Real-time reverse-transcriptase PCR for Salmonella Typhimurium detection from lettuce and tomatoes

Rapid and broad-spectrum detection of salmonella in various environments by magnetic enrichment-surface enhanced Raman spectroscopy

Rapid, accurate, and broad-spectrum detection of pathogenic bacteria in food is very important and an emerging need for increasing food safety concerns. Here, we present an ultrasensitive Surface-enhanced Raman spectroscopy (SERS) based aptasensor, which consists of core-shell structure (Ag@Au) and magnetic composites (Fe3O4@Au@Ag). 4-mercaptobenzoic acid (4MBA) as Raman reporter was embedded in Ag@Au nanoparticles (Ag@4MBA@Au) based on an internal standard. The combination of Ag@4MBA@Au and Fe3O4@Au@Ag are used to form the aptasensor with strongest Raman signal. Upon exposure to salmonella, the interaction between the SERS nanotags and the magnetic substrate was disrupted, causing an inverse correlation between the Raman intensity of 4MBA and the salmonella concentration. The result shows a wide linear range from 10 to 108 cfu/mL with five subtypes salmonella (S. Typhimurium, S. Enteritidis, S. Kentucky, S. Indiana, S. NO) and a low limit of detection of 1.782, 1.637, 1.941, 1.632, 1.875 cfu/mL, respectively. When applied to the detection of salmonella in actual samples (lake water, milk, shrimp), no pretreatment is required, and the results show no significant difference compared to the standard.

Colorimetric dual DNAzyme reaction triggered by loop-mediated isothermal amplification for the visual detection of Shiga toxin-producing Escherichia coli in food matrices

Shiga toxin-producing Escherichia coli (STEC) is causing outbreaks worldwide and a rapid detection method is urgently needed. Loop-mediated isothermal amplification (LAMP) has attracted attention in the development of pathogen detection methods; however, current methods for the detection of LAMP amplicon suffer some drawbacks. In this study, we designed a new LAMP method by incorporating peroxidase-mimicking G-quadruplex DNAzyme for a simple colorimetric detection of the LAMP amplicon. As the new method produces LAMP amplicon containing two DNAzyme molecules per amplification unit, the method was termed colorimetric Dual DNAzyme LAMP (cDDLAMP). cDDLAMP was developed targeting 3 common STEC's virulence genes (stx1, stx2, and eae) that are associated with serious human illnesses such hemorrhagic colitis and hemolytic-uremic syndrome. Immunomagnetic enrichment was used for specific, ultrasensitive, and fast detection of STEC in food samples (leafy vegetables and milk). The sensitivity of cDDLAMP ranged from 1-100 CFU/mL in pure culture to 100-103 CFU/mL in spiked milk, and 104-109 CFU/25g of lettuce. No cross-reaction with other generic E. coli strains and non-E. coli bacteria was observed. The color signal could be observed by the naked eye or analyzed by either UV-Vis spectra or smartphone platforms. Therefore, the cDDLAMP assay is a cost-effective method for detecting STEC strains without expensive machines or extraction methods.

Colorimetric and electrochemical analysis of DNAzyme-LAMP amplicons for the detection of Escherichia coli in food matrices

Foodborne bacteria like Escherichia coli threaten global food security, necessitating affordable, on-site detection methods, especially in resource-limited settings. This study optimized loop-mediated isothermal amplification (LAMP) integrated with peroxidase-mimicking G-quadruplex DNA structures (DNAzyme), termed DNAzyme-LAMP which was designed to incorporate two different catalytic DNAzymes per amplification unit, enabling colorimetric detection of E. coli in leafy vegetables and milk samples. Additionally, we introduce a novel electrochemical method that enhances analytical sensitivity. The optimized DNAzyme-LAMP achieved a detection limit below 6.3 CFU per reaction or 0.1 aM gene copies. This system lays the groundwork for the development of on-site biosensors and can be adapted for detecting other foodborne pathogens.

NMR Immunosensor Based on a Targeted Gadolinium Nanoprobe for Detecting Salmonella in Milk

Detecting harmful pathogens in food is not only a crucial aspect of food quality management but also an effective way to ensure public health. In this paper, a complete nuclear magnetic resonance biosensor based on a novel gadolinium (Gd)-targeting molecular probe was developed for the detection of Salmonella in milk. First, streptavidin was conjugated to the activated macromolecular polyaspartic acid (PASP) via an amide reaction to generate SA-PASP. Subsequently, the strong chelating and adsorption properties of PASP toward the lanthanide metal gadolinium ions were exploited to generate the magnetic complex (SA-PASP-Gd). Finally, the magnetic complex was linked to biotinylated antibodies to obtain the bioprobe and achieve the capture of Salmonella. Under optimal experimental conditions, the sensor we have constructed can achieve a rapid detection of Salmonella within 1.5 h, with a detection limit of 7.1 × 103 cfu mL-1.

Rapid detection of Salmonella enterica in leafy greens by a novel DNA microarray-based PathogenDx system

The diverse matrices pose great challenges for rapid detection of low Salmonella level (<10 CFU) in fresh produce. The applicability of microarray-based PathogenDx system for detecting low contamination of Salmonella Newport from leafy greens was evaluated. A pre-PCR preparation protocol including enrichment in universal pre-enrichment broth for 3 h followed by sample concentration using an InnovaPrep bio-concentrator or 6 h enrichment without a concentration step was used for detecting S. Newport from leafy greens with initial inoculum level at ∼6 CFU/25 g. Among 205 samples tested, 98%, 93%, 76%, and 60% of Romaine lettuce, Iceberg lettuce, kale, and spinach samples were tested positive after 3 h of enrichment with sample concentration. After 6 h of enrichment, 100%, 98%, 90%, and 82% of Romaine lettuce, Iceberg lettuce, kale, and spinach samples were positive. The samples were parallelly tested by the FDA bacterial analytical manual (BAM) method and 100% of spiked produce samples were tested positive. The overall analysis time of this methodology was between 8 and 11 h, including all pre-enrichment and concentration steps, in contrast to 4-5 days required for BAM method. The system correctly differentiated all 108 Salmonella strains and 35 non-Salmonella strains used in the study. This novel microarray approach provides a rapid method for detecting Salmonella in leafy greens.

Switchgrass extractives to mitigate Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium contamination of romaine lettuce at pre- and postharvest

The antimicrobial potential of switchgrass extractives (SE) was evaluated on cut lettuce leaves and romaine lettuce in planta, using rifampicin-resistant Escherichia coli O157:H7 and Salmonella Typhimurium strain LT2 as model pathogens. Cut lettuce leaves were swabbed with E. coli O157:H7 or S. Typhimurium followed by surface treatment with 0.8% SE, 0.6% sodium hypochlorite, or water for 1 to 45 min. For in planta studies, SE was swabbed on demarcated leaf surfaces either prior to or after inoculation of greenhouse-grown lettuce with E. coli O157:H7 or S. Typhimurium; the leaf samples were collected after 0, 24, and 48 h of treatment. Bacteria from inoculated leaves were enumerated on tryptic soy agar plates (and also on MacConkey's and XLT4 agar plates), and the recovered counts were statistically analyzed. Cut lettuce leaves showed E. coli O157:H7 reduction between 3.25 and 6.17 log CFU/leaf, whereas S. Typhimurium reductions were between 2.94 log CFU/leaf and 5.47 log CFU/leaf depending on the SE treatment durations, from initial levels of ∼7 log CFU/leaf. SE treatment of lettuce in planta, before bacterial inoculation, reduced E. coli O157:H7 and S. Typhimurium populations by 1.88 and 2.49 log CFU after 24 h and 3 h, respectively. However, SE treatment after bacterial inoculation of lettuce plants decreased E. coli O157:H7 populations by 3.04 log CFU (after 0 h) with negligible reduction of S. Typhimurium populations. Our findings demonstrate the potential of SE as a plant-based method for decontaminating E. coli O157:H7 on lettuce during pre- and postharvest stages in hurdle approaches.

Biosensors, modern technology for the detection of cancer-associated bacteria

Cancer is undoubtedly one of the major human challenges worldwide. A number of pathogenic bacteria are deemed to be potentially associated with the disease. Accordingly, accurate and specific identification of cancer-associated bacteria can play an important role in cancer control and prevention. A variety of conventional methods such as culture, serology, and molecular-based methods as well as PCR and real-time PCR have been adopted to identify bacteria. However, supply costs, machinery fees, training expenses, consuming time, and the need for advanced equipment are the main problems with the old methods. As a result, advanced and modern techniques are being developed to overcome the disadvantages of conventional methods. Biosensor technology is one of the innovative methods that has been the focus of researchers due to its numerous advantages. The main purpose of this study is to provide an overview of the latest developed biosensors for recognizing the paramount cancer-associated bacteria.

Use of Direct PCR Technique Without DNA Extraction in Confirmation Test for Salmonella typhimurium Bacteria on Meatball Samples

The use of direct PCR technique without DNA extraction in the confirmation test for Salmonella typhimurium ATCC 14028 bacteria on meatball samples was carried out in the Food and Drug molecular biology testing laboratory Administration in Gorontalo. The basis of this research is to have an impact on economic value in carrying out the confirmation test for S. typhimurium ATCC 14028, where testing is carried out conventionally, namely DNA extraction, which requires a large amount of money. Hence, it is necessary to innovate to modify the testing phase so that it is more effective and efficient. The purpose of this study was to see whether the direct PCR technique without DNA extraction can be done for the confirmation test of S. typhimurium ATCC 14028 on meatball samples. This study's sample consisted of 20 types of meatball samples spiked with S. typhimurium ATCC 14028 cultures. The method used in this study was qPCR analysis using the SYBR Green method. Data analysis was carried out based on 2 main criteria: (1) Ct analysis and (2) Tm analysis. Real-time PCR analysis results obtained Ct values ​​in the range 14.14 - 15.20 with an average of 14.82 and Tm values ​​85.20 - 86.30 with an average of 85.79. Based on these data, it can be concluded that using direct PCR can be used for testing confirmation of S. typhimurium ATCC 14028 on meatball samples.

Propidium monoazide for viable Salmonella enterica detection by PCR and LAMP assays in comparison to RNA-based RT-PCR, RT-LAMP, and culture-based assays

Rapid and sensitive detection of live/infectious foodborne pathogens is urgently needed in order to prevent outbreaks and food recalls. This study aimed to (1) evaluate the incorporation of propidium monoazide (PMA) into PCR or LAMP assays to selectively detect viable Salmonella Enteritidis following sublethal heat or UV treatment, and autoclave sterilization; and (2) compare the detection of PMA-PCR and PMA-LAMP to DNA-based PCR and LAMP (without PMA), RNA-based RT-PCR and RT-LAMP, and culture-based methods. Nucleic acids (DNA or RNA) from 1-mL S. Enteritidis samples were used for PCR, RT-PCR, LAMP, and RT-LAMP assays. Serially diluted samples were plated on Xylose Lysine Tergitol-4 agar for cultural enumeration. Comparable detection of overnight cultured S. Enteritidis was obtained by PMA-PCR, PCR, and RT-PCR, though 1 to 2 log less sensitive than cultural assays. PMA-LAMP and RT-LAMP showed similar detection of overnight cultures, being 1 to 2 log less sensitive than the LAMP assay, and ∼4 log less than culture-based detection. Autoclaved S. Enteritidis did not test positive by RNA-based methods or PMA-PCR, but PMA-LAMP showed detection of 1 log CFU/mL. PMA-PCR and RT-PCR showed comparable detection of sublethal heat-treated cells to cultural assays, while PMA-LAMP showed 1 to 2 log less detection. Our results suggest that PMA-PCR and PMA-LAMP assays are not suitable for selective viable cell detection after UV treatment. While PMA-LAMP assay needs optimization, PMA-PCR shows promise for live/viable S. Enteritidis detection. PMA-PCR shows potential for routine testing in the food industry with results within 1-day, albeit depending on the inactivation method employed.

Checkpoint enrichment for sensitive detection of target bacteria from large volume of food matrices

A gap in biosensor development is the ability to enrich and detect targets in large sample volumes in a complex matrix. To bridge this gap, our goal in this work is to propose a practical strategy, termed as checkpoint-style enrichment, for rapid enrichment of the target bacteria from large volume of food samples with particulates and evaluate its enrichment and improvement in detection. The checkpoint-style enrichment was conducted with antibody modified polyethylene terephthalate (PET) pads as capture substrates. In our approach, blended lettuce sample cocktail was circulated through antibody modified PET pads such as a checkpoint in the sample solution pathway, where target pathogens were selectively captured with immobilized antibodies. The obtained PET pads with the captured target pathogens were then used for enhanced detection by colorimetry. To render the checkpoint-style enrichment approach practical and applicable for on-site rapid screening tests, only a simple syringe-based setup with antibody modified PET pad was required. The developed method could process up to 50 ml of lettuce cocktail blended from 5g samples and purposefully inoculated with E. coli O157:H7. Overall, the enrichment method developed required only 40 min of sample processing time. After enrichment, as low as 100 CFU/ml of E. coli O157:H7 could be detected by a simple colorimetric procedure due to the enhancement from the proposed checkpoint-style enrichment in the presence of ∼3000 CFU/ml of non-target bacteria. A linear response was obtained from blank to 100000 CFU/ml of E. coli O157:H7 in blended lettuce samples. The conceptualized approach demonstrates a promising means to improve the detection of target bacteria with a high degree of sensitivity and specificity and could be used in low resourse settings.

A microfluidic biosensor for online and sensitive detection of Salmonella typhimurium using fluorescence labeling and smartphone video processing

Early screening of foodborne pathogens is a key to ensure food safety. In this study, we developed a microfluidic biosensor for online and sensitive detection of Salmonella based on immunomagnetic separation, fluorescence labeling and smartphone video processing. First, the immune magnetic nanoparticles were used to specifically separate and efficiently concentrate the target bacteria and the magnetic bacteria were formed. Then, the magnetic bacteria were labeled with the immune fluorescent microspheres and the fluorescent bacteria were formed. Finally, the fluorescent bacteria were continuously injected into the microfluidic chip on the smartphone-based fluorescent microscopic system, and the fluorescent spots were online counted using the smartphone App based on inter-frame difference algorithm to obtain the amount of the target bacteria. Under the optimal conditions, this proposed biosensor was able to quantitatively detect Salmonella typhimurium ranging from 1.4 × 10² to 1.4 × 10⁶ CFU/mL, and its lower detection limit was 58 CFU/mL. This biosensor could be extended for detection of multiple foodborne pathogens using different fluorescent materials.

A Novel qPCR Method for Simultaneous Detection and Quantification of Viable Pathogenic and Non-pathogenic Vibrio parahaemolyticus (tlh+ , tdh+ , and ureR + )

Pathogenic and non-pathogenic Vibrio parahaemolyticus strains were simultaneously detected and quantified using a novel viable multiplex real-time PCR (novel qPCR). We used a new PCR primer and probe, ureR, as a surrogate for detection of the toxin trh gene as the primer was better at identifying variant V. parahaemolyticus trh strains. The specificity of all primers and probes used in this study were validated on three standard strains of V. parahaemolyticus, 42 clinical strains, 12 wild strains, 4 strains of Vibrio spp., and 4 strains of other bacteria. Then, propidium monoazide (PMA) was applied to inhibit DNA of dead cell, and the results of PMA optimized treatments were 15 μM concentration, 5 min incubation periods, 15 min light exposure periods and 30 RPM rotational speed, which resulted in time and cost savings. Pathogenic and non-pathogenic strains were quantified using a two-reaction tube method where the tlh, tdh, and ureR genes were amplified. Additionally, standard curves with a 7-log dynamic range were generated for quantifying viable V. parahaemolyticus and the amplification efficiencies were 108.68, 105.17, and 115.61% for tlh⁺, tdh⁺, and ureR⁺. This novel qPCR accurately monitored V. parahaemolyticus contamination rates in shrimps (Penaeus vannamei) and clams (Ruditapes philippinarum) sampled from retail stores located in a major district in Shanghai. In conclusion, our assay can prioritize the detection and quantification of viable pathogenic V. parahaemolyticus and can prove to be a more effective tool for reducing infection risks from consumption of seafood in Shanghai.

Recombinant plasmid-based quantitative Real-Time PCR analysis of Salmonella enterica serotypes and its application to milk samples

The aim of the current study was to develop, a new, rapid, sensitive and quantitative Salmonella detection method using a Real-Time PCR technique based on an inexpensive, easy to produce, convenient and standardized recombinant plasmid positive control. To achieve this, two recombinant plasmids were constructed as reference molecules by cloning the two most commonly used Salmonella-specific target gene regions, invA and ttrRSBC. The more rapid detection enabled by the developed method (21 h) compared to the traditional culture method (90 h) allows the quantitative evaluation of Salmonella (quantification limits of 10(1)CFU/ml and 10(0)CFU/ml for the invA target and the ttrRSBC target, respectively), as illustrated using milk samples. Three advantages illustrated by the current study demonstrate the potential of the newly developed method to be used in routine analyses in the medical, veterinary, food and water/environmental sectors: I--The method provides fast analyses including the simultaneous detection and determination of correct pathogen counts; II--The method is applicable to challenging samples, such as milk; III--The method's positive controls (recombinant plasmids) are reproducible in large quantities without the need to construct new calibration curves.

A microfluidic nano-biosensor for the detection of pathogenic Salmonella

Rapid detection of pathogenic Salmonella in food products is extremely important for protecting the public from salmonellosis. The objective of the present study was to explore the feasibility of using a microfluidic nano-biosensor to rapidly detect pathogenic Salmonella. Quantum dot nanoparticles were used to detect Salmonella cells. For selective detection of Salmonella, anti-Salmonella polyclonal antibodies were covalently immobilized onto the quantum dot surface. To separate and concentrate the cells from the sample, superparamagnetic particles and a microfluidic chip were used. A portable fluorometer was developed to measure the fluorescence signal from the quantum dot nanoparticles attached to Salmonella in the samples. The sensitivity for detection of pathogenic Salmonella was evaluated using serially diluted Salmonella Typhimurium in borate buffer and chicken extract. The fluorescence response of the nano-biosensor increased with increasing cell concentration. The detection limit of the sensor was 10(3) CFU/mL Salmonella in both borate buffer and food extract.

An aptamer-based electrochemical biosensor for the detection of Salmonella

Salmonella is one of the most common causes of food-associated disease. An electrochemical biosensor was developed for Salmonella detection using a Salmonella-specific recognition aptamer. The biosensor was based on a glassy carbon electrode modified with graphene oxide and gold nanoparticles. Then, the aptamer ssDNA sequence could be linked to the electrode. Each assembly step was accompanied by changes to the electrochemical parameters. After incubation of the modified electrode with Salmonella, the electrochemical properties between the electrode and the electrolyte changed accordingly. The electrochemical impedance spectrum was measured to quantify the Salmonella. The results revealed that, when more Salmonella were added to the reaction system, the current between the electrode and electrolyte decreased; in other words, the impendence gradually increased. A detection limit as low as 3 cfu/mL was obtained. This novel method is specific and fast, and it has the potential for real sample detection.

A one-step homogeneous sandwich immunosensor for Salmonella detection based on magnetic nanoparticles (MNPs) and quantum Dots (QDs)

Simple immuno-magnetic separation tandem fluorescent probes based on quantum dots-antibody (QDs-Ab) were developed to detect Salmonella with sensitivity of 500 cfu mL-1. With two monoclonal antibodies, which recognize different antigenic determinant on the surface of Salmonella, we prepared antibody-coated magnetic nanoparticles (MNPs) and conjugates of QDs-Ab. The immune-magnetic beads were verified with high enrichment efficiency for Salmonella (90%). A sandwich structure formed if the Salmonella solution was mixed together with immune-beads and QDs-Ab, and the fluorescent single from QDs was related to the amount of Salmonella. A linear response between fluorescence intensity and various concentrations of Salmonella (2.5 × 103 to 1.95 × 108 cfu mL-1) were observed with this proposed method. The total assay time for Salmonella was 30 min, and no cross-reaction to other microbial strains, such as Staphylococcus aureus, Escherichia coli (E. coli) and Escherichia coli O157:H7 (E. coli O157:H7), were found using this detection system. All our results showed that the simple homogeneous immunoassay could be applied in Salmonella screening without time-consuming extra-enrichment of bacteria.

Development and application of reverse transcription loop-mediated isothermal amplification for detecting live Shewanella putrefaciens in preserved fish sample

Given that live Shewanella putrefaciens is one of the major causes of spoilage for aquatic products even in chill storage, the rapid and accurate detection process is the first priority. In the present study, a novel reverse transcription loop-mediated isothermal amplification (RT-LAMP) detecting assay was developed by targeting internal transcribed spacer (ITS) sequence between 16S and 23S rRNA. At the same time, a new procaryotic mRNA isolation strategy was also established by introducing a polyA tail to RNA during cDNA synthesis step. Under the optimal reaction time (60 min) and temperature (64.1 °C), S. putrefaciens could be specially identified from a variety of other tested bacteria by RT-LAMP. The sensitivity analysis showed that RT-LAMP could be identified as lower as 5.4 copies per reaction, which is over 200-fold higher than that of standard PCR (1.08 × 10³ copies per reaction). The method could be effectively identified S. putrefaciens in artificially contaminated or spoilaged fish samples with dose-dependent manners. To our knowledge, this is the first report using RT-LAMP assay to detect live S. putrefaciens in fish.

PRACTICAL APPLICATION

The study provided a rapid and accurate detection method for live bacteria in aquatic food and established a new procaryotic mRNA isolation strategy at the same time, which will be useful for food preservation.