1
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Sano T, Losakul R, Schmidt H. Dual optofluidic distributed feedback dye lasers for multiplexed biosensing applications. Sci Rep 2023; 13:16824. [PMID: 37803034 PMCID: PMC10558432 DOI: 10.1038/s41598-023-42671-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/12/2023] [Indexed: 10/08/2023] Open
Abstract
Integrated optofluidic devices have become subjects of high interest for rapid biosensor devices due to their unique ability to combine the fluidic processing of small volumes of microfluidics with the analysis capabilities of photonic structures. By integrating dynamically reconfigurable optofluidic lasers on-chip, complex coupling can be eliminated while further increasing the capabilities of sensors to detect an increasing number of target biomarkers. Here, we report a polydimethylsiloxane-based device with two on-chip fluidic distributed feedback (DFB) laser cavities that are integrated with an orthogonal analyte channel for multiplexed fluorescence excitation. One DFB grating is filled with 4-(dicyanomethylene)-2-methyl-6-(4-dimethylaminostyryl)-4H-pyran dissolved in dimethyl sulfoxide. The second grating is filled with rhodamine 6G dissolved in a diluted ethylene glycol solution. We present characterization of both lasers through analysis of the lasing spectra for spectral narrowing along with a power series to observe threshold behavior. We then demonstrate simultaneous detection of two different fluorescent microbeads as a proof of concept for scalable, single biomarker analysis using on-chip optofluidic lasers.
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Affiliation(s)
- Tyler Sano
- Department of Electrical and Computer Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA, 95064, USA.
| | - Ravipa Losakul
- Department of Electrical and Computer Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Holger Schmidt
- Department of Electrical and Computer Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA, 95064, USA
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2
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Ganjalizadeh V, Meena GG, Stott MA, Hawkins AR, Schmidt H. Machine learning at the edge for AI-enabled multiplexed pathogen detection. Sci Rep 2023; 13:4744. [PMID: 36959357 PMCID: PMC10034896 DOI: 10.1038/s41598-023-31694-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 03/15/2023] [Indexed: 03/25/2023] Open
Abstract
Multiplexed detection of biomarkers in real-time is crucial for sensitive and accurate diagnosis at the point of use. This scenario poses tremendous challenges for detection and identification of signals of varying shape and quality at the edge of the signal-to-noise limit. Here, we demonstrate a robust target identification scheme that utilizes a Deep Neural Network (DNN) for multiplex detection of single particles and molecular biomarkers. The model combines fast wavelet particle detection with Short-Time Fourier Transform analysis, followed by DNN identification on an AI-specific edge device (Google Coral Dev board). The approach is validated using multi-spot optical excitation of Klebsiella Pneumoniae bacterial nucleic acids flowing through an optofluidic waveguide chip that produces fluorescence signals of varying amplitude, duration, and quality. Amplification-free 3× multiplexing in real-time is demonstrated with excellent specificity, sensitivity, and a classification accuracy of 99.8%. These results show that a minimalistic DNN design optimized for mobile devices provides a robust framework for accurate pathogen detection using compact, low-cost diagnostic devices.
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Affiliation(s)
- Vahid Ganjalizadeh
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Gopikrishnan G Meena
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Matthew A Stott
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT, 84602, USA
| | - Aaron R Hawkins
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT, 84602, USA
| | - Holger Schmidt
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.
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3
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Fast custom wavelet analysis technique for single molecule detection and identification. Nat Commun 2022; 13:1035. [PMID: 35210454 PMCID: PMC8873225 DOI: 10.1038/s41467-022-28703-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 01/20/2022] [Indexed: 02/01/2023] Open
Abstract
Many sensors operate by detecting and identifying individual events in a time-dependent signal which is challenging if signals are weak and background noise is present. We introduce a powerful, fast, and robust signal analysis technique based on a massively parallel continuous wavelet transform (CWT) algorithm. The superiority of this approach is demonstrated with fluorescence signals from a chip-based, optofluidic single particle sensor. The technique is more accurate than simple peak-finding algorithms and several orders of magnitude faster than existing CWT methods, allowing for real-time data analysis during sensing for the first time. Performance is further increased by applying a custom wavelet to multi-peak signals as demonstrated using amplification-free detection of single bacterial DNAs. A 4x increase in detection rate, a 6x improved error rate, and the ability for extraction of experimental parameters are demonstrated. This cluster-based CWT analysis will enable high-performance, real-time sensing when signal-to-noise is hardware limited, for instance with low-cost sensors in point of care environments. The authors introduce an accurate, fast and efficient technique to analyze sensory data. They use a continuous wavelet transform concept to look for certain patterns in noisy raw data. The superiority of this approach is demonstrated with fluorescence signals from a chip-based, optofluidic single particle sensor.
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4
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Fernandez-Cuesta I, Llobera A, Ramos-Payán M. Optofluidic systems enabling detection in real samples: A review. Anal Chim Acta 2022; 1192:339307. [DOI: 10.1016/j.aca.2021.339307] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 12/20/2022]
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5
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Shi Y, Nguyen KT, Chin LK, Li Z, Xiao L, Cai H, Yu R, Huang W, Feng S, Yap PH, Liu J, Zhang Y, Liu AQ. Trapping and Detection of Single Viruses in an Optofluidic Chip. ACS Sens 2021; 6:3445-3450. [PMID: 34505501 DOI: 10.1021/acssensors.1c01350] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Accurate single virus detection is critical for disease diagnosis and early prevention, especially in view of current pandemics. Numerous detection methods have been proposed with the single virus sensitivity, including the optical approaches and immunoassays. However, few of them hitherto have the capability of both trapping and detection of single viruses in the microchannel. Here, we report an optofluidic potential well array to trap nanoparticles stably in the flow stream. The nanoparticle is bound with single viruses and fluorescence quantum dots through an immunolabeling protocol. Single viruses can be swiftly captured in the microchannel by optical forces and imaged by a camera. The number of viruses in solution and on each particle can be quantified via image processing. Our method can trap and detect single viruses in the 1 mL serum or water in 2 h, paving an avenue for the advanced, fast, and accurate clinical diagnosis, as well as the study of virus infectivity, mutation, drug inhibition, etc.
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Affiliation(s)
- Yuzhi Shi
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Electrical and Electronic Engineering, Nanyang Technological University, 639798 Singapore
| | - Kim Truc Nguyen
- School of Electrical and Electronic Engineering, Nanyang Technological University, 639798 Singapore
| | - Lip Ket Chin
- School of Electrical and Electronic Engineering, Nanyang Technological University, 639798 Singapore
| | - Zhenyu Li
- School of Electrical and Electronic Engineering, Nanyang Technological University, 639798 Singapore
| | - Limin Xiao
- Advanced Fiber Devices and Systems Group, Key Laboratory of Micro and Nano Photonic Structures (MoE), Key Laboratory for Information Science of Electromagnetic Waves (MoE), Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, School of Information Science and Technology, Fudan University, Shanghai 200433, China
| | - Hong Cai
- Institute of Microelectronics, A*STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-02 Innovis
Tower, 138634 Singapore
| | - Ruozhen Yu
- Chinese Research Academy of Environmental Science, 8, Anwai Dayanfang, Beijing 100012, China
| | - Wei Huang
- Key Laboratory of Multifunctional Nanomaterials and Smart Systems, Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences (CAS), Suzhou 215123, China
| | - Shilun Feng
- School of Electrical and Electronic Engineering, Nanyang Technological University, 639798 Singapore
| | - Peng Huat Yap
- Lee Kong Chian School of Medicine, Nanyang Technological University, 308232 Singapore
| | - Jingquan Liu
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yi Zhang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, 639798 Singapore
| | - Ai Qun Liu
- School of Electrical and Electronic Engineering, Nanyang Technological University, 639798 Singapore
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Stambaugh A, Stott MA, Meena GG, Tamhankar M, Carrion R, Patterson JL, Hawkins AR, Schmidt H. Optofluidic Amplification-free Multiplex Detection of Viral Hemorrhagic Fevers. IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS : A PUBLICATION OF THE IEEE LASERS AND ELECTRO-OPTICS SOCIETY 2021; 27:7200206. [PMID: 33390686 PMCID: PMC7774596 DOI: 10.1109/jstqe.2020.3024239] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Infectious disease outbreaks such as Ebola and other Viral Hemorrhagic Fevers (VHF) require low-complexity, specific, and differentiated diagnostics as illustrated by the recent outbreak in the Democratic Republic of Congo. Here, we describe amplification-free spectrally multiplex detection of four different VHF total RNA samples using multi-spot excitation on a multimode interference waveguide platform along with combinatorial fluorescence labeling of target nucleic acids. In these experiments, we observed an average of 8-fold greater fluorescence signal amplitudes for the Ebola total RNA sample compared to three other total RNA samples: Lake Victoria Marburg Virus, Ravn Marburg Virus, and Crimean-Congo Hemorrhagic Fever. We have attributed this amplitude amplification to an increased amount of RNA during synthesis of soluble glycoprotein in infection. This hypothesis is confirmed by single molecule detection of the total RNA sample after heat-activated release from the carrier microbeads. From these experiments, we observed at least a 5.3x higher RNA mass loading on the Ebola carrier microbeads compared to the Lake Victoria Marburg carrier microbeads, which is consistent with the known production of soluble glycoprotein during infection.
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Affiliation(s)
- Alexandra Stambaugh
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
| | - Matthew A Stott
- Department of Electrical and Computer Engineering, Brigham Young University, Provo UT 84602 USA
| | - Gopikrishnan G Meena
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
| | - Manasi Tamhankar
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227 USA
| | - Ricardo Carrion
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227 USA
| | - Jean L Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227 USA
| | - Aaron R Hawkins
- Department of Electrical and Computer Engineering, Brigham Young University, Provo UT 84602 USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
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7
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Meena GG, Stambaugh AM, Ganjalizadeh V, Stott MA, Hawkins AR, Schmidt H. Ultrasensitive detection of SARS-CoV-2 RNA and antigen using single-molecule optofluidic chip. APL PHOTONICS 2021; 6:066101. [PMID: 35693725 PMCID: PMC9186413 DOI: 10.1063/5.0049735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Nucleic acids and proteins are the two most important target types used in molecular diagnostics. In many instances, simultaneous sensitive and accurate detection of both biomarkers from the same sample would be desirable, but standard detection methods are highly optimized for one type and not cross-compatible. Here, we report the simultaneous multiplexed detection of SARS-CoV-2 RNAs and antigens with single molecule sensitivity. Both analytes are isolated and labeled using a single bead-based solid-phase extraction protocol, followed by fluorescence detection on a multi-channel optofluidic waveguide chip. Direct amplification-free detection of both biomarkers from nasopharyngeal swab samples is demonstrated with single molecule detection sensitivity, opening the door for ultrasensitive dual-target analysis in infectious disease diagnosis, oncology, and other applications.
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Affiliation(s)
- G. G. Meena
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA
| | - A. M. Stambaugh
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA
| | - V. Ganjalizadeh
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA
| | - M. A. Stott
- Electrical and Computer Engineering Department, Brigham Young University, Provo, Utah 84602, USA
| | - A. R. Hawkins
- Electrical and Computer Engineering Department, Brigham Young University, Provo, Utah 84602, USA
| | - H. Schmidt
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA
- Author to whom correspondence should be addressed:. Telephone: 831-459-1482
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8
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Shi Y, Li Z, Liu PY, Nguyen BTT, Wu W, Zhao Q, Chin LK, Wei M, Yap PH, Zhou X, Zhao H, Yu D, Tsai DP, Liu AQ. On-Chip Optical Detection of Viruses: A Review. ADVANCED PHOTONICS RESEARCH 2021; 2:2000150. [PMID: 33786535 PMCID: PMC7994989 DOI: 10.1002/adpr.202000150] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/31/2020] [Indexed: 05/17/2023]
Abstract
The current outbreak of the coronavirus disease-19 (COVID-19) pandemic worldwide has caused millions of fatalities and imposed a severe impact on our daily lives. Thus, the global healthcare system urgently calls for rapid, affordable, and reliable detection toolkits. Although the gold-standard nucleic acid amplification tests have been widely accepted and utilized, they are time-consuming and labor-intensive, which exceedingly hinder the mass detection in low-income populations, especially in developing countries. Recently, due to the blooming development of photonics, various optical chips have been developed to detect single viruses with the advantages of fast, label-free, affordable, and point of care deployment. Herein, optical approaches especially in three perspectives, e.g., flow-free optical methods, optofluidics, and surface-modification-assisted approaches, are summarized. The future development of on-chip optical-detection methods in the wave of emerging new ideas in nanophotonics is also briefly discussed.
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Affiliation(s)
- Yuzhi Shi
- School of Electrical and Electronic EngineeringNanyang Technological UniversitySingapore639798Singapore
| | - Zhenyu Li
- School of Electrical and Electronic EngineeringNanyang Technological UniversitySingapore639798Singapore
- National Key Laboratory of Science and Technology on Micro/Nano FabricationInstitute of MicroelectronicsPeking UniversityBeijing100871China
| | - Patricia Yang Liu
- School of Electrical and Electronic EngineeringNanyang Technological UniversitySingapore639798Singapore
| | - Binh Thi Thanh Nguyen
- School of Electrical and Electronic EngineeringNanyang Technological UniversitySingapore639798Singapore
| | - Wenshuai Wu
- School of Electrical and Electronic EngineeringNanyang Technological UniversitySingapore639798Singapore
| | - Qianbin Zhao
- School of Electrical and Electronic EngineeringNanyang Technological UniversitySingapore639798Singapore
| | - Lip Ket Chin
- School of Electrical and Electronic EngineeringNanyang Technological UniversitySingapore639798Singapore
- Center for Systems BiologyMassachusetts General HospitalBostonMA02141USA
| | - Minggui Wei
- School of Electrical and Electronic EngineeringNanyang Technological UniversitySingapore639798Singapore
| | - Peng Huat Yap
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingapore308232Singapore
| | - Xiaohong Zhou
- State Key Joint Laboratory of ESPCSchool of EnvironmentTsinghua UniversityBeijing100084China
| | - Hongwei Zhao
- State Key Laboratory of Marine Resource Utilization of South China SeaHainan UniversityHaikou570228China
| | - Dan Yu
- Beijing Pediatric Research InstituteBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijing100045China
| | - Din Ping Tsai
- Department of Electronic and Information EngineeringThe Hong Kong Polytechnic UniversityHung HomKowloonHong KongChina
| | - Ai Qun Liu
- School of Electrical and Electronic EngineeringNanyang Technological UniversitySingapore639798Singapore
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Sano T, Black J, Mitchell S, Zhang H, Schmidt H. Pneumatically tunable optofluidic DFB dye laser using corrugated sidewalls. OPTICS LETTERS 2020; 45:5978-5981. [PMID: 33137048 DOI: 10.1364/ol.404303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
Polydimethylsiloxane-based optofluidics provides a powerful platform for a complete analytical lab-on-chip. Here, we report on a novel on-chip laser source that can be integrated with sample preparation and analysis functions. A corrugated sidewall structure is integrated into a microfluidic channel to form a distributed feedback (DFB) laser using rhodamine 6G dissolved in an ethylene glycol and water solution. Lasing is demonstrated with a threshold pump power of 87.9 µW, corresponding to a pump intensity of 52.7mW/cm2. Laser threshold and output power are optimized with respect to rhodamine 6G concentration and core index and found to be in good agreement with a rate equation model. Additionally, the laser can be switched on and off mechanically using a pneumatic cell inducing positive pressure on the grating.
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Meena GG, Wall TA, Stott MA, Brown O, Robison R, Hawkins AR, Schmidt H. 7X multiplexed, optofluidic detection of nucleic acids for antibiotic-resistance bacterial screening. OPTICS EXPRESS 2020; 28:33019-33027. [PMID: 33114971 PMCID: PMC7679188 DOI: 10.1364/oe.402311] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Rapid and accurate diagnosis of bacterial infections resistant to multiple antibiotics requires development of new bio-sensors for differentiated detection of multiple targets. This work demonstrates 7x multiplexed detection for antibiotic-resistance bacterial screening on an optofluidic platform. We utilize spectrally multiplexed multi-spot excitation for simultaneous detection of nucleic acid strands corresponding to bacterial targets and resistance genes. This is enabled by multi-mode interference (MMI) waveguides integrated in an optofluidic device. We employ a combinatorial three-color labeling scheme for the nucleic acid assays to scale up their multiplexing capability to seven different nucleic acids, representing three species and four resistance genes.
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Affiliation(s)
- G. G. Meena
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA
| | - T. A. Wall
- Electrical and Computer Engineering Department, Brigham Young University, Provo, Utah 84602, USA
| | - M. A. Stott
- Electrical and Computer Engineering Department, Brigham Young University, Provo, Utah 84602, USA
| | - O. Brown
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah 84602, USA
| | - R. Robison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah 84602, USA
| | - A. R. Hawkins
- Electrical and Computer Engineering Department, Brigham Young University, Provo, Utah 84602, USA
| | - H. Schmidt
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA
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Meena GG, Hanson RL, Wood RL, Brown OT, Stott MA, Robison RA, Pitt WG, Woolley AT, Hawkins AR, Schmidt H. 3× multiplexed detection of antibiotic resistant plasmids with single molecule sensitivity. LAB ON A CHIP 2020; 20:3763-3771. [PMID: 33048071 PMCID: PMC7574402 DOI: 10.1039/d0lc00640h] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Bacterial pathogens resistant to antibiotics have become a serious health threat. Those species which have developed resistance against multiple drugs such as the carbapenems, are more lethal as these are last line therapy antibiotics. Current diagnostic tests for these resistance traits are based on singleplex target amplification techniques which can be time consuming and prone to errors. Here, we demonstrate a chip based optofluidic system with single molecule sensitivity for amplification-free, multiplexed detection of plasmids with genes corresponding to antibiotic resistance, within one hour. Rotating disks and microfluidic chips with functionalized polymer monoliths provided the upstream sample preparation steps to selectively extract these plasmids from blood spiked with E. coli DH5α cells. Waveguide-based spatial multiplexing using a multi-mode interference waveguide on an optofluidic chip was used for parallel detection of three different carbapenem resistance genes. These results point the way towards rapid, amplification-free, multiplex analysis of antibiotic-resistant pathogens.
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Affiliation(s)
- G G Meena
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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