Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
8.7
4.6
Journals
Antibiotics
Special Issues
Genomic Surveillance of Antimicrobial Resistance (AMR)
share announcement

Genomic Surveillance of Antimicrobial Resistance (AMR)

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 1222

Special Issue Editor

Dr. Linzy Elton

E-Mail Website
Guest Editor
Centre for Clinical Microbiology, University College London, London, UK
Interests: AMR; One Health; global health; infectious disease

Special Issue Information

Dear Colleagues,

Antimicrobial resistance (AMR) is a major global health threat. The rapid spread of resistance, driven by the overuse and misuse of antibiotics in humans, animals, and agriculture, increases the risk of untreatable infections, global outbreaks, and increased mortality. Surveillance is essential for combating AMR because it helps track the emergence, spread, and evolution of resistant pathogens. By monitoring resistance patterns in different regions and settings, surveillance systems provide critical data for guiding treatment decisions, informing public health strategies, and optimizing antibiotic use. Genomics plays a crucial role in AMR surveillance by providing detailed insights into the genetic mechanisms that drive resistance in pathogens. Genomic surveillance enhances our understanding of how resistance evolves and spreads within populations, both locally and globally, so we can track outbreaks, monitor transmission pathways, and identify potential reservoirs of resistance.

This Special Issue aims at showcasing the role that genomics can play in the surveillance of AMR across human, animal, and environmental sectors. We welcome original research, review articles, case studies, and opinion papers. Topics of particular interest include the following:

  • Cross-disciplinary/One Health research;
  • Fungal antimicrobial resistance;
  • Viral antimicrobial resistance;
  • Parasite antimicrobial resistance;
  • Research from low- and middle-income countries.

Dr. Linzy Elton
Guest Editor

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. 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

  • antimicrobial resistance
  • sequencing
  • genomics
  • surveillance
  • mobile genetic elements
  • multi-drug-resistant organisms
  • One Health
  • metagenomics
  • whole-genome sequencing

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

17 pages, 1188 KB  
Article
Comparative Phenotypic and Genotypic Analysis of Erysipelothrix rhusiopathiae Strains Isolated from Poultry
by Ádám Kerek, Gergely Tornyos, Eszter Kaszab, Enikő Fehér and Ákos Jerzsele
Antibiotics 2026, 15(1), 11; https://doi.org/10.3390/antibiotics15010011 (registering DOI) - 20 Dec 2025
Abstract
Background: Erysipelothrix rhusiopathiae is an important zoonotic pathogen in poultry, yet little is known about its antimicrobial resistance (AMR) dynamics in avian hosts. With growing concerns about subtherapeutic antimicrobial use in animal agriculture, poultry-origin isolates represent a potential but under-characterized reservoir of [...] Read more.
Background: Erysipelothrix rhusiopathiae is an important zoonotic pathogen in poultry, yet little is known about its antimicrobial resistance (AMR) dynamics in avian hosts. With growing concerns about subtherapeutic antimicrobial use in animal agriculture, poultry-origin isolates represent a potential but under-characterized reservoir of resistance genes. Methods: We phenotypically tested 38 E. rhusiopathiae strains isolated from geese, ducks, and turkeys in Hungary (2024) using broth microdilution against 18 antimicrobial agents, following Clinical Laboratory Standards Institute (CLSI) guidelines. Nineteen phenotypically resistant strains were selected for whole-genome sequencing (Illumina platform), followed by de novo hybrid assembly, gene annotation (Prokka, CARD, VFDB), mobile element detection (Mobile Element Finder), and phylogenetic inference (autoMLST). Results: All isolates were susceptible to β-lactams, including penicillin, amoxicillin, and third-generation cephalosporins. Resistance to tetracyclines (up to 10.5%) and florfenicol (5.3%) was most frequently detected. Genomic analysis revealed the presence of tetM (9/19), tetT (2/19), and erm(47) (2/19) genes, all associated with chromosomally integrated mobile elements, ICE Tn6009 and IS ISErh6. Phylogenomic analysis demonstrated tight clustering into four clades, suggesting clonal expansion. Notably, one strain harbored a 64.8 kb genomic island carrying ermC, the first such finding in poultry-derived E. rhusiopathiae. Conclusions: Our data highlights the early emergence of mobile AMR determinants in E. rhusiopathiae from poultry and suggests that horizontal gene transfer may drive resistance even in chromosomally encoded contexts. The genomic stability and phylogenetic homogeneity of avian isolates underscore the need for targeted AMR surveillance in poultry sectors to mitigate potential zoonotic transmission risks. Full article
(This article belongs to the Special Issue Genomic Surveillance of Antimicrobial Resistance (AMR))
►▼ Show Figures

Figure 1

17 pages, 886 KB  
Article
Genotypic Characterization of Virulence Factors in Extended-Spectrum Beta-Lactamase (ESBL)-Producing Escherichia coli Strains from Chickens in Hungary
by Ádám Kerek, Ábel Szabó, Gergely Tornyos, Eszter Kaszab, Krisztina Bali and Ákos Jerzsele
Antibiotics 2025, 14(11), 1083; https://doi.org/10.3390/antibiotics14111083 - 27 Oct 2025
Viewed by 583
Abstract
Background: The increasing attention on extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strains isolated from poultry flocks stems from concerns about their virulence potential and zoonotic risk. Of particular significance is the identification of extraintestinal pathogenic E. coli (ExPEC) pathotypes in poultry, as these [...] Read more.
Background: The increasing attention on extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strains isolated from poultry flocks stems from concerns about their virulence potential and zoonotic risk. Of particular significance is the identification of extraintestinal pathogenic E. coli (ExPEC) pathotypes in poultry, as these strains pose not only animal health concerns but also serious threats to food safety and public health. Mapping the genetic background of pathogenicity and antimicrobial resistance is essential for risk assessment and the development of effective control strategies. Methods: A total of 87 E. coli isolates were isolated from tracheal and cloacal swab samples collected from healthy chickens between 2022 and 2023. Whole-genome sequencing was performed using Illumina and MGI next-generation sequencing platforms. Bioinformatic analyses were conducted to identify virulence-associated genes and pathotype markers using multiple reference databases, including VirulenceFinder. The frequency of virulence genes was summarized both in tabular form and visualized through graphical representations. Results: A substantial proportion of the isolates harbored virulence genes linked to various ExPEC pathotypes, particularly uropathogenic E. coli (UPEC), avian pathogenic E. coli (APEC), and neonatal meningitis-causing E. coli (NMEC). The most frequently detected colonization factors included members of the fim, pap, ecp, and fae gene families. Among fitness-related genes, iron acquisition systems—ent, chu, iro, iuc, fep, and ybt—were especially prevalent. Classic UPEC-associated genes such as pap and fimH, along with the APEC-related iutA and vat, were found at high frequencies. Four isolates exhibited a virulence gene profile characteristic of the NMEC pathotype (ibeA, kpsD/M/T, fimH). In contrast, hallmark genes of enteric pathotypes were absent from all isolates. Conclusions: The predominance of extraintestinal virulence factors in the examined poultry-derived E. coli strains underscores their zoonotic potential. The complete absence of enteric pathotype markers indicates that the studied poultry populations primarily harbor ExPEC-like strains. These findings highlight the critical need for ongoing genomic surveillance and targeted preventive strategies within poultry production systems. Full article
(This article belongs to the Special Issue Genomic Surveillance of Antimicrobial Resistance (AMR))
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-2
Back to TopTop