A few years after I started my position as a veterinarian in Cornell University’s Ambulatory and Production Medicine Clinic, I inherited the primary vet work for a large dairy farm upon the retirement of my boss. At the same time I began working there, the dairy experienced an outbreak of infectious bovine keratoconjunctivitis, better known as pinkeye, in which the incidence of cases in 4- to 5-month-old heifers skyrocketed from 3% to 80% and much of the lactating herd became affected.

Mcart jessica
Associate Professor – Ambulatory and Production Medicine Clinic / Cornell University College of Veterinary Medicine

After my initial panic, I reviewed the scientific literature on pinkeye development, treatment and prevention, which I describe below along with my personal experiences creating and implementing an autogenous vaccine for pinkeye.   

Pinkeye pathogenesis and the importance of environment, management and nutrition

Pinkeye can be caused by several agents including viral, fungal and bacterial, with commonly implicated agents being moraxella spp., specifically M. bovis and M. bovoculi, and mycoplasma spp. Interestingly, these bacteria are also found on the ocular surface of healthy calves, which means presence of the bacteria alone is not enough to cause disease. As we know from many other bovine diseases, there is an important interaction among an animal, an infectious agent and the environment. The presence of flies, dust or other mechanical irritants and a weakened immune system due to poor nutrition, environmental stress or lack of antibodies can initiate a cascade of events that increase the ability of these bacteria to cause clinical disease.

Pinkeye is characterized by visual changes to the cornea (the clear part of the eye) and the conjunctiva (a clear covering over the white part of the eye) caused by the body’s response to bacterial invasion. We see this clinically as an increase in tear production, blinking, edema of the cornea (which turns it a bluish color), corneal ulceration, presence of small blood vessels in the cornea and light sensitivity. As you can imagine, this is quite painful.

Fortunately, pinkeye is a self-limiting disease, and most animals heal within 60 days with only a small, pinpoint corneal scar left as a reminder. However, a small percentage of animals develop more severe ocular inflammation which results in permanent blindness and/or eyeball perforation.


Unfortunately, few antibiotics are labeled for treatment of pinkeye, most antibiotic treatments minimally shorten the duration of the disease, and adequate pain control can be difficult. In addition, the sheer number of affected animals during an outbreak can make treatment logistically frustrating. As such, prevention of pinkeye is much more rewarding and successful.

Creating an autogenous pinkeye vaccine

Given the high incidence of cases in the herd I was working with, in addition to managing the current chaos, I decided to adjust the farm’s pinkeye vaccination program, as their current program was certainly not working. After some research and discussion with other bovine veterinarians, I decided to go with an autogenous vaccine.

Although there are commercial vaccines available for pinkeye, none contain multiple agents (M. bovis, M. bovoculi and mycoplasma spp.) responsible for the disease. Also, the large antigenic variation among bacterial strains (differences in the molecules the bacteria expose to the animal’s immune system) requires a vaccine that can keep up with these changing antigens over time. In addition, bacterial strains can differ between farms. So I wanted to use a vaccine that would continue to be effective on this specific farm.

Making an autogenous vaccine is not as complicated as you might think, and your herd veterinarian can follow these steps to create a farm-specific vaccination protocol.

Step 1: Collect swabs. “Swabbing eyeballs,” as I call it, is the most important step in the process. This tells us what organisms we are dealing with and becomes the foundation of our autogenous vaccine. For me, this step involves a call to my technical service veterinarian at Vaxxinova (formerly Newport Laboratories) to request shipment of “The Box.” The Box is my favorite part of pinkeye prevention, as it contains everything a veterinarian needs to collect and submit swabs including viral and bacterial media, a submission form and a prepaid shipment label (Image 1).


"The Box" containing swabbing supplies needed for identification of causative pinkeye agents. Photo provided by Jessica McArt.

I swab a total of five animals, each with swabs intended for viral and bacterial media. It is of utmost importance to swab the correct animals, which are those in the early stages of disease, seen with that tear-streaking stain running down their cheeks. Swabbing animals with more advanced disease, such as those with corneal edema or ulcers, will not provide helpful results.

After swabs have been collected, simply fill out the submission sheet and add a cold pack to the box along with the samples, and off it goes via overnight shipping to the diagnostic lab.

Step 2: Consult with diagnostic lab. Swabs are tested quickly for infectious agents and a first report is provided within one to two days of submission by my technical service veterinarian. If swabs did not find causative agents, or there is reason to suspect not all infectious agents were found, a re-swab might be necessary.

Once preliminary results are solidified, bacterial strains are “typed” to assess their antigenic potential and any shift in strain type since a previous swabbing event; this takes another four to six weeks due to the length of time needed to culture mycoplasma.

From here, a conversation between your herd veterinarian and technical service veterinarian will determine the number of bacterial strains to include in the vaccine, and vaccine production will begin. It is important to realize that vaccine production takes approximately 10 weeks, so staying on top of swabbing before outbreaks occur is critical. 

Step 3: Create a herd vaccination protocol. Work with your herd veterinarian to create a vaccination program aimed at disease prevention. Like other vaccines, autogenous pinkeye vaccines work best if administration of an initial and booster dose are completed a month before the peak of disease incidence. For my herd, this meant vaccinating calves at 3 months old with a booster at 4 months old. In addition, since much of the lactating herd was affected, we also gave two doses to all cows. From there, we integrated the vaccine into a routine herd schedule for calves, heifers and cows.

Response and adjustments to vaccine schedule

When the calves that received the pinkeye vaccine at 3 and 4 months old reached the barn where our pinkeye incidence usually skyrocketed, we found that the incidence of affected calves dropped dramatically to less than 5%. Similarly, new pinkeye cases in the lactating herd dropped to zero about a month after administration of the booster dose. My excitement (and relief) was immense.

Cases remained low for eight months when, much to my dismay, I walked through the heifer barn and saw a huge number of pinkeye cases again in our 4- to 5-month-old calves. Turns out that the calves were doing so well, and pinkeye cases were so low, that the heifer manager decided to stop vaccinating. After a brief and firm conversation, vaccination was again begun, and I took the opportunity to swab eyeballs to create an “updated” vaccine. As discussed above, we need to keep up with pinkeye – not only do bacterial species shift but strains of bacteria shift, and thus our vaccine needs to change over time to remain effective.

After switching to the updated pinkeye vaccine, the farm sailed along without issue for another 10 months, at which point we had a resurrection of pinkeye cases in calves. I tracked down the heifer manager again, and it turns out they ran out of vaccine without notifying me of their low stock. This, unfortunately, was a serious issue, as it takes a good four months from swabbing to vaccine shipment. I set off swabbing eyeballs for a third time and modified our vaccine notification protocol to attempt a continuous future supply of vaccine. Fortunately, after dealing with a high incidence of pinkeye in calves for the following four months, implementation of our newly produced autogenous vaccine again reduced the number of pinkeye cases to near zero.

Being a bovine veterinarian is never a boring job, and a year-and-a-half later we again had a pinkeye outbreak, but this time in 3- to 4-month-old calves. Discussion with the herd and heifer managers confirmed the vaccine was being given according to our usual schedule; however, they noted changes in barn movement patterns and barn cleaning frequency. It was clear these management adjustments had increased the social and environmental stress on the heifers, and we decided to add an additional dose of vaccine at 2 months old. This adjustment ended the pinkeye outbreak and remained an effective strategy for a year-and-a-half, at which time we had yet another pinkeye outbreak in 3- to 4-month-old heifers. No changes were reported in vaccine administration or heifer movement or management. I was concerned we had experienced a large shift in bacterial strain, so I swabbed eyeballs again. Lo and behold, we indeed had a large shift in several bacterial strains which had resulted in our vaccine’s ineffectiveness. An updated vaccine took care of the problem, and in discussion with the herd manager, I decided to maintain a six-month swabbing and vaccine production schedule going forward to stay on top of vaccine shifts.

What I learned about pinkeye and autogenous vaccines

Pinkeye can be a large and annoying issue on many dairy herds in both calves and cows. Treatment is often unrewarding and extremely labor-intensive, and the pain associated with pinkeye is a welfare concern.

To create the best environment for our calves and cows to succeed, we must remember that disease development depends on a triangle relationship among the animal, the infectious agent and the environment. In addition to good housing and nutrition, implementation of an autogenous vaccine for pinkeye can be a powerful tool to prevent disease. 

Four key points to remember when adding an autogenous pinkeye vaccine to your herd:

  1. Maintain good communication between your herd veterinarian and the farm management team to discuss changes in vaccination protocol or farm management practices.
  2. Be ready to adjust the vaccination schedule over time depending on the age of animals experiencing a pinkeye outbreak.
  3. Set up a regular schedule for the herd veterinarian to swab eyeballs to stay in front of bacterial strain shift events, as an updated vaccine takes four months to create from swabbing to delivery.
  4. There is great technical service support for pinkeye vaccine development and implementation, so do not be afraid to ask for help.