1
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Rafiee Z, Rezaie M, Choi S. Combined electrical-electrochemical phenotypic profiling of antibiotic susceptibility of in vitro biofilm models. Analyst 2024; 149:3224-3235. [PMID: 38686667 DOI: 10.1039/d4an00393d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
More than 65% of bacterial infections are caused by biofilms. However, standard biofilm susceptibility tests are not available for clinical use. All conventional biofilm models suffer from a long formation time and fail to mimic in vivo microbial biofilm conditions. Moreover, biofilms make it difficult to monitor the effectiveness of antibiotics. This work creates a powerful yet simple method to form a target biofilm and develops an innovative approach to monitoring the antibiotic's efficacy against a biofilm-associated infection. A paper-based culture platform can provide a new strategy for rapid microbial biofilm formation through capillary action. A combined electrical-electrochemical technique monitors bacterial metabolism rapidly and reliably by measuring microbial extracellular electron transfer (EET) and using electrochemical impedance spectroscopy (EIS) across a microbe-electrode interface. Three representative pathogens, Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus, form their biofilms controllably within an hour. Within another hour their susceptibilities to three frontline antibiotics with different action modes (gentamicin, ciprofloxacin, and ceftazidime) are examined. Our antibiotic susceptibility testing (AST) technique provides a quantifiable minimum inhibitory concentration (MIC) of those antibiotics against the in vitro biofilm models and characterizes their action mechanisms. The results will have an important positive effect because they provide immediately actionable healthcare information at a reduced cost, revolutionizing public healthcare.
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Affiliation(s)
- Zahra Rafiee
- Bioelectronics & Microsystems Laboratory, Department of Electrical & Computer Engineering, State University of New York at Binghamton, Binghamton, New York, 13902, USA.
| | - Maryam Rezaie
- Bioelectronics & Microsystems Laboratory, Department of Electrical & Computer Engineering, State University of New York at Binghamton, Binghamton, New York, 13902, USA.
| | - Seokheun Choi
- Bioelectronics & Microsystems Laboratory, Department of Electrical & Computer Engineering, State University of New York at Binghamton, Binghamton, New York, 13902, USA.
- Center for Research in Advanced Sensing Technologies & Environmental Sustainability, State University of New York at Binghamton, Binghamton, New York, 13902, USA
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2
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Benmamoun Z, Chandar P, Jankolovits J, Ducker WA. Time-Resolved Killing of Individual Bacterial Cells by a Polycationic Antimicrobial Polymer. ACS Biomater Sci Eng 2024; 10:3029-3040. [PMID: 38551901 PMCID: PMC11094676 DOI: 10.1021/acsbiomaterials.4c00263] [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: 02/07/2024] [Revised: 03/01/2024] [Accepted: 03/13/2024] [Indexed: 05/14/2024]
Abstract
Polycationic polymers are widely studied antiseptics, and their efficacy is usually quantified by the solution concentration required to kill a fraction of a population of cells (e.g., by Minimum Bactericidal Concentration (MBC)). Here we describe how the response to a polycationic antimicrobial varies greatly among members of even a monoclonal population of bacteria bathed in a single common antimicrobial concentration. We use fluorescence microscopy to measure the adsorption of a labeled cationic polymer, polydiallyldimethylammmonium chloride (PDADMAC, Mw ≈ 4 × 105 g mol-1) and the time course of cell response via a cell permeability indicator for each member of an ensemble of either Escherichia coli, Staphylococcus aureus, or Pseudomonas aeruginosa cells. This is a departure from traditional methods of evaluating synthetic antimicrobials, which typically measure the overall response of a collection of cells at a particular time and therefore do not assess the diversity within a population. Cells typically die after they reach a threshold adsorption of PDADMAC, but not always. There is a substantial time lag of about 5-10 min between adsorption and death, and the time to die of an individual cell is well correlated with the rate of adsorption. The amount adsorbed and the time-to-die differ among species but follow a trend of more adsorption on more negatively charged species, as expected for a cationic polymer. The study of individual cells via time-lapse microscopy reveals additional details that are lost when measuring ensemble properties at a particular time.
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Affiliation(s)
- Zachary Benmamoun
- Department
of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Prem Chandar
- Unilever
Research, Trumbull, Connecticut 06611, United States
| | - Joe Jankolovits
- Unilever
Research, Trumbull, Connecticut 06611, United States
| | - William A. Ducker
- Department
of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
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3
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Gao J, Zhou K, Li H, Li Y, Yang K, Wang W. Intermittent proton bursts of single lactic acid bacteria. Chem Sci 2024; 15:3516-3523. [PMID: 38455010 PMCID: PMC10915832 DOI: 10.1039/d3sc06238d] [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: 11/21/2023] [Accepted: 01/23/2024] [Indexed: 03/09/2024] Open
Abstract
Lactic acid bacteria are a kind of probiotic microorganisms that efficiently convert carbohydrates to lactic acids, thus playing essential roles in fermentation and food industry. While conventional wisdom often suggests continuous release of protons from bacteria during acidification, here we developed a methodology to measure the dynamics of proton release at the single bacteria level, and report on the discovery of a proton burst phenomenon, i.e., the intermittent efflux of protons, of single Lactobacillus plantarum bacteria. When placing an individual bacterium in an oil-sealed microwell, efflux and accumulation of protons consequently reduced the pH in the confined extracellular medium, which was monitored with fluorescent pH indicators in a high-throughput and real-time manner. In addition to the slow and continuous proton release behavior (as expected), stochastic and intermittent proton burst events were surprisingly observed with a typical timescale of several seconds. It was attributed to the regulatory response of bacteria by activating H+-ATPase to compensate the stochastic and transient depolarizations of membrane potential. These findings not only revealed an unprecedented proton burst phenomenon in lactic acid bacteria, but also shed new lights on the intrinsic roles of H+-ATPase in membrane potential homeostasis, with implications for both fermentation industry and bacterial electrophysiology.
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Affiliation(s)
- Jia Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University Nanjing 210023 China
| | - Kai Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University Nanjing 210023 China
| | - Haoran Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University Nanjing 210023 China
| | - Yaohua Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University Nanjing 210023 China
| | - Kairong Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University Nanjing 210023 China
| | - Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University Nanjing 210023 China
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4
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Lehnert T, Gijs MAM. Microfluidic systems for infectious disease diagnostics. LAB ON A CHIP 2024; 24:1441-1493. [PMID: 38372324 DOI: 10.1039/d4lc00117f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Microorganisms, encompassing both uni- and multicellular entities, exhibit remarkable diversity as omnipresent life forms in nature. They play a pivotal role by supplying essential components for sustaining biological processes across diverse ecosystems, including higher host organisms. The complex interactions within the human gut microbiota are crucial for metabolic functions, immune responses, and biochemical signalling, particularly through the gut-brain axis. Viruses also play important roles in biological processes, for example by increasing genetic diversity through horizontal gene transfer when replicating inside living cells. On the other hand, infection of the human body by microbiological agents may lead to severe physiological disorders and diseases. Infectious diseases pose a significant burden on global healthcare systems, characterized by substantial variations in the epidemiological landscape. Fast spreading antibiotic resistance or uncontrolled outbreaks of communicable diseases are major challenges at present. Furthermore, delivering field-proven point-of-care diagnostic tools to the most severely affected populations in low-resource settings is particularly important and challenging. New paradigms and technological approaches enabling rapid and informed disease management need to be implemented. In this respect, infectious disease diagnostics taking advantage of microfluidic systems combined with integrated biosensor-based pathogen detection offers a host of innovative and promising solutions. In this review, we aim to outline recent activities and progress in the development of microfluidic diagnostic tools. Our literature research mainly covers the last 5 years. We will follow a classification scheme based on the human body systems primarily involved at the clinical level or on specific pathogen transmission modes. Important diseases, such as tuberculosis and malaria, will be addressed more extensively.
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Affiliation(s)
- Thomas Lehnert
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland.
| | - Martin A M Gijs
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland.
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5
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Wu W, Kiat Goh SC, Cai G, Feng S, Zhang B. Digital metabolic activity assay enables fast assessment of 2D materials bactericidal efficiency. Anal Chim Acta 2024; 1285:342007. [PMID: 38057056 DOI: 10.1016/j.aca.2023.342007] [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: 10/04/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND The identification and quantification of viable Escherichia coli (E. coli) are important in multiple fields including the development of antimicrobial materials, water quality, food safety and infections diagnosis. However, the standard culture-based methods of viable E. coli detection suffer from long detection times (24 h) and complex operation, leaving the unmet requirement for fast assessing the efficiency of antimicrobial materials, early alerting the contamination of water and food, and immediately treatment of infections. RESULTS We present a digital β-d-glucuronidase (GUS) assay in a self-priming polydimethylsiloxane (PDMS) microfluidic chip for rapid E. coli identification and quantification. The GUS expression in viable bacteria was investigated to develop a fast GUS assay at the single-cell level. Single E. coli were stochastically discretized in picoliter chambers and identified by specific GUS activity. The digital GUS assay enabled identifying E. coli within 3 h and quantifying within 4 h for different E. coli subtypes. The specificity of our method was confirmed by using blended bacteria including E. coli, Bacillus, Shigella and Vibrio. We utilized digital GUS assay to enumerate viable E. coli after incubated with antibacterial materials for assessing the antibacterial efficiency. Moreover, the degassed chip can realize automatic sample distribution without external instruments. SIGNIFICANCE The results demonstrated the functionality and practicability of digital GUS assay for single E. coli identification and quantification. With air-tight packaging, the developed chip has the potential for on-site E. coli analysis and could be deployed for diagnosis of E. coli infections, antimicrobial susceptibility testing, and warning the fecal pollution of water. Digital GUS assay provides a paradigm, examining the activity of metabolic enzyme, for detecting the viable bacteria other than E. coli.
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Affiliation(s)
- Wenshuai Wu
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Simon Chun Kiat Goh
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Gaozhe Cai
- School of Microelectronics, Shanghai University, Shanghai, 200444, China
| | - Shilun Feng
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China.
| | - Boran Zhang
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore, 639798, Singapore.
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6
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Zhang H, Wang L, Zhang Z, Lin J, Ju F. Cost-Efficient Micro-Well Array-Based Colorimetric Antibiotic Susceptibility Testing (MacAST) for Bacteria from Culture or Community. BIOSENSORS 2023; 13:1028. [PMID: 38131788 PMCID: PMC10741774 DOI: 10.3390/bios13121028] [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: 11/07/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
Rapid and cost-efficient antibiotic susceptibility testing (AST) is key to timely prescription-oriented diagnosis and precision treatment. However, current AST methods have limitations in throughput or cost effectiveness, and are impractical for microbial communities. Here, we developed a high-throughput micro-well array-based colorimetric AST (macAST) system equipped with a self-developed smartphone application that could efficiently test sixteen combinations of bacteria strains and antibiotics, achieving comparable AST results based on resazurin metabolism assay. For community samples, we integrated immunomagnetic separation into the macAST (imacAST) system to specifically enrich the target cells before testing, which shortened bacterial isolation time from days to only 45 min and achieved AST of the target bacteria with a low concentration (~103 CFU/mL). This proof-of-concept study developed a high-throughput AST system with an at least ten-fold reduction in cost compared with a system equipped with a microscope or Raman spectrum. Based on colorimetric readout, the antimicrobial susceptibility of the bacteria from microbial communities can be delivered within 6 h, compared to days being required based on standard procedures, bypassing the need for precise instrumentation in therapy to combat bacterial antibiotic resistance in resource-limited settings.
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Affiliation(s)
- Huilin Zhang
- College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310027, China
- Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, China
| | - Lei Wang
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Zhiguo Zhang
- Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, China
| | - Jianhan Lin
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou 310024, China
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7
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Wu W, Zhang B, Yin W, Xia L, Suo Y, Cai G, Liu Y, Jin W, Zhao Q, Mu Y. Enzymatic Antimicrobial Susceptibility Testing with Bacteria Identification in 30 min. Anal Chem 2023; 95:16426-16432. [PMID: 37874622 DOI: 10.1021/acs.analchem.3c04316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Rapid antimicrobial susceptibility testing (AST) with the ability of bacterial identification is urgently needed for evidence-based antibiotic prescription. Herein, we propose an enzymatic AST (enzyAST) that employs β-d-glucuronidase as a biomarker to identify pathogens and profile phenotypic susceptibilities simultaneously. EnzyAST enables to offer binary AST results within 30 min, much faster than standard methods (>16 h). The general applicability of enzyAST was verified by testing the susceptibility of two Escherichia coli strains to three antibiotics with different action mechanisms. The pilot study also shows that the minimal inhibitory concentrations can be determined by enzyAST with the statistical analysis of enzymatic activity of the bacteria population exposed to varying antibiotic concentrations. With further development of multiple bacteria and sample treatment, enzyAST could be able to evaluate the susceptibility of pathogens in clinical samples directly to facilitate the evidence-based therapy.
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Affiliation(s)
- Wenshuai Wu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China
| | - Boran Zhang
- Department of Hydraulic Engineering, College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China
| | - Weihong Yin
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China
| | - Liping Xia
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China
| | - Yuanjie Suo
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China
| | - Gaozhe Cai
- School of Microelectronics, Shanghai University, Shanghai 200444, China
| | - Yang Liu
- School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 102401, China
| | - Wei Jin
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China
- Huzhou Institute of Zhejiang University, Huzhou 313002, China
| | - Qianbin Zhao
- Center of Health Science and Engineering, Hebei Key Laboratory of Biomaterials and Smart Theranostics, Hebei University of Technology, Tianjin 300131, China
| | - Ying Mu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China
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8
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Zeng K, Osaid M, van der Wijngaart W. Efficient filter-in-centrifuge separation of low-concentration bacteria from blood. LAB ON A CHIP 2023; 23:4334-4342. [PMID: 37712252 DOI: 10.1039/d3lc00594a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Separating bacteria from infected blood is an important step in preparing samples for downstream bacteria detection and analysis. However, the extremely low bacteria concentration and extremely high blood cell count make efficient separation challenging. In this study, we introduce a method for separating bacteria from blood in a single centrifugation step, which involves sedimentation velocity-based differentiation followed by size-based cross-flow filtration over an inclined filter. Starting from 1 mL spiked whole blood, we recovered 32 ± 4% of the bacteria (Escherichia coli, Klebsiella pneumonia, or Staphylococcus aureus) within one hour while removing 99.4 ± 0.1% of the red blood cells, 98.4 ± 1.4% of the white blood cells, and 90.0 ± 2.6% of the platelets. Changing the device material could further increase bacteria recovery to >50%. We demonstrated bacterial recovery from blood spiked with 10 CFU mL-1. Our simple hands-off efficient separation of low-abundant bacteria approaches clinical expectations, making the new method a promising candidate for future clinical use.
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Affiliation(s)
- Kaiyang Zeng
- Division of Micro and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Mohammad Osaid
- Division of Micro and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden.
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9
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Zhao R, Shen Y, Zhao C, Wu C, Liu Y, Wan H, Lu Z. A rapid screening platform for antibiotic susceptibility testing based on a simple colorimetric method. Analyst 2023; 148:4148-4155. [PMID: 37498542 DOI: 10.1039/d3an00611e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Rapid screening platforms for antibiotic susceptibility testing (AST) are important in inhibiting bacterial resistance in clinical practice. Herein, a rapid screening platform is reported for AST, which is based on nanofiber membrane enrichment bacteria-assisted cell counting Kit-8 (CCK8) colorimetry. The absorbance of CCK8 formazan has a linear relationship with the number of bacteria. The interference of antibiotics in the absorbance of CCK8 formazan could be eliminated by separating planktonic bacteria from the culture medium using nanofiber membranes. The total detection time is 7-9 h, using the new screening platform, which is significantly shorter than that with the traditional method, and the limit of detection of this method is 10 CFU mL-1. The evaluation results of antibiotic susceptibility are identical when using the new screening method and traditional methods. This method meets the definition of "rapid testing" for antibiotic susceptibility by most microbiologists. Furthermore, the new screening platform for antibiotic susceptibility testing ability in vitro was proved using E. coli in urine and blood, and S. aureus in wound fluid as practical samples. All the results showed that the new screening platform is a promising method for rapid antibiotic susceptibility testing in vitro.
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Affiliation(s)
- Rui Zhao
- Key Laboratory of Textile Fiber and Products Ministry of Education, School of Materials Science and Engineering, Hubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials & Application, Wuhan Textile University, Wuhan, 430200, China.
| | - Yubin Shen
- Key Laboratory of Textile Fiber and Products Ministry of Education, School of Materials Science and Engineering, Hubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials & Application, Wuhan Textile University, Wuhan, 430200, China.
| | - Chenyu Zhao
- Key Laboratory of Textile Fiber and Products Ministry of Education, School of Materials Science and Engineering, Hubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials & Application, Wuhan Textile University, Wuhan, 430200, China.
| | - Chengfeng Wu
- Key Laboratory of Textile Fiber and Products Ministry of Education, School of Materials Science and Engineering, Hubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials & Application, Wuhan Textile University, Wuhan, 430200, China.
| | - Yuyang Liu
- Key Laboratory of Textile Fiber and Products Ministry of Education, School of Materials Science and Engineering, Hubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials & Application, Wuhan Textile University, Wuhan, 430200, China.
| | - Huakun Wan
- Key Laboratory of Textile Fiber and Products Ministry of Education, School of Materials Science and Engineering, Hubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials & Application, Wuhan Textile University, Wuhan, 430200, China.
| | - Zhentan Lu
- Key Laboratory of Textile Fiber and Products Ministry of Education, School of Materials Science and Engineering, Hubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials & Application, Wuhan Textile University, Wuhan, 430200, China.
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10
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Baranova AA, Tyurin AP, Korshun VA, Alferova VA. Sensing of Antibiotic-Bacteria Interactions. Antibiotics (Basel) 2023; 12:1340. [PMID: 37627760 PMCID: PMC10451291 DOI: 10.3390/antibiotics12081340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Sensing of antibiotic-bacteria interactions is an important area of research that has gained significant attention in recent years. Antibiotic resistance is a major public health concern, and it is essential to develop new strategies for detecting and monitoring bacterial responses to antibiotics in order to maintain effective antibiotic development and antibacterial treatment. This review summarizes recent advances in sensing strategies for antibiotic-bacteria interactions, which are divided into two main parts: studies on the mechanism of action for sensitive bacteria and interrogation of the defense mechanisms for resistant ones. In conclusion, this review provides an overview of the present research landscape concerning antibiotic-bacteria interactions, emphasizing the potential for method adaptation and the integration of machine learning techniques in data analysis, which could potentially lead to a transformative impact on mechanistic studies within the field.
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Affiliation(s)
| | | | | | - Vera A. Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.B.); (A.P.T.); (V.A.K.)
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11
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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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12
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Wu T, Yagati AK, Min J. Electrochemical Detection of Different Foodborne Bacteria for Point-of-Care Applications. BIOSENSORS 2023; 13:641. [PMID: 37367006 DOI: 10.3390/bios13060641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023]
Abstract
Bacterial infections resulting from foodborne pathogenic bacteria cause millions of infections that greatly threaten human health and are one of the leading causes of mortality around the world. To counter this, the early, rapid, and accurate detection of bacterial infections is very important to address serious health issue concerns. We, therefore, present an electrochemical biosensor based on aptamers that selectively bind with the DNA of specific bacteria for the accurate and rapid detection of various foodborne bacteria for the selective determination of bacterial infection types. Different aptamers were synthesized and immobilized on Au electrodes for selective bindings of different types of bacterial DNA (Escherichia coli, Salmonella enterica, and Staphylococcus aureus) for the accurate detection and quantification of bacterial concentrations from 101 to 107 CFU/mL without using any labeling methods. Under optimized conditions, the sensor showed a good response to the various concentrations of bacteria, and a robust calibration curve was obtained. The sensor could detect the bacterial concentration at meager quantities and possessed an LOD of 4.2 × 101, 6.1 × 101, and 4.4 × 101 CFU/mL for S. Typhimurium, E. Coli, and S. aureus, respectively, with a linear range from 100 to 104 CFU/mL for the total bacteria probe and 100 to 103 CFU/mL for individual probes, respectively. The proposed biosensor is simple and rapid and has shown a good response to bacterial DNA detections and thus can be applied in clinical applications and food safety monitoring.
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Affiliation(s)
- Tailin Wu
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ajay Kumar Yagati
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Junhong Min
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
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13
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Wu W, Cai G, Liu Y, Suo Y, Zhang B, Jin W, Yu Y, Mu Y. Direct single-cell antimicrobial susceptibility testing of Escherichia coli in urine using a ready-to-use 3D microwell array chip. LAB ON A CHIP 2023; 23:2399-2410. [PMID: 36806255 DOI: 10.1039/d2lc01095j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Empirical antibiotic therapies are prescribed for treating uncomplicated urinary tract infections (UTIs) due to the long turnaround time of conventional antimicrobial susceptibility testing (AST), leading to the prevalence of multi-drug resistant pathogens. We present a ready-to-use 3D microwell array chip to directly conduct comprehensive AST of pathogenic agents in urine at the single-cell level. The developed device features a highly integrated 3D microwell array, offering a dynamic range from 102 to 107 CFU mL-1, and a capillary valve-based flow distributor for flow equidistribution in dispensing channels and uniform sample distribution. The chip with pre-loaded reagents and negative pressure inside only requires the user to initiate AST by loading samples (∼3 s) and can work independently. We demonstrate an accessible sample-to-result workflow, including syringe filter-based bacteria separation and rapid single-cell AST on chip, which enables us to bypass the time-consuming bacteria isolation and pre-culture, speeding up the AST in ∼3 h from 2 days of conventional methods. Moreover, the bacterial concentration and AST with minimum inhibitory concentrations can be assessed simultaneously to provide comprehensive information on infections. With further development for multiple antibiotic conditions, the Dsc-AST assay could contribute to timely prescription of targeted drugs for better patient outcomes and mitigation of the threat of drug-resistant bacteria.
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Affiliation(s)
- Wenshuai Wu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
| | - Gaozhe Cai
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | - Yang Liu
- School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 102401, China
| | - Yuanjie Suo
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
| | - Boran Zhang
- Department of Hydraulic Engineering, College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China
| | - Wei Jin
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
- Huzhou Institute of Zhejiang University, Huzhou 313002, China
| | - Yinghua Yu
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Ying Mu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
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Zhang L, Parvin R, Chen M, Hu D, Fan Q, Ye F. High-throughput microfluidic droplets in biomolecular analytical system: A review. Biosens Bioelectron 2023; 228:115213. [PMID: 36906989 DOI: 10.1016/j.bios.2023.115213] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Droplet microfluidic technology has revolutionized biomolecular analytical research, as it has the capability to reserve the genotype-to-phenotype linkage and assist for revealing the heterogeneity. Massive and uniform picolitre droplets feature dividing solution to the level that single cell and single molecule in each droplet can be visualized, barcoded, and analyzed. Then, the droplet assays can unfold intensive genomic data, offer high sensitivity, and screen and sort from a large number of combinations or phenotypes. Based on these unique advantages, this review focuses on up-to-date research concerning diverse screening applications utilizing droplet microfluidic technology. The emerging progress of droplet microfluidic technology is first introduced, including efficient and scaling-up in droplets encapsulation, and prevalent batch operations. Then the new implementations of droplet-based digital detection assays and single-cell muti-omics sequencing are briefly examined, along with related applications such as drug susceptibility testing, multiplexing for cancer subtype identification, interactions of virus-to-host, and multimodal and spatiotemporal analysis. Meanwhile, we specialize in droplet-based large-scale combinational screening regarding desired phenotypes, with an emphasis on sorting for immune cells, antibodies, enzymatic properties, and proteins produced by directed evolution methods. Finally, some challenges, deployment and future perspective of droplet microfluidics technology in practice are also discussed.
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Affiliation(s)
- Lexiang Zhang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Rokshana Parvin
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Mingshuo Chen
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Dingmeng Hu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Qihui Fan
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China; Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Fangfu Ye
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China; Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
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15
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李 政, 彭 显. [Application of Droplet-Based Microfluidics in Microbial Research]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2023; 54:673-678. [PMID: 37248604 PMCID: PMC10475413 DOI: 10.12182/20230560303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Indexed: 05/31/2023]
Abstract
Droplet-based microfluidics is a technology that generates and manipulates highly uniform droplets, ranging from picoliter to nanoliter droplets, in microchannels under precise control. In biological research, each droplet can be used to encapsulate a small group of cells or even a single cell, and then serve as an individual container for biochemical reaction, which is well suited for high-throughput and high-resolution biochemical analysis. In the field of microbial research, from cultivation and identification of microbes to the investigation of the spatiotemporal dynamics of microbial communities, from precise quantitation of microbiota to systematic study of microbial interactions, and from the isolation of rare and unculturable microbes to the development of genetically engineered strains, droplet microfluidic technology has played an important promotional role in all these aspects. Droplet microfluidics shows potential for becoming a basic tool for exploring single-cell microbes in microbiological research. In this review, we gave a brief overview of the technical basis of droplet microfluidics. Then, we presented its latest applications in microbial research and had some discussions, aiming to provide a reference for relevant research on microorganisms.
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Affiliation(s)
- 政毅 李
- 口腔疾病研究国家重点实验室 四川大学华西口腔医院 (成都 610041)State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 显 彭
- 口腔疾病研究国家重点实验室 四川大学华西口腔医院 (成都 610041)State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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16
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Li C, McCrone S, Warrick JW, Andes DR, Hite Z, Volk CF, Rose WE, Beebe DJ. Under-oil open microfluidic systems for rapid phenotypic antimicrobial susceptibility testing. LAB ON A CHIP 2023; 23:2005-2015. [PMID: 36883560 PMCID: PMC10581760 DOI: 10.1039/d3lc00066d] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Antimicrobial susceptibility testing (AST) remains the cornerstone of effective antimicrobial selection and optimization in patients. Despite recent advances in rapid pathogen identification and resistance marker detection with molecular diagnostics (e.g., qPCR, MALDI-TOF MS), phenotypic (i.e., microbial culture-based) AST methods - the gold standard in hospitals/clinics - remain relatively unchanged over the last few decades. Microfluidics-based phenotypic AST has been growing fast in recent years, aiming for rapid (i.e., turnaround time <8 h), high-throughput, and automated species identification, resistance detection, and antibiotics screening. In this pilot study, we describe the application of a multi-liquid-phase open microfluidic system, named under-oil open microfluidic systems (UOMS), to achieve a rapid phenotypic AST. UOMS provides an open microfluidics-based solution for rapid phenotypic AST (UOMS-AST) by implementing and recording a pathogen's antimicrobial activity in micro-volume testing units under an oil overlay. UOMS-AST allows free physical access (e.g., by standard pipetting) to the system and label-free, single-cell resolution optical access. UOMS-AST can accurately and rapidly determine antimicrobial activities [including susceptibility/resistance breakpoint and minimum inhibitory concentration (MIC)] from nominal sample/bacterial cells in a system aligned with clinical laboratory standards where open systems and optical microscopy are predominantly adopted. Further, we combine UOMS-AST with a cloud lab data analytic technique for real-time image analysis and report generation to provide a rapid (<4 h) sample-to-report turnaround time, shedding light on its utility as a versatile (e.g., low-resource setting and manual laboratory operation, or high-throughput automated system) phenotypic AST platform for hospital/clinic use.
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Affiliation(s)
- Chao Li
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sue McCrone
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jay W. Warrick
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David R. Andes
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zachary Hite
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Cecilia F. Volk
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Warren E. Rose
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - David J. Beebe
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
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17
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Li S, Wan C, Wang B, Chen D, Zeng W, Hong X, Li L, Pang Z, Du W, Feng X, Chen P, Li Y, Liu BF. Handyfuge Microfluidic for On-Site Antibiotic Susceptibility Testing. Anal Chem 2023; 95:6145-6155. [PMID: 36996249 DOI: 10.1021/acs.analchem.3c00557] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Low-cost, rapid, and accurate acquisition of minimum inhibitory concentrations (MICs) is key to limiting the development of antimicrobial resistance (AMR). Until now, conventional antibiotic susceptibility testing (AST) methods are typically time-consuming, high-cost, and labor-intensive, making them difficult to accomplish this task. Herein, an electricity-free, portable, and robust handyfuge microfluidic chip was developed for on-site AST, termed handyfuge-AST. With simply handheld centrifugation, the bacterial-antibiotic mixtures with accurate antibiotic concentration gradients could be generated in less than 5 min. The accurate MIC values of single antibiotics (including ampicillin, kanamycin, and chloramphenicol) or their combinations against Escherichia coli could be obtained within 5 h. To further meet the growing demands of point-of-care testing, we upgraded our handyfuge-AST with a pH-based colorimetric strategy, enabling naked eye recognition or intelligent recognition with a homemade mobile app. Through a comparative study of 60 clinical data (10 clinical samples corresponding to six commonly used antibiotics), the accurate MICs by handyfuge-AST with 100% categorical agreements were achieved compared to clinical standard methods (area under curves, AUCs = 1.00). The handyfuge-AST could be used as a low-cost, portable, and robust point-of-care device to rapidly obtain accurate MIC values, which significantly limit the progress of AMR.
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Affiliation(s)
- Shunji Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Chao Wan
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Bangfeng Wang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Dongjuan Chen
- Department of Laboratory Medicine, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430070, China
| | - Wenyi Zeng
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xianzhe Hong
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Lina Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zheng Pang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Wei Du
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaojun Feng
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Peng Chen
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yiwei Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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18
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Zhang Y, Kepiro I, Ryadnov MG, Pagliara S. Single Cell Killing Kinetics Differentiate Phenotypic Bacterial Responses to Different Antibacterial Classes. Microbiol Spectr 2023; 11:e0366722. [PMID: 36651776 PMCID: PMC9927147 DOI: 10.1128/spectrum.03667-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/19/2022] [Indexed: 01/19/2023] Open
Abstract
With the spread of multidrug-resistant bacteria, there has been an increasing focus on molecular classes that have not yet yielded an antibiotic. A key capability for assessing and prescribing new antibacterial treatments is to compare the effects antibacterial agents have on bacterial growth at a phenotypic, single-cell level. Here, we combined time-lapse microscopy with microfluidics to investigate the concentration-dependent killing kinetics of stationary-phase Escherichia coli cells. We used antibacterial agents from three different molecular classes, β-lactams and fluoroquinolones, with the known antibiotics ampicillin and ciprofloxacin, respectively, and a new experimental class, protein Ψ-capsids. We found that bacterial cells elongated when treated with ampicillin and ciprofloxacin used at their minimum inhibitory concentration (MIC). This was in contrast to Ψ-capsids, which arrested bacterial elongation within the first two hours of treatment. At concentrations exceeding the MIC, all the antibacterial agents tested arrested bacterial growth within the first 2 h of treatment. Further, our single-cell experiments revealed differences in the modes of action of three different agents. At the MIC, ampicillin and ciprofloxacin caused the lysis of bacterial cells, whereas at higher concentrations, the mode of action shifted toward membrane disruption. The Ψ-capsids killed cells by disrupting their membranes at all concentrations tested. Finally, at increasing concentrations, ampicillin and Ψ-capsids reduced the fraction of the population that survived treatment in a viable but nonculturable state, whereas ciprofloxacin increased this fraction. This study introduces an effective capability to differentiate the killing kinetics of antibacterial agents from different molecular classes and offers a high content analysis of antibacterial mechanisms at the single-cell level. IMPORTANCE Antibiotics act against bacterial pathogens by inhibiting their growth or killing them directly. Different modes of action determine different antibacterial responses, whereas phenotypic differences in bacteria can challenge the efficacy of antibiotics. Therefore, it is important to be able to differentiate the concentration-dependent killing kinetics of antibacterial agents at a single-cell level, in particular for molecular classes which have not yielded an antibiotic before. Here, we measured single-cell responses using microfluidics-enabled imaging, revealing that a novel class of antibacterial agents, protein Ψ-capsids, arrests bacterial elongation at the onset of treatment, whereas elongation continues for cells treated with β-lactam and fluoroquinolone antibiotics. The study advances our current understanding of antibacterial function and offers an effective strategy for the comparative design of new antibacterial therapies, as well as clinical antibiotic susceptibility testing.
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Affiliation(s)
- Yuewen Zhang
- Living Systems Institute and Biosciences, University of Exeter, Exeter, United Kingdom
- National Physical Laboratory, Teddington, United Kingdom
| | - Ibolya Kepiro
- National Physical Laboratory, Teddington, United Kingdom
| | - Maxim G. Ryadnov
- National Physical Laboratory, Teddington, United Kingdom
- Department of Physics, King’s College London, London, United Kingdom
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Exeter, United Kingdom
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19
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Wang Y, Cai D, Ouyang X, He H, Liu Y, Zou J, Chen Z, Wu B, Wu H, Liu D. Cascade filtration and droplet digital detection integrated microfluidic assay enables isolating culture-free phenotypic identification of carbapenem-resistant organisms. Biosens Bioelectron 2023; 220:114863. [DOI: 10.1016/j.bios.2022.114863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022]
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20
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Chen W, Chen H, Liu Y, Wei H, Wang Y, Rong Z, Liu X. An integrated fluorescent lateral flow assay for multiplex point-of-care detection of four respiratory viruses. Anal Biochem 2022; 659:114948. [PMID: 36216143 DOI: 10.1016/j.ab.2022.114948] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/24/2022] [Accepted: 10/03/2022] [Indexed: 12/14/2022]
Abstract
This work established a highly sensitive and specific quantum dot nanobeads-based lateral flow assay for multiplex detection of four respiratory virus markers at point of care. The respiratory virus antigens were detected by fluorescent lateral flow strips within 20 min. The limits of detection for SARS-CoV-2 antigen, IAV antigen, IBV antigen, and ADV antigen were 0.01 ng/mL, 0.05 ng/mL, 0.31 ng/mL, and 0.40 ng/mL, respectively, which were superior to that of conventional AuNPs-based colorimetric lateral flow assay. The coefficients of variation of the test strip were 6.09%, 2.24%, 7.92%, and 12.43% for these four antigens, which indicated that the proposed method had good repeatability. The specificity of the detection system was verified by different combinations of these four respiratory viruses and several other respiratory pathogens. These results indicated that this method could simultaneously detect SARS-CoV-2, IAV, IBV and ADV in a short assay time, showing the remarkable potential for the rapid and multiplex detection of respiratory viruses in resource-limited settings.
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Affiliation(s)
- Wenji Chen
- The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121012, PR China; Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Hong Chen
- Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Ye Liu
- Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Hongjuan Wei
- Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Yunxiang Wang
- Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Zhen Rong
- Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China.
| | - Xin Liu
- The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121012, PR China; Jinzhou Medical University Huludao Central Hospital Teaching Base, Huludao, 125001, PR China.
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21
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Interaction of a natural compound nanoemulsion with Gram negative and Gram positive bacterial membrane; a mechanism based study using a microfluidic chip and DESI technique. Int J Pharm 2022; 626:122181. [PMID: 36087628 DOI: 10.1016/j.ijpharm.2022.122181] [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: 05/09/2022] [Revised: 08/28/2022] [Accepted: 09/02/2022] [Indexed: 11/23/2022]
Abstract
The antibacterial activity of a nanoemulsion prepared from Satureja Khusitanica essential oil against a Gram-negative (Escherichia coli) and a Gram-positive (Bacillus atrophaeus) bacteria evaluated using microfluidic and conventional techniques. The effect of different residence time and concentrations on the antibacterial activity of nanoemulsion was studied by measuring the release of protein, nucleic acids, potassium, and also recording the MIC, MBC and time killing assays. Remarkable intensification was observed by employing microfluidic chip regarding a high-contact surface area between nanodroplets and bacterial membrane. The MIC and MBC values for E. coli and B. atrophaeus in conventional method were 400 and 1600 µg mL-1, respectively, whereas these values reduced to 11 to 50 µg mL-1 using microfluidic system. B. atrophaeus seemed to be more resistant than E. coli to the nanoemulsion treatment, perhaps due to different cell wall structures. Bacterial cell wall changes were examined using a desorption electrospray ionization (DESI) technique. It was found that the structural changes were more imminent in Gram negative E. coli by detecting a number of released lipids including phosphatidyl glycerol and phosphatidyl ethanolamines. The DESI spectra of B. atrophaeus revealed no M/Z related lipid release. These findings may help providing novel nano based natural antibacterials.
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22
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Li X, Liu X, Yu Z, Luo Y, Hu Q, Xu Z, Dai J, Wu N, Shen F. Combinatorial screening SlipChip for rapid phenotypic antimicrobial susceptibility testing. LAB ON A CHIP 2022; 22:3952-3960. [PMID: 36106408 DOI: 10.1039/d2lc00661h] [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
Antimicrobial resistance (AMR) by bacteria is a serious global threat, and a rapid, high-throughput, and easy-to-use phenotypic antimicrobial susceptibility testing (AST) method is essential for making timely treatment decisions and controlling the spread of antibiotic resistant micro-organisms. Traditional culture-based methods are time-consuming, and their capability to screen against a large number of different conditions is limited; meanwhile genotypic based methods, including sequencing and PCR based methods, are constrained by rarely identified resistance genes and complicated resistance mechanisms. Here, a combinatorial-screening SlipChip (cs-SlipChip) containing 192 nanoliter-sized compartments is developed which can perform high-throughput phenotypic AST within three hours by monitoring the bacterial growth within nanoliter-sized droplets with bright-field imaging and analyzing the changes in bacterial number and morphology. The minimum inhibitory concentration (MIC) of Escherichia coli ATCC 25922 against four antibiotics (ampicillin, ciprofloxacin, ceftazidime, and nitrofurantoin) can be measured in one chip within 3 hours. Furthermore, five antibiotic-resistant E. coli strains were isolated from patients diagnosed with urinary tract infections (UTIs), and an individual isolate was tested using four antibiotics and eleven antibiotic combinations simultaneously with three different concentrations of each. The results from the cs-SlipChip agree with those of a VITEK 2 automated system. This cs-SlipChip provides a practical high-throughput and rapid phenotypic method for AST and can also be used to screen different chemicals and antibiotic combinations for the treatment of multiple antibiotic-resistant bacteria.
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Affiliation(s)
- Xiang Li
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
| | - Xu Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
| | - Ziqing Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
| | - Yang Luo
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
| | - Qixin Hu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
| | - Zhenye Xu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
| | - Jia Dai
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Nannan Wu
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
- CreatiPhage Biotechnology Co., Ltd, Shanghai, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
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23
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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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Cao J, Chande C, Köhler JM. Microtoxicology by microfluidic instrumentation: a review. LAB ON A CHIP 2022; 22:2600-2623. [PMID: 35678285 DOI: 10.1039/d2lc00268j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microtoxicology is concerned with the toxic effects of small amounts of substances. This review paper discusses the application of small amounts of noxious substances for toxicological investigation in small volumes. The vigorous development of miniaturized methods in microfluidics over the last two decades involves chip-based devices, micro droplet-based procedures, and the use of micro-segmented flow for microtoxicological studies. The studies have shown that the microfluidic approach is particularly valuable for highly parallelized and combinatorial dose-response screenings. Accurate dosing and mixing of effector substances in large numbers of microcompartments supplies detailed data of dose-response functions by highly concentration-resolved assays and allows evaluation of stochastic responses in case of small separated cell ensembles and single cell experiments. The investigations demonstrate that very different biological targets can be studied using miniaturized approaches, among them bacteria, eukaryotic microorganisms, cell cultures from tissues of multicellular organisms, stem cells, and early embryonic states. Cultivation and effector exposure tests can be performed in small volumes over weeks and months, confirming that the microfluicial strategy is also applicable for slow-growing organisms. Here, the state of the art of miniaturized toxicology, particularly for studying antibiotic susceptibility, drug toxicity testing in the miniaturized system like organ-on-chip, environmental toxicology, and the characterization of combinatorial effects by two and multi-dimensional screenings, is discussed. Additionally, this review points out the practical limitations of the microtoxicology platform and discusses perspectives on future opportunities and challenges.
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Affiliation(s)
- Jialan Cao
- Techn. Univ. Ilmenau, Dept. Phys. Chem. and Microreaction Technology, Institute for Micro- und Nanotechnologies/Institute for Chemistry and Biotechnology, Ilmenau, Germany.
| | - Charmi Chande
- Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - J Michael Köhler
- Techn. Univ. Ilmenau, Dept. Phys. Chem. and Microreaction Technology, Institute for Micro- und Nanotechnologies/Institute for Chemistry and Biotechnology, Ilmenau, Germany.
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Liu X, Li X, Wu N, Luo Y, Zhang J, Yu Z, Shen F. Formation and Parallel Manipulation of Gradient Droplets on a Self-Partitioning SlipChip for Phenotypic Antimicrobial Susceptibility Testing. ACS Sens 2022; 7:1977-1984. [PMID: 35815869 DOI: 10.1021/acssensors.2c00734] [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: 11/29/2022]
Abstract
Flexible, robust, and user-friendly screening systems with a large dynamic range are highly desired in scientific research, industrial development, and clinical diagnostics. Droplet-based microfluidic systems with gradient concentrations of chemicals have been demonstrated as promising tools to provide confined microenvironments for screening tests with small reaction volumes. However, the generation and manipulation of gradient droplets, such as droplet merging, generally require sophisticated fluidic manipulation systems, potentially limiting their application in decentralized settings. We present a gradient-droplet SlipChip (gd-SlipChip) microfluidic device that enables instrument-free gradient droplet formation and parallel manipulation. The device can establish a gradient profile by free interfacial diffusion in a continuous fluidic channel. With a simple slipping step, gradient droplets can be generated by a surface tension-driven self-partitioning process. Additional reagents can be introduced in parallel to these gradient droplets with further slipping operations to initiate screening tests of the droplets over a large concentration range. To profile the concentration in the gradient droplets, we establish a numerical simulation model and verify it with hydrogen chloride (HCl) diffusion, as tested with a dual-color pH indicator (methyl orange and aniline blue). As a proof of concept, we tested this system with a gradient concentration of nitrofurantoin for the phenotypic antimicrobial susceptibility testing (AST) of Escherichia coli. The results of our gd-SlipChip-based AST on both reference and clinical strains of E. coli can be indicated by the bacterial growth profile within 3 h and are consistent with the clinical culture-based AST.
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Affiliation(s)
- Xu Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Xiang Li
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Nannan Wu
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200433, China
| | - Yang Luo
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Jiajie Zhang
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Ziqing Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
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Chen ZP, Yang P, Yang ZZ, Chai YQ, Yuan R, Zhuo Y, Liang WB. One-Step Digital Droplet Auto-Catalytic Nucleic Acid Amplification with High-Throughput Fluorescence Imaging and Droplet Tracking Computation. Anal Chem 2022; 94:9166-9175. [PMID: 35708271 DOI: 10.1021/acs.analchem.2c01754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Digital droplet technology has emerged as a powerful new tool for biomarker analysis. Temperature cycling, enzymes, and off-chip processes are, nevertheless, always required. Herein, we constructed a digital droplet auto-catalytic hairpin assembly (ddaCHA) microfluidic system to achieve digital quantification of single-molecule microRNA (miRNA). The designed continuous chip integrates droplet generation, incubation, and fluorescence imaging on the chip, avoiding the requirement for extra droplet re-collection and heating operations. Clearly, the digital readout was obtained by partitioning miRNA into many individual pL-sized small droplets in which the target molecule is either present ("positive") or absent ("negative"). Importantly, the suggested enzyme-free auto-catalytic hairpin assembly (aCHA) in droplets successfully mitigated the effects of the external environment and thermal cycling on droplets, and its reaction rate is significantly superior to that of traditional CHA. We got excellent sensitivity with a linear correlation from 1 pM to 10 nM and a detection limit of 0.34 pM in the fluorescence spectrum section, as well as high selectivity to other miRNAs. Furthermore, the minimum target concentration could be reduced to 10 fM based on the high-throughput tracking computation of fluorescent droplets with a self-developed Python script, and the fluorescence intensity distribution agreed well with the theoretical value, demonstrating that it is feasible to detect miRNA efficiently and accurately, which has great potential applications in clinical diagnostics and biochemical research.
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Affiliation(s)
- Zhao-Peng Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Peng Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ze-Zhou Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Wen-Bin Liang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
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Saxena S, Punjabi K, Ahamad N, Singh S, Bendale P, Banerjee R. Nanotechnology Approaches for Rapid Detection and Theranostics of Antimicrobial Resistant Bacterial Infections. ACS Biomater Sci Eng 2022; 8:2232-2257. [PMID: 35546526 DOI: 10.1021/acsbiomaterials.1c01516] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
As declared by WHO, antimicrobial resistance (AMR) is a high priority issue with a pressing need to develop impactful technologies to curb it. The rampant and inappropriate use of antibiotics due to the lack of adequate and timely diagnosis is a leading cause behind AMR evolution. Unfortunately, populations with poor economic status and those residing in densely populated areas are the most affected ones, frequently leading to emergence of AMR pathogens. Classical approaches for AMR diagnostics like phenotypic methods, biochemical assays, and molecular techniques are cumbersome and resource-intensive and involve a long turnaround time to yield confirmatory results. In contrast, recent emergence of nanotechnology-assisted approaches helps to overcome challenges in classical approaches and offer simpler, more sensitive, faster, and more affordable solutions for AMR diagnostics. Nanomaterial platforms (metallic, quantum-dot, carbon-based, upconversion, etc.), nanoparticle-based rapid point-of-care platforms, nano-biosensors (optical, mechanical, electrochemical), microfluidic-assisted devices, and importantly, nanotheranostic devices for diagnostics with treatment of AMR infections are examples of rapidly growing nanotechnology approaches used for AMR management. This review comprehensively summarizes the past 10 years of research progress on nanotechnology approaches for AMR diagnostics and for estimating antimicrobial susceptibility against commonly used antibiotics. This review also highlights several bottlenecks in nanotechnology approaches that need to be addressed prior to considering their translation to clinics.
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Affiliation(s)
- Survanshu Saxena
- Nanomedicine Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Kapil Punjabi
- Nanomedicine Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Nadim Ahamad
- Nanomedicine Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Subhasini Singh
- Nanomedicine Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Prachi Bendale
- Nanomedicine Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Rinti Banerjee
- Nanomedicine Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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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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Hsieh K, Mach KE, Zhang P, Liao JC, Wang TH. Combating Antimicrobial Resistance via Single-Cell Diagnostic Technologies Powered by Droplet Microfluidics. Acc Chem Res 2022; 55:123-133. [PMID: 34898173 PMCID: PMC10023138 DOI: 10.1021/acs.accounts.1c00462] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Antimicrobial resistance is a global threat that if left unchecked could lead to 10 million annual mortalities by 2050. One factor contributing to the rise of multi-drug-resistant (MDR) pathogens is the reliance on traditional culture-based pathogen identification (ID) and antimicrobial susceptibility testing (AST) that typically takes several days. This delay of objective pathogen ID and AST information to inform clinical decision making results in clinicians treating patients empirically often using first-line, broad-spectrum antibiotics, contributing to the misuse/overuse of antibiotics. To combat the rise in MDR pathogens, there is a critical demand for rapid ID and AST technologies. Among the advances in ID and AST technologies in the past decade, single-cell diagnostic technologies powered by droplet microfluidics offer great promise due to their potential for high-sensitivity detection and rapid turnaround time. Our laboratory has been at the forefront of developing such technologies and applying them to diagnosing urinary tract infections (UTIs), one of the most common infections and a frequent reason for the prescription of antimicrobials. For pathogen ID, we first demonstrated the highly sensitive, amplification-free detection of single bacterial cells by confining them in picoliter-scale droplets and detection with fluorogenic peptide nucleic acid (PNA) probes that target their 16S rRNA (rRNA), a well-characterized marker for phylogenic classification. We subsequently improved the PNA probe design and enhanced detection sensitivity. For single-cell AST, we first employed a growth indicator dye and engineered an integrated device that allows us to detect growth from single bacterial cells under antibiotic exposure within 1 h, equivalent to two to three bacterial replications. To expand beyond testing a single antibiotic condition per device, a common limitation for droplet microfluidics, we developed an integrated programmable droplet microfluidic device for scalable single-cell AST. Using the scalable single-cell AST platform, we demonstrated the generation of up to 32 droplet groups in a single device with custom antibiotic titers and the capacity to scale up single-cell AST, and providing reliable pathogen categories beyond a binary call embodies a critical advance. Finally, we developed an integrated ID and AST platform. To this end, we developed a PNA probe panel that can identify nearly 90% of uropathogens and showed the quantitative detection of 16S rRNA from single bacterial cells in droplet-enabled AST after as little as 10 min of antibiotic exposure. This platform achieved both ID and AST from minimally processed urine samples in 30 min, representing one of the fastest turnaround times to date. In addition to tracing the development of our technologies, we compare them with contemporary research advances and offer our perspectives for future development, with the vision that single-cell ID and AST technologies powered by droplet microfluidics can indeed become a useful diagnostic tool for combating antimicrobial resistance.
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Affiliation(s)
| | - Kathleen E Mach
- Department of Urology, Stanford University School of Medicine, Stanford, California 94305, United States
| | | | - Joseph C Liao
- Department of Urology, Stanford University School of Medicine, Stanford, California 94305, United States
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32
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Zhang P, Kaushik AM, Hsieh K, Li S, Lewis S, Mach KE, Liao JC, Carroll KC, Wang TH. A Cascaded Droplet Microfluidic Platform Enables High-Throughput Single Cell Antibiotic Susceptibility Testing at Scale. SMALL METHODS 2022; 6:e2101254. [PMID: 35041266 DOI: 10.1002/smtd.202101254] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Indexed: 06/14/2023]
Abstract
The global threat of antibiotic resistance underscores critical but unmet needs for rapid antibiotic susceptibility testing (AST) technologies. To this end, droplet microfluidic-based single-cell AST offers promise by achieving unprecedented rapidity, but its potential for clinical use is marred by the capacity of testing one to few antibiotic conditions per device, which falls short from the required scale in clinically relevant scenarios. To lift the scalability constraint in rapid single-cell AST technologies, a new cascaded droplet microfluidic platform that can streamline bacteria/antibiotic mixing, single-cell encapsulation within picoliter droplets, incubation, and detection in a continuous, assembly-line-like workflow is developed. The scalability of the platform is demonstrated by generating 32 groups of ≈10 000 droplets with custom antibiotic conditions within a single device, from which a new statistics-based method is used to analyze the single cell data and produce clinically useful antibiograms with minimum inhibitory concentrations in ≈90 min for the first antibiotic, plus 2 min for each subsequent antibiotic condition. Potential clinical utility of this platform is demonstrated by testing three clinical isolates and eight urine specimens against four frequently used antibiotics, and 100% and 93.8% categorical agreements are achieved compared to laboratory-based results that became available after 48 h.
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Affiliation(s)
- Pengfei Zhang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Aniruddha M Kaushik
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Sixuan Li
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Shawna Lewis
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Kathleen E Mach
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Joseph C Liao
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
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Heuer C, Bahnemann J, Scheper T, Segal E. Paving the Way to Overcome Antifungal Drug Resistance: Current Practices and Novel Developments for Rapid and Reliable Antifungal Susceptibility Testing. SMALL METHODS 2021; 5:e2100713. [PMID: 34927979 DOI: 10.1002/smtd.202100713] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/05/2021] [Indexed: 06/14/2023]
Abstract
The past year has established the link between the COVID-19 pandemic and the global spread of severe fungal infections; thus, underscoring the critical need for rapid and realizable fungal disease diagnostics. While in recent years, health authorities, such as the Centers for Disease Control and Prevention, have reported the alarming emergence and spread of drug-resistant pathogenic fungi and warned against the devastating consequences, progress in the diagnosis and treatment of fungal infections is limited. Early diagnosis and patient-tailored therapy are established to be key in reducing morbidity and mortality associated with fungal (and cofungal) infections. As such, antifungal susceptibility testing (AFST) is crucial in revealing susceptibility or resistance of these pathogens and initiating correct antifungal therapy. Today, gold standard AFST methods require several days for completion, and thus this much delayed time for answer limits their clinical application. This review focuses on the advancements made in developing novel AFST techniques and discusses their implications in the context of the practiced clinical workflow. The aim of this work is to highlight the advantages and drawbacks of currently available methods and identify the main gaps hindering their progress toward clinical application.
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Affiliation(s)
- Christopher Heuer
- Institute of Technical Chemistry, Leibniz University Hannover, 30167, Hannover, Germany
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 320003, Israel
| | - Janina Bahnemann
- Institute of Technical Chemistry, Leibniz University Hannover, 30167, Hannover, Germany
| | - Thomas Scheper
- Institute of Technical Chemistry, Leibniz University Hannover, 30167, Hannover, Germany
| | - Ester Segal
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 320003, Israel
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Sunkara V, Kumar S, Sabaté del Río J, Kim I, Cho YK. Lab-on-a-Disc for Point-of-Care Infection Diagnostics. Acc Chem Res 2021; 54:3643-3655. [PMID: 34516092 DOI: 10.1021/acs.accounts.1c00367] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Reliable, inexpensive, and rapid diagnostic tools are essential to control and prevent the spread of infectious diseases. Many commercial kits for coronavirus disease 2019 (COVID-19) diagnostics have played a crucial role in the fight against the COVID-19 pandemic. Most current standard in vitro diagnostic (IVD) protocols for infectious diseases are sensitive but time-consuming and require sophisticated laboratory equipment and specially trained personnel. Recent advances in biosensor technology suggest the potential to deliver point-of-care (POC) diagnostics that are affordable and provide accurate results in a short time. The ideal "sample-in-answer-out" type fully integrated POC infection diagnostic platforms are expected to be autonomous or easy-to-operate, equipment-free or infrastructure-independent, and high-throughput or easy to upscale. In this Account, we detail the recent progress made by our group and others in the development of centrifugal microfluidic devices or lab-on-a-disc (LOAD) systems. Unlike conventional pump-based fluid actuation, the centrifugal force generated by spinning the disc induces liquid pumping and no external fluidic interconnects are required. This allows a total fluidic network required for multiple steps of biological assays to be integrated on a disc, enabling fully automated POC diagnostics. Various applications have been demonstrated, including liquid biopsy for personalized cancer management, food applications, and environmental monitoring; here, we focus on IVD for infectious disease. First, we introduce various on-disc unit operation technologies, including reagent storage, sedimentation, filtration, valving, decanting, aliquoting, mixing, separation, serial dilution, washing, and calibration. Such centrifugal microfluidic technologies have already proved promising for micro-total-analysis systems for automated IVD ranging from molecular detection of pathogens to multiplexed enzyme-linked immunosorbent assays (ELISAs) that use raw samples such as whole blood or saliva. Some recent examples of LOAD systems for molecular diagnostics in which some or all steps of the assays are integrated on a disc, including pathogen enrichment, nucleic acid extraction, amplification, and detection, are discussed in detail. We then introduce fully automated ELISA systems with enhanced sensitivity. Furthermore, we demonstrate a toy-inspired fidget spinner that enables electricity-free and rapid analysis of pathogens from undiluted urine samples of patients with urinary tract infection symptoms and a phenotypic antimicrobial susceptibility test for an extreme POC diagnostics application. Considering the urgent need for cost-effective and reliable POC infection diagnostic tools, especially in the current pandemic crisis, the current limitations and future directions of fast and broad adaptation in real-world settings are also discussed. With proper attention to key challenges and leverage with recent advances in bio-sensing technologies, molecular biology, nanomaterials, analytical chemistry, miniaturization, system integration, and data management, LOAD systems hold the potential to deliver POC infection diagnostic tools with unprecedented performance regarding time, accuracy, and cost. We hope the new insight and promise of LOAD systems for POC infection diagnostics presented in this Account can spark new ideas and inspire further research and development to create better healthcare systems for current and future pandemics.
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Affiliation(s)
- Vijaya Sunkara
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Sumit Kumar
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Jonathan Sabaté del Río
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Insu Kim
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Yoon-Kyoung Cho
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
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Li N, Zhang T, Chen G, Xu J, Ouyang G, Zhu F. Recent advances in sample preparation techniques for quantitative detection of pharmaceuticals in biological samples. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116318] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Viri V, Arveiler M, Lehnert T, Gijs MAM. An In Vivo Microfluidic Study of Bacterial Load Dynamics and Absorption in the C. elegans Intestine. MICROMACHINES 2021; 12:832. [PMID: 34357242 PMCID: PMC8304684 DOI: 10.3390/mi12070832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 01/19/2023]
Abstract
Caenorhabditiselegans (C. elegans) has gained importance as a model for studying host-microbiota interactions and bacterial infections related to human pathogens. Assessing the fate of ingested bacteria in the worm's intestine is therefore of great interest, in particular with respect to normal bacterial digestion or intestinal colonization by pathogens. Here, we report an in vivo study of bacteria in the gut of C. elegans. We take advantage of a polydimethylsiloxane (PDMS) microfluidic device enabling passive immobilization of adult worms under physiological conditions. Non-pathogenic Escherichia coli (E. coli) bacteria expressing either pH-sensitive or pH-insensitive fluorescence reporters as well as fluorescently marked indigestible microbeads were used for the different assays. Dynamic fluorescence patterns of the bacterial load in the worm gut were conveniently monitored by time-lapse imaging. Cyclic motion of the bacterial load due to peristaltic activity of the gut was observed and biochemical digestion of E. coli was characterized by high-resolution fluorescence imaging of the worm's intestine. We could discriminate between individual intact bacteria and diffuse signals related to disrupted bacteria that can be digested. From the decay of the diffuse fluorescent signal, we determined a digestion time constant of 14 ± 4 s. In order to evaluate the possibility to perform infection assays with our platform, immobilized C. elegans worms were fed pathogenic Mycobacterium marinum (M. marinum) bacteria. We analyzed bacterial fate and accumulation in the gut of N2 worms and mitochondrial stress response in a hsp-6::gfp mutant.
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Affiliation(s)
| | | | | | - Martin A. M. Gijs
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland; (V.V.); (M.A.); (T.L.)
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Jusková P, Schmitt S, Kling A, Rackus DG, Held M, Egli A, Dittrich PS. Real-Time Respiration Changes as a Viability Indicator for Rapid Antibiotic Susceptibility Testing in a Microfluidic Chamber Array. ACS Sens 2021; 6:2202-2210. [PMID: 33900065 PMCID: PMC8240088 DOI: 10.1021/acssensors.1c00020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Rapid identification
of a pathogen and the measurement of its antibiotic
susceptibility are key elements in the diagnostic process of bacterial
infections. Microfluidic technologies offer great control over handling
and manipulation of low sample volumes with the possibility to study
microbial cultures on the single-cell level. Downscaling the dimensions
of cultivation systems directly results in a lower number of bacteria
required for antibiotic susceptibility testing (AST) and thus in a
reduction of the time to result. The developed platform presented
in this work allows the reading of pathogen resistance profiles within
2–3 h based on the changes of dissolved oxygen levels during
bacterial cultivation. The platform contains hundreds of individual
growth chambers prefilled with a hydrogel containing oxygen-sensing
nanoprobes and different concentrations of antibiotic compounds. The
performance of the developed platform is tested using quality control Escherichia coli strains (ATCC 25922 and ATCC 35218)
in response to clinically relevant antibiotics. The results are in
agreement with values given in reference guidelines and independent
measurements using a clinical AST protocol. Finally, the platform
is successfully used for the AST of an E. coli clinical isolate obtained from a patient blood culture.
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Affiliation(s)
- Petra Jusková
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Steven Schmitt
- Department of Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - André Kling
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Darius G. Rackus
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Martin Held
- Department of Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Adrian Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031 Basel, Switzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
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Trinh TND, Lee NY. Nucleic acid amplification-based microfluidic approaches for antimicrobial susceptibility testing. Analyst 2021; 146:3101-3113. [PMID: 33876805 DOI: 10.1039/d1an00180a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Because of the global spread of antimicrobials, there is an urgent need to develop rapid and effective tools for antimicrobial susceptibility testing to help clinicians prescribe accurate and appropriate antibiotic doses sooner. The conventional methods for antimicrobial susceptibility testing are usually based on bacterial culture methods, which are time-consuming, complicated, and labor-intensive. Therefore, other approaches are needed to address these issues. Recently, microfluidic technology has gained significant attention in infection management due to its advantages including rapid detection, high sensitivity and specificity, highly automated assay, simplicity, low cost, and potential for point-of-care testing in low-resource areas. Microfluidic advances for antimicrobial susceptibility testing can be classified into phenotypic (usually culture-based) and genotypic tests. Genotypic antimicrobial susceptibility testing is the detection of resistant genes in a microorganism using methods such as nucleic acid amplification. This review (with 107 references) surveys the different forms of nucleic acid amplification-based microdevices used for genotypic antimicrobial susceptibility testing. The first section reviews the serious threat of antimicrobial-resistant microorganisms and the urgent need for fast check-ups. Next, several conventional antimicrobial susceptibility testing methods are discussed, and microfluidic technology as a promising candidate for rapid detection of antimicrobial-resistant microorganisms is briefly introduced. The next section highlights several advancements of microdevices, with an emphasis on their working principles and performance. The review concludes with the importance of fully integrated microdevices and a discussion on future perspectives.
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Affiliation(s)
- Thi Ngoc Diep Trinh
- Department of Industrial Environmental Engineering, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, Korea.
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Azizi M, Nguyen AV, Dogan B, Zhang S, Simpson KW, Abbaspourrad A. Antimicrobial Susceptibility Testing in a Rapid Single Test via an Egg-like Multivolume Microchamber-Based Microfluidic Platform. ACS APPLIED MATERIALS & INTERFACES 2021; 13:19581-19592. [PMID: 33884865 DOI: 10.1021/acsami.0c23096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fast determination of antimicrobial agents' effectiveness (susceptibility/resistance pattern) is an essential diagnostic step for treating bacterial infections and stopping world-wide outbreaks. Here, we report an egg-like multivolume microchamber-based microfluidic (EL-MVM2) platform, which is used to produce a wide range of gradient-based antibiotic concentrations quickly (∼10 min). The EL-MVM2 platform works based upon testing a bacterial suspension in multivolume microchambers (microchamber sizes that range from a volume of 12.56 to 153.86 nL). Antibiotic molecules from a stock solution diffuse into the microchambers of various volumes at the same loading rate, leading to different concentrations among the microchambers. Therefore, we can quickly and easily produce a robust antibiotic gradient-based concentration profile. The EL-MVM2 platform's diffusion (loading) pattern was investigated for different antibiotic drugs using both computational fluid dynamics simulations and experimental approaches. With an easy-to-follow protocol for sample loading and operation, the EL-MVM2 platform was also found to be of high precision with respect to predicting the susceptibility/resistance outcome (>97%; surpassing the FDA-approval criterion for technology-based antimicrobial susceptibility testing instruments). These features indicate that the EL-MVM2 is an effective, time-saving, and precise alternative to conventional antibiotic susceptibility testing platforms currently being used in clinical diagnostics and point-of-care settings.
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Affiliation(s)
- Morteza Azizi
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, New York 14853, United States
| | - Ann V Nguyen
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, New York 14853, United States
| | - Belgin Dogan
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, 602 Tower Rd., Ithaca, New York 14853, United States
| | - Shiying Zhang
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, 602 Tower Rd., Ithaca, New York 14853, United States
| | - Kenneth W Simpson
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, 602 Tower Rd., Ithaca, New York 14853, United States
| | - Alireza Abbaspourrad
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, New York 14853, United States
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Hu B, Xu P, Ma L, Chen D, Wang J, Dai X, Huang L, Du W. One cell at a time: droplet-based microbial cultivation, screening and sequencing. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:169-188. [PMID: 37073344 PMCID: PMC10077293 DOI: 10.1007/s42995-020-00082-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/22/2020] [Indexed: 05/03/2023]
Abstract
Microbes thrive and, in turn, influence the earth's environment, but most are poorly understood because of our limited capacity to reveal their natural diversity and function. Developing novel tools and effective strategies are critical to ease this dilemma and will help to understand their roles in ecology and human health. Recently, droplet microfluidics is emerging as a promising technology for microbial studies with value in microbial cultivating, screening, and sequencing. This review aims to provide an overview of droplet microfluidics techniques for microbial research. First, some critical points or steps in the microfluidic system are introduced, such as droplet stabilization, manipulation, and detection. We then highlight the recent progress of droplet-based methods for microbiological applications, from high-throughput single-cell cultivation, screening to the targeted or whole-genome sequencing of single cells.
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Affiliation(s)
- Beiyu Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Peng Xu
- Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158 USA
| | - Liang Ma
- Department of Biomedical Devices, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510320 China
| | - Dongwei Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
| | - Jian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
| | - Xin Dai
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, 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
- Department of Biomedical Devices, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510320 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 100049 China
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Azizi M, Davaji B, Nguyen AV, Zhang S, Dogan B, Simpson KW, Abbaspourrad A. Gradient-Based Microfluidic Platform for One Single Rapid Antimicrobial Susceptibility Testing. ACS Sens 2021; 6:1560-1571. [PMID: 33851833 DOI: 10.1021/acssensors.0c02428] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Antimicrobial resistance is a growing problem, necessitating rapid antimicrobial susceptibility testing (AST) to enable effective in-clinic diagnostic testing and treatment. Conventional AST using broth microdilution or the Kirby-Bauer disk diffusion are time-consuming (e.g., 24-72 h), labor-intensive, and costly and consume reagents. Here, we propose a novel gradient-based microchamber microfluidic (GM2) platform to perform AST assay for a wide range of antibiotic concentrations plus zero (positive control) and maximum (negative control) concentrations all in a single test. Antibiotic lateral diffusion within enriched to depleted (Cmax and zero, respectively) cocurrent flowing fluids, moving alongside a micron-sized main channel, is led to form an antibiotic concentration profile in microchambers, connected to the depleted side of the main channel. We examined the tunability of the GM2 platform, in terms of producing a wide range of antibiotic concentrations in a gradient mode between two consecutive microchambers with changing either the loading fluids' flow rates or their initial concentrations. We also tested the GM2 platform for profiling bacteria associated with human Crohn's disease and bovine mastitis. Time to result for performing a complete AST assay was ∼ 3-4 h in the GM2 platform. Lastly, the GM2 platform tracked the bacterial growth independent of an antibiotic mechanism of action or bacterial species in a robust and easy-to-implement fashion.
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Affiliation(s)
- Morteza Azizi
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, New York 14853, United States
| | - Benyamin Davaji
- School of Electrical and Computer Engineering, Cornell University, Philips Hall, Ithaca, New York 8 14853, United States
| | - Ann V. Nguyen
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, New York 14853, United States
| | - Shiying Zhang
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, 602 Tower Rd., Ithaca, New York 14853, United States
| | - Belgin Dogan
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, 602 Tower Rd., Ithaca, New York 14853, United States
| | - Kenneth W. Simpson
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, 602 Tower Rd., Ithaca, New York 14853, United States
| | - Alireza Abbaspourrad
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, New York 14853, United States
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Song F, Shen Y, Wei Y, Yang C, Ge X, Wang A, Li C, Wan Y, Li J. Botulinum toxin as an ultrasensitive reporter for bacterial and SARS-CoV-2 nucleic acid diagnostics. Biosens Bioelectron 2021; 176:112953. [PMID: 33418182 PMCID: PMC7836976 DOI: 10.1016/j.bios.2020.112953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 01/18/2023]
Abstract
The rapid identification of pathogenic microorganisms plays a crucial role in the timely diagnosis and treatment strategies during a global pandemic, especially in resource-limited area. Herein, we present a sensitive biosensor strategy depended on botulinum neurotoxin type A light chain (BoNT/A LC) activated complex assay (BACA). BoNT/A LC, the surrogate of BoNT/A which embodying the most potent biological poisons, could serve as an ultrasensitive signal reporter with high signal-to-noise ratio to avoid common strong background response, poor stability and low intensity of current biosensor methods. A nanoparticle hybridization system, involving specific binding probes that recognize pathogenic 16S rRNAs or SARS-CoV-2 gene site, was developed to measure double-stranded biotinylated target DNA containing a single-stranded overhang using Fluorescence Resonance Energy Transfer (FRET)-based assay and colorimetric method. The method is validated widely by six different bacteria strains and severe acute respiratory related coronavirus 2 (SARS-CoV-2) nucleic acid, demonstrating a single cell or 1 aM nucleic acid detecting sensitivity. This detection strategy offers a solution for general applications and has a great prospect to be a simple instrument-free colorimetric tool, especially when facing public health emergency.
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Affiliation(s)
- Fengge Song
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Yuanyuan Shen
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Yangdao Wei
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Chunrong Yang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Xiaolin Ge
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Aimin Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Chaoyang Li
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China; Shandong Key Laboratory of Corrosion Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
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43
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Wang Y, Zhang Y, Chen J, Wang M, Zhang T, Luo W, Li Y, Wu Y, Zeng B, Zhang K, Deng R, Li W. Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. Anal Chem 2021; 93:3393-3402. [PMID: 33511840 PMCID: PMC7860141 DOI: 10.1021/acs.analchem.0c04303] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/13/2021] [Indexed: 02/08/2023]
Abstract
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a global health emergency, and its gene mutation and evolution further posed uncertainty of epidemic risk. Herein, we reported a light-up CRISPR-Cas13 transcription amplification method, which enables the detection of SARS-CoV-2 and its mutated variants. Sequence specificity was ensured by both the ligation process and Cas13a/crRNA recognition, allowing us to identify viral RNA mutation. Light-up RNA aptamer allows sensitive output of amplification signals via target-activated ribonuclease activity of CRISPR-Cas13a. The RNA virus assay has been designed to detect coronavirus, SARS-CoV-2, Middle East respiratory syndrome (MERS), and SARS, as well as the influenza viruses such as, H1N1, H7N9, and H9N2. It was accommodated to sense as low as 82 copies of SARS-CoV-2. Particularly, it allowed us to strictly discriminate key mutation of the SARS-CoV-2 variant, D614G, which may induce higher epidemic and pathogenetic risk. The proposed RNA virus assays are promising for point-of-care monitoring of SARS-CoV-2 and its risking variants.
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Affiliation(s)
- Yuxi Wang
- Department of Respiratory and Critical Care Medicine,
West China Medical School/West China Hospital, Sichuan
University, Chengdu 610041, China
| | - Yong Zhang
- College of Biomass Science and Engineering, Healthy
Food Evaluation Research Center, Sichuan University, Chengdu
610065, China
| | - Junbo Chen
- Analytical & Testing Center, Sichuan
University, Chengdu, Sichuan 610064, China
| | - Minjin Wang
- Department of Laboratory Medicine, West
China Hospital of Sichuan University, Chengdu 610041,
China
| | - Ting Zhang
- College of Biomass Science and Engineering, Healthy
Food Evaluation Research Center, Sichuan University, Chengdu
610065, China
| | - Wenxin Luo
- Department of Respiratory and Critical Care Medicine,
West China Medical School/West China Hospital, Sichuan
University, Chengdu 610041, China
| | - Yalun Li
- Department of Respiratory and Critical Care Medicine,
West China Medical School/West China Hospital, Sichuan
University, Chengdu 610041, China
| | - Yangping Wu
- Department of Respiratory and Critical Care Medicine,
West China Medical School/West China Hospital, Sichuan
University, Chengdu 610041, China
| | - Bo Zeng
- Department of Respiratory and Critical Care Medicine,
West China Medical School/West China Hospital, Sichuan
University, Chengdu 610041, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of
Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou
University, Zhengzhou 450001, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy
Food Evaluation Research Center, Sichuan University, Chengdu
610065, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine,
West China Medical School/West China Hospital, Sichuan
University, Chengdu 610041, China
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Sun J, Ren Y, Ji J, Guo Y, Sun X. A novel concentration gradient microfluidic chip for high-throughput antibiotic susceptibility testing of bacteria. Anal Bioanal Chem 2021; 413:1127-1136. [PMID: 33420534 DOI: 10.1007/s00216-020-03076-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 11/29/2022]
Abstract
Antibiotic resistance has become a serious threat to food safety and public health globally. Therefore, the development of a sensitive, quick, and simple method for antibiotic susceptibility testing is an urgent and crucial need. A novel concentration gradient microfluidic chip was designed in this work to generate antibiotic concentration gradient, culture bacteria, and produce fluorescence emission. An in-house-assembled fluorescence detection platform was constructed, and experiments were conducted to verify the linearity of the generated concentration gradient, explore the appropriate incubation time and flow rate for the microfluidic chip, and study the effect of long-term acid-based food processing on antibiotic susceptibility testing. Experimental results show that the concentration gradient generated by the microfluidic chip exhibited good linearity, stability, and controllability. The appropriate flow rate and incubation time for the microfluidic chip were 2 μL/min and 5 h, respectively. The use of this microfluidic chip for testing antibiotic resistance of Salmonella to ofloxacin and ampicillin generated results that were completely consistent with test results obtained using the gold-standard method. Furthermore, Salmonella showed greater sensitivity to antibiotics under strong acid conditions, confirming the potential influence of acid-based food processing on antibiotic susceptibility testing of real samples. The designed microfluidic chip provides a high-throughput, sensitive, and rapid antibiotic susceptibility testing method that combines the microfluidic chip and the fluorescence detection platform. The application of this method would facilitate determination of antibiotic-resistant bacterial strains for clinicians and researchers, and enable monitoring of changes in bacterial resistance during food processing.
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Affiliation(s)
- Jiadi Sun
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, 214122, Jiangsu, China.,State Key Laboratory of Dairy Biotechnology,Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai, 200436, Shanghai, China
| | - Yijing Ren
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Jian Ji
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Yu Guo
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, 214122, Jiangsu, China.,School of Internet of Things Engineering, Jiangnan University, Jiangsu, 214122, Wuxi, People's Republic of China
| | - Xiulan Sun
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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45
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Klein AK, Dietzel A. Microfluidic Systems for Antimicrobial Susceptibility Testing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 179:291-309. [PMID: 33851232 DOI: 10.1007/10_2021_164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Human health is threatened by the spread of antimicrobial resistance and resulting infections. One reason for the resistance spread is the treatment with inappropriate and ineffective antibiotics because standard antimicrobial susceptibility testing methods are time-consuming and laborious. To reduce the antimicrobial susceptibility detection time, minimize treatments with empirical broad-spectrum antibiotics, and thereby combat the further spread of antimicrobial resistance, faster and point-of-care methods are needed. This requires many different research approaches. Microfluidic systems for antimicrobial susceptibility testing offer the possibility to reduce the detection time, as small sample and reagent volumes can be used and the detection of single cells is possible. In some cases, the aim is to use human samples without pretreatment or pre-cultivation. This chapter first provides an overview of conventional detection methods. It then presents the potential of and various current approaches in microfluidics. The focus is on microfluidic methods for phenotypic antimicrobial susceptibility testing.
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Affiliation(s)
- Ann-Kathrin Klein
- Institute of Microtechnology Technische Universität Braunschweig, Braunschweig, Germany
| | - Andreas Dietzel
- Institute of Microtechnology Technische Universität Braunschweig, Braunschweig, Germany.
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