Viscoelastic Separation and Concentration of Fungi from Blood for Highly Sensitive Molecular Diagnostics

In the flow of molecular miniaturized fungal diagnosis

The diagnosis of fungal infections presents several challenges and limitations, stemming from the similarities in symptomatology, diversity of underlying pathogenic species, complexity of fungal biology, and scarcity of rapid, affordable, and point-of-care approaches. In this review, we assess technological advances enabling the conversion of cutting-edge laboratory molecular diagnostic methods to cost-effective microfluidic devices. The most promising strategies toward the design of DNA sequence-based fungal diagnostic systems, capable of capturing and deciphering the highly informative DNA of the pathogen and adapted for resource-limited settings, are discussed, bridging fungal biology, molecular genetics, microfluidics, and biosensors.

A Review of Research Progress in Microfluidic Bioseparation and Bioassay

With the rapid development of biotechnology, the importance of microfluidic bioseparation and bioassay in biomedicine, clinical diagnosis, and other fields has become increasingly prominent. Microfluidic technology, with its significant advantages of high throughput, automated operation, and low sample consumption, has brought new breakthroughs in the field of biological separation and bioassay. In this paper, the latest research progress in microfluidic technology in the field of bioseparation and bioassay is reviewed. Then, we focus on the methods of bioseparation including active separation, passive separation, and hybrid separation. At the same time, the latest research results of our group in particle separation are introduced. Finally, some application examples or methods for bioassay after particle separation are listed, and the current challenges and future prospects of bioseparation and bioassay are discussed.

Passive microfluidic devices for cell separation

The separation of specific cell populations is instrumental in gaining insights into cellular processes, elucidating disease mechanisms, and advancing applications in tissue engineering, regenerative medicine, diagnostics, and cell therapies. Microfluidic methods for cell separation have propelled the field forward, benefitting from miniaturization, advanced fabrication technologies, a profound understanding of fluid dynamics governing particle separation mechanisms, and a surge in interdisciplinary investigations focused on diverse applications. Cell separation methodologies can be categorized according to their underlying separation mechanisms. Passive microfluidic separation systems rely on channel structures and fluidic rheology, obviating the necessity for external force fields to facilitate label-free cell separation. These passive approaches offer a compelling combination of cost-effectiveness and scalability when compared to active methods that depend on external fields to manipulate cells. This review delves into the extensive utilization of passive microfluidic techniques for cell separation, encompassing various strategies such as filtration, sedimentation, adhesion-based techniques, pinched flow fractionation (PFF), deterministic lateral displacement (DLD), inertial microfluidics, hydrophoresis, viscoelastic microfluidics, and hybrid microfluidics. Besides, the review provides an in-depth discussion concerning cell types, separation markers, and the commercialization of these technologies. Subsequently, it outlines the current challenges faced in the field and presents a forward-looking perspective on potential future developments. This work hopes to aid in facilitating the dissemination of knowledge in cell separation, guiding future research, and informing practical applications across diverse scientific disciplines.

Separation and Washing of Candida Cells from White Blood Cells Using Viscoelastic Microfluidics

An early and accurate diagnosis of Candida albicans is critical for the rapid antifungal treatment of candidemia, a mortal bloodstream infection. This study demonstrates viscoelastic microfluidic techniques for continuous separation, concentration, and subsequent washing of Candida cells in the blood. The total sample preparation system contains two-step microfluidic devices: a closed-loop separation and concentration device and a co-flow cell-washing device. To determine the flow conditions of the closed-loop device, such as the flow rate factor, a mixture of 4 and 13 μm particles was used. Candida cells were successfully separated from the white blood cells (WBCs) and concentrated by 74.6-fold in the sample reservoir of the closed-loop system at 800 μL/min with a flow rate factor of 3.3. In addition, the collected Candida cells were washed with washing buffer (deionized water) in the microchannels with an aspect ratio of 2 at a total flow rate of 100 μL/min. Finally, Candida cells at extremely low concentrations (Ct > 35) became detectable after the removal of WBCs, the additional buffer solution in the closed-loop system (Ct = 30.3 ± 1.3), and further removal of blood lysate and washing (Ct = 23.3 ± 1.6).

Microfluidic Separation and Enrichment of Escherichia coli by Size Using Viscoelastic Flows

Here, we achieve the separation and enrichment of Escherichia coli clusters from its singlets in a viscoelastic microfluidic device. E. coli, an important prokaryotic model organism and a widely used microbial factory, can aggregate in clusters, leading to biofilm development that can be detrimental to human health and industrial processes. The ability to obtain high-purity populations of E. coli clusters is of significance for biological, biomedical, and industrial applications. In this study, polystyrene particles of two different sizes, 1 and 4.8 μm, are used to mimic E. coli singlets and clusters, respectively. Experimental results show that particles migrate toward the channel center in a size-dependent manner, due to the combined effects of inertial and elastic forces; 4.8 and 1 μm particles are found to have lateral equilibrium positions closer to the channel centerline and sidewalls, respectively. The size-dependent separation performance of the microdevice is demonstrated to be affected by three main factors: channel length, the ratio of sheath to sample flow rate, and poly(ethylene oxide) (PEO) concentration. Further, the separation of E. coli singlets and clusters is achieved at the outlets, and the separation efficiency is evaluated in terms of purity and enrichment factor.

A Continuous Microfluidic Concentrator for High-Sensitivity Detection of Bacteria in Water Sources

Water contamination is a critical issue that threatens global public health. To enable the rapid and precise monitoring of pathogen contamination in drinking water, a concentration technique for bacterial cells is required to address the limitations of current detection methods, including the culture method and polymerase chain reaction. Here we present a viscoelastic microfluidic device for the continuous concentration of bacterial cells. To validate the device performance for cell concentration, the flow characteristics of 2-μm particles were estimated in viscoelastic fluids at different concentrations and flow rates. Based on the particle flow distributions, the flow rate factor, which is defined as the ratio of the inlet flow rate to the outlet flow rate at the center outlet, was optimized to achieve highly concentrated bacterial cells by removal of the additional suspending medium. The flow characteristics of 0.5-, 0.7-, and 1.0-μm-diameter particles were evaluated to consider the effect of a wide spectrum of bacterial size distribution. Finally, the concentration factor of bacterial cells, Staphylococcus aureus, suspended in a 2000-ppm polyethylene oxide solution was found to be 20.6-fold at a flow rate of 20 μL/min and a flow rate factor of 40.

High-throughput concentration of rare malignant tumor cells from large-volume effusions by multistage inertial microfluidics

On-chip concentration of rare malignant tumor cells (MTCs) in malignant pleural effusions (MPEs) with a large volume is challenging. Previous microfluidic concentrators suffer from a low concentration factor (CF) and a limited processing throughput. This study describes a low-cost multiplexed microfluidic concentrator that can enable high-throughput (up to 16 mL min^-1) and high CF (over 40-fold for single run) concentration of rare cells from large-volume biofluids (up to hundreds of milliliters). The multiplexed device was fabricated using inexpensive polymer-film materials using a quick non-clean-room process within 30 min. The multiplexing and flow distribution approaches applied in the device achieved high-throughput processing. By adopting serial cascading, an ultrahigh CF of approximately 1400 was achieved. Moreover, the microfluidic concentrator was successfully applied for the concentration and purification of rare MTCs within MPEs collected from patients with advanced metastatic lung and breast cancers. The provision of concentrated samples with low background cells could improve the sensitivity of cytology and thus reduce the time required for cytological examination. This novel concentrator offers the distinct advantages of a remarkable CF, high throughput, low device cost, and label-free processing and can therefore be readily integrated with other on-chip cell sorters to enhance the identification of MPEs.

Paving the Way to Overcome Antifungal Drug Resistance: Current Practices and Novel Developments for Rapid and Reliable Antifungal Susceptibility Testing

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.

Cascaded contraction-expansion channels for bacteria separation from RBCs using viscoelastic microfluidics

Implementation of viscoelasticity-based particle migration techniques has attracted significant interest thanks to its simplicity to achieve particle separation and enrichment at high sensitivity and accuracy for the last decade. Many methods have previously been developed for particle focusing and separation, but they all require long fluidic channels to enable the desired elastic force on particles. Here, a cascade contraction-expansion microfluidic system with a much shorter channel length is presented. Experimental results show that this system achieved continuous, sheathless particle separation in a viscoelastic fluid, and Enterococcus faecalis was successfully separated from red blood cells (RBCs). Thanks to its small size, the system provides extra advantage for its integration into small chips.

High-Throughput Cell Concentration Using A Piezoelectric Pump in Closed-Loop Viscoelastic Microfluidics

Cell concentration is a critical process in biological assays and clinical diagnostics for the pre-treatment of extremely rare disease-related cells. The conventional technique for sample preconcentration and centrifugation has the limitations of a batch process requiring expensive and large equipment. Therefore, a high-throughput continuous cell concentration technique needs to be developed. However, in single-pass operation, the required concentration ratio is hard to achieve. In this study, we propose a closed-loop continuous cell concentration system using a viscoelastic non-Newtonian fluid. For miniaturized and integrated systems, two piezoelectric pumps were adopted. The pumping capability generated by a piezoelectric pump in a microfluidic channel was evaluated depending on the applied voltage, frequency, sample viscosity, and channel length. The concentration performance of the device was evaluated using 13 μm particles and white blood cells (WBCs) with different channel lengths and voltages. In the closed-loop system, the focused cells collected at the center outlet were sent back to the inlet, while the buffer solution was removed to the side outlets. Finally, to expand the clinical applicability of our closed-loop system, WBCs in lysed blood samples with 70% hematocrit and prostate cancer cells in urine samples were used. Using the closed-loop system, WBCs were concentrated by ~63.4 ± 0.8-fold within 20 min to a final volume of 160 μL using 10 mL of lysed blood sample with 70% hematocrit (~3 cP). In addition, prostate cancer cells in 10 mL urine samples were concentrated by ~64.1-fold within ~11 min due to low viscosity (~1 cP).

Molecular Diagnosis of Yeast Infections

PURPOSE OF REVIEW

The use of molecular tests to aid the diagnosis of invasive yeast infection, in particular invasive candidosis, has been described for over two decades, yet widespread application is limited, and diagnosis remains heavily dependent on classical microbiology. This article will review developments from the past decade in attempt to build on existing knowledge. It will highlight clinical performance and limitations while reviewing developments on recognized procedures; it will also provide insight into novel approaches incorporated in response to clinical demand (e.g. C. auris and antifungal resistance) or technological advances (e.g. next-generation sequencing).

RECENT FINDINGS

Limited methodological standardization and, until recently, unavailability of commercial options have hindered the integration of molecular diagnostics for yeasts. The development of certain, novel commercial methods has received considerable evaluation allowing a greater understanding of individual assay performance, but widespread multicentre evaluation of most commercial kits is lacking. The detection of emerging pathogens (e.g. C. auris) has been enhanced by the development of molecular tests. Molecular methods are providing a better understanding of the mycobiome, mechanisms of resistance and epidemiology/phylogeny.

SUMMARY

Despite over two decades of use, the incorporation of molecular methods to enhance the diagnosis of yeast infections remains limited to certain specialist centres. While the development of commercial tests will provide stimulus for broader application, further validation and reduced costs are required. Over the same period of time, Aspergillus PCR has become more widely accepted driven by international efforts to standardize methodology; it is critical that yeast PCR follows suit. Next-generation sequencing will provide significant information on the mycobiome, antifungal resistance mechanism and even broad-range detection directly from the specimen, which may be critical for the molecular detection of yeasts other than Candida species, which is currently limited.

Three-Dimensional Numerical Simulation of Particle Focusing and Separation in Viscoelastic Fluids

Particle focusing and separation using viscoelastic microfluidic technology have attracted lots of attention in many applications. In this paper, a three-dimensional lattice Boltzmann method (LBM) coupled with the immersed boundary method (IBM) is employed to study the focusing and separation of particles in viscoelastic fluid. In this method, the viscoelastic fluid is simulated by the LBM with two sets of distribution functions and the fluid-particle interaction is calculated by the IBM. The performance of particle focusing under different microchannel aspect ratios (AR) is explored and the focusing equilibrium positions of the particles with various elasticity numbers and particle diameters are compared to illustrate the mechanism of particle focusing and separation in viscoelastic fluids. The results indicate that, for particle focusing in the square channel (AR = 1), the centerline single focusing becomes a bistable focusing at the centerline and corners as El increases. In the rectangular channels (AR < 1), particles with different diameters have different equilibrium positions. The equilibrium position of large particles is closer to the wall, and large particles have a faster lateral migration speed and few large particles migrate towards the channel center. Compared with the square channel, the rectangular channel is a better design for particle separation.

Scaling of deterministic lateral displacement devices to a single column of bumping obstacles

We describe a deterministic lateral displacement (DLD) for particle separation with only a single column of bumping features. The bifurcation of fluid streams at obstacles is not set by the "tilt" of columns with respect to macroscopic current flow, but rather by the fluidic resistances for lateral flow at each obstacle. With one column of 14 bumping features and corresponding inlet/outlet channels, the single-column DLD can separate particles with diameters of 4.8 μm and 9.9 μm at 30 μL min^-1, with an area of only 0.37 mm × 1.5 mm (0.55 mm²). The large-cell output contains over 99% of the 9.9 μm particles and only 0.2% of the 4.8 m particles. The throughput per area of 54 μL min^-1 per mm² represents a 10× increase over previous selective harvesting reports for microfluidic devices in a similar particle size range.

Characterization of the Dielectrophoretic Response of Different Candida Strains Using 3D Carbon Microelectrodes

Bloodstream infection with Candida fungal cells remains one of the most life-threatening complications among hospitalized patients around the world. Although most of the cases are still due to Candida albicans, the rising incidence of infections caused by other Candida strains that may not respond to traditional anti-fungal treatments merits the development of a method for species-specific isolation of Candida. To this end, here we present the characterization of the dielectrophoresis (DEP) response of Candida albicans, Candida tropicalis and Candida parapsilosis. We complement such characterization with a study of the Candida cells morphology. The Candida strains exhibited subtle differences in their morphology and dimensions. All the Candida strains exhibited positive DEP in the range 10-500 kHz, although the strength of the DEP response was different for each Candida strain at different frequencies. Only Candida tropicalis showed positive DEP at 750 kHz. The current results show potential for manipulation and enrichment of a specific Candida strain at specific DEP conditions towards aiding in the rapid identification of Candida strains to enable the effective and timely treatment of Candida infections.

Viscoelastic microfluidics: progress and challenges

The manipulation of cells and particles suspended in viscoelastic fluids in microchannels has drawn increasing attention, in part due to the ability for single-stream three-dimensional focusing in simple channel geometries. Improvement in the understanding of non-Newtonian effects on particle dynamics has led to expanding exploration of focusing and sorting particles and cells using viscoelastic microfluidics. Multiple factors, such as the driving forces arising from fluid elasticity and inertia, the effect of fluid rheology, the physical properties of particles and cells, and channel geometry, actively interact and compete together to govern the intricate migration behavior of particles and cells in microchannels. Here, we review the viscoelastic fluid physics and the hydrodynamic forces in such flows and identify three pairs of competing forces/effects that collectively govern viscoelastic migration. We discuss migration dynamics, focusing positions, numerical simulations, and recent progress in viscoelastic microfluidic applications as well as the remaining challenges. Finally, we hope that an improved understanding of viscoelastic flows in microfluidics can lead to increased sophistication of microfluidic platforms in clinical diagnostics and biomedical research.

Label-free microfluidic sorting of microparticles

Massive growth of the microfluidics field has triggered numerous advances in focusing, separating, ordering, concentrating, and mixing of microparticles. Microfluidic systems capable of performing these functions are rapidly finding applications in industrial, environmental, and biomedical fields. Passive and label-free methods are one of the major categories of such systems that have received enormous attention owing to device operational simplicity and low costs. With new platforms continuously being proposed, our aim here is to provide an updated overview of the state of the art for passive label-free microparticle separation, with emphasis on performance and operational conditions. In addition to the now common separation approaches using Newtonian flows, such as deterministic lateral displacement, pinched flow fractionation, cross-flow filtration, hydrodynamic filtration, and inertial microfluidics, we also discuss separation approaches using non-Newtonian, viscoelastic flow. We then highlight the newly emerging approach based on shear-induced diffusion, which enables direct processing of complex samples such as untreated whole blood. Finally, we hope that an improved understanding of label-free passive sorting approaches can lead to sophisticated and useful platforms toward automation in industrial, environmental, and biomedical fields.

Sheathless separation of microalgae from bacteria using a simple straight channel based on viscoelastic microfluidics

Microalgae cells have been recognized as a promising sustainable resource to meet worldwide growing demands for renewable energy, food, livestock feed, water, cosmetics, pharmaceuticals, and materials. In order to ensure high-efficiency and high-quality production of biomass, biofuel, or bio-based products, purification procedures prior to the storage and cultivation of the microalgae from contaminated bacteria are of great importance. The present work proposed and developed a simple, sheathless, and efficient method to separate microalgae Chlorella from bacteria Bacillus Subtilis in a straight channel using the viscoelasticity of the medium. Microalgae and bacteria migrate to different lateral positions closer to the channel centre and channel walls respectively. Fluorescent microparticles with 1 μm and 5 μm diameters were first used to mimic the behaviours of bacteria and microalgae to optimize the separating conditions. Subsequently, size-based separation in Newtonian fluid and in viscoelastic fluid in straight channels with different aspect ratios was compared and demonstrated. Under the optimal condition, the removal ratio for 1 μm microparticles and separation efficiency for 5 μm particles can reach up to 98.28% and 93.85% respectively. For bacteria and microalgae cells separation, the removal ratio for bacteria and separation efficiency for microalgae cells is 92.69% and 100% respectively. This work demonstrated the continuous and sheathless separation of microalgae from bacteria for the first time by viscoelastic microfluidics. This technique can also be applied as an efficient and user-friendly method to separate mammalian cells or other kinds of cells.

Sheathless High-Throughput Circulating Tumor Cell Separation Using Viscoelastic non-Newtonian Fluid

Circulating tumor cells (CTCs) have attracted increasing attention as important biomarkers for clinical and biological applications. Several microfluidic approaches have been demonstrated to separate CTCs using immunoaffinity or size difference from other blood cells. This study demonstrates a sheathless, high-throughput separation of CTCs from white blood cells (WBCs) using a viscoelastic fluid. To determine the fluid viscoelasticity and the flow rate for CTC separation, and to validate the device performance, flow characteristics of 6, 13, and 27 μm particles in viscoelastic fluids with various concentrations were estimated at different flow rates. Using 0.2% hyaluronic acid (HA) solution, MCF-7 (Michigan Cancer Foundation-7) cells mimicking CTCs in this study were successfully separated from WBCs at 500 μL/min with a separation efficiency of 94.8%. Small amounts of MCF-7 cells (~5.2%) were found at the center outlet due to the size overlap with WBCs.