Name: Pathogen-agnostic surveillance with nanopore sequencing
Uploaded: 2023-12-18T00:00:00.0000000
Duration: T00H03M56S
Description: Pathogen-agnostic surveillance with nanopore sequencing

Name: Pathogen-agnostic surveillance with nanopore sequencing

Description: Pathogen-agnostic surveillance with nanopore sequencing

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Upload Date: 2023-12-18T00:00:00.0000000

Transcript: Language: EN.
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Genomic surveillance can be performed using different strategies. When studying a particular known pathogen, targeted methods can be used to enrich that pathogen for sequencing. If the pathogen is not known in advance and to gain the complete picture of microbes in a sample metagenomic sequencing can be utilized.
This pathogen-agnostic approach can enable broad, real-time pathogen surveillance and the ability to detect rare, novel or emerging infectious threats. Many approaches for identifying pathogens, such as PCR, typically rely on looking for a specific region by assaying small, highly conserved genomic regions. However, metagenomic approaches sequence all genetic material in a sample, which can contain multiple species with the potential to detect known and unknown pathogens in a hypothesis free manner.
Detect novel variants of known pathogens that escape routine detection methods, extract virulence and resistance information in the same assay, and deliver rapid results in situations where an urgent public health response may be required. Samples from a wide variety of sources can be used, including soil, animals, food and wastewater. Metagenomics has many applications, including clinical research for the rapid identification and analysis of microorganisms.
Outbreak surveillance and genomic epidemiology. Microbiome studies and environmental monitoring. Traditional short-read sequencing techniques lack the ability to sequence long stretches of DNA. This can result in misassembly of microbial genomes and assembly gaps in complex or repetitive regions. It can also limit the capacity to distinguish between different microbial species within a metagenomic sample, especially where sequences are highly similar.
Nanopore sequencing generates reads of any length from short to Ultra long, which provides benefits for metagenomics. Long nanopore reads can span large regions of microbial genomes, including those which can be challenging to sequence with traditional short read technologies. This greatly simplifies assembly even for highly similar microbial genomes, enabling complete, high quality microbial genome assembly from metagenomic data.
And entire microbial genomes may even be obtained in single reads. Metagenomic sequencing with nanopore technology improves our understanding of genetic variants in microbial genomes with the ability to generate highly accurate whole genome assemblies, resolve repeat rich sequences and structural variants, identify the locations and arrangement of antimicrobial resistance and virulence genes.
Determine which genes are present on the chromosome or mobile elements such as plasmids, and differentiate between closely related species. Nanopore sequencing technology provides rapid turnaround times with real time sequencing ideal for, for example, outbreak scenarios where rapid detection and response are required for effective pathogen surveillance. Oxford Nanopore offers a range of scalable devices from portable to benchtop.
So that metagenomic samples can be analyzed anywhere, including in the field. To find out more about pathogen surveillance using nanopore sequencing. Check out our In Focus on the topic.

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