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

Public health aspects of Vibrio spp. related to the consumption of seafood in the EU

Vibrio parahaemolyticus, Vibrio vulnificus and non-O1/non-O139 Vibrio cholerae are the Vibrio spp. of highest relevance for public health in the EU through seafood consumption. Infection with V. parahaemolyticus is associated with the haemolysins thermostable direct haemolysin (TDH) and TDH-related haemolysin (TRH) and mainly leads to acute gastroenteritis. V. vulnificus infections can lead to sepsis and death in susceptible individuals. V. cholerae non-O1/non-O139 can cause mild gastroenteritis or lead to severe infections, including sepsis, in susceptible individuals. The pooled prevalence estimate in seafood is 19.6% (95% CI 13.7-27.4), 6.1% (95% CI 3.0-11.8) and 4.1% (95% CI 2.4-6.9) for V. parahaemolyticus, V. vulnificus and non-choleragenic V. cholerae, respectively. Approximately one out of five V. parahaemolyticus-positive samples contain pathogenic strains. A large spectrum of antimicrobial resistances, some of which are intrinsic, has been found in vibrios isolated from seafood or food-borne infections in Europe. Genes conferring resistance to medically important antimicrobials and associated with mobile genetic elements are increasingly detected in vibrios. Temperature and salinity are the most relevant drivers for Vibrio abundance in the aquatic environment. It is anticipated that the occurrence and levels of the relevant Vibrio spp. in seafood will increase in response to coastal warming and extreme weather events, especially in low-salinity/brackish waters. While some measures, like high-pressure processing, irradiation or depuration reduce the levels of Vibrio spp. in seafood, maintaining the cold chain is important to prevent their growth. Available risk assessments addressed V. parahaemolyticus in various types of seafood and V. vulnificus in raw oysters and octopus. A quantitative microbiological risk assessment relevant in an EU context would be V. parahaemolyticus in bivalve molluscs (oysters), evaluating the effect of mitigations, especially in a climate change scenario. Knowledge gaps related to Vibrio spp. in seafood and aquatic environments are identified and future research needs are prioritised.

Establishment and application of a rapid visualization method for detecting Vibrio parahaemolyticus nucleic acid

Background

Swift and accurate detection of Vibrio parahaemolyticus, which is a prominent causative pathogen associated with seafood contamination, is required to effectively combat foodborne disease and wound infections. The toxR gene is relatively conserved within V. parahaemolyticus and is primarily involved in the expression and regulation of virulence genes with a notable degree of specificity. The aim of this study was to develop a rapid, simple, and constant temperature detection method for V. parahaemolyticus in clinical and nonspecialized laboratory settings.

Methods

In this study, specific primers and CRISPR RNA were used to target the toxR gene to construct a reaction system that combines recombinase polymerase amplification (RPA) with CRISPR‒Cas13a. The whole-genome DNA of the sample was extracted by self-prepared sodium dodecyl sulphate (SDS) nucleic acid rapid extraction reagent, and visual interpretation of the detection results was performed by lateral flow dipsticks (LFDs).

Results

The specificity of the RPA-CRISPR/Cas13a-LFD method was validated using V. parahaemolyticus strain ATCC-17802 and six other non-parahaemolytic Vibrio species. The results demonstrated a specificity of 100%. Additionally, the genomic DNA of V. parahaemolyticus was serially diluted and analysed, with a minimum detectable limit of 1 copy/µL for this method, which was greater than that of the TaqMan-qPCR method (102 copies/µL). The established methods were successfully applied to detect wild-type V. parahaemolyticus, yielding results consistent with those of TaqMan-qPCR and MALDI-TOF MS mass spectrometry identification. Finally, the established RPA-CRISPR/Cas13a-LFD method was applied to whole blood specimens from mice infected with V. parahaemolyticus, and the detection rate of V. parahaemolyticus by this method was consistent with that of the conventional PCR method.

Conclusions

In this study, we describe an RPA-CRISPR/Cas13a detection method that specifically targets the toxR gene and offers advantages such as simplicity, rapidity, high specificity, and visual interpretation. This method serves as a valuable tool for the prompt detection of V. parahaemolyticus in nonspecialized laboratory settings.

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.

Multiplex PCR-Lateral Flow Dipstick Method for Detection of Thermostable Direct Hemolysin (TDH) Producing V. parahaemolyticus

Vibrio parahaemolyticus is usually found in seafood and causes acute gastroenteritis in humans. Therefore, a detection method of pathogenic V. parahaemolyticus is necessary. Multiplex PCR combined with lateral flow dipstick (LFD) assay was developed to detect pathogenic V. parahaemolyticus. Biotin-, FAM-, and Dig-conjugated primers targeting thermolabile hemolysin (TLH) and thermostable direct hemolysin (TDH) genes were used for multiplex PCR amplification. The condition of the method was optimized and evaluated by agarose gel electrophoresis and universal lateral flow dipstick. The specificity assay was evaluated using strains belonging to seven foodborne pathogen species. The sensitivity of the method was also evaluated using DNA in the concentration range of 0.39-100 ng/reaction. The artificial spiking experiment was performed using 10 g of shrimp samples with an enrichment time of 0, 4, and 8 h with 10¹, 10², and 10³ CFU of V. parahaemolyticus. The developed multiplex PCR-LFD assay showed no non-specific amplification with a limit of the detection of 0.78 ng DNA/reaction visualized by agarose gel electrophoresis and 0.39 ng DNA with LFD assay. The artificial spiking experiment demonstrated that this method could detect pathogenic V. parahaemolyticus at 10 CFU/10 g shrimp samples following a 4 h of enrichment. Multiplex PCR-LFD assay was therefore established for detecting pathogenic V. parahaemolyticus with high sensitivity and specificity and might be a useful tool to develop a detection kit used in the food safety sector.

Quantitative Detection of Viable but Nonculturable Vibrio parahaemolyticus in Frozen Bivalve Molluscs

Vibrio parahaemolyticus is a foodborne pathogen diffusely distributed in the marine environment and often isolated from raw seafood belonging to different species, mostly shellfish. Ingestion of under- or uncooked seafood contaminated by V. parahaemolyticus can cause severe gastrointestinal symptoms in humans. Due to its ability to withstand low temperatures, Vibrio spp. could survive in frozen seafoods for long periods by entering the viable but nonculturable state (VBNC) and may constitute an unrecognized source of food contamination and infection. In the present study, seventy-seven frozen bivalve molluscs (35 mussels; 42 clams) were subjected to the detection and enumeration of viable V. parahaemolyticus using standard culture methods. VBNC forms were detected and quantified by applying an optimized protocol based on Propidium Monoazide (PMA) and Quantitative PCR (qPCR). All samples were negative for both the detection and enumeration of V. parahaemolyticus by the standard culture methods. VBNC forms were detected in 11.7% of the samples (9/77), with values ranging from 1.67 to 2.29 Log CFU/g. Only clam samples were positive for the detection of VBNC forms. The results of this study highlighted that VBNC V. parahaemolyticus may be present in frozen bivalve molluscs. Further data on the prevalence of VBNC V. parahaemolyticus in frozen seafood are needed in order to perform a robust risk assessment.

Analysis of Pathogenic Vibrio Contamination in Marine Products along China Based on Fluorescence Quantitative PCR

At present, aquatic product pollution has become the main root of frequent food safety problems and causes economic losses. Vibrio is one of the main pathogens causing foodborne diseases. In this study, in order to uncover the pollution status of pathogenic Vibrio in the marine products of China, a total of 646 aquatic products were collected and analyzed from 10 coastal cities in China. Five kinds of pathogenic Vibrio were separated from these samples and monitored to explore the relationship between pollution and the pathogen. Real-time fluorescence quantitative PCR was adopted to detect foodborne Vibrio quantitatively in marine aquatic products. Aquatic pathogenic Vibrio was collected in different regions, different types of aquatic products, and different sampling places, and the difference in detection rate was statistically significant through statistical analysis. This study made a frame for the pollution degree of pathogenic Vibrio in marine products in China and established the dominant flora of pathogenic Vibrio in different types of aquatic products, which provides a theoretical basis for food safety supervision departments to take targeted prevention and control measures.

Distinct dynamics of Vibrio parahaemolyticus populations in two farming models

AIMS

Despite the recent prosperity of shrimp cultivation in China, very little is known about how different shrimp farming models influence the dynamics of Vibrio parahaemolyticus populations and the antibiotic resistance of this bacterium.

METHODS AND RESULTS

To this end, we conducted continuous surveillance of V. parahaemolyticus on four farms over 3 years: two traditional shrimp farms with daily water exchange and two farms operated in the recirculating aquaculture systems (RAS). No antibiotics were used in these farms to exclude the potential impacts of antibiotics on the emergence of antibacterial resistance. Multilocus sequence typing was utilized to characterize the dynamics of V. parahaemolyticus populations. Whole-genome sequencing (WGS) was conducted to determine the representative sequence types (STs) at each farm. Results revealed that the population structure of V. parahaemolyticus remained stable over time in both RAS farms, with only nine and four STs observed at each. In contrast, annual replacement of V. parahaemolyticus populations was observed in traditional farms with 26 and 28 STs identified in rearing water. WGS of 50 isolates divided them into five clusters, of which ST917a isolates harboured a genomic island that disrupted the gene recA. Pair-wised genomic comparison of isolates from the same STs showed that they were genetically related but belonged to different clones associated with geographical distribution.

CONCLUSIONS

These results suggested that RAS presented a specific ecological niche by minimizing the water exchanges with the external environment. In contrast, traditional farming might pose a food safety issue by introducing new V. parahaemolyticus populations with antibiotic resistance genes.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results expose the potential food safety issue associated with conventional agriculture and should encourage the development of preventive strategies to reduce the emergence of resistant V. parahaemolyticus populations.

Quantification of Viable Brochothrix thermosphacta in Cold-Smoked Salmon Using PMA/PMAxx-qPCR

The aim of this study was to develop a rapid and accurate PMA-qPCR method to quantify viable Brochothrix thermosphacta in cold-smoked salmon. B. thermosphacta is one of the main food spoilage bacteria. Among seafood products, cold-smoked salmon is particularly impacted by B. thermosphacta spoilage. Specific and sensitive tools that detect and quantify this bacterium in food products are very useful. The culture method commonly used to quantify B. thermosphacta is time-consuming and can underestimate cells in a viable but not immediately culturable state. We designed a new PCR primer set from the single-copy rpoC gene. QPCR efficiency and specificity were compared with two other published primer sets targeting the rpoC and rpoB genes. The viability dyes PMA or PMAxx were combined with qPCR and compared with these primer sets on viable and dead B. thermosphacta cells in BHI broth and smoked salmon tissue homogenate (SSTH). The three primer sets displayed similar specificity and efficiency. The efficiency of new designed rpoC qPCR on viable B. thermosphacta cells in SSTH was 103.50%, with a linear determination coefficient (r²) of 0.998 and a limit of detection of 4.04 log CFU/g. Using the three primer sets on viable cells, no significant difference was observed between cells treated or untreated with PMA or PMAxx. When dead cells were used, both viability dyes suppressed DNA amplification. Nevertheless, our results did not highlight any difference between PMAxx and PMA in their efficiency to discriminate viable from unviable B. thermosphacta cells in cold-smoked salmon. Thus, this study presents a rapid, specific and efficient rpoC-PMA-qPCR method validated in cold-smoked salmon to quantify viable B. thermosphacta in foods.

Prevalence, detection of virulence genes and antimicrobial susceptibility of pathogen Vibrio species isolated from different types of seafood samples at "La Nueva Viga" market in Mexico City

Some Vibrio species are important human pathogens owing to they cause infectious diseases such as gastroenteritis, wound infections, septicemia or even death. Many of these illnesses are associated with consumption of contaminated seafood. In the present study, we evaluated the presence of pathogenic Vibrio species, their virulence and antimicrobial susceptibility from 285 different kind of seafood samples from "La Nueva Viga" market in Mexico City. The PCR assay was used for amplification the vppC (collagenase), vmh (hemolysin), tlh (thermolabile hemolysin), and vvhA (hemolytic cytolysin) genes that are specific to Vibrio alginolyticus (detected in 27%), Vibrio mimicus (23.2%), Vibrio parahaemolyticus (28.8%) and Vibrio vulnificus (21.1%), respectively. Several genes encoding virulence factors were amplified. These included V. alginolyticus: pvuA (17.9%), pvsA (50%), wza and lafA (100%); V. mimicus: iut A (60%), toxR (100%); V. parahaemolyticus: pvuA (58.7%), pvsA (26.1%), wza (2.2%), and lafA (100%); and V. vulnificus: wcrA (77.5%), gmhD (57.5%), lafA (100%) and motA (30%). The antibiotic susceptibility of the Vibrio species isolates revealed that most of them were resistant to ampicillin, cephalothin and carbenicillin but susceptible to pefloxacin and trimethoprim-sulfamethoxazole. Our results indicated a high prevalence of pathogenic Vibrio species in seafood, a high presence of virulence genes and that Vibrio species continuously exposed to antibiotics, therefore, consumption of these kind of seafood carries a potential risk for foodborne illness.

How to Evaluate Non-Growing Cells-Current Strategies for Determining Antimicrobial Resistance of VBNC Bacteria

Thanks to the achievements in sanitation, hygiene practices, and antibiotics, we have considerably improved in our ongoing battle against pathogenic bacteria. However, with our increasing knowledge about the complex bacterial lifestyles and cycles and their plethora of defense mechanisms, it is clear that the fight is far from over. One of these resistance mechanisms that has received increasing attention is the ability to enter a dormancy state termed viable but non-culturable (VBNC). Bacteria that enter the VBNC state, either through unfavorable environmental conditions or through potentially lethal stress, lose their ability to grow on standard enrichment media, but show a drastically increased tolerance against antimicrobials including antibiotics. The inability to utilize traditional culture-based methods represents a considerable experimental hurdle to investigate their increased antimicrobial resistance and impedes the development and evaluation of effective treatments or interventions against bacteria in the VBNC state. Although experimental approaches were developed to detect and quantify VBNCs, only a few have been utilized for antimicrobial resistance screening and this review aims to provide an overview of possible methodological approaches.

Vibrio and major commercially important vibriosis diseases in decapod crustaceans

Bacteria fromthe Vibriogenus are autochthonous to aquatic environments and ubiquitous in aquaculture production systems. Many Vibrio species are non-pathogenic and can be commonly found in healthy farmed aquatic animals. However, some Vibrio species and strains are pathogenic leading to a variety of 'vibriosis' diseases. These diseases can have a significant negative impact on animal production, including farmed crustaceans such as shrimps, lobsters, and crabs. As such, vibriosis can pose a threat to meeting growing food demand and global food security. Preventive management is essential to avoid the onset of vibriosis. This includes a robust health management plan, the use of prophylaxis and treatment measures, and enhancing animal health through nutrition. Furthermore, the use of probiotics, prebiotics, synbiotics, quorum sensing disruption, green water, biofloc, bacteriophages, and immune priming could also play a role in preventing and controlling a vibriosis outbreak. This review aims to inform and update the reader about the current state of knowledge about Vibrio and associated vibriosis in farmed crustaceans (i.e. shrimp, lobster, and crabs). Furthermore, the review will identify potential knowledge gaps in the literature, which serves as a basis for future research priorities.

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.

Managing the risk of Vibrio parahaemolyticus infections associated with oyster consumption: A review

Vibrio parahaemolyticus is a Gram-negative bacterium that is naturally present in the marine environment. Oysters, which are water filter feeders, may accumulate this pathogen in their soft tissues, thus increasing the risk of V. parahaemolyticus infection among people who consume oysters. In this review, factors affecting V. parahaemolyticus accumulation in oysters, the route of the pathogen from primary production to consumption, and the potential effects of climate change were discussed. In addition, intervention strategies for reducing accumulation of V. parahaemolyticus in oysters were presented. A literature review revealed the following information relevant to the present study: (a) managing the safety of oysters (for human consumption) from primary production to consumption remains a challenge, (b) there are multiple factors that influence the concentration of V. parahaemolyticus in oysters from primary production to consumption, (c) climate change could possibly affect the safety of oysters, both directly and indirectly, placing public health at risk, (d) many intervention strategies have been developed to control and/or reduce the concentration of V. parahaemolyticus in oysters to acceptable levels, but most of them are mainly focused on the downstream steps of the oyster supply chain, and (c) although available regulation and/or guidelines governing the safety of oyster consumption are mostly available in developed countries, limited food safety information is available in developing countries. The information provided in this review may serve as an early warning for managing the future effects of climate change on the safety of oyster consumption.

Comparison on the Growth Variability of Vibrio parahaemolyticus Coupled With Strain Sources and Genotypes Analyses in Simulated Gastric Digestion Fluids

Vibrio parahaemolyticus is a food-borne pathogen that causes pathogenic symptoms such as diarrhea and abdominal pain. Currently no studies have shown that either pathogenic and non-pathogenic V. parahaemolyticus possess growth heterogeneity in a human environment, such as in gastric and intestinal fluids. The tlh gene is present in both pathogenic and non-pathogenic V. parahaemolyticus strains, while the tdh and trh genes are only present in pathogenic strains. This study firstly applied simulated human gastric fluids to explore growth variability of 50 strains of V. parahaemolyticus at 37°C. The bacterial growth curves were fitted by primary modified Gompertz model, and the maximum growth rate (μ_max), lag time (LT), and their CV values were calculated to compare the stress response of pathogenic and non-pathogenic V. parahaemolyticus to simulated human gastric fluids. Results showed that the simulated human gastric fluids treatment significantly increased the μ_max of pathogenic strains and shortened the lag time, while decreased the μ_max of non-pathogenic strains and prolonged the lag time. Meanwhile, the CV values of genotypes (tlh⁺/tdh⁺/trh^–) evidently increased, showing that the pathogenic genotype (tlh⁺/tdh⁺/trh^–) strains had strong activity to simulated gastric fluids. All of the results indicated that the V. parahaemolyticus strains exhibited a great stress-resistant variability and growth heterogeneity to the simulated gastric fluids, which provides a novel insight to unlock the efficient control of pathogenic V. parahaemolyticus.

Quantitative Polymerase Chain Reaction Coupled With Sodium Dodecyl Sulfate and Propidium Monoazide for Detection of Viable Streptococcus agalactiae in Milk

Streptococcus agalactiae is an important pathogen causing bovine mastitis. The aim of this study was to develop a simple and specific method for direct detection of S. agalactiae from milk products. Propidium monoazide (PMA) and sodium dodecyl sulfate (SDS) were utilized to eliminate the interference of dead and injured cells in qPCR. Lysozyme (LYZ) was adopted to increase the extraction efficiency of target bacteria DNA in milk matrix. The specific primers were designed based on cfb gene of S. agalactiae for qPCR. The inclusivity and exclusivity of the assay were evaluated using 30 strains. The method was further determined by the detection of S. agalactiae in spiked milk. Results showed significant differences between the SDS–PMA–qPCR, PMA–qPCR and qPCR when a final concentration of 10 mg/ml (R² = 0.9996, E = 95%) of LYZ was added in DNA extraction. Viable S. agalactiae was effectively detected when SDS and PMA concentrations were 20 μg/ml and 10 μM, respectively, and it was specific and more sensitive than qPCR and PMA–qPCR. Moreover, the SDS–PMA–qPCR assay coupled with LYZ was used to detect viable S. agalactiae in spiked milk, with a limit of detection of 3 × 10³ cfu/ml. Therefore, the SDS–PMA–qPCR assay had excellent sensitivity and specificity for detection of viable S. agalactiae in milk.