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He R, Wang L, Wang F, Yang J, Yu X, Wang Y, Liu Z, Li C, Ma L. Combination of ultrashort PCR and Pyrococcus furiosus Argonaute for DNA detection. Analyst 2021; 147:35-39. [PMID: 34881761 DOI: 10.1039/d1an01521d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple and user-friendly nucleic acid sensing platform with 10 aM sensitivity, named USPCRP (combines ultrashort PCR with Pyrococcus furiosus Argonaute cleavage for nuleic acids detection) is reported. The product of this ultrashort PCR could be directly used as a DNA guide to mediate PfAgo cleavage of molecular beacons.
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Affiliation(s)
- Ruyi He
- School of Life Science and Technology, Wuhan Polytechnic University, China. .,State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, People's Republic of China.
| | - Longyu Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, People's Republic of China.
| | - Fei Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, People's Republic of China.
| | - Jun Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, People's Republic of China.
| | - Xiao Yu
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, Hubei, People's Republic of China
| | - Yuan Wang
- Medical College of Hubei University of Arts and Sciences, Xiangyang, Hubei, People's Republic of China
| | - Zhiguo Liu
- School of Life Science and Technology, Wuhan Polytechnic University, China.
| | - Chunhua Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, People's Republic of China.
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, People's Republic of China.
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Bouju-Albert A, Saltaji S, Dousset X, Prévost H, Jaffrès E. Quantification of Viable Brochothrix thermosphacta in Cold-Smoked Salmon Using PMA/PMAxx-qPCR. Front Microbiol 2021; 12:654178. [PMID: 34335490 PMCID: PMC8316974 DOI: 10.3389/fmicb.2021.654178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/17/2021] [Indexed: 11/17/2022] Open
Abstract
The aim of this study was to develop a rapid and accurate PMA-qPCR method to quantify viable Brochothrix thermosphacta in cold-smoked salmon. B. thermosphacta is one of the main food spoilage bacteria. Among seafood products, cold-smoked salmon is particularly impacted by B. thermosphacta spoilage. Specific and sensitive tools that detect and quantify this bacterium in food products are very useful. The culture method commonly used to quantify B. thermosphacta is time-consuming and can underestimate cells in a viable but not immediately culturable state. We designed a new PCR primer set from the single-copy rpoC gene. QPCR efficiency and specificity were compared with two other published primer sets targeting the rpoC and rpoB genes. The viability dyes PMA or PMAxx were combined with qPCR and compared with these primer sets on viable and dead B. thermosphacta cells in BHI broth and smoked salmon tissue homogenate (SSTH). The three primer sets displayed similar specificity and efficiency. The efficiency of new designed rpoC qPCR on viable B. thermosphacta cells in SSTH was 103.50%, with a linear determination coefficient (r2) of 0.998 and a limit of detection of 4.04 log CFU/g. Using the three primer sets on viable cells, no significant difference was observed between cells treated or untreated with PMA or PMAxx. When dead cells were used, both viability dyes suppressed DNA amplification. Nevertheless, our results did not highlight any difference between PMAxx and PMA in their efficiency to discriminate viable from unviable B. thermosphacta cells in cold-smoked salmon. Thus, this study presents a rapid, specific and efficient rpoC-PMA-qPCR method validated in cold-smoked salmon to quantify viable B. thermosphacta in foods.
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Kang S, Kim I, Vikesland PJ. Discriminatory Detection of ssDNA by Surface-Enhanced Raman Spectroscopy (SERS) and Tree-Based Support Vector Machine (Tr-SVM). Anal Chem 2021; 93:9319-9328. [PMID: 34196541 DOI: 10.1021/acs.analchem.0c04576] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We report label-free detection of 86-base single-stranded DNA (ssDNA) gene segments by surface-enhanced Raman spectroscopy (SERS). The use of a slippery liquid infused porous (SLIP) membrane induced aggregation of 43 nm gold nanoparticles and ssDNA upon pin-free droplet evaporation. The combined SLIPSERS approach generates significant numbers of SERS hot-spots and enabled detection at the 100 nM level of mecA and intI1 gene segments-two genes of interest in the context of antibiotic resistance. Tree-based multiclass support vector machine (Tr-SVM) classifiers were built to discriminate SERS spectra of 12 different gene sequences obtained by SLIPSERS: mecA, intI1, as well as analogues of mecA and intI1, respectively, with 2-10 base mismatches, and two random sequences. The trained predictive Tr-SVM classifiers correctly identified each gene sequence with a prediction accuracy of ∼90%. This study illustrates a novel means for discriminatory label-free SERS detection of ssDNA enabled by Tr-SVM.
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Affiliation(s)
- Seju Kang
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States.,Virginia Tech Institute of Critical Technology and Applied Science (ICTAS) Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Inyoung Kim
- Department of Statistics, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Peter J Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States.,Virginia Tech Institute of Critical Technology and Applied Science (ICTAS) Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
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Evaluation of DNA Extraction Methods for Culture-Independent Real-Time PCR-Based Detection of Listeria monocytogenes in Cheese. FOOD ANAL METHOD 2019. [DOI: 10.1007/s12161-019-01686-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Hu L, Deng X, Brown EW, Hammack TS, Ma LM, Zhang G. Evaluation of Roka Atlas Salmonella method for the detection of Salmonella in egg products in comparison with culture method, real-time PCR and isothermal amplification assays. Food Control 2018. [DOI: 10.1016/j.foodcont.2018.06.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Ricke SC, Kim SA, Shi Z, Park SH. Molecular-based identification and detection of Salmonella in food production systems: current perspectives. J Appl Microbiol 2018; 125:313-327. [PMID: 29675864 DOI: 10.1111/jam.13888] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 04/03/2018] [Accepted: 04/10/2018] [Indexed: 12/25/2022]
Abstract
Salmonella remains a prominent cause of foodborne illnesses and can originate from a wide range of food products. Given the continued presence of pathogenic Salmonella in food production systems, there is a consistent need to improve identification and detection methods that can identify this pathogen at all stages in food systems. Methods for subtyping have evolved over the years, and the introduction of whole genome sequencing and advancements in PCR technologies have greatly improved the resolution for differentiating strains within a particular serovar. This, in turn, has led to the continued improvement in Salmonella detection technologies for utilization in food production systems. In this review, the focus will be on recent advancements in these technologies, as well as potential issues associated with the application of these tools in food production. In addition, the recent and emerging research developments on Salmonella detection and identification methodologies and their potential application in food production systems will be discussed.
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Affiliation(s)
- S C Ricke
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - S A Kim
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - Z Shi
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - S H Park
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
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Azinheiro S, Carvalho J, Prado M, Garrido-Maestu A. Evaluation of Different Genetic Targets for Salmonella enterica Serovar Enteriditis and Typhimurium, Using Loop-Mediated Isothermal AMPlification for Detection in Food Samples. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2018. [DOI: 10.3389/fsufs.2018.00005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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Long Y, Li B, Liu H. Analysis of fluoroquinolones antibiotic residue in feed matrices using terahertz spectroscopy. APPLIED OPTICS 2018; 57:544-550. [PMID: 29400779 DOI: 10.1364/ao.57.000544] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 11/22/2017] [Indexed: 06/07/2023]
Abstract
As antibiotic residue becomes more and more serious all over the world, a rapid and effective detection method is needed to evaluate the antibiotic residue in feed matrices to ensure food safety for consumers. In this study, three different kinds of fluoroquinolones (norfloxacin, enrofloxacin, and ofloxacin) in feed matrices were analyzed using terahertz (THz) spectroscopy, respectively. Meanwhile, pure fluoroquinolones and pure feed matrices were also measured in the same way. Then, the absorption spectra of all of the samples were extracted in the transmission mode. Pure norfloxacin has two absorption peaks at 0.825 and 1.187 THz, and they could still be observed when mixing norfloxacin with feed matrices. Also, there was an obvious and strong absorption peak for ofloxacin at 1.044 THz. However, no obvious absorption peak for enrofloxacin was observed, and only a weak absorption peak was located at 0.8 THz. Then, the different models were established with different chemometrics to identify the fluoroquinolones in feed matrices and determined the fluoroquinolones content in the feed matrices. The least squares support vector machines, Naive Bayes, Mahalanobis distance, and back propagation neural network (BPNN) were used to build the identification model with a Savitzky-Golay filter and standardized normal variate pretreatments. The results show that the excellent classification model was acquired with the BPNN combined with no pretreatment. The optimal classification accuracy was 80.56% in the testing set. After that, multiple linear regression and stepwise regression were used to establish the quantitative detection model for different kinds of fluoroquinolones in feed matrices. The optimal correlation coefficients for norfloxacin, enrofloxacin, and ofloxacin in the prediction set were obtained with multiple linear regression that combined absorption peaks with wavelengths selected by stepwise regression, which were 0.867, 0.828, and 0.964, respectively. Overall, this research explored the potential of identifying the fluoroquinolones in feed matrices using THz spectroscopy without a complex pretreatment process and then quantitatively detecting the fluoroquinolones content in feed matrices. The results demonstrate that THz spectra could be used to identify fluoroquinolones in feed matrices and also detect their content quantitatively, which has great significance for the food safety industry.
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Hu L, Ma L, Zheng S, He X, Wang H, Brown E, Hammack T, Zhang G. Evaluation of 3M Molecular Detection System and ANSR Pathogen Detection System for rapid detection of Salmonella from egg products. Poult Sci 2017; 96:1410-1418. [DOI: 10.3382/ps/pew399] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/13/2016] [Indexed: 01/22/2023] Open
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Henrich N, Holmes B, Isaac-Renton J, Prystajecky N. Exploring readiness for the adoption of new molecular water quality tests: Insights from interviews with policy makers, laboratory managers and watershed managers. ENVIRONMENT INTERNATIONAL 2016; 89-90:12-20. [PMID: 26826358 DOI: 10.1016/j.envint.2016.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 06/05/2023]
Abstract
Adoption of molecular-based water quality tests has been limited despite their advantage over traditional culture-based tests. A better understanding of the factors affecting adoption of these tests is needed for effective implementation. The Consolidated Framework for Implementation Research (CFIR) was used to analyze interviews with policy makers, watershed managers and laboratory managers in British Columbia (BC), Canada about their perceptions of molecular water tests currently under development in order to assess readiness for adoption and identify factors that may impact implementation. Many of the CFIR constructs were addressed by study participants, thus confirming their validity in the water-testing context. Other constructs were not mentioned, which suggests that awareness about these constructs need to be increased to ensure that they are incorporated into implementation strategies. In general, there was much enthusiasm for the new tests, which were seen to provide valuable information that could enable improved management of watersheds and treatment of source water. However, prior to adopting the tests, stakeholders would require evidence supporting the tests' validity and reliability, would need to assess the complexity of introducing the tests into laboratories and water sampling processes, and would require support interpreting the test results. Even if all the aforementioned issues are satisfactorily addressed, the tests may not be adopted unless regulations and policies were changed to allow the use of these test results to inform decision making. The results support that implementation of new technologies, such as these water quality tests, need to address potential barriers that could hinder uptake despite the advantages of the new product.
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Affiliation(s)
- Natalie Henrich
- Center for Health Evaluation and Outcome Sciences, St. Paul's Hospital, 588-1081 Burrard Street, Vancouver, British Columbia V6Z 1Y6, Canada.
| | - Bev Holmes
- Michael Smith Foundation for Health Research, 200-1285 West Broadway, Vancouver, British Columbia V6H 3X8, Canada.
| | - Judith Isaac-Renton
- British Columbia Public Health Microbiology Reference Laboratory, Provincial Health Services Authority, 655 West 12th Avenue, Vancouver, British Columbia V5Z 4R4, Canada.
| | - Natalie Prystajecky
- British Columbia Public Health Microbiology Reference Laboratory, Provincial Health Services Authority, 655 West 12th Avenue, Vancouver, British Columbia V5Z 4R4, Canada.
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Souii A, M’hadheb-Gharbi MB, Gharbi J. Nucleic acid-based biotechnologies for food-borne pathogen detection using routine time-intensive culture-based methods and fast molecular diagnostics. Food Sci Biotechnol 2016; 25:11-20. [PMID: 30263230 PMCID: PMC6049363 DOI: 10.1007/s10068-016-0002-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 01/23/2023] Open
Abstract
Diseases caused by food-borne pathogens constitute a major burden to consumers, food business operators, and national governments. Bacterial and viral pathogens are the major biotic factors influencing food safety. A vast array of culture dependent analytical methods and protocols have been developed. Recently, nucleic acid-based methods have begun to replace or complement culture-based methods for routine use in food control laboratories. Basic advantages provided by nucleic acid-based technologies are faster speed and more information, such as sub-species identification, antibiotic resistance, and food microbiology. In particular, PCR and alternative methods have been developed to a stage that provides good speed, sensitivity, specificity, and reproducibility with minimized risk of carryover contamination. This review briefly summarizes currently available and developing molecular technologies that may be candidates for involvement in microbiological molecular diagnostic methods in the next decade.
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Affiliation(s)
- Amira Souii
- The Higher Institute of Applied Biological Sciences of Tunis, University of Tunis El manar-Tunis, Rommana, 1068 Tunisia
- The Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, 5000 Tunisia
| | | | - Jawhar Gharbi
- The Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, 5000 Tunisia
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Pastells C, Pascual N, Sanchez-Baeza F, Marco MP. Immunochemical Determination of Pyocyanin and 1-Hydroxyphenazine as Potential Biomarkers of Pseudomonas aeruginosa Infections. Anal Chem 2016; 88:1631-8. [DOI: 10.1021/acs.analchem.5b03490] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Carme Pastells
- Nanobiotechnology for Diagnostics (Nb4D), IQAC−CSIC, ‡Networking Research Center on Bioengineering, Biomaterials and Nanomedicine
(CIBER-BBN), Spain, Jordi
Girona, 18-26, 08034 Barcelona, Spain
| | - Nuria Pascual
- Nanobiotechnology for Diagnostics (Nb4D), IQAC−CSIC, ‡Networking Research Center on Bioengineering, Biomaterials and Nanomedicine
(CIBER-BBN), Spain, Jordi
Girona, 18-26, 08034 Barcelona, Spain
| | - Francisco Sanchez-Baeza
- Nanobiotechnology for Diagnostics (Nb4D), IQAC−CSIC, ‡Networking Research Center on Bioengineering, Biomaterials and Nanomedicine
(CIBER-BBN), Spain, Jordi
Girona, 18-26, 08034 Barcelona, Spain
| | - M.-Pilar Marco
- Nanobiotechnology for Diagnostics (Nb4D), IQAC−CSIC, ‡Networking Research Center on Bioengineering, Biomaterials and Nanomedicine
(CIBER-BBN), Spain, Jordi
Girona, 18-26, 08034 Barcelona, Spain
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Rapid Methods for Quality Assurance of Foods: the Next Decade with Polymerase Chain Reaction (PCR)-Based Food Monitoring. FOOD ANAL METHOD 2014. [DOI: 10.1007/s12161-014-9915-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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