Can Genomic Tests Identify the Infectious Causes of Reproductive Losses Better than Traditional Diagnostics?

Project Title

A Microbiome-supported Bovine Reproductive Sequencing Panel (BovReproSeq) for detecting, preventing and mitigating reproductive diseases in beef cattle


Yanyun Huang

Muhammad Anzar, Tim Dumonceaux, Jennifer Town (AAFC Saskatoon); Janet Hill, Cheryl Waldner, Gregg Adams, Jaswant Singh, Dinesh Dadarwal (Western College of Veterinary Medicine); William Hsiao (Simon Fraser University); Maodong Zhang, Anatoliy Trokhymchuk (Prairie Diagnostic Services)

Status Project Code
In progress. Results expected in October, 2026 ANH.10.22


At least a dozen different bacterial, viral, fungal and/or protozoal pathogens can be involved in reproductive failure. Unfortunately, there is no comprehensive diagnostic panel that can look for all of the potential causes of abortion all at the same time. This means that a separate diagnostic test needs to be run for each potential pathogen, one after the other. Producers can stop trying after some negative results, and the diagnosis can be missed. This can also get very costly, very quickly. As a result, most attempts to diagnose the cause(s) of abortion are abandoned before the question is answered, and many abortions end up going undiagnosed or even uninvestigated.

This team plans to develop and apply genomic diagnostic tools to identify (confirm or rule out) infectious causes of early embryonic death and late stage abortion, and build them into a diagnostic panel that can look for multiple reproductive pathogens at the same time.


  • Design a bovine reproductive sequencing panel (BovReproSeq) as a diagnostic tool for infectious reproductive failures (as well as a PCR panel for common and novel repro pathogens)
  • To study reproductive microbiomes in cows and bulls, and their relationships to herd fertility and breeding soundness (including differentiation of pathogenic vs. commensal microbes; this will also inform objective 1, as we as potential probiotics)

What they will do

They will first design a panel of around 15 diagnostic targets known to cause reproductive failure in cattle (BVDV, BHV-1 aka. IBR, Campylobacter fetus venerealis and fetus, Campylobacter jejuni, Chlamydophila abortus, Coxiella burnetii, Leptospira spp, Listeria monocytogenes, Neospora caninum, Tritrichomonas foetus, Trueperella pyogenes, Ureaplasma diversum, Salmonella spp. and Mycoplasma bovis). They will also use high throughput DNA sequencing to identify additional, unknown microbes; this will also help to detect new variants of known pathogens.

They’ll design the panel based on genomic sequencing technology. This panel will be first tested with known positive materials. PCR, a more traditional method will also be used to compare performance of this new panel.  After testing with known materials, a similar comparison will be done using diagnostic submissions from 200 reproductive failure cases (from the WCVM’s disease investigation unit, the C3SN, and PDS). The cost of the new panel will also be compared to current tests.

When diagnosing disease, its also helpful to know what “normal” looks like. But little is known about what microbes are normally found in healthy reproductive tracts of both cows and bulls. A related study will collect vaginal and uterine from cows and semen and preputial samples from bulls varying in age, breed, location, breeding soundness, and stage of the estrous cycle to characterize the microbial populations of healthy reproductive tracts. These microbial profiles will be related to reproductive outcomes in the breeding herd at the Livestock and Forage Centre of Excellence as well as with the results from the new diagnostic platform.


More rapid, accurate and cost-effective diagnostic tests will help producers and veterinarians respond more quickly and effectively to cases of reproductive failure.