Distribution, Sources and Risks of Bacteria and Their Antimicrobial Resistance Genes in the Environment, 2nd Edition

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: 30 April 2026 | Viewed by 512

Special Issue Editors


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Guest Editor
Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 80-233 Gdansk, Poland
Interests: environmental microbiology; antibiotic resistance genes (ARGs); micropollutants; water treatment; detection and monitoring of pharmaceutical‑resistant bacteria in diverse environmental niches

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Guest Editor
Genetics and Marine Biotechnology Department, Institute of Oceanology of the Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
Interests: environmental microbiology; antibiotic resistance genes; marine microbiology; Vibrio spp.; integrons’ antibiotic action; Aeromonas spp.

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Guest Editor
Leeds Institute of Medical Research, St James Campus, University of Leeds, Leeds, UK
Interests: metagenomics; metatranscriptomics; bioinformatics; biostatistics; microbiome

Special Issue Information

Dear Colleagues,

Following the success of the first volume of this Special Issue, we are pleased to launch the second edition, entitled “Distribution, Sources and Risks of Bacteria and Their Antimicrobial Resistance Genes in the Environment, 2nd Edition”.

Antimicrobial resistance (AMR) is a serious threat to human and animal health, and its investigation requires a One Health approach from an integrated perspective in which human, animal, and environmental compartments are interconnected. There is growing interest in the role that the environment plays in the selection, spread, and transmission of AMR to humans. Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) have been suggested as emerging environmental contaminants and potential health threats. Several ARB and ARG sources have been recognized, including sewage water discharged from homes, hospitals, pharmaceutical manufacturing facilities, and animal feedlots. However, there are still gaps in the reliable and efficient assessment of risks to human health from exposure to ARB and ARGs in the environment, as well as in the programs and tools used to systematically measure and record antimicrobial contamination and ARB in the environment. Filling in these critical research gaps is a prerequisite for the development of mitigation strategies and public health measures to limit environmental contamination from antimicrobial residues and AMR organisms.

Therefore, this Special Issue welcomes collaborative submissions from different research fields that further study and clarify the risks for AMR associated with the environmental compartment, with special reference to distribution dynamics, sources and transmission risks of bacteria, and their antimicrobial resistance genes in the environment.

Dr. Filip Gamoń
Dr. Ewa Kotlarska
Dr. Suparna Mitra
Guest Editors

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Keywords

  • antimicrobial resistance (AMR) and One Health
  • AMR dissemination in the environment
  • risk assessment of AMR in environmental reservoirs (agroecosystems)
  • antibiotic-resistant pathogenic and resident bacteria
  • antibiotic-resistance gene (ARG) transfer
  • ARG quantification
  • AMR and food/feed chain
  • antibiotics in animals
  • agrochemicals
  • antibiotic residues

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Research

28 pages, 3947 KB  
Article
Integrated Genetic Characterization and Quantitative Risk Assessment of Cephalosporin- and Ciprofloxacin-Resistant Salmonella in Pork from Thailand
by Thawanrut Kiatyingangsulee, Si Thu Hein, Rangsiya Prathan, Songsak Srisanga, Saharuetai Jeamsripong and Rungtip Chuanchuen
Antibiotics 2025, 14(12), 1198; https://doi.org/10.3390/antibiotics14121198 - 27 Nov 2025
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Abstract
Background/Objectives: This study assessed the risk associated with third-generation cephalosporin- and fluoroquinolone-resistant Salmonella from pork consumption by integrating phenotypic resistance profiles with genetic data to characterize the risks and transmission pathways. Methods: Salmonella were isolated from raw pork meat samples ( [...] Read more.
Background/Objectives: This study assessed the risk associated with third-generation cephalosporin- and fluoroquinolone-resistant Salmonella from pork consumption by integrating phenotypic resistance profiles with genetic data to characterize the risks and transmission pathways. Methods: Salmonella were isolated from raw pork meat samples (n = 793) collected from fresh markets and hypermarkets across Bangkok during 2021–2022, of which 150 were extended-spectrum β-lactamase (ESBL)-producing and 31 were fluoroquinolone-resistant isolates. Phenotypic and genotypic resistance profiles were characterized. Quantitative antimicrobial resistance risk assessment (AMR RA) was conducted using a dose–response model. Results: Salmonella spp. was detected in 42.75% of pork samples, with a higher prevalence in fresh markets (75.5%) than in hypermarket samples and with concentrations ranging from 1.3 to 180 MPN/g. Twenty-eight percent of isolates were ESBL producers, with ciprofloxacin and levofloxacin resistance observed in 5.3% and 3.0%, respectively. The blaCTX-M55 genes were located on conjugative plasmids. Whole genome sequencing revealed both vertical and horizontal gene transfer. IncHI2/N and IncC plasmids shared conserved backbones and resistance gene architectures, indicating horizontal dissemination of resistance genes. Phylogenomics suggested possible clonal transmission among pigs, pork, and humans. AMR RA estimated 88,194 annual illness cases per 100,000 people from ESBL-producing Salmonella and 61,877 from ciprofloxacin-resistant strain, compared with 95,328 cases predicted by QMRA from Salmonella contamination. Cooking pork at ≥64 °C for 3 min eliminated the risk in all scenarios. Sensitivity analysis identified initial contamination level and cooking temperature as key determinants. Conclusions: Raw pork meat consumption represents the highest risk, which can be mitigated by thorough cooking (>64 °C, ≥3 min), while integrating genomic data enhances AMR hazard identification, source attribution, and exposure assessment. Therefore, promoting well-cooked meat consumption and safe cooking practices, alongside the use of AMR genetic data to inform targeted interventions, is recommended. Full article
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