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If you ever want to see how bad a problem is, look at how much it costs. Tuberculosis alone costs India, Africa, and Brazil €300 billion / 27 Trillion INR a year in lost productivity and healthcare expenses. That’s one disease.

And here’s the thing: we already have tests for TB. The problem isn’t that we can’t detect it. The problem is how long it takes. Right now, clinicians rely on a combination of qPCR and phenotypic testing to diagnose infectious diseases. qPCR tells you what’s there, phenotypic testing tells you if it’s resistant to drugs, but neither does the job fast enough. You’re looking at days or weeks before you get a full resistance profile. That means more suffering, more spread, and more misuse of antibiotics, which fuels antimicrobial resistance (AMR)—one of the biggest health crises we’re facing.

The cost of this delay isn’t just financial. Every extra day a patient waits for results is another day they’re either getting worse or taking the wrong drugs, helping bacteria evolve defenses against our best treatments. And if AMR keeps accelerating, that €300 billion a year will look small.

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So what’s the fix?

Right now, qPCR and phenotypic testing work sequentially. First, you do a qPCR test to confirm the presence of a pathogen. Then, if the test finds something, you wait for culture-based phenotypic testing to determine if it’s resistant. But what if we could get both answers in one go?

That’s what Targeted Next Generation Sequencing (tNGS) does. Unlike qPCR, which can only test for a few predefined targets at a time, and phenotypic testing, which needs live cultures to grow before detecting resistance, tNGS works at the genetic level. It sequences key regions of the pathogen’s DNA to tell you exactly what’s there and exactly how resistant it is—in a single test.

And it doesn’t just speed things up. It sees more. qPCR can only confirm what it’s designed to look for. If a new resistance mutation emerges, qPCR will miss it. tNGS won’t. It sequences DNA directly, so if a novel mutation confers drug resistance, you’ll catch it before it becomes a problem. That’s how we get ahead of AMR instead of reacting to it.

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Why tNGS is better

If you had a way to test for multiple pathogens, identify resistance, and get results in hours instead of weeks, you’d take it, right? That’s what tNGS offers. Here’s how it compares to the current methods:

• Broad Diagnostic Capability → Detects multiple pathogens and all known resistance genes in a single test.
• Comprehensive Resistance Profiling → Instead of waiting for cultures to grow, tNGS detects resistance genes directly. Faster and more accurate.
• Speed → qPCR requires multiple tests. Phenotypic testing takes days or weeks. tNGS delivers results in hours. </aside>

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How tNGS works?

tNGS is a highly efficient sequencing method that hones in on specific regions of a pathogen’s genome rather than sequencing the entire thing. This makes it cheaper, faster, and more informative for diagnosing infectious diseases and tracking drug resistance.

There are two main ways to run tNGS diagnostic assays:

1. Hybridisation Capture Sequencing
   1. Uses biotin-labeled probes that selectively bind to genetic targets.
   2. These sequences are pulled down using magnetic beads, so only relevant DNA gets sequenced.
   3. Ideal for highly variable regions, like when we’re hunting for unknown mutations.
2. Amplicon-Based Sequencing
   1. Uses multiplex PCR to amplify specific genetic regions linked with drug resistance and/or pathogen identification.
   2. Gives ultra-high depth sequencing, meaning it can detect low-frequency ****variants that traditional methods might miss.
   3. Best for smaller, well-characterised targets.

Once the sequencing is done, bioinformatics tools align the reads to a reference database, detecting mutations—including ones linked to drug resistance.

Unlike qPCR, which only confirms known targets, tNGS can detect novel resistance mutations and co-infections in a single test. That means faster, more accurate diagnoses and fewer opportunities for AMR to develop unchecked.

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Why This Matters

AMR isn’t theoretical. It’s happening now. Every time an infection isn’t properly diagnosed, and a broad-spectrum antibiotic is thrown at it, resistance builds. Right now, 700,000 people a year die because antibiotics didn’t work for them. That number could hit 10 million per year by 2050.

We don’t need to throw more antibiotics at the problem. We need better diagnostics.

qPCR and phenotypic testing got us this far, but they’re not enough anymore. If we want to stay ahead of infectious diseases, we have to move beyond them.

tNGS isn’t just faster. It’s more precise, more scalable, and more future-proof. And that’s exactly what we need to fight AMR.

The question isn’t whether we need to replace outdated diagnostics—it’s how fast we can do it. I want to building a future where fast, affordable, and comprehensive infectious disease diagnostics are the norm in India.

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