Puzhu Road(S) Nanjing 211816 China
| | - Gongping Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering College of Chemical Engineering Nanjing Tech University NO.30 Puzhu Road(S) Nanjing 211816 China
| | - Guangru Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering College of Chemical Engineering Nanjing Tech University NO.30 Puzhu Road(S) Nanjing 211816 China
| | - Xiaoping Gu
- Nanjing Drum Tower Hospital The Affiliated Hospital of Nanjing University Medical School Nanjing 210008 P. R. China
| | - Zhengliang Ma
- Nanjing Drum Tower Hospital The Affiliated Hospital of Nanjing University Medical School Nanjing 210008 P. R. China
| | - Wanqin Jin
- State Key Laboratory of Materials-Oriented Chemical Engineering College of Chemical Engineering Nanjing Tech University NO.30 Puzhu Road(S) Nanjing 211816 China
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105
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Extraction of Small RNAs by Titanium Dioxide Nanofibers. Methods Mol Biol 2020. [PMID: 32797454 DOI: 10.1007/978-1-0716-0743-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
MicroRNAs (miRNAs) are small RNAs, that bind to mRNA targets and regulate their translation. Functional study of miRNAs and exploration of their utility as disease markers require miRNA extraction from biological samples, which contain large amounts of interfering compounds for downstream RNA identification and quantification. The most common extraction methods employ either silica columns or TRIzol reagent, but these approaches afford low recovery for small RNAs, possibly due to their short strand lengths. Here, we describe the fabrication of titanium dioxide nanofibers and the optimal extraction conditions to improve miRNA recovery from biological buffers, cell lysate, and serum.
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106
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Hur KH, Park K, Lim Y, Jeong YS, Sung H, Kim MN. Evaluation of Four Commercial Kits for SARS-CoV-2 Real-Time Reverse-Transcription Polymerase Chain Reaction Approved by Emergency-Use-Authorization in Korea. Front Med (Lausanne) 2020; 7:521. [PMID: 32903503 PMCID: PMC7438443 DOI: 10.3389/fmed.2020.00521] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 07/27/2020] [Indexed: 11/25/2022] Open
Abstract
SARS-CoV-2 real-time reverse-transcription PCR (rRT-PCR) is the most effective testing system currently available to counter COVID-19 epidemics when potent treatments and vaccines are unavailable. Therefore, four SARS-CoV-2 rRT-PCR kits have been approved by the emergency-use-authorization (EUA) without clinical validation in Korea until March 15, 2020. This study evaluated the analytical and clinical performance of these kits. Allplex 2019-nCoV Real-time PCR (Seegene, Seoul, Korea), PowerChek 2019-nCoV (KogeneBiotech, Seoul), Real-Q 2019-nCoV Real-Time Detection (BioSewoom, Seoul), and StandardM nCoV Detection (SD BIOSENSOR, Osong, Korea) were evaluated. The limit of detection (LODs) of Allplex, PowerChek, and Real-Q was determined by testing the transcribed RNA of SARS-CoV-2 E and the RNA of SARS-CoV Frankfurt1. A total of 27 consecutive samples comprising 13 sputum, 12 nasopharyngeal swab (NPS), 1 urine and 1 stool sample were collected from 2 COVID-19 patients for sensitivity analysis. Precision was assessed via daily tests of positive and negative controls in each kit for 5 d. Reproducibility was examined by repeating 21 samples and 10-fold dilutions of 14 samples in pairs using Allplex. Specificity was evaluated with 24 other respiratory virus-positive samples. LOD of Allplex, PowerChek, and Real-Q were 153.9, 84.1, and 80.6 copies/mL, respectively. The degrees of association between Cts and log viral concentrations by Allplex and PowerChek was expressed as y = −3.319 log (x) + 42.039 (R = 0.96) and y = −3.392 log(x) + 43.113 (R = 0.98), respectively. One or more of the 4 kits detected 20 out of 27 clinical samples positive. Of the 20 positive samples, the detection rates of positives for Allplex, PowerChek, Real-Q, and StandardM were 90.0, 82.3, 75.0, and 100.0%, respectively, but those of PowerChek and Real-Q would be 100% if out-of-cutoff Cts were counted as positives. Precision was 100%. Interpretation of Allplex results was reproducible when Ct of E ≤33. All 4 kits showed no cross-reactivity with other respiratory viruses. Performance of the 4 kits indicated the suitability of these for diagnosis and follow-up testing of COVID-19. Laboratory doctors who initially implement these EUA kits must be able to interpret quality control parameters.
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Affiliation(s)
- Kyu-Hwa Hur
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Kuenyoul Park
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Youngkuen Lim
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Yun Sil Jeong
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Heungsup Sung
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Mi-Na Kim
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
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107
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Valley BE, Crowell AD, Butler JE, Ladd AJC. Electro-hydrodynamic extraction of DNA from mixtures of DNA and bovine serum albumin. Analyst 2020; 145:5532-5538. [PMID: 32608411 DOI: 10.1039/d0an00961j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We report separation of genomic DNA (48 kbp) from bovine serum albumin (BSA) by the electro-hydrodynamic coupling between a pressure-driven flow and a parallel electric field. Electro-hydrodynamic extraction exploits this coupling to trap DNA molecules at the entrance of a microfluidic contraction channel, while allowing proteins and salts to be flushed from the device. Samples (10 μL) containing λ-DNA (1 ng) and BSA (0.3 mg) were injected directly into the device and convected to the contraction channel entrance by a flowing buffer solution. The DNA remains trapped in this region essentially indefinitely, while proteins and salts are eluted. The effectiveness of the concept has been assessed by fluorescence measurements of DNA and BSA concentrations. Electro-hydrodynamic extraction in a single-stage device was found to enhance the concentration of DNA 40-fold, while reducing the BSA concentration by four orders of magnitude. The relative concentrations of DNA to BSA at the contraction channel entrance can be as large as 1.5 : 1, corresponding to an A260/280 ratio of 1.9. The maximum yield of DNA from a salt-free solution is 50%, while salted (150 mM) solutions have a lower yield (38%).
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Affiliation(s)
- Benjamin E Valley
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA.
| | - Anne D Crowell
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA.
| | - Jason E Butler
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA.
| | - Anthony J C Ladd
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA.
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108
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Santos SB, Cunha AP, Macedo M, Nogueira CL, Brandão A, Costa SP, Melo LDR, Azeredo J, Carvalho CM. Bacteriophage‐receptor binding proteins for multiplex detection of
Staphylococcus
and
Enterococcus
in blood. Biotechnol Bioeng 2020; 117:3286-3298. [DOI: 10.1002/bit.27489] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/23/2020] [Accepted: 07/10/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Sílvio B. Santos
- Centre of Biological Engineering University of Minho Braga Portugal
| | | | - Mariana Macedo
- Centre of Biological Engineering University of Minho Braga Portugal
| | - Catarina L. Nogueira
- International Iberian Nanotechnology Laboratory Braga Portugal
- Instituto de Engenharia de Sistemas e Computadores – Microsistemas e Nanotecnologias (INESC MN) and IN – Institute of Nanoscience and Nanotechnolnology Lisbon Portugal
| | - Ana Brandão
- Centre of Biological Engineering University of Minho Braga Portugal
| | - Susana P. Costa
- Centre of Biological Engineering University of Minho Braga Portugal
- International Iberian Nanotechnology Laboratory Braga Portugal
- Instituto de Engenharia de Sistemas e Computadores – Microsistemas e Nanotecnologias (INESC MN) and IN – Institute of Nanoscience and Nanotechnolnology Lisbon Portugal
| | - Luís D. R. Melo
- Centre of Biological Engineering University of Minho Braga Portugal
| | - Joana Azeredo
- Centre of Biological Engineering University of Minho Braga Portugal
| | - Carla M. Carvalho
- Centre of Biological Engineering University of Minho Braga Portugal
- International Iberian Nanotechnology Laboratory Braga Portugal
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109
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Saechue B, Kamiyama N, Wang Y, Fukuda C, Watanabe K, Soga Y, Goto M, Dewayani A, Ariki S, Hirose H, Ozaka S, Sachi N, Hidano S, Faisal K, Chowdhury R, Anik Ashfaq Khan M, Hossain F, Ghosh P, Shirin T, Mondal D, Murakami K, Kobayashi T. Development of a portable reverse transcription loop-mediated isothermal amplification system to detect the E1 region of Chikungunya virus in a cost-effective manner. Genes Cells 2020; 25:615-625. [PMID: 32562326 DOI: 10.1111/gtc.12797] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 06/01/2020] [Accepted: 06/10/2020] [Indexed: 12/11/2022]
Abstract
Chikungunya fever is a mosquito-borne disease cause of persistent arthralgia. The current diagnosis of Chikungunya virus (CHIKV) relies on a conventional reverse transcription polymerase chain reaction assay. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a rapid and simple tool used for DNA-based diagnosis of a variety of infectious diseases. In this study, we established an RT-LAMP system to recognize CHIKV by targeting the envelope protein 1 (E1) gene that could also detect CHIKV at a concentration of 8 PFU without incorrectly detecting other mosquito-borne viruses. The system also amplified the E1 genome in the serum of CHIKV-infected mice with high sensitivity and specificity. Moreover, we established a dry RT-LAMP system that can be transported without a cold chain, which detected the virus genome in CHIKV-infected patient samples with high accuracy. Thus, the dry RT-LAMP system has great potential to be applied as a novel CHIKV screening kit in endemic areas.
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Affiliation(s)
- Benjawan Saechue
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Naganori Kamiyama
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Yinan Wang
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Chiaki Fukuda
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Kei Watanabe
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Yasuhiro Soga
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Mizuki Goto
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Astri Dewayani
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Shimpei Ariki
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Haruna Hirose
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Sotaro Ozaka
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Nozomi Sachi
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Shinya Hidano
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
| | - Khaledul Faisal
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Rajashree Chowdhury
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Md Anik Ashfaq Khan
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Faria Hossain
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Prakash Ghosh
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Tahmina Shirin
- Department of Virology, Institute of Epidemiology Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Dinesh Mondal
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Kazunari Murakami
- Department of Gastroenterology, Faculty of Medicine, Oita University, Oita, Japan
| | - Takashi Kobayashi
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita, Japan
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110
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Tsai HP, Yeh CS, Lin IT, Ko WC, Wang JR. Increasing Cytomegalovirus Detection Rate from Respiratory Tract Specimens by a New Laboratory-Developed Automated Molecular Diagnostic Test. Microorganisms 2020; 8:microorganisms8071063. [PMID: 32708818 PMCID: PMC7409230 DOI: 10.3390/microorganisms8071063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 11/16/2022] Open
Abstract
Lots of automated molecular methods for detecting cytomegalovirus (CMV) DNA in the blood are available, but seldom for various clinical specimens. This study was designed to establish a highly sensitive automated assay to detect CMV DNA in non-blood specimens. We designed a new QMT assay using QIAGEN artus CMV RG polymerase chain reaction (Q-CMV PCR) kit applied on the BD MAX system and compared with the other assays, including an RGQ assay (LabTurbo auto-extraction combined Q-CMV PCR kit on Rotor-Gene-Q instrument), and in-house PCR assay. A total of 1067 various clinical samples, including 426 plasma, 293 respiratory tract specimens (RTS), 127 stool, 101 cerebral spinal fluid, 90 vitreous humours were analysed. Examining CMV DNA in simultaneous specimens of the same immunocompromised patient with respiratory symptoms, the detection rate of RTS (93.6%, 88/94) was significant higher than plasma (65.9%, 62/94). The positive rates for plasma samples with a low CMV viral load (<137 IU/mL) and diagnostic sensitivity of QMT, RGQ, and in-house assays were 65% and 99.1%, 45% and 100%, 5% and 65.5%, respectively. The QMT assay performs better, with shorter operational and turnaround time than the other assays, enabling the effective and early detection of CMV infection in various clinical specimens, particularly for RTS.
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Affiliation(s)
- Huey-Pin Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan; (C.-S.Y.); (I.-T.L.)
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Correspondence: (H.-P.T.); (J.-R.W.); Tel.: +886-6-2353535 (ext. 2653) (H.-P.T.); Fax: +886-6-2094937 (H.-P.T.); Tel./Fax: +886-6-2760695 (J.-R.W.)
| | - Chun-Sheng Yeh
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan; (C.-S.Y.); (I.-T.L.)
| | - I-Ting Lin
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan; (C.-S.Y.); (I.-T.L.)
| | - Wen-Chien Ko
- Division of Infectious Diseases, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan;
- Department of Internal Medicine, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Jen-Ren Wang
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan; (C.-S.Y.); (I.-T.L.)
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 704, Taiwan
- Correspondence: (H.-P.T.); (J.-R.W.); Tel.: +886-6-2353535 (ext. 2653) (H.-P.T.); Fax: +886-6-2094937 (H.-P.T.); Tel./Fax: +886-6-2760695 (J.-R.W.)
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111
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Niksefat M, Guillen D, Moshayedi P, Rinaldo CR, Ojha A. Third time's a charm: diagnosis of herpes simplex encephalitis after two negative polymerase chain reaction results. Heliyon 2020; 6:e04247. [PMID: 32613121 PMCID: PMC7322049 DOI: 10.1016/j.heliyon.2020.e04247] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 06/13/2020] [Accepted: 06/15/2020] [Indexed: 11/23/2022] Open
Abstract
Introduction Polymerase chain reaction (PCR) testing of cerebrospinal fluid (CSF) is a sensitive and specific method in diagnosing herpes simplex virus (HSV) encephalitis. However there are increasing reports of false negative HSV PCR. Case description We present a patient in the 9th decade of life with abnormal behavior and focal seizures with MRI showing a right temporal T2 hyperintense non-enhancing lesion with electrographic evidence of right lateralized periodic discharges. CSF analysis and PCR for HSV-1 and 2 yielded negative results twice, and therefore acyclovir was discontinued. Patient initially improved following correction of hyponatremia. Patient however deteriorated and imaging revealed a new right parietal lesion. Third CSF sample showed lymphocytic pleocytosis with positive HSV-1 PCR. Patient improved following antiviral treatment. Discussion Acyclovir treatment should continue in high clinical suspicion scenarios despite negative HSV PCR. We further discuss causes of PCR false negatives and challenges it poses for patient care.
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Affiliation(s)
- Mahbobeh Niksefat
- UPMC Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Daniel Guillen
- UPMC Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Pouria Moshayedi
- Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Corresponding author.
| | - Charles R. Rinaldo
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Ajitesh Ojha
- Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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Haag E, Molitor A, Gregoriano C, Müller B, Schuetz P. The value of biomarker-guided antibiotic therapy. Expert Rev Mol Diagn 2020; 20:829-840. [PMID: 32529871 DOI: 10.1080/14737159.2020.1782193] [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] [Indexed: 01/20/2023]
Abstract
INTRODUCTION There is an increasing interest to individualize patient management and decisions regarding antibiotic treatment. Biomarkers may provide relevant information for this purpose. AREAS COVERED Despite a growing number of clinical trials investigating several biomarkers, there remain open questions regarding the best type of biomarker, timing or frequency of testing, and optimal cutoffs among others. The most promising results in regard to diagnosis of bacterial infection and therapy monitoring are found for procalcitonin (PCT), although some recent trials were not able to validate the promising earlier findings. Furthermore, less specific markers like C-reactive protein (CRP) and new prognostic biomarkers such as proadrenomedullin (MR-proADM) may improve the prognostic assessment of patients and proteomics may help shorten time to microbiological results. The aim of this review is to summarize the current concept of biomarker-guided management and provide an outlook of promising ongoing investigations. EXPERT OPINION 'Antibiotic stewardship' is complex and needs more than just the measurement of one single biomarker. However, when integrated into the context of a thorough clinical examination, standard blood parameters and a well done risk stratification by clinical scores such as the SOFA-score, biomarkers have great potential to improve the diagnostic and prognostic assessment of patients.
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Affiliation(s)
- Ellen Haag
- University Department of Medicine, Kantonsspital Aarau , Aarau, Switzerland
| | - Alexandra Molitor
- University Department of Medicine, Kantonsspital Aarau , Aarau, Switzerland
| | - Claudia Gregoriano
- University Department of Medicine, Kantonsspital Aarau , Aarau, Switzerland
| | - Beat Müller
- University Department of Medicine, Kantonsspital Aarau , Aarau, Switzerland
| | - Philipp Schuetz
- University Department of Medicine, Kantonsspital Aarau , Aarau, Switzerland
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113
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Selective capture of plasma cell-free tumor DNA on magnetic beads: a sensitive and versatile tool for liquid biopsy. Cell Oncol (Dordr) 2020; 43:949-956. [PMID: 32495293 DOI: 10.1007/s13402-020-00536-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 05/06/2020] [Accepted: 05/15/2020] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Recently, 'solid tumor biopsies' have been challenged by the emergence of 'liquid biopsies', which are aimed at the isolation and detection of circulating cell-free tumor DNA (ctDNA) in body fluids. Here, we developed and optimized a method for selective capture of ctDNA on magnetic beads (SCC-MAG) for mutation detection in plasma of patients with colorectal cancer (CRC). METHODS Blood and tissue samples from 28 CRC patients were included for the detection of KRAS mutations. For the tissue samples, mutation analysis was conducted by high resolution melting (HRM) analysis and sequencing. For the SCC-MAG method, ctDNA was isolated from 200 µl plasma from patients with a mutant KRAS gene. For comparison, ctDNA extraction was carried out using a silica membrane-based method, after which mutations were detected using Intplex allele-specific PCR. RESULTS The mean ctDNA integrity index in plasma samples of cancer patients was 1.03, comparable with that of silica membrane-derived ctDNA (1.011). Notably, the limit of detection for the SCC-MAG approach was lower than that of the silica membrane method and measured 2.25 pg/ml ctDNA in plasma. Our analyses showed that while the silica membrane-based approach was capable of collecting ctDNA from two out of six CRC patient samples (average Cq 34.23), the SCC-MAG captured ctDNA from all samples with an average Cq of 29.76. CONCLUSIONS We present a robust, reproducible, and highly sensitive method for the analysis of mutation statuses in liquid biopsies. The SCC-MAG method can readily be applied to any nucleic acid target for diagnostic purposes upon careful design of the specific capture probes, and can be multiplexed by several probes to identify multiple targets.
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114
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Albuquerque ALD, Araújo TAD, Melo DCTVD, Paiva MHS, Melo FLD, Oliveira CMFD, Ayres CFJ. Development of a molecular xenomonitoring protocol to assess filariasis transmission. Exp Parasitol 2020; 215:107918. [PMID: 32464220 DOI: 10.1016/j.exppara.2020.107918] [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: 10/17/2019] [Revised: 01/16/2020] [Accepted: 05/14/2020] [Indexed: 11/30/2022]
Abstract
According to the World Health Organization, lymphatic filariasis (LF), a mosquito-borne neglected tropical disease (NTD), should be eliminated as a public health concern by the end of 2020. To this end, the goals of the Global Programme to Eliminate Lymphatic Filariasis (GPELF) include interrupting transmission through mass drug administration (MDA). After two decades, several countries have implemented MDA and are now ready to confirm whether transmission has been interrupted. The method for detecting the parasites in mosquito vectors known as xenomonitoring is a non-invasive tool for assessing the current transmission status of the filarial nematode Wuchereria bancrofti (which is responsible for 90% of cases) by their vectors. There are several methods available for detection of the worm in mosquito samples, such as dissection or polymerase chain reaction (PCR). However, most of these techniques still produce a considerable number of false-negative results. The present study describes a new duplex PCR protocol, which is an improvement on the traditional PCR methodology, enhanced by introducing the actin gene as an endogenous control gene. After adjusting the mosquito pool size, DNA extraction, and WbCx PCR duplex design, we achieved a reliable and sensitive molecular xenomonitoring protocol. This assay was able to eliminate 5% of false negative samples and detected less than one Wb larvae. This high sensitivity is particularly valuable after MDA, when prevalence declines. This new method could reduce the number of false-negative samples, which will enable us to improve our ability to generate accurate results and aid the monitoring strategies used by LF elimination programmes.
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Affiliation(s)
| | | | | | - Marcelo Henrique Santos Paiva
- Departamento de Entomologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil; Universidade Federal de Pernambuco, Centro Acadêmico do Agreste, Caruaru, Pernambuco, Brazil.
| | - Fábio Lopes de Melo
- Departamento de Parasitologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil.
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Yin K, Ding X, Li Z, Zhao H, Cooper K, Liu C. Dynamic Aqueous Multiphase Reaction System for One-Pot CRISPR-Cas12a-Based Ultrasensitive and Quantitative Molecular Diagnosis. Anal Chem 2020; 92:8561-8568. [PMID: 32390420 DOI: 10.1021/acs.analchem.0c01459] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recently, CRISPR-Cas technology has opened a new era of nucleic acid-based molecular diagnostics. However, current CRISPR-Cas-based nucleic acid biosensing has a lack of the quantitative detection ability and typically requires separate manual operations. Herein, we reported a dynamic aqueous multiphase reaction (DAMR) system for simple, sensitive and quantitative one-pot CRISPR-Cas12a based molecular diagnosis by taking advantage of density difference of sucrose concentration. In the DAMR system, recombinase polymerase amplification (RPA) and CRISPR-Cas12a derived fluorescent detection occurred in spatially separated but connected aqueous phases. Our DAMR system was utilized to quantitatively detect human papillomavirus (HPV) 16 and 18 DNAs with sensitivities of 10 and 100 copies within less than 1 h. Multiplex detection of HPV16/18 in clinical human swab samples were successfully achieved in the DAMR system using 3D-printed microfluidic device. Furthermore, we demonstrated that target DNA in real human plasma samples can be directly amplified and detected in the DAMR system without complicated sample pretreatment. As demonstrated, the DAMR system has shown great potential for development of next-generation point-of-care molecular diagnostics.
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Affiliation(s)
- Kun Yin
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030, United States
| | - Xiong Ding
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030, United States
| | - Ziyue Li
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030, United States
| | - Hui Zhao
- Department of Mechanical Engineering, University of Nevada, Las Vegas, Las Vegas, Nevada 89154, United States
| | - Kumarasen Cooper
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3400 Spruce St. Philadelphia, Pennsylvania 19104, United States
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030, United States
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An evaluation of direct PCR assays for the detection and quantification of Porphyromonas gingivalis. Epidemiol Infect 2020; 148:e107. [PMID: 32418555 PMCID: PMC7325331 DOI: 10.1017/s0950268820001053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Porphyromonas gingivalis has been linked to the development and progression of oesophageal squamous cell carcinoma (ESCC), and is considered to be a high-risk factor for ESCC. Currently, the commonly used methods for P. gingivalis detection are culture or DNA extraction-based, which are either time and labour intensive especially for high-throughput applications. We aimed to establish and evaluate a rapid and sensitive direct quantitative polymerase chain reaction (qPCR) protocol for the detection of P. gingivalis without DNA extraction which is suitable for large-scale epidemiological studies. Paired gingival swab samples from 192 subjects undergoing general medical examinations were analysed using two direct and one extraction-based qPCR assays for P. gingivalis. Tris-EDTA buffer-based direct qPCR (TE-direct qPCR), lysis-based direct qPCR (lysis-direct qPCR) and DNA extraction-based qPCR (kit-qPCR) were used, respectively, in 192, 132 and 60 of these samples for quantification of P. gingivalis. The sensitivity and specificity of TE-direct qPCR was 95.24% and 100% compared with lysis-direct qPCR, which was 100% and 97.30% when compared with kit-qPCR; TE-direct qPCR had an almost perfect agreement with lysis-direct qPCR (κ = 0.954) and kit-qPCR (κ = 0.965). Moreover, the assay time used for TE-direct qPCR was 1.5 h. In conclusion, the TE-direct qPCR assay is a simple and efficient method for the quantification of oral P. gingivalis and showed high sensitivity and specificity compared with routine qPCR.
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Point-of-care multiplexed diagnosis of meningitis using the FilmArray® ME panel technology. Eur J Clin Microbiol Infect Dis 2020; 39:1573-1580. [DOI: 10.1007/s10096-020-03859-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/03/2020] [Indexed: 12/30/2022]
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118
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Lee K, Tripathi A. Parallel DNA Extraction From Whole Blood for Rapid Sample Generation in Genetic Epidemiological Studies. Front Genet 2020; 11:374. [PMID: 32411178 PMCID: PMC7201099 DOI: 10.3389/fgene.2020.00374] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/26/2020] [Indexed: 01/12/2023] Open
Abstract
Large-scale genetic epidemiological studies require high-quality analysis of samples such as blood or saliva from multiple patients, which is challenging at the point of care. To expand these studies’ impact, minimal sample storage time and less complex extraction of a substantial quantity and good purity of DNA or RNA for downstream applications are necessary. Here, a simple microfluidics-based system that performs genomic DNA (gDNA) extraction from whole blood was developed. In this system, a mixture of blood lysate, paramagnetic beads, and binding buffer are first placed into the input well. Then, the gDNA-bound paramagnetic beads are pulled using a magnet through a central channel containing a wash buffer to the output well, which contains elution buffer. The gDNA is eluted at 55°C off the chip. The 40-minute microfluidic protocol extracts gDNA from six samples simultaneously and requires an input of 4 μL of diluted blood and a total reagent volume of 75 μL per reaction. Techniques including quantitative PCR (qPCR) and spectrofluorimetry were used to test the purity and quantity of gDNA eluted from the chip following extraction. Bead transport and molecular diffusional analysis showed that an input of less than 4 ng of gDNA (∼667 white blood cells) is optimal for on-chip extraction. There was no observable transport of inhibitors into the eluate that would greatly affect qPCR, and a sample was successfully prepared for next-generation sequencing (NGS). The microfluidics-based extraction of DNA from whole blood described here is paramount for future work in DNA-based point-of-care diagnostics and NGS library workflows.
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Affiliation(s)
- Kiara Lee
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, United States
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, United States
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Lackey KA, Pace RM, Williams JE, Bode L, Donovan SM, Järvinen KM, Seppo AE, Raiten DJ, Meehan CL, McGuire MA, McGuire MK. SARS-CoV-2 and human milk: what is the evidence? MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.04.07.20056812. [PMID: 32511431 PMCID: PMC7217082 DOI: 10.1101/2020.04.07.20056812] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The novel coronavirus SARS-CoV-2 has emerged as one of the most compelling public health challenges of our time. To address the myriad issues generated by this pandemic, an interdisciplinary breadth of research, clinical, and public health communities have rapidly engaged to find answers and solutions. One area of active inquiry is understanding the mode(s) of SARS-CoV-2 transmission. While respiratory droplets are a known mechanism of transmission, other mechanisms are possible. Of particular importance to global health is the possibility of vertical transmission from infected mothers to infants through breastfeeding or consumption of human milk. However, there is limited published literature related to vertical transmission of any human coronavirus (including SARS-CoV-2) via human milk and/or breastfeeding. There is a single study providing some evidence of vertical transmission of human coronavirus 229E, a single study evaluating presence of SARS-CoV in human milk (it was negative), and no published data on MERS-CoV and human milk. There are 9 case studies of human milk tested for SARS-CoV-2; none detected the virus. Importantly, none of the published studies on coronaviruses and human milk report validation of their analytical methods for use in human milk. These reports are evaluated here, and their implications related to the possibility of vertical transmission of coronaviruses (in particular, SARS-CoV-2) during breastfeeding are discussed.
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Affiliation(s)
- Kimberly A. Lackey
- Margaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID, USA
| | - Ryan M. Pace
- Margaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID, USA
| | - Janet E. Williams
- Department of Animal and Veterinary Sciences, University of Idaho, Moscow, ID, USA
| | - Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), University of California, San Diego, La Jolla, CA, USA
| | - Sharon M. Donovan
- Department of Food Science and Human Nutrition and Institute of Genomic Biology, University of Illinois, Urbana, IL USA
| | - Kirsi M. Järvinen
- Department of Pediatrics, Division of Allergy and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Antti E. Seppo
- Department of Pediatrics, Division of Allergy and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Daniel J. Raiten
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Courtney L. Meehan
- Department of Anthropology, Washington State University, Pullman, WA, USA
| | - Mark A. McGuire
- Department of Animal and Veterinary Sciences, University of Idaho, Moscow, ID, USA
| | - Michelle K. McGuire
- Margaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID, USA
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120
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Browne DJ, Brady JL, Waardenberg AJ, Loiseau C, Doolan DL. An Analytically and Diagnostically Sensitive RNA Extraction and RT-qPCR Protocol for Peripheral Blood Mononuclear Cells. Front Immunol 2020; 11:402. [PMID: 32265908 PMCID: PMC7098950 DOI: 10.3389/fimmu.2020.00402] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/20/2020] [Indexed: 12/12/2022] Open
Abstract
Reliable extraction and sensitive detection of RNA from human peripheral blood mononuclear cells (PBMCs) is critical for a broad spectrum of immunology research and clinical diagnostics. RNA analysis platforms are dependent upon high-quality and high-quantity RNA; however, sensitive detection of specific responses associated with high-quality RNA extractions from human samples with limited PBMCs can be challenging. Furthermore, the comparative sensitivity between RNA quantification and best-practice protein quantification is poorly defined. Therefore, we provide herein a critical evaluation of the wide variety of current generation of RNA-based kits for PBMCs, representative of several strategies designed to maximize sensitivity. We assess these kits with a reverse transcription quantitative PCR (RT-qPCR) assay optimized for both analytically and diagnostically sensitive cell-based RNA-based applications. Specifically, three RNA extraction kits, one post-extraction RNA purification/concentration kit, four SYBR master-mix kits, and four reverse transcription kits were tested. RNA extraction and RT-qPCR reaction efficiency were evaluated with commonly used reference and cytokine genes. Significant variation in RNA expression of reference genes was apparent, and absolute quantification based on cell number was established as an effective RT-qPCR normalization strategy. We defined an optimized RNA extraction and RT-qPCR protocol with an analytical sensitivity capable of single cell RNA detection. The diagnostic sensitivity of this assay was sufficient to show a CD8+ T cell peptide epitope hierarchy with as few as 1 × 104 cells. Finally, we compared our optimized RNA extraction and RT-qPCR protocol with current best-practice immune assays and demonstrated that our assay is a sensitive alternative to protein-based assays for peptide-specific responses, especially with limited PBMCs number. This protocol with high analytical and diagnostic sensitivity has broad applicability for both primary research and clinical practice.
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Affiliation(s)
- Daniel J Browne
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia
| | - Jamie L Brady
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia
| | - Ashley J Waardenberg
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia
| | - Claire Loiseau
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia
| | - Denise L Doolan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, QLD, Australia
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121
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Sidstedt M, Rådström P, Hedman J. PCR inhibition in qPCR, dPCR and MPS-mechanisms and solutions. Anal Bioanal Chem 2020; 412:2009-2023. [PMID: 32052066 PMCID: PMC7072044 DOI: 10.1007/s00216-020-02490-2] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/29/2020] [Accepted: 02/04/2020] [Indexed: 12/24/2022]
Abstract
DNA analysis has seen an incredible development in terms of instrumentation, assays and applications over the last years. Massively parallel sequencing (MPS) and digital PCR are now broadly applied in research and diagnostics, and quantitative PCR is used for more and more practises. All these techniques are based on in vitro DNA polymerization and fluorescence measurements. A major limitation for successful analysis is the various sample-related substances that interfere with the analysis, i.e. PCR inhibitors. PCR inhibition affects library preparation in MPS analysis and skews quantification in qPCR, and some inhibitors have been found to quench the fluorescence of the applied fluorophores. Here, we provide a deeper understanding of mechanisms of specific PCR inhibitors and how these impact specific analytical techniques. This background knowledge is necessary in order to take full advantage of modern DNA analysis techniques, specifically for analysis of samples with low amounts of template and high amounts of background material. The classical solution to handle PCR inhibition is to purify or dilute DNA extracts, which leads to DNA loss. Applying inhibitor-tolerant DNA polymerases, either single enzymes or blends, provides a more straightforward and powerful solution. This review includes mechanisms of specific PCR inhibitors as well as solutions to the inhibition problem in relation to cutting-edge DNA analysis.
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Affiliation(s)
- Maja Sidstedt
- Swedish National Forensic Centre, Swedish Police Authority, 581 94, Linköping, Sweden
| | - Peter Rådström
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Johannes Hedman
- Swedish National Forensic Centre, Swedish Police Authority, 581 94, Linköping, Sweden.
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 221 00, Lund, Sweden.
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Haughan J, Jiang Z, Stefanovski D, Moss KL, Ortved KF, Robinson MA. Detection of intra-articular gene therapy in horses using quantitative real time PCR in synovial fluid and plasma. Drug Test Anal 2020; 12:743-751. [PMID: 32133745 DOI: 10.1002/dta.2785] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/18/2020] [Accepted: 02/24/2020] [Indexed: 12/29/2022]
Abstract
Gene therapy promotes the expression of missing or defective genes and can be curative following administration of a single dose. Gene therapy is prohibited in equine athletes by regulatory bodies due to the high potential for abuse and novel analytical methods are needed for detection. The goal of this study was to detect the administration of an experimental gene therapy: a recombinant adeno-associated viral vector (rAAV) carrying a transgene for the anti-inflammatory cytokine IL-10 (rAAV-IL10). Twelve horses were randomly assigned to receive an intra-articular injection of rAAV-IL10 or phosphate buffered saline (vehicle) into a middle carpal joint. Plasma and synovial fluid were collected on days 0, 1, 2, 4, 7, 14, 28, 56, and 84. Primer pairs were designed to detect two unique regions of rAAV. Using quantitative real time PCR, both sets of primers detected rAAV for 14-28 days in joints and up to 4 days in plasma, in all six treated horses. In synovial fluid, rAAV was detected on day 56 in 4/6 horses by both primer sets, and on day 84 in 1/6 horses by one primer set. In plasma, rAAV was detected for 7 days in 5/6 horses, 14 days in 2/6 horses, and 28 days in 1/6 horses by one primer set, and was detected for up to 14 days in 1/6 horses by the other primer set. This study is the first to validate that quantitative real time PCR can be used to systemically detect the local administration of a gene therapy product to horses.
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Affiliation(s)
- Joanne Haughan
- Department of Clinical Studies, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania
| | - Zibin Jiang
- Department of Clinical Studies, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania
| | - Darko Stefanovski
- Department of Clinical Studies, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania
| | - Kaitlyn L Moss
- Department of Clinical Studies, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania
| | - Kyla F Ortved
- Department of Clinical Studies, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania
| | - Mary A Robinson
- Department of Clinical Studies, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania.,Pennsylvania Equine Toxicology & Research Center, West Chester University, West Chester, PA, USA
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123
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Abafogi AT, Kim J, Lee J, Mohammed MO, van Noort D, Park S. 3D-Printed Modular Microfluidic Device Enabling Preconcentrating Bacteria and Purifying Bacterial DNA in Blood for Improving the Sensitivity of Molecular Diagnostics. SENSORS 2020; 20:s20041202. [PMID: 32098268 PMCID: PMC7070462 DOI: 10.3390/s20041202] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/19/2020] [Accepted: 02/20/2020] [Indexed: 01/22/2023]
Abstract
Molecular diagnostics for sepsis is still a challenge due to the presence of compounds that interfere with gene amplification and bacteria at concentrations lower than the limit of detection (LOD). Here, we report on the development of a 3D printed modular microfluidic device (3DpmμFD) that preconcentrates bacteria of interest in whole blood and purifies their genomic DNA (gDNA). It is composed of a W-shaped microchannel and a conical microchamber. Bacteria of interest are magnetically captured from blood in the device with antibody conjugated magnetic nanoparticles (Ab-MNPs) at 5 mL/min in the W-shaped microchannel, while purified gDNA of the preconcentrated bacteria is obtained with magnetic silica beads (MSBs) at 2 mL/min in the conical microchamber. The conical microchamber was designed to be connected to the microchannel after the capturing process using a 3D-printed rotary valve to minimize the exposure of the MSBs to interfering compounds in blood. The pretreatment process of spiked blood (2.5 mL) can be effectively completed within about 50 min. With the 3DpmμFD, the LOD for the target microorganism Escherichia coli O157:H7 measured by both polymerase chain reaction (PCR) with electrophoresis and quantitative PCR was 10 colony forming unit (CFU) per mL of whole blood. The results suggest that our method lowers the LOD of molecular diagnostics for pathogens in blood by providing bacterial gDNA at high purity and concentration.
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Affiliation(s)
- Abdurhaman Teyib Abafogi
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea; (A.T.A.); (J.K.); (J.L.)
| | - Jaewon Kim
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea; (A.T.A.); (J.K.); (J.L.)
| | - Jinyeop Lee
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea; (A.T.A.); (J.K.); (J.L.)
| | - Merem Omer Mohammed
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon 16419, Korea;
| | - Danny van Noort
- Division of Biotechnology, IFM, Linkoping University, 58183 Linkoping, Sweden;
- Chair of Micro Process Engineering and Technology (COMPETE), University of Ljubljana, 1000 Ljubljana, Slovenia
- Centro de Investigación en Bioingeniería -BIO, Universidad de Ingenieria y Tecnologia—UTEC, Barranco 15036, Peru
| | - Sungsu Park
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea; (A.T.A.); (J.K.); (J.L.)
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon 16419, Korea;
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Korea
- Correspondence: ; Tel.: +82-31-290-7431; Fax: +82-31-290-5889
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Chaouch M, Aoun K, Ben Othman S, Ben Abid M, Ben Sghaier I, Bouratbine A, Ben Abderrazak S. Development and Assessment of Leishmania major and Leishmania tropica Specific Loop-Mediated Isothermal Amplification Assays for the Diagnosis of Cutaneous Leishmaniasis in Tunisia. Am J Trop Med Hyg 2020; 101:101-107. [PMID: 31094311 DOI: 10.4269/ajtmh.19-0097] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Cutaneous leishmaniasis (CL) remains one of the world's most prevalent neglected diseases, particularly in developing countries. Identification of the involved Leishmania species is an important step in the diagnosis and case management process. In this study, we tested simple, rapid, and highly sensitive loop-mediated isothermal amplification (LAMP) assays for Leishmania DNA species-specific detection from cutaneous lesions. Two LAMP assays, targeting cysteine protease B (cpb) gene, were developed to detect and identify Leishmania major and Leishmania tropica species. Loop-mediated isothermal amplification specificity was examined using DNA samples from other Leishmania species and Trypanosoma species. No cross-reactions were detected. The developed LAMP assays exhibited sensitivity with a detection limit of 20 fg and 200 fg for L. major and L. tropica, respectively. Both tests were applied on clinical samples of CL suspected patients living in endemic Tunisian regions and compared with kinetoplast DNA quantitative PCR (qPCR), microscopic, and conventional cpb-based polymerase chain reaction (PCR) assays. Our LAMP tests were able to discriminate between L. major and L. tropica species and showed a sensitivity of 84% and a specificity of 100%. However, when compared with the performance of the diagnostic tests with latent class analysis (LCA), our LAMP assays show a sensitivity of 100%. These assays can be used as a first-line molecular test for early diagnosis and prompt management of CL cases in public health programs.
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Affiliation(s)
- Melek Chaouch
- Laboratory of Bioinformatics, Biomathematics and Biostatistics LR 16 IPT 09, Institut Pasteur de Tunis, Tunis, Tunisia.,Laboratory of Medical Parasitology, Biotechnology and Biomolecules LR 11 IPT 06, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Karim Aoun
- Laboratory of Parasitology and Mycology, Institut Pasteur de Tunis, Tunis, Tunisia.,Laboratory of Medical Parasitology, Biotechnology and Biomolecules LR 11 IPT 06, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Souad Ben Othman
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules LR 11 IPT 06, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Meriem Ben Abid
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules LR 11 IPT 06, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Ines Ben Sghaier
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules LR 11 IPT 06, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Aida Bouratbine
- Laboratory of Parasitology and Mycology, Institut Pasteur de Tunis, Tunis, Tunisia.,Laboratory of Medical Parasitology, Biotechnology and Biomolecules LR 11 IPT 06, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Souha Ben Abderrazak
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules LR 11 IPT 06, Institut Pasteur de Tunis, Tunis, Tunisia
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125
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Felekkis K, Papaneophytou C. Challenges in Using Circulating Micro-RNAs as Biomarkers for Cardiovascular Diseases. Int J Mol Sci 2020; 21:ijms21020561. [PMID: 31952319 PMCID: PMC7013987 DOI: 10.3390/ijms21020561] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 12/12/2022] Open
Abstract
Micro-RNAs (miRNAs) play a pivotal role in the development and physiology of the cardiovascular system while they have been associated with multiple cardiovascular diseases (CVDs). Several cardiac miRNAs are detectable in circulation (circulating miRNAs; c-miRNAs) and are emerging as diagnostic and therapeutic biomarkers for CVDs. c-miRNAs exhibit numerous essential characteristics of biomarkers while they are extremely stable in circulation, their expression is tissue-/disease-specific, and they can be easily detected using sequence-specific amplification methods. These features of c-miRNAs are helpful in the development of non-invasive assays to monitor the progress of CVDs. Despite significant progress in the detection of c-miRNAs in serum and plasma, there are many contradictory publications on the alterations of cardiac c-miRNAs concentration in circulation. The aim of this review is to examine the pre-analytical and analytical factors affecting the quantification of c-miRNAs and provide general guidelines to increase the accuracy of the diagnostic tests in order to improve future research on cardiac c-miRNAs.
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Abstract
Advanced prostate cancer (PC) patients commonly receive anti-hormonal drugs targeting the androgen receptor (AR) signaling pathways. However, almost all patients acquire therapy resistance that can be caused by AR amplification or expression of AR splice variant 7 (AR-V7). Therefore, AR-V7 and AR expression are potential biomarkers for early detection of therapy resistance. Here, we present our padlock probe (PLP)-based approach for the in situ detection of AR full length, AR-V7, and prostate-specific transcripts in PC cell lines, which is applicable for circulating tumor cells (CTCs) isolated from cancer patients. First, PC cell lines are seeded on glass slides. Then, cDNA is created using target-specific reverse transcription primers. PLPs are hybridized to the cDNA and ligated to form circular single-stranded DNA molecules. The PLP sequence is ligated and amplified by rolling circle amplification and the resulting rolling circle products can be detected using fluorescently labeled probes. Quantification can be automated using the image analysis software CellProfiler.
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127
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Medical Management and Diagnostic Approaches. THE LABORATORY RAT 2020. [PMCID: PMC7153319 DOI: 10.1016/b978-0-12-814338-4.00011-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
This chapter reviews the basic principles of medical management of rat colonies and diagnostic approaches to detect infectious diseases of rats. As is the case with all other species, rats are susceptible to a variety of injuries and diseases that can cause distress, morbidity, or mortality. Any facility that houses rats must develop monitoring programs designed to rapidly identify health-related problems so they can be communicated to appropriate veterinary or animal care personnel to be resolved. These programs generally consist of multiple components, some of which are directed toward individual animals and others that assess the health status of rat populations as a whole. Topics include individual animal monitoring and care, signs of illness and distress, colony health management, components of microbiological monitoring programs, including agents commonly targeted and sentinel programs, quarantine, biological material screening, diagnostic testing methodologies, including culture, serology, molecular diagnostic and histopathology, test profiles and interpretation, management of disease outbreaks, and treatment and prevention strategies for infectious agents.
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128
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Takano C, Kuramochi Y, Seki M, Kim DW, Omagari D, Sasano M, Chang B, Ohnishi M, Kim EJ, Fuwa K, Kilgore PE, Hoshino T, Hayakawa S. Molecular serotype-specific identification of Streptococcus pneumoniae using loop-mediated isothermal amplification. Sci Rep 2019; 9:19823. [PMID: 31882619 PMCID: PMC6934563 DOI: 10.1038/s41598-019-56225-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/09/2019] [Indexed: 11/14/2022] Open
Abstract
In children, the incidence of pneumococcal meningitis has decreased since the introduction of pneumococcal conjugate vaccine (PCV7 and PCV13). However, since the introduction of the vaccine, developed countries have seen the emergence of non-PCV13 serotypes. However, invasive pneumococcal disease (IPD) caused by PCV13-targeted serotypes still represents an important public health problem in resource-limited countries. To develop a rapid, simple, and cost-effective assay to detect serotypes of Streptococcus pneumoniae, we developed a novel loop-mediated isothermal amplification (LAMP) assay based on the sequences available for the 13 capsular types that are included in PCV13: 1, 3, 4, 5, 6 A, 6B, 7 F, 9 V, 14, 18 C, 19 A, 19 F, and 23 F. We evaluated test reactivity, specificity, sensitivity and performance, and compared the results between established LAMP and conventional PCR assays. To support its clinical use, the detection limits of the LAMP assay were evaluated using bacterial genomic DNA-spiked cerebrospinal fluid (CSF) and blood specimens. We confirmed the specificity of the LAMP assay using 41 serotypes of pneumococcal strains. The sensitivity of the LAMP assay was 10 to 100 copies per reaction, compared to 10 to 104 copies per reaction for PCR assays. The detection limits of the LAMP assay were comparable when using DNA-spiked CSF and blood specimens, as compared to using purified DNA as the template. In conclusion, a rapid and simple LAMP-based pneumococcal serotyping method has been developed. This is the first report of a LAMP method for a PCV13 serotype-specific identification assay, which could be a promising step to facilitate epidemiological studies of pneumococcal serotyping.
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Affiliation(s)
- Chika Takano
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, 173-8610, Japan.,Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Yoko Kuramochi
- Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Mitsuko Seki
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, 173-8610, Japan. .,Department of Pediatric Dentistry, School of Dentistry, Meikai University, Saitama, Japan.
| | - Dong Wook Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, 15588, Republic of Korea. .,Institute of Pharmacological Research, Hanyang University, Ansan, 15588, Republic of Korea.
| | - Daisuke Omagari
- Nihon University School of Dentistry, Tokyo, 101-8310, Japan
| | - Mari Sasano
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, 173-8610, Japan.,Department of Neurological Surgery, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Bin Chang
- Bacteriology I, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Makoto Ohnishi
- Bacteriology I, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Eun Jin Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, 15588, Republic of Korea.,Institute of Pharmacological Research, Hanyang University, Ansan, 15588, Republic of Korea
| | - Kazumasa Fuwa
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Paul E Kilgore
- Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Tomonori Hoshino
- Department of Pediatric Dentistry, School of Dentistry, Meikai University, Saitama, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, 173-8610, Japan
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129
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Identification and Validation Model for Informative Liquid Biopsy-Based microRNA Biomarkers: Insights from Germ Cell Tumor In Vitro, In Vivo and Patient-Derived Data. Cells 2019; 8:cells8121637. [PMID: 31847394 PMCID: PMC6952794 DOI: 10.3390/cells8121637] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/11/2019] [Accepted: 12/13/2019] [Indexed: 12/26/2022] Open
Abstract
Liquid biopsy-based biomarkers, such as microRNAs, represent valuable tools for patient management, but often do not make it to integration in the clinic. We aim to explore issues impeding this transition, in the setting of germ cell tumors, for which novel biomarkers are needed. We describe a model for identifying and validating clinically relevant microRNAs for germ cell tumor patients, using both in vitro, in vivo (mouse model) and patient-derived data. Initial wide screening of candidate microRNAs is performed, followed by targeted profiling of potentially relevant biomarkers. We demonstrate the relevance of appropriate (negative) controls, experimental conditions (proliferation), and issues related to sample origin (serum, plasma, cerebral spinal fluid) and pre-analytical variables (hemolysis, contaminants, temperature), all of which could interfere with liquid biopsy-based studies and their conclusions. Finally, we show the value of our identification model in a specific scenario, contradicting the presumed role of miR-375 as marker of teratoma histology in liquid biopsy setting. Our findings indicate other putative microRNAs (miR-885-5p, miR-448 and miR-197-3p) fulfilling this clinical need. The identification model is informative to identify the best candidate microRNAs to pursue in a clinical setting.
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130
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Abstract
The centrifuge is the gold standard for lab-based sample processing. While extremely efficient and robust, centrifuges are seldom used in the field due to the high-power requirements, size, and operational complexity. The lack of viable alternatives for remote sample collection has crippled the ability for mobile practitioners in human and animal medicine to reliably collect blood samples from their patients. There is no truly resource-independent solution that is able to perform highly efficient blood-plasma separation. Here, we describe our initial efforts in developing the High Efficiency Rapid Magnetic Erythrocyte Separator (H.E.R.M.E.S) sleeve, an apparatus that uses a magnetic bead-based separation assay in a scaled-up form factor to achieve highly efficient separation of erythrocytes from plasma within a short amount of time. The sleeve is easy-to-use, is completely resource independent, and achieves highly efficient separation in sample volumes as large as 1 mL by means of a unique mixing scheme. We demonstrate the performance of the sleeve with human blood samples and compare it against conventional end-over-end mixing.
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Affiliation(s)
- S Vemulapati
- Sibley School of Mechanical and Aerospace Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - D Erickson
- Sibley School of Mechanical and Aerospace Engineering , Cornell University , Ithaca , New York 14853 , United States.,Division of Nutritional Sciences , Cornell University , Ithaca , New York 14853 , United States
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131
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Clark DJ, Moore CM, Flanagan M, Bocxlaer KV, Piperaki ET, Yardley V, Croft SL, Tyson J, Whitehouse SP, O'Halloran J, Krishna S, Staines HM. An efficient and novel technology for the extraction of parasite genomic DNA from whole blood or culture. Biotechniques 2019; 68:79-84. [PMID: 31774301 PMCID: PMC7115988 DOI: 10.2144/btn-2019-0086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The aim of this study was to assess pathogen DNA extraction with a new spin column-based method (DNA-XT). DNA from either whole-blood samples spiked with Plasmodium falciparum or Leishmania donovani amastigote culture was extracted with DNA-XT and compared with that produced by a commercial extraction kit (DNeasy®). Eluates from large and small sample volumes were assessed by PCR and spectroscopy. Using a small volume (5 μl) of blood, the DNA-XT and DNeasy methods produced eluates with similar DNA concentrations (0.63 vs 1.06 ng/μl, respectively). The DNA-XT method produced DNA with lower PCR inhibition than DNeasy. The new technique was also twice as fast and required fewer plastics and manipulations but had reduced total recovered DNA compared with DNeasy. DNA-XT, which is designed for small sample volumes, uses a 5-min detergent and enzymatic lysis step to release DNA from cells. Contaminating proteins and lipids are then bound to a matrix within a spin column during a 1-min centrifugation step while DNA passes directly through.
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Affiliation(s)
- David J Clark
- Centre for Diagnostics & Antimicrobial Resistance, Institute for Infection & Immunity, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Catherine M Moore
- Centre for Diagnostics & Antimicrobial Resistance, Institute for Infection & Immunity, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | | | - Katrien Van Bocxlaer
- Infection & Immunity Department, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Evangelia-Theophano Piperaki
- Infection & Immunity Department, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Vanessa Yardley
- Infection & Immunity Department, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Simon L Croft
- Infection & Immunity Department, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - John Tyson
- QuantuMDx, Newcastle upon Tyne, NE1 2JQ, UK
| | | | | | - Sanjeev Krishna
- Centre for Diagnostics & Antimicrobial Resistance, Institute for Infection & Immunity, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Henry M Staines
- Centre for Diagnostics & Antimicrobial Resistance, Institute for Infection & Immunity, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK
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132
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Zhang C, Sun G, Senapati S, Chang HC. A bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput nucleic acid extraction and purification. LAB ON A CHIP 2019; 19:3853-3861. [PMID: 31621762 PMCID: PMC6982425 DOI: 10.1039/c9lc00818g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We report a bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput (20 min) extraction of nucleic acids from physiological samples. The design uses a membrane ionic transistor to sustain low-ionic strength in a localized region at a junction, such that the resulting high field can selectively isolate high-charge density nucleic acids from the main flow channel and insert them into a standardized buffer in a side channel that bifurcates from the junction. The high local electric field and the bifurcated field-flow design facilitate concentration reduction of both divalent cation (Ca2+) and molecular PCR inhibitors by more than two orders of magnitude, even with high-throughput continuous loading. The unique design with a large (>20 mM mm-1) on-chip ionic-strength gradient allows miniaturization into a high-throughput field-flow fractionation chip that can be integrated with upstream lysing and downstream PCR/sensor modules for various nucleic acid detection/quantification applications. A concentration-independent 85% yield for extraction and an overall post-PCR yield exceeding 60% are demonstrated for a 111 bp dsDNA in 10 μL of human plasma, compared to no amplification with the raw sample. A net yield four times larger than a commercial extraction kit is demonstrated for miR-39 in human plasma.
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Affiliation(s)
- Chenguang Zhang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. and Center for Microfluidics and Medical Diagnostics, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Gongchen Sun
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Satyajyoti Senapati
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. and Center for Microfluidics and Medical Diagnostics, University of Notre Dame, Notre Dame, IN 46556, USA and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. and Center for Microfluidics and Medical Diagnostics, University of Notre Dame, Notre Dame, IN 46556, USA and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA and Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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Yan L, Toohey-Kurth KL, Crossley BM, Bai J, Glaser AL, Tallmadge RL, Goodman LB. Inhibition monitoring in veterinary molecular testing. J Vet Diagn Invest 2019; 32:758-766. [PMID: 31735123 DOI: 10.1177/1040638719889315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Many of the sample matrices typically used for veterinary molecular testing contain inhibitory factors that can potentially reduce analytic sensitivity or produce false-negative results by masking the signal produced by the nucleic acid target. Inclusion of internal controls in PCR-based assays is a valuable strategy not only for monitoring for PCR inhibitors, but also for monitoring nucleic acid extraction efficiency, and for identifying technology errors that may interfere with the ability of an assay to detect the intended target. The Laboratory Technology Committee of the American Association of Veterinary Laboratory Diagnosticians reviewed the different types of internal controls related to monitoring inhibition of PCR-based assays, and provides information here to encourage veterinary diagnostic laboratories to incorporate PCR internal control strategies as a routine quality management component of their molecular testing.
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Affiliation(s)
- Lifang Yan
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
| | - Kathy L Toohey-Kurth
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
| | - Beate M Crossley
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
| | - Jianfa Bai
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
| | - Amy L Glaser
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
| | - Rebecca L Tallmadge
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
| | - Laura B Goodman
- Mississippi Veterinary Research and Diagnostic Laboratory, Mississippi State University, Pearl, MS (Yan).,California Animal Health and Food Safety Laboratory, University of California-Davis, Davis, CA (Toohey-Kurth, Crossley).,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS (Bai).,Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY (Glaser, Tallmadge, Goodman)
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134
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Kebede A, Beyene D, Yenew B, Diriba G, Mehamd Z, Alemu A, Amare M, Ameni G. Monitoring quality indicators for the Xpert MTB/RIF molecular assay in Ethiopia. PLoS One 2019; 14:e0225205. [PMID: 31714934 PMCID: PMC6850546 DOI: 10.1371/journal.pone.0225205] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/29/2019] [Indexed: 02/05/2023] Open
Abstract
INTRODUCTION In Ethiopia, >300 GeneXpert instruments have been deployed for tuberculosis (TB) testing using the Xpert MTB/RIF cartridge. Implementing quality indicators is necessary for monitoring and evaluating the quality of Xpert MTB/RIF diagnostic services. OBJECTIVE To assess the use of quality indicators for the Xpert MTB/RIF molecular assay in Ethiopia and to compare the findings with the predefined targets described in the literature. METHODS Clinical specimens collected from patients with suspected TB were subjected to Xpert MTB/RIF testing at the National TB Reference Laboratory (NTRL) between January and December 2018. Data were collected from GeneXpert software and Laboratory Information System (LIS) databases. Quality indicators were calculated and analyzed. Bivariate and multivariate analyses were performed using SPSS software version 20 (SPSS Inc., Chicago, Illinois, USA). RESULTS Of the 2515 specimens tested, 2274 (90.4%) had successful test results; 18.2% were positive for Mycobacterium tuberculosis (MTB). Among MTB positives (n = 413), 4.8% and 1.0% were rifampicin (RIF)-resistant and RIF-indeterminate cases, respectively. Unsuccessful results were 241 (9.6%); 8.9% of the total number of tests were errors, 0.04% had invalid results and 0.6% 'no result'. The most frequent error was probe check failure (error 5007). Instrument module A4, B2, B3, C3, and D3 (p<0.05) and tester experience (p<0.05) had a statistically significant association with errors in multivariate analysis. Additional 42 MTB cases (9.2% of the total cases) were detected among unsuccessful results by follow-up tests. Sixty-four percent of the initial test results were released within the turnaround time (TAT) ≤24 hours. CONCLUSION Most of the quality indicators for the Xpert MTB/RIF molecular assay were maintained within the targets. However, the error rate and TAT were out of the targets. Defective modules and lacking experience were the factors affecting successful test outcomes.
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Affiliation(s)
- Abebaw Kebede
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dereje Beyene
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Bazezew Yenew
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Getu Diriba
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Zemedu Mehamd
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Ayinalem Alemu
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Misikr Amare
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathology, Addis Ababa University, Addis Ababa, Ethiopia
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135
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Edgar RH, Cook J, Noel C, Minard A, Sajewski A, Fitzpatrick M, Fernandez R, Hempel JD, Kellum JA, Viator JA. Bacteriophage-mediated identification of bacteria using photoacoustic flow cytometry. JOURNAL OF BIOMEDICAL OPTICS 2019; 24:1-7. [PMID: 31758676 PMCID: PMC6874036 DOI: 10.1117/1.jbo.24.11.115003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/04/2019] [Indexed: 05/26/2023]
Abstract
Infection with resistant bacteria has become an ever increasing problem in modern medical practice. Currently, broad spectrum antibiotics are prescribed until bacteria can be identified through blood cultures, a process that can take two to three days and is unable to provide quantitative information. To detect and quantify bacteria rapidly in blood samples, we designed a method using labeled bacteriophage in conjunction with photoacoustic flow cytometry (PAFC). PAFC is the generation of ultrasonic waves created by the absorption of laser light in particles under flow. Bacteriophage is a virus that infects bacteria and possesses the ability to discriminate bacterial surface antigens, allowing the bacteriophage to bind only to their target bacteria. Bacteria can be tagged with dyed phage and processed through a photoacoustic flow cytometer where they are detected by the acoustic response. We demonstrate that E. coli; can be detected and discriminated from Salmonella; using this method. Our goal is to develop a method to determine bacterial content in blood samples. We hope to develop this technology into future clinical use and decrease the time required to identify bacterial species from 3 to 4 days to less than 1 hour.
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Affiliation(s)
- Robert H. Edgar
- University of Pittsburgh, Swanson School of Engineering, Department of Bioengineering, Pittsburgh, Pennsylvania, United States
| | - Justin Cook
- Duquesne University, Pittsburgh, Pennsylvania, United States
| | - Cierra Noel
- Duquesne University, Pittsburgh, Pennsylvania, United States
| | - Austin Minard
- Duquesne University, Pittsburgh, Pennsylvania, United States
| | - Andrea Sajewski
- Duquesne University, Pittsburgh, Pennsylvania, United States
| | | | | | - John D. Hempel
- Duquesne University, Pittsburgh, Pennsylvania, United States
| | - John A. Kellum
- University of Pittsburgh, Center for Critical Care Nephrology, Department of Critical Care Medicine, Pittsburgh, Pennsylvania, United States
| | - John A. Viator
- University of Pittsburgh, Swanson School of Engineering, Department of Bioengineering, Pittsburgh, Pennsylvania, United States
- Duquesne University, Pittsburgh, Pennsylvania, United States
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Rapid microbiological tests for bloodstream infections due to multidrug resistant Gram-negative bacteria: therapeutic implications. Clin Microbiol Infect 2019; 26:713-722. [PMID: 31610299 DOI: 10.1016/j.cmi.2019.09.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 09/20/2019] [Accepted: 09/27/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Treating severe infections due to multidrug-resistant Gram-negative bacteria (MDR-GNB) is one of the most important challenges for clinicians worldwide, partly because resistance may remain unrecognized until identification of the causative agent and/or antimicrobial susceptibility testing (AST). Recently, some novel rapid test for identification and/or AST of MDR-GNB from positive blood cultures or the blood of patients with bloodstream infections (BSIs) have become available. OBJECTIVES The objective of this narrative review is to discuss the advantages and limitations of different rapid tests for identification and/or AST of MDR-GNB from positive blood cultures or the blood of patients with BSI, as well as the available evidence on their possible role to improve therapeutic decisions and antimicrobial stewardship. SOURCES Inductive PubMed search for publications relevant to the topic. CONTENT The present review is structured in the following way: (a) rapid tests on positive blood cultures; (b) rapid tests directly on whole blood; (c) therapeutic implications. IMPLICATIONS Novel molecular and phenotypic rapid tests for identification and AST show the potential for favourably influencing patients' outcomes and results of antimicrobial stewardship interventions by reducing both the time to effective treatment and the misuse of antibiotics, although the interpretation about their impact on actual therapeutic decisions and patients' outcomes is still complex. Factors such as feasibility and personnel availability, as well as the detailed knowledge of the local microbiological epidemiology, need to be considered very carefully when implementing novel rapid tests in laboratory workflows and algorithms. Providing high-level, comparable evidence on the clinical impact of rapid identification and AST is becoming of paramount importance for MDR-GNB infections, since in the near future rapid identification of specific resistance mechanisms could be crucial for guiding rapid, effective, and targeted therapy against specific resistance mechanisms.
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Liu X, Zhang C, Hua K, Liang J, Li H, Ma T, Zhu J, Cui Y. Direct genotyping from whole blood using alkaline polyethylene glycol. Anal Biochem 2019; 582:113351. [DOI: 10.1016/j.ab.2019.113351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 02/07/2023]
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138
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Zheng H, Han F, Lin H, Cao L, Pavase TR, Sui J. Preparation of a novel polyethyleneimine functionalized sepharose-boronate affinity material and its application in selective enrichment of food borne pathogenic bacteria. Food Chem 2019; 294:468-476. [DOI: 10.1016/j.foodchem.2019.05.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 04/10/2019] [Accepted: 05/05/2019] [Indexed: 11/25/2022]
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139
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Advances in Directly Amplifying Nucleic Acids from Complex Samples. BIOSENSORS-BASEL 2019; 9:bios9040117. [PMID: 31574959 PMCID: PMC6955841 DOI: 10.3390/bios9040117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 12/15/2022]
Abstract
Advances in nucleic acid amplification technologies have revolutionized diagnostics for systemic, inherited, and infectious diseases. Current assays and platforms, however, often require lengthy experimental procedures and multiple instruments to remove contaminants and inhibitors from clinically-relevant, complex samples. This requirement of sample preparation has been a bottleneck for using nucleic acid amplification tests (NAATs) at the point of care (POC), though advances in “lab-on-chip” platforms that integrate sample preparation and NAATs have made great strides in this space. Alternatively, direct NAATs—techniques that minimize or even bypass sample preparation—present promising strategies for developing POC diagnostic tools for analyzing real-world samples. In this review, we discuss the current status of direct NAATs. Specifically, we surveyed potential testing systems published from 1989 to 2017, and analyzed their performances in terms of robustness, sensitivity, clinical relevance, and suitability for POC diagnostics. We introduce bubble plots to facilitate our analysis, as bubble plots enable effective visualization of the performances of these direct NAATs. Through our review, we hope to initiate an in-depth examination of direct NAATs and their potential for realizing POC diagnostics, and ultimately transformative technologies that can further enhance healthcare.
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140
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Roux G, Ravel C, Varlet-Marie E, Jendrowiak R, Bastien P, Sterkers Y. Inhibition of polymerase chain reaction: Pathogen-specific controls are better than human gene amplification. PLoS One 2019; 14:e0219276. [PMID: 31560697 PMCID: PMC6764677 DOI: 10.1371/journal.pone.0219276] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 08/23/2019] [Indexed: 11/21/2022] Open
Abstract
PCR inhibition is frequent in medical microbiology routine practice and may lead to false-negative results; however there is no consensus on how to detect it. Pathogen-specific and human gene amplifications are widely used to detect PCR inhibition. We aimed at comparing the value of PCR inhibitor detection using these two methods. We analysed Cp shifts (ΔCp) obtained from qPCRs targeting either the albumin gene or the pathogen-specific sequence used in two laboratory-developed microbiological qPCR assays. 3152 samples including various matrixes were included. Pathogen-specific amplification and albumin qPCR identified 62/3152 samples (2.0%), and 409/3152 (13.0%) samples, respectively, as inhibited. Only 16 samples were detected using both methods. In addition, the use of the Youden's index failed to determine adequate Cp thresholds for albumin qPCR, even when we distinguished among the different sample matrixes. qPCR targeting the albumin gene therefore appears not adequate to identify the presence of PCR inhibitors in microbiological PCR assays. Our data may be extrapolated to other heterologous targets and should discourage their use to assess the presence of PCR inhibition in microbiological PCR assays.
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Affiliation(s)
- Guillaume Roux
- Univ. Montpellier, and Laboratoire de Microbiologie, Centre Hospitalier Universitaire (CHU) of Nîmes, Nîmes, France
| | - Christophe Ravel
- Univ. Montpellier, Centre Hospitalier Universitaire (CHU) of Montpellier, Dept. of Parasitology-Mycology, Research Unit MiVEGEC, CNRS, IRD, Montpellier, France
| | - Emmanuelle Varlet-Marie
- Univ. Montpellier, Centre Hospitalier Universitaire (CHU) of Montpellier, Dept. of Parasitology-Mycology, Research Unit MiVEGEC, CNRS, IRD, Montpellier, France
| | - Rachel Jendrowiak
- Univ. Montpellier, Centre Hospitalier Universitaire (CHU) of Montpellier, Dept. of Parasitology-Mycology, Research Unit MiVEGEC, CNRS, IRD, Montpellier, France
| | - Patrick Bastien
- Univ. Montpellier, Centre Hospitalier Universitaire (CHU) of Montpellier, Dept. of Parasitology-Mycology, Research Unit MiVEGEC, CNRS, IRD, Montpellier, France
| | - Yvon Sterkers
- Univ. Montpellier, Centre Hospitalier Universitaire (CHU) of Montpellier, Dept. of Parasitology-Mycology, Research Unit MiVEGEC, CNRS, IRD, Montpellier, France
- * E-mail:
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141
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Prenatal diagnosis of genetic diseases directly using paper-dried cord blood as the starting material for PCR. Anal Bioanal Chem 2019; 411:6825-6835. [PMID: 31410536 DOI: 10.1007/s00216-019-02048-x] [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: 05/25/2019] [Revised: 07/05/2019] [Accepted: 07/22/2019] [Indexed: 10/26/2022]
Abstract
A rapid and low-cost method of diagnosis is becoming important for detecting fetal inherited diseases, including single-gene disorders and chromosomal abnormalities. Here, we demonstrated an innovation that use paper-dried cord blood (PCB) as the starting material for PCR and whole genome amplification without any DNA extraction step at a very low cost. A novel PCR buffer named "DDB buffer" containing ammonium sulfate and glycerol were used instead of the conventional 10× PCR buffer. The amplicons were directly analyzed through microchip electrophoresis and whole genome sequencing. Inhibitory substances in filter paper were effectively inactivated using DDB buffer. Direct PCR amplification of DNA fragments ranging from 100 to 900 bp using filter paper spotted with 0.5 to 5 μL of cord blood and various anticoagulants was successful. We were able to determine fetal single-gene disorders and chromosomal diseases in all 46 chromosomes using PCB samples successfully. Compared with prenatal diagnosis using purified DNA, the proposed method is simple, fast, less prone to cross-contamination at minimal cost. Researchers and clinical and healthcare workers may employ this method for genetic diagnosis using cord blood samples with minimum laboratory resources. This method is very promising for a variety of genetic diagnosis applications in underserved communities at the point of need in developing areas. Graphical abstract.
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Pilecky M, Schildberger A, Knabl L, Orth-Höller D, Weber V. Influence of antibiotic treatment on the detection of S. aureus in whole blood following pathogen enrichment. BMC Microbiol 2019; 19:180. [PMID: 31387527 PMCID: PMC6683330 DOI: 10.1186/s12866-019-1559-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/30/2019] [Indexed: 02/06/2023] Open
Abstract
Background Early pathogen detection and identification are crucial for an effective and targeted antibiotic therapy in patients suffering from blood stream infection. Molecular diagnostic methods can accelerate pathogen identification as compared to blood culture, but frequently suffer from the inhibition of polymerase chain reation (PCR) by sample matrix components, such as host DNA, anticoagulants, or plasma proteins. To overcome this limitation, molecular diagnostic methods commonly rely on pathogen enrichment by selective lysis of blood cells and pelleting of intact pathogens prior to analysis. Results Here, we investigated the impact of antibiotic treatment on the recovery of pathogen DNA using an established pathogen enrichment protocol. Based on the hypothesis that induction of bacterial cell wall disintegration following antibiotic administration leads to incomplete pelleting of pathogen DNA, S. aureus was grown in human whole blood with or without addition of cell wall active (vancomycin, piperacillin) or non cell wall active (ciprofloxacin, clindamycin) antibiotics at clinically relevant concentrations. Pathogen detection remained unaffected by non cell wall active antibiotics or even increased in the presence of cell wall active antibiotics, indicating improved accessibility of pathogen DNA. Likewise, mechanical lysis of S. aureus prior to pathogen enrichment resulted in increased recovery of pathogen DNA. Quantification of pathogen and human DNA after selective lysis of blood cells and pathogen enrichment confirmed partial depletion of human DNA, leading to a net enrichment of pathogen DNA over human DNA. Conclusion Concurrent antibiotic administration does not reduce the recovery of pathogen DNA during pathogen enrichment by selective lysis and centrifugation. Leads to a 10-fold human DNA depletion as compared to pathogen DNA. Moreover, we confirm that the recovery of pathogen DNA after pathogen enrichment is not negatively influenced by concurrent antibiotic administration. Electronic supplementary material The online version of this article (10.1186/s12866-019-1559-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthias Pilecky
- Center for Biomedical Technology, Department for Health Sciences and Biomedicine, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500, Krems, Austria
| | - Anita Schildberger
- Center for Biomedical Technology, Department for Health Sciences and Biomedicine, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500, Krems, Austria
| | - Ludwig Knabl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, A-6020, Innsbruck, Austria
| | - Dorothea Orth-Höller
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, A-6020, Innsbruck, Austria
| | - Viktoria Weber
- Center for Biomedical Technology, Department for Health Sciences and Biomedicine, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500, Krems, Austria. .,Christian Doppler Laboratory for Innovative Therapy Approaches in Sepsis, Department for Health Sciences and Biomedicine, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500, Krems, Austria. .,Department for Biomedical Research, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500, Krems, Austria.
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143
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Ivanov AV, Safenkova IV, Zherdev AV, Dzantiev BB. Recombinase polymerase amplification combined with a magnetic nanoparticle-based immunoassay for fluorometric determination of troponin T. Mikrochim Acta 2019; 186:549. [DOI: 10.1007/s00604-019-3686-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/07/2019] [Indexed: 02/07/2023]
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144
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WIJAYA YOGIKONKYSILVANA, NIBA EMMATABEEKO, ROCHMAH MAWADDAHAR, HARAHAP NURIMMAFATIMAH, AWANO HIROYUKI, TAKESHIMA YASUHIRO, SAITO TOSHIO, SAITO KAYOKO, TAKEUCHI ATSUKO, LAI POHSAN, BOUIKE YOSHIHIRO, NISHIO HISAHIDE, SHINOHARA MASAKAZU. Nested PCR Amplification Secures DNA Template Quality and Quantity in Real-time mCOP-PCR Screening for SMA. THE KOBE JOURNAL OF MEDICAL SCIENCES 2019; 65:E54-E58. [PMID: 31956257 PMCID: PMC7012193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/27/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Spinal Muscular Atrophy (SMA) is a common autosomal recessive disorder caused by SMN1 gene deletion. SMA has been considered an incurable disease. However, a newly-developed antisense oligonucleotide drug, nusinersen, brings about a good outcome to SMA patients in the clinical trials. Now, a screening for SMA is required for early diagnosis and early treatment so as to give a better clinical outcome to the patients. We have invented a new technology, mCOP-PCR, for SMA screening using dried blood spot (DBS) on the filter paper. One of the problems encountered in SMA screening is poor quality and quantity of DNA extracted from DBS. METHODS DNA was extracted from DBS of six individuals. Fresh blood DNA of each individual had already been genotyped using PCR/RFLP. The fragments including the sequence of SMN1/SMN2 exon 7 were pre-amplified with conventional PCR. To determine which pre-amplified product is a better template for the real-time mCOP-PCR, we did pre-amplification with a single PCR or pre-amplification with a nested PCR. RESULTS The real-time mCOP-PCR using pre-amplified products with a single PCR brought about ambiguous results in some SMN1-carrying individuals. However, the results of real-time mCOP-PCR following pre-amplification with a nested PCR were completely matched with those of PCR-RFLP. CONCLUSION In our study on the real-time mCOP-PCR screening system for SMA, a nested PCR secured the DNA template quality and quantity, leading to unambiguous results of SMA screening.
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Affiliation(s)
- YOGIK ONKY SILVANA WIJAYA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - EMMA TABE EKO NIBA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - MAWADDAH AR ROCHMAH
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - NUR IMMA FATIMAH HARAHAP
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - HIROYUKI AWANO
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | | | - TOSHIO SAITO
- Division of Child Neurology, Department of Neurology, National Hospital Organization Toneyama National Hospital, Toneyama, Japan
| | - KAYOKO SAITO
- Institute of Medical Genetics, Tokyo Women’s Medical University, Tokyo, Japan
| | | | - POH SAN LAI
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - HISAHIDE NISHIO
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
- Faculty of Rehabilitation, Kobe Gakuin University, Kobe, Japan
| | - MASAKAZU SHINOHARA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
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Peng Y, Zheng X, Kan B, Li W, Zhang W, Jiang T, Lu J, Qin A. Rapid detection of Burkholderia pseudomallei with a lateral flow recombinase polymerase amplification assay. PLoS One 2019; 14:e0213416. [PMID: 31283772 PMCID: PMC6613700 DOI: 10.1371/journal.pone.0213416] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/17/2019] [Indexed: 02/06/2023] Open
Abstract
Melioidosis is a severe infectious disease caused by gram-negative, facultative intracellular pathogen Burkholderia pseudomallei (B. pseudomallei). Although cases are increasing reported from other parts of the world, it is an illness of tropical and subtropical climates primarily found in southeast Asia and northern Australia. Because of a 40% mortality rate, this life-threatening disease poses a public health risk in endemic area. Early detection of B. pseudomallei infection is vital for prognosis of a melioidosis patient. In this study, a novel isothermal recombinase polymerase amplification combined with lateral flow dipstick (LF-RPA) assay was established for rapid detection of B. pseudomallei. A set of primer-probe targeting orf2 gene within the putative type III secretion system (T3SS) cluster genes was generated and parameters for the LF-RPA assay were optimized. Result can be easy visualized in 30 minutes with the limit of detection (LOD) as low as 20 femtogram (fg) (ca. 25.6 copies) of B. pseudomallei genomic DNA without a specific equipment. The assay is highly specific as no cross amplification was observed with Burkholderia mallei, members of the Burkholderia cepacia-complex and 35 non-B. pseudomallei bacteria species. Moreover, isolates from patients in Hainan (N = 19), Guangdong (N = 1), Guangxi (N = 3) province of China as well as in Australia (N = 3) and Thailand (N = 1) were retrospectively confirmed by the newly developed method. LODs for B. pseudomallei-spiked soil and blood samples were 2.1×103 CFU/g and 4.2×103 CFU/ml respectively. The sensitivity of the LF-RPA assay was comparable to TaqMan Real-Time PCR (TaqMan PCR). In addition, the LF-RPA assay exhibited a better tolerance to inhibitors in blood than TaqMan PCR. Our results showed that the LF-RPA assay is an alternative to existing PCR-based methods for detection of B. pseudomallei with a potentiality of early accurate diagnosis of melioidosis at point of care or in-field use.
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Affiliation(s)
- Yao Peng
- Department of Pestis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Xiao Zheng
- Department of Pestis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Biao Kan
- Department of Diarrheal Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Wei Li
- Department of Pestis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Wen Zhang
- Department of Bioinformatics, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Taozhen Jiang
- Department of Preservation Center for Standard Strain, China Institute of Veterinary Drug Control, Beijing, China
| | - Jinxing Lu
- Department of Hospital Antibiotics Resistance, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Aiping Qin
- State Key Laboratory of Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
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Detection of Coxiella burnetii Using Silicon Microring Resonator in Patient Blood Plasma. MICROMACHINES 2019; 10:mi10070427. [PMID: 31252533 PMCID: PMC6680664 DOI: 10.3390/mi10070427] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 06/21/2019] [Accepted: 06/25/2019] [Indexed: 11/16/2022]
Abstract
Blood plasma from patients is a powerful resource for diagnosing infectious disease due to it having many genetic materials as well as being relatively easy to obtain. Thus, various biosensors have been investigated for diagnosing diseases in blood plasma. However, there are no optimized and validated sensors for clinical use due to the low sensitivity, complexity, and difficulties of removing the inhibitors from plasma samples. In this study, we described a silicon microring resonator sensor used to detect Coxiella burnetii from the blood plasma of Q-fever patients in a label-free, real-time manner. Q-fever is an infectious disease caused by Coxiella burnetii via direct contact or inhalation aerosols. We validated this biosensor in the blood plasma of 35 clinical samples (including 16 Q fever samples infected with Coxiella burnetii and 19 samples infected with other febrile diseases. The biosensors are capable of rapid (10 min), highly sensitive (87.5%), and specific (89.5%) detection in plasma samples compared to the use of the conventional method.
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147
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Zheng H, Tao R, Zhang J, Zhang J, Wang S, Yang Z, Xu Q, Gao Y, Zhang S, Li C. Development and validation of a novel SiFaSTR
TM
23‐plex system. Electrophoresis 2019; 40:2644-2654. [DOI: 10.1002/elps.201900045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/22/2019] [Accepted: 05/23/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Hancheng Zheng
- Department of Forensic ScienceMedical School of Soochow University Suzhou P. R. China
- Shanghai Key Laboratory of Forensic MedicineShanghai Forensic Service PlatformAcademy of Forensic Sciences Shanghai P. R. China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic MedicineShanghai Forensic Service PlatformAcademy of Forensic Sciences Shanghai P. R. China
- Institute of Forensic MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan University Chengdu P. R. China
| | - Jingyi Zhang
- Department of Forensic ScienceMedical School of Soochow University Suzhou P. R. China
- Shanghai Key Laboratory of Forensic MedicineShanghai Forensic Service PlatformAcademy of Forensic Sciences Shanghai P. R. China
| | - Jiashuo Zhang
- Department of Forensic ScienceMedical School of Soochow University Suzhou P. R. China
- Shanghai Key Laboratory of Forensic MedicineShanghai Forensic Service PlatformAcademy of Forensic Sciences Shanghai P. R. China
| | - Shouyu Wang
- Institute of Forensic MedicineWest China School of Basic Medical Sciences & Forensic MedicineSichuan University Chengdu P. R. China
| | - Zihao Yang
- Shanghai Key Laboratory of Forensic MedicineShanghai Forensic Service PlatformAcademy of Forensic Sciences Shanghai P. R. China
- Department of Forensic MedicineSchool of Basic Medical ScienceWenzhou Medical University Wenzhou P. R. China
| | - Qiannan Xu
- Shanghai Key Laboratory of Forensic MedicineShanghai Forensic Service PlatformAcademy of Forensic Sciences Shanghai P. R. China
- Department of Forensic MedicineSchool of Basic Medical ScienceWenzhou Medical University Wenzhou P. R. China
| | - Yuzhen Gao
- Department of Forensic ScienceMedical School of Soochow University Suzhou P. R. China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic MedicineShanghai Forensic Service PlatformAcademy of Forensic Sciences Shanghai P. R. China
| | - Chengtao Li
- Department of Forensic ScienceMedical School of Soochow University Suzhou P. R. China
- Shanghai Key Laboratory of Forensic MedicineShanghai Forensic Service PlatformAcademy of Forensic Sciences Shanghai P. R. China
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Li L, He JA, Wang W, Xia Y, Song L, Chen ZH, Zuo HZ, Tan XP, Ho AHP, Kong SK, Loo JFC, Li HW, Gu D. Development of a direct reverse-transcription quantitative PCR (dirRT-qPCR) assay for clinical Zika diagnosis. Int J Infect Dis 2019; 85:167-174. [PMID: 31202908 DOI: 10.1016/j.ijid.2019.06.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/28/2019] [Accepted: 06/09/2019] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE The nucleic acid-based polymerase chain reaction (PCR) assay is commonly applied to detect infection with Zika virus (ZIKV). However, the time- and labor-intensive sample pretreatment required to remove inhibitors that cause false-negative results in clinical samples is impractical for use in resource-limited areas. The aim was to develop a direct reverse-transcription quantitative PCR (dirRT-qPCR) assay for ZIKV diagnosis directly from clinical samples. METHODS The combination of inhibitor-tolerant polymerases, polymerase enhancers, and dirRT-qPCR conditions was optimized for various clinical samples including blood and serum. Sensitivity was evaluated with standard DNA spiked in simulated samples. Specificity was evaluated using clinical specimens of other infections such as dengue virus and chikungunya virus. RESULTS High specificity and sensitivity were achieved, and the limit of detection (LOD) of the assay was 9.5×101 ZIKV RNA copies/reaction. The on-site clinical diagnosis of ZIKV required a 5μl sample and the diagnosis could be completed within 2h. CONCLUSIONS This robust dirRT-qPCR assay shows a high potential for point-of-care diagnosis, and the primer-probe combinations can also be extended for other viral detection. It realizes the goal of large-scale on-site screening for viral infections and could be used for early diagnosis and the prevention and control of viral outbreaks.
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Affiliation(s)
- Lang Li
- School of Public Health, The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, 523808, PR China; Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Customs District, Shenzhen, 518033, PR China
| | - Jian-An He
- Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Customs District, Shenzhen, 518033, PR China
| | - Wei Wang
- Department of Laboratory Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen, 518035, PR China
| | - Yun Xia
- Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Customs District, Shenzhen, 518033, PR China
| | - Li Song
- School of Public Health, The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, 523808, PR China; Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Customs District, Shenzhen, 518033, PR China
| | - Ze-Han Chen
- School of Public Health, The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, 523808, PR China
| | - Hang-Zhi Zuo
- School of Public Health, The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, 523808, PR China
| | - Xuan-Ping Tan
- Shenzhen gene-one Biotechnology Co., Ltd., 518000, PR China
| | - Aaron Ho-Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Siu-Kai Kong
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Jacky Fong-Chuen Loo
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, PR China; Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, PR China.
| | - Hua-Wen Li
- School of Public Health, The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, 523808, PR China.
| | - Dayong Gu
- Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Customs District, Shenzhen, 518033, PR China; Department of Laboratory Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen, 518035, PR China.
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Leelawong M, Adams NM, Gabella WE, Wright DW, Haselton FR. Detection of Single-Nucleotide Polymorphism Markers of Antimalarial Drug Resistance Directly from Whole Blood. J Mol Diagn 2019; 21:623-631. [PMID: 31204166 DOI: 10.1016/j.jmoldx.2019.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/12/2018] [Accepted: 02/22/2019] [Indexed: 02/01/2023] Open
Abstract
Monitoring of antimalarial resistance is important to prevent its further spread, but the available options for assessing resistance are less than ideal for field settings. Although molecular detection is perhaps the most efficient method, it is also the most complex because it requires DNA extraction and PCR instrumentation. To develop a more deployable approach, we designed new probes, which, when used in combination with an inhibitor-tolerant Taq polymerase, enable single-nucleotide polymorphism genotyping directly from whole blood. The probes feature two strategic design elements: locked nucleic acids to enhance specificity and the reporter dyes Cy5 and TEX615, which have less optical overlap with the blood absorbance spectra than other commonly used dyes. Probe performance was validated on a traditional laboratory-based instrument and then further tested on a field-deployable Adaptive PCR instrument to develop a point-of-care platform appropriate for use in malaria settings. The probes discriminated between wild-type Plasmodium falciparum and the chloroquine-resistant CRT PF3D7_0709000:c.227A>C (p.Lys76Thr) mutant in the presence of 2% blood. Additionally, in allelic discrimination plots with the new probes, samples clustered more closely to their respective axes compared with samples using minor groove binder probes with 6-FAM and VIC reporter dyes. Our strategy greatly simplifies single-nucleotide polymorphism detection and provides a more accessible alternative for antimalarial resistance surveillance in the field.
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Affiliation(s)
- Mindy Leelawong
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Nicholas M Adams
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - William E Gabella
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - David W Wright
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee.
| | - Frederick R Haselton
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee; Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee.
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Myklebust MP, Rosenlund B, Gjengstø P, Bercea BS, Karlsdottir Á, Brydøy M, Dahl O. Quantitative PCR Measurement of miR-371a-3p and miR-372-p Is Influenced by Hemolysis. Front Genet 2019; 10:463. [PMID: 31191602 PMCID: PMC6539204 DOI: 10.3389/fgene.2019.00463] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/30/2019] [Indexed: 12/12/2022] Open
Abstract
Cell-free microRNAs have been reported as biomarkers for several diseases. For testicular germ cell tumors (GCT), circulating microRNAs 371a-3p and 372-3p in serum and plasma have been proposed as biomarkers for diagnostic and disease monitoring purposes. The most widely used method for quantification of specific microRNAs in serum and plasma is reverse transcriptase real-time quantitative PCR (RT-qPCR) by the comparative Ct-method. In this method one or several reference genes or reference microRNAs are needed in order to normalize and calculate the relative microRNA levels across samples. One of the pitfalls in analysis of microRNAs from serum and plasma is the release of microRNAs from blood cells during hemolysis. This is an important issue because varying degrees of hemolysis are not uncommon in routine blood sampling. Thus, hemolysis must be taken into consideration when working with circulating microRNAs from blood. miR-93-5p, miR-30b-5p, and miR-20a-5p have been reported as reference microRNA in analysis of the miR-371a-373 cluster. We here show how these three microRNAs are influenced by hemolysis. We also propose a new reference microRNA, miR-191-5p, which is relatively stable in serum samples with mild hemolysis. In addition, we show how hemolysis can have effect on the reported microRNA levels in patient samples when these reference microRNAs are used in samples with varying levels of hemolysis.
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Affiliation(s)
| | - Benedikte Rosenlund
- Department of Oncology and Medical Physics, Haukeland University Hospital, Bergen, Norway
| | - Peder Gjengstø
- Department of Urology, Haukeland University Hospital, Bergen, Norway
| | | | - Ása Karlsdottir
- Department of Oncology and Medical Physics, Haukeland University Hospital, Bergen, Norway
| | - Marianne Brydøy
- Department of Oncology and Medical Physics, Haukeland University Hospital, Bergen, Norway
| | - Olav Dahl
- Department of Oncology and Medical Physics, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
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