1
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Doulcier G, Lambert A. Neutral diversity in experimental metapopulations. Theor Popul Biol 2024; 158:89-108. [PMID: 38493997 DOI: 10.1016/j.tpb.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 02/07/2024] [Accepted: 02/27/2024] [Indexed: 03/19/2024]
Abstract
New automated and high-throughput methods allow the manipulation and selection of numerous bacterial populations. In this manuscript we are interested in the neutral diversity patterns that emerge from such a setup in which many bacterial populations are grown in parallel serial transfers, in some cases with population-wide extinction and splitting events. We model bacterial growth by a birth-death process and use the theory of coalescent point processes. We show that there is a dilution factor that optimises the expected amount of neutral diversity for a given number of cycles, and study the power law behaviour of the mutation frequency spectrum for different experimental regimes. We also explore how neutral variation diverges between two recently split populations by establishing a new formula for the expected number of shared and private mutations. Finally, we show the interest of such a setup to select a phenotype of interest that requires multiple mutations.
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Affiliation(s)
- Guilhem Doulcier
- Macquarie University, Department of Philosophy, Sydney, Australia; Max Planck Institute for Evolutionary Biology, Department of Theoretical Biology, Plön, Germany.
| | - Amaury Lambert
- SMILE - Stochastic Models for the Inference of Life Evolution, Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS UMR8197, INSERM U1024, France; Centre Interdisciplinaire de Recherche en Biologie (CIRB), Collège de France, CNRS UMR7241, INSERM U1050, PSL Université, Paris, France.
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2
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Zhao X, Kolbinger FR, Distler M, Weitz J, Makarov D, Bachmann M, Baraban L. Portable droplet-based real-time monitoring of pancreatic α-amylase in postoperative patients. Biosens Bioelectron 2024; 251:116034. [PMID: 38359666 DOI: 10.1016/j.bios.2024.116034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/21/2023] [Accepted: 01/11/2024] [Indexed: 02/17/2024]
Abstract
Postoperative complications after pancreatic surgery are frequent and can be life-threatening. Current clinical diagnostic strategies involve time-consuming quantification of α-amylase activity in abdominal drain fluid, which is performed on the first and third postoperative day. The lack of real-time monitoring may delay adjustment of medical treatment upon complications and worsen prognosis for patients. We report a bedside portable droplet-based millifluidic device enabling real-time sensing of drain α-amylase activity for postoperative monitoring of patients undergoing pancreatic surgery. Here, a tiny amount of drain liquid of patient samples is continuously collected and co-encapsulated with a starch reagent in nanoliter-sized droplets to track the fluorescence intensity released upon reaction with α-amylase. Comparing the α-amylase levels of 32 patients, 97 % of the results of the droplet-based millifluidic system matched the clinical data. Our method reduces the α-amylase assay duration to approximately 3 min with the limit of detection 7 nmol/s·L, enabling amylase activity monitoring at the bedside in clinical real-time. The presented droplet-based platform can be extended for analysis of different body fluids, diseases, and towards a broader range of biomarkers, including lipase, bilirubin, lactate, inflammation, or liquid biopsy markers, paving the way towards new standards in postoperative patient monitoring.
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Affiliation(s)
- Xinne Zhao
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V, 01328, Dresden, Germany.
| | - Fiona R Kolbinger
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav. Carus, TUD Dresden University of Technology, Germany; Else Kröner Fresenius Center for Digital Health (EKFZ), TUD Dresden University of Technology, Germany.
| | - Marius Distler
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav. Carus, TUD Dresden University of Technology, Germany
| | - Jürgen Weitz
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav. Carus, TUD Dresden University of Technology, Germany; Else Kröner Fresenius Center for Digital Health (EKFZ), TUD Dresden University of Technology, Germany
| | - Denys Makarov
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf e. V, 01328, Dresden, Germany.
| | - Michael Bachmann
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V, 01328, Dresden, Germany.
| | - Larysa Baraban
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V, 01328, Dresden, Germany; Else Kröner Fresenius Center for Digital Health (EKFZ), TUD Dresden University of Technology, Germany.
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3
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Zhao X, Ruelens P, Farr AD, de Visser JAGM, Baraban L. Population dynamics of cross-protection against β-lactam antibiotics in droplet microreactors. Front Microbiol 2023; 14:1294790. [PMID: 38192289 PMCID: PMC10773670 DOI: 10.3389/fmicb.2023.1294790] [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: 09/15/2023] [Accepted: 12/06/2023] [Indexed: 01/10/2024] Open
Abstract
Introduction Bacterial strains that are resistant to antibiotics may protect not only themselves, but also sensitive bacteria nearby if resistance involves antibiotic degradation. Such cross-protection poses a challenge to effective antibiotic therapy by enhancing the long-term survival of bacterial infections, however, the current understanding is limited. Methods In this study, we utilize an automated nanoliter droplet analyzer to study the interactions between Escherichia coli strains expressing a β-lactamase (resistant) and those not expressing it (sensitive) when exposed to the β-lactam antibiotic cefotaxime (CTX), with the aim to define criteria contributing to cross-protection. Results We observed a cross-protection window of CTX concentrations for the sensitive strain, extending up to approximately 100 times its minimal inhibitory concentration (MIC). Through both microscopy and enzyme activity analyses, we demonstrate that bacterial filaments, triggered by antibiotic stress, contribute to cross-protection. Discussion The antibiotic concentration window for cross-protection depends on the difference in β-lactamase activity between co-cultured strains: larger differences shift the 'cross-protection window' toward higher CTX concentrations. Our findings highlight the dependence of opportunities for cross-protection on the relative resistance levels of the strains involved and suggest a possible specific role for filamentation.
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Affiliation(s)
- Xinne Zhao
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), Dresden, Germany
| | - Philip Ruelens
- Laboratory of Genetics, Wageningen University and Research, Wageningen, Netherlands
| | - Andrew D. Farr
- Laboratory of Genetics, Wageningen University and Research, Wageningen, Netherlands
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | | | - Larysa Baraban
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), Dresden, Germany
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4
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Payne EM, Murray BE, Penabad LI, Abbate E, Kennedy RT. Mass-Activated Droplet Sorting for the Selection of Lysine-Producing Escherichia coli. Anal Chem 2023; 95:15716-15724. [PMID: 37820298 PMCID: PMC11025463 DOI: 10.1021/acs.analchem.3c03080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Synthetic biology relies on engineering cells to have desirable properties, such as the production of select chemicals. A bottleneck in engineering methods is often the need to screen and sort variant libraries for potential activity. Droplet microfluidics is a method for high-throughput sample preparation and analysis which has the potential to improve the engineering of cells, but a limitation has been the reliance on fluorescent analysis. Here, we show the ability to select cell variants grown in 20 nL droplets at 0.5 samples/s using mass-activated droplet sorting (MADS), a method for selecting droplets based on the signal intensity measured by electrospray ionization mass spectrometry (ESI-MS). Escherichia coli variants producing lysine were used to evaluate the applicability of MADS for synthetic biology. E. coli were shown to be effectively grown in droplets, and the lysine produced by these cells was detectable using ESI-MS. Sorting of lysine-producing cells based on the MS signal was shown, yielding 96-98% purity for high-producing variants in the selected pool. Using this technique, cells were recovered after screening, enabling downstream validation via phenotyping. The presented method is translatable to whole-cell engineering for biocatalyst production.
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Affiliation(s)
- Emory M. Payne
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
| | - Bridget E. Murray
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
| | - Laura I. Penabad
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
| | - Eric Abbate
- Applications Development, Inscripta Inc., Pleasanton, CA 94588
| | - Robert T. Kennedy
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
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5
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Nguyen-Le TA, Zhao X, Bachmann M, Ruelens P, de Visser JAGM, Baraban L. High-Throughput Gel Microbeads as Incubators for Bacterial Competition Study. MICROMACHINES 2023; 14:645. [PMID: 36985052 PMCID: PMC10058504 DOI: 10.3390/mi14030645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Bacteria primarily live in structured environments, such as colonies and biofilms, attached to surfaces or growing within soft tissues. They are engaged in local competitive and cooperative interactions impacting our health and well-being, for example, by affecting population-level drug resistance. Our knowledge of bacterial competition and cooperation within soft matrices is incomplete, partly because we lack high-throughput tools to quantitatively study their interactions. Here, we introduce a method to generate a large amount of agarose microbeads that mimic the natural culture conditions experienced by bacteria to co-encapsulate two strains of fluorescence-labeled Escherichia coli. Focusing specifically on low bacterial inoculum (1-100 cells/capsule), we demonstrate a study on the formation of colonies of both strains within these 3D scaffolds and follow their growth kinetics and interaction using fluorescence microscopy in highly replicated experiments. We confirmed that the average final colony size is inversely proportional to the inoculum size in this semi-solid environment as a result of limited available resources. Furthermore, the colony shape and fluorescence intensity per colony are distinctly different in monoculture and co-culture. The experimental observations in mono- and co-culture are compared with predictions from a simple growth model. We suggest that our high throughput and small footprint microbead system is an excellent platform for future investigation of competitive and cooperative interactions in bacterial communities under diverse conditions, including antibiotics stress.
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Affiliation(s)
- Trang Anh Nguyen-Le
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), 01328 Dresden, Germany
| | - Xinne Zhao
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), 01328 Dresden, Germany
| | - Michael Bachmann
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), 01328 Dresden, Germany
- Tumor Immunology, University Cancer Center (UCC), University Hospital Carl Gustav Carus Dresden, Technische Universität Dresden, 01307 Dresden, Germany
- National Center for Tumor Diseases (NCT), Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 01309 Dresden, Germany
| | - Philip Ruelens
- Department of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - J. Arjan G. M. de Visser
- Department of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Larysa Baraban
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), 01328 Dresden, Germany
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01069 Dresden, Germany
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6
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Jian X, Guo X, Cai Z, Wei L, Wang L, Xing XH, Zhang C. Single-cell microliter-droplet screening system (MISS Cell): An integrated platform for automated high-throughput microbial monoclonal cultivation and picking. Biotechnol Bioeng 2023; 120:778-792. [PMID: 36477904 DOI: 10.1002/bit.28300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/18/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022]
Abstract
Solid plates have been used for microbial monoclonal isolation, cultivation, and colony picking since 1881. However, the process is labor- and resource-intensive for high-throughput requirements. Currently, several instruments have been integrated for automated and high-throughput picking, but complicated and expensive. To address these issues, we report a novel integrated platform, the single-cell microliter-droplet screening system (MISS Cell), for automated, high-throughput microbial monoclonal colony cultivation and picking. We verified the monoclonality of droplet cultures in the MISS Cell and characterized culture performance. Compared with solid plates, the MISS Cell generated a larger number of monoclonal colonies with higher initial growth rates using fewer resources. Finally, we established a workflow for automated high-throughput screening of Corynebacterium glutamicum using the MISS Cell and identified high glutamate-producing strains. The MISS Cell can serve as a universal platform to efficiently produce monoclonal colonies in high-throughput applications, overcoming the limitations of solid plates to promote rapid development in biotechnology.
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Affiliation(s)
- Xingjin Jian
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China
| | - Xiaojie Guo
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China
| | - Zhengshuo Cai
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China
| | - Longfeng Wei
- College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Liyan Wang
- Luoyang TMAXTREE Biotechnology Co., Ltd., Luoyang, China
| | - Xin-Hui Xing
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China
| | - Chong Zhang
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China
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7
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Pacocha N, Zapotoczna M, Makuch K, Bogusławski J, Garstecki P. You will know by its tail: a method for quantification of heterogeneity of bacterial populations using single-cell MIC profiling. LAB ON A CHIP 2022; 22:4317-4326. [PMID: 36222371 DOI: 10.1039/d2lc00234e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Severe non-healing infections are often caused by multiple pathogens or by genetic variants of the same pathogen exhibiting different levels of antibiotic resistance. For example, polymicrobial diabetic foot infections double the risk of amputation compared to monomicrobial infections. Although these infections lead to increased morbidity and mortality, standard antimicrobial susceptibility methods are designed for homogenous samples and are impaired in quantifying heteroresistance. Here, we propose a droplet-based label-free method for quantifying the antibiotic response of the entire population at the single-cell level. We used Pseudomonas aeruginosa and Staphylococcus aureus samples to confirm that the shape of the profile informs about the coexistence of diverse bacterial subpopulations, their sizes, and antibiotic heteroresistance. These profiles could therefore indicate the outcome of antibiotic treatment in terms of the size of remaining subpopulations. Moreover, we studied phenotypic variants of a S. aureus strain to confirm that the profile can be used to identify tolerant subpopulations, such as small colony variants, associated with increased risks for the development of persisting infections. Therefore, the profile is a versatile instrument for quantifying the size of each bacterial subpopulation within a specimen as well as their individual and joined heteroresistance.
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Affiliation(s)
- Natalia Pacocha
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Marta Zapotoczna
- Department of Molecular Microbiology, Institute of Microbiology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Karol Makuch
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Jakub Bogusławski
- International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
- Department of Physical Chemistry of Biological Systems, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
- Laser & Fiber Electronics Group, Faculty of Electronics, Wrocław University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Piotr Garstecki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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8
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Ardré M, Doulcier G, Brenner N, Rainey PB. A leader cell triggers end of lag phase in populations of Pseudomonas fluorescens. MICROLIFE 2022; 3:uqac022. [PMID: 37223352 PMCID: PMC10117806 DOI: 10.1093/femsml/uqac022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 10/25/2022] [Indexed: 05/25/2023]
Abstract
The relationship between the number of cells colonizing a new environment and time for resumption of growth is a subject of long-standing interest. In microbiology this is known as the "inoculum effect." Its mechanistic basis is unclear with possible explanations ranging from the independent actions of individual cells, to collective actions of populations of cells. Here, we use a millifluidic droplet device in which the growth dynamics of hundreds of populations founded by controlled numbers of Pseudomonas fluorescens cells, ranging from a single cell, to one thousand cells, were followed in real time. Our data show that lag phase decreases with inoculum size. The decrease of average lag time and its variance across droplets, as well as lag time distribution shapes, follow predictions of extreme value theory, where the inoculum lag time is determined by the minimum value sampled from the single-cell distribution. Our experimental results show that exit from lag phase depends on strong interactions among cells, consistent with a "leader cell" triggering end of lag phase for the entire population.
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Affiliation(s)
- Maxime Ardré
- Laboratoire Biophysique et Évolution, CBI, ESPCI Paris, Université PSL, CNRS, 75005 Paris, France
| | - Guilhem Doulcier
- Laboratoire Biophysique et Évolution, CBI, ESPCI Paris, Université PSL, CNRS, 75005 Paris, France
| | - Naama Brenner
- Network Biology Research Laboratories, and Department of Chemical Engineering, Technion–Israel Institute of Technology, Haifa, Israel
| | - Paul B Rainey
- Laboratoire Biophysique et Évolution, CBI, ESPCI Paris, Université PSL, CNRS, 75005 Paris, France
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
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9
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Postek W, Pacocha N, Garstecki P. Microfluidics for antibiotic susceptibility testing. LAB ON A CHIP 2022; 22:3637-3662. [PMID: 36069631 DOI: 10.1039/d2lc00394e] [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
The rise of antibiotic resistance is a threat to global health. Rapid and comprehensive analysis of infectious strains is critical to reducing the global use of antibiotics, as informed antibiotic use could slow down the emergence of resistant strains worldwide. Multiple platforms for antibiotic susceptibility testing (AST) have been developed with the use of microfluidic solutions. Here we describe microfluidic systems that have been proposed to aid AST. We identify the key contributions in overcoming outstanding challenges associated with the required degree of multiplexing, reduction of detection time, scalability, ease of use, and capacity for commercialization. We introduce the reader to microfluidics in general, and we analyze the challenges and opportunities related to the field of microfluidic AST.
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Affiliation(s)
- Witold Postek
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
- Broad Institute of MIT and Harvard, Merkin Building, 415 Main St, Cambridge, MA 02142, USA.
| | - Natalia Pacocha
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
| | - Piotr Garstecki
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
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10
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Postek W, Garstecki P. Droplet Microfluidics for High-Throughput Analysis of Antibiotic Susceptibility in Bacterial Cells and Populations. Acc Chem Res 2022; 55:605-615. [PMID: 35119826 PMCID: PMC8892833 DOI: 10.1021/acs.accounts.1c00729] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antibiotic-resistant bacteria are an increasing concern both in everyday life and specialized environments such as healthcare. As the rate of antibiotic-resistant infections rises, so do complications to health and the risk of disability and death. Urgent action is required regarding the discovery of new antibiotics and rapid diagnosis of the resistance profile of an infectious pathogen as well as a better understanding of population and single-cell distribution of the resistance level. High-throughput screening is the major affordance of droplet microfluidics. Droplet screens can be exploited both to look for combinations of drugs that could stop an infection of multidrug-resistant bacteria and to search for the source of resistance via directed-evolution experiments or the analysis of various responses to a drug by genetically identical bacteria. In droplet techniques that have been used in this way for over a decade, aqueous droplets containing antibiotics and bacteria are manipulated both within and outside of the microfluidic devices. The diagnostics problem was approached by producing a series of microfluidic systems with integrated dilution modules for automated preparation of antibiotic concentration gradients, achieving the speed that allowed for high-throughput combinatorial assays. We developed a method for automated emulsification of a series of samples that facilitated measuring the resistance levels of thousands of individual cells encapsulated in droplets and quantifying the inoculum effect, the dependence of resistance level on bacterial cell count. Screening of single cells encapsulated in droplets with varying antibiotic contents has revealed a distribution of resistance levels within populations of clonally identical cells. To be able to screen bacteria from clinical samples, a study of fluorescent dyes in droplets determined that a derivative of a popular viability marker is more suitable for droplet assays. We have developed a detection system that analyzes the growth or death state of bacteria with antibiotics for thousands of droplets per second by measuring the scattering of light hitting the droplets without labeling the cells or droplets. The droplet-based microchemostats enabled long-term evolution of resistance experiments, which will be integrated with high-throughput single-cell assays to better understand the mechanism of resistance acquisition and loss. These techniques underlie automated combinatorial screens of antibiotic resistance in single cells from clinical samples. We hope that this Account will inspire new droplet-based research on the antibiotic susceptibility of bacteria.
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Affiliation(s)
- Witold Postek
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland
| | - Piotr Garstecki
- Institute of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland
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11
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Needs SH, Saiprom N, Rafaque Z, Imtiaz W, Chantratita N, Runcharoen C, Thammachote J, Anun S, Peacock SJ, Ray P, Andrews S, Edwards AD. Miniaturised broth microdilution for simplified antibiotic susceptibility testing of Gram negative clinical isolates using microcapillary devices. Analyst 2022; 147:3558-3569. [DOI: 10.1039/d2an00305h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Miniaturised antibiotic susceptibility testing: 100 times smaller microcapillary broth microdilution gives equivalent result to standard microplate broth microdilution.
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Affiliation(s)
| | - Natnaree Saiprom
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Thailand
| | - Zara Rafaque
- Department of Microbiology, Faculty of Health Sciences, Hazara University, Mansehra, Pakistan
| | - Wajiha Imtiaz
- School of Biological Sciences, University of Reading, RG6 6DX, UK
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Thailand
| | - Chakkaphan Runcharoen
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Thailand
| | - Jeeranan Thammachote
- Division of Clinical Microbiology, Medical Technology Department, Bhuddhasothon Hospital, Chachoengsao, Thailand
| | - Suthatip Anun
- Division of Clinical Microbiology, Medical Technology Department, Bhuddhasothon Hospital, Chachoengsao, Thailand
| | | | - Partha Ray
- The Nature Conservancy, Virginia, USA
- School of Agriculture Policy and Development, University of Reading, UK
| | - Simon Andrews
- School of Biological Sciences, University of Reading, RG6 6DX, UK
| | - Alexander D. Edwards
- School of Pharmacy, University of Reading, RG6 6DX, UK
- CFT Ltd, Daux Road, Billingshurst, RH14 9SJ, UK
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12
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Yang L, Pijuan-Galito S, Rho HS, Vasilevich AS, Eren AD, Ge L, Habibović P, Alexander MR, de Boer J, Carlier A, van Rijn P, Zhou Q. High-Throughput Methods in the Discovery and Study of Biomaterials and Materiobiology. Chem Rev 2021; 121:4561-4677. [PMID: 33705116 PMCID: PMC8154331 DOI: 10.1021/acs.chemrev.0c00752] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Indexed: 02/07/2023]
Abstract
The complex interaction of cells with biomaterials (i.e., materiobiology) plays an increasingly pivotal role in the development of novel implants, biomedical devices, and tissue engineering scaffolds to treat diseases, aid in the restoration of bodily functions, construct healthy tissues, or regenerate diseased ones. However, the conventional approaches are incapable of screening the huge amount of potential material parameter combinations to identify the optimal cell responses and involve a combination of serendipity and many series of trial-and-error experiments. For advanced tissue engineering and regenerative medicine, highly efficient and complex bioanalysis platforms are expected to explore the complex interaction of cells with biomaterials using combinatorial approaches that offer desired complex microenvironments during healing, development, and homeostasis. In this review, we first introduce materiobiology and its high-throughput screening (HTS). Then we present an in-depth of the recent progress of 2D/3D HTS platforms (i.e., gradient and microarray) in the principle, preparation, screening for materiobiology, and combination with other advanced technologies. The Compendium for Biomaterial Transcriptomics and high content imaging, computational simulations, and their translation toward commercial and clinical uses are highlighted. In the final section, current challenges and future perspectives are discussed. High-throughput experimentation within the field of materiobiology enables the elucidation of the relationships between biomaterial properties and biological behavior and thereby serves as a potential tool for accelerating the development of high-performance biomaterials.
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Affiliation(s)
- Liangliang Yang
- University
of Groningen, W. J. Kolff Institute for Biomedical Engineering and
Materials Science, Department of Biomedical Engineering, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Sara Pijuan-Galito
- School
of Pharmacy, Biodiscovery Institute, University
of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| | - Hoon Suk Rho
- Department
of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired
Regenerative Medicine, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Aliaksei S. Vasilevich
- Department
of Biomedical Engineering, Eindhoven University
of Technology, 5600 MB Eindhoven, The Netherlands
| | - Aysegul Dede Eren
- Department
of Biomedical Engineering, Eindhoven University
of Technology, 5600 MB Eindhoven, The Netherlands
| | - Lu Ge
- University
of Groningen, W. J. Kolff Institute for Biomedical Engineering and
Materials Science, Department of Biomedical Engineering, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Pamela Habibović
- Department
of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired
Regenerative Medicine, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Morgan R. Alexander
- School
of Pharmacy, Boots Science Building, University
of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| | - Jan de Boer
- Department
of Biomedical Engineering, Eindhoven University
of Technology, 5600 MB Eindhoven, The Netherlands
| | - Aurélie Carlier
- Department
of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired
Regenerative Medicine, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Patrick van Rijn
- University
of Groningen, W. J. Kolff Institute for Biomedical Engineering and
Materials Science, Department of Biomedical Engineering, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Qihui Zhou
- Institute
for Translational Medicine, Department of Stomatology, The Affiliated
Hospital of Qingdao University, Qingdao
University, Qingdao 266003, China
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13
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Zhao X, Illing R, Ruelens P, Bachmann M, Cuniberti G, de Visser JAGM, Baraban L. Coexistence of fluorescent Escherichia coli strains in millifluidic droplet reactors. LAB ON A CHIP 2021; 21:1492-1502. [PMID: 33881032 DOI: 10.1039/d0lc01204a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Understanding competition and cooperation within microbiota is of high fundamental and clinical importance, helping to comprehend species' evolution and biodiversity. We co-encapsulated and cultured two isogenic Escherichia coli strains expressing blue (BFP) and yellow (YFP) fluorescent proteins into numerous emulsion droplets and quantified their growth by employing fluorescence measurements. To characterize and compare the bacterial growth kinetics and behavior in mono and co-culture, we compared the experimental observations with predictions from a simple growth model. Varying the initial ratio (R0) of both cell types injected, we observed a broad landscape from competition to cooperation between both strains in their confined microenvironments depending on start frequency: from a nearly symmetric situation at R0 = 1, up to the domination of one subpopulation when R0 ≫ 1 (or R0 ≪ 1). Due to competition between the strains, their doubling times and final biomass ratios (R1) continuously deviate from the monoculture behavior. The correlation map of the two strains' doubling times reveals that the R0 is one of the critical parameters affecting the competitive interaction between isogenic bacterial strains. Thanks to this strategy, different species of bacteria can be monitored simultaneously in real-time. Further advantages include high statistical output, unaffected bacteria growth, and long-time measurements in a well-mixed environment. We expect that the millifluidic droplet-based reactor can be utilized for practical clinical applications, such as bacterial antibiotic resistance and enzyme reaction kinetics studies.
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Affiliation(s)
- Xinne Zhao
- Institute for Materials Science, Max Bergmann Center of Biomaterials, Technische Universität Dresden, 01062 Dresden, Germany. and Helmholtz-Zentrum Dresden Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328 Dresden, Germany.
| | - Rico Illing
- Institute for Materials Science, Max Bergmann Center of Biomaterials, Technische Universität Dresden, 01062 Dresden, Germany. and Helmholtz-Zentrum Dresden Rossendorf, Institute of Ion Beam Physics and Materials Research, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Philip Ruelens
- Department of Genetics, Wageningen University, Arboretumlaan 4, 6703 BD Wageningen, The Netherlands
| | - Michael Bachmann
- Helmholtz-Zentrum Dresden Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328 Dresden, Germany.
| | - Gianaurelio Cuniberti
- Institute for Materials Science, Max Bergmann Center of Biomaterials, Technische Universität Dresden, 01062 Dresden, Germany.
| | - J Arjan G M de Visser
- Department of Genetics, Wageningen University, Arboretumlaan 4, 6703 BD Wageningen, The Netherlands
| | - Larysa Baraban
- Institute for Materials Science, Max Bergmann Center of Biomaterials, Technische Universität Dresden, 01062 Dresden, Germany. and Helmholtz-Zentrum Dresden Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328 Dresden, Germany.
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14
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Hsu KW, Lee WB, You HL, Lee MS, Lee GB. An automated and portable antimicrobial susceptibility testing system for urinary tract infections. LAB ON A CHIP 2021; 21:755-763. [PMID: 33503076 DOI: 10.1039/d0lc01315c] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Urinary tract infections (UTIs) are bacterial infections that 1) commonly affect females, 2) can pose high risks to impair kidney function, 3) are often treated with broad-spectrum antibiotics, and 4) are associated with high recurrence rates due to the evolution of drug-resistant strains. To choose the appropriate antibiotic, the minimum inhibitory concentration (MIC) among a panel of antibiotics should be determined before administration to avoid inadequate dosing or use of wrong antibiotics. To meet with the unmet needs, we developed a bead-based method for bacterial preconcentration with capture rates ranging from 20-50% and then automatically performed on-chip AST on an automated device which was composed of a pneumatic control module, a temperature control module and a chip image processing module. The developed portable system was capable of automatically conducting AST and MIC measurements using urine samples (via image analysis) in only 4.5-9 h and tested on four common UTIs bacterial strains. This compact system may therefore be promising for point-of-care personalized medicine in the near future.
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Affiliation(s)
- Kuo-Wei Hsu
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Wen-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Huey-Ling You
- Laboratory Medicine, 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. and Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan and Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan
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15
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Hengoju S, Tovar M, Man DKW, Buchheim S, Rosenbaum MA. Droplet Microfluidics for Microbial Biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 179:129-157. [PMID: 32888037 DOI: 10.1007/10_2020_140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Droplet microfluidics has recently evolved as a prominent platform for high-throughput experimentation for various research fields including microbiology. Key features of droplet microfluidics, like compartmentalization, miniaturization, and parallelization, have enabled many possibilities for microbiology including cultivation of microorganisms at a single-cell level, study of microbial interactions in a community, detection and analysis of microbial products, and screening of extensive microbial libraries with ultrahigh-throughput and minimal reagent consumptions. In this book chapter, we present several aspects and applications of droplet microfluidics for its implementation in various fields of microbial biotechnology. Recent advances in the cultivation of microorganisms in droplets including methods for isolation and domestication of rare microbes are reviewed. Similarly, a comparison of different detection and analysis techniques for microbial activities is summarized. Finally, several microbial applications are discussed with a focus on exploring new antimicrobials and high-throughput enzyme activity screening. We aim to highlight the advantages, limitations, and current developments in droplet microfluidics for microbial biotechnology while envisioning its enormous potential applications in the future.
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Affiliation(s)
- Sundar Hengoju
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University (FSU), Jena, Germany
| | - Miguel Tovar
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany
| | - DeDe Kwun Wai Man
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany
| | - Stefanie Buchheim
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University (FSU), Jena, Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University (FSU), Jena, Germany.
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16
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Huang HK, Cheng HW, Liao CC, Lin SJ, Chen YZ, Wang JK, Wang YL, Huang NT. Bacteria encapsulation and rapid antibiotic susceptibility test using a microfluidic microwell device integrating surface-enhanced Raman scattering. LAB ON A CHIP 2020; 20:2520-2528. [PMID: 32542276 DOI: 10.1039/d0lc00425a] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The antibiotic susceptibility test (AST) is a general laboratory procedure for bacterial identification and characterization and can be utilized to determine effective antimicrobials for individual patients. Due to the low bacterial concentration, conventional AST usually requires a prolonged bacterial culture time and a labor-intensive sample pretreatment process. Therefore, it cannot perform timely diagnosis or treatment, which results in a high mortality rate for seriously infected patients. To address this problem, we developed a microfluidic microwell device integrating surface-enhanced Raman scattering (SERS) technology, or the so called the Microwell-SERS system, to enable a rapid and high-throughput AST. Our results show that the Microwell-SERS system can successfully encapsulate bacteria in a miniaturized microwell with a greatly increased effective bacteria concentration, resulting in a shorter bacterial culture time. By attaching a microchannel onto the microwell, a smooth liquid and air exchange can purify the surrounding buffer and isolate bacteria in an individual microwell for independent SERS measurement. For proof-of-concept, we demonstrated a 2 h AST on susceptible and resistant E. coli and S. aureus with a concentration of 103 CFU mL-1 in the Microwell-SERS system, whereas the previous SERS-AST method required 108 CFU mL-1 bacterial suspension droplets dispensing on a SERS substrate. Based on the above features, we envision that the Microwell-SERS system could achieve highly sensitive, label-free, bacteria detection and rapid AST to enable timely and accurate bacterial infection disease diagnosis.
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Affiliation(s)
- Hsiu-Kang Huang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan.
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17
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Wang J, Jian X, Xing XH, Zhang C, Fei Q. Empowering a Methanol-Dependent Escherichia coli via Adaptive Evolution Using a High-Throughput Microbial Microdroplet Culture System. Front Bioeng Biotechnol 2020; 8:570. [PMID: 32733857 PMCID: PMC7363950 DOI: 10.3389/fbioe.2020.00570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/11/2020] [Indexed: 01/04/2023] Open
Abstract
Recently, a methanol-essential Escherichia coli was constructed; this strain is highly dependent on a supply of gluconate as a co-substrate for growth. Adaptive laboratory evolution is commonly applied to obtain mutants with specific phenotypes under certain selected pressure. However, conventional adaptive evolution approaches are not only laborious and time consuming, but they also come with lower throughput and inefficiency. In order to empower the aforementioned E. coli with reduced gluconate usage and enhanced growth rate, an irrational strategy based on a microbial microdroplet culture (MMC) platform was developed in this study. Given the automatic high-throughput selection of the MMC, a three-stage regime of an adaptive evolution experiment via gradually decreasing the availability of gluconate during the cultivation was performed for 50 days continuously in order to obtain the mutations. Finally, a candidate mutant was obtained with a 3-fold faster growth rate, a 43% shorter lag phase, and 40% less gluconate usage compared with the starting strain. Moreover, the gene mutations of gntU, idnT, edd, and pckA were identified by analyzing the whole-genome sequencing of mutants, which are strongly associated with the efficiency of gluconate uptake and cell growth. In conclusion, we have successfully demonstrated the feasibility of using MMC platform to empower the target strain with specific requirements in a manner of labor, time efficiency, and directed evolution.
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Affiliation(s)
- Jia Wang
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xingjin Jian
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Xin-Hui Xing
- Department of Chemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory for Industrial Biocatalysis of the Ministry of Education, Tsinghua University, Beijing, China
| | - Chong Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory for Industrial Biocatalysis of the Ministry of Education, Tsinghua University, Beijing, China
| | - Qiang Fei
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, China.,Shaanxi Key Laboratory of Energy Chemical Process Intensification, Xi'an Jiaotong University, Xi'an, China
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18
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Doulcier G, Lambert A, De Monte S, Rainey PB. Eco-evolutionary dynamics of nested Darwinian populations and the emergence of community-level heredity. eLife 2020; 9:e53433. [PMID: 32633717 PMCID: PMC7440921 DOI: 10.7554/elife.53433] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 06/12/2020] [Indexed: 01/23/2023] Open
Abstract
Interactions among microbial cells can generate new chemistries and functions, but exploitation requires establishment of communities that reliably recapitulate community-level phenotypes. Using mechanistic mathematical models, we show how simple manipulations to population structure can exogenously impose Darwinian-like properties on communities. Such scaffolding causes communities to participate directly in the process of evolution by natural selection and drives the evolution of cell-level interactions to the point where, despite underlying stochasticity, derived communities give rise to offspring communities that faithfully re-establish parental phenotype. The mechanism is akin to a developmental process (developmental correction) that arises from density-dependent interactions among cells. Knowledge of ecological factors affecting evolution of developmental correction has implications for understanding the evolutionary origin of major egalitarian transitions, symbioses, and for top-down engineering of microbial communities.
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Affiliation(s)
- Guilhem Doulcier
- Laboratoire de Génétique de l'Evolution, Chimie Biologie et Innovation, Université PSLParisFrance
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, Université PSLParisFrance
| | - Amaury Lambert
- Laboratoire de Probabilités, Statistique et Modélisation (LPSM), Sorbonne Université, CNRSParisFrance
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, Université PSL, CNRS, INSERMParisFrance
| | - Silvia De Monte
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, Université PSLParisFrance
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary BiologyPlönGermany
| | - Paul B Rainey
- Laboratoire de Génétique de l'Evolution, Chimie Biologie et Innovation, Université PSLParisFrance
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary BiologyPlönGermany
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19
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Benkova M, Soukup O, Marek J. Antimicrobial susceptibility testing: currently used methods and devices and the near future in clinical practice. J Appl Microbiol 2020; 129:806-822. [DOI: 10.1111/jam.14704] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 04/28/2020] [Accepted: 05/11/2020] [Indexed: 12/17/2022]
Affiliation(s)
- M. Benkova
- Department of Epidemiology Faculty of Military Health Sciences University of Defence Hradec Kralove Czech Republic
- Biomedical Research Center University Hospital Hradec Kralove Hradec Kralove Czech Republic
| | - O. Soukup
- Biomedical Research Center University Hospital Hradec Kralove Hradec Kralove Czech Republic
- Department of Toxicology and Military Pharmacy Faculty of Military Health Sciences University of Defence Hradec Kralove Czech Republic
| | - J. Marek
- Department of Epidemiology Faculty of Military Health Sciences University of Defence Hradec Kralove Czech Republic
- Biomedical Research Center University Hospital Hradec Kralove Hradec Kralove Czech Republic
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20
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Jian X, Guo X, Wang J, Tan ZL, Xing X, Wang L, Zhang C. Microbial microdroplet culture system (MMC): An integrated platform for automated, high‐throughput microbial cultivation and adaptive evolution. Biotechnol Bioeng 2020; 117:1724-1737. [DOI: 10.1002/bit.27327] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/14/2020] [Accepted: 03/08/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Xingjin Jian
- Department of Chemical Engineering, Institute of Biochemical EngineeringTsinghua University Beijing China
- Key Laboratory of Industrial Biocatalysis, Ministry of EducationTsinghua University Beijing China
| | - Xiaojie Guo
- Luoyang TMAXTREE Biotechnology Co., Ltd. Luoyang China
| | - Jia Wang
- Biochemical Engineering Research Group, School of Chemical Engineering and TechnologyXi'an Jiaotong University Xi'an China
| | - Zheng Lin Tan
- Department of Chemical Engineering, Institute of Biochemical EngineeringTsinghua University Beijing China
- Key Laboratory of Industrial Biocatalysis, Ministry of EducationTsinghua University Beijing China
- School of Life Science and TechnologyTokyo Institute of Technology, Midori‐ku Yokohama Kanagawa Prefecture Japan
| | - Xin‐hui Xing
- Department of Chemical Engineering, Institute of Biochemical EngineeringTsinghua University Beijing China
- Key Laboratory of Industrial Biocatalysis, Ministry of EducationTsinghua University Beijing China
- Center for Synthetic & Systems BiologyTsinghua University Beijing China
| | - Liyan Wang
- Luoyang TMAXTREE Biotechnology Co., Ltd. Luoyang China
| | - Chong Zhang
- Department of Chemical Engineering, Institute of Biochemical EngineeringTsinghua University Beijing China
- Key Laboratory of Industrial Biocatalysis, Ministry of EducationTsinghua University Beijing China
- Center for Synthetic & Systems BiologyTsinghua University Beijing China
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21
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Geyrhofer L, Brenner N. Coexistence and cooperation in structured habitats. BMC Ecol 2020; 20:14. [PMID: 32122337 PMCID: PMC7053132 DOI: 10.1186/s12898-020-00281-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/18/2020] [Indexed: 12/19/2022] Open
Abstract
Background Natural habitats are typically structured, imposing constraints on inhabiting populations and their interactions. Which conditions are important for coexistence of diverse communities, and how cooperative interaction stabilizes in such populations, have been important ecological and evolutionary questions. Results We investigate a minimal ecological framework of microbial population dynamics that exhibits crucial features to show coexistence: Populations repeatedly undergo cycles of separation into compartmentalized habitats and mixing with new resources. The characteristic time-scale is longer than that typical of individual growth. Using analytic approximations, averaging techniques and phase-plane methods of dynamical systems, we provide a framework for analyzing various types of microbial interactions. Population composition and population size are both dynamic variables of the model; they are found to be decoupled both in terms of time-scale and parameter dependence. We present specific results for two examples of cooperative interaction by public goods: collective antibiotics resistance, and enhanced iron-availability by pyoverdine. We find stable coexistence to be a likely outcome. Conclusions The two simple features of a long mixing time-scale and spatial compartmentalization are enough to enable coexisting strains. In particular, costly social traits are often stabilized in such an environment—and thus cooperation established.
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Affiliation(s)
- Lukas Geyrhofer
- Network Biology Research Laboratories, and Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel.
| | - Naama Brenner
- Network Biology Research Laboratories, and Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
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22
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On-chip MIC by Combining Concentration Gradient Generator and Flanged Chamber Arrays. MICROMACHINES 2020; 11:mi11020207. [PMID: 32079258 PMCID: PMC7074598 DOI: 10.3390/mi11020207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 01/31/2023]
Abstract
Minimum inhibition concentration (MIC) of antibiotic is an effective value to ascertain the agent and minimum dosage of inhibiting bacterial growth. However, current techniques to determine MIC are labor intensive and time-consuming, and require skilled operator and high initial concentration of bacteria. To simplify the operation and reduce the time of inhibition test, we developed a microfluidic system, containing a concentration generator and sub-micro-liter chambers, for rapid bacterial growth and inhibition test. To improve the mixing effect, a micropillar array in honeycomb-structure channels is designed, so the steady concentration gradient of amoxicillin can be generated. The flanged chambers are used to culture bacteria under the condition of continuous flow and the medium of chambers is refreshed constantly, which could supply the sufficient nutrient for bacteria growth and take away the metabolite. Based on the microfluidic platform, the bacterial growth with antibiotic inhibition on chip can be quantitatively measured and MIC can be obtained within six hours using low initial concentration of bacteria. Overall, this microfluidic platform has the potential to provide rapidness and effectiveness to screen bacteria and determine MIC of corresponding antibiotics in clinical therapies.
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23
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Merrin J. Frontiers in Microfluidics, a Teaching Resource Review. Bioengineering (Basel) 2019; 6:E109. [PMID: 31816954 PMCID: PMC6955790 DOI: 10.3390/bioengineering6040109] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 02/02/2023] Open
Abstract
This is a literature teaching resource review for biologically inspired microfluidics courses or exploring the diverse applications of microfluidics. The structure is around key papers and model organisms. While courses gradually change over time, a focus remains on understanding how microfluidics has developed as well as what it can and cannot do for researchers. As a primary starting point, we cover micro-fluid mechanics principles and microfabrication of devices. A variety of applications are discussed using model prokaryotic and eukaryotic organisms from the set of bacteria (Escherichia coli), trypanosomes (Trypanosoma brucei), yeast (Saccharomyces cerevisiae), slime molds (Physarum polycephalum), worms (Caenorhabditis elegans), flies (Drosophila melangoster), plants (Arabidopsis thaliana), and mouse immune cells (Mus musculus). Other engineering and biochemical methods discussed include biomimetics, organ on a chip, inkjet, droplet microfluidics, biotic games, and diagnostics. While we have not yet reached the end-all lab on a chip, microfluidics can still be used effectively for specific applications.
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Affiliation(s)
- Jack Merrin
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
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24
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Cross-Flow Filtration of Escherichia coli at a Nanofluidic Gap for Fast Immobilization and Antibiotic Susceptibility Testing. MICROMACHINES 2019; 10:mi10100691. [PMID: 31614761 PMCID: PMC6843207 DOI: 10.3390/mi10100691] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 01/17/2023]
Abstract
Infections with antimicrobial-resistant (AMR) bacteria are globally on the rise. In the future, multi-resistant infections will become one of the major problems in global health care. In order to enable reserve antibiotics to retain their effect as long as possible, broad-spectrum antibiotics must be used sparingly. This can be achieved by a rapid microfluidic phenotypic antibiotic susceptibility test, which provides the information needed for a targeted antibiotic therapy in less time than conventional tests. Such microfluidic tests must cope with a low bacteria concentration. On-chip filtering of the samples to accumulate bacteria can shorten the test time. By means of fluorescence microscopy, we examined a novel nanogap filtration principle to hold back Escherichia coli and to perform cultivation experiments with and without antibiotics present. Microfluidic chips based on the nanogap flow principle showed to be useful for the concentration and cultivation of E. coli. With a concentration of 106 cells/mL, a specific growth rate of 0.013 min-1 and a doubling time of 53 min were achieved. In the presence of an antibiotic, no growth was observed. The results prove that this principle can, in future, be used in fast and marker-free antimicrobial susceptibility testing (AST).
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25
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Behera B, Anil Vishnu GK, Chatterjee S, Sitaramgupta V VSN, Sreekumar N, Nagabhushan A, Rajendran N, Prathik BH, Pandya HJ. Emerging technologies for antibiotic susceptibility testing. Biosens Bioelectron 2019; 142:111552. [PMID: 31421358 DOI: 10.1016/j.bios.2019.111552] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/27/2019] [Accepted: 07/29/2019] [Indexed: 12/22/2022]
Abstract
Superbugs such as infectious bacteria pose a great threat to humanity due to an increase in bacterial mortality leading to clinical treatment failure, lengthy hospital stay, intravenous therapy and accretion of bacteraemia. These disease-causing bacteria gain resistance to drugs over time which further complicates the treatment. Monitoring of antibiotic resistance is therefore necessary so that bacterial infectious diseases can be diagnosed rapidly. Antimicrobial susceptibility testing (AST) provides valuable information on the efficacy of antibiotic agents and their dosages for treatment against bacterial infections. In clinical laboratories, most widely used AST methods are disk diffusion, gradient diffusion, broth dilution, or commercially available semi-automated systems. Though these methods are cost-effective and accurate, they are time-consuming, labour-intensive, and require skilled manpower. Recently much attention has been on developing rapid AST techniques to avoid misuse of antibiotics and provide effective treatment. In this review, we have discussed emerging engineering AST techniques with special emphasis on phenotypic AST. These techniques include fluorescence imaging along with computational image processing, surface plasmon resonance, Raman spectra, and laser tweezer as well as micro/nanotechnology-based device such as microfluidics, microdroplets, and microchamber. The mechanical and electrical behaviour of single bacterial cell and bacterial suspension for the study of AST is also discussed.
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Affiliation(s)
- Bhagaban Behera
- Biomedical and Electronic (10(-6)-10(-9)) Engineering Systems Laboratory, Department of Electronic Systems Engineering, Indian Institute of Science, Bangalore, India
| | - G K Anil Vishnu
- Biomedical and Electronic (10(-6)-10(-9)) Engineering Systems Laboratory, Department of Electronic Systems Engineering, Indian Institute of Science, Bangalore, India; Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Suman Chatterjee
- Biomedical and Electronic (10(-6)-10(-9)) Engineering Systems Laboratory, Department of Electronic Systems Engineering, Indian Institute of Science, Bangalore, India
| | - V S N Sitaramgupta V
- Biomedical and Electronic (10(-6)-10(-9)) Engineering Systems Laboratory, Department of Electronic Systems Engineering, Indian Institute of Science, Bangalore, India
| | - Niranjana Sreekumar
- Biomedical and Electronic (10(-6)-10(-9)) Engineering Systems Laboratory, Department of Electronic Systems Engineering, Indian Institute of Science, Bangalore, India
| | - Apoorva Nagabhushan
- Biomedical and Electronic (10(-6)-10(-9)) Engineering Systems Laboratory, Department of Electronic Systems Engineering, Indian Institute of Science, Bangalore, India
| | | | - B H Prathik
- Indira Gandhi Institute of Child Health, Bangalore, India
| | - Hardik J Pandya
- Biomedical and Electronic (10(-6)-10(-9)) Engineering Systems Laboratory, Department of Electronic Systems Engineering, Indian Institute of Science, Bangalore, India.
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27
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Tan ZL, Zheng X, Wu Y, Jian X, Xing X, Zhang C. In vivo continuous evolution of metabolic pathways for chemical production. Microb Cell Fact 2019; 18:82. [PMID: 31088458 PMCID: PMC6518619 DOI: 10.1186/s12934-019-1132-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/04/2019] [Indexed: 01/07/2023] Open
Abstract
Microorganisms have long been used as chemical plant to convert simple substrates into complex molecules. Various metabolic pathways have been optimised over the past few decades, but the progresses were limited due to our finite knowledge on metabolism. Evolution is a knowledge-free genetic randomisation approach, employed to improve the chemical production in microbial cell factories. However, evolution of large, complex pathway was a great challenge. The invention of continuous culturing systems and in vivo genetic diversification technologies have changed the way how laboratory evolution is conducted, render optimisation of large, complex pathway possible. In vivo genetic diversification, phenotypic selection, and continuous cultivation are the key elements in in vivo continuous evolution, where any human intervention in the process is prohibited. This approach is crucial in highly efficient evolution strategy of metabolic pathway evolution.
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Affiliation(s)
- Zheng Lin Tan
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama City, Kanagawa Prefecture, 226-8503 Japan
- Laboratory of Future Interdisciplinary Research and Science Technology, Tokyo Institute of Technology, Yokohama City, Kanagawa Prefecture, 226-8503 Japan
| | - Xiang Zheng
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Yinan Wu
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Xingjin Jian
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Xinhui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084 China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084 China
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Duarte LC, Figueredo F, Ribeiro LEB, Cortón E, Coltro WKT. Label-free counting of Escherichia coli cells in nanoliter droplets using 3D printed microfluidic devices with integrated contactless conductivity detection. Anal Chim Acta 2019; 1071:36-43. [PMID: 31128753 DOI: 10.1016/j.aca.2019.04.045] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 03/27/2019] [Accepted: 04/17/2019] [Indexed: 01/21/2023]
Abstract
This study describes for the first time the development of 3D printed microfluidic devices with integrated electrodes for label-free counting of E. coli cells incorporated inside droplets based on capacitively coupled contactless conductivity detection (C4D). Microfluidic devices were fully fabricated by 3D printing in the T-junction shape containing two channels for disperse and continuous phases and two sensing electrodes for C4D measurements. The disperse phase containing E. coli K12 cells and the continuous phase containing oil and 1% Span® 80 were pumped through flow rates fixed at 5 and 60 μL min-1, respectively. The droplets with incorporated cells were monitored in the C4D system applying a 500-kHz sinusoidal wave with 1 Vpp amplitude. The generated droplets exhibited a spherical shape with average diameter of 321 ± 9 μm and presented volume of 17.3 ± 0.5 nL. The proposed approach demonstrated ability to detect E. coli cells in the concentration range between 86.5 and 8650 CFU droplet-1. The number of cells per droplet was quantified through the plate counting method and revealed a good agreement with the Poisson distribution. The limit of detection achieved for counting E. coli cells was 63.66 CFU droplet-1. The label-free counting method has offered instrumental simplicity, low cost, high sensitivity and compatibility to be integrated on single microfluidic platforms entirely fabricated by 3D printing, thus opening new possibilities of applications in microbiology.
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Affiliation(s)
- Lucas C Duarte
- Instituto de Química, Universidade Federal de Goiás, Campus Samambaia, 74690-900, Goiânia, GO, Brazil
| | - Federico Figueredo
- Laboratorio de Biosensores y Bioanalisis (LABB), Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, CABA, Argentina
| | - Luiz E B Ribeiro
- Instituto de Química, Universidade Federal de Goiás, Campus Samambaia, 74690-900, Goiânia, GO, Brazil; Instituto Federal de Goiás - Campus Senador Canedo, 75250-000, Senador Canedo, GO, Brazil
| | - Eduardo Cortón
- Laboratorio de Biosensores y Bioanalisis (LABB), Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, CABA, Argentina
| | - Wendell K T Coltro
- Instituto de Química, Universidade Federal de Goiás, Campus Samambaia, 74690-900, Goiânia, GO, Brazil; Instituto Nacional de Ciência e Tecnologia de Bioanalítica, 13084-971, Campinas, SP, Brazil.
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29
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Li Y, Diddens C, Prosperetti A, Chong KL, Zhang X, Lohse D. Bouncing Oil Droplet in a Stratified Liquid and its Sudden Death. PHYSICAL REVIEW LETTERS 2019; 122:154502. [PMID: 31050512 DOI: 10.1103/physrevlett.122.154502] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/12/2019] [Indexed: 06/09/2023]
Abstract
Droplets can self-propel when immersed in another liquid in which a concentration gradient is present. Here we report the experimental and numerical study of a self-propelling oil droplet in a vertically stratified ethanol-water mixture: At first, the droplet sinks slowly due to gravity, but then, before having reached its density matched position, jumps up suddenly. More remarkably, the droplet bounces repeatedly with an ever increasing jumping distance, until all of a sudden it stops after about 30 min. We identify the Marangoni stress at the droplet-liquid interface as responsible for the jumping: its strength grows exponentially because it pulls down ethanol-rich liquid, which in turn increases its strength even more. The jumping process can repeat because gravity restores the system. Finally, the sudden death of the jumping droplet is also explained. Our findings have demonstrated a type of prominent droplet bouncing inside a continuous medium with no wall or sharp interface.
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Affiliation(s)
- Yanshen Li
- Physics of Fluids group, Max-Planck Center Twente for Complex Fluid Dynamics, Department of Science and Technology, Mesa+Institute, and J. M. Burgers Centre for Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede, Netherlands
| | - Christian Diddens
- Physics of Fluids group, Max-Planck Center Twente for Complex Fluid Dynamics, Department of Science and Technology, Mesa+Institute, and J. M. Burgers Centre for Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede, Netherlands
- Department of Mechanical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, Netherlands
| | - Andrea Prosperetti
- Physics of Fluids group, Max-Planck Center Twente for Complex Fluid Dynamics, Department of Science and Technology, Mesa+Institute, and J. M. Burgers Centre for Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede, Netherlands
- Department of Mechanical Engineering, University of Houston, Texas 77204-4006, USA
| | - Kai Leong Chong
- Physics of Fluids group, Max-Planck Center Twente for Complex Fluid Dynamics, Department of Science and Technology, Mesa+Institute, and J. M. Burgers Centre for Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede, Netherlands
| | - Xuehua Zhang
- Physics of Fluids group, Max-Planck Center Twente for Complex Fluid Dynamics, Department of Science and Technology, Mesa+Institute, and J. M. Burgers Centre for Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede, Netherlands
- Department of Chemical and Materials Engineering, University of Alberta, 12-380 Donadeo Innovation Centre for Engineering, Edmonton, T6G1H9 Alberta, Canada
| | - Detlef Lohse
- Physics of Fluids group, Max-Planck Center Twente for Complex Fluid Dynamics, Department of Science and Technology, Mesa+Institute, and J. M. Burgers Centre for Fluid Dynamics, University of Twente, P.O. Box 217, 7500 AE Enschede, Netherlands
- Max Planck Institute for Dynamics and Self-Organization, 37077 Göttingen, Germany
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30
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Kim S, Masum F, Jeon JS. Recent Developments of Chip-based Phenotypic Antibiotic Susceptibility Testing. BIOCHIP JOURNAL 2019. [DOI: 10.1007/s13206-019-3109-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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31
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Rapid serial diluting biomicrofluidic provides EC50 in minutes. MICRO AND NANO ENGINEERING 2019. [DOI: 10.1016/j.mne.2019.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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32
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Ferraro D, Serra M, Filippi D, Zago L, Guglielmin E, Pierno M, Descroix S, Viovy JL, Mistura G. Controlling the distance of highly confined droplets in a capillary by interfacial tension for merging on-demand. LAB ON A CHIP 2018; 19:136-146. [PMID: 30484796 DOI: 10.1039/c8lc01182f] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Droplet microfluidics is a powerful technology that finds many applications in chemistry and biomedicine. Among different configurations, droplets confined in a capillary (or plugs) present a number of advantages: they allow positional identification and simplify the integration of complex multi-steps protocols. However, these protocols rely on the control of droplet speed, which is affected by a complex and still debated interplay of various physico-chemical parameters like droplet length, viscosity ratio between droplets and carrier fluid, flow rate and interfacial tension. We present here a systematic investigation of the droplet speed as a function of their length and interfacial tension, and propose a novel, simple and robust methodology to control the relative distance between consecutive droplets flowing in microfluidic channels through the addition of surfactants either into the dispersed and/or into the continuous phases. As a proof of concept application, we present the possibility to accurately trigger in space and time the merging of two confined droplets flowing in a uniform cross-section circular capillary. This approach is further validated by monitoring a conventional enzymatic reaction used to quantify the concentration of H2O2 in a biological sample, showing its potentialities in both continuous and stopped assay methods.
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Affiliation(s)
- D Ferraro
- Dipartimento di Fisica e Astronomia G. Galilei, Università di Padova, via Marzolo 8, 35131 Padova, Italy.
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33
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Cui P, Wang S. Application of microfluidic chip technology in pharmaceutical analysis: A review. J Pharm Anal 2018; 9:238-247. [PMID: 31452961 PMCID: PMC6704040 DOI: 10.1016/j.jpha.2018.12.001] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 11/29/2018] [Accepted: 12/04/2018] [Indexed: 01/18/2023] Open
Abstract
The development of pharmaceutical analytical methods represents one of the most significant aspects of drug development. Recent advances in microfabrication and microfluidics could provide new approaches for drug analysis, including drug screening, active testing and the study of metabolism. Microfluidic chip technologies, such as lab-on-a-chip technology, three-dimensional (3D) cell culture, organs-on-chip and droplet techniques, have all been developed rapidly. Microfluidic chips coupled with various kinds of detection techniques are suitable for the high-throughput screening, detection and mechanistic study of drugs. This review highlights the latest (2010–2018) microfluidic technology for drug analysis and discusses the potential future development in this field.
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Affiliation(s)
- Ping Cui
- School of Pharmacy, Xi'an Jiaotong University Health Science Center, #76, Yanta West Road, Xi'an 710061, China.,Shaanxi Engineering Research Center of Cardiovascular Drugs Screening & Analysis, Xi'an 710061, China
| | - Sicen Wang
- School of Pharmacy, Xi'an Jiaotong University Health Science Center, #76, Yanta West Road, Xi'an 710061, China.,Shaanxi Engineering Research Center of Cardiovascular Drugs Screening & Analysis, Xi'an 710061, China
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34
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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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35
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Debski PR, Sklodowska K, Michalski JA, Korczyk PM, Dolata M, Jakiela S. Continuous Recirculation of Microdroplets in a Closed Loop Tailored for Screening of Bacteria Cultures. MICROMACHINES 2018; 9:E469. [PMID: 30424402 PMCID: PMC6187375 DOI: 10.3390/mi9090469] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/05/2018] [Accepted: 09/14/2018] [Indexed: 01/29/2023]
Abstract
Emerging microfluidic technology has introduced new precision controls over reaction conditions. Owing to the small amount of reagents, microfluidics significantly lowers the cost of carrying a single reaction. Moreover, in two-phase systems, each part of a dispersed fluid can be treated as an independent chemical reactor with a volume from femtoliters to microliters, increasing the throughput. In this work, we propose a microfluidic device that provides continuous recirculation of droplets in a closed loop, maintaining low consumption of oil phase, no cross-contamination, stabilized temperature, a constant condition of gas exchange, dynamic feedback control on droplet volume, and a real-time optical characterization of bacterial growth in a droplet. The channels (tubing) and junction cubes are made of Teflon fluorinated ethylene propylene (FEP) to ensure non-wetting conditions and to prevent the formation of biofilm, which is particularly crucial for biological experiments. We show the design and operation of a novel microfluidic loop with the circular motion of microdroplet reactors monitored with optical sensors and precision temperature controls. We have employed the proposed system for long term monitoring of bacterial growth during the antibiotic chloramphenicol treatment. The proposed system can find applications in a broad field of biomedical diagnostics and therapy.
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Affiliation(s)
- Pawel R Debski
- Department of Biophysics, Warsaw University of Life Sciences, 159 Nowoursynowska Street, 02776 Warsaw, Poland.
| | - Karolina Sklodowska
- Department of Biophysics, Warsaw University of Life Sciences, 159 Nowoursynowska Street, 02776 Warsaw, Poland.
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, 159 Nowoursynowska Street, 02776 Warsaw, Poland.
| | - Jacek A Michalski
- Faculty of Civil Engineering, Mechanics and Petrochemistry, Warsaw University of Technology, 17 Lukasiewicza Street, 09400 Plock, Poland.
| | - Piotr M Korczyk
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawinskiego 5B, 02106 Warsaw, Poland.
| | - Miroslaw Dolata
- Department of Econophysics and Physics Application, Warsaw University of Life Sciences, 159 Nowoursynowska Street, 02776 Warsaw, Poland.
| | - Slawomir Jakiela
- Department of Biophysics, Warsaw University of Life Sciences, 159 Nowoursynowska Street, 02776 Warsaw, Poland.
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36
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Abstract
Combinatorial drug treatment strategies perturb biological networks synergistically to achieve therapeutic effects and represent major opportunities to develop advanced treatments across a variety of human disease areas. However, the discovery of new combinatorial treatments is challenged by the sheer scale of combinatorial chemical space. Here, we report a high-throughput system for nanoliter-scale phenotypic screening that formulates a chemical library in nanoliter droplet emulsions and automates the construction of chemical combinations en masse using parallel droplet processing. We applied this system to predict synergy between more than 4,000 investigational and approved drugs and a panel of 10 antibiotics against Escherichia coli, a model gram-negative pathogen. We found a range of drugs not previously indicated for infectious disease that synergize with antibiotics. Our validated hits include drugs that synergize with the antibiotics vancomycin, erythromycin, and novobiocin, which are used against gram-positive bacteria but are not effective by themselves to resolve gram-negative infections.
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37
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Schumacher A, Vranken T, Malhotra A, Arts JJC, Habibovic P. In vitro antimicrobial susceptibility testing methods: agar dilution to 3D tissue-engineered models. Eur J Clin Microbiol Infect Dis 2018; 37:187-208. [PMID: 28871407 PMCID: PMC5780537 DOI: 10.1007/s10096-017-3089-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 07/20/2017] [Indexed: 12/22/2022]
Abstract
In the field of orthopaedic surgery, bacterial invasion of implants and the resulting periprosthetic infections are a common and unresolved problem. Antimicrobial susceptibility testing methods help to define the optimal treatment and identify antimicrobial resistance. This review discusses proven gold-standard techniques and recently developed models for antimicrobial susceptibility testing, while also providing a future outlook. Conventional, gold-standard methods, such as broth microdilution, are still widely applied in clinical settings. Although recently developed methods based on microfluidics and microdroplets have shown advantages over conventional methods in terms of testing speed, safety and the potential to provide a deeper insight into resistance mechanisms, extensive validation is required to translate this research to clinical practice. Recent optical and mechanical methods are complex and expensive and, therefore, not immediately clinically applicable. Novel osteoblast infection and tissue models best resemble infections in vivo. However, the integration of biomaterials into these models remains challenging and they require a long tissue culture, making their rapid clinical implementation unlikely. A method applicable for both clinical and research environments is difficult to realise. With a continuous increase in antimicrobial resistance, there is an urgent need for methods that analyse recurrent infections to identify the optimal treatment approaches. Graphical abstract Timeline of published and partly applied antimicrobial susceptibility testing methods, listed according to their underlying mechanism, complexity and application in research or clinics.
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Affiliation(s)
- A Schumacher
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, Room C3.577, 6229 ER, Maastricht, Netherlands.
- Science and Technology Faculty, University of Twente, Drienerlolaan 5, 7522 NB, Enschede, The Netherlands.
| | - T Vranken
- Department of Orthopaedic Surgery, CAPHRI Care and Public Health Research Institute, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - A Malhotra
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, Room C3.577, 6229 ER, Maastricht, Netherlands
| | - J J C Arts
- Department of Orthopaedic Surgery, CAPHRI Care and Public Health Research Institute, Maastricht University Medical Centre, Maastricht, The Netherlands
- Orthopaedic Biomechanics Group, Department of Biomedical Engineering, Eindhoven University of Technology (TU/e), Eindhoven, The Netherlands
| | - P Habibovic
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, Room C3.577, 6229 ER, Maastricht, Netherlands
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38
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Onishi K, Enomoto J, Araki T, Takagi R, Suzuki H, Fukuda J. Electrochemical microdevices for rapid and on-site determination of the minimum inhibitory concentration of antibiotics. Analyst 2018; 143:396-399. [DOI: 10.1039/c7an01873h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A tool for rapid selection of appropriate antibiotics may be useful to maximize the benefits of their effectiveness against severe infectious diseases.
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Affiliation(s)
- K. Onishi
- Faculty of Engineering
- Yokohama National University
- Yokohama 240-8501
- Japan
| | - J. Enomoto
- Faculty of Engineering
- Yokohama National University
- Yokohama 240-8501
- Japan
| | - T. Araki
- Faculty of Engineering
- Yokohama National University
- Yokohama 240-8501
- Japan
| | - R. Takagi
- Graduate School of Pure and Applied Sciences
- University of Tsukuba
- Tsukuba
- Japan
| | - H. Suzuki
- Graduate School of Pure and Applied Sciences
- University of Tsukuba
- Tsukuba
- Japan
| | - J. Fukuda
- Faculty of Engineering
- Yokohama National University
- Yokohama 240-8501
- Japan
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39
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Song W, Lin G, Ge J, Fassbender J, Makarov D. Encoding Microreactors with Droplet Chains in Microfluidics. ACS Sens 2017; 2:1839-1846. [PMID: 29183119 DOI: 10.1021/acssensors.7b00700] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Droplet-based high throughput biomolecular screening and combinatorial synthesis entail a viable indexing strategy to be developed for the identification of each microreactor. Here, we propose a novel indexing scheme based on the generation of droplet sequences on demand to form unique encoding droplet chains in fluidic networks. These codes are represented by multiunit and multilevel droplets packages, with each code unit possessing several distinct signal levels, potentially allowing large encoding capacity. For proof of concept, we use magnetic nanoparticles as the encoding material and a giant magnetoresistance (GMR) sensor-based active sorting system supplemented with an optical detector to generate and decode the sequence of one exemplar sample droplet reactor and a 4-unit quaternary magnetic code. The indexing capacity offered by 4-unit multilevel codes with this indexing strategy is estimated to exceed 104, which holds great promise for large-scale droplet-based screening and synthesis.
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Affiliation(s)
- Wenya Song
- Helmholtz-Zentrum
Dresden-Rossendorf e.V. (HZDR), Institute of Ion Beam Physics and Materials Research, Bautzner Landstr. 400, 01328 Dresden, Germany
| | - Gungun Lin
- Helmholtz-Zentrum
Dresden-Rossendorf e.V. (HZDR), Institute of Ion Beam Physics and Materials Research, Bautzner Landstr. 400, 01328 Dresden, Germany
- University of Technology Sydney, Institute for Biomedical Materials
and Devices (IBMD), School of Mathematical and Physical Sciences, Ultimo, NSW 2007, Australia
| | - Jin Ge
- Helmholtz-Zentrum
Dresden-Rossendorf e.V. (HZDR), Institute of Ion Beam Physics and Materials Research, Bautzner Landstr. 400, 01328 Dresden, Germany
| | - Jürgen Fassbender
- Helmholtz-Zentrum
Dresden-Rossendorf e.V. (HZDR), Institute of Ion Beam Physics and Materials Research, Bautzner Landstr. 400, 01328 Dresden, Germany
- Technische Universität Dresden, Zellescher Weg 16, 01069 Dresden, Germany
| | - Denys Makarov
- Helmholtz-Zentrum
Dresden-Rossendorf e.V. (HZDR), Institute of Ion Beam Physics and Materials Research, Bautzner Landstr. 400, 01328 Dresden, Germany
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40
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Liao S, Tao X, Ju Y, Feng J, Du W, Wang Y. Multichannel Dynamic Interfacial Printing: An Alternative Multicomponent Droplet Generation Technique for Lab in a Drop. ACS APPLIED MATERIALS & INTERFACES 2017; 9:43545-43552. [PMID: 29171252 DOI: 10.1021/acsami.7b16456] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Generation of uniform emulsion droplets mixed with multiple components is one of the key issues in the field of lab in a drop. Traditionally, droplet microfluidic chips are often served as the prime choice while designing and fabricating microfluidic chips always rely on skilled technician and specialized equipment, severely restricting its wide accessibility. In this work, an alternative technique, called multichannel dynamic interfacial printing (MC-DIP), was proposed for multicomponent droplet generation. The MC-DIP device was designed modularly and could be set up manually without any microfabrication process, exhibiting full accessibility for freshmen after a brief training. This new technique owns advantages in the generation of droplets with predictable sizes and composites. Quantitative experiments of measuring minimum inhibitory concentration (MIC) value via mixing microbes and antibiotics into droplet were conducted to proving its application potential for lab in a drop. Further research on a clinical pathogenic strain revealed that this technique could be potentially applied in the clinical laboratory for antibiotic susceptibility testing.
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Affiliation(s)
- Shenglong Liao
- Department of Chemistry, Renmin University of China , Beijing 100872, China
| | - Xinglei Tao
- Department of Chemistry, Renmin University of China , Beijing 100872, China
| | - Yingjiao Ju
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Yapei Wang
- Department of Chemistry, Renmin University of China , Beijing 100872, China
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41
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Ibarlucea B, Rim T, Baek CK, de Visser JAGM, Baraban L, Cuniberti G. Nanowire sensors monitor bacterial growth kinetics and response to antibiotics. LAB ON A CHIP 2017; 17:4283-4293. [PMID: 29119168 DOI: 10.1039/c7lc00807d] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Miniaturized and cost-efficient methods aiming at high throughput analysis of microbes are of great importance for the surveillance and control of infectious diseases and the related issue of antimicrobial resistance. Here we demonstrate a miniature nanosensor based on a honeycomb-patterned silicon nanowire field effect transistor (FET) capable of detection of bacterial growth and antibiotic response in microbiologically relevant nutrient media. We determine the growth kinetics and metabolic state of Escherichia coli cells in undiluted media via the quantification of changes in the source-drain current caused by varying pH values. Furthermore, by measuring the time dependent profile of pH change for bacterial cultures treated with antibiotics, we demonstrate for the first time the possibility of electrically distinguishing between bacteriostatic and bactericidal drug effects. We believe that the use of such nanoscopic FET devices enables addressing parameters that are not easily accessible by conventional optical methods in a label-free format, i.e. monitoring of microbial metabolic activity or stress response.
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Affiliation(s)
- B Ibarlucea
- Institute of Materials Science and Max Bergmann Center of Biomaterials, and, Center for Advancing Electronics Dresden (CfAED), Technische Universität Dresden, Budapester Str. 27, 01069, Dresden, Germany.
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42
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.Rainey PB, Remigi P, Farr AD, Lind PA. Darwin was right: where now for experimental evolution? Curr Opin Genet Dev 2017; 47:102-109. [DOI: 10.1016/j.gde.2017.09.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 01/02/2023]
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43
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Dressler OJ, Casadevall I Solvas X, deMello AJ. Chemical and Biological Dynamics Using Droplet-Based Microfluidics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:1-24. [PMID: 28375703 DOI: 10.1146/annurev-anchem-061516-045219] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Recent years have witnessed an increased use of droplet-based microfluidic techniques in a wide variety of chemical and biological assays. Nevertheless, obtaining dynamic data from these platforms has remained challenging, as this often requires reading the same droplets (possibly thousands of them) multiple times over a wide range of intervals (from milliseconds to hours). In this review, we introduce the elemental techniques for the formation and manipulation of microfluidic droplets, together with the most recent developments in these areas. We then discuss a wide range of analytical methods that have been successfully adapted for analyte detection in droplets. Finally, we highlight a diversity of studies where droplet-based microfluidic strategies have enabled the characterization of dynamic systems that would otherwise have remained unexplorable.
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Affiliation(s)
- Oliver J Dressler
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland;
| | | | - Andrew J deMello
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland;
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44
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Bleier BJ, Yezer BA, Freireich BJ, Anna SL, Walker LM. Droplet-based characterization of surfactant efficacy in colloidal stabilization of carbon black in nonpolar solvents. J Colloid Interface Sci 2017; 493:265-274. [DOI: 10.1016/j.jcis.2017.01.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 10/20/2022]
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45
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Davenport M, Mach KE, Shortliffe LMD, Banaei N, Wang TH, Liao JC. New and developing diagnostic technologies for urinary tract infections. Nat Rev Urol 2017; 14:296-310. [PMID: 28248946 PMCID: PMC5473291 DOI: 10.1038/nrurol.2017.20] [Citation(s) in RCA: 173] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Timely and accurate identification and determination of the antimicrobial susceptibility of uropathogens is central to the management of UTIs. Urine dipsticks are fast and amenable to point-of-care testing, but do not have adequate diagnostic accuracy or provide microbiological diagnosis. Urine culture with antimicrobial susceptibility testing takes 2-3 days and requires a clinical laboratory. The common use of empirical antibiotics has contributed to the rise of multidrug-resistant organisms, reducing treatment options and increasing costs. In addition to improved antimicrobial stewardship and the development of new antimicrobials, novel diagnostics are needed for timely microbial identification and determination of antimicrobial susceptibilities. New diagnostic platforms, including nucleic acid tests and mass spectrometry, have been approved for clinical use and have improved the speed and accuracy of pathogen identification from primary cultures. Optimization for direct urine testing would reduce the time to diagnosis, yet these technologies do not provide comprehensive information on antimicrobial susceptibility. Emerging technologies including biosensors, microfluidics, and other integrated platforms could improve UTI diagnosis via direct pathogen detection from urine samples, rapid antimicrobial susceptibility testing, and point-of-care testing. Successful development and implementation of these technologies has the potential to usher in an era of precision medicine to improve patient care and public health.
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Affiliation(s)
- Michael Davenport
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
| | - Kathleen E Mach
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
| | - Linda M Dairiki Shortliffe
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Avenue, Palo Alto, California 94304 USA
| | - Tza-Huei Wang
- Departments of Mechanical and Biomedical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA
| | - Joseph C Liao
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
- Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, California 94304 USA
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46
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Lee WB, Fu CY, Chang WH, You HL, Wang CH, Lee MS, Lee GB. A microfluidic device for antimicrobial susceptibility testing based on a broth dilution method. Biosens Bioelectron 2017; 87:669-678. [DOI: 10.1016/j.bios.2016.09.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/25/2016] [Accepted: 09/01/2016] [Indexed: 10/21/2022]
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47
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Doméjean H, de la Motte Saint Pierre M, Funfak A, Atrux-Tallau N, Alessandri K, Nassoy P, Bibette J, Bremond N. Controlled production of sub-millimeter liquid core hydrogel capsules for parallelized 3D cell culture. LAB ON A CHIP 2016; 17:110-119. [PMID: 27869911 DOI: 10.1039/c6lc00848h] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Liquid core capsules having a hydrogel membrane are becoming a versatile tool for three-dimensional culture of micro-organisms and mammalian cells. Making sub-millimeter capsules at a high rate, via the breakup of a compound jet in air, opens the way to high-throughput screening applications. However, control of the capsule size monodispersity, especially required for quantitative bioassays, was still lacking. Here, we report how the understanding of the underlying hydrodynamic instabilities that occur during the process can lead to calibrated core-shell bioreactors. The requirements are: i) damping the shear layer instability that develops inside the injector arising from the co-annular flow configuration of liquid phases having contrasting viscoelastic properties; ii) controlling the capillary instability of the compound jet by superposing a harmonic perturbation onto the shell flow; iii) avoiding coalescence of drops during jet fragmentation as well as during drop flight towards the gelling bath; iv) ensuring proper engulfment of the compound drops into the gelling bath for building a closed hydrogel shell. We end up with the creation of numerous identical compartments in which cells are able to form multicellular aggregates, namely spheroids. In addition, we implement an intermediate composite hydrogel layer, composed of alginate and collagen, allowing cell adhesion and thus the formation of epithelia or monolayers of cells.
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Affiliation(s)
- Hugo Doméjean
- Laboratoire Colloïdes et Matériaux Divisés, CNRS, Chemistry Biology & Innovation, ESPCI Paris, PSL Research University, 10 Rue Vauquelin, F-75005 Paris, France.
| | - Mathieu de la Motte Saint Pierre
- Laboratoire Colloïdes et Matériaux Divisés, CNRS, Chemistry Biology & Innovation, ESPCI Paris, PSL Research University, 10 Rue Vauquelin, F-75005 Paris, France.
| | - Anette Funfak
- Laboratoire Colloïdes et Matériaux Divisés, CNRS, Chemistry Biology & Innovation, ESPCI Paris, PSL Research University, 10 Rue Vauquelin, F-75005 Paris, France.
| | - Nicolas Atrux-Tallau
- Laboratoire Colloïdes et Matériaux Divisés, CNRS, Chemistry Biology & Innovation, ESPCI Paris, PSL Research University, 10 Rue Vauquelin, F-75005 Paris, France.
| | - Kevin Alessandri
- LP2N, Université de Bordeaux, F-33400 Talence, France and LP2N, UMR 5298, Institut d'Optique & CNRS, F-33400 Talence, France
| | - Pierre Nassoy
- LP2N, Université de Bordeaux, F-33400 Talence, France and LP2N, UMR 5298, Institut d'Optique & CNRS, F-33400 Talence, France
| | - Jérôme Bibette
- Laboratoire Colloïdes et Matériaux Divisés, CNRS, Chemistry Biology & Innovation, ESPCI Paris, PSL Research University, 10 Rue Vauquelin, F-75005 Paris, France.
| | - Nicolas Bremond
- Laboratoire Colloïdes et Matériaux Divisés, CNRS, Chemistry Biology & Innovation, ESPCI Paris, PSL Research University, 10 Rue Vauquelin, F-75005 Paris, France.
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48
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Horka M, Sun S, Ruszczak A, Garstecki P, Mayr T. Lifetime of Phosphorescence from Nanoparticles Yields Accurate Measurement of Concentration of Oxygen in Microdroplets, Allowing One To Monitor the Metabolism of Bacteria. Anal Chem 2016; 88:12006-12012. [DOI: 10.1021/acs.analchem.6b03758] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Michał Horka
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Shiwen Sun
- Institute
of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse9/2, 8010 Graz, Austria
| | - Artur Ruszczak
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Piotr Garstecki
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Torsten Mayr
- Institute
of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse9/2, 8010 Graz, Austria
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49
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Chen Z, Li W, Choi G, Yang X, Miao J, Cui L, Guan W. Arbitrarily Accessible 3D Microfluidic Device for Combinatorial High-Throughput Drug Screening. SENSORS (BASEL, SWITZERLAND) 2016; 16:E1616. [PMID: 27690055 PMCID: PMC5087404 DOI: 10.3390/s16101616] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 09/19/2016] [Accepted: 09/23/2016] [Indexed: 12/30/2022]
Abstract
Microfluidics-based drug-screening systems have enabled efficient and high-throughput drug screening, but their routine uses in ordinary labs are limited due to the complexity involved in device fabrication and system setup. In this work, we report an easy-to-use and low-cost arbitrarily accessible 3D microfluidic device that can be easily adopted by various labs to perform combinatorial assays for high-throughput drug screening. The device is capable of precisely performing automatic and simultaneous reagent loading and aliquoting tasks and performing multistep assays with arbitrary sequences. The device is not intended to compete with other microfluidic technologies regarding ultra-low reaction volume. Instead, its freedom from tubing or pumping systems and easy operation makes it an ideal platform for routine high-throughput drug screening outside traditional microfluidic labs. The functionality and quantitative reliability of the 3D microfluidic device were demonstrated with a histone acetyltransferase-based drug-screening assay using the recombinant Plasmodium falciparum GCN5 enzyme, benchmarked with a traditional microtiter plate-based method. This arbitrarily accessible, multistep capable, low-cost, and easy-to-use device can be widely adopted in various combinatorial assays beyond high-throughput drug screening.
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Affiliation(s)
- Zhuofa Chen
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
| | - Weizhi Li
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Gihoon Choi
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
| | - Xiaonan Yang
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
| | - Jun Miao
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Liwang Cui
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
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50
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Jepson AK, Schwarz-Linek J, Ryan L, Ryadnov MG, Poon WCK. What Is the 'Minimum Inhibitory Concentration' (MIC) of Pexiganan Acting on Escherichia coli?-A Cautionary Case Study. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 915:33-48. [PMID: 27193536 DOI: 10.1007/978-3-319-32189-9_4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
We measured the minimum inhibitory concentration (MIC) of the antimicrobial peptide pexiganan acting on Escherichia coli , and found an intrinsic variability in such measurements. These results led to a detailed study of the effect of pexiganan on the growth curve of E. coli, using a plate reader and manual plating (i.e. time-kill curves). The measured growth curves, together with single-cell observations and peptide depletion assays, suggested that addition of a sub-MIC concentration of pexiganan to a population of this bacterium killed a fraction of the cells, reducing peptide activity during the process, while leaving the remaining cells unaffected. This pharmacodynamic hypothesis suggests a considerable inoculum effect, which we quantified. Our results cast doubt on the use of the MIC as 'a measure of the concentration needed for peptide action' and show how 'coarse-grained' studies at the population level give vital information for the correct planning and interpretation of MIC measurements.
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Affiliation(s)
- Alys K Jepson
- SUPA and School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, Scotland, UK
| | - Jana Schwarz-Linek
- SUPA and School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, Scotland, UK
| | - Lloyd Ryan
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Wilson C K Poon
- SUPA and School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, Scotland, UK.
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