A Programmable Digital Microfluidic Assay for the Simultaneous Detection of Multiple Anti-Microbial Resistance Genes

Improved Teflon lift-off for droplet microarray generation and single-cell separation on digital microfluidic chips

Droplet microarrays (DMAs) leveraging wettability differences are instrumental in digital immunoassays, single-cell analysis, and high-throughput screening. This study introduces an enhanced Teflon lift-off process to fabricate hydrophilic-hydrophobic patterns on a digital microfluidic (DMF) chip, thereby integrating DMAs with DMF technology. By employing DMF for droplet manipulation and utilizing wettability differences, the automated generation of high-throughput DMAs was achieved. The volume of the microdroplets ranged from picoliters to nanoliters. For droplets with a diameter of 150 μm, the array density reached up to 1282 cm-2. We systematically investigated the influence of various DMF parameters on the formation of DMAs and applied this technique to particle distribution, achieving a single-cell isolation rate of approximately 30%. We believe that this method will be a potent tool to enhance the capabilities of DMAs and DMF technology and extend their applicability across more fields.

Democratizing digital microfluidics by a cloud-based design and manufacturing platform

Akin to the impact that digital microelectronics had on electronic devices for information technology, digital microfluidics (DMF) was anticipated to transform fluidic devices for lab-on-a-chip (LoC) applications. However, despite a wealth of research and publications, electrowetting-on-dielectric (EWOD) DMF has not achieved the anticipated wide adoption, and commercialization has been painfully slow. By identifying the technological and resource hurdles in developing DMF chip and control systems as the culprit, we envision democratizing DMF by building a standardized design and manufacturing platform. To achieve this vision, we introduce a proof-of-concept cloud platform that empowers any user to design, obtain, and operate DMF chips (https://edroplets.org). For chip design, we establish a web-based EWOD chip design platform with layout rules and automated wire routing. For chip manufacturing, we build a web-based EWOD chip manufacturing platform and fabricate four types of EWOD chips (i.e., glass, paper, PCB, and TFT) to demonstrate the foundry service workflow. For chip control, we introduce a compact EWOD control system along with web-based operating software. Although industrial fabrication services are beyond the scope of this work, we hope this perspective will inspire academic and commercial stakeholders to join the initiative toward a DMF ecosystem for the masses.

Microfluidic technologies for advanced antimicrobial susceptibility testing

Antimicrobial resistance is getting serious and becoming a threat to public health worldwide. The improper and excessive use of antibiotics is responsible for this situation. The standard methods used in clinical laboratories, to diagnose bacterial infections, identify pathogens, and determine susceptibility profiles, are time-consuming and labor-intensive, leaving the empirical antimicrobial therapy as the only option for the first treatment. To prevent the situation from getting worse, evidence-based therapy should be given. The choosing of effective drugs requires powerful diagnostic tools to provide comprehensive information on infections. Recent progress in microfluidics is pushing infection diagnosis and antimicrobial susceptibility testing (AST) to be faster and easier. This review summarizes the recent development in microfluidic assays for rapid identification and AST in bacterial infections. Finally, we discuss the perspective of microfluidic-AST to develop the next-generation infection diagnosis technologies.

Test Article for automation purposes

Digital recombinase polymerase amplification (dRPA) aims to quantify the initial amount of nucleic acid by dividing nucleic acid and all reagents required for the RPA reaction evenly into numerous individual reaction units, such as chambers or droplets. dRPA turns out to be a prominent technique for quantifying the absolute quantity of target nucleic acid because of its advantages including low equipment requirements, short time consumption, as well as high sensitivity and specificity. dRPA combined with microfluidics are recognized as simple, various, and high-throughput nucleic acid quantization systems. This paper classifies the microfluidic dRPA systems over the last decade. We analyze and summarize the vital technologies of various microfluidic dRPA systems (e.g., chip preparation process, segmentation principle, microfluidic control, and statistical analysis methods), and major efforts to address limitations (e.g., prevention of evaporation and contamination, accurate initiation, and reduction of manual operation). In addition, this paper summarizes key factors and potential constraints to the success of the microfluidic dRPA to help more researchers, and possible strategies to overcome the mentioned challenges. Lastly, actual suggestions and strategies are proposed for the subsequent development of microfluidic dRPA.

An Integrated Microfluidic Biosensing System Based on a Versatile Valve and Recombinase Polymerase Amplification for Rapid and Sensitive Detection of Salmonella typhimurium

Detecting foodborne pathogens on-site is crucial for ensuring food safety, necessitating the development of rapid, cost-effective, highly sensitive, and portable devices. This paper presents an integrated microfluidic biosensing system designed for the rapid and sensitive detection of Salmonella typhimurium (S. typhimurium). The biosensing system comprises a microfluidic chip with a versatile valve, a recombinase polymerase amplification (RPA) for nucleic acid detection, and a customized real-time fluorescence detection system. The versatile valve combines the functions of an active valve and a magnetic actuation mixer, enabling on-demand mixing and controlling fluid flow. Quantitative fluorescence is processed and detected through a custom-built smartphone application. The proposed integrated microfluidic biosensing system could detect Salmonella at concentrations as low as 1.0 × 102 copies/µL within 30 min, which was consistent with the results obtained from the real-time quantitative polymerase chain reaction (qPCR) tests. With its versatile valve, this integrated microfluidic biosensing system holds significant potential for on-site detection of foodborne pathogens.

Digital microfluidic platform assembled into a home-made studio for sample preparation and colorimetric sensing of S-nitrosocysteine

Digital microfluidics (DMF) is a versatile lab-on-a-chip platform that allows integration with several types of sensors and detection techniques, including colorimetric sensors. Here, we propose, for the first time, the integration of DMF chips into a mini studio containing a 3D-printed holder with previously fixed UV-LEDs to promote sample degradation on the chip surface before a complete analytical procedure involving reagent mixture, colorimetric reaction, and detection through a webcam integrated on the equipment. As a proof-of-concept, the feasibility of the integrated system was successfully through the indirect analysis of S-nitrosocysteine (CySNO) in biological samples. For this purpose, UV-LEDs were explored to perform the photolytic cleavage of CySNO, thus generating nitrite and subproducts directly on DMF chip. Nitrite was then colorimetrically detected based on a modified Griess reaction, in which reagents were prepared through a programable movement of droplets on DMF devices. The assembling and the experimental parameters were optimized, and the proposed integration exhibited a satisfactory correlation with the results acquired using a desktop scanner. Under the optimal experimental conditions, the obtained CySNO degradation to nitrite was 96%. Considering the analytical parameters, the proposed approach revealed linear behavior in the CySNO concentration range between 12.5 and 400 μmol L^-1 and a limit of detection equal to 2.8 μmol L^-1. Synthetic serum and human plasma samples were successfully analyzed, and the achieved results did not statistically differ from the data recorded by spectrophotometry at the confidence level of 95%, thus indicating the huge potential of the integration between DMF and mini studio to promote complete analysis of lowmolecular weight compounds.

Digital microfluidics as an emerging tool for bacterial protocols

Bacteria are widely studied in various research areas, including synthetic biology, sequencing and diagnostic testing. Protocols involving bacteria are often multistep, cumbersome and require access to a long list of instruments to perform experiments. In order to streamline these processes, the fluid handling technique digital microfluidics (DMF) has provided a miniaturized platform to perform various steps of bacterial protocols from sample preparation to analysis. DMF devices can be paired/interfaced with instrumentation such as microscopes, plate readers, and incubators, demonstrating their versatility with existing research tools. Alternatively, DMF instruments can be integrated into all-in-one packages with on-chip magnetic separation for sample preparation, heating/cooling modules to perform assay steps and cameras for absorbance and/or fluorescence measurements. This perspective outlines the beneficial features DMF offers to bacterial protocols, highlights limitations of current work and proposes future directions for this tool's expansion in the field.

Fabrication of planar monolayer microreactor array for visual statistical analysis and droplet-based digital quantitative analysis in situ

Planar monolayer microreactor arrays (PMMRAs) make droplet-based numerical measurements and statistical analysis cheap and easy. However, PMMRAs are typically produced in complex microfluidic devices and, moreover, still requires stringent control to reduce droplet loss during heating. In this paper, a simple, reliable, and flexible method for fabricating PMMRAs in a 96-well plate is described in detail by using simple materials and low-cost equipment. The partitioned droplets spontaneously assemble into PMMRAs in the plates, and this distribution is maintained even after incubation. This is advantageous for in situ analysis based on an individual droplet in droplet digital loop-mediated isothermal amplification (ddLAMP) and does not require the transfer of positive droplets. Precise and reproducible quantification of classical swine fever virus (CSFV) extracts was executed in these PMMRAs to verify its availability. Our results demonstrate that the proposed approach not only provides a flexible and controllable execution scheme for droplet-based nucleic acid quantification in resource-limited laboratories but also opens new perspectives for numerous analytical and biochemical applications using droplets as versatile plastic microreactors.

Overview and Future Perspectives of Microfluidic Digital Recombinase Polymerase Amplification (dRPA)

Digital recombinase polymerase amplification (dRPA) aims to quantify the initial amount of nucleic acid by dividing nucleic acid and all reagents required for the RPA reaction evenly into numerous individual reaction units, such as chambers or droplets. dRPA turns out to be a prominent technique for quantifying the absolute quantity of target nucleic acid because of its advantages including low equipment requirements, short time consumption, as well as high sensitivity and specificity. dRPA combined with microfluidics are recognized as simple, various, and high-throughput nucleic acid quantization systems. This paper classifies the microfluidic dRPA systems over the last decade. We analyze and summarize the vital technologies of various microfluidic dRPA systems (e.g., chip preparation process, segmentation principle, microfluidic control, and statistical analysis methods), and major efforts to address limitations (e.g., prevention of evaporation and contamination, accurate initiation, and reduction of manual operation). In addition, this paper summarizes key factors and potential constraints to the success of the microfluidic dRPA to help more researchers, and possible strategies to overcome the mentioned challenges. Lastly, actual suggestions and strategies are proposed for the subsequent development of microfluidic dRPA.

Progressing Antimicrobial Resistance Sensing Technologies across Human, Animal, and Environmental Health Domains

The spread of antimicrobial resistance (AMR) is a rapidly growing threat to humankind on both regional and global scales. As countries worldwide prepare to embrace a One Health approach to AMR management, which is one that recognizes the interconnectivity between human, animal, and environmental health, increasing attention is being paid to identifying and monitoring key contributing factors and critical control points. Presently, AMR sensing technologies have significantly progressed phenotypic antimicrobial susceptibility testing (AST) and genotypic antimicrobial resistance gene (ARG) detection in human healthcare. For effective AMR management, an evolution of innovative sensing technologies is needed for tackling the unique challenges of interconnected AMR across various and different health domains. This review comprehensively discusses the modern state-of-play for innovative commercial and emerging AMR sensing technologies, including sequencing, microfluidic, and miniaturized point-of-need platforms. With a unique view toward the future of One Health, we also provide our perspectives and outlook on the constantly changing landscape of AMR sensing technologies beyond the human health domain.

Bacterial classification and antibiotic susceptibility testing on an integrated microfluidic platform

With the prevalence of bacterial infections and increasing levels of antibiotic resistance comes the need for rapid and accurate methods for bacterial classification (BC) and antibiotic susceptibility testing (AST). Here we demonstrate the use of the fluid handling technique digital microfluidics (DMF) for automated and simultaneous BC and AST using growth metabolic markers. Custom instrumentation was developed for this application including an integrated heating module and a machine-learning-enabled low-cost colour camera for real-time absorbance and fluorescent sample monitoring on multipurpose devices. Antibiotic dilutions along with sample handling, mixing and incubation at 37 °C were all pre-programmed and processed automatically. By monitoring the metabolism of resazurin, resorufin beta-D-glucuronide and resorufin beta-D-galactopyranoside to resorufin, BC and AST were achieved in under 18 h. AST was validated in two uropathogenic E. coli strains with antibiotics ciprofloxacin and nitrofurantoin. BC was performed independently and simultaneously with ciprofloxacin AST for E. coli, K. pneumoniae, P. mirabilis and S. aureus. Finally, a proof-of-concept multiplexed system for breakpoint testing of two antibiotics, as well as E. coli and coliform classification was investigated with a multidrug-resistant E. coli strain. All bacteria were correctly identified, while AST and breakpoint test results were in essential and category agreement with reference methods. These results show the versatility and accuracy of this all-in-one microfluidic system for analysis of bacterial growth and phenotype.

Rapid detection of NDM and VIM carbapenemase encoding genes by recombinase polymerase amplification and lateral flow-based detection

Carbapenemase-producing organisms (CPOs) pose a serious clinical threat and rapid detection tools are essential to aid in patient management. We developed rapid and simple molecular tests to detect bla_NDM-type and bla_VIM-type carbapenemase genes using recombinase polymerase amplification (RPA) combined with a lateral flow detection. The tests could provide results in approximately 15 min when using DNA extracts, with limits of detection of 9.2 copies/μl for the bla_NDM-type assay and 7.5 copies/μl for bla_VIM-type assay, and successfully detected all isolates harbouring the carbapenemase encoding genes in a panel of 57 isolates. These RPA tests may be suitable for use in low-resource settings to tailor rapid implementation of infection control precautions and antibiotic stewardship.

Automated Miniaturized Digital Microfluidic Antimicrobial Susceptibility Test Using a Chip-Integrated Optical Oxygen Sensor

We present the first digital microfluidic (DMF) antimicrobial susceptibility test (AST) using an optical oxygen sensor film for in-situ and real-time continuous measurement of extracellular dissolved oxygen (DO). The device allows one to monitor bacterial growth across the entire cell culture area, and the fabricated device was utilized for a miniaturized and automated AST. The oxygen-sensitive probe platinum(II)-5,10,15,20-tetrakis-(2,3,4,5,6-pentafluorophenyl)-porphyrin was embedded in a Hyflon AD 60 polymer and spin-coated as a 100 nm thick layer onto an ITO glass serving as the DMF ground electrode. This DMF-integrated oxygen sensing film was found to cause no negative effects to the droplet manipulation or cell growth on the chip. The developed DMF platform was used to monitor the DO consumption during Escherichia coli (E. coli) growth caused by cellular respiration. A rapid and reliable twofold dilution procedure was developed and performed, and the AST with E. coli ATCC 25922 in the presence of ampicillin, chloramphenicol, and tetracycline at different concentrations from 0.5 to 8 μg mL^-1 was investigated. All sample dispensation, dilution, and mixing were performed automatically on the chip within 10 min. The minimum inhibitory concentration values measured from the DMF chip were consistent with those from the standard broth microdilution method but requiring only minimal sample handling and working with much smaller sample volumes.

Unravelling the menace: detection of antimicrobial resistance in aquaculture

One of the major problems to be addressed in aquaculture is the prominence of antimicrobial resistance (AMR). The occurrence of bacterial infections in cultured fishes promotes the continuous use of antibiotics in aquaculture, which results in the selection of proliferated antibiotic-resistant bacteria and increases the possibility of transfer to the whole environment through horizontal gene transfer. Hence, the accurate cultivation-dependent and cultivation-independent detection methods are very much crucial for the immediate and proper management of this menace. Antimicrobial resistance determinants carrying mobile genetic transfer elements such as transposons, plasmids, integrons and gene cassettes need to be specifically analysed through molecular detection techniques. The susceptibility of microbes to antibiotics should be tested at regular intervals along with various biochemical assays and conjugation studies so as to determine the extent of spread of AMR. Advanced omic-based and bioinformatic tools can also be incorporated for understanding of genetic diversity. The present review focuses on different detection methods to unearth the complexity of AMR in aquaculture. This monitoring helps the authorities to curb the use of antibiotics, commencement of appropriate management measures and adequate substitute strategies in aquaculture. The long battle of AMR could be overcome by the sincere implementation of One Health approach. SIGNIFICANCE AND IMPACT OF THE STUDY: The use of antibiotics and increased antimicrobial resistance (AMR) are of major concerns in aquaculture industry. This could result in global health risks through direct consumption of cultured fishes and dissemination of AMR to natural environment through horizontal gene transfer. Hence, timely detection of the antimicrobial-resistant pathogens and continuous monitoring programmes are inevitable. Advanced microbiological, molecular biological and omic-based tools can unravel the menace to a great extent. This will help the authorities to curb the use of antibiotics and implement appropriate management measures to overcome the threat.

Simultaneous detection of two growth factors from human single-embryo culture medium by a bead-based digital microfluidic chip

The measurement of growth factors released in a culture medium is considered to be an attractive non-invasive approach, apart from the embryo morphology, to identify the condition of an embryo development after fertilization in vitro (IVF), but the available embryo culture medium in the current method is only a few microlitres. This small sample volume, also of small concentration, makes difficult the application of a conventional detection method, such as an enzyme-linked immunosorbent assay (ELISA). A reliable detection of the growth factor from each embryo culture medium of such a small concentration hence remains a challenge. Here for the first time we report the results of measurement of not just one, but two, growth factors, human IL-1β and human TNF-α, from an individual droplet of embryo culture medium with a bead-based digital microfluidic chip. The required sample volume for a single measurement is only 520 nL; the total duration of the on-chip process is less than 40 min. Using the culture media of human embryos with normal morphologic features, we found that the concentrations of TNF-α change little from day 3 to day 5-6, but the concentrations of IL-1β for some embryos might double from day 3 to day 5-6. For other embryos even with similar normal morphologic features, some growth factors, such as IL-1β, might exhibit different expressions during the culture period. Those growth factors could serve to distinguish the development conditions of each embryo, not merely from an observation of embryo morphology.

Microfluidic-Based Nucleic Acid Amplification Systems in Microbiology

Rapid, sensitive, and selective bacterial detection is a hot topic, because the progress in this research area has had a broad range of applications. Novel and innovative strategies for detection and identification of bacterial nucleic acids are important for practical applications. Microfluidics is an emerging technology that only requires small amounts of liquid samples. Microfluidic devices allow for rapid advances in microbiology, enabling access to methods of amplifying nucleic acid molecules and overcoming difficulties faced by conventional. In this review, we summarize the recent progress in microfluidics-based polymerase chain reaction devices for the detection of nucleic acid biomarkers. The paper also discusses the recent development of isothermal nucleic acid amplification and droplet-based microfluidics devices. We discuss recent microfluidic techniques for sample preparation prior to the amplification process.

Review: a comprehensive summary of a decade development of the recombinase polymerase amplification

RPA is a versatile complement or replacement of PCR, and now is stepping into practice.

Sample pre-concentration on a digital microfluidic platform for rapid AMR detection in urine

There is a growing need for rapid diagnostic methods to support stewardship of antibiotics.

[Lab on a Chip]

BACKGROUND

Miniaturization has not only driven microelectronics and generated new unforeseen options but has also dramatically changed sensors and analytics.

DEVELOPMENTS

The Lab on a Chip (LOC) technology enables laboratory processes to run fully automated in canals in the micrometre range. The biggest challenge for LOC is to keep production costs low despite miniaturization and application-specific design. If this is achieved medical laboratory analyses can usually be carried out faster and with less hands on time. This explains why LOCs are already integrated into many laboratory instruments and why point-of-care testing (POCT) can no longer be imagined without it. New markers, such as in liquid biopsies and measurement techniques, such as Raman spectroscopy and mass spectroscopy, create further potentials that will enable faster and more specific laboratory analyses to be made using LOC technology.

CONCLUSION

The LOC technology has the potential of changing the medical practice especially in cases when the central laboratory is not available or is unable to provide results fast enough.

Recent Advances in the Race to Design a Rapid Diagnostic Test for Antimicrobial Resistance

Even with advances in antibiotic therapies, bacterial infections persistently plague society and have amounted to one of the most prevalent issues in healthcare today. Moreover, the improper and excessive administration of antibiotics has led to resistance of many pathogens to prescribed therapies, rendering such antibiotics ineffective against infections. While the identification and detection of bacteria in a patient's sample is critical for point-of-care diagnostics and in a clinical setting, the consequent determination of the correct antibiotic for a patient-tailored therapy is equally crucial. As a result, many recent research efforts have been focused on the development of sensors and systems that correctly guide a physician to the best antibiotic to prescribe for an infection, which can in turn, significantly reduce the instances of antibiotic resistance and the evolution of bacteria "superbugs." This review details the advantages and shortcomings of the recent advances (focusing from 2016 and onward) made in the developments of antimicrobial susceptibility testing (AST) measurements. Detection of antibiotic resistance by genomic AST techniques relies on the prediction of antibiotic resistance via extracted bacterial DNA content, while phenotypic determinations typically track physiological changes in cells and/or populations exposed to antibiotics. Regardless of the method used for AST, factors such as cost, scalability, and assay time need to be weighed into their design. With all of the expansive innovation in the field, which technology and sensing systems demonstrate the potential to detect antimicrobial resistance in a clinical setting?

Fast and sensitive isothermal DNA assay using microbead dielectrophoresis for detection of anti-microbial resistance genes

Antimicrobial resistant pathogens are a growing worldwide threat to human health. This study describes a novel method for rapid and sensitive detection of antimicrobial resistance (AMR) genes, specifically bla_CTX-M-15 which encodes for the enzyme that offers resistance to extended spectrum β-lactam antibiotics. The method combines isothermal DNA amplification by recombinase polymerase amplification (RPA), with microbead dielectrophoresis (DEP)-based DNA detection. The RPA amplicon is captured onto dielectric microbeads, and the amount of amplicon determined by dielectrophoretic impedance measurement (DEPIM) of the microbeads. Amplicon-labeled microbeads were prepared by either a two-step or one-step method. A purified recombinant plasmid containing bla_CTX-M-15 and genomic DNA (with plasmid) extracted from an AMR bacteria (Escherichia coli NCTC 13441) were used as target samples. A one-step method in which RPA and DNA immobilization on the microbeads is carried out simultaneously, has a detection limit of 2 copies/reaction for pure plasmid and 50 copies/reaction for genomic DNA. The assays are quantitative with a dynamic range up to 10⁵ copies/reaction, with a total detection time of 26 min. Both methods are easy, rapid, and unlike lateral flow detection are quantitative.

Multiplexed isothermal nucleic acid amplification

Multiplexed isothermal amplification and detection of nucleic acid sequences and biomarkers is of increasing importance in diverse areas including advanced diagnostics, food quality control and environmental monitoring. Whilst there are several very elegant isothermal amplification approaches, multiplexed amplification remains a challenge, requiring careful experimental design and optimisation, from judicious primer design in order to avoid the formation of primer dimers and non-specific amplification, applied temperature as well as the ratio and concentration of primers. In this review, we describe the various approaches that have been reported to date for multiplexed isothermal amplification, for both "one-pot" multiplexing as well as parallelised multiplexing using loop-mediated isothermal amplification, strand-displacement amplification, helicase-dependent amplification, rolling circle amplification, nucleic acid sequence-based amplification, with a particular focus on recombinase polymerase amplification.

Application of Microfluidic Methodology for the Analysis of DNA

Over the past 20 years, many of the developments and potential applications of microfluidic methodology have incorporated nucleic acid processes which have, in their own right, undergone a number of innovative changes [...].

Towards Multiplex Molecular Diagnosis-A Review of Microfluidic Genomics Technologies

Highly sensitive and specific pathogen diagnosis is essential for correct and timely treatment of infectious diseases, especially virulent strains, in people. Point-of-care pathogen diagnosis can be a tremendous help in managing disease outbreaks as well as in routine healthcare settings. Infectious pathogens can be identified with high specificity using molecular methods. A plethora of microfluidic innovations in recent years have now made it increasingly feasible to develop portable, robust, accurate, and sensitive genomic diagnostic devices for deployment at the point of care. However, improving processing time, multiplexed detection, sensitivity and limit of detection, specificity, and ease of deployment in resource-limited settings are ongoing challenges. This review outlines recent techniques in microfluidic genomic diagnosis and devices with a focus on integrating them into a lab on a chip that will lead towards the development of multiplexed point-of-care devices of high sensitivity and specificity.