Next-Generation Approaches to Foodborne Pathogens: Genomics, Resistance, and Emerging Risks

Dear Colleagues,

The global burden of foodborne illnesses continues to demand urgent scientific attention, particularly in light of increasing antimicrobial resistance (AMR), evolving food systems, and climate-driven shifts in pathogen ecology. Recent technological breakthroughs including whole-genome sequencing, metagenomics, transcriptomics, and proteomics have enabled researchers to study pathogens at unprecedented resolution. These approaches not only enhance surveillance and source tracking but also uncover the mechanisms of virulence, stress tolerance, and antimicrobial resistance that allow bacteria to persist in diverse food matrices and environments. Furthermore, smart detection technologies, such as CRISPR-based diagnostics and prediction models, are paving the way for rapid and precise pathogen monitoring. We particularly encourage submissions that take a systems biology, ecological, or predictive modeling perspective to understand pathogen behavior in complex food ecosystems.

This Special Issue aims to provide insights into the following:

• foodborne pathogens behavior mechanisms and evolution;
• gene regulation networks and dissemination routes of virulence and resistance genes;
• biofilm formation and surface persistence in processing environments;
• safety assessment of new and alternative food matrices;
• development of robust, rapid, and field-deployable detection tools;
• development of risk mitigation strategies in food models.

We particularly encourage submissions that take a systems biology, ecological, or predictive modeling perspective to understand pathogen behavior in complex food ecosystems.

We look forward to receiving your contributions.

Dr. Claudia Cortimiglia
Dr. Frédérique Pasquali
Dr. Giulia Tabanelli
Guest Editors

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 250 words) can be sent to the Editorial Office for assessment.

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.