How could nanopore sequencing in clinical labs combat infectious disease?

In hospitals around the world, against a backdrop of pathogens that evade detection and rising antimicrobial resistance (AMR), clinicians continue to fight infectious diseases. Timely access to reliable data is critical to this: what pathogen is causing this infection? Which treatments is it resistant to? Is this infection spreading from patient to patient? Are our control measures working?

Now, researchers are bringing Oxford Nanopore sequencing to this fight. By integrating nanopore technology directly into clinical microbiology labs, they are showcasing what could be possible with comprehensive pathogen data available in clinically relevant timeframes. Using targeted, whole-genome, and metagenomic approaches, researchers are demonstrating how a single sequencing platform can be applied across a range of clinical and public health challenges. The data they are generating has the potential to support treatment decisions, antimicrobial stewardship, and outbreak monitoring.

In this blog, we highlight six recent publications showing how researchers are using nanopore sequencing to potentially change the course of infectious disease treatment and control.

Gaining deep insights into infections and AMR with metagenomics

1. Rapid diagnosis of common, undetected, and uncultivable bloodstream infections from positive blood cultures using Oxford Nanopore sequencing: a metagenomic pipeline analysis. Lancet (2026)

Each year, bloodstream infections lead to approximately 11 million sepsis-related deaths¹. With every hour’s delay in treatment increasing the risk of mortality², fast identification (ID) of the pathogen responsible is critical. Govender et al. used metagenomic nanopore sequencing to rapidly identify the microbes behind these infections³.

The team used a GridION to sequence DNA from routine blood culture research samples taken at Oxford University hospitals, UK. Using real-time analysis, they identified the pathogen in under 3.5 hours — 10 hours earlier than routine diagnostics (Figure 1). As well as delivering faster results, their method detected 19 additional infections, including one in a culture-negative sample, highlighting its capacity to detect co-infections, false-negatives, and contaminants. Adjusting for these, their method demonstrated 100% precision and recall.

Crucially, their metagenomic approach also produced AMR data. For the ten most clinically relevant pathogens, this was available 20 hours earlier than classic antimicrobial susceptibility testing (AST), showing potential to identify effective treatments faster and, ultimately, save lives.

2. Clinical long-read metagenomic sequencing of culture-negative infective endocarditis reveals genomic features and antimicrobial resistance. BMC Infect. Dis. (2025)

At Siriraj Hospital, Thailand, researchers used metagenomic sequencing to characterise pathogens in infective endocarditis⁴. These life-threatening heart infections can be difficult to diagnose, especially where pathogens are unculturable.

Using DNA from two aortic valve tissue research samples, Kruasuwan and Pathomchareansukchai et al. made use of Adaptive Sampling — a software-based targeted nanopore sequencing method — to deplete host DNA without extra library prep. Within an hour of real-time analysis via EPI2ME, they identified the infecting pathogen in each sample. They then generated complete, circular metagenome-assembled genomes for both pathogens and annotated the AMR genes present, providing information that indicated the possibility of a de-escalation to β-lactam-based regimens rather than more intensive antibiotics in a future clinical context.

While the routine blood cultures remained negative after five days, the team’s proof-of-concept study showed the potential of metagenomics to identify infective endocarditis pathogens ‘within a matter of hours’⁴.

Pinpointing pathogens with rapid targeted sequencing

3. Implementing portable, real-time 16S rRNA sequencing in the healthcare sector enhances antimicrobial stewardship. Lancet (2026)

In the UK, Cunningham-Oakes et al. used nanopore 16S ribosomal RNA (rRNA) sequencing for rapid pathogen ID to tackle the ‘silent pandemic’ of AMR⁵. They validated their targeted, culture-free technique on over 100 samples from seven NHS hospitals, comparing against the commonly used Sanger sequencing and MALDI-TOF.

On average, just two hours of sequencing on a MinION Flow Cell was all they needed to identify the pathogen present. The only discrepancies between the workflow’s results and those of standard-of-care techniques were due to the higher resolution possible with nanopore sequencing, revealing additional pathogens or providing species-level ID instead of genus-level. For over half the samples, the data revealed information that could impact antibiotic stewardship, demonstrating its potential to aid effective treatment and cut unnecessary antibiotic use.

4. Clinical validation and utility of targeted nanopore sequencing for rapid pathogen diagnosis and precision therapy in lung cancer patients with pulmonary infections. Front. Cell. Infect. Microbiol. (2026)

Over half of patients with lung cancer develop pulmonary infections⁶, making rapid ID critical. At Hefei Cancer Hospital, Chinese Academy of Sciences, China, researchers investigated targeted sequencing as a method to characterise these infections⁷.

The team used a GridION to sequence targets covering the 16S and 18S ribosomal RNA (rRNA) genes, the internal transcribed spacer (ITS) region for fungal ID, virus-specific regions, and AMR genes. This non-invasive method, using sputum samples, revealed thousands of microbes and over 100 resistance genes.

The nanopore workflow not only showed strong concordance with metagenomic Illumina sequencing for respiratory pathogen detection but also identified significantly more potential pathogens in 40% less time. Results obtained from this research indicated the future potential for improved clinical outcomes, including rate of improvement, shortened antibiotic duration, and reduced broad-spectrum antibiotic exposure that could put immunocompromised cancer patients at further risk.

The researchers also discovered a correlation between lung microbiome features and different tumour treatment outcomes, highlighting the potential to reveal further information that could inform lung cancer treatment.

Protecting against hospital-associated infections through genomic pathogen surveillance

5. An open-source nanopore-only sequencing workflow for analysis of clonal outbreaks delivers short-read level accuracy. J. Clin. Microbiol. (2025)

Researchers are also using nanopore technology to understand and mitigate potential hospital outbreaks. In the USA, Vereeke et al. compared nanopore isolate sequencing performance against Illumina short-read sequencing, using core genome multilocus sequence typing (cgMLST) to infer how pathogen genomes were related⁸.

After seeing high concordance between the technologies in benchmarking, the team validated their approach on four research isolate sets from retrospective hospital outbreak clusters. This produced fully concordant phylogenies for all four sets compared to short-read references. As well as delivering the same accuracy as Illumina sequencing, the authors highlighted the low cost, speed, and portability of the Oxford Nanopore platform, representing key advantages for hospital outbreak detection.

6. Decentralised nanopore genomics reveals diverse Klebsiella pneumoniae and no evidence of patient–patient transmission in a New Zealand hospital. Microb. Genom. (2026)

Klebsiella pneumoniae is a prominent cause of healthcare-associated infections and is linked with high mortality⁹. In a 15-month prospective study at Wellington Regional Hospital, New Zealand, White et al. embedded the MinION into their onsite lab to gain detailed insights into the diversity and population dynamics of this pathogen¹⁰.

By sequencing 157 K. pneumoniae isolates in a 24–48-hour workflow, the group produced 118 complete whole-genome assemblies, revealing a highly diverse population (Figure 2).

This allowed the researchers to annotate AMR genes — which they identified as plasmid-borne in 35 isolates — plus virulence loci. Significantly, the data showed no evidence of patient-to-patient transmission, indicating that escalating infection control measures would be unnecessary and showcasing the power of onsite sequencing to deliver actionable data that could be used for hospital outbreak management.

From pathogen ID to outbreak surveillance: what's next?

These six studies highlight the breadth of infectious disease applications being explored with nanopore sequencing. From identifying bloodstream infections and characterising culture-negative samples, to informing antimicrobial stewardship and tracking potential hospital outbreaks, researchers are demonstrating how rapid access to comprehensive pathogen data could support clinical microbiology workflows and public health surveillance in the future.

Ready to explore the possibilities for your own research? Download our microbial sequencing getting started guide.

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