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Foods
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Prevalence and Antimicrobial Resistance of Foodborne Pathogens in Food
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Prevalence and Antimicrobial Resistance of Foodborne Pathogens in Food

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

Deadline for manuscript submissions: closed (15 December 2025) | Viewed by 5348

Special Issue Editors

Prof. Dr. Luciana Ruschel Dos Santos

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Guest Editor
Coordenadora do Programa de Pós-Graduação em Bioexperimentação, Escola de Ciências Agrárias, Inovação e Negócios, Universidade de Passo Fundo, BR 285, Passo Fundo, RS, Brazil
Interests: food microbiology; natural antimicobials; pathogenic bacteria
Special Issues, Collections and Topics in MDPI journals
Dr. Karen Apellanis Borges

E-Mail Website
Guest Editor
Centro de Diagnóstico e Pesquisa em Patologia Aviária, Departamento de Medicina Animal, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre 91540-000, RS, Brazil
Interests: bacterial resistance; Escherichia coli; Pasteurella multocida ; poultry; Salmonella
Special Issues, Collections and Topics in MDPI journals
Dr. Laura Beatriz Rodrigues

E-Mail Website
Guest Editor
Faculdade de Agronomia e Medicina Veterinária, Universidade de Passo Fundo, Passo Fundo, RS, Brazil
Interests: food

Special Issue Information

Dear Colleagues,

Antimicrobial use for non-therapeutic purposes in production animals far exceeds the amount used in humans, creating significant selective pressure for the emergence of resistant bacteria. Antimicrobial-resistant zoonotic pathogens present in food pose a direct risk to public health by increasing medical treatment costs, prolonging hospital stays, and raising mortality rates. Consequently, antimicrobial resistance is recognized as a global threat and a growing public health issue. The emergence of extended-spectrum beta-lactamase (ESBL)-producing and multidrug-resistant isolates has raised concerns within the scientific community. The rapid development of resistance to commonly used antimicrobials is primarily due to the spread of resistance genes among bacteria, which is mainly facilitated by their horizontal transfer through mobile genetic elements. Therefore, monitoring antimicrobial resistance is of paramount importance.

Prof. Dr. Luciana Ruschel Dos Santos
Dr. Karen Apellanis Borges
Dr. Laura Beatriz Rodrigues
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

  • antimicrobial resistance
  • foodborne pathogens
  • ESBL production
  • multidrug-resistant bacteria
  • antimicrobial resistance associated genes
  • horizontal tranfer
  • mobile genetic elements
  • alternative methods for controlling microorganisms
  • pathways of antimicrobial resistance
  • regulatory guidelines

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Published Papers (3 papers)

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Research

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20 pages, 1191 KB  
Article
Microarray-Based Serotyping and Molecular Characterization of Virulence and Antimicrobial Resistance of Salmonella enterica from Swine Meat Samples in Abattoirs and Wet Markets of Metro Manila, Philippines
by Rance Derrick N. Pavon, Jonah Feliza B. Mora, Michael Joseph M. Nagpala, Abbie Codia, Homer D. Pantua and Windell L. Rivera
Foods 2026, 15(2), 187; https://doi.org/10.3390/foods15020187 - 6 Jan 2026
Viewed by 233
Abstract
Salmonella is a globally prevalent and diverse group of pathogenic bacteria that reside in food animals, such as swine. They possess transmissible antimicrobial resistance (AMR) and virulence factors, causing outbreaks with varying disease outcomes. This study identified and characterized 110 Salmonella enterica isolates [...] Read more.
Salmonella is a globally prevalent and diverse group of pathogenic bacteria that reside in food animals, such as swine. They possess transmissible antimicrobial resistance (AMR) and virulence factors, causing outbreaks with varying disease outcomes. This study identified and characterized 110 Salmonella enterica isolates from swine meat in abattoirs and wet markets of Metro Manila, Philippines. Thirteen different S. enterica serovars were identified using the Check & Trace microarray platform. The most prevalent were Rissen, Typhimurium 1, 4, [5], 12:i:-, Anatum, and Derby. This study is also the first to report serovar Soerenga in the Philippines and Asia. A high prevalence of virulence genes was observed, namely, hilA (75.45%), avrA (73.64%), mgtC (72.73%), pipB (66.36%), sseC (58.18%), and spi4R (53.64%), with no plasmid-borne spvC and spvR. A high prevalence of blaTEM (44.55%) was also observed, consistent with the phenotypic AMR profiles. Additionally, 14.81% of the isolates exhibited multidrug resistance. Statistical associations and predictions were also found among virulence genes, serovars, and location types, which highlight implications of Salmonella contamination and serovar variations. These findings suggest the need for continuous surveillance of Salmonella, especially for emerging or rare serovars, the deeper investigation of virulence and AMR mechanisms, and improved regulation and sanitation throughout food animal industries. Full article
(This article belongs to the Special Issue Prevalence and Antimicrobial Resistance of Foodborne Pathogens in Food)
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18 pages, 3872 KB  
Article
Prevalence, Molecular Characterization, and Antimicrobial Resistance Profile of Enterotoxigenic Escherichia coli Isolates from Pig Farms in China
by Jiajia Zhu, Zewen Liu, Siyi Wang, Ting Gao, Wei Liu, Keli Yang, Fangyan Yuan, Qiong Wu, Chang Li, Rui Guo, Yongxiang Tian and Danna Zhou
Foods 2025, 14(7), 1188; https://doi.org/10.3390/foods14071188 - 28 Mar 2025
Cited by 4 | Viewed by 1353
Abstract
Enterotoxigenic Escherichia coli (ETEC) poses a critical threat to livestock health and food safety, particularly in regard to misuse of antimicrobial agents, which have accelerated the evolution of multidrug-resistant (MDR) ETEC strains, reshaping their virulence landscapes and epidemiological trajectories. In this study, 24 [...] Read more.
Enterotoxigenic Escherichia coli (ETEC) poses a critical threat to livestock health and food safety, particularly in regard to misuse of antimicrobial agents, which have accelerated the evolution of multidrug-resistant (MDR) ETEC strains, reshaping their virulence landscapes and epidemiological trajectories. In this study, 24 ETEC isolates from porcine diarrheal samples undergo genomic and phenotypic profiling, including virulence genotyping, bacterial adhesion, and antimicrobial resistance (AMR) analysis. Results show that multi-locus sequence typing (MLST) outputs (ST88, ST100) and serotypes (O9:H19, O116:H11, O149:H10) exhibited enhanced virulence, with F18ab-fimbriated strains carrying Shiga toxin genes (stx2A) demonstrating higher cytotoxicity than non-stx strains. There exists a significant negative correlation between bacterial growth rates and intestinal epithelial adhesion, with the expression of ETEC adhesion and virulence genes being growth-time-dependent. These relationships suggest evolutionary trade-offs favoring either rapid proliferation or virulence. Among these isolates, 95.8% were MDR, with alarming resistance to quinolones and aminoglycosides. Geospatial analysis identified region-specific AMR gene clusters, notably oqxB-aac(3) co-occurrence networks in 79% of ETEC isolates. These results highlight the urgent need for precision interventions, including vaccines targeting epidemic serotypes and AMR monitoring systems to disrupt resistance propagation across swine production networks. By underscoring the importance of current virulence and AMR profiles, this study provides actionable strategies to mitigate ETEC-associated threats to both animal welfare and meat safety ecosystems. Full article
(This article belongs to the Special Issue Prevalence and Antimicrobial Resistance of Foodborne Pathogens in Food)
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Review

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18 pages, 10970 KB  
Review
Role of Lysogenic Phages in the Dissemination of Antibiotic Resistance Genes Applied in the Food Chain
by Rafael Dorighello Cadamuro, Mariana Alves Elois, Giulia Von Tönnemann Pilati, Beatriz Pereira Savi, Leonardo Pessi, Yasmin Ferreira Souza Hoffmann Jempierre, David Rodríguez-Lázaro and Gislaine Fongaro
Foods 2025, 14(7), 1082; https://doi.org/10.3390/foods14071082 - 21 Mar 2025
Cited by 4 | Viewed by 3344
Abstract
Bacteriophages, first discovered in 1915, have re-emerged as critical players in microbial ecosystems, particularly in food production. Their ability to lysogenize bacterial hosts raises concerns about their role in the horizontal transfer of antibiotic resistance genes (ARGs) and virulence factors, contributing to the [...] Read more.
Bacteriophages, first discovered in 1915, have re-emerged as critical players in microbial ecosystems, particularly in food production. Their ability to lysogenize bacterial hosts raises concerns about their role in the horizontal transfer of antibiotic resistance genes (ARGs) and virulence factors, contributing to the global challenge of antimicrobial resistance. Key studies reveal that ARG-carrying phages are prevalent across various stages of the food chain, including soil, vegetables, meat, dairy, and wastewater associated with food production. These findings demonstrate the potential for lysogenic phages to act as vectors for resistance gene dissemination, posing risks to public health. The review also explores emerging genetic elements, such as phage-inducible chromosomal islands and gene transfer agents, that further enhance the mobility of resistance and virulence genes. Advancements in metagenomic tools have improved our understanding of phage-mediated gene transfer, but significant knowledge gaps remain. Future research should aim to quantify these processes in real-world settings and develop strategies to mitigate the risks associated with lysogenic phages in food systems. Full article
(This article belongs to the Special Issue Prevalence and Antimicrobial Resistance of Foodborne Pathogens in Food)
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