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There are many factors affecting the design of a control program:
- The reason the sheep are being raised
- The estimated flock prevalence of Johne's disease,
- The owner's perception of the importance of Johne's disease
control relative to other husbandry/health issues
- The capacity of the owner to pay for diagnostic tests and make
management changes to limit the spread of the infection
- The speed with which the owner wants to achieve control of Johne's
disease,
- And whether the goal is to control or to eradicate the infection.
Since an
effective program should closely reflect the particular resources
and requirement of each individual sheep operation, the following
is meant to provide a general framework only.
If M. paratuberculosis infection has been confirmed in one
sheep in a flock, it is likely that other animals are infected as
well. The next step should be to decide how aggressive the flock
manager needs/wants to be to address these other potential cases
and prevent the spread of the infection in the flock. To do so,
s/he needs to assess whether and when (at what age) other sheep
were exposed to the infected animal(s) and if there were other cases
in the recent past that fit a Johne's disease profile but may not
have been assessed for the infection. If the goal is to control
or eradicate the infection, it will be necessary to identify and
test these sheep. Test-positive animals should be culled or segregated
from the flock.

Since a single round of testing may not identify all infected animals,
the manager should begin longer term surveillance of the flock to
include if feasible:
- Regular assessment and recording of body condition to include weighing or palpation of ribs/spine under the fleece at least annually
- Annual AGID or fecal culture of the sheep exposed to manure from the confirmed case.
- More frequent testing for any offspring of the confirmed case(s) and animals exhibiting weight loss or diarrhea. Segregation of these animals until a diagnosis explaining these clinical signs is reached.
It is important to block the spread of the infection by preventing lambs from being exposed to potentially contaminated manure. Ways to help accomplish this include:
- Segregating the flock by level of infection risk so that likely-uninfected lambs are not exposed to adults with a higher risk of infection
- Preventing fecal pellets from contaminating feeders and waterers
- Conducting lambing in clean, manure-free areas
- Cleaning with a phenolic-based disinfectant since M. paratuberculosis is believed resistant to many disinfectants such as chlorine bleach, etc.
- Hand-rearing lambs
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