Development and evaluation of a loop-mediated isothermal amplification assay for the rapid detection of Staphylococcus aureus in food

Multiplex fluorescence loop-mediated isothermal amplification with lateral flow assay for rapid simultaneous detection of mecA and nuc genes in methicillin-resistant Staphylococcus aureus

BACKGROUND

Antibiotic-resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA), pose a significant threat to public health. Existing detection methods, like cultivation-based techniques, demand significant time and labor, while molecular diagnostic techniques, such as PCR, necessitate sophisticated instrumentation and skilled personnel. Although previous multiplex loop-mediated isothermal amplification assays based on fluorescent dyes (mfLAMP) offer simplicity and cost-effectiveness, they are prone to false-positive results. Therefore, developing a rapid and efficient multiplex assay for high-sensitivity MRSA is imperative to create a practical diagnostic tool for point-of-care testing.

RESULTS

Here, we developed a mfLAMP combined with a lateral flow assay (mfLAMP-LFA) for the visual and simultaneous detection of the mecA (PBP2a-specific marker) and nuc (S. aureus-specific marker) genes in MRSA. We optimized mfLAMP-LFA using graphene oxide (GO)-based purification and specific DNA probes and evaluated its sensitivity, specificity, and stability. Utilizing GO to mitigate false-positive results by acting as a trap for free DNA probes, the mfLAMP-LFA method successfully identified mecAf and nucf-probes, exhibiting distinct red, green, and yellow fluorescence signals. The detection sensitivity of the developed mfLAMP-LFA method (1 CFU mL-1 in phosphate-buffered saline (PBS)) was comparable to other highly sensitive MRSA detection methods (1 CFU mL-1 in PBS). Furthermore, the method demonstrated specificity for MRSA, detecting it in irrigation water samples within the desired range and achieving reliable recovery rates from spiked samples.

SIGNIFICANCE

This novel strategy is the first to incorporate GO into mfLAMP-LFA, enabling specific and sensitive MRSA detection and advancing rapid bacterial detection. This assay facilitates MRSA diagnostics, contributing to improved public health and food safety by delivering rapid, cost-effective point-of-care results. It enables the simultaneous detection of multiple bacteria, even in irrigation water samples artificially inoculated with MRSA, which contain aerobic bacteria at 2.7 × 102 CFU mL-1.

Rapid identification of Staphylococcus aureus based on a fluorescence imaging/detection platform that combines loop mediated isothermal amplification assay and the smartphone-based system

Food associated diseases pose significant public health threat in the United States. Health risks associated with food-borne pathogens drive the need for constant monitoring of food products. An efficient method that can diagnose food-borne pathogens rapidly will be invaluable and in high demand. In this study, we showed the feasibility of a novel rapid detection platform based on fluorescence imaging/detection that combines a user-friendly, portable loop mediated isothermal amplification (LAMP) reaction device and a smartphone-based detection system. The proposed platform was used to detect Staphylococcus aureus which is one of the most important food-borne pathogen especially dairy products. The complete protocol is quicker; the reaction is performed under isothermal conditions and completed in 1 h or less. Experimental results show that LAMP assays were ten-fold more sensitive than PCR-based detection. The proposed smartphone detection system was able to detect and quantify LAMP assay samples containing three different concentrations of S. aureus from 10⁹ CFU/mL down to 10³ CFU/mL. The present proof-of-concept study demonstrated that this platform offers a portable, easy to use method for measuring target pathogens with LAMP amplification.

A dual electrochemical/colorimetric magnetic nanoparticle/peptide-based platform for the detection of Staphylococcus aureus

Rapid and economical biosensor for Staphylococcus aureus, one of the main causes of food-borne illness, was developed based on dual colorimetric and electrochemical detection.

Electrochemical immunosensor based on an antibody-hierarchical mesoporous SiO2 for the detection of Staphylococcus aureus

The outbreak of food-borne pathogens has become a serious concern; therefore, the detection of pathogenic bacteria in food is required. Untreated, sensitive, and reliable sensors should be developed for the detection of Staphylococcus aureus (S. aureus). In this study, a sensitive antibody-based electrochemical immunosensor was developed using antibody (Ab)-hierarchical mesoporous silica (HMS) bio-conjugates for label-free detection of low concentrations of S. aureus. First, a bio-template method based on butterfly wings was used to prepare the HMS. Then, the carrier material was amino-functionalized to cross-link the antibody with glutaraldehyde. The Ab-HMS bio-conjugates were then immobilized on a glassy carbon electrode (GCE), and the presence of S. aureus was detected by analyzing the changes in the peak currents after the antigen-antibody complex formation. Differential pulse voltammetry (DPV) was performed with bacterial concentrations ranging from 10 to 2 × 103 colony forming units (CFU) mL-1. Selective tests were performed using Escherichia coli (E. coli), Listeria monocytogenes (L. monocytohenes), and Salmonella, and the selective assays showed specific detection of S. aureus using the sensor. In addition, the immunosensor showed a good linear relationship between the peak current increase and logarithmic S. aureus concentration (R 2 = 0.9759) with a fast detection time (20 min) and detection limit of 11 CFU mL-1. When the electrochemical impedance spectroscopy (EIS) was performed under the same conditions, the results showed a good linear relationship between the impedance change value and the bacterial concentration (R 2 = 0.9720), the limit of detection (LOD) was 12 CFU mL-1. The performance of the sensor was compared with that of the colony counting method in the spiked milk sample test. The results showed no significant difference in the test results. Hence, this electrochemical immunosensor can be used to quickly detect S. aureus in actual food samples with a high sensitivity, specificity and stability.

LAMP-on-a-chip: Revising microfluidic platforms for loop-mediated DNA amplification

Nucleic acid amplification for the detection of infectious diseases, food pathogens, or assessment of genetic disorders require a laboratory setting with specialized equipment and technical expertise. Isothermal deoxyribonucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), exhibit characteristics ideal for point-of-care (POC) applications, since their instrumentation is simpler in comparison with the standard method of polymerase chain reaction. Other key advantages of LAMP are robustness and the production of pyrophosphate in the presence of the target gene, enabling to detect the reaction products using the naked eye. Polymerase inhibitors, presented in clinical samples, do not affect the amplification process, making LAMP suitable for a simple sample-to-answer diagnostic systems with simplified sample preparation. In this review, we discuss the trends in miniaturized LAMP techniques, such as microfluidic, paper-based, and digital with their advantages and disadvantages, especially for POC applications alongside our opinion of the future development of miniaturized LAMP.

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Introduction of loop mediated isothermal amplification (LAMP) and its principle.

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Classical microfluidics-based LAMP for DNA/RNA detection.

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Paper-based LAMP.

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Microfluidic-based digital LAMP.

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Future of microfluidic LAMP development.

Bacterial pathogens were detected from human exhaled breath using a novel protocol

It is generally believed that influenza outbreak is associated with breath-borne transmission of viruses, however relevant evidence is little for that of respiratory bacterial infections. On another front, point-of-care infection diagnostic methods at the bedside are significantly lacking. Here, we used a newly developed protocol of integrating an exhaled breath condensate (EBC) collection device (PKU BioScreen) and Loop Mediated Isothermal Amplification (LAMP) to investigate what bacterial pathogens can be directly exhaled out from humans. Exhaled breath condensates were collected from human subjects with respiratory infection symptoms at Peking University 3rd hospital using the BioScreen. The screened bacterial pathogens included Streptococcus pneumoniae, Staphylococcus aureus, Methicillin-resistant Stphylococcus aureus (MRSA), Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Stenotrophomonas maltophilia, Haemophilus influenzae, Legionella pneumophila, Mycoplasma Pneumonia, Chlamydia pneumonia, and Mycobacterium tuberculosis. The results were further compared and validated using throat swabs from the same patients by a PCR method. Here, human bacterial pathogens such as H. influenzae, P. aeruginosa, E. coli, S. aureus and MRSA were detected in exhaled breath using the developed protocol that integrates the EBC collection and LAMP. For the patients recruited from the hospital, seven types of pathogens were detected from 36.5% of them, and for the remaining subjects none of those screened bacterial pathogens was detected. Importantly, some super resistant bacteria such as MRSA were detected from the exhaled breath, suggesting that breathing might be also an important bacterial transmission route. Results from throat swabs showed that 36.2% of the subjects were found to be infected with H. influenzae, P. aeruginosa, E. coli, S. maltophilia, S. aureus and MRSA. For the EBC samples, 33.3% were found to be infected with MRSA, E. coli and P. aeruginosa. Depending on the initial pathogen load in the sample, the entire protocol (EBC-LAMP) only takes 20-60 min to complete for a respiratory infection diagnosis. For different detection methods and pathogens, the agreements between the EBC and throat swabs from the same patients were found to range from 35% to 65%. Here, we have detected several bacterial pathogens including MRSA from exhaled breath, and the developed protocol could be very useful for the bedside pathogen screening particularly in remote areas where resources are significantly limited or prohibited.

Development of a novel loop-mediated isothermal amplification assay for the detection of lipolytic Pseudomonas fluorescens in raw cow milk from north China

Lipases secreted by psychrotrophic bacteria are known to be heat resistant and can remain active even after the thermal processing of milk products. Such enzymes are able to destabilize the quality of milk products by causing a rancid flavor. Rapid detection of a small amount of heat-resistant lipase-producing psychrotrophic bacteria is crucial for reducing their adverse effects on milk quality. In this study, we established and optimized a novel loop-mediated isothermal amplification (LAMP) assay for the detection of Pseudomonas fluorescens in raw cow milk, as the most frequently reported heat-resistant lipase-producing bacterial species. Pseudomonas fluorescens-specific DNA primers for LAMP were designed based on the lipase gene sequence. Reaction conditions of the LAMP assay were tested and optimized. The detection limit of the optimized LAMP assay was found to be lower than that of a conventional PCR-based method. In pure culture, the detection limit of the LAMP assay was found to be 4.8 × 10¹ cfu/reaction of the template DNA, whereas the detection limit of the PCR method was 4.8 × 10² cfu/reaction. Evaluation of the performance of the method in P. fluorescens-contaminated pasteurized cow milk revealed a detection limit of 7.4 × 10¹ cfu/reaction, which was 10² lower than that of the PCR-based method. If further developed, the LAMP assay could offer a favorable on-farm alternative to existing technologies for the detection of psychotrophic bacterial contamination of milk, enabling improved quality control of milk and milk products.

Endonuclease Restriction-Mediated Real-Time Polymerase Chain Reaction: A Novel Technique for Rapid, Sensitive and Quantitative Detection of Nucleic-Acid Sequence

The article reported a novel methodology for real-time PCR analysis of nucleic acids, termed endonuclease restriction-mediated real-time polymerase chain reaction (ET-PCR). Just like PCR, ET-PCR only required one pair of primers. A short sequence, which was recognized by restriction enzyme BstUI, was attached to the 5′ end of the forward (F) or reverse (R) PCR primer, and the new F or R primer was named EF or ER. EF/ER was labeled at the 5′ end with a reporter dye and in the middle with a quenching dye. BstUI cleaves the newly synthesized double-stranded terminal sequences (5′ end recognition sequences and their complementary sequences) during the extension phase, which separates the reporter molecule from the quenching dye, leading to a gain of fluorescence signal. This process is repeated in each amplification cycle and unaffected the exponential synthesis of the PCR amplification. ET-PCR allowed real-time analysis of single or multiple targets in a single vessel, and provided the reproducible quantitation of nucleic acids. The analytical sensitivity and specificity of ET-PCR were successfully evaluated, detecting down to 250 fg of genomic DNA per tube of target pathogen DNA examined, and the positive results were generated in a relatively short period. Moreover, the practical application of ET-PCR for simultaneous detection of multiple target pathogens was also demonstrated in artificially contaminated blood samples. In conclusion, due to the technique’s simplicity of design, reproducible data and low contamination risk, ET-PCR assay is an appealing alternative to conventional approaches currently used for real-time nucleic acid analysis.

A Comparison of In-House Real-Time LAMP Assays with a Commercial Assay for the Detection of Pathogenic Bacteria

Molecular detection of bacterial pathogens based on LAMP methods is a faster and simpler approach than conventional culture methods. Although different LAMP-based methods for pathogenic bacterial detection are available, a systematic comparison of these different LAMP assays has not been performed. In this paper, we compared 12 in-house real-time LAMP assays with a commercialized kit (Isothermal Master Mix) for the detection of Listeria monocytogenes, Salmonella spp, Staphylococcus aureus, Escherichia coli O157, E. coli O26, E. coli O45, E. coli O103, E. coli O111, E. coli O121, E. coli O145 and Streptococcus agalactiae. False-positive results were observed in all 12 in-house real-time LAMP assays, while all the negative controls of Isothermal Master Mix remained negative after amplification. The detection limit of Isothermal Master Mix for Listeria monocytogenes, Salmonella spp, Staphylococcus aureus, Escherichia coli O157, E. coli O26, E. coli O45, E. coli O103, E. coli O111, E. coli O121 and Streptococcus agalactiae was 1 pg, whereas the sensitivity of the commercialized kit for E. coli O145 was 100 pg. In conclusion, the 12 in-house real-time LAMP assays were impractical to use, while the commercialized kit Isothermal Master Mix was useful for the detection of most bacterial pathogens.

Loop-mediated isothermal amplification assay for the rapid detection of Staphylococcus aureus

Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), is an important human pathogen that produces a variety of toxins and causes a wide range of infections, including soft-tissue infections, bacteremia, and staphylococcal food poisoning. A loop-mediated isothermal amplification (LAMP) assay targeting the arcC gene of S. aureus was developed and evaluated with 119 S. aureus and 25 non-S. aureus strains. The usefulness of the assay was compared with the PCR method that targets spa and arcC genes. The optimal temperature for the LAMP assay was 58.5°C with a detection limit of 2.5 ng/μL and 10(2) CFU/mL when compared to 12.5 ng/μL and 10(3) CFU/mL for PCR (spa and arcC). Both LAMP and PCR assays were 100% specific, 100% sensitive, 100% positive predictive value (PPV), and 100% negative predictive value (NPV). When tested on 30 spiked blood specimens (21 MRSA, eight non-S. aureus and one negative control), the performance of LAMP and PCR was comparable: 100% specific, 100% sensitive, 100% PPV, and 100% NPV. In conclusion, the LAMP assay was equally specific with a shorter detection time when compared to PCR in the identification of S. aureus. The LAMP assay is a promising alternative method for the rapid identification of S. aureus and could be used in resource-limited laboratories and fields.