Center For Food Safety Research Articles

Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens.

We have developed and implemented an undergraduate microbiology course in which students isolate, characterize, and perform whole genome assembly and analysis of Salmonella enterica from stream sediments and poultry litter. In the development of the course and over three semesters, successive teams of undergraduate students collected field samples and performed enrichment and isolation techniques specific for the detection of S. enterica. Eighty-eight strains were confirmed using standard microbiological methods and PCR of the invA gene. The isolates’ genomes were Illumina-sequenced by the Center for Food Safety and Applied Nutrition at the FDA and the Virginia state Division of Consolidated Laboratory Services as part of the GenomeTrakr program. Students used GalaxyTrakr and other web- and non-web-based platforms and tools to perform quality control on raw and assembled sequence data, assemble, and annotate genomes, identify antimicrobial resistance and virulence genes, putative plasmids, and other mobile genetic elements. Strains with putative plasmid-borne antimicrobial resistance genes were further sequenced by students in our research lab using the Oxford Nanopore MinIONTM platform. Strains of Salmonella that were isolated include human infectious serotypes such as Typhimurium and Infantis. Over 31 of the isolates possessed antibiotic resistance genes, some of which were located on large, multidrug resistance plasmids. Plasmid pHJ-38, identified in a Typhimurium isolate, is an apparently self-transmissible 183 kb IncA/C2 plasmid that possesses multiple antimicrobial resistance and heavy-metal resistance genes. Plasmid pFHS-02, identified in an Infantis isolate, is an apparently self-transmissible 303 kb IncF1B plasmid that also possesses numerous heavy-metal and antimicrobial resistance genes. Using direct and indirect measures to assess student outcomes, results indicate that course participation contributed to cognitive gains in relevant content knowledge and research skills such as field sampling, molecular techniques, and computational analysis. Furthermore, participants self-reported a deeper interest in scientific research and careers as well as psychosocial outcomes (e.g., sense of belonging and self-efficacy) commonly associated with student success and persistence in STEM. Overall, this course provided a powerful combination of field, wet lab, and computational biology experiences for students, while also providing data potentially useful in pathogen surveillance, epidemiological tracking, and for the further study of environmental reservoirs of S. enterica.

In Case You Haven't Heard…

The U.S. Food and Drug Administration (FDA) announced warning letters to 10 companies for illegally selling dietary supplements that claim to cure, treat, mitigate or prevent depression and other mental health disorders, in violation of the Federal Food, Drug, and Cosmetic Act, an FDA news release stated. The warning letters were issued to: Enlifta LLC, Lifted Naturals, Mountain Peak Nutritionals, SANA Group LLC, Wholesome Wellness, Dr. Garber's Natural Solutions, ProHealth Inc., Blossom Nature LLC, FDC Nutrition Inc. and Silver Star Brands Inc. “Dietary supplements that claim to cure, treat, mitigate or prevent depression and other mental health disorders are unapproved new drugs that could potentially harm consumers who use these products instead of seeking proven treatments from qualified health care providers,” said Steven Tave, director of the Office of Dietary Supplement Programs in the FDA's Center for Food Safety and Applied Nutrition. “This is especially concerning during the ongoing pandemic, when consumers are even more susceptible to depression and mental health issues. The agency is committed to taking action to protect the public from unlawful dietary supplements.”

Integrating the Food and Drug Administration Office of the Coordinated Outbreak Response and Evaluation Network's foodborne illness outbreak surveillance and response activities with principles of the National Incident Management System.

The Food Safety Modernization Act mandates building a national Integrated Food Safety System, which represents a seamless partnership among federal, state, local, territorial, and tribal agencies. During multistate foodborne illness outbreak investigations, local and state partners, the Centers for Disease Control and Prevention, the United States Food and Drug Administration (FDA), or the United States Department of Agriculture Food Safety Inspection Service, depending on the regulated food product, become engaged and assist in coordinating the efforts between partners involved and determine the allocation of resources. The FDA Center for Food Safety and Applied Nutrition (CFSAN) Office of the Coordinated Outbreak Response and Evaluation (CORE) Network coordinates foodborne illness outbreak surveillance, response, and post-response activities related to incidents involving multiple illnesses linked to FDA-regulated human food, dietary supplements, and cosmetic products. FDA has implemented the National Incident Management System (NIMS) Incident Command System (ICS) principles across the agency to coordinate federal response efforts, and CORE has adapted NIMS ICS principles for the emergency management of multistate foodborne illness outbreaks. CORE's implementation of ICS principles has provided several benefits to the operational cycle of foodborne illness outbreak investigations, including establishing a consistent, standardized, and transparent step-by-step approach to outbreak investigations. ICS principles have been instrumental in the development of a national platform for rapid and systematic laboratory, traceback, and epidemiologic information sharing, data analysis, and decision-making. This allows for partners across jurisdictions to reach a consensus regarding outbreak goals and objectives, deploy resources, and take regulatory and public health actions.

GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians

BackgroundProcessing and analyzing whole genome sequencing (WGS) is computationally intense: a single Illumina MiSeq WGS run produces ~ 1 million 250-base-pair reads for each of 24 samples. This poses significant obstacles for smaller laboratories, or laboratories not affiliated with larger projects, which may not have dedicated bioinformatics staff or computing power to effectively use genomic data to protect public health. Building on the success of the cloud-based Galaxy bioinformatics platform (http://galaxyproject.org), already known for its user-friendliness and powerful WGS analytical tools, the Center for Food Safety and Applied Nutrition (CFSAN) at the U.S. Food and Drug Administration (FDA) created a customized ‘instance’ of the Galaxy environment, called GalaxyTrakr (https://www.galaxytrakr.org), for use by laboratory scientists performing food-safety regulatory research. The goal was to enable laboratories outside of the FDA internal network to (1) perform quality assessments of sequence data, (2) identify links between clinical isolates and positive food/environmental samples, including those at the National Center for Biotechnology Information sequence read archive (https://www.ncbi.nlm.nih.gov/sra/), and (3) explore new methodologies such as metagenomics. GalaxyTrakr hosts a variety of free and adaptable tools and provides the data storage and computing power to run the tools. These tools support coordinated analytic methods and consistent interpretation of results across laboratories. Users can create and share tools for their specific needs and use sequence data generated locally and elsewhere.ResultsIn its first full year (2018), GalaxyTrakr processed over 85,000 jobs and went from 25 to 250 users, representing 53 different public and state health laboratories, academic institutions, international health laboratories, and federal organizations. By mid-2020, it has grown to 600 registered users and processed over 450,000 analytical jobs. To illustrate how laboratories are making use of this resource, we describe how six institutions use GalaxyTrakr to quickly analyze and review their data. Instructions for participating in GalaxyTrakr are provided.ConclusionsGalaxyTrakr advances food safety by providing reliable and harmonized WGS analyses for public health laboratories and promoting collaboration across laboratories with differing resources. Anticipated enhancements to this resource will include workflows for additional foodborne pathogens, viruses, and parasites, as well as new tools and services.

Opioid exposure associated with poppy consumption reported to poison control centers and the U.S. Food and Drug Administration

Objective To assess characteristics of exposures to contaminated poppy and identify trends in exposure and poppy-related deaths. Methods Cross-sectional analysis of adverse events associated with exposure to poppy products (primarily poppy seeds) from the American Association of Poison Control Centers’ National Poison Data System (NPDS), 2000–2018, supplemented with analysis of overdoses and deaths related to poppy from the U.S. Food and Drug Administration (FDA) Center for Food Safety and Applied Nutrition’s Adverse Event Reporting System (CAERS) (2004–2018), and the FDA Adverse Event Reporting System (FAERS) (1968–2018). Results There were 591 NPDS exposure cases involving poppy between 2000 and 2018 including 392 in persons aged 13+. Rates of intentional exposures in NPDS increased among the age 13+ group over the study period. Most intentional exposures occurred in males in their teens and twenties. NPDS included 18 overdoses and three deaths likely attributable to poppy, most involving poppy seed tea. CAERS and FAERS included five additional deaths likely attributable to opioids in poppy. Conclusions Including previously reported cases, there are now at least 19 U.S. deaths associated with poppy seeds in the literature. We recommend that practitioners working in opioid treatment and recovery be alert to use of poppy to treat pain and symptoms of withdrawal.

Human Health Risk Assessments of Trace Metals on the Clam Corbicula javanica in a Tropical River in Peninsular Malaysia.

This study aimed to analyse ten trace metal concentrations in the edible part of the freshwater clam Corbicula javanica and to provide a critical assessment of the potential risks to human health through consumption of this clam as food based on well-established indices and food safety guidelines. The clams were captured from a pristine original site and transplanted to other sites with different environmental qualities. The trace metal levels in the edible total soft tissue (TST) of the clam were below those of the food safety guidelines referred to except for Pb, which exceeded the permissible limit set by the European Commission (2006) and the US Food and Drug Administration/ Center for Food Safety and Applied Nutrition); Interstate Shellfish Sanitation Conference. (USFDA/CFSAN; ISSC) (2007). The estimated daily intake (EDI) values of the clam were found to be lower than the oral reference dose and the calculated target hazard quotient (THQ) and total THQ were found to be less than 1. Therefore, in conclusion, the human health risk for consumption of TST of C. javanica at both average and high-level were insignificant regardless of the environment it was exposed to.

Screening of Kunun-zaki for Methicillin-Resistant Staphylococcus aureus (MRSA), Vancomycin-Resistant Staphylococcus aureus (VRSA) and Extended-Spectrum Beta-Lactamase (ESBL) Producing Salmonella spp.

Kunun-zaki is an indigenous, fermented, non-alcoholic cereal-based beverage produced and consumed primarily in Northern Nigeria. Due to its high nutritional and moisture content, it provides an ideal environment for the growth of foodborne pathogens. This study determined the presence of Methicillin resistant Staphylococcus aureus (MRSA), vancomycin resistant Staphylococcus aureus (VRSA) and Extended spectrum beta lactamase (ESBL) producing Salmonella spp in Kunun-zaki sold in Umuahia metropolis, Nigeria. Out of the 40 Kunun-zaki samples examined, Salmonella spp was detected in 19 (47.5%), whereas S. aureus was detected in 22 (55%) of the samples. The total Salmonella count ranged from 1.90×105-9.70×106 (CFU/ml), whereas the total S. aureus count ranged from 3.40×104-7.50×106 (CFU/ml); these microbial counts do not conform to the standard limits of detectable microbes in ready-to-eat food samples as stipulated by the Center for Food Safety. All the isolates were subjected to antibiotic susceptibility testing using the modified Kirby Bauer disc diffusion method. On the one hand, most of the Salmonella spp were resistant to the beta-lactam class of antibiotics used (IMP 58%, MEM 90%, AMP 53%). On the other hand, the Salmonella isolates showed the highest sensitivities to ceftazidime (95%) and ofloxacin (90%). The S. aureus isolates revealed high susceptibility to ofloxacin (96%), and major resistance to oxacillin (41%) and the oxyimino-cephalosporin antibiotics used (CAZ 55%, CTR 41%). MRSA, VRSA and ESBL producing Enterobacteriaceae are amongst the most critical multidrug-resistant bacterial pathogens. In this study, 26% of the Salmonella spp isolates were confirmed to be ESBL producers, whereas 41% of the isolates were MRSA, 23% were VRSA, and 68% were Vancomycin intermediate Staphylococcus aureus (VISA). Hence, the Kunun-zaki could constitute a reservoir for the dissemination of multidrug-resistant foodborne pathogens if not correctly quality controlled.

Adverse Events Reported to the United States Food and Drug Administration Related to Caffeine-Containing Products

ObjectiveTo examine differences in the frequency and severity of federally reported adverse events between caffeine-containing and non–caffeine-containing products while also identifying the category of caffeine-containing products associated with the highest frequency and severity of adverse events. Patients and MethodsAll adverse event reports that met specified eligibility criteria and were submitted to the Center for Food Safety and Applied Nutrition Adverse Event Reporting System between January 1, 2014, and June 29, 2018, were extracted. In this retrospective observational study, the most severe adverse event experienced, an ordinal variable, was categorized into death, life-threatening, hospitalization/disability, and emergency department visit. A nonproportional odds model was used to compare the odds of caffeine-containing products being associated with more severe adverse events relative to a noncaffeine group. The analysis is of data only from those reporting adverse events and may or may not be representative of the entire population exposed to these products, which is not known from the examined data. ResultsEnergy and preworkout products saw a significant increase in the odds of the adverse event experienced being death rather than the other less severe outcomes relative to the noncaffeinated group. Those products, along with weight loss products, had greater odds of the adverse event being death or life-threatening vs the less severe outcomes relative to the noncaffeinated group. ConclusionCaffeine-containing products have a greater association with severe adverse events compared with non–caffeine-containing products. Exposure to preworkout and weight loss products had greater odds of being associated with a more serious adverse event relative to noncaffeinated products. Health care practitioners should use these outcomes to better inform and educate patients about the many factors related to caffeine intake and adverse outcomes.

Do topically aplied skin creams containing retinyl palmitate affect the photocarcinogenecity of simulated solar light?

Retinyl palmitate (all-trans-retinyl palmitate; RP) was nominated in 2001 by the U.S. Food and Drug Administration's Center for Food Safety and Applied Nutrition (CFSAN) to the National Toxicology Program (NTP) as a high priority compound for phototoxicity and photocarcinogenicity studies at the National Center for Toxicological Research (NCTR). Studies with SKH-1 hairless mice are required to test whether topical application of RP enhances the phototoxicity and photocarcinogenicity of simulated solar light and UV light. Mechanistic studies are needed to provide insight into the disposition of RP in vitro and on the skin of mice, and to test thoroughly whether genotoxic damage by UV-induced radicals may participate in any toxicity of topically applied RP in the presence of UV light.

Groups sue EPA over glyphosate reauthorization

Environmental and farmworker groups are challenging the US Environmental Protection Agency’s January 2020 decision to allow the commonly used herbicide glyphosate to remain on the US market. In two separate lawsuits filed March 20, the petitioners argue that glyphosate poses health risks to humans and endangered species. In 2015, the World Health Organization’s cancer agency deemed the herbicide “probably carcinogenic,” but the EPA disputes that finding. The agency is still evaluating glyphosate’s potential endocrine-disrupting effects in humans and risks to endangered species. Glyphosate is the active ingredient in Monsanto’s Roundup, now produced by Bayer, and in several generic formulations made by other companies. “EPA’s half-completed, biased, and unlawful approval sacrifices the health of farmworkers and endangered species at the altar of Monsanto profits,” George Kimbrell, legal director for the Center for Food Safety and counsel for the petitioners in one of the lawsuits, says in a statement. The environmental groups

FRIED FOOD AND POSSIBLE HEALTH HAZARDS

FRIED FOOD AND POSSIBLE HEALTH HAZARDS

Prevalence, Distribution, and Phylogeny of Type Two Toxin-Antitoxin Genes Possessed by Cronobacter Species where C. sakazakii Homologs Follow Sequence Type Lineages.

Cronobacter species are a group of foodborne pathogenic bacteria that cause both intestinal and systemic human disease in individuals of all age groups. Little is known about the mechanisms that Cronobacter employ to survive and persist in foods and other environments. Toxin–antitoxin (TA) genes are thought to play a role in bacterial stress physiology, as well as in the stabilization of horizontally-acquired re-combinatorial elements such as plasmids, phage, and transposons. TA systems have been implicated in the formation of a persistence phenotype in some bacterial species including Escherichia coli and Salmonella. This project’s goal was to understand the phylogenetic relatedness among TA genes present in Cronobacter. Preliminary studies showed that two typical toxin genes, fic and hipA followed species evolutionary lines. A local database of 22 TA homologs was created for Cronobacter sakazakii and a Python version 3 shell script was generated to extract TA FASTA sequences present in 234 C. sakazakii genomes previously sequenced as part of Center for Food Safety and Applied Nutrition’s (CFSAN) GenomeTrakr project. BLAST analysis showed that not every C. sakazakii strain possessed all twenty-two TA loci. Interestingly, some strains contained either a toxin or an antitoxin component, but not both. Five common toxin genes: ESA_00258 (parDE toxin-antitoxin family), ESA_00804 (relBE family), ESA_01887 (relBE family), ESA_03838 (relBE family), and ESA_04273 (YhfG-Fic family) were selected for PCR analysis and the primers were designed to detect these genes. PCR analysis showed that 55 of 63 strains possessed three of these genes Sequence analysis identified homologs of the target genes and some of the strains were PCR-negative for one or more of the genes, pointing to potential nucleotide polymorphisms in those loci or that these toxin genes were absent. Phylogenetic studies using a Cronobacter pan genomic microarray showed that for the most part TAs follow species evolutionary lines except for a few toxin genes possessed by some C. malonaticus and C. universalis strains; this demonstrates that some TA orthologues share a common phylogeny. Within the C. sakazakii strains, the prevalence and distribution of these TA homologs by C. sakazakii strain BAA-894 (a powdered infant formula isolate) followed sequence-type evolutionary lineages. Understanding the phylogeny of TAs among the Cronobacter species is essential to design future studies to realize the physiological mechanisms and roles for TAs in stress adaptation and persistence of Cronobacter within food matrices and food processing environments.

The Reduction of Pathogen Load on Ross 708 Broilers when Using Different Sources of Commercial Peracetic Acid Sanitizers in a Pilot Processing Plant.

Peracetic acid (PAA) in poultry processing is not necessarily the same from company to company. Anecdotal evidence suggests that PeraClean may be more stable compared to the competition; however, it is not known what impact potential differences in chemical stability may have. In order to evaluate the antimicrobial effects of PAA, one PAA (PeraClean, P) was qualitatively compared against two competitor products (Competitors 1 and 2, C1 and C2) at the University of Arkansas Pilot Processing Plant. A total of 150 Ross 708 broilers (42 d) were used in the current study. Briefly, prior to treatment, 10 birds were sampled post-evisceration (C). Then, one of four treatment groups per PAA were applied (A1, A2, B1, and B2). The birds were dipped in either 400 ppm or 600 ppm PAA (A or B), chilled in either 25 ppm or 45 ppm PAA (1 or 2), and then manually agitated in 400 mL of nBPW for 1 min. There were 10 birds per treatment group in total. The resulting rinsates were transported to the Center for Food Safety and assessed for total microbiological load with total aerobic plate counts (Trypticase Soy Agar; APC), coliforms, (Eosin Methylene Blue Media; EMB), Salmonella (Xylose Lysine Deoxycholate agar, XLD), and Campylobacter (modified Charcoal Cefoperazone Deoxycholate Agar, mCCDA). The microbiological plates were incubated as per manufacturer’s directions. Statistical analyses were calculated in JMP 14.0, with a significance level of p ≤ 0.05. Data indicate that all three sources of PAA are effective sanitizers for poultry processing applications compared within treatment. Qualitatively, there were differences in efficacy between the treatments. However, additional studies will be required to determine if those differences are quantitatively distinctive and if they are attributable to differences in product stability.

Pesticides, biotech crops on wildlife refuges trigger lawsuit

The Center for Food Safety and Center for Biological Diversity are suing the Trump administration for reversing a 2014 decision that would have phased out the use of neonicotinoid pesticides and ge...

Electrochemical Study of Tartrazine Using a Carbon Paste Electrode Modified with Nanostructured Materials

Tartrazine (Trz) is one of the most widely used azoic dyes in the alimentary industry; it is added to a great variety of products, for this reason it is necessary to develop analytic methods and materials which allow its detection and quantification. For this purpose ultraviolet-visible spectrophotometry (UV-Vis), high performance liquid chromatography (HPLC), capillary electrophoresis and potentiometric and voltammetric sensors have been used. Potentiometric and voltammetric sensors have many advantages such as simplicity; rapid analysis and cost, besides most recently developed sensors are environmentally friendly and avoid the use of mercury which is toxic. In this regard, carbonaceous electrodes such as carbon paste electrodes have been employed due to its low cost, they are easy to manufacture and can be modified with a great diversity of materials an methods. Nanostructured materials such as bamboo-shaped multiwalled carbon nanotubes (BS-MWCNT) and Pt nanoparticles (Pt/NPs) allow great electrochemical activity and in this work are proposed to modify a CPE in order to detect and quantify Tartrazine samples. The electrochemical experiments were performed in a potentiostat/galvanostat AUTOLAB30, using NOVA 2.1 software, a typical three-electrode electrochemical cell was used. A Pt wire was employed as counter electrode; Ag/AgCl (3M NaCl) in a Luggin capillary as reference electrode, the working electrode was a CPE prepared by mixing graphite powder and mineral oil in a proportion 1:1, the CPE was modified by adding an aliquot of 5mL of BS-MWCNT dispersion and by adding an aliquot of 5mL of Pt/NPs and BS-MWCNT. Cyclic voltammograms obtained in 0.5M NaCl + 2.0x10-5 M Trz (adjusted to a pH=4.0) are shown in Figure 1. In the case of CPE, a peak due to Trz oxidation appears at 0.77V, the oxidation peak is positively shifted (0.15V) when BS-MWCNT are added and now appears at 0.92V, even though the oxidation potential is greater on BS-MWCNT the associated current is also greater. When the experiment is performed on BS-MWCNT + Pt/NPs the oxidation peak appears at 0.99V, the associated current in this last case is greater than in the previous cases, a great current leads to an improvement of some analytical parameters such as sensibility, which may help to detect and quantify Trz more accurately. S Food and Drug Administration Center for Food Safety and Applied Nutrition. (2003) U. S Department of Health and Human Services.López-de-Alba, P. L., López-Martínez, L., De-León-Rodríguez, L. M. Simultaneous Determination of Synthetic Dyes Tartrazine, Allura Red and Sunset Yellow by Differential Pulse Polarography and Partial Least Squares. A Multivariate Calibration Method. (2002). 14(3):197-205.Ramírez-Silva, T., Palomar-Pardavé, M. E. Gónzalez, I., Rojas-Hernández, A. (1995). Carbon Paste Electrodes with Electrolytic Binder: Influence of the Preparation Method. Electroanalysis. 7:184-188.Yu, L., Shi, M., Yue, X., Qu, L. (2016). Detection of Allura Red Based on the Composite of Poly (diallylmethylammonium chloride) Functionalized Graphene and Nickel Nanoparticles Modified Electrode. Sensors and Actuators B: Chemical. 225:398-404. Figure 1

PGE2 Augments Inflammasome Activation and M1 Polarization in Macrophages Infected with Salmonella Typhimurium and Yersinia enterocolitica

Prostaglandin E2 (PGE2) is an important immunomodulatory molecule that is part of a larger group of bioactive lipids known as eicosanoids. PGE2 has long been reported to have conflicting roles in the regulation of inflammation. For example, some effects are primarily anti‐inflammatory and other roles that mediate inflammation. During intracellular infection with Gram‐negative bacteria, host macrophages form complexes called inflammasomes. Inflammasomes drive activation and secretion of inflammatory cytokines such as IL‐1β that signal nearby cells in the process of inflammatory cell death called pyroptosis. PGE2 is reported to inhibit NLRP3 inflammasome activation and enhance NLRC4 inflammasome activation. Since both NLRP3 and NLRC4 inflammasomes mediate IL‐1β secretion, the PGE2's function in the inflammatory processes does not seem to be clear. Previous studies relied on LPS stimulation of macrophages in place of bacterial infection. In this study, we used an infection model of THP‐1 human macrophages with Salmonella enterica Typhimurium (St) and Yersinia enterocolitica (Ye) that suggests PGE2 plays a vital role in enhancing the transcription and secretion of IL‐1β upon inflammasome activation. Interestingly, distinct virulence strategies between St and Ye are reflected in the alteration of COX‐2 and resulting PGE2 biosynthesis by these pathogens. Ye virulence factors inhibit COX‐2 expression and thus decrease the amount of PGE2 secreted during infection. St, in contrast, activates COX‐2 and enhances PGE2 production. In our studies, PGE2 enhances bacterial load of St inside macrophages 48 hours post infection, but it decreases intracellular Ye. Finally, our results suggest that PGE2 primarily enhances the transcription of pro‐inflammatory cytokines while repressing anti‐inflammatory processes such as resource scavenging and matrix remodeling.Support or Funding InformationThis study was supported by a fund no. 2016‐31200‐06012 from the National Institute of Food and Agriculture (NIFA), https://doi.org/10.13039/100005825, National Institutes of Health (NIH) fund no. 5P20GM103646‐02, https://doi.org/10.13039/100000002, as well as MS Center for Food Safety and Post‐harvest Technology Grant Program (USDA‐ARS SCA 58‐6066‐7081) and NIH1R15ES015348‐02. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

US requires labeling of GMO foods as ‘bioengineered’

Food manufacturers must alert US consumers to the presence of genetically modified ingredients through labels, QR codes, or text messages, the US Department of Agriculture announced in late December. The new regulation, required under a 2016 law, opts for the term “bioengineered” food for this disclosure. It applies to foods containing “detectable genetic material that has been modified through lab techniques and cannot be created through conventional breeding or found in nature.” This includes resistance to specific pesticides. The Center for Food Safety, an activist group, faults USDA for prohibiting the terms best known to the public—genetically engineered or genetically modified organism—to describe organisms that scientists created by tweaking DNA. The organization says most consumers associate the word bioengineered with biomedical technology. The rule exempts highly refined items such as sugar or oil derived from a bioengineered crop because they don’t contain detectable amounts of modified genes. ...

Interpreting Whole-Genome Sequence Analyses of Foodborne Bacteria for Regulatory Applications and Outbreak Investigations.

Whole-genome sequence (WGS) analysis has revolutionized the food safety industry by enabling high-resolution typing of foodborne bacteria. Higher resolving power allows investigators to identify origins of contamination during illness outbreaks and regulatory activities quickly and accurately. Government agencies and industry stakeholders worldwide are now analyzing WGS data routinely. Although researchers have published many studies that assess the efficacy of WGS data analysis for source attribution, guidance for interpreting WGS analyses is lacking. Here, we provide the framework for interpreting WGS analyses used by the Food and Drug Administration’s Center for Food Safety and Applied Nutrition (CFSAN). We based this framework on the experiences of CFSAN investigators, collaborations and interactions with government and industry partners, and evaluation of the published literature. A fundamental question for investigators is whether two or more bacteria arose from the same source of contamination. Analysts often count the numbers of nucleotide differences [single-nucleotide polymorphisms (SNPs)] between two or more genome sequences to measure genetic distances. However, using SNP thresholds alone to assess whether bacteria originated from the same source can be misleading. Bacteria that are isolated from food, environmental, or clinical samples are representatives of bacterial populations. These populations are subject to evolutionary forces that can change genome sequences. Therefore, interpreting WGS analyses of foodborne bacteria requires a more sophisticated approach. Here, we present a framework for interpreting WGS analyses that combines SNP counts with phylogenetic tree topologies and bootstrap support. We also clarify the roles of WGS, epidemiological, traceback, and other evidence in forming the conclusions of investigations. Finally, we present examples that illustrate the application of this framework to real-world situations.

Cosmetics and Cancer: Adverse Event Reports Submitted to the Food and Drug Administration.

There have been numerous controversies surrounding cosmetic products and increased cancer risk. Such controversies include associations between parabens and breast cancer, hair dyes and hematologic malignancies, and talc powders and ovarian cancer. Despite the prominent media coverage and numerous scientific investigations, the majority of these associations currently lack conclusive evidence. In 2016, the US Food and Drug Administration (FDA) made publically available all adverse event reports in Center for Food Safety and Applied Nutrition’s Adverse Event Reporting System (CAERS), which includes complaints related to cosmetic products. We mined CAERS for cancer-related reports attributed to cosmetics. Between 2004 and 2017, cancer-related reports caused by cosmetics represented 41% of all adverse events related to cosmetics. This yielded 4427 individual reports of cancer related to a cosmetic product. Of these reports, the FDA redacted the specific product names in 95% of cancer-related reports under the Freedom of Information Act exemptions, most likely due to ongoing legal proceedings. For redacted reports, ovarian cancer reports dominated (n = 3992, 90%), followed by mesothelioma (n = 92, 2%) and malignant neoplasm unspecified (n = 46, 1%). For nonredacted reports, or those reports whose product names were not withheld (n = 218), 70% were related to ovarian cancer attributed to talc powders, followed by skin cancer (11%) and breast cancer (5%) attributed to topical moisturizers. Currently, CAERS is of limited utility, with the available data having been subjected to significant reporter bias and a lack of supportive information such as demographic data, medical history, or concomitant product use. Although the system has promise for safeguarding public health, the future utility of the database requires broader reporting participation and more complete reporting, paired with parallel investments in regulatory science and improved molecular methods.

The Foodborne Outbreak Challenge—Using Experiential Learning to Foster Interdisciplinary Training Among Students on Foodborne Disease Outbreak Investigations

AbstractThe Integrated Food Safety Centers of Excellence aim to develop novel learning methods to educate and train the future public health workforce to investigate foodborne outbreaks. The Foodborne Outbreak Challenge (FOC) was a one‐day event hosted by the Colorado Integrated Food Safety Center of Excellence at the Colorado School of Public Health. The FOC incorporated experiential, problem‐based, and interdisciplinary pedagogies from case studies, simulation exercises, and public health case competitions, to deliver a novel learning experience that met the training needs of a multidisciplinary foodborne outbreak response team with diverse skills sets. The event received positive feedback, and participants demonstrated knowledge gain. Event materials are available for other institutions to use.