Infectious disease

Offering comprehensive, real-time insights into infectious disease samples — 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 for effective control of infectious disease outbreaks. Sequence in the lab or at sample source at a scale to suit your needs, with powerful portable and high-throughput nanopore sequencing devices.

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)

Technology comparison

Oxford Nanopore sequencing

Legacy short-read technologies

Real-time data streaming

  • Immediate access to actionable results — pathogen identification, variant analysis, and AMR profiling
  • Stop sequencing when sufficient data generated — wash and reuse flow cell
  • Combine with intuitive, real-time EPI2ME data analysis workflows

Fixed run time with bulk data delivery

Increased time-to-result, which is less amenable to time-critical applications.

Sequence anywhere

  • Sequence at sample source, even in the most extreme environments, with the portable, low-cost MinION
  • Scale up with modular GridION and PromethION — suitable for ultra-high-throughput sequencing of pathogen and complex metagenomic samples alongside other experiments, such as host genomics

Constrained to the lab

Considerable site infrastructure and set-up requirements combined with high platform costs can limit accessibility.

Flexible and scalable

  • Scale your sequencing to your needs — run one to thousands of samples on a single device using flexible end-to-end workflows
  • Sequence what you want, when you want — no sample batching required

Limited flexibility

Sample batching may be required for optimal efficiency, potentially delaying results until sufficient samples are acquired.

Unrestricted read length (>4 Mb achieved)

Read length typically 50–300 bp

Short reads do not typically span entire regions of interest, including repeats and structural variants, or full-length RNA transcripts, resulting in fragmented assemblies and ambiguous transcript isoform identification.

Streamlined, automatable workflows

Laborious workflows

Lengthy sample preparation with requirement for amplification — removing base modifications (e.g. methylation) and increasing the potential for sequencing bias.

White paper

Delivering the future of genomic pathogen surveillance

From Ebola, Zika, and COVID-19, to AMR bacterial and fungal infections, discover how portable, real-time nanopore sequencing is being utilised by researchers worldwide to support rapid identification and control of infectious disease outbreaks. Read customer case studies on mpox virus, poliovirus, and AMR profiling, and find out how nanopore sequencing overcomes the limitations of legacy genomic pathogen surveillance techniques.

Get more infectious disease resources, including getting started guides, workflows, white papers, and videos in our Resource Centre.

Case study

Characterisation of drug resistance in Mycobacterium tuberculosis

Shannon Murphy and colleagues at the Wadsworth Center, New York State Department of Health, developed a rapid, culture-free, nanopore targeted sequencing assay to characterise drug resistance profiles of Mycobacterium tuberculosis directly from respiratory samples. The team demonstrated that their targeted assay was just as accurate at identifying resistance mutations as whole-genome sequencing analysis. But importantly, the assay turnaround time showed a more than two-week improvement compared with culture and whole-genome sequencing workflows at a similar cost, and their method also offers additional utility for cultures that are too low quality for whole-genome sequencing analysis.

... this assay was found to be accurate and generated susceptibility profiles comparable to those currently obtained with our existing WGS assay, which can only be performed on cultured isolates

Murphy et al. Front. Public Health (2023)


Real-time infectious disease outbreak investigations with nanopore sequencing and BugSeq analysis

Infectious disease outbreaks continue to pose significant challenges to public health, and solutions are needed that enable real-time, comprehensive genomic characterisation of pathogens and AMR.

Watch the webinar to hear from medical microbiologists sharing their experiences detecting and tracking bacterial outbreaks using real-time sequencing with Oxford Nanopore and analysis with BugSeq, as an end-to-end solution.

Discover more

Find out how nanopore sequencing enables real-time pathogen and AMR identification from mixed microbial samples.

Get started

Scalable sequencing of infectious disease samples

Fully scalable, real-time nanopore sequencing devices are available to suit all infectious disease sequencing requirements — from in-field pathogen surveillance and characterisation to high-volume analysis of outbreak samples and host genetics.

Recommended for infectious disease sequencing


Running up to five independent MinION or Flongle Flow Cells with powerful, integrated compute, GridION provides the flexibility to run multiple experiments, on-demand — ideal for rapid and scalable analysis of pathogen samples and tracking novel variants.


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