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Kilic T, Weissleder R, Lee H. Molecular and Immunological Diagnostic Tests of COVID-19: Current Status and Challenges. iScience 2020; 23:101406. [PMID: 32771976 PMCID: PMC7381402 DOI: 10.1016/j.isci.2020.101406] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/10/2020] [Accepted: 07/20/2020] [Indexed: 12/16/2022] Open
Abstract
Rapid spread of coronavirus disease 2019 (COVID-19) is ravaging the globe. Since its first report in December 2019, COVID-19 cases have exploded to over 14 million as of July 2020, claiming more than 600,000 lives. Implementing fast and widespread diagnostic tests is paramount to contain COVID-19, given the current lack of an effective therapeutic or vaccine. This review focuses on a broad description of currently available diagnostic tests to detect either the virus (SARS-CoV-2) or virus-induced immune responses. We specifically explain the working mechanisms of these tests and compare their analytical performance. These analyses will assist in selecting most effective tests for a given application, for example, epidemiology or global pandemic research, population screening, hospital-based testing, home-based and point-of-care testing, and therapeutic trials. Finally, we lay out the shortcomings of certain tests and future needs.
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Affiliation(s)
- Tugba Kilic
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital Research Institute, Harvard Medical School, Boston, MA 02114 USA
| | - Ralph Weissleder
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital Research Institute, Harvard Medical School, Boston, MA 02114 USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hakho Lee
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital Research Institute, Harvard Medical School, Boston, MA 02114 USA.
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Quantitative LAMP and PCR Detection of Salmonella in Chicken Samples Collected from Local Markets around Pathum Thani Province, Thailand. INTERNATIONAL JOURNAL OF FOOD SCIENCE 2020; 2020:8833173. [PMID: 32695808 PMCID: PMC7368944 DOI: 10.1155/2020/8833173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/08/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023]
Abstract
Salmonella is a bacterium that infects people when they consume contaminated food or liquids. To prevent humans from becoming ill, it is useful to have an efficient method of detecting Salmonella before the disease is passed on through the food chain. In this research, the efficiency of Salmonella detection was compared using the following four methods: conventional loop-mediated isothermal amplification (LAMP), PCR, quantitative LAMP (qLAMP), and qPCR. The artificial infection of chicken samples started with incubating of 10 mL of 108 CFU of S. typhimurium for 6 hr. and enriching for 2 hr. to represent real contamination of the samples. The results show that the sensitivity of Salmonella DNA detection in PCR, qPCR, LAMP, and qLAMP were 50 ng, 5 ng, 50 pg, and and 500 fg, respectively. Thirty samples of 10 g chicken were collected from 10 markets in Pathum Thani, Thailand; then, the infection was detected. The conventional LAMP, qLAMP, and qPCR methods detected Salmonella in all the chicken samples. However, the conventional PCR method detected Salmonella infection in only eight of the samples. Overall, the qLAMP method had the highest sensitivity of Salmonella DNA detection.
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Improvement of Loop-Mediated Isothermal Amplification Combined with Chromatographic Flow Dipstick Assay for Salmonella in Food Samples. FOOD ANAL METHOD 2020. [DOI: 10.1007/s12161-020-01760-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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54
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Priya GB, Agrawal RK, Prince Milton AA, Mishra M, Mendiratta S, Luke A, Inbaraj S, Singh BR, Kumar D, Kumar GR, Rajkhowa S. Rapid and visual detection of Salmonella in meat using invasin A (invA) gene-based loop-mediated isothermal amplification assay. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109262] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Highly Sensitive and Specific Detection and Serotyping of Five Prevalent Salmonella Serovars by Multiple Cross-Displacement Amplification. J Mol Diagn 2020; 22:708-719. [PMID: 32359725 DOI: 10.1016/j.jmoldx.2020.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 12/16/2019] [Accepted: 02/20/2020] [Indexed: 02/08/2023] Open
Abstract
Salmonella is a common cause of foodborne disease worldwide, including Australia. More than 85% of outbreaks of human salmonellosis in Australia were caused by five Salmonella serovars. Rapid, accurate, and sensitive identification of Salmonella serovars is vital for diagnosis and public health surveillance. Recently, an isothermal amplification technique, termed multiple cross-displacement amplification (MCDA), has been employed to detect Salmonella at the species level. Herein, seven MCDA assays were developed and evaluated for rapid detection and differentiation of the five most common Salmonella serovars in Australia: Typhimurium, Enteritidis, Virchow, Saintpaul, and Infantis. MCDA primer sets were designed by targeting seven serovar/lineage-specific gene markers identified through genomic comparisons. The sensitivity and specificity of the seven MCDA assays were evaluated using 79 target strains and 32 nontarget strains. The assays were all highly sensitive and specific to target serovars, with the sensitivity ranging from 92.9% to 100% and the specificity from 93.3% to 100%. The limit of detection of the seven MCDA assays was 50 fg per reaction (10 copies) from pure DNA, and positive results were detected in as little as 8 minutes. These seven MCDA assays offer a rapid, accurate, and sensitive serotyping method. With further validation in clinically relevant conditions, these assays could be used for culture-independent serotyping of common Salmonella serovars directly from clinical samples.
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Wen J, Gou H, Zhan Z, Gao Y, Chen Z, Bai J, Wang S, Chen K, Lin Q, Liao M, Zhang J. A rapid novel visualized loop-mediated isothermal amplification method for Salmonella detection targeting at fimW gene. Poult Sci 2020; 99:3637-3642. [PMID: 32616260 PMCID: PMC7597837 DOI: 10.1016/j.psj.2020.03.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/21/2020] [Accepted: 03/23/2020] [Indexed: 11/30/2022] Open
Abstract
Salmonella infection causes huge losses in the poultry industry worldwide. With the aim to prevent infectious diseases caused by Salmonella and to achieve rapid visualized Salmonella detection in poultry production, we used cresol red as an indicator to develop a novel visualized loop-mediated isothermal amplification method that targets the Salmonella fimW gene firstly in related field. The detection limit was 7.3 × 101 CFU/mL, and the method was highly specific and showed a high clinical detection rate. The entire reaction can be completed in about 40 min and only requires a water bath at 62°C, which makes the method extremely suitable for application to poultry production.
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Affiliation(s)
- Junping Wen
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Key Laboratory of Zoonoses, Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Hongchao Gou
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Zeqiang Zhan
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Key Laboratory of Zoonoses, Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yuan Gao
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Key Laboratory of Zoonoses, Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Zhengquan Chen
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Key Laboratory of Zoonoses, Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jie Bai
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Key Laboratory of Zoonoses, Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Shaojun Wang
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Key Laboratory of Zoonoses, Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Kaifeng Chen
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Key Laboratory of Zoonoses, Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Qijie Lin
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Key Laboratory of Zoonoses, Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Ming Liao
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Key Laboratory of Zoonoses, Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jianmin Zhang
- National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Key Laboratory of Zoonoses, Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
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Wang WH, Lin M, Li HL, Huang JY, Chen JT, Fang XS, Huang DM, Xi XX, Zhao QF, Song FL, Huang S, Zhong TY. <p>Establishment and Evaluation of a Novel Method Based on Loop-Mediated Isothermal Amplification for the Rapid Diagnosis of Thalassemia Genes</p>. Healthc Policy 2020; 13:303-311. [PMID: 32308513 PMCID: PMC7147610 DOI: 10.2147/rmhp.s241399] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 03/21/2020] [Indexed: 12/14/2022] Open
Abstract
Purpose Currently, thalassemia is commonly detected using gap-polymerase chain reaction (PCR) and deoxyribonucleic acid (DNA) reverse dot blot, which have high requirements of space, instruments, and personnel. Therefore, it is necessary to develop a new method for thalassemia detection with high sensitivity, low cost, and simple and fast operation. In this study, we aimed to design and evaluate a new method for detecting three α-thalassemia genes including –Southeast Asian (SEA), -α3.7, and -α4.2 and five β-thalassemia genes including 654M, 41/42M, −28M, 17M, and 27/28M based on loop-mediated isothermal amplification (LAMP). Methods Primer sequences were designed using Primer Explorer V4 software. Blood samples (5 mL) were collected from all participants in EDTA. DNA was extracted using Chelex 100 and was subjected to LAMP. LAMP products were detected by fluorescence development in ultraviolet light. Results We found that LAMP assays for positive samples of thalassemia reached a plateau before 60 minutes, whereas the negative control samples entered the plateau after 70 minutes or showed no amplification. The concentration range of positive reactions was between 20–60 pg/μL and 20–60 ng/μL. Additionally, there were no cross-reactivities among 8 thalassemia subtypes. For clinical samples, the positive sample tube showed strong green fluorescence, whereas the negative tube showed light green fluorescence. According to these results, the LAMP method has high sensitivity for detecting thalassemia (252/254). However, 43 false-positive results were obtained in the LAMP test. The LAMP assay was also of low cost and with simple and fast operation. Conclusion The novel LAMP assay can be completed within 60 min using a heating block or a water bath, and the result can be read visually based on color change to detect thalassemia. The LAMP assay fulfills the requirements of field application and resource-limited areas, especially those with primary hospitals and rural areas.
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Affiliation(s)
- Wei-hua Wang
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, People’s Republic of China
| | - Min Lin
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, Guangdong Province, People’s Republic of China
| | - Hai-liang Li
- Department of Hematology, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, People’s Republic of China
| | - Jun-yun Huang
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, People’s Republic of China
| | - Jiang-tao Chen
- The Chinese Medical Aid Team to the Republic of Equatorial Guinea, Guangzhou, Guangdong Province, People’s Republic of China
- Department of Medical Laboratory, Huizhou Central Hospital, Huizhou, Guangdong Province, People’s Republic of China
| | - Xian-song Fang
- Department of Blood Transfusion, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, People’s Republic of China
| | - Dong-mei Huang
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, People’s Republic of China
| | - Xu-xiang Xi
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, People’s Republic of China
| | - Qing-fei Zhao
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, People’s Republic of China
| | - Fang-li Song
- Jiangxi Shiningmed Medical Technology Ltd, Ganzhou, Jiangxi Province, People’s Republic of China
| | - Shao Huang
- Jiangxi Shiningmed Medical Technology Ltd, Ganzhou, Jiangxi Province, People’s Republic of China
- Correspondence: Shao Huang Jiangxi Shiningmed Medical Technology Ltd, Ganzhou, Jiangxi Province, People’s Republic of ChinaTel +86-18602004914 Email
| | - Tian-yu Zhong
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi Province, People’s Republic of China
- Tian-yu Zhong Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou341000, Jiangxi, People’s Republic of ChinaTel +86-797-8680632 Email
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58
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Bodulev OL, Sakharov IY. Isothermal Nucleic Acid Amplification Techniques and Their Use in Bioanalysis. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:147-166. [PMID: 32093592 PMCID: PMC7223333 DOI: 10.1134/s0006297920020030] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/01/2019] [Accepted: 11/01/2019] [Indexed: 12/16/2022]
Abstract
Recently, there has been a rapid progress in the development of techniques for isothermal amplification of nucleic acids as an alternative to polymerase chain reaction (PCR). The advantage of these methods is that the nucleic acids amplification can be carried out at constant temperature, unlike PCR, which requires cyclic temperature changes. Moreover, isothermal amplification can be conducted directly in living cells. This review describes the principles of isothermal amplification techniques and demonstrates their high efficiency in designing new highly sensitive detection methods of nucleic acids and enzymes involved in their modifications. The data on successful application of isothermal amplification methods for the analysis of cells and biomolecules with the use of DNA/RNA aptamers are presented.
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Affiliation(s)
- O L Bodulev
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia
| | - I Yu Sakharov
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
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Kumsiri R, Kanchanaphum P. A Comparison of Four Molecular Methods for Detection of Aflatoxin-Producing Aspergillus in Peanut and Dried Shrimp Samples Collected from Local Markets around Pathum Thani Province, Thailand. SCIENTIFICA 2020; 2020:8580451. [PMID: 33425428 PMCID: PMC7775171 DOI: 10.1155/2020/8580451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/30/2020] [Accepted: 12/15/2020] [Indexed: 05/22/2023]
Abstract
Aspergillus flavus is an aflatoxin-producing fungus which is poisonous to humans and animals when consumed. Detecting the fungus can help to prevent this danger. The four molecular methods, namely, conventional isothermal amplification (LAMP), PCR, quantitative LAMP (qLAMP), and qPCR, were compared to determine their efficiency for A. flavus detection. Thirty samples of peanut and dried shrimp were collected from 15 markets around Pathum Thani Province in Thailand. The samples were artificially infected with 108 conidia/ml of A. flavus for 1 hr and enriched for one day to represent real contamination. The results show that the sensitivity detection for A. flavus in PCR, LAMP, qPCR, and qLAMP was 50 ng, 5 ng, 5 pg, and 5 pg, respectively. Aspergillus in 30 peanut and dried shrimp from the market was detected by all four methods. The detection rate was about 20%, 60%, 100%, and 100% with PCR, LAMP, qPCR, and qLAMP, respectively. The molecular detection technique, especially LAMP, qPCR, and qLAMP, can detect this pathogenic fungi very rapidly with high sensitivity and reliability in comparison to conventional PCR.
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Affiliation(s)
- Ratchanok Kumsiri
- Pathobiology Unit, Faculty of Science, Rangsit University, Pathumthani, Thailand
| | - Panan Kanchanaphum
- Biochemistry Unit, Faculty of Science, Rangsit University, Pathumthani, Thailand
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60
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Development and application of a visual loop-mediated isothermal amplification combined with lateral flow dipstick (LAMP-LFD) method for rapid detection of Salmonella strains in food samples. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.04.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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61
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Papadakis G, Pantazis AK, Ntogka M, Parasyris K, Theodosi GI, Kaprou G, Gizeli E. 3D-printed Point-of-Care Platform for Genetic Testing of Infectious Diseases Directly in Human Samples Using Acoustic Sensors and a Smartphone. ACS Sens 2019; 4:1329-1336. [PMID: 30964650 DOI: 10.1021/acssensors.9b00264] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The objective of this work is to develop a methodology and associated platform for nucleic acid detection at the point-of-care (POC) that is sensitive, user-friendly, affordable, rapid, and robust. The heart of this system is an acoustic wave sensor, based on a Surface Acoustic Wave (SAW) or Quartz Crystal Microbalance (QCM) device, which is employed for the label-free detection of isothermally amplified target DNA. Nucleic acids amplification and detection is demonstrated inside three crude human samples, i.e., whole blood, saliva, and nasal swab, spiked in with 10-100 Salmonella cells. To qualify for POC applications, a portable platform was developed based on 3D printing, integrating inside a single box: (i) simple fluidics based on plastic tubing and a mini peristaltic pump, (ii) a heating plate combined with disposable reaction tubes for isothermal amplification; (iii) a mini antenna analyzer operated through a tablet; and (iv) an acoustic wave device housing unit. The simplicity of the method combined with smartphone operation and detection, rapid sample-to-answer analysis time (30 min), and high performance (detection limit 4 × 103 CFU/ml) in three of the most important human samples in diagnostics suggest that the methodology could become a tool of choice for nucleic acid detection at the POC. In addition, the low cost of the platform and assay holds promise for its adoption in resource limited areas. The acoustic detection method is shown to give similar results with a standard colorimetric assay carried out in saliva and nasal swab but can also be used to detect nucleic acids inside whole blood, where a colorimetric assay failed to perform.
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Affiliation(s)
- George Papadakis
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
| | - Alexandros K. Pantazis
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
| | - Maria Ntogka
- Department of Biology, University of Crete, Voutes, Heraklion 70013, Greece
| | | | - Gesthimani-Ioanna Theodosi
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
- Department of Biology, University of Crete, Voutes, Heraklion 70013, Greece
| | - Georgia Kaprou
- Department of Biology, University of Crete, Voutes, Heraklion 70013, Greece
- Institute of Nanoscience and Nanotechnology, NCSR-Demokritos, Patr. Gregoriou E’ and 27 Neapoleos Str., 15341 Aghia Paraskevi, Attiki, Greece
| | - Electra Gizeli
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
- Department of Biology, University of Crete, Voutes, Heraklion 70013, Greece
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Ge B, Domesle KJ, Yang Q, Hammack TS, Wang SS, Deng X, Hu L, Zhang G, Hu Y, Lai X, Chou KX, Dollete JR, Hirneisen KA, La SP, Richter RS, Rai DR, Yousefvand AA, Park PK, Wu CH, Eames T, Kiang D, Sheng J, Wu D, Hahn L, Ledger L, Logie C, You Q, Slavic D, Cai H, Ayers SL, Young SR, Pamboukian R. Multi-Laboratory Validation of a Loop-Mediated Isothermal Amplification Method for Screening Salmonella in Animal Food. Front Microbiol 2019; 10:562. [PMID: 30984125 PMCID: PMC6447708 DOI: 10.3389/fmicb.2019.00562] [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: 12/21/2018] [Accepted: 03/05/2019] [Indexed: 11/17/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) has gained wide popularity in the detection of Salmonella in foods owing to its simplicity, rapidity, and robustness. This multi-laboratory validation (MLV) study aimed to validate a Salmonella LAMP-based method against the United States Food and Drug Administration (FDA) Bacteriological Analytical Manual (BAM) Chapter 5 Salmonella reference method in a representative animal food matrix (dry dog food). Fourteen independent collaborators from seven laboratories in the United States and Canada participated in the study. Each collaborator received two sets of 24 blind-coded dry dog food samples (eight uninoculated; eight inoculated at a low level, 0.65 MPN/25 g; and eight inoculated at a high level, 3.01 MPN/25 g) and initiated the testing on the same day. The MLV study used an unpaired design where different test portions were analyzed by the LAMP and BAM methods using different preenrichment protocols (buffered peptone water for LAMP and lactose broth for BAM). All LAMP samples were confirmed by culture using the BAM method. BAM samples were also tested by LAMP following lactose broth preenrichment (paired samples). Statistical analysis was carried out by the probability of detection (POD) per AOAC guidelines and by a random intercept logistic regression model. Overall, no significant differences in POD between the Salmonella LAMP and BAM methods were observed with either unpaired or paired samples, indicating the methods were comparable. LAMP testing following preenrichment in buffered peptone water or lactose broth also resulted in insignificant POD differences (P > 0.05). The MLV study strongly supports the utility and applicability of this rapid and reliable LAMP method in routine regulatory screening of Salmonella in animal food.
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Affiliation(s)
- Beilei Ge
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Kelly J. Domesle
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Qianru Yang
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Thomas S. Hammack
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, MD, United States
| | - Shizhen S. Wang
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, MD, United States
| | - Xiaohong Deng
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, MD, United States
| | - Lijun Hu
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, MD, United States
| | - Guodong Zhang
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, MD, United States
| | - Yuan Hu
- Northeast Food and Feed Laboratory, Office of Regulatory Affairs, United States Food and Drug Administration, Jamaica, NY, United States
| | - Xiaokuang Lai
- Northeast Food and Feed Laboratory, Office of Regulatory Affairs, United States Food and Drug Administration, Jamaica, NY, United States
| | - Kyson X. Chou
- Pacific Southwest Food and Feed Laboratory, Office of Regulatory Affairs, United States Food and Drug Administration, Irvine, CA, United States
| | - Jan Ryan Dollete
- Pacific Southwest Food and Feed Laboratory, Office of Regulatory Affairs, United States Food and Drug Administration, Irvine, CA, United States
| | - Kirsten A. Hirneisen
- Pacific Southwest Food and Feed Laboratory, Office of Regulatory Affairs, United States Food and Drug Administration, Irvine, CA, United States
| | - Sammie P. La
- Pacific Southwest Food and Feed Laboratory, Office of Regulatory Affairs, United States Food and Drug Administration, Irvine, CA, United States
| | - Richelle S. Richter
- Pacific Southwest Food and Feed Laboratory, Office of Regulatory Affairs, United States Food and Drug Administration, Irvine, CA, United States
| | - Diyo R. Rai
- San Francisco Laboratory, Office of Regulatory Affairs, United States Food and Drug Administration, Alameda, CA, United States
| | - Azadeh A. Yousefvand
- San Francisco Laboratory, Office of Regulatory Affairs, United States Food and Drug Administration, Alameda, CA, United States
| | - Paul K. Park
- Food and Drug Laboratory Branch, California Department of Public Health, Richmond, CA, United States
| | - Cindy H. Wu
- Food and Drug Laboratory Branch, California Department of Public Health, Richmond, CA, United States
| | - Tameji Eames
- Food and Drug Laboratory Branch, California Department of Public Health, Richmond, CA, United States
| | - David Kiang
- Food and Drug Laboratory Branch, California Department of Public Health, Richmond, CA, United States
| | - Ju Sheng
- Office of Indiana State Chemist, Purdue University, West Lafayette, IN, United States
| | - Dancia Wu
- Office of Indiana State Chemist, Purdue University, West Lafayette, IN, United States
| | - Lori Hahn
- Animal Health Laboratory, University of Guelph, Guelph, ON, Canada
| | - Lisa Ledger
- Animal Health Laboratory, University of Guelph, Guelph, ON, Canada
| | - Cynthia Logie
- Animal Health Laboratory, University of Guelph, Guelph, ON, Canada
| | - Qiu You
- Animal Health Laboratory, University of Guelph, Guelph, ON, Canada
| | - Durda Slavic
- Animal Health Laboratory, University of Guelph, Guelph, ON, Canada
| | - Hugh Cai
- Animal Health Laboratory, University of Guelph, Guelph, ON, Canada
| | - Sherry L. Ayers
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Shenia R. Young
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Ruiqing Pamboukian
- Office of Regulatory Science, Office of Regulatory Affairs, United States Food and Drug Administration, Rockville, MD, United States
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Martzy R, Kolm C, Krska R, Mach RL, Farnleitner AH, Reischer GH. Challenges and perspectives in the application of isothermal DNA amplification methods for food and water analysis. Anal Bioanal Chem 2019; 411:1695-1702. [PMID: 30617408 PMCID: PMC6453865 DOI: 10.1007/s00216-018-1553-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/09/2018] [Accepted: 12/14/2018] [Indexed: 12/04/2022]
Abstract
Molecular diagnostic tools in the field of food and water quality analysis are becoming increasingly widespread. Usually, based on DNA amplification techniques such as polymerase chain reaction (PCR), these methods are highly sensitive and versatile but require well-equipped laboratories and trained personnel. To reduce analysis time and avoid expensive equipment, isothermal DNA amplification methods for detecting various target organisms have been developed. However, to make molecular diagnostics suitable for low-resource settings and in-field applications, it is crucial to continuously adapt the working steps associated with DNA amplification, namely sample preparation, DNA extraction, and visualization of the results. Many novel approaches have been evaluated in recent years to tackle these challenges, e.g., the use of ionic liquids for the rapid isolation of nucleic acids from organisms relevant for food and water analysis or the integration of entire analytical workflows on microfluidic chips. In any event, the future of applications in the field of isothermal amplification will probably lie in ready-to-use cartridges combined with affordable handheld devices for on-site analysis. This trend article aims to make prospective users more familiar with this technology and its potential for moving molecular diagnostics from the laboratory to the field. Graphical abstract ᅟ.
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Affiliation(s)
- Roland Martzy
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Molecular Diagnostics Group, Department of Agrobiotechnology (IFA-Tulln), 3430, Tulln, Austria
- ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
| | - Claudia Kolm
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Molecular Diagnostics Group, Department of Agrobiotechnology (IFA-Tulln), 3430, Tulln, Austria
- ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
| | - Rudolf Krska
- University of Natural Resources and Life Sciences, Vienna (BOKU), Department of Agrobiotechnology (IFA-Tulln), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
- Queen's University Belfast, Institute for Global Food Security, School of Biological Sciences, Belfast, Northern Ireland, BT71NN, UK
| | - Robert L Mach
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Research Area Biochemical Technology, Research Group of Synthetic Biology and Molecular Biotechnology, 1060, Vienna, Austria
| | - Andreas H Farnleitner
- ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
- Karl Landsteiner University of Health Sciences, Research Unit Water Quality and Health, 3500, Krems, Austria
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Research Area Biochemical Technology, Research Group of Environmental Microbiology and Molecular Diagnostics, 1060, Vienna, Austria
| | - Georg H Reischer
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Molecular Diagnostics Group, Department of Agrobiotechnology (IFA-Tulln), 3430, Tulln, Austria.
- TU Wien, Institute of Chemical, Environmental & Bioscience Engineering, Research Area Biochemical Technology, Research Group of Environmental Microbiology and Molecular Diagnostics, 1060, Vienna, Austria.
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Zhang H, Xu Y, Fohlerova Z, Chang H, Iliescu C, Neuzil P. LAMP-on-a-chip: Revising microfluidic platforms for loop-mediated DNA amplification. Trends Analyt Chem 2019; 113:44-53. [PMID: 32287531 PMCID: PMC7112807 DOI: 10.1016/j.trac.2019.01.015] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nucleic acid amplification for the detection of infectious diseases, food pathogens, or assessment of genetic disorders require a laboratory setting with specialized equipment and technical expertise. Isothermal deoxyribonucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), exhibit characteristics ideal for point-of-care (POC) applications, since their instrumentation is simpler in comparison with the standard method of polymerase chain reaction. Other key advantages of LAMP are robustness and the production of pyrophosphate in the presence of the target gene, enabling to detect the reaction products using the naked eye. Polymerase inhibitors, presented in clinical samples, do not affect the amplification process, making LAMP suitable for a simple sample-to-answer diagnostic systems with simplified sample preparation. In this review, we discuss the trends in miniaturized LAMP techniques, such as microfluidic, paper-based, and digital with their advantages and disadvantages, especially for POC applications alongside our opinion of the future development of miniaturized LAMP. Introduction of loop mediated isothermal amplification (LAMP) and its principle. Classical microfluidics-based LAMP for DNA/RNA detection. Paper-based LAMP. Microfluidic-based digital LAMP. Future of microfluidic LAMP development.
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Affiliation(s)
- Haoqing Zhang
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Ying Xu
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Zdenka Fohlerova
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, 61300 Brno, Czech Republic.,Faculty of Electrical Engineering, Brno University of Technology, Technická 3058/10, 61600 Brno, Czech Republic
| | - Honglong Chang
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Ciprian Iliescu
- Biomedical Institute for Global Health Research and Technology (BIGHEART), National University of Singapore, MD6, 14 Medical Drive #14-01, 117599, Singapore
| | - Pavel Neuzil
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China.,Central European Institute of Technology, Brno University of Technology, Purkyňova 123, 61300 Brno, Czech Republic
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Xu J, Hu Y, Guo J, Yang Y, Qiu J, Li X, Xin Z. A Loop-Mediated Isothermal Amplification Integrated G-Quadruplex Molecular Beacon (LAMP-GMB) Method for the Detection of Staphylococcus aureus in Food. FOOD ANAL METHOD 2018. [DOI: 10.1007/s12161-018-1373-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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