Meeting report: mobile genetic elements and genome plasticity 2018

Bacillus cytotoxicus is the thermotolerant representative of the Bacillus cereus group. This group, also known as B. cereus sensu lato, comprises both beneficial and pathogenic members and includes psychrotolerant and thermotolerant species. Bacillus cytotoxicus was originally recovered from a fatal outbreak in France in 1998. This species forms a remote cluster from the B. cereus group members and reliably contains the cytk-1 gene, coding for a cytotoxic variant of cytotoxin K. Although this species was originally thought to be homogenous, intra-species diversity has been recently described with four clades, six random amplified polymorphic DNA (RAPD) patterns, and 11 plasmids profiles. This study aimed to get new insights into the genomic diversity of B. cytotoxicus and to decipher the underlying chromosomal and plasmidial variations among six representative isolates through whole genome sequencing (WGS). Among the six sequenced strains, four fitted the previously described genomic clades A and D, while the remaining two constituted new distinct branches. As for the plasmid content of these strains, three large plasmids were putatively conjugative and three small ones potentially mobilizable, harboring coding genes for putative leaderless bacteriocins. Mobile genetic elements, such as prophages, Insertion Sequences (IS), and Bacillus cereus repeats (bcr) greatly contributed to the B. cytotoxicus diversity. As for IS elements and bcr, IS3 and bcr1 were the most abundant elements and, along with the group II intron B.c.I8, were found in all analyzed B. cytotoxicus strains. When compared to other B. cytotoxicus strains, the type-strain NVH 391-98 displayed a relatively low number of IS. Our results shed new light on the contribution of mobile genetic elements to the genome plasticity of B. cytotoxicus and their potential role in horizontal gene transfer.

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ISSR-PCR markers and mobile genetic elements in horse (Equus caballus) genome

Sel skokhozyaistvennaya Biologiya ◽

10.15389/agrobiology.2014.4.42eng ◽

2014 ◽

pp. 42-57 ◽

Cited By ~ 1

Author(s):

N.V. Bardukov ◽

◽

A.V. Feofilov ◽

T.T. Glazko ◽

V.I. Glazko ◽

...

Keyword(s):

Equus Caballus ◽

Mobile Genetic Elements ◽

Pcr Markers ◽

Genetic Elements ◽

Issr Pcr

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Faculty Opinions recommendation of Mobile genetic elements associated with antimicrobial resistance.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.733756730.793551360 ◽

2018 ◽

Author(s):

Fred Dyda

Keyword(s):

Antimicrobial Resistance ◽

Mobile Genetic Elements ◽

Genetic Elements

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Habitat determines the relationships among bacteria, resistance genes and mobile genetic elements in the soil‐plant system

European Journal of Soil Science ◽

10.1111/ejss.13132 ◽

2021 ◽

Author(s):

Ruilin Huang ◽

Jixian Ding ◽

Yuwei Guo ◽

Bo Sun ◽

Yuting Liang

Keyword(s):

Resistance Genes ◽

Mobile Genetic Elements ◽

Plant System ◽

Genetic Elements ◽

Bacteria Resistance

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Shotgun metagenomic analysis reveals the prevalence of antibiotic resistance genes and mobile genetic elements in full scale hospital wastewater treatment plants

Journal of Environmental Management ◽

10.1016/j.jenvman.2021.113270 ◽

2021 ◽

Vol 296 ◽

pp. 113270

Author(s):

Ranjith Kumar Manoharan ◽

Sathiyaraj Srinivasan ◽

Gnanendra Shanmugam ◽

Young-Ho Ahn

Keyword(s):

Antibiotic Resistance ◽

Wastewater Treatment ◽

Resistance Genes ◽

Wastewater Treatment Plants ◽

Antibiotic Resistance Genes ◽

Mobile Genetic Elements ◽

Full Scale ◽

Metagenomic Analysis ◽

Hospital Wastewater ◽

Genetic Elements

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Genomic evolution of antimicrobial resistance in Escherichia coli

Scientific Reports ◽

10.1038/s41598-021-93970-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Pimlapas Leekitcharoenphon ◽

Markus Hans Kristofer Johansson ◽

Patrick Munk ◽

Burkhard Malorny ◽

Magdalena Skarżyńska ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Virulence Genes ◽

Mobile Genetic Elements ◽

Whole Genome ◽

Sequencing Analysis ◽

Metagenomic Sequencing ◽

Fecal Samples ◽

E Coli ◽

Genetic Elements

AbstractThe emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.

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Microevolution within ST11 group Clostridioides difficile isolates through mobile genetic elements based on complete genome sequencing

BMC Genomics ◽

10.1186/s12864-019-6184-1 ◽

2019 ◽

Vol 20 (1) ◽

Author(s):

Yuan Wu ◽

Lin Yang ◽

Wen-Ge Li ◽

Wen Zhu Zhang ◽

Zheng Jie Liu ◽

...

Keyword(s):

Drug Resistance ◽

Resistance Genes ◽

Point Mutations ◽

Evolutionary Process ◽

Mobile Genetic Elements ◽

Genetic Elements ◽

Clostridioides Difficile ◽

Hospitalized Elderly ◽

Great Heterogeneity ◽

High Level

Abstract Background Clade 5 Clostridioides difficile diverges significantly from the other clades and is therefore, attracting increasing attention due its great heterogeneity. In this study, we used third-generation sequencing techniques to sequence the complete whole genomes of three ST11 C. difficile isolates, RT078 and another two new ribotypes (RTs), obtained from three independent hospitalized elderly patients undergoing antibiotics treatment. Mobile genetic elements (MGEs), antibiotic-resistance, drug resistance genes, and virulent-related genes were analyzed and compared within these three isolates. Results Isolates 10,010 and 12,038 carried a distinct deletion in tcdA compared with isolate 21,062. Furthermore, all three isolates had identical deletions and point-mutations in tcdC, which was once thought to be a unique characteristic of RT078. Isolate 21,062 (RT078) had a unique plasmid, different numbers of transposons and genetic organization, and harboring special CRISPR spacers. All three isolates retained high-level sensitivity to 11 drugs and isolate 21,062 (RT078) carried distinct drug-resistance genes and loss of numerous flagellum-related genes. Conclusions We concluded that capillary electrophoresis based PCR-ribotyping is important for confirming RT078. Furthermore, RT078 isolates displayed specific MGEs, indicating an independent evolutionary process. In the further study, we could testify these findings with more RT078 isolates of divergent origins.

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