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Pathogens
Special Issues
Antibiotic Resistance and Survival Strategies in Pathogens
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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: 25 September 2026 | Viewed by 3931

Special Issue Editors

Dr. Karolina Stojowska-Swędrzyńska

E-Mail Website
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
Dr. Dorota Kuczyńska-Wiśnik

E-Mail Website
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

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

  • 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 (3 papers)

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Research

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12 pages, 481 KB  
Article
Healthcare-Associated Conjunctivitis in the NICU: Microbiological Spectrum, Antimicrobial Resistance and Treatment Patterns
by Hatice Turgut, Elif Seren Tanrıverdi, Eda Karadoğan and Ramazan Özdemir
Pathogens 2026, 15(2), 209; https://doi.org/10.3390/pathogens15020209 - 13 Feb 2026
Cited by 1 | Viewed by 609
Abstract
Healthcare-associated bacterial conjunctivitis is an underrecognized yet preventable infection in neonatal intensive care units (NICUs). This study aimed to determine the incidence, risk factors, microbiological profile, and treatment approaches of healthcare-associated bacterial conjunctivitis in neonates. This descriptive, cross-sectional study included neonates diagnosed with [...] Read more.
Healthcare-associated bacterial conjunctivitis is an underrecognized yet preventable infection in neonatal intensive care units (NICUs). This study aimed to determine the incidence, risk factors, microbiological profile, and treatment approaches of healthcare-associated bacterial conjunctivitis in neonates. This descriptive, cross-sectional study included neonates diagnosed with bacterial conjunctivitis and followed in the NICU between January 2019 and January 2024. Pathogens were identified by MALDI-TOF MS and antimicrobial susceptibility determined using VITEK 2 according to EUCAST breakpoints. During the five-year period, 104 (2.5%) of 4107 neonates admitted to the NICU developed healthcare-associated bacterial conjunctivitis. Of the pathogens isolated in cultures, 70.2% were Gram-positive bacteria, with coagulase-negative staphylococci being the most common (52.9%), followed by Staphylococcus aureus, Klebsiella pneumoniae, and Serratia marcescens. Empirical treatment consisted of 0.3% topical gentamicin eye drops. In resistant cases, fortified vancomycin drops (32.7%), 0.5% moxifloxacin (4.8%), or 0.3% tobramycin (1.9%) eye drops were administered according to antibiogram results. Compared with Gram-positive infections, Gram-negative conjunctivitis was associated with longer durations of intubation, orogastric feeding, and hospitalization. These findings indicate a predominance of Gram-positive pathogens in NICU-acquired neonatal conjunctivitis, while Gram-negative infections confer greater clinical burden. Fortified antibiotic eye drops are an effective treatment option for resistant cases in high-risk newborns. Full article
(This article belongs to the Special Issue Antibiotic Resistance and Survival Strategies in Pathogens)
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Review

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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
Cited by 2 | Viewed by 2412
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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Other

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13 pages, 2190 KB  
Case Report
Detection and Identification of Paragyliauchen sp. (Trematoda) and Bacteria in Diseased Centropyge bicolor from the European Marine Aquarium Trade
by Leszek Guz, Anna Pastuszka, Michał Torbicz and Michał Oszust
Pathogens 2026, 15(3), 245; https://doi.org/10.3390/pathogens15030245 - 25 Feb 2026
Viewed by 524
Abstract
During the examination of a bicolor angelfish (Centropyge bicolor) imported from the Philippines and intended for sale on the Polish market, clinical signs of weakness and respiratory distress were observed. Mild hyperemia was noted along the lateral sides of the body [...] Read more.
During the examination of a bicolor angelfish (Centropyge bicolor) imported from the Philippines and intended for sale on the Polish market, clinical signs of weakness and respiratory distress were observed. Mild hyperemia was noted along the lateral sides of the body and around the mouth. Necropsy revealed the presence of five orange-colored trematodes in the intestinal lumen, with an average body length of 3.12 mm. Based on morphological features and molecular analyses, the parasite was identified as Paragyiauchen sp. The following gene loci were amplified: the gene-encoding component of the large ribosomal subunit (28S rRNA), the gene-encoding NADH dehydrogenase subunit 1 (ND1), the gene cluster 5.8S rRNA-ITS2-28S rRNA and the gene cluster ITS2-28S rRNA. Bacterial species identification using MALDI-TOF MS revealed the presence of three species: Shewanella putrefaciens and Brevundimonas diminuta isolated from the head kidney, and Aeromonas caviae isolated from the liver. This study documents the first detection of representatives of Paragyliauchen genus in C. bicolor imported to Europe and highlights the potential risk of introducing new parasites and opportunistic bacterial pathogens through the ornamental fish trade. These findings emphasize the need for parasitological and microbiological screening of imported ornamental fish. Full article
(This article belongs to the Special Issue Antibiotic Resistance and Survival Strategies in Pathogens)
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