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Microorganisms
Special Issues
Mobile Genetic Elements in Pathogens
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Mobile Genetic Elements in Pathogens

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Molecular Microbiology and Immunology".

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 3844

Special Issue Editors

Prof. Dr. Maria Santagati

E-Mail Website
Guest Editor
Department of Biomedical and Biotechnological Sciences (BIOMETEC), Section Microbiology, University of Catania, Catania, Italy
Interests: characterization of mobile genetic elements carrying resistance genes and their mobility by conjugation and transformation; genomics; microbiome; probiotics and bacteriocins
Prof. Dr. Francesco Iannelli

E-Mail Website
Guest Editor
Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
Interests: mobilome characterization in Gram positive bacteria; bacterial genetics and genomics

Special Issue Information

Dear Colleagues,

The microbial mobilome is defined as the complete set of mobile genetic elements (MGEs) present in the microbiome, including plasmids (conjugative and nonconjugative), transposons, integrative and conjugative elements (ICEs, formerly called conjugative transposons), bacteriophages, integrons, insertion sequences (ISs), mobilizable elements, and genomic islands. The acquisition of new genetic material by horizontal gene transfer (HGT) mediated by MGEs significantly drives bacterial genome evolution and is an important source of bacterial diversity, which shapes the structure of microbial communities. MGEs are responsible for the spread of antibiotic resistance and virulence genes in microbial communities by intracellular and intercellular DNA trafficking, which contributes to the adaptability of pathogenic microorganisms in the clinical setting. Metagenomic studies have recently implemented the characterization of MGEs, revealing further insights into the effects of MGEs in shaping the properties of the microbiota; however, functional studies of MGEs are still needed.

This Special Issue will focus on Mobile Genetic Elements and their mobility by horizontal gene transfer linking MGEs and HGT strategies and their complex interactions with the microbial host.

Knowledge in this field will help understanding how MGEs evolve and spread antibiotic resistance and virulence genes. Metagenomic studies will provide new genetic information on the evolutionary impact of MGEs on the microbiome and their functional effects.

We are pleased to invite you to contribute to this Special Issue of Microorganisms by submitting original research articles and review articles related to mobile genetic elements in pathogens.

Prof. Dr. Maria Santagati
Prof. Dr. Francesco Iannelli
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 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

  • Mobilome
  • Mobile Genetics Elements
  • Plasmids
  • Transposons
  • Integrative Conjugative Elements
  • Bacteriophages
  • Integrons
  • Genomic Islands
  • Horizontal Gene Transfer
  • Microbial Pathogens

Published Papers (3 papers)

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Research

15 pages, 2216 KiB  
Article
The Transposition of Insertion Sequences in Sigma-Factor- and LysR-Deficient Mutants of Deinococcus geothermalis
by Ji Hyun Park, Sohee Lee, Eunjung Shin, Sama Abdi Nansa and Sung-Jae Lee
Microorganisms 2024, 12(2), 328; https://doi.org/10.3390/microorganisms12020328 - 04 Feb 2024
Viewed by 829
Abstract
Some insertion sequence (IS) elements were actively transposed using oxidative stress conditions, including gamma irradiation and hydrogen peroxide treatment, in Deinococcus geothermalis, a radiation-resistant bacterium. D. geothermalis wild-type (WT), sigma factor gene-disrupted (∆dgeo_0606), and LysR gene-disrupted (∆dgeo_1692) mutants [...] Read more.
Some insertion sequence (IS) elements were actively transposed using oxidative stress conditions, including gamma irradiation and hydrogen peroxide treatment, in Deinococcus geothermalis, a radiation-resistant bacterium. D. geothermalis wild-type (WT), sigma factor gene-disrupted (∆dgeo_0606), and LysR gene-disrupted (∆dgeo_1692) mutants were examined for IS induction that resulted in non-pigmented colonies after gamma irradiation (5 kGy) exposure. The loss of pigmentation occurred because dgeo_0524, which encodes a phytoene desaturase in the carotenoid pathway, was disrupted by the transposition of IS elements. The types and loci of the IS elements were identified as ISDge2 and ISDge6 in the ∆dgeo_0606 mutant and ISDge5 and ISDge7 in the ∆dgeo_1692 mutant, but were not identified in the WT strain. Furthermore, 80 and 100 mM H2O2 treatments induced different transpositions of IS elements in ∆dgeo_0606 (ISDge5, ISDge6, and ISDge7) and WT (ISDge6). However, no IS transposition was observed in the ∆dgeo_1692 mutant. The complementary strain of the ∆dgeo_0606 mutation showed recovery effects in the viability assay; however, the growth-delayed curve did not return because the neighboring gene dgeo_0607 was overexpressed, probably acting as an anti-sigma factor. The expression levels of certain transposases, recognized as pivotal contributors to IS transposition, did not precisely correlate with active transposition in varying oxidation environments. Nevertheless, these findings suggest that specific IS elements integrated into dgeo_0524 in a target-gene-deficient and oxidation-source-dependent manner. Full article
(This article belongs to the Special Issue Mobile Genetic Elements in Pathogens)
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25 pages, 3051 KiB  
Article
Comparative Genomic Analysis Reveals the Emergence of ST-231 and ST-395 Klebsiella pneumoniae Strains Associated with the High Transmissibility of blaKPC Plasmids
by Muna AL-Muzahmi, Meher Rizvi, Munawr AL-Quraini, Zakariya AL-Muharrmi and Zaaima AL-Jabri
Microorganisms 2023, 11(10), 2411; https://doi.org/10.3390/microorganisms11102411 - 27 Sep 2023
Cited by 1 | Viewed by 934
Abstract
Conjugative transposons in Gram-negative bacteria have a significant role in the dissemination of antibiotic-resistance-conferring genes between bacteria. This study aims to genomically characterize plasmids and conjugative transposons carrying integrons in clinical isolates of Klebsiella pneumoniae. The genetic composition of conjugative transposons and phenotypic [...] Read more.
Conjugative transposons in Gram-negative bacteria have a significant role in the dissemination of antibiotic-resistance-conferring genes between bacteria. This study aims to genomically characterize plasmids and conjugative transposons carrying integrons in clinical isolates of Klebsiella pneumoniae. The genetic composition of conjugative transposons and phenotypic assessment of 50 multidrug-resistant K. pneumoniae isolates from a tertiary-care hospital (SQUH), Muscat, Oman, were investigated. Horizontal transferability was investigated by filter mating conjugation experiments. Whole-genome sequencing (WGS) was performed to determine the sequence type (ST), acquired resistome, and plasmidome of integron-carrying strains. Class 1 integrons were detected in 96% of isolates and, among integron-positive isolates, 18 stains contained variable regions. Horizontal transferability by conjugation confirmed the successful transfer of integrons between cells and WGS confirmed their presence in conjugative plasmids. Dihydrofolate reductase (dfrA14) was the most prevalent (34.8%) gene cassette in class 1 integrons. MLST analysis detected predominantly ST-231 and ST-395. BlaOXA-232 and blaCTX-M-15 were the most frequently detected carbapenemases and beta-lactamases in the sequenced isolates. This study highlighted the high transmissibility of MDR-conferring conjugative plasmids in clinical isolates of K. pneumoniae. Therefore, the wise use of antibiotics and the adherence to effective infection control measures are necessary to limit the further dissemination of multidrug-resistant bacteria. Full article
(This article belongs to the Special Issue Mobile Genetic Elements in Pathogens)
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17 pages, 3196 KiB  
Article
The Mobilome-Enriched Genome of the Competence-Deficient Streptococcus pneumoniae BM6001, the Original Host of Integrative Conjugative Element Tn5253, Is Phylogenetically Distinct from Historical Pneumococcal Genomes
by Lorenzo Colombini, Anna Maria Cuppone, Mariana Tirziu, Elisa Lazzeri, Gianni Pozzi, Francesco Santoro and Francesco Iannelli
Microorganisms 2023, 11(7), 1646; https://doi.org/10.3390/microorganisms11071646 - 23 Jun 2023
Cited by 3 | Viewed by 1373
Abstract
Streptococcus pneumoniae is an important human pathogen causing both mild and severe diseases. In this work, we determined the complete genome sequence of the S. pneumoniae clinical isolate BM6001, which is the original host of the ICE Tn5253. The BM6001 genome [...] Read more.
Streptococcus pneumoniae is an important human pathogen causing both mild and severe diseases. In this work, we determined the complete genome sequence of the S. pneumoniae clinical isolate BM6001, which is the original host of the ICE Tn5253. The BM6001 genome is organized in one circular chromosome of 2,293,748 base pairs (bp) in length, with an average GC content of 39.54%; the genome harbors a type 19F capsule locus, two tandem copies of pspC, the comC1-comD1 alleles and the type I restriction modification system SpnIII. The BM6001 mobilome accounts for 15.54% (356,521 bp) of the whole genome and includes (i) the ICE Tn5253 composite; (ii) the novel IME Tn7089; (iii) the novel transposon Tn7090; (iv) 3 prophages and 2 satellite prophages; (v) 5 genomic islands (GIs); (vi) 72 insertion sequences (ISs); (vii) 69 RUPs; (viii) 153 BOX elements; and (ix) 31 SPRITEs. All MGEs, except for the GIs, produce excised circular forms and attB site restoration. Tn7089 is 9089 bp long and contains 11 ORFs, of which 6 were annotated and code for three functions: integration/excision, mobilization and adaptation. Tn7090 is 9053 bp in size, flanked by two copies of ISSpn7, and contains seven ORFs organized as a single transcriptional unit, with genes encoding for proteins likely involved in the uptake and binding of Mg2+ cations in the adhesion to host cells and intracellular survival. BM6001 GIs, except for GI-BM6001.4, are variants of the pneumococcal TIGR4 RD5 region of diversity, pathogenicity island PPI1, R6 Cluster 4 and PTS island. Overall, prophages and satellite prophages contain genes predicted to encode proteins involved in DNA replication and lysogeny, in addition to genes encoding phage structural proteins and lytic enzymes carried only by prophages. ΦBM6001.3 has a mosaic structure that shares sequences with prophages IPP69 and MM1 and disrupts the competent comGC/cglC gene after chromosomal integration. Treatment with mitomycin C results in a 10-fold increase in the frequency of ΦBM6001.3 excised forms and comGC/cglC coding sequence restoration but does not restore competence for genetic transformation. In addition, phylogenetic analysis showed that BM6001 clusters in a small lineage with five other historical strains, but it is distantly related to the lineage due to its unique mobilome, suggesting that BM6001 has progressively accumulated many MGEs while losing competence for genetic transformation. Full article
(This article belongs to the Special Issue Mobile Genetic Elements in Pathogens)
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