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Traylor A, Lee PW, Hsieh K, Wang TH. Improving bacteria identification from digital melt assay via oligonucleotide-based temperature calibration. Anal Chim Acta 2024; 1297:342371. [PMID: 38438240 PMCID: PMC11082877 DOI: 10.1016/j.aca.2024.342371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 03/06/2024]
Abstract
BACKGROUND Bacterial infections, especially polymicrobial infections, remain a threat to global health and require advances in diagnostic technologies for timely and accurate identification of all causative species. Digital melt - microfluidic chip-based digital PCR combined with high resolution melt (HRM) - is an emerging method for identification and quantification of polymicrobial bacterial infections. Despite advances in recent years, existing digital melt instrumentation often delivers nonuniform temperatures across digital chips, resulting in nonuniform digital melt curves for individual bacterial species. This nonuniformity can lead to inaccurate species identification and reduce the capacity for differentiating bacterial species with similar digital melt curves. RESULTS We introduce herein a new temperature calibration method for digital melt by incorporating an unamplified, synthetic DNA fragment with a known melting temperature as a calibrator. When added at a tuned concentration to an established digital melt assay amplifying the commonly targeted 16S V1 - V6 region, this calibrator produced visible low temperature calibrator melt curves across-chip along with the target bacterial melt curves. This enables alignment of the bacterial melt curves and correction of heating-induced nonuniformities. Using this calibration method, we were able to improve the uniformity of digital melt curves from three causative species of bacteria. Additionally, we assessed calibration's effects on identification accuracy by performing machine learning identification of three polymicrobial mixtures comprised of two bacteria with similar digital melt curves in different ratios. Calibration greatly improved mixture composition prediction. SIGNIFICANCE To the best of our knowledge, this work represents the first DNA calibrator-supplemented assay and calibration method for nanoarray digital melt. Our results suggest that this calibration method can be flexibly used to improve identification accuracy and reduce melt curve variabilities across a variety of pathogens and assays. Therefore, this calibration method has the potential to elevate the diagnostic capabilities of digital melt toward polymicrobial bacterial infections and other infectious diseases.
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Affiliation(s)
- Amelia Traylor
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Pei-Wei Lee
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, 21205, United States; Institute of NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, United States.
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Lee SM, Balakrishnan HK, Doeven EH, Yuan D, Guijt RM. Chemical Trends in Sample Preparation for Nucleic Acid Amplification Testing (NAAT): A Review. BIOSENSORS 2023; 13:980. [PMID: 37998155 PMCID: PMC10669371 DOI: 10.3390/bios13110980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023]
Abstract
Nucleic acid amplification testing facilitates the detection of disease through specific genomic sequences and is attractive for point-of-need testing (PONT); in particular, the early detection of microorganisms can alert early response systems to protect the public and ecosystems from widespread outbreaks of biological threats, including infectious diseases. Prior to nucleic acid amplification and detection, extensive sample preparation techniques are required to free nucleic acids and extract them from the sample matrix. Sample preparation is critical to maximize the sensitivity and reliability of testing. As the enzymatic amplification reactions can be sensitive to inhibitors from the sample, as well as from chemicals used for lysis and extraction, avoiding inhibition is a significant challenge, particularly when minimising liquid handling steps is also desirable for the translation of the assay to a portable format for PONT. The reagents used in sample preparation for nucleic acid testing, covering lysis and NA extraction (binding, washing, and elution), are reviewed with a focus on their suitability for use in PONT.
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Affiliation(s)
- Soo Min Lee
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
| | - Hari Kalathil Balakrishnan
- Department of Chemical Engineering, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates;
| | - Egan H. Doeven
- School of Life and Environmental Sciences, Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia;
| | - Dan Yuan
- School of Mechanical and Mining Engineering, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Rosanne M. Guijt
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
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Bao M, Waitkus J, Liu L, Chang Y, Xu Z, Qin P, Chen J, Du K. Micro- and nanosystems for the detection of hemorrhagic fever viruses. LAB ON A CHIP 2023; 23:4173-4200. [PMID: 37675935 DOI: 10.1039/d3lc00482a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Hemorrhagic fever viruses (HFVs) are virulent pathogens that can cause severe and often fatal illnesses in humans. Timely and accurate detection of HFVs is critical for effective disease management and prevention. In recent years, micro- and nano-technologies have emerged as promising approaches for the detection of HFVs. This paper provides an overview of the current state-of-the-art systems for micro- and nano-scale approaches to detect HFVs. It covers various aspects of these technologies, including the principles behind their sensing assays, as well as the different types of diagnostic strategies that have been developed. This paper also explores future possibilities of employing micro- and nano-systems for the development of HFV diagnostic tools that meet the practical demands of clinical settings.
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Affiliation(s)
- Mengdi Bao
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Jacob Waitkus
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Li Liu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Yu Chang
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Zhiheng Xu
- Department of Industrial Engineering, Rochester Institute of Technology, Rochester, NY, USA
| | - Peiwu Qin
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
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Fan Y, Dai R, Guan X, Lu S, Yang C, Lv X, Li X. Rapid automatic nucleic acid purification system based on gas-liquid immiscible phase. J Sep Sci 2023; 46:e2200801. [PMID: 36661136 DOI: 10.1002/jssc.202200801] [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: 10/05/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/21/2023]
Abstract
The continuous expansion of nucleic acid detection applications has resulted in constant developments in rapid, low-consumption, and highly automated nucleic acid extraction methods. Nucleic acid extraction using magnetic beads across an immiscible phase interface offers significant simplification and parallelization potential. The gas-liquid immiscible phase valve eliminates the requirement for complicated cassettes and is suitable for automation applications. By analyzing the process of magnetic beads crossing the gas-liquid interface, we utilized a low magnetic field strength to drive large magnetic bead packages to cross the gas-liquid interface, providing a solution of high magnetic bead recovery rate for solid-phase extraction with a low-surfactant system based on gas-liquid immiscible phase valve. The recovery rate of magnetic beads was further improved to 90%-95% and the carryover of the reagents was below 1%. Consequently, a chip and an automatic system were developed to verify the applicability of this method for nucleic acid extraction. The Hepatitis B virus serum standard was used for the extraction test. The extraction of four samples was performed within 7 minutes, with nucleic acid recovery maintained above 80% and good purity. Thus, through analysis and experiments, a fast, highly automated, and low-consumption nucleic acid recovery method was proposed in this study.
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Affiliation(s)
- Yunlong Fan
- School of Life Science, Key Laboratory of Convergence Medical Engineering System and Healthcare Technology, Beijing Institute of Technology, Beijing, P. R. China
| | - Rongji Dai
- School of Life Science, Key Laboratory of Convergence Medical Engineering System and Healthcare Technology, Beijing Institute of Technology, Beijing, P. R. China
| | - Xuejun Guan
- School of Life Science, Key Laboratory of Convergence Medical Engineering System and Healthcare Technology, Beijing Institute of Technology, Beijing, P. R. China
| | - Shuyu Lu
- School of Life Science, Key Laboratory of Convergence Medical Engineering System and Healthcare Technology, Beijing Institute of Technology, Beijing, P. R. China
| | - Chunhua Yang
- School of Life Science, Key Laboratory of Convergence Medical Engineering System and Healthcare Technology, Beijing Institute of Technology, Beijing, P. R. China
| | - Xuefei Lv
- School of Life Science, Key Laboratory of Convergence Medical Engineering System and Healthcare Technology, Beijing Institute of Technology, Beijing, P. R. China
| | - Xiaoqiong Li
- School of Life Science, Key Laboratory of Convergence Medical Engineering System and Healthcare Technology, Beijing Institute of Technology, Beijing, P. R. China
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Hou Y, Chen S, Zheng Y, Zheng X, Lin JM. Droplet-based digital PCR (ddPCR) and its applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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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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Hsieh K, Melendez JH, Gaydos CA, Wang TH. Bridging the gap between development of point-of-care nucleic acid testing and patient care for sexually transmitted infections. LAB ON A CHIP 2022; 22:476-511. [PMID: 35048928 PMCID: PMC9035340 DOI: 10.1039/d1lc00665g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The incidence rates of sexually transmitted infections (STIs), including the four major curable STIs - chlamydia, gonorrhea, trichomoniasis and, syphilis - continue to increase globally, causing medical cost burden and morbidity especially in low and middle-income countries (LMIC). There have seen significant advances in diagnostic testing, but commercial antigen-based point-of-care tests (POCTs) are often insufficiently sensitive and specific, while near-point-of-care (POC) instruments that can perform sensitive and specific nucleic acid amplification tests (NAATs) are technically complex and expensive, especially for LMIC. Thus, there remains a critical need for NAAT-based STI POCTs that can improve diagnosis and curb the ongoing epidemic. Unfortunately, the development of such POCTs has been challenging due to the gap between researchers developing new technologies and healthcare providers using these technologies. This review aims to bridge this gap. We first present a short introduction of the four major STIs, followed by a discussion on the current landscape of commercial near-POC instruments for the detection of these STIs. We present relevant research toward addressing the gaps in developing NAAT-based STI POCT technologies and supplement this discussion with technologies for HIV and other infectious diseases, which may be adapted for STIs. Additionally, as case studies, we highlight the developmental trajectory of two different POCT technologies, including one approved by the United States Food and Drug Administration (FDA). Finally, we offer our perspectives on future development of NAAT-based STI POCT technologies.
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Affiliation(s)
- Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Johan H Melendez
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Charlotte A Gaydos
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
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