Search Results (445)

Deoxyribonucleic acid (DNA) is not only a fundamental biological molecule but also a versatile material for constructing sensitive and specific biosensing platforms. Its ability to undergo sequence-specific hybridization via Watson–Crick base pairing enables both precise target recognition and the programmable construction of nanoscale structures. The demand for ultrasensitive detection increases in fields such as disease diagnostics, therapeutics, and other areas, and the inherent characteristics of DNA have driven the development of a wide range of signal amplification strategies. Among these, polymerase chain reaction (PCR), rolling circle amplification (RCA), and loop-mediated isothermal amplification (LAMP) represent powerful target-based methods that enzymatically increase the concentration of nucleic acid targets, thereby boosting detection sensitivity. In parallel, structure-based strategies leverage the nanoscale spatial programmability of DNA to construct functional architectures with high precision. DNA can be used as a scaffold, such as DNA nanostructures, to organize sensing elements and facilitate signal transduction. It can also function as a probe, like aptamers, to recognize targets with high affinity. These versatilities enable the creation of highly sophisticated sensing platforms that integrate molecular recognition and signal amplification. Driven by DNA nano-assembly capability, both target-based and structure-based approaches are driving the advancement of highly sensitive, selective, and adaptable diagnostic technologies. This review highlights recent developments in DNA nano-assembly-driven amplification strategies. Full article

Tuberculosis (TB) is a global public health issue requiring early and accurate diagnosis. The loop-mediated isothermal amplification (LAMP) assay is a promising alternative recommended by the WHO for the initial diagnosis of pulmonary TB, particularly in resource-limited settings. This study evaluated the sensitivity and specificity of a commercial LAMP assay for TB detection using 198 samples from different countries including Mexico. The LAMP assay results were compared to the results of standard tests: AFB smear microscopy, cell culture, and Xpert PCR. Across all samples, LAMP showed a sensitivity of 96.20% and a specificity of 84.61%. When compared specifically to “true positives” and “true negatives” (defined by the consistency across the standard tests), LAMP demonstrated 100% sensitivity and 92.30% specificity. For context, the sensitivity of AFB smear microscopy against the culture and Xpert tests was 79.04%. A significant finding was that the LAMP test detected a high percentage (92.5%) of samples found positive by the culture and Xpert tests but negative by the AFB smear, highlighting its ability to identify cases missed by traditional microscopy. This study concluded that the LAMP assay is a sensitive and specific tool for TB diagnosis with potential for rapid and accurate diagnosis, especially in resource-limited areas. Full article

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne disease caused by the SFTS virus (SFTSV). A rapid and cost-effective point-of-care testing detection system is important for the early diagnosis of SFTS. Herein, we developed a ready-to-use dried reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the direct detection of SFTSV in clinical samples. The assay enables simple, RNA-extraction-free detection using heat-treated serum or plasma, followed by a 30 min incubation at 65 °C. The results are visually interpreted through the color emitted, which can be observed under LED light. The established assay demonstrated detection sensitivity for SFTSV at 10⁴ copies/µL and was effective in identifying infections in cats. Despite being less sensitive than real-time RT-PCR, this dried RT-LAMP method offers a rapid, cost-effective alternative suitable for point-of-care use, particularly in remote or resource-limited settings. The simplified workflow and visual readout make it a practical tool for the early detection and daily surveillance of SFTSV in animals. Full article

Accurate, rapid and inexpensive diagnosis of poultry respiratory pathogens remains a challenge, especially in many developing countries. Meanwhile, poultry respiratory pathogens are a major threat to poultry production worldwide, accounting for billions of dollars in economic loss to the sector. Early and accurate diagnosis of these diseases is critical for economic poultry production. Molecular diagnostic methods, including PCR-based techniques, have been developed and used to fill this gap, but unfortunately, these techniques require skilled technicians, relatively costly equipment and reagents and can only be performed in a laboratory setting. This warrants the development of other diagnostic tools, which can be used in the field even by unskilled personnel. In this review, we discussed the genesis, challenges, advances and prospects of loop-mediated isothermal amplification (LAMP) for the detection of poultry respiratory pathogens at the flock side, especially in resource-constrained countries. We highlighted the application of LAMP in routine poultry disease surveillance and early outbreak detection, underscoring its value as a transformative diagnostic tool in poultry production. The development and use of a point-of-care (POC) LAMP assay that can be used to screen for these poultry respiratory pathogens simultaneously enhance disease surveillance and diagnosis. Full article

Listeria monocytogenes, Staphylococcus aureus, Salmonella enterica, and Escherichia coli O157:H7 are four major foodborne pathogenic bacteria found in meat and meat products, which pose significant threats to human health. In this study, we developed specific loop-mediated isothermal amplification (LAMP) primers targeting these four pathogenic bacteria. Following the optimization of system components and reaction parameters, four rapid and simplified LAMP-based detection assays were established, which enabled the visual detection of these four pathogenic bacteria within 40–50 min. The three established LAMP assays targeting L. monocytogenes, S. aureus, and E. coli O157:H7 achieved species-level discrimination, whereas the LAMP method for Salmonella exhibited genus-level specificity. The detection limits of the LAMP assays were determined as follows: 1.8 × 10¹ colony forming units (CFU)/mL for L. monocytogenes, 5.1 × 10¹ CFU/mL for S. aureus, 1.2 × 10¹ CFU/mL for S. enterica, and 3.3 × 10³ CFU/mL for E. coli O157:H7, with sensitivity improved by 10–1000-fold compared to conventional PCR. The developed LAMP assays were used to analyze 52 meat and meat product samples, and 7 samples were positive, which was consistent with the results of the conventional PCR and culture-based methods, demonstrating an accuracy rate of 100% for the LAMP methods. In conclusion, the established LAMP assays exhibit high specificity, enhanced sensitivity, and result visualization, making them suitable for on-site rapid detection in food safety monitoring. Full article

This review presents information obtained over the past 10 years on the methods to control the widespread worldwide phytopathogen Pectobacterium carotovorum subsp. carotovorum (Pcc). This bacterium is among the ten most dangerous phytopathogens; it affects a wide range of cultivated plants: vegetables, ornamental and medicinal crops, both during vegetation and during the storage of fruits. Symptoms of Pcc damage include the wilting of plants, blackening of vessels on leaves, stems and petioles. At the flowering stage, the stem core gradually wilts and, starting from the root, the stem breaks and the plant dies. Pcc is a rod-shaped, non-capsule and endospore-forming facultative anaerobic Gram-negative bacterium with peritrichous flagellation. Pcc synthesizes bacteriocins—carocins. The main virulence factors of Pcc are the synthesis of N-acyl-homoserine lactone (AHL) and plant cell wall-degrading enzymes (PCWDEs) (pectinases, polygalacturonases, cellulases, and proteases). Diagnostic methods for this phytopathogen include polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), multilocus genotyping of strain-specific genes and detection of unique volatile organic compounds (VOCs). The main methods to control this microorganism include the use of various chemicals (acids, phenols, esters, salts, gases), plant extracts (from grasses, shrubs, trees, and algae), antagonistic bacteria (Bacillus, Pseudomonas, Streptomyces, and lactic acid bacteria), viruses (including a mixture of bacteriophages), and nanomaterials based on metals and chitosan. Full article

Candida auris (C. auris) is an emerging multidrug-resistant fungal pathogen recognized by the World Health Organization (WHO) as a critical global health threat. Its rapid transmission, high mortality rate, and frequent misidentification in clinical laboratories present significant challenges for diagnosis and infection control. This review provides a comprehensive overview of current and emerging diagnostic methods for C. auris detection, including culture-based techniques, biochemical assays, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and molecular diagnostics such as PCR and loop-mediated isothermal amplification (LAMP). We evaluate each method’s sensitivity, specificity, turnaround time, and feasibility in clinical and surveillance settings. While culture remains the diagnostic gold standard, it is limited by slow turnaround and phenotypic overlap with related species. Updated biochemical platforms and MALDI-TOF MS with expanded databases have improved identification accuracy. Molecular assays offer rapid, culture-independent detection. Antifungal susceptibility testing (AFST), primarily using broth microdilution, is essential for guiding treatment, although standardized breakpoints remain lacking. This review proposes an integrated diagnostic workflow and discusses key innovations and gaps in current practice. Our findings aim to support clinicians, microbiologists, and public health professionals in improving early detection, containment, and management of C. auris infections. Full article

Contamination of environmental surfaces by nosocomial pathogens like Pseudomonas aeruginosa (P. aeruginosa), Staphylococcus aureus (S. aureus), and Enterococcus spp. poses significant health risks worldwide. However, gold-standard detection methods are too time-consuming and labor-intensive. This study aimed to optimize loop-mediated isothermal amplification (LAMP) as a rapid, innovative, and cost-effective approach, comparing its effectiveness with the gold-standard cultural method. Sterile surfaces (24 cm²) were contaminated in duplicate with different concentrations of P. aeruginosa, S. aureus, and Enterococcus faecalis (E. faecalis) reference stains. For each pair of contaminated surfaces, one was analyzed using the agar contact plate method (UNI EN 17141:2021), while the other was analyzed using LAMP, following three different pre-incubation times (three, six, and nine hours). The sensitivity and accuracy of LAMP for P. aeruginosa improved with longer incubation times, reaching a value of 1.00 at nine hours, while the specificity and positive predictive value (PPV) remained at 1.00 regardless of the incubation time. For S. aureus, LAMP achieved a sensitivity, specificity, accuracy, PPV, and negative predictive value (NPV) of 1.00 across all incubation times. Finally, for E. faecalis, sensitivity increased from 0.57 at three hours to 1.00 at six and nine hours, with a high specificity, accuracy, PPV, and NPV from six hours onwards. These findings showed that LAMP can be used as a rapid and reliable alternative to gold-standard methods for detecting pathogens on surfaces. The high sensitivity and specificity achieved, especially at six and nine hours of pre-incubation, suggested its use for real-time monitoring in healthcare settings. Further research in real-world environments is needed to confirm these findings. Full article

Rice bakanae disease (RBD), a major threat in rice-cropping nations, can reduce rice yield and quality. As it is a seed-borne disease, effective seed detection is crucial. Loop-mediated isothermal amplification (LAMP) can rapidly and specifically amplify DNA at a constant temperature with high sensitivity. This research uses LAMP to develop rapid RBD pathogen detection systems. Primers were designed targeting the NRPS31 gene of Fusarium fujikuroi and conserved TEF1α sequences of Fusarium asiaticum, Fusarium proliferatum, and Fusarium andiyazi. These reactions at 60 °C for 60 min had a detection limit of 100 pg·μL⁻¹, and LAMP proved applicable in field trials. Full article

Neisseria meningitidis is a pathogenic bacterial agent that causes meningococcal meningitis in humans. Developing a rapid and low-cost N. meningitidis detection method is crucial, especially for developing countries. This study focuses on the development of an efficient loop-mediated isothermal amplification (LAMP) method for accurate N. meningitidis identification. A new LAMP primer set was designed, and a LAMP reaction was optimized. The colorimetric detection method was also applied, and the assay characteristics were evaluated using clinical samples. The results demonstrated a specific LAMP reaction for N. meningitidis detection of genotypes A, B, and C, with a limit of detection of 10² cfu/mL, 100% specificity and sensitivity, and a rapid detection time of only 40 min by colorimetric visual inspection. No cross-reactivity with reference strains of Streptococcus pneumoniae, Staphylococcus aureus, Neisseria lactamica, Mycobacterium tuberculosis, and Haemophilus influenzae type b was observed in the LAMP reaction with the new primer set. This result suggests that the LAMP reaction could be a promising tool for developing a rapid N. meningitidis detection method suitable for use in Vietnam and other developing countries. Full article

The growing human population has increased the need for food beyond what terrestrial sources can provide. This boosts aquaculture demand for molluscs, fish, and crustaceans. Molluscs are popular for their nutritional benefits, making them a profitable industry. Despite a 3% annual growth in mollusc populations, recent high mortality rates and population losses due to poor feeding practices and water pollution have made them more disease-prone. Limited treatment options exist for mollusc diseases in aquaculture systems. Hence, developing rapid, sensitive, and cost-effective diagnostic tools for field use is essential to identify and prevent infections promptly. Recently developed isothermal nucleic acid amplification technologies, like loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA), offer rapid results within an hour. This review examines these isothermal diagnostic techniques for mollusc pathogens and their potential for field application. Full article

Giardia duodenalis is a flagellated protozoan pathogen causing parasitic enteric disease outbreaks worldwide. Among detection methods, loop-mediated isothermal amplification (LAMP) has high selectivity and sensitivity, and the detection time is lower than that of conventional molecular methods. In this study, three published Giardia LAMP primer sets were tested and adapted to touchdown LAMP conditions. The measurement time, the volume of reagents, the effect of the denaturation step, different kinds of polymerases, and the presence or absence of betaine on the reaction were tested and evaluated. Based on the results of this study, the 66–60 °C range touchdown LAMP with the use of betaine, 90 °C denaturation step, Bst 2.0 WarmStart^® DNA Polymerase, and the primer set of Momoda et al. were the optimal conditions. We increased the analytical sensitivity of the LAMP reaction to 7.8- and 8-fold higher than the previously published methods for G. duodenalis assemblages A and B, with detection limits of 20 and 19.5 fg/assay, respectively, instead of 156 fg/assay. The detection time was less than 49 min for G. duodenalis assemblage A and less than 35 min for assemblage B, compared to the previously published 60 min. Our optimized LAMP protocol can be directly applied to improve Giardia LAMP tests in routine testing laboratories, could be implemented in standard diagnostic or environmental monitoring workflows, and can be used for the development of Giardia LAMP point-of-care devices or high-throughput systems. Full article

Detection of Salmonella, a highly diverse foodborne pathogen, is paramount to ensure safety and protection of the animal industry and its consumers. Salmonella enterica serovar Typhimurium is among the most important non-typhoidal serovars causing gastroenteritis worldwide. However, traditional serovar identification is labor- and resource-intensive, while typical molecular tools require expensive reagents and equipment. Hence, this study developed and optimized a calcein-based and closed-tube loop-mediated isothermal amplification (LAMP)-based assay to detect S. Typhimurium following enrichment steps compared with an optimized PCR assay. The PCR assay showed 100% specificity in silico confirmed through DNA sequencing. For actual specificity testing, both PCR and LAMP showed 100% specificity to S. Typhimurium. For DNA sensitivity, while PCR showed a limit of detection of 22 pg/μL, LAMP showed a 100-fold higher sensitivity at 220 fg/μL. Meanwhile, for pure culture sensitivity, both assays detected at least 4.98 × 10⁴ CFU/mL. Parallel testing of 208 raw meat samples from wet markets in Metro Manila, Philippines, showed corroboration and statistical association of the optimized PCR and LAMP with 89.42% and 90.87% positivity rates for S. Typhimurium, respectively. Hence, the developed closed-tube and calcein-based LAMP assay is potentially a powerful yet simple, sensitive, and fast method for S. Typhimurium detection. Full article

The increasing prevalence of antimicrobial-resistant (AMR) bacteria in humans, animals, and the environment underscores the necessity for a rapid, sensitive, and specific method to identify resistance genes. Objectives: This study aims to develop a reliable detection tool for identifying the tetracycline-resistant gene tet(M) in Enterococcus species using a real-time loop-mediated isothermal amplification (RT-LAMP) assay. Real-time visualization through a turbidimeter enabled precise estimation of time-to-positivity for gene detection. Methodology: Six primers were designed using PrimerExplorer v.5, and the assay was optimized across different temperatures and incubation times. Validation was conducted by testing 52 tet(M)-positive clinical enterococci isolates and spiking urine samples from a healthy volunteer and a cow with tet(M)-positive Enterococcus species. Results: The tet(M) gene was detected as early as 33 min, with optimal amplification occurring within 60 min at 60 °C. The assay demonstrated 100% specificity with the established primers. The sigmoidal graphs were corroborated with visual confirmation methods, including a green color change (visible to the naked eye), green fluorescence (under UV light), and a 200 bp PCR product observed via agarose gel electrophoresis. Notably, the tet(M) RT-LAMP assay exhibited a detection limit of 0.001 pg/μL, significantly surpassing conventional PCR, which had a detection limit of 0.1 pg/μL. Conclusions: This rapid, cost-effective, highly sensitive, and specific tet(M) RT-LAMP assay holds significant promise as a surveillance tool for antimicrobial resistance monitoring within a One Health framework, particularly in low-resource countries. Full article

Loop-mediated isothermal amplification (LAMP) was developed a quarter of a century ago, but it is still not exactly clear how this reaction proceeds. Only a few articles have focused on the kinetics of LAMP and the types of products formed. In this work, 10 types were identified and named. A basic dumbbell structure, Z6_dmb(1), consists of six zones and triggers the LAMP cycle. Due to self-priming, Z6_dmb(1) transforms into hairpin structure Z9_hp(1) and then into linearized strand Z9_li(1), carrying also strand Z6_dmb(2). Through similar transformations, it again generates strand Z6_dmb(1), completing the first LAMP cycle and starting a new one. The next stage of the exponential phase starts from two Z15_hp hairpin structures generated in the LAMP cycle, which next turn into Z15_li → Z27_hp → Z27_li → Z51_hp → and so forth. Modeling of a new type of the reaction, namely, pseudo-hemi-nested LAMP (phn-LAMP), was carried out. phn-LAMP involves three inner primers: two forward (FIP and extraFIP) and one backward inner primer, or vice versa. phn-LAMP has an advantage over LAMP involving loop or stem primers and over MIP-LAMP (multiple inner primers). Full article