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Pathogen Detection, Identification, and Analysis in Food Safety Control
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Pathogen Detection, Identification, and Analysis in Food Safety Control

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

Deadline for manuscript submissions: 31 July 2026 | Viewed by 6933

Special Issue Editors

Dr. Anastasia Kapetanakou

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Guest Editor
Institute of Technology of Agricultural Products, Hellenic Agricultural Organization, Lycovrissi, Greece
Interests: food safety and hygiene; predictive modelling; active packaging; food spoilage; shelf-life; fungi ecology; mycotoxins
Special Issues, Collections and Topics in MDPI journals
Dr. Olga Papadopoulou

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Guest Editor
Institute of Technology of Agricultural Products, Hellenic Agricultural Organization-DEMETER, 14123 Lycovrissi, Greece
Interests: food microbiology; food quality and safety; probiotic microorganisms; rapid technologies (FTIR, GC-MS, Raman, HPLC); data analytics; molecular biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Despite the technological advancements in food preservation and safety, foodborne pathogens remain a global concern, as they continue to be responsible for significant percentage of disease outbreaks, imposing a considerable economic burden. Thus, prompt and reliable detection of foodborne pathogens using rapid, accurate, highly sensitive as well as easy to use methods is essential for the effective control and prevention, serving as a critical step in minimizing both health risks and economic consequences.

This Special Issue, entitled “Pathogen Detection, Identification, and Analysis in Food Safety Control”, aims to feature original research articles and comprehensive reviews focusing on emerging and advanced methodologies—such as molecular diagnostics, next generation sequencing, biosensors, artificial intelligence etc.—for the detection and identification of foodborne pathogens (namely bacteria and fungi) and their toxins. Particular emphasis will be given on innovative techniques and their integration with conventional approaches—such as culture-based methods, biochemical test methods, immunological assays, and nucleic acid-based techniques—in order to enhance sensitivity and efficiency. Advanced detection and identification techniques of interest include, but are not limited to:

  • Array-based methods (e.g., DNA microarray)
  • Spectroscopy techniques (e.g., Fourier-transform infrared [FT-IR], Raman spectroscopy, Hyperspectral Imaging)
  • Loop-mediated Isothermal Amplification (LAMP)
  • Next-Generation Sequencing (NGS) technologies
  • Biosensors (e.g., optical, electrochemical, colorimetric, fluorescence-based)
  • Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS)
  • Microscopic techniques (e.g., fluorescence microscopy)

This special issue will provide information and highlight the dynamic of these advanced tools, especially when applied in tandem with established methodologies, to improve pathogen surveillance, outbreak investigation, and food safety monitoring.

Dr. Anastasia Kapetanakou
Dr. Olga Papadopoulou
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.

Keywords

  • foodborne pathogens
  • food safety
  • culture-based methods
  • PCR
  • array-based methods
  • spectroscopy
  • NGS
  • biosensors
  • MALDI-TOF MS
  • microscopy techniques

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (4 papers)

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20 pages, 1702 KB  
Article
Occurrence and Antimicrobial Resistance of Acinetobacter spp. in Processing Environments of Slaughterhouses and Meat Processing Facilities
by Alba Puente, Rebeca Cordero-García, Elena Fernández-Trapote, Victoria Crespo-Torbado, Márcia Oliveira, Mercedes López, Miguel Prieto, Avelino Alvarez-Ordóñez and José F. Cobo-Díaz
Foods 2026, 15(7), 1243; https://doi.org/10.3390/foods15071243 - 5 Apr 2026
Viewed by 634
Abstract
Several species of the genus Acinetobacter are nosocomial pathogens with a well-documented ability to acquire resistance to multiple antibiotics. Although Acinetobacter is one of the most abundant genera in meat processing environments, data on this genus outside of clinical environments remains limited. The [...] Read more.
Several species of the genus Acinetobacter are nosocomial pathogens with a well-documented ability to acquire resistance to multiple antibiotics. Although Acinetobacter is one of the most abundant genera in meat processing environments, data on this genus outside of clinical environments remains limited. The objective of this study was to ascertain the prevalence, diversity and antimicrobial resistance profile of Acinetobacter spp. in 200 samples collected from food contact surfaces, non-food contact surfaces, carcasses and final meat cuts across five pork, chicken and beef processing facilities, each comprising physically connected slaughterhouses and meat processing plants. Acinetobacter spp. were detected in 80% (95% CI = 71–87%) and 70% (95% CI = 60–79%) of samples from slaughterhouses and processing plants, respectively. The facilities harboured a wide diversity of Acinetobacter species, with 27 different species identified. Acinetobacter baumannii was the species most frequently detected. Whole-genome sequencing of 18 Acinetobacter spp. isolates revealed the presence of ARGs conferring resistance to beta-lactams, tetracyclines and aminoglycosides, and disclosed phylogenetic relationships with isolates from fresh meat. Phenotypic resistance to beta-lactams, fluoroquinolones, aminoglycosides, folate pathway inhibitors and/or tetracyclines was observed in 77.8% of the sequenced isolates, with 44.4% classified as multidrug-resistant. These findings identify meat processing environments as an important reservoir of Acinetobacter spp. and highlight the need for further investigation to prevent the dissemination of antimicrobial-resistant strains. Full article
(This article belongs to the Special Issue Pathogen Detection, Identification, and Analysis in Food Safety Control)
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17 pages, 2987 KB  
Article
Hybrid Genome Sequencing and Comparative Analysis of Three Novel Listeria monocytogenes Strains: Insights into Lineage Diversity, Virulence, Antibiotic Resistance, and Defense Systems
by Violeta Pemaj, Aleksandra Slavko, Konstantinos Konandreas, Dimitrios E. Pavlidis, Anastasios Ioannidis, Konstantinos Panousopoulos, Nikoletta Xydia, Vassiliki Antonopoulou, Marina Papadelli, Eleftherios H. Drosinos, Panagiotis N. Skandamis, Simon Magin and Konstantinos Papadimitriou
Foods 2026, 15(1), 88; https://doi.org/10.3390/foods15010088 - 28 Dec 2025
Viewed by 1091
Abstract
Listeria monocytogenes is a major foodborne pathogen, responsible for severe listeriosis outbreaks associated with contaminated foods. This study reports the comparative genomic analysis of three novel L. monocytogenes strains C5, A2D9 and A2D10, obtained from dairy and clinical sources. Hybrid genome sequencing with [...] Read more.
Listeria monocytogenes is a major foodborne pathogen, responsible for severe listeriosis outbreaks associated with contaminated foods. This study reports the comparative genomic analysis of three novel L. monocytogenes strains C5, A2D9 and A2D10, obtained from dairy and clinical sources. Hybrid genome sequencing with Oxford-Nanopore and Illumina technologies provided high-quality complete chromosomes. Phylogenomic analysis revealed a highly conserved core genome alongside accessory genome diversity. Strain C5 belonged to sequence type ST2, while A2D9 and A2D10 were assigned to ST155 and ST1, respectively. All strains exhibited close genomic relatedness to isolates from dairy animals and/or the dairy environment. Functional analysis identified conserved metabolic functions across all genomes. A total of 40 virulence genes were detected, including the LIPI-1 island in all strains and the LIPI-3 operon exclusively in A2D10, indicating a potential hypervirulent phenotype consistent with its ST1 background and the associated fatal clinical outcome. All strains exhibited similar antimicrobial resistance profiles typical of L. monocytogenes and diverse defense systems. The newly sequenced strains provide a valuable resource for functional analyses of the mechanisms underlying adaptation of L. monocytogenes to diverse environments. Full article
(This article belongs to the Special Issue Pathogen Detection, Identification, and Analysis in Food Safety Control)
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19 pages, 2627 KB  
Article
Monitoring Sublethal Injury in Listeria monocytogenes During Heat Treatment of Pork Frankfurter-Type Sausages: A Single-Cell vs. Population Level Approach
by Marianna Arvaniti, Eleni Vlachou, Maria Kourteli, Anastasia E. Kapetanakou and Panagiotis N. Skandamis
Foods 2025, 14(17), 3144; https://doi.org/10.3390/foods14173144 - 8 Sep 2025
Cited by 3 | Viewed by 3071
Abstract
Listeria monocytogenes is a foodborne pathogen capable of contaminating ready-to-eat meat products, e.g., frankfurters. Post-packaging mild heat treatment via water immersion is commonly employed; however, this may be sublethal to cells located in protected niches or beneath the product surface. The objectives of [...] Read more.
Listeria monocytogenes is a foodborne pathogen capable of contaminating ready-to-eat meat products, e.g., frankfurters. Post-packaging mild heat treatment via water immersion is commonly employed; however, this may be sublethal to cells located in protected niches or beneath the product surface. The objectives of this study were to evaluate thermal injury of L. monocytogenes on frankfurters at single-cell versus population level and to comparatively estimate pathogens’ physiological status. Pork frankfurter-type sausages were inoculated (ca. 7.0–7.5 log CFU/cm2) with L. monocytogenes strain EGDE-e. Heat treatment was performed at 61 °C (max. 60 min) and 64 °C (max. 12 min). To determine the injured subpopulation from the total, tryptic soy agar with 0.6% yeast extract (TSAYE), supplemented or not with 5% NaCl, was used. Plating-based quantification of injured cells was compared to CFDA/PIstained cells analysed by fluorescence microscopy and quantified with Fiji software. Injury was recorded mainly after 2 and 4 min at 64 °C, whereas no injury was detected at 61 °C, at population level. Following exposure to 61 °C for 60 min, culturable cells dropped below the enumeration limit (0.3 log CFU/cm2), while a considerable number of CFDA+/PI− and CFDA+/PI+ cells indicated viable-but-non-culturable induction and sublethal injury, respectively. These findings suggest that non-culturability may limit the accuracy of solely culture-based enumeration methods. Full article
(This article belongs to the Special Issue Pathogen Detection, Identification, and Analysis in Food Safety Control)
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35 pages, 509 KB  
Systematic Review
Systematic Literature Review to Determine Existing Data on the Growth of Listeria monocytogenes in Ready-to-Eat Foods Performed Based on the European Union Reference Laboratory (EURL) Lm Technical Guidance Documents
by Andrea Singer and Roger Stephan
Foods 2026, 15(8), 1402; https://doi.org/10.3390/foods15081402 - 17 Apr 2026
Viewed by 691
Abstract
With rising incidence in recent years, Listeriosis, a severe foodborne disease in humans primarily transmitted through ready-to-eat (RTE) foods contaminated with Listeria monocytogenes, became the most severe zoonotic disease in the European Union (EU) in 2024 with the highest hospitalization and mortality [...] Read more.
With rising incidence in recent years, Listeriosis, a severe foodborne disease in humans primarily transmitted through ready-to-eat (RTE) foods contaminated with Listeria monocytogenes, became the most severe zoonotic disease in the European Union (EU) in 2024 with the highest hospitalization and mortality rates, prompting stricter regulatory requirements under Regulation (EC) No 2073/2005 and its recent amendments. This systematic literature review aimed to evaluate the availability, validity and quality of published challenge test data on the growth potential and maximum growth rate of Listeria monocytogenes in RTE foods to identify data gaps and, if possible, to support the derivation of a classification of RTE foods into the two existing regulatory categories, a and b (not able and able to support the growth of Listeria monocytogenes). Conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and the Cochrane Handbook, a comprehensive database search was done to identify eligible challenge test studies on Listeria monocytogenes growth in RTE foods, followed by structured screening and quality assessment based on the EURL Lm Technical Guidance Documents. A limited and heterogeneous body of published challenge test data on the growth potential and maximum growth rate of Listeria monocytogenes in RTE foods was identified, with substantial data gaps across multiple food groups, precluding meta-analysis and limiting regulatory applicability under the current regulations. Overall, the available literature is insufficient to reliably support regulatory classification or to enable direct extrapolation by food business operators (FBO), underscoring the need for product-specific investigations and food group-specific guidance for food safety. Full article
(This article belongs to the Special Issue Pathogen Detection, Identification, and Analysis in Food Safety Control)
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