1
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Perchikov R, Cheliukanov M, Plekhanova Y, Tarasov S, Kharkova A, Butusov D, Arlyapov V, Nakamura H, Reshetilov A. Microbial Biofilms: Features of Formation and Potential for Use in Bioelectrochemical Devices. BIOSENSORS 2024; 14:302. [PMID: 38920606 PMCID: PMC11201457 DOI: 10.3390/bios14060302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 06/27/2024]
Abstract
Microbial biofilms present one of the most widespread forms of life on Earth. The formation of microbial communities on various surfaces presents a major challenge in a variety of fields, including medicine, the food industry, shipping, etc. At the same time, this process can also be used for the benefit of humans-in bioremediation, wastewater treatment, and various biotechnological processes. The main direction of using electroactive microbial biofilms is their incorporation into the composition of biosensor and biofuel cells This review examines the fundamental knowledge acquired about the structure and formation of biofilms, the properties they have when used in bioelectrochemical devices, and the characteristics of the formation of these structures on different surfaces. Special attention is given to the potential of applying the latest advances in genetic engineering in order to improve the performance of microbial biofilm-based devices and to regulate the processes that take place within them. Finally, we highlight possible ways of dealing with the drawbacks of using biofilms in the creation of highly efficient biosensors and biofuel cells.
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Affiliation(s)
- Roman Perchikov
- Federal State Budgetary Educational Institution of Higher Education, Tula State University, Tula 300012, Russia; (R.P.); (M.C.); (A.K.); (V.A.)
| | - Maxim Cheliukanov
- Federal State Budgetary Educational Institution of Higher Education, Tula State University, Tula 300012, Russia; (R.P.); (M.C.); (A.K.); (V.A.)
| | - Yulia Plekhanova
- Federal Research Center (Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia; (Y.P.); (S.T.)
| | - Sergei Tarasov
- Federal Research Center (Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia; (Y.P.); (S.T.)
| | - Anna Kharkova
- Federal State Budgetary Educational Institution of Higher Education, Tula State University, Tula 300012, Russia; (R.P.); (M.C.); (A.K.); (V.A.)
| | - Denis Butusov
- Computer-Aided Design Department, Saint Petersburg Electrotechnical University “LETI”, Saint Petersburg 197022, Russia;
| | - Vyacheslav Arlyapov
- Federal State Budgetary Educational Institution of Higher Education, Tula State University, Tula 300012, Russia; (R.P.); (M.C.); (A.K.); (V.A.)
| | - Hideaki Nakamura
- Department of Liberal Arts, Tokyo University of Technology, 1404-1 Katakura, Hachioji 192-0982, Tokyo, Japan;
| | - Anatoly Reshetilov
- Federal Research Center (Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia; (Y.P.); (S.T.)
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2
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Li X, Zhang Y, Hu X, Nie C, Li W, Ding Y, Chen H. A study on urinary tract infections based on a chemotactic microfluidic device. Minerva Gastroenterol (Torino) 2024; 70:268-270. [PMID: 37232144 DOI: 10.23736/s2724-5985.23.03387-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Xun Li
- Laboratory of Medicine, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, China
| | - Yuanyuan Zhang
- Laboratory of Medicine, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, China
| | - Xiefei Hu
- Chongqing University Central Hospital, Chongqing, China
| | - Cui Nie
- Laboratory of Medicine, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, China
| | - Wei Li
- Laboratory of Medicine, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, China
| | - Yan Ding
- Laboratory of Medicine, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, China
| | - Huajian Chen
- Laboratory of Medicine, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, China -
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3
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Jeong Y, Ahmad S, Irudayaraj J. Dynamic Effect of β-Lactam Antibiotic Inactivation Due to the Inter- and Intraspecies Interaction of Drug-Resistant Microbes. ACS Biomater Sci Eng 2024; 10:1461-1472. [PMID: 38315631 PMCID: PMC10936524 DOI: 10.1021/acsbiomaterials.3c01678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/07/2024]
Abstract
The presence of β-lactamase positive microorganisms imparts a pharmacological effect on a variety of organisms that can impact drug efficacy by influencing the function or composition of bacteria. Although studies to assess dynamic intra- and interspecies communication with bacterial communities exist, the efficacy of drug treatment and quantitative assessment of multiorganism response is not well understood due to the lack of technological advances that can be used to study coculture interactions in a dynamic format. In this study, we investigate how β-lactamase positive microorganisms can neutralize the effect of β-lactam antibiotics in a dynamic format at the inter- and intraspecies level using microbial bead technology. Three interactive models for the biological compartmentalization of organisms were demonstrated to evaluate the effect of β-lactam antibiotics on coculture systems. Our model at the intraspecies level attempts to mimic the biofilm matrix more closely as a community-level feature of microorganisms, which acknowledges the impact of nondrug-resistant species in shaping the dynamic response. In particular, the results of intraspecies studies are highly supportive of the biofilm mode of bacterial growth, which can provide structural support and protect the bacteria from an assault on host or environmental factors. Our findings also indicate that β-lactamase positive bacteria can neutralize the cytotoxic effect of β-lactam antibiotics at the interspecies level when cocultured with cancer cells. Results were validated using β-lactamase positive bacteria isolated from environmental niches, which can trigger phenotypical alteration of β-lactams when cocultured with other organisms. Our compartmentalization strategy acts as an independent ecosystem and provides a new avenue for multiscale studies to assess intra- and interspecies interactions.
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Affiliation(s)
- Yoon Jeong
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
- Cancer
Center at Illinois, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, Illinois 61801, United States
| | - Saeed Ahmad
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, Illinois 61801, United States
| | - Joseph Irudayaraj
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
- Cancer
Center at Illinois, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
- Biomedical
Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, Illinois 61801, United States
- Carle
R. Woese Institute for Genomic Biology, Beckman Institute, Urbana, Illinois 61801, United States
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4
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Heuberger L, Messmer D, dos Santos EC, Scherrer D, Lörtscher E, Schoenenberger C, Palivan CG. Microfluidic Giant Polymer Vesicles Equipped with Biopores for High-Throughput Screening of Bacteria. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307103. [PMID: 38158637 PMCID: PMC10953582 DOI: 10.1002/advs.202307103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Indexed: 01/03/2024]
Abstract
Understanding the mechanisms of antibiotic resistance is critical for the development of new therapeutics. Traditional methods for testing bacteria are often limited in their efficiency and reusability. Single bacterial cells can be studied at high throughput using double emulsions, although the lack of control over the oil shell permeability and limited access to the droplet interior present serious drawbacks. Here, a straightforward strategy for studying bacteria-encapsulating double emulsion-templated giant unilamellar vesicles (GUVs) is introduced. This microfluidic approach serves to simultaneously load bacteria inside synthetic GUVs and to permeabilize their membrane with the pore-forming peptide melittin. This enables antibiotic delivery or the influx of fresh medium into the GUV lumen for highly parallel cultivation and antimicrobial efficacy testing. Polymer-based GUVs proved to be efficient culture and analysis microvessels, as microfluidics allow easy selection and encapsulation of bacteria and rapid modification of culture conditions for antibiotic development. Further, a method for in situ profiling of biofilms within GUVs for high-throughput screening is demonstrated. Conceivably, synthetic GUVs equipped with biopores can serve as a foundation for the high-throughput screening of bacterial colony interactions during biofilm formation and for investigating the effect of antibiotics on biofilms.
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Affiliation(s)
- Lukas Heuberger
- Department of ChemistryUniversity of BaselMattenstrasse 22Basel4002Switzerland
| | - Daniel Messmer
- Department of ChemistryUniversity of BaselMattenstrasse 22Basel4002Switzerland
| | - Elena C. dos Santos
- Department of ChemistryUniversity of BaselMattenstrasse 22Basel4002Switzerland
| | - Dominik Scherrer
- IBM Research Europe–ZürichSäumerstrasse 4Rüschlikon8803Switzerland
| | - Emanuel Lörtscher
- IBM Research Europe–ZürichSäumerstrasse 4Rüschlikon8803Switzerland
- NCCR‐Molecular Systems EngineeringMattenstrasse 24a, BPR 1095Basel4058Switzerland
| | | | - Cornelia G. Palivan
- Department of ChemistryUniversity of BaselMattenstrasse 22Basel4002Switzerland
- NCCR‐Molecular Systems EngineeringMattenstrasse 24a, BPR 1095Basel4058Switzerland
- Swiss Nanoscience Institute (SNI)University of BaselKlingelbergstrasse 82Basel4056Switzerland
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Zoheir AE, Stolle C, Rabe KS. Microfluidics for adaptation of microorganisms to stress: design and application. Appl Microbiol Biotechnol 2024; 108:162. [PMID: 38252163 PMCID: PMC10803453 DOI: 10.1007/s00253-024-13011-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/22/2023] [Accepted: 01/11/2024] [Indexed: 01/23/2024]
Abstract
Microfluidic systems have fundamentally transformed the realm of adaptive laboratory evolution (ALE) for microorganisms by offering unparalleled control over environmental conditions, thereby optimizing mutant generation and desired trait selection. This review summarizes the substantial influence of microfluidic technologies and their design paradigms on microbial adaptation, with a primary focus on leveraging spatial stressor concentration gradients to enhance microbial growth in challenging environments. Specifically, microfluidic platforms tailored for scaled-down ALE processes not only enable highly autonomous and precise setups but also incorporate novel functionalities. These capabilities encompass fostering the growth of biofilms alongside planktonic cells, refining selection gradient profiles, and simulating adaptation dynamics akin to natural habitats. The integration of these aspects enables shaping phenotypes under pressure, presenting an unprecedented avenue for developing robust, stress-resistant strains, a feat not easily attainable using conventional ALE setups. The versatility of these microfluidic systems is not limited to fundamental research but also offers promising applications in various areas of stress resistance. As microfluidic technologies continue to evolve and merge with cutting-edge methodologies, they possess the potential not only to redefine the landscape of microbial adaptation studies but also to expedite advancements in various biotechnological areas. KEY POINTS: • Microfluidics enable precise microbial adaptation in controlled gradients. • Microfluidic ALE offers insights into stress resistance and distinguishes between resistance and persistence. • Integration of adaptation-influencing factors in microfluidic setups facilitates efficient generation of stress-resistant strains.
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Affiliation(s)
- Ahmed E Zoheir
- Department of Genetics and Cytology, Biotechnology Research Institute, National Research Centre (NRC), 33 El Buhouth St., Dokki, Cairo, 12622, Egypt
| | - Camilla Stolle
- Institute for Biological Interfaces 1 (IBG-1), Biomolecular Micro- and Nanostructures, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Institute for Biological Interfaces 1 (IBG-1), Biomolecular Micro- and Nanostructures, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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6
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Ardila CM, Jiménez-Arbeláez GA, Vivares-Builes AM. The Potential Clinical Applications of a Microfluidic Lab-on-a-Chip for the Identification and Antibiotic Susceptibility Testing of Enterococcus faecalis-Associated Endodontic Infections: A Systematic Review. Dent J (Basel) 2023; 12:5. [PMID: 38248213 PMCID: PMC10814515 DOI: 10.3390/dj12010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/12/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024] Open
Abstract
This systematic review evaluated the potential clinical use of microfluidic lab-on-a-chip (LOC) technology in the identification and antibiotic susceptibility testing of E. faecalis in endodontic infections. The search methodology employed in this review adhered to the PRISMA guidelines. Multiple scientific databases, including PubMed/MEDLINE, SCOPUS, and SCIELO, were utilized, along with exploration of grey literature sources. Up to September 2023, these resources were searched using specific keywords and MeSH terms. An initial comprehensive search yielded 202 articles. Ultimately, this systematic review incorporated 12 studies. Out of these, seven aimed to identify E. faecalis, while the remaining five evaluated its susceptibility to different antibiotics. All studies observed that the newly developed microfluidic chip significantly reduces detection time compared to traditional methods. This enhanced speed is accompanied by a high degree of accuracy, efficiency, and sensitivity. Most research findings indicated that the entire process took anywhere from less than an hour to five hours. It is important to note that this approach bypasses the need for minimum inhibitory concentration measurements, as it does not rely on traditional methodologies. Microfluidic devices enable the rapid identification and accurate antimicrobial susceptibility testing of E. faecalis, which are crucial for timely diagnosis and treatment in endodontic infections.
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Affiliation(s)
- Carlos M. Ardila
- Basic Studies Department, School of Dentistry, Universidad de Antioquia UdeA, Medellín 050010, Colombia
| | - Gustavo A. Jiménez-Arbeláez
- School of Dentistry, University Institution Visión de Las Américas, Medellín 050031, Colombia; (G.A.J.-A.); (A.M.V.-B.)
| | - Annie Marcela Vivares-Builes
- School of Dentistry, University Institution Visión de Las Américas, Medellín 050031, Colombia; (G.A.J.-A.); (A.M.V.-B.)
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7
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Childs SK, Jones AAD. A microtiter peg lid with ziggurat geometry for medium-throughput antibiotic testing and in situ imaging of biofilms. Biofilm 2023; 6:100167. [PMID: 38078058 PMCID: PMC10700155 DOI: 10.1016/j.bioflm.2023.100167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 01/12/2024] Open
Abstract
Bacteria biofilm responses to disinfectants and antibiotics are quantified and observed using multiple methods, though microscopy, particularly confocal laser scanning microscopy (CLSM) is preferred due to speed, a reduction in user error, and in situ analysis. CLSM can resolve biological and spatial heterogeneity of biofilms in 3D with limited throughput. The microplate peg-lid-based assay, described in ASTM E2799-22, is a medium-throughput method for testing biofilms but does not permit in situ imaging. Breaking off the peg, as recommended by the manufacturer, risks sample damage, and is limited to easily accessible pegs. Here we report modifications to the peg optimized for in situ visualization and visualization of all pegs. We report similar antibiotic challenge recovery via colony formation following the ASTM E2799-22 protocol and in situ imaging. We report novel quantifiable effects of antibiotics on biofilm morphologies, specifically biofilm streamers. The new design bridges the MBEC® assays design that selects for biofilm phenotypes with in situ imaging needs.
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Affiliation(s)
| | - A-Andrew D. Jones
- Department of Civil & Environmental Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
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8
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Zhang Y, Young P, Traini D, Li M, Ong HX, Cheng S. Challenges and current advances in in vitro biofilm characterization. Biotechnol J 2023; 18:e2300074. [PMID: 37477959 DOI: 10.1002/biot.202300074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/22/2023]
Abstract
Biofilms are structured communities of bacterial cells encased in a self-produced polymeric matrix, which develop over time and exhibit temporal responses to stimuli from internal biological processes or external environmental changes. They can be detrimental, threatening public health and causing economic loss, while they also play beneficial roles in ecosystem health, biotechnology processes, and industrial settings. Biofilms express extreme heterogeneity in their physical properties and structural composition, resulting in critical challenges in understanding them comprehensively. The lack of detailed knowledge of biofilms and their phenotypes has deterred significant progress in developing strategies to control their negative impacts and take advantage of their beneficial applications. A range of in vitro models and characterization tools have been developed and used to study biofilm growth and, specifically, to investigate the impact of environmental and growth factors on their development. This review article discusses the existing knowledge of biofilm properties and explains how external factors, such as flow condition, surface, interface, and host factor, may impact biofilm growth. The limitations of current tools, techniques, and in vitro models that are currently used for biofilms are also presented.
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Affiliation(s)
- Ye Zhang
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia
- Woolcock Institute of Medical Research, Sydney, New South Wales, Australia
| | - Paul Young
- Woolcock Institute of Medical Research, Sydney, New South Wales, Australia
- Department of Marketing, Macquarie Business School, Macquarie University, Sydney, New South Wales, Australia
| | - Daniela Traini
- Woolcock Institute of Medical Research, Sydney, New South Wales, Australia
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Ming Li
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Hui Xin Ong
- Woolcock Institute of Medical Research, Sydney, New South Wales, Australia
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Shaokoon Cheng
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia
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9
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Ardila CM, Jiménez-Arbeláez GA, Vivares-Builes AM. A Systematic Review of In Vitro Studies Using Microchip Platforms for Identifying Periodontopathogens from the Red Complex. Dent J (Basel) 2023; 11:245. [PMID: 37999009 PMCID: PMC10670886 DOI: 10.3390/dj11110245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/06/2023] [Accepted: 10/20/2023] [Indexed: 11/25/2023] Open
Abstract
Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola, collectively recognized as periodontopathogens within the red complex, have been extensively studied in clinical samples collected from individuals with periodontitis. A lab-on-a-chip (LOC) is a miniature mechanism that integrates various laboratory operations onto a single microchip or a small-scale platform. This systematic review evaluates the application of LOC technology in identifying microorganisms from the red complex. This study adhered to PRISMA recommendations, and the review process encompassed several databases. In the electronic search, a total of 58 reports were found, and ultimately, 10 studies were considered relevant for inclusion. All these studies described effective, rapid, and reliable LOC systems for detecting and amplifying P. gingivalis, T. forsythia, and T. denticola. Compared to traditional methods, the LOC approach demonstrated minimal reagent requirements. Additionally, the results indicated that the amplification process took approximately 2 to 8 min, while detection could be completed in as little as 2 min and 40 s, resulting in a total experimental duration of around 11 min. Integrating miniaturization, speed, accuracy, and automation within microchip platforms makes them promising tools for detecting and amplifying microorganisms associated with the red complex in periodontal diseases.
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Affiliation(s)
- Carlos M. Ardila
- Basic Studies Department, School of Dentistry, Universidad de Antioquia UdeA, Medellín 050010, Colombia
| | - Gustavo A. Jiménez-Arbeláez
- School of Dentistry, Institución Universitaria Visión de Las Américas, Medellín 050031, Colombia; (G.A.J.-A.); (A.M.V.-B.)
| | - Annie Marcela Vivares-Builes
- School of Dentistry, Institución Universitaria Visión de Las Américas, Medellín 050031, Colombia; (G.A.J.-A.); (A.M.V.-B.)
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10
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Ardila CM, Zuluaga-Gómez M, Vivares-Builes AM. Applications of Lab on a Chip in Antimicrobial Susceptibility of Staphylococcus aureus: A Systematic Review. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1719. [PMID: 37893437 PMCID: PMC10608121 DOI: 10.3390/medicina59101719] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023]
Abstract
Background and Objectives: Staphylococcus aureus is a prevalent bacterium capable of inducing various infections, including skin and soft tissue infections, bloodstream infections, pneumonia, and surgical site infections. The emergence of antimicrobial resistance in S. aureus, particularly methicillin-resistant S. aureus, has raised substantial concerns within global healthcare settings. Prior to antibiotic prescription, the ideal approach is antimicrobial susceptibility testing (AST); however, this is frequently perceived as excessively complex and time-intensive. Lab-on-a-chip (LOC) technology holds promise in addressing these challenges and advancing fundamental microbiological research while also aiding in the development of therapeutic strategies. This systematic review aims to evaluate the potential utility of LOC for AST of S. aureus. Materials and Methods: This study adhered to the PRISMA guidelines. Various databases, including SCOPUS, PubMed/MEDLINE, SCIELO, and LILACS, in addition to gray literature sources, were employed in the review process. Results: Sixteen studies were included in this systematic review. All these studies detailed the effectiveness, rapidity, and predictability of LOC systems for assessing S. aureus susceptibility to various antibiotics. When comparing the LOC approach to traditional manual methods, it was evident that LOC requires a minimal quantity of reagents. Furthermore, most studies reported that the entire LOC procedure took 10 min to 7 h, with results being equally accurate as those obtained through traditional AST protocols. Conclusions: The potential application of LOC for AST of S. aureus is emphasized by its ability to provide rapid access to minimum inhibitory concentration data, which can substantially aid in selecting the most suitable antibiotics and dosages for treating challenging infections caused by this microorganism. Moreover, the rapid AST facilitated by LOC holds promise for enhancing the appropriateness and efficacy of therapy in clinical settings.
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Affiliation(s)
- Carlos M. Ardila
- Basic Studies Department, School of Dentistry, Universidad de Antioquia UdeA, Medellín 050010, Colombia
| | - Mateo Zuluaga-Gómez
- Emergency Department, Universidad Pontificia Bolivariana, Medellín 050010, Colombia;
- Hospital San Vicente Fundación, Rionegro 054047, Colombia
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11
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Bhattacharyya A, Mavrodi O, Bhowmik N, Weller D, Thomashow L, Mavrodi D. Bacterial biofilms as an essential component of rhizosphere plant-microbe interactions. METHODS IN MICROBIOLOGY 2023; 53:3-48. [PMID: 38415193 PMCID: PMC10898258 DOI: 10.1016/bs.mim.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Affiliation(s)
- Ankita Bhattacharyya
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Olga Mavrodi
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Niladri Bhowmik
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - David Weller
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Linda Thomashow
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Dmitri Mavrodi
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
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12
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Yuan L, Straub H, Shishaeva L, Ren Q. Microfluidics for Biofilm Studies. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:139-159. [PMID: 37314876 DOI: 10.1146/annurev-anchem-091522-103827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Biofilms are multicellular communities held together by a self-produced extracellular matrix and exhibit a set of properties that distinguish them from free-living bacteria. Biofilms are exposed to a variety of mechanical and chemical cues resulting from fluid motion and mass transport. Microfluidics provides the precise control of hydrodynamic and physicochemical microenvironments to study biofilms in general. In this review, we summarize the recent progress made in microfluidics-based biofilm research, including understanding the mechanism of bacterial adhesion and biofilm development, assessment of antifouling and antimicrobial properties, development of advanced in vitro infection models, and advancement in methods to characterize biofilms. Finally, we provide a perspective on the future direction of microfluidics-assisted biofilm research.
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Affiliation(s)
- Lu Yuan
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China;
| | - Hervé Straub
- Laboratory for Biointerfaces, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland;
| | - Liubov Shishaeva
- Laboratory for Biointerfaces, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland;
| | - Qun Ren
- Laboratory for Biointerfaces, Empa, Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland;
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13
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Hervas-Raluy S, Wirthl B, Guerrero PE, Robalo Rei G, Nitzler J, Coronado E, Font de Mora Sainz J, Schrefler BA, Gomez-Benito MJ, Garcia-Aznar JM, Wall WA. Tumour growth: An approach to calibrate parameters of a multiphase porous media model based on in vitro observations of Neuroblastoma spheroid growth in a hydrogel microenvironment. Comput Biol Med 2023; 159:106895. [PMID: 37060771 DOI: 10.1016/j.compbiomed.2023.106895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/09/2023] [Accepted: 04/09/2023] [Indexed: 04/17/2023]
Abstract
To unravel processes that lead to the growth of solid tumours, it is necessary to link knowledge of cancer biology with the physical properties of the tumour and its interaction with the surrounding microenvironment. Our understanding of the underlying mechanisms is however still imprecise. We therefore developed computational physics-based models, which incorporate the interaction of the tumour with its surroundings based on the theory of porous media. However, the experimental validation of such models represents a challenge to its clinical use as a prognostic tool. This study combines a physics-based model with in vitro experiments based on microfluidic devices used to mimic a three-dimensional tumour microenvironment. By conducting a global sensitivity analysis, we identify the most influential input parameters and infer their posterior distribution based on Bayesian calibration. The resulting probability density is in agreement with the scattering of the experimental data and thus validates the proposed workflow. This study demonstrates the huge challenges associated with determining precise parameters with usually only limited data for such complex processes and models, but also demonstrates in general how to indirectly characterise the mechanical properties of neuroblastoma spheroids that cannot feasibly be measured experimentally.
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Affiliation(s)
- Silvia Hervas-Raluy
- Multiscale in Mechanical and Biological Engineering, Department of Mechanical Engineering, University of Zaragoza, Aragon Institute for Engineering Research (I3A), Maria de Luna 3, Zaragoza, 50018, Spain.
| | - Barbara Wirthl
- Institute for Computational Mechanics, Technical University of Munich, TUM School of Engineering and Design, Department of Engineering Physics & Computation, Boltzmannstraße 15, Garching b. Munich, 85748, Germany
| | - Pedro E Guerrero
- Multiscale in Mechanical and Biological Engineering, Department of Mechanical Engineering, University of Zaragoza, Aragon Institute for Engineering Research (I3A), Maria de Luna 3, Zaragoza, 50018, Spain
| | - Gil Robalo Rei
- Institute for Computational Mechanics, Technical University of Munich, TUM School of Engineering and Design, Department of Engineering Physics & Computation, Boltzmannstraße 15, Garching b. Munich, 85748, Germany
| | - Jonas Nitzler
- Institute for Computational Mechanics, Technical University of Munich, TUM School of Engineering and Design, Department of Engineering Physics & Computation, Boltzmannstraße 15, Garching b. Munich, 85748, Germany; Professorship for Data-Driven Materials Modeling, Technical University of Munich, TUM School of Engineering and Design, Department of Engineering Physics & Computation, Boltzmannstraße 15, Garching b. Munich, 85748, Germany
| | - Esther Coronado
- Clinical and Translational Oncology Research Group, Instituto de Investigación La Fe,, Fernando Abril Martorell 106, Valencia, 46026, Spain
| | - Jaime Font de Mora Sainz
- Clinical and Translational Oncology Research Group, Instituto de Investigación La Fe,, Fernando Abril Martorell 106, Valencia, 46026, Spain
| | - Bernhard A Schrefler
- Department of Civil, Environmental and Architectural Engineering, University of Padua, Marzolo 9, Padua, 35131, Italy; Institute for Advanced Study, Technical University of Munich, Boltzmannstraße 15, Garching b. Munich, 85748, Germany
| | - Maria Jose Gomez-Benito
- Multiscale in Mechanical and Biological Engineering, Department of Mechanical Engineering, University of Zaragoza, Aragon Institute for Engineering Research (I3A), Maria de Luna 3, Zaragoza, 50018, Spain
| | - Jose Manuel Garcia-Aznar
- Multiscale in Mechanical and Biological Engineering, Department of Mechanical Engineering, University of Zaragoza, Aragon Institute for Engineering Research (I3A), Maria de Luna 3, Zaragoza, 50018, Spain
| | - Wolfgang A Wall
- Institute for Computational Mechanics, Technical University of Munich, TUM School of Engineering and Design, Department of Engineering Physics & Computation, Boltzmannstraße 15, Garching b. Munich, 85748, Germany
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14
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Zhang Y, Gholizadeh H, Young P, Traini D, Li M, Ong HX, Cheng S. Real-time in-situ electrochemical monitoring of Pseudomonas aeruginosa biofilms grown on air-liquid interface and its antibiotic susceptibility using a novel dual-chamber microfluidic device. Biotechnol Bioeng 2023; 120:702-714. [PMID: 36408870 DOI: 10.1002/bit.28288] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 11/08/2022] [Accepted: 11/12/2022] [Indexed: 11/22/2022]
Abstract
Biofilms are communities of bacterial cells encased in a self-produced polymeric matrix that exhibit high tolerance toward environmental stress. Despite the plethora of research on biofilms, most P. aeruginosa biofilm models are cultured on a solid-liquid interface, and the longitudinal growth characteristics of P. aeruginosa biofilm are unclear. This study demonstrates the real-time and noninvasive monitoring of biofilm growth using a novel dual-chamber microfluidic device integrated with electrochemical detection capabilities to monitor pyocyanin (PYO). The growth of P. aeruginosa biofilms on the air-liquid interface (ALI) was monitored over 48 h, and its antibiotic susceptibility to 6 h exposure of 50, 400, and 1600 µg/ml of ciprofloxacin solutions was analyzed. The biofilm was treated directly on its surface and indirectly from the substratum by delivering the CIP solution to the top or bottom chamber of the microfluidic device. Results showed that P. aeruginosa biofilm developed on ALI produces PYO continuously, with the PYO production rate varying longitudinally and peak production observed between 24 and 30 h. In addition, this current study shows that the amount of PYO produced by the ALI biofilm is proportional to its viable cell numbers, which has not been previously demonstrated. Biofilm treated with ciprofloxacin solution above 400 µg/ml showed significant PYO reduction, with biofilms being killed more effectively when treatment was applied to their surfaces. The electrochemical measurement results have been verified with colony-forming unit count results, and the strong correlation between the PYO electrical signal and the viable cell number highlights the usefulness of this approach for fast and low-cost ALI biofilm study and antimicrobial tests.
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Affiliation(s)
- Ye Zhang
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia.,Woolcock Institute of Medical Research, Sydney, New South Wales, Australia
| | - Hanieh Gholizadeh
- Woolcock Institute of Medical Research, Sydney, New South Wales, Australia.,Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Paul Young
- Woolcock Institute of Medical Research, Sydney, New South Wales, Australia.,Department of Marketing, Macquarie Business School, Macquarie University, Sydney, New South Wales, Australia
| | - Daniela Traini
- Woolcock Institute of Medical Research, Sydney, New South Wales, Australia.,Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Ming Li
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Hui Xin Ong
- Woolcock Institute of Medical Research, Sydney, New South Wales, Australia.,Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Shaokoon Cheng
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia
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15
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Li Y, Yao H, Chen S, Xu N, Lin JM. Effect of Tryptophan Metabolites on Cell Damage Revealed by Bacteria-Cell Interactions in Hydrogel Microspheres. Anal Chem 2023; 95:1402-1408. [PMID: 36595555 DOI: 10.1021/acs.analchem.2c04355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
This work presented an alternative approach for studying bacteria-cell interactions in three-dimensional (3D) hydrogel microspheres formed by the cross-linking reaction of alginate and calcium-ethylenediaminetetraacetic acid (EDTA-Ca) produced in a microfluidic chip. During the co-culture process of hepatocytes (HepG2) and Escherichia coli (E. coli) 25922, we concluded that the content change of tryptophan metabolites detected via ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was related to the cell damage level and the change of interleukin (IL-22) detected by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) was related to the ways of co-cultivation. Compared to the two-dimensional (2D) adherent cell culture process in a Petri dish (2D), the co-culture process of HepG2 and E. coli 25922 in hydrogel microspheres indicated more information about metabolism such as the appearance of indole-3-propionic acid (IPA) and possibly IL-22. The method provides a new perspective to investigate the bacteria-cell interaction and it could be a promising tool in the study of gut microbiota and human health.
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Affiliation(s)
- Yuxuan Li
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Hongren Yao
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Shulang Chen
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Ning Xu
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
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16
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Sun Y, Zhang F, Li L, Chen K, Wang S, Ouyang Q, Luo C. Two-Layered Microfluidic Devices for High-Throughput Dynamic Analysis of Synthetic Gene Circuits in E. coli. ACS Synth Biol 2022; 11:3954-3965. [PMID: 36283074 DOI: 10.1021/acssynbio.2c00307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Escherichia coli is a common chassis for synthetic gene circuit studies. In addition to the dose-response of synthetic gene circuits, the analysis of dynamic responses is also an important part of the future design of more complicated synthetic systems. Recently, microfluidic-based methods have been widely used for the analysis of gene expression dynamics. Here, we established a two-layered microfluidic platform for the systematic characterization of synthetic gene circuits (eight strains in eight different culture environments could be observed simultaneously with a 5 min time resolution). With this platform, both dose responses and dynamic responses with a high temporal resolution could be easily derived for further analysis. A controlled environment ensures the stability of the bacterial growth rate, excluding changes in gene expression dynamics caused by changes of the growth dilution rate. The precise environmental switch and automatic micrograph shooting ensured that there was nearly no time lag between the inducer addition and the data recording. We studied four four-node incoherent-feedforward-loop (IFFL) networks with different operators using this device. The experimental results showed that as the effect of inhibition increased, two of the IFFL networks generated pulselike dynamic gene expressions in the range of the inducer concentrations, which was different from the dynamics of the two other circuits with only a simple pattern of rising to the platform. Through fitting the dose-response curves and the dynamic response curves, corresponding parameters were derived and introduced to a simple model that could qualitatively explain the generation of pulse dynamics.
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Affiliation(s)
- Yanhong Sun
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics School of Physics, Peking University, Beijing100871, China
| | - Fengyu Zhang
- School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
| | - Lusi Li
- Academy of Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Kaiyue Chen
- Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou, Zhejiang325001, China
| | - Shujing Wang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics School of Physics, Peking University, Beijing100871, China
| | - Qi Ouyang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics School of Physics, Peking University, Beijing100871, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Chunxiong Luo
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics School of Physics, Peking University, Beijing100871, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China.,Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou, Zhejiang325001, China
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17
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Richter F, Chen M, Schaub P, Wüst F, Zhang D, Schneider S, Groß GA, Mäder P, Dovzhenko O, Palme K, Köhler JM, Cao J. Induction of embryogenic development in haploid microspore stem cells in droplet-based microfluidics. LAB ON A CHIP 2022; 22:4292-4305. [PMID: 36196753 DOI: 10.1039/d2lc00788f] [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
This work presents the application of droplet-based microfluidics for the cultivation of microspores from Brassica napus using the doubled haploid technology. Under stress conditions (e.g. heat shock) or by chemical induction a certain fraction of the microspores can be reprogrammed and androgenesis can be induced. This process is an important approach for plant breeding because desired plant properties can be anchored in the germline on a genetic level. However, the reprogramming rate of the microspores is generally very low, increasing it by specific stimulation is, therefore, both a necessary and challenging task. In order to accelerate the optimisation and development process, the application of droplet-based microfluidics can be a promising tool. Here, we used a tube-based microfluidic system for the generation and cultivation of microspores inside nL-droplets. Different factors like cell density, tube material and heat shock conditions were investigated to improve the yield of vital plant organoids. Evaluation and analysis of the stimuli response were done on an image base aided by an artificial intelligence cell detection algorithm. Droplet-based microfluidics allowed us to apply large concentration programs in small test volumes and to screen the best conditions for reprogramming cells by the histone deacetylase inhibitor trichostatin A and for enhancing the yield of vital microspores in droplets. An enhanced reprogramming rate was found under the heat shock conditions at 32 °C for about 3 to 6 days. In addition, the comparative experiment with MTP showed that droplet cultivation with lower cell density (<10 cells per droplet) or adding media after 3 or 6 days significantly positively affects the microspore growth and embryo rate inside 120 nL droplets. Finally, the developed embryos could be removed from the droplets and further grown into mature plants. Overall, we demonstrated that the droplet-based tube system is suitable for implementation in an automated, miniaturized system to achieve the induction of embryogenic development in haploid microspore stem cells of Brassica napus.
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Affiliation(s)
- Felix Richter
- Institute for Chemistry and Biotechnologies, Dept. Physical Chemistry and Microreaction Technologies, Technische Universität Ilmenau, 98693 Ilmenau, Germany.
| | - Minqian Chen
- Technische Universität Ilmenau, Institute for Computer and Systems Engineering, Dept. Software Engineering for Safety-Critical Systems, 98693 Ilmenau, Germany
| | | | - Florian Wüst
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany
| | - Di Zhang
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany
| | - Steffen Schneider
- Institute for Chemistry and Biotechnologies, Dept. Physical Chemistry and Microreaction Technologies, Technische Universität Ilmenau, 98693 Ilmenau, Germany.
| | - G Alexander Groß
- Institute for Chemistry and Biotechnologies, Dept. Physical Chemistry and Microreaction Technologies, Technische Universität Ilmenau, 98693 Ilmenau, Germany.
| | - Patrick Mäder
- Technische Universität Ilmenau, Institute for Computer and Systems Engineering, Dept. Software Engineering for Safety-Critical Systems, 98693 Ilmenau, Germany
| | | | - Klaus Palme
- ScreenSYS GmbH, 79104 Freiburg, Germany
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany
- BIOSS Centre of Biological Signalling Studies, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany
- Sino-German Joint Research Center on Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
| | - J Michael Köhler
- Institute for Chemistry and Biotechnologies, Dept. Physical Chemistry and Microreaction Technologies, Technische Universität Ilmenau, 98693 Ilmenau, Germany.
| | - Jialan Cao
- Institute for Chemistry and Biotechnologies, Dept. Physical Chemistry and Microreaction Technologies, Technische Universität Ilmenau, 98693 Ilmenau, Germany.
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18
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Pérez-Rodríguez S, Borau C, García-Aznar JM, Gonzalo-Asensio J. A microfluidic-based analysis of 3D macrophage migration after stimulation by Mycobacterium, Salmonella and Escherichia. BMC Microbiol 2022; 22:211. [PMID: 36045335 PMCID: PMC9429415 DOI: 10.1186/s12866-022-02623-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/22/2022] [Indexed: 11/23/2022] Open
Abstract
Macrophages play an essential role in the process of recognition and containment of microbial infections. These immune cells are recruited to infectious sites to reach and phagocytose pathogens. Specifically, in this article, bacteria from the genus Mycobacterium, Salmonella and Escherichia, were selected to study the directional macrophage movement towards different bacterial fractions. We recreated a three-dimensional environment in a microfluidic device, using a collagen-based hydrogel that simulates the mechanical microarchitecture associated to the Extra Cellular Matrix (ECM). First, we showed that macrophage migration is affected by the collagen concentration of their environment, migrating greater distances at higher velocities with decreasing collagen concentrations. To recreate the infectious microenvironment, macrophages were exposed to lateral gradients of bacterial fractions obtained from the intracellular pathogens M. tuberculosis and S. typhimurium. Our results showed that macrophages migrated directionally, and in a concentration-dependent manner, towards the sites where bacterial fractions are located, suggesting the presence of attractants molecules in all the samples. We confirmed that purified M. tuberculosis antigens, as ESAT-6 and CFP-10, stimulated macrophage recruitment in our device. Finally, we also observed that macrophages migrate towards fractions from non-pathogenic bacteria, such as M. smegmatis and Escherichia coli. In conclusion, our microfluidic device is a useful tool which opens new perspectives to study the recognition of specific antigens by innate immune cells.
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19
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Xu A, Liu J, Cao S, Xu B, Guo C, Yu Z, Chen X, Zhou J, Dong W, Jiang M. Application of a novel fluorogenic polyurethane analogue probe in polyester-degrading microorganisms screening by microfluidic droplet. Microb Biotechnol 2022; 16:474-480. [PMID: 35881631 PMCID: PMC9871523 DOI: 10.1111/1751-7915.14121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/06/2022] [Accepted: 07/13/2022] [Indexed: 01/27/2023] Open
Abstract
Application of polyester-degrading microorganisms or enzymes should be considered as an eco-friendly alternative to chemical recycling due to the huge plastic waste disposal nowadays. However, current impranil DLN-based screening of polyester-degrading microorganisms is time-consuming, labour-intensive and unable to distinguish polyesterases from other protease- or amidase-like enzymes. Herein, we present an approach that combined a novel synthetic fluorescent polyurethane analogue probe (FPAP), along with the droplet-based microfluidics to screen polyurethane-degrading microorganisms through fluorescence-activated droplet sorting (FADS) pipeline. The fluorescent probe FPAP exhibited a fluorescence enhancement effect once hydrolysed by polyesterases, along with a strong specificity in discriminating polyesterases from other non-active enzymes. Application of FPAP in a microfluidic droplet system demonstrated that this probe exhibited high sensitivity and efficiency in selecting positive droplets containing leaf-branch compost cutinase (LCC) enzymes. This novel fluorogenic probe, FPAP, combined with the droplet microfluidic system has the potential to be used in the exploitation of novel PUR-biocatalysts for biotechnological and environmental applications.
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Affiliation(s)
- Anming Xu
- College of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina
| | - Jiawei Liu
- College of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina
| | - Shixiang Cao
- College of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina
| | - Bin Xu
- College of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina
| | - Chengzhi Guo
- State Key Laboratory of Materials‐Oriented Chemical EngineeringNanjing Tech UniversityNanjingChina
| | - Ziyi Yu
- State Key Laboratory of Materials‐Oriented Chemical EngineeringNanjing Tech UniversityNanjingChina
| | - Xiaoqiang Chen
- State Key Laboratory of Materials‐Oriented Chemical EngineeringNanjing Tech UniversityNanjingChina
| | - Jie Zhou
- College of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina,State Key Laboratory of Materials‐Oriented Chemical EngineeringNanjing Tech UniversityNanjingChina
| | - Weiliang Dong
- College of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina,State Key Laboratory of Materials‐Oriented Chemical EngineeringNanjing Tech UniversityNanjingChina
| | - Min Jiang
- College of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjingChina,State Key Laboratory of Materials‐Oriented Chemical EngineeringNanjing Tech UniversityNanjingChina
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20
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Tran VN, Khan F, Han W, Luluil M, Truong VG, Yun HG, Choi S, Kim YM, Shin JH, Kang HW. Real-time monitoring of mono- and dual-species biofilm formation and eradication using microfluidic platform. Sci Rep 2022; 12:9678. [PMID: 35690659 PMCID: PMC9188611 DOI: 10.1038/s41598-022-13699-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/26/2022] [Indexed: 11/17/2022] Open
Abstract
In a human host, bacterial Staphylococcus aureus and fungal Candida albicans pathogens form a mixed biofilm that causes severe mortality and morbidity. However, research on the formation and eradication of mixed biofilms under dynamic conditions is lacking. Thus, this study employed a microfluidic technique to analyze the real-time formation of mono- and dual-species (S. aureus and C. albicans) biofilms and noninvasive optical treatment of the established mature biofilm using 405-nm laser light. A herringbone mixer thoroughly mixed both bacterial and fungal cells in the growth media before being injected into the observation channels on the microfluidic chip. At a flow rate of 1.0 µL/min of growth media for 24 h, the bacterial biofilm coverage was up to 15% higher than that of the fungal biofilm (50% for bacteria vs. 35% for fungus). On the other hand, the dual-species biofilm yielded the highest coverage of ~ 96.5% because of the collective interaction between S. aureus and C. albicans. The number of cell proliferation events in S. aureus was higher than that of C. albicans for 12 h, which indicates that the S. aureus biofilm was developed faster than C. albicans. The novel in situ test platform showed a significant bactericidal effect (80%) of the 405-nm laser light at 1080 J/cm2 towards the established S. aureus biofilm, whereas the same treatment removed approximately 69% of the mixed cells in the dual-species biofilm. This study revealed that the developed microfluidic platform could be utilized to monitor the formation of dual-species biofilms in real-time and laser-induced antimicrobial effects on dual-species biofilms.
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Affiliation(s)
- Van Nam Tran
- Industry 4.0 Convergence Bionics Engineering and Marine-Integrated Biomedical Technology Center, Pukyong National University, Busan, 48513, South Korea
| | - Fazlurrahman Khan
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, 48513, South Korea
| | - Won Han
- Department of Biomedical Engineering, Pukyong National University, Busan, 48513, South Korea
| | - Maknuna Luluil
- Industry 4.0 Convergence Bionics Engineering and Marine-Integrated Biomedical Technology Center, Pukyong National University, Busan, 48513, South Korea
| | - Van Gia Truong
- Industry 4.0 Convergence Bionics Engineering and Marine-Integrated Biomedical Technology Center, Pukyong National University, Busan, 48513, South Korea
| | - Hyo Geun Yun
- Department of Electronic Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Sungyoung Choi
- Department of Electronic Engineering, Hanyang University, Seoul, 04763, South Korea.,Department of Biomedical Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Young-Mog Kim
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, 48513, South Korea.,Department of Food Science and Technology, Pukyong National University, Busan, 48513, South Korea
| | - Joong Ho Shin
- Industry 4.0 Convergence Bionics Engineering and Marine-Integrated Biomedical Technology Center, Pukyong National University, Busan, 48513, South Korea. .,Department of Biomedical Engineering, Pukyong National University, Busan, 48513, South Korea.
| | - Hyun Wook Kang
- Industry 4.0 Convergence Bionics Engineering and Marine-Integrated Biomedical Technology Center, Pukyong National University, Busan, 48513, South Korea. .,Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, 48513, South Korea. .,Department of Biomedical Engineering, Pukyong National University, Busan, 48513, South Korea.
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21
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Wang B, Park B. Microfluidic Sampling and Biosensing Systems for Foodborne Escherichia coli and Salmonella. Foodborne Pathog Dis 2022; 19:359-375. [PMID: 35713922 DOI: 10.1089/fpd.2021.0087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Developments of portable biosensors for field-deployable detections have been increasingly important to control foodborne pathogens in regulatory environment and in early stage of outbreaks. Conventional cultivation and gene amplification methods require sophisticated instruments and highly skilled professionals; while portable biosensing devices provide more freedom for rapid detections not only in research laboratories but also in the field; however, their sensitivity and specificity are limited. Microfluidic methods have the advantage of miniaturizing instrumental size while integrating multiple functions and high-throughput capability into one streamlined system at low cost. Minimal sample consumption is another advantage to detect samples in different sizes and concentrations, which is important for the close monitoring of pathogens at consumer end. They improve measurement or manipulation of bacteria by increasing the ratio of functional interface of the device to the targeted biospecies and in turn reducing background interference. This article introduces the major active and passive microfluidic devices that have been used for bacteria sampling and biosensing. The emphasis is on particle-based sorting/enrichment methods with or without external physical fields applied to the microfluidic devices and on various biosensing applications reported for bacteria sampling. Three major fabrication methods for microfluidics are briefly discussed with their advantages and limitations. The applications of these active and passive microfluidic sampling methods in the past 5 years have been summarized, with the focus on Escherichia coli and Salmonella. The current challenges to microfluidic bacteria sampling are caused by the small size and nonspherical shape of various bacterial cells, which can induce unpredictable deviations in sampling and biosensing processes. Future studies are needed to develop rapid prototyping methods for device manufacturing, which can facilitate rapid response to various foodborne pathogen outbreaks.
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Affiliation(s)
- Bin Wang
- U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia, USA
| | - Bosoon Park
- U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia, USA
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22
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Rebrosova K, Samek O, Kizovsky M, Bernatova S, Hola V, Ruzicka F. Raman Spectroscopy—A Novel Method for Identification and Characterization of Microbes on a Single-Cell Level in Clinical Settings. Front Cell Infect Microbiol 2022; 12:866463. [PMID: 35531343 PMCID: PMC9072635 DOI: 10.3389/fcimb.2022.866463] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/07/2022] [Indexed: 12/02/2022] Open
Abstract
Rapid and accurate identification of pathogens causing infections is one of the biggest challenges in medicine. Timely identification of causative agents and their antimicrobial resistance profile can significantly improve the management of infection, lower costs for healthcare, mitigate ever-growing antimicrobial resistance and in many cases, save lives. Raman spectroscopy was shown to be a useful—quick, non-invasive, and non-destructive —tool for identifying microbes from solid and liquid media. Modifications of Raman spectroscopy and/or pretreatment of samples allow single-cell analyses and identification of microbes from various samples. It was shown that those non-culture-based approaches could also detect antimicrobial resistance. Moreover, recent studies suggest that a combination of Raman spectroscopy with optical tweezers has the potential to identify microbes directly from human body fluids. This review aims to summarize recent advances in non-culture-based approaches of identification of microbes and their virulence factors, including antimicrobial resistance, using methods based on Raman spectroscopy in the context of possible use in the future point-of-care diagnostic process.
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Affiliation(s)
- Katarina Rebrosova
- Department of Microbiology, Faculty of Medicine of Masaryk University and St. Anne’s University Hospital, Brno, Czechia
| | - Ota Samek
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czechia
| | - Martin Kizovsky
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czechia
| | - Silvie Bernatova
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czechia
| | - Veronika Hola
- Department of Microbiology, Faculty of Medicine of Masaryk University and St. Anne’s University Hospital, Brno, Czechia
- *Correspondence: Veronika Hola,
| | - Filip Ruzicka
- Department of Microbiology, Faculty of Medicine of Masaryk University and St. Anne’s University Hospital, Brno, Czechia
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Sportelli MC, Kranz C, Mizaikoff B, Cioffi N. Recent advances on the spectroscopic characterization of microbial biofilms: A critical review. Anal Chim Acta 2022; 1195:339433. [DOI: 10.1016/j.aca.2022.339433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/30/2021] [Accepted: 01/02/2022] [Indexed: 02/07/2023]
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New Adapted In Vitro Technology to Evaluate Biofilm Formation and Antibiotic Activity Using Live Imaging under Flow Conditions. Diagnostics (Basel) 2021; 11:diagnostics11101746. [PMID: 34679444 PMCID: PMC8535051 DOI: 10.3390/diagnostics11101746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/11/2021] [Accepted: 09/19/2021] [Indexed: 12/19/2022] Open
Abstract
The polymicrobial nature of biofilms and bacterial interactions inside chronic wounds are keys for the understanding of bacterial cooperation. The aim of this present study was to develop a technique to study and visualize biofilm in live imaging under flow conditions (Bioflux™ 200, Fluxion Biosciences). The BiofluxTM system was adapted using an in vitro chronic wound-like medium (CWM) that mimics the environment encountered in ulcers. Two reference strains of Staphylococcus aureus (Newman) and Pseudomonas aeruginosa (PAO1) were injected in the BiofluxTM during 24 h to 72 h in mono and coculture (ratio 1:1, bacteria added simultaneously) in the CWM vs. a control medium (BHI). The quantification of biofilm formation at each time was evaluated by inverted microscopy. After 72 h, different antibiotics (ceftazidime, imipenem, linezolid, oxacillin and vancomycin) at 1x MIC, 10x MIC and 100x MIC were administrated to the system after an automatic increase of the flow that mimicked a debridement of the wound surface. Biofilm studies highlighted that the two species, alone or associated, constituted a faster and thicker biofilm in the CWM compared to the BHI medium. The effect of antibiotics on mature or “debrided” biofilm indicated that some of the most clinically used antibiotic such as vancomycin or imipenem were not able to disrupt and reduce the biofilm biomass. The use of a life cell imaging with an in vitro CWM represents a promising tool to study bacterial biofilm and investigate microbial cooperation in a chronic wound context.
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Rämä T, Quandt CA. Improving Fungal Cultivability for Natural Products Discovery. Front Microbiol 2021; 12:706044. [PMID: 34603232 PMCID: PMC8481835 DOI: 10.3389/fmicb.2021.706044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
The pool of fungal secondary metabolites can be extended by activating silent gene clusters of cultured strains or by using sensitive biological assays that detect metabolites missed by analytical methods. Alternatively, or in parallel with the first approach, one can increase the diversity of existing culture collections to improve the access to new natural products. This review focuses on the latter approach of screening previously uncultured fungi for chemodiversity. Both strategies have been practiced since the early days of fungal biodiscovery, yet relatively little has been done to overcome the challenge of cultivability of as-yet-uncultivated fungi. Whereas earlier cultivability studies using media formulations and biological assays to scrutinize fungal growth and associated factors were actively conducted, the application of modern omics methods remains limited to test how to culture the fungal dark matter and recalcitrant groups of described fungi. This review discusses the development of techniques to increase the cultivability of filamentous fungi that include culture media formulations and the utilization of known chemical growth factors, in situ culturing and current synthetic biology approaches that build upon knowledge from sequenced genomes. We list more than 100 growth factors, i.e., molecules, biological or physical factors that have been demonstrated to induce spore germination as well as tens of inducers of mycelial growth. We review culturing conditions that can be successfully manipulated for growth of fungi and visit recent information from omics methods to discuss the metabolic basis of cultivability. Earlier work has demonstrated the power of co-culturing fungi with their host, other microorganisms or their exudates to increase their cultivability. Co-culturing of two or more organisms is also a strategy used today for increasing cultivability. However, fungi possess an increased risk for cross-contaminations between isolates in existing in situ or microfluidics culturing devices. Technological improvements for culturing fungi are discussed in the review. We emphasize that improving the cultivability of fungi remains a relevant strategy in drug discovery and underline the importance of ecological and taxonomic knowledge in culture-dependent drug discovery. Combining traditional and omics techniques such as single cell or metagenome sequencing opens up a new era in the study of growth factors of hundreds of thousands of fungal species with high drug discovery potential.
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Affiliation(s)
- Teppo Rämä
- Marbio, Norwegian College of Fishery Science, University of Tromsø – The Arctic University of Norway, Tromsø, Norway
| | - C. Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
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Matilla MA. Facing crises in the 21st century: microfluidics approaches for antibiotic discovery. Microb Biotechnol 2021; 15:392-394. [PMID: 34333833 PMCID: PMC8867967 DOI: 10.1111/1751-7915.13908] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/28/2022] Open
Abstract
We urgently need new antibiotics to counteract the rising in the emergence of multidrug‐resistant microorganisms. To improve the identification of antimicrobial compounds of microbial origin, numerous multidisciplinary approaches are being implemented. However, the development of innovative microbial cultivation strategies is necessary to exploit the full biosynthetic potential of non‐culturable microorganisms. Here, I highlight various articles that employ high‐throughput microfluidic‐based strategies to identify novel antimicrobial metabolites based on bacterial activities. The rapid development of this technology will likely advance the field of antibiotic discovery.
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Affiliation(s)
- Miguel A Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, Granada, 18008, Spain
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