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Anagnostidis V, Tiwari A, Gielen F. Deep learning-assisted concentration gradient generation for the study of 3D cell cultures in hydrogel beads of varying stiffness. Front Bioeng Biotechnol 2024; 12:1364553. [PMID: 38665812 PMCID: PMC11044700 DOI: 10.3389/fbioe.2024.1364553] [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: 01/05/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
The study of dose-response relationships underpins analytical biosciences. Droplet microfluidics platforms can automate the generation of microreactors encapsulating varying concentrations of an assay component, providing datasets across a large chemical space in a single experiment. A classical method consists in varying the flow rate of multiple solutions co-flowing into a single microchannel (producing different volume fractions) before encapsulating the contents into water-in-oil droplets. This process can be automated through controlling the pumping elements but lacks the ability to adapt to unpredictable experimental scenarios, often requiring constant human supervision. In this paper, we introduce an image-based, closed-loop control system for assessing and adjusting volume fractions, thereby generating unsupervised, uniform concentration gradients. We trained a shallow convolutional neural network to assess the position of the laminar flow interface between two co-flowing fluids and used this model to adjust flow rates in real-time. We apply the method to generate alginate microbeads in which HEK293FT cells could grow in three dimensions. The stiffnesses ranged from 50 Pa to close to 1 kPa in Young modulus and were encoded with a fluorescent marker. We trained deep learning models based on the YOLOv4 object detector to efficiently detect both microbeads and multicellular spheroids from high-content screening images. This allowed us to map relationships between hydrogel stiffness and multicellular spheroid growth.
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Affiliation(s)
- Vasileios Anagnostidis
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| | - Anuj Tiwari
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Fabrice Gielen
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
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2
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Fevre R, Mary G, Vertti-Quintero N, Durand A, Tomasi RFX, Del Nery E, Baroud CN. Combinatorial drug screening on 3D Ewing sarcoma spheroids using droplet-based microfluidics. iScience 2023; 26:106651. [PMID: 37168549 PMCID: PMC10165258 DOI: 10.1016/j.isci.2023.106651] [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: 08/04/2022] [Revised: 02/02/2023] [Accepted: 04/05/2023] [Indexed: 05/13/2023] Open
Abstract
Culturing and screening cells in microfluidics, particularly in three-dimensional formats, has the potential to impact diverse areas from fundamental biology to cancer precision medicine. Here, we use a platform based on anchored droplets for drug screening. The response of spheroids of Ewing sarcoma (EwS) A673 cells to simultaneous or sequential combinations of etoposide and cisplatin was evaluated. This was done by culturing spheroids of EwS cells inside 500 nL droplets then merging them with secondary droplets containing fluorescent-barcoded drugs at different concentrations. Differences in EwS spheroid growth and viability were measured by microscopy. After drug exposure such measurements enabled estimation of their IC50 values, which were in agreement with values obtained in standard multiwell plates. Then, synergistic drug combination was evaluated. Sequential combination treatment of EwS with etoposide applied 24 h before cisplatin resulted in amplified synergistic effect. As such, droplet-based microfluidics offers the modularity required for evaluation of drug combinations.
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Affiliation(s)
- Romain Fevre
- Laboratoire d’ Hydrodynamique (LadHyX), CNRS, EcolePolytechnique, InstitutPolytechnique de Paris, 91128 Palaiseau, France
- Institut Pasteur, Université Paris Cité, Physical microfluidics and Bioengineering, 25-28 Rue du Dr. Roux, 75015 Paris, France
| | - Gaëtan Mary
- Okomera, iPEPS, the HealthTech Hub, Paris Brain Institute, HôpitalPitiéSalpêtrière, 75013 Paris, France
| | - Nadia Vertti-Quintero
- Institut Pasteur, Université Paris Cité, Physical microfluidics and Bioengineering, 25-28 Rue du Dr. Roux, 75015 Paris, France
| | - Aude Durand
- Institut Pasteur, Université Paris Cité, Physical microfluidics and Bioengineering, 25-28 Rue du Dr. Roux, 75015 Paris, France
| | - Raphaël F.-X. Tomasi
- Laboratoire d’ Hydrodynamique (LadHyX), CNRS, EcolePolytechnique, InstitutPolytechnique de Paris, 91128 Palaiseau, France
- Institut Pasteur, Université Paris Cité, Physical microfluidics and Bioengineering, 25-28 Rue du Dr. Roux, 75015 Paris, France
- Okomera, iPEPS, the HealthTech Hub, Paris Brain Institute, HôpitalPitiéSalpêtrière, 75013 Paris, France
| | - Elaine Del Nery
- Biophenics High-Content Screening Laboratory, Translational Research Department, PICT-IBiSA, Institut Curie, PSL Research University, 75005 Paris, France
- Corresponding author
| | - Charles N. Baroud
- Laboratoire d’ Hydrodynamique (LadHyX), CNRS, EcolePolytechnique, InstitutPolytechnique de Paris, 91128 Palaiseau, France
- Institut Pasteur, Université Paris Cité, Physical microfluidics and Bioengineering, 25-28 Rue du Dr. Roux, 75015 Paris, France
- Corresponding author
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3
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Gantz M, Neun S, Medcalf EJ, van Vliet LD, Hollfelder F. Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments. Chem Rev 2023; 123:5571-5611. [PMID: 37126602 PMCID: PMC10176489 DOI: 10.1021/acs.chemrev.2c00910] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >107-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >107 variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.
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Affiliation(s)
- Maximilian Gantz
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Stefanie Neun
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Elliot J Medcalf
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Liisa D van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
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4
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Neun S, van Vliet L, Hollfelder F, Gielen F. High-Throughput Steady-State Enzyme Kinetics Measured in a Parallel Droplet Generation and Absorbance Detection Platform. Anal Chem 2022; 94:16701-16710. [DOI: 10.1021/acs.analchem.2c03164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Stefanie Neun
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Liisa van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Fabrice Gielen
- Living Systems Institute and College of Engineering Mathematics and Physical Sciences, University of Exeter, Exeter EX4 4QD, U.K
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5
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Cao J, Russo DA, Xie T, Groß GA, Zedler JAZ. A droplet-based microfluidic platform enables high-throughput combinatorial optimization of cyanobacterial cultivation. Sci Rep 2022; 12:15536. [PMID: 36109626 PMCID: PMC9477827 DOI: 10.1038/s41598-022-19773-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/05/2022] [Indexed: 11/09/2022] Open
Abstract
Cyanobacteria are fast-growing, genetically accessible, photoautotrophs. Therefore, they have attracted interest as sustainable production platforms. However, the lack of techniques to systematically optimize cultivation parameters in a high-throughput manner is holding back progress towards industrialization. To overcome this bottleneck, here we introduce a droplet-based microfluidic platform capable of one- (1D) and two-dimension (2D) screening of key parameters in cyanobacterial cultivation. We successfully grew three different unicellular, biotechnologically relevant, cyanobacteria: Synechocystis sp. PCC 6803, Synechococcus elongatus UTEX 2973 and Synechococcus sp. UTEX 3154. This was followed by a highly-resolved 1D screening of nitrate, phosphate, carbonate, and salt concentrations. The 1D screening results suggested that nitrate and/or phosphate may be limiting nutrients in standard cultivation media. Finally, we use 2D screening to determine the optimal N:P ratio of BG-11. Application of the improved medium composition in a high-density cultivation setup led to an increase in biomass yield of up to 15.7%. This study demonstrates that droplet-based microfluidics can decrease the volume required for cyanobacterial cultivation and screening up to a thousand times while significantly increasing the multiplexing capacity. Going forward, microfluidics have the potential to play a significant role in the industrial exploitation of cyanobacteria.
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6
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Breukers J, Op de Beeck H, Rutten I, López Fernández M, Eyckerman S, Lammertyn J. Highly flexible and accurate serial picoinjection in droplets by combined pressure and flow rate control. LAB ON A CHIP 2022; 22:3475-3488. [PMID: 35943442 DOI: 10.1039/d2lc00368f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Picoinjection is a robust method for reagent addition into microfluidic droplets and has enabled the implementation of numerous multistep droplet assays. Although serial picoinjectors allow to screen many conditions in one run by injecting different combinations of reagents, their use is limited because it is complex to accurately control each injector independently. Here, we present a novel method for flexible, individual picoinjector control that allows to inject a predefined range of volumes by controlling the flow rate of the injector as well as turning off injection by setting the equilibrium pressure, which resulted in a stable interface of the injector liquid with the main microfluidic channel. Robust setting of the equilibrium pressure of an injector was achieved by applying accurate (R2 > 0.94) linear models between the injector and oil pressure in real-time. To illustrate the flexibility of this method, we performed several proof-of-concepts using 1, 2 or 3 picoinjectors loaded with fluorescent dyes. We successfully demonstrated picoinjection approaches using time-invariant settings, in which an injector setting was applied for prolonged times, and time-variant picoinjection, in which the injector settings were continuously varied in order to sweep the injected volumes, both resulting in monodisperse (CV < 3.4%) droplet libraries with different but reproducible fluorescent intensities. To illustrate the potential of the technology for fast compound concentration screenings, we studied the effect of a concentration range of a detergent on single-cell lysis. We anticipate that this robust and versatile methodology will make the serial picoinjection technology more accessible to researchers, allowing its wide implementation in numerous life science applications.
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Affiliation(s)
- Jolien Breukers
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Hannah Op de Beeck
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Iene Rutten
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Montserrat López Fernández
- Confo Therapeutics, Technologiepark-Zwijnaarde 30, Ghent 9052, Belgium
- Center for Medical Biotechnology, VIB-Ghent University, Technologiepark-Zwijnaarde 75, Ghent 9052, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, Ghent 9052, Belgium
| | - Sven Eyckerman
- Center for Medical Biotechnology, VIB-Ghent University, Technologiepark-Zwijnaarde 75, Ghent 9052, Belgium
- Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, Ghent 9052, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
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7
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Cao J, Chande C, Köhler JM. Microtoxicology by microfluidic instrumentation: a review. LAB ON A CHIP 2022; 22:2600-2623. [PMID: 35678285 DOI: 10.1039/d2lc00268j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microtoxicology is concerned with the toxic effects of small amounts of substances. This review paper discusses the application of small amounts of noxious substances for toxicological investigation in small volumes. The vigorous development of miniaturized methods in microfluidics over the last two decades involves chip-based devices, micro droplet-based procedures, and the use of micro-segmented flow for microtoxicological studies. The studies have shown that the microfluidic approach is particularly valuable for highly parallelized and combinatorial dose-response screenings. Accurate dosing and mixing of effector substances in large numbers of microcompartments supplies detailed data of dose-response functions by highly concentration-resolved assays and allows evaluation of stochastic responses in case of small separated cell ensembles and single cell experiments. The investigations demonstrate that very different biological targets can be studied using miniaturized approaches, among them bacteria, eukaryotic microorganisms, cell cultures from tissues of multicellular organisms, stem cells, and early embryonic states. Cultivation and effector exposure tests can be performed in small volumes over weeks and months, confirming that the microfluicial strategy is also applicable for slow-growing organisms. Here, the state of the art of miniaturized toxicology, particularly for studying antibiotic susceptibility, drug toxicity testing in the miniaturized system like organ-on-chip, environmental toxicology, and the characterization of combinatorial effects by two and multi-dimensional screenings, is discussed. Additionally, this review points out the practical limitations of the microtoxicology platform and discusses perspectives on future opportunities and challenges.
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Affiliation(s)
- Jialan Cao
- Techn. Univ. Ilmenau, Dept. Phys. Chem. and Microreaction Technology, Institute for Micro- und Nanotechnologies/Institute for Chemistry and Biotechnology, Ilmenau, Germany.
| | - Charmi Chande
- Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - J Michael Köhler
- Techn. Univ. Ilmenau, Dept. Phys. Chem. and Microreaction Technology, Institute for Micro- und Nanotechnologies/Institute for Chemistry and Biotechnology, Ilmenau, Germany.
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8
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Henkel T, Mayer G, Hampl J, Cao J, Ehrhardt L, Schober A, Groß GA. From Microtiter Plates to Droplets—There and Back Again. MICROMACHINES 2022; 13:mi13071022. [PMID: 35888839 PMCID: PMC9316479 DOI: 10.3390/mi13071022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 02/05/2023]
Abstract
Droplet-based microfluidic screening techniques can benefit from interfacing established microtiter plate-based screening and sample management workflows. Interfacing tools are required both for loading preconfigured microtiter-plate (MTP)-based sample collections into droplets and for dispensing the used droplets samples back into MTPs for subsequent storage or further processing. Here, we present a collection of Digital Microfluidic Pipetting Tips (DMPTs) with integrated facilities for droplet generation and manipulation together with a robotic system for its operation. This combination serves as a bidirectional sampling interface for sample transfer from wells into droplets (w2d) and vice versa droplets into wells (d2w). The DMPT were designed to fit into 96-deep-well MTPs and prepared from glass by means of microsystems technology. The aspirated samples are converted into the channel-confined droplets’ sequences separated by an immiscible carrier medium. To comply with the demands of dose-response assays, up to three additional assay compound solutions can be added to the sample droplets. To enable different procedural assay protocols, four different DMPT variants were made. In this way, droplet series with gradually changing composition can be generated for, e.g., 2D screening purposes. The developed DMPT and their common fluidic connector are described here. To handle the opposite transfer d2w, a robotic transfer system was set up and is described briefly.
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Affiliation(s)
- Thomas Henkel
- Leibniz Institute of Photonic Technology, Leibniz-IPHT, Albert-Einstein-Str. 9, 07745 Jena, Germany; (T.H.); (G.M.)
| | - Günter Mayer
- Leibniz Institute of Photonic Technology, Leibniz-IPHT, Albert-Einstein-Str. 9, 07745 Jena, Germany; (T.H.); (G.M.)
| | - Jörg Hampl
- Department of Nano-Biosystem Technology, Institute of Chemistry and Biotechnology, Technical University Ilmenau, Prof.-Schmidt-Str. 26, 98693 Ilmenau, Germany; (J.H.); (A.S.)
| | - Jialan Cao
- Department of Physical Chemistry and Microreaction Technologies, Institute of Chemistry and Biotechnology, Technical University Ilmenau, Prof.-Schmidt-Str. 26, 98693 Ilmenau, Germany; (J.C.); (L.E.)
| | - Linda Ehrhardt
- Department of Physical Chemistry and Microreaction Technologies, Institute of Chemistry and Biotechnology, Technical University Ilmenau, Prof.-Schmidt-Str. 26, 98693 Ilmenau, Germany; (J.C.); (L.E.)
| | - Andreas Schober
- Department of Nano-Biosystem Technology, Institute of Chemistry and Biotechnology, Technical University Ilmenau, Prof.-Schmidt-Str. 26, 98693 Ilmenau, Germany; (J.H.); (A.S.)
| | - Gregor Alexander Groß
- Department of Physical Chemistry and Microreaction Technologies, Institute of Chemistry and Biotechnology, Technical University Ilmenau, Prof.-Schmidt-Str. 26, 98693 Ilmenau, Germany; (J.C.); (L.E.)
- Correspondence: ; Tel.: +49-3677-69-3716
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9
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Microfluidically supported characterization of responses of Rhodococcus erythropolis strains isolated from different soils on Cu-, Ni-, and Co-stress. Braz J Microbiol 2021; 52:1405-1415. [PMID: 33956334 PMCID: PMC8324611 DOI: 10.1007/s42770-021-00495-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/08/2021] [Indexed: 10/26/2022] Open
Abstract
We present a new methodological approach for the assessment of the susceptibility of Rhodococcus erythropolis strains from specific sampling sites in response to increasing heavy metal concentration (Cu2+, Ni2+, and Co2+) using the droplet-based microfluid technique. All isolates belong to the species R. erythropolis identified by Sanger sequencing of the 16S rRNA. The tiny step-wise variation of metal concentrations from zero to the lower mM range in 500 nL droplets not only provided accurate data for critical metal ion concentrations but also resulted in a detailed visualization of the concentration-dependent response of bacterial growth and autofluorescence activity. As a result, some of the isolates showed similar characteristics in heavy metal tolerance against Cu2+, Ni2+, and Co2+. However, significantly different heavy metal tolerances were found for other strains. Surprisingly, samples from the surface soil of ancient copper mining areas supplied mostly strains with a moderate sensitivity to Cu2+, Ni2+, and Co2+, but in contrast, a soil sample from an excavation site of a medieval city that had been covered for about eight centuries showed an extremely high tolerance against cobalt ion (up to 36 mM). The differences among the strains not only may be regarded as results of adaptation to the different environmental conditions faced by the strains in nature but also seem to be related to ancient human activities and temporal partial decoupling of soil elements from the surface. This investigation confirmed that microfluidic screening offers empirical characterization of properties from same species which has been isolated from sites known to have different human activities in the past.
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10
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Vos M, Sibleyras L, Lo LK, Hesse E, Gaze W, Klümper U. Zinc can counteract selection for ciprofloxacin resistance. FEMS Microbiol Lett 2021; 367:5762671. [PMID: 32105320 PMCID: PMC7082703 DOI: 10.1093/femsle/fnaa038] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/26/2020] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial resistance (AMR) has emerged as one of the most pressing threats to public health. AMR evolution occurs in the clinic but also in the environment, where antibiotics and heavy metals can select and co-select for AMR. While the selective potential of both antibiotics and metals is increasingly well-characterized, experimental studies exploring their combined effects on AMR evolution are rare. It has previously been demonstrated that fluoroquinolone antibiotics such as ciprofloxacin can chelate metal ions. To investigate how ciprofloxacin resistance is affected by the presence of metals, we quantified selection dynamics between a ciprofloxacin-susceptible and a ciprofloxacin-resistant Escherichia coli strain across a gradient of ciprofloxacin concentrations in presence and absence of zinc. The presence of zinc reduced growth of both strains, while ciprofloxacin inhibited exclusively the susceptible one. When present in combination zinc retained its inhibitory effect, while ciprofloxacin inhibition of the susceptible strain was reduced. Consequently, the minimal selective concentration for ciprofloxacin resistance increased up to five-fold in the presence of zinc. Environmental pollution usually comprises complex mixtures of antimicrobial agents. In addition to the usual focus on additive or synergistic interactions in complex selective mixtures, our findings highlight the importance of antagonistic selective interactions when considering resistance evolution.
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Affiliation(s)
- Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital Truro, TR1 3HDTruro, Cornwall, UK
| | - Louise Sibleyras
- European Centre for Environment and Human Health, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital Truro, TR1 3HDTruro, Cornwall, UK.,Université Paris Saclay, Department of Biology, Espace Technologique Bat. Discovery - RD 128 - 2e ét, 91190 Saint-Aubin, France
| | - Lai Ka Lo
- European Centre for Environment and Human Health, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital Truro, TR1 3HDTruro, Cornwall, UK.,Institute for Evolution & Biodiversity, Universität Münster, Hüfferstraße 1, 48149 Münster, Germany.,College of Life and Environmental Science, University of Exeter, Penryn Campus, TR10 9FE Penryn, Cornwall, UK
| | - Elze Hesse
- College of Life and Environmental Science, University of Exeter, Penryn Campus, TR10 9FE Penryn, Cornwall, UK.,Environment and Sustainability Institute, University of Exeter, Penryn Campus, TR10 9FE Penryn, Cornwall, UK
| | - William Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital Truro, TR1 3HDTruro, Cornwall, UK
| | - Uli Klümper
- European Centre for Environment and Human Health, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital Truro, TR1 3HDTruro, Cornwall, UK.,College of Life and Environmental Science, University of Exeter, Penryn Campus, TR10 9FE Penryn, Cornwall, UK.,Environment and Sustainability Institute, University of Exeter, Penryn Campus, TR10 9FE Penryn, Cornwall, UK
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11
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Lee WB, Chien CC, You HL, Kuo FC, Lee MS, Lee GB. Rapid antimicrobial susceptibility tests on an integrated microfluidic device for precision medicine of antibiotics. Biosens Bioelectron 2020; 176:112890. [PMID: 33349537 DOI: 10.1016/j.bios.2020.112890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 01/07/2023]
Abstract
This study reports an integrated microfluidic device that was capable of executing rapid antimicrobial susceptibility tests with one, two, or even three antibiotics against two clinically isolated multi-drug-resistant bacteria strains (including carbapenem-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus). Bacteria were automatically mixed for 10 min with serially diluted antibiotics with a novel, membrane-type micromixer consisting of two circular micropumps, and the minimum inhibitory concentrations (MIC) were then determined via simple colorimetric reactions in only 4.5-6 h using only 3 μL of bacteria sample of each reaction (as opposed to 24 h and 50 μL, respectively, with the conventional broth micro-dilution method). In addition to determining MICs of antibiotics (ceftazidime, gentamicin, meropenem, vancomycin and linezolid), interaction effects across antibiotics combinations (gentamicin/meropenem or ceftazidime/gentamicin/meropenem) at different dosages were explored. The efficacy of polypharmacy showed additivity when gentamicin or ceftazidime/gentamicin were combined with meropenem to treat carbapenem-resistant Escherichia coli. This represents the first time that the perplexing clinical decision to choose multiple antibiotics for combination therapy against drug resistant bacteria can be realized on an integrated microfluidic device within 6 h.
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Affiliation(s)
- Wen-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Chun-Chih Chien
- Department of Laboratory Medicine, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University, Kaohsiung, 83301, Taiwan
| | - Huey-Ling You
- Department of Laboratory Medicine, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University, Kaohsiung, 83301, Taiwan
| | - Feng-Chih Kuo
- Department of Orthopaedic Surgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University, Kaohsiung, 83301, Taiwan
| | - Mel S Lee
- Department of Orthopaedic Surgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University, Kaohsiung, 83301, Taiwan.
| | - Gwo-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan; Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan; Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu, 30013, Taiwan.
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12
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Puentes PR, Henao MC, Torres CE, Gómez SC, Gómez LA, Burgos JC, Arbeláez P, Osma JF, Muñoz-Camargo C, Reyes LH, Cruz JC. Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches. Antibiotics (Basel) 2020; 9:E854. [PMID: 33265897 PMCID: PMC7759991 DOI: 10.3390/antibiotics9120854] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
One of the challenges of modern biotechnology is to find new routes to mitigate the resistance to conventional antibiotics. Antimicrobial peptides (AMPs) are an alternative type of biomolecules, naturally present in a wide variety of organisms, with the capacity to overcome the current microorganism resistance threat. Here, we reviewed our recent efforts to develop a new library of non-rationally produced AMPs that relies on bacterial genome inherent diversity and compared it with rationally designed libraries. Our approach is based on a four-stage workflow process that incorporates the interplay of recent developments in four major emerging technologies: artificial intelligence, molecular dynamics, surface-display in microorganisms, and microfluidics. Implementing this framework is challenging because to obtain reliable results, the in silico algorithms to search for candidate AMPs need to overcome issues of the state-of-the-art approaches that limit the possibilities for multi-space data distribution analyses in extremely large databases. We expect to tackle this challenge by using a recently developed classification algorithm based on deep learning models that rely on convolutional layers and gated recurrent units. This will be complemented by carefully tailored molecular dynamics simulations to elucidate specific interactions with lipid bilayers. Candidate AMPs will be recombinantly-expressed on the surface of microorganisms for further screening via different droplet-based microfluidic-based strategies to identify AMPs with the desired lytic abilities. We believe that the proposed approach opens opportunities for searching and screening bioactive peptides for other applications.
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Affiliation(s)
- Paola Ruiz Puentes
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogota DC 111711, Colombia; (P.R.P.); (P.A.)
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - María C. Henao
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogota DC 111711, Colombia;
| | - Carlos E. Torres
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Saúl C. Gómez
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Laura A. Gómez
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Juan C. Burgos
- Chemical Engineering Program, Universidad de Cartagena, Cartagena 130015, Colombia;
| | - Pablo Arbeláez
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogota DC 111711, Colombia; (P.R.P.); (P.A.)
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Johann F. Osma
- Department of Electrical and Electronic Engineering, Universidad de los Andes, Bogota DC 111711, Colombia;
| | - Carolina Muñoz-Camargo
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Luis H. Reyes
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogota DC 111711, Colombia;
| | - Juan C. Cruz
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide 5005, Australia
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13
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Microfluidic Chamber Design for Controlled Droplet Expansion and Coalescence. MICROMACHINES 2020; 11:mi11040394. [PMID: 32290165 PMCID: PMC7231328 DOI: 10.3390/mi11040394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 11/21/2022]
Abstract
The defined formation and expansion of droplets are essential operations for droplet-based screening assays. The volumetric expansion of droplets causes a dilution of the ingredients. Dilution is required for the generation of concentration graduation which is mandatory for many different assay protocols. Here, we describe the design of a microfluidic operation unit based on a bypassed chamber and its operation modes. The different operation modes enable the defined formation of sub-µL droplets on the one hand and the expansion of low nL to sub-µL droplets by controlled coalescence on the other. In this way the chamber acts as fluidic interface between two fluidic network parts dimensioned for different droplet volumes. Hence, channel confined droplets of about 30–40 nL from the first network part were expanded to cannel confined droplets of about 500 to about 2500 nL in the second network part. Four different operation modes were realized: (a) flow rate independent droplet formation in a self-controlled way caused by the bypassed chamber design, (b) single droplet expansion mode, (c) multiple droplet expansion mode, and (d) multiple droplet coalescence mode. The last mode was used for the automated coalescence of 12 droplets of about 40 nL volume to produce a highly ordered output sequence with individual droplet volumes of about 500 nL volume. The experimental investigation confirmed a high tolerance of the developed chamber against the variation of key parameters of the dispersed-phase like salt content, pH value and fluid viscosity. The presented fluidic chamber provides a solution for the problem of bridging different droplet volumes in a fluidic network.
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14
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Selection for antimicrobial resistance is reduced when embedded in a natural microbial community. ISME JOURNAL 2019; 13:2927-2937. [PMID: 31384011 PMCID: PMC6864104 DOI: 10.1038/s41396-019-0483-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 01/24/2023]
Abstract
Antibiotic resistance has emerged as one of the most pressing, global threats to public health. In single-species experiments selection for antibiotic resistance occurs at very low antibiotic concentrations. However, it is unclear how far these findings can be extrapolated to natural environments, where species are embedded within complex communities. We competed isogenic strains of Escherichia coli, differing exclusively in a single chromosomal resistance determinant, in the presence and absence of a pig faecal microbial community across a gradient of antibiotic concentration for two relevant antibiotics: gentamicin and kanamycin. We show that the minimal selective concentration was increased by more than one order of magnitude for both antibiotics when embedded in the community. We identified two general mechanisms were responsible for the increase in minimal selective concentration: an increase in the cost of resistance and a protective effect of the community for the susceptible phenotype. These findings have implications for our understanding of the evolution and selection of antibiotic resistance, and can inform future risk assessment efforts on antibiotic concentrations.
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15
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Kim S, Masum F, Kim JK, Chung HJ, Jeon JS. On-chip phenotypic investigation of combinatory antibiotic effects by generating orthogonal concentration gradients. LAB ON A CHIP 2019; 19:959-973. [PMID: 30768106 DOI: 10.1039/c8lc01406j] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Combinatory therapy using two or more kinds of antibiotics is attracting considerable attention for inhibiting multi-drug resistant pathogenic bacteria. Although the therapy mostly leads to more powerful antimicrobial effects than using a single antibiotic (synergy), interference may arise from certain antibiotic combinations, resulting in the antimicrobial effect being suppressed (antagonism). Here, we present a microfluidic-based phenotypic screening chip to investigate combinatory antibiotic effects by automatically generating two orthogonal concentration gradients on a bacteria-trapping agarose gel. Computational simulations and fluorescence experiments together verify the simultaneous establishment of 121 concentration combinations, facilitating on-chip drug testing with stability and efficiency. Against Gram-negative bacteria, Pseudomonas aeruginosa, our chip allows the measurement of phenotypic growth levels, and enables various types of analyses for all antibiotic pairs to be conducted in 7 h. Furthermore, by providing a specific amount of susceptibility data, our chip enables the two reference models, Loewe additivity and Bliss independence, to be implemented, which classify the antibiotic interaction types into synergy or antagonism. These results suggest the efficacy of our chip as a cell-based drug screening platform for exploring the underlying pharmacological patterns of antibiotic interactions, with potential applications in guidance in clinical therapies and in screening other cell-type agents.
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Affiliation(s)
- Seunggyu Kim
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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16
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Liao S, Tao Y, Du W, Wang Y. Interfacial Emulsification: An Emerging Monodisperse Droplet Generation Method for Microreactors and Bioanalysis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:11655-11666. [PMID: 29792711 DOI: 10.1021/acs.langmuir.8b01067] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The generation of uniform droplets has been extensively investigated owing to its profound potentials both in scientific research and engineering applications. Although various methods have been put forward to expand this area, new innovations are still needed to improve the technical convenience and save instrumental cost. In this feature article, we highlight an interfacial emulsification technique that we developed in the past several years. This technique serves as a platform for preparing uniform droplets that are formed on the air-liquid interface of the continuous phase based on interfacial shearing. Three specific aspects of interfacial emulsification are reviewed, including its basic design and principle, the preparation of droplets with controllable size and adjustable components, and practical applications of the method in bioanalysis, microreactors, and particle synthesis. Compared to other droplet generation methods, several attractive advantages and perspectives for further development have been summarized.
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Affiliation(s)
- Shenglong Liao
- Department of Chemistry , Renmin University of China , Beijing 100872 , China
| | - Yi Tao
- State Key Laboratory of Microbial Resources, Institute of Microbiology , Chinese Academy of Sciences , Beijing 100101 , China
- Savaid Medical School , University of the Chinese Academy of Sciences , Beijing 100049 , China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology , Chinese Academy of Sciences , Beijing 100101 , China
- Savaid Medical School , University of the Chinese Academy of Sciences , Beijing 100049 , China
| | - Yapei Wang
- Department of Chemistry , Renmin University of China , Beijing 100872 , China
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17
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Cao J, Hafermann L, Köhler JM. Stochastically reduced communities-Microfluidic compartments as model and investigation tool for soil microorganism growth in structured spaces. Eng Life Sci 2017; 17:792-800. [PMID: 32624825 DOI: 10.1002/elsc.201600264] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/03/2017] [Accepted: 02/20/2017] [Indexed: 11/09/2022] Open
Abstract
Microbial community in soil is a complex and dynamic system. Using traditional culture experiments it is difficult to model the stochastic distribution of single organisms of microbial communities in the soil pore's structure. Droplet-based micro-segmented flow technique allows the transfer of the principle of stochastic confinement of stochastically reduced communities from soil micro pores into nanoliter droplets. Microfluidics was applied for the investigation and comparison of soil samples from ancient mining areas by highly resolved concentration-dependent screenings. As results, the generation, incubation, and in situ optical characterization of nanoliter droplets of suspensions of unknown soil microbial communities allowed the identification of different response characteristics toward heavy metal exposition. The investigations proved the high potential of microfluidics for investigations of soil microbial communities. It may be in the future helpful to detect bacteria and consortia with special biosorption characteristics, which could be useful for the development of biological accumulation and detoxification strategies.
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Affiliation(s)
- Jialan Cao
- Physical Chemistry and Microreaction Technology, Institute for Micro- und Nanotechnologies / Institute for Chemistry and Biotechnique Ilmenau University of Technology Ilmenau Germany
| | - Lars Hafermann
- Physical Chemistry and Microreaction Technology, Institute for Micro- und Nanotechnologies / Institute for Chemistry and Biotechnique Ilmenau University of Technology Ilmenau Germany
| | - J Michael Köhler
- Physical Chemistry and Microreaction Technology, Institute for Micro- und Nanotechnologies / Institute for Chemistry and Biotechnique Ilmenau University of Technology Ilmenau Germany
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18
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Wang X, Liu Z, Pang Y. Concentration gradient generation methods based on microfluidic systems. RSC Adv 2017. [DOI: 10.1039/c7ra04494a] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Various concentration gradient generation methods based on microfluidic systems are summarized in this paper.
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Affiliation(s)
- Xiang Wang
- College of Mechanical Engineering and Applied Electronics Technology
- Beijing University of Technology
- Beijing 100124
- China
| | - Zhaomiao Liu
- College of Mechanical Engineering and Applied Electronics Technology
- Beijing University of Technology
- Beijing 100124
- China
| | - Yan Pang
- College of Mechanical Engineering and Applied Electronics Technology
- Beijing University of Technology
- Beijing 100124
- China
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19
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Campbell J, McBeth C, Kalashnikov M, Boardman AK, Sharon A, Sauer-Budge AF. Microfluidic advances in phenotypic antibiotic susceptibility testing. Biomed Microdevices 2016; 18:103. [PMID: 27796676 PMCID: PMC5473355 DOI: 10.1007/s10544-016-0121-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A strong natural selection for microbial antibiotic resistance has resulted from the extensive use and misuse of antibiotics. Though multiple factors are responsible for this crisis, the most significant factor - widespread prescription of broad-spectrum antibiotics - is largely driven by the fact that the standard process for determining antibiotic susceptibility includes a 1-2-day culture period, resulting in 48-72 h from patient sample to final determination. Clearly, disruptive approaches, rather than small incremental gains, are needed to address this issue. The field of microfluidics promises several advantages over existing macro-scale methods, including: faster assays, increased multiplexing, smaller volumes, increased portability for potential point-of-care use, higher sensitivity, and rapid detection methods. This Perspective will cover the advances made in the field of microfluidic, phenotypic antibiotic susceptibility testing (AST) over the past two years. Sections are organized based on the functionality of the chip - from simple microscopy platforms, to gradient generators, to antibody-based capture devices. Microfluidic AST methods that monitor growth as well as those that are not based on growth are presented. Finally, we will give our perspective on the major hurdles still facing the field, including the need for rapid sample preparation and affordable detection technologies.
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Affiliation(s)
- Jennifer Campbell
- Fraunhofer USA - Center for Manufacturing Innovation, Brookline, MA, 02446, USA
| | - Christine McBeth
- Fraunhofer USA - Center for Manufacturing Innovation, Brookline, MA, 02446, USA
| | - Maxim Kalashnikov
- Fraunhofer USA - Center for Manufacturing Innovation, Brookline, MA, 02446, USA
| | - Anna K Boardman
- Fraunhofer USA - Center for Manufacturing Innovation, Brookline, MA, 02446, USA
| | - Andre Sharon
- Fraunhofer USA - Center for Manufacturing Innovation, Brookline, MA, 02446, USA
- Department of Mechanical Engineering, Boston University, Boston, MA, 02215, USA
| | - Alexis F Sauer-Budge
- Fraunhofer USA - Center for Manufacturing Innovation, Brookline, MA, 02446, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
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20
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Dai J, Hamon M, Jambovane S. Microfluidics for Antibiotic Susceptibility and Toxicity Testing. Bioengineering (Basel) 2016; 3:bioengineering3040025. [PMID: 28952587 PMCID: PMC5597268 DOI: 10.3390/bioengineering3040025] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/30/2016] [Accepted: 09/30/2016] [Indexed: 12/23/2022] Open
Abstract
The recent emergence of antimicrobial resistance has become a major concern for worldwide policy makers as very few new antibiotics have been developed in the last twenty-five years. To prevent the death of millions of people worldwide, there is an urgent need for a cheap, fast and accurate set of tools and techniques that can help to discover and develop new antimicrobial drugs. In the past decade, microfluidic platforms have emerged as potential systems for conducting pharmacological studies. Recent studies have demonstrated that microfluidic platforms can perform rapid antibiotic susceptibility tests to evaluate antimicrobial drugs’ efficacy. In addition, the development of cell-on-a-chip and organ-on-a-chip platforms have enabled the early drug testing, providing more accurate insights into conventional cell cultures on the drug pharmacokinetics and toxicity, at the early and cheaper stage of drug development, i.e., prior to animal and human testing. In this review, we focus on the recent developments of microfluidic platforms for rapid antibiotics susceptibility testing, investigating bacterial persistence and non-growing but metabolically active (NGMA) bacteria, evaluating antibiotic effectiveness on biofilms and combinatorial effect of antibiotics, as well as microfluidic platforms that can be used for in vitro antibiotic toxicity testing.
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Affiliation(s)
- Jing Dai
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.
| | - Morgan Hamon
- Renal Regeneration Laboratory, VAGLAHS at Sepulveda, North Hills, CA 91343, USA.
- David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
| | - Sachin Jambovane
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (PNNL), Richland, WA 99354, USA.
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21
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Kaminski TS, Scheler O, Garstecki P. Droplet microfluidics for microbiology: techniques, applications and challenges. LAB ON A CHIP 2016; 16:2168-87. [PMID: 27212581 DOI: 10.1039/c6lc00367b] [Citation(s) in RCA: 241] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Droplet microfluidics has rapidly emerged as one of the key technologies opening up new experimental possibilities in microbiology. The ability to generate, manipulate and monitor droplets carrying single cells or small populations of bacteria in a highly parallel and high throughput manner creates new approaches for solving problems in diagnostics and for research on bacterial evolution. This review presents applications of droplet microfluidics in various fields of microbiology: i) detection and identification of pathogens, ii) antibiotic susceptibility testing, iii) studies of microbial physiology and iv) biotechnological selection and improvement of strains. We also list the challenges in the dynamically developing field and new potential uses of droplets in microbiology.
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Affiliation(s)
- Tomasz S Kaminski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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22
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Boken J, Soni SK, Kumar D. Microfluidic Synthesis of Nanoparticles and their Biosensing Applications. Crit Rev Anal Chem 2016; 46:538-61. [DOI: 10.1080/10408347.2016.1169912] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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23
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Microfluidics for cell-based high throughput screening platforms - A review. Anal Chim Acta 2015; 903:36-50. [PMID: 26709297 DOI: 10.1016/j.aca.2015.11.023] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 10/04/2015] [Accepted: 11/14/2015] [Indexed: 01/09/2023]
Abstract
In the last decades, the basic techniques of microfluidics for the study of cells such as cell culture, cell separation, and cell lysis, have been well developed. Based on cell handling techniques, microfluidics has been widely applied in the field of PCR (Polymerase Chain Reaction), immunoassays, organ-on-chip, stem cell research, and analysis and identification of circulating tumor cells. As a major step in drug discovery, high-throughput screening allows rapid analysis of thousands of chemical, biochemical, genetic or pharmacological tests in parallel. In this review, we summarize the application of microfluidics in cell-based high throughput screening. The screening methods mentioned in this paper include approaches using the perfusion flow mode, the droplet mode, and the microarray mode. We also discuss the future development of microfluidic based high throughput screening platform for drug discovery.
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24
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25
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Kürsten D, Möller F, Gross GA, Lenk C, Visaveliya N, Schüler T, Köhler JM. Identification of response classes from heavy metal‐tolerant soil microbial communities by highly resolved concentration‐dependent screenings in a microfluidic system. Methods Ecol Evol 2015. [DOI: 10.1111/2041-210x.12344] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Dana Kürsten
- Techn. Univ. Ilmenau, Institute for Micro‐ and Nanotechnologies Institute for Chemistry and Biotechnology PO box 100565 D‐98684 Ilmenau Germany
| | - Frances Möller
- Techn. Univ. Ilmenau, Institute for Micro‐ and Nanotechnologies Institute for Chemistry and Biotechnology PO box 100565 D‐98684 Ilmenau Germany
| | - Gregor Alexander Gross
- Techn. Univ. Ilmenau, Institute for Micro‐ and Nanotechnologies Institute for Chemistry and Biotechnology PO box 100565 D‐98684 Ilmenau Germany
| | - Claudia Lenk
- Techn. Univ. Ilmenau, Institute for Micro‐ and Nanotechnologies Institute for Chemistry and Biotechnology PO box 100565 D‐98684 Ilmenau Germany
| | - Nikunjkumar Visaveliya
- Techn. Univ. Ilmenau, Institute for Micro‐ and Nanotechnologies Institute for Chemistry and Biotechnology PO box 100565 D‐98684 Ilmenau Germany
| | - Tim Schüler
- TLDA Weimar Humboldtstr. 11 D‐99423 Weimar Germany
| | - Johann Michael Köhler
- Techn. Univ. Ilmenau, Institute for Micro‐ and Nanotechnologies Institute for Chemistry and Biotechnology PO box 100565 D‐98684 Ilmenau Germany
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26
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Wetzel K, Cao J, Kothe E, Köhler JM. Changing growth behavior of heavy-metal tolerant bacteria: Media optimization using droplet-based microfluidics. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Katharina Wetzel
- Institute for Micro and Nanotechnologies; Institute for Chemistry and Biotechnology, Technical University Ilmenau; Ilmenau Germany
| | - Jialan Cao
- Institute for Micro and Nanotechnologies; Institute for Chemistry and Biotechnology, Technical University Ilmenau; Ilmenau Germany
| | - Erika Kothe
- Institute of Microbiology; Friedrich Schiller University; Jena Germany
| | - J. Michael Köhler
- Institute for Micro and Nanotechnologies; Institute for Chemistry and Biotechnology, Technical University Ilmenau; Ilmenau Germany
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27
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Boitard L, Cottinet D, Bremond N, Baudry J, Bibette J. Growing microbes in millifluidic droplets. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400089] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Laurent Boitard
- Laboratoire de Colloïdes et Matériaux Divisés; UMR CBI 8231, ESPCI ParisTech, 10 rue Vauquelin; Paris France
| | - Denis Cottinet
- Laboratoire de Colloïdes et Matériaux Divisés; UMR CBI 8231, ESPCI ParisTech, 10 rue Vauquelin; Paris France
| | - Nicolas Bremond
- Laboratoire de Colloïdes et Matériaux Divisés; UMR CBI 8231, ESPCI ParisTech, 10 rue Vauquelin; Paris France
| | - Jean Baudry
- Laboratoire de Colloïdes et Matériaux Divisés; UMR CBI 8231, ESPCI ParisTech, 10 rue Vauquelin; Paris France
| | - Jérôme Bibette
- Laboratoire de Colloïdes et Matériaux Divisés; UMR CBI 8231, ESPCI ParisTech, 10 rue Vauquelin; Paris France
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28
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Affiliation(s)
- Jialan Cao
- Department of Physical Chemistry and Microreaction Technology; Institute for Micro and Nanotechnologies/Institute for Chemistry and Biotechnology; Ilmenau University of Technology; Ilmenau Germany
| | - Johann Michael Köhler
- Department of Physical Chemistry and Microreaction Technology; Institute for Micro and Nanotechnologies/Institute for Chemistry and Biotechnology; Ilmenau University of Technology; Ilmenau Germany
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29
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Gielen F, Buryska T, Vliet LV, Butz M, Damborsky J, Prokop Z, Hollfelder F. Interfacing Microwells with Nanoliter Compartments: A Sampler Generating High-Resolution Concentration Gradients for Quantitative Biochemical Analyses in Droplets. Anal Chem 2014; 87:624-32. [DOI: 10.1021/ac503336g] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Fabrice Gielen
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Tomas Buryska
- International
Centre for Clinical Research, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Liisa Van Vliet
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Maren Butz
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Jiri Damborsky
- International
Centre for Clinical Research, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Zbynek Prokop
- International
Centre for Clinical Research, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Florian Hollfelder
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
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30
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Generation of Nanoliter Droplets on Demand at Hundred-Hz Frequencies. MICROMACHINES 2014. [DOI: 10.3390/mi5041002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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31
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Oxygen sensor nanoparticles for monitoring bacterial growth and characterization of dose–response functions in microfluidic screenings. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1341-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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32
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Kalashnikov M, Campbell J, Lee JC, Sharon A, Sauer-Budge AF. Stress-induced antibiotic susceptibility testing on a chip. J Vis Exp 2014:e50828. [PMID: 24430495 DOI: 10.3791/50828] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
We have developed a rapid microfluidic method for antibiotic susceptibility testing in a stress-based environment. Fluid is passed at high speeds over bacteria immobilized on the bottom of a microfluidic channel. In the presence of stress and antibiotic, susceptible strains of bacteria die rapidly. However, resistant bacteria survive these stressful conditions. The hypothesis behind this method is new: stress activation of biochemical pathways, which are targets of antibiotics, can accelerate antibiotic susceptibility testing. As compared to standard antibiotic susceptibility testing methods, the rate-limiting step - bacterial growth - is omitted during antibiotic application. The technical implementation of the method is in a combination of standard techniques and innovative approaches. The standard parts of the method include bacterial culture protocols, defining microfluidic channels in polydimethylsiloxane (PDMS), cell viability monitoring with fluorescence, and batch image processing for bacteria counting. Innovative parts of the method are in the use of culture media flow for mechanical stress application, use of enzymes to damage but not kill the bacteria, and use of microarray substrates for bacterial attachment. The developed platform can be used in antibiotic and nonantibiotic related drug development and testing. As compared to the standard bacterial suspension experiments, the effect of the drug can be turned on and off repeatedly over controlled time periods. Repetitive observation of the same bacterial population is possible over the course of the same experiment.
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33
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Kürsten D, Kothe E, Wetzel K, Bergmann K, Köhler JM. Micro-segmented flow and multisensor-technology for microbial activity profiling. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2014; 16:2362-2370. [PMID: 25119668 DOI: 10.1039/c4em00255e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The combination of micro-segmented flow with miniaturized flow-through multisensor-technology has been utilized for metabolite profiling of soil bacteria. Series of sub-μl segments were generated containing soil sample slurry from historic copper mining sites and exposed to heavy metal salts of copper and nickel. Segments were examined for bacterial growth and spectral properties as well as for the effect of heavy metal-treatment after different incubation times. In order to evaluate microbial growth, extinction was recorded with 4 different spectral channels. Fluorescence was measured using a microflow-through fluorometer to detect both growth and production of fluorescent dyes or metabolites. The incidence of single segments with enhanced absorption in one of the spectral channels or enhanced fluorescence was scored to detect soil microorganisms with interesting properties for further screening. The study could show that the number of vegetated segments, the density of microorganisms in the segments after cultivation and the spectral response are different for separate soil samples and different metals. Thus, the highly parallelized and miniaturized segmented flow method is a promising tool for profiling of soil samples with regard to identifying micro-organisms with interesting profiles for secondary metabolite-production.
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Affiliation(s)
- Dana Kürsten
- Institute of Micro-and Nanotechnologies/Institute for Chemistry and Biotechnology, Dept. of Phys. Chem. and Microreaction Technology, Ilmenau University of Technology, PF 10 05 65, D-98684 Ilmenau, Germany.
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Churski K, Nowacki M, Korczyk PM, Garstecki P. Simple modular systems for generation of droplets on demand. LAB ON A CHIP 2013; 13:3689-97. [PMID: 23868204 DOI: 10.1039/c3lc50340b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This report provides practical guidelines for the use of inexpensive electromagnetic valves characterized by large dead volumes (tens to hundreds of μL) for the generation of small (nL) droplets on demand in microfluidic chips. We analyze the role of the ratio of resistances and of the elastic capacitance of the fluidic connectors between the reservoir of the liquid, the valve and the microfluidic chip in the reliable and precise formation of micro droplets on demand. We also demonstrate and examine the use of conventional electromagnetic squeeze valves in the generation of small droplets on demand with a similar set of design rules.
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Affiliation(s)
- Krzysztof Churski
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
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Application of micro-segmented flow for two-dimensional characterization of the combinatorial effect of zinc and copper ions on metal-tolerant Streptomyces strains. Appl Microbiol Biotechnol 2013; 97:8923-30. [DOI: 10.1007/s00253-013-5147-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/22/2013] [Accepted: 07/23/2013] [Indexed: 01/09/2023]
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Du GS, Pan JZ, Zhao SP, Zhu Y, den Toonder JMJ, Fang Q. Cell-based drug combination screening with a microfluidic droplet array system. Anal Chem 2013; 85:6740-7. [PMID: 23786644 DOI: 10.1021/ac400688f] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We performed cell-based drug combination screening using an integrated droplet-based microfluidic system based on the sequential operation droplet array (SODA) technique. In the system, a tapered capillary connected with a syringe pump was used for multistep droplet manipulations. An oil-covered two-dimensional droplet array chip fixed in an x-y-z translation stage was used as the platform for cell culture and analysis. Complex multistep operations for drug combination screening involving long-term cell culture, medium changing, schedule-dependent drug dosage and stimulation, and cell viability testing were achieved in parallel in the semiopen droplet array, using multiple droplet manipulations including liquid metering, aspirating, depositing, mixing, and transferring. Long-term cell culture as long as 11 days was performed in oil-covered 500 nL droplets by changing the culture medium in each droplet every 24 h. The present system was applied in parallel schedule-dependent drug combination screening for A549 nonsmall lung cancer cells with the cell cycle-dependent drug flavopiridol and two anticancer drugs of paclitaxel and 5-fluorouracil. The highest inhibition efficiency was obtained with a schedule combination of 200 nM flavopiridol followed by 100 μM 5-fluorouracil. The drug consumption for each screening test was substantially decreased to 5 ng-5 μg, corresponding to 10-1000-fold reductions compared with traditional drug screening systems with 96-well or 384-well plates. The present work provides a novel and flexible droplet-based microfluidic approach for performing cell-based screening with complex and multistep operation procedures.
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Affiliation(s)
- Guan-Sheng Du
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, China
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Gielen F, van Vliet L, Koprowski BT, Devenish SRA, Fischlechner M, Edel JB, Niu X, deMello AJ, Hollfelder F. A fully unsupervised compartment-on-demand platform for precise nanoliter assays of time-dependent steady-state enzyme kinetics and inhibition. Anal Chem 2013; 85:4761-9. [PMID: 23614771 PMCID: PMC3715888 DOI: 10.1021/ac400480z] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
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The ability to miniaturize biochemical
assays in water-in-oil emulsion
droplets allows a massive scale-down of reaction volumes, so that
high-throughput experimentation can be performed more economically
and more efficiently. Generating such droplets in compartment-on-demand
(COD) platforms is the basis for rapid, automated screening of chemical
and biological libraries with minimal volume consumption. Herein,
we describe the implementation of such a COD platform to perform high
precision nanoliter assays. The coupling of a COD platform to a droplet
absorbance detection set-up results in a fully automated analytical
system. Michaelis–Menten parameters of 4-nitrophenyl glucopyranoside
hydrolysis by sweet almond β-glucosidase can be generated based
on 24 time-courses taken at different substrate concentrations with
a total volume consumption of only 1.4 μL. Importantly, kinetic
parameters can be derived in a fully unsupervised manner within 20
min: droplet production (5 min), initial reading of the droplet sequence
(5 min), and droplet fusion to initiate the reaction and read-out
over time (10 min). Similarly, the inhibition of the enzymatic reaction
by conduritol B epoxide and 1-deoxynojirimycin was measured, and Ki values were determined. In both cases, the
kinetic parameters obtained in droplets were identical within error
to values obtained in titer plates, despite a >104-fold
volume reduction, from micro- to nanoliters.
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Affiliation(s)
- Fabrice Gielen
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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Knauer A, Köhler J. Screening of Multiparameter Spaces for Silver Nanoprism Synthesis by Microsegmented Flow Technique. CHEM-ING-TECH 2013. [DOI: 10.1002/cite.201200206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Kovarik ML, Ornoff DM, Melvin AT, Dobes NC, Wang Y, Dickinson AJ, Gach PC, Shah PK, Allbritton NL. Micro total analysis systems: fundamental advances and applications in the laboratory, clinic, and field. Anal Chem 2013; 85:451-72. [PMID: 23140554 PMCID: PMC3546124 DOI: 10.1021/ac3031543] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Michelle L. Kovarik
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Douglas M. Ornoff
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Adam T. Melvin
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Nicholas C. Dobes
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Yuli Wang
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Alexandra J. Dickinson
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Philip C. Gach
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Pavak K. Shah
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599 and North Carolina State University, Raleigh, NC 27695
| | - Nancy L. Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599 and North Carolina State University, Raleigh, NC 27695
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Kalashnikov M, Lee JC, Campbell J, Sharon A, Sauer-Budge AF. A microfluidic platform for rapid, stress-induced antibiotic susceptibility testing of Staphylococcus aureus. LAB ON A CHIP 2012; 12:4523-32. [PMID: 22968495 PMCID: PMC3489182 DOI: 10.1039/c2lc40531h] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The emergence and spread of bacterial resistance to ever increasing classes of antibiotics intensifies the need for fast phenotype-based clinical tests for determining antibiotic susceptibility. Standard susceptibility testing relies on the passive observation of bacterial growth inhibition in the presence of antibiotics. In this paper, we present a novel microfluidic platform for antibiotic susceptibility testing based on stress-activation of biosynthetic pathways that are the primary targets of antibiotics. We chose Staphylococcus aureus (S. aureus) as a model system due to its clinical importance, and we selected bacterial cell wall biosynthesis as the primary target of both stress and antibiotic. Enzymatic and mechanical stresses were used to damage the bacterial cell wall, and a β-lactam antibiotic interfered with the repair process, resulting in rapid cell death of strains that harbor no resistance mechanism. In contrast, resistant bacteria remained viable under the assay conditions. Bacteria, covalently-bound to the bottom of the microfluidic channel, were subjected to mechanical shear stress created by flowing culture media through the microfluidic channel and to enzymatic stress with sub-inhibitory concentrations of the bactericidal agent lysostaphin. Bacterial cell death was monitored via fluorescence using the Sytox Green dead cell stain, and rates of killing were measured for the bacterial samples in the presence and absence of oxacillin. Using model susceptible (Sanger 476) and resistant (MW2) S. aureus strains, a metric was established to separate susceptible and resistant staphylococci based on normalized fluorescence values after 60 min of exposure to stress and antibiotic. Because this ground-breaking approach is not based on standard methodology, it circumvents the need for minimum inhibitory concentration (MIC) measurements and long wait times. We demonstrate the successful development of a rapid microfluidic-based and stress-activated antibiotic susceptibility test by correctly designating the phenotypes of 16 additional clinically relevant S. aureus strains in a blinded study. In addition to future clinical utility, this method has great potential for studying the effects of various stresses on bacteria and their antibiotic susceptibility.
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Affiliation(s)
- Maxim Kalashnikov
- Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446, USA
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Churski K, Kaminski TS, Jakiela S, Kamysz W, Baranska-Rybak W, Weibel DB, Garstecki P. Rapid screening of antibiotic toxicity in an automated microdroplet system. LAB ON A CHIP 2012; 12:1629-37. [PMID: 22422170 DOI: 10.1039/c2lc21284f] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We report an automated microfluidic platform for 'digitally' screening the composition space of droplets containing cocktails of small molecules and demonstrate the features of this system by studying epistatic interactions between antibiotics and Escherichia coli ATCC 25922. This system has several key characteristics: (i) it uses small (<100 μL) samples of liquids and suspensions of bacteria that are introduced directly into the chip; (ii) it generates a sequence of droplets with compositions, including reagents and bacterial cell suspensions that are programmed by the user; (iii) it exports the sequence of droplets to an external segment of tubing that is subsequently disconnected for incubation and storage; and (iv) after incubation of bacteria in droplets, the droplets are injected into a second device equipped with an in-line fiber optic spectrophotometer that measures cell growth. The system generates and fuses droplets with precise (<1% in standard deviation) control of liquid volumes and of the concentrations of input substrates. We demonstrate the application of this technology in determining the minimum inhibitory concentration and pair-wise interactions of ampicillin, tetracycline, and chloramphenicol against E. coli. The experiments consumed small volumes of reagents and required minutes to create the droplets and several hours for their incubation and analysis.
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Affiliation(s)
- Krzysztof Churski
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
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