cows in field

Johnes Disease

by Dr. Hubert Karreman, Penn Dutch Cow Care

The inflammatory bowel disease caused by Mycobacterium paratuberculosis avium is better known by the name of the Danish veterinarian who discovered it in the early 1900’s: Johnes disease (pronounced Yo-neez). The hallmark sign of Johnes disease is chronic diarrhea, despite all attempts to treat it. Johnes has probably been in cattle and other ruminants for thousands of years. Due to more modern intensive farming for higher feeding for higher production, its prevalence (percent of the population) is noticeable in commercial cattle. At the beginning of the 1900’s when lots of cattle grazed, the disease was noticeable probably due to relatively poor nutrition and manure management. This article will discuss Johnes itself and best management practices for organic farms.

Signalment (category of animal affected)

Johnes can affect any breed of cow, generally beginning at two years of age or older. Jerseys and Guernseys have a historically higher incidence of Johnes (percent of animals at risk and showing disease) than Holsteins. However, due to the sheer number of Holsteins, there are simply more Holsteins that develop Johnes disease than other breeds at this point.


Though Johnes often develops with increasing age of an animal, a classic case would be a first calf heifer that freshens and starts to have diarrhea which does not quit. In most instances a stress of some sort, especially dietary or digestive stress, will trigger the diarrhea. Additionally, the natural stress involved with calving with the internal release of hormones can put them over the edge if Johnes has been simmering / sub-clinical.


Johnes exists in manure, and animals in contact with infected manure can be affected. If there is manure “everywhere”, there is a higher likelihood of Johnes being transmitted. Especially critical areas of Johnes bactera (in highest priority) are (1) calving pens, (2) areas where pre-weaned calves are kept, (3) areas where post-weaned calves are kept, and (4) bred heifer areas. Special attention and awareness needs to be paid to boots, shovels, pitch forks, water troughs, skid loaders and bucket loaders used for feeding and cleaning out areas (and their wheels). In a nut shell, the spread of Johnes management is dependent on direct contact of animals, especially the youngest ones, with manure.

Observable Signs

Typical signs of Johnes animals are fresh heifers or more mature cows with effortless pipe-stream diarrhea, eating normally, with progressively poor body condition. The diarrhea often (but not always) looks like thick pea soup oftentimes with small air bubbles. When these small air bubbles burst, the diarrhea then looks like a pancake ready to flip. As a cow continues with the diarrhea, there is a progressive loss of weight since the digestive tract is thickened and not absorbing the nutrition that the cow is eating. The cow’s bones will become more and more prominent. After a long time of diarrhea, Johnes cows sometimes get “bottle jaw” which is a fluid accumulation under their mouth that is soft. This is due to the circulatory system becoming leaky and proteins being lost.

Johnes cow with bottle jaw.

Physical Exam Findings

Beyond the Observable Signs shown above, there usually are not many remarkable findings on a standard physical exam since the pathology is in the thickening of the small bowel deep in the abdomen. A physical exam usually involves checking the eyes, ears, nose, mouth, heart, lungs, rumen activity, “pings” for any gas filled structures, udder secretions, superficial lymph nodes, and also rectal palpation to check for pregnancy status, kidneys and bladder, rumen fill, and internal lymph nodes. While a physical examination may reveal abnormal findings for one or more of the preceding items, a typical Johnes cow lacks abnormal findings on a physical exam (besides the readily observable ones stated in the paragraph above).

Physical Diagnosis

When a cow that is eating normally is continually skinny with chronic non-explosive diarrhea and also has bottle jaw, a barn diagnosis of Johnes can be made.

Initial Treatment

For any suspect animal which has not yet developed bottle jaw, I always recommend to feed only dry, grassy hay for at least five days. This will slow the gut down as much as possible. Such an animal being “tested” to see if she will revert back to normal manure should not be eating any pasture, baleage, silage, or grain. Just feed dry grassy hay. If the diarrhea does not stop, then I usually declare the cow a Johnes cow. If it does stop, be happy and hope that the individual cow just has a sensitive gut and needs more dry hay in her diet in general. However, be aware that Johnes diarrhea can stop temporarily and may well return when normal feeding resumes (this includes grazing).

Johnes’ diarrhea looks like pea soup with small air bubbles


While there may be some remedies and dietary changes that help Johnes cows (various probiotics, minerals and micro-minerals), there is no known, definitive cure for Johnes disease. Why might this be? The germs which cause Johnes disease most often initially infect the animal between birth and 6 months of age. Young, fragile calves whose immune system is not working completely yet are most susceptible to the germs which are shed in the manure of infected cows. Once infected, the germs slowly (very slowly) multiply in the small intestine. The animal’s immune system then reacts and plaques are created due to a constant battle between the germs and the immune system. It takes about two years by the time the gut is thickened enough to not be able to reabsorb fluids (and therefore break with diarrhea). At that point forward the gut is impaired by all the thickening and continues to thicken more, especially if noxious diets made up primarily of high starch diets are fed. Johnes is essentially inflammatory bowel disease of cattle. While I have occasionally heard of someone mentioning a treatment for this disease, I always keep in mind how the disease was triggered in the first place and the length of time it has been going on. Feeding a very gut-friendly diet will likely minimize signs but not clear an animal of infection. For the occasional treatment that I hear being offered to cure the disease, I would just ask that pre- and post manure samples are tested for the presence or clearance of the germ.


While there are no silver bullet treatments for Johnes, there are various testing programs which will help identify infected animals and help to decide what to do with them.

Bacteriology testing:

The gold standard is still the fecal test – a small sample of manure is incubated in a certain setting and left alone for 3-4 months to see if the germs show up. This is a very slow process, but if the germs are there, it is a true positive. Newer but costly DNA tests can be done on manure samples, but at least 100 colony forming units need to be present. A positive is a true positive, but if there aren’t enough germs present in the sample the test may not pick them up.

Immunologic testing:

The more common and quicker methods for testing include looking for evidence that the immune system has been challenged by the germ. This can be done via an ELISA test of milk or blood. While this test takes only about 5 days to run, it does not show that the germs are there, just that the body is reacting to the germs. However, there are other germs that can cause positive reactions. Therefore, the ELISA tests are best for screening purposes. This means that if a totally healthy, robust cow comes back positive on ELISA, she should be fecal tested to see if the Johnesgerms are actually present. However, if an animal is showing typical signs and tests positive on the ELISA test, she can be considered a true positive. The AGID test is a quick two day test which, if positive, indicates a true positive – but this test is only valid on obviously clinical animals. If a cow is positive on the AGID test and is pregnant, the calf will most likely be infected while still in the womb.


Most states have programs to help manage the spread of Johnes disease, both within herds and between herds. (See box, above.) Some programs will help pay for testing. Most require an on-farm analysis done by the herd veterinarian to identify weak spots which the farmer agrees to improve. The most common problem areas are calving areas and pre-weaned calf areas.


Milk from infected cows also carries the Johnes germs. Pasteurizing it before feeding it to calves is rational. However, if pasteurizing, always add back in probiotics to re-enliven the milk.

Nurse Cows:

Keeping in mind what was said about feeding a very gut-friendly diet, there is nothing more natural than calves suckling from cows. Not only will calves learn good grazing behavior, they will also be feeding on the most natural, nutritious diet possible. This is essentially the opposite of the conventional mind-set of feeding only grain and milk replacer, which often is the cause for digestive disturbances. However, it is CRITICAL to NOT have Johnes positive cows as nurse cows.


Most states have programs (see list above) to help in the vaccination of young calves against Johnes. This will not eliminate or completely prevent Johnes from happening, but it does significantly decrease the shedding of the germ in the manure. It’s worth looking into vaccinating if and only if other excellent manure management is already in place. It should not be considered as a tool to use if nothing else changes once Johnes is diagnosed in the herd. Vaccinating should be looked at as the final touch to a strong Johnes program.


In conclusion, Johnes doesn’t discriminate against organic or conventional cows. True victory over Johnes can take years and is based on smart manure management, identification and culling of fecal-positive infected animals. To minimize gut aggravation, feeding a high forage gut-friendly diet with lots of effective fiber in terms of dry hay to all animals from the beginning of life may minimize the signs and thus the shedding of Johnes germs into the barn and pasture environment. u

Dr. Karreman has been working with organic dairy cows since 1988, first as a herdsman on Seven Stars Farm then as a licensed veterinarian for 14 years. His interest in alternative medicine began in the early 1980’s as a soil sceintist while reading the Peterson Field Guide “Medicinal Plants, Eastern/Central” by Foster and Duke. Visit Dr. Karreman’s website: