A novel visual loop-mediated isothermal amplification assay targeting gene62181533 for the detection of Salmonella spp. in foods

Research progress of loop-mediated isothermal amplification in the detection of Salmonella for food safety applications

Salmonella, the prevailing zoonotic pathogen within the Enterobacteriaceae family, holds the foremost position in global bacterial poisoning incidents, thereby signifying its paramount importance in public health. Consequently, the imperative for expeditious and uncomplicated detection techniques for Salmonella in food is underscored. After more than two decades of development, loop-mediated isothermal amplification (LAMP) has emerged as a potent adjunct to the polymerase chain reaction, demonstrating significant advantages in the realm of isothermal amplification. Its growing prominence is evident in the increasing number of reports on its application in the rapid detection of Salmonella. This paper provides a systematic exposition of the technical principles and characteristics of LAMP, along with an overview of the research progress made in the rapid detection of Salmonella using LAMP and its derivatives. Additionally, the target genes reported in various levels, including Salmonella genus, species, serogroup, and serotype, are summarized, aiming to offer a valuable reference for the advancement of LAMP application in Salmonella detection. Finally, we look forward to the development direction of LAMP and expect more competitive methods to provide strong support for food safety applications.

Establishment of real-time fluorescence and visual LAMP for rapid detection of Escherichia coli O157:H7 and kits construction

Escherichia coli O157:H7 is a common pathogenic bacterium in food and water that can pose a threat to human health. The aim of this study was to develop loop-mediated isothermal amplification (LAMP) method for the detection of E. coli O157:H7 in food based on the specific gene Ecs_2840 and to construct rapid detection kits based on the established methods. Specifically, we established two methods of real-time fluorescent LAMP (RT-LAMP) and visual LAMP with calcein as an indicator. In pure bacterial culture, the cell sensitivity and genomic sensitivity of the RT-LAMP kit were 8.8 × 100 CFU ml-1 and 4.61 fg µl-1, respectively. The sensitivity of the visual LAMP kit was 2.35 × 100 CFU ml-1 and 4.61 fg µl-1. Both kits had excellent specificity and anti-interference performance. In addition, milk inoculated with 2.26 × 100 CFU ml-1E. coli O157:H7 could be detected within the reaction time after enrichment for 3 h. The results showed that the LAMP kits were rapid, sensitive, and specific for the detection of E. coli O157:H7 in food and had good application prospects in food safety surveillance.

Development of a lateral flow dipstick test for the detection of 4 strains of Salmonella spp. in animal products and animal production environmental samples based on loop-mediated isothermal amplification

OBJECTIVE

This study aimed to develop loop-mediated isothermal amplification (LAMP) combined with lateral flow dipstick (LFD) and compare it with LAMP-AGE, polymerase chain reaction (PCR), and standard Salmonella culture as reference methods for detecting Salmonella contamination in animal products and animal production environmental samples.

METHODS

The SalInvA01 primer, derived from the InvA gene and designed as a new probe for LFD detection, was used in developing this study. Adjusting for optimal conditions by temperature, time, and reagent concentration includes evaluating the specificity and limit of detection. The sampling of 120 animal product samples and 350 animal production environmental samples was determined by LAMP-LFD, comparing LAMP-AGE, PCR, and the culture method.

RESULTS

Salmonella was amplified using optimal conditions for the LAMP reaction and a DNA probe for LFD at 63°C for 60 minutes. The specificity test revealed no cross-reactivity with other microorganisms. The limit of detection of LAMP-LFD in pure culture was 3×102 CFU/mL (6 CFU/reaction) and 9.01 pg/μL in genomic DNA. The limit of detection of the LAMP-LFD using artificially inoculated in minced chicken samples with 5 hours of pre-enrichment was 3.4×104 CFU/mL (680 CFU/reaction). For 120 animal product samples, Salmonella was detected by the culture method, LAMP-LFD, LAMP-AGE, and PCR in 10/120 (8.3%). In three hundred fifty animal production environmental samples, Salmonella was detected in 91/350 (26%) by the culture method, equivalent to the detection rates of LAMP-LFD and LAMP-AGE, while PCR achieved 86/350 (24.6%). When comparing sensitivity, specificity, positive predictive value, and accuracy, LAMP-LFD showed the best results at 100%, 95.7%, 86.3%, and 96.6%, respectively. For Kappa index of LAMP-LFD, indicated nearly perfect agreement with culture method.

CONCLUSION

The LAMP-LFD Salmonella detection, which used InvA gene, was highly specific, sensitive, and convenient for identifying Salmonella. Furthermore, this method could be used for Salmonella monitoring and primary screening in animal products and animal production environmental samples.

Dual-color blending based visual LAMP for food allergen detection: A strategy with enlarged color variation range and contrast

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A near contrast color change was obtained by blending HNB and CR colorimetric LAMP detection process.

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The sensitivity of the dual-color blending method was comparable to the real-time LAMP.

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The ratio between the two visual dyes in the dual-color blending method is crucial.

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The reaction is conducted in one tube and no lid-opening was needed.

Food allergy has been a serious public health problem around the world. Its prevention relies heavily on the effective avoidance of any contaminated food, making clear and accurate detection very important. LAMP is one of the most potent methods for allergen rapid detection. However, its current colorimetric readouts usually have low color contrast and narrow color variation range. Thus, here we proposed a strategy based on color evolution to enlarge the variation range as well as the contrast to improve its suitability for naked-eye observation. By simply blending two commonly used color change processes during amplification, a wider color variation window, and a near contrast color change, purple-to-green with a hues difference of 10 were obtained. Three important allergens (walnuts, hazelnuts, and peanuts) were tested with a comparable sensitivity towards fluorescent real-time LAMP. Its feasibility for practical use has also been studied. This simple but effective strategy provides a new idea for the colorimetric detection of LAMP amplicons and can be applied to various fields.

One-step, multiplex, dual-function oligonucleotide of loop-mediated isothermal amplification assay for the detection of pathogenic Burkholderia pseudomallei

This study highlights the development of a multiplex real-time loop-mediated isothermal amplification assay. The developed assay employed a dual-function oligonucleotide (DFO) which simultaneously monitors the emitted amplification signals and accelerates the amplification process. The DFO was a modification of loop primer (LP); the 5'-end and 3'-end of the LP was tagged with fluorophore and quencher, respectively. The DFO was quenched in its unbound state and fluoresces only when it anneals to the specific target during the amplification process. With the same working mechanism as LP, DFO allowed the detection of target genes in less than 1 h in a real time monitoring system. We demonstrated this detection platform with Burkholderia pseudomallei, the causative agent of melioidosis. An internal amplification control (IAC) was incorporated in the assay to rule out false negative result and to demonstrate that the assay was successfully developed in a multiplex system. The assay was 100% specific when it was evaluated against 96 B. pseudomallei clinical isolates and 48 other bacteria species. The detection limit (sensitivity) of the developed assay was 1 fg/μl of B. pseudomallei genomic DNA and 18.2 CFU/ml at the bacterial cell level. In spiked blood samples, the assay's detection limit was 14 CFU/ml. The assay's diagnostic evaluation showed 100% diagnostic sensitivity, diagnostic specificity, positive predictive value, and negative predictive value. An integrated multiplex LAMP and real-time monitoring system was successfully developed, simplifying the workflow for the rapid and specific nucleic acid diagnostic test.

Rapid Screening for Salmonella in Raw Pet Food by Loop-Mediated Isothermal Amplification

ABSTRACT

Raw pet food, composed of raw meat and vegetables, has increased in popularity in recent years. Multiple surveys and frequent recalls indicate that this commodity has a high risk of contamination with Salmonella and other foodborne pathogens. Improved screening methods are needed to meet the growing demand for testing. This matrix verification study aimed to apply a Salmonella loop-mediated isothermal amplification (LAMP) method, recently completed multilaboratory validation in dry dog food, in several raw pet food matrices, following the U.S. Food and Drug Administration (FDA)'s method validation guidelines. Five types of raw pet food, consisting of freeze-dried beef and chicken treats and frozen beef, pork, and turkey complete foods, were evaluated. For each matrix, two sets of ten 25-g test portions (seven inoculated with ≤30 cells of Salmonella Typhimurium and three uninoculated controls) were examined. One set was preenriched in buffered peptone water and the other one was preenriched in lactose broth, which was followed by LAMP screening using two isothermal master mixes (ISO-001 and ISO-004). All results were confirmed by culture as specified in the FDA Bacteriological Analytical Manual (BAM). The LAMP method accurately detected Salmonella in all inoculated test portions of the five raw pet food samples, regardless of the preenrichment broth used. Positive results could be obtained within 4 min of the LAMP run using the ISO-004 master mix. All uninoculated controls tested negative using LAMP or BAM. In addition, one turkey-based complete pet food sample was found to be already contaminated with three Salmonella serovars harboring multiple antimicrobial resistance genes. The Salmonella LAMP method offers a rapid, reliable, and robust tool for routine screening of Salmonella in raw pet food, which will help better ensure product safety and protect public health.

HIGHLIGHTS

Evaluation of different target genes for the detection of Salmonella sp. by loop-mediated isothermal amplification

The loop-mediated isothermal amplification (LAMP) technique was used to investigate six salmonella-specific sequences for their suitability to serve as targets for the pathogen identification. Sequences selected for designing LAMP primers were genes invA, bcfD, phoP, siiA, gene62181533 and a region within the ttrRSBCA locus. Primers including single nucleotide polymorphisms were configured as degenerate primers. Specificity of the designed primer sets was determined by means of 46 salmonella and 32 other food- and waterborne bacterial reference species and strains. Primers targeting the ttrRSBCA locus showed 100 % inclusivity of target and exclusivity of other test species and strains. Other primer sets revealed deficiencies, especially regarding Salmonella enterica subsp. II-IV and Salmonella bongori. Additionally, primers targeting the siiA gene failed to detect S. enterica subsp. enterica serotypes Newport and Stanley, whereas bcfD primers did not amplify DNA of S. enterica subsp. enterica serotype Schleissheim. TtrRSBCA primers, providing short detection times and constant melting temperatures of amplification products, achieved best overall performance.

Electrochemical Immuno- and Aptamer-Based Assays for Bacteria: Pros and Cons over Traditional Detection Schemes

Microbiological safety of the human environment and health needs advanced monitoring tools both for the specific detection of bacteria in complex biological matrices, often in the presence of excessive amounts of other bacterial species, and for bacteria quantification at a single cell level. Here, we discuss the existing electrochemical approaches for bacterial analysis that are based on the biospecific recognition of whole bacterial cells. Perspectives of such assays applications as emergency-use biosensors for quick analysis of trace levels of bacteria by minimally trained personnel are argued.

Development of a test kit for visual loop-mediated isothermal amplification of Salmonella in spiked ready-to-eat fruits and vegetables

The purpose of this study was to assemble two types of loop-mediated isothermal amplification (LAMP) kit that have the ability to visually detect Salmonella in ready-to-eat fruits and vegetables. The reaction results were obtained within 20-40 min after addition of DNA and can be discerned by the naked eye or an amplification plot. The stability of the LAMP wet kit was evident after multiple freezing and thawing cycles, and the one-step LAMP lyophilized kit was further evolved to allow ambient temperature transport for deployment in resource-limited settings. The cost-effective wet kit had the ability to detect minimum amounts of 1.8 CFU/ml Salmonella DNA without enrichment, while the sensitivity of the one-step LAMP lyophilized kit was only 9.8 × 10³ CFU/ml. They both have good anti-interference, as they were both able to detect 2.1 × 10² CFU/ml Salmonella mixed with 10⁶ CFU/ml four non-Salmonella strain mixture. Moreover, cucumber and lettuce that were contaminated with an initial inoculation of 1.7 CFU of Salmonella/10 g showed detection within a reaction time of 30 min after 10 h enrichment. The present research setup is a convenient and practical kit for Salmonella rapid detection that has good application prospects in food safety monitoring.

Detection of Salmonella in Food Matrices, from Conventional Methods to Recent Aptamer-Sensing Technologies

Rapid detection of the foodborne pathogen Salmonella in food processing is of crucial importance to prevent food outbreaks and to ensure consumer safety. Detection and quantification of Salmonella species in food samples is routinely performed using conventional culture-based techniques, which are labor intensive, involve well-trained personnel, and are unsuitable for on-site and high-throughput analysis. To overcome these drawbacks, many research teams have developed alternative methods like biosensors, and more particularly aptasensors, were a nucleic acid is used as biorecognition element. The increasing interest in these devices is related to their high specificity, convenience, and relative rapid response. This review aims to present the advances made in these last years in the development of biosensors for the detection and the quantification of Salmonella, highlighting applications on meat from the chicken food chain.

Bisintercalating DNA redox reporters for real-time electrochemical qLAMP

The electrochemical detection methods have emerged as a potential alternative to the bench-top optical systems in monitoring nucleic acid amplification. DNA intercalating redox reporters play a crucial role in such monitoring schemes. Here, a series of bisintercalating redox probes have been tailor-made to meet specific requirements of electrochemical quantitative loop-mediated isothermal amplification (qLAMP). The probes composed of two naphthoquinone-imidazole (NQIM) derivatives as signal motifs that are covalently bridged by different linkers (R). They are bis-NQIM-R; R = Alkane (Ak), ethylene glycol (EG) and phenyl (Ph). The linkers allow the probes to be fine-tuned for securing ideal redox reporter. DNA binding studies via electrochemical and fluorescence techniques demonstrate that the bis-NQIM-R probes possess better ds-DNA bisintercalating ability compared to their mono-analogs. The bis-NQIM-Ph was implemented in a real-time electrochemical qLAMP, for which a prototype custom-made device that can perform fully automated multiplexed analyses is devised. A single copy of Salmonella DNA was quantified in just 10 min and the performance is comparable to the benchtop fluorescence method. Thus, the bisintercalating redox reporters incorporated electrochemical detection schemes hold great promise in qLAMP.

A rapid and eco-friendly isothermal amplification microdevice for multiplex detection of foodborne pathogens

In this study, a plastic microdevice based on loop-mediated isothermal amplification (LAMP) was fabricated for the amplification and on-chip fluorescence detection of multiple pathogens. Papers infused with LAMP reagents and specific primers were embedded inside the multiple reaction chambers of the microdevice. A solution containing the target pathogens was injected into the sample chamber, located in the center of the microdevice, and evenly distributed to the reaction chambers simultaneously via centrifugal force. For detection, fisetin, a plant-derived fluorophore, was used as the DNA-intercalating dye. Purified DNAs of Escherichia coli O157:H7 (E. coli O157:H7), Salmonella spp., Staphylococcus aureus (S. aureus), and Cochlodinium polykrikoides were successfully amplified and directly detected on the microdevice, where as low as 0.13 and 0.12 ng μL-1 of the DNA of E. coli O157:H7 and S. aureus, respectively, were identified. In addition, the potential of this microdevice for point-of-care testing was further examined by incorporating on-chip sample purification module and testing using a real sample - milk spiked with Salmonella spp. The thermally lysed milk sample was filtered using polydopamine-coated paper embedded inside a sample chamber and seamlessly transported into the reaction chambers by centrifugal force for subsequent LAMP followed by direct on-chip detection inside the reaction chambers in which fisetin-soaked papers were embedded. The limit of detection for Salmonella spp. was determined to be approximately 1.7 × 102 CFU mL-1 using the microdevice. This microdevice is safe, easy to use, selective, and sensitive enough for point-of-care testing to identify foodborne pathogens as well as environmentally harmful microorganisms.

Loop-Mediated Isothermal Amplification for Salmonella Detection in Food and Feed: Current Applications and Future Directions

Loop-mediated isothermal amplification (LAMP) has become a powerful alternative to polymerase chain reaction (PCR) for pathogen detection in clinical specimens and food matrices. Nontyphoidal Salmonella is a zoonotic pathogen of significant food and feed safety concern worldwide. The first study employing LAMP for the rapid detection of Salmonella was reported in 2005, 5 years after the invention of the LAMP technology in Japan. This review provides an overview of international efforts in the past decade on the development and application of Salmonella LAMP assays in a wide array of food and feed matrices. Recent progress in assay design, platform development, commercial application, and method validation is reviewed. Future perspectives toward more practical and wider applications of Salmonella LAMP assays in food and feed testing are discussed.

Development of uracil-DNA-glycosylase-supplemented loop-mediated isothermal amplification coupled with nanogold probe (UDG-LAMP-AuNP) for specific detection of Pseudomonas aeruginosa

Pseudomonas aeruginosa (P. aeruginosa) is an important opportunistic pathogen that causes serious infections in humans, including keratitis in contact lens wearers. Therefore, establishing a rapid, specific and sensitive method for the identification of P. aeruginosa is imperative. In the present study, the uracil-DNA-glycosylase-supplemented loop-mediated isothermal amplification combined with nanogold labeled hybridization probe (UDG-LAMP-AuNP) was developed for the detection of P. aeruginosa. UDG-LAMP was performed to prevent carry over contamination and the LAMP reactions can be readily observed using the nanogold probe. A set of 4 primers and a hybridization probe were designed based on the ecfX gene. The UDG-LAMP reactions were performed at 65°C for 60 min using the ratio of 40% deoxyuridine triphosphate to 60% deoxythymidine triphosphate. The detection of UDG-LAMP products using the nanogold labeled hybridization probe, which appeared as a red-purple color, was examined at 65°C for 5 min with 40 mM MgSO₄. The UDG-LAMP-AuNP demonstrated specificity to all tested isolates of P. aeruginosa without cross reaction to other bacteria. The sensitivity for the detection of pure culture was 1.6×10³ colony-forming units (CFU) ml⁻¹ or equivalent to 3 CFU per reaction while that of polymerase chain reaction was 30 CFU per reaction. The detection limit of spiked contact lenses was 1.1×10³ CFU ml⁻¹ or equivalent to 2 CFU per reaction. In conclusion, the UDG-LAMP-AuNP assay was rapid, simple, specific and was effective for the identification of P. aeruginosa in contaminated samples.

A disposable microcapsule array chip fabricated by ice printing combined with isothermal amplification for Salmonella DNA detection

In this work, a novel microcapsule array chip was fabricated for the detection of Salmonella DNA by integrating an ice-printing technique with DNA isothermal amplification. Reaction solutions were previously sealed in the microcapsule array chip via ice printing. To protect the relatively fragile DNA isothermal amplification system, an extra polystyrene (PS) film was introduced to isolate the reaction solution from photopolymer precursor, which was proved to be a vital step for providing a clean and stable environment for DNA amplification reaction. Detection operation can be done by simply injecting sample DNA into the microcapsule by an easily accessible syringe, and the result can be directly obtained through color change within 90 minutes. This method shows good sensitivity, specificity and stability.

An ice printing fabricated microcapsule array chip is demonstrated based on loop-mediated isothermal amplification for visual salmonella DNA detection.

Rapid visual detection of lily mottle virus using a loop-mediated isothermal amplification method

Lily mottle virus (LMoV; genus Potyvirus, family Potyviridae) infects plants of the genus Lilium, causing a reduction in flower and bulb quality. A rapid and sensitive loop-mediated isothermal amplification (LAMP) assay was developed to detect the coat protein gene of LMoV. This LAMP method was highly specific for LMoV, with no cross-reaction with other lily viruses. The sensitivity of LMoV using the LAMP assay was 100 times more sensitive than that using conventional polymerase chain reaction. A reverse transcription LAMP (RT-LAMP) was then successfully applied to detect LMoV RNA. The newly established LAMP and one-step RT-LAMP provide an alternative method for detecting LMoV in lily plants.