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Next Generation Microbial Food Safety: New Era on Pathogenic and...
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Next Generation Microbial Food Safety: New Era on Pathogenic and Beneficial Microorganisms

A Special Issue of Foods (ISSN 2304-8158) belonging to the section "Food Quality and Safety".

Deadline for manuscript submissions: 10 November 2026 | Viewed by 1246

Editors

Dr. Zeqiang Zhan

E-Mail Website
Guest Editor
Laboratory of Quality & Safety Risk Assessment for Agro-products (Zhaoqing), Ministry of Agriculture and Rural Affairs, School of Food and Pharmaceutical Engineering, Zhaoqing University, Zhaoqing 526061, China
Interests: prevention and control of foodborne pathogenic bacteria contamination; development and research of beneficial microorganisms
Dr. Jianmin Zhang

E-Mail Website
Guest Editor
College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
Interests: molecular identification; antimicrobial resistance; the pathogenicity of Salmonella, Haemophilus parasuis and Campylobacter
Dr. Shoukui He

E-Mail Website
Guest Editor
Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
Interests: food safety; food microbiology; foodborne pathogen; stress response; antimicrobial agent
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Ensuring microbial food safety is increasingly critical in the context of globalized food systems, evolving pathogens, and the expanding use of beneficial microorganisms. Next-generation approaches to microbial safety integrate insights from both pathogenic and beneficial microorganisms to better understand contamination dynamics, the emergence of antimicrobial resistance, and microbiome interactions across food production, processing, and storage environments. This Special Issue highlights cutting-edge research on pathogen detection, resistance mechanisms, microbial ecology, and the roles of probiotics and other beneficial microbes in enhancing food safety. Particular emphasis is placed on advanced genomics, metagenomics, high-throughput sequencing, and bioinformatics tools that enable comprehensive characterization of microbial communities, real-time risk assessment, and the development of innovative intervention strategies. We invite original research and review articles that advance knowledge of the dual roles of pathogenic and beneficial microorganisms and foster practical solutions for improving microbial safety in foods. The goal is to support a new era of science-driven, sustainable, and effective microbial food safety management.

Dr. Zeqiang Zhan
Dr. Jianmin Zhang
Dr. Shoukui He
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-anonymized 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

  • next-generation microbial food safety
  • foodborne pathogens
  • beneficial microorganisms
  • antimicrobial resistance
  • microbiome
  • pathogen detection
  • microbial risk assessment
  • intervention strategies

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Published Papers (3 papers)

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Research

19 pages, 38271 KB  
Article
Transferable IncHI2-Associated blaLAP-2 and blaCTX-M-55 Resistance Platforms in Foodborne Salmonella
by Zeqiang Zhan, Shaoping Zhang, Bingguo Wei, Yurui Zheng, Xingrui Li, Qiqi Lin, Jiang Chang, Shoukui He and Hongwu Wang
Foods 2026, 15(17), 3130; https://doi.org/10.3390/foods15173130 - 3 Sep 2026
Viewed by 242
Abstract
Extended-spectrum β-lactamase genes in foodborne Salmonella enterica can disseminate through mobile multidrug-resistance platforms. IncHI2 plasmids are important resistance vehicles capable of carrying complex resistance regions and facilitating their horizontal transfer across diverse bacterial backgrounds, but the transfer and genomic organization of IncHI2 elements [...] Read more.
Extended-spectrum β-lactamase genes in foodborne Salmonella enterica can disseminate through mobile multidrug-resistance platforms. IncHI2 plasmids are important resistance vehicles capable of carrying complex resistance regions and facilitating their horizontal transfer across diverse bacterial backgrounds, but the transfer and genomic organization of IncHI2 elements co-carrying blaLAP-2 and blaCTX-M-55 remain insufficiently characterized. This study investigated two multidrug-resistant foodborne isolates recovered in Shanghai in 2022: Salmonella Agona ST13 isolate Sal22C150 and Salmonella Havana ST1527 isolate Sal22P208. Antimicrobial susceptibility testing, whole-genome sequencing, conjugation, plasmid-retention analysis, comparative genomics, as well as strain- and plasmid-level phylogenetic analyses were performed. Both isolates exhibited broad antimicrobial resistance, including resistance to extended-spectrum cephalosporins. In both isolates, blaLAP-2 and blaCTX-M-55 co-transferred with the IncHI2 replicon to Escherichia coli J53 at frequencies of (4.95 ± 0.41) × 10−5 and (4.46 ± 0.42) × 10−6 transconjugants per donor cell, respectively. All tested plasmid markers remained detectable through 20 passages without antimicrobial selection. Complete assembly of Sal22P208 confirmed the location of the three β-lactamase genes on the 275,096 bp IncHI2 plasmid pSal22P208. The plasmid contained a conserved conjugative backbone and mosaic accessory regions carrying 15 antimicrobial-resistance determinants together with mercury- and tellurium-resistance loci. SNP-based analysis placed pSal22P208 within a closely related cluster containing six reference IncHI2 plasmids differing by fewer than 30 SNPs and recovered from Salmonella and E. coli of animal, food, and human origin, suggesting a broad distribution of this plasmid lineage across diverse bacterial and ecological backgrounds. Sal22P208 additionally contained a Tn3-associated chromosomal multidrug-resistance region between rpmJ and rpmE that shared extensive structural similarity with a region in Citrobacter braakii LBA3. These findings highlight the role of transferable IncHI2 resistance platforms in the horizontal dissemination and short-term post-transfer maintenance of linked resistance determinants, while chromosomally integrated resistance regions may provide an additional route for the accumulation and inheritance of multidrug resistance in foodborne Salmonella. Full article
(This article belongs to the Special Issue Next Generation Microbial Food Safety: New Era on Pathogenic and Beneficial Microorganisms)
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17 pages, 19137 KB  
Article
Preventive Effects of Fermented Yak Milk-Derived Lacticaseibacillus paracasei CD12-1 Against DSS-Induced Colitis in Mice
by Hongqiang Li, Teng Zhen, Junyang Li, Furong Han, Xian Guo, Defu Tang and Cheng Peng
Foods 2026, 15(17), 3120; https://doi.org/10.3390/foods15173120 - 2 Sep 2026
Viewed by 233
Abstract
Ulcerative colitis is a chronic inflammatory bowel disease characterized by mucosal barrier disruption, dysregulated immune responses, and gut microbial imbalance. However, limitations of current therapies highlight the need for safe probiotic interventions. This study evaluated the preventive effects of fermented yak milk-derived Lacticaseibacillus [...] Read more.
Ulcerative colitis is a chronic inflammatory bowel disease characterized by mucosal barrier disruption, dysregulated immune responses, and gut microbial imbalance. However, limitations of current therapies highlight the need for safe probiotic interventions. This study evaluated the preventive effects of fermented yak milk-derived Lacticaseibacillus paracasei CD12-1 on dextran sulfate sodium (DSS)-induced colitis in mice. The results showed that DSS caused body weight loss, an increased disease activity index, colon shortening, and severe histopathological injury. CD12-1 alleviated these abnormalities with differential effects across doses. The low-dose treatment produced the most comprehensive improvements in histopathological damage, goblet cell abundance, tight junction integrity, inflammatory cytokines, and short-chain fatty acids, whereas the high dose more effectively attenuated body weight loss. CD12-1 increased colonic ZO-1 and Occludin expression, reduced IL-1β, IL-6, and TNF-α levels, and increased IL-10. The low dose also elevated acetate and butyrate levels. Gut microbiota analysis showed that CD12-1 was associated with changes in the relative abundances of Lactobacillus, Bifidobacterium, Allobaculum, Akkermansia, and several inflammation-associated taxa. Correlation analysis associated Lactobacillus and Allobaculum with milder disease and improved barrier-related indicators, whereas Bacteroides and Sutterella were associated with greater disease severity and inflammation. Overall, CD12-1 alleviated DSS-induced colitis by improving intestinal barrier integrity and inflammatory homeostasis, accompanied by changes in microbial composition and short-chain fatty acid production. Full article
(This article belongs to the Special Issue Next Generation Microbial Food Safety: New Era on Pathogenic and Beneficial Microorganisms)
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16 pages, 9916 KB  
Article
Lauric Acid Microemulsions Inhibit Staphylococcus aureus Through Cell Membrane Disruption and Potential Interference with Peptidoglycan Biosynthesis
by Peipei Ma, Runrun Zhang, Chen Li, Qiao He, Xinhui Zhang and Zhixiang Cai
Foods 2026, 15(16), 2867; https://doi.org/10.3390/foods15162867 - 17 Aug 2026
Viewed by 346
Abstract
Staphylococcus aureus (S. aureus) is a prominent foodborne pathogen that poses a continuous threat to global public health and food safety due to its possession of a variety of toxins and its multidrug resistance. Medium-chain fatty acids (MCFAs), notably lauric acid [...] Read more.
Staphylococcus aureus (S. aureus) is a prominent foodborne pathogen that poses a continuous threat to global public health and food safety due to its possession of a variety of toxins and its multidrug resistance. Medium-chain fatty acids (MCFAs), notably lauric acid (LA), exhibit strong antimicrobial properties, but their application is heavily constrained by poor water solubility. In this study, optimized LA emulsions stabilized by chitosan (CS) and polyvinyl alcohol (PVA) were evaluated for their antibacterial activity and detailed mode of action against S. aureus ATCC 6538. The antibacterial activities were evaluated by the maximum inhibition zone, with the 20 CS-PVA/DLTA-LA formulation exhibiting stable dispersion and potent antibacterial activity at 1%. The underlying antibacterial mechanisms against S. aureus were specifically focused on cell membranes and peptidoglycan. Therein, the binding of emulsion droplets to the anionic bacterial surface was driven by electrostatic attraction. Membrane degradation was also observed with membrane dysfunctions involving membrane depolarization, increased permeability, and fluidity reduction triggered by their subsequent insertion into the lipid bilayer, which may cause cell dysmetabolism, disintegration, and eventual cell death. Overall, these findings substantiate that LA emulsions disrupt S. aureus by operating potentially multi-targeted effects involving cell membrane disruption and peptidoglycan interference, offering a promising alternative approach warranting further investigation for foodborne pathogen control. Full article
(This article belongs to the Special Issue Next Generation Microbial Food Safety: New Era on Pathogenic and Beneficial Microorganisms)
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