First Genome of Cryptosporidium serpentis Unlocks New Era in Exotic Animal Diagnostics MiDOG Animal Diagnostics

April 16, 2025

Advancing Veterinary Science Through Whole Genome Sequencing

In a major leap forward for microbial diagnostics and exotic animal health, MiDOG has completed and published the first genome sequence of Cryptosporidium serpentis – a dangerous parasite that poses a serious health risk to snakes.

This genomic achievement is not just a first-of-its-kind – it’s a clear signal that next-generation sequencing (NGS) is transforming how we approach parasitic infections in exotic pets and wildlife, providing new tools to identify and understand elusive pathogens that traditional methods often miss. At MiDOG, we are pushing the boundaries of science and advancing the field with every genome sequenced.

**What Is Cryptosporidium serpentis and Why Does It Matter?**

Cryptosporidium serpentis is a protist parasite that causes chronic, often fatal infections in snakes, especially those in captivity. Prior to this breakthrough, detection methods relied on PCR assays targeting small DNA fragments, which limited both diagnostic sensitivity and our broader understanding of this parasite’s genetic makeup.

Thanks to this genome assembly – spanning 6.5 million base pairs, with 86% genome completion and 0% contamination – and now publicly available on NCBI GenBank, MiDOG has delivered a critical resource that enables:

🧬 Species-level identification of C. serpentis
🔬 Comparative analysis with other Cryptosporidium strains, including those that affect humans
🦠 Discovery of potential virulence genes and antimicrobial resistance markers
🔍 Integration into shotgun metagenomic workflows for enhanced screening

“Before this, there was no genome for this parasite at all. Everything we knew was based on visual microscopy or small PCR targets,” said Mark Yacoub, MiDOG’s Microbiome Scientist. “Now, we can screen for it, study it, and compare it to other pathogens on a whole new level.”

How MiDOG Achieved It: A Precision Genomics Workflow

The sample was obtained through collaboration with Dr. Bogan from the Central Florida Zoo, who provided a stomach wash from an infected snake. The sequencing challenge lay in isolating the parasite’s DNA from the surrounding biological material – which included bacteria, digested food, and host tissue.

With support from the MicroBioMix sequencing team and MiDOG’s internal bioinformatics pipeline, the team achieved a high-quality, clean genomic assembly – an impressive feat considering the complexity of the raw sample.

Why This Is a Big Deal for Veterinary Microbiome Research

There are a large number of pathogens – especially in exotic mammals and reptiles – that we still know very little about. Traditional detection tools provide limited information, particularly when dealing with understudied species like Cryptosporidium serpentis. MiDOG’s sequencing efforts help fill the gaps in current knowledge, opening new pathways for diagnostics, treatment, and comparative research. This work reflects our drive to push the boundaries of science and advance the field of veterinary microbiome research.

This milestone marks several key advances:

🧫 Integration of exotic parasite genomes into shotgun sequencing pipelines
🧠 Improved diagnostic potential for chronic, unexplained infections
🌍 Shared genomic data for the global scientific and veterinary community
🔬 A stronger foundation for future research on reptile microbiomes and disease evolution

Importantly, this genome is now accessible to the broader community, helping researchers track genomic mutations, explore functional gene pathways, and better understand host-pathogen interactions in reptiles.

What’s Next?

Hot on the heels of this achievement, MiDOG has completed a second genome – this time for a canine bacterial pathogen – with another publication and database release on the horizon.

These developments are part of MiDOG’s broader mission to advance microbial diagnostics through precision sequencing, empowering both veterinarians and researchers with better tools to identify, treat, and prevent infection in animals of all species.

📂 Access the Genome

The Cryptosporidium serpentis genome is now live on NCBI GenBank and can be accessed here:
🔗 https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_049309605.1/

If you’re a veterinary professional, microbiologist, or research institution interested in applying this data or collaborating, reach out to our team at MiDOG.

Stay tuned – more genomic breakthroughs are coming soon.

Categories: Bacterial Infections, Exotic Pets, Gastrointestinal Health, Gut Microbiome, Next-Gen DNA Sequencing Technology

Validated by Veterinarians

“Clients expect their veterinarians to stay up to date on all matters that affect the health and well being of their non-human family members. The current technique that we have used to determine the presence and antibiotic sensitivity of organisms causing disease in our pets is over a century old.

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Martha Smith-Blackmore, DVM, President of Forensic Veterinary Investigations, LLC – Boston, MA

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Kathy Wentworth, DVM, Diplomate ABVP Canine and Feline Practice – PetPoint Medical Center, Irvine, CA

“The MiDOG staff was extremely helpful and supportive.”

Cathy Curtis, DVM – London, UK

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Michael Kavanagh, DVM, Practice owner – Saddleback Animal Hospital, Tustin, CA

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Richard Harvey BVSc DVD DipECVD PhD FRSB FRCVS – European Specialist in Veterinary Dermatology – Head of Dermatology, Willows Veterinary Centre & Referral Service – Solihull, England UK

“I have been using MiDog for over 4 years now and exclusively as my test of choice for all cultures for 3 years. It is so great to submit a culture and feel confident there will be a result when it comes back, especially for urine cultures. The reports were intimidating at first because they contain so much information. After the first few, I am now quickly able to glance over it and pick out the highlights. I can then come back later and pour over all the details. I have been extremely pleased with my patients’ results using the test as well. I don’t envision ever going back to traditional culture and susceptibilities again.”

Brian M. Urmson, DVM, Columbiana Veterinary Associates

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Dr. Melissa Giese, Chicago Exotics Animal Hospital

“MiDOG’s diagnostic approach offers the unique ability to identify pathogens that evade traditional culture and sensitivity testing. I have found that adding a molecular based testing approach in the form of Next Generation Sequencing (NGS) from MiDOG to my routine diagnostic cultures can be extremely helpful in the identification and diagnosis of uncommon pathogens in veterinary medicine.”

Dr. Wayne Rosenkrantz, Animal Dermatology Clinic – Tustin

“She [Dr. Krumbeck] really did a great job of making complicated concepts accessible and demonstrating the value of your services. I’m really looking forward to working with MiDOG on my research project!”

Dr. Yaicha Peters, Animal Dermatology Clinic – San Diego

“As a proud collaborator with MiDOG, I deeply appreciate their dedication to fostering partnerships between industry and veterinary experts. Their commitment to enhancing diagnostic quality for veterinarians is commendable. In my experience, their support has been invaluable, earning them a ‘Double A+, Triple Star’ rating. Their assistance has been faultless, contributing significantly to the success of my projects and studies. I eagerly anticipate our continued collaboration.”

Dr. Richard Harvey, BVSc DVD DipECVD PhD FRSB FRCVS; European Specialist in Veterinary Dermatology

“We’re seeing that, if we prescribe too many antibiotics or they’re taken too frequently, animals are developing inappropriate or pathogenic strains of bacteria. We’re also seeing that our antibiotics are just not working against them anymore… It’s a good example of why we need better diagnostic testing, like MiDOG, so that we’re selecting the correct antibiotic every time our patients have an infection.”

Dr. Alissa Rexo, DVM, CVA, DACVD, Mid-Atlantic Veterinary Dermatology

“The NGS technique as offered by MiDOG is wonderful because pathogens like Melissococcus plutonius, for example, are difficult to grow and keep alive in the laboratory. A standard laboratory cannot truly examine or even properly diagnose this pathogen in bee hives at this time. But with NGS, we can reliably diagnose it.”

Dr. Joerg Mayer, Entomologist and Microbiologist at the University of Georgia

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Dr. Jeremy Rayl – Veterinarian, Block House Creek Animal Hospital, Cedar Park, Texas

“With MiDog results I not only receive a list of organisms detected in the sample, but also cell counts which allow me to target the most abundant pathogens or the most pathogenic. The identification of antimicrobial resistance genes is also helpful in selecting an appropriate antibiotic. Another benefit is that sample handling is less prone to risk of overgrowth and is stable at room temperature. Easy and informative. A great tool in our diagnostic toolbox!!”

Lauren Palmer DVM, MPH, Marine mammal Care Center Los Angeles

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Patricia Latas, DVM, Wild Parrot Coalition

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Dr. Tara Klimovitz, Stay Pet Veterinary Hospital