Clinical metagenomics with Oxford Nanopore for bloodstream infection: species ID and AMR prediction
The Lancet Microbe · 2025
Clinical StudyExternal link only
Curated peer-reviewed / authoritative reference. Open the source link for the full text.
Genome Sequencing
Next-Generation & Whole Genome Sequencing (Oxford Nanopore)
Comprehensive pathogen genomic characterisation, resistance analysis and outbreak investigation using Oxford Nanopore long-read sequencing.
Method
NGS / Whole Genome Sequencing (Oxford Nanopore)
Turnaround
Data to be updated
Specimen
Whole Blood (EDTA), Sputum, Tissue / Biopsy, Pus / Aspirate
Sample volume
Data to be updated
Why This Test Matters
Next-Generation Sequencing (NGS) allows entire genomes to be sequenced quickly and affordably — processing millions of DNA strands simultaneously — and has revolutionised genetics, biology and medicine, including cancer research, genetic-disorder diagnostics and pathogen genomics. For infectious diseases, ID Labs performs NGS specifically through Oxford Nanopore sequencing technology.
Clinical Background
Whole Genome Sequencing determines the complete DNA sequence of an organism's genome at a single time — covering all chromosomes — to identify variations, mutations and anomalies linked to disease, traits or evolutionary change.
The Diagnostic Challenge
Current Diagnostic Methods
How the ID Labs Test Helps
How the Test Works
- 01Sample collection: DNA is extracted from the sample (blood, saliva, tissue, culture isolate)
- 02DNA fragmentation / library preparation with adapters
- 03Sequencing: as DNA or RNA strands pass through nanopores in a synthetic membrane, each nucleotide causes a unique disruption in the electric current
- 04Real-time data analysis determines the nucleotide sequence
- 05Data assembly into a continuous genome using bioinformatics tools
- 06Interpretation and report
Test Methodology
MethodologyNGS / Whole Genome Sequencing (Oxford Nanopore)
TechnologyOxford Nanopore sequencing
InstrumentOxford Nanopore platform
DetectionData to be updated
Specimen Information
Whole Blood (EDTA)
- Collection
- Venepuncture into EDTA tube using aseptic technique.
- Minimum volume
- 2 mL
- Recommended
- 3–5 mL
- Transport
- 2–8 °C, do not freeze
- Storage
- 2–8 °C
- Stability
- Data to be updated
- Rejection criteria
- Clotted, haemolysed or unlabelled samples; wrong anticoagulant.
Sputum
- Collection
- Deep cough specimen into a sterile wide-mouth container after rinsing the mouth.
- Minimum volume
- 1 mL
- Recommended
- 3–5 mL
- Transport
- 2–8 °C
- Storage
- 2–8 °C
- Stability
- Data to be updated
- Rejection criteria
- Saliva-only samples (watery, no purulent material).
Tissue / Biopsy
- Collection
- Aseptically collected tissue in sterile container with a small amount of sterile saline.
- Minimum volume
- Data to be updated
- Recommended
- Data to be updated
- Transport
- 2–8 °C
- Storage
- 2–8 °C
- Stability
- Data to be updated
- Rejection criteria
- Formalin-fixed tissue is unsuitable for culture and most molecular assays.
Pus / Aspirate
- Collection
- Aspirated pus in sterile container or swab in transport medium.
- Minimum volume
- 0.5 mL
- Recommended
- 1–2 mL
- Transport
- 2–8 °C
- Storage
- 2–8 °C
- Stability
- Data to be updated
- Rejection criteria
- Superficial swabs contaminated with skin flora.
Specimen Container
Container information: data to be updated.
Targets / Analytes / Organisms
Validated target list: data to be updated. Please contact ID Labs for the current configuration.
Technical Performance
| Characteristic | Value | Source |
|---|---|---|
| Analytical / clinical performance | Performance characteristics: please contact ID Labs — data to be updated. | ID Labs Validated Performance |
Clinical Utilization
Pathogen identification where conventional methods fail, comprehensive resistance-gene characterisation (including TB drug resistance), strain typing, outbreak investigation and epidemiology. WGS is not necessary for every routine infection — it is reserved for cases where its depth changes management or answers public-health questions.
Advantages
- Comprehensive analysis: complete view of the genome detecting a wide range of genetic variations
- Long-read, real-time data generation with portable devices
- Precise identification of genetic changes not detectable with other methods
Limitations
- Requires bioinformatics expertise and significant analysis time
- Not a first-line routine test for common infections
- Cost and turnaround exceed targeted tests
- Detection of resistance genes still benefits from phenotypic confirmation
Conventional vs Advanced Technology
| PCR vs Multiplex PCR vs NGS vs WGS | ||||
|---|---|---|---|---|
| Feature | PCR | Multiplex PCR | NGS | WGS |
| Scope | Single target | Dozens of defined targets | Millions of fragments | Entire genome |
| Question answered | Is this pathogen present? | Which of the likely pathogens? | Broad genomic survey | Complete characterisation |
| Routine use | Yes | Yes | Selected cases | Selected cases |
Publications & Scientific Evidence
Nanopore adaptive sampling for host depletion in clinical metagenomics
Briefings in Bioinformatics · 2022
Technical EvaluationExternal link only
Curated peer-reviewed / authoritative reference. Open the source link for the full text.
Discuss this test with our scientific team
Panel configuration, specimen logistics and turnaround details on request.
Information on this page is educational and does not replace professional clinical judgment. Performance values are labelled by source (ID Labs Specification / ID Labs Validated Performance / Manufacturer Specification / Published Scientific Evidence). Molecular results must be correlated clinically and, where appropriate, confirmed by culture and phenotypic susceptibility testing.