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Research Publications (Food Safety)

This page tracks research articles published in national and international peer-reviewed journals. Recent articles are available ahead of print and searchable by Journal, Article Title, and Category. Research publications are tracked across six categories: Bacterial Pathogens, Chemical Contaminants, Natural Toxins, Parasites, Produce Safety, and Viruses. Articles produced by USDA Grant Funding Agencies (requires login) and FDA Grant Funding Agencies (requires login) are also tracked in Scopus.

Displaying 1 - 25 of 83

  1. Inflammatory Responses Induced by the Monophasic Variant of Salmonella Typhimurium in Pigs Play a Role in the High Shedder Phenotype and Fecal Microbiota Composition

    • mSystems
    • mSystems, Ahead of Print. Pigs infected with Salmonella may excrete large amounts of Salmonella, increasing the risk of spread of this pathogen in the food chain. Identifying Salmonella high shedder pigs is therefore required to mitigate this risk. We analyzed immune-associated markers and composition of the gut microbiota in specific-pathogen-free pigs presenting different shedding levels after an oral infection with Salmonella.

      • Bacterial pathogens
      • Salmonella
  2. CRISPR-Cas-Guided Mutagenesis of Chromosome and Virulence Plasmid in Shigella flexneri by Cytosine Base Editing

    • mSystems
    • mSystems, Ahead of Print. Shigella is a Gram-negative bacterium that invades the human gut epithelium. The resulting infection, shigellosis, is the deadliest bacterial diarrheal disease. Much of the information about the genes dictating the pathophysiology of Shigella, both on the chromosome and the virulence plasmid, was obtained by classical reverse genetics.

      • Bacterial pathogens
      • Shigella
  3. Coordination of CcpA and CodY Regulators in Staphylococcus aureus USA300 Strains

    • mSystems
    • mSystems, Ahead of Print. The complex cross talk between metabolism and gene regulatory networks makes it difficult to untangle individual constituents and study their precise roles and interactions. To address this issue, we modularized the transcriptional regulatory network (TRN) of the Staphylococcus aureus USA300 strain by applying independent component analysis (ICA) to 385 RNA sequencing samples.

      • Bacterial pathogens
      • Staphylococcus aureus
  4. Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures

    • mSystems
    • mSystems, Ahead of Print. Establishing transcriptional regulatory networks (TRNs) in bacteria has been limited to well-characterized model strains. Using machine learning methods, we established the transcriptional regulatory networks of six Salmonella enterica serovar Typhimurium strains from their transcriptomes.

      • Bacterial pathogens
      • Salmonella
  5. Exploiting Violet-Blue Light to Kill Campylobacter jejuni: Analysis of Global Responses, Modeling of Transcription Factor Activities, and Identification of Protein Targets

    • mSystems
    • mSystems, Ahead of Print. Campylobacter jejuni is a microaerophilic foodborne zoonotic pathogen of worldwide concern as the leading cause of bacterial gastroenteritis. Many strains are increasingly antibiotic resistant and new methods of control are required to reduce food-chain contamination. One possibility is photodynamic inactivation (PDI) using violet-blue (VB) light, to which C. jejuni is highly susceptible.

      • Bacterial pathogens
      • Campylobacter
  6. Multilayered Networks of SalmoNet2 Enable Strain Comparisons of the Salmonella Genus on a Molecular Level

    • mSystems
    • mSystems, Ahead of Print. Serovars of the genus Salmonella primarily evolved as gastrointestinal pathogens in a wide range of hosts. Some serotypes later evolved further, adopting a more invasive lifestyle in a narrower host range associated with systemic infections. A system-level knowledge of these pathogens could identify the complex adaptations associated with the evolution of serovars with distinct pathogenicity, host range, and risk to human health.

      • Bacterial pathogens
      • Salmonella
  7. Dynamics of Antimicrobial Resistance and Genomic Epidemiology of Multidrug-Resistant Salmonella enterica Serovar Indiana ST17 from 2006 to 2017 in China

    • mSystems
    • mSystems, Ahead of Print. The genetic features of foodborne Salmonella have changed in recent years as multidrug-resistant (MDR) strains have become prevalent among various serovars.

      • Bacterial pathogens
      • Salmonella
  8. Staphylococcus aureus Infection Initiates Hypoxia-Mediated Transforming Growth Factor-β1 Upregulation to Trigger Osteomyelitis

    • mSystems
    • mSystems, Ahead of Print. Little is unknown about the regulatory mechanisms underlying the pathogenesis of osteomyelitis induced by Staphylococcus aureus. Hypoxia-inducible factor-1α (HIF-1α) and transforming growth factor β1 (TGF-β1) were both upregulated in S. aureus-infected MC3T3-E1 cells and osteomyelitis patients. HIF-1α directly targets the hypoxia-responsive elements (HREs) of TGF-β1 mRNA to induce its expression.

      • Bacterial pathogens
      • Staphylococcus aureus
  9. Forecasting Staphylococcus aureus Infections Using Genome-Wide Association Studies, Machine Learning, and Transcriptomic Approaches

    • mSystems
    • mSystems, Ahead of Print. Staphylococcus aureus is a major human and animal pathogen, colonizing diverse ecological niches within its hosts. Predicting whether an isolate will infect a specific host and its subsequent clinical fate remains unknown. In this study, we investigated the S. aureus pangenome using a curated set of 356 strains, spanning a wide range of hosts, origins, and clinical display and antibiotic resistance profiles.

      • Bacterial pathogens
      • Staphylococcus aureus
  10. Dietary Exposure to Antibiotic Residues Facilitates Metabolic Disorder by Altering the Gut Microbiota and Bile Acid Composition

    • mSystems
    • mSystems, Ahead of Print. Antibiotics used as growth promoters in livestock and animal husbandry can be detected in animal-derived food. Epidemiological studies have indicated that exposure to these antibiotic residues in food may be associated with childhood obesity. Herein, the effect of exposure to a residual dose of tylosin—an antibiotic growth promoter—on host metabolism and gut microbiota was explored in vivo.

      • Chemical contaminants
      • Antibiotic residues
  11. The Number and Type of Chaperone-Usher Fimbriae Reflect Phylogenetic Clade Rather than Host Range in Salmonella

    • mSystems
    • mSystems, Ahead of Print. Salmonella is one of the most successful foodborne pathogens worldwide, owing in part to its ability to colonize or infect a wide range of hosts. Salmonella serovars are known to encode a variety of different fimbriae (hairlike organelles that facilitate binding to surfaces); however, the distribution, number, and sequence diversity of fimbriae encoded across different lineages of Salmonella were unknown.

      • Bacterial pathogens
      • Salmonella
  12. Proteome Expression and Survival Strategies of a Proteorhodopsin-Containing Vibrio Strain under Carbon and Nitrogen Limitation

    • mSystems
    • mSystems, Volume 7, Issue 2, April 2022. Photoheterotrophy is a widespread mode of microbial metabolism, notably in the oligotrophic surface ocean, where microbes experience chronic nutrient limitation. One especially widespread form of photoheterotrophy is based on proteorhodopsin (PR), which uses light to generate proton motive force that can drive ATP synthesis, flagellar movement, or nutrient uptake.

      • Bacterial pathogens
      • Vibrio
  13. A Polysaccharide Biosynthesis Locus in Vibrio parahaemolyticus Important for Biofilm Formation Has Homologs Widely Distributed in Aquatic Bacteria Mainly from Gammaproteobacteria

    • mSystems
    • mSystems, Volume 7, Issue 2, April 2022. Vibrio parahaemolyticus is a seafood-borne pathogen that poses a great threat to public health worldwide. It is found in either a planktonic cell or a biofilm form in the natural environment. The cps locus has been the only extensively studied polysaccharide biosynthesis gene cluster involved in biofilm formation for this bacterium.

      • Bacterial pathogens
      • Vibrio
  14. Temporal Transcriptional Responses of a Vibrio alginolyticus Strain to Podoviridae Phage HH109 Revealed by RNA-Seq

    • mSystems
    • mSystems, Volume 7, Issue 2, April 2022. Phage are thought to exhibit control over host genes during infection. As a preliminary investigation of the kinetics and magnitude of co-expression between phage and bacteria, we compared the global transcriptional profiles for Vibrio alginolyticus strain E110 and its lytic phage HH109 by using RNA sequencing. In total, 24.7% (1,143/4,620) of the host protein-coding genes were differentially expressed genes during infection (DEGs).

      • Bacterial pathogens
      • Vibrio
  15. Evolutionary Trajectory of the Tet(X) Family: Critical Residue Changes towards High-Level Tigecycline Resistance

    • mSystems
    • ABSTRACT

      • Antibiotic residues
      • Chemical contaminants
  16. High-Content Imaging to Phenotype Antimicrobial Effects on Individual Bacteria at Scale

    • mSystems
    • ABSTRACT

      • Salmonella
      • Staphylococcus aureus
      • Bacterial pathogens
  17. Metagenomics and Quantitative Stable Isotope Probing Offer Insights into Metabolism of Polycyclic Aromatic Hydrocarbon Degraders in Chronically Polluted Seawater

    • mSystems
    • ABSTRACT

      • Chemical contaminants
  18. Marine Community Metabolomes Carry Fingerprints of Phytoplankton Community Composition

    • mSystems
    • ABSTRACT

      • Shellfish toxins
  19. Bacterial Microcompartments Coupled with Extracellular Electron Transfer Drive the Anaerobic Utilization of Ethanolamine in Listeria monocytogenes

    • mSystems
    • ABSTRACT

      • Listeria monocytogenes
      • Bacterial pathogens
  20. Calf Diarrhea Caused by Prolonged Expansion of Autochthonous Gut Enterobacteriaceae and Their Lytic Bacteriophages

    • mSystems
    • ABSTRACT

      • Salmonella
      • Bacterial pathogens
  21. Endophytic Lifestyle of Global Clones of Extended-Spectrum {beta}-Lactamase-Producing Priority Pathogens in Fresh Vegetables: a Trojan Horse Strategy Favoring Human Colonization?

    • mSystems
    • ABSTRACT

      • Chemical contaminants
      • Leafy Greens
      • Produce Safety
      • Pesticide residues
      • Bacterial pathogens
  22. Endogenous Metabolites Released by Sanitized Sprouting Alfalfa Seed Inhibit the Growth of Salmonella enterica

    • mSystems
    • ABSTRACT

      • Produce Safety
      • Salmonella
      • Bacterial pathogens
  23. Microbiota Assessments for the Identification and Confirmation of Slit Defect-Causing Bacteria in Milk and Cheddar Cheese

    • mSystems
    • ABSTRACT

      • Bacterial pathogens
  24. Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification

    • mSystems
    • ABSTRACT

  25. Manipulation of IRE1-Dependent MAPK Signaling by a Vibrio Agonist-Antagonist Effector Pair

    • mSystems
    • ABSTRACT

      • Vibrio
      • Bacterial pathogens