This week, I had every intention of writing about the Human Microbiome Project and exploring how we, as humans, may be more supra-organisms than individuals since our bacterial population outnumbers our actual human cells.
But something happened last Thursday that changed my focus.
I met with a senior colleague and mentor for a career update, and as always, our conversation was enriching.
We eventually landed on metagenomic next-generation sequencing (mNGS) testing, a topic that excites me.
Me: I've been writing about mNGS and advocating for its broader adoption. I’m an enthusiast, and I’d love to see this become the standard of care in infectious disease diagnostics.
Mentor: That’s great! I’m an enthusiast as well. It would be incredible to have mNGS as the standard of care.
Me: So why haven’t we seen widespread adoption across the country, considering its overwhelming advantages over traditional methods?
Mentor: One word— COST. The test is simply unaffordable.
Me: What do you think will bring the cost down?
Mentor: Competition. Until competition drives prices down further, we won’t see mNGS become the standard.
I’ve encountered two distinct groups of colleagues when it comes to mNGS: those who don’t even know it exists (because you can’t order a test you don’t know about) and my fellow enthusiasts who are restricted by cost and hospital policies.
So, what does a single mNGS test cost today? Around $2,500, with reports ranging from $1,000 to $3,000.
To put this into perspective, the total cost of sequencing the first human genome in 2003 was around $2.7 billion, but today, clinical whole-genome sequencing can be done for under $1,000.
This trajectory shows that with innovation and competition, prices can drop significantly; so why hasn't mNGS followed the same pattern?
Consider the case of a critically ill patient with an undiagnosed infection—mNGS could provide answers when traditional methods fail, yet many cannot afford it with prices still ranging from $1,000 to $3,000.
Compare that to traditional diagnostics— cultures, PCR — which typically cost $100 or less.
I understand that scientific discovery comes with a price, but this raises an important question:
It’s not just about the financial burden of the test.
The real cost is in the:
→ missed diagnoses that leave patients suffering needlessly,
→ extended hospital stays while doctors hunt for answers,
→ broad-spectrum antibiotic overuse when precise targeting would be possible
→ patients who continue to suffer from mysterious fevers of unknown origin because traditional methods fall short.
→ Lost opportunities to identify new or unexpected pathogens
Consider these real-world scenarios:
→ An immunocompromised patient requires rapid, precise diagnosis but can't afford the test.
→ A physician faces administrative barriers to ordering mNGS despite clear clinical need.
→ The insurance companies that refuse coverage, preventing patients from accessing a test that could change their clinical trajectory.
→ The patient with culture-negative endocarditis, where traditional testing fails to detect pathogens like Bartonella, Coxiella, Brucella .
→ The critically ill patient who was given broad-spectrum antibiotics on arrival per “ER sepsis protocols”, yet remains febrile days later with all negative cultures.
If we truly want to see mNGS become a widely used, life-saving tool, we need to tackle the cost issue from multiple angles:
➡️ Market Competition : We need more companies developing & refining mNGS assays, and optimizing processes. Competition historically drives innovation and reduces costs.
➡️ Insurance Coverage: Expanded coverage is essential for making these tests accessible to more patients. This requires demonstrating both clinical utility and cost-effectiveness.
➡️ Hospital Economics: Healthcare systems need to recognize that while mNGS has a higher upfront cost, it can reduce overall expenses through:
Shorter hospital stays
More targeted treatment
Reduced use of unnecessary medications
Fewer complications from delayed diagnosis
➡️ Government Support: Support for research and funding can ease the financial burden on laboratories, ultimately reducing the cost of the test.
➡️ Public funding for diagnostic innovation, similar to vaccine development support, could accelerate cost reduction and accessibility
Metagenomics has proven its worth in infectious disease diagnostics. Now, we need to remove the financial barriers preventing it from reaching its full potential.
As someone who is conscious of both the transformative potential of mNGS and its current limitations, I believe we're at a crucial juncture.
The question now isn't whether mNGS should become the standard of care, it's how we make that happen