Special Issue "Genetics and Genomics of Foodborne Pathogens"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: 31 December 2017

Special Issue Editors

Guest Editor
Dr. Kieran Jordan

Food Safety Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
Interests: Occurrence and persistence of foodborne pathogens, Listeria monocytogenes, pathogenic E. coli, whole genome sequencing, control of pathogens
Guest Editor
Dr. Avelino Alvarez-Ordonez

Department of Food Hygiene and Technology and Institute of Food Science and Technology, University of León, León, Spain
Interests: Microbial stress responses, antimicrobial resistance, occurrence and persistence of foodborne pathogens, biofilms, biocontrol, metagenomics
Guest Editor
Dr. Olivia McAuliffe

Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
Interests: Whole genome sequencing of foodborne pathogens and their bacteriophages, biocontrol and detection of foodborne pathogens with bacteriophages

Special Issue Information

Dear Colleagues,

Foodborne pathogens are a public health threat and their control is a challenge to the food industry. The occurrence and transcription of genes, which encode specialised functions, plays a vital role in survival of pathogens, growth under harsh conditions and in food, their ability to produce toxins and in virulence, pathogenicity and antimicrobial resistance. Controlling the expression of such genes can result in limiting the ability of pathogens to cause disease. Whole genome sequencing technologies are revolutionising epidemiology of foodborne pathogens and tracing of foodborne pathogens in food and the food processing environment. An increasing amount of information on genes, genomes and transcriptomes of foodborne pathogens is becoming available, which will lead to a greater understanding of survival and virulence of pathogens.

This Special Issue welcomes submissions on issues relating to the genetics and genomics of foodborne pathogens, including on topics such as persistence, virulence, gene detection, whole genome sequencing, transcriptomics, and characterisation of genes involved in toxin production, antimicrobial resistance and virulence, among others.

All contributions to this Special Issue must be in line with the scope of the journal. Manuscripts discovered, during any stage of peer review process, to be outside of the scope may be transferred to a suitable section or field, or withdrawn from review.

Dr. Kieran Jordan
Dr. Olivia McAuliffe
Dr. Avelino Alvarez-Ordonez
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. Genes 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 1200 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.


  • Bacterial virulence
  • Pathogenicity
  • Whole genome sequencing
  • Transcriptomics
  • Toxin production
  • Antimicrobial resistance

Published Papers (1 paper)

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Open AccessArticle Gene-Based Pathogen Detection: Can We Use qPCR to Predict the Outcome of Diagnostic Metagenomics?
Genes 2017, 8(11), 332; doi:10.3390/genes8110332
Received: 29 September 2017 / Revised: 2 November 2017 / Accepted: 14 November 2017 / Published: 20 November 2017
PDF Full-text (242 KB) | HTML Full-text | XML Full-text
In microbial food safety, molecular methods such as quantitative PCR (qPCR) and next-generation sequencing (NGS) of bacterial isolates can potentially be replaced by diagnostic shotgun metagenomics. However, the methods for pre-analytical sample preparation are often optimized for qPCR, and do not necessarily perform
[...] Read more.
In microbial food safety, molecular methods such as quantitative PCR (qPCR) and next-generation sequencing (NGS) of bacterial isolates can potentially be replaced by diagnostic shotgun metagenomics. However, the methods for pre-analytical sample preparation are often optimized for qPCR, and do not necessarily perform equally well for qPCR and sequencing. The present study investigates, through screening of methods, whether qPCR can be used as an indicator for the optimization of sample preparation for NGS-based shotgun metagenomics with a diagnostic focus. This was used on human fecal samples spiked with 103 or 106 colony-forming units (CFU)/g Campylobacter jejuni, as well as porcine fecal samples spiked with 103 or 106 CFU/g Salmonella typhimurium. DNA was extracted from the samples using variations of two widely used kits. The following quality parameters were measured: DNA concentration, qPCR, DNA fragmentation during library preparation, amount of DNA available for sequencing, amount of sequencing data, distribution of data between samples in a batch, and data insert size; none showed any correlation with the target ratio of the spiking organism detected in sequencing data. Surprisingly, diagnostic metagenomics can have better detection sensitivity than qPCR for samples spiked with 103 CFU/g C. jejuni. The study also showed that qPCR and sequencing results may be different due to inhibition in one of the methods. In conclusion, qPCR cannot uncritically be used as an indicator for the optimization of sample preparation for diagnostic metagenomics. Full article
(This article belongs to the Special Issue Genetics and Genomics of Foodborne Pathogens)

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Tentative title: Pathogenicity islands genes distribution in Shiga toxin-producing Escherichia coli (STEC) from Argentina

Putative authors: Jimena S. Cadona, Juliana González, Ana V. Bustamante, A. Mariel Sanso

Affiliation: Laboratorio de Inmunoquímica y Biotecnología, Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET-CIC-UNCPBA, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires, 7000 Tandil, Argentina

Abstract: Shiga toxin-producing Escherichia coli (STEC) are heterogeneous foodborne pathogens associated with outbreaks and hemolytic-uremic syndrome (HUS). Cattle are the main reservoir of STEC and human infections are acquired mainly by ingesting food or water contaminated directly or indirectly with cattle feces. E. coli O157:H7 is the serotype most associated to diseases, however, recent studies have shown that the number of non-O157 STEC infections sometimes surpasses the number of STEC O157 infections.

 Pathogenicity islands (PAIs) play an important role in STEC pathogenicity. Since PAIs are normally absent in nonpathogenic strains, they may serve as useful markers to distinguish highly virulent strains from less-virulent or harmless strains. In addition, PAIs can be used to identify new and emerging pathogenic bacteria. Non-LEE effector (nle) genes are present on PAIs and encode translocated substrates of the type III secretion system. A molecular risk assessment (MRA) approach based on the evaluation of the nle gene content has been used to predict which STEC strains pose a significant risk to human health.

The goal of this study was to investigate the distribution of OI-36, OI-57, OI-71 and OI-122 among clinical, food and animal STEC isolates from Argentina. More specific, the research aimed at identifying associations of the PAIs and individual virulence genes with STEC seropathotypes (SPTs), isolation sources, serogroups, intimin presence/absence and type of Shiga toxin.

 A total of 202 STEC strains belonging to 48 non-O157:H7 serotypes were screened by the presence of 20 markers virulence genes encoded by genomic O-islands OI-36  (nleB2, nleC, nleH1-1, nleD), OI-57 (nleG2-3, nleG5-2, nleG6-2), OI-71 (nleA, nleF, nleG, nleG2-1, nleG9, nleH1-2) and OI-122 (ent/espL2, nleB, nleE, Z4321, Z4326, Z4332, Z4333).

 We found a full spectrum of nle gene markers and differences in frequencies of genetic markers and PAI virulence genes profiles. The gene nleB encoded on the OI-122 was found as the most conserved marker.



Tentative title: Genome-wide profiling and novel applications of enterotoxigenic Staphylococcus aureus strains

Putative authors: Guerrino Macori1,*, Alberto Bellio1, Angelo Romano1, Silvia Gallina1, Jacques-Antoine Hennekinne2 and Lucia Decastelli1

1  National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154 Torino, Italy.

2   European Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Laboratory for food safety, ANSES, Université Paris-Est, Maisons-Alfort F-94700, France. 

Abstract: Staphylococcus aureus is a major human pathogen and an important cause of livestock infections. More than 20 staphylococcal enterotoxins with superantigenic activity can be produced by specific strains responsible of staphylococcal food poisoning, one of the most common food-borne diseases. In order to investigate enterotoxigenic S. aureus, the application of Whole Genome Sequencing provides the comprehensive view of the genome structure and gene content that is now being applied in outbreak investigations. In this study, six enterotoxigenic S.aureus strains have been genome-sequenced and analyzed with novel computational approaches, revealing the opportunity for the production of naturally contaminated materials and a database for genomic feature of this set of staphylococcal enterotoxins producers.

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