Antibiotic Resistance in Agricultural Environments: Emergence, Drivers and Mitigation

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Antibiotics in Animal Health".

Deadline for manuscript submissions: 30 June 2026 | Viewed by 1583

Special Issue Editors


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Guest Editor
1. National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
2. MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
Interests: antimicrobial resistance mechanism; zoonotic pathogen; antimicrobial resistance control strategy; multi-epitope vaccine against bacterial pathogen

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Guest Editor
Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
Interests: One Health; animal-derived food safety; bacterial resistance; bacterial pathogenicity; veterinary biological products

Special Issue Information

Dear Colleagues,

The emergence and spread of antibiotic resistance (AMR) in agricultural environments, especially in animal husbandry, poses a significant threat to both veterinary and public health. Excessive use of antibiotics in intensive farming practices has long been recognized as a key driver of AMR. However, increasing evidence implicates the role of non-antibiotic stressors such as heavy metals, biocides, feed additives, microplastics, etc., in the co-selection and persistence of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in various ecosystems.

Agricultural environments serve as hotspots and important reservoirs of horizontal gene transfer, facilitating the dissemination of diverse resistance determinants like ARGs across microbial communities. Thus, this Special Issue invites manuscript submissions that further our understanding regarding the ecological and evolutionary dynamics of AMR in animal-associated microbiomes. Topics of interest include, but are not limited to:

  1. The impact of selective pressures from antibiotics and non-antibiotics on AMR dynamics;
  2. Mechanistic insights into the emergence, persistence, and dissemination of ARB and ARGs in agricultural environments, especially animal-associated environments;
  3. Innovative strategies for mitigation and improved surveillance under a One Health Framework.

Dr. Guyue Cheng
Dr. Juan Wang
Guest Editors

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Keywords

  • antibiotic resistance (AMR)
  • animal husbandry
  • environmental resistome
  • livestock microbiome
  • co-selection
  • agricultural environments
  • One Health
  • antibiotic resistance genes (ARGs)
  • heavy metals
  • selective pressures

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Published Papers (2 papers)

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Research

22 pages, 5374 KB  
Article
Matrine Restores Porcine-Origin β-Lactam-Resistant Escherichia coli to Cefepime and Cefquinome: Association with Impaired Biofilm Formation and β-Lactamase Production
by Bo Yang, Wen Yang, Bingyan Hu, Jingchao Zhao, Hui Deng, Lingxian Yi, Penghua Jian, Zelin Hong and Daojin Yu
Antibiotics 2026, 15(5), 494; https://doi.org/10.3390/antibiotics15050494 - 14 May 2026
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Abstract
Background: The in vivo efficacy and mechanisms of matrine (MT) in reversing β-lactam resistance in E. coli remain unclear. Methods: β-lactam-resistant E. coli strains were treated with MT both in vitro and in a murine intestinal colonization model. Phenotypic changes (MIC, morphology, [...] Read more.
Background: The in vivo efficacy and mechanisms of matrine (MT) in reversing β-lactam resistance in E. coli remain unclear. Methods: β-lactam-resistant E. coli strains were treated with MT both in vitro and in a murine intestinal colonization model. Phenotypic changes (MIC, morphology, growth, biofilm, β-lactamase) were evaluated, and transcriptomic profiles were analyzed. Results: MT at sub-inhibitory concentrations significantly and concentration-dependently reduced the MICs of β-lactam-resistant E. coli strains by 2- to 32-fold in vitro. This reduction was also confirmed in vivo, and its magnitude became more pronounced as the number of doses increased. MT treatment dispersed bacterial aggregates and dissipated extracellular matrix, but did not alter the morphology of individual bacteria. At concentrations above 1024 μg/mL, MT significantly inhibited bacterial growth; lower concentrations (≤512 μg/mL) had no effect. Notably, MT inhibited biofilm formation and β-lactamase production both in vitro and in vivo. Conclusions: MT restored the susceptibility of β-lactam-resistant E. coli to cefepime and cefquinome. This effect was associated with suppression of biofilm formation and β-lactamase production, which correlated with the downregulation of key genes (ycgR, pgaB, pgaD, blaTEM and blaCTX-M). Full article
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11 pages, 7598 KB  
Article
ICECleSHZ29: Novel Integrative and Conjugative Element (ICE)-Carrying Tigecycline Resistance Gene tet(X6) in Chryseobacterium lecithinasegens
by Xi Chen, Yifei Zhang, Chunling Jiang, Yafang Lin, Xiaohui Yao, Wansen Nie, Lin Li, Jianchao Wei, Donghua Shao, Ke Liu, Zongjie Li, Yafeng Qiu, Zhiyong Ma, Beibei Li and Lining Xia
Antibiotics 2025, 14(10), 1002; https://doi.org/10.3390/antibiotics14101002 - 10 Oct 2025
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Abstract
Background/Objectives: The global dissemination of tet(X) variants critically threatens tigecycline efficacy as a last-resort antibiotic. The aim of this study was to characterize a tet(X6)-carrying integrative and conjugative element (ICE) in a multidrug-resistant Chryseobacterium lecithinasegens strain, SHZ29, isolated from Shanghai, China. [...] Read more.
Background/Objectives: The global dissemination of tet(X) variants critically threatens tigecycline efficacy as a last-resort antibiotic. The aim of this study was to characterize a tet(X6)-carrying integrative and conjugative element (ICE) in a multidrug-resistant Chryseobacterium lecithinasegens strain, SHZ29, isolated from Shanghai, China. Methods: Minimum inhibitory concentrations (MICs) were determined by broth microdilution for SHZ29. Whole genomic sequencing and bioinformatic analysis were performed to depict the structure of the novel tet(X6)-carrying ICE. Inverse PCR and conjugation experiments were conducted to investigate the transfer ability of the ICE. Results: We depicted a novel tet(X6)-carrying ICE, named ICECleSHZ29, which is 74,906 bp in size and inserted into the 3′ end of tRNA-Met-CAT gene of the C. lecithinasegens strain SHZ29, with 17 bp direct repeats (5′-tcccgtcttcgctacaa-3′). This ICE possesses a 38 kb conserved backbone and four variable regions (VR1-4), with VR3 aggregating multiple resistance genes, including tet(X6), tet(X2), erm(F), ere(D), floR, catB, sul2, ant(6)-I and blaOXA-1327. NCBI database searching identified 13 additional ICEs sharing a similar backbone to ICECleSHZ29. These ICECleSHZ29-like ICEs could be classified into two types based on their distinct insertion sites: Type I, inserted at the tRNA-Met-CAT gene; and Type II, inserted at the tRNA-Glu-TTC gene. Phylogenetic analysis indicated that differences in integrases may result in differences in the insertion site among these ICEs. A circular intermediate form of ICECleSHZ29 was detected by inverse PCR. However, the conjugation experiments using Escherichia coli EC600 as recipients failed. Conclusions: To our knowledge, this study provides the first report of tet(X6) in C. lecithinasegens and characterizes its carrier, a novel ICE: ICECleSHZ29. Full article
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