Accurate Prediction of Antimicrobial Susceptibility for Point-of-Care Testing of Urine in Less than 90 Minutes via iPRISM Cassettes

The extensive and improper use of antibiotics has led to a dramatic increase in the frequency of antibiotic resistance among human pathogens, complicating infectious disease treatments. In this work, a method for rapid antimicrobial susceptibility testing (AST) is presented using microstructured silicon diffraction gratings integrated into prototype devices, which enhance bacteria-surface interactions and promote bacterial colonization. The silicon microstructures act also as optical sensors for monitoring bacterial growth upon exposure to antibiotics in a real-time and label-free manner via intensity-based phase-shift reflectometric interference spectroscopic measurements (iPRISM). Rapid AST using clinical isolates of Escherichia coli (E. coli) from urine is established and the assay is applied directly on unprocessed urine samples from urinary tract infection patients. When coupled with a machine learning algorithm trained on clinical samples, the iPRISM AST is able to predict the resistance or susceptibility of a new clinical sample with an Area Under the Receiver Operating Characteristic curve (AUC) of ∼ 0.85 in 1 h, and AUC > 0.9 in 90 min, when compared to state-of-the-art automated AST methods used in the clinic while being an order of magnitude faster.

Shining light in blind alleys: deciphering bacterial attachment in silicon microstructures

With new advances in infectious disease, antifouling surfaces, and environmental microbiology research comes the need to understand and control the accumulation and attachment of bacterial cells on a surface. Thus, we employ intrinsic phase-shift reflectometric interference spectroscopic measurements of silicon diffraction gratings to non-destructively observe the interactions between bacterial cells and abiotic, microstructured surfaces in a label-free and real-time manner. We conclude that the combination of specific material characteristics (i.e., substrate surface charge and topology) and characteristics of the bacterial cells (i.e., motility, cell charge, biofilm formation, and physiology) drive bacteria to adhere to a particular surface, often leading to a biofilm formation. Such knowledge can be exploited to predict antibiotic efficacy and biofilm formation, and enhance surface-based biosensor development, as well as the design of anti-biofouling strategies.

Lab-on-a-Chip Devices for Point-of-Care Medical Diagnostics

The recent coronavirus (COVID-19) pandemic has underscored the need to move from traditional lab-centralized diagnostics to point-of-care (PoC) settings. Lab-on-a-chip (LoC) platforms facilitate the translation to PoC settings via the miniaturization, portability, integration, and automation of multiple assay functions onto a single chip. For this purpose, paper-based assays and microfluidic platforms are currently being extensively studied, and much focus is being directed towards simplifying their design while simultaneously improving multiplexing and automation capabilities. Signal amplification strategies are being applied to improve the performance of assays with respect to both sensitivity and selectivity, while smartphones are being integrated to expand the analytical power of the technology and promote its accessibility. In this chapter, we review the main technologies in the field of LoC platforms for PoC medical diagnostics and survey recent approaches for improving these assays.

Design considerations of aptasensors for continuous monitoring of biomarkers in digestive tract fluids

We present a porous Si (PSi)-based label-free optical biosensor for sensitive and continuous detection of a model target protein biomarker in gastrointestinal (GI) tract fluids. The biosensing platform is designed to continuously monitor its target protein within the complex GI fluids without sample preparation and washing steps. An oxidized PSi Fabry-Pérot thin films are functionalized with aptamers, which are used as the capture probes. The optical response of the aptamer-conjugated PSi is studied upon exposure to unprocessed GI fluids, originated from domestic pigs, spiked with the target protein. We investigate biological and chemical surface passivation methods to stabilize the surface and reduce non-specific adsorption of interfering proteins and molecules within the GI fluids. For the passivated PSi aptasensor we simulate continuous in vivo biosensing conditions, demonstrating that the aptasensor could successfully detect the target in a continuous manner without any need for surface washing after the target protein binding events, at a clinically relevant range. Furthermore, we simulate biosensing conditions within a smart capsule, in which the aptasensor is occasionally exposed to GI fluids in flow or via repeated cycles of injection and static incubation events. Such biosensor can be implemented within ingestible capsule devices and used for in situ biomarker detection in the GI tract.

Porous Silicon-Based Aptasensors: Toward Cancer Protein Biomarker Detection

The anterior gradient homologue-2 (AGR2) protein is an attractive biomarker for various types of cancer. In pancreatic cancer, it is secreted to the pancreatic juice by premalignant lesions, which would be an ideal stage for diagnosis. Thus, designing assays for the sensitive detection of AGR2 would be highly valuable for the potential early diagnosis of pancreatic and other types of cancer. Herein, we present a biosensor for label-free AGR2 detection and investigate approaches for enhancing the aptasensor sensitivity by accelerating the target mass transfer rate and reducing the system noise. The biosensor is based on a nanostructured porous silicon thin film that is decorated with anti-AGR2 aptamers, where real-time monitoring of the reflectance changes enables the detection and quantification of AGR2, as well as the study of the diffusion and target-aptamer binding kinetics. The aptasensor is highly selective for AGR2 and can detect the protein in simulated pancreatic juice, where its concentration is outnumbered by orders of magnitude by numerous proteins. The aptasensor's analytical performance is characterized with a linear detection range of 0.05-2 mg mL^-1, an apparent dissociation constant of 21 ± 1 μM, and a limit of detection of 9.2 μg mL^-1 (0.2 μM), which is attributed to mass transfer limitations. To improve the latter, we applied different strategies to increase the diffusion flux to and within the nanostructure, such as the application of isotachophoresis for the preconcentration of AGR2 on the aptasensor, mixing, or integration with microchannels. By combining these approaches with a new signal processing technique that employs Morlet wavelet filtering and phase analysis, we achieve a limit of detection of 15 nM without compromising the biosensor's selectivity and specificity.

Morlet Wavelet Filtering and Phase Analysis to Reduce the Limit of Detection for Thin Film Optical Biosensors

The ultimate detection limit of optical biosensors is often limited by various noise sources, including those introduced by the optical measurement setup. While sophisticated modifications to instrumentation may reduce noise, a simpler approach that can benefit all sensor platforms is the application of signal processing to minimize the deleterious effects of noise. In this work, we show that applying complex Morlet wavelet convolution to Fabry-Pérot interference fringes characteristic of thin film reflectometric biosensors effectively filters out white noise and low-frequency reflectance variations. Subsequent calculation of the average difference in extracted phase between the filtered analyte and reference signals enables a significant reduction in the limit of detection (LOD). This method is applied on experimental data sets of thin film porous silicon sensors (PSi) in buffered solution and complex media obtained from two different laboratories. The demonstrated improvement in the LOD achieved using wavelet convolution and average phase difference paves the way for PSi optical biosensors to operate with clinically relevant detection limits for medical diagnostics, environmental monitoring, and food safety.

3D-printed microfluidics integrated with optical nanostructured porous aptasensors for protein detection

Microfluidic integration of biosensors enables improved biosensing performance and sophisticated lab-on-a-chip platform design for numerous applications. While soft lithography and polydimethylsiloxane (PDMS)-based microfluidics are still considered the gold standard, 3D-printing has emerged as a promising fabrication alternative for microfluidic systems. Herein, a 3D-printed polyacrylate-based microfluidic platform is integrated for the first time with a label-free porous silicon (PSi)-based optical aptasensor via a facile bonding method. The latter utilizes a UV-curable adhesive as an intermediate layer, while preserving the delicate nanostructure of the porous regions within the microchannels. As a proof-of-concept, a generic model aptasensor for label-free detection of his-tagged proteins is constructed, characterized, and compared to non-microfluidic and PDMS-based microfluidic setups. Detection of the target protein is carried out by real-time monitoring reflectivity changes of the PSi, induced by the target binding to the immobilized aptamers within the porous nanostructure. The microfluidic integrated aptasensor has been successfully used for detection of a model target protein, in the range 0.25 to 18 μM, with a good selectivity and an improved limit of detection, when compared to a non-microfluidic biosensing platform (0.04 μM vs. 2.7 μM, respectively). Furthermore, a superior performance of the 3D-printed microfluidic aptasensor is obtained, compared to a conventional PDMS-based microfluidic platform with similar dimensions.

Aptamers vs. antibodies as capture probes in optical porous silicon biosensors

Over the past decade aptamers have emerged as a promising class of bioreceptors for biosensing applications with significant advantages over conventional antibodies. However, experimental studies comparing aptasensors and immunosensors, under equivalent conditions, are limited and the results are inconclusive, in terms of benefits and limitations of each bioreceptor type. In the present work, the performance of aptamer and antibody bioreceptors for the detection of a his-tagged protein, used as a model target, is compared. The bioreceptors are immobilized onto a nanostructured porous silicon (PSi) thin film, used as the optical transducer, and the target protein is detected in a real-time and label-free format by reflective interferometric Fourier transform spectroscopy. For the antibodies, random-oriented immobilization onto the PSi nanostructure results in a poor biosensing performance. Contrary, Fc-oriented immobilization of the antibodies shows a similar biosensing performance to that exhibited by the aptamer-based biosensor, in terms of binding rate, dynamic detection range, limit of detection and selectivity. The aptasensor outperforms in terms of its reusability and storability, while the immunosensor could not be regenerated for subsequent experiments.

Lab-on-a-Chip Devices for Point-of-Care Medical Diagnostics

The recent coronavirus (COVID-19) pandemic has underscored the need to move from traditional lab-centralized diagnostics to point-of-care (PoC) settings. Lab-on-a-chip (LoC) platforms facilitate the translation to PoC settings via the miniaturization, portability, integration, and automation of multiple assay functions onto a single chip. For this purpose, paper-based assays and microfluidic platforms are currently being extensively studied, and much focus is being directed towards simplifying their design while simultaneously improving multiplexing and automation capabilities. Signal amplification strategies are being applied to improve the performance of assays with respect to both sensitivity and selectivity, while smartphones are being integrated to expand the analytical power of the technology and promote its accessibility. In this chapter, we review the main technologies in the field of LoC platforms for PoC medical diagnostics and survey recent approaches for improving these assays.

On Chip Protein Pre-Concentration for Enhancing the Sensitivity of Porous Silicon Biosensors

Porous silicon (PSi) nanomaterials have been widely studied as label-free optical biosensors for protein detection. However, these biosensors' performance, specifically in terms of their sensitivity (which is typically in the micromolar range), is insufficient for many applications. Herein, we present a proof-of-concept application of the electrokinetic isotachophoresis (ITP) technique for real-time preconcentration of a target protein on a PSi biosensor. With ITP, a highly concentrated target zone is delivered to the sensing area, where the protein target is captured by immobilized aptamers. The detection of the binding events is conducted in a label-free manner by reflective interferometric Fourier transformation spectroscopy (RIFTS). Up to 1000-fold enhancement in local concentration of the protein target and the biosensor's sensitivity are achieved, with a measured limit of detection of 7.5 nM. Furthermore, the assay is successfully performed in complex media, such as bacteria lysate samples, while the selectivity of the biosensor is retained. The presented assay could be further utilized for other protein targets, and to promote the development of clinically useful PSi biosensors.

Whole-cell detection of live lactobacillus acidophilus on aptamer-decorated porous silicon biosensors

This work describes the design of optical aptamer-based porous silicon (PSi) biosensors for the direct capture of Lactobacillus acidophilus. Aptamers are oligonucleotides (single-stranded DNA or RNA) that can bind their targets with high affinity and specificity, making them excellent recognition elements for biosensing applications. Herein, aptamer Hemag1P, which specifically targets the important probiotic L. acidophilus, was utilized for direct bacteria capture onto oxidized PSi Fabry-Pérot thin films. Monitoring changes in the reflectivity spectrum (using reflective interferometric Fourier transform spectroscopy) allows for bacteria detection in a label-free, simple and rapid manner. The performance of the biosensor was optimized by tuning the PSi nanostructure, its optical properties, as well as the immobilization density of the aptamer. We demonstrate the high selectivity and specificity of this simple "direct-capture" biosensing scheme and show its ability to distinguish between live and dead bacteria. The resulting biosensor presents a robust and rapid method for the specific detection of live L. acidophilus at concentrations relevant for probiotic products and as low as 10(6) cells per mL. Rapid monitoring of probiotic bacteria is crucial for quality, purity and safety control as the use of probiotics in functional foods and pharmaceuticals is becoming increasingly popular.