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Gradisteanu Pircalabioru G, Raileanu M, Dionisie MV, Lixandru-Petre IO, Iliescu C. Fast detection of bacterial gut pathogens on miniaturized devices: an overview. Expert Rev Mol Diagn 2024; 24:201-218. [PMID: 38347807 DOI: 10.1080/14737159.2024.2316756] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 02/06/2024] [Indexed: 03/23/2024]
Abstract
INTRODUCTION Gut microbes pose challenges like colon inflammation, deadly diarrhea, antimicrobial resistance dissemination, and chronic disease onset. Development of early, rapid and specific diagnosis tools is essential for improving infection control. Point-of-care testing (POCT) systems offer rapid, sensitive, low-cost and sample-to-answer methods for microbe detection from various clinical and environmental samples, bringing the advantages of portability, automation, and simple operation. AREAS COVERED Rapid detection of gut microbes can be done using a wide array of techniques including biosensors, immunological assays, electrochemical impedance spectroscopy, mass spectrometry and molecular biology. Inclusion of Internet of Things, machine learning, and smartphone-based point-of-care applications is an important aspect of POCT. In this review, the authors discuss various fast diagnostic platforms for gut pathogens and their main challenges. EXPERT OPINION Developing effective assays for microbe detection can be complex. Assay design must consider factors like target selection, real-time and multiplex detection, sample type, reagent stability and storage, primer/probe design, and optimizing reaction conditions for accuracy and sensitivity. Mitigating these challenges requires interdisciplinary collaboration among scientists, clinicians, engineers, and industry partners. Future efforts are essential to enhance sensitivity, specificity, and versatility of POCT systems for gut microbe detection and quantification, advancing infectious disease diagnostics and management.
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Affiliation(s)
- Gratiela Gradisteanu Pircalabioru
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
- Division of Earth, Environmental and Life Sciences, The Research Institute of University of Bucharest (ICUB), Bucharest, Romania
- Academy of Romanian Scientists, Bucharest, Romania
| | - Mina Raileanu
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
- Department of Life and Environmental Physics, Horia Hulubei National Institute of Physics and Nuclear Engineering, Magurele, Romania
| | - Mihai Viorel Dionisie
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
| | - Irina-Oana Lixandru-Petre
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
| | - Ciprian Iliescu
- eBio-hub Research Centre, National University of Science and Technology "Politehnica" Bucharest, Bucharest, Romania
- Academy of Romanian Scientists, Bucharest, Romania
- Microsystems in Biomedical and Environmental Applications, National Research and Development Institute for Microtechnology, Bucharest, Romania
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Vinayaka AC, Quyen TL, Huynh VN, Madsen M, Bang DD, Wolff A. Rapid detection of Salmonella enterica in primary production samples by eliminating DNA amplification inhibitors using an improved sample pre-treatment method. Microb Biotechnol 2023; 16:2105-2113. [PMID: 37776205 PMCID: PMC10616646 DOI: 10.1111/1751-7915.14343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 09/09/2023] [Accepted: 09/13/2023] [Indexed: 10/02/2023] Open
Abstract
Sensitive detection of pathogens in livestock farms is an integral part of the One Health Action Plan of the European Union (EU). Ensuring this requires on-site testing devices that are compatible with complex matrices such as primary production samples. Among all, faeces are considered the most challenging matrix type that makes it difficult to identify pathogens because of complexity in sample preparation for molecular testing. We have developed a loop-mediated isothermal amplification (LAMP) based veterinary point-of-care (POC) device (VETPOD) and adapted it to detect Salmonella enterica in primary production samples. Three different sampling methods (semi-wet chicken faeces, boot socks collection and dust samples from poultry shed) were iteratively tested to assess their nature of complexity and possibility for adapting them as suitable sampling methods for on-site testing. During the study, the sample preparation method that included a two-step centrifugation combined with washing of the enriched Salmonella cells was found crucial in eliminating amplification inhibitors originating from the faecal matrices. A total of 90 samples were tested that included 60 samples for sensitivity study and 30 samples for relative level of detection (RLOD, a level of detection in comparison to ISO 6579:1 reference method). Overall, the VETPOD had a sensitivity of 90%, 84.62% and 81.82% for boot sock, faecal and dust samples, respectively. The RLOD was 2.23 CFU/25 g which was found to be 1.33 times higher than the ISO 6579:1. Performing with an excellent agreement with ISO 6579:1, the VETPOD proved as a promising alternative to detect Salmonella spp. in primary production and animal husbandry samples.
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Affiliation(s)
- Aaydha Chidambara Vinayaka
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), DTU‐Bioengineering (Department of Biotechnology and Biomedicine)Technical University of DenmarkKgs. LyngbyDenmark
| | - Than Linh Quyen
- Biolabchip group, DTU‐Bioengineering (Department of Biotechnology and Biomedicine)Technical University of DenmarkKgs. LyngbyDenmark
| | - Van Ngoc Huynh
- Biolabchip group, DTU‐Bioengineering (Department of Biotechnology and Biomedicine)Technical University of DenmarkKgs. LyngbyDenmark
| | - Mogens Madsen
- Biolabchip group, DTU‐Bioengineering (Department of Biotechnology and Biomedicine)Technical University of DenmarkKgs. LyngbyDenmark
| | - Dang Duong Bang
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), DTU‐Bioengineering (Department of Biotechnology and Biomedicine)Technical University of DenmarkKgs. LyngbyDenmark
| | - Anders Wolff
- Biolabchip group, DTU‐Bioengineering (Department of Biotechnology and Biomedicine)Technical University of DenmarkKgs. LyngbyDenmark
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3
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Kopler I, Marchaim U, Tikász IE, Opaliński S, Kokin E, Mallinger K, Neubauer T, Gunnarsson S, Soerensen C, Phillips CJC, Banhazi T. Farmers' Perspectives of the Benefits and Risks in Precision Livestock Farming in the EU Pig and Poultry Sectors. Animals (Basel) 2023; 13:2868. [PMID: 37760267 PMCID: PMC10525424 DOI: 10.3390/ani13182868] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 08/28/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
More efficient livestock production systems are necessary, considering that only 41% of global meat demand will be met by 2050. Moreover, the COVID-19 pandemic crisis has clearly illustrated the necessity of building sustainable and stable agri-food systems. Precision Livestock Farming (PLF) offers the continuous capacity of agriculture to contribute to overall human and animal welfare by providing sufficient goods and services through the application of technical innovations like digitalization. However, adopting new technologies is a challenging issue for farmers, extension services, agri-business and policymakers. We present a review of operational concepts and technological solutions in the pig and poultry sectors, as reflected in 41 and 16 European projects from the last decade, respectively. The European trend of increasing broiler-meat production, which is soon to outpace pork, stresses the need for more outstanding research efforts in the poultry industry. We further present a review of farmers' attitudes and obstacles to the acceptance of technological solutions in the pig and poultry sectors using examples and lessons learned from recent European projects. Despite the low resonance at the research level, the investigation of farmers' attitudes and concerns regarding the acceptance of technological solutions in the livestock sector should be incorporated into any technological development.
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Affiliation(s)
- Idan Kopler
- European Wing Unit, Galilee Research Institute, Kiryat Shmona 11016, Israel;
| | - Uri Marchaim
- European Wing Unit, Galilee Research Institute, Kiryat Shmona 11016, Israel;
| | - Ildikó E. Tikász
- Agricultural Economics Directorate, Institute of Agricultural Economics, H-1093 Budapest, Hungary;
| | - Sebastian Opaliński
- Department of Environmental Hygiene and Animal Welfare, Wroclaw University of Environmental and Life Sciences, 50-375 Wrocław, Poland;
| | - Eugen Kokin
- Institute of Forestry and Engineering, Estonian University of Life Science, 51014 Tartu, Estonia; (E.K.); (C.J.C.P.)
| | | | | | - Stefan Gunnarsson
- Department of Animal Environment and Health, Swedish University of Agricultural Sciences, SE-532 23 Skara, Sweden;
| | - Claus Soerensen
- Department of Electrical and Computer Engineering, Aarhus University, 8000 Aarhus, Denmark;
| | - Clive J. C. Phillips
- Institute of Forestry and Engineering, Estonian University of Life Science, 51014 Tartu, Estonia; (E.K.); (C.J.C.P.)
- CUSP Institute, Curtin University, Bentley, WA 6102, Australia
| | - Thomas Banhazi
- AgHiTech Kft, H-1101 Budapest, Hungary;
- International College, National Taiwan University, Taipei 10617, Taiwan
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4
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Tao D, Liu J, Li Q, Jiang Y, Xu B, Khazalwa EM, Gong P, Xu J, Ma Y, Ruan J, Niu L, Xie S. A Simple, Affordable, and Rapid Visual CRISPR-Based Field Test for Sex Determination of Earlier Porcine Embryos and Pork Products. Mol Biotechnol 2023; 65:263-272. [PMID: 35840848 DOI: 10.1007/s12033-022-00532-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 06/29/2022] [Indexed: 01/18/2023]
Abstract
Sex selection technologies have immensely impacted swine production globally. Conventional earlier embryo sex identification methods require professional technicians and sophisticated laboratory instruments. Rapid on-site gender identification of porcine embryos and pork products remains challenging. In this study, we developed a CRISPR/Cas12a-based fluorescence visualization point-of-care sex determination test that is rapid, accurate and easy to implement on-site. The CRISPR/Cas12a assay coupled with either the polymerase chain reaction (PCR) or loop-mediated isothermal amplification (LAMP) employs precisely designed primers and single-guide RNAs targeting the sex-determining region Y (SRY) and the zinc finger protein X-linked (ZFX) genes. PCR and LAMP amplicons were cleaved with the subsequent generation of fluorescing products detectable with portable blue and ultraviolet light transilluminators. Approximately two copies per microliter of the ZFX and SRY genes were detected using the RApid VIsual CRISPR (RAVI-CRISPR) assay. This method is a sensitive, inexpensive, versatile, and point-of-care test. The technology has other potential applications like determining the sex of diverse livestock species, detecting livestock disease-causing pathogens and evaluating the quality of meat products.
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Affiliation(s)
- Dagang Tao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jiajia Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Qiushi Li
- College of Biological Engineering and Food Science, Hubei University of Technology, Wuhan, 430070, People's Republic of China
| | - Yu Jiang
- Yangshan Customs, Shanghai, 201306, People's Republic of China
| | - Bingrong Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | | | - Ping Gong
- Institute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, 430208, People's Republic of China
| | - Jing Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yunlong Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jinxue Ruan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, People's Republic of China
| | - Lili Niu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China.
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China. .,Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, People's Republic of China.
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Detection of Campylobacter jejuni Based on a Real-Time Fluorescence Loop-Mediated Isothermal Amplification Method. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3613757. [PMID: 36093400 PMCID: PMC9453007 DOI: 10.1155/2022/3613757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 06/24/2022] [Accepted: 07/28/2022] [Indexed: 11/20/2022]
Abstract
Campylobacter jejuni (C. jejuni), a foodborne pathogenic bacterium, is among the most prevalent causes of human gastroenteritis globally. We developed and evaluated a loop-mediated isothermal amplification (LAMP) method to detect C. jejuni. Outer primers and inner primers were designed based on the hipO gene. The ratio between the concentrations of the inner and outer primers and the reaction temperature were then optimized to achieve optimal assay conditions. The analytical specificity tests showed that, among 12 genera of 74 pure bacterial culture strains, only four C. jejuni isolates could be detected, whereas no amplification was observed in C. coli, C. lari, and the other 11 genera of foodborne pathogens (n = 70). Moreover, the LAMP assay showed a higher analytical sensitivity (34.2 fg μL−1) than the conventional PCR method (342 fg μL−1). The limit of detection of C. jejuni based on the LAMP assay was 103 CFU g−1 in the artificially spiked samples of chicken meat. In conclusion, the developed LAMP assay will be a powerful and practical tool for the fast, specific, and sensitive detection of C. jejuni.
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Saito Y, Matsui A, Michiyuki S, Morooka H, Ibi T, Yamauchi Y, Takahashi N, Shimizu Y, Ikeya T, Hoshi E, Sakao Y, Kawamura M. Loop-Mediated Isothermal Amplification as Point-of-Care Testing for EGFR-Mutated Lung Adenocarcinoma. MICROMACHINES 2022; 13:mi13060897. [PMID: 35744511 PMCID: PMC9230792 DOI: 10.3390/mi13060897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 12/10/2022]
Abstract
Liquid biopsy has been adapted as a diagnostic test for EGFR mutations in patients with advanced or metastatic non-small cell lung cancer (NSCLC). Loop-mediated isothermal amplification (LAMP) has been widely used for the rapid detection of pathogens through DNA amplification. This study investigated the efficacy of an EGFR-LAMP assay using plasma samples of patients with resected NSCLC tumors. The EGFR status was investigated using both LAMP and next-generation sequencing (NGS) assays in cases that met the following criteria: (1) pulmonary adenocarcinoma with EGFR mutation detected by the Therascreen EGFR PCR Kit and (2) preoperative plasma samples contained enough DNA for the LAMP and NGS experiments. Among 51 specimens from patients with EGFR-mutated tumors or metastatic lymph nodes, the LAMP assay detected 1 EGFR mutation that was also detected in the NGS assay. However, a plasma sample that demonstrated EGFR wild type in the LAMP assay showed an EGFR mutant status in NGS. The detection rates (1.9% in LAMP and 3.9% in NGS) were very low in both assays, demonstrating a similar performance in detecting EGFR mutations in NSCLC tumors; therefore, it could be a more suitable test for the advanced stage, not the early stage. Notably, the LAMP assay was more time-saving, cost-effective, and straightforward. However, further investigation is required to develop a more sensitive assay.
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Affiliation(s)
- Yuichi Saito
- Department of Surgery, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku 173-8605, Tokyo, Japan; (Y.Y.); (Y.S.); (M.K.)
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, 1696 Itai, Kumagaya 360-0197, Saitama, Japan; (H.M.); (T.I.); (N.T.); (T.I.); (E.H.)
- Correspondence: ; Tel.: +81-33-964-1211; Fax: +81-33-964-6888
| | - Atsuka Matsui
- Biochemical Research Laboratory II, Eiken Chemical Co., Ltd., 1381-3 Shimoishigami, Otawara-shi 324-0036, Tochigi, Japan; (A.M.); (S.M.)
| | - Satoru Michiyuki
- Biochemical Research Laboratory II, Eiken Chemical Co., Ltd., 1381-3 Shimoishigami, Otawara-shi 324-0036, Tochigi, Japan; (A.M.); (S.M.)
| | - Hiroaki Morooka
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, 1696 Itai, Kumagaya 360-0197, Saitama, Japan; (H.M.); (T.I.); (N.T.); (T.I.); (E.H.)
| | - Takayuki Ibi
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, 1696 Itai, Kumagaya 360-0197, Saitama, Japan; (H.M.); (T.I.); (N.T.); (T.I.); (E.H.)
| | - Yoshikane Yamauchi
- Department of Surgery, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku 173-8605, Tokyo, Japan; (Y.Y.); (Y.S.); (M.K.)
| | - Nobumasa Takahashi
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, 1696 Itai, Kumagaya 360-0197, Saitama, Japan; (H.M.); (T.I.); (N.T.); (T.I.); (E.H.)
| | - Yoshihiko Shimizu
- Department of Pathology, Saitama Cardiovascular and Respiratory Center, 1696 Itai, Kumagaya 360-0197, Saitama, Japan;
| | - Tomohiko Ikeya
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, 1696 Itai, Kumagaya 360-0197, Saitama, Japan; (H.M.); (T.I.); (N.T.); (T.I.); (E.H.)
| | - Eishin Hoshi
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, 1696 Itai, Kumagaya 360-0197, Saitama, Japan; (H.M.); (T.I.); (N.T.); (T.I.); (E.H.)
| | - Yukinori Sakao
- Department of Surgery, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku 173-8605, Tokyo, Japan; (Y.Y.); (Y.S.); (M.K.)
| | - Masafumi Kawamura
- Department of Surgery, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku 173-8605, Tokyo, Japan; (Y.Y.); (Y.S.); (M.K.)
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Paruch L. Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:5128. [PMID: 35564522 PMCID: PMC9105083 DOI: 10.3390/ijerph19095128] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022]
Abstract
Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications.
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Affiliation(s)
- Lisa Paruch
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research-NIBIO Oluf Thesens vei 43, 1433 Aas, Norway
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8
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Quyen TL, Vinayaka AC, Golabi M, Ngoc HV, Bang DD, Wolff A. Elimination of Carryover Contamination in Real-Time Reverse Transcriptase Loop-Mediated Isothermal Amplification for Rapid Detection of the SARS-CoV-2 Virus in Point-of-Care Testing. Front Cell Infect Microbiol 2022; 12:856553. [PMID: 35521217 PMCID: PMC9065284 DOI: 10.3389/fcimb.2022.856553] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is being used as a robust rapid diagnostic tool to prevent the transmission of infectious diseases. However, carryover contamination of LAMP-amplified products originating from previous tests has been a problem in LAMP-based bio-analytical assays. In this study, we developed a Cod-uracil-DNA-glycosylase real-time reverse transcriptase LAMP assay (Cod-UNG-rRT-LAMP) for the elimination of carryover contamination and the rapid detection of SARS-CoV-2 in point-of-care (POC) testing. Using the Cod-UNG-rRT-LAMP assay, the SARS-CoV-2 virus could be detected as low as 2 copies/µl (8 copies/reaction) within 45 min of amplification and 2.63 ± 0.17 pg (equivalent to 2.296 × 109 copies) of contaminants per reaction could be eliminated. Analysis of clinical SARS-CoV-2 samples using the Cod-UNG-rRT-LAMP assay showed an excellent agreement with a relative accuracy of 98.2%, sensitivity of 97.1%, and specificity of 95.2% in comparison to rRT-PCR. The results obtained in this study clearly demonstrate the feasibility of the use of the Cod-UNG-rRT-LAMP assay for applications toward the POC diagnosis of SARS-CoV-2 and on-site testing of other pathogens.
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Affiliation(s)
- Than Linh Quyen
- Biolabchip Group, Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Aaydha Chidambara Vinayaka
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Mohsen Golabi
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Huynh Van Ngoc
- Biolabchip Group, Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Dang Duong Bang
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Anders Wolff
- Biolabchip Group, Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
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9
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A Cutoff Determination of Real-Time Loop-Mediated Isothermal Amplification (LAMP) for End-Point Detection of Campylobacter jejuni in Chicken Meat. Vet Sci 2022; 9:vetsci9030122. [PMID: 35324850 PMCID: PMC8953776 DOI: 10.3390/vetsci9030122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/22/2022] [Accepted: 03/05/2022] [Indexed: 02/01/2023] Open
Abstract
Campylobacter jejuni is one of the leading causes of foodborne illness worldwide. C. jejuni is commonly found in poultry. It is the most frequent cause of contamination and thus resulting in not only public health concerns but also economic impacts. To test for this bacterial contamination in food processing plants, this study attempted to employ a simple and rapid detection assay called loop-mediated isothermal amplification (LAMP). The best cutoff value for the positive determination of C. jejuni calculated using real-time LAMP quantification cycle (Cq) was derived from the receiver operating characteristic (ROC) curve modeling. The model showed an area under curve (AUC) of 0.936 (95% Wald CI: 0.903–0.970). Based on Youden’s J statistic, the optimal cutoff value which had the highest sensitivity and specificity from the model was calculated as 18.07. The LAMP assay had 96.9% sensitivity, 95.8% specificity, and 93.9 and 97.9% positive and negative predictive values, respectively, compared to a standard culture approach for C. jejuni identification. Among all non-C. jejuni strains, the LAMP assay gave each of 12.5% false-positive results to C. coli and E. coli (1 out of 8 samples). The assay can detect C. jejuni at the lowest concentration of 103 CFU/mL. Our results suggest a preliminary indicator for the application of end-point LAMP assays, such as turbidity and UV fluorescence tests, to detect C. jejuni in field operations. The LAMP assay is an alternative screening test for C. jejuni contamination in food samples. The method provides a rapid detection, which requires only 9 min with a cutoff value of Cq. We performed the extraction of DNA from pure cultures and the detection of C. jejuni using the LAMP assay within 3 h. However, we were not able to reduce the time for the process of enrichment involved in our study. Therefore, we suggest that alternative enrichment media and rapid DNA extraction methods should be considered for further study. Compared to other traditional methods, our proposed assay requires less equipment and time, which is applicable at any processing steps in the food production chain.
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10
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Moore KJM, Cahill J, Aidelberg G, Aronoff R, Bektaş A, Bezdan D, Butler DJ, Chittur SV, Codyre M, Federici F, Tanner NA, Tighe SW, True R, Ware SB, Wyllie AL, Afshin EE, Bendesky A, Chang CB, Dela Rosa R, Elhaik E, Erickson D, Goldsborough AS, Grills G, Hadasch K, Hayden A, Her SY, Karl JA, Kim CH, Kriegel AJ, Kunstman T, Landau Z, Land K, Langhorst BW, Lindner AB, Mayer BE, McLaughlin LA, McLaughlin MT, Molloy J, Mozsary C, Nadler JL, D'Silva M, Ng D, O'Connor DH, Ongerth JE, Osuolale O, Pinharanda A, Plenker D, Ranjan R, Rosbash M, Rotem A, Segarra J, Schürer S, Sherrill-Mix S, Solo-Gabriele H, To S, Vogt MC, Yu AD, Mason CE. Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications. J Biomol Tech 2021; 32:228-275. [PMID: 35136384 PMCID: PMC8802757 DOI: 10.7171/jbt.21-3203-017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.
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Affiliation(s)
- Keith J M Moore
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | | | - Guy Aidelberg
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
| | - Rachel Aronoff
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- Action for Genomic Integrity Through Research! (AGiR!), Lausanne, Switzerland
- Association Hackuarium, Lausanne, Switzerland
| | - Ali Bektaş
- Oakland Genomics Center, Oakland, CA 94609, USA
| | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, 72076 Tübingen, Germany
- Poppy Health, Inc, San Francisco, CA 94158, USA
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital, 72076 Tübingen, Germany
| | - Daniel J Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sridar V Chittur
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | - Martin Codyre
- GiantLeap Biotechnology Ltd, Wicklow A63 Kv91, Ireland
| | - Fernan Federici
- ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | | | | | - Randy True
- FloodLAMP Biotechnologies, San Carlos, CA 94070, USA
| | - Sarah B Ware
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- BioBlaze Community Bio Lab, 1800 W Hawthorne Ln, Ste J-1, West Chicago, IL 60185, USA
- Blossom Bio Lab, 1800 W Hawthorne Ln, Ste K-2, West Chicago, IL 60185, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Evan E Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andres Bendesky
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY 10027, USA
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Connie B Chang
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, 59717, USA
| | - Richard Dela Rosa
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Eran Elhaik
- Department of Biology, Lund University, Sölvegatan 35, Lund, Sweden
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14850, USA
| | | | - George Grills
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Kathrin Hadasch
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
- IANUS Verein für Friedensorientierte Technikgestaltung eV, 64289 Darmstadt, Germany
| | - Andrew Hayden
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | | | - Julie A Karl
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | | | | | | | - Zeph Landau
- Department of Computer Science, University of California, Berkeley, Berkeley, 94720, USA
| | - Kevin Land
- Mologic, Centre for Advanced Rapid Diagnostics, (CARD), Bedford Technology Park, Thurleigh MK44 2YA, England
- Department of Electrical, Electronic and Computer Engineering, University of Pretoria, 0028 Pretoria, South Africa
| | | | - Ariel B Lindner
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
| | - Benjamin E Mayer
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
| | | | - Matthew T McLaughlin
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jenny Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, England
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jerry L Nadler
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - Melinee D'Silva
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - David Ng
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jerry E Ongerth
- University of Wollongong, Environmental Engineering, Wollongong NSW 2522, Australia
| | - Olayinka Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara Mokin, Nigeria
| | - Ana Pinharanda
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Dennis Plenker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ravi Ranjan
- Genomics Resource Laboratory, Institute for Applied Life Sciences, University of Massachusetts, Amherst, 01003, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | | | | | | | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | | | - Shaina To
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Merly C Vogt
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Albert D Yu
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
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11
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Petersen M, Ma L, Lu X. Rapid determination of viable but non-culturable Campylobacter jejuni in food products by loop-mediated isothermal amplification coupling propidium monoazide treatment. Int J Food Microbiol 2021; 351:109263. [PMID: 34116344 DOI: 10.1016/j.ijfoodmicro.2021.109263] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/12/2021] [Accepted: 05/25/2021] [Indexed: 11/19/2022]
Abstract
Campylobacter is the leading cause of foodborne human diarrhea worldwide. This microbe in the viable but non-culturable (VBNC) state can evade detection by routinely used culture-based methods and remain viable for extended periods of time. Bacteria in this dormancy state can resume their metabolic activity and virulence by resuscitation under favorable conditions, and subsequently cause infections. In this study, an assay combining loop-mediated isothermal amplification (LAMP) and propidium monoazide (PMA) treatment was developed for the detection and quantification of VBNC C. jejuni in agri-foods. PMA-qLAMP targeting the hipO gene demonstrated 100% high specificity to C. jejuni. A linear detection of C. jejuni was achieved between 8.77 × 102 and 8.77 × 07 CFU/mL with a coefficient of determination (R2) of 0.9956, indicating a good quantitative capacity. C. jejuni was effectively induced into the VBNC state by osmotic stress (i.e., 7% NaCl, w/v) over 48 h. VBNC C. jejuni cells were spiked into three representative food products and determined by PMA-qLAMP coupled with plating assay. The detection limits of PMA-qLAMP were 1.58 × 102 CFU/mL in milk, 3.78 × 102 CFU/g in chicken breast meat, and 4.33 × 102 CFU/g in romaine lettuce. PMA-qLAMP demonstrated rapid (25-40 min), specific (100% inclusivity and 100% exclusivity) and sensitive (~102 CFU/mL) determination of VBNC C. jejuni. This method can be applied in the agri-food industry to decrease the risks related to the consumption of contaminated agri-foods with pathogenic bacteria in the VBNC state and reduce the burden of C. jejuni infections to public health.
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Affiliation(s)
- Marlen Petersen
- Food Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Luyao Ma
- Food Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Xiaonan Lu
- Food Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Ste Anne de Bellevue, QC H9X 3V9, Canada.
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12
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Kreitlow A, Becker A, Ahmed MFE, Kittler S, Schotte U, Plötz M, Abdulmawjood A. Combined Loop-Mediated Isothermal Amplification Assays for Rapid Detection and One-Step Differentiation of Campylobacter jejuni and Campylobacter coli in Meat Products. Front Microbiol 2021; 12:668824. [PMID: 34177847 PMCID: PMC8219907 DOI: 10.3389/fmicb.2021.668824] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/29/2021] [Indexed: 11/25/2022] Open
Abstract
A loop-mediated isothermal amplification (LAMP) assay system was established, allowing rplD gene-based simultaneous detection of Campylobacter jejuni and Campylobacter coli in enriched meat products. Additionally, one-step differentiation of target species on agar plates was enabled by cdtC gene- and gyrA gene-based duplex LAMP. Both the rplD and cdtC–gyrA LAMP assays amplified the target sequences in all 62 C. jejuni and 27 C. coli strains used for determining inclusivity and revealed 100% exclusivity toward 85 tested non-target species. Throughout the entire experiments, C. jejuni and C. coli strains were 100% distinguishable by melting curves of cdtC and gyrA LAMP products. After 24-h enrichment, the rplD LAMP assay reliably detected initial inoculation levels of 10–100 CFU/g in artificially contaminated minced meat. Investigation of naturally contaminated meat samples revealed a diagnostic accuracy of 95% toward real-time PCR and 94.1% toward the standard culture method applying the 24-h incubation period. Diagnostic sensitivity and specificity, and positive and negative predictive values were 89.8, 100, 100, and 91.2%, respectively, when measured against real-time PCR, and 89.6, 98.1, 97.7, and 91.2%, respectively, when measured against the standard culture method. After 48-h enrichment, the detection limit of the rplD LAMP assay improved to initial inoculation levels of 1–10 CFU/g in artificially contaminated minced meat. Applying the 48-h incubation period on naturally contaminated meat samples resulted in 100% concordant results between rplD LAMP, real-time PCR, and the standard culture method. The established LAMP assay system was proved to be suitable for rapid meat sample screening. Furthermore, it constitutes a promising tool for investigating other Campylobacter sources and could therefore make a valuable contribution to protect consumers from foodborne illness.
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Affiliation(s)
- Antonia Kreitlow
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hanover, Germany
| | - André Becker
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Marwa F E Ahmed
- Institute for Animal Hygiene, Animal Welfare and Farm Animal Behavior, University of Veterinary Medicine Hannover, Hanover, Germany.,Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Sophie Kittler
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Ulrich Schotte
- Department A-Veterinary Medicine, Central Institute of the Bundeswehr Medical Service Kiel, Kronshagen, Germany
| | - Madeleine Plötz
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Amir Abdulmawjood
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hanover, Germany
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13
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Thornval NR, Hoorfar J. Progress in detection of Campylobacter in the food production chain. Curr Opin Food Sci 2021. [DOI: 10.1016/j.cofs.2020.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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14
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Zendrini A, Carta V, Filipello V, Ragni L, Cosciani-Cunico E, Arnaboldi S, Bertasi B, Franceschi N, Ajmone-Marsan P, De Medici D, Losio MN. One-Day Molecular Detection of Salmonella and Campylobacter in Chicken Meat: A Pilot Study. Foods 2021; 10:foods10051132. [PMID: 34069582 PMCID: PMC8161052 DOI: 10.3390/foods10051132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 11/16/2022] Open
Abstract
Salmonella and Campylobacter ssp. are bacterial pathogens responsible for most foodborne infections in EU countries. Poultry serves as a reservoir for these pathogens, and its important role in the meat industry makes it essential to develop a rapid detection assay able to provide results in one day. Indeed, the rapid identification of foodborne pathogens is an important instrument for the monitoring and prevention of epidemic outbreaks. To date, Salmonella and Campylobacter screening is mainly conducted through molecular methods (PCR or real-time PCR) performed after 18–24 h long enrichments. In this study, we evaluated short enrichments (0, 2, 4, and 6 h) combined with a colorimetric loop-mediated isothermal AMPlification (LAMP) or real-time PCR to detect Salmonella and Campylobacter in poultry meat contaminated at different concentration levels (101, 103, and 105 CFU/g). Our results show that real-time PCR allows the detection of Salmonella and Campylobacter, even after shorter enrichment times than prescribed by ISO references; particularly, it detected Salmonella down to 101 CFU/g since T0 and Campylobacter from 103 CFU/g since T0. Detection with LAMP was comparable to real-time PCR without the requirement of a thermal cycler and with shorter execution times. These characteristics make colorimetric LAMP a valid alternative when one-day results are needed, improving the timely identification of positive meat batches, even in the absence of specialized instrumentation.
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Affiliation(s)
- Andrea Zendrini
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via E. Parmense, 84, 29122 Piacenza, Italy; (A.Z.); (N.F.); (P.A.-M.)
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa, 11, 25123 Brescia, Italy
| | - Valentina Carta
- Department of Food Safety, Istituto Zooprofilattico della Lombardia e dell’Emilia Romagna, Via A. Bianchi, 9, 25124 Brescia, Italy; (V.C.); (L.R.); (E.C.-C.); (S.A.); (B.B.); (M.N.L.)
| | - Virginia Filipello
- Department of Food Safety, Istituto Zooprofilattico della Lombardia e dell’Emilia Romagna, Via A. Bianchi, 9, 25124 Brescia, Italy; (V.C.); (L.R.); (E.C.-C.); (S.A.); (B.B.); (M.N.L.)
- National Reference Centre for Emerging Risks in Food Safety—CRESA, Istituto Zooprofilattico della Lombardia e dell’Emilia Romagna, Via G. Celoria, 12, 20133 Milan, Italy
- Correspondence: ; Tel.: +39-030-2290-781
| | - Laura Ragni
- Department of Food Safety, Istituto Zooprofilattico della Lombardia e dell’Emilia Romagna, Via A. Bianchi, 9, 25124 Brescia, Italy; (V.C.); (L.R.); (E.C.-C.); (S.A.); (B.B.); (M.N.L.)
| | - Elena Cosciani-Cunico
- Department of Food Safety, Istituto Zooprofilattico della Lombardia e dell’Emilia Romagna, Via A. Bianchi, 9, 25124 Brescia, Italy; (V.C.); (L.R.); (E.C.-C.); (S.A.); (B.B.); (M.N.L.)
| | - Sara Arnaboldi
- Department of Food Safety, Istituto Zooprofilattico della Lombardia e dell’Emilia Romagna, Via A. Bianchi, 9, 25124 Brescia, Italy; (V.C.); (L.R.); (E.C.-C.); (S.A.); (B.B.); (M.N.L.)
| | - Barbara Bertasi
- Department of Food Safety, Istituto Zooprofilattico della Lombardia e dell’Emilia Romagna, Via A. Bianchi, 9, 25124 Brescia, Italy; (V.C.); (L.R.); (E.C.-C.); (S.A.); (B.B.); (M.N.L.)
| | - Niccolò Franceschi
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via E. Parmense, 84, 29122 Piacenza, Italy; (A.Z.); (N.F.); (P.A.-M.)
| | - Paolo Ajmone-Marsan
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via E. Parmense, 84, 29122 Piacenza, Italy; (A.Z.); (N.F.); (P.A.-M.)
| | - Dario De Medici
- Department of Food Safety and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy;
| | - Marina Nadia Losio
- Department of Food Safety, Istituto Zooprofilattico della Lombardia e dell’Emilia Romagna, Via A. Bianchi, 9, 25124 Brescia, Italy; (V.C.); (L.R.); (E.C.-C.); (S.A.); (B.B.); (M.N.L.)
- National Reference Centre for Emerging Risks in Food Safety—CRESA, Istituto Zooprofilattico della Lombardia e dell’Emilia Romagna, Via G. Celoria, 12, 20133 Milan, Italy
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15
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Rapid and simultaneous detection of fluoroquinolone- and macrolide-resistant Campylobacter jejuni/coli in retail chicken meat using CAMpylobacter Express Resistance Array (CAMERA). Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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16
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Saito Y, Takahashi N, Matsui A, Michiyuki S, Yamauchi Y, Shimizu Y, Hoshi E, Sakao Y, Kawamura M. Comparative study of the loop-mediated isothermal amplification method and the QIAGEN therascreen PCR kit for the detection of EGFR mutations in non-small cell lung cancer. J Thorac Dis 2021; 13:743-753. [PMID: 33717546 PMCID: PMC7947485 DOI: 10.21037/jtd-20-2642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background Epidermal growth factor receptor (EGFR) mutations are important biomarkers in the treatment of patients with advanced or metastatic diseases. The therascreen EGFR Rotor-Gene Q (RGQ) PCR Kit® (Qiagen, Inc.) is an approved diagnostic test for EGFR mutations in non-small cell lung cancer (NSCLC). This study aims to investigate the diagnostic capability of a loop-mediated isothermal amplification (LAMP) assay as an accurate, efficient, and cost-effective alternative to the therascreen assay. Methods EGFR mutations were investigated by LAMP and therascreen assays using tissue samples that were surgically resected or biopsied from 117 consecutive patients with NSCLC tumors. The EGFR status from the LAMP assay was compared with that of the therascreen assay. Next-generation sequencing (NGS) was performed to confirm EGFR status of tumors that did not match in both assays. To establish an optimal LAMP AUC value, receiver operating characteristics (ROC) curve analysis was performed within tumors with exon 19 deletion or L858R point mutation. Results Of the 117 tumors assayed, 45 tumors with EGFR mutations and 68 tumors with EGFR wild type were matched in both assays, four tumors having mismatched EGFR statuses. NGS further confirmed that two of the four discordant tumors had the same EGFR status that was determined by the LAMP assay. The AUC values were 0.973 (95% CI: 0.929–1.00) in exon 19 deletion, and 0.952 (95% CI: 0.885–1.00) in L858R point mutation. In exon 19 deletion, sensitivity, specificity, and accuracy were 89.3%, 98.9%, and 96.6%, respectively, and 94.7%, 95.9%, and 95.7%, respectively, in L858R using AUC value of 0.222. Conclusions The LAMP assay compared favorably with the therascreen assay and has potential as an effective, simple, rapid, and low-cost diagnostic alternative. Based on these results, a liquid biopsy LAMP system should be developed for point-of-care testing of oncogenes in the near future.
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Affiliation(s)
- Yuichi Saito
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan.,Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, Saitama, Japan
| | - Nobumasa Takahashi
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, Saitama, Japan
| | - Atsuka Matsui
- Fundamental Research Laboratory, Fundamental Technology Research Department, Eiken Chemical Co., Ltd., Tochigi, Japan
| | - Satoru Michiyuki
- Fundamental Research Laboratory, Fundamental Technology Research Department, Eiken Chemical Co., Ltd., Tochigi, Japan
| | - Yoshikane Yamauchi
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Yoshihiko Shimizu
- Department of Pathology, Saitama Cardiovascular and Respiratory Center, Saitama, Japan
| | - Eishin Hoshi
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, Saitama, Japan
| | - Yukinori Sakao
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Masafumi Kawamura
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
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