ECCMID 2024
)
Oxford Nanopore are sponsors of ECCMID 2024 and will be exhibiting and presenting at this event.
The Oxford Nanopore Sundowner Symposium, Rapid genomic detection and characterisation of pathogens using nanopore sequencing, will take place in Hall L on Monday 29th April 2024 between 4:00 pm - 5:30 pm CET.
This session delves into the transformative impact of genomics in clinical microbiology and infectious disease research. Genomic technologies have unlocked new possibilities, from whole-genome characterisation of microbial pathogens and plasmids to comprehensive profiling of infectious agents and antimicrobial resistance. Despite their potential, legacy sequencing platforms suffer from long turnaround times, high costs, and technical limitations. Join us to hear how our speakers are overcoming these challenges using nanopore sequencing.
The ESCMID-appointed chair for the symposium is Dr Natacha Couto, University of Oxford, Big Data Institute.
Please register below to save your seat at the symposium.
Please also visit us at Booth #C3 if you are able to attend the event.
Agenda
16:00 – 17:30 hrs CEST | Agenda (subject to change) | |
|---|---|---|
16:00 - 16:10 hrs | Welcome and introductions | Justin O'Grady, Oxford Nanopore Technologies |
16:10 - 16:25 hrs | Bringing nanopore sequencing into the clinical microbiology setting with targeted approaches | Patricia Simner, Johns Hopkins University |
16:25 - 16:40 hrs | Genomic surveillance of multidrug-resistant organisms based on long-read sequencing | Fabian Landman, National Institute for Public Health and the Environment |
16:40 - 16:55 hrs | Seq&Treat: targeted sequencing for drug-resistant TB detection and treatment | Swapna Uplekar, FIND |
16:55 - 17:10 hrs | Clinical metagenomics and infection - where are we today | David Eyre, Oxford Big Data Institute |
17:10 - 17:30 hrs | Q&A and audience discussion | Panel, facilitated by Justin O'Grady, Oxford Nanopore Technologies |
Please note; the ESCMID-appointed symposium chair is Dr Natacha Couto, University of Oxford, Big Data Institute |
Speakers
)
Justin O'Grady, Senior Director, Translational Applications, Oxford Nanopore TechnologiesProf Justin O'Grady gained his BSc, MSc and PhD in microbiology and infectious diseases at the National University of Ireland Galway (NUIG). He remained at NUIG for his first post-doc, focussing on foodborne pathogens. This was followed by a two-year stint in industry (Beckman Coulter) developing real-time PCR based tests for infectious diseases. Prof O’Grady then returned to academia, taking a post-doc position at University College London on TB diagnostics. In January 2013 he was appointed Assistant Professor in Medical Microbiology at the University of East Anglia (Norwich, UK), was promoted to Associate Professor in August 2016 and promoted to Professor in January 2021. He 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 June 2021. His research continues to focus on the development of rapid diagnostic tests, to maximise community and patient benefit.
)
Patricia Simner, John Hopkins UniversityBackground Multidrug-resistant organisms (MDRO) pose a significant threat to public health world-wide. National reference and public health laboratories (NRLs, PHLs) monitor trends in antimicrobial resistance and transmission of MDRO for surveillance purposes. The aim of this study was to develop automated genomic MDRO surveillance based on long-read sequencing. Methods Genomic DNA of 221 MDRO obtained from May-September 2023 was automatically extracted and purified using the Maxwell RSC48 (Promega). The 221 MDRO comprised of 70 Klebsiella pneumoniae (Kpn), 69 Escherichia coli (Eco), 11 Enterobacter cloacae complex (Ecl), 9 Citrobacter freundii (Cfr), 11 Pseudomonas aeruginosa (Pae), 7 Acinetobacter baumannii (Aba) and 44 methicillin-resistant Staphylococcus aureus (MRSA). MDRO were sequenced using both short-read (Illumina NextSeq 550, Nextera DNA Flex Library Prep kit) and long-read (Oxford Nanopore Technologies [ONT], Rapid Barcoding Kit 24 V14, SQK-RBK114.24, MinION flow cell R10.4.1) whole-genome sequencing (WGS). Basecalling was performed using Dorado 0.3.2 duplex mode and Rerio model (for Kpn only). Long-read data was assembled using Flye v2.9.2, Canu v2.2, Miniasm v0.3 and Unicycler v0.5.0. WGS data with >30x coverage was used for multilocus sequence typing (MLST), whole-genome MLST (wgMLST), and identification of resistance genes (Abricate v1.0.1). Results Comparison of 221 Illumina-sequenced and 221 ONT-sequenced MDRO using species-specific wgMLST schemes and cluster cut-offs revealed that 43/70 (61%) Kpn, 65/69 (94%) Eco, 11/11 (100%) Ecl, 8/9 (89%) Cfr, 1/11 (9%) Pae, 7/7 (100%) Aba and 43/44 (98%) MRSA yielded nearly identical genomes and varied, on average 24, 4, 3, 3, 52, 2, and 2 wgMLST alleles, respectively. Flye ONT-assemblies had the best performance. MLST sequence types were 99% identical between Illumina and ONT long-read WGS data. Sensitivity and specificity for antimicrobial resistance genes of Flye assembled ONT long-read sequencing data was 98%/100% Kpn, 99%/100% Eco, 95%/100% Ecl, 100%/99% Cfr, 94%/90% Pae, 97%/100% Aba, and 99%/97% MRSA, respectively. Conclusions We demonstrate that automated DNA extraction followed by ONT long-read sequencing is an accurate, reliable, fast, and cost-effective method for genomic surveillance of MDRO for NRLs and PHLs. Two out of seven species, K. pneumoniae and P. aeruginosa, require further improvement of basecalling algorithms.
Background Multidrug-resistant organisms (MDRO) pose a significant threat to public health world-wide. National reference and public health laboratories (NRLs, PHLs) monitor trends in antimicrobial resistance and transmission of MDRO for surveillance purposes. The aim of this study was to develop automated genomic MDRO surveillance based on long-read sequencing. Methods Genomic DNA of 221 MDRO obtained from May-September 2023 was automatically extracted and purified using the Maxwell RSC48 (Promega). The 221 MDRO comprised of 70 Klebsiella pneumoniae (Kpn), 69 Escherichia coli (Eco), 11 Enterobacter cloacae complex (Ecl), 9 Citrobacter freundii (Cfr), 11 Pseudomonas aeruginosa (Pae), 7 Acinetobacter baumannii (Aba) and 44 methicillin-resistant Staphylococcus aureus (MRSA). MDRO were sequenced using both short-read (Illumina NextSeq 550, Nextera DNA Flex Library Prep kit) and long-read (Oxford Nanopore Technologies [ONT], Rapid Barcoding Kit 24 V14, SQK-RBK114.24, MinION flow cell R10.4.1) whole-genome sequencing (WGS). Basecalling was performed using Dorado 0.3.2 duplex mode and Rerio model (for Kpn only). Long-read data was assembled using Flye v2.9.2, Canu v2.2, Miniasm v0.3 and Unicycler v0.5.0. WGS data with >30x coverage was used for multilocus sequence typing (MLST), whole-genome MLST (wgMLST), and identification of resistance genes (Abricate v1.0.1). Results Comparison of 221 Illumina-sequenced and 221 ONT-sequenced MDRO using species-specific wgMLST schemes and cluster cut-offs revealed that 43/70 (61%) Kpn, 65/69 (94%) Eco, 11/11 (100%) Ecl, 8/9 (89%) Cfr, 1/11 (9%) Pae, 7/7 (100%) Aba and 43/44 (98%) MRSA yielded nearly identical genomes and varied, on average 24, 4, 3, 3, 52, 2, and 2 wgMLST alleles, respectively. Flye ONT-assemblies had the best performance. MLST sequence types were 99% identical between Illumina and ONT long-read WGS data. Sensitivity and specificity for antimicrobial resistance genes of Flye assembled ONT long-read sequencing data was 98%/100% Kpn, 99%/100% Eco, 95%/100% Ecl, 100%/99% Cfr, 94%/90% Pae, 97%/100% Aba, and 99%/97% MRSA, respectively. Conclusions We demonstrate that automated DNA extraction followed by ONT long-read sequencing is an accurate, reliable, fast, and cost-effective method for genomic surveillance of MDRO for NRLs and PHLs. Two out of seven species, K. pneumoniae and P. aeruginosa, require further improvement of basecalling algorithms.
)
Fabian Landman, National Institute for Public Health and the Environment (RIVM)Drug-resistant tuberculosis (DR-TB) is a major contributor to antimicrobial resistance worldwide and continues to be a public health threat. Targeted next-generation sequencing (tNGS) direct from clinical specimens has the potential to transform DR-TB management by providing rapid and comprehensive drug resistance testing to inform timely and treatment, including new shortened drug regimens. Findings from the recently completed clinical evaluation of the Oxford Nanopore DR-TB test will be presented. This evaluation is part of the Unitaid-funded Seq&Treat grant, designed to generate evidence for global policy and accelerate the use of tNGS for DR-TB diagnosis in high TB burden countries.
Drug-resistant tuberculosis (DR-TB) is a major contributor to antimicrobial resistance worldwide and continues to be a public health threat. Targeted next-generation sequencing (tNGS) direct from clinical specimens has the potential to transform DR-TB management by providing rapid and comprehensive drug resistance testing to inform timely and treatment, including new shortened drug regimens. Findings from the recently completed clinical evaluation of the Oxford Nanopore DR-TB test will be presented. This evaluation is part of the Unitaid-funded Seq&Treat grant, designed to generate evidence for global policy and accelerate the use of tNGS for DR-TB diagnosis in high TB burden countries.
)
Swapna Uplekar, FINDPotential scenarios for use of clinical metagenomics will be discussed, ranging from use as a reference laboratory test through to aspirations for metagenomics to become a routine first-line microbiology diagnostic. Diagnostic performance for species identification and antimicrobial resistance prediction will be reviewed. Example applications will then be described, before considering future directions for clinical metagenomics
Potential scenarios for use of clinical metagenomics will be discussed, ranging from use as a reference laboratory test through to aspirations for metagenomics to become a routine first-line microbiology diagnostic. Diagnostic performance for species identification and antimicrobial resistance prediction will be reviewed. Example applications will then be described, before considering future directions for clinical metagenomics
)
David Eyre, Oxford Big Data Institute
Register for symposium
Oxford Nanopore will also be hosting an evening reception on Sunday 28th April.
During the reception, we are looking forward to hosting an informal panel session, where we will be joined by Jonathan Edgeworth, Clinical Microbiologist and Director of the Kings College London Centre for Clinical Infection and Diagnostics Research, Abdul Sesay from the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine and Ela Sauerborn, Clinical microbiologist and PhD student from the Helmholtz AI institute.
There will be opportunity to ask questions on the topics of building effective pathogen surveillance programs and the potential of real-time genomics in this informal setting.
This event is now fully booked. Completing the registration form below will add you to a wait list.
Register for evening reception
Booth demos
Demo title | Description | Date |
|---|---|---|
Flow cell loading/initiating a sequencing run | Learn how to load a flow cell and initiate a sequencing run using Oxford Nanopore technology. | Saturday 27 April - 3:45 pm Sunday 28 April - 10:45 am Monday 29 April - 3:45 pm |
AmPORE-TB & Beyond: Workflows for infectious agent identification and characterisation plus Bacterial Genomes (NO-MISS) | Multi-drug resistant Mycobacterium tuberculosis infections are a global health issue. AmPORE-TB is a same day (<6hrs) assay for the identification of antimicrobial resistance. Extraction, PCR and library preparation is followed by a simplified sequencing and analysis interface. Analysis is performed locally on the GridION at the end of sequencing using the latest WHO mutation catalogue to produce a summary report of any resistance detected in sequenced samples. Join our demo to learn about this new end-to-end product coming later this year. (Approximately 10 minutes) | Saturday 27 April - 12:15 pm Sunday 28 April - 12:15 pm Monday 29 April - 12:15 pm |
Bacterial Genomes (NO-MISS) | 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! (Approximately 10 minutes) | |
TurBOT: Streamlining sample-to-answer microbial sequencing | Effortlessly go from sample to ultra-rich sequencing data with a push of a button. Discover how our newest device, TurBOT, accelerates your sequencing workflow, from extraction to analysis, ensuring rapid answers in labs of every size. Join our demo to see how TurBOT transforms sample-to-answer Nanopore-only Microbial Isolate Sequencing (NO-MISS) into seamless, straightforward science. Leap into the future of automated genomics. | Saturday 27 April - 10:45 am Sunday 28 April - 3:45 pm Monday 29 April - 10:45 am |
Visit our booth for Data for Breakfast.
The Oxford Nanopore team will present on Sunday 28th April from 09:30 — 09:50 AM on EPI2ME: Oxford Nanopore data analysis for anyone.
