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Antibiotics
Special Issues
Genomic Insights into Dissemination of Multi-Drug Resistance Pathogens
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Genomic Insights into Dissemination of Multi-Drug Resistance Pathogens

A special issue of Antibiotics (ISSN 2079-6382).

Deadline for manuscript submissions: closed (31 December 2025) | Viewed by 2575

Special Issue Editors

Dr. Vanessa Silva

E-Mail Website
Guest Editor
1. Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
2. Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
3. LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
Interests: microbiology; One Health; antimicrobial resistance; biofilms; microbial genetics; infectious diseases
Special Issues, Collections and Topics in MDPI journals
Dr. Gilberto Igrejas

E-Mail Website
Guest Editor
1. Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
2. Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
3. LAQV@REQUIMTE, Chemistry Department, Faculty of Science and Technology, NOVA University of Lisbon, Almada, Portugal
Interests: microbiology; One Health; antimicrobial resistance; biofilms; microbial genetics; infectious diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The global rise of antimicrobial resistance (AMR) represents a critical public health challenge, threatening the effectiveness of existing therapies and the control of infectious diseases. The advent of whole-genome sequencing (WGS) and other genomic tools has revolutionized our ability to investigate the evolution, transmission, and persistence of multidrug-resistant (MDR) pathogens across human, animal, and environmental reservoirs. This Special Issue will gather original research and comprehensive reviews exploring genomic aspects of MDR pathogens, including, but not limited to, the identification of resistance genes, mobile genetic elements, virulence factors, and phylogenetic relationships.

We welcome studies focusing on genomic surveillance, One Health perspectives, and the role of horizontal gene transfer in resistance dissemination. Contributions involving emerging MDR clones, environmental and zoonotic reservoirs, and the integration of genomics into phenotypic data are particularly encouraged. This Special Issue will foster interdisciplinary collaboration and enhance our understanding of how MDR pathogens spread and evolve, ultimately supporting the development of effective containment and mitigation strategies.

Dr. Vanessa Silva
Dr. Gilberto Igrejas
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 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
  • genomic surveillance
  • MDR
  • gene transfer
  • One Health

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

Published Papers (2 papers)

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16 pages, 12268 KB  
Article
Whole-Genome Sequencing and Antibiotic Resistance Profiling of Helicobacter pylori Isolates from a Tertiary Hospital in Southern Thailand
by Chonticha Romyasamit, Apichat Kaewdech, Pimsiri Sripongpun, Naichaya Chamroonkul, Komwit Surachat, Sirikan Suwannasin, Yosita Leepromma, Morteza Saki, Maseetoh Samaeng and Phoomjai Sornsenee
Antibiotics 2025, 14(9), 944; https://doi.org/10.3390/antibiotics14090944 - 18 Sep 2025
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Abstract
Background: Helicobacter pylori is associated with a wide range of gastroduodenal diseases, including chronic gastritis, peptic ulcer disease, and gastric cancer. Eradication efforts are challenged by increasing antimicrobial resistance rates, particularly in Southeast Asia. We sequenced the whole genomes of clinical H. [...] Read more.
Background: Helicobacter pylori is associated with a wide range of gastroduodenal diseases, including chronic gastritis, peptic ulcer disease, and gastric cancer. Eradication efforts are challenged by increasing antimicrobial resistance rates, particularly in Southeast Asia. We sequenced the whole genomes of clinical H. pylori isolates from Southern Thailand to elucidate their resistance profiles, virulence determinants, and evolutionary relationships. Methods: Three clinical H. pylori isolates (004, 117, and 189) were subjected to whole-genome sequencing, phenotypic antimicrobial susceptibility testing, and comparative genomic analyses. Results: All strains exhibited high-level resistance to metronidazole. Additionally, H. pylori 117 was resistant to both amoxicillin and levofloxacin, classifying it as multidrug-resistant. Genomic analysis revealed mutations in rdxA, frxA, and rpoB, as well as in penicillin-binding protein genes (pbp2 and pbp3), supporting the phenotypic findings. While all isolates harboured clarithromycin resistance mutations (A2142G and A2143G in the 23S rRNA gene), they were phenotypically susceptible, highlighting a potential discordance that requires further investigation. Virulence gene profiling identified 115–118 conserved genes per strain, including cagA, vacA, oipA, babA, and flagellar, urease, and lipopolysaccharide biosynthesis genes. Phylogenetic analysis using core-genome single-nucleotide polymorphisms demonstrated that these strains formed a distinct Southern Thai monophyletic clade, suggesting localised clonal expansion driven by regional selective pressures. Conclusions: Region-specific surveillance strategies and treatment guidelines are urgently needed in Thailand. The combination of high-risk virulence genes and rising antimicrobial resistance in H. pylori strains necessitates tailored therapeutic approaches, the integration of genomic surveillance into clinical diagnostics, and expanded studies linking genotype to clinical outcomes in diverse populations. Full article
(This article belongs to the Special Issue Genomic Insights into Dissemination of Multi-Drug Resistance Pathogens)
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11 pages, 280 KB  
Case Report
Antimicrobial-Resistant Enteric Gram-Negative Bacteria Isolated from a Fatal Diarrhea in a Horse: Genomic Characterization of CTX-M-2-Producing Escherichia coli
by Gabriel Augusto Marques Rossi, Fábio Parra Sellera, Carolina Magri Ferraz, Renan Silva de Carvalho, Alvaro de Paula Lage de Oliveira, Camila Angela Marques, Enzo Bernardes Rocha Fávaro, Rafael da Silva Rosa, Leandro Augusto Mariano Silva, Marita Vedovelli Cardozo, Eliana Guedes Stehling and João Pedro Rueda Furlan
Antibiotics 2025, 14(12), 1185; https://doi.org/10.3390/antibiotics14121185 - 21 Nov 2025
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Abstract
Background: Infections caused by antimicrobial-resistant bacteria are difficult to treat and increase the risk of death in animals. This report describes a fatal case of diarrhea in a horse that, despite intensive treatment including surgery and broad-spectrum antimicrobials (ceftiofur and amikacin), experienced a [...] Read more.
Background: Infections caused by antimicrobial-resistant bacteria are difficult to treat and increase the risk of death in animals. This report describes a fatal case of diarrhea in a horse that, despite intensive treatment including surgery and broad-spectrum antimicrobials (ceftiofur and amikacin), experienced a worsening of its condition and subsequent death. Methods: A fecal swab sample was subjected to microbiological culture for the identification of bacteria and assessment of their phenotypical antimicrobial susceptibility profiles using the disk-diffusion and broth microdilution methods. The double-disk synergy test, polymerase chain reactions for the detection of genes encoding extended-spectrum β-lactamases, and whole-genome sequence-based analysis were also performed. Results: Strains of Salmonella enterica and Escherichia coli were isolated, with the E. coli strain DSL-HVUVV-2025 presenting resistance to a third-generation cephalosporin. Accordingly, the blaCTX-M-2 gene was identified in the DSL-HVUVV-2025 strain, which was submitted to whole-genome sequencing. Genomic analysis showed several antimicrobial resistance determinants, as well as virulence genes, including those associated with the enteroaggregative pathotype. The blaCTX-M-2 gene was surrounded by an ISCR1 element and embedded in a complex class 1 integron that is part of the Tn7337 transposon. Strain DSL-HVUVV-2025 belonged to a novel sequence type. Conclusions: This case highlights the importance of monitoring antimicrobial resistance and performing genomic characterization of bacteria involved in equine diarrhea to guide effective clinical management in veterinary hospitals. It also reinforces the role of horses as potential carriers of WHO critical priority pathogens and the need for responsible antimicrobial use. Full article
(This article belongs to the Special Issue Genomic Insights into Dissemination of Multi-Drug Resistance Pathogens)
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