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Antibiotics
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Distribution, Sources and Risks of Bacteria and Their Antimicrobial Resistance...
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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: 31 December 2026 | Viewed by 1488

Special Issue Editors

Dr. Filip Gamoń

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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: anammox; wastewater treatment; environmental biotechnology; antibiotic impact; micropollutants
Special Issues, Collections and Topics in MDPI journals
Dr. Ewa Kotlarska

E-Mail Website
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.
Dr. Suparna Mitra

E-Mail Website
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

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

  • 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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Related Special Issue

Published Papers (2 papers)

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Research

28 pages, 9761 KB  
Article
West Siberian Soil Resistome: Mobile Antibiotic Resistance in Agricultural Microbiomes
by Anna Evgenevna Skotareva, Ekaterina Alexeevna Sokolova and Elena Nikolaevna Voronina
Antibiotics 2026, 15(5), 502; https://doi.org/10.3390/antibiotics15050502 - 17 May 2026
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Abstract
Background/Objectives: Soil microbiomes in agroecosystems are natural reservoirs of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), creating conditions for horizontal gene transfer (HGT) to clinically relevant bacteria. Southern West Siberia—a globally significant grain-producing region—lacks metagenomic characterization of its soil resistome. This [...] Read more.
Background/Objectives: Soil microbiomes in agroecosystems are natural reservoirs of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), creating conditions for horizontal gene transfer (HGT) to clinically relevant bacteria. Southern West Siberia—a globally significant grain-producing region—lacks metagenomic characterization of its soil resistome. This study aimed to establish the first baseline profile of resistome and mobilome composition for West Siberian agricultural soils. Methods: Twelve composite soil samples were collected from agroecosystems under seven crop types across diverse soil types in southern West Siberia (September 2022). Shotgun metagenomics was performed on an Illumina NovaSeq 6000 platform. Taxonomic profiling used Kraken2/Bracken; ARG annotation used Prokka/DeepARG (identity ≥ 70%, probability score ≥ 0.8); while MGE characterization used Platon, HMMER v3.3.2, and Prokka-based integrase annotation. Resistome load was normalized to the single-copy housekeeping gene rpoB; ARG–MGE associations were defined as co-localization within 10 kb on the same contig. Results: Microbial communities were dominated by Pseudomonadota and Bacillota, with a stable core of Streptomycetaceae, Nitrobacteraceae, and Sphingomonadaceae. Normalized resistome load (N/rpoB 2.30–5.37) indicated moderate anthropogenic pressure. Dominant ARGs included efflux pumps (emrA, drrA, tetA, bcr, fsr), target modification (lnrL), and lipid A modification (arnA) genes. Class 1 integron integrase (intI1/rpoB 0.64–1.59) was detected in all 12 samples, exceeding unity in 9 of 12. ARG–MGE co-localizations were found in 11 of 12 samples. In sample Mg_155, genes emrA–emrB and bcr (NODE_16) and arnA and lnrL (NODE_6) were each independently associated with distinct prophage IntA integrase copies within Pseudomonas contigs, documenting multiple parallel horizontal transfer events encompassing resistance to five antibiotic classes. Conclusions: This work establishes the first metagenomic baseline of resistome and mobilome for West Siberian agroecosystems. The obtained data indicate moderate anthropogenic pressure on soil microbiomes, consistent with temperate agricultural systems with limited organic fertilizer input. The detected ARG–MGE co-localizations and evidence of prophage-mediated transfer of resistance determinants beyond their natural hosts suggest that mobilization potential in the region warrants consideration in future AMR monitoring programs. Full article
(This article belongs to the Special Issue Distribution, Sources and Risks of Bacteria and Their Antimicrobial Resistance Genes in the Environment, 2nd Edition)
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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
(This article belongs to the Special Issue Distribution, Sources and Risks of Bacteria and Their Antimicrobial Resistance Genes in the Environment, 2nd Edition)
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