Nanopore sequencing for bacterial mobilome characterization

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F23%3A00130871" target="_blank" >RIV/00216224:14310/23:00130871 - isvavai.cz</a>

Výsledek na webu

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DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

Nanopore sequencing for bacterial mobilome characterization

Popis výsledku v původním jazyce

Bacterial mobile genetic elements like phages or chromosomal islands represent a fundamental force in bacterial evolution. We focus on staphylococcal phages, which genophores are mostly linear dsDNA of 15-150 kb with different types of physical ends depending on the DNA-packaging mechanism. Some phages can persist in hosts by integrating their genomes (prophages) into the bacterial chromosome. They can also mediate the transfer of bacterial genes or whole genomic regions, e.g., chromosomal islands, between strains and species across ecosystems. Some chromosomal islands have mechanisms that alter the phage particles to enhance their spread. The altered capsid of smaller size can contain the whole island genome but not a much bigger phage one. On the other hand, strictly lytic phages can be used in the therapy of bacterial infections as an alternative to antibiotics. To reveal interactions with their host, roles in evolution, and safe use in therapy, phages must be described in detail, including their genomics and capability to transfer bacterial genes. The favorite method of WGS nowadays is the Illumina platform. Its benefits are high accuracy, extensive coverage, low price per sample, and optimized workflows. However, this short-read method has at least one significant disadvantage; it cannot resolve long repeat regions. The third-generation platform, Oxford Nanopore, is relatively new and still developing, but it already offers not only very long reads and reasonable quality. ONT sequencing can be used to resolve (I) long repeats of physical ends of phages, to determine (II) the transduced regions, and (III) to detect methylations.

Název v anglickém jazyce

Nanopore sequencing for bacterial mobilome characterization

Popis výsledku anglicky

Bacterial mobile genetic elements like phages or chromosomal islands represent a fundamental force in bacterial evolution. We focus on staphylococcal phages, which genophores are mostly linear dsDNA of 15-150 kb with different types of physical ends depending on the DNA-packaging mechanism. Some phages can persist in hosts by integrating their genomes (prophages) into the bacterial chromosome. They can also mediate the transfer of bacterial genes or whole genomic regions, e.g., chromosomal islands, between strains and species across ecosystems. Some chromosomal islands have mechanisms that alter the phage particles to enhance their spread. The altered capsid of smaller size can contain the whole island genome but not a much bigger phage one. On the other hand, strictly lytic phages can be used in the therapy of bacterial infections as an alternative to antibiotics. To reveal interactions with their host, roles in evolution, and safe use in therapy, phages must be described in detail, including their genomics and capability to transfer bacterial genes. The favorite method of WGS nowadays is the Illumina platform. Its benefits are high accuracy, extensive coverage, low price per sample, and optimized workflows. However, this short-read method has at least one significant disadvantage; it cannot resolve long repeat regions. The third-generation platform, Oxford Nanopore, is relatively new and still developing, but it already offers not only very long reads and reasonable quality. ONT sequencing can be used to resolve (I) long repeats of physical ends of phages, to determine (II) the transduced regions, and (III) to detect methylations.

Druh

O - Ostatní výsledky

CEP obor

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OECD FORD obor

10607 - Virology

Projekt

<a href="/cs/project/NU21J-05-00035" target="_blank" >NU21J-05-00035: Synergie lytických bakteriofágů a antibiotik v léčbě povrchových infekcí způsobených Staphylococcus aureus</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2023

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů