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Sogore T, Guo M, Sun N, Jiang D, Shen M, Ding T. Microbiological and chemical hazards in cultured meat and methods for their detection. Compr Rev Food Sci Food Saf 2024; 23:e13392. [PMID: 38865212 DOI: 10.1111/1541-4337.13392] [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: 02/16/2024] [Revised: 04/23/2024] [Accepted: 05/19/2024] [Indexed: 06/14/2024]
Abstract
Cultured meat, which involves growing meat in a laboratory rather than breeding animals, offers potential benefits in terms of sustainability, health, and animal welfare compared to conventional meat production. However, the cultured meat production process involves several stages, each with potential hazards requiring careful monitoring and control. Microbial contamination risks exist in the initial cell collection from source animals and the surrounding environment. During cell proliferation, hazards may include chemical residues from media components such as antibiotics and growth factors, as well as microbial issues from improper bioreactor sterilization. In the differentiation stage where cells become muscle tissue, potential hazards include residues from scaffolding materials, microcarriers, and media components. Final maturation and harvesting stages risk environmental contamination from nonsterile conditions, equipment, or worker handling if proper aseptic conditions are not maintained. This review examines the key microbiological and chemical hazards that must be monitored and controlled during the manufacturing process for cultured meats. It describes some conventional and emerging novel techniques that could be applied for the detection of microbial and chemical hazards in cultured meat. The review also outlines the current evolving regulatory landscape around cultured meat and explains how thorough detection and characterization of microbiological and chemical hazards through advanced analytical techniques can provide crucial data to help develop robust, evidence-based food safety regulations specifically tailored for the cultured meat industry. Implementing new digital food safety methods is recommended for further research on the sensitive and effective detection of microbiological and chemical hazards in cultured meat.
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Affiliation(s)
- Tahirou Sogore
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Meimei Guo
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Na Sun
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China
| | - Donglei Jiang
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, China
| | - Mofei Shen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Zhongyuan Institute, Zhejiang University, Zhengzhou, China
| | - Tian Ding
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, China
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2
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Alissa M, Hjazi A. Utilising biosensor-based approaches for identifying neurotropic viruses. Rev Med Virol 2024; 34:e2513. [PMID: 38282404 DOI: 10.1002/rmv.2513] [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: 11/13/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 01/30/2024]
Abstract
Neurotropic viruses, with their ability to invade the central nervous system, present a significant public health challenge, causing a spectrum of neurological diseases. Clinical manifestations of neurotropic viral infections vary widely, from mild to life-threatening conditions, such as HSV-induced encephalitis or poliovirus-induced poliomyelitis. Traditional diagnostic methods, including polymerase chain reaction, serological assays, and imaging techniques, though valuable, have limitations. To address these challenges, biosensor-based methods have emerged as a promising approach. These methods offer advantages such as rapid results, high sensitivity, specificity, and potential for point-of-care applications. By targeting specific biomarkers or genetic material, biosensors utilise technologies like surface plasmon resonance and microarrays, providing a direct and efficient means of diagnosing neurotropic infections. This review explores the evolving landscape of biosensor-based methods, highlighting their potential to enhance the diagnostic toolkit for neurotropic viruses.
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Affiliation(s)
- Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz, Al-Kharj, Saudi Arabia
| | - Ahmed Hjazi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz, Al-Kharj, Saudi Arabia
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3
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Ndraha N, Lin HY, Tsai SK, Hsiao HI, Lin HJ. The Rapid Detection of Salmonella enterica, Listeria monocytogenes, and Staphylococcus aureus via Polymerase Chain Reaction Combined with Magnetic Beads and Capillary Electrophoresis. Foods 2023; 12:3895. [PMID: 37959014 PMCID: PMC10649415 DOI: 10.3390/foods12213895] [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: 09/29/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Food safety concerns regarding foodborne pathogen contamination have gained global attention due to its significant implications. In this study, we developed a detection system utilizing a PCR array combined with an automated magnetic bead-based system and CE technology to enable the detection of three foodborne pathogens, namely Salmonella enterica, Listeria monocytogenes, and Staphylococcus aureus. The results showed that our developed method could detect these pathogens at concentrations as low as 7.3 × 101, 6.7 × 102, and 6.9 × 102 cfu/mL, respectively, in the broth samples. In chicken samples, the limit of detection for these pathogens was 3.1 × 104, 3.5 × 103, and 3.9 × 102 cfu/g, respectively. The detection of these pathogens was accomplished without the necessity for sample enrichment, and the entire protocols, from sample preparation to amplicon analysis, were completed in approximately 3.5 h. Regarding the impact of the extraction method on detection capability, our study observed that an automated DNA extraction system based on the magnetic bead method demonstrated a 10-fold improvement or, at the very least, yielded similar results compared to the column-based method. These findings demonstrated that our developed model is effective in detecting low levels of these pathogens in the samples analyzed in this study. The PCR-CE method developed in this study may help monitor food safety in the future. It may also be extended to identify other foodborne pathogens across a wide range of food samples.
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Affiliation(s)
- Nodali Ndraha
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan; (N.N.); (H.-Y.L.)
| | - Hung-Yun Lin
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan; (N.N.); (H.-Y.L.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202301, Taiwan
| | | | - Hsin-I Hsiao
- Department of Food Science, National Taiwan Ocean University, Keelung 202301, Taiwan;
| | - Han-Jia Lin
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 202301, Taiwan; (N.N.); (H.-Y.L.)
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Ji S, Wang X, Wang Y, Sun Y, Su Y, Lv X, Song X. Advances in Cas12a-Based Amplification-Free Nucleic Acid Detection. CRISPR J 2023; 6:405-418. [PMID: 37751223 DOI: 10.1089/crispr.2023.0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023] Open
Abstract
In biomedicine, rapid and sensitive nucleic acid detection technology plays an important role in the early detection of infectious diseases. However, most traditional nucleic acid detection methods require the amplification of nucleic acids, resulting in problems such as long detection time, complex operation, and false-positive results. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR) systems have been widely used in nucleic acid detection, especially the CRISPR-Cas12a system, which can trans cleave single-stranded DNA and can realize the detection of DNA targets. But, amplification of nucleic acids is still required to further improve detection sensitivity, which makes Cas12a-based amplification-free nucleic acid detection methods a great challenge. This article reviews the recent progress of Cas12a-based amplification-free detection methods for nucleic acids. These detection methods apply electrochemical detection methods, fluorescence detection methods, noble metal nanomaterial detection methods, and lateral flow assay. Under various optimization strategies, unamplified nucleic acids have the same sensitivity as amplified nucleic acids. At the same time, the article discusses the advantages and disadvantages of each method and further discusses the current challenges such as off-target effects and the ability to achieve high-throughput detection. Amplification-free nucleic acid detection technology based on CRISPR-Cas12a has great potential in the biomedical field.
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Affiliation(s)
- Shixin Ji
- School of Life Sciences, Changchun Normal University, Changchun, China; and Jilin Business and Technology College, Changchun, China
| | - Xueli Wang
- School of Grain, Jilin Business and Technology College, Changchun, China
| | - Yangkun Wang
- School of Life Sciences, Changchun Normal University, Changchun, China; and Jilin Business and Technology College, Changchun, China
| | - Yingqi Sun
- School of Life Sciences, Changchun Normal University, Changchun, China; and Jilin Business and Technology College, Changchun, China
| | - Yingying Su
- School of Life Sciences, Changchun Normal University, Changchun, China; and Jilin Business and Technology College, Changchun, China
| | - Xiaosong Lv
- School of Life Sciences, Changchun Normal University, Changchun, China; and Jilin Business and Technology College, Changchun, China
| | - Xiangwei Song
- School of Life Sciences, Changchun Normal University, Changchun, China; and Jilin Business and Technology College, Changchun, China
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Liu J, Zeng S, Wan Y, Liu T, Chen F, Wang A, Tang W, Wang J, Yuan H, Negahdary M, Lin Y, Li Y, Wang L, Wu Z. Hybridization chain reaction cascaded amplification platform for sensitive detection of pathogen. Talanta 2023; 265:124829. [PMID: 37352781 DOI: 10.1016/j.talanta.2023.124829] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 06/25/2023]
Abstract
Rapid, sensitive, and accurate identification of pathogens is vital for preventing and controlling fish disease, reducing economic losses in aquaculture, and interrupting the spread of food-borne diseases in human populations. Herein, we proposed a hybridization chain reaction (HCR) cascaded dual-signal amplification platform for the ultrasensitive and specific detection of pathogenic microorganisms. A couple of specific primers for target bacterial 16S rRNAs were used to obtain amplified target single-stranded DNAs (AT-ssDNA). Then, AT-ssDNA initiated HCR amplification along with the opening of fluorophore (FAM) and a quencher (BHQ1) labeled hairpin reporter probe (H1), and the FAM fluorescence signal recovered. The proposed strategy could achieve a detection limit down to 0.31 CFU/mL for Staphylococcus aureus (S. aureus), 0.49 CFU/mL for Escherichia coli (E. coli) in buffer, and a linear range from 1 to 1 × 106 CFU/mL for S. aureus, 1 to 1 × 107 CFU/mL for E. coli. Furthermore, this platform enabled sensitive and precise detection of pathogenic microorganisms in complex samples such as fish blood and different organ tissues (large intestine, gallbladder, heart, liver, ren, gill, skin), which shows great potential in disease prevention and control in aquatic products.
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Affiliation(s)
- Jiaxin Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 56 Renmin Road, Haikou, 570228, China; Marine College, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Shu Zeng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 56 Renmin Road, Haikou, 570228, China; Marine College, Hainan University, 56 Renmin Road, Haikou, 570228, China.
| | - Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 56 Renmin Road, Haikou, 570228, China; Marine College, Hainan University, 56 Renmin Road, Haikou, 570228, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
| | - Tianmi Liu
- Testing Center of Aquatic Product Quality Safety of Hainan Province, Haikou, 570206, China
| | - Fei Chen
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Anwei Wang
- Testing Center of Aquatic Product Quality Safety of Hainan Province, Haikou, 570206, China
| | - Wenning Tang
- Products Quality Supervision and Inspection Institute of Hainan Province, Haikou, 570206, China
| | - Jiali Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 56 Renmin Road, Haikou, 570228, China; Marine College, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Haoyu Yuan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 56 Renmin Road, Haikou, 570228, China; Marine College, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Masoud Negahdary
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, 05508-000, Brazil
| | - Yutong Lin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Yajing Li
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Lingxuan Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Zijing Wu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 56 Renmin Road, Haikou, 570228, China
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Yee BJ, Shafiqah NF, Mohd-Naim NF, Ahmed MU. A CRISPR/Cas12a-based fluorescence aptasensor for the rapid and sensitive detection of ampicillin. Int J Biol Macromol 2023:125211. [PMID: 37271263 DOI: 10.1016/j.ijbiomac.2023.125211] [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: 03/28/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/06/2023]
Abstract
This study introduces CRISPR/Cas-based aptasensor for the highly sensitive and specific detection of the antibiotic, ampicillin. Ampicillin (AMPI) is a commonly used antibiotic for treating pathogenic bacteria and is additionally added to livestock feed in agriculture. This study can enable early detection of antibiotic residues, prevent their accumulation in the environment, and ensure compliance with food safety regulations. Herein, the aptasensor was developed with the CRISPR/Cas system by utilizing three different ampicillin-specific aptamers, each conjugated with a biotin at the 5'-end. The ssDNA activator was bound to the aptamers through complementary base pairings. The attraction of the aptamers to the ampicillin target released the bound ssDNA, causing the activation of the CRISPR/Cas system. The DNA reporter probe, labelled with Cy3 and a quencher, turns on the fluorescence signal when cleaved by the activated Cas12a through trans-cleavage measured using a fluorescence spectrophotometer at 590 nm. The fluorescence signal was linearly proportional to the ampicillin target concentration with a 0.01 nM limit of detection and a read-out time of 30 min. This aptasensor showed high sensitivity towards ampicillin even in the presence of other antibiotics. The method was also successfully implemented for ampicillin detection in spiked food samples.
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Affiliation(s)
- Bong Jing Yee
- Biosensors and Nanobiotechnology Laboratory, Chemical Science Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE 1410, Brunei Darussalam
| | - Nurul Faizeemah Shafiqah
- Biosensors and Nanobiotechnology Laboratory, Chemical Science Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE 1410, Brunei Darussalam
| | - Noor Faizah Mohd-Naim
- PAPRSB Institute of Health Science, Univesiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE 1410, Brunei Darussalam
| | - Minhaz Uddin Ahmed
- Biosensors and Nanobiotechnology Laboratory, Chemical Science Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE 1410, Brunei Darussalam.
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Pawar AA, Patwardhan SB, Barage S, Raut R, Lakkakula J, Roy A, Sharma R, Anand J. Smartphone-based diagnostics for biosensing infectious human pathogens. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 180-181:120-130. [PMID: 37164166 DOI: 10.1016/j.pbiomolbio.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/01/2023] [Accepted: 05/07/2023] [Indexed: 05/12/2023]
Abstract
The widespread usage of smartphones has made accessing vast troves of data easier for everyone. Smartphones are powerful, handy, and easy to operate, making them a valuable tool for improving public health through diagnostics. When combined with other devices and sensors, smartphones have shown potential for detecting, visualizing, collecting, and transferring data, enabling rapid disease diagnosis. In resource-limited settings, the user-friendly operating system of smartphones allows them to function as a point-of-care platform for healthcare and disease diagnosis. Herein, we critically reviewed the smartphone-based biosensors for the diagnosis and detection of diseases caused by infectious human pathogens, such as deadly viruses, bacteria, and fungi. These biosensors use several analytical sensing methods, including microscopic imaging, instrumental interface, colorimetric, fluorescence, and electrochemical biosensors. We have discussed the diverse diagnosis strategies and analytical performances of smartphone-based detection systems in identifying infectious human pathogens, along with future perspectives.
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Affiliation(s)
- Aditya Amrut Pawar
- Amity Institute of Biotechnology, Amity University Maharashtra, Mumbai-Pune Expressway, Bhatan, Panvel, Mumbai, Maharashtra, 410206, India
| | - Sanchita Bipin Patwardhan
- Amity Institute of Biotechnology, Amity University Maharashtra, Mumbai-Pune Expressway, Bhatan, Panvel, Mumbai, Maharashtra, 410206, India
| | - Sagar Barage
- Amity Institute of Biotechnology, Amity University Maharashtra, Mumbai-Pune Expressway, Bhatan, Panvel, Mumbai, Maharashtra, 410206, India; Centre for Computational Biology and Translational Research, Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, 410206, India
| | - Rajesh Raut
- Department of Botany, The Institute of Science, 15 Madame Cama Roads, Mumbai, 32, India
| | - Jaya Lakkakula
- Amity Institute of Biotechnology, Amity University Maharashtra, Mumbai-Pune Expressway, Bhatan, Panvel, Mumbai, Maharashtra, 410206, India; Centre for Computational Biology and Translational Research, Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, 410206, India.
| | - Arpita Roy
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida, India.
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Jigisha Anand
- Department of Biotechnology, Graphic Era Deemed to Be University, Dehradun, Uttarakhand, India
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Venbrux M, Crauwels S, Rediers H. Current and emerging trends in techniques for plant pathogen detection. FRONTIERS IN PLANT SCIENCE 2023; 14:1120968. [PMID: 37223788 PMCID: PMC10200959 DOI: 10.3389/fpls.2023.1120968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/21/2023] [Indexed: 05/25/2023]
Abstract
Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.
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Affiliation(s)
- Marc Venbrux
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
| | - Sam Crauwels
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
| | - Hans Rediers
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
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Peng C, Wang Y, Chen X, Wang X, Ding L, Xu X, Wei W, Yang L, Wu J, Sun M, Xu J. A Localized CRISPR Assay that Detects Short Nucleic Acid Fragments in Unamplified Genetically Modified Samples. ACS Sens 2023; 8:1054-1063. [PMID: 36802509 DOI: 10.1021/acssensors.2c01955] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Detecting short genetically modified (GM) nucleic acid fragments in GM crops and associated products is critically important for the global agriculture industry. Although nucleic acid amplification-based technologies have been widely used for genetically modified organism (GMO) detection, they still struggle to amplify and detect these ultra-short nucleic acid fragments in highly processed products. Here, we used a multiple-CRISPR-derived RNA (crRNA) strategy to detect ultra-short nucleic acid fragments. By combining confinement effects on local concentrations, an amplification-free CRISPR-based short nucleic acid (CRISPRsna) system was established to detect the cauliflower mosaic virus 35S promoter in GM samples. Moreover, we demonstrated assay sensitivity, specificity, and reliability by directly detecting nucleic acid samples from GM crops with a wide genomic range. The CRISPRsna assay avoided possible aerosol contamination from nucleic acid amplification and saved time due to an amplification-free approach. Given that our assay displayed distinct advantages over other technologies in detecting ultra-short nucleic acid fragments, it may have wide applications for detecting GM in highly processed products.
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Affiliation(s)
- Cheng Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yuling Wang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xiaoyun Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaofu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Lin Ding
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaoli Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wei Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Lei Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Meihao Sun
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Junfeng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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10
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Liang S, Sutham P, Wu K, Mallikarjunan K, Wang JP. Giant Magnetoresistance Biosensors for Food Safety Applications. SENSORS (BASEL, SWITZERLAND) 2022; 22:s22155663. [PMID: 35957220 PMCID: PMC9371012 DOI: 10.3390/s22155663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 05/25/2023]
Abstract
Nowadays, the increasing number of foodborne disease outbreaks around the globe has aroused the wide attention of the food industry and regulators. During food production, processing, storage, and transportation, microorganisms may grow and secrete toxins as well as other harmful substances. These kinds of food contamination from microbiological and chemical sources can seriously endanger human health. The traditional detection methods such as cell culture and colony counting cannot meet the requirements of rapid detection due to some intrinsic shortcomings, such as being time-consuming, laborious, and requiring expensive instrumentation or a central laboratory. In the past decade, efforts have been made to develop rapid, sensitive, and easy-to-use detection platforms for on-site food safety regulation. Herein, we review one type of promising biosensing platform that may revolutionize the current food surveillance approaches, the giant magnetoresistance (GMR) biosensors. Benefiting from the advances of nanotechnology, hundreds to thousands of GMR biosensors can be integrated into a fingernail-sized area, allowing the higher throughput screening of food samples at a lower cost. In addition, combined with on-chip microfluidic channels and filtration function, this type of GMR biosensing system can be fully automatic, and less operator training is required. Furthermore, the compact-sized GMR biosensor platforms could be further extended to related food contamination and the field screening of other pathogen targets.
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Affiliation(s)
- Shuang Liang
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Phanatchakorn Sutham
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108, USA;
| | - Kai Wu
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, TX 79409, USA
| | - Kumar Mallikarjunan
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108, USA;
| | - Jian-Ping Wang
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA;
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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11
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Loop mediated isothermal amplification for detection of foodborne parasites: A journey from lab to lab-on-a-chip. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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12
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Wang Y, Liang X, Xu J, Nan L, Liu F, Duan G, Yang H. Rapid and Ultrasensitive Detection of Methicillin-Resistant Staphylococcus aureus Based on CRISPR-Cas12a Combined With Recombinase-Aided Amplification. Front Microbiol 2022; 13:903298. [PMID: 35722329 PMCID: PMC9204182 DOI: 10.3389/fmicb.2022.903298] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/09/2022] [Indexed: 12/26/2022] Open
Abstract
Staphylococcus aureus is one of the main pathogens causing hospital and community-acquired infections, in particular, infections caused by methicillin-resistant Staphylococcus aureus (MRSA) cause a higher mortality rate than those caused by methicillin-sensitive strains, which poses a serious global public health problem. Therefore, rapid and ultrasensitive detection of patients with clinical MRSA infection and timely control of infection are essential. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) based on nucleic acid detection methods are well-known for its high specificity and sensitivity and programmability. Here, we successfully proposed a method based on CRISPR-Cas12a combined with recombinase-aided amplification (RAA) through fluorescent readout to achieve accurate identification and highly sensitive detection of MRSA in clinical samples. Results showed that the limit of detection (LoD) of the RAA-Cas12a method could reach 10 copies/μl at 60 min of reaction. Specificity tests showed that the method could distinguish MRSA from clinically common bacteria. The results of RAA-Cas12a were consistent with that of antimicrobial susceptibility tests (AST) and polymerase chain reaction (PCR) in 83 clinical samples. These results indicated that the detection method based on RAA-Cas12a has high sensitivity and specificity, and provides important value for rapid detection of MRSA.
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Affiliation(s)
- Ying Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xuan Liang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Jie Xu
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Lan Nan
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Fang Liu
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Haiyan Yang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
- *Correspondence: Haiyan Yang
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Kao YT, Calabrese S, Borst N, Lehnert M, Lai YK, Schlenker F, Juelg P, Zengerle R, Garstecki P, von Stetten F. Microfluidic One-Pot Digital Droplet FISH Using LNA/DNA Molecular Beacons for Bacteria Detection and Absolute Quantification. BIOSENSORS 2022; 12:bios12040237. [PMID: 35448297 PMCID: PMC9032532 DOI: 10.3390/bios12040237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/06/2022] [Accepted: 04/10/2022] [Indexed: 02/06/2023]
Abstract
We demonstrate detection and quantification of bacterial load with a novel microfluidic one-pot wash-free fluorescence in situ hybridization (FISH) assay in droplets. The method offers minimal manual workload by only requiring mixing of the sample with reagents and loading it into a microfluidic cartridge. By centrifugal microfluidic step emulsification, our method partitioned the sample into 210 pL (73 µm in diameter) droplets for bacterial encapsulation followed by in situ permeabilization, hybridization, and signal detection. Employing locked nucleic acid (LNA)/DNA molecular beacons (LNA/DNA MBs) and NaCl-urea based hybridization buffer, the assay was characterized with Escherichia coli, Klebsiella pneumonia, and Proteus mirabilis. The assay performed with single-cell sensitivity, a 4-log dynamic range from a lower limit of quantification (LLOQ) at ~3 × 103 bacteria/mL to an upper limit of quantification (ULOQ) at ~3 × 107 bacteria/mL, anda linearity R2 = 0.976. The total time-to-results for detection and quantification was around 1.5 hours.
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Affiliation(s)
- Yu-Ting Kao
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
| | - Silvia Calabrese
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Nadine Borst
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Michael Lehnert
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Yu-Kai Lai
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Franziska Schlenker
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Peter Juelg
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Roland Zengerle
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Piotr Garstecki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
| | - Felix von Stetten
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
- Correspondence: ; Tel.: +49-761-203-73243
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Qian S, Chen Y, Xu X, Peng C, Wang X, Wu H, Liu Y, Zhong X, Xu J, Wu J. Advances in amplification-free detection of nucleic acid: CRISPR/Cas system as a powerful tool. Anal Biochem 2022; 643:114593. [DOI: 10.1016/j.ab.2022.114593] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/28/2022] [Accepted: 02/05/2022] [Indexed: 12/26/2022]
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Chen XF, Zhao X, Yang Z. Aptasensors for the detection of infectious pathogens: design strategies and point-of-care testing. Mikrochim Acta 2022; 189:443. [PMID: 36350388 PMCID: PMC9643942 DOI: 10.1007/s00604-022-05533-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/10/2022] [Indexed: 11/11/2022]
Abstract
The epidemic of infectious diseases caused by contagious pathogens is a life-threatening hazard to the entire human population worldwide. A timely and accurate diagnosis is the critical link in the fight against infectious diseases. Aptamer-based biosensors, the so-called aptasensors, employ nucleic acid aptamers as bio-receptors for the recognition of target pathogens of interest. This review focuses on the design strategies as well as state-of-the-art technologies of aptasensor-based diagnostics for infectious pathogens (mainly bacteria and viruses), covering the utilization of three major signal transducers, the employment of aptamers as recognition moieties, the construction of versatile biosensing platforms (mostly micro and nanomaterial-based), innovated reporting mechanisms, and signal enhancement approaches. Advanced point-of-care testing (POCT) for infectious disease diagnostics are also discussed highlighting some representative ready-to-use devices to address the urgent needs of currently prevalent coronavirus disease 2019 (COVID-19). Pressing issues in aptamer-based technology and some future perspectives of aptasensors are provided for the implementation of aptasensor-based diagnostics into practical application.
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Affiliation(s)
- Xiao-Fei Chen
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou, 510070, People's Republic of China
| | - Xin Zhao
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou, 510070, People's Republic of China.
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, People's Republic of China.
- Guangzhou Laboratory, Guangzhou, 510320, People's Republic of China.
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, Guangzhou, 510005, People's Republic of China.
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Schuele L, Cassidy H, Peker N, Rossen JWA, Couto N. Future potential of metagenomics in clinical laboratories. Expert Rev Mol Diagn 2021; 21:1273-1285. [PMID: 34755585 DOI: 10.1080/14737159.2021.2001329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Rapid and sensitive diagnostic strategies are necessary for patient care and public health. Most of the current conventional microbiological assays detect only a restricted panel of pathogens at a time or require a microbe to be successfully cultured from a sample. Clinical metagenomics next-generation sequencing (mNGS) has the potential to unbiasedly detect all pathogens in a sample, increasing the sensitivity for detection and enabling the discovery of unknown infectious agents. AREAS COVERED High expectations have been built around mNGS; however, this technique is far from widely available. This review highlights the advances and currently available options in terms of costs, turnaround time, sensitivity, specificity, validation, and reproducibility of mNGS as a diagnostic tool in clinical microbiology laboratories. EXPERT OPINION The need for a novel diagnostic tool to increase the sensitivity of microbial diagnostics is clear. mNGS has the potential to revolutionise clinical microbiology. However, its role as a diagnostic tool has yet to be widely established, which is crucial for successfully implementing the technique. A clear definition of diagnostic algorithms that include mNGS is vital to show clinical utility. Similarly to real-time PCR, mNGS will one day become a vital tool in any testing algorithm.
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Affiliation(s)
- Leonard Schuele
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Hayley Cassidy
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Nilay Peker
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - John W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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Mollasalehi H, Vahedipour N, Taghvamanesh A, Minai-Tehrani D. Development of one-pot single specific primer-LAMP (SSP-LAMP) for identification of Shigella genus using 16S rDNA. Anal Biochem 2021; 636:114452. [PMID: 34762873 DOI: 10.1016/j.ab.2021.114452] [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: 08/10/2021] [Revised: 11/03/2021] [Accepted: 11/07/2021] [Indexed: 11/16/2022]
Abstract
Ribosomal RNA gene as a high-copy number nucleo-biomarker is extremely conserved among bacteria which limits its application to the discriminative detection approaches. We have developed a colorimetric isothermal amplification method called "single specific primer-LAMP (SSP-LAMP)" requiring only one specific primer for the amplification of the target and applied to the identification of the 16S rRNA gene in the Shigella genus. A region with high sequence homology in the genus and low homology with other bacteria was considered as the most appropriate. In that regard, a 23 bp sequence in the 16S rRNA gene of the genus was targeted based on the alignment of the gene with fifty-three closely related bacterial species, and a single specific primer along with five degenerate primers were designed. Using hydroxy-naphthol blue (HNB) as an indicator and gel electrophoresis, the proposed approach of SSP-LAMP was able to detect S. boydii, S. sonnei, S. flexneri and S. dysenteriae specifically while other species remained unidentified. The SSP-LAMP method could provide a rapid one-pot point-of-care method for molecular diagnostics of pathogens in many circumstances mainly samples with high genetic homogeneity.
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Affiliation(s)
- Hamidreza Mollasalehi
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983969411, Iran.
| | - Narges Vahedipour
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983969411, Iran
| | - Ahang Taghvamanesh
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983969411, Iran
| | - Dariush Minai-Tehrani
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983969411, Iran
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18
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Lee CY, Degani I, Cheong J, Weissleder R, Lee JH, Cheon J, Lee H. Development of Integrated Systems for On-Site Infection Detection. Acc Chem Res 2021; 54:3991-4000. [PMID: 34677927 DOI: 10.1021/acs.accounts.1c00498] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The modern healthcare system faces an unrelenting threat from microorganisms, as evidenced by global outbreaks of new viral diseases, emerging antimicrobial resistance, and the rising incidence of healthcare-associated infections (HAIs). An effective response to these threats requires rapid and accurate diagnostic tests that can identify causative pathogens at the point of care (POC). Such tests could eliminate diagnostic uncertainties, facilitating patient triaging, minimizing the empiric use of antimicrobial drugs, and enabling targeted treatments. Current standard methods, however, often fail to meet the needs of rapid diagnosis in POC settings. Culture-based assays entail long processing times and require specialized laboratory infrastructure; nucleic acid (NA) tests are often limited to centralized hospitals due to assay complexity and high costs. Here we discuss two new POC tests developed in our groups to enable the rapid diagnosis of infection. The first is nanoPCR that takes advantages of core-shell magnetoplasmonic nanoparticles (MPNs): (i) Au shell significantly accelerates thermocycling via volumetric, plasmonic light-to-heat conversion and (ii) a magnetic core enables sensitive in situ fluorescent detection via magnetic clearing. By adopting a Ferris wheel module, the system expedites multisamples in parallel with a minimal setup. When applied to COVID-19 diagnosis, nanoPCR detected SARS-CoV-2 RNA down to 3.2 copy/μL within 17 min. In particular, nanoPCR diagnostics accurately identified COVID-19 cases in clinical samples (n = 150), validating its clinical applicability. The second is a polarization anisotropy diagnostic (PAD) system that exploits the principle of fluorescence polarization (FP) as a detection modality. Fluorescent probes were designed to alter their molecular weight upon recognizing target NAs. This event modulates the probes' tumbling rate (Brownian motion), which leads to changes in FP. The approach is robust against environmental noise and benefits from the ratiometric nature of the signal readout. We applied PAD to detect clinically relevant HAI bacteria (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Staphylococcus aureus). The PAD assay demonstrated detection sensitivity down to the single bacterium level and determined both drug resistance and virulence status. In summary, these new tests have the potential to become powerful tools for rapid diagnosis in the infectious disease space. They do not require highly skilled personnel or labor-intensive analyses, and the assays are quick and cost-effective. These attributes will make nanoPCR and PAD well-aligned with a POC workflow to aid physicians to initiate prompt and informed patient treatment.
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Affiliation(s)
- Chang Yeol Lee
- Center for Systems Biology, Massachusetts General Hospital Research Institute, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, Massachusetts 02114, United States
- Institute for Basic Science (IBS), Center for NanoMedicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Ismail Degani
- Center for Systems Biology, Massachusetts General Hospital Research Institute, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 50 Vassar Street, Cambridge, Massachusetts 02142, United States
| | - Jiyong Cheong
- Institute for Basic Science (IBS), Center for NanoMedicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital Research Institute, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, Massachusetts 02114, United States
- Department of Systems Biology, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jae-Hyun Lee
- Institute for Basic Science (IBS), Center for NanoMedicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Jinwoo Cheon
- Institute for Basic Science (IBS), Center for NanoMedicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
- Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital Research Institute, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, Massachusetts 02114, United States
- Institute for Basic Science (IBS), Center for NanoMedicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
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Fu J, Li J, Chen J, Li Y, Liu J, Su X, Shi S. Ultra-specific nucleic acid testing by target-activated nucleases. Crit Rev Biotechnol 2021; 42:1061-1078. [PMID: 34706599 DOI: 10.1080/07388551.2021.1983757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Specific and sensitive detection of nucleic acids is essential to clinical diagnostics and biotechnological applications. Currently, amplification steps are necessary for most detection methods due to the low concentration of nucleic acid targets in real samples. Although amplification renders high sensitivity, poor specificity is prevalent because of the lack of highly accurate precise strategies, resulting in significant false positives and false negatives. Nucleases exhibit high catalytic activity for nucleic acid cleavage which is regulated in a programmable manner. This review focuses on the latest progress in nucleic acid testing methods based on the target-activated nucleases. It summarizes the property of enzymes such as CRISPR/Cas, Argonautes, and some gene-editing irrelevant nucleases, which have been leveraged to create highly specific and sensitive nucleic acid testing tools. We elaborate on recent advances in the field of nuclease-mediated DNA recognition techniques for nucleic acid detection, and discuss its future applications and challenges in molecular diagnostics.
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Affiliation(s)
- Jinyu Fu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Junjie Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jing Chen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yabei Li
- Department of Neurosurgery, People's Hospital of Shijiazhuang, Shijiazhuang, China
| | - Jiajia Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xin Su
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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Experimental Performance Analysis of a Small Thermoelectric System Applicable to Real-Time PCR Devices. Symmetry (Basel) 2020. [DOI: 10.3390/sym12121963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
At the International Space Station (ISS), not only observation of the space environment, but also biological and medical research under weightlessness has been conducted. The efficient use of energy from waste heat from the ISS away from the Earth is very important to the efficient operation of the ISS. To develop a thermoelectric module that can be used for real-time polymerase chain reaction (PCR) machinery used in biological and medical research, we simulated and evaluated the thermoelectric waste heat recovery system. Specifically, the thermoelectric module was attached to a stainless steel duct, and a hot air blower was faced with the duct inlet. The power of the thermoelectric system was measured by controlling the temperature of the hot air inlet. Additionally, the thermoelectric performance was evaluated according to the heat sink attached to the cold side of the thermoelectric module. Here, we also found the optimal heat exchange factors to improve the power and efficiency of the thermoelectric module. In this regard, it is expected that the thermoelectric module development and analysis study using waste heat will play an important role in the biological and medical research that is being conducted at ISS by developing a real-time PCR utilizing it.
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21
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Moeini-Zanjani A, Pournajaf A, Ferdosi-Shahandashti E, Gholami M, Masjedian F, Khafri S, Rajabnia R. Comparison of loop-mediated isothermal amplification and conventional PCR tests for diagnosis of common Brucella species. BMC Res Notes 2020; 13:533. [PMID: 33187548 PMCID: PMC7666441 DOI: 10.1186/s13104-020-05377-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Rapid, reliable, and affordable detection of Brucella species via the molecular methods remains a challenge. In recent years, loop-mediated isothermal amplification (LAMP) is a functional nucleic acid amplification technique offering a substitute to polymerase chain reaction (PCR). So, we compared the LAMP assay with the conventional PCR for the identification of common Brucella species in Iran. In this study, LAMP assay was comprehensively evaluated against the common PCR method. A group of specific LAMP primers were used to amplify a highly specific fragment from the sequence of the Brucella abortus, bcsp31 gene. Sensitivity and specificity values of tests were done with a set of 78 (50 Brucella and 28 non-Brucella) strains. RESULTS A dilution series of B. abortus DNA indicated that the LAMP reaction could reliably detect 10 (fg/µl) DNA target copies per reaction within 36 min, which is 10 times greater than the PCR assay. In summary, we conclude that LAMP assay provide accurate and fast test results to identify of common Brucella species in low-complexity labs, mainly in low and lower middle income countries.
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Affiliation(s)
- Ali Moeini-Zanjani
- Department of Microbiology, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Abazar Pournajaf
- Department of Microbiology, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
- Infectious Diseases and Tropical Medicine Research Center, Babol University of Medical Sciences, Babol, Iran
| | - Elaheh Ferdosi-Shahandashti
- Infectious Diseases and Tropical Medicine Research Center, Babol University of Medical Sciences, Babol, Iran
- Department of Medical Biotechnology, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Mehrdad Gholami
- Department of Microbiology and Virology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Faramarz Masjedian
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Soraya Khafri
- Department of Biostatistics and Epidemiology, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Ramazan Rajabnia
- Department of Microbiology, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.
- Infectious Diseases and Tropical Medicine Research Center, Babol University of Medical Sciences, Babol, Iran.
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22
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Label-free capacitive assaying of biomarkers for molecular diagnostics. Nat Protoc 2020; 15:3879-3893. [PMID: 33106679 DOI: 10.1038/s41596-020-0390-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 07/28/2020] [Indexed: 11/08/2022]
Abstract
The label-free analysis of biomarkers offers important advantages in developing point-of-care (PoC) biosensors. In contrast to label-based methodologies, such as ELISA, label-free analysis enables direct detection of targets without additional steps and labeled reagents. Nonetheless, label-free approaches require high sensitivity to detect the intrinsic features of a biomarker and low levels of nonspecific signals. Electrochemical capacitance, [Formula: see text], is a feature of electroactive nanoscale films that can be measured using electrochemical impedance spectroscopy. [Formula: see text] is promising as an electrochemical transducing signal for the development of high-sensitivity, reagentless and label-free molecular diagnostic assays. We used a proprietary ferrocene (Fc)-tagged peptide that is able to self-assemble onto gold electrodes (thicknesses <2 nm) to which any biological receptor can be coupled. When coupled with biological receptors (e.g., a monoclonal antibody), [Formula: see text] exhibited by the redox-tagged peptide changes as a function of the target concentration. We provide herein the steps for the qualitative and quantitative detection of dengue non-structural protein 1 (NS1) biomarker. Detection of NS1 can be used to diagnose dengue virus infection, which causes epidemics each year in tropical and subtropical regions of the world. Including the pre-treatment of the electrode surface, the analysis takes ~25 h. This time can be reduced to minutes if the electrode surface is fabricated separately, demonstrating that [Formula: see text] is promising for PoC applications. We hope this protocol will serve as a reference point for researchers and companies that intend to further develop capacitive devices for molecular diagnostic assays.
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23
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Ríos-Castillo A, Ripolles-Avila C, Rodríguez-Jerez J. Detection of Salmonella Typhimurium and Listeria monocytogenes biofilm cells exposed to different drying and pre-enrichment times using conventional and rapid methods. Int J Food Microbiol 2020; 324:108611. [DOI: 10.1016/j.ijfoodmicro.2020.108611] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 01/28/2023]
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Nucleic acid amplification free biosensors for pathogen detection. Biosens Bioelectron 2020; 153:112049. [DOI: 10.1016/j.bios.2020.112049] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 12/11/2022]
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25
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Geissler M, Brassard D, Clime L, Pilar AVC, Malic L, Daoud J, Barrère V, Luebbert C, Blais BW, Corneau N, Veres T. Centrifugal microfluidic lab-on-a-chip system with automated sample lysis, DNA amplification and microarray hybridization for identification of enterohemorrhagic Escherichia coli culture isolates. Analyst 2020; 145:6831-6845. [DOI: 10.1039/d0an01232g] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Automated workflow that starts with a colony isolate and ends with a fluorescence signal on a DNA microarray.
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Affiliation(s)
- Matthias Geissler
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Daniel Brassard
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Liviu Clime
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | | | - Lidija Malic
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Jamal Daoud
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | | | | | - Burton W. Blais
- Ontario Laboratory Network
- Canadian Food Inspection Agency
- Ottawa
- Canada
| | | | - Teodor Veres
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
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Li Y, Liu H, Huang H, Deng J, Fang L, Luo J, Zhang S, Huang J, Liang W, Zheng J. A sensitive electrochemical strategy via multiple amplification reactions for the detection of E. coli O157: H7. Biosens Bioelectron 2019; 147:111752. [PMID: 31630033 DOI: 10.1016/j.bios.2019.111752] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/10/2019] [Accepted: 09/30/2019] [Indexed: 12/17/2022]
Abstract
The sensitive and efficient strategy remains a central challenge for early diagnosis of pathogenic bacteria. Herein, an ultrasensitive electrochemical biosensor was proposed based on the multiple amplification strategy via the 3D DNA walker, rolling circle amplification (RCA) and hybridization chain reaction (HCR) for the accurate detection of Escherichiacoli O157:H7 (E. coli O157:H7). Firstly, the target sequence extracted from E. coli O157:H7 was transformed and amplified by the DNA walker firstly. Subsequently, a large number of transformed nucleic acid sequences were amplified by the RCA reaction. And then, the progress of HCR was triggered by every fragment in RCA products to form a long double-stranded DNA sequence to immobilize electrochemical indicators, generating a significantly enhanced electrochemical signal. As expected, a high sensitivity with a detection limit of 7 CFU/mL was achieved based on the proposed multiple amplification strategy, which is superior to most current methods for E. coli O157: H7 assay. The multiple amplification strategy could be readily expanded for the detection of various pathogenic bacteria, providing a new approach for early diagnosis of pathogenic microorganisms or other diseases.
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Affiliation(s)
- Yan Li
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Huamin Liu
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China; Department of Materials and Energy, Southwest University, Chongqing, 400715, PR China
| | - Hui Huang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Jun Deng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Lichao Fang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Jing Luo
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China; Department of Materials and Energy, Southwest University, Chongqing, 400715, PR China
| | - Shu Zhang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Jian Huang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Wenbin Liang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China.
| | - Junsong Zheng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China.
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Zhang J, Yang Y, Jiang X, Dong C, Song C, Han C, Wang L. Ultrasensitive SERS detection of nucleic acids via simultaneous amplification of target-triggered enzyme-free recycling and multiple-reporter. Biosens Bioelectron 2019; 141:111402. [DOI: 10.1016/j.bios.2019.111402] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/21/2019] [Accepted: 05/31/2019] [Indexed: 01/28/2023]
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Idelevich EA, Reischl U, Becker K. New Microbiological Techniques in the Diagnosis of Bloodstream Infections. DEUTSCHES ARZTEBLATT INTERNATIONAL 2019; 115:822-832. [PMID: 30678752 DOI: 10.3238/arztebl.2018.0822] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/04/2017] [Accepted: 10/12/2018] [Indexed: 01/12/2023]
Abstract
BACKGROUND When a bloodstream infection is suspected, the preliminary and definitive results of culture-based microbiological testing arrive too late to have any influence on the initial choice of empirical antibiotic treatment. METHODS This review is based on pertinent publications retrieved by a selective search of the literature and on the authors' clinical and scientific experience. RESULTS A number of technical advances now enable more rapid microbiological diagnosis of bloodstream infections. DNA- based techniques for the direct detection of pathogenic organisms in whole blood have not yet become established in routine use because of various limitations. On the other hand, matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become available for routine use in clinical laboratories and has markedly shortened the time to diagnosis after blood samples that have been cultured in automated blood-culture systems turn positive. Further developments of this technique now enable it to be used directly for blood cultures that have been flagged positive, as well as for subcultures that have been incubated for only a short time on a solid nutrient medium. The microbial biomass of the subculture can also be used in parallel for more rapid susceptibility testing with conventional methods, or, in future, with MALDI-TOF MS. CONCLUSION The potential of all of these new techniques will only be realizable in practice if they are optimally embedded in the diagnostic process and if sufficient attention is paid to pre-analytical issues, particularly storage and transport times.
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Lee SH, Park SM, Kim BN, Kwon OS, Rho WY, Jun BH. Emerging ultrafast nucleic acid amplification technologies for next-generation molecular diagnostics. Biosens Bioelectron 2019; 141:111448. [PMID: 31252258 DOI: 10.1016/j.bios.2019.111448] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/31/2019] [Accepted: 06/17/2019] [Indexed: 02/07/2023]
Abstract
Over the last decade, nucleic acid amplification tests (NAATs) including polymerase chain reaction (PCR) were an indispensable methodology for diagnosing cancers, viral and bacterial infections owing to their high sensitivity and specificity. Because the NAATs can recognize and discriminate even a few copies of nucleic acid (NA) and species-specific NA sequences, NAATs have become the gold standard in a wide range of applications. However, limitations of NAAT approaches have recently become more apparent by reason of their lengthy run time, large reaction volume, and complex protocol. To meet the current demands of clinicians and biomedical researchers, new NAATs have developed to achieve ultrafast sample-to-answer protocols for the point-of-care testing (POCT). In this review, ultrafast NA-POCT platforms are discussed, outlining their NA amplification principles as well as delineating recent advances in ultrafast NAAT applications. The main focus is to provide an overview of NA-POCT platforms in regard to sample preparation of NA, NA amplification, NA detection process, interpretation of the analysis, and evaluation of the platform design. Increasing importance will be given to innovative, ultrafast amplification methods and tools which incorporate artificial intelligence (AI)-associated data analysis processes and mobile-healthcare networks. The future prospects of NA POCT platforms are promising as they allow absolute quantitation of NA in individuals which is essential to precision medicine.
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Affiliation(s)
- Sang Hun Lee
- Department of Bioengineering, University of California Berkeley, CA, USA
| | | | - Brian N Kim
- Department of Electrical and Computer Engineering, University of Central Florida, FL, USA
| | - Oh Seok Kwon
- Infectious Disease Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, South Korea
| | - Won-Yep Rho
- School of International Engineering and Science, Chonbuk National University, Jeonju, South Korea
| | - Bong-Hyun Jun
- Department of Bioscience and Biotechnology, Konkuk University, South Korea.
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Masud MK, Na J, Younus M, Hossain MSA, Bando Y, Shiddiky MJA, Yamauchi Y. Superparamagnetic nanoarchitectures for disease-specific biomarker detection. Chem Soc Rev 2019; 48:5717-5751. [DOI: 10.1039/c9cs00174c] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Synthesis, bio-functionalization, and multifunctional activities of superparamagnetic-nanostructures have been extensively reviewed with a particular emphasis on their uses in a range of disease-specific biomarker detection and associated challenges.
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Affiliation(s)
- Mostafa Kamal Masud
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
- Department of Biochemistry & Molecular Biology
| | - Jongbeom Na
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
- International Center for Materials Nanoarchitechtonics (MANA)
| | - Muhammad Younus
- Department of Chemistry
- School of Physical Sciences
- Shahjalal University of Science & Technology
- Sylhet 3114
- Bangladesh
| | - Md. Shahriar A. Hossain
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
- School of Mechanical and Mining Engineering
| | - Yoshio Bando
- International Center for Materials Nanoarchitechtonics (MANA)
- National Institute for Materials Science (NIMS)
- Ibaraki 305-0044
- Japan
- Institute of Molecular Plus
| | - Muhammad J. A. Shiddiky
- School of Environment and Sciences and Queensland Micro- and Nanotechnology Centre (QMMC)
- Griffith University
- QLD 4111
- Australia
| | - Yusuke Yamauchi
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
- International Center for Materials Nanoarchitechtonics (MANA)
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Microbial Proteomics and Their Importance in Medical Microbiology. RECENT DEVELOPMENTS IN APPLIED MICROBIOLOGY AND BIOCHEMISTRY 2019. [PMCID: PMC7149639 DOI: 10.1016/b978-0-12-816328-3.00003-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microbial infection is a leading cause of death around the world. Most of the infectious diseases are caused by drug-resistant microbes; this may lead to a delay in the administration of microbiologically effective therapy (Chen et al., 2017; Del Chierico et al., 2014). Therefore, exhaustive understanding of microbial physiologies, infection and defense systems, and survival strategies is of great interest in order to actively defeat microbial infection. Microbial proteomics provides complete information of microbial physiology and expression and function of the proteins that are involved in infection and also gives a clue in clinical diagnosis and antimicrobial therapy (Pérez-Llarena and Bou, 2016; Vranakis et al., 2014). Microbial proteomics helps to identify the proteins associated with microbial activity, microbial host-pathogen interactions, and antimicrobial resistant mechanism. Microbial activity of pathogens can be confirmed by using the 2-D gel-based and gel-free method with the combination of MALDI-TOF-LC-MS/MS. Proteomic analysis of microbial host-pathogen interaction reveals valuable information about the virulence of the pathogen and its resistance; it helps in better understanding of the infection and for developing strategies against microbial infections (Cheng et al., 2016). Fig. 3.1 schematically illustrates the proteomic analysis of the bacterial samples.
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A new single-tube platform of melting temperature curve analysis based on multiplex real-time PCR using EvaGreen for simultaneous screening detection of Shiga toxin-producing Escherichia coli, Salmonella spp. and Listeria monocytogenes in food. Food Control 2018. [DOI: 10.1016/j.foodcont.2018.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Sub-femtomolar detection of DNA and discrimination of mutant strands using microwell-array assisted digital enzyme-linked oligonucleotide assay. Anal Chim Acta 2018; 1041:122-130. [PMID: 30340684 DOI: 10.1016/j.aca.2018.08.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 07/12/2018] [Accepted: 08/28/2018] [Indexed: 02/01/2023]
Abstract
Detection methods that do not rely on the amplification of DNA but can reach sensitivity, specificity and throughput of gold standard methods, such as qPCR, have been extensively explored in recent years. Here, we present a hydrophilic-in-hydrophobic (HIH)-microwell array platform that empowers a panel of different amplification-free DNA bioassays: digital enzyme-linked oligonucleotide assay (ELONA), ligation-assisted (LA) digital ELONA and so-called 'analog' bioassays. We developed all three bioassays by using magnetic beads for capturing DNA target, followed by hybridization of enzyme-labelled detection probes and sealing of the built complexes into the femtoliter HIH microwells to achieve the fluorescent readout of single DNA molecules. With the optimized digital ELONA bioassay, we successfully detected 97 and 200 nt-long ssDNA molecules down to 68 and 92 aM, respectively, demonstrating extremely high sensitivity of the bioassay and its flexibility towards targets of different lengths. Importantly, we also proved that the same bioassay concept was suited to detect substantially higher concentrations of ssDNA (up to picomolar levels) by quantifying the total fluorescent intensity rather than counting fluorescent events for digital quantification. Finally, we advanced this concept towards LA digital ELONA capable of differentiating wildtype strands from those carrying single-point mutations even when the former were constituting only 1% of the DNA mixture and were present at 2 fM concentration. In conclusion, the developed platform showed remarkably high sensitivity, specificity and versatility for amplification-free detection of DNA and as such can be valuable for numerous applications in medical diagnostics, gene analysis, food safety and environmental monitoring.
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Di Pietro V, Yakoub KM, Scarpa U, Di Pietro C, Belli A. MicroRNA Signature of Traumatic Brain Injury: From the Biomarker Discovery to the Point-of-Care. Front Neurol 2018; 9:429. [PMID: 29963002 PMCID: PMC6010584 DOI: 10.3389/fneur.2018.00429] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/22/2018] [Indexed: 12/21/2022] Open
Abstract
Traumatic brain injury (TBI) is a serious problem that causes high morbidity and mortality around the world. Currently, no reliable biomarkers are used to assess the severity and predict the recovery. Many protein biomarkers were extensively studied for diagnosis and prognosis of different TBI severities such as S-100β, glial fibrillary acidic protein (GFAP), neuron-specific enolase (NSE), neurofilament light chain (NFL), cleaved tau protein (C-tau), and ubiquitin C-terminal hydrolase-L1 (UCH-L1). However, none of these candidates is currently used in the clinical practice, due to relatively low sensitivity, for the diagnosis of mild TBI (mTBI) or mild to moderate TBI (MMTBI) patients who are clinically well and do not have a detectable intracranial pathology on the scans. MicroRNAs (miRNAs or miRs) are a class of small endogenous molecular regulators, which showed to be altered in different pathologies, including TBI and for this reason, their potential role in diagnosis, prognosis and therapeutic applications, is explored. Promising miRNAs such as miR-21, miR-16 or let-7i were identified as suitable candidate biomarkers for TBI and can differentiate mild from severe TBI. Also, they might represent new potential therapeutic targets. Identification of miRNA signature in tissue or biofluids, for several pathological conditions, is now possible thanks to the introduction of new high-throughput technologies such as microarray platform, Nanostring technologies or Next Generation Sequencing. This review has the aim to describe the role of microRNA in TBI and to explore the most commonly used techniques to identify microRNA profile. Understanding the strengths and limitations of the different methods can aid in the practical use of miRNA profiling for diverse clinical applications, including the development of a point-of-care device.
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Affiliation(s)
- Valentina Di Pietro
- Neurotrauma and Ophthalmology Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom.,Surgical Reconstruction and Microbiology Research Centre, National Institute for Health Research, Queen Elizabeth Hospital, Birmingham, United Kingdom.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Illinois, IL, United States
| | - Kamal M Yakoub
- Surgical Reconstruction and Microbiology Research Centre, National Institute for Health Research, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Ugo Scarpa
- Surgical Reconstruction and Microbiology Research Centre, National Institute for Health Research, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Cinzia Di Pietro
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of Biomedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - Antonio Belli
- Neurotrauma and Ophthalmology Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom.,Surgical Reconstruction and Microbiology Research Centre, National Institute for Health Research, Queen Elizabeth Hospital, Birmingham, United Kingdom
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Shin WR, Sekhon SS, Rhee SK, Ko JH, Ahn JY, Min J, Kim YH. Aptamer-Based Paper Strip Sensor for Detecting Vibrio fischeri. ACS COMBINATORIAL SCIENCE 2018; 20:261-268. [PMID: 29553704 DOI: 10.1021/acscombsci.7b00190] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Aptamer-based paper strip sensor for detecting Vibrio fischeri was developed. Our method was based on the aptamer sandwich assay between whole live cells, V. fischeri and DNA aptamer probes. Following 9 rounds of Cell-SELEX and one of the negative-SELEX, V. fischeri Cell Aptamer (VFCA)-02 and -03 were isolated, with the former showing approximately 10-fold greater avidity (in the subnanomolar range) for the target cells when arrayed on a surface. The colorimetric response of a paper sensor based on VFCA-02 was linear in the range of 4 × 101 to 4 × 105 CFU/mL of target cell by using scanning reader. The linear regression correlation coefficient ( R2) was 0.9809. This system shows promise for use in aptamer-conjugated gold nanoparticle probes in paper strip format for in-field detection of marine bioindicating bacteria.
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Affiliation(s)
- Woo-Ri Shin
- School of Biological Sciences, Chungbuk National University 1 Chungdae-Ro, Seowon-Gu, Cheongju 28644, South Korea
| | - Simranjeet Singh Sekhon
- School of Biological Sciences, Chungbuk National University 1 Chungdae-Ro, Seowon-Gu, Cheongju 28644, South Korea
| | - Sung-Keun Rhee
- School of Biological Sciences, Chungbuk National University 1 Chungdae-Ro, Seowon-Gu, Cheongju 28644, South Korea
| | - Jung Ho Ko
- College of Veterinary Medicine, Western University of Health Sciences, 309 East Second Street, Pomona California 91766, United States
| | - Ji-Young Ahn
- School of Biological Sciences, Chungbuk National University 1 Chungdae-Ro, Seowon-Gu, Cheongju 28644, South Korea
| | - Jiho Min
- Department of Bioprocess Engineering, Chonbuk National University, 567 Baekje-daero, Deokjin-Gu Jeonju, Jeonbuk 54896, South Korea
| | - Yang-Hoon Kim
- School of Biological Sciences, Chungbuk National University 1 Chungdae-Ro, Seowon-Gu, Cheongju 28644, South Korea
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Abstract
Microbiological diagnostic procedures have changed rapidly in recent years. This is especially true in the field of molecular diagnostics. Classical culture-based techniques are still the gold standard in many areas; however, they are already complemented by automated and also molecular techniques to guarantee faster and better quality results. The most commonly used techniques include real-time polymerase chain reaction (RT-PCR) based systems and nucleic acid hybridization. These procedures are used most powerfully from direct patient samples or in assays to detect the presence of nonculturable or fastidious organisms. Further techniques such as DNA sequencing are not yet used routinely for urological samples and can be considered experimental. However, in conjunction with dropping prices and further technical developments, these techniques promise to be used much more in the near future. Regarding bacterial identification from culture, mass spectrometry (MALDI-TOF MS) has become the technique of choice in recent years especially in Europe. It has tremendously shortened the time to result. This is now going to be extended to antibiotic susceptibility testing. This is of paramount importance in view of ever rising antimicrobial resistance rates. Techniques described in this review offer a faster and better microbiological diagnosis. Such continuous improvements are critical especially in times of cost pressure and rising antimicrobial resistance rates. It is in our interest to provide the best possible care for patients and in this regard a good and effective communication between the laboratory and the clinician is of vital importance.
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Affiliation(s)
- S Schubert
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-Universität München, Marchioninistr. 17, 81377, München, Deutschland.
| | - A Wieser
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-Universität München, Marchioninistr. 17, 81377, München, Deutschland.,Abteilung für Infektions- und Tropenmedizin der LMU, Leopoldstrasse 5, 80802, München, Deutschland.,Deutsches Zentrum für Infektionsforschung (DZIF), Standort München, München, Deutschland
| | - G Bonkat
- alta uro AG, Centralbahnplatz 6, 4051, Basel, Schweiz
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Srisa-Art M, Boehle KE, Geiss BJ, Henry CS. Highly Sensitive Detection of Salmonella typhimurium Using a Colorimetric Paper-Based Analytical Device Coupled with Immunomagnetic Separation. Anal Chem 2017; 90:1035-1043. [PMID: 29211962 DOI: 10.1021/acs.analchem.7b04628] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Salmonella causes over a million foodborne illnesses per year in the United States resulting in more hospitalizations and deaths than any other foodborne bacterial pathogen. To help prevent outbreaks, a rapid, portable, sensitive, and reliable method for onsite detection of bacteria that can be used in different sample matrices would be beneficial. Herein, we present a colorimetric paper-based analytical device (PAD) combined with immunomagnetic separation (IMS) for detecting Salmonella typhimurium. IMS anti-Salmonella coated magnetic beads were applied to capture and separate bacteria from the sample matrix and preconcentrate it into small volumes before testing on paper. To directly detect S. typhimurium after IMS, a sandwich immunoassay was implemented into the procedure with β-galactosidase (β-gal) as the detection enzyme. Using the antibody/enzyme complex, we performed a colorimetric assay with chlorophenol red-β-d-galactopyranoside (CPRG) for bacteria quantification. The method was confirmed to be highly specific to S. typhimurium without interference from other pathogenic bacteria like Escherichia coli. Using this system, the limit of detection of S. typhimurium was found to be 102 CFU mL-1 in culturing solution without any pre-enrichment. In addition, distance-based detection where the concentration is read as the length of colored band formed on the reaction was also demonstrated. This assay had a detection limit of 102 CFU mL-1 for S. typhimurium, providing an instrument-free quantitative analysis alternative to spot tests, which require image analysis. Finally, the proposed platform was applied for detection of S. typhimurium in inoculated Starling bird fecal samples and whole milk with detection limits of 105 CFU g-1 and 103 CFU mL-1, respectively, and this is the first published paper-based detection method for S. typhimurium in bird feces and whole milk.
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Affiliation(s)
- Monpichar Srisa-Art
- Department of Chemistry, Faculty of Science, Chulalongkorn University , Bangkok, 10330, Thailand
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Ali MM, Brown CL, Jahanshahi-Anbuhi S, Kannan B, Li Y, Filipe CDM, Brennan JD. A Printed Multicomponent Paper Sensor for Bacterial Detection. Sci Rep 2017; 7:12335. [PMID: 28951563 PMCID: PMC5615064 DOI: 10.1038/s41598-017-12549-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/12/2017] [Indexed: 12/14/2022] Open
Abstract
We present a simple all-in-one paper-based sensor for E. coli detection using a composite ink made of a fluorogenic DNAzyme probe for bacterial recognition and signal generation, lysozyme that lyses whole bacterial cells, and pullulan/trehalose sugars that stabilize printed bioactive molecules. The paper sensor is capable of producing a fluorescence signal as a readout within 5 minutes upon contacting E. coli, can achieve a limit of detection of 100 cells/mL, in a variety of sample matrixes, without sample enrichment, and remains stable for at least 6 months when stored at ambient temperature. Therefore, this simple paper sensor provides rapid bacterial testing on site, and can be shipped and stored under ambient conditions to benefit users living in resource-limited regions.
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Affiliation(s)
- M Monsur Ali
- Biointerfaces Institute, McMaster University, 1280 Main St W, Hamilton, Ontario, L8S 0A3, Canada
| | - Christine L Brown
- Department of Chemical Engineering, McMaster University, 1280 Main St W, Hamilton, Ontario, L8S 4L7, Canada
| | - Sana Jahanshahi-Anbuhi
- Department of Chemical Engineering, McMaster University, 1280 Main St W, Hamilton, Ontario, L8S 4L7, Canada
| | - Balamurali Kannan
- Biointerfaces Institute, McMaster University, 1280 Main St W, Hamilton, Ontario, L8S 0A3, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St. W, Hamilton, ON L8S 4K1, Canada
| | - Carlos D M Filipe
- Department of Chemical Engineering, McMaster University, 1280 Main St W, Hamilton, Ontario, L8S 4L7, Canada.
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main St W, Hamilton, Ontario, L8S 0A3, Canada.
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McVey C, Huang F, Elliott C, Cao C. Endonuclease controlled aggregation of gold nanoparticles for the ultrasensitive detection of pathogenic bacterial DNA. Biosens Bioelectron 2017; 92:502-508. [DOI: 10.1016/j.bios.2016.10.072] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/22/2016] [Accepted: 10/25/2016] [Indexed: 11/26/2022]
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Jain P, Chakma B, Singh N, Patra S, Goswami P. Metal-DNA Interactions Improve signal in High-Resolution Melting of DNA for Species Differentiation of Plasmodium Parasite. Mol Biotechnol 2017; 59:179-191. [PMID: 28421327 DOI: 10.1007/s12033-017-0004-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The success of high-resolution melting (HRM) analysis for distinguishing similar DNAs with minor base mismatch differences is limited. Here, metal-mediated structural change in DNA has been exploited to amplify HRM signals leading to differentiation of target DNAs in an orthologous gene corresponding to four Plasmodium species. Conserved 26-mer ssDNAs from ldh gene of the four Plasmodium species were employed as targets. A capture probe (CP) that is fully complementary to the Plasmodium falciparum target (FT) and has two base mismatches each, with the targets of Plasmodium vivax (VT), Plasmodium malariae, (MT), and Plasmodium ovale (OT), was considered. The DNA duplexes were treated with metal ions for structural perturbation and analyzed by HRM. Distinct resolution of melting fluorescence signal in otherwise identical HRM profiles for each of the DNA duplexes was achieved by using Ca+2 or Mg+2 ions, where, Ca+2 conferred higher resolution. The increase in resolution for CP-FT versus CP-OT, CP-FT versus CP-VT, CP-FT versus CP-MT, CP-VT versus CP-OT, and CP-MT versus CP-OT with Ca-DNA as compared to control was 67.3-, 20.4-, 22.0-, 10.9-, and 8.3-fold, respectively. The signal resolution was the highest at pH 8. The method could detect 0.25 pmol/µl of the target DNA. Structural analysis showed that Ca+2 and Mg+2 ions perturbed the structure of DNA. This perturbation helped to improve HRM signal resolution among DNA targets corresponding to the orthologous gene of four Plasmodium species. This novel approach has potential application not only for Plasmodium species-specific diagnosis but also for differentiation of DNAs with minor sequence variation.
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Affiliation(s)
- Priyamvada Jain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Babina Chakma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Naveen Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Sanjukta Patra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Pranab Goswami
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India.
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Valderrama WB, Dudley EG, Doores S, Cutter CN. Commercially Available Rapid Methods for Detection of Selected Food-borne Pathogens. Crit Rev Food Sci Nutr 2017; 56:1519-31. [PMID: 25749054 DOI: 10.1080/10408398.2013.775567] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Generally, the enumeration and isolation of food-borne pathogens is performed using culture-dependent methods. These methods are sensitive, inexpensive, and provide both qualitative and quantitative assessment of the microorganisms present in a sample, but these are time-consuming. For this reason, researchers are developing new techniques that allow detection of food pathogens in shorter period of time. This review identifies commercially available methods for rapid detection and quantification of Listeria monocytogenes, Salmonella spp., Staphylococcus aureus, and Shiga toxin-producing Escherichia coli in food samples. Three categories are discussed: immunologically based methods, nucleic acid-based assays, and biosensors. This review describes the basic mechanism and capabilities of each method, discusses the difficulties of choosing the most convenient method, and provides an overview of the future challenges for the technology for rapid detection of microorganisms.
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Affiliation(s)
- Wladir B Valderrama
- a Department of Food Science , Pennsylvania State University , University Park , Pennsylvania , USA
| | - Edward G Dudley
- a Department of Food Science , Pennsylvania State University , University Park , Pennsylvania , USA
| | - Stephanie Doores
- a Department of Food Science , Pennsylvania State University , University Park , Pennsylvania , USA
| | - Catherine N Cutter
- a Department of Food Science , Pennsylvania State University , University Park , Pennsylvania , USA
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Moore MD, Goulter RM, Jaykus LA. Human norovirus as a foodborne pathogen: challenges and developments. Annu Rev Food Sci Technol 2015; 6:411-33. [PMID: 25884284 DOI: 10.1146/annurev-food-022814-015643] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human noroviruses (NoVs) are the leading cause of foodborne illness in the United States, and they exact a considerable human and economic burden worldwide. In fact, the many challenging aspects of human NoV have caused some to call it the nearly perfect foodborne pathogen. In this review, a brief overview of NoVs and their genetic structure is provided. Additionally, the challenges and recent developments related to human NoVs regarding viral evolution, transmission, epidemiology, outbreak identification, cultivation, animal and human models, and detection are presented.
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Affiliation(s)
- Matthew D Moore
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695;
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Sun Y, Quyen TL, Hung TQ, Chin WH, Wolff A, Bang DD. A lab-on-a-chip system with integrated sample preparation and loop-mediated isothermal amplification for rapid and quantitative detection of Salmonella spp. in food samples. LAB ON A CHIP 2015; 15:1898-904. [PMID: 25715949 DOI: 10.1039/c4lc01459f] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Foodborne disease is a major public health threat worldwide. Salmonellosis, an infectious disease caused by Salmonella spp., is one of the most common foodborne diseases. Isolation and identification of Salmonella by conventional bacterial culture or molecular-based methods are time consuming and usually take a few hours to days to complete. In response to the demand for rapid on line or on site detection of pathogens, in this study, we describe for the first time an eight-chamber lab-on-a-chip (LOC) system with integrated magnetic bead-based sample preparation and loop-mediated isothermal amplification (LAMP) for rapid and quantitative detection of Salmonella spp. in food samples. The whole diagnostic procedures including DNA isolation, isothermal amplification, and real-time detection were accomplished in a single chamber. Up to eight samples could be handled simultaneously and the system was capable to detect Salmonella at concentration of 50 cells per test within 40 min. The simple design, together with high level of integration, isothermal amplification, and quantitative analysis of multiple samples in short time, will greatly enhance the practical applicability of the LOC system for rapid on-site screening of Salmonella for applications in food safety control, environmental surveillance, and clinical diagnostics.
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Affiliation(s)
- Yi Sun
- Department of Micro and Nanotechnology (DTU-Nanotech), Technical University of Denmark, Ørsteds Plads, DK-2800 Kgs. Lyngby, Denmark
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Bartsch MS, Edwards HS, Lee D, Moseley CE, Tew KE, Renzi RF, Van de Vreugde JL, Kim H, Knight DL, Sinha A, Branda SS, Patel KD. The rotary zone thermal cycler: a low-power system enabling automated rapid PCR. PLoS One 2015; 10:e0118182. [PMID: 25826708 PMCID: PMC4380418 DOI: 10.1371/journal.pone.0118182] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 01/09/2015] [Indexed: 12/17/2022] Open
Abstract
Advances in molecular biology, microfluidics, and laboratory automation continue to expand the accessibility and applicability of these methods beyond the confines of conventional, centralized laboratory facilities and into point of use roles in clinical, military, forensic, and field-deployed applications. As a result, there is a growing need to adapt the unit operations of molecular biology (e.g., aliquoting, centrifuging, mixing, and thermal cycling) to compact, portable, low-power, and automation-ready formats. Here we present one such adaptation, the rotary zone thermal cycler (RZTC), a novel wheel-based device capable of cycling up to four different fixed-temperature blocks into contact with a stationary 4-microliter capillary-bound sample to realize 1-3 second transitions with steady state heater power of less than 10 W. We demonstrate the utility of the RZTC for DNA amplification as part of a highly integrated rotary zone PCR (rzPCR) system that uses low-volume valves and syringe-based fluid handling to automate sample loading and unloading, thermal cycling, and between-run cleaning functionalities in a compact, modular form factor. In addition to characterizing the performance of the RZTC and the efficacy of different online cleaning protocols, we present preliminary results for rapid single-plex PCR, multiplex short tandem repeat (STR) amplification, and second strand cDNA synthesis.
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Affiliation(s)
- Michael S. Bartsch
- Sandia National Laboratories, Livermore, CA, United States of America
- * E-mail:
| | | | - Daniel Lee
- Sandia National Laboratories, Livermore, CA, United States of America
| | | | - Karen E. Tew
- Sandia National Laboratories, Livermore, CA, United States of America
| | - Ronald F. Renzi
- Sandia National Laboratories, Livermore, CA, United States of America
| | | | - Hanyoup Kim
- Sandia National Laboratories, Livermore, CA, United States of America
| | | | - Anupama Sinha
- Sandia National Laboratories, Livermore, CA, United States of America
| | - Steven S. Branda
- Sandia National Laboratories, Livermore, CA, United States of America
| | - Kamlesh D. Patel
- Sandia National Laboratories, Livermore, CA, United States of America
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Benami M, Gillor O, Gross A. The question of pathogen quantification in disinfected graywater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 506-507:496-504. [PMID: 25437766 DOI: 10.1016/j.scitotenv.2014.11.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 11/15/2014] [Accepted: 11/15/2014] [Indexed: 05/26/2023]
Abstract
Graywater (GW) reuse for irrigation is recognized as a sustainable solution for water conservation. One of the major impediments to GW reuse is the presence of pathogenic microorganisms. This study monitored three similar on-site GW treatment systems bi-monthly over the course of a year to compare the presence of pathogens and indicators in raw, biologically treated, and biologically treated and disinfected [by chlorine and ultraviolet light (UV)] GW. The systems were designed to allow the testing of the same batch (collection) of water as it passed through the treatment chain. The samples were analyzed using standard culture-dependent methods and the data were compared to culture-independent DNA-based methods. Results suggested that the presence and abundance of fecal coliforms, Escherichia coli, Salmonella enterica, Enterococcus spp., Staphylococcus aureus and Pseudomonas aeruginosa differ among the various GW streams (e.g. raw, biologically treated, and disinfected). The culture-dependent analyses suggested that both chlorine and UV inactivate most of the bacteria tested in the biologically treated GW, albeit at different efficiencies. Conversely, the DNA-based analyses indicated no significant differences in pathogenic bacterial abundance between the biologically treated GW with or without disinfection. To better understand the discrepancies between the results, we repeated the analysis in the laboratory under controlled conditions using Enterococcus faecalis as a model bacterium and obtained similar results. We suggest that disinfection of biologically treated GW with chlorine or UV is effective for treating pathogens, but that the inactivation efficiency cannot be estimated by DNA-based qPCR.
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Affiliation(s)
- Maya Benami
- Zuckerberg Institute for Water Research, Israel; Albert Katz International School for Desert Studies,; The Jacob Blaustein Institutes for Desert Research,; Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben Gurion 84990, Israel
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Israel; Albert Katz International School for Desert Studies,; The Jacob Blaustein Institutes for Desert Research,; Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben Gurion 84990, Israel.
| | - Amit Gross
- Zuckerberg Institute for Water Research, Israel; Albert Katz International School for Desert Studies,; The Jacob Blaustein Institutes for Desert Research,; Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben Gurion 84990, Israel.
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48
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Law JWF, Ab Mutalib NS, Chan KG, Lee LH. Rapid methods for the detection of foodborne bacterial pathogens: principles, applications, advantages and limitations. Front Microbiol 2015. [PMID: 25628612 DOI: 10.3389/fmicb.2014.00770.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The incidence of foodborne diseases has increased over the years and resulted in major public health problem globally. Foodborne pathogens can be found in various foods and it is important to detect foodborne pathogens to provide safe food supply and to prevent foodborne diseases. The conventional methods used to detect foodborne pathogen are time consuming and laborious. Hence, a variety of methods have been developed for rapid detection of foodborne pathogens as it is required in many food analyses. Rapid detection methods can be categorized into nucleic acid-based, biosensor-based and immunological-based methods. This review emphasizes on the principles and application of recent rapid methods for the detection of foodborne bacterial pathogens. Detection methods included are simple polymerase chain reaction (PCR), multiplex PCR, real-time PCR, nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP) and oligonucleotide DNA microarray which classified as nucleic acid-based methods; optical, electrochemical and mass-based biosensors which classified as biosensor-based methods; enzyme-linked immunosorbent assay (ELISA) and lateral flow immunoassay which classified as immunological-based methods. In general, rapid detection methods are generally time-efficient, sensitive, specific and labor-saving. The developments of rapid detection methods are vital in prevention and treatment of foodborne diseases.
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Affiliation(s)
- Jodi Woan-Fei Law
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Selangor Darul Ehsan, Malaysia ; School of Science, Monash University Malaysia Selangor Darul Ehsan, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, Bandar Tun Razak Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Learn-Han Lee
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Selangor Darul Ehsan, Malaysia
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49
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Law JWF, Ab Mutalib NS, Chan KG, Lee LH. Rapid methods for the detection of foodborne bacterial pathogens: principles, applications, advantages and limitations. Front Microbiol 2015; 5:770. [PMID: 25628612 PMCID: PMC4290631 DOI: 10.3389/fmicb.2014.00770] [Citation(s) in RCA: 514] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/17/2014] [Indexed: 12/11/2022] Open
Abstract
The incidence of foodborne diseases has increased over the years and resulted in major public health problem globally. Foodborne pathogens can be found in various foods and it is important to detect foodborne pathogens to provide safe food supply and to prevent foodborne diseases. The conventional methods used to detect foodborne pathogen are time consuming and laborious. Hence, a variety of methods have been developed for rapid detection of foodborne pathogens as it is required in many food analyses. Rapid detection methods can be categorized into nucleic acid-based, biosensor-based and immunological-based methods. This review emphasizes on the principles and application of recent rapid methods for the detection of foodborne bacterial pathogens. Detection methods included are simple polymerase chain reaction (PCR), multiplex PCR, real-time PCR, nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP) and oligonucleotide DNA microarray which classified as nucleic acid-based methods; optical, electrochemical and mass-based biosensors which classified as biosensor-based methods; enzyme-linked immunosorbent assay (ELISA) and lateral flow immunoassay which classified as immunological-based methods. In general, rapid detection methods are generally time-efficient, sensitive, specific and labor-saving. The developments of rapid detection methods are vital in prevention and treatment of foodborne diseases.
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Affiliation(s)
- Jodi Woan-Fei Law
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University MalaysiaSelangor Darul Ehsan, Malaysia
- School of Science, Monash University MalaysiaSelangor Darul Ehsan, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, Bandar Tun RazakKuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of MalayaKuala Lumpur, Malaysia
| | - Learn-Han Lee
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University MalaysiaSelangor Darul Ehsan, Malaysia
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50
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Review of Salmonella detection and identification methods: Aspects of rapid emergency response and food safety. Food Control 2015. [DOI: 10.1016/j.foodcont.2014.07.011] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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