Antibiotic Resistance and Survival Strategies in Pathogens

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Bacterial Pathogens".

Deadline for manuscript submissions: 20 April 2026 | Viewed by 150

Special Issue Editors


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Guest Editor
Laboratory of Microbial Biochemistry, Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Gdańsk, Poland
Interests: persister cells; bacterial dormancy; resuscitation mechanisms; molecular mechanisms of persistence; biochemical adaptation of bacteria; stress response in bacteria; antibiotic tolerance; non-growing bacterial states; VBNC cells; bacterial biofilms

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Guest Editor
Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Gdańsk, Poland
Interests: biofilm; desiccation stress; multidrug resistance; persisters; proteostasis

Special Issue Information

Dear Colleagues,

Antibiotic resistance poses a significant challenge to public health worldwide. While the emergence and spread of genetically encoded resistance mechanisms is well-recognized, bacterial survival strategies extend beyond resistance alone. Increasing attention is being paid to tolerance mechanisms that enable pathogens to persist under antimicrobial pressure without exhibiting traditional resistance traits.

This Special Issue of Pathogens aims to highlight recent advances in our understanding of both antibiotic resistance and bacterial tolerance in pathogenic microorganisms. We welcome contributions focusing on molecular mechanisms of resistance, the prevalence of resistant strains in clinical and environmental settings, and novel resistance genes or phenotypes.

In addition, we strongly encourage submissions addressing antibiotic tolerance and non-replicative survival strategies, such as the formation of persister cells and the viable but non-culturable (VBNC) state. These phenotypes allow pathogens to withstand hostile conditions, evade immune responses, and survive antibiotic treatment, contributing to recurrent and chronic infections.

We invite original research articles, reviews, and short communications that provide new insights into how pathogenic bacteria adapt to and survive in adverse conditions. Studies proposing novel diagnostic, therapeutic, or preventive strategies targeting both resistant and tolerant populations are particularly welcome.

Researchers within microbiology, infectious diseases, molecular biology, and related fields are encouraged to contribute to this Special Issue.

Dr. Karolina Stojowska-Swędrzyńska
Dr. Dorota Kuczyńska-Wiśnik
Guest Editors

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Keywords

  • antibiotic resistance
  • antibiotic tolerance
  • persister cells
  • VBNC state
  • multidrug resistance
  • resistant pathogens
  • mechanisms of antimicrobial resistance
  • antibiotic-resistant genes
  • alternative antimicrobial strategies
  • chronic infections

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Published Papers (1 paper)

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Review

29 pages, 1443 KB  
Review
From Methylomes to CRISPR Epigenetic Editing: New Paths in Antibiotic Resistance
by Nada M. Nass and Kawther A. Zaher
Pathogens 2025, 14(12), 1267; https://doi.org/10.3390/pathogens14121267 - 10 Dec 2025
Abstract
Antibiotic resistance (AR) has long been interpreted through the lens of genetic mutations and horizontal gene transfer. Yet, mounting evidence suggests that epigenetic regulation, including DNA and RNA methylation, histone-like proteins, and small non-coding RNAs, plays a similarly critical role in bacterial adaptability. [...] Read more.
Antibiotic resistance (AR) has long been interpreted through the lens of genetic mutations and horizontal gene transfer. Yet, mounting evidence suggests that epigenetic regulation, including DNA and RNA methylation, histone-like proteins, and small non-coding RNAs, plays a similarly critical role in bacterial adaptability. These reversible modifications reshape gene expression without altering the DNA sequence, enabling transient resistance, phenotypic heterogeneity, and biofilm persistence under antimicrobial stress. Advances in single-molecule sequencing and methylome mapping have uncovered diverse DNA methyltransferase systems that coordinate virulence, efflux, and stress responses. Such epigenetic circuits allow pathogens to survive antibiotic exposure, then revert to susceptibility once pressure subsides, complicating clinical treatment. Parallel advances in CRISPR-based technologies now enable direct manipulation of these regulatory layers. CRISPR interference (CRISPRi) and catalytically inactive dCas9-fused methyltransferases can silence or reactivate genes in a programmable, non-mutational manner, offering a new route to reverse resistance or sensitize pathogens. Integrating methylomic data with transcriptomic and proteomic profiles further reveals how epigenetic plasticity sustains antimicrobial tolerance across environments. This review traces the continuum from natural bacterial methylomes to engineered CRISPR-mediated epigenetic editing, outlining how this emerging interface could redefine antibiotic stewardship. Understanding and targeting these reversible, heritable mechanisms opens the door to precision antimicrobial strategies that restore the effectiveness of existing drugs while curbing the evolution of resistance. Full article
(This article belongs to the Special Issue Antibiotic Resistance and Survival Strategies in Pathogens)
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