1
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Peng K, Wu Z, Feng Z, Deng R, Ma X, Fan B, Liu H, Tang Z, Zhao Z, Li Y. A highly integrated digital PCR system with on-chip heating for accurate DNA quantitative analysis. Biosens Bioelectron 2024; 253:116167. [PMID: 38422813 DOI: 10.1016/j.bios.2024.116167] [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: 09/27/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/02/2024]
Abstract
Digital polymerase chain reaction (dPCR) is extensively used for highly sensitive disease diagnosis due to its single-molecule detection ability. However, current dPCR systems require intricate DNA sample distribution, rely on cumbersome external heaters, and exhibit sluggish thermal cycling, hampering efficiency and speed of the dPCR process. Herein, we presented the development of a microwell array based dPCR system featuring an integrated self-heating dPCR chip. By utilizing hydrodynamic and electrothermal simulations, the chip's structure is optimized, resulting in improved partitioning within microwells and uniform thermal distribution. Through strategic hydrophilic/hydrophobic modifications on the chip's surface, we effectively secured the compartmentalization of sample within the microwells by employing an overlaying oil phase, which renders homogeneity and independence of samples in the microwells. To achieve precise, stable, uniform, and rapid self-heating of the chip, the ITO heating layer and the temperature control algorithm are deliberately designed. With a capacity of 22,500 microwells that can be easily expanded, the system successfully quantified EGFR plasmid solutions, exhibiting a dynamic linear range of 105 and a detection limit of 10 copies per reaction. To further validate its performance, we employed the dPCR platform for quantitative detection of BCR-ABL1 mutation gene fragments, where its performance was compared against the QuantStudio 3D, and the self-heating dPCR system demonstrated similar analytical accuracy to the commercial dPCR system. Notably, the individual chip is produced on a semiconductor manufacturing line, benefiting from mass production capabilities, so the chips are cost-effective and conducive to widespread adoption and accessibility.
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Affiliation(s)
- Kang Peng
- BOE Technology Group Co Ltd., Beijing, 100176, PR China
| | - Zhihong Wu
- BOE Technology Group Co Ltd., Beijing, 100176, PR China
| | - Zhongxin Feng
- Affiliated Hospital of Guizhou Medical University, Guiyang, 550002, Guizhou, PR China
| | - Ruijun Deng
- BOE Technology Group Co Ltd., Beijing, 100176, PR China
| | - Xiangguo Ma
- BOE Technology Group Co Ltd., Beijing, 100176, PR China
| | - Beiyuan Fan
- BOE Technology Group Co Ltd., Beijing, 100176, PR China
| | - Haonan Liu
- BOE Technology Group Co Ltd., Beijing, 100176, PR China
| | - Zhuzhu Tang
- Affiliated Hospital of Guizhou Medical University, Guiyang, 550002, Guizhou, PR China
| | - Zijian Zhao
- BOE Technology Group Co Ltd., Beijing, 100176, PR China.
| | - Yanzhao Li
- BOE Technology Group Co Ltd., Beijing, 100176, PR China.
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2
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Sancha Dominguez L, Cotos Suárez A, Sánchez Ledesma M, Muñoz Bellido JL. Present and Future Applications of Digital PCR in Infectious Diseases Diagnosis. Diagnostics (Basel) 2024; 14:931. [PMID: 38732345 PMCID: PMC11083499 DOI: 10.3390/diagnostics14090931] [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: 03/19/2024] [Revised: 04/19/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
Infectious diseases account for about 3 million deaths per year. The advent of molecular techniques has led to an enormous improvement in their diagnosis, both in terms of sensitivity and specificity and in terms of the speed with which a clinically useful result can be obtained. Digital PCR, or 3rd generation PCR, is based on a series of technical modifications that result in more sensitive techniques, more resistant to the action of inhibitors and capable of direct quantification without the need for standard curves. This review presents the main applications that have been developed for the diagnosis of viral, bacterial, and parasitic infections and the potential prospects for the clinical use of this technology.
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Affiliation(s)
- Laura Sancha Dominguez
- Department of Microbiology, Hospital Universitario de Salamanca, 37007 Salamanca, Spain; (L.S.D.); (A.C.S.)
- Research Group IIMD-16, Institute for Biomedical Research of Salamanca (IBSAL), SACYL, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
| | - Ana Cotos Suárez
- Department of Microbiology, Hospital Universitario de Salamanca, 37007 Salamanca, Spain; (L.S.D.); (A.C.S.)
- Research Group IIMD-16, Institute for Biomedical Research of Salamanca (IBSAL), SACYL, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
| | - María Sánchez Ledesma
- Infectious Diseases Unit, Hospital Universitario de Salamanca, 37007 Salamanca, Spain;
| | - Juan Luis Muñoz Bellido
- Department of Microbiology, Hospital Universitario de Salamanca, 37007 Salamanca, Spain; (L.S.D.); (A.C.S.)
- Research Group IIMD-16, Institute for Biomedical Research of Salamanca (IBSAL), SACYL, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
- Department of Biomedical and Diagnosis Sciences, Faculty of Medicine, Universidad de Salamanca, 37007 Salamanca, Spain
- Center for Research on Tropical Diseases, Universidad de Salamanca (CIETUS), 37007 Salamanca, Spain
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3
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Mao Y, Zhou X, Hu W, Yang W, Cheng Z. Dynamic video recognition for cell-encapsulating microfluidic droplets. Analyst 2024; 149:2147-2160. [PMID: 38441128 DOI: 10.1039/d4an00022f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Droplet microfluidics is a highly sensitive and high-throughput technology extensively utilized in biomedical applications, such as single-cell sequencing and cell screening. However, its performance is highly influenced by the droplet size and single-cell encapsulation rate (following random distribution), thereby creating an urgent need for quality control. Machine learning has the potential to revolutionize droplet microfluidics, but it requires tedious pixel-level annotation for network training. This paper investigates the application software of the weakly supervised cell-counting network (WSCApp) for video recognition of microdroplets. We demonstrated its real-time performance in video processing of microfluidic droplets and further identified the locations of droplets and encapsulated cells. We verified our methods on droplets encapsulating six types of cells/beads, which were collected from various microfluidic structures. Quantitative experimental results showed that our approach can not only accurately distinguish droplet encapsulations (micro-F1 score > 0.94), but also locate each cell without any supervised location information. Furthermore, fine-tuning transfer learning on the pre-trained model also significantly reduced (>80%) annotation. This software provides a user-friendly and assistive annotation platform for the quantitative assessment of cell-encapsulating microfluidic droplets.
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Affiliation(s)
- Yuanhang Mao
- Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Xiao Zhou
- Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Weiguo Hu
- Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Weiyang Yang
- Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Zhen Cheng
- Department of Automation, Tsinghua University, Beijing, 100084, China.
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4
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Gao S, Xu T, Wu L, Zhu X, Wang X, Chen Y, Li G, Li X. Complete Prevention of Bubbles in a PDMS-Based Digital PCR Chip with a Multifunction Cavity. BIOSENSORS 2024; 14:114. [PMID: 38534221 DOI: 10.3390/bios14030114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/04/2024] [Accepted: 01/09/2024] [Indexed: 03/28/2024]
Abstract
In a chamber-based digital PCR (dPCR) chip fabricated with polydimethylsiloxane (PDMS), bubble generation in the chambers at high temperatures is a critical issue. Here, we found that the main reason for bubble formation in PDMS chips is the too-high saturated vapor pressure of water at an elevated temperature. The bubbles should be completely prevented by reducing the initial pressure of the system to under 13.6 kPa to eliminate the effects of increased-pressure water vapor. Then, a cavity was designed and fabricated above the PCR reaction layer, and Parylene C was used as a shell covering the chip. The cavity was used for the negative generator in sample loading, PDMS degassing, PCR solution degassing in the digitization process and water storage in the thermal reaction process. The analysis was confirmed and finally achieved a desirable bubble-free, fast-digitization, valve-free and no-tubing connection dPCR.
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Affiliation(s)
- Shiyuan Gao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Tiegang Xu
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Wu
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyue Zhu
- Metabolomics Center, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuefeng Wang
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Chen
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gang Li
- Key Laboratory of Optoelectronic Technology and Systems, Ministry of Education, Defense Key Disciplines Lab of Novel Micro-Nano Devices and System Technology, Chongqing University, Chongqing 400044, China
| | - Xinxin Li
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
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5
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Zhang X, Wang S, Wang J, Sun X, Xue J, Wang Z, Yang T, Weng L, Wang B, Luo G. A ddPCR platform based on a microfluidic chip with a dual-function flow-focusing structure for sample-to-result DNA quantification analysis. LAB ON A CHIP 2024; 24:738-750. [PMID: 38192250 DOI: 10.1039/d3lc01078c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Droplet digital PCR (ddPCR) is a powerful method for absolute nucleic acid quantification with high precision and accuracy. However, complicated operational steps have hampered the use and diffusion of ddPCR. Therefore, an automated, easy-to-use, low-sample-consumption, and portable ddPCR platform is urgently needed. This paper proposes a microfluidic ddPCR platform based on a microfluidic chip that can realize the sample-to-result function by switching the rotary valve, achieving the dual function of the flow-focusing structure for droplet generation and readout. Sample, generation oil, and analysis oil were pre-added to the reservoirs. Droplets were generated due to focusing flow, and after passing through the integrated temporary storage bin in the rotary valve, the droplets and oil subsequently entered the collecting tube, improving the droplet-to-oil volume ratio for enhanced thermal cycle performance. Droplets with an average diameter of 107.44 μm and a CV of 2.38% were generated using our chip under the optimal pressures. High-performance thermal cycling was achieved through improvements of the droplet-to-oil volume ratio of the sample, the integrated heating lid, the pure copper heating base, and the temperature-controlling algorithm. Gradient quantification experiments were conducted for the HER2 and CEP17 genes extracted from breast cancer cells, yielding strong linear correlations with R2 values of 0.9996 for FAM and 0.9989 for CY5. Moreover, pronounced linearity was obtained between the detected concentrations of HER2 and CEP17, indicated by a slope of 1.0091 and an R2 of 0.9997, signifying consistent HER2 : CEP17 ratios across various sample dilutions. The outcomes of the quantitative analysis, encompassing the dynamic range and the consistency of the HER2 : CEP17 ratio using our ddPCR platform, meet the standards required for breast cancer assessment and therapy. Our ddPCR platform is automated, portable, and capable of stable droplet generation, high-efficiency amplification, realization of the sample-to-result function based on dual-function flow-focusing structure, and accuracy absolute quantification, underscoring its significant potential for ddPCR analysis in clinical diagnostics.
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Affiliation(s)
- Xiaoliang Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China.
| | - Shun Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China.
| | - Jinxian Wang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China.
| | - Xiaojie Sun
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China.
| | - Jinbing Xue
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China.
| | - Zhenya Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China.
| | - Tianhang Yang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China.
| | - Liangfei Weng
- Suzhou Guoke Medical Science & Technology Development Co. Ltd, Suzhou 215163, People's Republic of China
| | - Bidou Wang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China.
| | - Gangyin Luo
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China.
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6
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Zhang W, Cui L, Wang Y, Xie Z, Wei Y, Zhu S, Nawaz M, Mak WC, Ho HP, Gu D, Zeng S. An Integrated ddPCR Lab-on-a-Disc Device for Rapid Screening of Infectious Diseases. BIOSENSORS 2023; 14:2. [PMID: 38275303 PMCID: PMC10813669 DOI: 10.3390/bios14010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/14/2023] [Accepted: 12/16/2023] [Indexed: 01/27/2024]
Abstract
Digital droplet PCR (ddPCR) is a powerful amplification technique for absolute quantification of viral nucleic acids. Although commercial ddPCR devices are effective in the lab bench tests, they cannot meet current urgent requirements for on-site and rapid screening for patients. Here, we have developed a portable and fully integrated lab-on-a-disc (LOAD) device for quantitively screening infectious disease agents. Our designed LOAD device has integrated (i) microfluidics chips, (ii) a transparent circulating oil-based heat exchanger, and (iii) an on-disc transmitted-light fluorescent imaging system into one compact and portable box. Thus, droplet generation, PCR thermocycling, and analysis can be achieved in a single LOAD device. This feature is a significant attribute for the current clinical application of disease screening. For this custom-built ddPCR setup, we have first demonstrated the loading and ddPCR amplification ability by using influenza A virus-specific DNA fragments with different concentrations (diluted from the original concentration to 107 times), followed by analyzing the droplets with an external fluorescence microscope as a standard calibration test. The measured DNA concentration is linearly related to the gradient-dilution factor, which validated the precise quantification for the samples. In addition to the calibration tests using DNA fragments, we also employed this ddPCR-LOAD device for clinical samples with different viruses. Infectious samples containing five different viruses, including influenza A virus (IAV), respiratory syncytial virus (RSV), varicella zoster virus (VZV), Zika virus (ZIKV), and adenovirus (ADV), were injected into the device, followed by analyzing the droplets with an external fluorescence microscope with the lowest detected concentration of 20.24 copies/µL. Finally, we demonstrated the proof-of-concept detection of clinical samples of IAV using the on-disc fluorescence imaging system in our fully integrated device, which proves the capability of this device in clinical sample detection. We anticipate that this integrated ddPCR-LOAD device will become a flexible tool for on-site disease detection.
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Grants
- GRF14204621, GRF14207920, GRF14207419, GRF14207121, N_CUHK407/16 Hong Kong Research Grants Council
- No.2021A1515220084, No. 2022B1111020001 the National Key Research and Development Program of China
- ZDSYS20210623092001003, GJHZ20200731095604013, JSGG20220301090003004, No. 201906133000069, No. SGLH20180625171602058, and JCYJ20200109120205924 Shenzhen Science and Technology Foundation
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Affiliation(s)
- Wanyi Zhang
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China; (W.Z.); (Z.X.); (Y.W.); (S.Z.); (M.N.); (W.-C.M.)
| | - Lili Cui
- School of Public Health, Guangdong Medical University, Dongguan 523808, China;
- Laboratory Medicine, Shenzhen Key Laboratory of Medical Laboratory and Molecular Diagnostics, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen 518035, China;
| | - Yuye Wang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Zhenming Xie
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China; (W.Z.); (Z.X.); (Y.W.); (S.Z.); (M.N.); (W.-C.M.)
| | - Yuanyuan Wei
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China; (W.Z.); (Z.X.); (Y.W.); (S.Z.); (M.N.); (W.-C.M.)
| | - Shaodi Zhu
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China; (W.Z.); (Z.X.); (Y.W.); (S.Z.); (M.N.); (W.-C.M.)
- Light, Nanomaterials & Nanotechnologies (L2n), CNRS-EMR 7004, Université de Technologie de Troyes, 10000 Troyes, France
| | - Mehmood Nawaz
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China; (W.Z.); (Z.X.); (Y.W.); (S.Z.); (M.N.); (W.-C.M.)
| | - Wing-Cheung Mak
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China; (W.Z.); (Z.X.); (Y.W.); (S.Z.); (M.N.); (W.-C.M.)
| | - Ho-Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China; (W.Z.); (Z.X.); (Y.W.); (S.Z.); (M.N.); (W.-C.M.)
| | - Dayong Gu
- Laboratory Medicine, Shenzhen Key Laboratory of Medical Laboratory and Molecular Diagnostics, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen 518035, China;
| | - Shuwen Zeng
- Light, Nanomaterials & Nanotechnologies (L2n), CNRS-EMR 7004, Université de Technologie de Troyes, 10000 Troyes, France
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7
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Song X, Wang Q, Liu Q, Yu L, Wang S, Yao N, Tong L, Zhang L. Twisted Optical Micro/Nanofibers Enabled Detection of Subtle Temperature Variation. ACS APPLIED MATERIALS & INTERFACES 2023; 15:47177-47183. [PMID: 37755699 DOI: 10.1021/acsami.3c07831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
The detection of subtle temperature variation plays an important role in many applications, including proximity sensing in robotics, temperature measurements in microfluidics, and tumor monitoring in healthcare. Herein, a flexible miniaturized optical temperature sensor is fabricated by embedding twisted micro/nanofibers in a thin layer of polydimethylsiloxane. Enabled by the dramatic change of the coupling ratio under subtle temperature variation, the sensor exhibits an ultrahigh sensitivity (-30 nm/°C) and high resolution (0.0012 °C). As a proof-of-concept demonstration, a robotic arm equipped with our sensor can avoid undesired collisions by detecting the subtle temperature variation caused by the existence of a human. Moreover, benefiting from the miniaturized and engineerable sensing structure, real-time measurement of subtle temperature variation in microfluidic chips is realized. These initial results pave the way toward a category of optical sensing devices ranging from robotic skin to human-machine interfaces and implantable healthcare sensors.
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Affiliation(s)
- Xingda Song
- Research Center for Humanoid Sensing, Zhejiang Lab, Hangzhou 311121, China
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Qi Wang
- Research Center for Humanoid Sensing, Zhejiang Lab, Hangzhou 311121, China
| | - Qiulan Liu
- Research Center for Intelligent Chips and Devices, Zhejiang Lab, Hangzhou 311121, China
| | - Longteng Yu
- Research Center for Humanoid Sensing, Zhejiang Lab, Hangzhou 311121, China
| | - Shipeng Wang
- Research Center for Humanoid Sensing, Zhejiang Lab, Hangzhou 311121, China
| | - Ni Yao
- Research Center for Humanoid Sensing, Zhejiang Lab, Hangzhou 311121, China
| | - Limin Tong
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Lei Zhang
- Research Center for Humanoid Sensing, Zhejiang Lab, Hangzhou 311121, China
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, China
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8
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Li J, Cheng J, Li S, Wu JJ, Li J. Virtual Multiplexing Chamber-Based Digital PCR for Camel Milk Authentication Applications. MICROMACHINES 2023; 14:1619. [PMID: 37630155 PMCID: PMC10456615 DOI: 10.3390/mi14081619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023]
Abstract
In this work, we proposed a chamber-based digital PCR (cdPCR) microfluidic device that is compatible with fluorescence imaging systems for milk adulteration detection. The device enables the digitalization of PCR reagents, which are loaded into microchambers, and subsequent thermocycling for DNA amplification. Then, fluorescence images of the microchambers are captured and analyzed to obtain the total number of positive chambers, which is used to calculate the copy numbers of the target DNA, enabling accurate quantitative detections to determine intentional milk adulteration from accidental contaminations. The validation of this device is performed by camel milk authentication. We performed 25,600-chamber virtual multiplexing cdPCR tests using 40 × 40 chamber devices for the detection of DNA templates extracted from pure or mixed milk with different dilutions. Then, the cdPCR chip was used to authenticate blind milk samples, demonstrating its efficacy in real biotechnical applications.
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Affiliation(s)
- Jinchao Li
- Hebei Key Laboratory of Smart Sensing and Human-Robot Interactions, School of Mechanical Engineering, Hebei University of Technology, Tianjin 300130, China
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300130, China
| | - Jingmeng Cheng
- Hebei Key Laboratory of Smart Sensing and Human-Robot Interactions, School of Mechanical Engineering, Hebei University of Technology, Tianjin 300130, China
| | - Shanshan Li
- Hebei Key Laboratory of Smart Sensing and Human-Robot Interactions, School of Mechanical Engineering, Hebei University of Technology, Tianjin 300130, China
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300130, China
| | - Jie Jayne Wu
- Department of Electrical Engineering and Computer Science, The University of Tennessee, Knoxville, TN 37996, USA
| | - Junwei Li
- Institute of Biophysics, School of Health Sciences and Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
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9
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Kang BH, Jang KW, Yu ES, Na H, Lee YJ, Ko WY, Bae N, Rho D, Jeong KH. Ultrafast Plasmonic Nucleic Acid Amplification and Real-Time Quantification for Decentralized Molecular Diagnostics. ACS NANO 2023; 17:6507-6518. [PMID: 36971140 PMCID: PMC10081571 DOI: 10.1021/acsnano.2c11831] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 03/23/2023] [Indexed: 06/18/2023]
Abstract
Point-of-care real-time reverse-transcription polymerase chain reaction (RT-PCR) facilitates the widespread use of rapid, accurate, and cost-effective near-patient testing that is available to the public. Here, we report ultrafast plasmonic nucleic acid amplification and real-time quantification for decentralized molecular diagnostics. The plasmonic real-time RT-PCR system features an ultrafast plasmonic thermocycler (PTC), a disposable plastic-on-metal (PoM) cartridge, and an ultrathin microlens array fluorescence (MAF) microscope. The PTC provides ultrafast photothermal cycling under white-light-emitting diode illumination and precise temperature monitoring with an integrated resistance temperature detector. The PoM thin film cartridge allows rapid heat transfer as well as complete light blocking from the photothermal excitation source, resulting in real-time and highly efficient PCR quantification. Besides, the MAF microscope exhibits close-up and high-contrast fluorescence microscopic imaging. All of the systems were fully packaged in a palm size for point-of-care testing. The real-time RT-PCR system demonstrates the rapid diagnosis of coronavirus disease-19 RNA virus within 10 min and yields 95.6% of amplification efficiency, 96.6% of classification accuracy for preoperational test, and 91% of total percent agreement for clinical diagnostic test. The ultrafast and compact PCR system can decentralize point-of-care molecular diagnostic testing in primary care and developing countries.
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Affiliation(s)
- Byoung-Hoon Kang
- Department
of Bio and Brain Engineering, Korea Advanced
Institute of Science and Technology (KAIST), 291 Daehak-ro,
Yuseong-gu, Daejeon 34141, Republic of Korea
- KAIST
Institute for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro,
Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Kyung-Won Jang
- Department
of Bio and Brain Engineering, Korea Advanced
Institute of Science and Technology (KAIST), 291 Daehak-ro,
Yuseong-gu, Daejeon 34141, Republic of Korea
- KAIST
Institute for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro,
Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Eun-Sil Yu
- Department
of Bio and Brain Engineering, Korea Advanced
Institute of Science and Technology (KAIST), 291 Daehak-ro,
Yuseong-gu, Daejeon 34141, Republic of Korea
- KAIST
Institute for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro,
Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hamin Na
- Department
of Bio and Brain Engineering, Korea Advanced
Institute of Science and Technology (KAIST), 291 Daehak-ro,
Yuseong-gu, Daejeon 34141, Republic of Korea
- KAIST
Institute for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro,
Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yun-Jae Lee
- OSANG
Healthcare Co., Ltd., 132, Anyangcheondong-ro, Dongan-gu, Anyang-si, Gyeonggi-do 14040, Korea
| | - Woong-Yeol Ko
- OSANG
Healthcare Co., Ltd., 132, Anyangcheondong-ro, Dongan-gu, Anyang-si, Gyeonggi-do 14040, Korea
| | - NamHo Bae
- Center
for Nano Bio Development, National NanoFab
Center (NNFC), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Donggee Rho
- Center
for Nano Bio Development, National NanoFab
Center (NNFC), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Ki-Hun Jeong
- Department
of Bio and Brain Engineering, Korea Advanced
Institute of Science and Technology (KAIST), 291 Daehak-ro,
Yuseong-gu, Daejeon 34141, Republic of Korea
- KAIST
Institute for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro,
Yuseong-gu, Daejeon 34141, Republic of Korea
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10
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Hu Q, Kanwal F, Lyu W, Zhang J, Liu X, Qin K, Shen F. Multiplex Digital Polymerase Chain Reaction on a Droplet Array SlipChip for Analysis of KRAS Mutations in Pancreatic Cancer. ACS Sens 2023; 8:114-121. [PMID: 36520653 DOI: 10.1021/acssensors.2c01776] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pancreatic cancer is a terminal disease with high mortality and very poor prognosis. A sensitive and quantitative analysis of KRAS mutations in pancreatic cancer provides a tool not only to understand the biological mechanisms of pancreatic cancer but also for diagnosis and treatment monitoring. Digital polymerase chain reaction (PCR) is a promising tool for KRAS mutation analysis, but current methods generally require a complex microfluidic handling system, which can be challenging to implement in routine research and point-of-care clinical diagnostics. Here, we present a droplet-array SlipChip (da-SlipChip) for the multiplex quantification of KRAS G12D, V, R, and C mutant genes with the wild-type (WT) gene background by dual color (FAM/ROX) fluorescence detection. This da-SlipChip is a high-density microwell array of 21,696 wells of 200 pL in 4 by 5424 microwell format with simple loading and slipping operation. It does not require the same precise alignment of microfeatures on the different plates that are acquired by the traditional digital PCR SlipChip. This device can provide accurate quantification of both mutant genes and the WT KRAS gene. We collected tumor tissue, paired normal pancreatic tissue, and other normal tissues from 18 pancreatic cancer patients and analyzed the mutation profiles of KRAS G12D, V, R, and C in these samples; the results from the multiplex digital PCR on da-SlipChip agree well with those of next-generation sequencing (NGS). This da-SlipChip moves digital PCR closer to the practical point-of-care applications not only for detecting KRAS mutations in pancreatic cancer but also for other applications that require precise nucleic acid quantification with high sensitivity.
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Affiliation(s)
- Qixin Hu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Fariha Kanwal
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Weiyuan Lyu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Jiajie Zhang
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Xu Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Kai Qin
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
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11
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Fast Track Diagnostic Tools for Clinical Management of Sepsis: Paradigm Shift from Conventional to Advanced Methods. Diagnostics (Basel) 2023; 13:diagnostics13020277. [PMID: 36673087 PMCID: PMC9857847 DOI: 10.3390/diagnostics13020277] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/24/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Sepsis is one of the deadliest disorders in the new century due to specific limitations in early and differential diagnosis. Moreover, antimicrobial resistance (AMR) is becoming the dominant threat to human health globally. The only way to encounter the spread and emergence of AMR is through the active detection and identification of the pathogen along with the quantification of resistance. For better management of such disease, there is an essential requirement to approach many suitable diagnostic techniques for the proper administration of antibiotics and elimination of these infectious diseases. The current method employed for the diagnosis of sepsis relies on the conventional culture of blood suspected infection. However, this method is more time consuming and generates results that are false negative in the case of antibiotic pretreated samples as well as slow-growing microbes. In comparison to the conventional method, modern methods are capable of analyzing blood samples, obtaining accurate results from the suspicious patient of sepsis, and giving all the necessary information to identify the pathogens as well as AMR in a short period. The present review is intended to highlight the culture shift from conventional to modern and advanced technologies including their limitations for the proper and prompt diagnosing of bloodstream infections and AMR detection.
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12
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Pudasaini S, Thapa G, Marasini BP, Giri B. Smartphone-operated affordable PCR thermal cycler for the detection of antimicrobial resistant bacterial genes. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001120. [PMID: 36962978 PMCID: PMC10021165 DOI: 10.1371/journal.pgph.0001120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 01/27/2023] [Indexed: 03/03/2023]
Abstract
Antimicrobial resistance (AMR) is a global public health threat. Surveillance of AMR requires affordable, rapid, and user-friendly diagnostic methods. Our aim was to develop a low-cost thermocycler to perform polymerase chain reaction (PCR). We developed a smartphone-operated PCR thermal cycler using locally available recycled materials. The thermal cycler was used for the amplification for three bacterial genes-bla-TEM, bla-CTXM and 16s rRNA in human urine samples. The performance of custom-built thermal cycler was compared with commercial thermal cycler. The thermal cycler was portable (<1kg weight), required 12 V power supply, 25 μL of solution, and cost only USD50.0. Temperature and time conditions were instructed using a custom-built smartphone application. The ramping rate of was 0.23°C for heating and 0.43°C for cooling. The reported temperatures were within ± 0.5°C of set temperature. The human urine samples were highly resistance and multi-resistant. Nearly 46% (n = 54) E. coli isolates were positive in ESBL screening test. The custom-built thermocycler was able to accurately predict the presence of bla-TEM, bla-CTXM genes, and 16s rRNA (n = 6). We developed and demonstrated a portable, low-cost, easy-to-use, and smartphone-operated PCR thermal cycler. Since it is portable, it can be used in remote location and field settings, including places without stable power supply. The use of the thermal cycler system can be extended, beyond the detection of AMR genes, e.g., in clinical diagnosis, genetics, forensic analysis, and environmental protection.
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Affiliation(s)
- Sanam Pudasaini
- Center for Analytical Sciences, Kathmandu Institute of Applied Sciences, Kathmandu, Nepal
| | - Garima Thapa
- Center for Analytical Sciences, Kathmandu Institute of Applied Sciences, Kathmandu, Nepal
- Department of Biotechnology, National College, Tribhuvan University, Kathmandu, Nepal
| | - Bishnu P Marasini
- Department of Biotechnology, National College, Tribhuvan University, Kathmandu, Nepal
| | - Basant Giri
- Center for Analytical Sciences, Kathmandu Institute of Applied Sciences, Kathmandu, Nepal
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13
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Advantages and Limitations of Microscopy and Molecular Detections for Diagnosis of Soil-transmitted Helminths: An Overview. Helminthologia 2022; 59:321-340. [PMID: 36875683 PMCID: PMC9979072 DOI: 10.2478/helm-2022-0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 10/31/2022] [Indexed: 02/05/2023] Open
Abstract
World Health Organization (WHO) reported that over 1.5 billion people are infected by soil-transmitted helminths (STH) worldwide in sub-Saharan Africa, the United States of America, China, and East Asia. Heavy infections and polyparasitism are associated with higher morbidity rates, and the patients are exposed to increased vulnerability to other diseases. Therefore, accurate diagnosis followed by mass treatment for morbidity control is necessary.STH diagnosis commonly involves the microscopic observation of the presence of the STH eggs and larvae in the faecal samples. Furthermore, molecular approaches are increasingly utilised in monitoring and surveillance as they show higher sensitivity. Their capability to differentiate hookworm species is an advantage over the Kato-Katz technique. This review discusses the advantages and limitations of microscopy and various molecular tools used for STH detection.
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14
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Xiang X, Diao E, Shang Y, Song M, He Y. Rapid quantitative detection of Vibrio parahaemolyticus via high-fidelity target-based microfluidic identification. Food Res Int 2022; 162:112032. [PMID: 36461252 DOI: 10.1016/j.foodres.2022.112032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/12/2022] [Accepted: 10/04/2022] [Indexed: 11/26/2022]
Abstract
With the rapid development of logistics, a growing number of pathogenic microorganisms has the means to spread worldwide using food as a carrier; thus, there is an urgent need to develop effective detection strategies to ensure food safety. By combining novel markers identified by pan-genome analysis and a digital recombinase-aided amplification (RAA) detection method based on a microfluidic chip, a strategy of high-fidelity target-based microfluidic identification (HFTMI) has been developed. Herein, a proof-of-concept study of HFTMI for rapid pathogen detection of V. parahaemolyticus was investigated. Specific primers designed for the gene group_41170 identified in the pan-genome analysis showed high sensitivity and a broad spectrum for the detection of V. parahaemolyticus. Different power systems were investigated to increase the partition rate on specifically designed chamber-based digital chips. The performance of HFTMI was greatly improved compared with qPCR. Collectively, this novel HFTMI system provides more reliable guidance for food safety testing.
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Affiliation(s)
- Xinran Xiang
- Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Science, Huaiyin Normal University, Huai'an 223300, China; School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Enjie Diao
- Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Science, Huaiyin Normal University, Huai'an 223300, China
| | - Yuting Shang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Minghui Song
- Hainan Hospital of Chinese PLA General Hospital, Sanya 572000, China.
| | - Yinglong He
- College of Agriculture/Tree Peony, Henan University of Science and Technology, Luoyang 471023, China.
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15
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Takei T, Tomimatsu R, Matsumoto T, Sreejith KR, Nguyen NT, Yoshida M. Hydrophobically Modified Gelatin Particles for Production of Liquid Marbles. Polymers (Basel) 2022; 14:polym14224849. [PMID: 36432975 PMCID: PMC9695580 DOI: 10.3390/polym14224849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/12/2022] Open
Abstract
The unique properties and morphology of liquid marbles (LMs) make them potentially useful for various applications. Non-edible hydrophobic organic polymer particles are widely used to prepare LMs. It is necessary to increase the variety of LM particles to extend their use into food and pharmaceuticals. Herein, we focus on hydrophobically modified gelatin (HMG) as a base material for the particles. The surface tension of HMG decreased as the length of alkyl chains incorporated into the gelatin and the degree of substitution (DS) of the alkyl chains increased. HMG with a surface tension of less than 37.5 mN/m (determined using equations based on the Young-Dupré equation and Kaelble-Uy theory) successfully formed LMs of water. The minimum surface tension of a liquid in which it was possible to form LMs using HMG particles was approximately 53 mN/m. We also showed that the liquid-over-solid spreading coefficient SL/S is a potential new factor for predicting if particles can form LMs. The HMG particles and the new system for predicting LM formation could expand the use of LMs in food and pharmaceuticals.
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Affiliation(s)
- Takayuki Takei
- Department of Chemical Engineering, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima 890-0065, Japan
- Correspondence:
| | - Rio Tomimatsu
- Department of Chemical Engineering, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima 890-0065, Japan
| | - Takanori Matsumoto
- Department of Chemical Engineering, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima 890-0065, Japan
| | - Kamalalayam Rajan Sreejith
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
| | - Masahiro Yoshida
- Department of Chemical Engineering, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima 890-0065, Japan
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16
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Xia Y, Chu X, Zhao C, Wang N, Yu J, Jin Y, Sun L, Ma S. A Glass-Ultra-Thin PDMS Film-Glass Microfluidic Device for Digital PCR Application Based on Flexible Mold Peel-Off Process. MICROMACHINES 2022; 13:mi13101667. [PMID: 36296020 PMCID: PMC9608979 DOI: 10.3390/mi13101667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/29/2022] [Accepted: 10/01/2022] [Indexed: 05/27/2023]
Abstract
The microfluidic device (MFD) with a glass−PDMS−glass (G-P-G) structure is of interest for a wide range of applications. However, G-P-G MFD fabrication with an ultra-thin PDMS film (especially thickness less than 200 μm) is still a big challenge because the ultra-thin PDMS film is easily deformed, curled, and damaged during demolding and transferring. This study aimed to report a thickness-controllable and low-cost fabrication process of the G-P-G MFD with an ultra-thin PDMS film based on a flexible mold peel-off process. A patterned photoresist layer was deposited on a polyethylene terephthalate (PET) film to fabricate a flexible mold that could be demolded softly to achieve a rigid structure of the glass−PDMS film. The thickness of ultra-thin patterned PDMS could reach less than 50 μm without damage to the PDMS film. The MFD showcased the excellent property of water evaporation inhibition (water loss < 10%) during PCR thermal cycling because of the ultra-thin PDMS film. Its low-cost fabrication process and excellent water evaporation inhibition present extremely high prospects for digital PCR application.
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Affiliation(s)
- Yanming Xia
- Department of Mechanical & Electrical Engineering, Xiamen University, Xiamen 361005, China
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Xianglong Chu
- Department of Mechanical & Electrical Engineering, Xiamen University, Xiamen 361005, China
| | - Caiming Zhao
- Department of Mechanical & Electrical Engineering, Xiamen University, Xiamen 361005, China
| | - Nanxin Wang
- School of Electronic and Computer Engineering, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Juan Yu
- Department of Mechanical & Electrical Engineering, Xiamen University, Xiamen 361005, China
| | - Yufeng Jin
- School of Electronic and Computer Engineering, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Lijun Sun
- School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Shenglin Ma
- Department of Mechanical & Electrical Engineering, Xiamen University, Xiamen 361005, China
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17
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Cao Z, Ye Y, Li G, Zhang R, Dong S, Liu Y. Monolithically integrated microchannel plate functionalized with ZnO nanorods for fluorescence-enhanced digital polymerase chain reaction. Biosens Bioelectron 2022; 213:114499. [DOI: 10.1016/j.bios.2022.114499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/08/2022] [Accepted: 06/21/2022] [Indexed: 11/27/2022]
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18
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Zhu M, Shan Z, Ning W, Wu X. Image Segmentation and Quantification of Droplet dPCR Based on Thermal Bubble Printing Technology. SENSORS (BASEL, SWITZERLAND) 2022; 22:7222. [PMID: 36236321 PMCID: PMC9573249 DOI: 10.3390/s22197222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Thermal inkjet printing can generate more than 300,000 droplets of picoliter scale within one second stably, and the image analysis workflow is used to quantify the positive and negative values of the droplets. In this paper, the SimpleBlobDetector detection algorithm is used to identify and localize droplets with a volume of 24 pL in bright field images and suppress bright spots and scratches when performing droplet location identification. The polynomial surface fitting of the pixel grayscale value of the fluorescence channel image can effectively compensate and correct the image vignetting caused by the optical path, and the compensated fluorescence image can accurately classify positive and negative droplets by the k-means clustering algorithm. 20 µL of the sample solution in the result reading chip can produce more than 100,000 effective droplets. The effective droplet identification correct rate of 20 images of random statistical samples can reach more than 99% and the classification accuracy of positive and negative droplets can reach more than 98% on average. This paper overcomes the problem of effectively classifying positive and negative droplets caused by the poor image quality of photographed picolitre ddPCR droplets caused by optical hardware limitations.
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Affiliation(s)
- Mingjie Zhu
- School of Microelectronics, Shanghai University, Shanghai 200444, China
| | - Zilong Shan
- School of Microelectronics, Shanghai University, Shanghai 200444, China
| | - Wei Ning
- Shanghai Industrial µTechnology Research Institute, Shanghai 201800, China
| | - Xuanye Wu
- School of Microelectronics, Shanghai University, Shanghai 200444, China
- Shanghai Industrial µTechnology Research Institute, Shanghai 201800, China
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19
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Emerging digital PCR technology in precision medicine. Biosens Bioelectron 2022; 211:114344. [DOI: 10.1016/j.bios.2022.114344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/23/2022] [Accepted: 05/03/2022] [Indexed: 12/20/2022]
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20
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Curtin K, Fike BJ, Binkley B, Godary T, Li P. Recent Advances in Digital Biosensing Technology. BIOSENSORS 2022; 12:bios12090673. [PMID: 36140058 PMCID: PMC9496261 DOI: 10.3390/bios12090673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/27/2022]
Abstract
Digital biosensing assays demonstrate remarkable advantages over conventional biosensing systems because of their ability to achieve single-molecule detection and absolute quantification. Unlike traditional low-abundance biomarking screening, digital-based biosensing systems reduce sample volumes significantly to the fL-nL level, which vastly reduces overall reagent consumption, improves reaction time and throughput, and enables high sensitivity and single target detection. This review presents the current technology for compartmentalizing reactions and their applications in detecting proteins and nucleic acids. We also analyze existing challenges and future opportunities associated with digital biosensing and research opportunities for developing integrated digital biosensing systems.
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Affiliation(s)
- Kathrine Curtin
- Department of Mechanical and Aerospace Engineering, West Virginia University, Morgantown, WV 26506, USA
| | - Bethany J. Fike
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Brandi Binkley
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Toktam Godary
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA
- Correspondence:
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21
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Wang K, Li B, Guo Y, Wu Y, Li Y, Wu W. An integrated digital PCR system with high universality and low cost for nucleic acid detection. Front Bioeng Biotechnol 2022; 10:947895. [PMID: 36061433 PMCID: PMC9437218 DOI: 10.3389/fbioe.2022.947895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Digital PCR is the most advanced PCR technology. However, due to the high price of the digital PCR analysis instrument, this powerful nucleic acid detection technology is still difficult to be popularized in the general biochemistry laboratory. Moreover, one of the biggest disadvantages of commercial digital PCR systems is the poor versatility of reagents: each instrument can only be used for a few customized kits. Herein, we built a low-cost digital PCR system. The system only relies on low-cost traditional flat-panel PCR equipment to provide temperature conditions for commercial dPCR chips, and the self-made fluorescence detection system is designed and optically optimized to meet a wide range of reagent requirements. More importantly, our system not only has a low cost (<8000 US dollars) but also has a much higher universality for nucleic acid detection reagents than the traditional commercial digital PCR system. In this study, several samples were tested. The genes used in the experiment were plasmids containing UPE-1a fragment, TP53 reference DNA, hepatitis B virus DNA, leukemia sample, SARS-COV-2 DNA, and SARS-COV-2 RNA. Under the condition that DNA can be amplified normally, the function of the dPCR system can be realized with simpler and low-price equipment. Some DNA cannot be detected by using the commercial dPCR system because of the special formula when it is configured as the reaction solution, but these DNA fluorescence signals can be clearly detected by our system, and the concentration can be calculated. Our system is more applicable than the commercial dPCR system to form a new dPCR system that is smaller and more widely applicable than commercially available machinery.
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Affiliation(s)
- Kangning Wang
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Bin Li
- Institute of Microbiology Chinese Academy of Sciences, Beijing, China
| | - Yu Guo
- School of Mechanical and Electrical Engineering, Guangdong University of Technology, Guangzhou, China
| | - Yanqi Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, China
| | - Yan Li
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Wenming Wu
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
- *Correspondence: Wenming Wu,
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22
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Yin J, Xia L, Zou Z, Zhuang J, Mu Y. A direct and multiplex digital PCR chip for EGFR mutation. Talanta 2022; 250:123725. [PMID: 35834974 DOI: 10.1016/j.talanta.2022.123725] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/24/2022] [Accepted: 07/04/2022] [Indexed: 12/25/2022]
Abstract
Digital PCR is a sensitive detection method, which has important applicability in liquid biopsy through the measurement of ctDNA. However, the current sample pre-processing of ctDNA and the multiplex detection capability of digital PCR have limitations. In view of the above two aspects, we developed a digital PCR chip with multiplex capability and established a direct amplification detection method without nucleic acid extraction. Through the design and processing of the chip, we established a self-priming multiplex digital PCR chip, which can detect 4 targets using single fluorescence. This method can be applied to most digital PCR chips. In addition, we used the plasma of lung cancer patients to establish a direct digital PCR detection method based on the chip, thereby avoiding disadvantages caused by the ctDNA extraction process. As a proof of concept, we prepared blood plasma samples with different concentration of ctDNA to prove the chip's multiplex detection capabilities and the results suggested that this multiplex digital PCR is accurate. Overall, our platform provides a novel and promising option for the detection of ctDNA.
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Affiliation(s)
- Juxin Yin
- School of Information and Electrical Engineering, Zhejiang University City College, Hangzhou, Zhejiang Province, 310015, China
| | - Liping Xia
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province, 310027, China
| | - Zheyu Zou
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province, 310027, China
| | - Jianjian Zhuang
- Department of Clinical Pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Cancer Center, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Ying Mu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province, 310027, China.
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23
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Wang Y, Xu H, Dong Z, Wang Z, Yang Z, Yu X, Chang L. Micro/nano biomedical devices for point-of-care diagnosis of infectious respiratory diseases. MEDICINE IN NOVEL TECHNOLOGY AND DEVICES 2022; 14:100116. [PMID: 35187465 PMCID: PMC8837495 DOI: 10.1016/j.medntd.2022.100116] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/14/2021] [Accepted: 01/18/2022] [Indexed: 12/12/2022] Open
Abstract
Corona Virus Disease 2019 (COVID-19) has developed into a global pandemic in the last two years, causing significant impacts on our daily life in many countries. Rapid and accurate detection of COVID-19 is of great importance to both treatments and pandemic management. Till now, a variety of point-of-care testing (POCT) approaches devices, including nucleic acid-based test and immunological detection, have been developed and some of them has been rapidly ruled out for clinical diagnosis of COVID-19 due to the requirement of mass testing. In this review, we provide a summary and commentary on the methods and biomedical devices innovated or renovated for the quick and early diagnosis of COVID-19. In particular, some of micro and nano devices with miniaturized structures, showing outstanding analytical performances such as ultra-sensitivity, rapidness, accuracy and low cost, are discussed in this paper. We also provide our insights on the further implementation of biomedical devices using advanced micro and nano technologies to meet the demand of point-of-care diagnosis and home testing to facilitate pandemic management. In general, our paper provides a comprehensive overview of the latest advances on the POCT device for diagnosis of COVID-19, which may provide insightful knowledge for researcher to further develop novel diagnostic technologies for rapid and on-site detection of pathogens including SARS-CoV-2.
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Affiliation(s)
- Yang Wang
- Key Laboratory for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Huiren Xu
- School of Biomedical Information and Engineering, Hainan Medical University, Haikou, 471100, China
| | - Zaizai Dong
- Key Laboratory for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Zhiying Wang
- Key Laboratory for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Zhugen Yang
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, United Kingdom,Corresponding author
| | - Xinge Yu
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, China,Corresponding author.
| | - Lingqian Chang
- Key Laboratory for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China,Corresponding author.
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24
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Merino I, de la Fuente A, Domínguez-Gil M, Eiros JM, Tedim AP, Bermejo-Martín JF. Digital PCR applications for the diagnosis and management of infection in critical care medicine. Crit Care 2022; 26:63. [PMID: 35313934 PMCID: PMC8935253 DOI: 10.1186/s13054-022-03948-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/11/2022] [Indexed: 12/15/2022] Open
Abstract
Infection (either community acquired or nosocomial) is a major cause of morbidity and mortality in critical care medicine. Sepsis is present in up to 30% of all ICU patients. A large fraction of sepsis cases is driven by severe community acquired pneumonia (sCAP), which incidence has dramatically increased during COVID-19 pandemics. A frequent complication of ICU patients is ventilator associated pneumonia (VAP), which affects 10–25% of all ventilated patients, and bloodstream infections (BSIs), affecting about 10% of patients. Management of these severe infections poses several challenges, including early diagnosis, severity stratification, prognosis assessment or treatment guidance. Digital PCR (dPCR) is a next-generation PCR method that offers a number of technical advantages to face these challenges: it is less affected than real time PCR by the presence of PCR inhibitors leading to higher sensitivity. In addition, dPCR offers high reproducibility, and provides absolute quantification without the need for a standard curve. In this article we reviewed the existing evidence on the applications of dPCR to the management of infection in critical care medicine. We included thirty-two articles involving critically ill patients. Twenty-three articles focused on the amplification of microbial genes: (1) four articles approached bacterial identification in blood or plasma; (2) one article used dPCR for fungal identification in blood; (3) another article focused on bacterial and fungal identification in other clinical samples; (4) three articles used dPCR for viral identification; (5) twelve articles quantified microbial burden by dPCR to assess severity, prognosis and treatment guidance; (6) two articles used dPCR to determine microbial ecology in ICU patients. The remaining nine articles used dPCR to profile host responses to infection, two of them for severity stratification in sepsis, four focused to improve diagnosis of this disease, one for detecting sCAP, one for detecting VAP, and finally one aimed to predict progression of COVID-19. This review evidences the potential of dPCR as a useful tool that could contribute to improve the detection and clinical management of infection in critical care medicine.
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Affiliation(s)
- Irene Merino
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.,Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Marta Domínguez-Gil
- Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - José María Eiros
- Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain. .,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.
| | - Jesús F Bermejo-Martín
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
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25
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Annese VF, Giagkoulovits C, Hu C, Al-Rawhani MA, Grant J, Patil SB, Cumming DRS. Micromolar Metabolite Measurement in an Electronically Multiplexed Format. IEEE Trans Biomed Eng 2022; 69:2715-2722. [PMID: 35104208 DOI: 10.1109/tbme.2022.3147855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The detection of metabolites such as choline in blood are important in clinical care for patients with cancer and cardiovascular disease. Choline is only present in human blood at low concentrations hence accurate measurement in an affordable point-of-care format is extremely challenging. Integration of microfluidics on to complementary metal-oxide semiconductor (CMOS) technology has the potential to enable advanced sensing technologies with extremely low limit of detection that are well suited to multiple clinical metabolite measurements. Although CMOS and microfluidics are individually mature technologies, their integration has presented challenges that we overcome in a novel, cost-effective, single-step process. To demonstrate the process, we present the microfluidic integration of a metabolomics-on-CMOS point-of-care platform with four capillary microfluidic channels on top of a CMOS optical sensor array. The fabricated device was characterised to verify the required structural profile, mechanical strength, optical spectra, and fluid flow. As a proof of concept, we used the device for the in-vitro quantification of choline in human blood plasma with a limit of detection of 3.2 M and a resolution of 1.6 M.
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26
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Advances in improvement strategies of digital nucleic acid amplification for pathogen detection. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116568] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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27
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Gaňová M, Wang X, Yan Z, Zhang H, Lednický T, Korabečná M, Neužil P. Temperature non-uniformity detection on dPCR chips and temperature sensor calibration. RSC Adv 2022; 12:2375-2382. [PMID: 35425215 PMCID: PMC8979175 DOI: 10.1039/d1ra08138a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 01/08/2022] [Indexed: 12/12/2022] Open
Abstract
A microfluidic-based digital polymerase chain reaction (dPCR) chip requires precise temperature control as well as uniform temperature distribution to ensure PCR efficiency. However, measuring local temperature and its distribution over thousands of μL/nL-volume samples with minimum disturbance is challenging. Here, we present a method of non-contact localized temperature measurement for determination of the non-uniformity of temperature distribution over a dPCR chip. We filled the dPCR chip with a PCR solution containing amplified DNA fragments with a known melting temperature (TM). We then captured fluorescent images of the chip when it was heated from 70 to 99 °C, plotted the fluorescence intensity of each partition as a function of temperature, and calculated measured TM values from each partition. Finally, we created a 3-D map of the dPCR chip with the measured TM as the parameter. Even when the actual TM of the PCR solution was constant, the measured TM value varied between locations due to temperature non-uniformity in the dPCR chip. The method described here thereby characterized the distribution of temperature non-uniformity using a PCR solution with known TM as a temperature sensor. Among the non-contact temperature measurement methods, the proposed TM-based method can determine the temperature distribution within the chip, instead of only at the chip surface. The method also does not suffer from the undesirable photobleaching effect of fluorescein-based temperature measurement method. Temperature determination over the dPCR chip based on TM allowed us to calibrate the temperature sensor and improve the dPCR configuration and precision. This method is also suitable for determining the temperature uniformity of other microarray systems where there is no physical access to the system and thus direct temperature measurement is not possible. We present a method of non-contact localized temperature measurement for determination of the non-uniformity of temperature distribution over a dPCR chip mounted on two different thermal cycling configurations.![]()
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Affiliation(s)
- Martina Gaňová
- Central European Institute of Technology, Brno University of Technology Purkyňova 123 612 00 Brno Czech Republic
| | - Xinlu Wang
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering 127 West Youyi Road Xi'an Shaanxi 710072 PR China
| | - Zhiqiang Yan
- Northwestern Polytechnical University, School of Marine Science and Technology 127 West Youyi Road Xi'an Shaanxi 710072 PR China
| | - Haoqing Zhang
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering 127 West Youyi Road Xi'an Shaanxi 710072 PR China
| | - Tomáš Lednický
- Central European Institute of Technology, Brno University of Technology Purkyňova 123 612 00 Brno Czech Republic
| | - Marie Korabečná
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague Albertov 4 128 00 Prague Czech Republic
| | - Pavel Neužil
- Northwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering 127 West Youyi Road Xi'an Shaanxi 710072 PR China
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28
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Jo D, Kim SY, Kang HW, Pyo SH, Jeong NK, Bae NH, Lee SJ, Kim YT, Lee KG. Micro-injection Molded Droplet Generation System for Digital PCR Application. BIOCHIP JOURNAL 2022; 16:433-440. [PMID: 36091641 PMCID: PMC9446600 DOI: 10.1007/s13206-022-00079-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 12/29/2022]
Abstract
Sensitive, effective, and quantitative analysis of infectious pathogens is an important task for the prevention of human health threats. Herein, we present an advanced approach to producing gene-encapsulated microdroplets for quantitative analysis using a micropatterned metal mold and injection molding technique with an automatically operated system. An injection molded microdroplet generation device was successfully fabricated with a minimum channel width of 30 μm and optimized to produce 100 μm diameter droplets. The optimized microchannel design and flow rate also enable the production of stable numbers of microdroplets (~ 16,000 droplets). To verify the applicability of our device and system to droplet-based digital PCR analysis, Escherichia coli (E. coli) O157:H7 was selected as a model bacterial pathogen, and the stx2 gene was amplified in the microdroplets. The generated microdroplets exhibit both chemical and mechanical stability, and our results are similar to those obtained by a commercially available method. Accordingly, the usefulness of the microdroplet generative device and system is confirmed as a simple, fast, and reliable tool for the quantitative molecular analysis of infectious diseases.
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Affiliation(s)
- Daae Jo
- National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - So Young Kim
- Bio R&D Lab, BioTNS Co.Ltd, 19-12 Daehak-ro 76 beonan-gil, Daejeon, 34141 Republic of Korea
- Department of Biology, Soon Chun Hyang University, 22 Soonchunhyang-ro, Chungcheongnam-do, Asan-si, 31538 Republic of Korea
| | - Hyeon Woo Kang
- Bio R&D Lab, BioTNS Co.Ltd, 19-12 Daehak-ro 76 beonan-gil, Daejeon, 34141 Republic of Korea
- Department of Biology, Soon Chun Hyang University, 22 Soonchunhyang-ro, Chungcheongnam-do, Asan-si, 31538 Republic of Korea
| | - Sung Han Pyo
- National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Nam Kyu Jeong
- National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Nam ho Bae
- National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Seok Jae Lee
- National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Yong Tae Kim
- Department of Chemical Engineering and Biotechnology, Tech University of Korea, 237 Sangidaehak-ro, Siheung-si, Gyeonggi-do 15073 Republic of Korea
| | - Kyoung G. Lee
- National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
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29
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A plasmonic gold nanofilm-based microfluidic chip for rapid and inexpensive droplet-based photonic PCR. Sci Rep 2021; 11:23338. [PMID: 34857792 PMCID: PMC8639772 DOI: 10.1038/s41598-021-02535-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/12/2021] [Indexed: 12/23/2022] Open
Abstract
Polymerase chain reaction (PCR) is a powerful tool for nucleic acid amplification and quantification. However, long thermocycling time is a major limitation of the commercial PCR devices in the point-of-care (POC). Herein, we have developed a rapid droplet-based photonic PCR (dpPCR) system, including a gold (Au) nanofilm-based microfluidic chip and a plasmonic photothermal cycler. The chip is fabricated by adding mineral oil to uncured polydimethylsiloxane (PDMS) to suppress droplet evaporation in PDMS microfluidic chips during PCR thermocycling. A PDMS to gold bonding technique using a double-sided adhesive tape is applied to enhance the bonding strength between the oil-added PDMS and the gold nanofilm. Moreover, the gold nanofilm excited by two light-emitting diodes (LEDs) from the top and bottom sides of the chip provides fast heating of the PCR sample to 230 °C within 100 s. Such a design enables 30 thermal cycles from 60 to 95 °C within 13 min with the average heating and cooling rates of 7.37 ± 0.27 °C/s and 1.91 ± 0.03 °C/s, respectively. The experimental results demonstrate successful PCR amplification of the alcohol oxidase (AOX) gene using the rapid plasmonic photothermal cycler and exhibit the great performance of the microfluidic chip for droplet-based PCR.
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30
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Ou Y, Cao S, Zhang J, Dong W, Yang Z, Yu Z. Droplet microfluidics on analysis of pathogenic microbes for wastewater-based epidemiology. Trends Analyt Chem 2021; 143:116333. [PMID: 34720276 PMCID: PMC8547957 DOI: 10.1016/j.trac.2021.116333] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Infectious diseases caused by pathogenic microbes have posed a major health issue for the public, such as the ongoing COVID-19 global pandemic. In recent years, wastewater-based epidemiology (WBE) is emerging as an effective and unbiased method for monitoring public health. Despite its increasing importance, the advancement of WBE requires more competent and streamlined analytical platforms. Herein we discuss the interactions between WBE and droplet microfluidics, focusing on the analysis of pathogens in droplets, which is hard to be tackled by traditional analytical tools. We highlight research works from three aspects, namely, quantitation of pathogen biomarkers in droplets, single-cell analysis in droplets, and living cell biosensors in droplets, as well as providing future perspectives on the synergy between WBE and droplet microfluidics.
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Affiliation(s)
- Yangteng Ou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China.,Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Shixiang Cao
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China
| | - Jing Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China
| | - Zhugen Yang
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK
| | - Ziyi Yu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China
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31
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Cao L, Guo X, Mao P, Ren Y, Li Z, You M, Hu J, Tian M, Yao C, Li F, Xu F. A Portable Digital Loop-Mediated Isothermal Amplification Platform Based on Microgel Array and Hand-Held Reader. ACS Sens 2021; 6:3564-3574. [PMID: 34606243 DOI: 10.1021/acssensors.1c00603] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Digital polymerase chain reaction (dPCR) has found widespread applications in molecular diagnosis of various diseases owing to its sensitive single-molecule detection capability. However, the existing dPCR platforms rely on the auxiliary procedure to disperse DNA samples, which needs complicated operation, expensive apparatus, and consumables. Besides, the complex and costly dPCR readers also impede the applications of dPCR for point-of-care testing (POCT). Herein, we developed a portable digital loop-mediated isothermal amplification (dLAMP) platform, integrating a microscale hydrogel (microgel) array chip for sample partition, a miniaturized heater for DNA amplification, and a hand-held reader for digital readout. In the platform, the chip with thousands of isolated microgels holds the capability of self-absorption and partition of DNA samples, thus avoiding auxiliary equipment and professional personnel operations. Using the integrated dLAMP platform, λDNA templates have been quantified with a good linear detection range of 2-1000 copies/μL and a detection limit of 1 copy/μL. As a demonstration, the epidermal growth factor receptor L858R gene mutation, a crucial factor for the susceptibility of the tyrosine kinase inhibitor in non-small-cell lung cancer treatment, has been accurately identified by the dLAMP platform with a spiked plasma sample. This work shows that the developed dLAMP platform provides a low-cost, facile, and user-friendly solution for the absolute quantification of DNA, showing great potential for the POCT of nucleic acids.
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Affiliation(s)
- Lei Cao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Xiaojin Guo
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
- Department of Chemistry, School of Science, Xi’an Jiaotong University, Xi’an 710049, China
| | - Ping Mao
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Yulin Ren
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Zedong Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Minli You
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Jie Hu
- Suzhou DiYinAn Biotechnology Company Ltd., Suzhou 215000, China
| | - Miao Tian
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Chunyan Yao
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Fei Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
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32
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He Y, Lu Z, Fan H, Zhang T. A photofabricated honeycomb micropillar array for loss-free trapping of microfluidic droplets and application to digital PCR. LAB ON A CHIP 2021; 21:3933-3941. [PMID: 34636815 DOI: 10.1039/d1lc00629k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Droplet microfluidics is a promising platform for various biological and biomedical applications. Among which, droplet-based digital PCR (ddPCR) is one of the most challenging examples, with practical issues involving possible fusion/fission of droplets during PCR thermocycling and difficulties of indexing them for real-time monitoring. While spatially trapped droplet arrays may be helpful, they currently are either of low trapping density or suffer from high droplet loss. In this paper, we, for the first time, report a photofabricated honeycomb micropillar array (PHMA) for high-density and loss-free droplet trapping. By rationally designing high-aspect-ratio micropillars into a honeycomb configuration, droplets can be captured at a density of 160-250 droplets per mm2 and, more interestingly, without any loss. The PHMA device can be fabricated from several photocurable materials, with one gasproof photopolymer being optimally selected herein to enable the simple design to avoid sample evaporation and tedious surface modification, thereby making the fabrication very convenient. Moreover, by using a photocurable oil as a continuous phase, the trapped droplets can be further immobilized, and thus, become more stable even in PCR thermocycling. With these features, the proposed PHMA has shown promising potential in ddPCR, and is expected to find a wide range of applications in various biological and biomedical research.
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Affiliation(s)
- Yu He
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310023, China.
| | - Zefan Lu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310023, China.
| | - Hongliang Fan
- Department of Environmental Medicine, Institute of Hygiene, Zhejiang Academy of Medical Sciences, Hangzhou 310013, China
| | - Tao Zhang
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310023, China.
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33
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Park J, Park JK. Pushbutton-activated microfluidic cartridge as a user-friendly sample preparation tool for diagnostics. BIOMICROFLUIDICS 2021; 15:041302. [PMID: 34257794 PMCID: PMC8270647 DOI: 10.1063/5.0056580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/18/2021] [Indexed: 06/13/2023]
Abstract
Microfluidic technologies have several advantages in sample preparation for diagnostics but suffer from the need for an external operation system that hampers user-friendliness. To overcome this limitation in microfluidic technologies, a number of user-friendly methods utilizing capillary force, degassed poly(dimethylsiloxane), pushbutton-driven pressure, a syringe, or a pipette have been reported. Among these methods, the pushbutton-driven, pressure-based method has a great potential to be widely used as a user-friendly sample preparation tool for point-of-care testing or portable diagnostics. In this Perspective, we focus on the pushbutton-activated microfluidic technologies toward a user-friendly sample preparation tool. The working principle and recent advances in pushbutton-activated microfluidic technologies are briefly reviewed, and future perspectives for wide application are discussed in terms of integration with the signal analysis system, user-dependent variation, and universal and facile use.
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Affiliation(s)
| | - Je-Kyun Park
- Author to whom correspondence should be addressed:
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34
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Dong X, Liu L, Tu Y, Zhang J, Miao G, Zhang L, Ge S, Xia N, Yu D, Qiu X. Rapid PCR powered by microfluidics: A quick review under the background of COVID-19 pandemic. Trends Analyt Chem 2021; 143:116377. [PMID: 34188341 PMCID: PMC8223007 DOI: 10.1016/j.trac.2021.116377] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
PCR has been widely used in different fields including molecular biology, pathogen detection, medical diagnosis, food detection and etc. However, the difficulty of promoting PCR in on-site point-of-care testing reflects on challenges relative to its speed, convenience, complexity, and even cost. With the emerging state-of-art of microfluidics, rapid PCR can be achieved with more flexible ways in micro-reactors. PCR plays a critical role in the detection of SARS-CoV-2. Under this special background of COVID-19 pandemic, this review focuses on the latest rapid microfluidic PCR. Rapid PCR is concluded in two main features, including the reactor (type, size, material) and the implementation of thermal cycling. Especially, the compromise between speed and sensitivity with microfluidic PCR is explored based on the system ratio of (thermal cycling time)/(reactor size). Representative applications about the detection of pathogens and SARS-CoV-2 viruses based on rapid PCR or other isothermal amplification are discussed as well.
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Affiliation(s)
- Xiaobin Dong
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Luyao Liu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yunping Tu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jing Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Guijun Miao
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Lulu Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shengxiang Ge
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361005, China
| | - Ningshao Xia
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361005, China
| | - Duli Yu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing, 100029, China
| | - Xianbo Qiu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
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35
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Yue H, Shu B, Tian T, Xiong E, Huang M, Zhu D, Sun J, Liu Q, Wang S, Li Y, Zhou X. Droplet Cas12a Assay Enables DNA Quantification from Unamplified Samples at the Single-Molecule Level. NANO LETTERS 2021; 21:4643-4653. [PMID: 34038136 DOI: 10.1021/acs.nanolett.1c00715] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
DNA quantification is important for biomedical research, but the routinely used techniques rely on nucleic acid amplification which have inherent issues like cross-contamination risk and quantification bias. Here, we report a CRISPR-Cas12a-based molecular diagnostic technique for amplification-free and absolute quantification of DNA at the single-molecule level. To achieve this, we first screened out the optimal reaction parameters for high-efficient Cas12a assay, yielding over 50-fold improvement in sensitivity compared with the reported Cas12a assays. We further leveraged the microdroplet-enabled confinement effect to perform an ultralocalized droplet Cas12a assay, obtaining excellent specificity and single-molecule sensitivity. Moreover, we demonstrated its versatility and quantification capability by direct counting of diverse virus's DNAs (African swine fever virus, Epstein-Barr virus, and Hepatitis B virus) from clinical serum samples with a wide range of viral titers. Given the flexible programmability of crRNA, we envision this amplification-free technique as a versatile and quantitative platform for molecular diagnosis.
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Affiliation(s)
- Huahua Yue
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
- College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Bowen Shu
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
- Department of Laboratory Medicine, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
| | - Tian Tian
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Erhu Xiong
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Mengqi Huang
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Debin Zhu
- Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry, South China Normal University, Guangzhou 510006, China
| | - Jian Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, China
| | - Qing Liu
- Department of Molecular Diagnostics, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510700, China
| | - Shichan Wang
- Department of Laboratory Medicine, Zhongnan Hospital, Wuhan University, Wuhan 430071, China
| | - Yirong Li
- Department of Laboratory Medicine, Zhongnan Hospital, Wuhan University, Wuhan 430071, China
| | - Xiaoming Zhou
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
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36
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Gaňová M, Zhang H, Zhu H, Korabečná M, Neužil P. Multiplexed digital polymerase chain reaction as a powerful diagnostic tool. Biosens Bioelectron 2021; 181:113155. [PMID: 33740540 DOI: 10.1016/j.bios.2021.113155] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/13/2021] [Accepted: 03/06/2021] [Indexed: 01/30/2023]
Abstract
The digital polymerase chain reaction (dPCR) multiplexing method can simultaneously detect and quantify closely related deoxyribonucleic acid sequences in complex mixtures. The dPCR concept is continuously improved by the development of microfluidics and micro- and nanofabrication, and different complex techniques are introduced. In this review, we introduce dPCR techniques based on sample compartmentalization, droplet- and chip-based systems, and their combinations. We then discuss dPCR multiplexing methods in both laboratory research settings and advanced or routine clinical applications. We focus on their strengths and weaknesses with regard to the character of biological samples and to the required precision of such analysis, as well as showing recently published work based on those methods. Finally, we envisage possible future achievements in this field.
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Affiliation(s)
- Martina Gaňová
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic
| | - Haoqing Zhang
- School of Mechanical Engineering, Northwestern Polytechnical University, Xi'an, 710072, PR China
| | - Hanliang Zhu
- School of Mechanical Engineering, Northwestern Polytechnical University, Xi'an, 710072, PR China
| | - Marie Korabečná
- 1st Faculty of Medicine, Institute of Biology and Medical Genetics, Charles University and General University Hospital, 12800, Prague, Czech Republic
| | - Pavel Neužil
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; School of Mechanical Engineering, Northwestern Polytechnical University, Xi'an, 710072, PR China; The Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic.
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Del Giudice F, D'Avino G, Maffettone PL. Microfluidic formation of crystal-like structures. LAB ON A CHIP 2021; 21:2069-2094. [PMID: 34002182 DOI: 10.1039/d1lc00144b] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Crystal-like structures find application in several fields ranging from biomedical engineering to material science. For instance, droplet crystals are critical for high throughput assays and material synthesis, while particle crystals are important for particles and cell encapsulation, Drop-seq technologies, and single-cell analysis. Formation of crystal-like structures relies entirely on the possibility of manipulating with great accuracy the micrometer-size objects forming the crystal. In this context, microfluidic devices offer versatile tools for the precise manipulation of droplets and particles, thus enabling fabrication of crystal-like structures that form due to hydrodynamic interactions among droplets or particles. In this review, we aim at providing an holistic representation of crystal-like structure formation mediated by hydrodynamic interactions in microfluidic devices. We also discuss the physical origin of these hydrodynamic interactions and their relation to parameters such as device geometry, fluid properties, and flow conditions.
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Affiliation(s)
- Francesco Del Giudice
- System and Process Engineering Centre, College of Engineering, Fabian Way, Swansea, SA1 8EN, UK.
| | - Gaetano D'Avino
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Universitá degli Studi di Napoli Federico II, Piazzale Tecchio 80, 80125 Naples, Italy
| | - Pier Luca Maffettone
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Universitá degli Studi di Napoli Federico II, Piazzale Tecchio 80, 80125 Naples, Italy
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38
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Min YK, Park KS. The Application of Control Materials for Ongoing Quality Management of Next-Generation Sequencing in a Clinical Genetic Laboratory. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:543. [PMID: 34071304 PMCID: PMC8227145 DOI: 10.3390/medicina57060543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 11/16/2022]
Abstract
Next-generation sequencing (NGS) has played an important role in detecting genetic variants with pathologic and therapeutic potential. The advantages of NGS, such as high-throughput sequencing capacity and massively parallel sequencing, have a significant impact on realization of genetic profiling in clinical genetic laboratories. These changes have enabled clinicians to execute precision medicine in diagnosis, prognosis, and treatment for patients. However, to adapt targeted gene panels in diagnostic use, analytical validation and ongoing quality control should be implemented and applied with both practical guidelines and appropriate control materials. Several guidelines for NGS quality control recommend usage of control materials such as HapMap cell lines, synthetic DNA fragments, and genetically characterized cell lines; however, specifications or applications of such usage are insufficient to guideline method development. This review focuses on what factors should be considered before control material selection for NGS assay and practical methods of how they could be developed in clinical genetic laboratories. This review also provides the detailed sources of critical information related to control materials.
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Affiliation(s)
- Young-Kyu Min
- Department of Medical Laser, Dankook University, Chungnam 31116, Korea;
- Department of Laboratory Medicine, Severance Hospital, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Kyung-Sun Park
- Department of Laboratory Medicine, Kyung Hee University School of Medicine and Kyung Hee University Medical Center, Seoul 02447, Korea
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Ooi CH, Vadivelu R, Jin J, Sreejith KR, Singha P, Nguyen NK, Nguyen NT. Liquid marble-based digital microfluidics - fundamentals and applications. LAB ON A CHIP 2021; 21:1199-1216. [PMID: 33656019 DOI: 10.1039/d0lc01290d] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Liquid marbles are droplets with volume typically on the order of microliters coated with hydrophobic powder. Their versatility, ease of use and low cost make liquid marbles an attractive platform for digital microfluidics. This paper provides the state of the art of discoveries in the physics of liquid marbles and their practical applications. The paper first discusses the fundamental properties of liquid marbles, followed by the summary of different techniques for the synthesis of liquid marbles. Next, manipulation techniques for handling liquid marbles are discussed. Applications of liquid marbles are categorised according to their use as chemical and biological reactors. The paper concludes with perspectives on the future development of liquid marble-based digital microfluidics.
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Affiliation(s)
- Chin Hong Ooi
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Queensland 4111, Australia.
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40
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A narrative review of single-nucleotide polymorphism detection methods and their application in studies of Staphylococcus aureus. JOURNAL OF BIO-X RESEARCH 2021. [DOI: 10.1097/jbr.0000000000000071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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41
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Choi Y, Song Y, Kim YT, Lee SJ, Lee KG, Im SG. Multifunctional Printable Micropattern Array for Digital Nucleic Acid Assay for Microbial Pathogen Detection. ACS APPLIED MATERIALS & INTERFACES 2021; 13:3098-3108. [PMID: 33423455 DOI: 10.1021/acsami.0c16862] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The digital nucleic acid assay is a precise, sensitive, and reproducible method for determining the presence of individual target molecules separated in designated partitions; thus, this technique can be used for the nucleic acid detection. Here, we propose a multifunctional micropattern array capable of isolating individual target molecules into partitions and simultaneous on-site cell lysis to achieve a direct DNA extraction and digitized quantification thereof. The multifunctional micropattern array is fabricated by the deposition of a copolymer film, poly(2-dimethylaminomethyl styrene-co-hydroxyethyl methacrylate) (pDH), directly on a microfluidic chip surface via the photoinitiated chemical vapor deposition process, followed by hydrophobic microcontact printing (μCP) to define each partition for the nucleic acid isolation. The pDH layer is a positively charged surface, which is desirable for the bacterial lysis and DNA capture, while showing exceptional water stability for more than 24 h. The hydrophobic μCP-treated pDH surface is stable under aqueous conditions at a high temperature (70 °C) for 1 h and enables the rapid and reliable formation of thousands of sessile microdroplets for the compartmentalization of an aqueous sample solution without involving bulky and costly microfluidic devices. By assembling the multifunctional micropattern array into the microfluidic chip, the isothermal amplification in each partition can detect DNA templates over a concentration range of 0.01-2 ng/μL. The untreated bacterial cells can also be directly compartmentalized via the microdroplet formation, followed by the on-site cell lysis and DNA capture on the compartmentalized pDH surface. For Escherichia coli O157:H7, Salmonella enteritidis, and Staphylococcus aureus cells, cell numbers ranging from 1.4 × 104 to 1.4 × 107 can be distinguished by using the multifunctional micropattern array, regardless of the cell type. The multifunctional micropattern array developed in this study provides a novel multifunctional compartmentalization method for rapid, simple, and accurate digital nucleic acid assays.
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Affiliation(s)
- Yunho Choi
- Department of Chemical & Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Younseong Song
- Department of Chemical & Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yong Tae Kim
- Department of Chemical Engineering & Biotechnology, Korea Polytechnic University, 237 Sangidaehak-ro, Siheung-si, Gyeonggi-do 15073, Republic of Korea
| | - Seok Jae Lee
- National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Kyoung G Lee
- National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sung Gap Im
- Department of Chemical & Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- KAIST Institute for NanoCentury, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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42
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Centrifugal Microfluidic Integration of 4-Plex ddPCR Demonstrated by the Quantification of Cancer-Associated Point Mutations. Processes (Basel) 2021. [DOI: 10.3390/pr9010097] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We present the centrifugal microfluidic implementation of a four-plex digital droplet polymerase chain reaction (ddPCR). The platform features 12 identical ddPCR units on a LabDisk cartridge, each capable of generating droplets with a diameter of 82.7 ± 9 µm. By investigating different oil–surfactant concentrations, we identified a robust process for droplet generation and stabilization. We observed high droplet stability during thermocycling and endpoint fluorescence imaging, as is required for ddPCRs. Furthermore, we introduce an automated process for four-color fluorescence imaging using a commercial cell analysis microscope, including a customized software pipeline for ddPCR image evaluation. The applicability of ddPCRs is demonstrated by the quantification of three cancer-associated KRAS point mutations (G12D, G12V and G12A) in a diagnostically relevant wild type DNA background. The four-plex assay showed high sensitivity (3.5–35 mutant DNA copies in 15,000 wild type DNA copies) and linear performance (R² = 0.99) across all targets in the LabDisk.
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43
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Abstract
Nanoparticles and biological molecules high throughput robust separation is of significant interest in many healthcare and nanoscience industrial applications. In this work, we report an on-chip automatic efficient separation and preconcentration method of dissimilar sized particles within a microfluidic platform using integrated membrane valves controlled microfiltration. Micro-sized E. coli bacteria are sorted from nanoparticles and preconcentrated on a microfluidic chip with six integrated pneumatic valves (sub-100 nL dead volume) using hydrophilic PVDF filter with 0.45 μm pore diameter. The proposed on-chip automatic sorting sequence includes a sample filtration, dead volume washout and retentate backflush in reverse flow. We showed that pulse backflush mode and volume control can dramatically increase microparticles sorting and preconcentration efficiency. We demonstrate that at the optimal pulse backflush regime a separation efficiency of E. coli cells up to 81.33% at a separation throughput of 120.45 μL/min can be achieved. A trimmed mode when the backflush volume is twice smaller than the initial sample results in a preconcentration efficiency of E. coli cells up to 121.96% at a throughput of 80.93 μL/min. Finally, we propose a cyclic on-chip preconcentration method which demonstrates E. coli cells preconcentration efficiency of 536% at a throughput of 1.98 μL/min and 294% preconcentration efficiency at a 10.9 μL/min throughput.
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44
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Hai X, Li Y, Zhu C, Song W, Cao J, Bi S. DNA-based label-free electrochemical biosensors: From principles to applications. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116098] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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45
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Compressed Air-Driven Continuous-Flow Thermocycled Digital PCR for HBV Diagnosis in Clinical-Level Serum Sample Based on Single Hot Plate. Molecules 2020; 25:molecules25235646. [PMID: 33266146 PMCID: PMC7731400 DOI: 10.3390/molecules25235646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/16/2022] Open
Abstract
We report a novel compressed air-driven continuous-flow digital PCR (dPCR) system based on a 3D microfluidic chip and self-developed software system to realize real-time monitoring. The system can ensure the steady transmission of droplets in long tubing without an external power source and generate stable droplets of suitable size for dPCR by two needles and a narrowed Teflon tube. The stable thermal cycle required by dPCR can be achieved by using only one constant temperature heater. In addition, our system has realized the real-time detection of droplet fluorescence in each thermal cycle, which makes up for the drawbacks of the end-point detection method used in traditional continuous-flow dPCR. This continuous-flow digital PCR by the compressed air-driven method can meet the requirements of droplet thermal cycle and diagnosis in a clinical-level serum sample. Comparing the detection results of clinical samples (hepatitis B virus serum) with commercial instruments (CFX Connect; Bio Rad, Hercules, CA, USA), the linear correlation reached 0.9995. Because the system greatly simplified the traditional dPCR process, this system is stable and user-friendly.
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46
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Wang X, Li F, Guo Y. Recent Trends in Nanomaterial-Based Biosensors for Point-of-Care Testing. Front Chem 2020; 8:586702. [PMID: 33195085 PMCID: PMC7596383 DOI: 10.3389/fchem.2020.586702] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/07/2020] [Indexed: 12/15/2022] Open
Abstract
In recent years, nanomaterials of different shape, size, and composition have been prepared and characterized, such as gold and silver nanoparticles, quantum dots, mesoporous silica nanoparticles, carbon nanomaterials, and hybrid nanocomposites. Because of their unique physical and chemical properties, these nanomaterials are increasingly used in point-of-care testing (POCT) to improve analytical performance and simplify detection process. They are used either as carriers for immobilizing biorecognition elements, or as labels for signal generation, transduction and amplification. In this commentary, we highlight recent POCT technologies that employ nanotechnology for the analysis of disease biomarkers, including small-molecule metabolites, enzymes, proteins, nucleic acids, cancer cells, and pathogens. Recent advances in lateral flow tests, printable electrochemical biosensors, and microfluidics-based devices are summarized. Existing challenges and future directions are also discussed.
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Affiliation(s)
- Xu Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
| | - Feng Li
- College of Chemistry, Sichuan University, Chengdu, China.,Department of Chemistry, Brock University, St. Catharines, ON, Canada
| | - Yirong Guo
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
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47
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Abstract
DNA libraries are predisposed to template mispairing during conventional “bulk” PCR, leading to the loss of unique sequences. The latter is facilitated by the nonuniform distribution of templates frequently observed in DNA libraries. These effects result in a prominent reduction of the original diversity. The encapsulation of DNA repertoires in liquid droplets abolishes the effects of mispairing in DNA libraries. The fundamental advantages of emulsion PCR (ePCR) over bulk PCR are illustrated by deep sequencing and mathematical modeling, which provide the general strategy for ePCR rationalization. The quasi single-molecule ePCR reveals total genetic information by counteracting the degeneration of DNA libraries’ diversity. Conventional “bulk” PCR often yields inefficient and nonuniform amplification of complex templates in DNA libraries, introducing unwanted biases. Amplification of single DNA molecules encapsulated in a myriad of emulsion droplets (emulsion PCR, ePCR) allows the mitigation of this problem. Different ePCR regimes were experimentally analyzed to identify the most robust techniques for enhanced amplification of DNA libraries. A phenomenological mathematical model that forms an essential basis for optimal use of ePCR for library amplification was developed. A detailed description by high-throughput sequencing of amplified DNA-encoded libraries highlights the principal advantages of ePCR over bulk PCR. ePCR outperforms PCR, reduces gross DNA errors, and provides a more uniform distribution of the amplified sequences. The quasi single-molecule amplification achieved via ePCR represents the fundamental requirement in case of complex DNA templates being prone to diversity degeneration and provides a way to preserve the quality of DNA libraries.
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48
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Li B, Li Y, Jiang Y, Manz A, Wu W. A digital PCR system based on the thermal cycled chip with multi helix winding capillary. Sci Rep 2020; 10:17824. [PMID: 33082428 PMCID: PMC7576587 DOI: 10.1038/s41598-020-74711-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 10/05/2020] [Indexed: 12/19/2022] Open
Abstract
This paper presents a digital PCR system based on a novel thermal cycled chip, which wraps microchannels on a trapezoidal structure made of polydimethylsiloxane (PDMS) in a multi-helix manner for the first time. It is found that compared to the single helix chip commonly used in previous reports, this kind of novel multi-helix chip can make the surface temperature in the renaturation zone more uniform, and even in the case of rapid fluid flow, it can improve the efficiency of the polymerase chain reaction. What's more, the winding method of multi helix (such as double helix, six helix and eight helix) can obtain better temperature uniformity than the winding of odd helix (such as single helix and three helix). As a proof of concept, the temperature-optimized double-helical chip structure is applied to continuous-flow digital PCR and there is no need to add any surfactant to both the oil phase and reagent. In addition, we successfully analyzed the fluorescence signal of continuous-flow digital PCR by using CMOS camera. Finally, this method is applied for the absolute quantification of the clinical serum sample infected by HBV. The accuracy of the test results has been confirmed by commercial instruments.
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Affiliation(s)
- Bin Li
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanming Li
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China
| | - Yangyang Jiang
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China
| | - Andreas Manz
- Systems Engineering Department, Saarland University, 66123, Saarbrücken, Germany
- Bio Sensor & Materials Group, KIST Europe, 66123, Saarbrücken, Germany
| | - Wenming Wu
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China.
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49
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Moniri A, Miglietta L, Holmes A, Georgiou P, Rodriguez-Manzano J. High-Level Multiplexing in Digital PCR with Intercalating Dyes by Coupling Real-Time Kinetics and Melting Curve Analysis. Anal Chem 2020; 92:14181-14188. [PMID: 32954724 DOI: 10.1021/acs.analchem.0c03298] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Digital polymerase chain reaction (dPCR) is a mature technique that has enabled scientific breakthroughs in several fields. However, this technology is primarily used in research environments with high-level multiplexing, representing a major challenge. Here, we propose a novel method for multiplexing, referred to as amplification and melting curve analysis (AMCA), which leverages the kinetic information in real-time amplification data and the thermodynamic melting profile using an affordable intercalating dye (EvaGreen). The method trains a system composed of supervised machine learning models for accurate classification, by virtue of the large volume of data from dPCR platforms. As a case study, we develop a new 9-plex assay to detect mobilized colistin resistant genes as clinically relevant targets for antimicrobial resistance. Over 100,000 amplification events have been analyzed, and for the positive reactions, the AMCA approach reports a classification accuracy of 99.33 ± 0.13%, an increase of 10.0% over using melting curve analysis. This work provides an affordable method of high-level multiplexing without fluorescent probes, extending the benefits of dPCR in research and clinical settings.
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Affiliation(s)
- Ahmad Moniri
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Luca Miglietta
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Alison Holmes
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London W12 0NN, U.K
| | - Pantelis Georgiou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Jesus Rodriguez-Manzano
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London W12 0NN, U.K
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50
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Moniri A, Miglietta L, Malpartida-Cardenas K, Pennisi I, Cacho-Soblechero M, Moser N, Holmes A, Georgiou P, Rodriguez-Manzano J. Amplification Curve Analysis: Data-Driven Multiplexing Using Real-Time Digital PCR. Anal Chem 2020; 92:13134-13143. [PMID: 32946688 DOI: 10.1021/acs.analchem.0c02253] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Information about the kinetics of PCR reactions is encoded in the amplification curve. However, in digital PCR (dPCR), this information is typically neglected by collapsing each amplification curve into a binary output (positive/negative). Here, we demonstrate that the large volume of raw data obtained from real-time dPCR instruments can be exploited to perform data-driven multiplexing in a single fluorescent channel using machine learning methods, by virtue of the information in the amplification curve. This new approach, referred to as amplification curve analysis (ACA), was shown using an intercalating dye (EvaGreen), reducing the cost and complexity of the assay and enabling the use of melting curve analysis for validation. As a case study, we multiplexed 3 carbapenem-resistant genes to show the impact of this approach on global challenges such as antimicrobial resistance. In the presence of single targets, we report a classification accuracy of 99.1% (N = 16188), which represents a 19.7% increase compared to multiplexing based on the final fluorescent intensity. Considering all combinations of amplification events (including coamplifications), the accuracy was shown to be 92.9% (N = 10383). To support the analysis, we derived a formula to estimate the occurrence of coamplification in dPCR based on multivariate Poisson statistics and suggest reducing the digital occupancy in the case of multiple targets in the same digital panel. The ACA approach takes a step toward maximizing the capabilities of existing real-time dPCR instruments and chemistries, by extracting more information from data to enable data-driven multiplexing with high accuracy. Furthermore, we expect that combining this method with existing probe-based assays will increase multiplexing capabilities significantly. We envision that once emerging point-of-care technologies can reliably capture real-time data from isothermal chemistries, the ACA method will facilitate the implementation of dPCR outside of the lab.
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Affiliation(s)
- Ahmad Moniri
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Luca Miglietta
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Kenny Malpartida-Cardenas
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Ivana Pennisi
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K.,Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London W2 1NY, U.K
| | - Miguel Cacho-Soblechero
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Nicolas Moser
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Alison Holmes
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London W12 0NN, U.K
| | - Pantelis Georgiou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Jesus Rodriguez-Manzano
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London W12 0NN, U.K
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