Detection, quantification and vitality of Listeria monocytogenes in food as determined by quantitative PCR

Boron nitride nanoplate-based strand exchange amplification with enhanced sensitivity and rapidity for quantitative detection of Staphylococcus aureus in food samples

Staphylococcus aureus is one of the most common foodborne pathogens that can cause serious food poisoning and infectious diseases in humans. Standard identification approaches include nucleic acid amplification, but current amplification tools suffer from low amplification efficiency, resulting in the risk of low sensitivity and long detection time. Herein, boron nitride nanoplates (BNNPs) were chosen as an additive for enhancing the sensitivity and rapidity of strand exchange amplification (SEA), thereby successfully expanding the application of nucleic acid detection for detecting Staphylococcus aureus in food samples. As a result, SEA based on boron nitride nanoplates (BNNP-SEA) was employed for sensitive and rapid detection of foodborne pathogen Staphylococcus aureus. Compared with classical SEA, the BNNP-based SEA assay was more than 10-fold sensitive, and the detection time was reduced by 15 minutes. The optimized BNNP-based SEA shows a wide linear range from 40 pg to 50 ng in a diluted solution of the target DNA with a low detection limit of 40 pg. Moreover, the BNNP-based SEA achieves the quantitative detection of Staphylococcus aureus in different food samples (pork, beef, mutton, duck, milk and shrimp). In contrast to the classical SEA, the BNNP-based SEA method enabled sensitive and rapid detection of Staphylococcus aureus in the above food samples at concentrations as low as 5 × 103 CFU mL-1. The BNNP-based SEA assay is specific, sensitive and reliable, offering a valuable diagnostic technology for routine analysis in food safety research.

Verification of a Rapid Analytical Method for the Qualitative Detection of Listeria spp. and Listeria monocytogenes by a Real-Time PCR Assay according to EN UNI ISO 16140-3:2021

Microbial contamination and foodborne infections are a significant global public health concern. For this reason, the detection, monitoring, and characterization of pathogens represent a significant challenge in quality control settings. Standard approaches, such as culture methods and biochemical tests, are known to be very time-consuming and intensive. Conversely, molecular technologies based on the genomic identification of bacteria are quick and low-cost. Listeria monocytogenes is an opportunistic pathogen and a major concern especially in food industries. It is important to understand and implement multiple quality control measures to control Listeria infection risk and prevent the contamination of products. Standardized detection and confirmation tests such as the API Listeria test, MALDI-TOF MS, and PCR analysis are available. The aim of our work is to provide a specific molecular method, designed according to the EN UNI ISO 16140-3:2021, for the specific detection, monitoring, and characterization of Listeria spp. and Listeria monocytogenes contamination. The verification of this new rapid approach by real-time PCR (qPCR) overcomes the limitations of culture-based techniques, meeting all the verification criteria required by ISO guidelines, including implementation and item confirmation. This system offers a powerful approach to the real-time assessment of food safety, useful for industry self-monitoring and regulatory inspection.

Optical Sensors for Bacterial Detection

Analytical devices for bacterial detection are an integral part of modern laboratory medicine, as they permit the early diagnosis of diseases and their timely treatment. Therefore, special attention is directed to the development of and improvements in monitoring and diagnostic methods, including biosensor-based ones. A promising direction in the development of bacterial detection methods is optical sensor systems based on colorimetric and fluorescence techniques, the surface plasmon resonance, and the measurement of orientational effects. This review shows the detecting capabilities of these systems and the promise of electro-optical analysis for bacterial detection. It also discusses the advantages and disadvantages of optical sensor systems and the prospects for their further improvement.

Viability and Virulence of Listeria monocytogenes in Poultry

The prevalence of Listeria monocytogenes in 30 samples of poultry was determined using culture-dependent (isolation on OCLA and confirmation by conventional polymerase chain reaction -PCR-, OCLA&PCR) and culture-independent (real-time polymerase chain reaction, q-PCR) methods. L. monocytogenes was detected in 15 samples (50.0%) by OCLA&PCR and in 20 (66.7%) by q-PCR. The concentrations (log10 cfu/g) of L. monocytogenes (q-PCR) ranged from 2.40 to 5.22 (total cells) and from <2.15 to 3.93 (viable cells). The two methods, q-PCR using a viability marker (v-PCR) and OCLA&PCR (gold standard), were compared for their capacity to detect viable cells of L. monocytogenes, with the potential to cause human disease. The values for sensitivity, specificity and efficiency of the v-PCR were 100%, 66.7% and 83.3%, respectively. The agreement between the two methods (kappa coefficient) was 0.67. The presence of nine virulence genes (hlyA, actA, inlB, inlA, inlC, inlJ, prfA, plcA and iap) was studied in 45 L. monocytogenes isolates (three from each positive sample) using PCR. All the strains harbored between six and nine virulence genes. Fifteen isolates (33.3% of the total) did not show the potential to form biofilm on a polystyrene surface, as determined by a crystal violet assay. The remaining strains were classified as weak (23 isolates, 51.1% of the total), moderate (one isolate, 2.2%) or strong (six isolates, 13.3%) biofilm producers. The strains were tested for susceptibility to a panel of 15 antibiotics. An average of 5.11 ± 1.30 resistances per isolate was observed. When the values for resistance and for reduced susceptibility were taken jointly, this figure rose to 6.91 ± 1.59. There was a prevalence of resistance or reduced susceptibility of more than 50.0% for oxacillin, cefoxitin, cefotaxime, cefepime ciprofloxacin, enrofloxacin and nitrofurantoin. For the remaining antibiotics tested, the corresponding values ranged from 0.0% for chloramphenicol to 48.9% for rifampicin. The high prevalence and level of L. monocytogenes with numerous virulence factors in poultry underline how crucial it is to follow correct hygiene procedures during the processing of this foodstuff in order to reduce the risk of human listeriosis.

Quantification of Total and Viable Cells and Determination of Serogroups and Antibiotic Resistance Patterns of Listeria monocytogenes in Chicken Meat from the North-Western Iberian Peninsula

Twenty samples of minced chicken meat procured from butcher’s shops in León (Spain; 10 samples) and Vila Real (Portugal; 10 samples) were analyzed. Microbial concentrations (log10 cfu/g) of 7.53 ± 1.02 (viable aerobic microbiota), 7.13 ± 1.07 (psychrotrophic microorganisms), and 4.23 ± 0.88 (enterobacteria) were found. The detection method described in the UNE-EN ISO 11290-1 standard (based on isolation from the chromogenic medium OCLA) with confirmation by the polymerase chain reaction (PCR; lmo1030) (OCLA−PCR), revealed Listeria monocytogenes in 14 samples (70.0% of the total), nine of Spanish origin and five of Portuguese (p > 0.05). The levels of viable and inactivated L. monocytogenes in the samples were determined with a q-PCR using propidium monoazide (PMAxx) as a viability marker. Seven samples tested positive both with the OCLA−PCR and with the q-PCR, with estimated concentrations of viable cells varying between 2.15 log10 cfu/g (detection limit) and 2.94 log10 cfu/g. Three samples tested negative both with the OCLA−PCR and with the q-PCR. Seven samples were positive with the OCLA−PCR, but negative with the q-PCR, and three samples tested negative with the OCLA−PCR and positive with the q-PCR. The percentage of viable cells relative to the total ranged between 2.4% and 86.0%. Seventy isolates of L. monocytogenes (five from each positive sample) were classified in PCR serogroups with a multiplex PCR assay. L. monocytogenes isolates belonged to serogroups IIa (52 isolates; 74.3%), IIc (7; 10.0%), IVa (2; 2.9%), and IVb (9; 12.9%). The susceptibility of the 70 isolates to 15 antibiotics of clinical interest was tested. The strains presented resistance to between three and eight antibiotics. The average number of resistances was greater (p < 0.001) among strains isolated from Spanish samples (6.20 ± 1.08), than in those from Portugal (5.00 ± 1.08). In both groups of strains, a prevalence of resistance higher than 95% was observed for oxacillin, cefoxitin, cefotaxime, and cefepime. The need to handle minced chicken meat correctly, taking care to cook it sufficiently and to avoid cross-contamination, so as to reduce the danger of listeriosis, is emphasized. A combination of culture-dependent and culture-independent methods offers complementary routes for the detection in food of the cells of L. monocytogenes in various different physiological states.

Challenges and perspectives of quantitative microbiome profiling in food fermentations

Spontaneously fermented foods are consumed and appreciated for thousands of years although they are usually produced with fluctuated productivity and quality, potentially threatening both food safety and food security. To guarantee consistent fermentation productivity and quality, it is essential to control the complex microbiota, the most crucial factor in food fermentations. The prerequisite for the control is to comprehensively understand the structure and function of the microbiota. How to quantify the actual microbiota is of paramount importance. Among various microbial quantitative methods evolved, quantitative microbiome profiling, namely to quantify all microbial taxa by absolute abundance, is the best method to understand the complex microbiota, although it is still at its pioneering stage for food fermentations. Here, we provide an overview of microbial quantitative methods, including the development from conventional methods to the advanced quantitative microbiome profiling, and the application examples of these methods. Moreover, we address potential challenges and perspectives of quantitative microbiome profiling methods, as well as future research needs for the ultimate goal of rational and optimal control of microbiota in spontaneous food fermentations. Our review can serve as reference for the traditional food fermentation sector for stable fermentation productivity, quality and safety.

Development of a rapid qPCR method to quantify lactic acid bacteria in cold-smoked salmon

Quantification of lactic acid bacteria (LAB) is essential to control quality of seafood products like cold-smoked salmon (CSS). In the present study, we report the design and optimization of a dual-labelled TaqMan ™ probe targeting the V7 region of 16S rRNA gene for the detection of LAB in CSS. This quantitative PCR (qPCR) assays is useful for the simultaneous detection of the ten LAB genera communally encountered in CSS as Aerococcus, Carnobacterium, Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Macrococcus, Streptococcus, Vagococcus and Weissella. The specificity of this method was demonstrated against 14 genera (44 isolates, 35 species) of Gram-positive bacteria and 19 genera of Gram-negative (40 isolates, 34 species). Calibration of the method was performed in CSS matrix using a mix of equimolar cultured solution of five LAB. Quantification with the qPCR method range from 3.5 to 8.5 Log CFU/g in CSS matrix, covering 5 orders of magnitude. On these artificially contaminated CSS slices, PCR method results correlated successfully (R² = 0.9945) with the conventional enumeration on Elliker medium. In addition, the new method was successful on commercial CSS from five different origins with a quantification range from 3.7 Log CFU/g to 8.0 Log CFU/g. This one-step quantitative methodology is proposed as a rapid and complementary tool of the cultural methods to investigate the LAB microbiota and biodiversity of CSS.

In vitro virulence potential, surface attachment and transcriptional response of sublethally injured Listeria monocytogenes following exposure to peracetic acid

The disinfectant Peracetic acid (PAA) can cause high levels of sublethal injury to L. monocytogenes. This study aims to evaluate phenotypic and transcriptional characteristics concerning surface attachment and virulence potential of sublethally injured L. monocytogenes ScottA and EGDe after exposure to 0.75 ppm PAA for 90 min at 4°C and subsequent incubation in TSBY at 4°C. Results showed that injured L. monocytogenes cells (99% of total population) were able to attach (after 2 and 24h) on stainless steel coupons at 4°C and 20°C. In vitro virulence assays using human intestinal epithelial Caco-2 cells showed that injured L. monocytogenes could invade host cells but could not proliferate intracellularly. In vitro virulence response was strain-dependent; injured ScottA was more invasive than EGDe. Assessment of PAA-injury at the transcriptional level showed upregulation of genes (motB, flaA) involved in flagellum motility and surface attachment. The transcriptional response of L. monocytogenes EGDe and ScottA was different; only injured ScottA demonstrated upregulation of the virulence genes inlA and plcA. Downregulation of the stress-related genes fri and kat, and upregulation of lmo0669 was observed in injured ScottA. The obtained results indicate that sublethally-injured L. monocytogenes cells may retain part of their virulence properties as well as their ability to adhere on food processing surfaces. Transmission to food products and introduction of these cells in the food chain is therefore a plausible scenario that is worth taking into consideration in terms of risk assessment. Importance L. monocytogenes is the causative agent of listeriosis a serious food-borne illness. Antimicrobial practices, such as disinfectants used for the elimination of this pathogen in food industry can produce a sublethally injured population fraction. Injured cells of this pathogen, that may survive an antimicrobial treatment, may pose a food safety-risk. Nevertheless, knowledge regarding how sublethal injury may impact important cellular traits and phenotypic responses of this pathogen is limited. This work suggests that sublethally injured L. monocytogenes cells maintain the virulence and surface attachment potential and highlights the importance of the occurrence of sublethally injured cells regarding food safety.

Surveillance of Fresh Artisanal Cheeses Revealed High Levels of Listeria monocytogenes Contamination in the Department of Quindío, Colombia

Listeriosis is a foodborne disease caused by Listeria monocytogenes. Because outbreaks of listeriosis are associated with the ingestion of contaminated dairy products, surveillance of artisanal cheeses to detect the presence of this microorganism is necessary. We collected three types of artisanal non-acid fresh cheese (Campesino, Costeño, and Cuajada) from 12 municipalities of the Department of Quindío, Colombia. L. monocytogenes was identified using VIDAS^® and confirmed with API^® Listeria Rapid Kit. L. monocytogenes was detected in 104 (53.6%) of the 194 artisanal fresh-cheese samples analyzed. The highest percentages of contamination were detected in Salento (90.9%), Calracá (65.5%), Armenia (64.9%), and Filandia (50%). A significant association between municipality and contamination with L. monocytogenes was identified. However, no association could be established between the type of cheese and the occurrence of the bacterium. This is the first study on the presence of L. monocytogenes in artisanal fresh cheeses sold in the municipalities of the Department of Quindío, and the findings revealed very high percentages of contaminated samples. The presence of L. monocytogenes in artisanal cheeses remains a public health threat in developing countries, especially Colombia, where existing legislation does not require the surveillance of L. monocytogenes in food.

Real-Time PCR Method Combined with a Matrix Lysis Procedure for the Quantification of Listeria monocytogenes in Meat Products

In this study a real-time PCR method has been developed for the specific quantification of the foodborne pathogen Listeria monocytogenes on meat products through the gene hlyA. The PCR was combined with a matrix lysis that allowed the obtaining of the microorganisms without sample dilution and the elimination the PCR inhibitors from dry-cured ham. The qPCR method calibration curve had an efficiency of 100.4%, limits of detection and quantification were 30.1 ± 6.2 CFU/g which is under the legal limit of L. monocytogenes in ready-to-eat products, and an analytical variability <0.25 log hlyA gene copies/reaction. The analysis was performed simultaneously with the reference method ISO 11290-2. The comparison of the qPCR-matrix lysis results with the reference method showed an excellent correspondence, with a relative accuracy between 95.83-105.20%. Finally, the method was applied to commercial derived meat samples and the pathogen was quantified in one of the commercial samples assayed in 69.1 ± 13.9 CFU/g while the reference method did not quantify it. The optimized qPCR showed higher precision and sensitivity than the reference method at low concentrations of the microorganism in a shorter time. Therefore, qPCR-matrix lysis shows a potential application in the meat industry for L. monocytogenes routine control.

A review of Listeria monocytogenes from meat and meat products: Epidemiology, virulence factors, antimicrobial resistance and diagnosis

Listeria monocytogenes is a zoonotic food-borne pathogen that is associated with serious public health and economic implications. In animals, L. monocytogenes can be associated with clinical listeriosis, which is characterised by symptoms such as abortion, encephalitis and septicaemia. In human beings, listeriosis symptoms include encephalitis, septicaemia and meningitis. In addition, listeriosis may cause gastroenteric symptoms in human beings and still births or spontaneous abortions in pregnant women. In the last few years, a number of reported outbreaks and sporadic cases associated with consumption of contaminated meat and meat products with L. monocytogenes have increased in developing countries. A variety of virulence factors play a role in the pathogenicity of L. monocytogenes. This zoonotic pathogen can be diagnosed using both classical microbiological techniques and molecular-based methods. There is limited information about L. monocytogenes recovered from meat and meat products in African countries. This review strives to: (1) provide information on prevalence and control measures of L. monocytogenes along the meat value chain, (2) describe the epidemiology of L. monocytogenes (3) provide an overview of different methods for detection and typing of L. monocytogenes for epidemiological, regulatory and trading purposes and (4) discuss the pathogenicity, virulence traits and antimicrobial resistance profiles of L. monocytogenes.

Differential Modulation of Listeria monocytogenes Fitness, In Vitro Virulence, and Transcription of Virulence-Associated Genes in Response to the Presence of Different Microorganisms

Interactions between Listeria monocytogenes and food-associated or environmental bacteria are critical not only for the growth but also for a number of key biological processes of the microorganism. In this regard, limited information exists on the impact of other microorganisms on the virulence of L. monocytogenes In this study, the growth of L. monocytogenes was evaluated in a single culture or in coculture with L. innocua, Bacillus subtilis, Lactobacillus plantarum, or Pseudomonas aeruginosa in tryptic soy broth (10°C/10 days and 37°C/24 h). Transcriptional levels of 9 key virulence genes (inlA, inlB, inlC, inlJ, sigB, prfA, hly, plcA, and plcB) and invasion efficiency and intracellular growth in Caco-2 cells were determined for L. monocytogenes following growth in mono- or coculture for 3 days at 10°C or 9 h at 37°C. The growth of L. monocytogenes was negatively affected by the presence of L. innocua and B. subtilis, while the effect of cell-to-cell contact on L. monocytogenes growth was dependent on the competing microorganism. Cocultivation affected the in vitro virulence properties of L. monocytogenes in a microorganism-specific manner, with L. innocua mainly enhancing and B. subtilis reducing the invasion of the pathogen in Caco-2 cells. Assessment of the mRNA levels of L. monocytogenes virulence genes in the presence of the four tested bacteria revealed a complex pattern in which the observed up- or downregulation was only partially correlated with growth or in vitro virulence and mainly suggested that L. monocytogenes may display a microorganism-specific transcriptional response.IMPORTANCE Listeria monocytogenes is the etiological agent of the severe foodborne disease listeriosis. Important insight regarding the physiology and the infection biology of this microorganism has been acquired in the past 20 years. However, despite the fact that L. monocytogenes coexists with various microorganisms throughout its life cycle and during transmission from the environment to foods and then to the host, there is still limited knowledge related to the impact of surrounding microorganisms on L. monocytogenes' biological functions. In this study, we showed that L. monocytogenes modulates specific biological activities (i.e., growth and virulence potential) as a response to coexisting microorganisms and differentially alters the expression of virulence-associated genes when confronted with different bacterial genera and species. Our work suggests that the interaction with different bacteria plays a key role in the survival strategies of L. monocytogenes and supports the need to incorporate biotic factors into the research conducted to identify mechanisms deployed by this organism for establishment in different environments.

Microbiological and Metagenomic Analysis to Assess the Effect of Container Material on the Microbiota of Feta Cheese during Ripening

The aim of the present study was to assess the influence of ripening container’s material on the bacterial diversity of Feta cheese PDO (Protected Designation of Origin). The microbiota of fresh and mature cheese produced in plastic and stainless steel container was monitored by microbial enumeration and 16s rRNA gene sequencing. According to the obtained results, lactic acid bacteria (LAB) was the dominant microbiota of fresh and mature cheese. Metagenomics data revealed that fresh cheese was dominated by Lactococcus followed by members of Enterobacteriaceae family and Pseudomonas. Similarly, Lactococcus was the most abundant genus detected in mature cheese (54 days and 120 days), regardless of the container’s material. In both fresh and mature cheese, species of Pseudomonas, Streptococcus, Acinetobacter, Lactobacillus, Flavobacterium, and Carnobacterium were detected. The abundance of Enterobacteriaceae, Moraxellaceae and Pseudomonadaceae in mature cheese ripened in stainless steel container seems to be numerically reduced after 120 days of storage compared to the cheese ripened in plastic container but not significant differences were observed (p > 0.05). In conclusion, metagenomic analysis suggests that ripening container’s material does not affect the microbial community responsible for the ripening of feta cheese PDO.

Effect of Atmospheric Pressure Plasma on Listeria monocytogenes Attached to Abiotic Surfaces

Listeria monocytogenes can be introduced into food processing plants via raw material of animal or plant origin and can establish endemic populations through formation of biofilms. Biofilms are a continuous source of contamination for food products, and L. monocytogenes cells in biofilms are more resistant to stress and sanitizing agents than are planktonic cells. The use of gas-discharge plasmas may offer a feasible alternative to conventional sanitization methods. Plasmas are a mixture of charged particles, chemically reactive species, and UV radiation and can be used to destroy microorganisms. The purpose of this study was to measure the effectiveness of cold atmospheric pressure plasma (APP) treatments against bacteria attached to a solid surface and to evaluate the individual susceptibility of various L. monocytogenes strains. Attention was focused on the state of the cells after treatment, combining detection by viable counts and quantitative PCR (qPCR). Most of the culturable cells were inactivated after APP treatment, but the qPCR assay targeting the 16S rRNA revealed the presence of injured cells or their entrance into the viable but nonculturable state. These results were at least partly confirmed by a resuscitation experiment. After APP treatment, L. monocytogenes cell suspensions were incubated in brain heart infusion broth; some cells grew in the medium and therefore had survived the treatment. An understanding of the effects of APP on L. monocytogenes can inform the development of sanitation programs incorporating APP for pathogen removal. Methods other than those based of the culturability of the cells should be used to monitor pathogens in food processing plants because cultivation alone may underestimate the actual microbial load.

Brotes de enfermedades transmitidas por los alimentos estudiados mediante técnicas moleculares

Objetivo Aplicar una técnica de reacción en cadena de la polimerasa (PCR) múltiple en tiempo real para la detección de Salmonella spp., Listeria monocytogenes y Yersinia enterocolitica, como herramienta de apoyo diagnóstico en la vigilancia de brotes de enfermedad transmitida por alimentos.Materiales y Métodos Se aplicó la metodología molecular en muestras clínicas provenientes de individuos que estaban asociados a brotes de enfermedad transmitida por alimentos de dos departamentos de Colombia. Los resultados se compararon con los datos arrojados por la metodología convencional de cultivo. Adicionalmente a los aislamientos obtenidos se les evaluó relación clonal mediante la técnica de electroforesis de campo pulsado (PFGE).Resultados Se determinó un total de 123 casos de enfermedad transmitida por alimentos de los cuales 45 muestras biológicas fueron confirmadas por laboratorio y 88 mediante nexo epidemiológico. La metodología molecular detectó 35/45 muestras positivas frente a 17/45 muestras positivas detectadas mediante la metodología convencional. La PFGE demostró relación clonal en cada brote.Conclusión Los resultados del estudio demuestran la aplicabilidad de la técnica molecular como herramienta útil de apoyo diagnóstico en la caracterización de brotes de enfermedad transmitida por alimentos, permitiendo una respuesta oportuna y confiable.

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.

Microbiota of an Italian Grana-Like Cheese during Manufacture and Ripening, Unraveled by 16S rRNA-Based Approaches

The microbial ecology of cheese involves a rich and complex interaction between starter lactic acid bacteria and nonstarter lactic acid bacteria (NSLAB), mainly originating from raw milk and/or from the environment, that can contribute to the final characteristics of cheese. The aim of the present research was the exploration of the active microbiota by RNA-based approaches during the manufacturing and ripening of a Grana-like cheese. Reverse transcriptase PCR (RT-PCR)-denaturing gradient gel electrophoresis (DGGE) and RNA-based high-throughput sequencing were applied to profile microbial populations, while the enumeration of active bacteria was carried out by using quantitative PCR (qPCR). Three different cheese productions (named D, E, and F) collected in the same month from the same dairy plant were analyzed. The application of the qPCR protocol revealed the presence of 7 log CFU/ml of bacterial load in raw milk, while, during ripening, active bacterial populations ranged from <4 to 8 log CFU/ml. The natural whey starters used in the three productions showed the same microbiota composition, characterized by the presence of Lactobacillus helveticus and Lactobacillus delbrueckii Nevertheless, beta-diversity analysis of the 16S rRNA sequencing data and RT-PCR-DGGE showed a clear clustering of the samples according to the three productions, probably driven by the different milks used. Milk samples were found to be characterized by the presence of several contaminants, such as Propionibacterium acnes, Acidovorax, Acinetobacter, Pseudomonas, and NSLAB. The core genera of the starter tended to limit the development of the spoilage bacteria only in two of the three batches. This study underlines the influence of different factors that can affect the final microbiota composition of the artisanal cheese.

IMPORTANCE

This study highlights the importance of the quality of the raw milk in the production of a hard cheese. Independent from the use of a starter culture, raw milk with low microbiological quality can negatively affect the populations of lactic acid bacteria and, as a consequence, impact the quality of the final product due to metabolic processes associated with spoilage bacteria.

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.

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.

Analytical bioconjugates, aptamers, enable specific quantitative detection of Listeria monocytogenes

As a major human pathogen in the Listeria genus, Listeria monocytogenes causes the bacterial disease listeriosis, which is a serious infection caused by eating food contaminated with the bacteria. We have developed an aptamer-based sandwich assay (ABSA) platform that demonstrates a promising potential for use in pathogen detection using aptamers as analytical bioconjugates. The whole-bacteria SELEX (WB-SELEX) strategy was adopted to generate aptamers with high affinity and specificity against live L. monocytogenes. Of the 35 aptamer candidates tested, LMCA2 and LMCA26 reacted to L. monocytogenes with high binding, and were consequently chosen as sensing probes. The ABSA platform can significantly enhance the sensitivity by employing a very specific aptamer pair for the sandwich complex. The ABSA platform exhibited a linear response over a wide concentration range of L. monocytogenes from 20 to 2×10(6) CFU per mL and was closely correlated with the following relationship: y=9533.3x+1542.3 (R(2)=0.99). Our proposed ABSA platform also provided excellent specificity for the tests to distinguish L. monocytogenes from other Listeria species and other bacterial genera (3 Listeria spp., 4 Salmonella spp., 2 Vibrio spp., 3 Escherichia coli and 3 Shigella spp.). Improvements in the sensitivity and specificity have not only facilitated the reliable detection of L. monocytogenes at extremely low concentrations, but also allowed for the development of a 96-well plate-based routine assay platform for multivalent diagnostics.

Rapid detection of Listeria monocytogenes in raw milk and soft cheese by a redox potential measurement based method combined with real-time PCR

The incidence of outbreaks of foodborne listeriosis has indicated the need for a reliable and rapid detection of the microbe in different foodstuffs. A method combining redox potential measurement and real-time polymerase chain reaction (PCR) was developed to detect Listeria monocytogenes in artificially contaminated raw milk and soft cheese. Food samples of 25 g or 25 ml were homogenised in 225 ml of Listeria Enrichment Broth (LEB) with Oxford supplement, and the redox potential measurement technique was applied. For Listeria species the measuring time was maximum 34 h. The absence of L. monocytogenes could reliably be proven by the redox potential measurement method, but Listeria innocua and Bacillus subtilis could not be differentiated from L. monocytogenes on the basis of the redox curves. The presence of L. monocytogenes had to be confirmed by real-time PCR. The combination of these two methods proved to detect < 10 cfu/g of L. monocytogenes in a cost- and time-effective manner. This method can potentially be used as an alternative to the standard nutrient method for the rapid detection of L. monocytogenes in food.

Rapid detection of Listeria monocytogenes by real-time PCR in processed meat and dairy products

The objectives of this study were to evaluate the detection of Listeria monocytogenes in different ready-to-eat foods using real-time PCR (RT-PCR). Various concentrations (10(0) to 10(5) CFU/ml) of L. monocytogenes ATCC 19115 were inoculated into ham, sausage, ground meat, processed milk, cheese, and infant formula. L. monocytogenes ATCC 19115 in the samples was then enumerated on Oxford agar, and DNA was extracted from the samples before and after incubation at 36°C for 4 h. A set of primers and hybridization probe designed in this study was then used to detect the pathogen. The standard curve was then prepared by plotting cycle threshold values for each dilution versus L. monocytogenes cell counts (log CFU). The specificity of the set of primers and hybridization probe was appropriate. A 4-h incubation at 36°C before DNA extraction produced optimum standard curves in comparison to the results for a 0-h incubation. Thus, a 4-h incubation at 36°C was applied for monitoring L. monocytogenes in collected food samples. To monitor L. monocytogenes in foods, 533 samples (ham, 129; sausage, 226; ground meat, 72; processed cheese, 54; processed milk, 42; and infant formula, 10) were collected from retail markets and from the step before pasteurization in plants. Of all 533 samples, 4 samples (0.8%) showed positive signals in RT-PCR. Two samples from hams (1.6%) and two samples from sausages (0.9%) were determined to be positive for L. monocytogenes at < 100 CFU/g. The results indicate that the RT-PCR detection method with the set of primers and hybridization probe designed in this study should be useful in monitoring for L. monocytogenes in processed meat and milk products.

Nation-wide study of the occurrence of Listeria monocytogenes in French soils using culture-based and molecular detection methods

Soil is a potential reservoir of human pathogens and a possible source of contamination of animals, crops and water. In order to study the distribution of Listeria monocytogenes in French soils, a real-time PCR TaqMan assay targeting the phosphoribosylpyrophosphate synthetase (prs) gene of L. monocytogenes was developed for the specific detection and quantification of this bacterium within a collection of 1315 soil DNAs originated from the French Soil Quality Monitoring Network. The prs real-time PCR TaqMan assay was specific for L. monocytogenes and could quantify accurately down to 10(4)L. monocytogenes per gram of dry soil. Among the 1315 soil DNAs, prs was not detected. This suggested that the level of L. monocytogenes in French soils is generally less than 10(4)L. monocytogenes per gram of dry soil. In order to confirm this hypothesis, we investigated the occurrence of L. monocytogenes in samples collected in the Burgundy region by culture-based and molecular detection methods on the same samples. By using cultivation-based detection, 17% of samples were positive for the presence of L. monocytogenes while only 2% were found positive by the molecular detection method. L. monocytogenes was repeatedly isolated from cow pasture soils but not from cultivated soils, meadows or forest soils. Isolates were grouped in the serovar 1/2a or 3a and 4b or 4d or 4e. Taken as a whole, molecular detection results globally demonstrate that the level of L. monocytogenes in French soils does not exceed 10(4)CFU per gram of dry soil. However, in comparison with culture-based method, PCR-based detection underestimates the occurrence of L. monocytogenes in soils. Soil sampling procedure also appears critical and may also lead to the underestimation of the incidence of L. monocytogenes.

Peptide-bacteria interactions using engineered surface-immobilized peptides from class IIa bacteriocins

Specificity of the class IIa bacteriocin Leucocin A (LeuA), an antimicrobial peptide active against Gram-positive bacteria, including Listeria monocytogenes , is known to be dictated by the C-terminal amphipathic helical region, including the extended hairpin-like structure. However, its specificity when attached to a substrate has not been investigated. Exploiting properties of LeuA, we have synthesized two LeuA derivatives, which span the amphipathic helical region of the wild-type LeuA, consisting of 14- (14AA LeuA, CWGEAFSAGVHRLA) and 24-amino acid residues (24AA LeuA, CSVNWGEAFSAGVHRLANGGNGFW). The peptides were purified to >95% purity, as shown by analytical RP-HPLC and mass spectrometry. By including an N-terminal cysteine group, the tailored peptide fragments were readily immobilized at the gold interfaces. The resulting thickness and molecular orientation, determined by ellipsometry and grazing angle infrared spectroscopy, respectively, indicated that the peptides were covalently immobilized in a random helical orientation. The bacterial specificity of the anchored peptide fragments was tested against Gram-positive and Gram-negative bacteria. Our results showed that the adsorbed 14AA LeuA exhibited no specificity toward the bacterial strains, whereas the surface-immobilized 24AA LeuA displayed significant binding toward Gram-positive bacteria with various binding affinities from one strain to another. The 14AA LeuA did not show binding as this fragment is most likely too short in length for recognition by the membrane-bound receptor on the target bacterial cell membrane. These results support the potential use of class IIa bacteriocins as molecular recognition elements in biosensing platforms.

Multiplex T-RFLP allows for increased target number and specificity: detection of Salmonella enterica and six species of Listeria in a single test

A multiplex T-RFLP test was developed to detect and identify Salmonella enterica and all six species of Listeria inoculated into milk at minimal levels. Extensive in silico analysis was used to design a fifteen-primer, six-amplimer methodology and in vitro application showed target organism DNA, when amplified individually, yielded the predicted terminal restriction fragments (TRFs) following digestion. Non-target organisms were either not-amplified or yielded TRFs which did not interfere with target identification. Multiple target DNA analysis gave over 86% detection of total TRFs predicted, and this was improved to over 90% detection of total TRFs predicted when only two target DNA extracts were combined analysed. Co-inoculation of milk with five strains each of the target species of S. enterica and L. monocytogenes, along with five strains of the non-target species E. coli was followed by enrichment in SEL medium for M-TRFLP analysis. This allowed for detection of both target species in all samples, with detection of one S. enterica and two Listeria TRFs in all cases, and detection of a second S. enterica TRF in 91% of cases. This was from an initial inoculum of <5 cfu per 25 ml milk with a background of competing E. coli present, and gave a result from sampling of under 20 hours. The ability to increase target species number without loss of sensitivity means that extensive screening can be performed at reduced cost due to a reduction in the number of tests required.