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Pathogens
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Antimicrobial Resistance in Foodborne Pathogens: Prevalence, Mechanisms, and Interventions
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Antimicrobial Resistance in Foodborne Pathogens: Prevalence, Mechanisms, and Interventions

A special issue of Pathogens (ISSN 2076-0817).

Deadline for manuscript submissions: closed (15 October 2025) | Viewed by 2616

Special Issue Editors

Dr. Byeonghwa Jeon

E-Mail Website
Guest Editor
Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
Interests: foodborne pathogens; stress tolerance; antibiotic resistance; phage therapy
Special Issues, Collections and Topics in MDPI journals
Dr. Jinshil Kim

E-Mail Website
Guest Editor
Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
Interests: foodborne pathogens; gene expression regulation; bacteriophage therapy
Dr. Jisun Haan

E-Mail Website
Guest Editor
Enterics Unit, Infectious Disease Laboratory Section, Public Health Laboratory Division, Minnesota Department of Health, St. Paul, MN 55164, USA
Interests: foodborne outbreak surveillance system; WGS subtyping and clustering; antibiotic resistance monitoring in foodborne pathogens

Special Issue Information

Dear Colleagues,

We are delighted to announce our new Special Issue entitled "Antimicrobial Resistance in Foodborne Pathogens: Prevalence, Mechanisms, and Interventions". This comprehensive Special Issue seeks to address critical knowledge gaps concerning the emergence, dissemination, and persistence of antimicrobial resistance across the food production continuum. Our focus encompasses high-priority foodborne pathogens, including Salmonella spp., Campylobacter spp., Escherichia coli, and Listeria monocytogenes, with isolates sourced from diverse food production environments and clinical settings to provide a holistic understanding of resistance ecology.

We welcome investigations elucidating the genetic and phenotypic determinants governing resistance acquisition, expression dynamics, and transmission pathways. Additionally, we seek innovative research on intervention strategies to combat resistant foodborne pathogens. Submissions exploring novel approaches, such as bacteriophage therapy, competitive exclusion strategies, vaccination, and alternative antimicrobial compounds, are strongly encouraged, particularly those demonstrating translational potential for implementation across the farm-to-fork continuum. We sincerely invite contributions from researchers across multiple disciplines, including microbiology, genomics, epidemiology, food science, veterinary medicine, and public health. Original research, comprehensive reviews, and perspective articles addressing these critical aspects of antimicrobial resistance in foodborne pathogens are welcome for consideration.

Dr. Byeonghwa Jeon
Dr. Jinshil Kim
Dr. Jisun Haan
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. Pathogens 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 2200 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
  • resistance genes
  • interventions

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Published Papers (2 papers)

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Research

23 pages, 2765 KB  
Article
Analysis of Multi-Antimicrobial Resistance Patterns in U.S. Foodborne Pathogens (2015–2025) Using Data from the NCBI Pathogen Isolates Browser
by Daniel Lao, Leo Pan-Wang, Kenneth Tianyi Yu, Yanzhi Chen, Erin Yang, Tailin Chen and Zuyi Huang
Pathogens 2026, 15(1), 27; https://doi.org/10.3390/pathogens15010027 - 24 Dec 2025
Cited by 1 | Viewed by 718
Abstract
Antimicrobial resistance (AMR) in foodborne pathogens poses a major threat to global public health and food safety. Using 9393 U.S. isolates of Salmonella enterica, Campylobacter jejuni, and Escherichia coli/Shigella collected from poultry, cattle, and swine between 2015 and 2025 [...] Read more.
Antimicrobial resistance (AMR) in foodborne pathogens poses a major threat to global public health and food safety. Using 9393 U.S. isolates of Salmonella enterica, Campylobacter jejuni, and Escherichia coli/Shigella collected from poultry, cattle, and swine between 2015 and 2025 and archived in the NCBI Pathogen Isolates Browser, we applied multivariate statistical analysis to characterize antimicrobial resistance patterns in isolates showing resistance to one to six antimicrobials (AMR-1 to AMR-6). Six antimicrobials—tetracycline, streptomycin, sulfisoxazole, ampicillin, nalidixic acid, and ciprofloxacin—were identified through PCA-guided clustering and frequency profiling as the principal axes of co-resistance across pathogens. Tetracycline emerged as a foundational driver of multidrug resistance, while C. jejuni contributed almost exclusively to single-drug resistance and Salmonella enterica dominated higher-order AMR categories, reflecting species-specific ecological and genomic constraints. Gene analyses revealed a progressive, modular accumulation of resistance determinants, led by efflux pumps (mdsA, mdsB), tetracycline genes (tetA/B/O), aminoglycoside-modifying enzymes, sulfonamide genes (sul1/sul2), quinolone resistance determinants (gyrA, acrF, mdtM), and β-lactamases (blaEC, blaOXA, blaCTX). Together, these results demonstrate that multidrug resistance in U.S. foodborne pathogens evolves through coordinated gene–drug–pathogen interactions rather than isolated events, underscoring the need for integrated surveillance and targeted stewardship strategies focused on the dominant antimicrobials and high-risk foodborne pathogens. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Foodborne Pathogens: Prevalence, Mechanisms, and Interventions)
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16 pages, 947 KB  
Article
Comparative Analysis of Concentration and Quantification Methods for Antibiotic Resistance Genes and Their Phage-Mediated Dissemination in Treated Wastewater and Biosolids
by Irene Falcó, Ana Allende, Francesca Cutrupi, Rosa Aznar, Gloria Sánchez and Pilar Truchado
Pathogens 2025, 14(10), 1050; https://doi.org/10.3390/pathogens14101050 - 18 Oct 2025
Viewed by 1449
Abstract
Antimicrobial resistance poses a growing threat to public health, and integrated surveillance strategies across environmental compartments such as treated wastewater and biosolids can substantially improve monitoring efforts. A key challenge is the diversity of available protocols, which complicates comparability for the concentration and [...] Read more.
Antimicrobial resistance poses a growing threat to public health, and integrated surveillance strategies across environmental compartments such as treated wastewater and biosolids can substantially improve monitoring efforts. A key challenge is the diversity of available protocols, which complicates comparability for the concentration and detection of antibiotic resistance genes (ARGs), particularly in complex matrices. In this study, we compared two commonly used concentration methods—filtration–centrifugation (FC) and aluminum-based precipitation (AP)—and two detection techniques, quantitative PCR (qPCR) and droplet digital PCR (ddPCR), for the quantification of four clinically relevant ARGs: tet(A), blaCTX-M group 1, qnrB, and catI. Analyses were performed in both secondary treated wastewater and biosolid samples, including their purified bacteriophage-associated DNA fractions. Results showed that the AP method provided higher ARG concentrations than FC, particularly in wastewater samples. ddPCR demonstrated greater sensitivity than qPCR in wastewater, whereas in biosolids, both methods performed similarly, although ddPCR yielded weaker detection. Importantly, ARGs were detected in the phage fraction of both matrices, with ddPCR generally offering higher detection levels. These results provide comparative insights into established methodologies and highlight the value of selecting appropriate protocols based on matrix characteristics and surveillance objectives. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Foodborne Pathogens: Prevalence, Mechanisms, and Interventions)
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