Foodborne Pathogens, Antimicrobial Resistance and Contaminants Risk Assessment and Management Along the Animal-Based Food Chain

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

Deadline for manuscript submissions: 31 August 2026 | Viewed by 1601

Special Issue Editors


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Guest Editor
Division of Microbiology, Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Ciszewskiego 8, 02-786 Warsaw, Poland
Interests: food microbiology; zoonotic pathogens; antimicrobial resistance; molecular diagnostics of foodborne bacteria; microbiological food safety; One Health approach in foodborne zoonoses; risk assessment in the food chain; bacterial virulence profiling; genomic epidemiology of pathogens isolated from animal-origin food

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Guest Editor
Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Ciszewskiego 8, 02-786 Warsaw, Poland
Interests: antimicrobial resistance in commensal and pathogenic bacteria; microbiota of animals; mechanisms of bacterial resistance; antibiotic alternatives; gut health; bacterial infections in companion and farm animals; foodborne zoonotic pathogens; One Health in veterinary microbiology

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Guest Editor Assistant
Department of Food Gastronomy and Food Hygiene, Institute of Human Nutrition Sciences, Warsaw University of Life Sciences (WULS), 166 Nowoursynowska Str., 02-787 Warsaw, Poland
Interests: classical and instrumental methods of analysis of microbiological quality of food; predictive mathematical models; microbiological risk assessment of food; phenomenon of biofilm formation by food microorganisms

Special Issue Information

Dear Colleagues,

Problems related to the occurrence of pathogenic microorganisms stem from their remarkable diversity and continuously evolving defence and adaptation mechanisms. Furthermore, emerging chemical hazards in food may result from changes associated with modern civilization and industrial development.

To effectively protect human health, food law and safety management should be firmly based on risk analysis, with risk assessment as its cornerstone. This assessment must rely on current scientific evidence and be performed in an independent, objective, and transparent manner to ensure proper information flow and risk management.

Since contamination and food safety hazards may occur at any stage of the food chain, it is essential that all aspects of risk are assessed using scientifically validated methodologies.

We invite you to contribute your most recent research to this Special Issue, particularly studies focused on the following areas:

  • Detection and identification of foodborne pathogens of animal origin;
  • Diagnosis and characterization of microbial contaminants;
  • Antimicrobial resistance in bacteria isolated from food of animal origin;
  • Risk assessment strategies related to microbiological and chemical hazards in food production and distribution.

Submissions focusing on any point in the food chain are welcome.

Prof. Dr. Joanna Pławińska-Czarnak
Dr. Magdalena Kizerwetter-Świda
Guest Editors

Dr. Elżbieta Rosiak
Guest Editor Assistant

Manuscript Submission Information

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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

  • food-born pathogens (Listeria monocytogenes, Salmonella spp., Campylobacter spp.
  • antibiotic resistance of microorganisms
  • antimicrobial bioactive compounds
  • safety in the supply chain
  • microbial contamination
  • pathogenic microorganisms
  • risk analysis in food safety
  • One Health approach
  • food processing hygiene

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Published Papers (3 papers)

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Research

20 pages, 2194 KB  
Article
Osmotic Stress Adaptation of Poultry-Associated Salmonella Infantis and Its Implications for Food Safety
by Gabriel I. Krüger, Ana Oviedo, Coral Pardo-Esté, Nicolás Avilés-Núñes, Sofía Quintana, Alejandro A. Hidalgo, Javiera Álvarez, Francisca Urbina, Catalina Kusch, Katterinne N. Mendez, Jorge Olivares-Pacheco, Luis Alvarez-Thon, Francisco Remonsellez, Juan Castro-Severyn and Claudia P. Saavedra
Foods 2026, 15(11), 1938; https://doi.org/10.3390/foods15111938 - 31 May 2026
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Abstract
Salmonella enterica serovar Infantis, an important zoonotic pathogen with increasing prevalence in the poultry industry, often persists despite rigorous disinfection. This study characterized the transcriptomic response of the multidrug-resistant Salmonella Infantis strain SE016, isolated from a poultry plant, to osmotic stress, a condition [...] Read more.
Salmonella enterica serovar Infantis, an important zoonotic pathogen with increasing prevalence in the poultry industry, often persists despite rigorous disinfection. This study characterized the transcriptomic response of the multidrug-resistant Salmonella Infantis strain SE016, isolated from a poultry plant, to osmotic stress, a condition frequently induced by the use of industrial disinfectants. Phenotypic assays demonstrated that stress induced by 15% sucrose simulated osmotic stress, producing a drastic reduction in flagellar motility and a significant increase in biofilm formation in SE016, compared with a susceptible control strain. RNA-seq analysis indicated that SE016 undergoes coordinated transcriptional changes consistent with altered metabolic activity under osmotic stress. Key mechanisms include metabolic braking through repression of tricarboxylic acid (TCA) cycle genes (icd, mdh) and induction of anaerobic nitrate respiration (narGHI, narZWV) as an energy contingency. Furthermore, SE016 showed increased expression of genes involved in osmoprotectant uptake, including the proU transport system and endogenous trehalose synthesis (ostAB) while repressing proline degradation (putA). Furthermore, robust biofilm formation was observed despite repression of the master regulator csgD. This was mediated by the CsgD-independent induction of the diguanylate cyclase adrA, activating cellulose synthesis (bcs). These results suggest that pathways associated with the OmpR/EnvZ two-component system may contribute to energy balance and persistence-related phenotypes under industrial-like stress conditions. Full article
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25 pages, 1955 KB  
Article
Microbiological Quality of Maize Silage in Relation to Agricultural Practices: A Four-Year Study
by Elżbieta Kukier, Łukasz Bocian and Monika Pytka
Foods 2026, 15(9), 1518; https://doi.org/10.3390/foods15091518 - 27 Apr 2026
Viewed by 554
Abstract
Silage is a fundamental component of cattle feed, and its microbiological quality is critical for animal health and human safety. Improper ensiling conditions, such as oxygen exposure or inadequate acidification, can promote the growth of pathogens like Listeria monocytogenes, Clostridium botulinum, [...] Read more.
Silage is a fundamental component of cattle feed, and its microbiological quality is critical for animal health and human safety. Improper ensiling conditions, such as oxygen exposure or inadequate acidification, can promote the growth of pathogens like Listeria monocytogenes, Clostridium botulinum, and Bacillus cereus. This study aimed to evaluate the microbial status of maize silages and identify pre-ensiling factors influencing its hygienic safety. Over a four-year period, 406 silage samples were collected from cattle farms across Poland. The research evaluated general hygiene indicators and screened for specific pathogens using standard culture methods, polymerase chain reaction toxotyping, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The impact of agricultural practices, including soil quality, organic fertilization, and microbial inoculation, was also analyzed. The analysis revealed that 32.1% of silages fell outside the reference pH range, indicating potential aerobic instability. While Salmonella and Campylobacter were not detected, Clostridium spp. were highly prevalent (81.0%), and C. perfringens was confirmed in 24.9% of samples. Listeria species occurred in 2.9% of silages, with L. innocua being the most frequent isolate. Statistical analysis showed that organic fertilization was significantly linked to specific C. perfringens toxotypes, though it did not increase the overall microbial burden. Conversely, microbial inoculation generally reduced the counts of several undesirable bacteria, although these differences were not statistically significant across all parameters. High pH values and significant contamination with Clostridium, B. cereus, and fungi remain critical challenges for silage safety. The results underscore the necessity for improved agricultural practices—specifically the minimization of soil and manure contamination during harvest—and the broader adoption of microbial inoculation to ensure the microbiological stability of fermented forage. Full article
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18 pages, 764 KB  
Article
Molecular Characterization, Virulence Profiling, and Antimicrobial Susceptibility of Listeria monocytogenes Isolated from Smoked Fish in Poland: A Preliminary Study
by Zuzanna J. Strzałkowska, Ewa D. Domańska, Karolina Wódz, Magdalena Kizerwetter-Świda, Dorota Chrobak-Chmiel, Tomasz Nowak, Piotr Kwieciński, Elżbieta Rosiak, Kamil Stańczak and Joanna Pławińska-Czarnak
Foods 2026, 15(8), 1406; https://doi.org/10.3390/foods15081406 - 17 Apr 2026
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Abstract
Listeria monocytogenes remains a major foodborne pathogen associated with ready-to-eat (RTE) products, including smoked fish. This study investigated the occurrence, molecular characteristics, virulence gene profiles, and antimicrobial susceptibility of L. monocytogenes isolated from retail smoked fish in Poland. A total of 46 samples [...] Read more.
Listeria monocytogenes remains a major foodborne pathogen associated with ready-to-eat (RTE) products, including smoked fish. This study investigated the occurrence, molecular characteristics, virulence gene profiles, and antimicrobial susceptibility of L. monocytogenes isolated from retail smoked fish in Poland. A total of 46 samples (cold- and hot-smoked products) collected from 15 producers and five retail chains were analyzed using ISO 11290-1:2017 for qualitative detection and ISO 11290-2:2017 for enumeration. Listeria spp. were detected in 5/46 samples (10.9%), including 4 isolates confirmed as L. monocytogenes (8.7%). All positive samples originated from cold-smoked salmon, with a prevalence of 4/13 (30.8%) in this product category. The quantitative analysis indicated that contamination levels in all positive samples were below 100 CFU/g. Molecular serogrouping and multiplex PCR demonstrated the presence of key virulence-associated genes, including hlyA, prfA, plcB, and actA, consistent with potentially pathogenic profiles. Pulsed-field gel electrophoresis (PFGE) revealed clustering of isolates, indicating genetic relatedness among strains obtained from different retail sources. Antimicrobial susceptibility testing using the MICRONAUT system showed that all L. monocytogenes isolates were susceptible to first-line therapeutic agents, including ampicillin and penicillin, according to EUCAST/CLSI criteria. Although contamination levels were low and isolates remained susceptible to clinically relevant antimicrobials, the detection of virulence-associated strains in RTE smoked fish highlights the need for continuous monitoring and strict hygienic control in the production and retail chain. These findings contribute to regional surveillance data on L. monocytogenes in smoked fish products in Poland. Full article
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