Oxford Nanopore releases new protocol for sequencing complete microbial isolate genomes ahead of ESCMID

New protocol for use in infectious disease research part of packed activity lineup for ESCMID Global 2024

OXFORD, UK — April 25, 2024 — Oxford Nanopore Technologies (Oxford Nanopore), the company behind a new generation of molecular sensing technology based on nanopores, today announced its lineup of speakers and conference activities for the upcoming annual meeting of the European Society of Clinical Microbiology and Infectious Diseases, taking place April 27 – 30, 2024, in Barcelona, Spain. Ahead of the event, the company announced the release of its new Nanopore-Only Microbial Isolate Sequencing Solution (NO-MISS), an end-to-end workflow for sequencing complete microbial isolate genomes designed for the infectious disease community.

“This conference is such an important event for the infectious disease and microbiology community, and we look forward to attending every year,” said Rosemary Sinclair Dokos, SVP Product and Programme Management, Oxford Nanopore Technologies. “We are eager to hear from many scientists reporting their latest advances based on nanopore sequencing, and we look forward to connecting with the community to demonstrate our technology’s latest capabilities. This year we are particularly excited to share our new protocol for sequencing complete microbial isolate genomes, offering the community another powerful tool for studying infectious disease.”

NO-MISS Protocol

The new NO-MISS protocol is an end-to-end solution designed for sequencing complete microbial isolate genomes, from DNA extraction to comprehensive data analysis. NO-MISS works seamlessly with the MinION Flow Cells and is capable of sequencing four to 24 genomes per run, typically generating a minimum of 50x coverage, which is optimal for achieving accurate, high-quality genome and plasmid assembly and robust downstream analysis, including AMR profiling, core genome and whole genome multi-locus sequence typing, and SNP typing.

Comparison of short-read and nanopore sequencing in bacterial genome assembly, highlighting gene placement on plasmids and chromosomes for outbreak analysis.

Figure 1. Most bacterial genome assemblies produced with short-read sequencing technologies are fragmented and incomplete. Conversely, nanopore sequencing enhances microbial genome assemblies, offering the capability to discern gene placement on plasmids versus chromosomes, which can be integral for unravelling transmission patterns and identifying antimicrobial resistance drivers during outbreak investigations.

The NO-MISS protocol includes several DNA extraction methods tailored to different organisms, including bacteria and fungi, and employs specific kits for DNA purification and sequencing. The workflow includes quality checks, sample preparation, library preparation with tagging and barcoding, and loading the samples onto the flow cell for sequencing. Users can analyse their sequencing data using the EPI2ME wf-bacterial-genomes workflow, which provides user-friendly bioinformatics analyses and reports.

Whole-genome sequencing of microbial isolates provides valuable information for public health, clinical microbiology research, food safety, and microbial ecology.

The full NO-MISS protocol can be found here.

ESCMID 2024 Activities

Nearly 35 presentations at ESCMID Global 2024 (formerly known as ECCMID) will feature data from Oxford Nanopore sequencing devices. These will cover a range of diverse topics, including viral whole-genome sequencing, 16S rRNA sequencing, bacterial isolate whole-genome sequencing, tuberculosis drug resistance profiling, and metagenomics. The full poster list is available here.

Oxford Nanopore will host a symposium on Monday, April 29, about the transformative impact of genomics in clinical microbiology and infectious disease research. Please register here to attend.

Symposium: Rapid genomic detection and characterisation of pathogens using nanopore sequencing, Hall L, Monday, April 29




16:00 – 16:10

Welcome and Introductions

Justin O'Grady, Oxford Nanopore Technologies

16:10 – 16:25

Bringing nanopore sequencing into the clinical microbiology setting with targeted approaches

Patricia Simner, Johns Hopkins University

16:25 – 16:40

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

Seq&Treat: targeted sequencing for drug-resistant TB detection and treatment

Swapna Uplekar, FIND

16:55 – 17:10

Clinical metagenomics and infection - where are we today

David Eyre, Oxford Big Data Institute

17:10 – 17:30

Q&A and audience discussion

Panel, facilitated by Justin O'Grady, Oxford Nanopore Technologies

In addition, Oxford Nanopore will host an evening reception on Sunday, April 28, from 6:00 pm - 8:00 pm CEST, at the Hotel SB Plaza Europa near the conference venue. Register here to enjoy drinks, food, music and networking.

ESCMID attendees can also learn more about nanopore sequencing and the NO-MISS protocol through a variety of demonstrations and presentations at the Oxford Nanopore booth (C3).

Demo Title


Date and Time

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.

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!

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