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Dissecting diagnostic testing: What you need to know

Theresa Ollivett for Progressive Dairyman Published on 09 June 2017

It is not uncommon to hear layers of skepticism from veterinarians and producers when it comes to testing for pathogens associated with scours and respiratory disease. “Every farm has every pathogen” is a common misconception and rationale for not testing.

“Most farms have most pathogens at one time or another” might be a more appropriate perspective and implies the profile of pathogens associated with dairy can vary from farm to farm, and may change over time.



Working as a team with your veterinarian and diagnostic laboratory is important for having a good grasp on appropriate diagnostic testing and which pathogens to look for when you do. Interpretation of results is another critical step that should involve expert input because not all positive test results are equivalent, nor necessarily an indication of a major problem.

This article will not focus on all of the different diagnostic tests available for diagnosing specific conditions in cattle. Instead, it will highlight an approach to testing and focus on how a couple of common diagnostic tests can be integrated into routine calf health monitoring and when investigating any new problems associated with calf scours and respiratory disease.

The results from diagnostic tests can answer several questions regarding gastrointestinal and respiratory health. Is a specific pathogen present? How much of that pathogen is present? If it is a bacteria, is it sensitive to the antibiotic used to treat that condition on the farm? If samples are not collected from the right animals or submitted properly for the correct tests, interpreting the test results can be difficult.

The worst case scenario occurs when time and money are wasted to obtain results that are not capable of answering the questions being asked and additional samples need to be submitted. This strains both relationships and everyone’s faith in the whole process.

Our approach has been to take fresh samples from at least six calves that have not been administered antibiotics and submit for pathogen testing in each individual calf. This process creates a pathogen profile for the herd specific to the age of the calves sampled and the time of year when the samples were submitted.


Variation in the pathogen profile in a herd over time often suggests protocol drifts or breaks in biosecurity.

Fecal samples should be tested for the pathogens typically associated with diarrhea in calves of the age represented on the farm. It is common for diagnostic laboratories to be proactive about developing different panels for investigating calf problems.

This is more efficient and cost effective than submitting samples and requesting a whole bunch of individual tests. Most commonly, these panels include some combination of tests for cryptosporidium, rotavirus, coronavirus, and Salmonella spp. and E. coli.

For example, if the problem is diarrhea in 10- to 14-day-old calves, the most appropriate panel would not include testing for E. coli, since this is mainly a problem in calves less than a few days old.

Understanding how to interpret the test results is important and typically related to the type of testing performed. At this point, many fecal pathogens can be identified and quantified using PCR, a test for the DNA from a specific pathogen. The results are presented in two ways.

The first is a numerical answer – the CT value or cycle threshold. The CT value is indicative of how much pathogen DNA was detected. Lower CT values indicate more pathogen DNA (and therefore more shedding of the pathogen) and vice versa. The second result categorizes the response depending on the CT result into positive, negative or suspect. Bacterial organisms can be cultured and assessed for their sensitivity to a variety of antibiotics.


Diagnostic laboratories can vary in which testing strategies they prefer or commonly run, which is why it is important to communicate and work as a team to investigate problems or establish baseline information in your calves. Before submitting samples, consider how you will use the test results.

The purpose of this diagnostic testing for fecal pathogen is, in this case, to understand how much challenge there is in the environment. In other words, how many calves are exposed and then infected with these organisms.

In general, we are going to find most, if not all, of these pathogens on our dairy farms. What we’re really trying to figure out is whether or not too many calves are being exposed due to excessive environmental contamination.

A general rule of thumb we use at the University of Wisconsin – Madison, and which has been recommended for a long time by Dr. Sheila McGuirk, a professor at the University of Wisconsin – Madison, is: If we test six calves, we do not want to see any more than two of them positive for rotavirus, coronavirus or cryptosporidium.

If we see more, this suggests the environment is too heavily contaminated and the challenge is too overwhelming. We have a zero-tolerance policy for most types of salmonella, however. At the end of the day, we are looking for the proportion of calves that are positive. We need to submit individual fecal samples to determine this, not pooled or combined samples.

Mixing fecal samples from several areas, called composite sampling, however, can be useful to determine the presence of salmonella and the location of hot zones of environmental contamination.

Common places would be the feed alley or parlor holding area or calving pen. Again, the question here is: “Do I have this organism on the farm, and if I do, where is it located?”

Pooling fecal samples is slightly different and implies we’re taking fecal samples from individual calves, mixing a certain number of them together and then sub-sampling from that mixture for the test. Results from pooled fecal samples do not indicate the proportion of calves affected and rarely provide useful information.

Relative to respiratory disease testing deep nasal pharyngeal swabs for bacterial and viral pathogens are one of the more common means of understanding the pathogens involved in respiratory disease on the farm.

Again, we often find most of these organisms on most farms, but a greater relative proportion of one versus the other can help guide management decisions regarding vaccination protocols, disease detection problems and treatment strategies.

Again, PCR is commonly performed in conjunction with culturing and identifying sensitivity patterns for the bacterial organisms. Viral pathogens are also identified by PCR for respiratory disease.

Having a good working relationship among the farm, the veterinarian and the diagnostic lab is critical for understanding what samples should be collected from which calves and where they should be submitted.

Resource personnel at the diagnostic lab can assist your veterinarian and help develop your testing strategy and interpretation of results. Remember, testing is only useful if you are going to do something with the results. Plan ahead to reduce unnecessary testing and expense, and glean the most useful information for managing your calves.  end mark

Theresa Ollivett is an assistant professor of food animal production medicine at University of Wisconsin – Madison.

The author wrote this article on behalf of Agri-Plastics.