Prevalence of Escherichia coli generic and pathogenic in pork meat: systematic review and meta-analysis

This research aimed to analyze scientific information regarding the prevalence of generic and pathogenic E. coli in the production and supply chain of pork meat, considering different types of samples, places of sampling, and pathotypes using a systematic review and meta-analysis tools. The meta-analysis for the prevalence of generic and pathogenic E. coli was conducted by estimating the effects within subgroups. Data subsets were analyzed using the DerSimonian-Laird method for binary random effects. The average prevalence of generic E. coli in different types of pork meat samples was determined to be 35.6% (95% CI 19.3-51.8), with no significant differences observed between pork meat and carcasses. Conversely, the average prevalence of E. coli pathotypes in samples related to the supply chain of pork meat was found to be 4.7% (95% CI 3.7-5.7). In conclusion, these findings suggest the possibility of establishing an objective threshold for E. coli prevalence as a benchmark for comparison within the meat industry. By utilizing this data, it becomes possible to propose a standardized limit that can serve as a reference point for evaluating and improving processes in the industry.

Exploring thermosonication as non-chemical disinfection technology for strawberries

The scope of this work was to study the efficacy of the combination of sonication at 35 or 130 kHz with three temperature treatments: 20, 50 and 55 ºC, on the population of artificially inoculated Listeria innocua in strawberries, and on their overall quality. Prior in vitro results showed that temperature was the main factor in decreasing L. innocua population: a maximum of 3.8 log reductions was obtained with sonication at 130 kHz and 55 ºC for 15 min Treatments combining—or not—sonication at 130 kHz with mild temperatures (50 and 55 ºC) for 5 or 10 min were able to decrease about 3 log units of artificially inoculated L. innocua in strawberries and about 2 log units of total aerobic mesophilic and yeasts and molds populations naturally occurring in strawberries. Thermosonication treatments did not exert a detrimental impact on fruit quality, except for those at the higher temperatures and times, which caused a change in color to more purplish and a little softening of the strawberries, which were proposed to be assessed for further processing other than fresh commercialization. Overall, the impact of sonication in fresh strawberries needs to be further investigated to find the adequate conditions to enhance the effects of temperature itself.

Complete Whole Genome Sequences of Escherichia coli Surrogate Strains and Comparison of Sequence Methods with Application to the Food Industry

In 2013, the U.S. Department of Agriculture Food Safety and Inspection Service (USDA-FSIS) began transitioning to whole genome sequencing (WGS) for foodborne disease outbreak- and recall-associated isolate identification of select bacterial species. While WGS offers greater precision, certain hurdles must be overcome before widespread application within the food industry is plausible. Challenges include diversity of sequencing platform outputs and lack of standardized bioinformatics workflows for data analyses. We sequenced DNA from USDA-FSIS approved, non-pathogenic E. coli surrogates and a derivative group of rifampicin-resistant mutants (rif^R) via both Oxford Nanopore MinION and Illumina MiSeq platforms to generate and annotate complete genomes. Genome sequences from each clone were assembled separately so long-read, short-read, and combined sequence assemblies could be directly compared. The combined sequence data approach provides more accurate completed genomes. The genomes from these isolates were verified to lack functional key E. coli elements commonly associated with pathogenesis. Genetic alterations known to confer rif^R were also identified. As the food industry adopts WGS within its food safety programs, these data provide completed genomes for commonly used surrogate strains, with a direct comparison of sequence platforms and assembly strategies relevant to research/testing workflows applicable for both processors and regulators.

Emerging Applications of Machine Learning in Food Safety

Food safety continues to threaten public health. Machine learning holds potential in leveraging large, emerging data sets to improve the safety of the food supply and mitigate the impact of food safety incidents. Foodborne pathogen genomes and novel data streams, including text, transactional, and trade data, have seen emerging applications enabled by a machine learning approach, such as prediction of antibiotic resistance, source attribution of pathogens, and foodborne outbreak detection and risk assessment. In this article, we provide a gentle introduction to machine learning in the context of food safety and an overview of recent developments and applications. With many of these applications still in their nascence, general and domain-specific pitfalls and challenges associated with machine learning have begun to be recognized and addressed, which are critical to prospective use and future deployment of large data sets and their associated machine learning models for food safety applications.

Current status of food safety hazards and health risks connected with aquatic food products from Southeast Asian region

Food safety issues associated with aquatic food products become more important with the increasing consumption and followed by its ongoing challenges. The objective of this paper is to review the food safety hazards and health risks related to aquatic food products for the Southeast Asian region. These hazards can be categorized as microplastics (MPs) hazard, biological hazards (pathogenic bacteria, biogenic amines, viruses, parasites), and chemical hazards (antimicrobial, formaldehyde, heavy metal). In different Southeast Asian countries, the potential health risks of aquatic food products brought by food hazards to consumers were at different intensity and classes. Among all these hazards, pathogenic bacteria, antimicrobials, and heavy metal were a particular concern in the Southeast Asian region. With environmental changes, evolving consumption patterns, and the globalization of trade, new food safety challenges are created, which put forward higher requirements on food technologies, food safety regulations, and international cooperation.

Genome-Guided Mass Spectrometry Expedited the Discovery of Paraplantaricin TC318, a Lantibiotic Produced by Lactobacillus paraplantarum Strain Isolated From Cheese

The quest for potent alternatives to the currently used antimicrobials is urged by health professionals, considering the rapid rise in resistance to preservatives and antibiotics among pathogens. The current study was initiated to search for novel and effective bacteriocins from food microbes, preferably lactic acid bacteria (LAB), for potential use as preservatives. Advances in genome-guided mass spectrometry (MS) were implemented to expedite identifying and elucidating the structure of the recovered antimicrobial agent. A LAB strain, OSY-TC318, was isolated from a Turkish cheese, and the crude extract of the cultured strain inhibited the growth of various pathogenic and spoilage bacteria such as Bacillus cereus, Clostridium sporogenes, Enterococcus faecalis, Listeria monocytogenes, Salmonella enterica ser. Typhimurium, and Staphylococcus aureus. The antimicrobial producer was identified as Lactobacillus paraplantarum using MS biotyping and genomic analysis. Additionally, L. paraplantarum OSY-TC318 was distinguished from closely related strains using comparative genomic analysis. Based on in silico analysis, the genome of the new strain contained a complete lantibiotic biosynthetic gene cluster, encoding a novel lantibiotic that was designated as paraplantaricin TC318. The bioinformatic analysis of the gene cluster led to the prediction of the biosynthetic pathway, amino acid sequence, and theoretical molecular mass of paraplantaricin TC318. To verify the genomic analysis predictions, paraplantaricin TC318 was purified from the producer cellular crude extract using liquid chromatography, followed by structural elucidation using Fourier transform ion cyclotron resonance MS analysis. This genome-guided MS analysis revealed that the molecular mass of paraplantaricin TC318 is 2,263.900 Da, its chemical formula is C₁₀₆H₁₃₃N₂₇O₂₂S₄, and its primary sequence is F-K-S-W-S-L-C-T-F-G-C-G-H-T-G-S-F-N-S-F-C-C. This lantibiotic, which differs from mutacin 1140 at positions 9, 12, 13, and 20, is considered a new member of the epidermin group in class I lantibiotics. In conclusion, the study revealed a new L. paraplantarum strain producing a novel lantibiotic that is potentially useful in food and medical applications.

Detecting reports of unsafe foods in consumer product reviews

OBJECTIVES

Access to safe and nutritious food is essential for good health. However, food can become unsafe due to contamination with pathogens, chemicals or toxins, or mislabeling of allergens. Illness resulting from the consumption of unsafe foods is a global health problem. Here, we develop a machine learning approach for detecting reports of unsafe food products in consumer product reviews from Amazon.com.

MATERIALS AND METHODS

We linked Amazon.com food product reviews to Food and Drug Administration (FDA) food recalls from 2012 to 2014 using text matching approaches in a PostGres relational database. We applied machine learning methods and over- and under-sampling methods to the linked data to automate the detection of reports of unsafe food products.

RESULTS

Our data consisted of 1 297 156 product reviews from Amazon.com. Only 5149 (0.4%) were linked to recalled food products. Bidirectional Encoder Representation from Transformations performed best in identifying unsafe food reviews, achieving an F1 score, precision and recall of 0.74, 0.78, and 0.71, respectively. We also identified synonyms for terms associated with FDA recalls in more than 20 000 reviews, most of which were associated with nonrecalled products. This might suggest that many more products should have been recalled or investigated.

DISCUSSION AND CONCLUSION

Challenges to improving food safety include, urbanization which has led to a longer food chain, underreporting of illness and difficulty in linking contaminated food to illness. Our approach can improve food safety by enabling early identification of unsafe foods which can lead to timely recall thereby limiting the health and economic impact on the public.

Combining Quantitative Risk Assessment of Human Health, Food Waste, and Energy Consumption: The Next Step in the Development of the Food Cold Chain?

The preservation of perishable food via refrigeration in the supply chain is essential to extend shelf life and provide consumers with safe food. However, electricity consumed in refrigeration processes has an economical and an environmental impact. This study focuses on the cold chain of cooked ham, including transport, cold room in supermarket, display cabinet, transport by consumer, and domestic refrigerator, and aims to predict the risk for human health associated with Listeria monocytogenes, the amount of food wasted due to the growth of spoilage bacteria, and the electrical consumption to maintain product temperature through the cold chain. A set of eight intervention actions were tested to evaluate their impact on the three criteria. Results show that the modification of the thermostat of the domestic refrigerator has a high impact on food safety and food waste and a limited impact on the electrical consumption. Inversely, the modification of the airflow rate in the display cabinet has a high impact on electrical consumption and a limited impact on food safety and food waste. A cost-benefit analysis approach and two multicriteria decision analysis methods were used to rank the intervention actions. These three methodologies show that setting the thermostat of the domestic refrigerator to 4 °C presents the best compromise between the three criteria. The impact of decisionmaker preferences (criteria weight) and limitations of these three approaches are discussed. The approaches proposed by this study may be useful in decision making to evaluate global impact of intervention actions in issues involving conflicting outputs.

Public health investigation and response to a hepatitis A outbreak from imported scallops consumed raw—Hawaii, 2016

During the summer of 2016, the Hawaii Department of Health responded to the second-largest domestic foodborne hepatitis A virus (HAV) outbreak in the post-vaccine era. The epidemiological investigation included case finding and investigation, sequencing of RNA positive clinical specimens, product trace-back and virologic testing and sequencing of HAV RNA from the product. Additionally, an online survey open to all Hawaii residents was conducted to estimate baseline commercial food consumption. We identified 292 confirmed HAV cases, of whom 11 (4%) were possible secondary cases. Seventy-four (25%) were hospitalised and there were two deaths. Among all cases, 94% reported eating at Oahu or Kauai Island branches of Restaurant Chain A, with 86% of those cases reporting raw scallop consumption. In contrast, a food consumption survey conducted during the outbreak indicated 25% of Oahu residents patronised Restaurant Chain A in the 7 weeks before the survey. Product trace-back revealed a single distributor that supplied scallops imported from the Philippines to Restaurant Chain A. Recovery, amplification and sequence comparison of HAV recovered from scallops revealed viral sequences matching those from case-patients. Removal of product from implicated restaurants and vaccination of those potentially exposed led to the cessation of the outbreak. This outbreak further highlights the need for improved imported food safety.

Human microbiome versus food-borne pathogens: friend or foe

As food safety advances, there is a great need to maintain, distribute, and provide high-quality food to a much broader consumer base. There is also an ever-growing "arms race" between pathogens and humans as food manufacturers. The human microbiome is a collective organ of microbes that have found community niches while associating with their host and other microorganisms. Humans play an important role in modifying the environment of these organisms through their life choices, especially through individual diet. The composition of an individual's diet influences the digestive system-an ecosystem with the greatest number and largest diversity of organisms currently known. Organisms living on and within food have the potential to be either friends or foes to the consumer. Maintenance of this system can have multiple benefits, but lack of maintenance can lead to a host of chronic and preventable diseases. Overall, this dynamic system is influenced by intense competition from food-borne pathogens, lifestyle, overall diet, and presiding host-associated microbiota.

Antimicrobial Resistance, Food Safety, and One Health: The Need for Convergence

Antimicrobial resistance is a complex, multifaceted, urgent global health problem. There is increasing concern about the emergence of multidrug-resistant superbugs. These superbugs result in infections responsive to treatment with few if any currently available antimicrobial agents, reviving memories of the preantibiotic era and evoking concerns about a postantibiotic era. Use of antibiotics exerts selective pressure on pathogens as well as on commensal organisms that are part of the normal flora of humans, animals, and the environment; this favors the emergence of resistant strains and sometimes involves the food supply. Addressing this urgent threat requires implementation of a multifaceted strategy that has been articulated in the past few years; implementation will require sustained political will, investment in systems and research, and a One Health approach involving improved communication, cooperation, and collaboration among the many professional disciplines and organizations with important roles to play at the intersection of human, animal, and environmental health. Priorities include strengthened human and animal health surveillance and monitoring for resistant organisms, antimicrobial stewardship programs, infection-control programs, development and approval of new antimicrobial agents, research on innovative therapeutic approaches, development of rapid diagnostic tests and new vaccines, and educational programs that target professional groups and the public.

Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens

As we are approaching the twentieth anniversary of PulseNet, a network of public health and regulatory laboratories that has changed the landscape of foodborne illness surveillance through molecular subtyping, public health microbiology is undergoing another transformation brought about by so-called next-generation sequencing (NGS) technologies that have made whole-genome sequencing (WGS) of foodborne bacterial pathogens a realistic and superior alternative to traditional subtyping methods. Routine, real-time, and widespread application of WGS in food safety and public health is on the horizon. Technological, operational, and policy challenges are still present and being addressed by an international and multidisciplinary community of researchers, public health practitioners, and other stakeholders.