Development of a multiplex real-time PCR method for simultaneous detection of Vibrio parahaemolyticus, Listeria monocytogenes and Salmonella spp. in raw shrimp

A Stand-Off Laser-Induced Breakdown Spectroscopy (LIBS) System for Remote Bacteria Identification

Bacteria are the primary cause of infectious diseases, making rapid and accurate identification crucial for timely pathogen diagnosis and disease control. However, traditional identification techniques such as polymerase chain reaction and loop-mediated isothermal amplification are complex, time-consuming, and pose infection risks. This study explores remote (~3 m) bacterial identification using laser-induced breakdown spectroscopy (LIBS) with a Cassegrain reflective telescope. Principal component analysis (PCA) was employed to reduce the dimensionality of the LIBS spectral data, and the accuracy of support vector machine (SVM) and Random Forest (RF) algorithms was compared. Multiple repeated experiments showed that the RF model achieved a classification accuracy, recall, precision, and F1-score of 99.81%, 99.80%, 99.79%, and 0.9979, respectively, outperforming the SVM model and providing more accurate remote bacterial identification. The method based on laser-induced plasma spectroscopy and machine learning has broad application prospects, supporting noncontact disease diagnosis, improving public health, and advancing medical research and technological development.

Modeling naturally-occurring Vibrio parahaemolyticus in post-harvest raw shrimps

There is little known about the growth and survival of naturally-occurring Vibrio parahaemolyticus in harvested raw shrimps. In this study, the fate of naturally-occurring V. parahaemolyticus in post-harvest raw shrimps was investigated from 4℃ to 30℃ using real-time PCR combined with propidium monoazide (PMA-qPCR). The Baranyi-model was used to fit the growth and survival data. A square root model and non-linear Arrhenius model was then used to quantify the parameters derived from the Baranyi-model. The results showed that naturally-occurring V. parahaemolyticus were slowly inactivated at 4℃ and 7℃ with deactivation rates of 0.019 Log CFU/g/h and 0.025 Log CFU/g/h. Conversely, at 15, 20, 25, and 30 °C, the average maximum growth rates (μmax) of naturally-occurring V. parahaemolyticus were determined to be 0.044, 0.105, 0.179 and 0.336 Log CFU/g/h, accompanied by the average lag phases (λ) of 15.5 h, 7.3 h, 4.4 h and 3.7 h. The validation metrics, Af and Bf, for both the square root model and non-linear, indicating that the model had a good ability to predict the growth behavior of naturally-occurring V. parahaemolyticus in post-harvest raw shrimps. Furthermore, a comparative exploration between the growth of artificially contaminated V. parahaemolyticus in cooked shrimps and naturally-occurring V. parahaemolyticus in post-harvest raw shrimps revealed intriguing insights. While no substantial distinction in deactivation rates emerged at 4 °C and 7 °C (P > 0.05), a discernible disparity in growth rates was observable at 15 °C, 20 °C, 25 °C, and 30 °C, with the former surpassing the latter. Which indicated the risk of V. parahaemolyticus using models derived from cooked shrimps may be biased. Our study also unveiled a discernible seasonal effect. The μmax and λ of V. parahaemolyticus in shrimps harvested in summer were similar to those harvested in autumn, while the initial and maximum bacterial concentration harvested in summer were higher than those harvested in autumn. This predictive microbiology model of naturally-occurring V. parahaemolyticus in raw shrimps provides relevance to modelling growth in situ.

Construction of classification models for pathogenic bacteria based on LIBS combined with different machine learning algorithms

Bacteria, especially foodborne pathogens, seriously threaten human life and health. Rapid discrimination techniques for foodborne pathogens are still urgently needed. At present, laser-induced breakdown spectroscopy (LIBS), combined with machine learning algorithms, is seen as fast recognition technology for pathogenic bacteria. However, there is still a lack of research on evaluating the differences between different bacterial classification models. In this work, five species of foodborne pathogens were analyzed via LIBS; then, the preprocessing effect of five filtering methods was compared to improve accuracy. The preprocessed spectral data were further analyzed with a support vector machine (SVM), a backpropagation neural network (BP), and k-nearest neighbor (KNN). Upon comparing the capacity of the three algorithms to classify pathogenic bacteria, the most suitable one was selected. The signal-to-noise ratio and mean square error of the spectral data after applying a Savitzky-Golay filter reached 17.4540 and 0.0020, respectively. The SVM algorithm, BP algorithm, and KNN algorithm attained the highest classification accuracy for pathogenic bacteria, reaching 98%, 97%, and 96%, respectively. The results indicate that, with the support of a machine learning algorithm, LIBS technology demonstrates superior performance, and the combination of the two is expected to be a powerful tool for pathogen classification.

A Review on Metal- and Metal Oxide-Based Nanozymes: Properties, Mechanisms, and Applications

Since the ferromagnetic (Fe3O4) nanoparticles were firstly reported to exert enzyme-like activity in 2007, extensive research progress in nanozymes has been made with deep investigation of diverse nanozymes and rapid development of related nanotechnologies. As promising alternatives for natural enzymes, nanozymes have broadened the way toward clinical medicine, food safety, environmental monitoring, and chemical production. The past decade has witnessed the rapid development of metal- and metal oxide-based nanozymes owing to their remarkable physicochemical properties in parallel with low cost, high stability, and easy storage. It is widely known that the deep study of catalytic activities and mechanism sheds significant influence on the applications of nanozymes. This review digs into the characteristics and intrinsic properties of metal- and metal oxide-based nanozymes, especially emphasizing their catalytic mechanism and recent applications in biological analysis, relieving inflammation, antibacterial, and cancer therapy. We also conclude the present challenges and provide insights into the future research of nanozymes constituted of metal and metal oxide nanomaterials.

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.

A turn-on-type fluorescence resonance energy transfer aptasensor for vibrio detection using aptamer-modified polyhedral oligomeric silsesquioxane-perovskite quantum dots/Ti3C2 MXenes composite probes

A pair of composite probes based on aptamer modified polyhedral oligomeric silsesquioxane-perovskite quantum dots (POSS-PQDs-Apt) as signal probe and titanium carbide (Ti₃C₂) MXenes as quencher were prepared for the first time. They were employed to fabricate one turn-on-type aptasensor relying on fluorescence resonance energy transfer (FRET) for Vibrio parahaemolyticus (VP) determination. The POSS-PQDs-Apt can be adsorbed on the MXenes nanosheets, and its fluorescence was quenched due to the FRET. After the composite probes were incubated with VP for 50 min, the POSS-PQDs-Apt binding with VP can be released from the surface of MXenes, and the signal recovered due to its higher affinity to the VP than MXenes. The fluorescence intensity from 519 nm emission of the system was measured at 480 nm excitation. Under In optimized conditions, the assay can determine VP in the concentration range 10² - 10⁶ cfu/mL, and the detection limit (LOD) was 30 cfu/mL using fluorescence detection. The LOD is still 100 cfu/mL by naked eye detection which is proper for on-line monitoring VP in aquaculture water. This method was also used to detect VP in actual samples of seawater, the recovery of spiked samples was between 93% and 106%, and relative standard deviation (RSD) was between 2.7% and 6.7%. The result is consistent with the plate count. Therefore, this assay could provide a candidate platform for screening VP in aquaculture industry.

Chitosan-riboflavin composite film based on photodynamic inactivation technology for antibacterial food packaging

Photodynamic inactivation (PDI) is a novel sterilization technology that has proven effective in medicine. This study focused on applying PDI to food packaging, where chitosan (CS) films containing photosensitizing riboflavin (RB) were prepared via solution casting. The CS-RB composite films exhibited good ultraviolet (UV)-barrier properties, and had a visually appealing highly transparent yellow appearance. Scanning electron microscopy (SEM) confirmed even dispersion of RB throughout the CS film. The addition of RB led to improved film characteristics, including the thickness, mechanical properties, solubility, and water barrier properties. The CS-RB⁵ composite films produced sufficient singlet oxygen under blue LED irradiation for 2 h to inactivate two food-borne pathogens (Listeria monocytogenes and Vibrio parahaemolyticus) and one spoilage bacteria (Shewanella baltica). The CS-RB composite films were assessed as a salmon packaging material, where inhibition of bacterial growth was observed. The film is biodegradable, and has the potential to alleviate the issues associated with the excessive use of petrochemical materials, such as environmental pollution and limited resources. The CS-RB composite films showed potential as a novel environmentally friendly packaging material for shelf-life extension of refrigerated food products.

A sensitive SERS-based sandwich immunoassay platform for simultaneous multiple detection of foodborne pathogens without interference

A reliable and sensitive sensing of multiple foodborne pathogens is critical for timely diagnosis and human health. To meet this need, herein, we designed a sandwich immunoassay platform, using functionalized SERS probes and magnetic beads, for the interference-free simultaneous detection of Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) in food samples by surface-enhanced Raman scattering (SERS) technology. The signal of two SERS probes coded by triple bonds (C[triple bond, length as m-dash]C and C[triple bond, length as m-dash]N) located at 2105 and 2227 cm-1, respectively, could perfectly avoid the spectral overlap with coexisting materials in the Raman fingerprint region, which ensured the accuracy of the immunoassay platform. The application of functional magnetic beads, integrating enrichment and separation, greatly improved the sensitivity of the detection system. Under magnetic force, due to the mature interaction between the antigen and antibody, the sandwich immunoassay platform could be fabricated. Its limit of detection (LOD) for the simultaneous detection of E. coli and S. aureus was as low as 10 and 25 cfu mL-1, respectively, and the sandwich immunoassay platform was successfully applied for the detection of E. coli and S. aureus in bottled water and milk. As a sensitive and highly selective analytical technique for the simultaneous multiple detection of pathogens, this SERS-based method has great potential to be applied in the field of food safety.

Microbial detection and identification methods: Bench top assays to omics approaches

Rapid detection of foodborne pathogens, spoilage microbes, and other biological contaminants in complex food matrices is essential to maintain food quality and ensure consumer safety. Traditional methods involve culturing microbes using a range of nonselective and selective enrichment methods, followed by biochemical confirmation among others. The time-to-detection is a key limitation when testing foods, particularly those with short shelf lives, such as fresh meat, fish, dairy products, and vegetables. Some recent detection methods developed include the use of spectroscopic techniques, such as matrix-assisted laser desorption ionization-time of flight along with hyperspectral imaging protocols.This review presents a comprehensive overview comparing insights into the principles, characteristics, and applications of newer and emerging techniques methods applied to the detection and identification of microbes in food matrices, to more traditional benchtop approaches. The content has been developed to provide specialist scientists a broad view of bacterial identification methods available in terms of their benefits and limitations, which may be useful in the development of future experimental design. The case is also made for incorporating some of these emerging methods into the mainstream, for example, underutilized potential of spectroscopic techniques and hyperspectral imaging.

Multiplex Detection of Salmonella spp., E. coli O157 and L. monocytogenes by qPCR Melt Curve Analysis in Spiked Infant Formula

Food poisoning continue to be a threat in the food industry showing a need to improve the detection of the pathogen responsible for the hospitalization cases and death. DNA-based techniques represent a real advantage and allow the detection of several targets at the same time, reducing cost and time of analysis. The development of new methodology using SYBR Green qPCR for the detection of L. monocytogenes, Salmonella spp. and E. coli O157 simultaneously was developed and a non-competitive internal amplification control (NC-IAC) was implemented to detect reaction inhibition. The formulation and supplementation of the enrichment medium was also optimized to allow the growth of all pathogens. The limit of detection (LoD) 95% obtained was <1 CFU/25 g for E. coli O157, and 2 CFU/25 g for Salmonella spp. and L. monocytogenes and regarding the multiplex detection a LoD 95% of 1.7 CFU/25 g was observed. The specificity, relative sensitivity and accuracy of full methodology were 100% and the use of the NC-IAC allowed the reliability of the results without interfering with the sensitivity of the methodology. The described study proved to obtain results comparable to those of probe-based qPCR, and more economically than classical high resolution melting qPCR, being both important aspects for its implementation in the food industry.

A 4-plex Droplet Digital PCR Method for Simultaneous Quantification and Differentiation of Pathogenic and Non-pathogenic Vibrio parahaemolyticus Based on Single Intact Cells

Vibrio parahaemolyticus is a significant seafood-borne pathogen, leading to serious acute gastrointestinal diseases worldwide. In this study, a reliable 4-plex droplet digital PCR (ddPCR) was successfully established and evaluated for the simultaneous detection of V. parahaemolyticus based on tlh, tdh, ureR, and orf8 in food samples using single intact cells. The targets tlh and ureR were labeled with 6-Carboxyfluorescein (FAM), and the targets tdh and orf8 were labeled with 5’-Hexachlorofluorescein (HEX). Due to reasonable proration of primers and probes corresponding into the two fluorescence channels of the ddPCR detecting platforms, the clearly separated 16 (2⁴) clusters based on fluorescence amplitude were obtained. For better results, the sample hot lysis time and the cycle number were optimized. The results showed that the minimum number of “rain” and maximum fluorescence amplification were presented for precise detection in the condition of 25 min of the sample hot lysis time and 55 cycles. The sensitivity of this 4-plex ddPCR assay was 39 CFU/mL, which was in accordance with that of the conventional plate counting and was 10-fold sensitive than that of qPCR. In conclusion, the 4-plex ddPCR assay presented in this paper was a rapid, specific, sensitive, and accurate tool for the detection of V. parahaemolyticus including pandemic group strains and could be applied in the differentiation of V. parahaemolyticus in a wide variety of samples.

A universal signal-on electrochemical assay for rapid on-site quantitation of vibrio parahaemolyticus using aptamer modified magnetic metal-organic framework and phenylboronic acid-ferrocene co-immobilized nanolabel

Sensitive and rapid detection of pathogenic bacteria remains important and challenging for food safety and preventing outbreaks of foodborne disease. The major limitations of standard analytical methods for detecting vibrio parahaemolyticus (V.P) lie in their bulky equipment and tedious and long-time operation. This study presents an electrochemical aptasensor for the rapid on-site quantification of V.P in seafood. Magnetic nanoscale metal-organic frameworks (Fe₃O₄@NMOF) labeled with an aptamer against V.P served as capture probes, while gold nanoparticles combined with phenylboronic acid and ferrocene acted as the nanolabels. When detecting V.P, the sandwich-type complex of capture probe-V.P-nanolabel was formed and magnetically attached to a screen-printed electrode (SPE) for signal measurement. Under optimal conditions, the increase in the ferrocene electrochemical signals could assess the V.P amount; the quantified concentration range was 10-10⁹ cfu/mL. Then, the developed signal-on sensor successfully detected V.P in real seafood samples, exhibiting many advantages. It could not only specifically enrich and rapidly separate the V.P in complex samples but also largely amplify the signal. Moreover, using compact SPE with a detection time of maximum 20 min as the measurement platform allows rapid on-site assays. Thus, the proposed method is a feasible strategy for screening V.P in seafood.

A SERS aptasensor for simultaneous multiple pathogens detection using gold decorated PDMS substrate

An aptamer-based sensitive method was developed here for detection of multiple foodborne pathogens in food matrix by surface-enhanced Raman scattering (SERS) technology. Polydimethylsiloxane (PDMS) film was first prepared and then coated with gold nanoparticles (AuNP) to act as an active substrate for the enhancement of Raman scattering. The as-prepared Au-PDMS film was functionalized with specific pathogen aptamers (Apt) to capture the targets. In addition, aptamers functionalized AuNP integrated with Raman reporters (4-Mercaptobenzoic acid (4-MBA)/Nile blue A (NBA)) were fabricated as pathogen-specific SERS probes. In this scheme, pathogens were first captured by Apt-Au-PDMS film and then bind with SERS probes to allow the formation of a sandwich assay to complete the sensor module for the detection of multiple pathogens. With Vibrio parahaemolyticus and Salmonella typhimurium as model targets, this protocol can selectively detect 18 cfu/mL and 27 cfu/mL, respectively. Furthermore, this platform can be successfully applied to detect pathogens in seafood samples with recoveries ranging from 82.9% to 95.1%.

Multiplex Recombinase Polymerase Amplification Assay for the Simultaneous Detection of Three Foodborne Pathogens in Seafood

Foodborne pathogens can cause foodborne illness. In reality, one food sample may carry more than one pathogen. A rapid, sensitive, and multiple target method for bacteria detection is crucial in food safety. For the simultaneous detection of Staphylococcus aureus, Vibrio parahaemolyticus, and Salmonella Enteritidis, multi-objective recombinase polymerase amplification (RPA) combined with a lateral flow dipstick (LFD) was developed in this study. The whole process, including amplification and reading, can be completed in 15 min at 37 °C. The detection limits were 2.6 × 101 CFU/mL for Staphylococcus aureus, 7.6 × 101 CFU/mL for Vibrio parahaemolyticus, and 1.29 × 101 CFU/mL for Salmonella Enteritidis. Moreover, colored signal intensities on test lines were measured by a test strip reader to achieve quantitative detection for Staphylococcus aureus (R2 = 0.9903), Vibrio parahaemolyticus (R2 = 0.9928), and Salmonella Enteritidis (R2 = 0.9945). In addition, the method demonstrated good recoveries (92.00%-107.95%) in the testing of spiked food samples. Therefore, the multiplex LFD-RPA assay is a feasible method for the rapid, sensitive, and quantitative detection of bacterial pathogens in seafood.

Rapid visualized isothermal nucleic acid testing of Vibrio parahaemolyticus by polymerase spiral reaction

The aim of this study was to develop an effective and specific visual method to rapidly detect and identify Vibrio parahaemolyticus (V. parahaemolyticus) based on the polymerase spiral reaction (PSR). The method utilized only two pairs of primers designed specifically to target the conserved tlh gene sequence of V. parahaemolyticus. Nucleic acid amplification can be achieved under isothermal conditions using DNA polymerase. The reaction could be accomplished in < 40 min with high specificity and sensitivity. The limits of detection of V. parahaemolyticus in purified genomic DNA and pure culture were 300 fg/μL and 2.4 CFU/mL per reaction, respectively, which were 100-fold more sensitive than with conventional PCR. The model food samples showed consistent specificity and sensitivity to the pure bacterial culture. With these encouraging results, it is expected that the novel, effortless and reliable isothermal nucleic acid testing assay developed in this study has potential to be applied to screening for V. parahaemolyticus in seafood samples.

Characterization of Mixed-Species Biofilm Formed by Vibrio parahaemolyticus and Listeria monocytogenes

Mixed-species biofilms are the predominant form of biofilms found in nature. Research on biofilms have typically concentrated on single species biofilms and this study expands the horizon of biofilm research, where the characterization and dynamic changes of mono and mixed-species biofilms formed by the pathogens, Vibrio parahaemolyticus and Listeria monocytogenes were investigated. Compared to mono-species biofilm, the biomass, bio-volume, and thickness of mixed-species biofilms were significantly lower, which were confirmed using crystal violet staining, confocal laser scanning microscopy and scanning electron microscopy. Further experimental analysis showed these variations might result from the reduction of bacterial numbers, the down-regulation of biofilm-regulated genes and loss of metabolic activity in mixed-species biofilm. In addition, V. parahaemolyticus was located primarily on the surface layers of the mixed-species biofilms thus accruing competitive advantage. This competitive advantage was evidenced in a higher V. parahaemolyticus population density in the mixed-species biofilms. The adhesion to surfaces of the mixed-species biofilms were also reduced due to lower concentrations of extracellular polysaccharide and protein when the structure of the mixed-species was examined using Raman spectral analysis, phenol-sulfuric acid method and Lowry method. Furthermore, the minimum biofilm inhibitory concentration to antibiotics obviously decreased when V. parahaemolyticus co-exited with L. monocytogenes. This study firstly elucidated the interactive behavior in biofilm development of two foodborne pathogens, and future studies for biofilm control and antibiotic therapy should take into account interactions in mixed-species biofilms.

Multicolor and Ultrasensitive Enzyme-Linked Immunosorbent Assay Based on the Fluorescence Hybrid Chain Reaction for Simultaneous Detection of Pathogens

Various pathogens may coexist in one sample; however, detection methods that rely on traditional selective culture media or immune agents designed specifically for a certain target are unsuitable for multiple targets. It is important to develop a simultaneous and sensitive detection method for multiple pathogens. Here, a multicolor and ultrasensitive enzyme-linked immunosorbent assay (ELISA) platform based on the fluorescence hybridization chain reaction (HCR) was developed. In the assay, multicolor fluorescence concatemers formed as signal amplifiers and signal reporters in the presence of target pathogens. When HCR occurred, Escherichia coli O157:H7, Salmonella serotype Choleraesuis, and Listeria monocytogenes were detected simultaneously with three different fluorescences. Additionally, the limits of detection for E. coli O157:H7, Salmonella Choleraesuis, and L. monocytogenes were 3.4 × 10¹, 6.4 × 10⁰, and 7.0 × 10¹ CFU/mL, respectively. The assay achieved ultrasensitive, specific, and simultaneous detection of three pathogens and can be applied to the detection of pathogens in milk samples. Therefore, this multicolor and ultrasensitive ELISA platform has great potential in the application of simultaneous detection of pathogens.

Discrimination of viable and dead Vibrio parahaemolyticus subjected to low temperatures using Propidium Monoazide - Quantitative loop mediated isothermal amplification (PMA-qLAMP) and PMA-qPCR

The aim of this study was to determine the effect of cold (4 °C) and subzero (-18 °C, -45 °C) temperatures on the occurrence time of membrane damage to provide Propidium Monoazide (PMA) penetration of Vibrio parahaemolyticus inoculated to the sea bass. Direct plate counting (DPC) and PMA-based quantitative loop-mediated isothermal amplification (qLAMP) and qPCR was utilized for discrimination of dead and live bacteria on the designated storage days (1, 3, 7, and 14). The optimum amount of PMA was 50 μM for inhibition of amplification derived from dead cells in spiked samples. The number of live V. parahaemolyticus was detectable at the end of the 14. day using PMA-qLAMP and PMA-qPCR at all the temperatures. On the 7th day, culturability has lost at any of the storage temperatures and DPCs at -18 °C and -45 °C revealed a difference of about 1 log₁₀ CFU/ml between 1st and 3rd days. The same difference was also observed in PMA-qLAMP and PMA-qPCR on the same days (0.59-0.95 log₁₀ CFU/ml). Subzero temperatures have the highest rate of viability while causing the fastest decrease in culturability in sample groups as a result of the higher level of transition to VBNC state. qLAMP and qPCR methods in the PMA-treated and nontreated groups on the storage days at all temperatures gave similar results (p > 0.05).

The Effect of Disease and Season to Hepatopancreas and Intestinal Mycobiota of Litopenaeus vannamei

Increasing evidence has manifested that the gut bacterial microbiota of shrimps is closely related to the environmental factors, host developmental stage and health status like that of humans and animals does. These studies have provided an important guidance for improving shrimp culture benefits. In practice, aside from bacteria, eukaryotic microorganisms dominated by fungal microbiota (mycobiota), also play a key role in host growth, metabolism and homeostasis. However, little so far is known about the mycobiota in the digestive tract of shrimp. In this study, we used high-throughput sequencing of internal transcribed spacer 1 region to characterize the hepatopancreas and intestinal mycobiota of Pacific white shrimp and their connections with disease incidence and seasonal variation. The results showed that the hepatopancreas and intestinal mycobiota of Litopenaeus vannamei are dominated by the phyla Ascomycota and Basidiomycota, and the genera Alternaria, Tuber, Hortaea, Sarocladium, and Stagonospora. The fungal microbiota significantly varies under the influence of disease and seasonal variation. Sick shrimps had a higher level of potential pathogenic fungus, Candida in the intestine. Healthy shrimps had a higher abundance of the genera Didymella and Filobasidium in the gut, and Pyrenochaetopsis in the hepatopancreas. Of note, most of the fungi carried by Pacific white shrimps were pathogens to humans. This study has revealed the intestinal and hepatopancreas mycobiota of L. vannamei and the effects of diseases and seasonal variation to the mycobiota. Our study provides important guidance for Pacific white shrimp farming and sheds further insight on the fungal microbiota.

Colorimetric Aptasensor Based on Truncated Aptamer and Trivalent DNAzyme for Vibrio parahemolyticus Determination

In this work, after optimizing the original aptamer sequence by truncation and site-directed mutagenesis, a simple and sensitive colorimetric aptasensor was established for detecting the widespread food-borne pathogen Vibrio parahemolyticus ( V. parahemolyticus). The detection strategy was based on the competition for an V. parahemolyticus specific aptamer between its complementary DNA (cDNA) and V. parahemolyticus. The aptamer-conjugated magnetic nanoparticles (MNPs) were used as capture probes, and the G-quadruplex (G4) DNAzyme was employed as the signal amplifying element. Under optimal conditions, a wide linear detection range (from 10² to 10⁷ cfu/mL) was available, and the detection limit could be as low as 10 cfu/mL. This method was also used to detect V. parahemolyticus in contaminated salmon samples, and the results showed good consistency with those obtained from standard plate counting method. Therefore, this novel aptasensor could be a good candidate for sensitive and selective detection of V. parahemolyticus without complicated operations.

Visualized Detection of Vibrio parahaemolyticus in Food Samples Using Dual-Functional Aptamers and Cut-Assisted Rolling Circle Amplification

A biosensor using two aptamers (Dual-Apt) and cut-assisted rolling circle amplification (CA-RCA) for rapid and visualized detection of Vibrio parahaemolyticus was established. The anchoring aptamer (A-Apt) that specifically binds to the surface of V. parahaemolyticus was applied to separate and enrich the bacterium from the food matrix with the help of streptavidin magnetic beads. While the detecting aptamer (D-Apt), binding on the different sites of the cell surface, was used as a signal reporter. CA-RCA with an enhanced amplification rate was fabricated here to amplify the D-Apt to produce the monomeric G4 sequence that catalyzes the oxidation of ABTS^2-, resulting in the coloration visible to the naked eye. Under optimal conditions, as low as 10 colony-forming units (CFU)/mL (g) of V. parahaemolyticus can be visibly detected in real food samples. Free from DNA extraction, visualized signal output and no need for expensive instruments enable Dual-Apt and CA-RCA to be a promising strategy for on-spot rapid detection.

Colorimetric Immunoassay for Rapid Detection of Vibrio parahemolyticus Based on Mn2+ Mediates the Assembly of Gold Nanoparticles

Vibrio parahemolyticus ( V. parahemolyticus) is an important food-borne pathogen that causes food poisoning and acute gastroenteritis in humans. Herein, a novel colorimetric immunoassay was presented for rapid detection of V. parahemolyticus using gold nanoparticles (18.1 nm diameter) as chromogenic substrate, whose combination of a magnetic bead-based sandwich immunoassay and an optical sensing system via Mn²⁺ ions mediated aggregation of gold nanoparticles. MnO₂ nanoparticles coated with polyclonal IgG antibodies (7.8 nm diameter) are used to recognize the target and can be etched to generate manganese ions by ascorbic acid. A color change ranging from red to purple to blue can be easily discerned by bare eye, corresponding to V. parahemolyticus concentration in the range between 10 and 10⁶ cfu·mL^-1. The proposed method possesses high specificity with a limit of detection of 10 cfu·mL^-1 and was successfully applied to determination of V. parahemolyticus in oyster samples without pre-enrichment. In our perception, it shows promise in rapid instrumental and on-site visual detection of V. parahemolyticus.

Nanoparticle Enhanced Antibody and DNA Biosensors for Sensitive Detection of Salmonella

Bacteria-related pathogenic diseases are one of the major health problems throughout the world. Salmonella is a genus of rod-shaped Gram-negative enterobacteria of which more than 2600 serotypes have been identified. Infection with Salmonella can cause salmonellosis, a serious bacterial toxi-infection syndrome associated with gastroenteritis, and paralyphoid and typhoid fevers. Its rapid and sensitive detection is a key to the prevention of problems related to health. This paper describes the development of antibody and DNA sensors for Salmonella detection using a microfluidic-based electrochemical system. Commercial Salmonella typhimurium and Salmonella typhimurium from human stool samples were investigated using standard and nanomaterial-amplified antibody sensors. S. typhimurium could be detected down to 1 cfu mL^-1. The specificity of immunoassay was tested by studying with non-specific bacteria including E. coli and S. aureus that revealed only 2.01% and 2.66% binding when compared to the target bacterium. On the other hand, the quantification of Salmonella DNA was investigated in a concentration range of 0.002⁻200 µM using the developed DNA biosensor that demonstrated very high specificity and sensitivity with a detection limit of 0.94 nM. Our custom-designed microfluidic sensor offers rapid, highly sensitive, and specific diagnostic assay approaches for pathogen detection.

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.

Giant Gold Nanowire Vesicle-Based Colorimetric and SERS Dual-Mode Immunosensor for Ultrasensitive Detection of Vibrio parahemolyticus

Conventional methods for the detection of Vibrio parahemolyticus (VP) usually need tedious, labor-intensive processes, and have low sensitivity, which further limits their practical applications. Herein, we developed a simple and efficient colorimetry and surface-enhanced Raman scattering (SERS) dual-mode immunosensor for sensitive detection of VP, by employing giant Au vesicles with anchored tiny gold nanowires (AuNW) as a smart probe. Due to the larger specific surface and special hollow structure of giant Au vesicles, silver staining would easily lead to vivid color change for colorimetric analysis and further amplify SERS signals. The t-test was further used to determine if two sets of data from colorimetry and SERS were significantly different from each other. The result shows that there was no significant difference between data from the two methods. Two sets of data can mutually validate each other and avoid false positive and negative detection. The designed colorimetry-SERS dual-mode sensor would be very promising in various applications such as food safety inspection, personal healthcare, and on-site environmental monitoring.

Application of molecular tools to elucidate the microbiota of seafood

The aim of this review is to present the methodologies currently applied to identify microbiota and pathogens transmitted to humans through seafood consumption, focusing on molecular techniques and pointing out their importance, advantages, disadvantages and applicability. Knowledge of available techniques allows researchers to identify which technique best fits their expectations. With such discernment, it will be possible to infer which disadvantages will be present and, therefore, not interfering with the final result. Two methodologies can be employed for this purpose, dependent and independent cultures. However, the dependent culture has certain limitations that can be solved through the independent cultivation techniques, such as PCR, PFGE and NGS, especially through the sequencing of the 16S rRNA region, providing a complete view of microbial diversity. These have revolutionized microbiological knowledge, mainly because they allow for the identification of uncultivable micro-organisms, which represent a substantial portion of total micro-organisms, making it possible to elucidate not yet described taxa which may display pathogenic potential, besides quantifying microbial communities, microbiota genetics, translated proteins and produced metabolites. In addition, transcriptomic and metabolomic techniques also allow for the evaluation of possible impacts that microbial communities may create in their environment, as well as the determination of potential pathogenicity to humans.

Detection of Total and Pathogenic Vibrio parahaemolyticus in Shellfish Growing along the South Yellow Sea and the East China Sea

This study was conducted to monitor the densities of total and pathogenic Vibrio parahaemolyticus in 300 samples of nine shellfish species harvested from the coasts of the South Yellow Sea and the East China Sea (N 23° to 34°, E 116° to 124°), People's Republic of China, between May and October 2015. Total V. parahaemolyticus densities were measured, and V. parahaemolyticus isolates were biochemically identified with probes for the thermostable direct hemolysin gene (tdh) and the thermostable direct hemolysin-related hemolysin gene (trh). We found that 202 of the 300 samples were positive for V. parahaemolyticus from all the sites: 58 of the 100 samples from the Fujian province, 71 of the 100 samples from the Zhejiang province, and 73 of the 100 samples from the Jiangsu province. In most (170) of the 300 samples, V. parahaemolyticus densities were 0.3 to 10 most probable number (MPN)/g; five lots exceeded 110 MPN/g, and two lots were estimated at 110 MPN/g. Among the 202 V. parahaemolyticus strains, only one was trh positive. Densities of V. parahaemolyticus in these shellfish were temperature dependent, with highest densities in June and July. Among the nine mollusk species, V. parahaemolyticus was most abundant in the agemaki clam (Sinonovacula constricta). The highest and lowest V. parahaemolyticus prevalences were found in oriental cyclina (Cyclina sinensis, 93.8%) and mussels (Mytilus edulis, 28.1%), respectively. Overall, although V. parahaemolyticus is widely distributed in marine environments, the density of V. parahaemolyticus was low and the prevalence of the main virulence factor was very low in shellfish along the coasts of the South Yellow Sea and East China Sea, which is important from a public health perspective. Data presented here will be useful for correlational research and can be utilized for developing risk management plans that establish food safety guidelines for V. parahaemolyticus in Chinese shellfish.

Rapid and simultaneous quantification of viable Escherichia coli O157:H7 and Salmonella spp. in milk through multiplex real-time PCR

Escherichia coli O157:H7 and Salmonella spp. in milk are 2 common pathogens that cause foodborne diseases. An accurate, rapid, specific method has been developed for the simultaneous detection of viable E. coli O157:H7 and Salmonella spp. in milk. Two specific genes, namely, fliC from E. coli O157:H7 and invA from Salmonella spp., were selected to design primers and probes. A combined treatment containing sodium deoxycholate (SDO) and propidium monoazide (PMA) was applied to detect viable E. coli O157:H7 and Salmonella spp. only. Traditional culture methods and SDO-PMA-multiplex real-time (mRT) PCR assay were applied to determine the number of viable E. coli O157:H7 and Salmonella spp. in cell suspensions with different proportions of dead cells. These methods revealed consistent findings regarding the detected viable cells. The detection limit of the SDO-PMA-mRT-PCR assay reached 10² cfu/mL for Salmonella spp. and 10² cfu/mL for E. coli O157:H7 in milk. The detection limit of SDO-PMA-mRT-PCR for E. coli O157:H7 and Salmonella spp. in milk was significantly similar even in the presence of 10⁶ cfu/mL of 2 nontarget bacteria. The proposed SDO-PMA-mRT-PCR assay is a potential approach for the accurate and sensitive detection of viable E. coli O157:H7 and Salmonella spp. in milk.

A Multiplex RT-PCR Assay for S. aureus, L. monocytogenes, and Salmonella spp. Detection in Raw Milk with Pre-enrichment

This study firstly developed a multiplex real-time PCR (RT-PCR) technique combined with a pre-enrichment step to simultaneously detect Staphylococcus aureus (S. aureus), Listeria monocytogenes (L. monocytogenes) and Salmonella spp. in raw milk and the dairy farm environment (feces, soil, feed, water) in one reaction. Brain heart infusion (BHI) broth was selected for the enrichment step to increase the density of the target bacteria by using an incubation of 4 h before multiplex RT-PCR. The results showed that the detection limit of the multiplex real-time assay was approximately 102 CFU/mL for pure cultures and artificially contaminated milk without enrichment, while 12, 14, and 10 CFU/25 mL, respectively, for S. aureus, L. monocytogenes, and Salmonella spp. after pre-enrichment. The newly developed multiplex RT-PCR assay was applied to 46 dairy farm environmental samples and raw milk samples covering a wide variety of sample types. The results demonstrated that the multiplex RT-PCR assay coupled with the BHI enrichment broth was suitable for the simultaneous screening of S. aureus, L. monocytogenes, and Salmonella spp. in the pasture environment and in raw milk. The multiplex RT-PCR assay clearly and successfully shortened the total detection time and reduced labor compared to conventional culture-based methods for testing natural samples.

Prevalence of Vibrio parahaemolyticus in seafood products from hypermarkets in Shanghai

BACKGROUND

Vibrio parahaemolyticus is an important gastroenteritis pathogen contaminating seafood in China. In this study a total of 992 seafood samples from major hypermarkets in Shanghai were monitored for prevalence and burden of V. parahaemolyticus from January 2011 to December 2012. Additionally, appropriate probability distributions for describing V. parahaemolyticus concentrations were assessed based on these surveillance data.

RESULTS

Seventeen of 992 samples were positive for V. parahaemolyticus and the geometric mean was 0.1581 most probable number (MPN) g^-1 . The variation in prevalence of V. parahaemolyticus was seasonal and the burden of contamination in August (0.1942 MPN g^-1 ) was significant (P < 0.01) between 2011 and 2012. Also, the prevalence of V. parahaemolyticus was higher in shellfish and cephalopods than in other seafood (P < 0.05). By comparison, the lognormal distribution and integrated distribution showed no obvious difference for characterizing V. parahaemolyticus contamination.

CONCLUSION

The low prevalence and burden found indicated that seafood from hypermarkets may not be an important risk source for V. parahaemolyticus infection in Shanghai, and more attention should be paid to other areas for selling seafood, such as farmlands or farmers' markets. The simple and effective lognormal distribution is recommended as a better choice for describing V. parahaemolyticus contamination in future risk assessment studies. © 2016 Society of Chemical Industry.