Survey of five food-borne pathogens in commercial cold food dishes and their detection by multiplex PCR

Development and Application of Four Foodborne Pathogens by TaqMan Multiplex Real-Time PCR

A TaqMan multiplex real-time PCR (mRT-PCR) was developed to detect simultaneously Salmonella spp., Escherichia coli O157, Staphylococcus aureus, and Listeria monocytogenes in food samples. The method involves four sets of primers and probes tailored to the unique DNA sequences found in the invA, nuc, rfbE, and hly genes of each pathogen. The generated standard curves, correlating gene copy numbers with Ct values, demonstrated high accuracy (R2 > 0.99) and efficiency (92%-104%). Meanwhile, the limit of detection was 100 CFU/mL for the four target bacteria in artificially contaminated food samples after 6-8 h of enrichment. The assay's effectiveness was further verified by testing 80 naturally contaminated food samples, showing results largely in agreement with traditional culture methods. Overall, this newly developed TaqMan mRT-PCR, inclusive of a pre-enrichment step, proves to be a dependable and effective tool for detecting single or multiple pathogens in diverse food items, offering significant potential for in vitro diagnostics.

Quercetin-Mediated Silver Nanoparticle Formation for the Colorimetric Detection of Infectious Pathogens Coupled with Loop-Mediated Isothermal Amplification

Here, quercetin-mediated silver nanoparticle (AgNP) formation combined with loop-mediated isothermal amplification (LAMP) was introduced to colorimetrically detect two major infectious pathogens, SARS-CoV-2 and Enterococcus faecium, using a foldable PMMA microdevice. The nitrogenous bases of LAMP amplicons can readily form a complex with Ag⁺ ions, and the catechol moiety in quercetin, which acted as a reducing agent, could be chelated with Ag⁺ ions, resulting in the easy electron transfer from the oxidant to the reductant and producing brown-colored AgNPs within 5 min. The introduced method exhibited higher sensitivity than agarose gel electrophoresis due to more active redox centers in quercetin. The detection limit was attained at 10¹ copies μL^-1 and 10¹ CFU mL^-1 for SARS-CoV-2 RNA and E. faecium, respectively. A foldable microdevice made of two pieces of PMMA that fully integrates DNA extraction, amplification, and detection processes was fabricated to establish practical applicability. On one PMMA, DNA extraction was performed in a reaction chamber inserted with an FTA card, and then LAMP reagents were added for amplification. Silver nitrate was added to the reaction chamber after LAMP. On the other PMMA, quercetin-soaked paper discs loaded in the detection chamber were folded toward the reaction chamber for colorimetric detection. An intense brown color was produced within 5 min when heated at 65 °C. The introduced colorimetric assay, which is highly favorable for laboratory and on-site applications, could be a valuable alternative to conventional methods for detecting infectious diseases, given its unique principle, simplicity, and naked-eye detection.

Development and Evaluation of a Next-Generation Sequencing Panel for the Multiple Detection and Identification of Pathogens in Fermented Foods

These days, bacterial detection methods have some limitations in sensitivity, specificity, and multiple detection. To overcome these, novel detection and identification method is necessary to be developed. Recently, NGS panel method has been suggested to screen, detect, and even identify specific foodborne pathogens in one reaction. In this study, new NGS panel primer sets were developed to target 13 specific virulence factor genes from five types of pathogenic Escherichia coli, Listeria monocytogenes, and Salmonella enterica serovar Typhimurium, respectively. Evaluation of the primer sets using singleplex PCR, crosscheck PCR and multiplex PCR revealed high specificity and selectivity without interference of primers or genomic DNAs. Subsequent NGS panel analysis with six artificially contaminated food samples using those primer sets showed that all target genes were multi-detected in one reaction at 10⁸-10⁵ CFU of target strains. However, a few false-positive results were shown at 10⁶-10⁵ CFU. To validate this NGS panel analysis, three sets of qPCR analyses were independently performed with the same contaminated food samples, showing the similar specificity and selectivity for detection and identification. While this NGS panel still has some issues for detection and identification of specific foodborne pathogens, it has much more advantages, especially multiple detection and identification in one reaction, and it could be improved by further optimized NGS panel primer sets and even by application of a new real-time NGS sequencing technology. Therefore, this study suggests the efficiency and usability of NGS panel for rapid determination of origin strain in various foodborne outbreaks in one reaction.

Hydrazone chemistry-mediated CRISPR/Cas12a system for bacterial analysis

In this study, a hydrazone chemistry-mediated clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 12a (Cas12a) system has been proposed for the fist time and constructed. In our system, hydrazone chemistry is designed and employed to accelerate the formation of a whole activation strand by taking advantage of the proximity effect induced by complementary base pairing, thus activating the CRISPR/Cas12a system quickly and efficiently. Moreover, the introduction of hydrazone chemistry can improve the specificity of the CRISPR/Cas12a system, allowing it to effectively distinguish single-base mismatches. The established system has been further applied to analyze Pseudomonas aeruginosa by specific recognition of the probe strand with a characteristic fragment in 16S rDNA to release the hydrazine group-modified activation strand. The method shows a wide linear range from 3.8 × 10² colony-forming units (CFU)/ml to 3.8 × 10⁶ CFU/ml, with the lowest detection limit of 24 CFU/ml. Therefore, the introduction of hydrazone chemistry may also broaden the application of the CRISPR/Cas12a system.

Evaluation of Microbial Contamination in Cold Dishes and Prevalence of Foodborne Pathogens in Jilin Province

ABSTRACT

This study evaluated the microbial contamination status of cold dishes consumed by residents of Jilin Province and investigated to determine the incidence of four pathogenic bacteria in cold dishes. A total of 300 samples of cold dishes, including meat, vegetable, and mixed products, were collected from three purchasing places: supermarkets, farmers' markets, and mobile vendors. Viable bacteria were isolated using conventional culture methods. After separation, a quick and easy PCR was used to detect Listeria monocytogenes, Staphylococcus aureus, enterotoxigenic Escherichia coli, and Salmonella. The results showed that the total number of microbial colonies in the vegetable samples exceeded the standard rate of 8% and the total number of microbial colonies in the meat and mixed samples did not exceed the standard. The total microbial colony count exceeded the standard in all three procurement sites, with the highest exceedance of 7.4% in the mobile vendor sites. The detection rates of enterotoxigenic E. coli, S. aureus, L. monocytogenes, and Salmonella, among the four pathogenic bacteria detected in all samples, were 4.3, 3.3, 3.0, and 1.0%, respectively. This study can be used to qualitatively assess the microbiological quality associated with cold dishes. It provides data to support the detection of possible food safety problems.

HIGHLIGHTS

Risk factors for sporadic listeriosis in Beijing, China: A matched case-control study

Listeriosis is a rare but serious foodborne disease caused by Listeria monocytogenes . This matched case–control study (1:1 ratio) aimed to identify the risk factors associated with food consumption and food-handling habits for the occurrence of sporadic listeriosis in Beijing, China. Cases were defined as patients from whom Listeria was isolated, in addition to the presence of symptoms, including fever, bacteraemia, sepsis and other clinical manifestations corresponding to listeriosis, which were reported via the Beijing Foodborne Disease Surveillance System. Basic patient information and possible risk factors associated with food consumption and food-handling habits were collected through face-to-face interviews. One hundred and six cases were enrolled from 1 January 2018 to 31 December 2020, including 52 perinatal cases and 54 non-perinatal cases. In the non-perinatal group, the consumption of Chinese cold dishes increased the risk of infection by 3.43-fold (95% confidence interval 1.27–9.25, χ 2 = 5.92, P = 0.02). In the perinatal group, the risk of infection reduced by 95.2% when raw and cooked foods were well-separated (χ 2 = 5.11, P = 0.02). These findings provide important scientific evidence for preventing infection by L. monocytogenes and improving the dissemination of advice regarding food safety for vulnerable populations.

Touchable 3D hierarchically structured polyaniline nanoweb for capture and detection of pathogenic bacteria

A bacteria-capturing platform is a critical function of accurate, quantitative, and sensitive identification of bacterial pathogens for potential usage in the detection of foodborne diseases. Despite the development of various nanostructures and their surface chemical modification strategies, relative to the principal physical contact propagation of bacterial infections, mechanically robust and nanostructured platforms that are available to capture bacteria remain a significant problem. Here, a three-dimensional (3D) hierarchically structured polyaniline nanoweb film is developed for the efficient capture of bacterial pathogens by hand-touching. This unique nanostructure ensures sufficient mechanical resistance when exposed to compression and shear forces and facilitates the 3D interfacial interactions between bacterial extracellular organelles and polyaniline surfaces. The bacterial pathogens (Escherichia coli O157:H7, Salmonella enteritidis, and Staphylococcus aureus) are efficiently captured through finger-touching, as verified by the polymerase chain reaction (PCR) analysis. Moreover, the real-time PCR results of finger-touched cells on a 3D nanoweb film show a highly sensitive detection of bacteria, which is similar to those of the real-time PCR using cultured cells without the capturing step without any interfering of fluorescence signal and structural deformation during thermal cycling.

A fluorescence biosensor for Salmonella typhimurium detection in food based on the nano-self-assembly of alendronic acid modified upconversion and gold nanoparticles

A simple and quick-response fluorescent biosensor for Salmonella typhimurium detection based on the recognition of an aptamer coupled with alendronic acid (ADA)@upconversion nanoparticles (UCNPs) and gold nanoparticles (AuNPs) has been developed. Briefly, the aptamer can adsorb on the surfaces of the AuNPs via a "Au-S" bond to protect the AuNPs from aggregation in highly concentrated salt solution. Then, the AuNPs and UCNPs are linked by electrostatic adsorption, which leads to a decrease in the fluorescence peak at 541 nm based on fluorescence resonance energy transfer (FRET) between the UCNPs and AuNPs. In the presence of Salmonella typhimurium, the "Au-S" bond was broken, and the fluorescence intensity at 541 nm was recovered. Under optimal conditions, the correlation between the concentration of S. typhimurium and the intensity of the fluorescent biosensor signals was observed to be linear within the range of 1.16 × 10² to 1.16 × 10⁷ CFU mL^-1 (R² = 0.9912), and the detection limit of the developed biosensor was observed to be 36 CFU mL^-1. Furthermore, the proposed method was successfully used to detect the Salmonella typhimurium pathogen in food samples with satisfactory results.

Magnetic Bead Chain-Based Continuous-Flow DNA Extraction for Microfluidic PCR Detection of Salmonella

Nucleic acid extraction is crucial for PCR detection of pathogenic bacteria to ensure food safety. In this study, a new magnetic extraction method was developed using 3D printing and magnetic silica beads (MSBs) to extract the target DNA from a large volume of bacterial sample and combined with microfluidic PCR to determine the bacteria. After proteinase K was added into a bacterial sample to lyse the bacteria and release the DNA, it was continuous-flow injected into the serpentine channel of the extraction chip, where magnetic silica bead chains had been formed in advance using a homogeneous magnetic field generated by two concentric semicircle magnets to capture the MSBs. Then, the flowing DNA was captured by the MSB chains, washed with alcohol, dried with gas, and eluted with deionized water to obtain the purified and concentrated DNA. Finally, the extracted DNA templates were injected into a microfluidic PCR chip with lyophilized amplification reagents and determined using a commercial qPCR device. The experimental results showed that the DNA extraction efficiency was more than 90%, and the lower detection limit of Salmonella was 10² CFU/mL. This new Salmonella detection method is promising to provide the rapid, sensitive, and simultaneous detection of multiple foodborne pathogens.

Simultaneous detection of Salmonella spp., Pseudomonas aeruginosa, Bacillus cereus, and Escherichia coli O157:H7 in environmental water using PMA combined with mPCR

A multiplex polymerase chain reaction (mPCR) with propidium monoazide (PMA) and internal amplification control (IAC) for the simultaneous detection of waterborne pathogens Salmonella spp., Pseudomonas aeruginosa, Bacillus cereus, and Escherichia coli O157:H7, was developed. This PMA-IAC-mPCR assay used four new specific primers based on the genes for invA, ecfX, cesB, and fliC, respectively. A 16S rRNA primer was chosen for IAC to eliminate false negative results. The photosensitive dye, propidium monoazide (PMA) was used to exclude signals from dead bacteria that could lead to false positive results. In pure culture, the limits of detection (LOD) were 10¹ CFU/ml for P. aeruginosa, 10² CFU/ml for both Salmonella spp. and E. coli O157:H7, and 10³ CFU/ml for B. cereus, respectively. In addition, with a 6-8 h enrichment of all four bacteria that were combined in a mixture that was spiked in water sample matrix, the LOD was 3 CFU/ml for Salmonella spp., 7 CFU/ml for E. coli O157:H7, 10 CFU/ml for B. cereus and 2 CFU/ml for P. aeruginosa. This PMA-IAC-mPCR assay holds potential for application in the multiplex assay of waterborne pathogens.

A Rapid and Sensitive Salmonella Biosensor Based on Viscoelastic Inertial Microfluidics

Salmonella is a main cause of foodborne illnesses and rapid screening of Salmonella is the key to prevent Salmonella outbreaks, however available detection methods either require a long time, or need complex pretreatment, or have low sensitivity. In this study, a microfluidic biosensor was developed for Salmonella detection using viscoelastic inertial microfluidics for separating magnetic bacteria from unbound magnetic nanoparticles (MNPs) and enzyme catalytic colorimetry for amplifying biological signals. The polyclonal antibodies and horseradish peroxidase (HRP) modified MNPs were first used to specifically capture Salmonella to form magnetic HRP-bacteria. Both magnetic HRP-bacteria and unbound MNPs were magnetically separated from background and resuspended in viscoelastic polyvinylpyrrolidone solution as sample flow. When sample flow was injected with polyvinylpyrrolidone sheath flow into a T-shaped microchannel, larger-sized magnetic HRP-bacteria could penetrate the sample flow, however smaller-sized MNPs remained in the sample flow due to weaker inertial lift force and elastic lift force, resulting in continuous-flow separation of magnetic HRP-bacteria. Finally, magnetic HRP-bacteria were collected and concentrated to catalyze tetramethyl benzidine, and absorbance was measured to determine the bacteria. This biosensor was able to detect Salmonella as low as 30 CFU/mL in 1 h and featured the advantages of shorter time due to a one-step immunoreaction, easier extension due to only one antibody and one label, and lower cost due to less expensive materials.

Review of Electrochemical DNA Biosensors for Detecting Food Borne Pathogens

The vital importance of rapid and accurate detection of food borne pathogens has driven the development of biosensor to prevent food borne illness outbreaks. Electrochemical DNA biosensors offer such merits as rapid response, high sensitivity, low cost, and ease of use. This review covers the following three aspects: food borne pathogens and conventional detection methods, the design and fabrication of electrochemical DNA biosensors and several techniques for improving sensitivity of biosensors. We highlight the main bioreceptors and immobilizing methods on sensing interface, electrochemical techniques, electrochemical indicators, nanotechnology, and nucleic acid-based amplification. Finally, in view of the existing shortcomings of electrochemical DNA biosensors in the field of food borne pathogen detection, we also predict and prospect future research focuses from the following five aspects: specific bioreceptors (improving specificity), nanomaterials (enhancing sensitivity), microfluidic chip technology (realizing automate operation), paper-based biosensors (reducing detection cost), and smartphones or other mobile devices (simplifying signal reading devices).

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.

Saltatory rolling circle amplification for sensitive visual detection of Staphylococcus aureus in milk

Monitoring Staphylococcus aureus with high sensitivity is very important for ensuring milk quality and food safety. In this study, we used a rapid nucleic acid isothermal amplification method, saltatory rolling circle amplification (SRCA), for the detection of Staph. aureus in milk. The results of the SRCA method can be assessed visually by the presence of white precipitate or by fluorescence measurement. Thirteen Staph. aureus strains and 31 non-Staph. aureus strains were used to evaluate the specificity of SRCA. The method exhibited excellent detection of Staph. aureus genomic DNA at a concentration of 7.8 × 10¹ fg/µL when assessed by visible precipitate, and at 7.8 × 10⁰ fg/µL when detected by fluorescence after addition of the fluorochrome SYBR Green I. In artificially inoculated milk, the detection limits of SRCA were 5.6 × 10² cfu/mL by precipitate and 5.6 × 10¹ cfu/mL by fluorescence, respectively. Compared with conventional PCR approaches, the SRCA assay achieved at least 100-fold higher sensitivity. Moreover, the sensitivity, specificity, and accuracy of the SRCA-based system were calculated to be 100.00, 97.73, and 97.78%, respectively. These results indicate that SRCA has potential application as a sensitive and visual technique for the detection of Staph. aureus in milk.

Multiplex touchdown PCR assay to enhance specificity and sensitivity for concurrent detection of four foodborne pathogens in raw milk

AIMS

The aim of this study was to develop a multiplex touchdown PCR (multiplex TD-PCR) for rapid and simultaneous detection of four major foodborne pathogens to avoid mispriming and unwanted production during gene amplification. Touchdown PCR is the modified form of standard PCR, which enhances specificity, sensitivity.

METHODS AND RESULTS

For this reason, a multiplex TD-PCR assay with a pre-enrichment step was developed to detect four foodborne pathogens namely Escherichia coli O157:H7, Listeria monocytogenes, Staphylococcus aureus, and Salmonella enterica serovar Enteritidis in pure culture and raw milk samples. The results showed that this protocol can eliminate the unwanted band or reduce significantly. The detection sensitivity of the single and multiplex TD-PCR was one cell per ml in pure culture. Furthermore, the detection limit of multiplex TD-PCR was one cell per 25 ml for artificially contaminated raw milk. We obtained similar results for detection of aforementioned pathogens in raw milk, after comparing the multiplex TD-PCR method with the traditional culture, except in one or two samples.

CONCLUSIONS

Hence, the proposed multiplex TD-PCR method could be confirmed as an effective way for rapid optimization of PCR reactions to increase specificity, sensitivity during gene amplification.

SIGNIFICANCE AND IMPACT OF THE STUDY

Hence, due to its simplicity, cost-effectiveness and being time-saving, it seems that this method is reasonable and economical for rapid optimization of PCR reactions.

Developing a multiplex real-time PCR with a new pre-enrichment to simultaneously detect four foodborne bacteria in milk

Aim: The aim of this study is to formulate a new single nonselective pre-enrichment medium (ELSS) that can support the concurrent growth of four major foodborne pathogens containing E. coli O157: H7, L. monocytogenes, S. aureus and S. enterica serovar Entertidis to develop a multiplex TaqMan Real-time PCR (mRT-PCR). Methods: The mRT-PCR with a new pre-enrichment was carried out for simultaneous detection and quantification of these foodborne bacteria. Results: By using mRT-PCR after 16 h pre-enrichment in ELSS, the detection limit of each pathogen was 1 CFU/25 ml contaminated milk, as well as inclusivity and exclusivity reached 100%. Conclusion: The mRT-PCR assay with pre-enrichment step is a fast and reliable technique for detecting single or multiple pathogens in food products.

Rapid and sensitive detection of Staphylococcus aureus assisted by polydopamine modified magnetic nanoparticles

Pathogens cause significant morbidity and mortality to humans. Thus, development of fast and reliable methods for detection and identification of pathogens is urgently needed to increase protection level of public health and ensure the safety of consumers. Herein, a rapid and sensitive method has been developed for Staphylococcus aureus (S. aureus) detection based on the dual role of polydopamine modified magnetic nanoparticles (PDA@Fe₃O₄ NPs) combined with polymerase chain reaction (PCR) and capillary electrophoresis (CE). The core-shell type structure PDA@Fe₃O₄ NPs were prepared, which are spherical, about 152 ± 20 nm in diameter and the PDA shell is about 17.5 ± 1.6 nm. PDA@Fe₃O₄ NPs play a dual role including efficient capture of bacteria and extraction of DNA. In the pH range of 3.0-7.0, the capture efficiency of S. aureus by PDA@Fe₃O₄ NPs was more than 95% in 5 min. The adsorption capacity of the PDA@Fe₃O₄ NPs for S. aureus is 1.2 × 10⁸ cfu mg^-1. The efficient capture and concentration of bacteria from large volumes of samples by PDA@Fe₃O₄ NPs avoids the time-consuming culture-enrichment prior to PCR. Interestingly, PDA@Fe₃O₄ NPs were also found to be efficient adsorbents for extraction of genomic DNA from pathogens based on the electrostatic interaction. The process can be finished in 25 min. The PDA@Fe₃O₄ NPs based solid phase extraction combined with PCR and CE allows for detecting the order of 10² cfu mL^-1S. aureus in tap water and orange juice samples. The whole process takes < 5.5 h. The developed method would provide a promising platform for rapid and sensitive detection of pathogens.

Characterization of microbial community composition and pathogens risk assessment in typical Italian-style salami by high-throughput sequencing technology

The structure of microbial communities in a typical Italian-style salami, including bacterial and fungal diversity, was investigated by high-throughput sequencing technology. A total of 6 phyla, 7 classes, 19 orders, 20 families and 28 genera were obtained from 16S rDNA sequences, and a total of 2 phyla, 4 classes, 4 orders, 5 families, 10 genera and 12 Species were obtained from 18S rDNA sequences. The core microbiota was composed of Staphylococcaceae, representing up to 97.52% of the total 16S rRNA, and Penicillium digitatum, accounting for 99.74% of the total classified 18S rRNA. Lactobacillales and Saccharomycetales were detected with a quite low proportion of 1.71 and 0.007%, respectively. This study contributes to the knowledge of the microbial diversity involved in salami and presents high-throughput sequencing as a useful tool to evaluate microbial diversity and monitor the food-borne pathogens in fermented sausage.

Multiplex PCR assay and lyophilization for detection of Salmonella spp., Staphylococcus aureus and Bacillus cereus in pork products

Multiplex PCR (m-PCR) has the potential for more rapid detection of pathogens compared to simple PCR through the simultaneous amplification of multiple gene targets using several sets of specific primers. Here, we developed an m-PCR assay which combined dry reagent mixtures for ready-to-use simultaneous detection of Salmonella spp., Bacillus cereus, and Staphylococcus aureus. The assay did not show cross-reactivity with several common bacterial pathogens and the detection limit was 10³ CFU/mL for mixed genomic DNA in pure culture. Lyophilized m-PCR reagents are stable for 2 months stored at 4 °C and for 1 month stored at 25 °C. Detection sensitivities of both dry and fresh mixes were able to simultaneously detect 10 CFU/mL of each pathogen in artificially inoculated samples after enrichment for 6 and 12 h. Results demonstrated that this method is both sensitive and specific and can be used for rapid detection and differentiation of foodborne diseases.