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Journals
Microorganisms
Special Issues
Next-Generation Sequencing in Antimicrobial Resistance
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Next-Generation Sequencing in Antimicrobial Resistance

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Antimicrobial Agents and Resistance".

Deadline for manuscript submissions: 31 July 2025 | Viewed by 3779

Special Issue Editors

Prof. Dr. Efthymia Petinaki

E-Mail Website
Guest Editor
Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece
Interests: biopathology; clinical microbiology
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Artemis G. Hatzigeorgiou

E-Mail Website
Guest Editor
DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece
Interests: bioinformatics; genetics; sequences
Dr. Skoulakis Anargyros

E-Mail Website
Guest Editor Assistant
DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece
Interests: microbiology; bioinformatics; metagenomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Antimicrobial resistance (AMR) is a serious threat with impacts on public health, food sustainability and security, environmental wellbeing, and socio-economic development. So, globally, there has been much emphasis placed on the so called “One Health” approach that involves connecting the health of humans, animals, and the environment to tackle AMR. Today, the improvements of diagnostic methods have deeply transformed our ability to address AMR. Next-generation sequencing (NGS) offers the possibility to sequence microbial genomes either from colonies (genome of bacteria and fungi) or directly from clinical samples (metagenome). The NGS data analyzed by bioinformatics tools enable the rapid and accurate detection of a variety of known and new genes or mutations conferring resistance of microorganisms (bacteria, viruses, fungi and parasites) to antimicrobial agents. The introduction of NGS in “One Health” appears to be a new perspective in the diagnostic field of AMR, with a focus on personalized therapy and on the limitation of the spread of resistant pathogens. Moreover, NGS could help in tracking how antimicrobial determinants from human and animal pathogens can be transferred to environmental commensals and vice versa.

In this Special Issue entitled “Next-Generation Sequencing and Antimicrobial Resistance”, we welcome reviews, original research, and short communications that share new insights into the application of NGS in human, animal and environmental samples for detecting AMR.

Prof. Dr. Efthymia Petinaki
Prof. Dr. Artemis G. Hatzigeorgiou
Guest Editors

Dr. Skoulakis Anargyros
Guest Editor Assistant

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. Microorganisms 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 2700 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

  • next-generation sequencing
  • genome
  • metagenome
  • bioinformatics
  • clinical samples
  • One Health

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Published Papers (2 papers)

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Research

14 pages, 5031 KiB  
Article
Unveiling Antibiotic Resistance: Genome Sequencing of Streptomycin-Resistant Erwinia amylovora Isolate
by Lin He, Yuna Kim, Seohyun Kim, Mi-Hyun Lee and Jun Myoung Yu
Microorganisms 2024, 12(12), 2494; https://doi.org/10.3390/microorganisms12122494 - 3 Dec 2024
Viewed by 781
Abstract
Erwinia amylovora, the causal agent of fire blight, poses a serious threat to several rosaceous plants, especially apples and pears. In this study, a spontaneous streptomycin-resistant E. amylovora strain (EaSmR) was isolated under laboratory conditions. Compared with the parental strain TS3128, the [...] Read more.
Erwinia amylovora, the causal agent of fire blight, poses a serious threat to several rosaceous plants, especially apples and pears. In this study, a spontaneous streptomycin-resistant E. amylovora strain (EaSmR) was isolated under laboratory conditions. Compared with the parental strain TS3128, the EaSmR strain exhibited high resistance to streptomycin (>100,000 µg/mL) and showed a significant reduction in both swimming and swarming motility. To investigate the mechanisms underlying streptomycin resistance, the genome of EaSmR was sequenced, and four single nucleotide variants (SNVs) were identified in comparison with the EaSmR genome with TS3128. Two genes in EaSmR were found to contain SNVs relative to TS3128, including a point mutation at codon 43 in the rpsL gene, the primary target of streptomycin, which was identified as the cause of the resistance. Additionally, three other point mutations were detected within the gene encoding type I methionyl aminopeptidase (MetAP1), resulting in an amino acid substitution from serine to valine (S76V). Furthermore, we analyzed the nonsynonymous single nucleotide variants (nsSNVs) between the EaSmR isolate and the reference type strain, CFBP1430. A total of 111 nsSNVs were found in EaSmR, including three stop-gain mutations, across 102 genes, which likely account for potential differences between the Korean strain TS3128 (EaSmR) and the reference strain CFBP1430. Whole-genome sequencing of EaSmR reveals significant genetic changes and provides valuable insights into the role of single nucleotide variants in antibiotic resistance and altered physiological traits. As the first report of a laboratory-induced, streptomycin-resistant E. amylovora strain from South Korea, this study provides essential insights into resistance mechanisms and highlights key genomic differences that may contribute to the unique characteristics of the Korean strain, establishing a valuable foundation for future disease management strategies. Full article
(This article belongs to the Special Issue Next-Generation Sequencing in Antimicrobial Resistance)
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16 pages, 8354 KiB  
Article
Genomic Investigation and Comparative Analysis of European High-Risk Clone of Acinetobacter baumannii ST2
by David Hummel, Janos Juhasz, Katalin Kamotsay, Katalin Kristof, Basil Britto Xavier, Sien De Koster, Dora Szabo and Bela Kocsis
Microorganisms 2024, 12(12), 2474; https://doi.org/10.3390/microorganisms12122474 - 2 Dec 2024
Viewed by 2678
Abstract
Multidrug-resistant Acinetobacter baumannii is a major concern in healthcare institutions worldwide. Several reports described the dissemination of A. baumannii high-risk clones that are responsible for a high number of difficult-to-treat infections. In our study, 19 multidrug-resistant A. baumannii strains from Budapest, Hungary, were [...] Read more.
Multidrug-resistant Acinetobacter baumannii is a major concern in healthcare institutions worldwide. Several reports described the dissemination of A. baumannii high-risk clones that are responsible for a high number of difficult-to-treat infections. In our study, 19 multidrug-resistant A. baumannii strains from Budapest, Hungary, were investigated based on whole-genome sequencing (WGS). The obtained results were analysed together with data from 433 strains of A. baumannii from the Pathogenwatch database. WGS analysis of 19 A. baumannii strains detected that 12 belonged to ST2 and seven belonged to ST636. Among ST2 strains, 11 out of 12 carried either blaOXA-23 or blaOXA-58 genes; however, all strains of ST636 uniformly carried blaOXA-72 gene. All strains of ST2 and ST636 carried blaOXA-66 and blaADC-25 genes. Based on core genome multilocus sequence typing (cgMLST), 10 strains of ST2 belonged to cgMLST906, one strain to cgMLST458, and one strain to cgMLST1320; by contrast, all strains of ST636 belonged to cgMLST1178. Certain virulence determinants were present in all strains of both ST2 and ST636, namely, Ata, Bap, BfmRS, T2SS and PNAG. Interestingly, OmpA was present in all strains of ST2, but it was absent in all strains of ST636. Comparative analysis of 19 strains of this study and the collection of 433 isolates from Pathogenwatch database, proved a diverse clonal distribution of high-risk A. baumannii clones in Europe. The major clone in Europe is ST2, which is present all over the continent. However, ST636 has been mainly reported in Eastern Europe. Interestingly, cgMLSTs of ST2 correspond to the production of different beta-lactamases, namely, OXA-82 in cgMLST116, OXA-72 in cgMLST506, and cgMLST556, PER-1 in cgMLST456 and cgMLST1041. Our study demonstrates that the ST2 high-risk clone of A. baumannii is the most widespread in Europe; however, based on cgMLST analysis, a detailed detection of beta-lactamase production can be determined. Full article
(This article belongs to the Special Issue Next-Generation Sequencing in Antimicrobial Resistance)
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