Infectious disease

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This method will save time in obtaining high-quality complete genomes of bacteria for antimicrobial resistance surveillance, and is likely to become a valuable tool for monitoring the transmission of plasmid-borne drug resistance genes

Zhao et al. Front. Microbiol. (2023)

  • Real-time icon blue
    Immediate access to actionable results with real-time data — including pathogen identification and AMR profiling
  • Workflow_icon_RGB_roundel_blue
    Rapidly characterise and identify pathogens using fast and flexible end-to-end workflows in the lab or field
  • Icon displaying a graphic of any length nanopore reads
    Resolve complete bacterial and viral genomes and mobile genetic elements with long nanopore reads
Intro

Rapid access to results

Offering comprehensive, real-time insights into the genomics of infectious diseases — from pathogen identification and antimicrobial resistance (AMR) profiling to the assembly of high-quality genomes and variant identification — nanopore sequencing delivers immediate access to the critical genomic epidemiology data required to effectively control infectious disease outbreaks. Sequence in the lab or at sample source at a scale that suits your needs, with powerful portable and high-throughput nanopore sequencing devices.

Technology comparison

Oxford Nanopore sequencing

Legacy short-read sequencing

Any read length (20 bp to >4 Mb)

Short read length (<300 bp)

  • Generate complete, high-quality genomes with fewer contigs and simplify de novo assembly
  • Resolve genomic regions inaccessible to short reads, including complex structural variants (SVs) and repeats
  • Analyse long-range haplotypes, accurately phase single nucleotide variants (SNVs) and base modifications, and identify parent-of-origin effects
  • Sequence short DNA fragments, such as amplicons and cell-free DNA (cfDNA)
  • Resolve mobile genetic elements — including plasmids and transposons — to generate critical genomic insights
  • Enhance taxonomic resolution using full-length reads of informative loci, such as the entire 16S gene
  • Assembly contiguity is reduced and complex computational analyses are required to infer results
  • Complex genomic regions such as SVs and repeat elements typically cannot be sequenced in single reads (e.g. transposons, gene duplications, and prophage sequences)
  • Important genetic information is missed

Direct sequencing of native DNA/RNA

Amplification required

  • Eliminate amplification- and GC-bias, along with read length limitations, and access genomic regions that are difficult to amplify
  • Create cost-effective, amplification-free, targeted panels with adaptive sampling to detect SVs, repeats, SNVs, and methylation in a single assay
  • Amplification is often required and can introduce bias
  • Uniformity of coverage is reduced, resulting in assembly gaps

Real-time data streaming

Fixed run time with bulk data delivery

  • Analyse data as it is generated for immediate access to actionable results
  • Stop sequencing when sufficient data is obtained — wash and reuse flow cell
  • Combine real-time data streaming with intuitive, real-time EPI2ME data analysis workflows for deeper insights
  • Time to result is increased
  • Workflow errors cannot be identified until it is too late
  • Additional complexities of handling large volumes of bulk data

Accessible and affordable sequencing

Constrained to centralised labs

  • Sequence on demand with flexible end-to-end workflows that suit your throughput needs
  • Sequence at sample source, even in the most extreme or remote environments, with the portable MinION device — minimise potential sample degradation caused by storage and shipping
  • Scale up with modular GridION and PromethION devices — suitable for high-output, high-throughput sequencing to generate ultra-rich data
  • Perform cost-effective targeted analyses with single-use Flongle Flow Cells
  • Sequence as and when needed using low-cost, independently addressable flow cells — no sample batching needed
  • Use sample barcodes to multiplex samples on a single flow cell
  • Bulky, expensive devices that require substantial site infrastructure — use is restricted to well-resourced, centralised locations, limiting global accessibility
  • High sample batching is required for optimal efficiency, delaying time to results

Streamlined, automatable workflows

Laborious workflows

  • Lengthy sample prep is required
  • Long sequencing run times
  • Workflow efficiency is reduced, and time to result is increased