ESCMID Global 2025
)
ESCMID Global is one of the largest and foremost congresses in the field of infection and the comprehensive programme is a collaboration built by the ESCMID Global Programme Committee (EPC), ESCMID entities and partners and industry sponsors.
Oxford Nanopore will be located at booth B52 in the exhibit hall, and will host a Sundowner Symposium on Monday, 14th April, 2025. Session details below.
Unlocking rapid, comprehensive pathogen genomics with real-time nanopore sequencing
Date: Monday, 14th April, 2025
Time: 16:15 - 17:45 CET
Location: Hall 6
This session will explore how nanopore sequencing is transforming the clinical microbiology and public health landscape by providing rapid, decentralized, and comprehensive pathogen genomics solutions. From the ability to generate complete whole-genome sequencing of microbial isolates, to the agnostic detection of pathogens and antimicrobial resistance (AMR) genes directly from samples, nanopore sequencing offers cost-effective, timely, and automatable sample-to-answer workflows. These innovative capabilities tackle key challenges such as uncovering hidden outbreaks, tracking plasmid transmission, and identifying potential drug resistance within hours. The session will feature experts applying nanopore technology for outbreak detection, pathogen identification, and AMR profiling, showcasing how real-time genomics can deliver actionable insights faster than traditional methods, potentially advancing precision medicine, and improving responses to infectious diseases and public health challenges.
Implementing next generation sequencing for rapid diagnostics and public health investigations
(Kim Musser, Wadsworth Center)
Implementing portable, real-time 16S rRNA sequencing in the healthcare sector enhances antimicrobial stewardship
(Anna Smielewska, Royal Liverpool Hospitals)
Reliable whole-genome genotyping for bacterial surveillance using nanopore sequencing data
(Gabriel Wagner, Medical University of Graz)
Utilizing nanopore metagenomic sequencing for rapid identification of infections
(Judith Breuer, University College London)
Symposium Speakers
)
Justin O'Grady, VP, Translational Applications, Oxford Nanopore TechnologiesProf Justin O'Grady gained his BSc, MSc and PhD in microbiology and infectious diseases at the University of Galway. Following postdocs and a two-year stint in industry (Beckman Coulter) developing real-time PCR based tests for infectious diseases, Prof O’Grady was appointed Assistant Professor in Medical Microbiology at the University of East Anglia (Norwich, UK) in 2013. He was promoted to Associate Professor in 2016 and Professor in 2021. Prof O’Grady was seconded to the University of Cambridge during the COVID pandemic, as Deputy Director of COG-UK, to help lead the UK’s SARS-CoV-2 sequencing effort. He then joined Oxford Nanopore Technologies as Senior Director of Translational Applications in 2021 and was promoted to Vice President in 2024. His work continues to focus on the development of rapid diagnostic tests, to maximise community and patient benefit.
The objective of this project is to develop and validate nanopore sequencing tests for use on clinical specimens and isolates with improved performance, cost and efficiency for applications ranging from Mycobacterium tuberculosis (MTB) whole genome and targeted sequencing, bacterial identification, and for healthcare associated transmission investigations of antimicrobial resistant and other bacterial pathogens.
The objective of this project is to develop and validate nanopore sequencing tests for use on clinical specimens and isolates with improved performance, cost and efficiency for applications ranging from Mycobacterium tuberculosis (MTB) whole genome and targeted sequencing, bacterial identification, and for healthcare associated transmission investigations of antimicrobial resistant and other bacterial pathogens.
)
Kim Musser, Clinical Director, Wadsworth Center, David Axelrod InstituteDespite recent advances in error rate reduction, Oxford Nanopore Technology (ONT) sequences have until recently lacked the accuracy for reliable fine-scale bacterial genomic analysis. Here, we evaluated recent improvements of ONT's tools (Dorado basecalling and Medaka polishing) and the ONT cgMLST polisher (Ridom, Germany) on bacterial genotyping.
Despite recent advances in error rate reduction, Oxford Nanopore Technology (ONT) sequences have until recently lacked the accuracy for reliable fine-scale bacterial genomic analysis. Here, we evaluated recent improvements of ONT's tools (Dorado basecalling and Medaka polishing) and the ONT cgMLST polisher (Ridom, Germany) on bacterial genotyping.
)
Gabriel Wagner-Lichtenegger, Molecular Biologist, Medical University of GrazRapid identification of microbiological organisms is especially important in today’s healthcare setting as we face increased antimicrobial resistance. Diagnostically there is a clear need for a rapid, accurate and flexible bacterial identification assay that could be run in a routine diagnostic laboratory, while remaining cost effective and lean.
Rapid identification of microbiological organisms is especially important in today’s healthcare setting as we face increased antimicrobial resistance. Diagnostically there is a clear need for a rapid, accurate and flexible bacterial identification assay that could be run in a routine diagnostic laboratory, while remaining cost effective and lean.
)
Anna Smielewska, Clinical Director, Royal Liverpool Hospitals NHS Foundation TrustIn this talk I will discuss the experience of Great Ormond Street Hospital in implementing the respiratory metagenomics protocol developed by Oxford Nanopore Technologies in collaboration with Guys and St Thomas Hospital (GSTT) and review the first 5-6 months of our results. I will examine the lessons learnt during the process of establishing the existing protocol within a busy diagnostic laboratory and the particular challenges of applying the pipeline to severely ill and often immunocompromised paediatric patients. In addition I will present the measures taken to facilitate useful interpretation of polymicrobial upper respiratory tract specimens, which are more commonly taken from children. GOSH has also since 2014 delivered a metagenomics service (UKAS accredited in 2024) for detection (and exclusion) of pathogens in sterile sites and tissue, in cases where infection is suspected but conventional methods remain negative. The current sterile-site pipeline is slow and ONT technology offers the potential for faster turnaround times, provided comparable sensitivity can be achieved. I will present the work in our lab to develop sufficient improvement in ONT sensitivity to potentially enable rapid (12-48 hour) detection and exclusion of pathogens in sterile sites.
In this talk I will discuss the experience of Great Ormond Street Hospital in implementing the respiratory metagenomics protocol developed by Oxford Nanopore Technologies in collaboration with Guys and St Thomas Hospital (GSTT) and review the first 5-6 months of our results. I will examine the lessons learnt during the process of establishing the existing protocol within a busy diagnostic laboratory and the particular challenges of applying the pipeline to severely ill and often immunocompromised paediatric patients. In addition I will present the measures taken to facilitate useful interpretation of polymicrobial upper respiratory tract specimens, which are more commonly taken from children. GOSH has also since 2014 delivered a metagenomics service (UKAS accredited in 2024) for detection (and exclusion) of pathogens in sterile sites and tissue, in cases where infection is suspected but conventional methods remain negative. The current sterile-site pipeline is slow and ONT technology offers the potential for faster turnaround times, provided comparable sensitivity can be achieved. I will present the work in our lab to develop sufficient improvement in ONT sensitivity to potentially enable rapid (12-48 hour) detection and exclusion of pathogens in sterile sites.
)
Judith Breuer, Clinical Professor of Virology, University College London
On-booth demos
Saturday, 12th April | Sunday, 13th April | Monday, 14th April |
|---|---|---|
10:45 am — ElysION: bring automated, sample-to-answer microbial sequencing into your lab Kinga Sedzielewska Toro, Oxford Nanopore Technologies | 10:45 am — Flow cell loading/initiating a sequencing run Isabel Sophie Abellan Schneyder & Sebastian Ganschow, Oxford Nanopore Technologies | 10:45 am — ElysION: bring automated, sample-to-answer microbial sequencing into your lab Kinga Sedzielewska Toro, Oxford Nanopore Technologies |
12:15 pm — Microbial isolate sequencing Christopher Alder, Oxford Nanopore Technologies | 12:15 pm — Microbial isolate sequencing Christopher Alder, Oxford Nanopore Technologies | 12:15 pm — Microbial isolate sequencing Christopher Alder, Oxford Nanopore Technologies |
3:45 pm — Flow cell loading/initiating a sequencing run Isabel Sophie Abellan Schneyder & Sebastian Ganschow, Oxford Nanopore Technologies | 3:45 pm – ElysION: bring automated, sample-to-answer microbial sequencing into your lab Kinga Sedzielewska Toro, Oxford Nanopore Technologies | 3:45 pm — Flow cell loading/initiating a sequencing run Isabel Sophie Abellan Schneyder & Sebastian Ganschow, Oxford Nanopore Technologies |
Flow cell loading/initiating a sequencing run:
Learn about Nanopore sequencing technologies, including flow cell architecture. Discover how to load a flow cell and start a sequencing run using Oxford Nanopore technology. After the demonstration, you can ask questions, e.g., about sample handling and reviewing a run report.
Microbial isolate sequencing:
Whole-genome sequencing of microbial isolates provides valuable information for public health, clinical microbiology research, food safety, and microbial ecology. Nanopore-only microbial isolate sequencing solution (NO-MISS) is a new rapid end-to-end workflow for the sequencing and analysis of bacterial isolates. Join our demo to learn how this workflow provides assembly, antimicrobial resistance and more in one easy to perform experiment!
ElysION: bring automated, sample-to-answer microbial sequencing into your lab
Effortlessly go from sample to ultra-rich microbial sequencing data with fully automated, hands-off workflows on ElysION. From respiratory metagenomics to microbial isolate sequencing, ElysION accelerates every step — extraction, sequencing, and analysis — in a single, intuitive solution. Join our demo and discover how to perform streamlined microbial genomics research in your lab with ElysION.
Join the Oxford Nanopore team and other nanopore users at booth B52 to chat about current applications of our technology!
Date: Sunday, 13th April, 2025
Time: 16:00 CEST
