Pneumonia in pre-weaned calves is frustrating for cattle producers and veterinarians. A previous iGrow article introduced the concept of using the diagnostic lab to better understand these occurrences. In some cases, diagnostic testing can help veterinarians in guiding treatment and future preventive practices; it’s good for cattle producers to understand these methods. Lung tissue is a common post-mortem sample for the identification of specific pneumonia germs. But what about outbreaks where no calves have died? What samples, if any, might be useful from a diagnostic standpoint?

Nasal Swabs

A calf’s nose is the entry route for germs into the respiratory tract. Sampling the nasal passages is relatively easy. However, the germs present in the nostrils may not be the same as those causing the infection in the lower lungs, due to clearance mechanisms that keep them from descending deeper into the lungs. This complicates the interpretation of nasal swabs.

Special skill is not required to collect nasal swabs, but using the right sampling materials (swabs and preservative) is important. Swabs with plastic shafts and Dacron or rayon ends should be used, as should preservatives without antibiotics that could inhibit bacterial growth. Veterinarians will have access to the appropriate materials; sometimes the swabs and preservatives come in a pre-packaged kit. The tubes should be put on ice to keep cool and shipped appropriately to the lab.

Normally, it’s sufficient to sample one nostril per calf. The swab should be inserted as deeply as possible without forcing it. Aiming it toward the outer side of the nostril as it’s inserted sometimes helps. Avoid contamination with dirt, manure, and the calf’s skin; get a new swab and start over if this occurs.

An alternative to these superficial nasal swabs is that of deep nasal swabs. The concept behind their use is that a sample taken deeper in the pharynx more closely represents the bacteria and viruses in the lungs. A guarded swab (to avoid contamination from bacteria in the outer nasal passages) is inserted almost to the back of the throat then the swab is pushed through the outer sheath to get the sample.

Which calves – and how many – to sample?

It’s not economically feasible – nor is it necessary - to sample every calf in an outbreak. Diagnostic testing is not inexpensive. But veterinarians should take a sufficient number of samples to ensure the results represent the group rather than just a handful of animals. Sample size calculations can quickly make a person’s head spin, but in general 10 samples from a moderate- to large-sized herd will likely suffice.

Calves should be sampled relatively early in their course of disease – soon after they’re detected. Those that have recently been treated with antibiotics should be avoided, as this will suppress the growth of bacteria at the lab. In addition, calves that have been recently vaccinated (within the past month) with modified live viral vaccines – whether intranasal or injectable – should not be sampled. Virus recovered from these samples may be due to the vaccine and not the disease process.

Another strategy that veterinarians often consider is to sample sick calves as well as a similar number of non-affected calves. If there are differences between the two groups, this may help identify which pathogens are significant.

Depending on the wishes of the veterinarian, the diagnostic lab may perform several different procedures on the swabs. They will attempt to grow bacteria from the swabs, and may perform polymerase chain reaction (PCR) testing, a very sensitive method for detecting the presence of respiratory viruses. Bacterial culture is a see-what-grows-and-identify-it procedure, while PCR testing is a yes-or-no test for the particular virus. The laboratory can perform antimicrobial sensitivity testing on bacteria grown to aid treatment choices. Veterinarians will want to check with their laboratory regarding current test availability.

Interpreting the results

Because many potentially virulent bacteria can be found normally in the nasal passages, positive results should be interpreted cautiously. However, many investigators are inclined to believe that a consistent finding of a specific bacterial species across a high percentage of sampled calves means a significant problem with that particular bacteria. Sporadic and inconsistent findings of different bacteria may simply represent “normal” inhabitants of the upper respiratory tract.

Identifying respiratory viruses in nasal swabs is usually meaningful, however. Viruses such as BRSV, IBR, and BVD should not normally be found in the upper respiratory tract. These positive findings should be interpreted in terms of recent vaccine use too, as previously mentioned. At the SDSU ADRDL, we commonly identify bovine coronavirus in nasal swab samples. Some of these coronaviruses can be associated with respiratory illness; however, there is a lot yet to learn about their role.

Other diagnostic methods

Veterinarians have a couple other tools available in the attempt to identify germs in the lower respiratory tract of live affected calves. These are more involved procedures that take some skill and practice to master, such as tracheobronchial lavage and transtracheal washes. Both of these techniques aim to get around the problem of contamination from normal bacteria in the nasal passages.

The first step in any diagnostic testing strategy is a clear idea of how the results will be used to help the calves at hand, as well as future groups. Sometimes the most appropriate testing strategy is to not do testing at all. It all starts with a good conversation with the herd veterinarian.