Antibiotic Resistance Genes: Mechanisms, Evolution and Dissemination

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Mechanism and Evolution of Antibiotic Resistance".

Deadline for manuscript submissions: 31 May 2026 | Viewed by 2238

Special Issue Editors


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Guest Editor
Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, 1431 Sofia, Bulgaria
Interests: molecular virology; sequencing; phylogenetic; diagnosis
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Guest Editor
Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, 10-907 Olsztyn, Poland
Interests: antimicrobial agents; gut microbiome; metaomics; microbial biopolymers; microbial diversity; prokaryotic gene regulation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Antibiotic resistance develops through various well-known mechanisms, such as enzymatic degradation or modification of antimicrobial agents, alteration of target sites, reduced membrane permeability, and active efflux of drugs. These mechanisms have made infection control increasingly challenging worldwide. One main question remains unanswered: “Where do antibiotic resistance genes come from, and how is resistance acquired?”. Do they derive from the microbiome of humans and animals, from microorganisms in the environment, from the adaptation of the pathogens themselves (mutations in certain genes), a combination of these factors, or for another reason?

This Special Issue welcomes collaborative proposals across different research fields, inviting original scientific articles and reviews related to antibiotic resistance and the future consequences of its development. Research areas may include (but are not limited to) the following:

- Bacterial resistance;

- Viral resistance;

- Fungal resistance;

- Resistance gene transfer;

- Mutations in the genome of microorganisms;

- Evolution and adaptation of microorganisms;

- Mechanisms of resistance;

- Diagnostics of resistance;

- Therapy.

Dr. Ivo Nikolaev Sirakov
Prof. Dr. Slawomir Ciesielski
Guest Editors

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Keywords

  • antibiotic resistance genes
  • transposons
  • integrons
  • gene transfer
  • therapy

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Published Papers (3 papers)

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21 pages, 2188 KB  
Article
High-Resolution Genomic Surveillance of Carbapenem-Resistant Acinetobacter baumannii: IC-2 Clonal Diversity, Resistance Determinants, and Virulence Signatures
by Arianna Basile, Valentina Antonelli, Claudia Rotondo, Michele Properzi, Francesco Messina, Silvia D’Arezzo, Valentina Dimartino, Ivano Petriccione, Laura Loiacono, Maria Grazia Bocci, Giulia Capecchi, Alessia Arcangeli, Alessandra Marani, Filippo Pasquale Riggio, Massimiliano Lucidi, Francesco Imperi, Paolo Visca and Carla Fontana
Antibiotics 2026, 15(5), 464; https://doi.org/10.3390/antibiotics15050464 - 4 May 2026
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Abstract
Background/Objectives: Acinetobacter baumannii is a critical opportunistic pathogen causing severe healthcare-associated infections, particularly in intensive care units. The global dissemination of carbapenem-resistant A. baumannii (CRAB) and its environmental persistence necessitate continuous genomic surveillance to monitor high-risk clones. Methods: We conducted whole-genome sequencing [...] Read more.
Background/Objectives: Acinetobacter baumannii is a critical opportunistic pathogen causing severe healthcare-associated infections, particularly in intensive care units. The global dissemination of carbapenem-resistant A. baumannii (CRAB) and its environmental persistence necessitate continuous genomic surveillance to monitor high-risk clones. Methods: We conducted whole-genome sequencing (WGS), core genome multi-locus sequence typing (cgMLST), and phylogenomic analyses on 26 CRAB isolates collected at the National Institute for Infectious Diseases (INMI) “Lazzaro Spallanzani” IRCCS (September 2023–September 2024). Antimicrobial resistance determinants, virulence-related genes, and capsular (KL) and lipooligosaccharide outer core (OCL) loci were characterized by interrogation of comprehensive bioinformatic pipelines. Results: All CRAB isolates displayed an extensively drug-resistant (XDR) phenotype, with a shared resistance pattern to carbapenems, aminoglycosides, fluoroquinolones, fosfomycin, and sulfonamides, while being susceptible only to colistin and cefiderocol. The carbapenemase gene blaOXA-23 was detected in all CRAB isolates, together with clone-specific blaOXA-51-like variants. For all isolates, the resistome profile fully matched the observed resistance phenotype. All isolates belonged to the International Clonal Lineage II (ICL II), Pasteur Sequence Type (ST) 2, and Oxford ST369, ST208, and ST455. Integration of cgMLST data with phylogenomic analyses and genome-based classification of KL and OCL loci revealed five distinct clusters, each one including nearly identical isolates, indicating both intra-hospital dissemination and possible inter-hospital transmission. Virulome profiling revealed heterogeneous repertoires of virulence-associated genes, resulting in cluster-specific patterns, while patristic analysis identified phylogenetic clusters linking the study isolates to other Italian and other European lineages. Conclusions: This study underscores the complex genomic landscape of CRAB in our setting, driven by the circulation of different ICL II clonal types, and reinforces the urgency of integrated genomic surveillance and robust antimicrobial stewardship to mitigate the spread of high-risk XDR A. baumannii clones. Full article
(This article belongs to the Special Issue Antibiotic Resistance Genes: Mechanisms, Evolution and Dissemination)
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18 pages, 2621 KB  
Article
Genetic and Phenotypic Characterization of a Salmonella Enteritidis ST11 Clinical Isolate Carrying blaNDM-13 in Jiaxing City, China
by Ping Li, Weiming Yang, Zhongwen Chen, Henghui Wang, Miaomiao Jia, Xuejuan Liu, Yong Yan and Guoying Zhu
Antibiotics 2026, 15(4), 381; https://doi.org/10.3390/antibiotics15040381 - 9 Apr 2026
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Abstract
Background/Objectives: Multidrug-resistant Salmonella enterica serovar Enteritidis, especially those isolated from humans, remains a public concern. In the present study, S. Enteritidis strain 31404 was obtained clinically from a fecal sample of a fifteen-year-old girl, who was positive for blaNDM-13. [...] Read more.
Background/Objectives: Multidrug-resistant Salmonella enterica serovar Enteritidis, especially those isolated from humans, remains a public concern. In the present study, S. Enteritidis strain 31404 was obtained clinically from a fecal sample of a fifteen-year-old girl, who was positive for blaNDM-13. Methods: Antibiotic susceptibility testing and whole genome sequencing were performed. Core genome MLST and hierarchical clustering (HierCC) were performed using EnteroBase. Population structure analysis of 57 S. Enteritidis isolates collected between 2023 and 2025 in Jiaxing city was conducted. A comparative structure analysis of blaNDM-13-positive plasmids was also performed. Results: S. Enteritidis strain 31404 was resistant to 13 antimicrobial agents. We found that strain 31404 belonged to ST11 and carried resistance genes, such as blaNDM-13, blaCTX-M-14, bleMBL, fosA3, qnrS, and tet (A). blaNDM-13 was located on an IncI1-I (α) plasmid designated as p31404-NDM13. S. Enteritidis isolate 31404 was closely related to PNUSAS514422, which was isolated from the United States in 2025. Comparative genetic environment related to blaNDM-13-positive plasmids available in the NCBI database indicates that ΔTn125-mediated contexts were commonly associated with blaNDM-13. IS1294 (IS91 family), which replaces ISAba125, is likely to mobilize blaNDM-13. Conclusions: The findings in this study provide insights into the molecular characterization and diversification of blaNDM-13. The identification of blaNDM-13-containing transferable plasmids in different serotypes of Salmonella isolates (such as S. Rissen, S. Typhimurium, and S. Enteritidis) in different cities in China highlights the risk of the spread of carbapenem-resistant genes among Salmonella isolates. Full article
(This article belongs to the Special Issue Antibiotic Resistance Genes: Mechanisms, Evolution and Dissemination)
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27 pages, 2459 KB  
Systematic Review
Mobile Genetic Elements Associated with Antimicrobial Resistance Across One Health Interfaces in Africa: A Systematic Review and Meta-Analysis
by Kedir A. Hassen, Jose Fafetine, Laurinda Augusto, Inacio Mandomando, Marcelino Garrine, Rogerio Marcos and Gudeta W. Sileshi
Antibiotics 2026, 15(5), 456; https://doi.org/10.3390/antibiotics15050456 - 30 Apr 2026
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Abstract
Background: High infectious disease burden and uncontrolled antibiotic usage across human, animal, and environmental contaminants make antimicrobial resistance (AMR) a growing public health problem in Africa. Mobile genetic elements (MGEs) such plasmids, transposons, integrons, conjugative elements, and phages help spread AMR via horizontal [...] Read more.
Background: High infectious disease burden and uncontrolled antibiotic usage across human, animal, and environmental contaminants make antimicrobial resistance (AMR) a growing public health problem in Africa. Mobile genetic elements (MGEs) such plasmids, transposons, integrons, conjugative elements, and phages help spread AMR via horizontal gene transfer (HGT) across human, animal, food, and environmental sources. Despite growing evidence for antibiotic resistance genes (ARGs), Africa lacks a one-health-focused synthesis of mobile genetic element-mediated AMR. Objective: This systematic review and meta-analysis aimed to consolidate information on MGEs and ARGs in AMR dissemination throughout Africa’s one health interface. Methods: The literature was searched using PubMed, Scopus, and ScienceDirect. Observational. molecular epidemiology, whole genome sequencing (WGS), and metagenomic investigations of MGE-associated AMR in Africa were eligible. The study selection, data extraction, and quality assessment were performed by two independent reviewer and quality was graded using ROBVIS 2 utilizing Rayyan software. Narrative synthesis, random-effect meta-analysis, subgroup analysis, and meta-regression were utilized. Results: A total of 109 studies were included, with 91 studies contributing to the meta-analysis. MGEs reported were plasmids (71.7%) and integrons (54.8%). ARGs carried by MGEs were blaCTMX-M-15 (78.6%), Sul2 (69.6%), blaTEM (59.1%), and tetA (49.9%). Horizontal gene transfer was seen in 259 instances; however, transmission was unclear. In 442 observations, transmission pathways across human, animal, and environmental interfaces showed AMR prevalence of 75.1% in human, 98.0% in human–animal, and 61.3% in one health interface. Whole-genome sequencing was the most frequently used method for detecting MGEsThe pooled pathogen and AMR prevalence rates were 73.3% (95% CI: 60.5–83.7%) and 94% (95% CI: 85–98%), with significant heterogeneity (I2 = 97.8% and 97.4%, respectively). The prevalence of Escherichia coli was 93% and Salmonella enterica 85% in subgroup analysis. Fluoroquinolones, aminoglycosides, and beta-lactams were prevalent in humans (89.7%) and human–animal interactions (98.0%) according to AMR Class. Conclusions: Horizontal gene transfer has propagated MGE-mediated antimicrobial resistance across human, animal, and environmental interfaces in Africa. To combat AMR in Africa, coordinated, genomics-informed One Health surveillance and antibiotic stewardship are needed. Due to variability and publication bias, these data should be considered cautiously. Pooled data may only show descriptive patterns, and not necessarily precise continent-wide prevalence estimates. Full article
(This article belongs to the Special Issue Antibiotic Resistance Genes: Mechanisms, Evolution and Dissemination)
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