Development and validation of qualitative SYBR®Green real-time PCR for detection and discrimination of Listeria spp. and Listeria monocytogenes

Comparison of commercial DNA kits for allergen detection of celery in food matrices

For correct allergen risk management by industry, retail and food safety authorities, sensitive and reliable fast allergen detection methods are required, even more when precautionary allergen labelling based on reference doses will be implemented in legislation. This study aimed to perform a comparative assessment of three commercially available quantitative or qualitative test kits, for DNA analysis of celery in food products. Five product groups, representing different sectors of the AOAC food-matrix triangle, being (plant-based) meat products, snacks, sauces, dried herbs and spices, and smoothies, were identified to potentially contain celery. From each group, blank and incurred (labelled to contain celery) food products were selected, of which the blank food products were additionally spiked with low protein levels of celery prior to qPCR assessment. Results show that the assessed test kits perform according to their specifications, however, a clear influence of the matrix on the detection ability of celery was observed. In addition, quantification of the amount of celery in the different food products showed to be challenging in all food product groups using the two quantification kits.

Profiling and source tracking of the microbial populations and resistome present in fish products

Microorganisms in processing environments significantly impact the quality and safety of food products and can serve as potential reservoirs for antibiotic-resistant genes, contributing to public health concerns about antimicrobial resistance (AMR). Fish processing plants represent an understudied environment for microbiome mapping. This study investigated the microbial composition, prevalence of Listeria spp., and resistome structures in three catfish processing facilities in the southeastern United States. The 16S rRNA gene sequencing revealed that the observed richness and Shannon diversity index increased significantly from fish to fillet. Beta diversity analysis showed distinct clustering of microbial communities between fish, environment, and fillet samples. Fast expectation-maximization microbial source tracking (FEAST) algorithm demonstrated that the microbiota presents in the processing environment contributed 48.2 %, 62.4 %, and 53.7 % to the microbiota present on fillet in Facility 1 (F1), F2, and F3, respectively. Food contact surfaces made larger contributions compared to the non-food contact surfaces. The linear discriminant analysis of effect size (LEfSe) identified specific microbial genera (e.g., Plesiomohas, Brochothrix, Chryseobacterium and Cetobacterium) that significantly varied between Listeria spp. positive and negative samples in all three processing plants. The metagenomic sequencing results identified 212 antimicrobial resistance genes (ARGs) belonging to 72 groups from the raw fish and fish fillet samples collected from three processing plants. Although there was a significant decrease in the overall diversity of ARGs from fish to fillet samples, the total abundance of ARGs did not change significantly (P > 0.05). ARGs associated with resistance to macrolide-lincosamide-streptogramin (MLS), cationic antimicrobial peptides, aminoglycosides, and beta-lactams were found to be enriched in the fillet samples when compared to fish samples. Results of this study highlight the profound impact of processing environment on shaping the microbial populations present on the final fish product and the need for additional strategies to mitigate AMR in fish products.

Longitudinal Survey of Aeromonas hydrophila and Foodborne Pathogens in a Commercial Aquaponics System

Aquaponic production of fresh produce is a sustainable agricultural method becoming widely adopted, though few studies have investigated potential food safety hazards within commercial systems. A longitudinal study was conducted to isolate and quantify several foodborne pathogens from a commercial, aquaponic farm, and to elucidate their distribution throughout. The survey was conducted over 2 years on a controlled-environment farm containing Nile tilapia (Oreochromis niloticus) and lettuce (Lactuca sativa). Samples (N = 1,047) were collected bimonthly from three identical, independent systems, and included lettuce leaves, roots, fingerlings (7-126 d old), feces from mature fish (>126 d old), water, and sponge swabs collected from the tank interior surface. Most probable number of generic Escherichia coli were determined using IDEXX Colilert Quanti-Tray. Enumeration and enrichment were used to detect Shiga toxin-producing E. coli (STEC), Salmonella enterica, Listeria monocytogenes, Aeromonas spp., Aeromonas hydrophilia, and Pseudomonas aeruginosa. Generic E. coli, STEC, L. monocytogenes, and S. enterica were not detected in collected samples. P. aeruginosa was isolated from water (7/351; 1.99%), swabs (3/351; 0.85%), feces (2/108; 1.85%), and lettuce leaves (2/99; 2.02%). A. hydrophila was isolated from all sample types (623/1047; 59.50%). The incidence of A. hydrophila in water (X2 = 23.234, p < 0.001) and sponge samples (X2 = 21.352, p < 0.001) increased over time.

Detection of Listeria Species by Conventional Culture-Dependent and Alternative Rapid Detection Methods in Retail Ready-to-Eat Foods in Turkey

Foodborne pathogens, like Listeria monocytogenes, continue to inflict substantial financial losses on the food industry. Various methods for detecting Listeria in food have been developed and numerous studies have been conducted to compare the different methods. But, in recent years, new Listeria species have been identified, and currently the genus comprises 26 species. Therefore, it would be a more accurate approach to re-evaluate existing detection methods by considering new species. The present investigation involved the analysis of 42 ready-to-eat (RTE) foods, encompassing a variety of food categories, such as mezes, salads, dairy products, and meat products, with the aim of ascertaining the presence of Listeria. Among the traditional culture-dependent reference methods, the ISO 11290 method was preferred. The process of strain identification was conducted with the API Identification System. Furthermore, to ascertain the existence of L. monocytogenes and Listeria spp., the samples underwent additional analysis employing the VIDAS Immunoassay System, ELISA, and RT-PCR methodologies. Thus, four alternative approaches were employed in this study to compare not only the different methods used to determine Listeria while taking into account the newly identified Listeria species, but also to assess the compliance of retail RTE food items with microbiological criteria pertaining to the genus Listeria. Based on the conducted analyses, L. monocytogenes was conclusively determined to be present in one sample. The presence of Listeria spp. was detected in 30.9% of the samples, specifically in Turkish cig kofte, sliced salami, and salads.

Duplex real-time PCR assay with high-resolution melt analysis for the detection and quantification of Listeria species and Listeria monocytogenes in meat products

Listeria contamination in foods of animal origin is one of the most concerning food safety issues. A duplex, SYBR green-based, real-time PCR assay was developed with high-resolution melting analysis-based differentiation of the genus Listeria and Listeria monocytogenes. The primers were designed and tested against other related foodborne pathogens. The assay was optimized for standard parameters in a non-orthogonal fashion and validated following international standards. The LODabs and LOQ of the assay were calculated to be 0.78 and 1.56 ng of the target DNA. The LODrel of the assay was found to be 1% Listeria DNA in background DNA. The assay was evaluated for applicability in artificially spiked samples, providing a 120 CFU/ml detection. The assay was validated with proficiency test samples and also with samples collected for surveillance analysis. This well-established and validated assay can be utilized as a qualitative and quantitative tool for addressing the Listeria contamination in the food safety contexts.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05695-2.

Listeria monocytogenes in foods-From culture identification to whole-genome characteristics

Listeria monocytogenes is an important foodborne pathogen, which is able to persist in the food production environments. The presence of these bacteria in different niches makes them a potential threat for public health. In the present review, the current information on the classical and alternative methods used for isolation and identification of L. monocytogenes in food have been described. Although these techniques are usually simple, standardized, inexpensive, and are routinely used in many food testing laboratories, several alternative molecular-based approaches for the bacteria detection in food and food production environments have been developed. They are characterized by the high sample throughput, a short time of analysis, and cost-effectiveness. However, these methods are important for the routine testing toward the presence and number of L. monocytogenes, but are not suitable for characteristics and typing of the bacterial isolates, which are crucial in the study of listeriosis infections. For these purposes, novel approaches, with a high discriminatory power to genetically distinguish the strains during epidemiological studies, have been developed, e.g., whole-genome sequence-based techniques such as NGS which provide an opportunity to perform comparison between strains of the same species. In the present review, we have shown a short description of the principles of microbiological, alternative, and modern methods of detection of L. monocytogenes in foods and characterization of the isolates for epidemiological purposes. According to our knowledge, similar comprehensive papers on such subject have not been recently published, and we hope that the current review may be interesting for research communities.

Quantitative characterization and effective inactivation of biological hazards in struvite recovered from digested poultry slurry

Struvite formed from digested poultry slurries can serve as an alternative to chemical fertilizers; however, the biological safety of such products is questionable. Therefore, quantification and inactivation of foodborne pathogens existing in struvite are important. Herein, the dynamics of foodborne pathogens' (Streptococcus faecalis, S. typhimurium, Clostridium perfringens, and Escherichia coli) living status, whether culturable and viable but non-culturable (VBNC) in struvite, were quantified for the first time. Meanwhile, inactivation technologies, namely high-humidity hot air impingement blanching (HHAIB), cold plasma, and hot air treatment, were evaluated and compared for their potential to inactivate/kill foodborne pathogens in struvite. An increase in precipitation pH from 9.0 to 11.0 decreased the culturable count of pathogens in the struvite from 75 to 86% to 7-20%, while the VBNC pathogen counts increased from 16 to 24% to 35-55%. Among the tested inactivation technologies, the HHAIB treatment at 130 °C for 120 s killed approximately 68-79% of foodborne pathogens in struvite precipitated at pH 9.0. VBNC pathogens increased from 16 to 24% to 57-68% after HHAIB treatment at 130 °C for 120 s. Struvite treatment with different inactivation technologies did not change its crystalline structure; however, it reduced functional group abundance. Therefore, further research on inactivation technologies is required to achieve better pathogen reduction efficiency in struvite to make it a biologically safe fertilizer for crop production.

Cecal microbiome profile of Hawaiian feral chickens and pasture-raised broiler (commercial) chickens determined using 16S rRNA amplicon sequencing

This study investigated the taxonomic profile and abundance distribution of the bacterial community in the ceca of feral and pasture-raised broiler (commercial) chickens. Cecal content from feral and commercial chickens (n = 7 each) was collected, and total DNA was isolated. Next-Generation Sequencing (Illumina MiSeq) was performed to characterize the cecal microbiota. Specific bacteria explored were: Bacteroides, Bifidobacterium, Lactobacillus, Enterococcus, Escherichia, and Clostridium. At the phylum level, 92% of the bacteria belonged to Firmicutes, Bacteroidetes, and Proteobacteria for both feral and commercial chickens. The proportional abundance of Firmicutes was 55.3% and 63.3%, Bacteroidetes was 32.5% and 24.4%, and Proteobacteria was 7.0% and 5.9% in the feral and commercial chickens, respectively. The alpha-diversity Shannon index (P = 0.017) and Simpson index (P = 0.038) were significantly higher for commercial than for feral chickens. Predictive functional profiling by PICRUSt showed enriched microbial metabolic pathways for L-proline biosynthesis in the feral group (P < 0.01). There were a greater percentage of specific bacteria in the feral than commercial chickens, albeit with lower diversity but a more functional microbiota. In conclusion, feral birds have distinguished microbial communities, and further microbiome analysis is mandated to know the specific functional role of individual microbiota. The difference in microbiota level between feral and commercial birds could be accounted to the scavenging nature, diverse feed ingredients, and distinct rearing localities.

Detection of spore forming Paenibacillus macerans in raw milk

Paenibacillus macerans can cause spoilage of milk during extended storage. However, the natural milk microbiota interferes with the enumeration of Paenibacillus species in raw milk. In this study, a qualitative SYBR Green real-time PCR assay based on the groEL gene was developed for detecting P. macerans (PMassay) in raw milk and compared with one designed for total Paenibacillus detection (TPassay). The specificity of the PMassay was confirmed against a panel of dairy-related spore forming isolates. In the presence of background DNA substituted up to 95%, P. macerans DNA could still be detected by the PMassay although interference occurred as non-target DNA substitution increased. The PMassay was sensitive (detection limit of 2 log CFU/ml in milk) and specific as non-P. macerans isolates gave a Ct > 30. After enrichment of raw milk for 7 days at 37 °C in Reinforced Clostridial Medium with D-cycloserine (RCM-D) under anaerobiosis, Paenibacillus was detected in 10 of the 16 raw milk samples tested. Enrichment in RCM-D yielded about 0.5 to 5.8 log CFU/ml total Paenibacillus and 0.3 to 4.6 log CFU/ml P. macerans in the samples. The assay could be useful in commercial settings, allowing a sensitive detection of P. macerans.

p53 Hinders CRISPR/Cas9-Mediated Targeted Gene Disruption in Memory CD8 T Cells In Vivo

CRISPR/Cas9 technology has revolutionized rapid and reliable gene editing in cells. Although many cell types have been subjected to CRISPR/Cas9-mediated gene editing, there is no evidence of success in genetic alteration of Ag-experienced memory CD8 T cells. In this study, we show that CRISPR/Cas9-mediated gene editing in memory CD8 T cells precludes their proliferation after Ag re-encounter in vivo. This defect is mediated by the proapoptotic transcription factor p53, a sensor of DNA damage. Temporarily inhibiting p53 function offers a window of opportunity for the memory CD8 T cells to repair the DNA damage, facilitating robust recall responses on Ag re-encounter. We demonstrate this by functionally altering memory CD8 T cells using CRISPR/Cas9-mediated targeted gene disruption under the aegis of p53siRNA in the mouse model. Our approach thus adapts the CRISPR/Cas9 technology for memory CD8 T cells to undertake gene editing in vivo, for the first time, to our knowledge.

Prevalence, characterization and antimicrobial resistance of Listeria monocytogenes isolated from beef meat in Meknes city, Morocco

Introduction

Listeria monocytogenes is one of the most pathogenic bacteria related to the consumption of contaminated food. This study aims to determine the prevalence of L. monocytogenes in raw beef meat in Meknes city of Morocco, to evaluate its pathogenicity and resistance to antimicrobials.

Methods

During four seasons, a total of 140 samples were collected from supermarkets, butcheries and Souk (weekly traditional market). The PCR method was used to examine the presence of specific and virulence genes in the isolated strains, and also to identify their serotypes. The antimicrobial resistance was determined.

Results

The results show a prevalence of 7.14% which depends on retail sites and also on the season's variation. The majority of the strains were detected in butcheries (6 strains), and supermarkets (4 strains). Moreover, the majority of strains were detected during summer (50%). Concerning virulence genes, the seven researched genes were detected in 100% of isolated strains. The majority of strains were of the (1/2a, 1/2c, 3a and 3c) serogroup (70%), while two of them were of the (1/2b, 3b, 4b and 4d) serogroup (20%). All isolates were resistant to at least one antimicrobial, while three strains were resistant to nine tested antimicrobials. However, they were highly susceptible to amikacin, imipenem, gentamicin, sulfamethoxazole and chloramphenicol.

Conclusions

According to results, isolated L. monocytogenes from analyzed beef meat shows a high level of pathogenicity and resistance to the most used antimicrobials in listeriosis therapy, which calls for the severe application of quality systems at the slaughterhouses and retail sites level.

Development of a loop-mediated isothermal amplification assay targeting lmo0753 gene for detection of Listeria monocytogenes in wastewater

Contaminated wastewater plays an important role in the transmission of Listeria monocytogenes in the environment. In this study, a loop-mediated isothermal amplification (LAMP) assay for sensitive detection of L.  monocytogenes in wastewater from treatment plants was developed, validated and compared to conventional PCR. The lmo0753 gene which codes for a Crp/Fnr family transcription factor, was targeted to design four specific primers to detect L.  monocytogenes in 60 min at 63°C in a water bath. Amplification products were visualized by agarose gel electrophoresis. The detection limit of the LAMP assay was 65 fg µl^-1 of DNA and 38 CFU per ml. Conventional PCR was 10 times less sensitive than LAMP assay with primers targeting the HlyA gene. A total of 70 crude wastewater samples collected at different treatment stages (aeration tank, pre chlorination and post chlorination), were tested directly by LAMP and PCR. Samples from aeration and pre-chlorination stages tested positive with LAMP and culture method but not with conventional PCR. LAMP assay was tolerant to inhibitors present in wastewater and circumvented the need for isolation of pure DNA for detection. Both LAMP assay and culture method failed to detect L.  monocytogenes in post-chlorinated wastewater, confirming the efficiency of the treatment process in the removal of L.  monocytogenes. SIGNIFICANCE AND IMPACT OF THE STUDY: Treated wastewater effluent contains Listeria monocytogenes which survives conventional wastewater treatment processes and can re-enter human food chain, thus it is imperative to detect L.  monocytogenes using a rapid and an inexpensive method. To the best of our knowledge, this is the first report of a loop-mediated isothermal amplification (LAMP) assay, targeting the lmo0753 gene for detection of L.  monocytogenes in wastewater from treatment plants. The LAMP assay detects L.  monocytogenes in 60 min at 63°C in a water bath. LAMP does not require isolation of pure genomic DNA hence it is a user friendly method for L.  monocytogenes detection.

Development of a real-time PCR method for the genoserotyping of Salmonella Paratyphi B variant Java

Discriminating between D-tartrate fermenting and non-fermenting strains of Salmonella enterica subsp. enterica serotype Paratyphi B is of major importance as these two variants have different pathogenic profiles. While D-tartrate non-fermenting S. Paratyphi B isolates are the causative agent of typhoid-like fever, D-tartrate fermenting isolates (also called variant Java) of the same serotype trigger the less dangerous gastroenteritis. The determination of S. Paratyphi B variants requires a time-consuming process and complex biochemical tests. Therefore, a quadruplex real-time PCR method, based on the allelic discrimination of molecular markers selected from the scientific literature and from whole genome sequencing data produced in-house, was developed in this study, to be applied to Salmonella isolates. This method was validated with the analysis of 178 S. Paratyphi B (D-tartrate fermenting and non-fermenting) and other serotypes reaching an accuracy, compared with the classical methods, of 98% for serotyping by slide agglutination and 100% for replacement of the biochemical test. The developed real-time PCR permits to save time and to obtain an accurate identification of a S. Paratyphi B serotype and its D-tartrate fermenting profile, which is needed in routine laboratories for fast and efficient diagnostics.

Toxigenic and pathogenic potential of enteric bacterial pathogens prevalent in the traditional fermented foods marketed in the Northeast region of India

The microbial risk involved with natural food fermentation is largely unknown. Here, we report the prevalence of enteric bacterial pathogens in the traditional fermented foods marketed in Northeast region of India. A total of 682 samples of 39 food types (broadly categorized into fermented soybean, bamboo shoot, fish, milk and pork products) collected over four different seasons from seven states of India were analyzed in this study. Cultivation-independent analysis by MiSeq amplicon sequencing of V4-V5 region of the 16S rRNA gene showed the bacterial community structure in the foods. Among the WHO prioritized foodborne bacterial pathogens, we detected the prevalence of phylotypes related to Clostridium botulinum, Bacillus cereus, Staphylococcus aureus, Clostridium perfringens, Listeria monocytogenes, and Escherichia coli in these ethnic foods. We also observed the occurrence of other well known human enteric pathogens like Proteus mirabilis, Clostridium difficile, and Yersinia enterocolitica. Further pathogen-specific qPCR assays confirmed a higher population (>107 cells/g) of B. cereus, P. mirabilis, and a C. botulinum related phylotype in the fermented soybean, fish, and pork products. We noticed a general trend of higher pathogen occurrence during the colder months without any seasonal variation of total bacterial load in the fermented foods. Further qPCR analysis on toxigenic and pathogenic potential, and toxins production by immunoassays showed that all the soybean samples and the isolated B. cereus cultures were positive for diarrheal toxins (Nhe and Hb1), and nearly half of the samples were positive for emetic toxin (cereulide). Similarly, the food samples and associated swarming P. mirabilis cultures were positive with the pathogenic factors like hemolysin (hpm), urease (ure) and multidrug resistance. However, we could not confirm the presence of botulinum neurotoxin (toxins A, B, E, and F) in the C. botulinum positive food samples. This is the first baseline data of the enteric bacterial pathogens prevalent in the traditional fermented foods of India, which will support the sustained effort of WHO to estimate the global foodborne disease burden. The unusual presence of P. mirabilis in the fermented foods marketed in the Indian region with high incidence of urolithiasis cases is a concern. Our study emphasizes the need of the hour to have a coordinated action to control and prevent the spread of enteric bacterial pathogens through fermented foods marketed in India. Moreover, replacing the indigenous process with a defined starter culture based controlled fermentation will enhance the safety of Indian fermented foods.

Detection and discrimination of five E. coli pathotypes using a combinatory SYBR® Green qPCR screening system

A detection and discrimination system for five Escherichia coli pathotypes, based on a combination of 13 SYBR® Green qPCR, has been developed, i.e., combinatory SYBR® Green qPCR screening system for pathogenic E. coli (CoSYPS Path E. coli). It allows the discrimination on isolates and the screening of potential presence in food of the following pathotypes of E. coli: shigatoxigenic (STEC) (including enterohemorrhagic (EHEC)), enteropathogenic (EPEC), enteroaggregative (EAggEC), enteroaggregative shigatoxigenic (EAggSTEC), and enteroinvasive (EIEC) E. coli. The SYBR® Green qPCR assays target the uidA, ipaH, eae, aggR, aaiC, stx1, and stx2 genes. uidA controls for E. coli presence and all the other genes are specific targets of E. coli pathotypes. For each gene, two primer pairs have been designed to guarantee a sufficient detection even in case of deletion or polymorphisms in the target gene. Moreover, all the qPCR have been designed to be run together in a single analytical PCR plate. This study includes the primer pairs' design, in silico and in situ selectivity, sensitivity, repeatability, and reproducibility evaluation of the 13 SYBR® Green qPCR assays. Each target displayed a selectivity of 100%. The limit of detection of the 13 assays is between 1 and 10 genomic copies. Their repeatability and reproducibility comply with the European requirements. As a preliminary feasibility study on food, the CoSYPS Path E. coli system was subsequently evaluated on four food matrices artificially contaminated with pathogenic E. coli. It allowed the detection of an initial contamination level as low as 2 to 7 cfu of STEC/25 g of food matrix after 24 h of enrichment.

Development of a Novel Listeria Enrichment Broth for the Isolation of Pathogenic Listeria

Listeriosis, the disease caused by pathogenic Listeria species, can present severe symptoms in susceptible people. The goal of this study was to develop a novel enrichment broth, Listeria allose enrichment broth (LAEB), to improve isolation of Listeria monocytogenes and Listeria ivanovii from samples through incorporating a specific carbohydrate and reducing inhibitor concentrations. Other coexisting bacteria, particularly Listeria innocua, can interfere with the isolation of pathogenic Listeria in such ways as overgrowth of L. innocua and the generation of inhibitory metabolites. The incorporation of allose into the novel LAEB was effective for slowing the growth of L. innocua and other nontarget microorganisms. We determined that 35°C and pH 7.0 under aerobic conditions are optimal for Listeria growth in this medium. The novelty of the use of LAEB is the single enrichment procedure at 35°C for 24 h, obviating the need for a secondary enrichment medium. In 50 simulated samples, the sensitivity of the LAEB method (86%) was higher than that of the International Organization for Standardization (EN ISO) method (70%). In 142 naturally contaminated samples tested, the isolation rate for pathogenic Listeria with the LAEB method was 26.0% (37 of 142 samples), which was significantly higher than the 17.6% (25 of 142 samples) for the EN ISO method. Higher isolation rates and a quicker and easier protocol make the novel LAEB method an appropriate alternative for the isolation of pathogenic Listeria.

Development and performance assessment of a luminex xMAP® direct hybridization assay for the detection and identification of indoor air fungal contamination

Considered as a public health problem, indoor fungal contamination is generally monitored using classical protocols based on culturing. However, this culture dependency could influence the representativeness of the fungal population detected in an analyzed sample as this includes the dead and uncultivable fraction. Moreover, culture-based protocols are often time-consuming. In this context, molecular tools are a powerful alternative, especially those allowing multiplexing. In this study a Luminex xMAP® assay was developed for the simultaneous detection of 10 fungal species which are most frequently in indoor air and that may cause health problems. This xMAP® assay was found to be sensitive, i.e. its limit of detection is ranging between 0.05 and 0.01 ng of gDNA. The assay was subsequently tested with environmental air samples which were also analyzed with a classical protocol. All the species identified with the classical method were also detected with the xMAP® assay, however in a shorter time frame. These results demonstrate that the Luminex xMAP® fungal assay developed in this study could contribute to the improvement of public health and specifically to the indoor fungal contamination treatment.

The Continuous Challenge of Characterizing the Foodborne Pathogen Listeria monocytogenes

Listeria monocytogenes is an important foodborne pathogen commonly isolated from food processing environments and food products. This organism can multiply at refrigeration temperatures, form biofilms on different materials and under various conditions, resist a range of environmental stresses, and contaminate food products by cross-contamination. L. monocytogenes is recognized as the causative agent of listeriosis, a serious disease that affects mainly individuals from high-risk groups, such as pregnant women, newborns, the elderly, and immunocompromised individuals. Listeriosis can be considered a disease that has emerged along with changing eating habits and large-scale industrial food processing. This disease causes losses of billions of dollars every year with recalls of contaminated foods and patient medical treatment expenses. In addition to the immune status of the host and the infecting dose, the virulence potential of each strain is crucial for the development of disease symptoms. While many isolates are naturally virulent, other isolates are avirulent and unable to cause disease; this may vary according to the presence of molecular determinants associated with virulence. In the last decade, the characterization of genetic profiles through the use of molecular methods has helped track and demonstrate the genetic diversity among L. monocytogenes isolates obtained from various sources. The purposes of this review were to summarize the main methods used for isolation, identification, and typing of L. monocytogenes and also describe its most relevant virulence characteristics.

Locked nucleic acid probe-based real-time PCR for the diagnosis of Listeria monocytogenes in ruminants

Because of its high fatality rate, listeriosis ranks among the most important infectious diseases worldwide. Although ruminants are known as natural reservoirs for Listeria monocytogenes and a possible source of human listeriosis, studies of the prevalence and risk factors associated with ruminant listeriosis are limited to some developed countries. Therefore, this report describes the development of a real-time PCR targeting the hly gene for the absolute quantification of L. monocytogenes based on circular and linear DNA standards. Results show that the PCR that uses circular plasmid as a template gave a 2.6-7.89 greater threshold cycle number than did equimolar linear standards. No cross-amplification was observed when bacteria commonly found in bovine and ovine diseases were tested. The PCR achieved good intra and inter-run reproducibility and a detection limit of 6.1 copies of linear plasmid per reaction. This PCR was then applied to 1134 samples taken from 378 Tunisian ruminants. Based on the test sensitivity (90%) and specificity (100%), the true individual animal prevalence of listeriosis was 5.7% in cattle and 10.2% in sheep. In addition, the true herd-level prevalence was 50.1% in cattle and 26.7% in sheep. A multivariable logistic regression analysis at the animal-population level indicated that for cattle, the variables strata and mastitis were important risk factors, whereas for sheep, the variables strata, age and abortion were found to be associated with listeriosis. At the herd level, risk factors for Listeria test-positivity they were: abortion, herd composition and silage storage for cattle, whereas for sheep were: management system, cleaning frequency, silage storage and floor type. Animal hygiene, food quality and sanitary practices on the farm should be applied as strategies to control this pathogen in ruminant herds.

A molecular approach for the rapid, selective and sensitive detection of Exophiala jeanselmei in environmental samples: development and performance assessment of a real-time PCR assay

Exophiala jeanselmei is an opportunistic pathogenic black yeast growing in humid environments such as water reservoirs of air-conditioning systems. Because this fungal contaminant could be vaporized into the air and subsequently cause health problems, its monitoring is recommended. Currently, this monitoring is based on culture and microscopic identification which are complex, sometimes ambiguous and time-demanding, i.e., up to 21 days. Therefore, molecular, culture-independent methods could be more advantageous for the monitoring of E. jeanselmei. In this study, we developed a SYBR®green real-time PCR assay based on the internal transcribed spacer 2 from the 18S ribosomal DNA complex for the specific detection of E. jeanselmei. The selectivity (100 %), PCR efficiency (95.5 %), dynamic range and repeatability of this qPCR assay were subsequently evaluated. The limit of detection for this qPCR assay was determined to be 1 copy of genomic DNA of E. jeanselmei. Finally, water samples collected from cooling reservoirs were analyzed using this qPCR assay to deliver a proof of concept for the molecular detection of E. jeanselmei in environmental samples. The results obtained by molecular analysis were compared with those of classical methods (i.e., culture and microscopic identification) used in routine analysis and were 100 % matching. This comparison demonstrated that this SYBR®green qPCR assay can be used as a molecular alternative for monitoring and routine investigation of samples contaminated by E. jeanselmei, while eliminating the need for culturing and thereby considerably decreasing the required analysis time to 2 days.

Use of next generation sequencing data to develop a qPCR method for specific detection of EU-unauthorized genetically modified Bacillus subtilis overproducing riboflavin

Background

Recently, the presence of an unauthorized genetically modified (GM) Bacillus subtilis bacterium overproducing vitamin B2 in a feed additive was notified by the Rapid Alert System for Food and Feed (RASFF). This has demonstrated that a contamination by a GM micro-organism (GMM) may occur in feed additives and has confronted for the first time,the enforcement laboratories with this type of RASFF. As no sequence information of this GMM nor any specific detection or identification method was available, Next GenerationSequencing (NGS) was used to generate sequence information. However, NGS data analysis often requires appropriate tools, involving bioinformatics expertise which is not alwayspresent in the average enforcement laboratory. This hampers the use of this technology to rapidly obtain critical sequence information in order to be able to develop a specific qPCRdetection method.

Methods

Data generated by NGS were exploited using a simple BLAST approach. A TaqMan® qPCR method was developed and tested on isolated bacterial strains and on the feed additive directly.

Results

In this study, a very simple strategy based on the common BLAST tools that can be used by any enforcement lab without profound bioinformatics expertise, was successfully used toanalyse the B. subtilis data generated by NGS. The results were used to design and assess a new TaqMan® qPCR method, specifically detecting this GM vitamin B2 overproducing bacterium. The method complies with EU critical performance parameters for specificity, sensitivity, PCR efficiency and repeatability. The VitB2-UGM method also could detect the B. subtilis strain in genomic DNA extracted from the feed additive, without prior culturing step.

Conclusions

The proposed method, provides a crucial tool for specifically and rapidly identifying this unauthorized GM bacterium in food and feed additives by enforcement laboratories. Moreover, this work can be seen as a case study to substantiate how the use of NGS data can offer an added value to easily gain access to sequence information needed to develop qPCR methods to detect unknown andunauthorized GMO in food and feed.

Electronic supplementary material

The online version of this article (doi:10.1186/s12896-015-0216-y) contains supplementary material, which is available to authorized users.

An insight into the isolation, enumeration, and molecular detection of Listeria monocytogenes in food

Listeria monocytogenes, a foodborne pathogen that can cause listeriosis through the consumption of food contaminated with this pathogen. The ability of L. monocytogenes to survive in extreme conditions and cause food contaminations have become a major concern. Hence, routine microbiological food testing is necessary to prevent food contamination and outbreaks of foodborne illness. This review provides insight into the methods for cultural detection, enumeration, and molecular identification of L. monocytogenes in various food samples. There are a number of enrichment and plating media that can be used for the isolation of L. monocytogenes from food samples. Enrichment media such as buffered Listeria enrichment broth, Fraser broth, and University of Vermont Medium (UVM) Listeria enrichment broth are recommended by regulatory agencies such as Food and Drug Administration-bacteriological and analytical method (FDA-BAM), US Department of Agriculture-Food and Safety (USDA-FSIS), and International Organization for Standardization (ISO). Many plating media are available for the isolation of L. monocytogenes, for instance, polymyxin acriflavin lithium-chloride ceftazidime aesculin mannitol, Oxford, and other chromogenic media. Besides, reference methods like FDA-BAM, ISO 11290 method, and USDA-FSIS method are usually applied for the cultural detection or enumeration of L. monocytogenes. most probable number technique is applied for the enumeration of L. monocytogenes in the case of low level contamination. Molecular methods including polymerase chain reaction, multiplex polymerase chain reaction, real-time/quantitative polymerase chain reaction, nucleic acid sequence-based amplification, loop-mediated isothermal amplification, DNA microarray, and next generation sequencing technology for the detection and identification of L. monocytogenes are discussed in this review. Overall, molecular methods are rapid, sensitive, specific, time- and labor-saving. In future, there are chances for the development of new techniques for the detection and identification of foodborne with improved features.

Mining of novel species-specific primers for PCR detection of Listeria monocytogenes based on genomic approach

Listeria monocytogenes in contaminated food is considered as a serious health threat for consumers due to its high mortality rate. The objective of this study was to obtain novel species-specific target-genes and primers for the molecular detection of L. monocytogenes using a comparative genomic approach. By comparative analysis of L. monocytogenes and non-L. monocytogenes genome sequences in the GenBank database with BLAST program, 26 specific target sequences were used as candidates and the primers were designed for L. monocytogenes species-specificity verification by using PCR assay. Finally, the three genes LMOf2365_0970, LMOf2365_2721 and mpl were identified to have L. monocytogenes species-specificity and be unique as detection targets for diagnostic application. The species-specific primer Lm8 of gene LMOf2365_0970, Lm13 of gene LMOf2365_2721 and Lm20 of gene mpl showed better specificity and sensitivity than the primers described previously. The PCR detection limits of the three specific primer sets were 430, 43, 4.3 fg/μL for genomic DNA, and 5 × 10(3), 50, 5 cfu/mL for pure culture of L. monocytogenes. There was no interference in specificity of detecting L. monocytogenes by co-culture with other foodborne pathogens in high concentration. Moreover, after 6-8 h of enrichment, L. monocytogenes in the artificially contaminated milk samples at an inoculum dose of 38 cfu/10 mL milk could be detected successfully with the studied three primers. Therefore, the three specific genes and primers can be applied to establish a novel rapid and accurate method for detecting L. monocytogenes in food materials.

The challenge of enumerating Listeria monocytogenes in food

Listeria monocytogenes is recognised as a serious foodborne pathogen in humans. However, food products are usually contaminated at low levels (i.e. <100 CFU/g) and there is still no adequate enumeration method for testing food. Much research has been carried out to improve Listeria enumeration methods, leading to several proposed alternative methods such as the most probable number technique, molecular-based methods and bacterial cell concentration techniques. Here, we catalogue the current knowledge concerning L. monocytogenes enumeration, with a particular focus on the problem of enumerating low level contamination.

Development and performance assessment of a qualitative SYBR® green real-time PCR assay for the detection of Aspergillus versicolor in indoor air

Currently, contamination of indoor environment by fungi and molds is considered as a public health problem. The monitoring of indoor airborne fungal contamination is a common tool to help understanding the link between fungi in houses and respiratory problems. Classical analytical monitoring methods, based on cultivation and microscopic identification, depend on the growth of the fungi. Consequently, they are biased by difficulties to grow some species on certain culture media and under certain conditions or by noncultivable or dead fungi that can consequently not be identified. However, they could have an impact on human health as they might be allergenic. Since molecular methods do not require a culture step, they seem an excellent alternative for the monitoring of indoor fungal contaminations. As a case study, we developed a SYBR® green real-time PCR-based assay for the specific detection and identification of Aspergillus versicolor, which is frequently observed in indoor environment and known to be allergenic. The developed primers amplify a short region of the internal transcribed spacer 1 from the 18S ribosomal DNA complex. Subsequently, the performance of this quantitative polymerase chain reaction (qPCR) method was assessed using specific criteria, including an evaluation of the selectivity, PCR efficiency, dynamic range, and repeatability. The limit of detection was determined to be 1 or 2 copies of genomic DNA of A. versicolor. In order to demonstrate that this SYBR® green qPCR assay is a valuable alternative for monitoring indoor fungal contamination with A. versicolor, environmental samples collected in contaminated houses were analyzed and the results were compared to the ones obtained with the traditional methods.

A new rapid method for detecting epidermal growth factor receptor mutations in non-small cell lung cancer

Mutations in the epidermal growth factor receptor (EGFR) gene are associated with a favorable clinical response to the EGFR tyrosine kinase inhibitors gefitinib and erlotinib in non-small cell lung cancer (NSCLC). We present here, a new method for the rapid detection of the two most common EGFR mutations (delE746-A750 and L858R) from clinical samples. The methodology involves the combination of newly designed mutation-specific primers and a novel real-time PCR machine with an innovative thermo-control mechanism that enables ultrarapid PCR. We evaluated this method using a cell mixture composed of various ratios of lung cancer cells harboring mutated or wild-type EGFR, lung cancer tissues obtained by surgery, and a cytology sample obtained by bronchoscopy from a lung cancer patient. In the cell mixture analysis, our method detected 0.1% of cells with delE746-A750 and 1% of cells with L858R among cells with wild-type EGFR. In 143 lung cancer tissues, the result of this assay was concordant with those of direct sequencing in 138 samples. The five samples with discordant results were tested using a PCR-Invader assay and the result matched those of our method at 100%. We also successfully detected EGFR mutations in the lavage obtained from a lung cancer patient. The turnaround time for this method was <10 min, and all steps could be accomplished in <50 min after sample collection. Thus, our novel PCR method offers a rapid, simple, and less expensive test for EGFR mutations and can be applied as a point-of-care diagnostic test.

Bacteriocin production and inhibition of Listeria monocytogenes by Lactobacillus sakei subsp. sakei 2a in a potentially synbiotic cheese spread

Survival, bacteriocin(s) production, and antilisterial effect of Lactobacillus sakei subsp. sakei 2a were evaluated in a potentially synbiotic cheese spread, throughout storage at 4 °C and 15 °C for up to 28 days, using culture-dependent (plate count) and culture-independent (qPCR) methods. Bacteriocin(s) production in the food product was monitored by phenotypic and molecular (RT-qPCR) techniques. Three cheese spread trials (T) containing the prebiotic fiber inulin were produced in duplicates and studied: T1 (control - without inoculation of lactic acid bacteria); T2 (inoculated with the non-bacteriocinogenic Lb. sakei ATCC 15521 strain), and T3 (inoculated with the bacteriocinogenic Lb. sakei 2a strain). The cheese spreads were challenged with Listeria monocytogenes serotypes 4b and 1/2a, individually added to the food product. The counts of Lb. sakei 2a in the cheese spread T3 remained high during storage and the growth of L. monocytogenes was inhibited at both temperatures, especially L. monocytogenes 4b in the food product kept at 15 °C due to the production of bacteriocins (up to 6,400 AU/mL). Expression of the genes sakP and sakQ encoding for bacteriocins production during the cheese spread storage was demonstrated. Lb. sakei 2a can be used for production of potentially synbiotic cheese spreads with increased safety.

Fast and discriminative CoSYPS detection system of viable Salmonella spp. and Listeria spp. in carcass swab samples

In this study, the complete CoSYPS Path Food workflow including all steps, namely swab sample enrichment, SYBR®Green qPCR detection of Salmonella spp. and Listeria spp., isolation and confirmation of the detected strain, was validated on beef carcass swabs. To perform the validation, the results of the complete workflow were compared, according to the ISO 16140:2003, with the ISO reference methods for detection, isolation and confirmation of Listeria monocytogenes and Salmonella spp. The results showed that the relative level of detection and the limit of detection of the complete workflow and ISO reference methods are in a range from 2 to 16 CFU/swab for both bacteria. The relative specificity, sensitivity and accuracy identified during this validation were all 100% since the results obtained with the complete CoSYPS Path Food workflow and the ISO reference methods were identical (Cohen's kappa index=1.00). In addition the complete CoSYPS Path Food workflow is able to provide detection results (negative or presumptive positive) in half the time needed as for the ISO reference methods. These results demonstrate that the performance of the complete CoSYPS Path Food workflow is not only comparable to the ISO reference methods but also provides a faster response for the verification of beef carcasses before commercial distribution.

Identification of six Listeria species by real-time PCR assay

The Listeria genus comprises 10 recognized species. Listeria monocytogenes causes listeriosis in humans and other animals primarily via contaminated food or animal feed. Listeria ivanovii causes listeriosis in animals and on rare occasions in humans. The identification of nonpathogenic species of Listeria in foods indicates that conditions exist that support the growth of pathogenic strains and is used to facilitate the implementation of control and prevention measures. This study shows the development and evaluation of a 5'exonuclease real-time PCR assay for the rapid identification of Listeria seeligeri, Listeria welshimeri, L. monocytogenes, L. ivanovii, Listeria grayi and Listeria innocua. The assay consists of two triplexes that were evaluated using 53 cultures of Gram-positive bacteria, including 49 Listeria spp. from human, animal, food or food-processing environments. The assay was rapid, specific and reproducible and could identify each of the six species from a mixture of strains. The developed assay proved to be a powerful means of rapidly identifying Listeria species and could be usefully implemented in busy specialist reference laboratories.

SIGNIFICANCE AND IMPACT OF THE STUDY

The identification of species of Listeria from foods is important to monitor pathogenic strains and facilitates the implementation of control measures. This study shows the development and evaluation of a 5'exonuclease real-time PCR assay for the rapid identification of L. seeligeri, L. welshimeri, L. monocytogenes and L. ivanovii, L. grayi, L. innocua. The developed assay proved to be specific, rapid and reproducible and therefore could be implemented in busy specialist reference laboratories.

SYBR®Green qPCR Salmonella detection system allowing discrimination at the genus, species and subspecies levels

In this work, a three-level Salmonella detection system based on a combination of seven SYBR®Green qPCR was developed. This detection system discriminates Salmonella at the genus, species and subspecies levels using a single 96-well plate. The SYBR®Green qPCR assays target the invA, rpoD, iroB and safC genes, as well as the STM0296 locus, putatively coding for a cytoplasmic protein. This study includes the design of primer pairs, in silico and in situ selectivity, sensitivity, repeatability and reproducibility evaluations of the seven SYBR®Green qPCR assays. Each detection level displayed a selectivity of 100 %. This combinatory SYBR®Green qPCR system was also compared with three commercially available Salmonella qPCR detection kits. This comparison highlighted the importance of using a multi-gene detection system to be able to detect every target strain, even those with deletion or mutation of important genes.

Application of Real Time PCR for the Detection and Enumeration of Vibrio parahaemolyticus from Seafood in Sarawak (Malaysia)

Vibrio parahaemolyticus has been associated as the major cause of food poisoning and gastroenteritis in manycountries including Southeast Asia. Their human infection is regularly associated with the consumption of rawor undercooked seafood and contaminated water supplies. A rapid method of detection is important to monitorthe occurrence of V. parahaemolyticus in both food and environment samples especially in Malaysia. Thus, theaim of this study was to detect and enumerate V. parahaemolyticus from seafood by using the real-time PCRbased on the SYBR green assay. targeting the thermolabile (tl) gene. The assay was applied on 24 seafoodsamples comprised of 6 cockles, 6 prawns, 6 squids and 6 fishes. In this study, all of the six cockles and prawnswere positive for the presence of V. parahaemolyticus while fish samples have only 2 positive isolates.However, this study recorded no presence of V. parahaemolyticus in squids. Overall, the real-time PCR assaywas proven to be highly specific, and is sensitive in detecting and enumerating V. parahaemolyticus in theseafood samples. In addition, this study has proven that seafood (especially cockles and prawns) are potentialsources for V. parahaemolyticus.