Genomic First: MiDOG Uncovers New Castellaniella Species in Critical Respiratory Case MiDOG Animal Diagnostics

June 25, 2025

When two dogs presented with severe, ultimately fatal respiratory disease, the clinical team turned to MiDOG for help identifying the causative agent. What followed was not only a landmark diagnostic effort, but it was also a scientific breakthrough. In a collaboration between veterinary clinician Dr. Lina Crespo Bilhalva and MiDOG scientist Dr. Mark Yacoub, PhD, a complex canine respiratory case became the gateway to something extraordinary: the discovery of a previously unknown bacterial species, now formally sequenced and deposited in NCBI’s public genome repository.

🔗 GCA_049446255.1 – Castellaniella sp.

This case marks a turning point for how next-generation diagnostics can uncover hidden pathogens and reshape our understanding of emerging infectious diseases.

The Case: Two Dogs, Severe Lung Disease, and a Diagnostic Puzzle

The clinical scenario involved two unrelated canine patients with aggressive pulmonary infections. Both cases were advanced, with significant lung damage. Traditional diagnostics failed to produce a conclusive answer, prompting the veterinary team to submit tissue samples to MiDOG.

MiDOG’s initial next-generation sequencing (NGS) analysis revealed the presence of Castellaniella species in both samples, but with a twist:

Sample 1: Castellaniella denitrificans
Sample 2: Castellaniella sp. (unclassified at the species level)

This immediately raised a red flag: despite similar presentations, the infections were caused by different bacterial species, and one of them appeared to be previously uncharacterized.

Whole Genome Sequencing: From DNA Fragment to Scientific First

To dig deeper, MiDOG offered the clinical team whole genome sequencing (WGS) of the second sample process typically reserved for research labs, not routine diagnostics. The team removed all host (dog) DNA from the lung sample, isolating the microbial genome.

This sample had a high bacterial load, which made it ideal for deep sequencing. MiDOG’s team then:

Conducted de novo genome assembly
Mapped the entire bacterial chromosome and plasmid content
Classified the organism down to its closest relatives
Performed functional annotation of over 4,000 genes

The result: a complete genome belonging to a new, previously unidentified species of Castellaniella, a genus known for its resilience in toxic environments.

View of the Genome on NCBI

You can now explore the full genome, publicly available on the National Center for Biotechnology Information (NCBI):

🔗 GCA_049446255.1 – Castellaniella sp.

Key Findings from the Genome

This novel Castellaniella species is far from benign. The genetic architecture revealed a host of traits that explain both its survivability in extreme environments and its pathogenic potential in hosts:

Toxin-Antitoxin Systems

These genes allow the bacterium to secrete toxins that kill surrounding competitors—while simultaneously producing antitoxins that protect itself. This biological warfare mechanism makes it highly competitive within the microbiome and difficult to treat, as it can eliminate both competitors and potentially beneficial flora.

Environmental Resilience Genes

Castellaniella is known to thrive in acidic, polluted, and nitrate-rich environments. This strain carries genes for:

Nitric oxide reduction
Decomposition of heavy metals and toxic compounds

These features, while adaptive in nature, translate into high virulence when infecting a host.

Virulence Factors

The genome is “riddled” with virulence genes, including:

Genes for injecting toxins into host cells
Secretion systems for host cell manipulation
Genetic mechanisms for evading immune response

These features suggest this bacterium is well-equipped to cause tissue damage and resist typical immune clearance.

Plasmids with Antimicrobial Resistance (AMR) Genes

The organism harbored several plasmids, circular DNA molecules that move easily between bacteria. These plasmids carried putative AMR genes, which:

Confer resistance to drugs like ampicillin and trimethoprim
May spread to other bacteria in the environment or host

This adds to the growing concern around plasmid-mediated resistance, particularly in veterinary and zoonotic pathogens.

Structural Genomics: A Deeper Layer of Insight

One of the most striking aspects of the genome analysis was the identification of a mobile genetic elemental segment of DNA that appeared distinct from the rest of the genome due to an abrupt change in GC content (a method called nucleotide skew analysis).

Inside this mobile element?
The cluster of virulence and toxin-antitoxin genes, suggesting that this segment may have been acquired via horizontal gene transfer and may continue to move between organisms.

In other words: this dangerous trait cluster is both portable and likely to spread.

Scientific Integrity Meets Curiosity

MiDOG’s bioinformatics lead didn’t stop just assembling the genome. In an effort well beyond typical diagnostic scope, each of the ~4,000 genes were functionally annotated to determine its potential role in the organism’s pathogenicity and survival strategy.

This level of dedication reflects MiDOG’s mission: to not just diagnose, but to investigate, understand, and advance what’s possible in microbial diagnostics.

Why It Matters

This discovery underscores the future of diagnostic microbiology:

Traditional cultures can miss fastidious or novel pathogens.
NGS identifies everything present, not just what grows.
The whole genome sequencing reveals how and why an organism causes disease.
Publicly available genomes support open science, comparative research, and downstream innovation.

By offering real-time insights into microbial evolution, resistance, and virulence, MiDOG provides clinicians with the tools needed to treat, not guess.

Closing Thoughts

The identification and genome assembly of a novel Castellaniella species from a canine lung infection wasn’t just a diagnostic win, it was a scientific milestone. It reaffirms MiDOG’s role as a leader in precision veterinary diagnostics and microbial discovery.

Want to partner on whole-genome sequencing or advanced microbial analysis? Let’s uncover the unseen, together.

Connect with our team

Categories: Antibiotic Resistance, Antimicrobial Resistance, Bacterial Infections, Dogs, Next-Gen DNA Sequencing Technology, Respiratory Infection

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.

With the emergence of dangerous antibacterial resistance, it is critical that veterinarians are able to offer laser-focused diagnostics and treatment. MiDOG enables us to offer care that exceeds the typical standard of care.”

Bernadine Cruz, DVM, Laguna Hills Animal Hospital Laguna Woods, CA

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Michael Morgan, DVMQuail Animal Hospital, Tustin, CA

“The MiDOG All-in-One Test is amazing, I would use it instead of culture and sensitivity. Such rapid and detailed results, I will reach for MiDOG before culture next time!

Thank you very much MiDOG, for sharing the opportunity to try your technology.”

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

“The MiDOG All-in-One Microbial Test is our new gold standard of pathogen identification. The results are so accurate and valuable – especially with assessing both bacterial and fungal infections with the same sample.

Thank you MiDOG!”

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

“I have had great results using the MiDOG Test. Compared to traditional culture tests, I am better able to target the treatment for dogs because the MiDOG Test is so sensitive that it identifies all pathogens, including bacteria and fungi, as well as antibiotic sensitivity.

The cost and turnaround time are about the same as a culture test, but I get much more data. The test has great performance, and I believe the NGS technology will be a game changer for veterinarians treating dogs with lesions or other infections.”

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

“It’s helpful to have an NGS spectrum because it gives you a broader insight of what’s happening and what might be going on.”

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 that 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 pore 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

“As an exotic veterinarian, there are numerous tests we have to consider to check specific bacterial and fungal organisms based on the species. MiDOG eliminates the need for many of these separate samples and provides definitive results quickly to help us treat our patients more efficiently and effectively. The lab is wonderful to work with and has never rejected our samples- they even processed a lizard toe we amputated and determined the cause of skin infection.”

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

“For me, as a clinician and as a researcher, I see the immense value in the product [the All-in-One Test]. I have had great success using MiDOG clinically, including identifying Mycoplasma in a 24 year old pigeon, a Nannizziopsis spp in a ball python from a large pet distributor, Mycoplasma and Fusobacterium necrophorum co-infection in a peacock, and to identify an abnormal gut GI in a technician’s dog that tested negative for everything else (but we were able to establish what was abnormal, and work toward fixing it).”

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 the 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

“If every rescue and sanctuary could run a scan on new admissions, I think it would open everyone’s eyes. These birds have been through so much and damaged by human pathogens. Plus, the MiDOG test was much more affordable than a battery of PCRs, several c&s, repeated tests, etc. AND non-invasive. Thank you. I would advise every sanctuary and other parrot facility to run MiDOG screening. I know it might reveal more than we want to know.”

Patricia Latas, DVM, Wild Parrot Coalition

“Quality testing is invaluable in my mind, and so far, I am putting my support behind MiDOG because it gives me this great plethora of information but also the expertise in discerning what is normal, not supportive of disease versus the alternative…. I really didn’t understand at first but once I read through all of the information – that it is using DNA of bacteria to isolate instead of lab media that our reference labs do – that is wild and limitless and I love it!”

Dr. Tara Klimovitz, Stay Pet Veterinary Hospital