Loop-mediated Isothermal Amplification Primer Sets Research Articles

Study on producing a LAMP kit for diagnosis of small liver fluke Clonorchis sinensisinfection in humans

Background: Clonorchis sinensis is one of the three species of small liver flukes that cause infections in humans. C. sinensis is found mainly in several Asian countries and Northern, Vietnam. The Loop-mediated isothermal amplification (LAMP) with a sensitivity and specificity comparable to that of the PCR method, which requires less complex equipment and facilities for performance. Methods:The research design describes the laboratory experiment and evaluates a LAMP kit for the diagnosis of C. sinensis in the laboratory and the small-scale field assessment, using 150 human stool samples from fascioliasis endemic areas. Results: The LAMP primer sets have been designed and selected; the conditions and components of the LAMP reaction for C. sinensisdiagnosis have been optimised. Evaluation results of the LAMP kit in the laboratory showed a sensitivity of the test was 98.63% (95% CI: 91.92-99.99%); a specificity was 100% (95% CI: 85.25-100%); the limit of detection was 26 gene copies/μl. The LAMP test kit was found to be stable within 12 months at -20±5oC, and 6 months after opening the tubes. The field assessment of the LAMP kit in Ninh Binh province showed a C. sinensis rate of 6.66%, which was similar to the rate obtained from the studies using the real-time PCR method. Conclusions: The research has successfullyproduced a LAMP kit for the diagnosis of C. sinensis that is sensitive >95% and highly specific >95%. The LAMP kit is stable within 12 months at -20±5oC and for 6 months after opening the tubes

Comparison of Warmstart colorimetric LAMP using heat-treated samples with two Plasmodium-detection methods in Ekiti state, southwestern Nigeria

Background: Malaria remains a deadly disease responsible for numerous deaths worldwide, especially in tropi-cal developing countries. Widely used methods for diagnosis include microscopy, which is laborious, lengthy, and error-prone, and rapid diagnostic tests (RDT), which have recently faced limitations on accuracy. Molecular methods like the polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) have emerged as accurate, sensitive, and rapid ways of detecting the disease. While PCR requires expensive equip-ment, LAMP is less expensive to perform. However, contemporary malaria LAMP still requires DNA extraction kits from patient samples. DNA extraction by heating can be used to lower the cost, time, and level of training required from end-users to perform LAMP in low-resource settings. Methods: Blood samples were screened for Plasmodium parasites using microscopy, followed by a commonly used RDT kit. Heat treatment was used for quick DNA extraction from the blood samples, and LAMP primer sets were then used together with Warmstart colorimetric LAMP reagents for isothermal DNA amplification. Agarose gel electrophoresis was used to confirm that the colorimetric observations in LAMP reactions were due to successful DNA amplification. The data obtained were analysed in GraphPad Prism and subjected to chi-square tests with 95% confidence level. Results: Warmstart colorimetric LAMP using heat-treated blood samples achieved successful DNA amplifica-tion and detected Plasmodium parasites in 43.3% of samples, compared to 40% and 30% Plasmodium parasite detection yielded by antigen RDT kit and microscopy respectively. However, the difference between the percent-ages obtained using the different methods was not statistically significant. LAMP approach further enabled the identification/discrimination of different Plasmodium species. Conclusion: The Warmstart LAMP using heat-treated samples can be used as a rapid, cheaper, and easier-to-perform molecular method for the detection and species-level differentiation of malaria parasites.

A handheld isothermal fluorescence detector for duplex visualization of aquatic pathogens via enhanced one-pot LAMP-PfAgo assay

The expansion of large-scale aquaculture has exacerbated the challenge of aquatic diseases, resulting in substantial economic losses annually. Currently, traditional laboratory-based diagnostic methods are time-consuming and costly, hindering on-site testing for individual farmers. We address this issue by developing a state-of-the-art handheld isothermal nucleic acid amplification device (WeD-1) capable of fluorescence tracking of reactions and integrating it with an enhanced one-pot Prokaryotic Argonaute based nucleic acid detection method, enabling duplex visual detection of aquatic pathogens. WeD-1 is portable, reusable, user-friendly, and cost-effective, offering real-time smartphone interaction and enabling real-time fluorescence observation during the reaction. The enhanced one-pot Loop-Mediated Isothermal Amplification (LAMP)-PfAgo method, incorporating paraffin-encapsulated lyophilized PfAgo protein, achieves precise target-specific cleavage, significantly enhancing multiplex nucleic acid detection. This innovation streamlines on-site testing, negating the need for specialized laboratory conditions while ensuring an aerosol-free system. With newly developed and highly sensitive LAMP primer sets, our compact WeD-1/LAMP-PfAgo nucleic acid rapid testing system exhibits remarkable sensitivity, readily detecting aquatic pathogens with naked eyes from rapidly prepared fish and shrimp samples within 40 min, even when the Ct values are as high as 34.

Colorimetric LAMP assay for detection of Xanthomonas phaseoli pv. manihotis in cassava through genomics: a new approach to an old problem.

Bacterial spot caused by Xanthomonas phaseoli pv. manihotis (Xpm) is considered the main bacterial disease that affects cassava, causing significant losses when not properly managed. In the present study, a fast, sensitive, and easy-to-apply method to detect Xpm via colorimetric loop-mediated isothermal amplification (LAMP) was developed. In order to ensure the use of a unique to the target pathovar core region for primer design, 74 complete genomic sequences of Xpm together with different bacterial species and pathovars were used for comparative genomics. A total of 42 unique genes were used to design 27 LAMP primer sets, from which nine primers were synthesized and only one (Xpm_Lp1 primer set) showed sufficient efficiency in preliminary tests. The sensitivity, assessed by a serial dilution of the type strain (IBSBF 278) DNA, yielded high sensitivity, detecting up to 100 fg. The LAMP primers showed high specificity, not cross-reacting with other bacterial species or other pathovars tested, and amplifying only the Xpm isolates. Tests confirmed the high efficiency of the protocol using infected or inoculated macerated cassava leaves, without the need for additional sample treatment. The LAMP test developed in this study was able to detect Xpm in a fast, simple, and sensitive way, and it can be used to monitor the disease under laboratory and field conditions.

Development of Loop-Mediated Isothermal Amplification Assays for the Rapid and Accurate Diagnosis of Exserohilum turcicum for Field Applications.

Northern corn leaf blight (NCLB), caused by Exserohilum turcicum, is one of the most devastating foliar diseases of maize. Rapid and accurate diagnosis for this disease is urgently needed but still limited. Here, we establish a field-deployable diagnostic method to detect E. turcicum based on loop-mediated isothermal amplification (LAMP) assays. A software application called K-mer Elimination by Cross-reference was used to search for the specific sequences belonging to E. turcicum by comparing the whole genome sequence between E. turcicum and other known maize pathogens. Five LAMP primer sets were designed based on specific and single-copy fragments of E. turcicum. Post-LAMP analyses indicated that only the primer set, Et9468_set1, was the most suitable, producing a ladder-like amplification pattern in the agarose gel electrophoresis and a strong fluorescence signal in the presence of SYBR Green I. The LAMP assay using Et9468_set1 primers demonstrated a high level of specificity in distinguishing E. turcicum from six other common fungal pathogens of maize, as well as 12 more fungal and oomycete strains including the epiphytic fungi from maize leaves and other crop pathogens. Moreover, it exhibited remarkable sensitivity by detecting five copies per reaction, which was approximately 104 times more sensitive compared with conventional PCR. The LAMP assay successfully detected E. turcicum in field maize leaves without DNA extraction, demonstrating its suitability for rapid on-spot detection of NCLB. Our study provides a direct LAMP diagnostic method to detect E. turcicum, which enables on-site pathogen detection in the field and the development of preventive strategies for NCLB management.

Loop-mediated isothermal amplification (LAMP) assays for rapid on-site detection of Lacticaseibacillus casei, Lacticaseibacillus paracasei, and Lacticaseibacillus rhamnosus in probiotic products

We developed the colorimetric loop-mediated isothermal amplification (LAMP) and a real-time LAMP with direct DNA extraction for the on-site detection of the three closely related Lacticaseibacillus species, such as Lacticaseibacillus casei, Lacticaseibacillus paracasei, and Lacticaseibacillus rhamnosus in probiotic products. Species-specific LAMP primers were designed targeting a unique gene in each species through comparative genomic analysis. Each LAMP primer set amplified target species specifically, distinguishing between the closely related species within the Lacticaseibacillus species. Based on the designed LAMP primers, two LAMP-based assays with direct DNA extraction were compared; their limit of detection was 103 CFU/mL for the Lacticaseibacillus species. In addition, both methods were applied to 44 commercial probiotic products and obtained identical results; it took about 45 min from sample preparation to confirming the presence or absence of the Lacticaseibacillus species. Thus, these methods can be rapid and simple in-field tests to detect L. casei, L. paracasei, and L. rhamnosus in probiotic products.

Application of multiple binding sites for LAMP primers across P. falciparum genome improves detection of the parasite from whole blood samples

IntroductionMalaria remains a significant health concern, particularly in regions with widespread prevalence. As the transmission rates decrease, there is a rise in low-density infections with the causative parasite, P. falciparum, that often escape detection through standard point-of-care diagnostic tools. In-low transmission areas, even few undetected cases can trigger outbreaks, necessitating rapid and sensitive diagnostics. Loop-mediated isothermal Amplification (LAMP) stands out as a nucleic acid technique that can easily utilizes un-processed samples such of saliva, urine, and lysed whole blood templates for a sensitive detection. However, most nucleic acid tests detect genes with few copies per parasite making it difficult to detect low-density parasitaemia.MethodsWe selected Pfr364 multi-copy repeats of the P. falciparum genome as a target for amplification due to their higher copy number, ideal for rapid amplification, addressing amplification drawbacks of limited parasites DNA. We used a sequence clustering approach to design a novel set of LAMP primers, capable of binding to multiple sites. Subsequently, we developed a hydroxynaphthol blue (HNB) colorimetric LAMP assay, using genomic DNA obtained from the 3D7 strain cultivated in vitro. This assay’s performance was validated using archived clinical samples of both whole blood and matched saliva, ensuring accuracy through comparative analysis against gold standard, nested PCR, targeting the 18S RNA gene.ResultsThe HNB-LAMP assay achieved rapid amplification within 15 minutes and exhibited high sensitivity with a limit of detection of 1 parasite. Further, the LAMP assay was robust in whole blood lysed with Triton X-100 and heat-treated saliva clinical samples. Against nested PCR, the assay showed sensitivity of 100% for whole blood and 40% for saliva samples. Moreover, co-analysis with the nested PCR showed a perfect agreement between the two techniques. (K = 0.99 for whole blood, and 0.66 for saliva).ConclusionOur study presents a method for detecting P. falciparum using LAMP, which results in increased sensitivity, shorter assay times, and a simpler workflow than nucleic acid tests relying on conventional DNA extraction and additional equipment for result interpretation. These findings hold great promise for improved malaria diagnosis, especially in settings where low-density parasitaemia is prevalent and rapid and accurate malaria detection is crucial.

Loop-mediated isothermal amplification coupled with nanoparticle-based lateral flow biosensor for monkeypox virus detection

Monkeypox virus (MPXV) infection is currently an evolving public health concern, highlighting an urgent need for early and rapid detection of MPXV. Here, we present a diagnostic test called MPXV-LAMP-LFB, which combines loop-mediated isothermal amplification (LAMP) and nanoparticle-based lateral flow biosensor (LFB) for the simple, sensitive and specific detection of MPXV and differentiation of its two clades. The MPXV-LAMP-LFB can be conducted at a heating block and the detection results can be visually indicated with the biosensor without any specialized apparatus. Two sets of LAMP primers targeting the D14L and ATI genes were designed for the Central and West African MPXV isolates, respectively. The optimal amplification condition was 64 °C for 40 min. Thus, the MPXV-LAMP-LFB test can be completed within 1 h, incorporating rapid DNA extraction (∼15 min), LAMP reaction (∼40 min) and result indicating (∼5 min). The MPXV-LAMP-LFB assay could detect down to 5 copies of plasmid template and 12.5 copies of pseudotyped virus in simulated blood samples. Furthermore, the MPXV-LAMP-LFB assay correctly identified all the positive controls and successfully avoided cross-reactivity with the non-MPXV pathogens or clinical samples, demonstrating its high specificity. Overall, the MPXV-LAMP-LFB test developed in this study showed great promise as a rapid, sensitive and accurate molecular tool for diagnosing MPXV infection.

Rapid on-site detection of Leuconostoc citreum in commercially processed products using loop-mediated isothermal amplification(LAMP) technique

Leuconostoc citreum is widely utilized across numerous industries due to its beneficial properties. Thus, a detection method for this target species is essential to track the presence of L. citreum in commercial products. We developed a rapid, on-site L. citreum detection method using the loop-mediated isothermal amplification (LAMP) technique in this study. The designed LAMP primer set exhibited high specificity, only targeting the intended species among the 76 tested. Moreover, this assay demonstrated a sensitivity of 2 pg of target DNA. To evaluate the LAMP assay's applicability, we selected 20 varied types of processed products. The results confirmed these products' successful and precise detection of L. citreum within 35 min. Additionally, we used samples spiked with L. citreum to determine the detection limit, revealing L. citreum detection up to 102 or 103 CFU/mL. Thus, the LAMP assay developed herein is a specific, sensitive, precise, and rapid on-site detection method for L. citreum in various processed products.

Real-Time and Rapid Detection of Phytopythium vexans Using Loop-Mediated Isothermal Amplification Assay.

Phytopythium vexans (de Bary) Abad, de Cock, Bala, Robideau, A. M. Lodhi & Levesque is an important waterborne and soil-inhabiting oomycete pathogen causing root and crown rot of various plants including certain woody ornamentals, fruit, and forest trees. Early and accurate detection of Phytopythium in the nursery production system is critical, as this pathogen is quickly transported to neighboring healthy plants through the irrigation system. Conventional methods for the detection of this pathogen are tedious, frequently inconclusive, and costly. Hence, a specific, sensitive, and rapid molecular diagnostic method is required to overcome the limitations of traditional identification. In the current study, loop-mediated isothermal amplification (LAMP) for DNA amplification was developed for the identification of P. vexans. It was evaluated using real-time and colorimetric assays. Several sets of LAMP primers were designed and screened, but PVLSU2 was found to be specific to P. vexans as it did not amplify other closely related oomycetes, fungi, and bacteria. Moreover, the developed assays were sensitive enough to amplify DNA up to 102 fg per reaction. The real-time LAMP assay was more sensitive than traditional PCR and culture-based methods to detect infected plant samples. In addition, both LAMP assays detected as few as 100 zoospores suspended in 100 ml water. These LAMP assays are anticipated to save time in P. vexans detection by disease diagnostic laboratories and research institutions and enable early preparedness in the event of disease outbreaks.

Development of a Loop-Mediated Isothermal Amplification (LAMP) Method to Detect the Potato Zebra Chip Pathogen 'Candidatus Liberibacter solanacearum' (Lso) and Differentiate Haplotypes A and B.

'Candidatus Liberibacter solanacearum' (Lso) is the causal agent of zebra chip of potato (Solanum tuberosum), which can significantly reduce potato yield. In this study, a loop-mediated isothermal amplification (LAMP) method for the detection of Lso haplotypes A and B was developed and evaluated. Two sets of LAMP primers named LAMP-A and LAMP-B were designed and tested for specificity and sensitivity. Both LAMP-A and LAMP-B were specific to Lso in in silico analysis using the Primer-Blast tool. The LAMP-A and LAMP-B could only produce positive signals from DNA mixtures of Lso-infected tomato but not from the genomic DNA of 37 nontarget plant pathogens. The sensitivity of LAMP-A and LAMP-B on Lso haplotypes A and B were tested on gBlocks and genomic DNA from Lso-infected tomato. On the genomic DNA for LAMP-A, the lowest amount of template DNA for a positive LAMP reaction was 2 to 20 ng on four haplotype A strains and 20 to 80 ng on four haplotype B strains; for LAMP-B, the lowest amount of template DNA for a positive LAMP reaction was 0.02 to 2 ng on four haplotype B strains and 20 ng to no amplification on four haplotype A strains. On gBlocks for LAMP-A, the lowest number of copies for a positive LAMP reaction was 60 on haplotype A and 600 on haplotype B; for LAMP-B, the lowest number of copies for a positive LAMP reaction was 60 on haplotype B and 600 on haplotype A. Therefore, considering the convenience of the LAMP technique, as well as the high specificity and sensitivity, the LAMP-A and LAMP-B primers can be used together to test the probable Lso-infected plant or psyllid samples to rapidly, accurately, and directly differentiate haplotypes A and B. We highly recommend this LAMP system to plant pathology practitioners and diagnostic labs for routine detection of Lso and confirmation of zebra chip disease on potato or tomato.

Closed-tube visual detection of Atlantic cod (Gadus morhua) using self-quenched primer coupled with a designed loop-mediated isothermal amplification vessel.

Species adulteration has been widely revealed around the world, and the possible reasons include declining stocks in most source areas of the world, poor transparency in the global supply chain, and difficulty in distinguishing the features of processed products. The present work selected Atlantic cod (Gadus morhua) as a case study, and developed a novel loop-mediated isothermal amplification (LAMP) assay for Atlantic cod authentication, where a self-quenched primer and a newly designed reaction vessel were used to realize the endpoint visual detection of the target-specific products. A novel LAMP primer set was designed for Atlantic cod, and the inner primer BIP was selected to label the self-quenched fluorogenic element. The fluorophore's dequenching only occurred along with LAMP elongation for the target species. No fluorescence could be observed with both single-stranded DNA and partially complementary dsDNA of the non-target species. With the novel reaction vessel, both amplification as well as detection were operated in an enclosed device, and visual differentiation of Atlantic cod, negative control, and false positive generated from primer dimers was achieved. The novel assay has proved its specificity and applicability, and could detect as little as 1 pg of Atlantic cod DNA. Moreover, Atlantic cod adulteration as low as 10% could be detected in haddock (Melanogrammus aeglefinus), and no cross-reactivity was observed. The established assay could be a useful tool to detect mislabeling incidents involving Atlantic cod considering the advantages of speed, simplicity and accuracy. © 2023 Society of Chemical Industry.

Development of a colorimetric loop-mediated isothermal amplification diagnostic assay for deer tick virus

Deer tick virus (DTV) is an emerging pathogen in North America. This virus can cause nervous system complications such as encephalitis in humans. Further, no data are available regarding long-term effects of infection from DTV patients across variable age groups. Diagnostic tools of DTV used by government laboratories are based on RT-PCR using patient serum or ticks. This paper explores the feasibility of a colorimetric loop-mediated isothermal amplification (LAMP) assay to create a point-of-care diagnostic methodology for use in field and in primary care. LAMP consists of six primers that bind to target DNA and amplify variable length nucleotide strands that can be visualized through side reactions or via electrophoresis. First, a viable LAMP primer set, and a primer set that/ dimerizes and amplifies DNA regardless of compatibility were created in silico and validated in vitro. Then, a specific LAMP assay was developed. Our findings showed this method can be performed within 30 min and can measure with limits of detection comparable to PCR.

Development and Evaluation of a Loop-Mediated Isothermal Amplification (LAMP) Method for Detection of the Potato Powdery Scab Pathogen Spongospora subterranea.

Spongospora subterranea is the causal agent of powdery scab of potato (Solanum tuberosum), which can significantly reduce potato quality. In this study, we developed and evaluated a loop-mediated isothermal amplification (LAMP) method for the detection of S. subterranea. A set of LAMP primers named PS-LAMP was designed and tested for specificity and sensitivity. In the specificity test, in silico analysis using the NCBI Primer-BLAST tool indicated that PS-LAMP was specific to S. subterranea. The in vitro tests confirmed specificity, showing that PS-LAMP could produce positive signals from DNA isolated from each of three potato tubers with powdery scab symptoms but did not produce positive signals from DNA isolated from 38 nontarget plant pathogens. The sensitivity of PS-LAMP was tested on both gBlocks and DNA isolated from potato samples with powdery scab symptoms. On gBlocks, the lowest number of copies for a positive LAMP reaction was six, which was similar to results obtained via qPCR, but it was 10 times more sensitive than conventional PCR. On a DNA sample from S. subterranea-infected potato, the lowest amount of template DNA for a positive LAMP reaction was 2 pg, which was incomparable with the sensitivity of qPCR. Considering the convenience of the LAMP technique, as well as the high specificity and sensitivity, this assay can be very useful for plant pathology practitioners and diagnostic labs interested in rapid, accurate, and routine detection of S. subterranea and confirmation of powdery scab disease.

Optimization and application of loop-mediated isothermal amplification technique for sex identification in red-whiskered bulbul (Pycnonotus jocosus).

The red‐whiskered bulbul (Pycnonotus jocosus) is a popular avian species in Thailand and many other countries. The red‐whiskered bulbul has a high economic value, but breeding is challenging since sex identification is difficult. The PCR method is now used for sex identification. However, PCR amplification and post‐PCR analysis necessitate the use of a laboratory equipped with specialized scientific instruments, which is inconvenient for field operations. This research describes a method for amplification of DNA samples using the loop‐mediated isothermal amplification (LAMP) approach, which is a molecular biology methodology for isothermal amplification that is extremely sensitive, fast, and easy for post‐LAMP product visualization. Herein, total of 23 blood samples were collected and DNA was extracted. Two sets of LAMP primers were designed for CHD‐Z and CHD‐W genes. The colorimetric assay was used to investigate the best conditions for LAMP reactions and post‐LAMP product visualization. LAMP reactions for sex identification were compared to traditional PCR in terms of sensitivity and specificity. LAMP reactions were found to be 10‐fold more sensitive than PCR at 1 ng of DNA. When compared to electrophoresis analysis, the visualization with colorimetric assay using GelRed® and SYTO™ 9 was 100% accurate. The optimal LAMP condition tested simple DNA extracted from bird feathers using the HotSHOT technique. The result showed that the optimal condition could distinguish the sex of red‐whiskered bulbuls totally and accurately. A powerful method for red‐whiskered bulbul sex identification is demonstrated in this study, which can be used in field studies because it is quick and easy to perform, has high sensitivity, and does not require advanced scientific equipment.

Loop-mediated isothermal amplification of PBAN gene for molecular diagnosis of Bemisia tabaci biotype Q (Hemiptera: Aleyrodidae)

• LAMP assay for PBAN of the whitefly was developed. • The PBAN-based LAMP primer set showed specific amplification of the target region. • The PBAN-based LAMP assay can be applicable for monitoring B. tabaci biotype Q. The tobacco whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae), is a serious pest that transmits tomato yellow leaf curl virus (TYLCV) in tomato. The tobacco whitefly exhibits morphological similarity with the greenhouse whitefly, Trialeurodes vaporariorum (Hemiptera: Aleyrodidae) which also damages various plants in the greenhouse. Therefore, it is very important to quickly and accurately diagnose whiteflies for applying pest management strategies. In this study, we used a loop-mediated isothermal amplification (LAMP) assay to quickly and effectively detect B. tabaci . Primer sets were investigated for the specificity of B. tabaci by visible detection of the target DNA fragment. Two primer sets for pheromone biosynthesis activating neuropeptide (PBAN) gene were obtained from transcriptomic analysis of B. tabaci biotype Q. The PBAN-based LAMP primer set showed specific amplification of the target region. The optimal conditions for B. tabaci detection were 60 °C for 60 min with four LAMP primers of PBAN. The minimum amount of genomic DNA required for visible detection was 100 ng. These results suggest that the PBAN-based LAMP assay can be applicable for field monitoring of B. tabaci .

Analysis and validation of silica-immobilised BST polymerase in loop-mediated isothermal amplification (LAMP) for malaria diagnosis

Bacillus stearothermophilus large fragment (BSTLF) DNA polymerase is reported, isolated on silica via a fused R5 silica-affinity peptide and used in nucleic acid diagnostics. mCherry (mCh), included in the fusion construct, was shown as an efficient fluorescent label to follow the workflow from gene to diagnostic. The R5 immobilisation on silica from cell lysate was consistent with cooperative R5-specific binding of R52-mCh-FL-BSTLF or R52-mCh-H10-BSTLF fusion proteins followed by non-specific protein binding (including E. coli native proteins). Higher R5-binding could be achieved in the presence of phosphate, but phosphate residue reduced loop-mediated isothermal amplification (LAMP) performance, possibly blocking sites on the BSTLF for binding of β- and γ-phosphates of the dNTPs. Quantitative assessment showed that cations (Mg2+ and Mn2+) that complex the PPi product optimised enzyme activity. In malaria testing, the limit of detection depended on Plasmodium species and primer set. For example, 1000 copies of P. knowlesi 18S rRNA could be detected with the P.KNO-LAU primer set with Si-R52-mCh-FL-BSTLF , but 10 copies of P. ovale 18S rRNA could be detected with the P.OVA-HAN primer set using the same enzyme. The Si-immobilised BSTLF outperformed the commercial enzyme for four of the nine Plasmodium LAMP primer sets tested. Si-R52-mCh-FL-BSTLF production was transferred from Cambridge to Accra and set up de novo for a trial with clinical samples. Different detection limits were found, targeting the mitochondrial DNA or the 18S rRNA gene for P. falciparum. The results are discussed in comparison with qPCR and sampling protocol and show that the Si-BSTLF polymerase can be optimised to meet the WHO recommended guidelines.Graphical abstract

Rapid on-site identification of Lepiota brunneoincarnata-induced mushroom poisoning by simple DNA extraction and loop-mediated isothermal amplification strategy

Lepiota brunneoincarnata-induced mushroom poisoning has occurred widely in some areas of the world in recent years, resulting in high mortality and posing potential health risks to humans and pets. However, a rapid and sensitive method for the identification of L. brunneoincarnata is scarce. Loop-mediated isothermal amplification (LAMP) combined with visual dye reaction or lateral flow dipstick (LFD) was established for rapid on-site detection of L. brunneoincarnata. Simple DNA extraction was completed by the heating lysis method within 15 min. In addition, a specific LAMP primer set was designed targeting the internal transcribed spacer (ITS) sequence of L. brunneoincarnata, with no cross-reactivity against 22 other mushroom species. Sensitivity evaluation showed that the detection limits of visual LAMP and LAMP-LFD assays were 10 and 0.1 pg/μL genomic DNA of L. brunneoincarnata, respectively. Moreover, the developed method was successfully applied to cooked mushroom and simulated vomitus, with detection limits of 1% admixture for the visual LAMP assay and 0.1% admixture for the LAMP-LFD assay. The whole detection protocol can be completed in 60 min without expensive instruments, which is suitable for the rapid identification of Lepiota brunneoincarnata-induced mushroom poisoning in the field.

CRISPR/Cas12a-Based Diagnostic Platform Accurately Detects Nocardia farcinica Targeting a Novel Species-Specific Gene.

Under the COVID-19 pandemic background, nucleic acid detection has become the gold standard to rapidly diagnose the infectious disease. A rapid, low cost, reliable nucleic acid detection platform will be the key to control next potential pandemic. In this study, a nucleic acid detection platform, which combined CRISPR/Cas12a-based detection with loop-mediated isothermal amplification (LAMP), was developed and termed CRISPR-CLA. In the CRISPR-CLA system, LAMP preamplification was employed, and CRISPR/Cas12a-based detection was used to monitor the preamplicons. The forward inner primer (FIP) was engineered with a protospacer adjacent motif (PAM) site TTTA of Cas12a effector at the linker region; thus, the CRISPR-CLA platform can detect any sequence as long as the primer design meets the requirement of LAMP. To demonstrate the validity of the CRISPR-CLA system, it was applied for the molecular diagnosis of nocardiosis caused by Nocardia farcinica (N. farcinica). A highly conserved and species-specific gene pbr1 of N. farcinica, which was first reported in this study, was used as the target of detection. A set of LAMP primers targeting a fragment of pbr1 of the N. farcinica reference strain IFM 10152 was designed according to the principle of CRISPR-CLA. Three CRISPR RNAs (crRNAs) with different lengths were designed, and the most efficient crRNA was screened out. Additionally, three single-strand DNA (ssDNA) probes were tested to further optimize the detection system. As a result, the N. farcinica CRISPR-CLA assay was established, and the whole detection process, including DNA extraction (20 min), LAMP preamplification (70°C, 40 min), and CRISPR/Cas12a-mediated detection (37°C, 8 min), can be completed within 70 min. A fluorescence reader (for fluorescence CRISPR-CLA) or a lateral flow biosensor (for lateral-flow CRISPR-CLA) can be the media of the result readout. Up to 132 strains were used to examine the specificity of N. farcinica CRISPR-CLA assay, and no cross-reaction was observed with non-N. farcinica templates. The limit of detection (LoD) of the N. farcinica CRISPR-CLA assay was 100 fg double-strand DNA per reaction. N. farcinica was detected accurately in 41 sputum specimens using the N. farcinica CRISPR-CLA assay, which showed higher specificity than a real-time qPCR method. Hence, the N. farcinica CRISPR-CLA assay is a rapid, economic and accurate method to diagnose N. farcinica infection.

Simultaneous detection of multiple foodborne bacteria by loop-mediated isothermal amplification on a microfluidic chip through colorimetric and fluorescent assay

The integration of loop-mediated isothermal amplification (LAMP) onto a microfluidic chip adds more simplicity and portability for food safety control. However, this system for multiple-target detection was less used on foodborne bacteria. Here, we utilized a ten-well microfluidic chip with pre-loaded LAMP primer sets for the quantitative and qualitative detection of Salmonella , Staphylococcus aureus , Escherichia coli O157:H7, and Shigella . The specificity and sensitivity of designed primers targeting sirA , spA , fliC , and ipaH genes were validated. Using regular tubes and the ten-well microfluidic chips, these four pathogens could be simultaneously detected within 45 min by LAMP with fluorescent and colorimetric readouts, respectively. Finally, the results demonstrated that the limit of detection reached 8 × 10 3 CFU mL −1 genomic DNA with a recovery rate of 86.1%∼110%. In summary, our microfluidic chip platform displayed obvious advantages in time-saving, cost-effectiveness, and sensitivity, which is applicable for in-field monitoring of food pathogens. ● LAMP reaction is integrated on a 10-well microfluidic chip for food detection. ● The microfluidic chip is used for both quantitative and qualitative detection. ● The fluorescent intensity and colorimetric amplification readouts can be obtained. ● This microfluidic chip platform simultaneously detects four bacteria within 45 min.