A microfluidic cartridge for fast and accurate diagnosis of Mycobacterium tuberculosis infections on standard laboratory equipment

Fully integrated and automated centrifugal microfluidic chip for point-of-care multiplexed molecular diagnostics

Public health events caused by pathogens have imposed significant economic and societal burdens. However, conventional methods still face challenges including complex operations, the need for trained operators, and sophisticated instruments. Here, we proposed a fully integrated and automated centrifugal microfluidic chip, also termed IACMC, for point-of-care multiplexed molecular diagnostics by harnessing the advantages of active and passive valves. The IACMC incorporates multiple essential components including a pneumatic balance module for sequential release of multiple reagents, a pneumatic centrifugation-assisted module for on-demand solution release, an on-chip silicon membrane module for nucleic acid extraction, a Coriolis force-mediated fluid switching module, and an amplification module. Numerical simulation and visual validation were employed to iterate and optimize the chip's structure. Upon sample loading, the chip automatically executes the entire process of bacterial sample lysis, nucleic acid capture, elution quantification, and isothermal LAMP amplification. By optimizing crucial parameters including centrifugation speed, direction of rotation, and silicone membrane thickness, the chip achieves exceptional sensitivity (twenty-five Salmonella or forty Escherichia coli) and specificity in detecting Escherichia coli and Salmonella within 40 min. The development of IACMC will drive advancements in centrifugal microfluidics for point-of-care testing and holds potential for broader applications in precision medicine including high-throughput biochemical analysis immune diagnostics, and drug susceptibility testing.

Microfluidic systems for infectious disease diagnostics

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.

Fast and on-site animal species identification in processed meat via centrifugal microfluidics and isothermal amplification

We present a novel centrifugal microfluidic approach to rapidly identify animal species in meat products. The workflow requires a centrifugal cartridge for DNA extraction and for preparation of a recombinant polymerase amplification (RPA) reaction, a programmable centrifuge for processing the cartridge and an isothermal reader to perform the RPA. Liquid reagents are pre-stored on the cartridge and the meat sample can be added directly without any pre-treatment. With this system, we are able to identify six different animal species in a single run within one hour. In pork salami containing horse, turkey, sheep, chicken and beef meat, it was possible to identify species levels as low as 0.01%. In beef salami and cooked pork sausages 0.1% of foreign meat could be detected. This novel workflow enables rapid and sensitive species identification in processed meat at the point of need.

Two-stage tuberculosis diagnostics: combining centrifugal microfluidics to detect TB infection and Inh and Rif resistance at the point of care with subsequent antibiotic resistance profiling by targeted NGS

Globally, tuberculosis (TB) remains the deadliest bacterial infectious disease, and spreading antibiotic resistances is the biggest challenge for combatting the disease. Rapid and comprehensive diagnostics including drug susceptibility testing (DST) would assure early treatment, reduction of morbidity and the interruption of transmission chains. To date, rapid genetic resistance testing addresses only one to four drug groups while complete DST is done phenotypically and takes several weeks. To overcome these limitations, we developed a two-stage workflow for rapid TB diagnostics including DST from a single sputum sample that can be completed within three days. The first stage is qPCR detection of M. tuberculosis complex (MTBC) including antibiotic resistance testing against the first-line antibiotics, isoniazid (Inh) and rifampicin (Rif). The test is automated by centrifugal microfluidics and designed for point of care (PoC). Furthermore, enriched MTBC DNA is provided in a detachable sample tube to enable the second stage: if the PCR detects MTBC and resistance to either Inh or Rif, the MTBC DNA is shipped to specialized facilities and analyzed by targeted next generation sequencing (tNGS) to assess the complete resistance profile. Proof-of-concept testing of the PoC test revealed an analytical sensitivity of 44.2 CFU ml-1, a diagnostic sensitivity of 96%, and a diagnostic specificity of 100% for MTBC detection. Coupled tNGS successfully provided resistance profiles, demonstrated for samples from 17 patients. To the best of our knowledge, the presented combination of PoC qPCR with tNGS allows for the fastest comprehensive TB diagnostics comprising decentralized pathogen detection with subsequent resistance profiling in a facility specialized in tNGS.

Advances in Simple, Rapid, and Contamination-Free Instantaneous Nucleic Acid Devices for Pathogen Detection

Pathogenic pathogens invade the human body through various pathways, causing damage to host cells, tissues, and their functions, ultimately leading to the development of diseases and posing a threat to human health. The rapid and accurate detection of pathogenic pathogens in humans is crucial and pressing. Nucleic acid detection offers advantages such as higher sensitivity, accuracy, and specificity compared to antibody and antigen detection methods. However, conventional nucleic acid testing is time-consuming, labor-intensive, and requires sophisticated equipment and specialized medical personnel. Therefore, this review focuses on advanced nucleic acid testing systems that aim to address the issues of testing time, portability, degree of automation, and cross-contamination. These systems include extraction-free rapid nucleic acid testing, fully automated extraction, amplification, and detection, as well as fully enclosed testing and commercial nucleic acid testing equipment. Additionally, the biochemical methods used for extraction, amplification, and detection in nucleic acid testing are briefly described. We hope that this review will inspire further research and the development of more suitable extraction-free reagents and fully automated testing devices for rapid, point-of-care diagnostics.

Rapid on-site nucleic acid testing: On-chip sample preparation, amplification, and detection, and their integration into all-in-one systems

As nucleic acid testing is playing a vital role in increasingly many research fields, the need for rapid on-site testing methods is also increasing. The test procedure often consists of three steps: Sample preparation, amplification, and detection. This review covers recent advances in on-chip methods for each of these three steps and explains the principles underlying related methods. The sample preparation process is further divided into cell lysis and nucleic acid purification, and methods for the integration of these two steps on a single chip are discussed. Under amplification, on-chip studies based on PCR and isothermal amplification are covered. Three isothermal amplification methods reported to have good resistance to PCR inhibitors are selected for discussion due to their potential for use in direct amplification. Chip designs and novel strategies employed to achieve rapid extraction/amplification with satisfactory efficiency are discussed. Four detection methods providing rapid responses (fluorescent, optical, and electrochemical detection methods, plus lateral flow assay) are evaluated for their potential in rapid on-site detection. In the final section, we discuss strategies to improve the speed of the entire procedure and to integrate all three steps onto a single chip; we also comment on recent advances, and on obstacles to reducing the cost of chip manufacture and achieving mass production. We conclude that future trends will focus on effective nucleic acid extraction via combined methods and direct amplification via isothermal methods.

Application of Microfluidics for Bacterial Identification

Bacterial infections continue to pose serious public health challenges. Though anti-bacterial therapeutics are effective remedies for treating these infections, the emergence of antibiotic resistance has imposed new challenges to treatment. Often, there is a delay in prescribing antibiotics at initial symptom presentation as it can be challenging to clinically differentiate bacterial infections from other organisms (e.g., viruses) causing infection. Moreover, bacterial infections can arise from food, water, or other sources. These challenges have demonstrated the need for rapid identification of bacteria in liquids, food, clinical spaces, and other environments. Conventional methods of bacterial identification rely on culture-based approaches which require long processing times and higher pathogen concentration thresholds. In the past few years, microfluidic devices paired with various bacterial identification methods have garnered attention for addressing the limitations of conventional methods and demonstrating feasibility for rapid bacterial identification with lower biomass thresholds. However, such culture-free methods often require integration of multiple steps from sample preparation to measurement. Research interest in using microfluidic methods for bacterial identification is growing; therefore, this review article is a summary of current advancements in this field with a focus on comparing the efficacy of polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and emerging spectroscopic methods.

Culture-Free Quantification of Bacteria Using Digital Fluorescence Imaging in a Tunable Magnetic Capturing Cartridge for Onsite Food Testing

Accurate, onsite detection of pathogenic bacteria from food matrices is required to rapidly respond to pathogen outbreaks. However, accurately detecting whole-cell bacteria in large sample volumes without an enrichment step remains a challenge. Therefore, bacterial samples must be concentrated, identified, and quantified. We developed a tunable magnetic capturing cartridge (TMCC) and combined it with a portable digital fluorescence reader for quick, onsite, quantitative detection of Staphylococcus aureus. The TMCC platform integrates an absorption pad impregnated with water-soluble polyvinyl alcohol (PVA) with an injection-molded polycarbonate (PC) plate that has a hard magnet on its back and an acrylonitrile-butadiene-styrene case. An S. aureus-specific antibody conjugated with magnetic nanoparticles was used to concentrate bacteria from a large-volume sample and capture bacteria within the TMCC. The retention time for capturing bacteria on the TMCC was adjusted by controlling the concentration and volume of the PVA solution. Concentrated bacterial samples bound to target-specific aptamer probes conjugated with quantum dots were loaded into the TMCC for a controlled time, followed by attachment of the bacteria to the PC plate and removal of unbound aptamer probes with wash buffer. The captured bacteria were quantified using a digital fluorescence reader equipped with an embedded program that automatically counts fluorescently tagged bacteria. The bacterial count made using the TMCC was comparable to a standard plate count (R² = 0.9898), with assay sensitivity and specificity of 94.3 and 100%, respectively.

Correlation between Sputum Bacterial Culture Positive Rate and Drug Sensitivity Test Results and Disease Severity inInpatients and Its Clinical Significance: A SystematicReview and Meta-Analysis

Objective. To systematically evaluate the correlation between the positive rate of sputum bacterial culture and the results of drug sensitivity test and the severity of the disease and its clinical significance, so as to provide evidence-based medicine for clinical application. Methods. PubMed, Embase, ScienceDirect, Cochrane Library, China Knowledge Network Database (CNKI), China VIP Database, Wanfang Database, and China Biomedical Literature Database (CBM) online database were used. The retrieval time limit was from the establishment of the database to the present. Data for all included studies were extracted by two independent researchers, and the risk of bias for the quality of each included study was assessed by the Cochrane Handbook 5.1.0 criteria. RevMan5.4 statistical software was used to analyze the collected data by meta. Results. In the end, 6 RCT articles were included. Overall, 613 samples were included in 6 RCT studies. The correlation between the positive rate of sputum bacterial culture in inpatients and the severity of the disease was meta-analyzed. The heterogeneity test results showed that Chi2 = 177.20, df = 3, P < 0.00001, and I2 = 98%, indicating that there was obvious heterogeneity among the included research data. It was considered that there was a correlation between the positive rate of sputum bacterial culture and the severity of the disease. The correlation between the results of the drug sensitivity test of inpatients and the severity of the disease was evaluated. The results of the heterogeneity test showed that Chi2 = 0.00, df = 1, P = 1 > 0.05, and I2 = 0%, indicating that there was no heterogeneity among the included research data. In addition, the combined effect of WMD was analyzed by the fixed effect model. The combined effect dose WMD test was Z = 6.58 (P < 0.00001). It was considered that there was a correlation between the results of the drug sensitivity test and the severity of the disease. Conclusion. There is a correlation between positive sputum culture and drug sensitivity test results and the severity of the disease in hospitalized patients. In clinical practice, for hospitalized patients, the positive sputum bacterial culture rate and drug sensitivity test results can be used to guide the appropriate use of antibiotics. Due to the low input from the literature, more studies with higher methodological quality and longer follow-up are needed for further validation.

Autonomous electrochemical biosensing of glial fibrillary acidic protein for point-of-care detection of central nervous system injuries

The integration of electrochemical biosensors into fluid handling units such as paper-based, centrifugal, and capillary microfluidic devices has been explored with the purpose of developing point-of-care platforms for quantitative detection of bodily fluid markers. However, the present fluidic device designs largely lack the capacity of full assay automation, needing manual loading of one or multiple reagents or requiring external devices for liquid manipulation. Such fluidic handing platforms also require universality for detecting various biomarkers. These platforms are also largely produced using materials unsuitable for scalable manufacturing and with a high production cost. The mechanism of fluid flow also often induces noise to the embedded biosensors which adversely impacts the accuracy of biosensing. This work addresses these challenges by presenting a reliable design of a fully automated and universal capillary-driven microfluidic platform that automates several steps of label-free electrochemical biosensing assays. These steps include sample aliquoting, controlled incubation, removal of non-specific bindings, reagent mixing and delivery to sensing electrodes, and electrochemical detection. The multilayer architecture of the microfluidic device is made of polymeric and adhesive materials commercially used for the fabrication of point-of-care devices. The design and geometry of different components of the device (e.g., sampling unit, mixer, resistances, delay valves, interconnecting components) were optimized using a combined experimental testing and numerical fluid flow modeling to reach high reproducibility and minimize the noise-induced to the biosensor. As a proof of concept, the performance of this on-chip immunosensing platform was demonstrated for rapid and autonomous detection of glial fibrillary acidic proteins (GFAP) in phosphate-buffered saline (PBS). The microfluidic immunosensing device exhibited a linear detection range of 10-1000 pg mL^-1 for the detection of GFAP within 30 min, with a limit of detection (LoD) and sensitivity of 3 pg mL^-1 and 39 mL pg^-1 mm^-2 in PBS, respectively. Owing to its simplicity, sample-to-result performance, universality for handing different biofluids, low cost, high reproducibility, compatibility with scalable production, and short analysis time, the proposed biosensing platform can be further adapted for the detection of other biomarkers in different clinical bodily fluids for rapid diagnostic and prognostic applications.

Automatic and multi-channel detection of bacteria on a slidable centrifugal disc based on FTA card nucleic acid extraction and recombinase aided amplification

Rapid screening of foodborne pathogens is key to preventing food poisoning. In this study, a slidable centrifugal disc was developed for automatic and multi-channel detection of Salmonella typhimurium using Flinders Technology Associates (FTA) cards for nucleic acid extraction and recombinase aided amplification (RAA) for nucleic acid detection. The slidable FTA switching and centrifugal fluidic control were elaborately combined to achieve fully automatic operations, including centrifugation of the bacterial sample to obtain the concentrated bacteria, heating and drying of the FTA card to extract the nucleic acids, washing of the FTA card to remove the impurities, and RAA detection of the extracted DNA to determine the concentration. Under the optimal conditions, this slidable centrifugal disc was able to detect 10 CFU mL^-1 in a spiked chicken meat supernatant in 1 h with an average recovery of 101.8% and an average standard deviation of 6.5%. This disc has been demonstrated as an alternative for sample-in-result-out detection of Salmonella and has shown potential for simultaneous detection of multiple bacteria.

Systematic review of centrifugal valving based on digital twin modeling towards highly integrated lab-on-a-disc systems

Current, application-driven trends towards larger-scale integration (LSI) of microfluidic systems for comprehensive assay automation and multiplexing pose significant technological and economical challenges to developers. By virtue of their intrinsic capability for powerful sample preparation, centrifugal systems have attracted significant interest in academia and business since the early 1990s. This review models common, rotationally controlled valving schemes at the heart of such "Lab-on-a-Disc" (LoaD) platforms to predict critical spin rates and reliability of flow control which mainly depend on geometries, location and liquid volumes to be processed, and their experimental tolerances. In absence of larger-scale manufacturing facilities during product development, the method presented here facilitates efficient simulation tools for virtual prototyping and characterization and algorithmic design optimization according to key performance metrics. This virtual in silico approach thus significantly accelerates, de-risks and lowers costs along the critical advancement from idea, layout, fluidic testing, bioanalytical validation, and scale-up to commercial mass manufacture.

Design Optimization of Centrifugal Microfluidic “Lab-on-a-Disc” Systems towards Fluidic Larger-Scale Integration

Enhancing the degree of functional multiplexing while assuring operational reliability and manufacturability at competitive costs are crucial ingredients for enabling comprehensive sample-to-answer automation, e.g., for use in common, decentralized “Point-of-Care” or “Point-of-Use” scenarios. This paper demonstrates a model-based “digital twin” approach, which efficiently supports the algorithmic design optimization of exemplary centrifugo-pneumatic (CP) dissolvable-film (DF) siphon valves toward larger-scale integration (LSI) of well-established “Lab-on-a-Disc” (LoaD) systems. Obviously, the spatial footprint of the valves and their upstream laboratory unit operations (LUOs) have to fit, at a given radial position prescribed by its occurrence in the assay protocol, into the locally accessible disc space. At the same time, the retention rate of a rotationally actuated CP-DF siphon valve and, most challengingly, its band width related to unavoidable tolerances of experimental input parameters need to slot into a defined interval of the practically allowed frequency envelope. To accomplish particular design goals, a set of parametrized metrics is defined, which are to be met within their practical boundaries while (numerically) minimizing the band width in the frequency domain. While each LSI scenario needs to be addressed individually on the basis of the digital twin, a suite of qualitative design rules and instructive showcases structures are presented.

Secure Air Traffic Control at the Hub of Multiplexing on the Centrifugo-Pneumatic Lab-on-a-Disc Platform

Fluidic larger-scale integration (LSI) resides at the heart of comprehensive sample-to-answer automation and parallelization of assay panels for frequent and ubiquitous bioanalytical testing in decentralized point-of-use/point-of-care settings. This paper develops a novel "digital twin" strategy with an emphasis on rotational, centrifugo-pneumatic flow control. The underlying model systematically connects retention rates of rotationally actuated valves as a key element of LSI to experimental input parameters; for the first time, the concept of band widths in frequency space as the decisive quantity characterizing operational robustness is introduced, a set of quantitative performance metrics guiding algorithmic optimization of disc layouts is defined, and the engineering principles of advanced, logical flow control and timing are elucidated. Overall, the digital twin enables efficient design for automating multiplexed bioassay protocols on such "Lab-on-a-Disc" (LoaD) systems featuring high packing density, reliability, configurability, modularity, and manufacturability to eventually minimize cost, time, and risk of development and production.