Topics

Differential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing O145:H28.

07:00 EST 14th January 2020 | BioPortfolio

Summary of "Differential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing O145:H28."

Phages and plasmids play important roles in bacterial evolution and diversification. Although many draft genomes have been generated, phage and plasmid genomes are usually fragmented, limiting our understanding of their dynamics. Here, we performed a systematic analysis of 239 draft genomes and 7 complete genomes of Shiga toxin (Stx)-producing O145:H28, the major virulence factors of which are encoded by prophages (PPs) or plasmids. The results indicated that PPs are more stably maintained than plasmids. A set of ancestrally acquired PPs was well conserved, while various PPs, including Stx phages, were acquired by multiple sublineages. In contrast, gains and losses of a wide range of plasmids have frequently occurred across the O145:H28 lineage, and only the virulence plasmid was well conserved. The different dynamics of PPs and plasmids have differentially impacted the pangenome of O145:H28, with high proportions of PP- and plasmid-associated genes in the variably present and rare gene fractions, respectively. The dynamics of PPs and plasmids have also strongly impacted virulence gene repertoires, such as the highly variable distribution of genes and the high conservation of a set of type III secretion effectors, which probably represents the core effectors of O145:H28 and the genes on the virulence plasmid in the entire O145:H28 population. These results provide detailed insights into the dynamics of PPs and plasmids, and show the application of genomic analyses using a large set of draft genomes and appropriately selected complete genomes.

Affiliation

Journal Details

This article was published in the following journal.

Name: Microbial genomics
ISSN: 2057-5858
Pages:

Links

DeepDyve research library

PubMed Articles [15276 Associated PubMed Articles listed on BioPortfolio]

Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence of bla, bla and bla, along with sophisticated iron acquisition strategies.

Enterobacter bugandensis is a recently described species that has been largely associated with nosocomial infections. We report the genome of a non-clinical E. bugandensis strain, which was integrated...

Prophages contribute to remarkable genome plasticity of Klebsiella pneumoniae and may involve the chromosomal integration of ARGs in CG258.

Klebsiella pneumoniae is an important multidrug-resistant pathogen carrying prophages. Here we explore the contribution of prophages to bacterial evolution and fitness in silico. This study showed pro...

Legume Pangenome Construction Using an Iterative Mapping and Assembly Approach.

A pangenome is a collection of genomic sequences found in the entire species rather than a single individual. It allows for comprehensive, species-wide characterization of genetic variations and minin...

Population analysis of D6-like plasmid prophage variants associated with specific IncC plasmid types in the emerging Salmonella Typhimurium ST213 genotype.

The Salmonella enterica serovar Typhimurium sequence type 213 (ST213) emerged as a predominant genotype in Mexico. It is characterized by harboring multidrug resistance (MDR) IncC plasmids (previously...

ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database.

Prophages play a significant role in prokaryotic evolution, often altering the function of the cell that they infect via transfer of new genes e.g., virulence or antibiotic resistance factors, inactiv...

Clinical Trials [3780 Associated Clinical Trials listed on BioPortfolio]

Dermal HIV-1 Immunization During Anti-retroviral Therapy Followed by Repeated Treatment Interruptions

In this study, the investigators evaluated a therapeutic HIV-1 DNA vaccine administered with a novel topical application method to 12 chronically HIV-infected cART treated patients. The HI...

Co-adaptation Between HIV and CD8 Cellular Immunity

Our objective here is to characterize the viral evolution and viral factors determining HIV virulence, the evolution of the HIV reservoir in PBMC and the co-evolution of anti-HIV CD8 T cel...

Clostridium Difficile Virulence Mechanism Study (CDVM Study)

This study is an observational study to collect stool samples from patients with Clostridium difficile infection (CDI) to investigate the virulence mechanisms of C. difficile ribotypes in ...

HIV-DNA Dynamics in HIV Monoinfected or HIV/HCV Coinfected Patients

New markers of viral activity are now under investigation. Aim of the study is to investigate the efficacy of new antiretroviral drugs by monitoring HIV-DNA dynamics in HIV-positive popula...

Application of Ultrasound Artificial Intelligence and Elastography in Differential Diagnosis of Thyroid Nodules

The application of computer-aided diagnosis (CAD) technology "S-DetectTM" enables qualitative and quantitative automated analysis of ultrasound images to obtain objective, repeatable and m...

Medical and Biotech [MESH] Definitions

Genomes of temperate BACTERIOPHAGES integrated into the DNA of their bacterial host cell. The prophages can be duplicated for many cell generations until some stimulus induces its activation and virulence.

Plasmids encoding bacterial exotoxins (BACTERIOCINS).

Differential thermal analysis in which the sample compartment of the apparatus is a differential calorimeter, allowing an exact measure of the heat of transition independent of the specific heat, thermal conductivity, and other variables of the sample.

The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its VIRULENCE FACTORS.

Plasmids coding for proteins which induce PLANT TUMORS. The most notable example of a plant tumor inducing plasmid is the Ti plasmid found associated with AGROBACTERIUM TUMEFACIENS.

Quick Search


DeepDyve research library

Relevant Topic

Bioinformatics
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...


Searches Linking to this Article