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Daniel F, Kesterson D, Lei K, Hord C, Patel A, Kaffenes A, Congivaram H, Prakash S. Application of Microfluidics for Bacterial Identification. Pharmaceuticals (Basel) 2022; 15:ph15121531. [PMID: 36558982 PMCID: PMC9781190 DOI: 10.3390/ph15121531] [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: 10/23/2022] [Revised: 11/29/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Bacterial infections continue to pose serious public health challenges. Though anti-bacterial therapeutics are effective remedies for treating these infections, the emergence of antibiotic resistance has imposed new challenges to treatment. Often, there is a delay in prescribing antibiotics at initial symptom presentation as it can be challenging to clinically differentiate bacterial infections from other organisms (e.g., viruses) causing infection. Moreover, bacterial infections can arise from food, water, or other sources. These challenges have demonstrated the need for rapid identification of bacteria in liquids, food, clinical spaces, and other environments. Conventional methods of bacterial identification rely on culture-based approaches which require long processing times and higher pathogen concentration thresholds. In the past few years, microfluidic devices paired with various bacterial identification methods have garnered attention for addressing the limitations of conventional methods and demonstrating feasibility for rapid bacterial identification with lower biomass thresholds. However, such culture-free methods often require integration of multiple steps from sample preparation to measurement. Research interest in using microfluidic methods for bacterial identification is growing; therefore, this review article is a summary of current advancements in this field with a focus on comparing the efficacy of polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and emerging spectroscopic methods.
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Affiliation(s)
- Fraser Daniel
- Department of Mechanical and Aerospace Engineering, College of Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Delaney Kesterson
- Center for Life Sciences Education, The Ohio State University, Columbus, OH 43210, USA
| | - Kevin Lei
- Department of Chemical and Biomolecular Engineering, College of Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Catherine Hord
- Center for Life Sciences Education, The Ohio State University, Columbus, OH 43210, USA
| | - Aarti Patel
- Department of Biomedical Engineering, College of Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Anastasia Kaffenes
- Department of Neuroscience, College of Arts and Sciences and College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Harrshavasan Congivaram
- School of Health and Rehabilitation Sciences, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Shaurya Prakash
- Department of Mechanical and Aerospace Engineering, College of Engineering, The Ohio State University, Columbus, OH 43210, USA
- Correspondence:
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Tsai HF, Carlson DW, Koldaeva A, Pigolotti S, Shen AQ. Optimization and Fabrication of Multi-Level Microchannels for Long-Term Imaging of Bacterial Growth and Expansion. MICROMACHINES 2022; 13:mi13040576. [PMID: 35457881 PMCID: PMC9028424 DOI: 10.3390/mi13040576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 02/01/2023]
Abstract
Bacteria are unicellular organisms whose length is usually around a few micrometers. Advances in microfabrication techniques have enabled the design and implementation of microdevices to confine and observe bacterial colony growth. Microstructures hosting the bacteria and microchannels for nutrient perfusion usually require separate microfabrication procedures due to different feature size requirements. This fact increases the complexity of device integration and assembly process. Furthermore, long-term imaging of bacterial dynamics over tens of hours requires stability in the microscope focusing mechanism to ensure less than one-micron drift in the focal axis. In this work, we design and fabricate an integrated multi-level, hydrodynamically-optimized microfluidic chip to study long-term Escherichia coli population dynamics in confined microchannels. Reliable long-term microscopy imaging and analysis has been limited by focus drifting and ghost effect, probably caused by the shear viscosity changes of aging microscopy immersion oil. By selecting a microscopy immersion oil with the most stable viscosity, we demonstrate successful captures of focally stable time-lapse bacterial images for ≥72 h. Our fabrication and imaging methodology should be applicable to other single-cell studies requiring long-term imaging.
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Affiliation(s)
- Hsieh-Fu Tsai
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan;
- Department of Biomedical Engineering, Chang Gung University, Taoyuan 333, Taiwan
- Correspondence: (H.-F.T.); (A.Q.S.); Tel.: +886-3-2118800 (ext. 3079) (H.-F.T.)
| | - Daniel W. Carlson
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan;
| | - Anzhelika Koldaeva
- Biological Complexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan; (A.K.); (S.P.)
| | - Simone Pigolotti
- Biological Complexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan; (A.K.); (S.P.)
| | - Amy Q. Shen
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan;
- Correspondence: (H.-F.T.); (A.Q.S.); Tel.: +886-3-2118800 (ext. 3079) (H.-F.T.)
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Zhou WM, Yan YY, Guo QR, Ji H, Wang H, Xu TT, Makabel B, Pilarsky C, He G, Yu XY, Zhang JY. Microfluidics applications for high-throughput single cell sequencing. J Nanobiotechnology 2021; 19:312. [PMID: 34635104 PMCID: PMC8507141 DOI: 10.1186/s12951-021-01045-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 09/16/2021] [Indexed: 12/22/2022] Open
Abstract
The inherent heterogeneity of individual cells in cell populations plays significant roles in disease development and progression, which is critical for disease diagnosis and treatment. Substantial evidences show that the majority of traditional gene profiling methods mask the difference of individual cells. Single cell sequencing can provide data to characterize the inherent heterogeneity of individual cells, and reveal complex and rare cell populations. Different microfluidic technologies have emerged for single cell researches and become the frontiers and hot topics over the past decade. In this review article, we introduce the processes of single cell sequencing, and review the principles of microfluidics for single cell analysis. Also, we discuss the common high-throughput single cell sequencing technologies along with their advantages and disadvantages. Lastly, microfluidics applications in single cell sequencing technology for the diagnosis of cancers and immune system diseases are briefly illustrated.
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Affiliation(s)
- Wen-Min Zhou
- Key Laboratory of Molecular Target & Clinical Pharmacology , The State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, People's Republic of China
| | - Yan-Yan Yan
- School of Medicine, Shanxi Datong University, Datong, 037009, People's Republic of China
| | - Qiao-Ru Guo
- Key Laboratory of Molecular Target & Clinical Pharmacology , The State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, People's Republic of China
| | - Hong Ji
- Key Laboratory of Molecular Target & Clinical Pharmacology , The State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, People's Republic of China
| | - Hui Wang
- Guangzhou Institute of Pediatrics/Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, People's Republic of China
| | - Tian-Tian Xu
- Guangzhou Institute of Pediatrics/Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, People's Republic of China
| | - Bolat Makabel
- Xinjiang Institute of Materia Medica, Urumqi, 830004, People's Republic of China
| | - Christian Pilarsky
- Department of Surgery, Friedrich-Alexander University of Erlangen-Nuremberg (FAU), University Hospital of Erlangen, Erlangen, Germany
| | - Gen He
- Key Laboratory of Molecular Target & Clinical Pharmacology , The State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, People's Republic of China.
| | - Xi-Yong Yu
- Key Laboratory of Molecular Target & Clinical Pharmacology , The State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, People's Republic of China.
| | - Jian-Ye Zhang
- Key Laboratory of Molecular Target & Clinical Pharmacology , The State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, People's Republic of China.
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Dettinger P, Wang W, Ahmed N, Zhang Y, Loeffler D, Kull T, Etzrodt M, Lengerke C, Schroeder T. An automated microfluidic system for efficient capture of rare cells and rapid flow-free stimulation. LAB ON A CHIP 2020; 20:4246-4254. [PMID: 33063816 DOI: 10.1039/d0lc00687d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cell fates are controlled by environmental stimuli that rapidly change the activity of intracellular signaling. Studying these processes requires rapid manipulations of micro-environmental conditions while continuously observing single cells over long periods of time. Current microfluidic devices are unable to simultaneously i) efficiently capture and concentrate rare cells, ii) conduct automated rapid media exchanges via diffusion without displacing non-adherent cells, and iii) allow sensitive high-throughput long-term time-lapse microscopy. Hematopoietic stem and progenitor cells pose a particular challenge for these types of experiments as they are impossible to obtain in very large numbers and are displaced by the fluid flow usually used to change culture media, thus preventing cell tracking. Here, we developed a programmable automated system composed of a novel microfluidic device for efficient capture of rare cells in independently addressable culture chambers, a custom incubation system, and user-friendly control software. The chip's culture chambers are optimized for efficient and sensitive fluorescence microscopy and their media can be individually and quickly changed by diffusion without non-adherent cell displacement. The chip allows efficient capture, stimulation, and sensitive high-frequency time-lapse observation of rare and sensitive murine and human primary hematopoietic stem cells. Our 3D-printed humidification and incubation system minimizes gas consumption, facilitates chip setup, and maintains stable humidity and gas composition during long-term cell culture. This approach now enables the required continuous long-term single-cell quantification of rare non-adherent cells with rapid environmental manipulations, e.g. of rapid signaling dynamics and the later stem cell fate choices they control.
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Affiliation(s)
- Philip Dettinger
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Weijia Wang
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Nouraiz Ahmed
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Yang Zhang
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Dirk Loeffler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Tobias Kull
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Martin Etzrodt
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Claudia Lengerke
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
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