Changing the Molecular Testing Playing Field: PathogenDx’s D³ Array

February 16, 2023

By Susan Evans

What if you could create a testing environment that enhances the ability for a clinical sample, such as a bacterium responsible for an infection, to find and bind to a molecular detection probe? If you could, you would have the potential to significantly increase the testing speed, improving patient outcome and care, while also increasing the accuracy and sensitivity of the laboratory test. The future of molecular testing.

If only, well—PathogenDx’s proprietary D³ Array technology can do just that. It is a novel, new approach to a multiplexed array, and very exciting. Designed to emulate a three-dimensional structure or scaffold, the D³ Array has a greater surface area than traditional two-dimensional microarrays, allowing for a higher density of molecular probes attached to the surface. The sample can move freely within the 3D structure, in a solution-like environment, increasing the probability of probe sample binding events, while decreasing the time required for hybridization and clinical result reporting.

Before we move on, we should not forget that the ability to print probes and create microarrays was a major advancement in multiplexed molecular testing. The question today is how we can make it better? What are the limitations that can be overcome to take array testing to the next level providing more rapid, sensitive, cost-effective testing results?

Enter the D³ Array. To help us develop an image of what is different, let’s take a walk within a traditional array. If you could shrink, like in the movies, and become very tiny, you would find yourself walking up and down rows of probes bound to the surface of the plate or microtiter well, like rows of grape vines with roots in the ground ensuring each vine stays in place. One of the limitations of a traditional 2D array like this is often steric hindrance. Although the probe has some freedom of movement, it is often limited. The roots are holding them in place and the rows do not always allow for fluidity. In addition, some sample DNA fragments can be quite large. Once the sample and probe find each other, and it may take quite a bit of time, the tail of the sample DNA can often sterically block other binding sites on the 2D array, making it more challenging for additional binding/hybridization events to occur in the surrounding area. Bottom line, the binding is more challenging, taking much longer, requiring more heating and cooling steps, and is cumbersome.

Now, let’s take a walk within a D³ Array. When the sample is added the D³ Array swells to create a unique and fluid-like 3D architecture with probes attached everywhere. If you are walking, the probes are attached to a lacey vine-like molecular structure. The probes are above you, next to you, behind you, all around you. Imagine yourself swimming around the array, as the sample does. You would be surrounded by probes attached, with increased freedom of movement, hanging from every branch of the 3D structure. More probes for the sample DNA to bind to, easier to find, more fluidity facilitating rapid room temperature hybridization, less steric hindrance blocking probes sites for other samples. It’s a totally new environment—more than an incremental next-generation array approach—enabling rapid detection of pathogens and the promise of additional applications in other diseases with molecular biomarkers.

Why is this so important? Rapid and accurate detection of infectious pathogens is critical to optimize patient care, resulting in positive outcomes. Rapid ID of the causative organism and the presence or absence of drug resistant genes will optimize and guide therapy. Effective therapy drives effective patient management, preventing the development of serious complications.

The availability of molecular testing approaches has changed the playing field, moving what has historically been a 2–4-day testing cycle based on culturing and then identification, to a same day or 1–2-day cycle. Amazing progress but there is still room for advancement, and PathogenDx’s D³ Array is a valuable tool in the continuum of major advances in infectious disease testing. D³ Array is fast, reducing the time to result, it can provide both ID and drug-resistant results in a single test, and can simultaneously detect the presence of a wide range of organisms (bacteria, viruses, fungi), as well as the identification of drug-resistant genes enabling the creation of advanced, multiplexed panels in a single ‘well’ test.

A practical example of how this plays out today is researching the cause of the chronic recurrence of Urinary Tract Infections (UTIs). For most cases, UTIs are easy to diagnose and treat, but for a subset of the population this is not true. It gets complicated. In fact, the common terminology to describe this condition is ‘complicated UTIs’. Traditional treatments are not enough, and the infection requires a selection of antibiotics and treatments specifically for treating each unique case of ‘complicated UTI’. We probably all know someone who has dealt with a UTI infection that was difficult to treat, or someone who has had multiple or continuous recurrent bouts with UTI infections. PathogenDx’s D³ Array has the potential to be a valuable tool in the ongoing research to better understand and detect ‘complicated’ UTI infections. There is also a driving need from infectious disease physicians to better understand the surrounding ‘microbiome’ and its relationship to the pathogen causing the infection, and this is where the D³ Array’s potential and power comes through to provide meaningful information to improve diagnosis and treatment. In the case of PathogenDx’s first UTI assay, in a single test the D³ Array can detect 20+ organisms and a wide range of drug-resistant genes enabling the creation of targeted treatment plans that optimize therapy.

The D³ Array is not the only way to get answers, but it is the most cost effective, rapid approach, especially when you know what you are looking for. On one end of the continuum, PCR-based assays are a proven approach for pathogen identification and on the other end, NGS sequencing has emerged as an important discovery tool. The D³ Array is a perfect “best of both worlds” fit when multiple PCR -based assays are needed, which can be time consuming and expensive, and NGS to far more than what is needed. The D³ Array, if needed, can detect 100+ targets in a single reaction, with a single shift time to result. The unique 3D architecture optimizes the speed and sensitivity of the test and enables simplified multiplexed testing.

The D³ Array is a Dynamic, Dimensional, Detection Technology that fills an important technology gap between traditional PCR-based assays and arrays and NGS. The D3 Array provides multiplexed targeted sequence detection that is cost-effective, rapid, and highly accurate and sensitive.  This exciting new technology is perfectly suited for a wide range of research and diagnostic applications.