Special Issue "Applications of Whole Genome Sequencing and Metagenomics to Food Safety"

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

Deadline for manuscript submissions: 15 September 2021.

Special Issue Editors

Dr. Frédérique Pasquali
Guest Editor
Department of Agricultural and Food Sciences, Alma Mater Studiorum – University of Bologna, Italy
Interests: food safety; food of animal origin; food borne bacterial pathogens; whole genome sequencing; antimicrobial resistance; poultry production
Prof. Dr. Alessandra De Cesare
Guest Editor
Department of Veterinary Medical Sciences, Alma Mater Studiorum – University of Bologna, Italy
Interests: food safety; food metagenomics; food borne bacterial pathogens; microbiological risk assessment
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

In recent years, next generation sequencing has opened unprecedent opportunities. In food safety, whole genome sequencing (WGS) and metagenomics have been successfully applied to trace back the source of contamination, investigate reservoirs of foodborne pathogens, assess the likelihood and magnitude of a food safety hazard to cause illness; study the effect of intervention strategies on the microbiome, virulome and resistome of a particular animal or food microbiota; and, predict the likelihood of pathogen/gene transfer. WGS has the advantage of fine tuning the focus from the species/genus level to subtypes associated to a higher risk of infection or disease in humans. Metagenomics has the advantage of studying not only a narrow number of bacterial populations but the entire microbiome of a specific animal, food, or environment. However, these methods bring specific challenges: 1) they investigate genotypes which are not always reliable for phenotype predictions; 2) their implementation is challenged by lack of standards in the wet lab aspects and a wide variety of available platforms and bioinformatic pipelines.

This Special Issue deals with all applications of whole genome sequencing and metagenomics to food safety including but not limited to trace back sources of environmental contamination, outbreak investigation, source attribution, microbial risk assessment, antimicrobial resistance and virulence characterisation, evaluation of the effect of intervention strategies on microbiota in the farm to fork chain. The full range of microbial foodborne pathogens are expected to be assessed from bacteria to parasites, fungi, and viruses. 

Dr. Frédérique Pasquali
Prof. Dr. Alessandra De Cesare
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 papers will be 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 monthly 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 2000 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.


  • Whole genome sequencing
  • Metagenomics
  • Outbreak investigation
  • Source attribution
  • Microbial risk assessment
  • Microbial food-borne pathogens
  • Antimicrobial resistance
  • Virulence
  • Farm-to-fork chains
  • Intervention strategies

Published Papers

This special issue is now open for submission.
Back to TopTop