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Antibiotics
Special Issues
Origins and Evolution of Antibiotic Resistance in the Environment
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Origins and Evolution of Antibiotic Resistance in the Environment

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: closed (31 December 2025) | Viewed by 8312

Special Issue Editors

Dr. Damian Rolbiecki

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Guest Editor
European Regional Centre for Ecohydrology of the Polish Academy of Sciences, 90-364 Lodz, Poland
Interests: antibiotic resistance; environmental microbiology; WHO pathogens; surface water; wastewater
Dr. Małgorzata Czatzkowska

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Guest Editor
Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, 10-720 Olsztyn, Poland
Interests: anaerobic digestion; antibiotic resistance; soil; health hazard; wastewater treatment plant

Special Issue Information

Dear Colleagues,

Antimicrobial resistance (AMR) represents one of the most significant global threats and challenges to public health faced by humanity today. Extensive research on AMR conducted worldwide has demonstrated that antimicrobial resistance is a complex issue that requires a holistic approach, integrating insights from various scientific disciplines. The crisis of AMR has been linked to the concept of "One Health," which highlights the interconnectedness of human, animal, and environmental health. The "One Health" framework underscores the necessity of investigating potential pathways for the transmission and evolution of antimicrobial resistance  across the domains encompassed within "One Health". Investigating the dynamics of antibiotic resistant bacteria—encompassing their persistence, modes of transmission, and evolutionary adaptations across diverse environments—represents a pivotal and urgent research priority. Insights gained from such studies will be instrumental in developing effective strategies to mitigate the spread of AMR in the environment.

In this Special Issue, we aim to compile inspiring works that focus on the origins and evolution of AMR in the environment, with particular emphasis on the following themes:

  • Analysis of transmission pathways for antimicrobial-resistant bacteria and resistance determinants into natural environments, as well as their transfer from the environment to humans and animals.
  • Persistence, variability, and evolution of clinically relevant antimicrobial-resistant pathogens in natural settings, such as surface waters and soils.
  • Dynamics and ecological aspects of resistance dissemination within and between ecosystems.
  • Exploratory studies uncovering bacteria and resistance determinants in underexplored or pristine environments.
  • Strategies to limit the evolution and transmission of AMR through environmental vectors.

This Special Issue seeks to advance the understanding of the complex interactions driving the development and spread of AMR in environmental contexts, and also contribute to the identification of action directions for preventing further AMR progress.

Dr. Damian Rolbiecki
Dr. Małgorzata Czatzkowska
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

  • surface water
  • soil
  • wastewater
  • antibiotic resistance genes
  • antibiotic resistant bacteria
  • One Health
  • WHO pathogens
  • anthropogenic pressure

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Published Papers (3 papers)

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Research

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24 pages, 3176 KB  
Article
Influence of Seasonality and Pollution on the Presence of Antibiotic Resistance Genes and Potentially Pathogenic Bacteria in a Tropical Urban River
by Kenia Barrantes-Jiménez, Bradd Mendoza-Guido, Eric Morales-Mora, Luis Rivera-Montero, José Montiel-Mora, Luz Chacón-Jiménez, Keilor Rojas-Jiménez and María Arias-Andrés
Antibiotics 2025, 14(8), 798; https://doi.org/10.3390/antibiotics14080798 - 5 Aug 2025
Cited by 4 | Viewed by 3169
Abstract
Background/Objectives: This study examines how seasonality, pollution, and sample type (water and sediment) influence the presence and distribution of antibiotic resistance genes (ARGs), with a focus on antibiotic resistance genes (ARGs) located on plasmids (the complete set of plasmid-derived sequences, including ARGs) in [...] Read more.
Background/Objectives: This study examines how seasonality, pollution, and sample type (water and sediment) influence the presence and distribution of antibiotic resistance genes (ARGs), with a focus on antibiotic resistance genes (ARGs) located on plasmids (the complete set of plasmid-derived sequences, including ARGs) in a tropical urban river. Methods: Samples were collected from three sites along a pollution gradient in the Virilla River, Costa Rica, during three seasonal campaigns (wet 2021, dry 2022, and wet 2022). ARGs in water and sediment were quantified by qPCR, and metagenomic sequencing was applied to analyze chromosomal and plasmid-associated resistance profiles in sediments. Tobit and linear regression models, along with multivariate ordination, were used to assess spatial and seasonal trends. Results: During the wet season of 2021, the abundance of antibiotic resistance genes (ARGs) such as sul-1, intI-1, and tetA in water samples decreased significantly, likely due to dilution, while intI-1 and tetQ increased in sediments, suggesting particle-bound accumulation. In the wet season 2022, intI-1 remained low in water, qnrS increased, and sediments showed significant increases in tetQ, tetA, and qnrS, along with decreases in sul-1 and sul-2. Metagenomic analysis revealed spatial differences in plasmid-associated ARGs, with the highest abundance at the most polluted site (Site 3). Bacterial taxa also showed spatial differences, with greater plasmidome diversity and a higher representation of potential pathogens in the most contaminated site. Conclusions: Seasonality and pollution gradients jointly shape ARG dynamics in this tropical river. Plasmid-mediated resistance responds rapidly to environmental change and is enriched at polluted sites, while sediments serve as long-term reservoirs. These findings support the use of plasmid-based monitoring for antimicrobial resistance surveillance in aquatic systems. Full article
(This article belongs to the Special Issue Origins and Evolution of Antibiotic Resistance in the Environment)
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Review

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27 pages, 3905 KB  
Review
Silent Threat Evolution: Critically Important Carbapenem and Colistin Resistance Genes in the Natural Aquatic Environment
by Małgorzata Czatzkowska and Damian Rolbiecki
Antibiotics 2026, 15(2), 113; https://doi.org/10.3390/antibiotics15020113 - 23 Jan 2026
Cited by 2 | Viewed by 1485
Abstract
The rise in antimicrobial resistance (AMR) among the most clinically significant bacteria presents a global threat. The coexistence of resistance mechanisms to both carbapenems and colistin is particularly concerning, as these are last-line treatments, specifically reserved for the most challenging infections caused by [...] Read more.
The rise in antimicrobial resistance (AMR) among the most clinically significant bacteria presents a global threat. The coexistence of resistance mechanisms to both carbapenems and colistin is particularly concerning, as these are last-line treatments, specifically reserved for the most challenging infections caused by clinically multidrug-resistant Enterobacterales. Natural aquatic environments have become environmental reservoirs for the transmission of AMR, particularly concerning mechanisms against these two types of critically important drugs. The crucial role of environmental settings as a driving force for the spread and evolution of AMR associated with these drugs is underestimated, and scientific knowledge on this topic is limited. This review aims to fill an important gap in the scientific literature and comprehensively consolidate the available data on carbapenem- and colistin-associated AMR in the aquatic environment. This study provides a comprehensive synthesis of the current knowledge by integrating bibliographic data with a detailed genomic analysis of 278 bacterial genomes sourced from natural waters. It explores the distribution of carbapenemase and mobile colistin resistance (mcr) genes, identifying their hosts, geographical spread, and complex gene–plasmid–host associations. This review distinguishes two critical host groups for genes that provide resistance to last-resort drugs, Enterobacterales and autochthonous aquatic microbiota, highlighting both confirmed and potential interactions between them. Crucially, genomic analysis highlights the alarming co-occurrence of carbapenem and colistin resistance in single cells and on single plasmids, contributing to the spread of multidrug resistance phenotypes. These findings clearly indicate that aquatic environments are not merely passive recipients but active, evolving hubs for high-risk AMR determinants. Future research should focus on the interplay between allochthonous vectors and autochthonous microbiota to better understand the long-term stabilization of carbapenemase and mcr genes. Such efforts, combined with advanced sequencing technologies, are essential to ensure that carbapenems and colistin remain viable treatment options in clinical settings. Full article
(This article belongs to the Special Issue Origins and Evolution of Antibiotic Resistance in the Environment)
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51 pages, 1350 KB  
Review
Enrichment of Antibiotic Resistance Genes on Plastic Waste in Aquatic Ecosystems, Aquatic Animals, and Fishery Products
by Franca Rossi, Serena Santonicola and Giampaolo Colavita
Antibiotics 2025, 14(11), 1106; https://doi.org/10.3390/antibiotics14111106 - 2 Nov 2025
Cited by 6 | Viewed by 3008
Abstract
This comprehensive review compiles current knowledge about the connection between plastic waste and the selection and transmission of antibiotic resistance genes (ARGs) in aquatic ecosystems, which can result in ARG contamination of fishery products—a significant source of microplastic (MP) introduction into the food [...] Read more.
This comprehensive review compiles current knowledge about the connection between plastic waste and the selection and transmission of antibiotic resistance genes (ARGs) in aquatic ecosystems, which can result in ARG contamination of fishery products—a significant source of microplastic (MP) introduction into the food chain. Plastic debris in aquatic environments is covered by a biofilm (the plastisphere) in which antibiotic-resistant bacteria (ARB) are selected and horizontal gene transfer (HGT) of ARGs is facilitated. The types of plastic waste considered in this study for their role in ARG enrichment are mainly microplastics (MPs), and also nanoplastics (NPs) and macroplastics. Studies regarding freshwaters, seawaters, aquaculture farms, and ARG accumulation favored by MPs in aquatic animals were considered. Most studies focused on the identification of the microbiota and its correlation with ARGs in plastic biofilms, while a few evaluated the effect of MPs on ARG selection in aquatic animals. A higher abundance of ARGs in the plastisphere than in the surrounding water or natural solid substrates such as sand, rocks, and wood was repeatedly reported. Studies regarding aquatic animals showed that MPs alone, or in association with antibiotics, favored the increase in ARGs in exposed organisms, with the risk of their introduction into the food chain. Therefore, reducing plastic pollution in water bodies and aquaculture waters could mitigate the ARG threat. Further investigations focused on ARG selection in aquatic animals should be conducted to better assess health risks and increase awareness of this ARG transmission route, enabling the adoption of appropriate countermeasures. Full article
(This article belongs to the Special Issue Origins and Evolution of Antibiotic Resistance in the Environment)
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