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Antibiotics
Special Issues
Genomic Insights and Implications of Emerging Antimicrobial Resistance
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Genomic Insights and Implications of Emerging Antimicrobial Resistance

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: 30 September 2025 | Viewed by 1411

Special Issue Editors

Dr. Daniela Bencardino

E-Mail Website
Guest Editor
Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
Interests: antimicrobial-resistance; infectious diseases; epidemiological surveillance; methicillin-resistant Staphylococcus aureus (MRSA); molecular typing of resistant strains; food pathogens; healthcare-associated infections; community-acquired infections
Dr. Christian Berens

E-Mail Website
Guest Editor
Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, 07743 Jena, Germany
Interests: antibiotic resistance mechanisms; regulation of antibiotic resistance; mechanisms of antibiotic action; tetracycline activity and resistance; molecular genetics

Special Issue Information

Dear Colleagues,

Antimicrobial resistance (AMR) is a critical global health challenge requiring urgent attention and a multifaceted One Health approach. Genomic technologies offer actionable insights to help prioritize and implement AMR mitigation strategies and assess the effectiveness of interventions. Whole-genome sequencing (WGS) has revealed the noteworthy speed at which bacteria can adapt to antimicrobial agents, providing high-resolution, precise characterization of multidrug resistance (MDR) and enabling a more comprehensive analysis of AMR mechanisms. Data sharing from genomic surveillance is crucial for tracking evolutionary trends and population dynamics, as well as for identifying highly adaptable resistant clones as they emerge and spread.

A genomics-based approach for AMR surveillance enables the identification of new resistant microorganisms, mobile genetic elements (MGEs) that spread AMR, and hotspots for horizontal gene transfer (HGT). These insights support stewardship practices, establish baseline resistance data important for assessing mitigation efforts, and facilitate tracking of pathogen transmission within hospitals, veterinary clinics, and environmental settings. This Special Issue brings together research that highlights the vital role of genomics in monitoring resistance within healthcare settings and community-acquired infections, with important implications for future control and therapeutic strategies.

All studies on the One Health genomic surveillance of AMR will be highly appreciated and  included in this Special Issue.

Dr. Daniela Bencardino
Dr. Christian Berens
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 100 words) can be sent to the Editorial Office for announcement on this website.

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

  • antibiotic-resistance
  • molecular typing
  • genomic technologies
  • high-threat pathogens
  • epidemiological surveillance
  • emerging and re-emerging infectious diseases
  • one health approach

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Published Papers (2 papers)

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Research

17 pages, 2372 KiB  
Article
Emergence and Clonal Spread of Extended-Spectrum β-Lactamase-Producing Salmonella Infantis Carrying pESI Megaplasmids in Korean Retail Poultry Meat
by Yeona Kim, Hyeonwoo Cho, Miru Lee, Amany Hassan, Soo-Jin Yang, Jong-Chan Chae and Kun Taek Park
Antibiotics 2025, 14(4), 366; https://doi.org/10.3390/antibiotics14040366 - 1 Apr 2025
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Abstract
Background/Objectives: Salmonella is a major cause of foodborne illnesses, with multidrug-resistant (MDR) strains posing significant threats to public health worldwide. This study investigated the prevalence and antimicrobial resistance (AMR) of Salmonella, focusing on extended-spectrum β-lactamase (ESBL)-producing Salmonella in retail poultry meat [...] Read more.
Background/Objectives: Salmonella is a major cause of foodborne illnesses, with multidrug-resistant (MDR) strains posing significant threats to public health worldwide. This study investigated the prevalence and antimicrobial resistance (AMR) of Salmonella, focusing on extended-spectrum β-lactamase (ESBL)-producing Salmonella in retail poultry meat in Korea. Methods: A total of 300 poultry meat samples were collected nationwide from retail markets. Multi-locus sequence typing, serotyping, and antimicrobial susceptibility testing were performed. Whole-genome sequencing (WGS) analysis was conducted against 28 representative ESBL-producing S. Infantis isolates to identify the genetic characteristics and phylogenetic relationship. Results: Salmonella was detected in 81.3% of raw poultry meat samples, with S. Infantis ST32 being the dominant serotype in chicken (53.0%) and S. Typhimurium ST19 predominant in duck (39.0%). MDR was identified in 58.2% of samples, with a significantly higher rate in chicken isolates than in duck isolates (p < 0.001). Notably, 75.3% of chicken MDR isolates were ESBL-producing S. Infantis carrying blaCTX-M-65. WGS of 28 geographically and phenotypically representative ESBL-producing S. Infantis revealed five clonal clusters, suggesting the widespread dissemination of ESBL-producing S. Infantis across Korea’s poultry supply chain. All 28 ESBL-producing S. Infantis isolates contained a pESI-like megaplasmid, carrying multiple resistance and virulence genes, with sequences highly identical to plasmids reported in the United States, indicating potential international transmission. Conclusions: This study emphasizes the urgent need for continuous surveillance and responsible antibiotic use in livestock under a One Health framework. WGS can provide an effective tool for tracking AMR evolution and clonal spread within and across regions. Full article
(This article belongs to the Special Issue Genomic Insights and Implications of Emerging Antimicrobial Resistance)
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16 pages, 2086 KiB  
Article
Multiplex Real-Time Polymerase Chain Reaction and Recombinase Polymerase Amplification: Methods for Quick and Cost-Effective Detection of Vancomycin-Resistant Enterococci (VRE)
by Ibukun Elizabeth Osadare, Abdinasir Abdilahi, Martin Reinicke, Celia Diezel, Maximilian Collatz, Annett Reissig, Stefan Monecke and Ralf Ehricht
Antibiotics 2025, 14(3), 295; https://doi.org/10.3390/antibiotics14030295 - 12 Mar 2025
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Abstract
Background/Objectives: Vancomycin-resistant enterococci (VRE) are one of the leading causes of antibiotic-resistant infections in the hospital setting worldwide, and this has become a major issue, because most patients infected with this strain are difficult to treat. Multiplex real-time polymerase chain [...] Read more.
Background/Objectives: Vancomycin-resistant enterococci (VRE) are one of the leading causes of antibiotic-resistant infections in the hospital setting worldwide, and this has become a major issue, because most patients infected with this strain are difficult to treat. Multiplex real-time polymerase chain reaction (RT PCR) is an advantageous technique that can amplify multiple targets in a single reaction, and can be used to quickly detect specific targets in VRE within two hours, starting from suspected colonies of bacterial cultures, without sample preparation. Methods: In this study, we selected the glycopeptide/vancomycin resistance genes that are most common in clinical settings, vanA and vanB, in combination with the species markers ddl_faecium and ddl_faecalis for the most common VRE species—Enterococcus faecium and Enterococcus faecalis. Results: DNA from forty clinical VRE strains was prepared using a fast and economic heat lysis method, and a multiplex real-time PCR assay was optimized and carried out subsequently. The results were in concordance with the results from recombinase polymerase amplification (RPA) of the same VRE samples. Conclusions: Multiplex RT PCR and RPA for VRE detection proffers a second method for the confirmation of vancomycin resistance, and it can be developed as a fast screening assay for patients before admission into high-risk settings. Full article
(This article belongs to the Special Issue Genomic Insights and Implications of Emerging Antimicrobial Resistance)
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