Particle Diffusometry: An Optical Detection Method for Vibrio cholerae Presence in Environmental Water Samples

Real-Time Visualization of HIV-1 RNA Detection Using Loop-Mediated Isothermal Amplification-Enabled Particle Diffusometry

Isothermal nucleic acid amplification tests, NAATs, such as reverse transcription-loop-mediated isothermal amplification (RT-LAMP), offer promising capabilities to perform real-time semiquantitative detection of viral pathogens. These tests provide rapid results, utilize simple instrumentation for single-temperature reactions, support efficient user workflows, and are suitable for field use. Herein, we present a novel and robust method for real-time monitoring of HIV-1 RNA RT-LAMP utilizing a novel implementation of particle diffusometry (PD), a diffusivity quantification technique using fluorescent particles, to quantify viral concentration in nuclease-free water. We monitor changes in particle diffusion dynamics of 400 nm fluorescently labeled particles throughout the RT-LAMP of HIV-1 RNA in nuclease-free water, enabling measurement within 20 min and detection of concentrations as low as 25 virus particles per μL. Moreover, in a single-blind study, we demonstrate semiquantitative detection by accurately determining the initial concentration of an unknown HIV-1 RNA within a 10% absolute error margin. These results highlight the potential of real-time PD readout for quantifying HIV-1 RNA via RT-LAMP, offering promise for viral load monitoring of HIV and other chronic infections.

Biomolecular Interaction Analysis Quantification with a Low-Volume Microfluidic Chip and Particle Diffusometry

Microfluidic techniques are widely applied in biomolecular analysis and disease diagnostic assays. While the volume of the sample that is directly used in such assays is often only femto-to microliters, the "dead volume" of solutions supplied in syringes and tubing can be much larger, even up to milliliters, increasing overall reagent use and making analysis significantly more expensive. To reduce the difficulty and cost, we designed a new chip using a low volume solution for analysis and applied it to obtain real-time data for protein-protein interaction measurements. The chip takes advantage of air/aqueous two-phase droplet flow, on-chip rapid mixing within milliseconds, and a droplet capture method, that ultimately requires only 2 μL of reagent solution. The interaction is analyzed by particle diffusometry, a nonintrusive and precise optical detection method to analyze the properties of microparticle diffusion in solution. Herein, we demonstrate on-chip characterization of human immunodeficiency virus p24 antibody-antigen protein binding kinetics imaged via fluorescence microscopy and analyzed by PD. The measured kon and koff are 1 × 106 M-1 s-1 and 3.3 × 10-4 s-1, respectively, and agree with independent measurement via biolayer interferometry and previously calculated p24-antibody binding kinetics. This new microfluidic chip and the protein-protein interaction analysis method can also be applied in other fields that require low-volume solutions to perform accurate measurement, analysis, and detection.

Review of Rapid Diagnostic Methods for Vibrio Cholerae Detection in the Last Decade (2011-2022)

Introduction

Cholera epidemic poses a global public health threat, heavily impacting the global economy and societies, with Africa and Asia particularly affected due to factors like; inadequate sanitation, contaminated water, and overcrowding. The associated high rates of morbidity and mortality strain productivity and healthcare costs while complicating control measures. Consequently, the World Health Organization's cholera control initiative and the Diarrhoeal Diseases Laboratory Network advocate for rapid responses to outbreaks and continuous environmental surveillance, since traditional cholera detection methods relying on phenotypic fingerprinting, although considered the gold standard, suffer from labour-intensiveness, time-consumption, and skill requirements. This results in inadequate surveillance and delayed treatment in remote areas lacking well-equipped laboratories.

Methods

A systematic review was conducted to evaluate the development and performance of cholera rapid diagnostic techniques for detecting cholera in clinical samples and for environmental surveillance purposes over the past decade.

Results

Twenty-four commercially produced diagnostics were identified in January 2011. Ten more were mentioned in the literature and yet did not provide enough relevant data due to suspected production withdrawal or fall-back. The vast bulk of tests were discovered to be based on antigen or antibody detection, with DNA accounting for a large proportion of the residual tests. This study revealed a plethora of diagnostic methods, some of which have not yet made it to the commercial market. Promising approaches, such as; Loop-mediated isothermal amplification (LAMP), ELISA, and simplified PCR protocols, are likely to play a significant role in future cholera screening. Findings are herein summarised in tables and figures.

Conclusion

Cholera epidemic continues to present a formidable global health challenge with economic and social repercussions. Traditional detection methods fall short in resource-limited areas, necessitating the exploration of advanced molecular techniques, like aptamers, to improve diagnosis, surveillance, and control measures, especially in regions vulnerable to cholera outbreaks.

Quantifying Brownian motion in the presence of simple shear flow with particle diffusometry

Particle diffusometry, a technology derived from particle image velocimetry, quantifies the Brownian motion of particles suspended in a quiescent solution by computing the diffusion coefficient. Particle diffusometry has been used for pathogen detection by measuring the change in solution viscosity due to amplified DNA from a specific gene target. However, particle diffusometry fails to calculate accurate measurements at elevated temperatures and fluid flow. Therefore, these two current limitations hinder the potential application where particle diffusometry can further be used. In this work, we expanded the usability of particle diffusometry to be applied to fluid samples with simple shear flow and at various temperatures. A range of diffusion coefficient videos is created to simulate the Brownian motion of particles under flow and temperature conditions. Our updated particle diffusometry analysis forms a correction equation under three different polynomial degrees of shear flow with varying flow rates and temperatures between 25 and 65 °C. An experiment in a channel with a rectangular cross section using a syringe pump to generate a constant flow is done to analyze the modified algorithm. In simulation analysis, the modified algorithm successfully computes the diffusion coefficients with ±  10% error for an average flow rate of up to 8 pixel / Δ t on all three flow types. Complementary experiments confirm the simulation results.

Graphical abstract

LAMP-Based Point-of-Care Biosensors for Rapid Pathogen Detection

Seeking optimized infectious pathogen detection tools is of primary importance to lessen the spread of infections, allowing prompt medical attention for the infected. Among nucleic-acid-based sensing techniques, loop-mediated isothermal amplification is a promising method, as it provides rapid, sensitive, and specific detection of microbial and viral pathogens and has enormous potential to transform current point-of-care molecular diagnostics. In this review, the advances in LAMP-based point-of-care diagnostics assays developed during the past few years for rapid and sensitive detection of infectious pathogens are outlined. The numerous detection methods of LAMP-based biosensors are discussed in an end-point and real-time manner with ideal examples. We also summarize the trends in LAMP-on-a-chip modalities, such as classical microfluidic, paper-based, and digital LAMP, with their merits and limitations. Finally, we provide our opinion on the future improvement of on-chip LAMP methods. This review serves as an overview of recent breakthroughs in the LAMP approach and their potential for use in the diagnosis of existing and emerging diseases.

Translating diagnostics and drug delivery technologies to low-resource settings

Diagnostics and drug delivery technologies engineered for low-resource settings aim to meet their technical design specifications using strategies that are compatible with limited equipment, infrastructure, and operator training. Despite many preclinical successes, very few of these devices have been translated to the clinic. Here, we identify factors that contribute to the clinical success of diagnostics and drug delivery systems for low-resource settings, including the need to engage key stakeholders at an early stage, and provide recommendations for the clinical translation of future medical technologies.

Rotational diffusometric sensor with isothermal amplification for ultra-sensitive and rapid detection of SARS-CoV-2 nsp2 cDNA

In the wake of a pandemic, the development of rapid, simple, and accurate molecular diagnostic tests can significantly aid in reducing the spread of infections. By combining particle imaging with molecular assays, a quick and highly sensitive biosensor can readily identify a pathogen at low concentrations. Here, we implement functionalized particle-enabled rotational diffusometry in combination with loop-mediated isothermal amplification for the rapid detection of the SARS-CoV-2 nsp2 gene in the recombinant plasmid as a proof of concept for COVID-19 diagnostics. By analyzing the images of blinking signals generated by these modified particles, the change in micro-level viscosity due to nucleic acid amplification was measured. The high sensitivity of rotational diffusometry enabled facile detection within 10 min, with a limit of detection of 70 ag/μL and a sample volume of 2 μL. Tenfold higher detection sensitivity was observed for rotational diffusometry in comparison with real-time PCR. In addition, the system stability and the effect of temperature on rotational diffusometric measurements were studied and reported. These results demonstrated the utility of a rotational diffusometric platform for the rapid and sensitive detection of SARS-CoV-2 cDNA fragments.

PD-LAMP smartphone detection of SARS-CoV-2 on chip

In 2019 the COVID-19 pandemic, caused by SARS-CoV-2, demonstrated the urgent need for rapid, reliable, and portable diagnostics. The COVID-19 pandemic was declared in January 2020 and surges of the outbreak continue to reoccur. It is clear that early identification of infected individuals, especially asymptomatic carriers, plays a huge role in preventing the spread of the disease. The current gold standard diagnostic for SARS-CoV-2 is quantitative reverse transcription polymerase chain reaction (qRT-PCR) test based on the detection of the viral RNA. While RT-PCR is reliable and sensitive, it requires expensive centralized equipment and is time consuming (∼2 h or more); limiting its applicability in low resource areas. The FDA issued Emergency Use Authorizations (EUAs) for several COVID-19 diagnostics with an emphasis on point-of care (PoC) testing. Numerous RT-PCR and serological tests were approved for use at the point of care. Abbott's ID NOW, and Cue Health's COVID-19 test are of particular interest, which use isothermal amplification methods for rapid detection in under 20 min. We look to expand on the range of current PoC testing platforms with a new rapid and portable isothermal nucleic acid detection device. We pair reverse transcription loop mediated isothermal amplification (RT-LAMP) with a particle imaging technique, particle diffusometry (PD), to successfully detect SARS-CoV-2 in only 35 min on a portable chip with integrated heating. A smartphone device is used to image the samples containing fluorescent beads post-RT-LAMP and correlates decreased diffusivity to positive samples. We detect as little as 30 virus particles per μL from a RT-LAMP reaction in a microfluidic chip using a portable heating unit. Further, we can perform RT-LAMP from a diluted unprocessed saliva sample without RNA extraction. Additionally, we lyophilize SARS-CoV-2-specific RT-LAMP reactions that target both the N gene and the ORF1ab gene in the microfluidic chip, eliminating the need for cold storage. Our assay meets specific target product profiles outlined by the World Health Organization: it is specific to SARS-CoV-2, does not require cold storage, is compatible with digital connectivity, and has a detection limit of less than 35 × 10⁴ viral particles per mL in saliva. PD-LAMP is rapid, simple, and attractive for screening and use at the point of care.

Towards the use of a smartphone imaging-based tool for point-of-care detection of asymptomatic low-density malaria parasitaemia

BACKGROUND

Globally, there are over 200 million cases of malaria annually and over 400,000 deaths. Early and accurate detection of low-density parasitaemia and asymptomatic individuals is key to achieving the World Health Organization (WHO) 2030 sustainable development goals of reducing malaria-related deaths by 90% and eradication in 35 countries. Current rapid diagnostic tests are neither sensitive nor specific enough to detect the low parasite concentrations in the blood of asymptomatic individuals.

METHODS

Here, an imaging-based sensing technique, particle diffusometry (PD), is combined with loop mediated isothermal amplification (LAMP) on a smartphone-enabled device to detect low levels of parasitaemia often associated with asymptomatic malaria. After amplification, PD quantifies the Brownian motion of fluorescent nanoparticles in the solution during a 30 s video taken on the phone. The resulting diffusion coefficient is used to detect the presence of Plasmodium DNA amplicons. The coefficients of known negative samples are compared to positive samples using a one-way ANOVA post-hoc Dunnett's test for confirmation of amplification.

RESULTS

As few as 3 parasite/µL of blood was detectable in 45 min without DNA extraction. Plasmodium falciparum parasites were detected from asymptomatic individuals' whole blood samples with 89% sensitivity and 100% specificity when compared to quantitative polymerase chain reaction (qPCR).

CONCLUSIONS

PD-LAMP is of value for the detection of low density parasitaemia especially in areas where trained personnel may be scarce. The demonstration of this smartphone biosensor paired with the sensitivity of LAMP provides a proof of concept to achieve widespread asymptomatic malaria testing at the point of care.

Pocket MUSE: an affordable, versatile and high-performance fluorescence microscope using a smartphone

Smartphone microscopes can be useful tools for a broad range of imaging applications. This manuscript demonstrates the first practical implementation of Microscopy with Ultraviolet Surface Excitation (MUSE) in a compact smartphone microscope called Pocket MUSE, resulting in a remarkably effective design. Fabricated with parts from consumer electronics that are readily available at low cost, the small optical module attaches directly over the rear lens in a smartphone. It enables high-quality multichannel fluorescence microscopy with submicron resolution over a 10× equivalent field of view. In addition to the novel optical configuration, Pocket MUSE is compatible with a series of simple, portable, and user-friendly sample preparation strategies that can be directly implemented for various microscopy applications for point-of-care diagnostics, at-home health monitoring, plant biology, STEM education, environmental studies, etc.

LAMP Diagnostics at the Point-of-Care: Emerging Trends and Perspectives for the Developer Community

Introduction: Over the past decade, loop-mediated isothermal amplification (LAMP) technology has played an important role in molecular diagnostics. Amongst numerous nucleic acid amplification assays, LAMP stands out in terms of sample-to-answer time, sensitivity, specificity, cost, robustness, and accessibility, making it ideal for field-deployable diagnostics in resource-limited regions.Areas covered: In this review, we outline the front-end LAMP design practices for point-of-care (POC) applications, including sample handling and various signal readout methodologies. Next, we explore existing LAMP technologies that have been validated with clinical samples in the field. We summarize recent work that utilizes reverse transcription (RT) LAMP to rapidly detect SARS-CoV-2 as an alternative to standard PCR protocols. Finally, we describe challenges in translating LAMP from the benchtop to the field and opportunities for future LAMP assay development and performance reporting.Expert opinion: Despite the popularity of LAMP in the academic research community and a recent surge in interest in LAMP due to the COVID-19 pandemic, there are numerous areas for improvement in the fundamental understanding of LAMP, which are needed to elevate the field of LAMP assay development and characterization.

Developing Rapid Antimicrobial Susceptibility Testing for Motile/Non-Motile Bacteria Treated with Antibiotics Covering Five Bactericidal Mechanisms on the Basis of Bead-Based Optical Diffusometry

Rapid antimicrobial susceptibility testing (AST) is an effective measure in the treatment of infections and the prevention of bacterial drug resistance. However, diverse antibiotic types and bacterial characteristics have formed complicated barriers to rapid diagnosis. To counteract these limitations, we investigated the interactions between antibiotic-treated bacteria and functionalized microbeads in optical diffusometry. The conjugation with bacteria increased the effective microbead complex size, thereby resulting in a temporal diffusivity change. The yielded data were sorted and analyzed to delineate a pattern for the prediction of antimicrobial susceptibility. The outcome showed that a completed rapid AST based on the trend of microbead diffusivity could provide results within 3 h (2 h measurement + 1 h computation). In this research, we studied four bacterial strains, including Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Staphylococcus aureus, and six antibiotics. Despite the different inhibitory effects caused by various antibiotics, similar trends in diffusivity alteration for all susceptible and resistant cases in the last 40 min of the 2-h measurement period were deduced. In addition, the AST results obtained using optical diffusometry showed good agreement with those acquired from the commercial instrument and conventional culture methods. Finally, we conducted a single-blinded clinical test, and the sensitivity, specificity, and accuracy of the system reached 92.9%, 91.4%, and 91.8%, respectively. Overall, the developed optical diffusometry showcased rapid AST with a small sample volume (20 μL) and low initial bacterial count (10⁵ CFU/mL). This technique provided a promising way to achieve early therapy against microbial diseases in the future.

A smartphone-based particle diffusometry platform for sub-attomolar detection of Vibrio cholerae in environmental water

Each year, 3.4 million people die from waterborne diseases worldwide. Development of a rapid and portable platform for detecting and monitoring waterborne pathogens would significantly aid in reducing the incidence and spread of infectious diseases. By combining optical methods and smartphone technology with molecular assays, the sensitivity required to detect exceedingly low concentrations of waterborne pathogens can readily be achieved. Here, we implement smartphone-based particle diffusometry (PD) detection of loop-mediated isothermal amplification (LAMP) targeting the waterborne pathogen Vibrio cholerae (V. cholerae). By measuring the diffusion of 400 nm streptavidin-coated fluorescent nanoparticles imaged at 68X magnification on a smartphone, we can detect as few as 6 V. cholerae cells per reaction (0.66 aM) in just 35 minutes. In a double-blinded study with 132 pond water samples, we establish a 91.8% sensitivity, 95.2% specificity, and 94.3% accuracy of the smartphone-based PD platform for detection of V. cholerae. Together, these results demonstrate the utility of this smartphone-based PD platform for rapid and sensitive detection of V. cholerae at the point of use.

Polymerization-Based Amplification for Target-Specific Colorimetric Detection of Amplified Mycobacterium tuberculosis DNA on Cellulose

Loop-mediated isothermal amplification (LAMP) is an appealing method for low-cost, point-of-care nucleic acid diagnostic assays due to high sensitivity, minimal equipment requirements, and compatibility with user-friendly colorimetric detection methods. The enhanced sensitivity LAMP offers comes with vulnerability to cross-contamination, where negative samples are exposed to minute amounts of nucleic acids from positive samples. These amounts are insignificant in less sensitive amplification methods, but visible when LAMP is paired with common colorimetric methods. Here, we examined the use of eosin photopolymerization, a tunable reaction, for colorimetric detection of LAMP products to reduce this false positive risk. Using eosin and biotin end-labeled primers, we successfully amplified target regions of the Mycobacterium tuberculosis (MTB) genome using PCR and LAMP, captured amplicons on streptavidin-coated cellulose, and detected DNA targets via eosin photopolymerization, producing a bright pink color only if MTB DNA was present in the sample. Consistent with previous reports, the LAMP-based method exhibited high background signal, but tuning the illumination time for the photopolymerization reaction allowed readouts from samples with no added MTB DNA to remain blank and visually distinct from pink positives. This method yielded limits of detection of 30 and 300 copies/μL for LAMP and PCR amplification, respectively. When confronted with boiled MTB culture samples, this method gave clear positive readouts, compared to negligible signal from other Mycobacterium boiled culture samples. This new method of LAMP colorimetric detection has the potential to increase the utility of LAMP as a nucleic acid assay technique by mitigating sensitivity to cross-contamination.

Microfluidic rapid and autonomous analytical device (microRAAD) to detect HIV from whole blood samples

While identifying acute HIV infection is critical to providing prompt treatment to HIV-positive individuals and preventing transmission, existing laboratory-based testing methods are too complex to perform at the point of care. Specifically, molecular techniques can detect HIV RNA within 8-10 days of transmission but require laboratory infrastructure for cold-chain reagent storage and extensive sample preparation performed by trained personnel. Here, we demonstrate our point-of-care microfluidic rapid and autonomous analysis device (microRAAD) that automatically detects HIV RNA from whole blood. Inside microRAAD, we incorporate vitrified amplification reagents, thermally-actuated valves for fluidic control, and a temperature control circuit for low-power heating. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) products are visualized using a lateral flow immunoassay (LFIA), resulting in an assay limit of detection of 100 HIV-1 RNA copies when performed as a standard tube reaction. Even after three weeks of room-temperature reagent storage, microRAAD automatically isolates the virus from whole blood, amplifies HIV-1 RNA, and transports amplification products to the internal LFIA, detecting as few as 3 × 105 HIV-1 viral particles, or 2.3 × 107 virus copies per mL of whole blood, within 90 minutes. This integrated microRAAD is a low-cost and portable platform to enable automated detection of HIV and other pathogens at the point of care.