Metagenomics for pathogen surveillance
)
View the recording here
Rapid metagenomic sequencing is a powerful approach for identifying bacteria, fungi, and viruses in respiratory samples by directly sequencing their genetic material. While traditional next-generation sequencing (NGS) methods are widely used, Oxford Nanopore sequencing offers significant advantages for rapid and comprehensive pathogen surveillance.
Join this Knowledge Exchange webinar to learn how Oxford Nanopore sequencing can provide a rapid and comprehensive metagenomic approach for characterising bacteria, fungi, and viruses directly from respiratory samples. Participants will learn two sample preparation methods: one for DNA-only targeting of bacterial and fungal pathogens, and the other for both DNA and RNA, focused on viral pathogens. We will cover the necessary reagents for amplification and sequencing using a shotgun approach.
Additionally, we'll demonstrate the powerful bioinformatics tools for taxonomic classification, antimicrobial resistance (AMR) gene identification, and the generation of taxonomic profiles from metagenomic samples. Attendees will learn how to use the EPI2ME metagenomics workflow (wf-metagenomics) for data analysis and generate publication-ready figures, with interactive plots to explore sample data.
The webinar will conclude with a live Q&A from our speakers.
In this webinar, viewers will learn:
How to extract nucleic acids and prepare sequencing libraries, to explore viral, bacterial, and fungal pathogens.
An understanding of the technical performance, limitations, and quality control requirements for metagenomic sequencing.
An overview of the EPI2ME bioinformatic analysis workflow, wf-metagenomics, as well as the challenges and methods associated with bioinformatic analysis of complex samples.
The benefits of Oxford Nanopore sequencing to enhance your pathogen surveillance capabilities.
View the recording here
Meet the speakers
)
Anna Maria Niewiadomska, Segment market manger – public health, Oxford Nanopore TechnologiesIn her role as segment market manager, Anna drives the development of new markets in the infectious disease and public health space. She received her Ph.D. in molecular microbiology and immunology from the Johns Hopkins School of Public Health. Prior to joining Oxford Nanopore, Anna worked on multiple projects focusing on host/virus interactions, mathematical modeling of antimicrobial resistance, microbial bioinformatics, and emerging infectious disease outbreaks. She combines a deep knowledge of experimental and in silico methods for generation and analysis of microbial genomic data.
)
Alex Trotter, Development scientist – translational development, Oxford Nanopore TechnologiesAs part of Translational Development in Oxford Nanopore Technologies, Alex works on prototyping and developing clinical applications of nanopore technology in the infection space. His background is in infection diagnostics and his PhD was on the application of nanopore sequencing to the rapid identification of prosthetic joint infection through metagenomics. Following that, Alex worked as part of the COVID-19 Genomics UK Consortium (COG-UK) using sequencing to track SARS-CoV2 variants at the Quadram Institute in Norwich, before moving to Oxford Nanopore.
)
Natalia Garcia, Bioinformatics Software Developer, Oxford Nanopore TechnologiesAs a Bioinformatics Workflow Developer in the Customer Workflow team, Natalia creates and maintains workflows that help non-expert users to reliably analyse their data with minimal training. Our open-source workflows, implemented using Nextflow, allow life science researchers to go from raw reads to informative reports designed to help them make the most of their data. In particular, she is focused on the analysis of microbial communities through metagenomics data. Before joining Oxford Nanopore in 2023, she worked on microbial ecology at the Microbiome Analysis Laboratory in the Spanish National Biotechnology Center (CNB)| CSIC.
