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Antibiotics
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Drivers of Virulence and Antimicrobial Resistance in Emerging and Re-Emerging...
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Drivers of Virulence and Antimicrobial Resistance in Emerging and Re-Emerging Pathogens

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Genetic and Biochemical Studies of Antibiotic Activity and Resistance".

Deadline for manuscript submissions: 31 March 2026 | Viewed by 1761

Special Issue Editors

Dr. Opeyemi U. Lawal

E-Mail Website
Guest Editor
School of the Environment & Great Lakes Institute for Environmental Research (GLIER), University of Windsor, Windsor, ON N9B 3P4, Canada
Interests: AMR; microbiology; microbial ecology; pathogen dynamics; environmental and public health genomics; multi-omics; microbiome; microbial interactions; bioinformatics; AI/ML
Dr. Ons Bouchami

E-Mail Website
Guest Editor
Laboratory of Human Microbiota – Xenobiotics Interactions, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
Interests: AMR; microbiome; pathogen evolution; microbiology; xenobiotic interaction; public health; bioinformatics; genomics; multi-omics
Special Issues, Collections and Topics in MDPI journals
Dr. Ingrid Maria Cecilia Rubin

E-Mail Website
Guest Editor
Statens Serum Institut, Denmark & Copenhagen Microbiome Center, COPMICS, Hvidovre University Hospital, Hvidovre, Denmark
Interests: AMR; microbiome; clinical microbiology; host-pathogen interaction; public health; emerging infections

Special Issue Information

Dear Colleagues,

The rise of antimicrobial resistance (AMR) and virulence among emerging and re-emerging pathogens poses a significant threat to global health. AMR is not limited to human health or clinical settings, but spans diverse environments in which pathogens, hosts, and various ecological forces intersect. These "hotspots" for the evolution of resistance and virulence include healthcare facilities, agricultural settings, urban wastewater systems, soil matrices, and aquatic ecosystems. Understanding the complexity of these interactions necessitates an innovative approach that provides a holistic view of AMR and virulence dynamics. This Special Issue, entitled “Drivers of Virulence and Antimicrobial Resistance in Emerging and Re-Emerging Pathogens”, will explore the folliwng key areas: the ecological and environmental factors that contribute to the evolution and spread of pathogens with enhanced virulence and resistance profiles; the molecular and genetic mechanisms underlying virulence and AMR, including the role of mobile genetic elements, plasmids, and horizontal gene transfer; host–pathogen interactions that drive immune evasion and adaptation strategies; and innovative approaches that utilize advanced genomics tools, artificial intelligence, and machine learning technologies to monitor AMR hotspots and develop predictive models for understanding and mitigating this global threat. By addressing these critical aspects, this Special Issue aims to advance our understanding of the drivers of virulence and AMR, ultimately informing strategies to combat these urgent public health challenges.

Dr. Opeyemi U. Lawal
Dr. Ons Bouchami
Dr. Ingrid Maria Cecilia Rubin
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

  • AMR
  • microbial pathogenesis
  • microbial ecology
  • pathogen dynamics
  • genomic epidemiology
  • multiomics
  • microbial interactions
  • AI/ML

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Published Papers (3 papers)

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Research

15 pages, 2081 KB  
Article
Clinical and Environmental Plasmids: Antibiotic Resistance, Virulence, Mobility, and ESKAPEE Pathogens
by Célia P. F. Domingues, João S. Rebelo, Francisco Dionisio and Teresa Nogueira
Antibiotics 2026, 15(1), 29; https://doi.org/10.3390/antibiotics15010029 - 31 Dec 2025
Viewed by 316
Abstract
Background/Objectives: Plasmids are autonomous DNA molecules that can replicate independently and transfer horizontally between bacterial cells. They play a key role in disseminating adaptive traits, such as antimicrobial resistance and virulence. Our study investigates the fundamental differences between plasmid populations originating from clinical/isolates [...] Read more.
Background/Objectives: Plasmids are autonomous DNA molecules that can replicate independently and transfer horizontally between bacterial cells. They play a key role in disseminating adaptive traits, such as antimicrobial resistance and virulence. Our study investigates the fundamental differences between plasmid populations originating from clinical/isolates and environmental/metagenomes. Methods: We compare three distinct plasmid genome datasets—the NCBI Reference Sequence Database (RefSeq), the Integrated Microbial Genomes & Microbiomes system (IMG/PR) from bacterial isolates (I) and microbiomes (M)—to assess how plasmid origin shapes their characteristics, including mobility types, antimicrobial resistance genes (ARGs), virulence genes (VGs) and host taxonomy. Results: We show that plasmids originating from bacterial isolates, more enriched in clinical samples, are fundamentally distinct from recovered from metagenomic data. Plasmids from isolates are larger, enriched in conjugative plasmids and display a higher frequency of ARGs and VGs than the ones assembled from metagenomes. Furthermore, ARGs are more frequently associated with highly mobile plasmids, particularly pCONJ. Conclusions: These findings highlight the importance of plasmid origins in studies of plasmid epidemiology, functional potential and mobility. Full article
(This article belongs to the Special Issue Drivers of Virulence and Antimicrobial Resistance in Emerging and Re-Emerging Pathogens)
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14 pages, 898 KB  
Article
Occurrence of Virulence and Antibiotic Resistance in Pseudomonas aeruginosa Isolated from the Environmental Water from Tamaulipas, Mexico
by Jessica I. Licea-Herrera, Abraham Guerrero, Paulina Guel, Virgilio Bocanegra-García, Gildardo Rivera and Ana Verónica Martínez-Vázquez
Antibiotics 2025, 14(12), 1278; https://doi.org/10.3390/antibiotics14121278 - 17 Dec 2025
Viewed by 487
Abstract
Background/Objectives: Antibiotic-resistant strains have been reported in aquatic ecosystems, with varying prevalence and resistance patterns by region. In Tamaulipas, Mexico, little information has been generated on this topic, making it difficult to estimate their potential risk to environmental and human health. Therefore, the [...] Read more.
Background/Objectives: Antibiotic-resistant strains have been reported in aquatic ecosystems, with varying prevalence and resistance patterns by region. In Tamaulipas, Mexico, little information has been generated on this topic, making it difficult to estimate their potential risk to environmental and human health. Therefore, the objective of this study was to evaluate the presence and virulence of antibiotic-resistant strains of Pseudomonas aeruginosa in environmental water from Tamaulipas, Mexico. Methods: One hundred water samples were collected from different water bodies in Tamaulipas to identify P. aeruginosa by PCR and MALDI-TOF, virulence gene detection, antimicrobial susceptibility testing, and detection class 1 integrons. Results: In this study, 109 P. aeruginosa strains were isolated. Eight virulence genes were identified in 47.7% to 80.7% of the strains, with the rhlAB gene being the most frequent. The strains showed resistance or intermedia resistance to 10 of the 16 antibiotics tested, in a range of resistance values 0.9–66.2%. In total, 100% (109/109) were susceptible to ceftazidime (CAZ), gentamicin (GM), amikacin (AN), netilmicin (NET), tobramycin (NN) and norfloxacin (NOR), and 65.7% were resistant to ticarcillin/clavulanic acid and 53.5% to ticarcillin; the resistance to the remaining antibiotics was between 19.4% and 0.9%. The class 1 integron was not identified in any of the strains analyzed. Conclusions:P. aeruginosa in environmental waters of Tamaulipas showed potential to cause infections and low rates of resistance to most of the antibiotics tested. However, 20% were resistant to one of the most common treatments, which could pose a risk to public health. Full article
(This article belongs to the Special Issue Drivers of Virulence and Antimicrobial Resistance in Emerging and Re-Emerging Pathogens)
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15 pages, 2951 KB  
Article
Comparative Relatedness of Clostridioides difficile Strains Isolated from Humans and Companion Dogs in South Korea
by Joo Yeol Kim, Su Min Kwak, Jae Hong Jeong, Jae Young Oh, Kwang-Won Seo, Dongheui An, Dokyun Kim, Seok Hoon Jeong, Chang-Ki Kim, Kwang Jun Lee and Jong-Chan Chae
Antibiotics 2025, 14(12), 1231; https://doi.org/10.3390/antibiotics14121231 - 6 Dec 2025
Viewed by 439
Abstract
Background/Objectives: Clostridioides difficile is an anaerobic Gram-positive bacterium and a leading cause of healthcare-associated diarrhea. In this study, C. difficile strains isolated from human patients with diarrhea and companion dogs in South Korea were compared to reveal the potential transmission between different [...] Read more.
Background/Objectives: Clostridioides difficile is an anaerobic Gram-positive bacterium and a leading cause of healthcare-associated diarrhea. In this study, C. difficile strains isolated from human patients with diarrhea and companion dogs in South Korea were compared to reveal the potential transmission between different hosts. Methods: A total of 304 C. difficile strains were isolated, including 217 human isolates and 87 dog isolates. The strains were characterized for antimicrobial susceptibility and genotypic features, including antimicrobial resistant genes and toxin genes. In addition, comparative genomic analyses were performed to investigate their genetic relatedness. Results: Although antimicrobial susceptibility test revealed no significant difference in overall resistance, human isolates had higher resistance to moxifloxacin and cefotetan, while dog isolates showed slightly higher resistance to clindamycin and ampicillin. Resistance to vancomycin (3.7%), rifampin (8.3%), and chloramphenicol (0.9%) was observed only in human isolates. Toxin genes (tcdA and tcdB) were found in 57.1% of human isolates and 43.7% of dog isolates, while binary toxin genes (cdtA and cdtB) were detected only in isolates from humans. Multilocus sequence typing (MLST) analysis identified 34 sequence types (STs) in human isolates and 16 in dog isolates. Among them, 15 STs were detected in the isolates from both origins; notably, ST203 and ST42 were the predominant taxa that were equally derived from humans and dogs. Although tcdA and tcdB have not been previously reported in ST203, they were detected in 7 out of 34 ST203 isolates. The whole genomes of 36 representative isolates belonging to ST42 and ST203 were classified according to the STs of the source origin. Conclusions: These results indicate that similar C. difficile strain populations are present in both humans and companion dogs, which is compatible with interspecies dissemination or circulation of shared strain populations, and may also reflect host adaptation. Full article
(This article belongs to the Special Issue Drivers of Virulence and Antimicrobial Resistance in Emerging and Re-Emerging Pathogens)
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