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Toxics
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Antibiotics and Resistance Genes in Environment
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Antibiotics and Resistance Genes in Environment

A special issue of Toxics (ISSN 2305-6304). This special issue belongs to the section "Emerging Contaminants".

Deadline for manuscript submissions: 30 June 2026 | Viewed by 14624

Special Issue Editors

Dr. Fengxia Yang

E-Mail Website
Guest Editor
Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
Interests: emerging contaminants; antibiotic resistance genes; antimicrobial resistance; livestock farming; agricultural environment; risk assessment
Special Issues, Collections and Topics in MDPI journals
Dr. Shimei Zheng

E-Mail Website
Guest Editor
College of Chemistry and Chemical and Environmental Engineering, Weifang University, Weifang 261061, China
Interests: emerging contaminants; ecological risk; antibiotic; environmental toxicology; microplastics; soil environment

Special Issue Information

Dear Colleagues,

The emergence and spread of antibiotic resistance is one of the greatest threats to global public health. Antibiotics are widely used in human and veterinary medicine to treat bacterial infections, but their overuse and misuse have led to the development of resistant bacteria. Resistance genes can be transferred between bacteria, spreading antibiotic resistance rapidly and making it difficult to treat infections. In addition, antibiotics and resistance genes can enter the environment through various routes, such as wastewater discharge, agricultural runoff, and land application of manure, posing a potential risk to human health and the ecosystem. Understanding the sources, fate, and transport of these contaminants in the environment is crucial for developing effective strategies to mitigate their impact on human health and the ecosystem.

This Special Issue will focus on highlighting timely research studies addressing antibiotics and resistance genes in the environment. Authors are invited and welcome to submit original research papers, reviews, and short communications.

Topics may include, but are not limited, to the following:

(1) Studies on the occurrence, distribution, and persistence of antibiotics and resistance genes in various environmental matrices (e.g., water, soil, sediment, air);
(2) Investigation of the sources and pathways of antibiotic and resistance gene contamination in the environment;
(3) Development and application of novel detection methods for antibiotics and resistance genes;
(4) Assessment of the ecological and human health risks associated with antibiotic and resistance gene pollution;
(5) Evaluation of the effectiveness of mitigation strategies for reducing antibiotic and resistance gene levels in the environment;
(6) Insights into the mechanisms of antibiotic resistance development and spread in environmental settings;
(7) Studies on the interaction between antibiotics, resistance genes, and microbial communities in the environment.

Dr. Fengxia Yang
Dr. Shimei Zheng
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. Toxics 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 2600 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

  • antibiotics
  • antibiotic resistance genes
  • environmental fate
  • human health
  • ecosystem impact
  • risk assessment
  • mitigation strategies

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Published Papers (5 papers)

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Research

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22 pages, 3529 KB  
Article
Optimization of the Quantification of Antibiotic Resistance Genes in Media from the Yangtze River Estuary
by Jiadai Wu, Xinran Liu, Min Liu, Yawen Song, Qian Li, Jian Wang and Ye Huang
Toxics 2026, 14(2), 151; https://doi.org/10.3390/toxics14020151 - 2 Feb 2026
Viewed by 689
Abstract
Antibiotic resistance gene (ARG) monitoring in environmental systems increasingly relies on DNA-based molecular approaches; however, the extent to which DNA extraction strategies bias downstream resistome interpretation remains insufficiently understood. This study systematically evaluated the effects of single versus successive DNA extraction on DNA [...] Read more.
Antibiotic resistance gene (ARG) monitoring in environmental systems increasingly relies on DNA-based molecular approaches; however, the extent to which DNA extraction strategies bias downstream resistome interpretation remains insufficiently understood. This study systematically evaluated the effects of single versus successive DNA extraction on DNA recovery, microbial community composition, and the abundance and diversity of 385 genes related to antibiotic resistance including ARGs and mobile genetic elements (MGEs) across three contrasting matrices: water, sediment, and fish intestinal tissue. Successive extraction markedly increased DNA yield and detection of functional genes in water and sediment, particularly for low-abundance and particle-associated taxa. Enhanced recovery resulted in higher richness and abundance of ARGs and MGEs and strengthened correlations between intI1, ARGs, and bacterial taxa, indicating that single-cycle extraction may underestimate resistome magnitude and potential host associations in complex matrices. Conversely, fish intestinal tissue, used here as a representative biological matrix, showed limited benefit or even reduced gene abundance with repeated extraction, likely due to rapid depletion of extractable nucleic acids and DNA degradation. While successive extraction improves recovery efficiency, the potential inclusion of extracellular or relic DNA suggests caution in interpreting inflated ARG abundance. Overall, our findings demonstrate that DNA extraction is a matrix-dependent methodological driver that can reshape both quantitative outcomes and ecological inference. Matrix-specific optimization and careful protocol selection are therefore essential for improving data comparability and minimizing methodological underestimation in environmental resistome assessments. Full article
(This article belongs to the Special Issue Antibiotics and Resistance Genes in Environment)
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21 pages, 2443 KB  
Article
Quantification of Pharmaceuticals in Sludge Produced from Wastewater Treatment Plants in Jordan and Environmental Risk Assessment
by Othman Almashaqbeh, Christina Emmanouil and Layal Alsalhi
Toxics 2026, 14(1), 62; https://doi.org/10.3390/toxics14010062 - 8 Jan 2026
Viewed by 847
Abstract
Sewage sludge is increasingly recognized as a major reservoir for pharmaceuticals and emerging contaminants that are only partially removed by conventional wastewater treatment. This study provides the first comprehensive assessment of these contaminants in biosolids generated from ten major wastewater treatment plants (WWTPs) [...] Read more.
Sewage sludge is increasingly recognized as a major reservoir for pharmaceuticals and emerging contaminants that are only partially removed by conventional wastewater treatment. This study provides the first comprehensive assessment of these contaminants in biosolids generated from ten major wastewater treatment plants (WWTPs) across Jordan. Different pharmaceuticals were quantified in the sludge samples generated. The results revealed concentrations ranging from 10 to over 2000 µg kg−1, with antibiotics typically showing the highest enrichment (e.g., ciprofloxacin up to 2165 µg kg−1, ofloxacin up to 303 µg kg−1). Anti-inflammatory compounds such as diclofenac reached 196 µg kg−1, while the antimicrobial triclosan exceeded 4700 µg kg−1 in some sludge samples. Carbamazepine, a recalcitrant antiepileptic drug, ranged between 50 and 223 µg kg−1, reflecting both widespread use and strong persistence. Elevated levels of quaternary ammonium compounds (QACs) were also detected. The highest levels were generally associated with large urban WWTPs and plants receiving industrial discharges. Environmental risk assessment (ERA) indicated that the risk for soil biota was acceptable for most cases for low application doses (5–10 t/ha) except for WWTP6-MD, WWTP8-S, and WWTP9-IC, where the risk was non-acceptable. Severe limitations in the risk assessment were noted: reliable toxicity endpoints in terrestrial soil organisms such as microbiota, collembola, and earthworms are few, while deriving endpoints via aquatic available data is not always reliable. Overall, the findings demonstrate that Jordanian sewage sludge contains environmentally relevant levels of pharmaceuticals and QACs and that risk assessment is, therefore, pertinent before any stabilization and realistic land application scenarios are chosen. Full article
(This article belongs to the Special Issue Antibiotics and Resistance Genes in Environment)
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21 pages, 10443 KB  
Article
Contamination Characteristics of Antibiotic Resistance Genes in Multi-Vector Environment in Typical Regional Fattening House
by Kai Wang, Dan Shen, Zhendong Guo, Qiuming Zhong and Kai Huang
Toxics 2024, 12(12), 916; https://doi.org/10.3390/toxics12120916 - 18 Dec 2024
Cited by 2 | Viewed by 1639
Abstract
Antibiotic resistance genes (ARGs) are emerging as significant environmental contaminants, posing potential health risks worldwide. Intensive livestock farming, particularly swine production, is a primary contributor to the escalation of ARG pollution. In this study, we employed metagenomic sequencing and quantitative polymerase chain reaction [...] Read more.
Antibiotic resistance genes (ARGs) are emerging as significant environmental contaminants, posing potential health risks worldwide. Intensive livestock farming, particularly swine production, is a primary contributor to the escalation of ARG pollution. In this study, we employed metagenomic sequencing and quantitative polymerase chain reaction to analyze the composition of microorganisms and ARGs across four vectors in a typical swine fattening facility: dung, soil, airborne particulate matter (PM), and fodder. Surprisingly, soil and PM harbored a higher abundance of microorganisms and ARGs than dung. At the same time, fodder was more likely to carry eukaryotes. Proteobacteria exhibited the highest propensity for carrying ARGs, with proportions 9–20 times greater than other microorganisms. Furthermore, a strong interrelation among various ARGs was observed, suggesting the potential for cooperative transmission mechanisms. These findings underscore the importance of recognizing soil and PM as significant reservoirs of ARGs in swine facilities alongside dung. Consequently, targeted measures should be implemented to mitigate their proliferation, mainly focusing on airborne PM, which can rapidly disseminate via air currents. Proteobacteria, given their remarkable carrying capacity for ARGs with the primary resistance mechanism of efflux, represent a promising avenue for developing novel control strategies against antibiotic resistance. Full article
(This article belongs to the Special Issue Antibiotics and Resistance Genes in Environment)
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Review

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26 pages, 970 KB  
Review
A Review on the Degradation of Antibiotic Resistance Genes During Composting of Livestock Manure
by Enwang Zhao, Yongchao Li, Jin Zhang and Bing Geng
Toxics 2025, 13(8), 667; https://doi.org/10.3390/toxics13080667 - 8 Aug 2025
Cited by 3 | Viewed by 3692
Abstract
As emerging pollutants, antibiotic resistance genes (ARGs) have been recognized as originating from diverse sources. Among these, the use of livestock feed and veterinary drugs was identified as the primary source of ARGs in livestock manure. ARGs were found to be widely distributed [...] Read more.
As emerging pollutants, antibiotic resistance genes (ARGs) have been recognized as originating from diverse sources. Among these, the use of livestock feed and veterinary drugs was identified as the primary source of ARGs in livestock manure. ARGs were found to be widely distributed in global environments, particularly in agriculture-related soils, water bodies, and the atmosphere, posing potential threats to ecological environments and human health. This paper reviewed the degradation mechanisms of ARGs during aerobic composting of livestock manure and the safety evaluation of compost products. Aerobic composting was demonstrated to be an effective method for degrading ARGs, primarily through mechanisms such as high-temperature elimination of ARG-carrying microorganisms, reduction in host bacterial abundance, and inhibition of horizontal gene transfer. Factors including the physicochemical properties of the composting substrate, the use of additives, and the presence of antibiotic and heavy metal residues were shown to influence the degradation efficiency of ARGs, with compost temperature being the core factor. The safety of organic fertilizers encompassed multiple aspects, including heavy metal content, seed germination index, and risk assessments based on ARG residues. The analysis indicated that deficiencies existed in areas such as the persistence of thermotolerant bacteria carrying ARGs, the dissemination of extracellular antibiotic resistance genes (eARGs), and virus-mediated gene transfer. Future research should focus on (1) the removal of thermotolerant bacteria harboring ARGs; (2) the decomposition of eARGs or the blocking of their transmission pathways; (3) the optimization of ultra-high temperature composting parameters; and (4) the analysis of interactions between viruses and resistant hosts. This study reviews the mechanisms, influencing factors, and safety assessment of aerobic composting for degrading ARGs in livestock manure. It not only deepens the understanding of this important environmental biotechnology process but also provides a crucial knowledge base and practical guidance for effectively controlling ARG pollution, ensuring agricultural environmental safety, and protecting public health. Additionally, it clearly outlines the key paths for future technological optimization, thus holding significant implications for the environment, agriculture, and public health. Full article
(This article belongs to the Special Issue Antibiotics and Resistance Genes in Environment)
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19 pages, 1799 KB  
Review
Solutions to the Dilemma of Antibiotics Use in Livestock and Poultry Farming: Regulation Policy and Alternatives
by Shimei Zheng, Yongchao Li, Cuihong Chen, Naiyu Wang and Fengxia Yang
Toxics 2025, 13(5), 348; https://doi.org/10.3390/toxics13050348 - 27 Apr 2025
Cited by 24 | Viewed by 6886
Abstract
While the application of antibiotics in livestock production has undeniably propelled the rapid growth of animal husbandry, the escalating crisis of antimicrobial resistance stemming from antibiotic use poses significant threats to global public health and sustainable agricultural development. To address this critical challenge, [...] Read more.
While the application of antibiotics in livestock production has undeniably propelled the rapid growth of animal husbandry, the escalating crisis of antimicrobial resistance stemming from antibiotic use poses significant threats to global public health and sustainable agricultural development. To address this critical challenge, multifaceted strategies have been implemented through coordinated policy interventions and scientific innovations. This review systematically examines two pivotal dimensions: (1) evolving regulatory frameworks governing antibiotic usage and (2) emerging non-antibiotic alternatives, with a particular focus on their implementation mechanisms and technological maturation. The analysis of transnational antibiotic governance encompasses comparative policy evolution in the European Union, the United States, and China. These regulatory paradigms address critical control points including registration management policies, usage monitoring systems, and integrated surveillance programs. Concerning technological alternatives, six categories of antibiotic substitutes are critically evaluated: Chinese herbal formulations, plant-derived essential oils, antimicrobial peptides, microecological agents, acidifiers, and enzyme preparations. These solutions are functionally categorized into prophylactic agents (enhancing disease resilience) and zootechnical additives (optimizing feed efficiency). These antibiotic alternatives demonstrate certain efficacy in alleviating the challenges of antibiotic overuse, yet they still face multiple implementation barriers. Further investigations are warranted to establish standardized efficacy evaluation protocols and conduct technoeconomic feasibility assessments under commercial-scale production conditions. Ultimately, resolving the antibiotic dilemma requires synergistic collaboration between regulatory bodies, pharmaceutical innovators, and academic researchers. This work emphasizes the crucial interplay between evidence-based policymaking and technological advancement in shaping sustainable livestock production systems. Full article
(This article belongs to the Special Issue Antibiotics and Resistance Genes in Environment)
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