A capillary-based multiplexed isothermal nucleic acid-based test for sexually transmitted diseases in patients

A dual signal amplification system with specific signal identification for rapid and sensitive detection of miRNA

False positive which is mostly caused by the nonspecific amplification has severely hindered the development of nucleic acid detection and it is hard to avoid. Therefore, specific signals recognition and output in nucleic acid amplification are crucial to reliability of clinical diagnosis. Herein, we proposed a one-step and rapid miRNA detection strategy with specific signal identification, dual amplification and output. And this strategy was named as high-temperature hybridization chain reaction coupled with strand displacement amplification (HSA). In HSA, we well designed a target signal recognition, replication, and output probe (RRO probe). If the target miRNA exists, RRO probe can initiate a strand displacement amplification and output a target-related special single-stranded DNA (trigger). And the trigger can be identified by a high-temperature hybridization chain reaction and initiate a secondary signal amplification. As a result, the quantitative determination of HSA for miRNA-21 was in the range of 100 fM to 100 pM in 30 min, and with a detection limit of 82 fM. Moreover, with high sensitivity and rapidity, HSA has been successfully used to detect miRNA-21 in real samples.

Naked-eye visualization of nucleic acid amplicons using hierarchical nanoassembly

This study reports the development of a rapid visualization method for DNA amplicons. Oligonucleotide-coated gold nanoparticles hierarchically assemble on DNA networks to form globular nanostructures, which precipitate into a distinct visible red pellet. This aims to overcome challenges associated with nanoparticle aggregation and dye-based colorimetric detection in LAMP assays.

Bridging the gap between development of point-of-care nucleic acid testing and patient care for sexually transmitted infections

The incidence rates of sexually transmitted infections (STIs), including the four major curable STIs - chlamydia, gonorrhea, trichomoniasis and, syphilis - continue to increase globally, causing medical cost burden and morbidity especially in low and middle-income countries (LMIC). There have seen significant advances in diagnostic testing, but commercial antigen-based point-of-care tests (POCTs) are often insufficiently sensitive and specific, while near-point-of-care (POC) instruments that can perform sensitive and specific nucleic acid amplification tests (NAATs) are technically complex and expensive, especially for LMIC. Thus, there remains a critical need for NAAT-based STI POCTs that can improve diagnosis and curb the ongoing epidemic. Unfortunately, the development of such POCTs has been challenging due to the gap between researchers developing new technologies and healthcare providers using these technologies. This review aims to bridge this gap. We first present a short introduction of the four major STIs, followed by a discussion on the current landscape of commercial near-POC instruments for the detection of these STIs. We present relevant research toward addressing the gaps in developing NAAT-based STI POCT technologies and supplement this discussion with technologies for HIV and other infectious diseases, which may be adapted for STIs. Additionally, as case studies, we highlight the developmental trajectory of two different POCT technologies, including one approved by the United States Food and Drug Administration (FDA). Finally, we offer our perspectives on future development of NAAT-based STI POCT technologies.

Recent advances and challenges of biosensing in point-of-care molecular diagnosis

Molecular diagnosis, which plays a major role in infectious disease screening with successful understanding of the human genome, has attracted more attention because of the outbreak of COVID-19 recently. Since point-of-care testing (POCT) can expand the application of molecular diagnosis with the benefit of rapid reply, low cost, and working in decentralized environments, many researchers and commercial institutions have dedicated tremendous effort and enthusiasm to POCT-based biosensing for molecular diagnosis. In this review, we firstly summarize the state-of-the-art techniques and the construction of biosensing systems for POC molecular diagnosis. Then, the application scenarios of POCT-based biosensing for molecular diagnosis were also reviewed. Finally, several challenges and perspectives of POC biosensing for molecular diagnosis are discussed. This review is expected to help researchers deepen comprehension and make progresses in POCT-based biosensing field for molecular diagnosis applications.

All-in-One DNA Extraction Tube for Facilitated Real-Time Detection of Infectious Pathogens

An "all-in-one tube" platform is developed, where the genetic analysis involving DNA extraction, amplification, and detection can be performed in a single tube. The all-in-one tube consists of a polymerase chain reaction (PCR) tube in which the inner surface is conformally modified with a tertiary-amine-containing polymer to generate a strong electrostatic interaction with DNA. The all-in-one tube provides high DNA capture efficiency exceeding 80% from Escherichia coli O157: H7 pathogen at a wide range of DNA amount from 0.003 to 3 ng. Indeed, the use of the surface-functionalized PCR tube enables direct amplification and detection of the surface-captured DNA without the modification of standard real-time PCR instrument. Besides, this platform has sensitivity, selectivity, and reliability enough for accurate detection at the minimal infective dose of both gram-positive and negative pathogens. The all-in-one tube enables the direct molecular diagnosis, substantially reducing the labor-intensive pathogen detection steps while providing high compatibility with the currently established real-time PCR instruments, and illustrates its on-site applicability with convenience expandable to various genetic analyses including food safety testing, forensic analysis, and clinical diagnosis.

How does DNA 'meet' capillary-based microsystems?

DNA possesses various chemical and physical properties which make it important in biological analysis. The opportunity for DNA to 'meet' capillary-based microsystems is rapidly increasing owing to the expanding development of miniaturization. Novel capillary-based methods can provide favourable platforms for DNA-ligand interaction assay, DNA translocation study, DNA separation, DNA aptamer selection, DNA amplification assay, and DNA digestion. Meanwhile, DNA exhibits great potential in the fabrication of new capillary-based biosensors and enzymatic bioreactors. Moreover, DNA has received significant research interest in improving capillary electrophoresis (CE) performance. We focus on highlighting the advantages of combining DNA and capillary-based microsystems. The general trend presented in this review suggests that the 'meeting' has offered a stepping stone for the application of DNA and capillary-based microsystems in the field of analytical chemistry.

Advances in Mutation Detection Using Loop-Mediated Isothermal Amplification

Detection of mutations and single-nucleotide polymorphisms is highly important for diagnostic applications. Loop-mediated isothermal amplification (LAMP) is a powerful technique for the rapid and sensitive detection of nucleic acids. However, LAMP traditionally does not possess the ability to resolve single-nucleotide differences within the target sequence. Because of its speed and isothermal nature, LAMP is ideally suited for point-of-care applications in resource-limited settings. Recently, different approaches have been developed and applied to enable single-nucleotide differentiation within target sequences. This Mini-Review highlights advancements in mutation detection using LAMP. Methods involving primer design and modification to enable sequence differentiation are discussed. In addition, the development of probe-based detection methods for mutation detection are also covered.

Current and Future Trends in the Laboratory Diagnosis of Sexually Transmitted Infections

Sexually transmitted infections (STIs) continue to exert a considerable public health and social burden globally, particularly for developing countries. Due to the high prevalence of asymptomatic infections and the limitations of symptom-based (syndromic) diagnosis, confirmation of infection using laboratory tools is essential to choose the most appropriate course of treatment and to screen at-risk groups. Numerous laboratory tests and platforms have been developed for gonorrhea, chlamydia, syphilis, trichomoniasis, genital mycoplasmas, herpesviruses, and human papillomavirus. Point-of-care testing is now a possibility, and microfluidic and high-throughput omics technologies promise to revolutionize the diagnosis of STIs. The scope of this paper is to provide an updated overview of the current laboratory diagnostic tools for these infections, highlighting their advantages, limitations, and point-of-care adaptability. The diagnostic applicability of the latest molecular and biochemical approaches is also discussed.

Microcapillary LAMP for rapid and sensitive detection of pathogen in bovine semen

A microcapillary-based loop-mediated isothermal amplification (µcLAMP) has been described for specific detection of infectious reproductive pathogens in semen samples of cattle without sophisticated instrumentation. Brucella abortus, Leptospira interrogans serovar Pomona and bovine herpesvirus 1 (BoHV-1) cultures were mixed in bovine semen samples. The µcLAMP assay is portable, user-friendly, cost-effective, and suitable to be performed as a POC diagnostic test. We have demonstrated high sensitivity and specificity of µcLAMP for detection of Brucella, Leptospira, and BoHV-1 in bovine semen samples comparable to PCR and qPCR assays. Thus, µcLAMP would be a promising field-based test for monitoring various infectious pathogens in biological samples.HighlightsDetect infectious organism in bovines semenReduction in carryover contamination is an important attribute, which may reduce the false-positive reaction.µcLAMP is a miniaturized form, which could be performed with a minimum volume of reagents.The µcLAMP assay is portable, user-friendly, and suitable to be performed as a POC diagnostic test.

Mini-Disk Capillary Array Coupling with LAMP for Visual Detection of Multiple Nucleic Acids using Genetically Modified Organism Analysis as an Example

Convenient, portable, and low-cost multiplex nucleic acid testing (NAT) systems are the trends in the fields of food safety, environmental microorganisms, molecular diagnosis, etc. In this study, we developed a novel system for visual monitoring of multiple nucleic acids combining a mini-disk capillary array (diameter = 17 mm, embedded with 6-10 capillaries), visual loop-mediated isothermal amplification (LAMP), and quick DNA extraction called mDC-LAMP. The performance and applicability of mDC-LAMP in testing multiple nucleic acids were evaluated and verified employing genetically modified contents analysis as an example. All of the results confirmed that mDC-LAMP has the advantages of high specificity without any cross contamination, high sensitivity with a limit of detection of 25 copies/reaction, high throughput with flexible channel sensors, easy fabrication, and low costs. We believe that mDC-LAMP is a competitive choice for on-spot monitoring of multiple nucleic acids in terms of the easy fabrication/operation, low costs, and suitable performance presented in the nucleic acids test.

Point-of-care detection of 16S rRNA of Staphylococcus aureus based on multiple biotin-labeled DNA probes

A visual method that combines multiple biotin-labeled DNA probes and lateral-flow nucleic acid biosensor was developed to detect Staphylococcus aureus. The 16S rRNA from Staphyloccocus aureus (S. aureus), coupled with multiple biotin-labeled DNA probes, was functionalized in a signal structure for lateral-flow point-of-care detection. The secondary structure of the 16S rRNA was unwound by two specific capture probes modified by Fam and multiple bridge probes, which extended additional sequences for use as initiators. By utilizing the initiators, each target 16S rRNA with multiple DNA probes could tether a number of biotin molecules, so that a large number of streptavidin-labeled gold nanoparticles could be introduced in the lateral flow assay. The images of the lateral flow detection results obtained using a smartphone were transmitted to a computer via Wi-Fi or Bluetooth connection for quantitative processing by ImageJ. The limit of detection was 10³ cfu/mL without sample enrichment, and decreased to 0.12 cfu/mL following a 3-h enrichment of samples in growth medium. Notably, this method presented high specificity and applicability for the detection of S. aureus in food samples. In short, the developed visual non-specific operation method is very suitable for point-of-care diagnosis of pathogens in resource-limited countries.

Single-color multiplexing by the integration of high-resolution melting pattern recognition with loop-mediated isothermal amplification

We develop a single-color multiplexing strategy by the integration of high-resolution melting pattern recognition with loop-mediated isothermal amplification (LAMP). This strategy can identify multiple amplicons with a small DNA melting temperature (Tm) difference (∼0.2 °C) without the involvement of either multicolor labels or parallelized multiplexing, and it can sensitively detect LAMP amplicons with the initial DNA concentrations ranging from 10 to 108 copies.

Multiplex sample-to-answer detection of bacteria using a pipette-actuated capillary array comb with integrated DNA extraction, isothermal amplification, and smartphone detection

A pipette-actuated capillary array comb (PAAC) system operated on a smartphone-based hand-held device has been successfully developed for the multiplex detection of bacteria in a "sample-to-answer" manner. The PAAC consists of eight open capillaries inserted into a cylindrical plastic base with a piece of chitosan-modified glass filter paper embedded in each capillary. During the sample preparation, a PAAC was mounted into a 1 mL pipette tip with an enlarged opening and was operated with a 1 mL pipette for liquid handling. The cell lysate was drawn and expelled through the capillaries three times to facilitate the DNA capture on the embedded filter discs. Following washes with water, the loop-mediated isothermal amplification (LAMP) reagents were aspirated into the capillaries, in which the primers were pre-fixed with chitosan. After that, the PAAC was loaded into the smartphone-based device for a one-hour amplification at 65 °C and end-point detection of calcein fluorescence in the capillaries. The DNA capture efficiency of a 1.1 mm-diameter filter disc was determined to be 97% of λ-DNA and the coefficient of variation among the eight capillaries in the PAAC was only 2.2%. The multiplex detection of genomic DNA extracted from Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus provided limits of detection of 200, 500, and 500 copies, respectively, without any cross-contamination and cross reactions. "Sample-to-answer" detection of E. coli samples was successfully completed in 85 minutes, demonstrating a sensitivity of 200 cfu per capillary. The multiplex "sample-to-answer" detection, the streamlined operation, and the compact device should facilitate a broad range of applications of our PAAC system in point-of-care testing.

Rapid Veterinary Diagnosis of Bovine Reproductive Infectious Diseases from Semen Using Paper-Origami DNA Microfluidics

The health and well-being of cattle is an important issue in maintaining and increasing global agricultural output. In dairy production within low and middle income countries (LMICs), there is a significant biosensing challenge in detecting sexually transmitted infection (STI) pathogens during animal husbandry, due in part to difficulties associated with the limited infrastructure for veterinary medicine. Here we demonstrate low-cost, multiplexed, and sample-to-answer paper-origami tests for the detection of three bovine infectious reproductive diseases in semen samples, collected at a test site in rural India. Pathogen DNA from one viral pathogen, bovine herpes virus-1 (BoHV-1), and two bacteria (Brucella and Leptospira) was extracted, amplified (using loop-mediated isothermal amplification, LAMP), and detected fluorescently, enabling <1 pg (∼ from 115 to 274 copies per reaction) of target genomic DNA to be measured. Data was collected as a fluorescence signal either visually, using a low-cost hand-held torch, or digitally with a mobile-phone camera. Limits of detection and sensitivities of the paper-origami device for the three pathogens were also evaluated using pathogen-inoculated semen samples and were as few as 50 Leptospira organisms, 50 CFU Brucella, and 1 TCID₅₀ BoHV-1. Semen samples from elite bulls at a germplasm center were also tested in double-blind tests, as a demonstrator for a low-cost, user-friendly point-of-care sensing platform, for in-the-field resource-limited regions. The sensors showed excellent levels of sensitivity and specificity, and for the first time a demonstrated ability of the application of paper microfluidics devices for the diagnosis multiple infectious diseases from semen samples.

Monitoring Genetic Population Biomarkers for Wastewater-Based Epidemiology

We report a rapid "sample-to-answer" platform that can be used for the quantitative monitoring of genetic biomarkers within communities through the analysis of wastewater. The assay is based on the loop-mediated isothermal amplification (LAMP) of nucleic acid biomarkers and shows for the first time the ability to rapidly quantify human-specific mitochondrial DNA (mtDNA) from raw untreated wastewater samples. mtDNA provides a model population biomarker associated with carcinogenesis including breast, renal and gastric cancers. To enable a sample-to-answer, field-based technology, we integrated a filter to remove solid impurities and perform DNA extraction and enrichment into a low cost lateral flow-based test. We demonstrated mtDNA detection over seven consecutive days, achieving a limit of detection of 40 copies of human genomic DNA per reaction volume. The assay can be performed at the site of sample collection, with minimal user intervention, yielding results within 45 min and providing a method to monitor public health from wastewater.