The Future of Metagenomics in Clinical Diagnostics

Highlights from the IBMS Congress 2025 on advancements in metagenomics in microbiology  

As the year draws to a close, the IBMS Congress in Birmingham offered an ideal moment to reflect on how rapidly clinical microbiology is evolving. One of the clearest messages from this year’s programme was the growing momentum behind metagenomics as a diagnostic tool. The field is still maturing, but the discussions, case studies, and accredited workflows presented at IBMS showed just how close routine clinical implementation is becoming. 

This blog summarises the key insights from the medical microbiology session “The future is now: how do we move to metagenomics for microbiology?” and explores what these developments could mean for laboratories preparing for the next phase of molecular diagnostics. 

Metagenomics is entering the clinical mainstream 

The first major takeaway from the session was simple: metagenomics is no longer a distant aspiration. Several UK centres have now built or are building pipelines capable of identifying pathogens directly from complex clinical samples. As sequencing platforms become faster and more affordable, the question is shifting away from “Is this possible?” and toward “How do we implement this safely, consistently, and within quality frameworks?” 

The presence of accredited methods on the conference stage signalled a step change. Although still limited in scope, these early workflows are beginning to demonstrate what future diagnostics could look like when unbiased sequencing is incorporated alongside conventional microbiology. 

A significant milestone: the first UKAS-accredited metagenomics workflow 

One of the most anticipated talks came from Great Ormond Street Hospital (GOSH), who have successfully implemented the UK’s first UKAS-accredited metagenomic workflow under ISO 15189:2022. Their method, developed for brain biopsies and CSF, removes host DNA at the bioinformatics stage and has been in development since 2020. 

For laboratories considering their own metagenomic pipeline, hearing the GOSH team’s journey was particularly valuable. Their experience highlighted both the promise of the technology and the practical challenges of meeting UKAS expectations. 

 Key challenges they encountered included: 

1. Validation complexity
   Metagenomics can theoretically detect any microorganism, but validating performance across all potential pathogens is impossible. GOSH approached this by designing model groups of organisms to represent key pathogen categories.
2. Comparing results to existing methods
   Because some pathogens detected by metagenomics cannot be identified through conventional diagnostics, validation cannot always rely on comparator methods. Clear rationale and structured validation become essential.
3. Determining limits of detection
   Using mock tissue spiked with known viral copies, they assessed sensitivity while accounting for variables such as sample type, biomass, and host DNA burden.
4. Bioinformatics as a quality-critical component
   GOSH reinforced that bioinformatics must meet the same quality, reproducibility, and traceability standards as the wet lab workflow.
5. External Quality Assurance (EQA)
   UKAS cannot accredit any test where an applicable EQA scheme does not exist. Current EQA availability for metagenomics remains limited to CSF and certain viral targets. GOSH resolved this by running EQA samples on alternative validated methods for comparison.

This EQA challenge will be one of the major constraints for UK laboratories seeking broader accreditation in the coming years. 

Other clinical centres are pushing the field forward 

Two additional presentations demonstrated how UK hospitals are already applying NGS and metagenomics to real clinical problems. 

Whole genome sequencing in wound care 

One talk focused on bacterial whole genome sequencing to support wound management. Human DNA can dominate wound swab samples, often masking clinically relevant microbial signals. Approaches that deplete host DNA make it easier to detect pathogens and identify antimicrobial resistance genes. 

This aligns with the product solutions offered by VH Bio partner Molzym, whose host DNA depletion technologies selectively remove human DNA while preserving microbial cell integrity. By improving sensitivity and reducing sequencing noise, these methods support more informed antimicrobial decisions and better stewardship practices. 

The presentation also highlighted the translational benefit of genomics, demonstrating how sequencing can complement established microbiology rather than competing with it. 

A metagenomic pipeline at St Thomas’ Hospital 

Another talk showcased a metagenomic workflow in development at St Thomas’ Hospital. Their approach uses manual bead beating for host DNA depletion, which they have refined since presenting earlier in the year at ESCMID. Although this introduces longer hands-on time, the team has paired it with a custom bioinformatics pipeline capable of generating incremental automated reports throughout the day. Under certain conditions, this could make same-day metagenomic results feasible. 

Their method differs from Molzym’s  SelectNA™plus workflow used by several VH Bio customers, particularly in its mechanical host-depletion strategy versus Molzym’s chaotropic chemistry. While both approaches demonstrate strong performance, the automated Molzym workflow provides a reproducible, standardised route that fits naturally into accreditation pathways. St Thomas’ plan to pursue UKAS accreditation in the future, and their work highlights the range of approaches being explored within the NHS. 

Our customers are already ahead of the curve 

Alongside the academic and clinical presentations, IBMS reinforced the progress being made by some of VH Bio’s partners and customers. ELDA Biotech, for example, has already implemented an INAB-accredited workflow incorporating Molzym’s host depletion and microbial DNA extraction technologies. Their experience provides a real-world demonstration of how selective host removal enhances sequencing efficiency and improves downstream microbial detection. 

For laboratories considering their own metagenomics journey, ELDA’s example shows that accredited, high-quality host-depletion workflows are not only achievable but already in routine use.
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What these developments mean for the wider diagnostic community 

Across all three talks, several consistent themes emerged. 

1. Workflow design must prioritise quality and reproducibility

Accreditation success will depend on transparent validation, structured documentation, and clinically meaningful outcomes. The sequencing platform alone will not differentiate laboratories. 

2. Host DNA depletion is becoming a key enabler

Whether mechanical, chemical, or computational, host depletion improves sensitivity, lowers sequencing costs, and enhances the interpretability of metagenomic results. Molzym’s automated solutions offer a streamlined route for labs who require high reproducibility and consistent sample quality. 

3. Accreditation pathways remain challenging but navigable

EQA availability remains the biggest constraint. Early adopters provide a useful blueprint, but national coordination will be required for metagenomics to scale. 

4. The diagnostic landscape is shifting

What was once a research tool is now progressing toward routine use. As accreditation frameworks mature and sequencing becomes more accessible, metagenomics is likely to join the mainstream diagnostic repertoire for complex infections. 

Looking ahead 

IBMS 2025 showed that metagenomics in clinical diagnostics is no longer theoretical. Accredited workflows exist. Innovative laboratories are testing new models. Bioinformatics infrastructures are strengthening. Host-depletion technologies such as those provided by Molzym are proving central to improving analytical performance. And VH Bio customers like Elda Biotech are already demonstrating what accredited sequencing pipelines can look like in practice. 

Over the next few years, an increasing number of UK laboratories are likely to evaluate or pilot metagenomic approaches. As technology improves and more EQA schemes emerge, the pathway to routine implementation will become clearer. 

For now, IBMS provided an encouraging glimpse of a future where sequencing sits alongside conventional diagnostics to deliver faster, broader, and more accurate insights into infectious disease – supported by partners such as VH Bio who can help laboratories navigate the evolving landscape. 

Interested in finding out how VH Bio can help implement metagenomics into your lab’s clinical diagnostics? Get in touch for a chat or to arrange a product demo.