Microbial Food Safety in China: Past, Present, and Future.

Food safety is a major public health issue worldwide, especially in heavily populated countries such as China. As in other countries, the predominant food safety issues in China are foodborne diseases caused by microbial pathogens. Hence, this review provides a systematic overview on microbial food safety in the past, present, and future in China. Management of microbial food safety in China is generally divided into three stages: Stage I before 2000, Stage II from 2000 to 2009, and Stage III from 2010 to present. At Stage I, China's main food concern gradually shifted from food security to food safety. At Stage II, foodborne pathogen surveillance was initiated and gradually became a focus of microbial food safety marked by the establishment of national food contamination monitoring system in 2000 and the promulgation of China Food Safety Law in 2009, although chemical food safety was considered a priority issue during this stage. At Stage III, microbial food safety was recognized as a high priority supported by many national food safety policies such as the launch of a national foodborne disease molecular tracing network in 2013 and the revision of China Food Safety Law in 2015. Advancement in food safety education and research support by central and local governments has also made significant contributions to tackling and solving microbial food safety problems. Management in the future should be focused on active involvement of food industries in mitigating microbial risks by introducing ISO 22000, regulatory enforcement to oversee compliances to standards and rules, and application of molecular tools for fast detection and source tracking to support decision-making. Future research efforts may include, but are not limited to, exploitation of interaction mechanisms among pathogenic bacteria, food and gut microbiota, smart traceability of microbial hazards, and development of novel antimicrobial strategies.

The China National Foodborne Pathogen Surveillance System: Twenty Years of Experience and Achievements.

National foodborne pathogen surveillance is a system that collects data regarding food contamination by pathogenic bacteria, viruses, parasites, and other harmful microbial factors. The surveillance data are used to understand the potential microbial risks in different categories of food and to provide science-based data for risk assessment and development of reference standards in the form of maximum limits. This review introduces stepwise expansion of the foodborne pathogen surveillance in China, relevant policies, function and duties of different organizations and institutions, surveillance plans, and quality control. Achievements of the surveillance system and future challenges are also presented.

Whole Genome Sequencing Applied to Pathogen Source Tracking in Food Industry: Key Considerations for Robust Bioinformatics Data Analysis and Reliable Results Interpretation.

Whole genome sequencing (WGS) has arisen as a powerful tool to perform pathogen source tracking in the food industry thanks to several developments in recent years. However, the cost associated to this technology and the degree of expertise required to accurately process and understand the data has limited its adoption at a wider scale. Additionally, the time needed to obtain actionable information is often seen as an impairment for the application and use of the information generated via WGS. Ongoing work towards standardization of wet lab including sequencing protocols, following guidelines from the regulatory authorities and international standardization efforts make the technology more and more accessible. However, data analysis and results interpretation guidelines are still subject to initiatives coming from distinct groups and institutions. There are multiple bioinformatics software and pipelines developed to handle such information. Nevertheless, little consensus exists on a standard way to process the data and interpret the results. Here, we want to present the constraints we face in an industrial setting and the steps we consider necessary to obtain high quality data, reproducible results and a robust interpretation of the obtained information. All of this, in a time frame allowing for data-driven actions supporting factories and their needs.

Probiotic triangle of success; strain production, clinical studies and product development.

The successful development of probiotic foods and dietary supplements rests on three pillars; each with their specific challenges and opportunities. First, strain production; this depends on selecting the right strain with promising technological properties and safety profile. Further the manufacturing of the strain in a stable format at sufficiently high yield, following regulatory and customer requirements on culture media ingredients and other processing aids. The second pillar are the preclinical and clinical studies to document that the strain is a probiotic and exerts a health benefit on the host, the consumer. Especially when aiming for a regulator approved health claim, clinical studies need to be thoroughly performed; following appropriate ethical, scientific and regulatory guidelines. Finally, the probiotic will need to be incorporated in a product that can be brought to the consumer; a dietary supplement or a functional food. Because of the live nature of probiotics, specific challenges may need to be dealt with. Although experience from other strains is helpful in the process, the development is strain specific. Commercialisation and marketing of probiotics are strictly but differently regulated in most jurisdictions; defining what can and cannot be claimed.

[Microbiological safety of food: development of normative and methodical base].

The main results and prospects of fundamental and applied hygienic research of the laboratory of biosafety and nutrimicrobiome analysis of the Federal Research Centre of Nutrition, Biotechnology and Food Safety (hereinafter - the Institute of Nutrition) in the direction of developing a regulatory and methodological framework for assessing the microbiological safety of food are reviewed. The formation of microbiological regulation as a scientific analytical and administrative managerial process in the former USSR and the Russian Federation is considered in the context of historical data, including personal contribution of the scientists of the Institute of Nutrition and other specialists. The basic principles of regulation are emphasized: the scientific validity of the established criteria and requirements, the feasibility, technological attainability, differentiation according to the degree of danger to the health of consumers, preventive nature. The resource of the national normative and methodological base in the field of microbiological food safety at the turn of the century is characterized, the features of the introduction of the microbiological risk assessment (MRA) methodology in the substantiation of Russian norms and measures for the prevention of food infections are described. The information is given on the developed guidance documents on MRA and on the examples of norms adopted on its basis. The article covers the issues of reglamentation the requirements for food safety and reducing the spread of new pathogens Stx-Escherichia coli, Listeria monocytogenes, Enterobacter sakazakii, Campylobacter spp. in the food chain based on risk-oriented approaches. The necessity of taking specific measures for the prevention of cross-contamination in the poultry processing industry is substantiated, taking into account the evidence of the high adaptability of C. jejuni isolated from domestic raw poultry. In the sanitarian-mycological aspect, the monitoring perspective of mould fungi, taking into account their chemotypes, in cereals and non-grain plant products is shown to predict the risk of mycotoxin accumulation and take timely measures. The need to assess the impact on the population, taking into account the characteristics of consumption in the country, as well as the development of criteria for indirect risk of residues are argued for regulation of the antibiotics in food. In light of the challenges in the field of agro- and food technologies to public health at the present stage, contributing to the acceleration of microbial evolution and the emergence of new risks in food, the priority tasks of improving the regulatory and methodological base for assessing microbiological safety have been identified, with an emphasis on the introduction into the process of substantiating the norms of innovative OMICs-technologies based on the achievements of genomics, transcriptomics, proteomics, metabolomics, bioinformatics.

A Review on the Effect of High Pressure Processing (HPP) on Gelatinization and Infusion of Nutrients.

High pressure processing (HPP) is a novel technology that involves subjecting foods to high hydrostatic pressures of the order of 100-600 MPa. This technology has been proven successful for inactivation of numerous microorganisms, spores and enzymes in foods, leading to increased shelf life. HPP is not limited to cold pasteurization, but has many other applications. The focus of this paper is to explore other applications of HPP, such as gelatinization, forced water absorption and infusion of nutrients. The use of high pressure in producing cold gelatinizing effects, imparting unique properties to food and improving food quality will be also discussed, highlighting the latest published studies and the innovative methods adopted.

Methods for detection of viable foodborne pathogens: current state-of-art and future prospects.

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.

Investigation of Incidents and Trends of Antimicrobial Resistance in Foodborne Pathogens in Eight Countries from Historical Sample Data.

Antimicrobial resistance (AMR) causes millions of illnesses every year, threatening the success of lifesaving antibiotic therapy and, thus, public health. To examine the rise and spread of antimicrobial resistance around the world, our study performs a multivariate statistical analysis of antimicrobial resistance gene data from eight different countries: the US, the UK, China, Brazil, Mexico, Canada, Australia, and South Africa. Multi-dimensional data points were projected onto a two-dimensional plane using principal component analysis and organized into a dendrogram utilizing hierarchical clustering to identify significant AMR genes and pathogens. Outlier genes/pathogens were typically involved in high occurrences of antimicrobial resistance, and they were able to indicate the trend of antimicrobial resistance in the future. Statistical analysis of the data identified: (1) tet(A), aph(3'')-Ib, aph(6)-Id, blaEC, blaTEM-1, qacEdelta1, sul1, sul2, and aadA1 as the nine most common AMR genes among the studied countries; (2) Salmonella enterica and E. coli and Shigella as the most common AMR foodborne pathogens; and (3) chicken as the most prevalent meat carrier of antimicrobial resistance. Our study shows that the overall number of reported antimicrobial resistance cases in foodborne pathogens is generally rising. One potential contributing factor for this is the increasing antimicrobial usage in the growing livestock industry.

Novel mutagenesis and screening technologies for food microorganisms: advances and prospects.

Microorganisms are indispensable in the food industry, but wild-type strains hardly meet the current industrial demands due to several undesirable traits. Therefore, microbial strain improvement offers a critical solution to enhance the food industry. Traditional techniques for food microbial improvement, such as the use of chemical mutagens and manual isolation/purification, are inefficient, time-consuming, and laborious, restricting further progress in the area of food fermentation. In this review, the applications of novel mutagenesis and screening technologies used for the improvement of food microbes were summarized, including random mutagenesis based on physical irradiation, microbial screening facilitated by a microtiter plate, fluorescence-activated cell or droplet sorting, and microscaled fermentation in a microtiter plate or microbioreactor. In comparison with conventional methods, these new tools have the potential in accelerating microbial strain improvement and their combined applications could create a new trend for strain development. However, several problems that could affect its potential application may include the following: the lack of specific mutagenesis devices and biosensing systems, the insufficient improvement of the mixed culture system, the low efficiency when using filamentous fungi and flocculating bacteria, and the insufficient safety assessment on harnessing genome-editing technology. Therefore, future works on strain improvement remain challenging for the food industry.

A colorimetric Loop-mediated isothermal amplification (LAMP) assay based on HRP-mimicking molecular beacon for the rapid detection of Vibrio parahaemolyticus.

In the world wide, food poisoning accidents related to Vibrio spp. are on the rise, even numbers of food poisoning by other foodborne pathogens are decreasing. Therefore, the requirement of the rapid, sensitive and convenient detection method for V. parahaemolyticus has been grown. The objective of this study is to develop a colorimetric loop-mediated isothermal amplification (LAMP) assay using a molecular beacon (HRPzyme connected with complementary oligonucleotides at the 5' and 3' ends) for the rapid, sensitive, and convenient detection of V. parahaemolyticus. The colorimetric LAMP assay optimized at 58.8°C showed a detection limit of 1 × 100 CFU/mL and was confirmed to be specific to V. parahaemolyticus. The colorimetric LAMP assay can be finished within 1 h including DNA extraction step. The method was successfully applied to flatfish samples artificially inoculated with known amount of V. parahaemolyticus, and its cut-off value for the flatfish samples was 1 × 101 CFU/g. In addition, the colorimetric LAMP assay developed in the study was found to be able to correct false-positive results, which are known to be a disadvantage of conventional LAMP assays. Therefore, these results indicated that the colorimetric LAMP method is a useful tool for the rapid, sensitive and convenient detection of V. parahaemolyticus in fishes and can also be used as a point-of-care molecular diagnostic technique since it does not require any expensive equipment such as a thermocycler and detectors.

Tasting the terroir of wine yeast innovation.

Wine is an archetypal traditional fermented beverage with strong territorial and socio-cultural connotations. Its 7000 year history is patterned by a tradition of innovation. Every value-adding innovation - whether in the vineyard, winery, supply chain or marketplace - that led to the invention of a new tradition spurred progress and created a brighter future from past developments. In a way, wine traditions can be defined as remembered innovations from the distant past - inherited knowledge and wisdom that withstood the test of time. Therefore, it should not be assumed a priori that tradition and innovation are polar opposites. The relations between the forces driven by the anchors of tradition and the wings of innovation do not necessarily involve displacement, conflict or exclusiveness. Innovation can strengthen wine tradition, and the reinvention of a tradition-bound practice, approach or concept can foster innovation. In cases where a paradigm-shifting innovation disrupts a tradition, the process of such an innovation transitioning into a radically new tradition can become protracted while proponents of divergent opinions duke it out. Sometimes these conflicting opinions are based on fact, and sometimes not. The imperfections of such a debate between the 'ancients' and the 'moderns' can, from time to time, obscure the line between myth and reality. Therefore, finding the right balance between traditions worth keeping and innovations worth implementing can be complex. The intent here is to harness the creative tension between science fiction and science fact when innovation's first-principles challenge the status quo by re-examining the foundational principles about a core traditional concept, such as terroir. Poignant questions are raised about the importance of the terroir (biogeography) of yeasts and the value of the microbiome of grapes to wine quality. This article imagines a metaphorical terroir free from cognitive biases where diverse perspectives can converge to uncork the effervescent power of territorial yeast populations as well as 'nomadic' yeast starter cultures. At the same time, this paper also engages in mental time-travel. A future scenario is imagined, explored, tested and debated where terroir-less yeast avatars are equipped with designer genomes to safely and consistently produce, individually or in combination with region-specific wild yeasts and or other starter cultures, high-quality wine according to the preferences of consumers in a range of markets. The purpose of this review is to look beyond the horizon and to synthesize a link between what we know now and what could be. This article informs readers where to look without suggesting what they must see as a way forward. In the context of one of the world's oldest fermentation industries - steeped in a rich history of tradition and innovation - the mantra here is: respect the past, lead the present and secure the future of wine.

100 Years Since Tolaas: Bacterial Blotch of Mushrooms in the 21st Century.

Among the biotic constraints of common mushroom (Agaricus bisporus) production, bacterial blotch is considered the most important mushroom disease in terms of global prevalence and economic impact. Etiology and management of bacterial blotch has been a major concern since its original description in 1915. Although Pseudomonas tolaasii is thought to be the main causal agent, various Pseudomonas species, as well as organisms from other genera have been reported to cause blotch symptoms on mushroom caps. In this review, we provide an updated overview on the etiology, epidemiology, and management strategies of bacterial blotch disease. First, diversity of the causal agent(s) and utility of high throughput sequencing-based approaches in the precise characterization and identification of blotch pathogen(s) is explained. Further, due to the limited options for use of conventional pesticides in mushroom farms against blotch pathogen(s), we highlight the role of balanced threshold of relative humidity and temperature in mushroom farms to combat the disease in organic and conventional production. Additionally, we discuss the possibility of the use of biological control agents (either antagonistic mushroom-associated bacterial strains or bacteriophages) for blotch management as one of the sustainable approaches for 21st century agriculture. Finally, we aim to elucidate the association of mushroom microbiome in cap development and productivity on one hand, and blotch incidence/outbreaks on the other hand.

The impacts of Schizosaccharomyces on winemaking.

In the past century, yeasts from the genus Saccharomyces represented the only option in fermentation industries, such as winemaking, to produce wine, beer, and other fermented products. However, other genera are currently emerging to solve challenges in modern enology. Schizosaccharomyces pombe is showing promising results in solving specific challenges in northern, cool viticulture regions with highly acidic wines by deacidifying these wines through its malic acid metabolism. In addition, this microorganism is considered beneficial in warm growing regions with challenges such as the control of wine food safety problems such as the presence of biogenic amines, ochratoxin A, or ethyl carbamate. Indeed, the genus Schizosaccharomyces positively influences other important wine quality parameters, such as color and polysaccharide content. However, the main challenge of using this genus remains the selection of proper strains that alleviate problems such as the production of high acetate concentrations. Industries other than wine production such as ginger fermentation, apple wine, Kei-apple fermentation, plum wine, sparkling wine, and bilberry fermentation industries have also started to study Schizosaccharomyces species as an alternative tool for solving specific related problems. The review discusses the influence of Schizosaccharomyces on different fermentation quality parameters and its main applications in different industries.

Fermentation as a driver for food innovation.

The following paper is reviewing the current trends in research connected to fermentation, highlighting the work carried out in the various research kitchens that have gained a new understanding of fermentation in the recent years. The reflection on the developments made both on microbiological as well on the technological level aims to create pathways within the research fields in order to foster new innovations within the food production system.

The use of next generation sequencing for improving food safety: Translation into practice.

Next Generation Sequencing (NGS) combined with powerful bioinformatic approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of single isolates allows the most detailed comparison possible hitherto of individual strains. The two principle approaches for strain discrimination, single nucleotide polymorphism (SNP) analysis and genomic multi-locus sequence typing (MLST) are showing concordant results for phylogenetic clustering and are complementary to each other. Metabarcoding and metagenomics, applied to total DNA isolated from either food materials or the production environment, allows the identification of complete microbial populations. Metagenomics identifies the entire gene content and when coupled to transcriptomics or proteomics, allows the identification of functional capacity and biochemical activity of microbial populations. The focus of this review is on the recent use and future potential of NGS in food microbiology and on current challenges. Guidance is provided for new users, such as public health departments and the food industry, on the implementation of NGS and how to critically interpret results and place them in a broader context. The review aims to promote the broader application of NGS technologies within the food industry as well as highlight knowledge gaps and novel applications of NGS with the aim of driving future research and increasing food safety outputs from its wider use.

The qualified presumption of safety assessment and its role in EFSA risk evaluations: 15 years past.

Microorganisms are intentionally added at different stages of the food and feed chain (food or feed additive, novel food or plant protection product) and are subjected to regulation and safety assessment by the European Food Safety Authority. Safety evaluation is based on application dossiers for market authorisation to the European Commission. The qualified presumption of safety (QPS) concept was developed in 20031 to provide a harmonised generic safety pre-appraisal of the above microorganisms. Unambiguously defined biological taxonomic units (TUs) are assessed for their body of knowledge, their safety and their end use. Identified safety concerns for a certain TU can be, where reasonable in number and not universally present, reflected as 'qualifications.' Strains belonging to TUs having QPS status may benefit of a fast track evaluation. The lowest TU for which the QPS status is granted is the species level for bacteria and yeasts and the family for viruses. The QPS concept is also applicable to genetically modified microorganisms used for production purposes. Based on the current body of knowledge and/or the ambiguous taxonomic position, some TUs, such as filamentous fungi, bacteriophages, Enterococcus faecium, Escherichia coli, Streptomyces spp. and Oomycetes, are not considered liable for QPS status.

Polyunsaturated fatty acids in marine bacteria and strategies to enhance their production.

Polyunsaturated fatty acids (PUFAs) play an important role in human diet. Despite the wide-ranging importance and benefits from heart health to brain functions, humans and mammals cannot synthesize PUFAs de novo. The primary sources of PUFA are fish and plants. Due to the increasing concerns associated with food security as well as issues of environmental contaminants in fish oil, there has been considerable interest in the production of polyunsaturated fatty acids from alternative resources which are more sustainable, safer, and economical. For instance, marine bacteria, particularly the genus of Shewanella, Photobacterium, Colwellia, Moritella, Psychromonas, Vibrio, and Alteromonas, are found to be one among the major microbial producers of polyunsaturated fatty acids. Recent developments in the area with a focus on the production of polyunsaturated fatty acids from marine bacteria as well as the metabolic engineering strategies for the improvement of PUFA production are discussed.

Next generation microbiological risk assessment-Potential of omics data for hazard characterisation.

According to the World Health Organization estimates in 2015, 600 million people fall ill every year from contaminated food and 420,000 die. Microbial risk assessment (MRA) was developed as a tool to reduce and prevent risks presented by pathogens and/or their toxins. MRA is organized in four steps to analyse information and assist in both designing appropriate control options and implementation of regulatory decisions and programs. Among the four steps, hazard characterisation is performed to establish the probability and severity of a disease outcome, which is determined as function of the dose of toxin and/or pathogen ingested. This dose-response relationship is subject to both variability and uncertainty. The purpose of this review/opinion article is to discuss how Next Generation Omics can impact hazard characterisation and, more precisely, how it can improve our understanding of variability and limit the uncertainty in the dose-response relation. The expansion of omics tools (e.g. genomics, transcriptomics, proteomics and metabolomics) allows for a better understanding of pathogenicity mechanisms and virulence levels of bacterial strains. Detection and identification of virulence genes, comparative genomics, analyses of mRNA and protein levels and the development of biomarkers can help in building a mechanistic dose-response model to predict disease severity. In this respect, systems biology can help to identify critical system characteristics that confer virulence and explain variability between strains. Despite challenges in the integration of omics into risk assessment, some omics methods have already been used by regulatory agencies for hazard identification. Standardized methods, reproducibility and datasets obtained from realistic conditions remain a challenge, and are needed to improve accuracy of hazard characterisation. When these improvements are realized, they will allow the health authorities and government policy makers to prioritize hazards more accurately and thus refine surveillance programs with the collaboration of all stakeholders of the food chain.