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Antibiotics
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Genomic Surveillance of Antimicrobial Resistance (AMR)
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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 3652

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

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Published Papers (5 papers)

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Research

24 pages, 2800 KB  
Article
Genomic Epidemiology of ESBL and Non-ESBL-Producing Escherichia coli Across One Health Interfaces in Oman
by Hibatallah Sultan Al-Habsi, Zaaima Al Jabri, Amina Al-Jardani, Amira ElBaradei, Hafidha Al-Hattali, Faiza Syed, Zakariya Al Muharrmi, Wafa Al Alawi, Hatim Ali Eltahir and Meher Rizvi
Antibiotics 2026, 15(4), 411; https://doi.org/10.3390/antibiotics15040411 - 17 Apr 2026
Viewed by 192
Abstract
Background: Antimicrobial resistance is a One Health problem driven by the intricate interactions across human, animal, and environmental interfaces that enable microbial exchange and movement of mobile genetic elements encoding resistance and virulence. This study investigated the genomic epidemiology of ESBL and [...] Read more.
Background: Antimicrobial resistance is a One Health problem driven by the intricate interactions across human, animal, and environmental interfaces that enable microbial exchange and movement of mobile genetic elements encoding resistance and virulence. This study investigated the genomic epidemiology of ESBL and non-ESBL Escherichia coli across One Health interfaces in Oman. Methods: This prospective cross-sectional study analyzed 295 non-duplicate Escherichia coli isolates derived from 104 clinical, 173 animal [diseased (123) and healthy (50)], 14 sewage and four water sources. Antimicrobial susceptibility testing was performed phenotypically, and a representative subset of 50 ESBL and non-ESBL Escherichia coli from the three interfaces underwent whole genome sequencing to determine MLST, phylogroups, resistance genes, virulence determinants and plasmid replicons. Results: ESBL prevalence was highest in human isolates (73%), followed by sewage (28.6%) and animals (16.3% diseased; 8% healthy). blaCTX-M-15 predominated in humans, whereas blaCTX-M-55 dominated in animals and sewage, suggesting ecological partitioning with partial overlap. Quinolone resistance was lowest in the animal interface. Sewage isolates harbored the most complex resistome, including rmtB and plasmid-mediated quinolone resistance genes. MLST analysis revealed high diversity in human isolates, including globally recognized ExPEC lineages (ST10, ST38, ST73, ST127, ST131), while ST224 dominated in animals with evidence of possible spillover to humans. ST167 was confined to sewage, consistent with environmental maintenance of high-risk clones. Phylogroup structuring showed predominance of A, B2 and D among human isolates and A, B1, and E among animal and sewage isolates. Virulence profiling demonstrated broader virulome diversity in humans, but shared core determinants (fimH, sitA, traT) across all domains. IncFIB(AP001918) was the dominant plasmid replicon, particularly among ESBL isolates, underscoring its role in horizontal gene dissemination. Alarmingly, mutation in pmrB (V161G) was identified in a healthy animal isolate, pointing to a need for greater colistin restriction in animal husbandry. Conclusions: This study highlights plasmid-mediated resistance and shared virulence determinants linking reservoirs; although AMR profile was quite distinct across the three interfaces, human isolates demonstrated greater resistance than animal isolates, suggesting healthcare-driven AMR in Oman. Continued integrated genomic surveillance is essential to monitor gene flow and inform coordinated antimicrobial stewardship strategies. Full article
(This article belongs to the Special Issue Genomic Surveillance of Antimicrobial Resistance (AMR))
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16 pages, 1097 KB  
Article
Inferred Mobility-Resolved Resistome Architecture Suggests Recurrent Co-Resistance Modules on a Conserved Chromosomal Backbone in Multidrug-Resistant Escherichia coli from Intensive Swine Production in Hungary
by Ádám Kerek, Balázs Nagyházi, Gergely Álmos Tornyos, Levente Hunor Husz, Máté Hetyésy, Eszter Kaszab, Enikő Fehér, Patrik Mag and Ákos Jerzsele
Antibiotics 2026, 15(4), 367; https://doi.org/10.3390/antibiotics15040367 - 2 Apr 2026
Viewed by 362
Abstract
Background: Multidrug-resistant (MDR) Escherichia coli in intensive pig production represents a persistent animal health and One Health concern. Here, we integrated quantitative phenotypic susceptibility data with whole-genome sequencing (WGS) to characterize the resistome and its inferred genomic context (chromosomal vs. plasmid-predicted contigs and [...] Read more.
Background: Multidrug-resistant (MDR) Escherichia coli in intensive pig production represents a persistent animal health and One Health concern. Here, we integrated quantitative phenotypic susceptibility data with whole-genome sequencing (WGS) to characterize the resistome and its inferred genomic context (chromosomal vs. plasmid-predicted contigs and mobile genetic element (MGE)-proximal regions) in swine-associated MDR E. coli from Hungary. Methods: A total of 203 E. coli isolates from large-scale pig farms were tested by broth microdilution. Based on resistance-oriented screening from an extended-spectrum β-lactamase (ESBL)-screen-positive pool, 116 isolates were subjected to whole-genome sequencing (WGS) as a resistance-enriched subset. Resistance determinants were annotated using the Comprehensive Antibiotic Resistance Database (CARD). Results: Resistance-oriented screening indicated frequent β-lactamase activity and ESBL screening positivity (110/203 and 127/203 isolates, respectively), consistent with strong antimicrobial selection pressure in the source population. Across the full phenotypic panel, 78/203 isolates (38.4%) met the MDR definition (non-susceptible to ≥3 antimicrobial classes), with marked between-farm variation (p < 0.001) but no age-group effect (p = 0.75). Non-β-lactam minimum inhibitory concentration (MIC) distributions showed pronounced, site-dependent high-MIC “tails”, most notably for tetracyclines, trimethoprim–sulfamethoxazole, fluoroquinolones, and colistin. In the WGS cohort (n = 116), we detected 82 distinct resistance determinants (5433 total occurrences), featuring a conserved chromosomal backbone enriched for intrinsic multidrug resistance components and lipid A modification pathways, alongside common plasmid- and MGE-associated acquired ARG modules involving tetracycline (tetA/tetB), sulfonamide/trimethoprim (sul/dfrA), aminoglycoside-modifying enzymes, and phenicol determinants (floR/cat). High-priority mobile determinants were rare but present, including mcr-1 (3/116; plasmid-associated) and plasmid-mediated quinolone resistance qnrB5 (2/116). Conclusions: Importantly, mobility/context inferences are restricted to this ESBL-screen-enriched WGS subset. Swine-associated E. coli from Hungarian large-scale farms harbors complex resistance architectures shaped by co-selection of mobile ARG modules on top of a pervasive chromosomal resistance backbone. Mobility-aware surveillance and stewardship are warranted to mitigate dissemination risks at the animal–environment–human interface. Full article
(This article belongs to the Special Issue Genomic Surveillance of Antimicrobial Resistance (AMR))
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14 pages, 1224 KB  
Article
Comprehensive Shotgun Metagenomic Profiling of Antibiotic Resistance Genes in Sheep and Goat Farming Environments
by Sara Gomes-Gonçalves, Jaqueline T. Bento, Guilherme Moreira, Joana Mourão, Rita Cruz, Fernando Esteves, Alexandra Lameira Baptista, Maria Aires Pereira, Pedro Caseiro, Pedro Carreira, Luís Figueira and João R. Mesquita
Antibiotics 2026, 15(3), 277; https://doi.org/10.3390/antibiotics15030277 - 9 Mar 2026
Viewed by 596
Abstract
Background: Antimicrobial resistance (AMR) is a growing global health concern, driven in part by antibiotic use in animal production systems. Despite its relevance, the microbiome and resistome of small ruminant farm environments remain largely underexplored. Methods: In this study, shotgun metagenomics was applied [...] Read more.
Background: Antimicrobial resistance (AMR) is a growing global health concern, driven in part by antibiotic use in animal production systems. Despite its relevance, the microbiome and resistome of small ruminant farm environments remain largely underexplored. Methods: In this study, shotgun metagenomics was applied to environmental samples from 46 sheep, goat and mixed-species farms across 14 municipalities in central Portugal. Results: Microbial profiling revealed a well-preserved microbiome with Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota (syn. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes respectively) as the most dominant phylum across different farm types. Regarding AMR, a total of 706 unique antimicrobial resistance genes (ARGs), covering 15 antibiotic classes, were detected. Tetracycline, aminoglycoside and macrolide resistance genes dominated across all samples, forming a conserved core resistome. While overall resistome profiles were broadly similar among farm types, significant differences were observed in specific ARG classes, such as pleuromutilin and fosfomycin. Conclusions: These findings highlight small ruminant farm environments as potential reservoirs of clinically relevant ARGs, including WHO highest priority critically important antimicrobial (HPCIA) resistance genes for macrolides (mph(c), erm(f), erm(b)) and fluoroquinolones (qnrD1), as well as critically important antimicrobial (CIA) resistance genes for glycopeptides (vanR-SC, vanR-O) and aminoglycosides (str, aadA), supporting the need to incorporate these environments into surveillance strategies. Full article
(This article belongs to the Special Issue Genomic Surveillance of Antimicrobial Resistance (AMR))
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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 - 20 Dec 2025
Viewed by 689
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))
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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 943
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))
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