Precision diagnostics: A Q&A on next-generation sequencing with Janina Krumbeck, PhD

Traditional diagnostic culture has changed very little since the 1880s, with lengthy turnaround times and "no growth" rates that can reach 70% in some cases. Janina Krumbeck, PhD, cofounder of MiDog Animal Diagnostics, is working to modernize this workflow through next-generation sequencing (NGS). In this Q&A, Krumbeck explains how moving from the petri dish to genomic markers allows for 48-hour pathogen identification, more precise antimicrobial stewardship, and a clear look at the 99% of microbes that traditional methods simply cannot detect.

To start, could you provide some background on yourself and the mission behind MiDog?

Krumbeck: I am a cofounder of MiDog Animal Diagnostics. We founded the company in 2019 to bring next-generation DNA sequencing to the veterinary market as a primary diagnostic tool. My background is in molecular genetics and microbiology; my PhD research focused on how commensal microbes influence gastrointestinal health through probiotics, prebiotics, and synbiotics.

In research, NGS is the standard tool for studying the microbiome. We realized that [although] it was the gold standard in research, no one was utilizing it as a diagnostic tool to identify pathogens causing active infections in pets. We have since expanded from bacterial testing to include fungal and parasite diagnostics, offering an all-inclusive diagnostic for any animal species.

For the clinician, what is the fundamental difference between the NGS technology MiDog utilizes and traditional culture testing?

Krumbeck: Culture testing is based on technology from the 1880s developed by Robert Koch and Louis Pasteur. [Although] groundbreaking at the time, we now know—based on modern molecular markers—that only 1% to 3% of all microorganisms on the planet can actually grow in a petri dish.

There are roughly 100 trillion microbes on the average dog that walks into a clinic. If you rely on culture, you are missing the vast majority of the picture. Molecular diagnostics rely on genomic markers to identify bacteria, fungi, viruses, and parasites. It allows us to see who they are and what they are doing without the limitations of "culturability," allowing for more efficient treatment.

What are the specific clinical advantages of this approach for a practicing veterinarian?

Krumbeck: According to the [American Veterinary Medical Association], 10% to 30% of all diagnostic tests sent out in veterinary medicine return with "no growth" results. In cases of urinary tract infections, that failure rate can climb to nearly 70%. If you use a test with a 30% to 70% failure rate, you aren't getting the information needed to treat the patient efficiently.

We extract DNA from all bacteria, fungi, and parasites in a sample to showcase exactly which pathogens are present. Furthermore, we provide these results in 48 hours. Compare that [with] a fungal culture, which can take 4 to 5 weeks and often still returns with no growth. In many cases, especially with systemic infections, that time difference is literally a matter of life or death.

Is there published research or a specific case study that highlights the efficacy of this technology in a clinical setting?

Krumbeck: We are very research-driven and have published 34 peer-reviewed publications. These range from direct comparisons between culture and NGS to case reports and studies establishing healthy microbiome baselines for various species.

One case that stands out involved a golden retriever named Cooper who suffered from deep tissue pyoderma. The initial culture suggested a Pseudomonas-like organism. [Although] Pseudomonas and Burkholderia are both Gram-negative rods that look similar under a microscope, they are genetically as diverse as a butterfly and an elephant.

Our NGS test identified the pathogen as Burkholderia gladioli within 48 hours. This is an organism typically associated with "onion rot" in plants, but human literature shows it can cause rare pyoderma cases. Identifying it as Burkholderia rather than Pseudomonas significantly changed the treatment protocol. The clinician was able to resolve the case within 2 weeks after previous treatments had failed.

How does the sampling process work? Is there a steep learning curve for hospital staff?

Krumbeck: The same principles apply as they would for culture or PCR [polymerase chain reaction]. We provide collection devices containing a DNA preservation reagent. You simply use the provided swab—or any standard swab used in the clinic—and mix the sample with the reagent.

One major advantage is that the samples are stabilized at ambient temperature for up to a year. This allows a pet owner to take time to decide on testing. Or, if an initial empirical treatment fails, the veterinarian can send the original sample in weeks later because the DNA is preserved as a "snapshot in time."

What is the cost to the clinic, and what does the report actually provide?

Krumbeck: We offer the test at $170 to the veterinarian. This includes the collection devices, FedEx overnight shipping, and the results. The report screens against a database of 65,000 bacteria, 4000 fungi, and 800 protozoa and parasites. It also includes a free veterinary consultation to help interpret results and make treatment decisions.

How does this technology aid in antimicrobial stewardship?

Krumbeck: Accurate diagnosis is the cornerstone of the One Health approach. We often see cases, particularly in otitis, where both Staphylococcus and Malassezia are present. If a culture only catches the bacteria, the clinician might miss the fungal component. By providing a more accurate "bug-to-drug" match, treatment is more targeted. We provide treatment options for 46 different antibacterial drugs, organized in tiers to support responsible antibiotic use.

Can this test be used on patients already receiving antibiotics?

Krumbeck: Yes. Unlike culture, which is often inhibited by antibiotics, NGS is sensitive enough to see [whether] the treatment is working. You can see [whether] the main pathogen is responding or if a secondary resistant pathogen is emerging. Ideally, you test before treatment to select the drug, during treatment to monitor the microbiome profile, and after to ensure the pathogen is eliminated and the commensal flora is restored.

What is next on the horizon for MiDog?

Krumbeck: We are launching our parasite testing this month, and we are expanding our testing to include toxin and biofilm genes. According to the [National Institutes of Health], 80% of all infections are caused by biofilms; we can now identify those markers in clinical samples. Later this year, we also hope to launch whole genome sequencing for viral testing.

To wrap up, what is the most common misconception about NGS that you'd like to clear up for DVMs?

Krumbeck: Many people think of NGS as a PCR panel. It is actually untargeted sequencing. We aren't just looking for 10 or 20 specific things; we sequence every bacterial, fungal, and parasite molecule in the sample. You can imagine it like running millions of PCR panels in parallel without having to preselect what you are looking for. It takes the guesswork out of the diagnostic process.