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Shi J, Ding S, Li C, Chen G, Du F, Wang S, Yue A, Ren K, Yang Z, Xu P, Dong J, Zhao J, Tang Z. Ultrafast DNA detection based on turn-back loop primer-accelerated LAMP (TLAMP). Anal Chim Acta 2024; 1321:343041. [PMID: 39155098 DOI: 10.1016/j.aca.2024.343041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 07/08/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024]
Abstract
Rapid DNA detection is a long-pursuing goal in molecular detection, especially in combating infectious diseases. Loop-mediated isothermal amplification (LAMP) is a robust and prevailing DNA detection method in pathogen detection, which has been drawing broad interest in improving its performance. Herein, we reported a new strategy and developed a new LAMP variant named TLAMP with a superior amplification rate. In this strategy, the turn-back loop primers (TLPs) were devised by ingeniously extending the 5' end of the original loop primer, which conferred the new role of being the inner primer for TLPs while retaining its original function as the loop primer. In theory, based on the bifunctional TLPs, a total of eight basic dumbbell-like structures and four cyclic amplification pathways were produced to significantly enhance the amplification efficiency of TLAMP. With the enhancing effect of TLPs, TLAMP exhibited a significantly reduced amplification-to-result time compared to the conventional six-primer LAMP (typically 1 h), enabling rapid DNA detection within 20 min. Furthermore, TLAMP proved to be about 10 min faster than the fast LAMP variants reported so far, while still presenting comparable sensitivity and higher repeatability. Finally, TLAMP successfully achieved an ultrafast diagnosis of Monkeypox virus (MPXV), capable of detecting as few as 10 copies (0.67copies/μL) of pseudovirus within 20 min using real-time fluorescence assay or within 30 min using a colorimetric assay, suggesting that the proposed TLAMP offers a sensitive, specific, reliable, and, most importantly, ultrafast DNA detection method when facing the challenges posed by infectious diseases.
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Affiliation(s)
- Jinyi Shi
- Shanxi Agricultural University, Dept Basic Sci, Taigu, 030801, Shanxi, PR China; Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Sheng Ding
- School of Clinical Medical College & Affiliated Hospital, Chengdu University, Chengdu, 610052, PR China
| | - Chen Li
- Shanxi Agricultural University, Dept Basic Sci, Taigu, 030801, Shanxi, PR China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China
| | - Feng Du
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China
| | - Sifan Wang
- Shanxi Agricultural University, Dept Basic Sci, Taigu, 030801, Shanxi, PR China
| | - Aiqin Yue
- Shanxi Agricultural University, Dept Basic Sci, Taigu, 030801, Shanxi, PR China
| | - Kaiyuan Ren
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China
| | - Zhirong Yang
- People's Hospital of De Yang City, Deyang, 618099, PR China
| | - Pei Xu
- People's Hospital of De Yang City, Deyang, 618099, PR China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China.
| | - Jinzhong Zhao
- Shanxi Agricultural University, Dept Basic Sci, Taigu, 030801, Shanxi, PR China.
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China.
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Gayathri SL, Bhakat M, Mohanty TK. Early Detection of Sub-clinical Mastitis in Murrah Buffaloes through Udder Thermogram Analysis during the Natural Progression of Infection. Vet J 2024; 306:106176. [PMID: 38901760 DOI: 10.1016/j.tvjl.2024.106176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 06/05/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
Mastitis is a global production disease that needs an intelligent solution to tackle effectively. Infrared Thermography (IRT) is a non-invasive technology that could be incorporated into routine day-to-day farm activities to monitor the health status of the animals. In this study, the udder health status was routinely monitored for 30 days among 41 Murrah buffaloes via IRT and the California Mastitis Test (CMT). Further, somatic cell count (SCC), microbial identification, and milk quality parameters were also estimated for representative samples. The thermal imaging data obtained was tabulated and back propagated from the 0th day to the -10th day and front propagated from the 0th day to +10th day for all the udder quarters. Results revealed that on the 0th day, the mean of udder skin surface temperature (USST) and teat skin surface temperature (TSST) showed a difference (p < 0.05) in the sub-clinical mastitis (SCM) and clinical mastitis (CM) affected quarters to the healthy quarters, and their degree of difference was the highest. The indication of infection was signaled during the -9th to -5th day to the 0th day in SCM and CM cases. There was a steep increment in the temperature from -2nd and -1st day to the 0th day of infection. Sometimes, some quarters show an increment in temperature due to mastitis during morning hours but recover by evening milking due to the animal's innate immune system. Thus, the initiation period in which the udder gets assaulted is crucial in the early assessment of SCM by monitoring temperature change using IRT.
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Affiliation(s)
- S L Gayathri
- Livestock Production Management Division, ICAR, National Dairy Research Institute, Karnal, Haryana 132001, India.
| | - M Bhakat
- Livestock Production Management Division, ICAR, National Dairy Research Institute, Karnal, Haryana 132001, India.
| | - T K Mohanty
- Livestock Production Management Division, ICAR, National Dairy Research Institute, Karnal, Haryana 132001, India.
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Sakatoku A, Suzuki T, Hatano K, Seki M, Tanaka D, Nakamura S, Suzuki N, Isshiki T. Inhibitors of LAMP used to detect Tenacibaculum sp. strain Pbs-1 associated with black-spot shell disease in Akoya pearl oysters, and additives to reduce the effect of the inhibitors. J Microbiol Methods 2024; 223:106986. [PMID: 38969181 DOI: 10.1016/j.mimet.2024.106986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 06/30/2024] [Accepted: 06/30/2024] [Indexed: 07/07/2024]
Abstract
Black-spot shell disease is an unresolved disease that decreases pearl quality and threatens pearl oyster survival. In previous studies, the bacterium Tenacibaculum sp. strain Pbs-1 was isolated from diseased Akoya pearl oysters Pinctada fucata, and a rapid, specific, and sensitive loop-mediated isothermal amplification (LAMP) assay for detecting this pathogen was established. This technology has considerable potential for routine diagnosis of strain Pbs-1 in oyster hatcheries and/or pearl farms; therefore, it is vital to identify substances in environmental samples that might inhibit LAMP and to find additives that can reduce the inhibition. In this study, we investigated the effects of six chemicals or proteins, otherwise known as conventional PCR inhibitors, on LAMP, using the DNA of strain Pbs-1 as template: humic acid, urea, iron (III) chloride hexahydrate, melanin, myoglobin, and Ethylenediamine-N,N,N',N'-tetraacetic acid, disodium salt, dihydrate (EDTA; pH 6.5). Next, to reduce the effects of identified inhibitors, we tested the addition of bovine serum albumin (BSA) or T4 gene 32 protein (gp32) to the LAMP assay. When 50 ng of DNA template was used, 4 ng/μL of humic acid, 0.05% melanin, and 10 mM of EDTA (pH 6.5) inhibited the LAMP reaction, whereas myoglobin, urea, and FeCl3 had no effect. When 50 pg of DNA template was used, 4 ng/μL of humic acid, 0.05% melanin, 4 μg/μL of myoglobin, 10 μg/μL of urea, and 10 mM of EDTA inhibited the LAMP reaction. Thus, it was shown that the gene-amplification inhibitory effect of melanin, humic acid, and urea could be reduced by adding BSA or gp32 to the LAMP reaction mixture. This technique could be applied as part of a protocol to prevent mass mortalities of pearl oysters; moreover, the results enhance our knowledge about substances that inhibit LAMP and methods to reduce the inhibition, which have rarely been reported.
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Affiliation(s)
- Akihiro Sakatoku
- School of Science, Academic Assembly, University of Toyama, Toyama 930-8555, Japan.
| | - Takaya Suzuki
- School of Science, Academic Assembly, University of Toyama, Toyama 930-8555, Japan
| | - Kaito Hatano
- Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Ogi, Noto-cho, Ishikawa 927-0553, Japan
| | - Makoto Seki
- School of Science, Academic Assembly, University of Toyama, Toyama 930-8555, Japan
| | - Daisuke Tanaka
- School of Science, Academic Assembly, University of Toyama, Toyama 930-8555, Japan
| | - Shogo Nakamura
- School of Science, Academic Assembly, University of Toyama, Toyama 930-8555, Japan
| | - Nobuo Suzuki
- Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Ogi, Noto-cho, Ishikawa 927-0553, Japan
| | - Tadashi Isshiki
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu, Mie 514-8507, Japan
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Natsuhara D, Kiba Y, Saito R, Okamoto S, Nagai M, Yamauchi Y, Kitamura M, Shibata T. A sequential liquid dispensing method in a centrifugal microfluidic device operating at a constant rotational speed for the multiplexed genetic detection of foodborne pathogens. RSC Adv 2024; 14:22606-22617. [PMID: 39021458 PMCID: PMC11253859 DOI: 10.1039/d4ra04055d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
This study proposes a sequential liquid dispensing method using a centrifugal microfluidic device operating at a constant rotational speed for the multiplexed genetic detection of nucleic acid targets across multiple samples in a single operation. A pair of passive valves integrated into each microchamber enabled the liquid to fill towards the center of rotation against the centrifugal force, facilitating the complete removal of air inside the microchamber. Liquid manipulation can be achievable without any surface coating of the device by exploiting the inherent hydrophobicity of the polymer. Furthermore, design guidelines for the optimization of microfluidic devices are clarified. Consequently, our proposed method allows direct liquid dispensing into the reaction chambers without cross-contamination while simultaneously metering the sample/reagent volume for the colorimetric loop-mediated isothermal amplification (LAMP) reaction. In addition, we demonstrated the simultaneous detection of four foodborne pathogens (Salmonella spp., Vibrio parahaemolyticus, Campylobacter spp., and norovirus genogroup II (GII)) across four samples in a centrifugal microfluidic device within 60 min. Furthermore, the device exhibited high quantitation (R 2 > 0.98) of the DNA concentration in the sample. Our proposed method enables a more compact design by eliminating the need for metering chambers and offers a point-of-care testing platform with high simplicity as it operates at a constant rotational speed.
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Affiliation(s)
- Daigo Natsuhara
- Department of Materials Process Engineering, Graduate School of Engineering, Nagoya University Nagoya Aichi 464-8603 Japan
| | - Yuka Kiba
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University Sakado Saitama 350-0295 Japan
| | - Ryogo Saito
- Department of Mechanical Engineering, Toyohashi University of Technology Toyohashi Aichi 441-8580 Japan
| | - Shunya Okamoto
- Department of Mechanical Engineering, Toyohashi University of Technology Toyohashi Aichi 441-8580 Japan
| | - Moeto Nagai
- Department of Mechanical Engineering, Toyohashi University of Technology Toyohashi Aichi 441-8580 Japan
- Institute for Research on Next-generation Semiconductor and Sensing Science (IRES2), Toyohashi University of Technology Aichi 441-8580 Japan
| | - Yusuke Yamauchi
- Department of Materials Process Engineering, Graduate School of Engineering, Nagoya University Nagoya Aichi 464-8603 Japan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland St. Lucia QLD 4072 Australia
| | - Masashi Kitamura
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University Sakado Saitama 350-0295 Japan
| | - Takayuki Shibata
- Department of Mechanical Engineering, Toyohashi University of Technology Toyohashi Aichi 441-8580 Japan
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Panich W, Jaruboonyakorn P, Raksaman A, Tejangkura T, Chontananarth T. Development and utilization of a visual loop-mediated isothermal amplification coupled with a lateral flow dipstick (LAMP-LFD) assay for rapid detection of Echinostomatidae metacercaria in edible snail samples. Int J Food Microbiol 2024; 418:110732. [PMID: 38728973 DOI: 10.1016/j.ijfoodmicro.2024.110732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/12/2024]
Abstract
Trematodes belonging to the family Echinostomatidae are food-borne parasites which cause echinostomiasis in animals and humans. This is a global public health issue, particularly in East and Southeast Asia. A method to detect the infective stage of Echinostomatidae species is required to prevent transmission to humans. In this study, a loop-mediated isothermal amplification coupled with a lateral flow dipstick (LAMP-LFD) assay was developed for visual detection of the metacercarial stage in edible snails of the genus Filopaludina from local markets in Thailand. The LAMP-LFD method can be performed within 70 min at a consistent temperature of 66 °C, and the results can be interpreted with the naked eye. The detection limits of the assay using Echinostoma mekongi, E. macrorchis, E. miyagawai and Hypoderaeum conoideum genomic DNA were equal between the four species at 50 pg/μL. A specificity evaluation demonstrated that the LAMP-LFD assay had no cross-reaction with another parasite (Thapariella species) or with the snail host species (Filopaludina martensi martensi, F. sumatrensis speciosa, and F. s. polygramma). Clinical test assessments were compared to microscopic examination in 110 edible snail samples. The clinical sensitivity and specificity of the tests were 84.62 % and 100 %, respectively, with a strong level of agreement based on the kappa statistic and the results of both methods were not significantly different (p > 0.05) per McNemar's test. The test successfully developed in this study may be useful for the detection of the metacercarial stage in edible snails for epidemiological investigations, control, surveillance, and to prevent future echinostomiasis health issues.
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Affiliation(s)
- Wasin Panich
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Phonkawin Jaruboonyakorn
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Awika Raksaman
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Thanawan Tejangkura
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand; Research and Innovation Unit for Diagnosis of Medical and Veterinary Important Parasites, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Thapana Chontananarth
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand; Research and Innovation Unit for Diagnosis of Medical and Veterinary Important Parasites, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand.
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Čermáková E, Mukherjee S, Nováková D, Horká P, Zdeňková K, Demnerová K. Parvalbumin Gene: A Valuable Marker for Pike Authentication and Allergen Risk Assessment. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12788-12797. [PMID: 38778779 PMCID: PMC11157528 DOI: 10.1021/acs.jafc.4c01410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/02/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Fish from the pike (Esox) genus are valued in gastronomy for their superior meat quality. However, they can cause allergic reactions in sensitive consumers. This work aimed to fill the gap in the detection of pike allergens using molecular-biological techniques. New, fast, and accurate loop-mediated isothermal amplification (LAMP) and real-time PCR (qPCR) assays were designed to detect pike DNA using the parvalbumin gene as a marker. LAMP was assessed by electrophoresis, SYBR green optical detection, and real-time fluorescence detection. The latter was the most sensitive, detecting as little as 0.78 ng of pike DNA; the qPCR detection limit was 0.1 ng. The LAMP analysis took 20-70 min, which is significantly faster than qPCR. The study provides reliable detection and quantification of the parvalbumin gene in both fresh and processed samples and further highlights the versatility of the use of the parvalbumin gene for the authentication of food products and consumer protection via refined allergen risk assessment that is independent of the type of tissue or food processing method used.
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Affiliation(s)
- Eliška Čermáková
- Department
of Chemistry, Biochemistry and Food Microbiology, Food Research Institute Prague, Radiová 1285/7, Prague
10 102 00, Czech Republic
- Department
of Biochemistry and Microbiology, University
of Chemistry and Technology, Prague, Technická 5, Prague 6 166 28, Czech Republic
| | - Subham Mukherjee
- Department
of Chemistry, Biochemistry and Food Microbiology, Food Research Institute Prague, Radiová 1285/7, Prague
10 102 00, Czech Republic
- Lennard-Jones
School of Chemical and Physical Sciences, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institute
for Environmental Studies, Faculty of Science, Charles University, Benatska 2, Prague 2 128
01, Czech Republic
| | - Denisa Nováková
- Department
of Biochemistry and Microbiology, University
of Chemistry and Technology, Prague, Technická 5, Prague 6 166 28, Czech Republic
| | - Petra Horká
- Institute
for Environmental Studies, Faculty of Science, Charles University, Benatska 2, Prague 2 128
01, Czech Republic
| | - Kamila Zdeňková
- Department
of Biochemistry and Microbiology, University
of Chemistry and Technology, Prague, Technická 5, Prague 6 166 28, Czech Republic
| | - Kateřina Demnerová
- Department
of Biochemistry and Microbiology, University
of Chemistry and Technology, Prague, Technická 5, Prague 6 166 28, Czech Republic
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Wulandari DA, Hartati YW, Ibrahim AU, Pitaloka DAE, Irkham. Multidrug-resistant tuberculosis. Clin Chim Acta 2024; 559:119701. [PMID: 38697459 DOI: 10.1016/j.cca.2024.119701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/05/2024]
Abstract
One of predominant contributors to global mortality is tuberculosis (TB), an infection caused by Mycobacterium tuberculosis (MTB). Inappropriate and ineffectual treatment can lead to the development of drug-resistant TB. One of the most common forms of drug-resistant TB is multidrug-resistant tuberculosis (MDR-TB), caused by mutations in the rpoB and katG genes that lead to resistance to anti-TB drugs, rifampicin (RIF) and isoniazid (INH), respectively. Although culturing remains the gold standard, it is not rapid thereby delaying potential treatment and potentially increasing the incidence of MDR-TB. In contrast, molecular techniques provide a highly sensitive and specific alternative. This review discusses the classification of biomarkers used to detect MDR-TB, some of the commonly used anti-TB drugs, and DNA mutations in MTB that lead to anti-TB resistance. The objective of this review is to increase awareness of the need for rapid and precise detection of MDR-TB cases to decrease morbidity and mortality of this infectious disease worldwide.
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Affiliation(s)
- Dika Apriliana Wulandari
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang Km 21, 45363, Indonesia
| | - Yeni Wahyuni Hartati
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang Km 21, 45363, Indonesia
| | - Abdullahi Umar Ibrahim
- Department of Biomedical Engineering, Near East University, Mersin 10, Nicosia 99010, Turkey; Research Center for Science, Technology and Engineering (BILTEM), Near East University, 99138 Nicosia, TRNC, Mersin 10, Turkey
| | - Dian Ayu Eka Pitaloka
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Bandung, Indonesia
| | - Irkham
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung-Sumedang Km 21, 45363, Indonesia.
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Oslan SNH, Yusof NY, Lim SJ, Ahmad NH. Rapid and sensitive detection of Salmonella in agro-Food and environmental samples: A review of advances in rapid tests and biosensors. J Microbiol Methods 2024; 219:106897. [PMID: 38342249 DOI: 10.1016/j.mimet.2024.106897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/13/2024]
Abstract
Salmonella is as an intracellular bacterium, causing many human fatalities when the host-specific serotypes reach the host gastrointestinal tract. Nontyphoidal Salmonella are responsible for numerous foodborne outbreaks and product recalls worldwide whereas typhoidal Salmonella are responsible for Typhoid fever cases in developing countries. Yet, Salmonella-related foodborne disease outbreaks through its food and water contaminations have urged the advancement of rapid and sensitive Salmonella-detecting methods for public health protection. While conventional detection methods are time-consuming and ineffective for monitoring foodstuffs with short shelf lives, advances in microbiology, molecular biology and biosensor methods have hastened the detection. Here, the review discusses Salmonella pathogenic mechanisms and its detection technology advancements (fundamental concepts, features, implementations, efficiency, benefits, limitations and prospects). The time-efficiency of each rapid test method is discussed in relation to their limit of detections (LODs) and time required from sample enrichment to final data analysis. Importantly, the matrix effects (LODs and sample enrichments) were compared within the methods to potentially speculate Salmonella detection from environmental, clinical or food matrices using certain techniques. Although biotechnological advancements have led to various time-efficient Salmonella-detecting techniques, one should consider the usage of sophisticated equipment to run the analysis by moderately to highly trained personnel. Ultimately, a fast, accurate Salmonella screening that is readily executed by untrained personnels from various matrices, is desired for public health procurement.
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Affiliation(s)
- Siti Nur Hazwani Oslan
- Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia; Food Security Research Laboratory, Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia.
| | - Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Si Jie Lim
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Nurul Hawa Ahmad
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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Shi Y, Zhou Q, Dong S, Zhao Q, Wu X, Yang P, Zeng X, Yang X, Tan Y, Luo X, Xiao Z, Chen X. Rapid, visual, label-based biosensor platform for identification of hepatitis C virus in clinical applications. BMC Microbiol 2024; 24:68. [PMID: 38413863 PMCID: PMC10900634 DOI: 10.1186/s12866-024-03220-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 02/09/2024] [Indexed: 02/29/2024] Open
Abstract
OBJECTIVES In the current study, for the first time, we reported a novel HCV molecular diagnostic approach termed reverse transcription loop-mediated isothermal amplification integrated with a gold nanoparticles-based lateral flow biosensor (RT-LAMP-AuNPs-LFB), which we developed for rapid, sensitive, specific, simple, and visual identification of HCV. METHODS A set of LAMP primer was designed according to 5'untranslated region (5'UTR) gene from the major HCV genotypes 1b, 2a, 3b, 6a, and 3a, which are prevalent in China. The HCV-RT-LAMP-AuNPs-LFB assay conditions, including HCV-RT-LAMP reaction temperature and time were optimized. The sensitivity, specificity, and selectivity of our assay were evaluated in the current study. The feasibility of HCV-RT-LAMP-AuNPs-LFB was confirmed through clinical serum samples from patients with suspected HCV infections. RESULTS An unique set of HCV-RT-LAMP primers were successfully designed targeting on the 5'UTR gene. The optimal detection process, including crude nucleic acid extraction (approximately 5 min), RT-LAMP reaction (67℃, 30 min), and visual interpretation of AuNPs-LFB results (~ 2 min), could be performed within 40 min without specific instruments. The limit of detection was determined to be 20 copies per test. The HCV-RT-LAMP-AuNPs-LFB assay exhibited high specificity and anti-interference. CONCLUSIONS These preliminary results confirmed that the HCV-RT-LAMP-AuNPs-LFB assay is a sensitive, specific, rapid, visual, and cost-saving assay for identification of HCV. This diagnostic approach has great potential value for point-of-care (POC) diagnostic of HCV, especially in resource-challenged regions.
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Affiliation(s)
- Yuanfang Shi
- The Second Clinical Medical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China
| | - Qingxue Zhou
- Clinical Laboratory, Hangzhou Women's Hospital, Hangzhou, Zhejiang, 310008, People's Republic of China
| | - Shilei Dong
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, Zhejiang, 310013, People's Republic of China
| | - Qi Zhao
- Department of gastroenterology, the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China
| | - Xue Wu
- Department of Scientific Research, the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China
| | - Peng Yang
- Clinical Laboratory, the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China
| | - Xiaoyan Zeng
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China
| | - Xinggui Yang
- Experiment Center, Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, Guizhou, 550004, People's Republic of China
| | - Yan Tan
- Clinical Laboratory, Guizhou Provincial Center for Clinical Laboratory, Guiyang, Guizhou, 550002, People's Republic of China
| | - Xinhua Luo
- Department of Infectious Disease, Guizhou Provincial People's Hospital, Guiyang, Guizhou, 550002, People's Republic of China
| | - Zhenghua Xiao
- The Second Clinical Medical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China.
- Department of gastroenterology, the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China.
| | - Xu Chen
- The Second Clinical Medical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China.
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China.
- Department of Scientific Research, the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China.
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10
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Kim D, DeBriere TJ, Eastmond BH, Alomar AA, Yaren O, McCarter J, Bradley KM, Benner SA, Alto BW, Burkett-Cadena ND. Rapid detection of West Nile and Dengue viruses from mosquito saliva by loop-mediated isothermal amplification and displaced probes. PLoS One 2024; 19:e0298805. [PMID: 38394282 PMCID: PMC10889885 DOI: 10.1371/journal.pone.0298805] [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: 09/01/2023] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Arthropod-borne viruses are major causes of human and animal disease, especially in endemic low- and middle-income countries. Mosquito-borne pathogen surveillance is essential for risk assessment and vector control responses. Sentinel chicken serosurveillance (antibody testing) and mosquito pool screening (by RT-qPCR or virus isolation) are currently used to monitor arbovirus transmission, however substantial time lags of seroconversion and/or laborious mosquito identification and RNA extraction steps sacrifice their early warning value. As a consequence, timely vector control responses are compromised. Here, we report on development of a rapid arbovirus detection system whereby adding sucrose to reagents of loop-mediated isothermal amplification with displaced probes (DP-LAMP) elicits infectious mosquitoes to feed directly upon the reagent mix and expectorate viruses into the reagents during feeding. We demonstrate that RNA from pathogenic arboviruses (West Nile and Dengue viruses) transmitted in the infectious mosquito saliva was detectable rapidly (within 45 minutes) without RNA extraction. Sucrose stabilized viral RNA at field temperatures for at least 48 hours, important for transition of this system to practical use. After thermal treatment, the DP-LAMP could be reliably visualized by a simple optical image sensor to distinguish between positive and negative samples based on fluorescence intensity. Field application of this technology could fundamentally change conventional arbovirus surveillance methods by eliminating laborious RNA extraction steps, permitting arbovirus monitoring from additional sites, and substantially reducing time needed to detect circulating pathogens.
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Affiliation(s)
- Dongmin Kim
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida, United States of America
| | | | - Bradley H. Eastmond
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida, United States of America
| | - Abdullah A. Alomar
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida, United States of America
| | - Ozlem Yaren
- Firebird Biomolecular Sciences LLC, Alachua, Florida, United States of America
- Foundation for Applied Molecular Evolution, Alachua, Florida, United States of America
| | - Jacquelyn McCarter
- Firebird Biomolecular Sciences LLC, Alachua, Florida, United States of America
- Foundation for Applied Molecular Evolution, Alachua, Florida, United States of America
| | - Kevin M. Bradley
- Foundation for Applied Molecular Evolution, Alachua, Florida, United States of America
| | - Steven A. Benner
- Firebird Biomolecular Sciences LLC, Alachua, Florida, United States of America
- Foundation for Applied Molecular Evolution, Alachua, Florida, United States of America
| | - Barry W. Alto
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida, United States of America
| | - Nathan D. Burkett-Cadena
- Florida Medical Entomology Laboratory, University of Florida, Vero Beach, Florida, United States of America
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11
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Pan B, El-Moghazy AY, Norwood M, Nitin N, Sun G. Rapid and Ultrasensitive Colorimetric Biosensors for Onsite Detection of Escherichia coli O157:H7 in Fluids. ACS Sens 2024; 9:912-922. [PMID: 38320289 PMCID: PMC10897931 DOI: 10.1021/acssensors.3c02339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/08/2024]
Abstract
This study presents a breakthrough in the field of onsite bacterial detection, offering an innovative, rapid, and ultrasensitive colorimetric biosensor for the detection of Escherichia coli (E. coli) O157:H7, using chemically modified melamine foam (MF). Different from conventional platforms, such as 96-well plates and fiber-based membranes, the modified MF features a macroporous reticulated three-dimensional (3D) framework structure, allowing fast and free movement of large biomolecules and bacteria cells through the MF structure in every direction and ensuring good accessibility of entire active binding sites of the framework structure with the target bacteria, which significantly increased sensitive and volume-responsive detection of whole-cell bacteria. The biosensing platform requires less than 1.5 h to complete the quantitative detection with a sensitivity of 10 cfu/mL, discernible by the naked eye, and an enhanced sensitivity of 5 cfu/mL with the help of a smartphone. Following a short enrichment period of 1 h, the sensitivity was further amplified to 2 cfu/mL. The biosensor material is volume responsive, making the biosensing platform sensitivity increase as the volume of the sample increases, and is highly suitable for testing large-volume fluid samples. This novel material paves the way for the development of volume-flexible biosensing platforms for the record-fast, onsite, selective, and ultrasensitive detection of various pathogenic bacteria in real-world applications.
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Affiliation(s)
- Bofeng Pan
- Biological
and Agricultural Engineering, University
of California, Davis, California 95616, United States
| | - Ahmed Y. El-Moghazy
- Department
of Food Science and Technology, University
of California, Davis, California 95616, United States
| | - Makela Norwood
- Biological
and Agricultural Engineering, University
of California, Davis, California 95616, United States
| | - Nitin Nitin
- Biological
and Agricultural Engineering, University
of California, Davis, California 95616, United States
- Department
of Food Science and Technology, University
of California, Davis, California 95616, United States
| | - Gang Sun
- Biological
and Agricultural Engineering, University
of California, Davis, California 95616, United States
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12
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Trippa D, Scalenghe R, Basso MF, Panno S, Davino S, Morone C, Giovino A, Oufensou S, Luchi N, Yousefi S, Martinelli F. Next-generation methods for early disease detection in crops. PEST MANAGEMENT SCIENCE 2024; 80:245-261. [PMID: 37599270 DOI: 10.1002/ps.7733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/21/2023] [Indexed: 08/22/2023]
Abstract
Plant pathogens are commonly identified in the field by the typical disease symptoms that they can cause. The efficient early detection and identification of pathogens are essential procedures to adopt effective management practices that reduce or prevent their spread in order to mitigate the negative impacts of the disease. In this review, the traditional and innovative methods for early detection of the plant pathogens highlighting their major advantages and limitations are presented and discussed. Traditional techniques of diagnosis used for plant pathogen identification are focused typically on the DNA, RNA (when molecular methods), and proteins or peptides (when serological methods) of the pathogens. Serological methods based on mainly enzyme-linked immunosorbent assay (ELISA) are the most common method used for pathogen detection due to their high-throughput potential and low cost. This technique is not particularly reliable and sufficiently sensitive for many pathogens detection during the asymptomatic stage of infection. For non-cultivable pathogens in the laboratory, nucleic acid-based technology is the best choice for consistent pathogen detection or identification. Lateral flow systems are innovative tools that allow fast and accurate results even in field conditions, but they have sensitivity issues to be overcome. PCR assays performed on last-generation portable thermocyclers may provide rapid detection results in situ. The advent of portable instruments can speed pathogen detection, reduce commercial costs, and potentially revolutionize plant pathology. This review provides information on current methodologies and procedures for the effective detection of different plant pathogens. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Daniela Trippa
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Riccardo Scalenghe
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | | | - Stefano Panno
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Salvatore Davino
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Chiara Morone
- Regione Piemonte - Phytosanitary Division, Torino, Italy
| | - Antonio Giovino
- Council for Agricultural Research and Economics (CREA)-Research Centre for Plant Protection and Certification (CREA-DC), Palermo, Italy
| | - Safa Oufensou
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Nicola Luchi
- National Research Council, Institute for Sustainable Plant Protection, (CNR-IPSP), Florence, Italy
| | - Sanaz Yousefi
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Federico Martinelli
- Department of Biology, University of Florence, Florence, Italy
- National Research Council, Institute for Sustainable Plant Protection, (CNR-IPSP), Florence, Italy
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13
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Akter J, Smith WJM, Gebrewold M, Kim I, Simpson SL, Bivins A, Ahmed W. Evaluation of colorimetric RT-LAMP for screening of SARS-CoV-2 in untreated wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167964. [PMID: 37865239 DOI: 10.1016/j.scitotenv.2023.167964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
This study compared reverse transcription-loop-mediated isothermal amplification (RT-LAMP) and three reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays targeting the N and E genes of the SARS-CoV-2 genome for detecting RNA in untreated wastewater samples. RT-qPCR assays exhibited consistent amplification down to 2 × 102 GC/reaction, with greater analytical sensitivity at 2 × 101 GC/reaction by US CDC N1 and US CDC N2 assays. In contrast, RT-LAMP exhibited lower sensitivity, detecting SARS-CoV-2 only at or above 2 × 103 GC/reaction. For SARS-CoV-2 seeded wastewater samples, the US CDC N1 assay exhibited greater analytical sensitivity than the US CDC N2, E_Sarbeco, and RT-LAMP assays. Out of 30 wastewater samples, RT-qPCR detected endogenous SARS-CoV-2 RNA in 29 samples, while RT-LAMP identified 27 positive samples, with 20 displaying consistent amplifications in all three RT-LAMP technical replicates. Agreement analysis revealed a strong concordance between RT-LAMP and the US CDC N1 and E_Sarbeco RT-qPCR assays (κ = 0.474) but lower agreement with the US CDC N2 RT-qPCR assay (κ = 0.359). Quantification of SARS-CoV-2 RNA in positive samples revealed a strong correlation between the US CDC N1 and E_Sarbeco assays, while the US CDC N1 and US CDC N2 assays exhibited weak correlation. Logistic regression analysis indicated that RT-LAMP results correlated with RNA quantified by the US CDC N1 and E_Sarbeco assays, with 95 % limits of detection of 3.99 and 3.47 log10 GC/15 mL, respectively. In conclusion, despite lower sensitivity compared to RT-qPCR assays, RT-LAMP may offer advantages for wastewater surveillance, such as rapid results (estimated as twice as fast), and simplicity, making it a valuable tool in the shifting landscape of COVID-19 wastewater surveillance. Furthermore, LAMP positive wastewater samples might be prioritized for SARS-CoV-2 sequencing due to reduced analytical sensitivity. These findings support the use of RT-LAMP as a specific and efficient method for screening wastewater samples for SARS-CoV-2, particularly in resource-limited settings.
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Affiliation(s)
- Jesmin Akter
- Department of Civil and Environmental Engineering, University of Science and Technology, Republic of Korea; Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Republic of Korea; CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy J M Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Metasebia Gebrewold
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Ilho Kim
- Department of Civil and Environmental Engineering, University of Science and Technology, Republic of Korea; Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Republic of Korea
| | | | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA 70803, United States of America
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
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14
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Moon YJ, Lee SY, Kim U, Oh SW. Naked-eye detection with loop-mediated isothermal amplification for P. carotovorum subsp. carotovorum in agricultural products. Food Sci Biotechnol 2024; 33:203-209. [PMID: 38186613 PMCID: PMC10766909 DOI: 10.1007/s10068-023-01315-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/04/2023] [Accepted: 04/17/2023] [Indexed: 01/09/2024] Open
Abstract
Pectobacterium carotovorum causing soft-rot disease requires on-site detection before the distribution of agricultural products. Loop-mediated isothermal amplification (LAMP), which is resistant to food inhibitors, is known for its high detection sensitivity for pathogens and when coupled with lateral flow immunoassay (LFA) enables visualizations. For detection of soft-rot disease, we developed a LAMP-LFA system targeting 16S ribosomal RNA, a partial sequence gene of P. carotovorum subsp. carotovorum. The LAMP-LFA was performed at 60 °C for 50 min followed by hybridization of digoxygenin-labeled LAMP amplicon and biotinylated probe. Detection sensitivity was 3.22 × 101 CFU/mL in pure culture, which specifically detected the target. In Chinese cabbage and potato, the target was detected up to low levels of 1.57 × 102 CFU/g and 1.29 × 102 CFU/g, respectively. This study showed potential applicability as a sensitive point-of-care system for soft-rot disease bacteria detection in agricultural products. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-023-01315-z.
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Affiliation(s)
- Ye-Ji Moon
- Department of Food and Nutrition, Kookmin University, Seoul, 02727 Republic of Korea
| | - So-Young Lee
- Department of Food and Nutrition, Kookmin University, Seoul, 02727 Republic of Korea
| | - Unji Kim
- Department of Food and Nutrition, Kookmin University, Seoul, 02727 Republic of Korea
| | - Se-Wook Oh
- Department of Food and Nutrition, Kookmin University, Seoul, 02727 Republic of Korea
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15
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Zhu W, Xiao L, Yuan R, Lin Y, Wang T, Wen Z, Ding L, Wang K. Isothermal nucleic acid amplification combined with gold nanoparticles assisted electrochemical impedance for the sensitive and efficient porcine delta coronavirus detection. Talanta 2024; 266:125109. [PMID: 37633037 DOI: 10.1016/j.talanta.2023.125109] [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: 06/25/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 08/28/2023]
Abstract
The emergence of porcine delta coronavirus (PDCoV) has caused huge economic losses in the global pig industry. How to realize the sensitive and efficient detection for it is a difficult problem that need to be resolved. In this work, loop-mediated isothermal amplification (LAMP)-electrochemical impedance spectroscopy (EIS) detection platform for PDCoV based on nucleic acid level was constructed by combining the advantages of efficient amplification for LAMP and sensitive detection for EIS. Referring to a 159 bp fragment of PDCoV N gene (Genbank:KY078891, 641 bp-799 bp), primers (HS-FIP、BIP、F3、B3) were designed to screened and sulfhydryl groups were activated, and then loop-mediated isothermal amplification was carried out. Subsequently, gold nanoparticles were loaded on indium tin oxide glass by electrodeposition technology, and the amplified products were connected to the electrode surface through the formation of Au-S bonds. According to the difference of charge transfer resistance after double-stranded DNA was connected on the electrode surface, the detection platform can achieve valid detection of PDCoV in the concentration range of 102-107 copies/μL, the limit of detection is 28 copies/μL, and can be used for practical analysis of pig small intestine samples.
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Affiliation(s)
- Weiran Zhu
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China
| | - Liting Xiao
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China
| | - Ruishuang Yuan
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China
| | - Yuhang Lin
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China
| | - Tianshuo Wang
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China
| | - Zuorui Wen
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China
| | - Lijun Ding
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China
| | - Kun Wang
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China; School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, PR China.
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16
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Gieroń M, Żarnowiec P, Zegadło K, Gmiter D, Czerwonka G, Kaca W, Kręcisz B. Loop-Mediated Isothermal Amplification of DNA (LAMP) as an Alternative Method for Determining Bacteria in Wound Infections. Int J Mol Sci 2023; 25:411. [PMID: 38203582 PMCID: PMC10778741 DOI: 10.3390/ijms25010411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
The increasing number of patients with chronic wounds requires the development of quick and accurate diagnostics methods. One of the key and challenging aspects of treating ulcers is to control wound infection. Early detection of infection is essential for the application of suitable treatment methods, such as systemic antibiotics or other antimicrobial agents. Clinically, the most frequently used method for detecting microorganisms in wounds is through a swab and culture on appropriate media. This test has major limitations, such as the long bacterial growth time and the selectivity of bacterial growth. This article presents an overview of molecular methods for detecting bacteria in wounds, including real-time polymerase chain reaction (rtPCR), quantitative polymerase chain reaction (qPCR), genotyping, next-generation sequencing (NGS), and loop-mediated isothermal amplification (LAMP). We focus on the LAMP method, which has not yet been widely used to detect bacteria in wounds, but it is an interesting alternative to conventional detection methods. LAMP does not require additional complicated equipment and provides the fastest detection time for microorganisms (approx. 30 min reaction). It also allows the use of many pairs of primers in one reaction and determination of up to 15 organisms in one sample. Isothermal amplification of DNA is currently the easiest and most economical method for microbial detection in wound infection. Direct visualization of the reaction with dyes, along with omitting DNA isolation, has increased the potential use of this method.
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Affiliation(s)
- Monika Gieroń
- Faculty of Medicine, Jan Kochanowski University in Kielce, 25-369 Kielce, Poland; (M.G.); (B.K.)
- Dermatology Department, Provincial General Hospital, 25-317 Kielce, Poland
| | - Paulina Żarnowiec
- Department of Microbiology, Institute of Biology, Jan Kochanowski University in Kielce, 25-406 Kielce, Poland; (P.Ż.); (K.Z.); (D.G.); (W.K.)
| | - Katarzyna Zegadło
- Department of Microbiology, Institute of Biology, Jan Kochanowski University in Kielce, 25-406 Kielce, Poland; (P.Ż.); (K.Z.); (D.G.); (W.K.)
| | - Dawid Gmiter
- Department of Microbiology, Institute of Biology, Jan Kochanowski University in Kielce, 25-406 Kielce, Poland; (P.Ż.); (K.Z.); (D.G.); (W.K.)
| | - Grzegorz Czerwonka
- Department of Microbiology, Institute of Biology, Jan Kochanowski University in Kielce, 25-406 Kielce, Poland; (P.Ż.); (K.Z.); (D.G.); (W.K.)
| | - Wiesław Kaca
- Department of Microbiology, Institute of Biology, Jan Kochanowski University in Kielce, 25-406 Kielce, Poland; (P.Ż.); (K.Z.); (D.G.); (W.K.)
| | - Beata Kręcisz
- Faculty of Medicine, Jan Kochanowski University in Kielce, 25-369 Kielce, Poland; (M.G.); (B.K.)
- Dermatology Department, Provincial General Hospital, 25-317 Kielce, Poland
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17
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Zhou J, Liu Y, Du X, Gui Y, He J, Xie F, Cai J. Recent Advances in Design and Application of Nanomaterials-Based Colorimetric Biosensors for Agri-food Safety Analysis. ACS OMEGA 2023; 8:46346-46361. [PMID: 38107919 PMCID: PMC10720297 DOI: 10.1021/acsomega.3c06409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/12/2023] [Accepted: 11/03/2023] [Indexed: 12/19/2023]
Abstract
A colorimetric sensor detects an analyte by utilizing the optical properties of the sensor unit, such as absorption or reflection, to generate a structural color that serves as the output signal to detect an analyte. Detecting the refractive index of an analyte by recording the color change of the sensor structure on its surface has several advantages, including simple operation, low cost, suitability for onsite analysis, and real-time detection. Colorimetric sensors have drawn much attention owing to their rapidity, simplicity, high sensitivity and selectivity. This Review discusses the use of colorimetric sensors in the food industry, including their applications for detecting food contaminants. The Review also provides insight into the scope of future research in this area.
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Affiliation(s)
- Jiaojiao Zhou
- National
R&D Center for Se-Rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-Rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yuantao Liu
- National
R&D Center for Se-Rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-Rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Xiaoping Du
- Ankang
R&D Center for Se-enriched Products, Key Laboratory of Se-enriched
Products Development and Quality Control, Ministry of Agriculture and Rural Affairs, Ankang Shaanxi 725000, China
| | - Yue Gui
- National
R&D Center for Se-Rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-Rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jiangling He
- National
R&D Center for Se-Rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-Rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Fang Xie
- National
R&D Center for Se-Rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-Rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jie Cai
- National
R&D Center for Se-Rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-Rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
- Key
Laboratory for Deep Processing of Major Grain and Oil, Ministry of
Education, Hubei Key Laboratory for Processing and Transformation
of Agricultural Products, Wuhan Polytechnic
University, Wuhan 430023, China
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18
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Saengsawang N, Ruang-Areerate P, Kaeothaisong N, Leelayoova S, Mungthin M, Juntanawiwat P, Hanyanunt P, Potisuwan P, Kesakomol P, Butsararattanagomen P, Wichaiwong P, Dungchai W, Ruang-Areerate T. Validation of quantitative loop-mediated isothermal amplification assay using a fluorescent distance-based paper device for detection of Escherichia coli in urine. Sci Rep 2023; 13:18781. [PMID: 37907677 PMCID: PMC10618465 DOI: 10.1038/s41598-023-46001-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) causes up to 90% of urinary tract infections (UTI) which is more prevalent among females than males. In urine, patients with symptomatic UTI usually have a high concentration of bacterial infection, ≥ 105 colony-forming units (CFU) per mL, in which the culture method is regularly the gold standard diagnosis. In this study, a simple and inexpensive distance-based paper device (dPAD) combined with the fluorescent closed tube LAMP assay was validated for simultaneously screening and semi-quantifying the infection level of E. coli in 440 urine samples of patients with UTI. The dPAD could measure the LAMP amplicons and semi-quantify the levels of E. coli infection in heavy (≥ 104 CFU/mL), light (≤ 103 CFU/mL) and no infection. The sensitivity and specificity had reliable performances, achieving as high as 100 and 92.7%, respectively. The one step LAMP assay could be performed within 3 h, which was 7.5 times faster than the culture method. To empower early UTI diagnosis and fast treatment, this inexpensive dPAD tool combined with the fluorescent closed tube LAMP assay is simple, reliably fast and practically portable for point-of-care settings, particularly in resource-limited areas, which can be set up in all levels of healthcare facilities.
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Affiliation(s)
- Natkrittaya Saengsawang
- Analytical Chemistry, Department of Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - Panthita Ruang-Areerate
- BIOTEC, National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Nuanlaong Kaeothaisong
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Saovanee Leelayoova
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Mathirut Mungthin
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Piraporn Juntanawiwat
- Division of Microbiology, Department of Clinical Pathology, Phramongkutklao Hospital, Bangkok, 10400, Thailand
| | - Patomroek Hanyanunt
- Division of Microbiology, Department of Clinical Pathology, Phramongkutklao Hospital, Bangkok, 10400, Thailand
| | - Patsanun Potisuwan
- Division of Microbiology, Department of Clinical Pathology, Phramongkutklao Hospital, Bangkok, 10400, Thailand
| | - Piyanate Kesakomol
- Department of Microbiology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Pornphan Butsararattanagomen
- Analytical Chemistry, Department of Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - Pattarawadee Wichaiwong
- Analytical Chemistry, Department of Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - Wijitar Dungchai
- Analytical Chemistry, Department of Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand.
| | - Toon Ruang-Areerate
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand.
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19
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Guo J, Liang Q, Zhang H, Tian M, Zhang H, Wei G, Zhang W. Exo-III Enzyme-Assisted Triple Cycle Signal Amplifications for Sensitive and Accurate Identification of Pathogenic Bacteria. Appl Biochem Biotechnol 2023; 195:6203-6211. [PMID: 36847983 DOI: 10.1007/s12010-023-04391-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2023] [Indexed: 03/01/2023]
Abstract
Early determination of infectious pathogens is vitally important to select appropriate antibiotics, and to manage nosocomial infection. Herein, we propose a target recognition triggered triple signal amplification-based approach for sensitive pathogenic bacteria detection. In the proposed approach, a double-strand DNA probe (capture probe) that is composed of an aptamer sequence and a primer sequence is designed for specific identification of target bacteria and initiation of following triple signal amplification. After recognition of target bacteria, primer sequence is released from capture probe to bind with the designed H1 probe, forming a blunt terminal in the H1 probe. Exonuclease-III (Exo-III enzyme) specifically recognizes the blunt terminal in H1 probe and degrades the sequence from 3' terminal, resulting a single-strand DNA to induce the following signal amplification. Eventually, the approach exhibits a low detection limit of 36 cfu/mL with a broad dynamic range. The high selectivity endows the method a promising prospective for clinical sample analysis.
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Affiliation(s)
- Jie Guo
- Department of Endoscopy Center, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Hubei Province, Huangshi, People's Republic of China
| | - Qun Liang
- Health Commission of Huangshi, Hubei Province, Huangshi, People's Republic of China
| | - Huifang Zhang
- Department of Gastroenterology, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Hubei Province, Huangshi, People's Republic of China
| | - Miao Tian
- Department of Endoscopy Center, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Hubei Province, Huangshi, People's Republic of China
| | - Huajun Zhang
- Department of Operation Management, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Hubei Province, Huangshi, People's Republic of China.
| | - Guo Wei
- Department of Pediatric, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei, People's Republic of China.
| | - Wantao Zhang
- Department of Operation Management, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Hubei Province, Huangshi, People's Republic of China.
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20
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Meinecke CD, Vos LD, Yilmaz N, Steenkamp ET, Wingfield MJ, Wingfield BD, Villari C. A LAMP Assay for Rapid Detection of the Pitch Canker Pathogen Fusarium circinatum. PLANT DISEASE 2023; 107:2916-2923. [PMID: 36867583 DOI: 10.1094/pdis-04-22-0972-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The pine pitch canker pathogen Fusarium circinatum is endemic in the southeastern United States and Central America and represents an invasive threat globally. This ecologically adaptable fungus readily infects all parts of its pine hosts, leading to widespread mortality of nursery seedlings and decline in the health and productivity of forest stands. Because trees infected by F. circinatum can remain asymptomatic for long periods of time, accurate and rapid tools are needed for real-time diagnostics and surveillance at ports, in nurseries, and in plantations. To meet this need and to limit the spread and impact of the pathogen, we developed a molecular test using loop-mediated isothermal amplification (LAMP), a technology that allows for the rapid detection of pathogen DNA on portable, field-capable devices. LAMP primers were designed and validated to amplify a gene region unique to F. circinatum. Using a globally representative collection of F. circinatum isolates and other closely related species, we have demonstrated that the assay can be used to identify F. circinatum across its genetic diversity and that it is sensitive to as few as 10 cells from purified DNA extracts. The assay can also be used with a simple, pipette-free DNA extraction method and is compatible with testing symptomatic pine tissues in the field. This assay has the potential to facilitate diagnostic and surveillance efforts both in the laboratory and in the field and, thus, to reduce the spread and impact of pitch canker worldwide.
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Affiliation(s)
- Colton D Meinecke
- D. B. Warnell School of Forestry of Natural Resources, University of Georgia, Athens, GA 30602, U.S.A
| | - Lieschen De Vos
- Forestry and Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Neriman Yilmaz
- Forestry and Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Emma T Steenkamp
- Forestry and Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Michael J Wingfield
- Forestry and Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Brenda D Wingfield
- Forestry and Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Caterina Villari
- D. B. Warnell School of Forestry of Natural Resources, University of Georgia, Athens, GA 30602, U.S.A
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21
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Okella H, Tonooka K, Okello E. A Systematic Review of the Recent Techniques Commonly Used in the Diagnosis of Mycoplasma bovis in Dairy Cattle. Pathogens 2023; 12:1178. [PMID: 37764986 PMCID: PMC10535753 DOI: 10.3390/pathogens12091178] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Early detection of Mycoplasmal mastitis is greatly hampered by late seroconversion, slow growth of Mycoplasma organisms, intermittent shedding, and the high cost of diagnostic tests. To improve future diagnostic development, examining the available techniques is necessary. Accordingly, the present study systematically reviewed M. bovis diagnostic studies published between January 2000 and April 2023 utilizing the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) protocol. The protocol registration was performed according to the Open Science Framework (osf.io/ug79h), and the electronic search was conducted in the World Catalog, Mendeley, ProQuest, ScienceDirect, Semantic Scholar, PubMed, Google Scholar, Prime Scholar, and PubMed Central databases using a Boolean operator and inclusion and exclusion criteria. Of the 1194 pieces of literature retrieved, 67 studies were included. Four broad categories of up to 16 diagnostic approaches were reported: microbial culture, serological, DNA-based, and mass spectrometry. Overall, DNA-based techniques were the most published (48.0%), with recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP) as the most promising user-friendly, equipment-free techniques. On the other hand, mass spectrometry was reported as the least utilized (2.9%) given the high equipment cost. Though costly and laboratory-allied, DNA-based techniques, particularly PCRs, were reported as the most rapid and specific approach.
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Affiliation(s)
- Hedmon Okella
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California Davis, Tulare, CA 93274, USA
| | - Karen Tonooka
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California Davis, Tulare, CA 93274, USA
| | - Emmanuel Okello
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California Davis, Tulare, CA 93274, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
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22
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Hanze M, Khaliliazar S, Réu P, Toldrà A, Hamedi MM. Toward Continuous Molecular Testing Using Gold-Coated Threads as Multi-Target Electrochemical Biosensors. BIOSENSORS 2023; 13:844. [PMID: 37754078 PMCID: PMC10526339 DOI: 10.3390/bios13090844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/14/2023] [Accepted: 08/23/2023] [Indexed: 09/28/2023]
Abstract
Analytical systems based on isothermal nucleic acid amplification tests (NAATs) paired with electroanalytical detection enable cost-effective, sensitive, and specific digital pathogen detection for various in situ applications such as point-of-care medical diagnostics, food safety monitoring, and environmental surveillance. Self-assembled monolayers (SAMs) on gold surfaces are reliable platforms for electroanalytical DNA biosensors. However, the lack of automation and scalability often limits traditional chip-based systems. To address these challenges, we propose a continuous thread-based device that enables multiple electrochemical readings on a functionalized working electrode Au thread with a single connection point. We demonstrate the possibility of rolling the thread on a spool, which enables easy manipulation in a roll-to-roll architecture for high-throughput applications. As a proof of concept, we have demonstrated the detection of recombinase polymerase amplification (RPA) isothermally amplified DNA from the two toxic microalgae species Ostreopsis cf. ovata and Ostreopsis cf. siamensis by performing a sandwich hybridization assay (SHA) with electrochemical readout.
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Affiliation(s)
| | | | | | - Anna Toldrà
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Teknikringen 56, 10044 Stockholm, Sweden
| | - Mahiar M. Hamedi
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Teknikringen 56, 10044 Stockholm, Sweden
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23
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Wu R, Meng B, Corredig M, Griffiths MW. Rapid Detection of Hepatitis A Virus in Foods Using a Bioluminescent Assay in Real-Time (BART) and Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Technology. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:144-157. [PMID: 36640204 PMCID: PMC9839959 DOI: 10.1007/s12560-022-09548-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 12/30/2022] [Indexed: 06/13/2023]
Abstract
Foodborne hepatitis A infections have been considered as a major threat for public health worldwide. Increased incidences of hepatitis A virus (HAV) infection has been associated with growing global trade of food products. Rapid and sensitive detection of HAV in foods is very essential for investigating the outbreaks. Real-time RT-PCR has been most widely used for the detection of HAV by far. However, the technology relies on fluorescence determination of the amplicon and requires sophisticated, high-cost instruments and trained personnel, limiting its use in low resource settings. In this study, a robust, affordable, and simple assay, reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in combination with a bioluminescence-based determination of amplification in real-time (BART), was developed for the detection of HAV in different food matrices, including green onion, strawberry, mussel, and milk. The efficiencies of a one-step RT-LAMP-BART and a two-step RT-LAMP-BART were investigated for the detection of HAV in different food matrices and was compared with that of real-time RT-PCR. The sensitivity of the RT-LAMP-BART assay was significantly affected by Mg2+ concentration (P < 0.05), in addition to primer quality. The optimal Mg2+ concentration was 2 mM for one-step RT-LAMP-BART and 4 mM for two-step RT-LAMP-BART. Compared with cartridge-purified primers, HPLC-purified primers could greatly improve the sensitivity of the RT-LAMP-BART assay (P < 0.05). For detecting HAV in different food matrices, the performance of two-step RT-LAMP-BART was comparable with that of real-time RT-PCR and was better than that of one-step RT-LAMP-BART. The detection limit of the two-step RT-LAMP-BART for HAV in green onion, strawberry, mussel, and milk was 8.3 × 100 PFU/15 g, 8.3 × 101 PFU/50 g, 8.3 × 100 PFU/5 g, and 8.3 × 100 PFU/40 mL, respectively. The developed RT-LAMP-BART was an effective, simple, sensitive, and robust method for foodborne HAV detection.
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Affiliation(s)
- Ruiqin Wu
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
- Canadian Research Institute for Food Safety, 43 McGilvray Street, Guelph, ON, N1G 2W1, Canada.
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Milena Corredig
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Mansel W Griffiths
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
- Canadian Research Institute for Food Safety, 43 McGilvray Street, Guelph, ON, N1G 2W1, Canada
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Chen X, Yuan W, Yang X, Shi Y, Zeng X, Huang J, Wang Y, Li S. Ultrasensitive and Specific Identification of Monkeypox Virus Congo Basin and West African Strains Using a CRISPR/Cas12b-Based Platform. Microbiol Spectr 2023; 11:e0403522. [PMID: 36821485 PMCID: PMC10100855 DOI: 10.1128/spectrum.04035-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/29/2023] [Indexed: 02/24/2023] Open
Abstract
Human monkeypox (MPX) is a severe and reemerging infectious disease caused by monkeypox virus (MPXV) and forms two distinct lineages, including Congo Basin and West African clades. Due to the absence of specific vaccines and antiviral drugs, developing a point-of-care (POC) testing system to identify MPXV is critical for preventing and controlling MPX transmission. Here, a CRISPR/Cas12b diagnostic platform was integrated with loop-mediated isothermal amplification (LAMP) to devise a novel CRISPR-MPXV approach for ultrasensitive, highly specific, rapid, and simple detection of MPXV Congo Basin and West African strains, and the detection results were interpreted with real-time fluorescence and a gold nanoparticle-based lateral flow biosensor (AuNP-LFB). The optimal detection process, including genomic DNA extraction (15 min), LAMP preamplification (35 min at 66°C), CRISPR/Cas12b-based detection (5 min at 45°C), and AuNP-LFB readout (~2 min), can be completed within 60 min without expensive instruments. Our assay has a limit of detection of 10 copies per test and produces no cross-reaction with any other types of pathogens. Hence, our CRISPR-MPXV assay exhibited considerable potential for POC testing for identifying and distinguishing MPXV Congo Basin and West African strains, especially in regions with resource shortages. IMPORTANCE Monkeypox (MPX), a reemerging zoonotic disease caused by monkeypox virus (MPXV), causes a smallpox-like disease in humans. Early diagnosis is critical to prevent MPX epidemics. Here, CRISPR/Cas12b was integrated with LAMP amplification to devise a novel CRISPR-MPXV approach to achieve highly specific, ultrasensitive, rapid, and visual identification of MPXV Congo Basin and West African strains.
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Affiliation(s)
- Xu Chen
- The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, People’s Republic of China
- Clinical Medical Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, People’s Republic of China
| | - Wei Yuan
- Department of Quality Control, Guizhou Provincial Center for Clinical Laboratory, Guiyang, Guizhou, People’s Republic of China
| | - Xinggui Yang
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, Guizhou, People’s Republic of China
| | - Yuanfang Shi
- The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, People’s Republic of China
| | - Xiaoyan Zeng
- The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, People’s Republic of China
- Clinical Medical Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, People’s Republic of China
| | - Junfei Huang
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, Guizhou, People’s Republic of China
| | - Yi Wang
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, People’s Republic of China
| | - Shijun Li
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, Guizhou, People’s Republic of China
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25
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Wang M, Tang Z, Liao M, Cao H, Zhao N. Loop-mediated isothermal amplification for detecting the Ile-2041-Asn mutation in fenoxaprop-P-ethyl-resistant Alopecurus aequalis. PEST MANAGEMENT SCIENCE 2023; 79:711-718. [PMID: 36258292 DOI: 10.1002/ps.7239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/26/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Shortawn foxtail (Alopecurus aequalis Sobol.), a competitive grass weed severely infesting overwintering crops worldwide, has evolved resistance to the highly efficient acetyl-CoA carboxylase (ACCase)-inhibiting herbicide fenoxaprop-P-ethyl. The Ile-to-Asn substitution at codon position 2041 of ACCase is a dominant resistance mutation that has been associated with fenoxaprop-P-ethyl resistance in A. aequalis. However, its detection based on conventional methods such as polymerase chain reaction (PCR) and gene sequencing is rather labor- and time-consuming. RESULTS In order to facilitate its detection in field populations of A. aequalis, a simple and efficient method with high sensitivity to the Ile-2041-Asn mutation was developed based on loop-mediated isothermal amplification (LAMP). A set of four primers was designed to target a 244-bp fragment of ACCase comprising codon position 2041. Using the special primers and genomic DNA of A. aequalis, the concentrations of reaction components, temperature and time each were optimized. The LAMP reaction for the detection of the Ile-2041-Asn mutation was processed at 65 °C for 45 min followed by 80 °C for 10 min to stop the reaction. The LAMP method developed was 1000-fold more sensitive than the conventional PCR method, and the detection was also practicable when using crude DNA of A. aequalis as a template. CONCLUSION The low cost, simplicity and high sensitivity of the developed LAMP assay make the detection of the Ile-2041-Asn mutation easier and quicker, which may contribute to the monitoring and management of resistance development to fenoxaprop-P-ethyl in A. aequalis. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Mali Wang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Zhi Tang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Min Liao
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Haiqun Cao
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Ning Zhao
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
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26
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Zamzami M, Alamoudi S, Ahmad A, Choudhry H, Khan MI, Hosawi S, Rabbani G, Shalaan ES, Arkook B. Direct Identification of Label-Free Gram-Negative Bacteria with Bioreceptor-Free Concentric Interdigitated Electrodes. BIOSENSORS 2023; 13:179. [PMID: 36831945 PMCID: PMC9953431 DOI: 10.3390/bios13020179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/05/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
This investigation demonstrates an electrochemical method for directly identifying unlabeled Gram-negative bacteria without other additives or labeling agents. After incubation, the bacterial cell surface is linked to the interdigitated electrode through electroadsorption. Next, these cells are exposed to a potential difference between the two electrodes. The design geometry of an electrode has a significant effect on the electrochemical detection of Gram-negative bacteria. Therefore, electrode design geometry is a crucial factor that needs to be considered when designing electrodes for electrochemical sensing. They provide the area for the reaction and are responsible for transferring electrons from one electrode to another. This work aims to study the available design in the commercial market to determine the most suitable electrode geometry with a high detection sensitivity that can be used to identify and quantify bacterial cells in normal saline solutions. To work on detecting bacterial cells without the biorecognition element, we have to consider the microelectrode's design, which makes it very susceptible to bacteria size. The concentration-dilution technique measures the effect of the concentration on label-free Gram-negative bacteria in a normal saline solution without needing bio-recognized elements for a fast screening evaluation. This method's limit of detection (LOD) cannot measure concentrations less than 102 CFU/mL and cannot distinguish between live and dead cells. Nevertheless, this approach exhibited excellent detection performance under optimal experimental conditions and took only a few hours.
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Affiliation(s)
- Mazin Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Samer Alamoudi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Abrar Ahmad
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mohammad Imran Khan
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Salman Hosawi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Gulam Rabbani
- Department of Medical Biotechnology, Yeungnam University, 280 Daehak-ro, Gyeongsan 38541, Gyeongbuk, Republic of Korea
| | - El-Sayed Shalaan
- Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Bassim Arkook
- Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Physics and Astronomy, University of California, Riverside, CA 92521, USA
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27
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Identification of Fish Species and Targeted Genetic Modifications Based on DNA Analysis: State of the Art. Foods 2023; 12:foods12010228. [PMID: 36613444 PMCID: PMC9818732 DOI: 10.3390/foods12010228] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023] Open
Abstract
Food adulteration is one of the most serious problems regarding food safety and quality worldwide. Besides misleading consumers, it poses a considerable health risk associated with the potential non-labeled allergen content. Fish and fish products are one of the most expensive and widely traded commodities, which predisposes them to being adulterated. Among all fraud types, replacing high-quality or rare fish with a less valuable species predominates. Because fish differ in their allergen content, specifically the main one, parvalbumin, their replacement can endanger consumers. This underlines the need for reliable, robust control systems for fish species identification. Various methods may be used for the aforementioned purpose. DNA-based methods are favored due to the characteristics of the target molecule, DNA, which is heat resistant, and the fact that through its sequencing, several other traits, including the recognition of genetic modifications, can be determined. Thus, they are considered to be powerful tools for identifying cases of food fraud. In this review, the major DNA-based methods applicable for fish meat and product authentication and their commercial applications are discussed, the possibilities of detecting genetic modifications in fish are evaluated, and future trends are highlighted, emphasizing the need for comprehensive and regularly updated online database resources.
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28
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Chen N, Li G, Si Y, Ye Y, Zhang T, Chi D, Zhang W, Pan L, Qu G, Lu Y, Zong M, Sui G, Fan L. Development and evaluation of a centrifugal disk system for the rapid detection of multiple pathogens and their antibiotic resistance genes in urinary tract infection. Front Microbiol 2023; 14:1157403. [PMID: 37200917 PMCID: PMC10187633 DOI: 10.3389/fmicb.2023.1157403] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/08/2023] [Indexed: 05/20/2023] Open
Abstract
Background Urinary tract infections (UTIs) are some of the most common bacterial infections in the world. Nevertheless, as uncomplicated UTIs are treated empirically without culturing the urine, adequate knowledge of the resistance pattern of uropathogens is essential. Conventional urine culture and identification take at least 2 days. Here, we developed a platform based on LAMP and centrifugal disk system (LCD) to simultaneously detect the main pathogens and antibiotic resistant genes (ARGs) of urgent concern multidrug-resistant among UTIs. Methods We designed specific primers to detect the target genes above and evaluated their sensitivity and specificity. We also assessed the result of our preload LCD platform on 645 urine specimens with a conventional culturing method and Sanger sequencing. Results The results obtained with the 645 clinical samples indicated that the platform has high specificity (0.988-1) and sensitivity (0.904-1) for the studied pathogens and ARGs. Moreover, the kappa value of all pathogens was more than 0.75, revealing an excellent agreement between the LCD and culture method. Compared to phenotypic tests, the LCD platform is a practical and fast detection approach for methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococci, carbapenem-resistant Enterobacteriaceae, carbapenem-resistant Acinetobacter, carbapenem-resistant Pseudomonas aeruginosa (kappa value of all >0.75), and non-extended-spectrum β-lactamase producers. Conclusion We developed a detection platform that has high accuracy and that meets the need for rapid diagnosis, which can be completed within 1.5 h from specimen collection. It may be a powerful tool for evidence-based UTIs diagnosis, which has essential support for the rational use of antibiotics. More high-quality clinical studies are required to prove the effectiveness of our platform.
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Affiliation(s)
- Nianzhen Chen
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Gen Li
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yuying Si
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yangqin Ye
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tong Zhang
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, China
| | - Dali Chi
- Fosun Diagnostics Co., Ltd., Shanghai, China
| | - Wenyan Zhang
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lifeng Pan
- Department of Microbiology, Pudong New Area Center for Disease Control and Prevention, Shanghai, China
| | - Guoying Qu
- Weifang Community Health Service Center, Shanghai, China
| | - Yun Lu
- Huamu Community Health Service Center, Shanghai, China
| | - Ming Zong
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Ming Zong,
| | - Guodong Sui
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, China
- Guodong Sui,
| | - Lieying Fan
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Lieying Fan,
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Cabrales-Arellano P, Park E, Minor M, Delgado E, Valles-Rosales D, Taboada H, Espiritu J, Su J, Park YH. Rapid identification of Staphylococcus aureus based on a fluorescence imaging/detection platform that combines loop mediated isothermal amplification assay and the smartphone-based system. Sci Rep 2022; 12:20655. [PMID: 36450878 PMCID: PMC9712598 DOI: 10.1038/s41598-022-25190-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
Food associated diseases pose significant public health threat in the United States. Health risks associated with food-borne pathogens drive the need for constant monitoring of food products. An efficient method that can diagnose food-borne pathogens rapidly will be invaluable and in high demand. In this study, we showed the feasibility of a novel rapid detection platform based on fluorescence imaging/detection that combines a user-friendly, portable loop mediated isothermal amplification (LAMP) reaction device and a smartphone-based detection system. The proposed platform was used to detect Staphylococcus aureus which is one of the most important food-borne pathogen especially dairy products. The complete protocol is quicker; the reaction is performed under isothermal conditions and completed in 1 h or less. Experimental results show that LAMP assays were ten-fold more sensitive than PCR-based detection. The proposed smartphone detection system was able to detect and quantify LAMP assay samples containing three different concentrations of S. aureus from 109 CFU/mL down to 103 CFU/mL. The present proof-of-concept study demonstrated that this platform offers a portable, easy to use method for measuring target pathogens with LAMP amplification.
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Affiliation(s)
- Patricia Cabrales-Arellano
- grid.24805.3b0000 0001 0687 2182Family and Consumer Science Department, New Mexico State University, Las Cruces, NM 88003 USA
| | - Edward Park
- grid.24805.3b0000 0001 0687 2182Biology Department, New Mexico State University, Las Cruces, NM 88003 USA
| | - Martha Minor
- grid.24805.3b0000 0001 0687 2182Family and Consumer Science Department, New Mexico State University, Las Cruces, NM 88003 USA
| | - Efren Delgado
- grid.24805.3b0000 0001 0687 2182Family and Consumer Science Department, New Mexico State University, Las Cruces, NM 88003 USA
| | - Delia Valles-Rosales
- grid.264760.10000 0004 0387 0036Industrial Management and Technology Department, Texas A&M University Kingsville, Kingsville, TX 78363 USA
| | - Heidi Taboada
- grid.264760.10000 0004 0387 0036Mechanical and Industrial Engineering Department, Texas A&M University Kingsville, Kingsville, TX 78363 USA
| | - José Espiritu
- grid.264760.10000 0004 0387 0036Mechanical and Industrial Engineering Department, Texas A&M University Kingsville, Kingsville, TX 78363 USA
| | - Jianzhong Su
- grid.267315.40000 0001 2181 9515Department of Mathematics, University of Texas at Arlington, Arlington, TX 76019 USA
| | - Young Ho Park
- grid.24805.3b0000 0001 0687 2182Mechanical Engineering Department, New Mexico State University, Las Cruces, NM 88003 USA
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30
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Das D, Lin CW, Chuang HS. LAMP-Based Point-of-Care Biosensors for Rapid Pathogen Detection. BIOSENSORS 2022; 12:bios12121068. [PMID: 36551035 PMCID: PMC9775414 DOI: 10.3390/bios12121068] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 06/01/2023]
Abstract
Seeking optimized infectious pathogen detection tools is of primary importance to lessen the spread of infections, allowing prompt medical attention for the infected. Among nucleic-acid-based sensing techniques, loop-mediated isothermal amplification is a promising method, as it provides rapid, sensitive, and specific detection of microbial and viral pathogens and has enormous potential to transform current point-of-care molecular diagnostics. In this review, the advances in LAMP-based point-of-care diagnostics assays developed during the past few years for rapid and sensitive detection of infectious pathogens are outlined. The numerous detection methods of LAMP-based biosensors are discussed in an end-point and real-time manner with ideal examples. We also summarize the trends in LAMP-on-a-chip modalities, such as classical microfluidic, paper-based, and digital LAMP, with their merits and limitations. Finally, we provide our opinion on the future improvement of on-chip LAMP methods. This review serves as an overview of recent breakthroughs in the LAMP approach and their potential for use in the diagnosis of existing and emerging diseases.
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Affiliation(s)
- Dhrubajyoti Das
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Cheng-Wen Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 404, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Wufeng, Taichung 413, Taiwan
| | - Han-Sheng Chuang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan
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31
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Atçeken N, Yigci D, Ozdalgic B, Tasoglu S. CRISPR-Cas-Integrated LAMP. BIOSENSORS 2022; 12:1035. [PMID: 36421156 PMCID: PMC9688180 DOI: 10.3390/bios12111035] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/10/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Pathogen-specific point-of-care (PoC) diagnostic tests have become an important need in the fight against infectious diseases and epidemics in recent years. PoC diagnostic tests are designed with the following parameters in mind: rapidity, accuracy, sensitivity, specificity, and ease of use. Molecular techniques are the gold standard for pathogen detection due to their accuracy and specificity. There are various limitations in adapting molecular diagnostic methods to PoC diagnostic tests. Efforts to overcome limitations are focused on the development of integrated molecular diagnostics by utilizing the latest technologies available to create the most successful PoC diagnostic platforms. With this point of view, a new generation technology was developed by combining loop-mediated isothermal amplification (LAMP) technology with clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas) technology. This integrated approach benefits from the properties of LAMP technology, namely its high efficiency, short turnaround time, and the lack of need for a complex device. It also makes use of the programmable function of CRISPR-Cas technology and the collateral cleavage activity of certain Cas proteins that allow for convenient reporter detection. Thus, this combined technology enables the development of PoC diagnostic tests with high sensitivity, specificity, and ease of use without the need for complicated devices. In this review, we discuss the advantages and limitations of the CRISPR/Cas combined LAMP technology. We review current limitations to convert CRISPR combined LAMP into pathogen-specific PoC platforms. Furthermore, we point out the need to design more useful PoC platforms using microfabrication technologies by developing strategies that overcome the limitations of this new technology, reduce its complexity, and reduce the risk of contamination.
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Affiliation(s)
- Nazente Atçeken
- Koç University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
| | - Defne Yigci
- School of Medicine, Koç University, Istanbul 34450, Turkey
| | - Berin Ozdalgic
- Koç University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
- Department of Mechanical Engineering, Engineering Faculty, Koç University, Istanbul 34450, Turkey
- School of Medical Services & Techniques, Dogus University, Istanbul 34775, Turkey
| | - Savas Tasoglu
- Koç University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
- Department of Mechanical Engineering, Engineering Faculty, Koç University, Istanbul 34450, Turkey
- Boğaziçi Institute of Biomedical Engineering, Boğaziçi University, Istanbul 34684, Turkey
- Koç University Arçelik Research Center for Creative Industries (KUAR), Koç University, Istanbul 34450, Turkey
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32
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Neculai-Valeanu AS, Ariton AM. Udder Health Monitoring for Prevention of Bovine Mastitis and Improvement of Milk Quality. Bioengineering (Basel) 2022; 9:608. [PMID: 36354519 PMCID: PMC9687184 DOI: 10.3390/bioengineering9110608] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 08/05/2023] Open
Abstract
To maximize milk production, efficiency, and profits, modern dairy cows are genetically selected and bred to produce more and more milk and are fed copious quantities of high-energy feed to support ever-increasing milk volumes. As demands for increased milk yield and milking efficiency continue to rise to provide for the growing world population, more significant stress is placed on the dairy cow's productive capacity. In this climate, which is becoming increasingly hotter, millions of people depend on the capacity of cattle to respond to new environments and to cope with temperature shocks as well as additional stress factors such as solar radiation, animal crowding, insect pests, and poor ventilation, which are often associated with an increased risk of mastitis, resulting in lower milk quality and reduced production. This article reviews the impact of heat stress on milk production and quality and emphasizes the importance of udder health monitoring, with a focus on the use of emergent methods for monitoring udder health, such as infrared thermography, biosensors, and lab-on-chip devices, which may promote animal health and welfare, as well as the quality and safety of dairy products, without hindering the technological flow, while providing significant benefits to farmers, manufacturers, and consumers.
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Mastitis: What It Is, Current Diagnostics, and the Potential of Metabolomics to Identify New Predictive Biomarkers. DAIRY 2022. [DOI: 10.3390/dairy3040050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
Periparturient diseases continue to be the greatest challenge to both farmers and dairy cows. They are associated with a decrease in productivity, lower profitability, and a negative impact on cows’ health as well as public health. This review article discusses the pathophysiology and diagnostic opportunities of mastitis, the most common disease of dairy cows. To better understand the disease, we dive deep into the causative agents, traditional paradigms, and the use of new technologies for diagnosis, treatment, and prevention of mastitis. This paper takes a systems biology approach by highlighting the relationship of mastitis with other diseases and introduces the use of omics sciences, specifically metabolomics and its analytical techniques. Concluding, this review is backed up by multiple studies that show how earlier identification of mastitis through predictive biomarkers can benefit the dairy industry and improve the overall animal health.
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Jiang W, Hu D, Xu Y, Chen Y, Zhu X, Han Z, Ye X, Li X. Loop-mediated isothermal amplification-microfluidic chip for the detection of Trichophyton infection. Front Microbiol 2022; 13:1031388. [PMID: 36312927 PMCID: PMC9606667 DOI: 10.3389/fmicb.2022.1031388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Trichophyton is the most pathogenic type of fungal skin infection. It often invades and grows in a keratin-rich matrix, and lesions include human skin, hair, and fingernails (toenails). We designed LAMP primers for Trichophyton and developed a LAMP-Microfluidic chip detection system for Trichophyton. This system detects six common species of Trichophyton in the genus Trichophyton, including Trichophyton rubrum, Trichophyton mentagrophyte, Trichophyton violaceum, Trichophyton tonsurans, Trichophyton verrucosum, and Trichophyton schoenleinii. The specificity reached 100%, and the sensitivity could reach about 1 × 102 copies/μl. The entire detection process can be completed within 60 min and does not cross-react with other dermatophytes. The established LAMP-Microfluidic chip detection system has the advantages of simple operation, high specificity, and high sensitivity, and has the potential for clinical application.
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Affiliation(s)
- Weiwei Jiang
- Department of Dermatology, 72nd Group Army Hospital of PLA, Huzhou, Zhejiang, China
| | - Dongying Hu
- Department of Dermatology, 72nd Group Army Hospital of PLA, Huzhou, Zhejiang, China
| | - Yanyan Xu
- Affiliated Hospital of Hebei University of Engineering, Handan, Hebei, China
| | - Yang Chen
- Department of Dermatology, 72nd Group Army Hospital of PLA, Huzhou, Zhejiang, China
| | - Xiaoyang Zhu
- Department of Dermatology, 72nd Group Army Hospital of PLA, Huzhou, Zhejiang, China
| | - Zhao Han
- Affiliated Hospital of Hebei University of Engineering, Handan, Hebei, China
- *Correspondence: Zhao Han,
| | - Xin Ye
- Department of Laboratory Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Xin Ye,
| | - Xiaojing Li
- Affiliated Hospital of Hebei University of Engineering, Handan, Hebei, China
- Xiaojing Li,
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Yalley AK, Ahiatrogah S, Kafintu-Kwashie AA, Amegatcher G, Prah D, Botwe AK, Adusei-Poku MA, Obodai E, Nii-Trebi NI. A Systematic Review on Suitability of Molecular Techniques for Diagnosis and Research into Infectious Diseases of Concern in Resource-Limited Settings. Curr Issues Mol Biol 2022; 44:4367-4385. [PMID: 36286015 PMCID: PMC9601131 DOI: 10.3390/cimb44100300] [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: 08/23/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Infectious diseases significantly impact the health status of developing countries. Historically, infectious diseases of the tropics especially have received insufficient attention in worldwide public health initiatives, resulting in poor preventive and treatment options. Many molecular tests for human infections have been established since the 1980s, when polymerase chain reaction (PCR) testing was introduced. In spite of the substantial innovative advancements in PCR technology, which currently has found wide application in most viral pathogens of global concern, the development and application of molecular diagnostics, particularly in resource-limited settings, poses potential constraints. This review accessed data from sources including PubMed, Google Scholar, the Web of Knowledge, as well as reports from the World Health Organization’s Annual Meeting on infectious diseases and examined these for current molecular approaches used to identify, monitor, or investigate some neglected tropical infectious diseases. This review noted some growth efforts in the development of molecular techniques for diagnosis of pathogens that appear to be common in resource limited settings and identified gaps in the availability and applicability of most of these molecular diagnostics, which need to be addressed if the One Health goal is to be achieved.
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Affiliation(s)
- Akua K. Yalley
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box KB 143, Ghana
| | - Selasie Ahiatrogah
- Department of Obstetrics and Gynaecology, College of Medicine, Pan African University of Life and Earth Sciences Institute, University of Ibadan, Ibadan P.O. Box 22133, Nigeria
| | - Anna A. Kafintu-Kwashie
- Department of Medical Microbiology, University of Ghana Medical School, Accra GA-221-1570, Ghana
| | - Gloria Amegatcher
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box KB 143, Ghana
| | - Diana Prah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Akua K. Botwe
- Molecular Biology Unit, Kintampo Health Research Centre, Ghana Health Service, Kintampo P.O. Box 200, Ghana
| | - Mildred A. Adusei-Poku
- Department of Medical Microbiology, University of Ghana Medical School, Accra GA-221-1570, Ghana
| | - Evangeline Obodai
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Nicholas I. Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box KB 143, Ghana
- Correspondence: ; Tel.: +233-54-827-6424
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Gui Z, Cai H, Wu L, Miao Q, Yu JF, Cai T, Mao R. Visual closed dumbbell-mediated isothermal amplification (CDA) for on-site detection of Rickettsia raoultii. PLoS Negl Trop Dis 2022; 16:e0010747. [PMID: 36084136 PMCID: PMC9491570 DOI: 10.1371/journal.pntd.0010747] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 09/21/2022] [Accepted: 08/18/2022] [Indexed: 11/28/2022] Open
Abstract
Spotted fever group (SFG) rickettsioses are important zoonoses, threatening human health seriously and gradually attracting more attention in the world. SFG rickettsiae are classified as neglected pathogens. If these pathogens are detected at all, they are usually recognized very late in the infection through indirect detection of specific antibodies. Previous studies have shown that Rickettsia raoultii (R. raoultii), a member of the SFG rickettsiae, occurs with increasing incidence in remote countries. Therefore, a rapid detection method for R. raoultii is in urgently need. In this study, a R. raoultii diagnosis method by closed dumbbell-mediated isothermal amplification (R-CDA) assay targeting a conserved sequence of the outer membrane protein A (OmpA) gene with high sensitivity and specificity was developed. This assay offered a rapid and simple method for on-site detection of R. raoultii. Firstly, four pairs of R-CDA primers were designed and the optimum primer set was selected to amplify target gene specifically and effectively. Then, a pair of outer primer was designed to accelerate the reaction based on the inner primers to establish the RO-CDA reaction. In addition, the results of real-time amplification curves, melting curves and end-point colorimetric judgements showed that the established visual RO-CDA reaction could accurately detect R. raoultii without cross-reaction with other closely related pathogens. Furthermore, the detection limit of visual RO-CDA assay was 10 copies/μL, which was feasible for on-site detection with merits of easy-operation, rapidity, high sensitivity, and specificity. In conclusion, the developed RO-CDA detection method could be helpful for pathogen screening and epidemic prevention at the point of care. Spotted fever group (SFG) rickettsioses are important neglected zoonoses throughout the world, with expanding known distribution, among which R. raoultii is an emerging member. As the clinical symptoms of R. raoultii is similar to other diseases, the accurate diagnosis of the pathogen based on the detection of genome plays a vital role in effective treatment and control at low infection levels. Due to the lack of on-site detection technology of Rickettsia raoultii in remote areas, the pathogen can only be treated in the late infection stage with specific clinical symptoms. Closed dumbbell-mediated isothermal amplification (CDA) is a method that rapidly amplifies nucleic acids under isothermal condition, which can help to resolve the problem of point of care detection for R. raoultii. The established R. raoultii detection approach based on CDA was feasible for on-site detection with merits of easy-operation, rapidity, high sensitivity, and specificity. At last, compared with PCR and LAMP, CDA method is simpler and more efficient to detect R. raoultii, which helps to improve the efficiency of detection and strengthen the prevention and control of this neglected but widely distributed disease.
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Affiliation(s)
- Zheng Gui
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Hao Cai
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Lin Wu
- Graduate School, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Qing Miao
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Jing feng Yu
- Department of Parasitology, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
- * E-mail: (JY); (TC); (RM)
| | - Ting Cai
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- * E-mail: (JY); (TC); (RM)
| | - Rui Mao
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- * E-mail: (JY); (TC); (RM)
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Wu H, Cao X, Meng Y, Richards D, Wu J, Ye Z, deMello AJ. DropCRISPR: A LAMP-Cas12a based digital method for ultrasensitive detection of nucleic acid. Biosens Bioelectron 2022; 211:114377. [DOI: 10.1016/j.bios.2022.114377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 12/26/2022]
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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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Probe-based Loop-Mediated Isothermal Amplification Assay for Multi-target Quantitative Detection of Three Foodborne Pathogens in Seafood. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-022-02381-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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40
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Zhi S, Shen J, Li X, Jiang Y, Xue J, Fang T, Xu J, Wang X, Cao Y, Yang D, Yao Z, Yu D. Development of Recombinase-Aided Amplification (RAA)-Exo-Probe and RAA-CRISPR/Cas12a Assays for Rapid Detection of Campylobacter jejuni in Food Samples. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9557-9566. [PMID: 35857318 DOI: 10.1021/acs.jafc.2c02581] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Campylobacter jejuni is the major cause of campylobacteriosis, one of the most common foodborne illnesses worldwide. Here, we report the development of RAA-exo-probe and RAA-CRIPSR/Cas12a assays for the detection of C. jejuni in food samples. The two assays were found to be highly specific to C. jejuni and highly sensitive, as they were one log more sensitive compared to the traditional culture method, with detection thresholds of 9 and 5 copies per reaction, respectively. These assays successfully detected C. jejuni in spiked chicken samples and natural meat samples (chicken, beef, mutton, etc.) and were overall less dependent on expensive equipment, only requiring a fluorescent reader. Their ease of use compared to other nucleic acid amplification-based methods indicates that these assays could be adapted for the rapid, routine surveillance of C. jejuni contamination in food samples, particularly for work done in the field or poorly equipped labs.
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Affiliation(s)
- Shuai Zhi
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315211, China
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Jinling Shen
- Technology Center for Animal Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai 200135, China
| | - Xingang Li
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Yuan Jiang
- Nanjing Customs District People's Republic of China, Nanjing 210001, China
| | - Junxin Xue
- Technology Center for Animal Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai 200135, China
| | - Taisong Fang
- Technology Center for Animal Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai 200135, China
| | - Jin Xu
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Xuan Wang
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Yuhao Cao
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Danting Yang
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo 315211, China
| | - Daniel Yu
- School of Public Health, University of Alberta, Edmonton, Alberta T6G 1C9, Canada
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Cardona-Trujillo MC, Ocampo-Cárdenas T, Tabares-Villa FA, Zuluaga-Vélez A, Sepúlveda-Arias JC. Recent molecular techniques for the diagnosis of Zika and Chikungunya infections: A systematic review. Heliyon 2022; 8:e10225. [PMID: 36033321 PMCID: PMC9404361 DOI: 10.1016/j.heliyon.2022.e10225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/05/2022] [Accepted: 08/03/2022] [Indexed: 11/26/2022] Open
Abstract
Zika virus (ZIKV) and Chikungunya virus (CHIKV) are arboviruses that cause important viral diseases affecting the world population. Both viruses can produce remarkably similar clinical manifestations, co-circulate in a geographic region, and coinfections have been documented, thus making clinical diagnosis challenging. Therefore, it is urgent to have better molecular techniques that allow a differential, sensitive and rapid diagnosis from body fluid samples. This systematic review explores evidence in the literature regarding the advances in the molecular diagnosis of Zika and Chikungunya in humans, published from 2010 to March 2021. Four databases were consulted (Scopus, PubMed, Web of Science, and Embase) and a total of 31 studies were included according to the selection criteria. Our analysis highlights the need for standardization in the report and interpretation of new promising diagnostic methods. It also examines the benefits of new alternatives for the molecular diagnosis of these arboviruses, in contrast to established methods.
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Affiliation(s)
- María C Cardona-Trujillo
- Grupo Infección e Inmunidad, Facultad de Ciencias de la Salud, Universidad Tecnológica de Pereira, Pereira, Colombia
| | - Tatiana Ocampo-Cárdenas
- Grupo Infección e Inmunidad, Facultad de Ciencias de la Salud, Universidad Tecnológica de Pereira, Pereira, Colombia
| | - Fredy A Tabares-Villa
- Grupo Infección e Inmunidad, Facultad de Ciencias de la Salud, Universidad Tecnológica de Pereira, Pereira, Colombia
| | - Augusto Zuluaga-Vélez
- Grupo Infección e Inmunidad, Facultad de Ciencias de la Salud, Universidad Tecnológica de Pereira, Pereira, Colombia
| | - Juan C Sepúlveda-Arias
- Grupo Infección e Inmunidad, Facultad de Ciencias de la Salud, Universidad Tecnológica de Pereira, Pereira, Colombia
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42
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Nnachi RC, Sui N, Ke B, Luo Z, Bhalla N, He D, Yang Z. Biosensors for rapid detection of bacterial pathogens in water, food and environment. ENVIRONMENT INTERNATIONAL 2022; 166:107357. [PMID: 35777116 DOI: 10.1016/j.envint.2022.107357] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/10/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Conventional techniques (e.g., culture-based method) for bacterial detection typically require a central laboratory and well-trained technicians, which may take several hours or days. However, recent developments within various disciplines of science and engineering have led to a major paradigm shift in how microorganisms can be detected. The analytical sensors which are widely used for medical applications in the literature are being extended for rapid and on-site monitoring of the bacterial pathogens in food, water and the environment. Especially, within the low-resource settings such as low and middle-income countries, due to the advantages of low cost, rapidness and potential for field-testing, their use is indispensable for sustainable development of the regions. Within this context, this paper discusses analytical methods and biosensors which can be used to ensure food safety, water quality and environmental monitoring. In brief, most of our discussion is focused on various rapid sensors including biosensors and microfluidic chips. The analytical performances such as the sensitivity, specificity and usability of these sensors, as well as a brief comparison with the conventional techniques for bacteria detection, form the core part of the discussion. Furthermore, we provide a holistic viewpoint on how future research should focus on exploring the synergy of different sensing technologies by developing an integrated multiplexed, sensitive and accurate sensors that will enable rapid detection for food safety, water and environmental monitoring.
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Affiliation(s)
- Raphael Chukwuka Nnachi
- School of Water, Energy and Environment, Cranfield University, Milton Keynes MK43, 0AL, United Kingdom
| | - Ning Sui
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Bowen Ke
- Laboratory of Anesthesiology & Critical Care Medicine, Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan 61004, PR China
| | - Zhenhua Luo
- School of Water, Energy and Environment, Cranfield University, Milton Keynes MK43, 0AL, United Kingdom
| | - Nikhil Bhalla
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, Shore Road, BT37 0QB Jordanstown, Northern Ireland, United Kingdom; Healthcare Technology Hub, Ulster University, Jordanstown Shore Road, BT37 0QB, Northern Ireland, United Kingdom
| | - Daping He
- School of Science, Wuhan University of Technology, Wuhan 430070, China
| | - Zhugen Yang
- School of Water, Energy and Environment, Cranfield University, Milton Keynes MK43, 0AL, United Kingdom.
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43
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Chen X, Zhou Q, Tan Y, Wang R, Wu X, Liu J, Liu R, Wang S, Dong S. Nanoparticle-Based Lateral Flow Biosensor Integrated With Loop-Mediated Isothermal Amplification for Rapid and Visual Identification of Chlamydia trachomatis for Point-of-Care Use. Front Microbiol 2022; 13:914620. [PMID: 35903464 PMCID: PMC9318599 DOI: 10.3389/fmicb.2022.914620] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
Chlamydial infection, caused by Chlamydia trachomatis, is the most common bacterial sexually transmitted infection and remains a major public health problem worldwide, particularly in underdeveloped regions. Developing a rapid and sensitive point-of-care (POC) testing for accurate screening of C. trachomatis infection is critical for earlier treatment to prevent transmission. In this study, a novel diagnostic assay, loop-mediated isothermal amplification integrated with gold nanoparticle-based lateral flow biosensor (LAMP-LFB), was devised and applied for diagnosis of C. trachomatis in clinical samples. A set of LAMP primers based on the ompA gene from 14 C. trachomatis serological variants (serovar A-K, L1, L2, L3) was successfully designed and used for the development of C. trachomatis-LAMP-LFB assay. The optimal reaction system can be performed at a constant temperature of 67°C for 35 min. The total assay process, including genomic DNA extraction (~15 min), LAMP reaction (35 min), and LFB readout (~2 min), could be finished within 60 min. The C. trachomatis-LAMP-LFB could detect down to 50 copies/ml, and the specificity was 100%, no cross-reactions with other pathogens were observed. Hence, our C. trachomatis-LAMP-LFB was a rapid, reliable, sensitive, cost-effective, and easy-to-operate assay, which could offer an attractive POC testing tool for chlamydial infection screening, especially in resource starvation settings.
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44
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Sharma M, Singh P. Advances in the Diagnosis of Leprosy. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.893653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Leprosy is a public health issue, and early detection is critical to avert disability. Despite the global attempt to eradicate this disease as a public health problem, it remains an important cause of global neurological disability. India, Brazil and Indonesia share more than 70% of the cases. The reduction of new cases is a priority in the WHO global strategy 2021-2030 which aims to reduce disease transmission in the community by diagnosing cases and identifying subclinical infection. The clinical manifestations of leprosy range from a few to several lesions. The identification remains difficult due to the limited sensitivity of traditional approaches based on bacillary counts of skin smears and histology. To aid in the diagnosis of this disease, molecular biology, and biotechnological technologies have been applied, each with its own set of benefits and downsides despite providing an essential tool to validate the clinical diagnosis of leprosy. Because of this, it is strongly recognized that specific, inexpensive point of care technologies should be developed, particularly to identify asymptomatic M. leprae infections or leprosy nearer to the suspected cases seeking medical attention. Thus, this review will provide an overview of the advancements in leprosy diagnosis over the world. The purpose of this review is to improve our understanding of the outcomes of current tests and technologies used in leprosy diagnosis and to emphasize critical aspects concerning the detection of leprosy bacilli.
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45
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Wen Y, Tan Y, Zhao L, Lv X, Lin L, Liang D, Wang L. Rapid on-site detection of viable Escherichia coli O157: H7 in lettuce using immunomagnetic separation combined with PMAxx-LAMP and nucleic acid lateral flow strip. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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46
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Li JY, Chen XP, Tie YQ, Sun XL, Zhang RQ, He AN, Nie MZ, Fan GH, Li FY, Tian FY, Shen XX, Feng ZS, Ma XJ. Detection of low-load Epstein-Barr virus in blood samples by enriched recombinase aided amplification assay. AMB Express 2022; 12:71. [PMID: 35689713 PMCID: PMC9188631 DOI: 10.1186/s13568-022-01415-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 06/03/2022] [Indexed: 11/10/2022] Open
Abstract
Epstein-Barr virus (EBV), a common human γ-herpesvirus, infects more than 90% of adults worldwide. The purpose of this study was to establish a novel EBV detection method by combining the recombinase aided amplification (RAA) assay with an initial enrichment step that utilizes magnetic beads coated with a recombinant human mannan-binding lectin (rhMBL, M1 protein). An M1 protein–protein A magnetic bead complex (M1 beads) was prepared and used to achieve separation and enrichment of EBV from blood. After nucleic acid extraction, DNA was amplified by RAA. Using 388 whole blood samples and 1 serum sample, we explored the specificity, sensitivity and applicability of the newly developed detection method and compared it with commercial quantitative real-time polymerase chain reaction (qPCR) following M1 bead enrichment, traditional qPCR and traditional RAA. After enrichment, the positivity rate of EBV was increased from 15.94% to 17.74% by RAA (P < 0.05) and from 7.20% to 15.17% by qPCR (P < 0.05). The viral loads after enrichment were increased by 1.13 to 23.19-fold (P < 0.05). Our data demonstrates that an RAA assay incorporating M1 bead enrichment is a promising tool for detecting low EBV viral loads in blood samples that will facilitate an early response to EBV infection. The RAA with an enrichment step that utilizes magnetic beads coated with M1 protein. A very effective method for detecting low-load virus in blood samples. The first report describing virus detection using this method.
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Affiliation(s)
- Jing-Yi Li
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Xiao-Ping Chen
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Yan-Qing Tie
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China
| | - Xiu-Li Sun
- Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.,North China University of Science and Technology, No. 46 West Xinhua Road, Tangshan, 063009, Hebei, China
| | - Rui-Qing Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - An-Na He
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.,North China University of Science and Technology, No. 46 West Xinhua Road, Tangshan, 063009, Hebei, China
| | - Ming-Zhu Nie
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Guo-Hao Fan
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Feng-Yu Li
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Feng-Yu Tian
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Xin-Xin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.
| | - Zhi-Shan Feng
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China. .,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.
| | - Xue-Jun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.
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Abstract
The COVID-19 pandemic remains a significant problem involving health systems worldwide. Several diagnostic methods are reported for detecting the coronavirus in clinical, research, and public health laboratories. rRT-PCR is considered the gold standard; however, as it required skilled personnel and special equipment, rapid antigen tests have been developed and used as first-line screening. The serologic testing of antibodies can also be used to enhance the detection sensitivity and accuracy, which are used to assess the overall infection rate. This review summarizes the molecular techniques and serologic assays widely used in China and discusses the advantages and disadvantages of these techniques.
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Affiliation(s)
- Yanjun Lu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ziyong Sun
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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48
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Shi X, Sun H, Li H, Wei S, Jin J, Zhao C, Wang J, Li H. Preparation of IgY Oriented Conjugated Fe3O4 MNPs as Immunomagnetic Nanoprobe for Increasing Enrichment Efficiency of Staphylococcus aureus Based on Adjusting the pH of the Solution System. Front Public Health 2022; 10:865828. [PMID: 35669739 PMCID: PMC9163370 DOI: 10.3389/fpubh.2022.865828] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Immunomagnetic separation based on Fe3O4 magnetic nanoparticles (MNPs) has been widely performed in sample pretreatment. The oriented conjugation strategy can achieve a better capture effect than the N-(3-dimethylamlnopropyl)-N'-ethylcarbodiimide hydrochloride (EDC) /N-hydroxysuccinimide (NHS) method. However, immunoglobulin yolk (IgY) cannot be oriented through an SPA strategy like immunoglobulin G (IgG). In this article, an oriented conjugation nanoprobe was prepared for the enrichment of bacteria based on pH adjusting. The main factors affecting the enrichment efficiency were studied, such as the pH of the buffer system, the concentration of IgY, the concentration of nanoprobe, and the enrichment time. Under the optimal conditions, the enrichment efficiency toward target bacteria could reach 92.8%. Combined with PCR, the limit of detection (LOD) was found to be 103 CFU/ml, which was lower than the PCR only. In conclusion, we provided a new protocol for the oriented conjugation of IgY and high sensitivity detection with simple pretreatment.
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Affiliation(s)
- Xuening Shi
- School of Public Health, Jilin University, Changchun, China
| | - Hongbin Sun
- China-Japan Union Hospital of Jilin University, Changchun, China
| | - Hang Li
- School of Public Health, Jilin University, Changchun, China
| | - Shengnan Wei
- School of Public Health, Jilin University, Changchun, China
| | - Jin Jin
- School of Public Health, Jilin University, Changchun, China
| | - Chao Zhao
- School of Public Health, Jilin University, Changchun, China
| | - Juan Wang
- School of Public Health, Jilin University, Changchun, China
- *Correspondence: Juan Wang
| | - Hui Li
- School of Public Health, Jilin University, Changchun, China
- Hui Li
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49
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Savonnet M, Aubret M, Laurent P, Roupioz Y, Cubizolles M, Buhot A. Kinetics of Isothermal Dumbbell Exponential Amplification: Effects of Mix Composition on LAMP and Its Derivatives. BIOSENSORS 2022; 12:bios12050346. [PMID: 35624647 PMCID: PMC9138685 DOI: 10.3390/bios12050346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/16/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is an exponential amplification method of DNA strands that is more and more used for its high performances. Thanks to its high sensitivity and selectivity, LAMP found numerous applications from the detection of pathogens or viruses through their genome amplification to its incorporation as an amplification strategy in protein or miRNA biomarker quantification. The LAMP method is composed of two stages: the first one consists in the transformation of the DNA strands into dumbbell structures formed of two stems and loops thanks to four primers; then, in the second stage, only two primers are required to amplify the dumbbells exponentially in numerous hairpins of increasing lengths. In this paper, we propose a theoretical framework to analyze the kinetics of the second stage of LAMP, the isothermal dumbbell exponential amplification (IDEA) as function of the physico-chemical parameters of the amplification reaction. Dedicated experiments validate the models. We believe these results may help the optimization of LAMP performances by reducing the number of experiments necessary to find the best parameters.
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Affiliation(s)
- Maud Savonnet
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-SyMMES, 38000 Grenoble, France; (M.S.); (M.A.); (Y.R.)
- Microfluidic Systems and Bioengineering Lab, Technologies for Healthcare and Biology Department, Univ. Grenoble Alpes, CEA, LETI, 38000 Grenoble, France;
| | - Mathilde Aubret
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-SyMMES, 38000 Grenoble, France; (M.S.); (M.A.); (Y.R.)
- Microfluidic Systems and Bioengineering Lab, Technologies for Healthcare and Biology Department, Univ. Grenoble Alpes, CEA, LETI, 38000 Grenoble, France;
| | - Patricia Laurent
- Microfluidic Systems and Bioengineering Lab, Technologies for Healthcare and Biology Department, Univ. Grenoble Alpes, CEA, LETI, 38000 Grenoble, France;
| | - Yoann Roupioz
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-SyMMES, 38000 Grenoble, France; (M.S.); (M.A.); (Y.R.)
| | - Myriam Cubizolles
- Microfluidic Systems and Bioengineering Lab, Technologies for Healthcare and Biology Department, Univ. Grenoble Alpes, CEA, LETI, 38000 Grenoble, France;
- Correspondence: (M.C.); (A.B.)
| | - Arnaud Buhot
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-SyMMES, 38000 Grenoble, France; (M.S.); (M.A.); (Y.R.)
- Correspondence: (M.C.); (A.B.)
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50
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Zhou Y, Ren M, Zhang P, Jiang D, Yao X, Luo Y, Yang Z, Wang Y. Application of Nanopore Sequencing in the Detection of Foodborne Microorganisms. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:1534. [PMID: 35564242 PMCID: PMC9100974 DOI: 10.3390/nano12091534] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 12/21/2022]
Abstract
Foodborne pathogens have become the subject of intense interest because of their high incidence and mortality worldwide. In the past few decades, people have developed many methods to solve this challenge. At present, methods such as traditional microbial culture methods, nucleic acid or protein-based pathogen detection methods, and whole-genome analysis are widely used in the detection of pathogenic microorganisms in food. However, these methods are limited by time-consuming, cumbersome operations or high costs. The development of nanopore sequencing technology offers the possibility to address these shortcomings. Nanopore sequencing, a third-generation technology, has the advantages of simple operation, high sensitivity, real-time sequencing, and low turnaround time. It can be widely used in the rapid detection and serotyping of foodborne pathogens. This review article discusses foodborne diseases, the principle of nanopore sequencing technology, the application of nanopore sequencing technology in foodborne pathogens detection, as well as its development prospects.
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Affiliation(s)
| | | | | | | | | | | | | | - Yin Wang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (M.R.); (P.Z.); (D.J.); (X.Y.); (Y.L.); (Z.Y.)
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