mNGS Diagnostics: Reducing the Unnecessary Use of Antibiotics

 Do you know that, on average, almost 35,000 Americans die every year just because of misusing antibiotics?

The horrific tale of antibiotic misuse is not a concern in just the US anymore. Instead, it has become a global issue that poses severe threats to global health, food security, and development. According to the World Bank, if we don’t pay due attention to the issue of antibiotic resistance, we could see a GDP fall of 1.1%~8% by 2050. The body also believes that this negligence could push up to 24 million people into extreme poverty by 2030. These numbers indicate the gravity of situation. Widespread resistance to antibiotics prompts changes in empirical treatment options. This affects adverse health outcomes, which could lead to extreme financial constraints on the healthcare systems worldwide. If there is one thing that the COVID-19 pandemic that taught us, it is that health & economy are inseparable.

Antibiotics are a popular choice for treating and alleviating the symptoms of bacterial infections. But when a particular antibiotic is used against a specific strain of bacteria exaggeratedly, things can get complicated. Such bacteria can become resistant to antibiotics. As a consequence, the infections caused by antibiotic-resistant bacteria are even harder to treat. In the USA alone, this resistance accounts for $20 billion in excess direct costs, such as healthcare expenses, and $35 billion in societal costs, such as loss in productivity every year!

In a nutshell, antibiotic resistance leads to increased medical costs and mortality rates.

Dangers of Antibiotic Misuse

The troubling bit about antibiotic resistance is that it is happening everywhere globally, that too at an alarming pace! Can you imagine living in a world where suddenly nothing works against the most common bacterial infections? Here, we are talking about diseases like pneumonia, botulism, and tuberculosis. Meds are not even working against common sinus infections! 

Limitations of Antibiotics

Should one rely on antibiotics to the extent that we have described in the previous lines? Again, not belittling their efficacy, but there is another side of the coin as well. An extensive antibiotic routine can hamper the immune system’s proper functioning by a significant factor. What is more, is that antibiotics have specific side effects too. For example, certain antibiotics can lead to digestive disorders, skeletal system problems, and sunlight sensitivity issues. 

Conventional Methods of Bacterial Detection

Could the problem of antibiotic misuse be mitigated if we knew which type of bacteria we are dealing with precisely? Unfortunately, conventional diagnostic tools don’t give as accurate results as one would like them.

Popular methods for detecting and quantifying bacteria include:

  1. Culture tests
  2. Spectrophotometer method of optical density (OD) measurement
  3. Flow cytometry
  4. PCR testing

However, relying on these tests for accurate diagnostic testing is a big mistake since these tests are prone to false negatives.

But it is desperate times like these in which hope dawns! In this case, that hope is metagenomic next-generation sequencing (mNGS).

mNGS: An Introduction

mNGS works by running all the nucleic acids in a sample containing a mixed population of microbes. Then, assigning these microorganisms to their reference genomes can help determine their proportions present in the sample. This technique is certainly more specific and sensitive as compared to other methods of bacterial detection.

In fact, mNGS can be just the antidote to antibiotic resistance that scientists seek desperately!

Let us back our claim with an example. Psittacosis is a zoonotic infectious disease s transmitted from parrots to humans by transmitting the bacterium Chlamydia psittaci. Signs and symptoms of this disease include fever, headache, chills, and muscle aches.

Here, the critical thing to note is that most cases of Psittacosis are treated without diagnostic testing. And when one relies on culture testing, serologic testing, or PCR testing, there is always a risk of false negatives. That’s where mNGS comes to our aid.

The technique allows detection of the causative bacterium in the respiratory tract samples. Once the presence of C. psittaci nucleic acid in the sample is confirmed, doctors can prescribe the proper antibiotic treatment at the right time. In this case, only tetracycline is enough. Hence, the patient doesn’t have to take any other antibiotics that wouldn’t have helped their cause but would have contributed to the development of antibiotic resistance in C.psittaci.

Isn’t it clever how mNGS saves both patient and the doctor from a lot of guesswork?   However, even though mNGS is much faster, it is also much more expensive compared to a bacterial culture test. One of the major reasons for this is that mNGS has to deal with excessive human DNA contamination in patients’ samples so most of resources are spent to deplete host DNA from the sequencing reads. Imagine how much cost is wasted as host DNA makes up to 99% of sample material!

Micronbane Medical addresses this problem with Devin® filter which helps to deplete host DNA within just 5 minutes and thus enables to reduce sequencing cost in more than a half. PaRTI-Seq® (Micronbane’s proprietary technology of Pathogen Real-Time Identification by Sequencing) build upon Devin® filter optimizes the whole workflow of pathogen identification making it possible to detect even small amounts of pathogens within less than 24 hours upon sample receival.

Accurate diagnosis can help doctors prescribe the antibiotics that a patient needs timely and precisely. Moreover, once an accurate diagnosis of bacterial infections becomes a norm worldwide, it will help to gradually address antibiotic resistance issues.

Find out more about precision medicine and microbial diagnostics developed by Micronbane Medical right here!