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Garrido-Maestu A, Prado M. Naked-eye detection strategies coupled with isothermal nucleic acid amplification techniques for the detection of human pathogens. Compr Rev Food Sci Food Saf 2022; 21:1913-1939. [PMID: 35122372 DOI: 10.1111/1541-4337.12902] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/26/2022]
Abstract
Nucleic acid amplification-based techniques have gained acceptance by the scientific, and general, community as reference methodologies for many different applications. Since the development of the gold standard of these techniques, polymerase chain reaction (PCR), back in the 1980s many improvements have been made, and alternative techniques emerged reporting improvements over PCR. Among these, isothermal amplification approaches resulted of particular interest as could overcome the need of specialized equipment to accurately control temperature changes, but it was after year 2000 that these techniques have flourished in a huge number of novel alternatives with many different degrees of complexities and requirements. An added value is their possibility to be combined with many different naked-eye detection strategies, simplifying the resources needed, allowing to reduce cost, and serving as the basis for novel developments of lab-on-chip systems, and miniaturized devices, for point-of-care testing. In this review, we will go over different types of naked-eye detection strategies, combined with isothermal amplification. This will provide the readers up-to-date information for them to select the most appropriate strategies depending on the particular needs and resources for their experimental setup.
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Affiliation(s)
- Alejandro Garrido-Maestu
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Marta Prado
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
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Chen Z, Zhao K, He Z, Luo X, Qin Z, Tan Y, Zheng X, Wu Z, Deng Y, Chen H, Guo Y, Li S. Development and evaluation of a thermostatic nucleic acid testing device based on magnesium pyrophosphate precipitation for detecting Enterocytozoon hepatopenaei. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.01.072] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Bucher BJ, Muchaamba G, Kamber T, Kronenberg PA, Abdykerimov KK, Isaev M, Deplazes P, Alvarez Rojas CA. LAMP Assay for the Detection of Echinococcus multilocularis Eggs Isolated from Canine Faeces by a Cost-Effective NaOH-Based DNA Extraction Method. Pathogens 2021; 10:pathogens10070847. [PMID: 34357996 PMCID: PMC8308659 DOI: 10.3390/pathogens10070847] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/23/2021] [Accepted: 06/29/2021] [Indexed: 12/13/2022] Open
Abstract
The detection of Echinococcus multilocularis in infected canids and the environment is pivotal for a better understanding of the epidemiology of alveolar echinococcosis in endemic areas. Necropsy/sedimentation and counting technique remain the gold standard for the detection of canid infection. PCR-based detection methods have shown high sensitivity and specificity, but they have been hardly used in large scale prevalence studies. Loop-mediated isothermal amplification (LAMP) is a fast and simple method to detect DNA with a high sensitivity and specificity, having the potential for field-application. A specific LAMP assay for the detection of E. multilocularis was developed targeting the mitochondrial nad1 gene. A crucial step for amplification-based detection methods is DNA extraction, usually achieved utilising silica-gel membrane spin columns from commercial kits which are expensive. We propose two cost-effective and straightforward methods for DNA extraction, using NaOH (method 1A) and InstaGeneTM Matrix (method 1B), from isolated eggs circumventing the need for commercial kits. The sensitivity of both assays with fox samples was similar (72.7%) with multiplex-PCR using protocol 1A and LAMP using protocol 1B. Sensitivity increased up to 100% when testing faeces from 12 foxes infected with more than 100 intestinal stages of E. multilocularis. For dogs, sensitivity was similar (95.4%) for LAMP and multiplex-PCR using protocol 1B and for both methods when DNA was extracted using protocol 1A (90.9%). The DNA extraction methods used here are fast, cheap, and do not require a DNA purification step, making them suitable for field studies in low-income countries for the prevalence study of E. multilocularis.
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Affiliation(s)
- Barbara J. Bucher
- Institute of Parasitology, Vetsuisse and Medical Faculty, University of Zurich, 8057 Zurich, Switzerland; (B.J.B.); (G.M.); (T.K.); (P.A.K.); (P.D.)
| | - Gillian Muchaamba
- Institute of Parasitology, Vetsuisse and Medical Faculty, University of Zurich, 8057 Zurich, Switzerland; (B.J.B.); (G.M.); (T.K.); (P.A.K.); (P.D.)
| | - Tim Kamber
- Institute of Parasitology, Vetsuisse and Medical Faculty, University of Zurich, 8057 Zurich, Switzerland; (B.J.B.); (G.M.); (T.K.); (P.A.K.); (P.D.)
| | - Philipp A. Kronenberg
- Institute of Parasitology, Vetsuisse and Medical Faculty, University of Zurich, 8057 Zurich, Switzerland; (B.J.B.); (G.M.); (T.K.); (P.A.K.); (P.D.)
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Kubanychbek K. Abdykerimov
- Section of Epidemiology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland;
- Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland
| | - Myktybek Isaev
- Department of Parasitology, Kyrgyz Research Institute of Veterinary Medicine Arstanbek Duisheev, Ministry of Education and Science of the Kyrgyz Republic, Bishkek 720033, Kyrgyzstan;
| | - Peter Deplazes
- Institute of Parasitology, Vetsuisse and Medical Faculty, University of Zurich, 8057 Zurich, Switzerland; (B.J.B.); (G.M.); (T.K.); (P.A.K.); (P.D.)
| | - Cristian A. Alvarez Rojas
- Institute of Parasitology, Vetsuisse and Medical Faculty, University of Zurich, 8057 Zurich, Switzerland; (B.J.B.); (G.M.); (T.K.); (P.A.K.); (P.D.)
- Correspondence:
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