Sheathless and high-throughput elasto-inertial bacterial sorting for enhancing molecular diagnosis of bloodstream infection

Identification of sepsis-causing bacteria from whole blood without culture using primers with no cross-reactivity to human DNA

Sepsis is a major health concern globally, and identification of the causative organism usually takes several days. Furthermore, molecular amplification using whole blood from patients with sepsis remains challenging because of primer cross-reactivity with human DNA, which can delay appropriate clinical intervention. To address these concerns, we designed primers that could reduce cross-reactivity. By evaluating these primers against human DNA, we confirmed that the cross-reactivity observed with conventional primers was notably absent. In silico PCR further demonstrated the specificity and efficiency of the designed primers across 23 bacterial species that are often associated with sepsis. When tested using blood samples from sepsis patients, the designed primers showed moderate sensitivity and high specificity. Surprisingly, our method identified bacteria even in samples that were detected at other sites but tested negative using conventional blood culture methods. Although we identified some challenges, such as contamination with Acetobacter aceti due to the saponin pretreatment of samples, the developed method demonstrates remarkable potential for rapid identification of the causative organisms of sepsis and provides a new avenue for diagnosis in clinical practice.

Cascaded elasto-inertial separation of malignant tumor cells from untreated malignant pleural and peritoneal effusions

Separation of malignant tumor cells (MTCs) from large background cells in untreated malignant pleural and peritoneal effusions (MPPEs) is critical for improving the sensitivity and efficiency of cytological diagnosis. Herein, we proposed a cascaded elasto-inertial cell separation (CEICS) device integrating an interfacial elasto-inertial microfluidic channel with a symmetric contraction expansion array (CEA) channel for pretreatment-free, high-recovery-ratio, and high-purity separation of MTCs from clinical MPPEs. First, the effects of flow-rate ratio, cell concentration, and cell size on separation performances in two single-stage channels were investigated. Then, the performances of the integrated CEICS device were characterized using blood cells spiked with three different tumor cells (MCF-7, MDA-MB-231, and A549 cells) at a high total throughput of 240 μL min-1. An average recovery ratio of ∼95% and an average purity of ∼61% for the three tumor cells were achieved. Finally, we successfully applied the CEICS device for the pretreatment-free separation of MTCs from clinical MPPEs of different cancers. Our CEICS device may provide a preparation tool for improving the sensitivity and efficiency of cytological examination.

Sheathless inertial particle focusing methods within microfluidic devices: a review

The ability to manipulate and focus particles within microscale fluidic environments is crucial to advancing biological, chemical, and medical research. Precise and high-throughput particle focusing is an essential prerequisite for various applications, including cell counting, biomolecular detection, sample sorting, and enhancement of biosensor functionalities. Active and sheath-assisted focusing techniques offer accuracy but necessitate the introduction of external energy fields or additional sheath flows. In contrast, passive focusing methods exploit the inherent fluid dynamics in achieving high-throughput focusing without external actuation. This review analyzes the latest developments in strategies of sheathless inertial focusing, emphasizing inertial and elasto-inertial microfluidic focusing techniques from the channel structure classifications. These methodologies will serve as pivotal benchmarks for the broader application of microfluidic focusing technologies in biological sample manipulation. Then, prospects for future development are also predicted. This paper will assist in the understanding of the design of microfluidic particle focusing devices.

Efficient filter-in-centrifuge separation of low-concentration bacteria from blood

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.

Separation of bacteria smaller than 4 µm from other blood components using insulator-based dielectrophoresis: numerical simulation approach

Bloodstream infection (BSI) is a life-threatening infection that causes more than 80,000 deaths and more than 500,000 infections annually in North America. The rapid diagnosis of infection reduces BSI mortality. We proposed bacterial enrichment and separation approach in the current work that may reduce culturing time and accelerate the diagnosis of infection. Over the last two decades, multiple separation methods have been developed, and among these methods, insulator-based dielectrophoresis (iDEP) is considered a powerful technique for separating biological particles. Bacterial separation in the blood is challenging due to the presence of other blood cells, such as white blood cells, red blood cells, and platelets. In the present study, a model is presented which is capable of blood cells separation and directing each cell to a specific outlet using continuous flows of particles with sizes larger than 8 µm, 8-4 µm, and smaller than 4 µm. Compared to other methods, such as filtration, the main advantage of this model is that particles larger than 8 µm are separated from the flow before other particles, which prevents the accumulation of particles in the channel. The outcomes of simulations demonstrated that the factors such as applied voltage and channel dimensions significantly affect the separation efficiency. If these values are properly selected (for example voltage of 70 V that was causing an electric field of 200 V/cm), the proposed model can completely (100%) separate particles larger than 8 µm and smaller than 4 µm (8-4 µm particles separation efficiency is 95%).

Tuning particle inertial separation in sinusoidal channels by embedding periodic obstacle microstructures

Inertial microfluidics functions solely based on the fluid dynamics at relatively high flow speed. Thus, channel geometry is the critical design parameter that contributes to the performance of the device. Four basic channel geometries (i.e., straight, expansion-contraction, spiral and serpentine) have been proposed and extensively studied. To further enhance the performance, innovative channel design through combining two or more geometries is promising. This work explores embedding periodic concave and convex obstacle microstructures in sinusoidal channels and investigates their influence on particle inertial focusing and separation. The concave obstacles could significantly enhance the Dean flow and tune the flow range for particle inertial focusing and separation. Based on this finding, we propose a cascaded device by connecting two sinusoidal channels consecutively for rare cell separation. The concave obstacles are embedded in the second channel to adapt its operational flow rates and enable the functional operation of both channels. Polystyrene beads and breast cancer cells (T47D) spiking in the blood were respectively processed by the proposed device. The results indicate an outstanding separation performance, with 3 to 4 orders of magnitude enhancement in purity for samples with a primary cancer cells ratio of 0.01% and 0.001%, respectively. Embedding microstructures as obstacles brings more flexibility to the design of inertial microfluidic devices, offering a feasible new way to combine two or more serial processing units for high-performance separation.

Automatic Microfluidic Cell Wash Platform for Purifying Cells in Suspension: Puriogen

Cell wash is an essential cell sample preparation procedure to eliminate or minimize interfering substances for various subsequent cell analyses. The commonly used cell wash method is centrifugation which separates cells from other biomolecules in a solution with manual pipetting and has many drawbacks such as being labor-intensive and time-consuming with substantial cell loss and cell clumping. To overcome these issues, a centrifuge-free and automatic cell wash platform for cell purity generation, termed Puriogen, has been developed in this work. Compared with other developed products such as AcouWash, Puriogen can process samples with a high throughput of above 500 μL/min. Puriogen utilizes a uniquely designed inertial microfluidic device to complete the automatic cell wash procedure. One single-cell wash procedure with the Puriogen platform can remove more than 90% ambient proteins and nucleic acids from the cell sample. It can also remove most of the residual fluorescent dye after cell staining to significantly reduce the background signals for subsequent cell analysis. By removing the dead cell debris, it can increase the live cell percentage in the sample by 2-fold. Moreover, the percentage of single-cell population is also increased by 20% because of further disassociation of small-cell aggregates (e.g., doublets and triplets) into singlets. To freely adjust cell concentrations, the Puriogen platform can concentrate cells 5 times in a single flow-through process. The presented Puriogen cell wash solution has broad applications in cell preparation with its excellent simplicity in operation and wash efficiency, especially in single-cell sequencing.

Diagnosis of Bloodstream Infections: An Evolution of Technologies towards Accurate and Rapid Identification and Antibiotic Susceptibility Testing

Bloodstream infections (BSI) are a leading cause of death worldwide. The lack of timely and reliable diagnostic practices is an ongoing issue for managing BSI. The current gold standard blood culture practice for pathogen identification and antibiotic susceptibility testing is time-consuming. Delayed diagnosis warrants the use of empirical antibiotics, which could lead to poor patient outcomes, and risks the development of antibiotic resistance. Hence, novel techniques that could offer accurate and timely diagnosis and susceptibility testing are urgently needed. This review focuses on BSI and highlights both the progress and shortcomings of its current diagnosis. We surveyed clinical workflows that employ recently approved technologies and showed that, while offering improved sensitivity and selectivity, these techniques are still unable to deliver a timely result. We then discuss a number of emerging technologies that have the potential to shorten the overall turnaround time of BSI diagnosis through direct testing from whole blood—while maintaining, if not improving—the current assay’s sensitivity and pathogen coverage. We concluded by providing our assessment of potential future directions for accelerating BSI pathogen identification and the antibiotic susceptibility test. While engineering solutions have enabled faster assay turnaround, further progress is still needed to supplant blood culture practice and guide appropriate antibiotic administration for BSI patients.

High resolution and rapid separation of bacteria from blood using elasto-inertial microfluidics

Improved sample preparation has the potential to address unmet needs for fast turnaround sepsis tests. In this work, we report elasto-inertial based rapid bacteria separation from diluted blood at high separation efficiency. In viscoelastic flows, we demonstrate novel findings where blood cells prepositioned at the outer wall entering a spiral device remain fully focused throughout the channel length while smaller bacteria migrate to the opposite wall. Initially, using microparticles, we show that particles above a certain size cut-off remain fully focused at the outer wall while smaller particles differentially migrate toward the inner wall. We demonstrate particle separation at 1 μm resolution at a total throughput of 1 mL/min. For blood-based experiments, a minimum of 1:2 dilution was necessary to fully focus blood cells at the outer wall. Finally, Escherichia coli spiked in diluted blood were continuously separated at a total flow rate of 1 mL/min, with efficiencies between 82 and 90% depending on the blood dilution. Using a single spiral, it takes 40 min to process 1 mL of blood at a separation efficiency of 82%. The label-free, passive, and rapid bacteria isolation method has a great potential for speeding up downstream phenotypic and genotypic analysis.