Molecular Characterization of Multidrug-Resistant Pathogens

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Genetic and Biochemical Studies of Antibiotic Activity and Resistance".

Deadline for manuscript submissions: 30 September 2025 | Viewed by 31

Special Issue Editors


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Guest Editor
Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
Interests: genomics; transcriptomics; MDR microorganisms; biofilm; molecular resistance mechanisms
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Medical Molecular Microbiology and Antibiotic Resistance Laboratory (MMARLab), Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Catania, Italy
Interests: screening and characterization of probiotic strains including strains producing bacteriocins involved in antimicrobial activity; microbial genome analysis and microbiome studies; sequencing and characterization of mobile genetic elements responsible for antibiotic resistance and production of bacteriocin genes
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The rapid emergence and global spread of multidrug-resistant (MDR) pathogens pose a global health challenge, impacting human, animal, and environmental health. Understanding the molecular mechanisms underlying antimicrobial resistance is crucial for developing targeted therapeutic strategies and effective control measures in all environments. In this context, this Special Issue aims to collect studies of MDR pathogens’ molecular characterization.

Original research articles, short communications, or review articles describing recent advances in the field of antimicrobial resistance mechanisms and evolution will be considered.

Potential topics include, but are not limited to, the following:

  • Molecular mechanisms involved in bacterial resistance mechanisms;
  • Omics to investigate molecular mechanisms and their evolutionary trends;
  • Impact of environmental factors on resistance dissemination;
  • One-Health approach for the dissemination of MDR pathogens and resistance mechanisms;
  • Response to antimicrobials or antibiotics;
  • Genetics on microorganisms to improve antimicrobial effects;
  • Genetic elements involved in antimicrobial resistance;
  • Molecular epidemiology, phylogenomics, evolution, genomics, phylogenetic reconstruction, and lineage replacement;
  • Persistence and tolerance.

Dr. Viviana Cafiso
Dr. Maria Santagati
Guest Editors

Manuscript Submission Information

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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. Antibiotics 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 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

  • MDR pathogens
  • One-Health
  • genomic
  • transcriptomic
  • phylogenomics
  • molecular epidemiology
  • AMR

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Published Papers (1 paper)

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Research

23 pages, 1575 KiB  
Article
Mutation- and Transcription-Driven Omic Burden of Daptomycin/Dalbavancin-R and Glycopeptide-RS Fitness Costs in High-Risk MRSA: A Nexus in Antimicrobial Resistance Mechanisms—Genome Proneness—Compensatory Adaptations
by Eleonora Chines, Gaia Vertillo Aluisio, Maria Lina Mezzatesta, Maria Santagati and Viviana Cafiso
Antibiotics 2025, 14(5), 465; https://doi.org/10.3390/antibiotics14050465 (registering DOI) - 2 May 2025
Abstract
Background: In Staphylococcus aureus, antimicrobial resistance (AMR) imposes significant fitness costs (FCs), including reduced growth rate, interbacterial competitiveness, and virulence. However, the FC molecular basis remains poorly understood. This study investigated the FC omic basis and compensatory adaptations in high-risk HA-, LA-, [...] Read more.
Background: In Staphylococcus aureus, antimicrobial resistance (AMR) imposes significant fitness costs (FCs), including reduced growth rate, interbacterial competitiveness, and virulence. However, the FC molecular basis remains poorly understood. This study investigated the FC omic basis and compensatory adaptations in high-risk HA-, LA-, and CA-MRSA, acquiring mono- or cross-resistance to second-line daptomycin (DAP) and dalbavancin (DAL), as well as reduced susceptibility (RS) to first-line glycopeptides, i.e., vancomycin and teicoplanin (GLYs, i.e., VAN, TEC), related to the specific mechanism of action (MOA)-related AMR-mechanisms and genomic backgrounds, paying increasing FCs. Methods: The FC omic basis associated with mono- or cross- DAP-/DAL-R and GLY-RS were investigated by integrated omics. This study focused on core-genome essential (EG) and accessory virulence gene (VG) SNPomics and transcriptomics by Illumina MiSeq whole-genome sequencing, RNA-seq, and bioinformatic analysis. Results: Moderate impact nsSNPs were identified in EGs related to vital cellular functions and VGs. Comparative EG transcriptomics revealed differential expressions and key dysregulations—via asRNAs—prevalently affecting the protein synthesis and cell-envelope EG clusters, as well as the VG cluster. Conclusions: Our data, firstly, underlined the EG and VG mutation- and transcription-driven omic-based FC burden and the compensatory adaptations associated with the emergence of mono-DAP-R, cross-DAP-R/hGISA, and DAP-R/DAL-R/GISA, linked to specific MOA-related AMR-mechanisms and genomic backgrounds in high-risk HA-, LA-, and CA-MRSA. Full article
(This article belongs to the Special Issue Molecular Characterization of Multidrug-Resistant Pathogens)
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