ECCMID: An Oxford Nanopore guide to ECCMID

If you're in Amsterdam this weekend for ECCMID 2019, please do come and say hello at booth 1.23. PromethION, GridION, MinION and Flongle will be on display and we're bringing a range of technology and application experts to answer any questions you might have about nanopore sequencing.

We're also hosting an evening event on Monday 15th April where you'll have the opportunity to network with scientists, both new to, and already working with the technology, over some drinks and food.

The event is free to attend, you just need to register to confirm your place with our events team.

If you're looking for some pre-reading material ahead of the conference you might like to download our microbiology, clinical research and tuberculosis white papers, or browse recent publications in our resource centre.

There will be plenty of opportunities to find out more about nanopore technology at ECCMID with an excellent line up of speakers presenting talks and posters that will explore the use of nanopore technology across a broad range of topics:


Session: Microbiology by DNA: moving towards clinical metagenomics. 2-hour symposium (Hall K, 10:00 – 12:00)

E. Ruppé: Promises and hurdles of metagenomics

T. Street: Clinical metagenomics in bone and joint infections

C. Chiu: Metagenomics to unveil undetected micro-organisms

L. Kafetzopoulou: Clinical metagenomics in the field: outbreak investigation in limited-resource settings

Session: Respiratory viruses: what's out there and what is the impact? Mini-oral ePoster session (Arena 1, 14:45 – 15:45)

S. Pullan: Metagenomic nanopore sequencing for the detection and genomic characterisation of influenza and other RNA viruses direct from respiratory samples.


Session: Diagnostic assays in tuberculosis (12.30 - 13.30)

P1008 Constructing the rapid detection methods of drug-resistance mutation of tuberculosis using mobile nanopore sequencer MinION. K. Misawa et al.

P1023 Next-generation sequencing technologies for the identification of Mycobacterium tuberculosis resistance patterns. N. Peker et al.

Session: 16S rRNA methyltransferases (13.30 - 14.30)

P1135 Unravelling 16S rRNA methyltransferase-carrying plasmid dynamics in wastewater treatment plants by Nanopore Whole Genome Sequencing analysis. J. Delgado Blas et al.

Session: Insights from WGS: one world, one health

Session: On the forefront of respiratory viral diagnostic methods

Session: Omics, Omics and even more Omics

Session: What else is new: emerging viruses

Time: 15.30 - 16.30

P0501 Metagenomic MinION sequencing for Campylobacter surveillance in air samples from Italian poultry farms. L. Di Marcantonio et al.

P0502 Rapid detection of Coxiella burnetii in a goat abortion by MinION. M. Di Domenico et al.

P0070 Rapid genomic characterisation of UK-imported monkeypox virus by next-generation sequencing. K. Lewandowski et al.

P0106 Nanopore metagenomic sequencing of full length human metapneumovirus within a unique sublineage. Y. Xu et al.

P0454 Nanopore sequencing of large fosmid-inserts for rapid characterisation of tetracycline resistance genes in genomic context. L. E. De Vries et al.


Session: Emerging infectious surveillance. 2-hour symposium (Hall D, 8:45 – 10:45)

M. P. G. Koopmans: Emerging infections preparedness research in a One Health context

Session: Polymyxin resistance around the globe. 2-hour oral session (Arena J, 13:30 – 15:30)

G. Fleres: Detection of a mobile colistin resistance (mcr-5) gene in hospital tap water using short- and long-read shotgun metagenomics sequencing

Session: Performance and utility of broad-range molecular diagnostics. Mini-oral ePoster session (Arena 5, 14:45 – 15:45)

S. M. Neuenschwander: An improved bacterial identification workflow based on single-molecule sequencing


Session: Molecular methods for carbapenemase detection (13.30 - 14.30)

P1232 Rapid nanopore detection for carbapenem-resistant Klebsiella pneumoniae. W. Zhang et al.


Session: Clinical metagenomics: practical applications. 1-hour oral session (Hall F, 11:00 – 12:00)

L. Barker: Metagenomic sequencing for culture-independent diagnosis of Neisseria gonorrhoeae in urine: a pilot study

Session: Practical aspects of implementing whole-genome sequencing. 2-hour oral session (Hall F, 13:30 – 15:30)

Selene Garcia: Rapid identification and molecular characterisation of clinical isolates by using whole genome nanopore sequencing in a children’s hospital

Session: Optimised diagnosis of bacterial infection. Mini-oral flash session (Hall E, 14:45 – 15:45)

Dewi Rhys Owen: Prediction of the antimicrobial resistance profiles of Escherichia coli and Klebsiella pneumoniae directly from respiratory samples using MinION nanopore metagenomic sequencing


Session: Enterobacterales: virulence and pathogenesis

Session: Promiscuous plasmids on the attack: mobile genetic elements and their impact on antibiotic resistance

Time: 12.30 - 13.30

P1476 Characterisation of beta-lactamase CMY-2 gene and bacteriocin-encoding plasmids of ST131 ExPEC using MinION and Illumina sequencing and evaluation of its potential role in the virulence mechanisms. A. Da Cruz Campos et al.

P1612 MinION sequencing of Escherichia coli blaNDM-5 carriage isolates indicates huge variation in IncF plasmids. D. Paul et al.


Session: How to implement and use metagenomics in infectious disease diagnostics and management? Meet-the-Expert session (Hall D, 7:30 – 8:30)

Justin O'Grady


Session: Detection of antibacterial resistance mechanisms

Session: Surveillance of healthcare-associated infections

Time: 12.30 - 13.30

P2767 A method using the MinION nanopore sequencer for detecting bacteria and ESBL-producing species in the bloodstream. K. Imai et al.

P2588 Molecular epidemiology of carbapenemase-producing Enterobacteriaceae at a United Kingdom teaching hospital, 2014-2018. J. Bryan et al.