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Many foodborne diseases are associated with consumption of meat and poultry. Some pathogens were not previously known (new pathogens), others have newly arisen as foodborne (emerging pathogens), and others have become more potent or associated with other products (evolving pathogens). Many of these pathogens may cause severe illness, besides gastroenteritis. Campylobacter jejuni is a leading cause of food-associated bacterial illness; Campylobacter jejuni O:19 and other serotypes are common etiological agents of Guillain-Barré syndrome, a neuropathy due to autoimmune response. Salmonella Typhimurium DT104 and other serotypes have been found to be multi-drug resistant; salmonellosis may lead to chronic reactive arthritis. Many outbreaks of enterohemorrhagic Escherichia coli have been associated with consumption of undercooked contaminated ground beef; complication may occur (e.g., hemolytic uremic syndrome and thrombotic thrombocytopenic purpura). Listeria monocytogenes is ubiquitous; listeriosis is of major public health concern because of the severity and non-enteric nature of the disease (meningitis or meningoencephalitis, septicemia, and abortion) and its ability to multiply at refrigeration temperature. Arcobacter butzleri is a potential foodborne pathogen, and has been isolated from raw poultry, meat, and meat products; but its role in causing human illness is not fully understood. Mycobacterium avium subsp. paratuberculosis can be transmitted by ingestion of raw and processed meats; the organism may contribute to Crohn's disease, a chronic intestinal enteritis. Beef, pork, lamb, and/or poultry have been reported as sources of infection for the abovementioned organisms but have not been generally associated with disease outbreaks of some of the pathogens.

Food packaging is tailored to keep food fresh by increasing shelf life and preventing microbial deterioration. However, traditional food packaging is commonly made from non-degradable polymers without antimicrobial properties and that pose an environmental threat if not disposed properly. To address this issue, here we describe the preparation of cellulose nanofibril (CNF) films and hydrogels with antimicrobial activity against common foodborne pathogens such as verotoxigenic E. coli, L. monocytogenes and S. Typhimurium. Furthermore, two grades of negatively charged CNFs with different fibrillation degrees were modified with ethyl lauroyl arginate (LAE), which is an antimicrobial agent. CNF films were able to bind LAE molecules up to a maximum concentration of 145–160 ppm. LAE–CNF biocomposite films exerted a bactericidal activity against a major foodborne pathogen present in ready-to-eat food (L. monocytogenes) even at 1% LAE. Our work describes a novel biopolymer-based strategy that overcomes the current hurdles with LAE incorporation into packaging materials, offering a green and antimicrobial alternative for packaging of ready-to-eat (RTE) meat products.

The detection and identification of foodborne pathogens continue to rely on conventional culturing techniques. These are very elaborate, time-consuming, and have to be completed in a microbiology laboratory and are therefore not suitable for on-site monitoring. The need for a more rapid, reliable, specific, and sensitive method of detecting a target analyte, at low cost, is the focus of a great deal of research. Biosensor technology has the potential to speed up the detection, increase specificity and sensitivity, enable high-throughput analysis, and to be used for monitoring of critical control points in food production. This article reviews food pathogen detection methods based on electrochemical biosensors, specifically amperometric, potentiometric, and impedimetric biosensors. The underlying principles and application of these biosensors are discussed with special emphasis on new biorecognition elements, nanomaterials, and lab on a chip technology.

With continued development of novel molecular-based technologies for rapid, high-throughput detection of foodborne pathogenic bacteria, the future of conventional microbiological methods such as viable cell enumeration, selective isolation of bacteria on commercial media, and immunoassays seems tenuous. In fact, a number of unique approaches and variations on existing techniques are currently on the market or are being implemented that offer ease of use, reliability, and low cost compared with molecular tools. Approaches that enhance recovery of sublethally injured bacteria, differentiation among species using fluorogenics or chromogenics, dry plate culturing, differentiation among bacteria of interest using biochemical profiling, enumeration using impedence technology, techniques to confirm the presence of target pathogens using immunological methods, and bioluminescence applications for hygiene monitoring are summarized here and discussed in relation to their specific advantages or disadvantages when implemented in a food microbiology setting.Key words: food pathogen, detection, enumeration methods, food safety.

The need for pre-analytical sample processing prior to the application of rapid molecular-based detection of pathogens in food and environmental samples is well established. Although immunocapture has been applied in this regard, alternative ligands such as nucleic acid aptamers have advantages over antibodies such as low cost, ease of production and modification, and comparable stability. To identify DNA aptamers demonstrating binding specificity to Campylobacter jejuni cells, a whole-cell Systemic Evolution of Ligands by EXponential enrichment (SELEX) method was applied to a combinatorial library of FAM-labeled single-stranded DNA molecules. FAM-labeled aptamer sequences with high binding affinity to C. jejuni A9a as determined by flow cytometric analysis were identified. Aptamer ONS-23, which showed particularly high binding affinity in preliminary studies, was chosen for further characterization. This aptamer displayed a dissociation constant (K d value) of 292.8 ± 53.1 nM with 47.27 ± 5.58% cells fluorescent (bound) in a 1.48-μM aptamer solution. Binding assays to assess the specificity of aptamer ONS-23 showed high binding affinity (25-36%) for all other C. jejuni strains screened (inclusivity) and low apparent binding affinity (1-5%) with non-C. jejuni strains (exclusivity). Whole-cell SELEX is a promising technique to design aptamer-based molecular probes for microbial pathogens without tedious isolation and purification of complex markers or targets.

This Opinion considers the application of whole genome sequencing (WGS) and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne pathogens. WGS offers the highest level of bacterial strain discrimination for food‐borne outbreak investigation and source‐attribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management. WGS improves linking of sporadic cases associated with different food products and geographical regions to a point source outbreak and can facilitate epidemiological investigations, allowing also the use of previously sequenced genomes. Source attribution may be favoured by improved identification of transmission pathways, through the integration of spatial‐temporal factors and the detection of multidirectional transmission and pathogen–host interactions. Metagenomics has potential, especially in relation to the detection and characterisation of non‐culturable, difficult‐to‐culture or slow‐growing microorganisms, for tracking of hazard‐related genetic determinants and the dynamic evaluation of the composition and functionality of complex microbial communities. A SWOT analysis is provided on the use of WGS and metagenomics for Salmonella and Shigatoxin‐producing Escherichia coli (STEC) serotyping and the identification of antimicrobial resistance determinants in bacteria. Close agreement between phenotypic and WGS‐based genotyping data has been observed. WGS provides additional information on the nature and localisation of antimicrobial resistance determinants and on their dissemination potential by horizontal gene transfer, as well as on genes relating to virulence and biological fitness. Interoperable data will play a major role in the future use of WGS and metagenomic data. Capacity building based on harmonised, quality controlled operational systems within European laboratories and worldwide is essential for the investigation of cross‐border outbreaks and for the development of international standardised risk assessments of food‐borne microorganisms.

Meat and meat products are excellent sources of nutrients for humans; however, they also provide a favorable environment for microbial growth. To prevent the microbiological contamination of livestock foods, synthetic preservatives, including nitrites, nitrates, and sorbates, have been widely used in the food industry due to their low cost and strong antibacterial activity. Use of synthetic chemical preservatives is recently being considered by customers due to concerns related to negative health issues. Therefore, the demand for natural substances as food preservatives has increased with the use of plant-derived and animal-derived products, and microbial metabolites. These natural preservatives inhibit the growth of spoilage microorganisms or food-borne pathogens by increasing the permeability of microbial cell membranes, interruption of protein synthesis, and cell metabolism. Natural preservatives can extend the shelf-life and inhibit the growth of microorganisms. However, they can also influence food sensory properties, including the flavor, taste, color, texture, and acceptability of food. To increase the applicability of natural preservatives, a number of strategies, including combinations of different preservatives or food preservation methods, such as active packaging systems and encapsulation, have been explored. This review summarizes the current applications of natural preservatives for meat and meat products.

The ability to rapidly detect viable pathogens in food is important for public health and food safety reasons. Culture-based detection methods, the traditional means of demonstrating microbial viability, tend to be laborious, time consuming and slow to provide results. Several culture-independent methods to detect viable pathogens have been reported in recent years, including both nucleic acid–based (PCR combined with use of cell viability dyes or reverse-transcriptase PCR to detect messenger RNA) and phage-based (plaque assay or phage amplification and lysis plus PCR/qPCR, immunoassay or enzymatic assay to detect host DNA, progeny phages or intracellular components) methods. Some of these newer methods, particularly phage-based methods, show promise in terms of speed, sensitivity of detection and cost compared with culture for food testing. This review provides an overview of these new approaches and their food testing applications, and discusses their current limitations and future prospects in relation to detection of viable pathogens in food.Key points• Cultural methods may be ‘gold standard’ for assessing viability of pathogens, but they are too slow.• Nucleic acid–based methods offer speed of detection but not consistently proof of cell viability.• Phage-based methods appear to offer best alternative to culture for detecting viable pathogens.

Over the last 10 to 15 years, increasing evidence suggests that persistence of Listeria monocytogenes in food processing plants for years or even decades is an important factor in the transmission of this foodborne pathogen and the root cause of a number of human listeriosis outbreaks. L. monocytogenes persistence in other food-associated environments (e.g., farms and retail establishments) may also contribute to food contamination and transmission of the pathogen to humans. Although L. monocytogenes persistence is typically identified through isolation of a specific molecular subtype from samples collected in a given environment over time, formal (statistical) criteria for identification of persistence are undefined. Environmental factors (e.g., facilities and equipment that are difficult to clean) have been identified as key contributors to persistence; however, the mechanisms are less well understood. Although some researchers have reported that persistent strains possess specific characteristics that may facilitate persistence (e.g., biofilm formation and better adaptation to stress conditions), other researchers have not found significant differences between persistent and nonpersistent strains in the phenotypic characteristics that might facilitate persistence. This review includes a discussion of our current knowledge concerning some key issues associated with the persistence of L. monocytogenes, with special focus on (i) persistence in food processing plants and other food-associated environments, (ii) persistence in the general environment, (iii) phenotypic and genetic characteristics of persistent strains, (iv) niches, and (v) public health and economic implications of persistence. Although the available data clearly indicate that L. monocytogenes persistence at various stages of the food chain contributes to contamination of finished products, continued efforts to quantitatively integrate data on L. monocytogenes persistence (e.g., meta-analysis or quantitative microbial risk assessment) will be needed to advance our understanding of persistence of this pathogen and its economic and public health impacts.

The aim of this work was to examine the effect of modified atmosphere packaging on the physicochemical and microbiological changes of Graviera Agraphon cheese during refrigerated storage. Blocks of Graviera Agraphon cheese weighing around 200 g were packaged under natural (control) or modified atmosphere packaging (MAP) conditions (50% N 2 – 50% CO 2 ) and stored at 4 °C or 10 °C for up to 85 d. Prior to packaging, groups of cheese blocks were inoculated with one each of the following foodborne pathogens at around 10 4 log cfu/g: Listeria monocytogenes, Salmonella Typhimurium, Escherichia coli O157:H7 or Staphylococcus aureus, whilst further groups of cheese blocks were not inoculated. The protein, fat, moisture and salt contents as well as the pH of control and MAP cheese samples did not change significantly ( P > 0.05) throughout 4 °C storage, while the pH values of control and MAP cheese samples were significantly ( P < 0.05) reduced at 10 °C storage. At 10 °C storage, yeasts and molds, psychrotrophs and lactic acid bacteria (LAB) were significantly higher ( P < 0.05) for the normal atmosphere than the MAP cheese samples after the 4 th , 8 th and 4 th days, respectively. At 4 °C storage, the yeasts and molds or psychrotrophs were significantly higher ( P < 0.05) than those of control after the 6 th and 15 th days, respectively at 4 °C storage. All foodborne pathogens showed a higher decrease ( P < 0.05) at 10 °C than 4 °C storage. S. aureus proved more sensitive in inactivation in the MAP conditions than atmospheric conditions. L. monocytogenes and S . aureus presented a higher decrease than that of E. coli O157:H7 and S. Typhimurium. In conclusion, MAP proved efficient in retarding the growth of yeasts, molds, psychrotrophs and E. coli O157:H7, L. monocytogenes , S. Typhimurium and S. aureus in Graviera Agraphon cheese during refrigerated storage at 4 and 10 °C.