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Antibiotics
Special Issues
Antimicrobial Resistance (AMR) in Plant and Soil Microbiome
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Antimicrobial Resistance (AMR) in Plant and Soil Microbiome

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: closed (30 November 2022) | Viewed by 9515

Special Issue Editor

Dr. Qinglin Chen

E-Mail Website
Guest Editor
Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
Interests: antimicrobial resistance; soil microbiology; plant microbiome
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Antimicrobial resistance (AMR) has been recognized as a major health issue of global concerns of the 21st century. Emerging evidence suggests that the environment is the single largest source and reservoir of antibiotic resistance determinants. Currently, more than 700,000 people die globally per year from antibiotic-resistant diseases, and if no action is taken, more than 10 million deaths per year are projected by 2050. At its heart, the influence of antibiotic resistance on human, animal, and plant health and welfare, as well as its ecological and economic consequences, has reinforced the need for a concerted effort to track and control its emergence and dissemination

Despite a longstanding interest in this topic, currently, we lack a comprehensive understanding of how environmental resistomes change in the context of a changing environment as well as the contribution of the environmental state factors to those changes. This Special Issue will center on metagenomic and population genomic studies on the environmental resistome and its connection to environmental state factors. We are especially interested in the processes that drive the dissemination of AMR between soil and plant.

Dr. Qinglin Chen
Guest Editor

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 100 words) can be sent to the Editorial Office for announcement on this website.

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
  • soil microbiology
  • plant microbiome

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Published Papers (3 papers)

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Research

19 pages, 2932 KiB  
Article
High Genomic Identity between Clinical and Environmental Strains of Herbaspirillum frisingense Suggests Pre-Adaptation to Different Hosts and Intrinsic Resistance to Multiple Drugs
by Willian Klassen Oliveira, Hugo Leonardo Ávila, Michelle Zibeti Tadra, Rodrigo Luiz Cardoso, Cyntia Maria Teles Fadel-Pichet, Emanuel Maltempi de Souza, Fábio de Oliveira Pedrosa and Helisson Faoro
Antibiotics 2021, 10(11), 1409; https://doi.org/10.3390/antibiotics10111409 - 18 Nov 2021
Cited by 4 | Viewed by 2395
Abstract
The genus Herbaspirillum is widely studied for its ability to associate with grasses and to perform biological nitrogen fixation. However, the bacteria of the Herbaspirillum genus have frequently been isolated from clinical samples. Understanding the genomic characteristics that allow these bacteria to switch [...] Read more.
The genus Herbaspirillum is widely studied for its ability to associate with grasses and to perform biological nitrogen fixation. However, the bacteria of the Herbaspirillum genus have frequently been isolated from clinical samples. Understanding the genomic characteristics that allow these bacteria to switch environments and become able to colonize human hosts is essential for monitoring emerging pathogens and predicting outbreaks. In this work, we describe the sequencing, assembly, and annotation of the genome of H. frisingense AU14559 isolated from the sputum of patients with cystic fibrosis, and its comparison with the genomes of the uropathogenic strain VT-16–41 and the environmental strains GSF30, BH-1, IAC152, and SG826. The genes responsible for biological nitrogen fixation were absent from all strains except for GSF30. On the other hand, genes encoding virulence and host interaction factors were mostly shared with environmental strains. We also identified a large set of intrinsic antibiotic resistance genes that were shared across all strains. Unlike other strains, in addition to unique genomic islands, AU14559 has a mutation that renders the biosynthesis of rhamnose and its incorporation into the exopolysaccharide unfeasible. These data suggest that H. frisingense has characteristics that provide it with the metabolic diversity needed to infect and colonize human hosts. Full article
(This article belongs to the Special Issue Antimicrobial Resistance (AMR) in Plant and Soil Microbiome)
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18 pages, 1196 KiB  
Article
D-Mannoside FimH Inhibitors as Non-Antibiotic Alternatives for Uropathogenic Escherichia coli
by Alfredo Montes-Robledo, Rosa Baldiris-Avila and Johan Fabian Galindo
Antibiotics 2021, 10(9), 1072; https://doi.org/10.3390/antibiotics10091072 - 4 Sep 2021
Cited by 7 | Viewed by 4017
Abstract
FimH is a type I fimbria of uropathogenic Escherichia coli (UPEC), recognized for its ability to adhere and infect epithelial urinary tissue. Due to its role in the virulence of UPEC, several therapeutic strategies have focused on the study of FimH, including vaccines, [...] Read more.
FimH is a type I fimbria of uropathogenic Escherichia coli (UPEC), recognized for its ability to adhere and infect epithelial urinary tissue. Due to its role in the virulence of UPEC, several therapeutic strategies have focused on the study of FimH, including vaccines, mannosides, and molecules that inhibit their assembly. This work has focused on the ability of a set of monosubstituted and disubstituted phenyl mannosides to inhibit FimH. To determine the 3D structure of FimH for our in silico studies, we obtained fifteen sequences by PCR amplification of the fimH gene from 102 UPEC isolates. The fimH sequences in BLAST had a high homology (97–100%) to our UPEC fimH sequences. A search for the three-dimensional crystallographic structure of FimH proteins in the PDB server showed that proteins 4X5P and 4XO9 were found in 10 of the 15 isolates, presenting a 67% influx among our UPEC isolates. We focused on these two proteins to study the stability, free energy, and the interactions with different mannoside ligands. We found that the interactions with the residues of aspartic acid (ASP 54) and glutamine (GLN 133) were significant to the binding stability. The ligands assessed demonstrated high binding affinity and stability with the lectin domain of FimH proteins during the molecular dynamic simulations, based on MM-PBSA analysis. Therefore, our results suggest the potential utility of phenyl mannoside derivatives as FimH inhibitors to mitigate urinary tract infections produced by UPEC; thus, decreasing colonization, disease burden, and the costs of medical care. Full article
(This article belongs to the Special Issue Antimicrobial Resistance (AMR) in Plant and Soil Microbiome)
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9 pages, 1359 KiB  
Article
Molecular Epidemiology of Fosfomycin Resistant E. coli from a Pigeon Farm in China
by Lu Han, Xiao-Qing Lu, Xu-Wei Liu, Mei-Na Liao, Ruan-Yang Sun, Yao Xie, Xiao-Ping Liao, Ya-Hong Liu, Jian Sun and Rong-Min Zhang
Antibiotics 2021, 10(7), 777; https://doi.org/10.3390/antibiotics10070777 - 25 Jun 2021
Cited by 8 | Viewed by 2177
Abstract
We determined the prevalence and molecular characteristics of fosfomycin-resistant Escherichia coli from a domestic pigeon farm. A total of 79 samples collected from pigeons and their surrounding environments were screened for the presence of fosfomycin resistant isolates and these included 49 E. coli [...] Read more.
We determined the prevalence and molecular characteristics of fosfomycin-resistant Escherichia coli from a domestic pigeon farm. A total of 79 samples collected from pigeons and their surrounding environments were screened for the presence of fosfomycin resistant isolates and these included 49 E. coli isolates that displayed high-level resistance (MIC ≥ 256 mg L−1) and carried the fosA3 gene on plasmids with sizes ranging from 80 to 370 kb. MLST analysis of these fosA3-positive E. coli isolates indicated the presence of nine sequence types (ST6856, ST8804, ST457, ST746, ST533, ST165, ST2614, ST362 and ST8805) of which ST6856 was the most prevalent (24.5%, 12/49). PFGE combined with genomic context comparative analyses indicated that the fosA3 gene was spread by horizontal transfer as well as via clonal transmission between E. coli in the pigeon farm, and IS26 played an important role in fosA3 transmission. The high prevalence of fosA3 in the pigeon farm and the high similarity of the fosA3 genomic environment between E. coli isolates from humans and pigeons indicated that the pigeon farm served as a potential reservoir for human infections. The pigeon farm was found to be an important reservoir for the fosA3 gene and this should be further monitored. Full article
(This article belongs to the Special Issue Antimicrobial Resistance (AMR) in Plant and Soil Microbiome)
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