Unraveling Genomic Mechanisms of Stress Tolerance and Antimicrobial Resistance in Foodborne Pathogens

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (25 January 2026) | Viewed by 1303

Special Issue Editors


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Guest Editor
Food Molecular Microbiology Laboratory (LabMMA), Federal University of Mato Grosso (UFMT), Boa Esperança Avenue, Cuiabá 78060-900, MT, Brazil
Interests: foodborne bacterial characterization using genomic approach
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Food Molecular Microbiology Laboratory (LABMMA), Federal University of Mato Grosso (UFMT), Boa Esperança Avenue, Cuiabá 78060-900, MT, Brazil
Interests: foodborne bacterial characterization using genomic approach
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent years, there has been a noticeable increase in stress tolerance among foodborne pathogens in response to various stimuli such as heat, sanitizers, antibiotics, and acidity, among others. Additionally, some bacteria like Escherichia coli have demonstrated the presence of not just individual resistance genes but entire genomic loci, such as the Transmissible Locus of Stress Tolerance (tLST). Other genomic elements, including the Listeria monocytogenes Stress Survival Islet 1 (SSI-1) and the Salmonella Genomic Island 1 (SGI1), have also been implicated in enhancing survival and multidrug resistance. In other cases, bacteria like Salmonella have acquired resistance through megaplasmids, such as the pESI-like plasmid, which facilitates the rapid spread of antimicrobial resistance. The emergence of additional plasmids, such as the IncX4, IncHI2, and IncI1 types, carrying critical resistance genes (e.g., mcr-1 for colistin resistance or blaCTX-M for extended-spectrum β-lactamase production) is of growing concern.

This Special Issue aims to address existing gaps and showcase cutting-edge research in this field. We invite researchers to contribute manuscripts exploring all aspects of stress tolerance and antimicrobial resistance in foodborne pathogens. Studies focusing on stressors such as heat, sanitizers, acidity, salinity, and osmolarity, as well as mechanisms of antimicrobial resistance, including the role of emerging resistance genes, genomic islands, and mobile genetic elements, are especially welcome.

Dr. Eduardo Eustáquio de Souza Figueiredo
Dr. Vinicius Silva Castro
Guest Editors

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Keywords

  • foodborne pathogens
  • AMR
  • survivability
  • thermal resistance
  • in silico analysis
  • DNA sequencing
  • RNA sequencing
  • environmental stress condition

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Published Papers (1 paper)

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Research

18 pages, 1613 KB  
Article
Antibiotic-Driven Evolutionary Engineering in Salmonella Heidelberg Reveals Genomic Signatures of Attenuation
by Ruy D. Chacón, Manuel Ramírez, Claudete S. Astolfi-Ferreira and Antonio J. Piantino Ferreira
Genes 2026, 17(2), 235; https://doi.org/10.3390/genes17020235 - 12 Feb 2026
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Abstract
Background/Objectives: Salmonella Heidelberg (SH) is a globally distributed pathogen associated with gastrointestinal disease in humans and animals and frequently affects poultry. Among the classic strategies used in vaccine development, evolutionary engineering enables the generation of attenuated bacterial strains through exposure to selective [...] Read more.
Background/Objectives: Salmonella Heidelberg (SH) is a globally distributed pathogen associated with gastrointestinal disease in humans and animals and frequently affects poultry. Among the classic strategies used in vaccine development, evolutionary engineering enables the generation of attenuated bacterial strains through exposure to selective pressures such as antibiotics. In this study, spontaneous antibiotic-resistant mutant strains of SH were generated by exposure to high concentrations of streptomycin and rifampicin, after which their phenotypic and genotypic characteristics were evaluated. Methods: The wild-type strain SA628 wt was subjected to continuous and discontinuous selection under antibiotic pressure. Phenotypic characterization included biochemical profiling and antibiotic susceptibility testing. Whole-genome sequencing was performed to identify genetic changes affecting virulence- and resistance-associated genes, plasmid content, and point mutations using variant calling approaches. The potential functional relationships of the mutated genes were further analyzed through genetic network analysis. Results: The mutant strains SA628 mut1 and SA628 mut3 were obtained through discontinuous selection, whereas strain SA628 mut2 was generated under continuous selection. Phenotypically, all the mutant strains exhibited resistance to streptomycin, whereas SA628 mut2 and SA628 mut3 also exhibited resistance to rifampicin. Genomic analyses revealed mutations in rpoS, ascD, ynfE, rpoB, and cyaA associated with discontinuous selection and in iscU, ybiO, rpoB, and rsmG associated with continuous selection. Network analysis indicated that these genes are functionally connected within regulatory and metabolic interaction networks, including global transcriptional regulation, anaerobic metabolism, cAMP-mediated signaling, translation, and iron–sulfur cluster biogenesis. Conclusions: Collectively, these findings suggest that antibiotic-driven selection promotes coordinated genetic changes affecting stress responses and metabolism, which may contribute to reduced virulence. This work provides insights into bacterial adaptation under antibiotic stress and supports the potential use of evolutionary engineering for the development of attenuated strains. Full article
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