Nanopore metagenomic sequencing vs culture

When an infection needs to be investigated, Nanopore metagenomic sequencing can complement culture, but it does not replace it in every case. The two techniques answer different questions: culture looks for viable microorganisms, while Nanopore analyses the genetic material present in the sample.

In summary:

• Microbiological culture makes it possible to recover viable microorganisms and can facilitate phenotypic antimicrobial susceptibility testing, but it depends on whether they grow under the conditions used.
• Metagenomic sequencing analyses genetic material and can detect, simultaneously, microorganisms that are difficult to culture or were not initially suspected.
• A metagenomic result must be interpreted alongside the sample, the amount of genetic material, possible contamination and clinical data.
• Detecting resistance-associated genes does not always demonstrate phenotypic resistance; the technique should be selected according to the clinical question.

The 2026 mLife review and the prospective study of bloodstream infections published in Microbiology Spectrum (2025) support its potential value, although their findings do not allow the usefulness of Nanopore to be generalised to all samples or infections.

What is the difference between Nanopore metagenomic sequencing and culture?

Culture attempts to grow viable microorganisms under specific conditions, whereas Nanopore metagenomic sequencing directly analyses the genetic material in a sample. As a result, they may produce different findings and should be compared according to the suspected microorganism, the type and quality of the sample, and the treatment received.

Metagenomics is the simultaneous analysis of the genetic material in a sample, without necessarily being limited to a microorganism selected in advance. Nanopore is a sequencing technology that makes it possible to study this genetic material and provide a broad view of the microorganisms detected.

Culture can provide a viable isolate for further microbiological testing. By contrast, sequencing can detect genetic material without, on its own, showing that the microorganism is alive or causing the infection. According to the mLife review (2026), interpreting metagenomic results requires integrating sample quality and the clinical context; the prospective study in blood published in Microbiology Spectrum (2025) is limited to that sample type and syndrome. For bloodstream infections, see the blood metagenomic test.

When can Nanopore metagenomic sequencing offer advantages?

Nanopore metagenomic sequencing may offer advantages when several microorganisms need to be explored at once, when difficult-to-culture agents are being considered, or when studying an infection after antibiotics. However, this technical possibility does not by itself demonstrate clinical utility: the result must be consistent with the sample, the pre-test probability and the patient’s clinical situation (mLife, 2026).

It may be particularly useful for guiding the assessment when:

• a polymicrobial infection is suspected;
• there is no single microbiological hypothesis;
• difficult-to-culture or slow-growing agents are being considered;
• previous antimicrobial treatment may make culture recovery more difficult;
• several microbial groups need to be analysed in the same sample.

In blood, a prospective study evaluated rapid metagenomic sequencing of cell-free microbial DNA using Nanopore to support the investigation of bloodstream infections (Microbiology Spectrum, 2025). This result cannot automatically be extrapolated to the usefulness of the technique for all sample types or clinical syndromes. To explore the available options, see the Xenogene test catalogue.

What are the limitations of Nanopore compared with microbiological culture?

Nanopore metagenomic sequencing has limitations: it can detect DNA or RNA without demonstrating that the microorganism is alive or causing the symptoms, it can be affected by contamination or colonisation, and it cannot rule out an infection when the sample contains little genetic material or the material is degraded, according to a 2026 review.

In practice, it is particularly important to consider:

• A contaminated sample may lead to detections that do not represent the infection.
• Finding several microorganisms does not, on its own, demonstrate a polymicrobial infection.
• A negative result may be due to a low quantity of genetic material, degradation or inadequate sample collection.
• Detecting a gene associated with resistance is not equivalent to demonstrating resistance to a specific antibiotic.

The report should therefore be assessed alongside the clinical findings, culture results and previous treatments. In severe infections, the AMC Critical test requires professional assessment; Nanopore may help guide decisions, but it does not, on its own, establish the cause or antimicrobial susceptibility.

What information about antimicrobial resistance can it provide?

Metagenomic sequencing can identify genes or markers associated with resistance, but their presence does not always predict how a microorganism will respond to each antibiotic. Phenotypic susceptibility, measured using microbiological methods on a viable microorganism, provides additional evidence that must be considered alongside the sample, the clinical context and the applicable guidelines (mNGS review).

In practice, it is useful to distinguish between:

• Genotypic detection: identifies genetic material associated with resistance mechanisms.
• Phenotypic testing: observes whether the microorganism grows in the presence of specific antimicrobials.
• Interpretation: depends on the microorganism, the detected gene, its genetic context, the sample and the databases used.

A gene may not be expressed, may belong to another microorganism in the sample or may not allow a response to all drugs to be inferred. For this reason, the result can provide guidance, but it does not determine treatment on its own. If you need help assessing a report or understanding the scope of the analysis, you can contact the technical team.

How should a Nanopore result be interpreted alongside culture?

A Nanopore result should be interpreted together with the quality and origin of the sample, signs and symptoms, clinical examination, previous treatments, culture and other tests, as well as the detected signal and the plausibility of the microorganism; on its own, it can provide guidance, but it does not establish the diagnosis or determine treatment.

The detected signal or relative abundance does not necessarily correspond to viable microbial load or demonstrate causality. It is important to consider:

• whether the microorganism is compatible with the anatomical site and clinical presentation;
• whether the sample may contain normal microbiota or contaminants;
• whether the culture was positive, negative or inconclusive;
• whether antimicrobials were given before the sample was collected.

Integrated interpretation is particularly important when Nanopore and culture results do not agree. The mLife mNGS review (2026) highlights that the result should be incorporated into the clinical and microbiological context, rather than read in isolation (review of metagenomic diagnostics). The report can support the assessment, while diagnosis remains the responsibility of the healthcare professional. Sophia can help interpret clinical reports, but does not replace clinical judgement.

Frequently asked questions

Can metagenomic sequencing detect an infection after antibiotics have been started?

It can detect genetic material even after antimicrobial treatment has begun, but the result depends on the sample, the amount of genetic material and the microorganism involved. Previous treatment may also reduce recovery in culture. According to the mLife review (2026), this context should be reported and incorporated into the clinical interpretation.

Does a negative Nanopore result rule out an infection?

No. A negative Nanopore result does not, on its own, rule out an infection. The sample may contain an insufficient amount of genetic material, deteriorate during processing or not represent the site of infection. The mLife review (2026) notes that the result should be assessed alongside the clinical suspicion, sample type and other microbiological tests.

Does metagenomic sequencing identify every microorganism present in the sample?

Not necessarily. It identifies genetic material that reaches a sufficient quantity and quality for analysis, within the capabilities of the assay. It may detect microorganisms that were not initially anticipated, but it may also find colonisers or contaminants with no causal relationship to the symptoms. For this reason, taxonomic identification does not, on its own, confirm an infection.

What type of sample is needed for a clinical metagenomic analysis?

The sample required depends on the site of infection and the clinical question, so it should be selected by a healthcare professional. Its origin, quality, volume and possible contamination affect interpretation. There is no universal sample suitable for all infections. Before analysis, it is advisable to check the accepted sample type and the intended use of the test.

Can Nanopore determine which antibiotic should be used?

Nanopore does not, on its own, determine which antibiotic should be used. It can identify genes or markers associated with resistance, but this finding does not always predict the microorganism’s susceptibility to each drug. When the treatment decision requires it, the professional may need culture, phenotypic susceptibility testing and clinical assessment. The mLife review (2026) highlights this distinction.

How long does it take for a metagenomic result to become available?

Turnaround time depends on the sample type, the laboratory workflow, quality controls and the interpretation required. A single timeframe should not be assumed for all analyses. The prospective study of bloodstream infections published in Microbiology Spectrum (2025) evaluated a rapid strategy, but its results do not support generalising a timeframe to every sample or service.

View the clinical metagenomic tests for infections available from Xenogene

Sources

• Emerging role of metagenomic next-generation sequencing in infectious disease diagnostics: Clinical integration and future directions — mLife — 2026-04-01
• Application of rapid Nanopore metagenomic cell-free DNA sequencing to diagnose bloodstream infections: a prospective observational study — Microbiology Spectrum — 2025-05-06