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Antibiotics
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Antibiotics and Antibiotic Resistance Genes in the Environment: Transmission, Fate...
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Antibiotics and Antibiotic Resistance Genes in the Environment: Transmission, Fate and Mitigation Strategies

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

Deadline for manuscript submissions: 31 December 2026 | Viewed by 5839

Special Issue Editors

Dr. Yongzhen Ding

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Guest Editor
Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
Interests: antibiotics residue; antibiotic resistance genes; drug-resistant bacteria; polymicrobial interaction
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Zulin Zhang

E-Mail Website
Guest Editor
The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
Interests: environmental geochemical behavior; effect and risk assessment of organic contaminants; developing new analytical and monitoring techniques
Special Issues, Collections and Topics in MDPI journals
Dr. Hui Lin

E-Mail Website
Guest Editor
Institute of Environment, Resource, Soil & Fertilizer, Zhejiang Academy of Agriculture Sciences, Hangzhou 310021, China
Interests: agricultural waste treatment; antimicrobial resistance; emerging organic contaminants; biodegradation and bioremediation; biogeochemical cycling and microbial processes
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The widespread use of antibiotics in agriculture—primarily to promote growth, prevent disease, and treat infections in livestock and aquaculture—has made the agro-environment a critical hotspot for the dissemination of antibiotic resistance. Although antibiotics play an essential role in safeguarding animal health and ensuring food security, their release into the environment via manure application, wastewater irrigation, and surface runoff poses a serious threat to global public health. This environmental reservoir of antibiotics and antibiotic resistance genes (ARGs) creates continuous selection pressure, fostering the enrichment of resistant bacteria and facilitating the horizontal transfer of ARGs to human pathogens.

This Special Issue of Antibiotics seeks to gather high-quality research and review articles that address the complex challenges associated with antibiotics and antibiotic resistance genes in the environment. We aim to advance understanding of the full lifecycle of antibiotics—from their use and environmental fate to their ecological impacts and the development of resistance. Particular emphasis will be placed on innovative strategies for monitoring, risk assessment, and mitigation. By integrating insights from diverse disciplines, this Special Issue aspires to inform sustainable agricultural practices and policy development, ultimately helping preserve the effectiveness of existing antibiotics for future generations.

Prof. Dr. Yongzhen Ding
Dr. Zulin Zhang
Dr. Hui Lin
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

  • antibiotic resistance genes (ARGs)
  • veterinary antibiotic
  • manure and soil amendment
  • horizontal gene transfer
  • one health
  • environmental impact assessment
  • biodegradation and bioremediation
  • antimicrobial stewardship in agriculture
  • emerging contaminants

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Published Papers (5 papers)

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Research

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25 pages, 3955 KB  
Article
Root Exudates Are Linked to Antibiotic Resistance Gene Variation by Modulating Rhizosphere Microbial Community Assembly Under Swine Wastewater Irrigation
by Liwei Liu, Meng Wang, Xiuzhi Wang, Yuan Liu and Zhongyang Li
Antibiotics 2026, 15(5), 444; https://doi.org/10.3390/antibiotics15050444 - 29 Apr 2026
Viewed by 362
Abstract
Background: Irrigation with swine wastewater may increase the dissemination risk of antibiotic resistance genes (ARGs) in the rhizosphere and alter root exudate composition. However, the relationship between root exudates and ARG dynamics under swine wastewater irrigation remains poorly understood. This study therefore [...] Read more.
Background: Irrigation with swine wastewater may increase the dissemination risk of antibiotic resistance genes (ARGs) in the rhizosphere and alter root exudate composition. However, the relationship between root exudates and ARG dynamics under swine wastewater irrigation remains poorly understood. This study therefore aimed to clarify how root exudates are connected with ARG dynamics under swine wastewater irrigation. Methods: To address this, untargeted metabolomics and metagenomic sequencing were combined to characterize rhizosphere ARG composition, microbial community structure, and root exudate profiles in different soybean cultivars under swine wastewater irrigation. Results: The results showed that irrigation water source and soybean cultivar were associated with variation in soil ARG composition and changes in plant root metabolic profiles. Under wastewater irrigation, the relative abundances of secondary metabolites in root exudates were generally elevated, particularly those of organic nitrogen compounds and organic oxygenated compounds. Cultivar-related variation remained evident in rhizosphere microbial communities and ARG profiles, and differences in exudate composition among cultivars became smaller. Irrigation water source and soybean cultivar were associated with changes in ARG dynamics. This association was mainly linked to variation in rhizosphere microbial community structure rather than direct effects of root exudates on ARGs. Xanthine and 3-isobutylpentanedioic acid, identified as key root exudates, increased under wastewater irrigation and were related to variation in the potential ARG host genus SCGC-AG-212-J23 and the related ARGs. In contrast, 5-methylheptan-3-one decreased under wastewater irrigation and was correlated with variation in SCGC-AG-212-J23, Gp6-AA40, and the related ARGs. Conclusions: Swine wastewater irrigation and soybean cultivar altered root metabolism, which were linked to variation in rhizosphere microbial communities. These changes may have collectively contributed to shifts in rhizosphere ARGs. This could provide a basis for understanding the ecological relationships among root exudates, microorganisms, and ARGs under swine wastewater irrigation. Full article
(This article belongs to the Special Issue Antibiotics and Antibiotic Resistance Genes in the Environment: Transmission, Fate and Mitigation Strategies)
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21 pages, 3389 KB  
Article
In Situ Electrochemically Generating High-Valent Iron Species Activated by Nitrogen-Doped Biochar for Efficient Degradation of Antibiotics
by Yuhang Lin, Anting Ding, Zhikang Deng, Ya-Nan Zhang, Chenyu Zeng, Fuyu Xie, Yumu Luo, Minle Li, Junwei Ma and Zulin Zhang
Antibiotics 2026, 15(3), 254; https://doi.org/10.3390/antibiotics15030254 - 1 Mar 2026
Viewed by 655
Abstract
Background: Traditional methods exhibit an extremely low removal efficiency for antibiotics in water, making an efficient and energy-saving approach urgently needed. Methods and Results: In this study, a novel catalytic approach based on the in situ generation of high-valent iron (Fe(IV)/Fe(V)) has been [...] Read more.
Background: Traditional methods exhibit an extremely low removal efficiency for antibiotics in water, making an efficient and energy-saving approach urgently needed. Methods and Results: In this study, a novel catalytic approach based on the in situ generation of high-valent iron (Fe(IV)/Fe(V)) has been developed by adding biochar instead of modifying the electrode materials (in previous studies) for the efficient removal of sulfamethoxazole (SMX) from water. Fe(IV)/Fe(V) was produced by the anodic oxidation of low concentrations of Fe(III) and subsequently activated by nitrogen-doped corn stalk biochar (NBC). The results showed that the degradation efficiency increased from 50.83% to 90.67% within 60 min after the addition of nitrogen-modified biochar. The abundant defect structures, graphitic N and oxygen-containing functional groups in NBC endowed the catalyst with excellent activation capability. Quenching experiments and methyl phenyl sulfoxide (PMSO) probe experiments revealed that singlet oxygen (1O2) and Fe(IV)/Fe(V) were the main contributors to SMX degradation. Degradation pathways were inferred based on transformation products (TPs) and density functional theory (DFT) calculations. Ecotoxicity prediction using the ECOSAR program indicated that the TPs formed in the E/Fe(III)/NBC system exhibited markedly lower toxicity to aquatic organisms than the parent SMX. Furthermore, the E/Fe(III)/NBC system maintained a high degradation efficiency for SMX in real aquatic environments. Additionally, the E/Fe(III)/NBC system showed high removal rates for other sulfonamides such as sulfadiazine (SDZ), sulfamethoxypyridazine (SMP), sulfathiazole (STZ) and sulfadoxine (SDX). Conclusions: Overall, the E/Fe(III)/NBC system was demonstrated to be a highly efficient and sustainable technology for removing various antibiotics from water. Full article
(This article belongs to the Special Issue Antibiotics and Antibiotic Resistance Genes in the Environment: Transmission, Fate and Mitigation Strategies)
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17 pages, 5155 KB  
Article
Plasmid-Mediated Spread of Antibiotic Resistance by Arsenic and Microplastics During Vermicomposting
by Rui Xin, Huai Lin, Zijun Li and Fengxia Yang
Antibiotics 2025, 14(12), 1230; https://doi.org/10.3390/antibiotics14121230 - 6 Dec 2025
Viewed by 1206
Abstract
Background: The efficiency of vermicomposting in reducing antibiotic resistance genes (ARGs) in dairy manure may be compromised by co-pollutants like arsenic (As) and microplastics. Specifically, plasmids serving as carriers and vectors of ARGs were largely distributed in this process. However, the impact of [...] Read more.
Background: The efficiency of vermicomposting in reducing antibiotic resistance genes (ARGs) in dairy manure may be compromised by co-pollutants like arsenic (As) and microplastics. Specifically, plasmids serving as carriers and vectors of ARGs were largely distributed in this process. However, the impact of As and microplastics on plasmids carrying ARGs during vermicomposting is largely unknown. Methods: This study utilized a controlled experimental design and applied plasmid metagenomics to investigate the individual and combined effects of As and polyethylene terephthalate (PET) microplastics on plasmid-mediated ARG dynamics during vermicomposting. Results: We found that vermicomposting alone mainly enriched non-mobilizable plasmids, while PET microplastics selectively promoted conjugative and mobilizable plasmids, whereas As significantly increased all plasmid types. Moreover, both PET or As alone and combined exposure (PET and As) increased total ARG abundance, with their combination inducing synergistic ARG enrichment despite unchanged total plasmid abundance. Furthermore, co-occurrence network analysis combined with ARGs/plasmid ratio assessments demonstrated that As influences ARGs through co-selective pressure by enriching ARGs co-localized with As resistance genes (e.g., the ars operon) on plasmids while simultaneously promoting horizontal gene transfer (HGT) via activation of oxidative stress and SOS response pathways. In contrast, PET primarily facilitates ARG dissemination through a “metabolism-resistance” coupling strategy by enriching colonizing bacteria with PET-degrading capacity. Their co-exposure formed As-enrichment hotspots on PET microplastic surfaces, functioning as a “super-mixer” that selectively screened for superbugs carrying potent resistance mechanisms (e.g., blaOXA-50 and mdtB/mdtE). Conclusions: This study provides the first plasmidome-level evidence of synergistic ARG propagation by As and PET microplastics during vermicomposting, highlighting mobile genetic elements’ critical role in co-pollutant risk assessments. Full article
(This article belongs to the Special Issue Antibiotics and Antibiotic Resistance Genes in the Environment: Transmission, Fate and Mitigation Strategies)
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Review

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23 pages, 1493 KB  
Review
Research Progress and Prospects of Modified Biochar in the Adsorption and Degradation of Sulfonamide Antibiotics
by Junjie Wang, Yingxia Hou, Xue Li, Ran Zhao, Xiaoquan Mu, Yifan Liu, Chengcheng Huang, Frank Fu and Fengxia Yang
Antibiotics 2026, 15(3), 268; https://doi.org/10.3390/antibiotics15030268 - 4 Mar 2026
Cited by 1 | Viewed by 1479
Abstract
Sulfonamide antibiotics (SAs) are ubiquitous and persistent organic contaminants in aquatic and soil ecosystems due to their extensive application and high structural stability, causing rising environmental hazards. Conventional treatment approaches, generally based on physical adsorption or biological processes, remain limited in achieving efficient [...] Read more.
Sulfonamide antibiotics (SAs) are ubiquitous and persistent organic contaminants in aquatic and soil ecosystems due to their extensive application and high structural stability, causing rising environmental hazards. Conventional treatment approaches, generally based on physical adsorption or biological processes, remain limited in achieving efficient and stable removal as well as deep molecular modification of SAs. In recent years, modified biochar has developed as a flexible environmental functional material incorporating adsorption and reaction regulation capabilities, owing to its customizable pore structure, surface chemistry, and electronic characteristics. This study comprehensively highlights current achievements in the adsorption and degradation of sulfonamide antibiotics by modified biochar, with specific emphasis on modification techniques, structural modulation, structure–performance connections, and interfacial reaction processes. Through physical activation, heteroatom doping, defect engineering, and metal integration, biochar has developed from a traditional adsorbent into a carbon-based interfacial reactor capable of pollutant adsorption, molecular activation, and directed transformation. Surface-confined reaction interfaces, where π–π interactions, hydrogen bonding, electrostatic interactions, and metal coordination cooperatively control adsorption and transformation processes, are primarily responsible for the elimination of SAs. Moreover, the dual functions of modified biochar in driving both radical and non-radical pathways are explored, showing the vital importance of interfacial electronic structure modulation and electron-transfer mechanisms in influencing reaction efficiency and selectivity. The impact of sulfonamide molecular configurations, ambient circumstances, and concomitant chemicals on removal performance are also explored. Unlike previous reviews that mainly summarize adsorption efficiency or oxidant activation systems separately, this work integrates structural modulation, interfacial electronic regulation, and bond-selective transformation mechanisms into a unified structure–chemistry–reactivity framework. By correlating sulfonamide molecular configuration with biochar electronic structure, this review provides a mechanistic roadmap for the rational design of next-generation catalytic biochar systems. Finally, key challenges related to structural controllability, long-term stability, and engineering scalability are identified, and future research directions are proposed to support the rational design of high-performance biochar materials and the practical control of sulfonamide antibiotic pollution. Full article
(This article belongs to the Special Issue Antibiotics and Antibiotic Resistance Genes in the Environment: Transmission, Fate and Mitigation Strategies)
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27 pages, 1481 KB  
Review
Exploring the Relationship Between Farmland Management and Manure-Derived Antibiotic Resistance Genes and Their Prevention and Control Strategies
by Chengcheng Huang, Yuanye Zeng, Fengxia Yang, Qixin Wu and Yongzhen Ding
Antibiotics 2025, 14(11), 1117; https://doi.org/10.3390/antibiotics14111117 - 5 Nov 2025
Cited by 1 | Viewed by 1499
Abstract
Background/Objectives: The application of manure introduces antibiotic resistance genes (ARGs) into farmland, posing a significant public health risk. While tillage and fertilization practices are known to influence soil ecosystems, a systematic synthesis of how tillage patterns specifically regulate the fate of manure-derived ARGs [...] Read more.
Background/Objectives: The application of manure introduces antibiotic resistance genes (ARGs) into farmland, posing a significant public health risk. While tillage and fertilization practices are known to influence soil ecosystems, a systematic synthesis of how tillage patterns specifically regulate the fate of manure-derived ARGs is lacking. Methods: This review bridges this critical knowledge gap by systematically analyzing the interactions between conventional/conservation tillage and the distribution, persistence, and transmission of these ARGs. Results: It is observed that conservation tillage (e.g., no tillage), while beneficial for soil health, can lead to ARG accumulation at the soil surface, potentially increasing runoff risks, whereas conventional tillage promotes vertical mixing and dilution. A key unique contribution of this review is the systematic comparison of conventional versus conservation tillage, revealing quantitative reductions in ARG abundance. under practices like no till or deep plowing. Conclusions: We further con-solidate and propose integrated management strategies, combining precision agriculture, optimized fertilization, and scientific soil management, to mitigate ARG pollution. This work provides a targeted framework for developing more effective intervention measures to ensure agricultural sustainability and safeguard human health. Full article
(This article belongs to the Special Issue Antibiotics and Antibiotic Resistance Genes in the Environment: Transmission, Fate and Mitigation Strategies)
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