Genomic Technologies for the Characterization, Typing, and Detection of Food-Borne Pathogens

A special issue of Foods (ISSN 2304-8158). This special issue belongs to the section "Foodomics".

Deadline for manuscript submissions: 31 August 2025 | Viewed by 974

Special Issue Editors


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Guest Editor
Eastern Regional Research Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Washington, DC, USA
Interests: foodborne pathogen detection; campylobacter genomics; antimicrobial nanoparticle research

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Guest Editor Assistant
Eastern Regional Research Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Washington, DC, USA
Interests: food-borne pathogen detection and characterization; microbial genomics; antimicrobial research; microbial ecology

Special Issue Information

Dear Colleagues,

We cordially invite you to submit articles related to the upcoming Special Issue on “Genomic Technologies for the Characterization, Typing, and Detection of Food-Borne Pathogens”.

Next-generation sequencing (NGS) combined with bioinformatics analysis is revolutionizing food microbiology research. Sequencing DNA or RNA using NGS technologies enables genomic and transcriptomic studies of food-borne pathogens, revealing single-nucleotide polymorphisms (SNPs) and multi-locus sequence types (MLSTs) for genotyping bacterial strains and the identification of microbial contamination in a particular food or food process environment.

This Special Issue will address the most recent trends in the application of next-generation sequencing technologies for detecting, genotyping, and characterizing food-borne pathogens to ensure food safety. The scope of this Special Issue will broadly encompass well-known microbial food-borne pathogens in addition to emerging food-borne pathogens. Research articles, reviews, technical notes, and case reports that highlight advancements in the utilization of next-generation sequencing technologies for investigating microbial genomics or microbiomes associated with food or food process environments are welcome.

The main goal of this Special Issue is to promote the broad application of DNA and RNA sequencing technologies in food safety testing. In addition, we endeavor to highlight novel applications of microbial genomics with the ultimate aim of increasing food safety by driving further research in this area.

Dr. Yiping He
Guest Editor

Dr. Gretchen Dykes
Guest Editor Assistant

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Foods is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • next-generation sequencing (NGS)
  • food-borne pathogen
  • food safety
  • bioinformatics
  • microbial genomics
  • detection
  • typing

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Published Papers (2 papers)

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Research

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16 pages, 1535 KiB  
Article
Exploratory Genomic Marker Analysis of Virulence Patterns in Listeria monocytogenes Human and Food Isolates
by Valeria Russini, Maria Laura De Marchis, Cinzia Sampieri, Cinzia Onorati, Piero Zucchitta, Paola De Santis, Bianca Maria Varcasia, Laura De Santis, Alexandra Chiaverini, Antonietta Gattuso, Annarita Vestri, Laura Gasperetti, Roberto Condoleo, Luigi Palla and Teresa Bossù
Foods 2025, 14(10), 1669; https://doi.org/10.3390/foods14101669 - 9 May 2025
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Abstract
Listeria monocytogenes causes listeriosis, a severe foodborne disease with high mortality. Contamination with it poses significant risks to food safety and public health. Notably, genetic characteristic differences exist between strains causing human infections and those found in routine food inspections. This study examined [...] Read more.
Listeria monocytogenes causes listeriosis, a severe foodborne disease with high mortality. Contamination with it poses significant risks to food safety and public health. Notably, genetic characteristic differences exist between strains causing human infections and those found in routine food inspections. This study examined the genotypic factors influencing the pathogenicity of L. monocytogenes, focusing on virulence gene profiles and key integrity genes like inlA to explain these divergences. The dataset included 958 strains isolated from human, food, and environmental samples. Whole-genome sequencing identified virulence genes, and principal component analysis (PCA) examined 92 virulence genes and inlA integrity to uncover potentially pathogenic patterns. The results highlight differences in virulence characteristics between strains of different origins. The integrity of inlA and genes such as inlD, inlG, and inlL were pivotal to pathogenicity. Strains with premature stop codons (PMSCs) in inlA, associated with reduced virulence, accounted for a low percentage of human cases but over 30% of food isolates. Sequence types (STs) like ST121, ST580, and ST199 showed unique profiles, while ST9, dominant in food, occasionally caused human cases, posing risks to vulnerable individuals. This research highlights the complexity of the pathogenicity of L. monocytogenes and emphasizes the importance of genomic surveillance for effective risk assessment. Full article
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Review

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11 pages, 201 KiB  
Review
Application of Comparative Genomics for the Development of PCR Primers for the Detection of Harmful or Beneficial Microorganisms in Food: Mini-Review
by Sang-Soon Kim
Foods 2025, 14(6), 1060; https://doi.org/10.3390/foods14061060 - 20 Mar 2025
Cited by 1 | Viewed by 455
Abstract
Gene markers are widely utilized for detecting harmful and beneficial microorganisms in food products. Primer sequences targeting the 16S rRNA region, recognized as a conserved region, have been conventionally employed in PCR analyses. However, several studies have highlighted limitations and false-positive results associated [...] Read more.
Gene markers are widely utilized for detecting harmful and beneficial microorganisms in food products. Primer sequences targeting the 16S rRNA region, recognized as a conserved region, have been conventionally employed in PCR analyses. However, several studies have highlighted limitations and false-positive results associated with the use of these primer sequences. Consequently, pan-genome analysis, a comparative genomic approach, has been increasingly applied to design more selective gene markers. This mini-review explores the application of pan-genome analysis in developing PCR primers for the detection of harmful microorganisms, such as Salmonella, Cronobacter, Staphylococcus, and Listeria, as well as beneficial microorganisms like Lactobacillus. Additionally, the review discusses the applicability, advantages, limitations, and future directions of pan-genome analysis for primer design. A comparative overview of bioinformatics tools, recent trends, and verification methods is also provided, offering valuable insights for researchers interested in leveraging pan-genome analysis for advanced primer design. Full article
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